From ec9464528fbe3b95d86d30c4361722746196b854 Mon Sep 17 00:00:00 2001 From: Shyue Ping Ong Date: Wed, 18 May 2022 13:31:33 -0700 Subject: [PATCH] Update docs --- docs/_static/documentation_options.js | 2 +- docs/addons.html | 4 +- docs/change_log.html | 11 +- docs/compatibility.html | 4 +- docs/contributing.html | 4 +- docs/genindex.html | 6 +- docs/index.html | 10 +- docs/installation.html | 4 +- docs/introduction.html | 12 +- docs/latest_changes.html | 10 +- docs/modules.html | 4 +- docs/objects.inv | Bin 51015 -> 51023 bytes docs/py-modindex.html | 4 +- docs/pymatgen.alchemy.filters.html | 42 +- docs/pymatgen.alchemy.html | 4 +- docs/pymatgen.alchemy.materials.html | 38 +- docs/pymatgen.alchemy.transmuters.html | 36 +- docs/pymatgen.analysis.adsorption.html | 46 +- docs/pymatgen.analysis.bond_dissociation.html | 14 +- docs/pymatgen.analysis.bond_valence.html | 20 +- ...env.connectivity.connected_components.html | 48 +- ...menv.connectivity.connectivity_finder.html | 10 +- 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zMg>z$Hrti%;7Y%!Nr@xgDXkoW^;f<6bOKw+pH+7yY(GoUC)mq>VL2~R3F%g}kDvR& z`_{0lPn*0r+F#BHM z`r`>?ljh8Nngqs6A!kw=eEoH{M#65V{h~TXv#mB_hLCtCGCCqn@Vn;ws|X5XCXgaJ ze3f1cpP-FP9vU%!9nBF(OT|Y{V&T-nR7>fI8WcT`c<;6PO?NIpC#+>X!PJwx*`U?_ z^tLB2943%c@|(T_DQGRk|**O;H`EP1)}6+6&Ep_GA_Xdw5P&6KfH@)ttGnKlUM}Jtytu2RY!P z(}eO|tdFOEi_=fVyH-;%sqekuDrGOKc+J`fTM6{x)@l2J51AQPe(!}XR) z_$orTqdeSpNz~tz=u&-u t7PVR6ZrnlfyOO%YI~>zYu7$ktzy2hjt8dF5->?7qyZG^^{~y!R;9XfNaOMC2 diff --git a/docs/py-modindex.html b/docs/py-modindex.html index 263c7569ae6..6a15a6b4c8c 100644 --- a/docs/py-modindex.html +++ b/docs/py-modindex.html @@ -3,7 +3,7 @@ - Python Module Index — pymatgen 2022.5.18 documentation + Python Module Index — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
        - 2022.5.18 + 2022.5.18.1
        diff --git a/docs/pymatgen.alchemy.filters.html b/docs/pymatgen.alchemy.filters.html index 6a336fa3f33..4b1ffe39804 100644 --- a/docs/pymatgen.alchemy.filters.html +++ b/docs/pymatgen.alchemy.filters.html @@ -4,7 +4,7 @@ - pymatgen.alchemy.filters module — pymatgen 2022.5.18 documentation + pymatgen.alchemy.filters module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
        - 2022.5.18 + 2022.5.18.1
        @@ -118,14 +118,14 @@

        This module defines filters for Transmuter object.

        -class AbstractStructureFilter[source]
        +class AbstractStructureFilter[source]

        Bases: monty.json.MSONable

        AbstractStructureFilter that defines an API to perform testing of Structures. Structures that return True to a test are retained during transmutation while those that return False are removed.

        -abstract test(structure)[source]
        +abstract test(structure)[source]

        Method to execute the test.

        Parameters
        @@ -142,7 +142,7 @@
        -class ChargeBalanceFilter[source]
        +class ChargeBalanceFilter[source]

        Bases: pymatgen.alchemy.filters.AbstractStructureFilter

        This filter removes structures that are not charge balanced from the transmuter. This only works if the structure is oxidation state @@ -151,7 +151,7 @@

        No args required.

        -test(structure)[source]
        +test(structure)[source]

        Method to execute the test.

        Parameters
        @@ -165,7 +165,7 @@
        -class ContainsSpecieFilter(species, strict_compare=False, AND=True, exclude=False)[source]
        +class ContainsSpecieFilter(species, strict_compare=False, AND=True, exclude=False)[source]

        Bases: pymatgen.alchemy.filters.AbstractStructureFilter

        Filter for structures containing certain elements or species. By default compares by atomic number.

        @@ -183,13 +183,13 @@
        -as_dict()[source]
        +as_dict()[source]

        Returns: MSONAble dict

        -classmethod from_dict(d)[source]
        +classmethod from_dict(d)[source]
        Parameters

        d (dict) – Dict representation

        @@ -202,7 +202,7 @@
        -test(structure)[source]
        +test(structure)[source]

        Method to execute the test.

        Returns: True if structure do not contain specified species.

        @@ -211,7 +211,7 @@
        -class RemoveDuplicatesFilter(structure_matcher=<pymatgen.analysis.structure_matcher.StructureMatcher object>, symprec=None)[source]
        +class RemoveDuplicatesFilter(structure_matcher=<pymatgen.analysis.structure_matcher.StructureMatcher object>, symprec=None)[source]

        Bases: pymatgen.alchemy.filters.AbstractStructureFilter

        This filter removes exact duplicate structures from the transmuter.

        Remove duplicate structures based on the structure matcher @@ -229,7 +229,7 @@

        -test(structure)[source]
        +test(structure)[source]
        Parameters

        structure (Structure) – Input structure to test

        @@ -242,7 +242,7 @@
        -class RemoveExistingFilter(existing_structures, structure_matcher=<pymatgen.analysis.structure_matcher.StructureMatcher object>, symprec=None)[source]
        +class RemoveExistingFilter(existing_structures, structure_matcher=<pymatgen.analysis.structure_matcher.StructureMatcher object>, symprec=None)[source]

        Bases: pymatgen.alchemy.filters.AbstractStructureFilter

        This filter removes structures existing in a given list from the transmuter.

        Remove existing structures based on the structure matcher @@ -261,13 +261,13 @@

        -as_dict()[source]
        +as_dict()[source]

        Returns: MSONable dict

        -test(structure)[source]
        +test(structure)[source]

        Method to execute the test.

        Parameters
        @@ -281,7 +281,7 @@
        -class SpecieProximityFilter(specie_and_min_dist_dict)[source]
        +class SpecieProximityFilter(specie_and_min_dist_dict)[source]

        Bases: pymatgen.alchemy.filters.AbstractStructureFilter

        This filter removes structures that have certain species that are too close together.

        @@ -297,13 +297,13 @@
        -as_dict()[source]
        +as_dict()[source]

        Returns: MSONable dict

        -classmethod from_dict(d)[source]
        +classmethod from_dict(d)[source]
        Parameters

        d (dict) – Dict representation

        @@ -316,7 +316,7 @@
        -test(structure)[source]
        +test(structure)[source]

        Method to execute the test.

        Parameters
        @@ -333,7 +333,7 @@
        -class SpeciesMaxDistFilter(sp1, sp2, max_dist)[source]
        +class SpeciesMaxDistFilter(sp1, sp2, max_dist)[source]

        Bases: pymatgen.alchemy.filters.AbstractStructureFilter

        This filter removes structures that do have two particular species that are not nearest neighbors by a predefined max_dist. For instance, if you are @@ -353,7 +353,7 @@

        -test(structure)[source]
        +test(structure)[source]

        Method to execute the test.

        Parameters
        diff --git a/docs/pymatgen.alchemy.html b/docs/pymatgen.alchemy.html index 28c586b3013..889d8dd5b15 100644 --- a/docs/pymatgen.alchemy.html +++ b/docs/pymatgen.alchemy.html @@ -4,7 +4,7 @@ - pymatgen.alchemy package — pymatgen 2022.5.18 documentation + pymatgen.alchemy package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
        - 2022.5.18 + 2022.5.18.1
        diff --git a/docs/pymatgen.alchemy.materials.html b/docs/pymatgen.alchemy.materials.html index bf47b912c56..60452fd6799 100644 --- a/docs/pymatgen.alchemy.materials.html +++ b/docs/pymatgen.alchemy.materials.html @@ -4,7 +4,7 @@ - pymatgen.alchemy.materials module — pymatgen 2022.5.18 documentation + pymatgen.alchemy.materials module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
        - 2022.5.18 + 2022.5.18.1
        @@ -120,7 +120,7 @@ series of transformations.

        -class TransformedStructure(structure: Structure, transformations: list[AbstractTransformation] = None, history: list[AbstractTransformation | dict[str, Any]] = None, other_parameters: dict[str, Any] = None)[source]
        +class TransformedStructure(structure: Structure, transformations: list[AbstractTransformation] = None, history: list[AbstractTransformation | dict[str, Any]] = None, other_parameters: dict[str, Any] = None)[source]

        Bases: monty.json.MSONable

        Container object for new structures that include history of transformations.

        @@ -140,7 +140,7 @@
        -append_filter(structure_filter: pymatgen.alchemy.filters.AbstractStructureFilter) → None[source]
        +append_filter(structure_filter: pymatgen.alchemy.filters.AbstractStructureFilter) → None[source]

        Adds a filter.

        Parameters
        @@ -152,7 +152,7 @@
        -append_transformation(transformation, return_alternatives=False, clear_redo=True)[source]
        +append_transformation(transformation, return_alternatives=False, clear_redo=True)[source]

        Appends a transformation to the TransformedStructure.

        Parameters
        @@ -174,13 +174,13 @@
        -as_dict() → dict[str, Any][source]
        +as_dict() → dict[str, Any][source]

        Dict representation of the TransformedStructure.

        -extend_transformations(transformations: list[pymatgen.transformations.transformation_abc.AbstractTransformation], return_alternatives: bool = False) → None[source]
        +extend_transformations(transformations: list[pymatgen.transformations.transformation_abc.AbstractTransformation], return_alternatives: bool = False) → None[source]

        Extends a sequence of transformations to the TransformedStructure.

        Parameters
        @@ -197,7 +197,7 @@
        -static from_cif_string(cif_string: str, transformations: Optional[list[pymatgen.transformations.transformation_abc.AbstractTransformation]] = None, primitive: bool = True, occupancy_tolerance: float = 1.0) → pymatgen.alchemy.materials.TransformedStructure[source]
        +static from_cif_string(cif_string: str, transformations: Optional[list[pymatgen.transformations.transformation_abc.AbstractTransformation]] = None, primitive: bool = True, occupancy_tolerance: float = 1.0) → pymatgen.alchemy.materials.TransformedStructure[source]

        Generates TransformedStructure from a cif string.

        Parameters
        @@ -225,13 +225,13 @@
        -classmethod from_dict(d) → pymatgen.alchemy.materials.TransformedStructure[source]
        +classmethod from_dict(d) → pymatgen.alchemy.materials.TransformedStructure[source]

        Creates a TransformedStructure from a dict.

        -static from_poscar_string(poscar_string: str, transformations: Optional[list[pymatgen.transformations.transformation_abc.AbstractTransformation]] = None) → pymatgen.alchemy.materials.TransformedStructure[source]
        +static from_poscar_string(poscar_string: str, transformations: Optional[list[pymatgen.transformations.transformation_abc.AbstractTransformation]] = None) → pymatgen.alchemy.materials.TransformedStructure[source]

        Generates TransformedStructure from a poscar string.

        Parameters
        @@ -246,7 +246,7 @@
        -classmethod from_snl(snl: pymatgen.util.provenance.StructureNL) → pymatgen.alchemy.materials.TransformedStructure[source]
        +classmethod from_snl(snl: pymatgen.util.provenance.StructureNL) → pymatgen.alchemy.materials.TransformedStructure[source]

        Create TransformedStructure from SNL.

        Parameters
        @@ -260,7 +260,7 @@
        -get_vasp_input(vasp_input_set: type[pymatgen.io.vasp.sets.VaspInputSet] = <class 'pymatgen.io.vasp.sets.MPRelaxSet'>, **kwargs) → dict[str, Any][source]
        +get_vasp_input(vasp_input_set: type[pymatgen.io.vasp.sets.VaspInputSet] = <class 'pymatgen.io.vasp.sets.MPRelaxSet'>, **kwargs) → dict[str, Any][source]

        Returns VASP input as a dict of vasp objects.

        Parameters
        @@ -272,7 +272,7 @@
        -redo_next_change() → None[source]
        +redo_next_change() → None[source]

        Redo the last undone change in the TransformedStructure.

        Raises
        @@ -283,7 +283,7 @@
        -set_parameter(key: str, value: Any) → None[source]
        +set_parameter(key: str, value: Any) → None[source]

        Set a parameter

        Parameters
        @@ -297,14 +297,14 @@
        -property structures: list[pymatgen.core.structure.Structure][source]
        +property structures: list[pymatgen.core.structure.Structure][source]

        Copy of all structures in the TransformedStructure. A structure is stored after every single transformation.

        -to_snl(authors, **kwargs) → pymatgen.util.provenance.StructureNL[source]
        +to_snl(authors, **kwargs) → pymatgen.util.provenance.StructureNL[source]

        Generate SNL from TransformedStructure.

        Parameters
        @@ -322,7 +322,7 @@
        -undo_last_change() → None[source]
        +undo_last_change() → None[source]

        Undo the last change in the TransformedStructure.

        Raises
        @@ -333,7 +333,7 @@
        -property was_modified: bool[source]
        +property was_modified: bool[source]

        Boolean describing whether the last transformation on the structure made any alterations to it one example of when this would return false is in the case of performing a substitution transformation on the @@ -342,7 +342,7 @@

        -write_vasp_input(vasp_input_set: type[pymatgen.io.vasp.sets.VaspInputSet] = <class 'pymatgen.io.vasp.sets.MPRelaxSet'>, output_dir: str = '.', create_directory: bool = True, **kwargs) → None[source]
        +write_vasp_input(vasp_input_set: type[pymatgen.io.vasp.sets.VaspInputSet] = <class 'pymatgen.io.vasp.sets.MPRelaxSet'>, output_dir: str = '.', create_directory: bool = True, **kwargs) → None[source]

        Writes VASP input to an output_dir.

        Parameters
        diff --git a/docs/pymatgen.alchemy.transmuters.html b/docs/pymatgen.alchemy.transmuters.html index 4b9d388fd0d..aa2d0d00cf1 100644 --- a/docs/pymatgen.alchemy.transmuters.html +++ b/docs/pymatgen.alchemy.transmuters.html @@ -4,7 +4,7 @@ - pymatgen.alchemy.transmuters module — pymatgen 2022.5.18 documentation + pymatgen.alchemy.transmuters module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
        - 2022.5.18 + 2022.5.18.1
        @@ -123,7 +123,7 @@ entire directory of vasp input files for running.

        -class CifTransmuter(cif_string, transformations=None, primitive=True, extend_collection=False)[source]
        +class CifTransmuter(cif_string, transformations=None, primitive=True, extend_collection=False)[source]

        Bases: pymatgen.alchemy.transmuters.StandardTransmuter

        Generates a Transmuter from a cif string, possibly containing multiple structures.

        @@ -145,7 +145,7 @@
        -static from_filenames(filenames, transformations=None, primitive=True, extend_collection=False)[source]
        +static from_filenames(filenames, transformations=None, primitive=True, extend_collection=False)[source]

        Generates a TransformedStructureCollection from a cif, possibly containing multiple structures.

        @@ -165,7 +165,7 @@
        -class PoscarTransmuter(poscar_string, transformations=None, extend_collection=False)[source]
        +class PoscarTransmuter(poscar_string, transformations=None, extend_collection=False)[source]

        Bases: pymatgen.alchemy.transmuters.StandardTransmuter

        Generates a transmuter from a sequence of POSCARs.

        @@ -181,7 +181,7 @@
        -static from_filenames(poscar_filenames, transformations=None, extend_collection=False)[source]
        +static from_filenames(poscar_filenames, transformations=None, extend_collection=False)[source]

        Convenient constructor to generates a POSCAR transmuter from a list of POSCAR filenames.

        @@ -200,7 +200,7 @@
        -class StandardTransmuter(transformed_structures, transformations=None, extend_collection=0, ncores=None)[source]
        +class StandardTransmuter(transformed_structures, transformations=None, extend_collection=0, ncores=None)[source]

        Bases: object

        An example of a Transmuter object, which performs a sequence of transformations on many structures to generate TransformedStructures.

        @@ -225,7 +225,7 @@
        -add_tags(tags)[source]
        +add_tags(tags)[source]

        Add tags for the structures generated by the transmuter.

        Parameters
        @@ -237,7 +237,7 @@
        -append_transformation(transformation, extend_collection=False, clear_redo=True)[source]
        +append_transformation(transformation, extend_collection=False, clear_redo=True)[source]

        Appends a transformation to all TransformedStructures.

        Parameters
        @@ -264,7 +264,7 @@
        -append_transformed_structures(tstructs_or_transmuter)[source]
        +append_transformed_structures(tstructs_or_transmuter)[source]

        Method is overloaded to accept either a list of transformed structures or transmuter, it which case it appends the second transmuter”s structures.

        @@ -278,7 +278,7 @@
        -apply_filter(structure_filter)[source]
        +apply_filter(structure_filter)[source]

        Applies a structure_filter to the list of TransformedStructures in the transmuter.

        @@ -290,7 +290,7 @@
        -extend_transformations(transformations)[source]
        +extend_transformations(transformations)[source]

        Extends a sequence of transformations to the TransformedStructure.

        Parameters
        @@ -301,7 +301,7 @@
        -static from_structures(structures, transformations=None, extend_collection=0)[source]
        +static from_structures(structures, transformations=None, extend_collection=0)[source]

        Alternative constructor from structures rather than TransformedStructures.

        @@ -324,7 +324,7 @@
        -redo_next_change()[source]
        +redo_next_change()[source]

        Redo the last undone transformation in the TransformedStructure.

        Raises
        @@ -335,7 +335,7 @@
        -set_parameter(key, value)[source]
        +set_parameter(key, value)[source]

        Add parameters to the transmuter. Additional parameters are stored in the as_dict() output.

        @@ -350,7 +350,7 @@
        -undo_last_change()[source]
        +undo_last_change()[source]

        Undo the last transformation in the TransformedStructure.

        Raises
        @@ -361,7 +361,7 @@
        -write_vasp_input(**kwargs)[source]
        +write_vasp_input(**kwargs)[source]

        Batch write vasp input for a sequence of transformed structures to output_dir, following the format output_dir/{formula}_{number}.

        @@ -375,7 +375,7 @@
        -batch_write_vasp_input(transformed_structures, vasp_input_set=<class 'pymatgen.io.vasp.sets.MPRelaxSet'>, output_dir='.', create_directory=True, subfolder=None, include_cif=False, **kwargs)[source]
        +batch_write_vasp_input(transformed_structures, vasp_input_set=<class 'pymatgen.io.vasp.sets.MPRelaxSet'>, output_dir='.', create_directory=True, subfolder=None, include_cif=False, **kwargs)[source]

        Batch write vasp input for a sequence of transformed structures to output_dir, following the format output_dir/{group}/{formula}_{number}.

        diff --git a/docs/pymatgen.analysis.adsorption.html b/docs/pymatgen.analysis.adsorption.html index acc1b88b1e1..b8aff4fbb01 100644 --- a/docs/pymatgen.analysis.adsorption.html +++ b/docs/pymatgen.analysis.adsorption.html @@ -4,7 +4,7 @@ - pymatgen.analysis.adsorption module — pymatgen 2022.5.18 documentation + pymatgen.analysis.adsorption module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
        - 2022.5.18 + 2022.5.18.1
        @@ -119,7 +119,7 @@ and to find adsorption sites on slabs

        -class AdsorbateSiteFinder(slab, selective_dynamics=False, height=0.9, mi_vec=None)[source]
        +class AdsorbateSiteFinder(slab, selective_dynamics=False, height=0.9, mi_vec=None)[source]

        Bases: object

        This class finds adsorbate sites on slabs and generates adsorbate structures according to user-defined criteria. @@ -167,7 +167,7 @@

        -add_adsorbate(molecule, ads_coord, repeat=None, translate=True, reorient=True)[source]
        +add_adsorbate(molecule, ads_coord, repeat=None, translate=True, reorient=True)[source]

        Adds an adsorbate at a particular coordinate. Adsorbate represented by a Molecule object and is translated to (0, 0, 0) if translate is True, or positioned relative to the input adsorbate @@ -190,7 +190,7 @@

        -adsorb_both_surfaces(molecule, repeat=None, min_lw=5.0, translate=True, reorient=True, find_args=None)[source]
        +adsorb_both_surfaces(molecule, repeat=None, min_lw=5.0, translate=True, reorient=True, find_args=None)[source]

        Function that generates all adsorption structures for a given molecular adsorbate on both surfaces of a slab. This is useful for calculating surface energy where both surfaces need to be @@ -213,7 +213,7 @@

        -classmethod assign_selective_dynamics(slab)[source]
        +classmethod assign_selective_dynamics(slab)[source]

        Helper function to assign selective dynamics site_properties based on surface, subsurface site properties

        @@ -225,13 +225,13 @@
        -assign_site_properties(slab, height=0.9)[source]
        +assign_site_properties(slab, height=0.9)[source]

        Assigns site properties.

        -classmethod ensemble_center(site_list, indices, cartesian=True)[source]
        +classmethod ensemble_center(site_list, indices, cartesian=True)[source]

        Finds the center of an ensemble of sites selected from a list of sites. Helper method for the find_adsorption_sites algorithm.

        @@ -250,7 +250,7 @@
        -find_adsorption_sites(distance=2.0, put_inside=True, symm_reduce=0.01, near_reduce=0.01, positions=['ontop', 'bridge', 'hollow'], no_obtuse_hollow=True)[source]
        +find_adsorption_sites(distance=2.0, put_inside=True, symm_reduce=0.01, near_reduce=0.01, positions=['ontop', 'bridge', 'hollow'], no_obtuse_hollow=True)[source]

        Finds surface sites according to the above algorithm. Returns a list of corresponding Cartesian coordinates.

        @@ -280,7 +280,7 @@
        -find_surface_sites_by_height(slab, height=0.9, xy_tol=0.05)[source]
        +find_surface_sites_by_height(slab, height=0.9, xy_tol=0.05)[source]

        This method finds surface sites by determining which sites are within a threshold value in height from the topmost site in a list of sites

        @@ -302,7 +302,7 @@
        -classmethod from_bulk_and_miller(structure, miller_index, min_slab_size=8.0, min_vacuum_size=10.0, max_normal_search=None, center_slab=True, selective_dynamics=False, undercoord_threshold=0.09)[source]
        +classmethod from_bulk_and_miller(structure, miller_index, min_slab_size=8.0, min_vacuum_size=10.0, max_normal_search=None, center_slab=True, selective_dynamics=False, undercoord_threshold=0.09)[source]

        This method constructs the adsorbate site finder from a bulk structure and a miller index, which allows the surface sites to be determined from the difference in bulk and slab coordination, @@ -330,7 +330,7 @@

        -generate_adsorption_structures(molecule, repeat=None, min_lw=5.0, translate=True, reorient=True, find_args=None)[source]
        +generate_adsorption_structures(molecule, repeat=None, min_lw=5.0, translate=True, reorient=True, find_args=None)[source]

        Function that generates all adsorption structures for a given molecular adsorbate. Can take repeat argument or minimum length/width of precursor slab as an input

        @@ -354,7 +354,7 @@
        -generate_substitution_structures(atom, target_species=None, sub_both_sides=False, range_tol=0.01, dist_from_surf=0)[source]
        +generate_substitution_structures(atom, target_species=None, sub_both_sides=False, range_tol=0.01, dist_from_surf=0)[source]
        Function that performs substitution-type doping on the surface and

        returns all possible configurations where one dopant is substituted per surface. Can substitute one surface or both.

        @@ -378,7 +378,7 @@
        -get_extended_surface_mesh(repeat=(5, 5, 1))[source]
        +get_extended_surface_mesh(repeat=(5, 5, 1))[source]

        Gets an extended surface mesh for to use for adsorption site finding by constructing supercell of surface sites

        @@ -390,7 +390,7 @@
        -near_reduce(coords_set, threshold=0.0001)[source]
        +near_reduce(coords_set, threshold=0.0001)[source]

        Prunes coordinate set for coordinates that are within threshold

        @@ -405,19 +405,19 @@
        -subsurface_sites()[source]
        +subsurface_sites()[source]

        convenience method to return list of subsurface sites

        -property surface_sites[source]
        +property surface_sites[source]

        convenience method to return a list of surface sites

        -symm_reduce(coords_set, threshold=1e-06)[source]
        +symm_reduce(coords_set, threshold=1e-06)[source]

        Reduces the set of adsorbate sites by finding removing symmetrically equivalent duplicates

        @@ -435,20 +435,20 @@
        -get_mi_vec(slab)[source]
        +get_mi_vec(slab)[source]

        Convenience function which returns the unit vector aligned with the miller index.

        -get_rot(slab)[source]
        +get_rot(slab)[source]

        Gets the transformation to rotate the z axis into the miller index

        -plot_slab(slab, ax, scale=0.8, repeat=5, window=1.5, draw_unit_cell=True, decay=0.2, adsorption_sites=True, inverse=False)[source]
        +plot_slab(slab, ax, scale=0.8, repeat=5, window=1.5, draw_unit_cell=True, decay=0.2, adsorption_sites=True, inverse=False)[source]

        Function that helps visualize the slab in a 2-D plot, for convenient viewing of output of AdsorbateSiteFinder.

        @@ -470,13 +470,13 @@
        -put_coord_inside(lattice, cart_coordinate)[source]
        +put_coord_inside(lattice, cart_coordinate)[source]

        converts a Cartesian coordinate such that it is inside the unit cell.

        -reorient_z(structure)[source]
        +reorient_z(structure)[source]

        reorients a structure such that the z axis is concurrent with the normal to the A-B plane

        diff --git a/docs/pymatgen.analysis.bond_dissociation.html b/docs/pymatgen.analysis.bond_dissociation.html index 2adb1a72e22..a61a2d295cb 100644 --- a/docs/pymatgen.analysis.bond_dissociation.html +++ b/docs/pymatgen.analysis.bond_dissociation.html @@ -4,7 +4,7 @@ - pymatgen.analysis.bond_dissociation module — pymatgen 2022.5.18 documentation + pymatgen.analysis.bond_dissociation module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
        - 2022.5.18 + 2022.5.18.1
        @@ -118,7 +118,7 @@

        Module for BondDissociationEnergies.

        -class BondDissociationEnergies(molecule_entry, fragment_entries, allow_additional_charge_separation=False, multibreak=False)[source]
        +class BondDissociationEnergies(molecule_entry, fragment_entries, allow_additional_charge_separation=False, multibreak=False)[source]

        Bases: monty.json.MSONable

        Standard constructor for bond dissociation energies. All bonds in the principle molecule are looped through and their dissociation energies are calculated given the energies of the resulting @@ -143,7 +143,7 @@

        -build_new_entry(frags, bonds)[source]
        +build_new_entry(frags, bonds)[source]

        Simple function to format a bond dissociation entry that will eventually be returned to the user.

        Parameters
        @@ -160,7 +160,7 @@
        -filter_fragment_entries(fragment_entries)[source]
        +filter_fragment_entries(fragment_entries)[source]

        Filter the fragment entries.

        Parameters
        @@ -174,7 +174,7 @@
        -fragment_and_process(bonds)[source]
        +fragment_and_process(bonds)[source]

        Fragment and process bonds.

        Parameters
        @@ -188,7 +188,7 @@
        -search_fragment_entries(frag)[source]
        +search_fragment_entries(frag)[source]

        Search all fragment entries for those isomorphic to the given fragment. We distinguish between entries where both initial and final molgraphs are isomorphic to the given fragment (entries) vs those where only the initial molgraph is isomorphic to the given diff --git a/docs/pymatgen.analysis.bond_valence.html b/docs/pymatgen.analysis.bond_valence.html index 1297ed143b7..87537c05e7f 100644 --- a/docs/pymatgen.analysis.bond_valence.html +++ b/docs/pymatgen.analysis.bond_valence.html @@ -4,7 +4,7 @@ - pymatgen.analysis.bond_valence module — pymatgen 2022.5.18 documentation + pymatgen.analysis.bond_valence module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

        - 2022.5.18 + 2022.5.18.1
        @@ -118,7 +118,7 @@

        This module implements classes to perform bond valence analyses.

        -class BVAnalyzer(symm_tol=0.1, max_radius=4, max_permutations=100000, distance_scale_factor=1.015, charge_neutrality_tolerance=1e-05, forbidden_species=None)[source]
        +class BVAnalyzer(symm_tol=0.1, max_radius=4, max_permutations=100000, distance_scale_factor=1.015, charge_neutrality_tolerance=1e-05, forbidden_species=None)[source]

        Bases: object

        This class implements a maximum a posteriori (MAP) estimation method to determine oxidation states in a structure. The algorithm is as follows: @@ -158,12 +158,12 @@

        -CHARGE_NEUTRALITY_TOLERANCE = 1e-05[source]
        +CHARGE_NEUTRALITY_TOLERANCE = 1e-05[source]
        -get_oxi_state_decorated_structure(structure)[source]
        +get_oxi_state_decorated_structure(structure)[source]

        Get an oxidation state decorated structure. This currently works only for ordered structures only.

        @@ -181,7 +181,7 @@
        -get_valences(structure)[source]
        +get_valences(structure)[source]

        Returns a list of valences for the structure. This currently works only for ordered structures only.

        @@ -205,7 +205,7 @@
        -add_oxidation_state_by_site_fraction(structure, oxidation_states)[source]
        +add_oxidation_state_by_site_fraction(structure, oxidation_states)[source]

        Add oxidation states to a structure by fractional site.

        Parameters
        @@ -218,7 +218,7 @@
        -calculate_bv_sum(site, nn_list, scale_factor=1.0)[source]
        +calculate_bv_sum(site, nn_list, scale_factor=1.0)[source]

        Calculates the BV sum of a site.

        Parameters
        @@ -236,7 +236,7 @@
        -calculate_bv_sum_unordered(site, nn_list, scale_factor=1)[source]
        +calculate_bv_sum_unordered(site, nn_list, scale_factor=1)[source]

        Calculates the BV sum of a site for unordered structures.

        Parameters
        @@ -254,7 +254,7 @@
        -get_z_ordered_elmap(comp)[source]
        +get_z_ordered_elmap(comp)[source]

        Arbitrary ordered elmap on the elements/species of a composition of a given site in an unordered structure. Returns a list of tuples ( element_or_specie: occupation) in the arbitrary order.

        diff --git a/docs/pymatgen.analysis.chemenv.connectivity.connected_components.html b/docs/pymatgen.analysis.chemenv.connectivity.connected_components.html index 200c9c01777..90107592cdf 100644 --- a/docs/pymatgen.analysis.chemenv.connectivity.connected_components.html +++ b/docs/pymatgen.analysis.chemenv.connectivity.connected_components.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.connectivity.connected_components module — pymatgen 2022.5.18 documentation + pymatgen.analysis.chemenv.connectivity.connected_components module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
        - 2022.5.18 + 2022.5.18.1
        @@ -120,7 +120,7 @@

        Connected components.

        -class ConnectedComponent(environments=None, links=None, environments_data=None, links_data=None, graph=None)[source]
        +class ConnectedComponent(environments=None, links=None, environments_data=None, links_data=None, graph=None)[source]

        Bases: monty.json.MSONable

        Class used to describe the connected components in a structure in terms of coordination environments.

        Constructor for the ConnectedComponent object.

        @@ -143,7 +143,7 @@
        -as_dict()[source]
        +as_dict()[source]

        Bson-serializable dict representation of the ConnectedComponent object.

        Returns
        @@ -157,7 +157,7 @@
        -compute_periodicity(algorithm='all_simple_paths')[source]
        +compute_periodicity(algorithm='all_simple_paths')[source]
        Parameters

        () (algorithm) –

        @@ -168,19 +168,19 @@
        -compute_periodicity_all_simple_paths_algorithm()[source]
        +compute_periodicity_all_simple_paths_algorithm()[source]

        Returns:

        -compute_periodicity_cycle_basis()[source]
        +compute_periodicity_cycle_basis()[source]

        Returns:

        -coordination_sequence(source_node, path_size=5, coordination='number', include_source=False)[source]
        +coordination_sequence(source_node, path_size=5, coordination='number', include_source=False)[source]

        Get the coordination sequence for a given node.

        Parameters
        @@ -230,7 +230,7 @@
        -description(full=False)[source]
        +description(full=False)[source]
        Parameters

        () (full) –

        @@ -241,7 +241,7 @@
        -elastic_centered_graph(start_node=None)[source]
        +elastic_centered_graph(start_node=None)[source]
        Parameters

        () (start_node) –

        @@ -252,7 +252,7 @@
        -classmethod from_dict(d)[source]
        +classmethod from_dict(d)[source]

        Reconstructs the ConnectedComponent object from a dict representation of the ConnectedComponent object created using the as_dict method.

        @@ -270,7 +270,7 @@
        -classmethod from_graph(g)[source]
        +classmethod from_graph(g)[source]

        Constructor for the ConnectedComponent object from a graph of the connected component

        Parameters
        @@ -287,7 +287,7 @@
        -property graph[source]
        +property graph[source]

        Return the graph of this connected component.

        Returns
        @@ -305,37 +305,37 @@
        -property is_0d[source]
        +property is_0d[source]

        Returns:

        -property is_1d[source]
        +property is_1d[source]

        Returns:

        -property is_2d[source]
        +property is_2d[source]

        Returns:

        -property is_3d[source]
        +property is_3d[source]

        Returns:

        -property is_periodic[source]
        +property is_periodic[source]

        Returns:

        -make_supergraph(multiplicity)[source]
        +make_supergraph(multiplicity)[source]
        Parameters

        () (multiplicity) –

        @@ -346,19 +346,19 @@
        -property periodicity[source]
        +property periodicity[source]

        Returns:

        -property periodicity_vectors[source]
        +property periodicity_vectors[source]

        Returns:

        -show_graph(graph=None, save_file=None, drawing_type='internal', pltshow=True)[source]
        +show_graph(graph=None, save_file=None, drawing_type='internal', pltshow=True)[source]
        Parameters
          @@ -376,7 +376,7 @@
          -draw_network(env_graph, pos, ax, sg=None, periodicity_vectors=None)[source]
          +draw_network(env_graph, pos, ax, sg=None, periodicity_vectors=None)[source]

          Draw network of environments in a matplotlib figure axes.

          Parameters
          @@ -394,7 +394,7 @@
          -make_supergraph(graph, multiplicity, periodicity_vectors)[source]
          +make_supergraph(graph, multiplicity, periodicity_vectors)[source]

          Make supergraph from a graph of environments.

          Parameters
          diff --git a/docs/pymatgen.analysis.chemenv.connectivity.connectivity_finder.html b/docs/pymatgen.analysis.chemenv.connectivity.connectivity_finder.html index 78ba58f86eb..c3b22b97bcf 100644 --- a/docs/pymatgen.analysis.chemenv.connectivity.connectivity_finder.html +++ b/docs/pymatgen.analysis.chemenv.connectivity.connectivity_finder.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.connectivity.connectivity_finder module — pymatgen 2022.5.18 documentation + pymatgen.analysis.chemenv.connectivity.connectivity_finder module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
          - 2022.5.18 + 2022.5.18.1
          @@ -120,7 +120,7 @@

          Module implementing connectivity finding.

          -class ConnectivityFinder(multiple_environments_choice=None)[source]
          +class ConnectivityFinder(multiple_environments_choice=None)[source]

          Bases: object

          Main class used to find the structure connectivity of a structure

          Constructor for the ConnectivityFinder.

          @@ -133,7 +133,7 @@ coordination environments.

          -get_structure_connectivity(light_structure_environments)[source]
          +get_structure_connectivity(light_structure_environments)[source]

          Get the structure connectivity from the coordination environments provided as an input.

          @@ -148,7 +148,7 @@
          -setup_parameters(multiple_environments_choice)[source]
          +setup_parameters(multiple_environments_choice)[source]

          Setup of the parameters for the connectivity finder.

          diff --git a/docs/pymatgen.analysis.chemenv.connectivity.environment_nodes.html b/docs/pymatgen.analysis.chemenv.connectivity.environment_nodes.html index 00c28406d0f..9c8a40450db 100644 --- a/docs/pymatgen.analysis.chemenv.connectivity.environment_nodes.html +++ b/docs/pymatgen.analysis.chemenv.connectivity.environment_nodes.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.connectivity.environment_nodes module — pymatgen 2022.5.18 documentation + pymatgen.analysis.chemenv.connectivity.environment_nodes module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
          - 2022.5.18 + 2022.5.18.1
          @@ -120,7 +120,7 @@

          Environment nodes module.

          -class AbstractEnvironmentNode(central_site, i_central_site)[source]
          +class AbstractEnvironmentNode(central_site, i_central_site)[source]

          Bases: monty.json.MSONable

          Abstract class used to define an environment as a node in a graph.

          Constructor for the AbstractEnvironmentNode object.

          @@ -135,104 +135,104 @@
          -ATOM = 6[source]
          +ATOM = 6[source]
          -CE_NNBCES_NBCES_LIGANDS = -1[source]
          +CE_NNBCES_NBCES_LIGANDS = -1[source]
          -COORDINATION_ENVIRONMENT = 0[source]
          +COORDINATION_ENVIRONMENT = 0[source]
          -DEFAULT_EXTENSIONS = (6, 0)[source]
          +DEFAULT_EXTENSIONS = (6, 0)[source]
          -LIGANDS_ARRANGEMENT = 4[source]
          +LIGANDS_ARRANGEMENT = 4[source]
          -NEIGHBORING_CES = 2[source]
          +NEIGHBORING_CES = 2[source]
          -NEIGHBORING_COORDINATION_ENVIRONMENTS = 2[source]
          +NEIGHBORING_COORDINATION_ENVIRONMENTS = 2[source]
          -NEIGHBORS_LIGANDS_ARRANGEMENT = 5[source]
          +NEIGHBORS_LIGANDS_ARRANGEMENT = 5[source]
          -NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_CE = 3[source]
          +NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_CE = 3[source]
          -NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_COORDINATION_ENVIRONMENT = 3[source]
          +NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_COORDINATION_ENVIRONMENT = 3[source]
          -NUMBER_OF_NEIGHBORING_CES = 1[source]
          +NUMBER_OF_NEIGHBORING_CES = 1[source]
          -NUMBER_OF_NEIGHBORING_COORDINATION_ENVIRONMENTS = 1[source]
          +NUMBER_OF_NEIGHBORING_COORDINATION_ENVIRONMENTS = 1[source]
          -property atom_symbol[source]
          +property atom_symbol[source]

          Symbol of the atom on the central site.

          -property ce[source]
          +property ce[source]

          Coordination environment of this node.

          -property ce_symbol[source]
          +property ce_symbol[source]

          Coordination environment of this node.

          -abstract property coordination_environment[source]
          +abstract property coordination_environment[source]

          Coordination environment of this node.

          -everything_equal(other)[source]
          +everything_equal(other)[source]

          Checks equality with respect to another AbstractEnvironmentNode using the index of the central site as well as the central site itself.

          -property isite[source]
          +property isite[source]

          Index of the central site.

          -property mp_symbol[source]
          +property mp_symbol[source]

          Coordination environment of this node.

          @@ -240,7 +240,7 @@
          -class EnvironmentNode(central_site, i_central_site, ce_symbol)[source]
          +class EnvironmentNode(central_site, i_central_site, ce_symbol)[source]

          Bases: pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode

          Class used to define an environment as a node in a graph.

          Constructor for the EnvironmentNode object.

          @@ -256,13 +256,13 @@
          -property coordination_environment[source]
          +property coordination_environment[source]

          Coordination environment of this node.

          -everything_equal(other)[source]
          +everything_equal(other)[source]

          Compare with another environment node.

          Returns
          @@ -275,7 +275,7 @@
          -get_environment_node(central_site, i_central_site, ce_symbol)[source]
          +get_environment_node(central_site, i_central_site, ce_symbol)[source]

          Get the EnvironmentNode class or subclass for the given site and symbol.

          Parameters
          diff --git a/docs/pymatgen.analysis.chemenv.connectivity.html b/docs/pymatgen.analysis.chemenv.connectivity.html index d85b61796de..2653ebfd4ff 100644 --- a/docs/pymatgen.analysis.chemenv.connectivity.html +++ b/docs/pymatgen.analysis.chemenv.connectivity.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.connectivity package — pymatgen 2022.5.18 documentation + pymatgen.analysis.chemenv.connectivity package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
          - 2022.5.18 + 2022.5.18.1
          diff --git a/docs/pymatgen.analysis.chemenv.connectivity.structure_connectivity.html b/docs/pymatgen.analysis.chemenv.connectivity.structure_connectivity.html index d5a9719d0cc..d250db6f5e8 100644 --- a/docs/pymatgen.analysis.chemenv.connectivity.structure_connectivity.html +++ b/docs/pymatgen.analysis.chemenv.connectivity.structure_connectivity.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.connectivity.structure_connectivity module — pymatgen 2022.5.18 documentation + pymatgen.analysis.chemenv.connectivity.structure_connectivity module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
          - 2022.5.18 + 2022.5.18.1
          @@ -120,7 +120,7 @@

          Structure connectivity class.

          -class StructureConnectivity(light_structure_environment, connectivity_graph=None, environment_subgraphs=None)[source]
          +class StructureConnectivity(light_structure_environment, connectivity_graph=None, environment_subgraphs=None)[source]

          Bases: monty.json.MSONable

          Main class containing the connectivity of a structure.

          Constructor for the StructureConnectivity object.

          @@ -141,7 +141,7 @@
          -add_bonds(isite, site_neighbors_set)[source]
          +add_bonds(isite, site_neighbors_set)[source]

          Add the bonds for a given site index to the structure connectivity graph.

          Parameters
          @@ -155,19 +155,19 @@
          -add_sites()[source]
          +add_sites()[source]

          Add the sites in the structure connectivity graph.

          -as_dict()[source]
          +as_dict()[source]

          Returns:

          -environment_subgraph(environments_symbols=None, only_atoms=None)[source]
          +environment_subgraph(environments_symbols=None, only_atoms=None)[source]
          Parameters
            @@ -181,7 +181,7 @@
            -classmethod from_dict(d)[source]
            +classmethod from_dict(d)[source]
            Parameters

            () (d) –

            @@ -192,7 +192,7 @@
            -get_connected_components(environments_symbols=None, only_atoms=None)[source]
            +get_connected_components(environments_symbols=None, only_atoms=None)[source]
            Parameters
              @@ -206,13 +206,13 @@
              +print_links()[source]

              Returns:

              -setup_atom_environment_subgraph(atom_environment)[source]
              +setup_atom_environment_subgraph(atom_environment)[source]
              Parameters

              () (atom_environment) –

              @@ -223,7 +223,7 @@
              -setup_atom_environments_subgraph(atoms_environments)[source]
              +setup_atom_environments_subgraph(atoms_environments)[source]
              Parameters

              () (atoms_environments) –

              @@ -234,13 +234,13 @@
              -setup_connectivity_description()[source]
              +setup_connectivity_description()[source]

              Returns:

              -setup_environment_subgraph(environments_symbols, only_atoms=None)[source]
              +setup_environment_subgraph(environments_symbols, only_atoms=None)[source]

              Set up the graph for predefined environments and optionally atoms.

              Parameters
              @@ -254,7 +254,7 @@
              -setup_environments_subgraph(environments_symbols)[source]
              +setup_environments_subgraph(environments_symbols)[source]
              Parameters

              () (environments_symbols) –

              @@ -267,7 +267,7 @@
              -get_delta_image(isite1, isite2, data1, data2)[source]
              +get_delta_image(isite1, isite2, data1, data2)[source]

              Helper method to get the delta image between one environment and another from the ligand’s delta images.

              diff --git a/docs/pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html b/docs/pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html index 86bcc7ffc0e..551e038f8f8 100644 --- a/docs/pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html +++ b/docs/pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies module — pymatgen 2022.5.18 documentation + pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
              - 2022.5.18 + 2022.5.18.1
              @@ -123,7 +123,7 @@ fraction. The choice of the strategy depends on the purpose of the user.

              -class AbstractChemenvStrategy(structure_environments=None, symmetry_measure_type='csm_wcs_ctwcc')[source]
              +class AbstractChemenvStrategy(structure_environments=None, symmetry_measure_type='csm_wcs_ctwcc')[source]

              Bases: monty.json.MSONable

              Class used to define a Chemenv strategy for the neighbors and coordination environment to be applied to a StructureEnvironments object

              @@ -134,39 +134,39 @@
              -AC = <pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions object>[source]
              +AC = <pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions object>[source]
              -DEFAULT_SYMMETRY_MEASURE_TYPE = 'csm_wcs_ctwcc'[source]
              +DEFAULT_SYMMETRY_MEASURE_TYPE = 'csm_wcs_ctwcc'[source]
              -STRATEGY_DESCRIPTION: str = None[source]
              +STRATEGY_DESCRIPTION: str = None[source]
              -STRATEGY_INFO_FIELDS: List = [][source]
              +STRATEGY_INFO_FIELDS: List = [][source]
              -STRATEGY_OPTIONS: Dict[str, Dict] = {}[source]
              +STRATEGY_OPTIONS: Dict[str, Dict] = {}[source]
              -abstract as_dict()[source]
              +abstract as_dict()[source]

              Bson-serializable dict representation of the SimplestChemenvStrategy object. :return: Bson-serializable dict representation of the SimplestChemenvStrategy object.

              -equivalent_site_index_and_transform(psite)[source]
              +equivalent_site_index_and_transform(psite)[source]

              Get the equivalent site and corresponding symmetry+translation transformations.

              Parameters
              @@ -180,7 +180,7 @@
              -classmethod from_dict(d)[source]
              +classmethod from_dict(d)[source]

              Reconstructs the SimpleAbundanceChemenvStrategy object from a dict representation of the SimpleAbundanceChemenvStrategy object created using the as_dict method. :param d: dict representation of the SimpleAbundanceChemenvStrategy object @@ -189,7 +189,7 @@

              -get_site_ce_fractions_and_neighbors(site, full_ce_info=False, strategy_info=False)[source]
              +get_site_ce_fractions_and_neighbors(site, full_ce_info=False, strategy_info=False)[source]

              Applies the strategy to the structure_environments object in order to get coordination environments, their fraction, csm, geometry_info, and neighbors :param site: Site for which the above information is seeked @@ -199,7 +199,7 @@

              -abstract get_site_coordination_environment(site)[source]
              +abstract get_site_coordination_environment(site)[source]

              Applies the strategy to the structure_environments object in order to define the coordination environment of a given site. :param site: Site for which the coordination environment is looked for @@ -211,7 +211,7 @@

              -abstract get_site_coordination_environments(site)[source]
              +abstract get_site_coordination_environments(site)[source]

              Applies the strategy to the structure_environments object in order to define the coordination environment of a given site. :param site: Site for which the coordination environment is looked for @@ -223,7 +223,7 @@

              -abstract get_site_coordination_environments_fractions(site, isite=None, dequivsite=None, dthissite=None, mysym=None, ordered=True, min_fraction=0.0, return_maps=True, return_strategy_dict_info=False)[source]
              +abstract get_site_coordination_environments_fractions(site, isite=None, dequivsite=None, dthissite=None, mysym=None, ordered=True, min_fraction=0.0, return_maps=True, return_strategy_dict_info=False)[source]

              Applies the strategy to the structure_environments object in order to define the coordination environment of a given site. :param site: Site for which the coordination environment is looked for @@ -235,7 +235,7 @@

              -abstract get_site_neighbors(site)[source]
              +abstract get_site_neighbors(site)[source]

              Applies the strategy to the structure_environments object in order to get the neighbors of a given site. :param site: Site for which the neighbors are looked for :param structure_environments: StructureEnvironments object containing all the information needed to get the

              @@ -252,13 +252,13 @@
              -prepare_symmetries()[source]
              +prepare_symmetries()[source]

              Prepare the symmetries for the structure contained in the structure environments.

              -set_option(option_name, option_value)[source]
              +set_option(option_name, option_value)[source]

              Set up a given option for this strategy.

              Parameters
              @@ -275,7 +275,7 @@
              -set_structure_environments(structure_environments)[source]
              +set_structure_environments(structure_environments)[source]

              Set the structure environments to this strategy.

              Parameters
              @@ -289,7 +289,7 @@
              -setup_options(all_options_dict)[source]
              +setup_options(all_options_dict)[source]

              Set up options for this strategy based on a dict.

              Parameters
              @@ -303,13 +303,13 @@
              -property symmetry_measure_type[source]
              +property symmetry_measure_type[source]

              Type of symmetry measure.

              -property uniquely_determines_coordination_environments[source]
              +property uniquely_determines_coordination_environments[source]

              Returns True if the strategy leads to a unique coordination environment, False otherwise. :return: True if the strategy leads to a unique coordination environment, False otherwise.

              @@ -318,29 +318,29 @@
              -class AdditionalConditionInt(integer)[source]
              +class AdditionalConditionInt(integer)[source]

              Bases: int, pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.StrategyOption

              Integer representing an additional condition in a strategy.

              Special int representing additional conditions.

              -allowed_values: Optional[str] = 'Integer amongst :\n - 0 for "No additional condition"\n - 1 for "Only anion-cation bonds"\n - 2 for "No element-element bonds (same elements)"\n - 3 for "Only anion-cation bonds and no element-element bonds (same elements)"\n - 4 for "Only element-oxygen bonds"\n'[source]
              +allowed_values: Optional[str] = 'Integer amongst :\n - 0 for "No additional condition"\n - 1 for "Only anion-cation bonds"\n - 2 for "No element-element bonds (same elements)"\n - 3 for "Only anion-cation bonds and no element-element bonds (same elements)"\n - 4 for "Only element-oxygen bonds"\n'[source]
              -as_dict()[source]
              +as_dict()[source]

              MSONable dict

              -description = 'Only element-oxygen bonds'[source]
              +description = 'Only element-oxygen bonds'[source]
              -classmethod from_dict(d)[source]
              +classmethod from_dict(d)[source]

              Initialize additional condition from dict.

              Parameters
              @@ -351,14 +351,14 @@
              -integer = 4[source]
              +integer = 4[source]
              -class AngleCutoffFloat(myfloat)[source]
              +class AngleCutoffFloat(myfloat)[source]

              Bases: float, pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.StrategyOption

              Angle cutoff in a strategy

              Special float that should be between 0.0 and 1.0.

              @@ -369,18 +369,18 @@
              -allowed_values: Optional[str] = 'Real number between 0.0 and 1.0'[source]
              +allowed_values: Optional[str] = 'Real number between 0.0 and 1.0'[source]
              -as_dict()[source]
              +as_dict()[source]

              MSONAble dict

              -classmethod from_dict(d)[source]
              +classmethod from_dict(d)[source]

              Initialize angle cutoff from dict.

              Parameters
              @@ -393,7 +393,7 @@
              -class AngleNbSetWeight(aa=1.0)[source]
              +class AngleNbSetWeight(aa=1.0)[source]

              Bases: pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.NbSetWeight

              Weight of neighbors set based on the angle.

              Initialize AngleNbSetWeight estimator.

              @@ -404,12 +404,12 @@
              -SHORT_NAME = 'AngleWeight'[source]
              +SHORT_NAME = 'AngleWeight'[source]
              -static angle_sum(nb_set)[source]
              +static angle_sum(nb_set)[source]

              Sum of all angles in a neighbors set.

              Parameters
              @@ -423,7 +423,7 @@
              -angle_sumn(nb_set)[source]
              +angle_sumn(nb_set)[source]

              Sum of all angles to a given power in a neighbors set.

              Parameters
              @@ -437,13 +437,13 @@
              -as_dict()[source]
              +as_dict()[source]

              MSONAble dict

              -classmethod from_dict(dd)[source]
              +classmethod from_dict(dd)[source]

              From dict :param dd: :return:

              @@ -451,7 +451,7 @@
              -weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]
              +weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]

              Get the weight of a given neighbors set.

              Parameters
              @@ -472,7 +472,7 @@
              -class AnglePlateauNbSetWeight(angle_function=None, weight_function=None)[source]
              +class AnglePlateauNbSetWeight(angle_function=None, weight_function=None)[source]

              Bases: pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.NbSetWeight

              Weight of neighbors set based on the angle.

              Initialize AnglePlateauNbSetWeight.

              @@ -486,18 +486,18 @@
              -SHORT_NAME = 'AnglePlateauWeight'[source]
              +SHORT_NAME = 'AnglePlateauWeight'[source]
              -as_dict()[source]
              +as_dict()[source]

              MSONable dict

              -classmethod from_dict(dd)[source]
              +classmethod from_dict(dd)[source]

              Initialize from dict.

              Parameters
              @@ -511,7 +511,7 @@
              -weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]
              +weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]

              Get the weight of a given neighbors set.

              Parameters
              @@ -532,7 +532,7 @@
              -class CNBiasNbSetWeight(cn_weights, initialization_options)[source]
              +class CNBiasNbSetWeight(cn_weights, initialization_options)[source]

              Bases: pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.NbSetWeight

              Weight of neighbors set based on specific biases towards specific coordination numbers.

              Initialize CNBiasNbSetWeight.

              @@ -546,18 +546,18 @@
              -SHORT_NAME = 'CNBiasWeight'[source]
              +SHORT_NAME = 'CNBiasWeight'[source]
              -as_dict()[source]
              +as_dict()[source]

              MSONable dict

              -classmethod explicit(cn_weights)[source]
              +classmethod explicit(cn_weights)[source]

              Initializes weights explicitly for each coordination.

              Parameters
              @@ -571,7 +571,7 @@
              -classmethod from_description(dd)[source]
              +classmethod from_description(dd)[source]

              Initializes weights from description.

              Parameters
              @@ -585,7 +585,7 @@
              -classmethod from_dict(dd)[source]
              +classmethod from_dict(dd)[source]

              Initialize from dict.

              Parameters
              @@ -599,7 +599,7 @@
              -classmethod geometrically_equidistant(weight_cn1, weight_cn13)[source]
              +classmethod geometrically_equidistant(weight_cn1, weight_cn13)[source]

              Initializes geometrically equidistant weights for each coordination.

              Parameters
              @@ -616,7 +616,7 @@
              -classmethod linearly_equidistant(weight_cn1, weight_cn13)[source]
              +classmethod linearly_equidistant(weight_cn1, weight_cn13)[source]

              Initializes linearly equidistant weights for each coordination.

              Parameters
              @@ -633,7 +633,7 @@
              -weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]
              +weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]

              Get the weight of a given neighbors set.

              Parameters
              @@ -654,7 +654,7 @@
              -class CSMFloat(myfloat)[source]
              +class CSMFloat(myfloat)[source]

              Bases: float, pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.StrategyOption

              Real number representing a Continuous Symmetry Measure

              Special float that should be between 0.0 and 100.0.

              @@ -665,18 +665,18 @@
              -allowed_values: Optional[str] = 'Real number between 0.0 and 100.0'[source]
              +allowed_values: Optional[str] = 'Real number between 0.0 and 100.0'[source]
              -as_dict()[source]
              +as_dict()[source]

              MSONable dict

              -classmethod from_dict(d)[source]
              +classmethod from_dict(d)[source]

              Initialize CSM from dict.

              Parameters
              @@ -689,7 +689,7 @@
              -class DeltaCSMNbSetWeight(effective_csm_estimator={'function': 'power2_inverse_decreasing', 'options': {'max_csm': 8.0}}, weight_estimator={'function': 'smootherstep', 'options': {'delta_csm_max': 3.0, 'delta_csm_min': 0.5}}, delta_cn_weight_estimators=None, symmetry_measure_type='csm_wcs_ctwcc')[source]
              +class DeltaCSMNbSetWeight(effective_csm_estimator={'function': 'power2_inverse_decreasing', 'options': {'max_csm': 8.0}}, weight_estimator={'function': 'smootherstep', 'options': {'delta_csm_max': 3.0, 'delta_csm_min': 0.5}}, delta_cn_weight_estimators=None, symmetry_measure_type='csm_wcs_ctwcc')[source]

              Bases: pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.NbSetWeight

              Weight of neighbors set based on the differences of CSM.

              Initialize SelfCSMNbSetWeight.

              @@ -705,34 +705,34 @@
              -DEFAULT_EFFECTIVE_CSM_ESTIMATOR = {'function': 'power2_inverse_decreasing', 'options': {'max_csm': 8.0}}[source]
              +DEFAULT_EFFECTIVE_CSM_ESTIMATOR = {'function': 'power2_inverse_decreasing', 'options': {'max_csm': 8.0}}[source]
              -DEFAULT_SYMMETRY_MEASURE_TYPE = 'csm_wcs_ctwcc'[source]
              +DEFAULT_SYMMETRY_MEASURE_TYPE = 'csm_wcs_ctwcc'[source]
              -DEFAULT_WEIGHT_ESTIMATOR = {'function': 'smootherstep', 'options': {'delta_csm_max': 3.0, 'delta_csm_min': 0.5}}[source]
              +DEFAULT_WEIGHT_ESTIMATOR = {'function': 'smootherstep', 'options': {'delta_csm_max': 3.0, 'delta_csm_min': 0.5}}[source]
              -SHORT_NAME = 'DeltaCSMWeight'[source]
              +SHORT_NAME = 'DeltaCSMWeight'[source]
              -as_dict()[source]
              +as_dict()[source]

              MSONable dict. :return:

              -classmethod delta_cn_specifics(delta_csm_mins=None, delta_csm_maxs=None, function='smootherstep', symmetry_measure_type='csm_wcs_ctwcc', effective_csm_estimator={'function': 'power2_inverse_decreasing', 'options': {'max_csm': 8.0}})[source]
              +classmethod delta_cn_specifics(delta_csm_mins=None, delta_csm_maxs=None, function='smootherstep', symmetry_measure_type='csm_wcs_ctwcc', effective_csm_estimator={'function': 'power2_inverse_decreasing', 'options': {'max_csm': 8.0}})[source]

              Initializes DeltaCSMNbSetWeight from specific coordination number differences.

              Parameters
              @@ -752,7 +752,7 @@
              -classmethod from_dict(dd)[source]
              +classmethod from_dict(dd)[source]

              Initialize from dict.

              Parameters
              @@ -766,7 +766,7 @@
              -weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]
              +weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]

              Get the weight of a given neighbors set.

              Parameters
              @@ -787,7 +787,7 @@
              -class DeltaDistanceNbSetWeight(weight_function=None, nbs_source='voronoi')[source]
              +class DeltaDistanceNbSetWeight(weight_function=None, nbs_source='voronoi')[source]

              Bases: pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.NbSetWeight

              Weight of neighbors set based on the difference of distances.

              Initialize DeltaDistanceNbSetWeight.

              @@ -801,18 +801,18 @@
              -SHORT_NAME = 'DeltaDistanceNbSetWeight'[source]
              +SHORT_NAME = 'DeltaDistanceNbSetWeight'[source]
              -as_dict()[source]
              +as_dict()[source]

              MSONable dict

              -classmethod from_dict(dd)[source]
              +classmethod from_dict(dd)[source]

              Initialize from dict.

              Parameters
              @@ -826,7 +826,7 @@
              -weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]
              +weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]

              Get the weight of a given neighbors set.

              Parameters
              @@ -847,7 +847,7 @@
              -class DistanceAngleAreaNbSetWeight(weight_type='has_intersection', surface_definition={'angle_bounds': {'lower': 0.1, 'upper': 0.8}, 'distance_bounds': {'lower': 1.2, 'upper': 1.8}, 'type': 'standard_elliptic'}, nb_sets_from_hints='fallback_to_source', other_nb_sets='0_weight', additional_condition=1, smoothstep_distance=None, smoothstep_angle=None)[source]
              +class DistanceAngleAreaNbSetWeight(weight_type='has_intersection', surface_definition={'angle_bounds': {'lower': 0.1, 'upper': 0.8}, 'distance_bounds': {'lower': 1.2, 'upper': 1.8}, 'type': 'standard_elliptic'}, nb_sets_from_hints='fallback_to_source', other_nb_sets='0_weight', additional_condition=1, smoothstep_distance=None, smoothstep_angle=None)[source]

              Bases: pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.NbSetWeight

              Weight of neighbors set based on the area in the distance-angle space.

              Initialize CNBiasNbSetWeight.

              @@ -866,28 +866,28 @@
              -AC = <pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions object>[source]
              +AC = <pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions object>[source]
              -DEFAULT_SURFACE_DEFINITION = {'angle_bounds': {'lower': 0.1, 'upper': 0.8}, 'distance_bounds': {'lower': 1.2, 'upper': 1.8}, 'type': 'standard_elliptic'}[source]
              +DEFAULT_SURFACE_DEFINITION = {'angle_bounds': {'lower': 0.1, 'upper': 0.8}, 'distance_bounds': {'lower': 1.2, 'upper': 1.8}, 'type': 'standard_elliptic'}[source]
              -SHORT_NAME = 'DistAngleAreaWeight'[source]
              +SHORT_NAME = 'DistAngleAreaWeight'[source]
              -as_dict()[source]
              +as_dict()[source]

              MSONable dict

              -classmethod from_dict(dd)[source]
              +classmethod from_dict(dd)[source]

              Initialize from dict.

              Parameters
              @@ -901,7 +901,7 @@
              -rectangle_crosses_area(d1, d2, a1, a2)[source]
              +rectangle_crosses_area(d1, d2, a1, a2)[source]

              Whether a given rectangle crosses the area defined by the upper and lower curves.

              Parameters
              @@ -920,7 +920,7 @@
              -w_area_has_intersection(nb_set, structure_environments, cn_map, additional_info)[source]
              +w_area_has_intersection(nb_set, structure_environments, cn_map, additional_info)[source]

              Get intersection of the neighbors set area with the surface.

              Parameters
              @@ -939,7 +939,7 @@
              -w_area_has_intersection_smoothstep(nb_set, structure_environments, cn_map, additional_info)[source]
              +w_area_has_intersection_smoothstep(nb_set, structure_environments, cn_map, additional_info)[source]

              Get intersection of the neighbors set area with the surface.

              Parameters
              @@ -958,7 +958,7 @@
              -w_area_intersection_nbsfh_fbs_onb0(nb_set, structure_environments, cn_map, additional_info)[source]
              +w_area_intersection_nbsfh_fbs_onb0(nb_set, structure_environments, cn_map, additional_info)[source]

              Get intersection of the neighbors set area with the surface.

              Parameters
              @@ -977,7 +977,7 @@
              -weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]
              +weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]

              Get the weight of a given neighbors set.

              Parameters
              @@ -998,7 +998,7 @@
              -class DistanceCutoffFloat(myfloat)[source]
              +class DistanceCutoffFloat(myfloat)[source]

              Bases: float, pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.StrategyOption

              Distance cutoff in a strategy.

              Special float that should be between 1.0 and infinity.

              @@ -1009,18 +1009,18 @@
              -allowed_values: Optional[str] = 'Real number between 1.0 and +infinity'[source]
              +allowed_values: Optional[str] = 'Real number between 1.0 and +infinity'[source]
              -as_dict()[source]
              +as_dict()[source]

              MSONAble dict

              -classmethod from_dict(d)[source]
              +classmethod from_dict(d)[source]

              Initialize distance cutoff from dict.

              Parameters
              @@ -1033,7 +1033,7 @@
              -class DistanceNbSetWeight(weight_function=None, nbs_source='voronoi')[source]
              +class DistanceNbSetWeight(weight_function=None, nbs_source='voronoi')[source]

              Bases: pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.NbSetWeight

              Weight of neighbors set based on the distance.

              Initialize DistanceNbSetWeight.

              @@ -1047,18 +1047,18 @@
              -SHORT_NAME = 'DistanceNbSetWeight'[source]
              +SHORT_NAME = 'DistanceNbSetWeight'[source]
              -as_dict()[source]
              +as_dict()[source]

              MSOnable dict

              -classmethod from_dict(dd)[source]
              +classmethod from_dict(dd)[source]

              Initialize from dict.

              Parameters
              @@ -1072,7 +1072,7 @@
              -weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]
              +weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]

              Get the weight of a given neighbors set.

              Parameters
              @@ -1093,7 +1093,7 @@
              -class DistancePlateauNbSetWeight(distance_function=None, weight_function=None)[source]
              +class DistancePlateauNbSetWeight(distance_function=None, weight_function=None)[source]

              Bases: pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.NbSetWeight

              Weight of neighbors set based on the distance.

              Initialize DistancePlateauNbSetWeight.

              @@ -1107,18 +1107,18 @@
              -SHORT_NAME = 'DistancePlateauWeight'[source]
              +SHORT_NAME = 'DistancePlateauWeight'[source]
              -as_dict()[source]
              +as_dict()[source]

              MSONable dict

              -classmethod from_dict(dd)[source]
              +classmethod from_dict(dd)[source]

              Initialize from dict.

              Parameters
              @@ -1132,7 +1132,7 @@
              -weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]
              +weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]

              Get the weight of a given neighbors set.

              Parameters
              @@ -1153,7 +1153,7 @@
              -class MultiWeightsChemenvStrategy(structure_environments=None, additional_condition=1, symmetry_measure_type='csm_wcs_ctwcc', dist_ang_area_weight=None, self_csm_weight=None, delta_csm_weight=None, cn_bias_weight=None, angle_weight=None, normalized_angle_distance_weight=None, ce_estimator={'function': 'power2_inverse_power2_decreasing', 'options': {'max_csm': 8.0}})[source]
              +class MultiWeightsChemenvStrategy(structure_environments=None, additional_condition=1, symmetry_measure_type='csm_wcs_ctwcc', dist_ang_area_weight=None, self_csm_weight=None, delta_csm_weight=None, cn_bias_weight=None, angle_weight=None, normalized_angle_distance_weight=None, ce_estimator={'function': 'power2_inverse_power2_decreasing', 'options': {'max_csm': 8.0}})[source]

              Bases: pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.WeightedNbSetChemenvStrategy

              Constructor for the MultiWeightsChemenvStrategy. :param structure_environments: StructureEnvironments object containing all the information on the

              @@ -1162,29 +1162,29 @@
          -DEFAULT_CE_ESTIMATOR = {'function': 'power2_inverse_power2_decreasing', 'options': {'max_csm': 8.0}}[source]
          +DEFAULT_CE_ESTIMATOR = {'function': 'power2_inverse_power2_decreasing', 'options': {'max_csm': 8.0}}[source]
          -DEFAULT_DIST_ANG_AREA_WEIGHT: Dict = {}[source]
          +DEFAULT_DIST_ANG_AREA_WEIGHT: Dict = {}[source]
          -STRATEGY_DESCRIPTION: str = '    Multi Weights ChemenvStrategy'[source]
          +STRATEGY_DESCRIPTION: str = '    Multi Weights ChemenvStrategy'[source]
          -as_dict()[source]
          +as_dict()[source]

          Bson-serializable dict representation of the MultiWeightsChemenvStrategy object. :return: Bson-serializable dict representation of the MultiWeightsChemenvStrategy object.

          -classmethod from_dict(d)[source]
          +classmethod from_dict(d)[source]

          Reconstructs the MultiWeightsChemenvStrategy object from a dict representation of the MultipleAbundanceChemenvStrategy object created using the as_dict method. :param d: dict representation of the MultiWeightsChemenvStrategy object @@ -1193,13 +1193,13 @@

          -classmethod stats_article_weights_parameters()[source]
          +classmethod stats_article_weights_parameters()[source]

          Initialize strategy used in the statistics article.

          -property uniquely_determines_coordination_environments[source]
          +property uniquely_determines_coordination_environments[source]

          Whether this strategy uniquely determines coordination environments.

          @@ -1207,18 +1207,18 @@
          -class NbSetWeight[source]
          +class NbSetWeight[source]

          Bases: monty.json.MSONable

          Abstract object for neighbors sets weights estimations.

          -abstract as_dict()[source]
          +abstract as_dict()[source]

          A JSON-serializable dict representation of this neighbors set weight.

          -abstract weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]
          +abstract weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]

          Get the weight of a given neighbors set.

          Parameters
          @@ -1239,7 +1239,7 @@
          -class NormalizedAngleDistanceNbSetWeight(average_type, aa, bb)[source]
          +class NormalizedAngleDistanceNbSetWeight(average_type, aa, bb)[source]

          Bases: pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.NbSetWeight

          Weight of neighbors set based on the normalized angle/distance.

          Initialize NormalizedAngleDistanceNbSetWeight.

          @@ -1254,12 +1254,12 @@
          -SHORT_NAME = 'NormAngleDistWeight'[source]
          +SHORT_NAME = 'NormAngleDistWeight'[source]
          -static ang(nb_set)[source]
          +static ang(nb_set)[source]

          Angle weight.

          Parameters
          @@ -1273,7 +1273,7 @@
          -static anginvdist(nb_set)[source]
          +static anginvdist(nb_set)[source]

          Angle/distance weight.

          Parameters
          @@ -1287,7 +1287,7 @@
          -anginvndist(nb_set)[source]
          +anginvndist(nb_set)[source]

          Angle/power distance weight.

          Parameters
          @@ -1301,7 +1301,7 @@
          -angn(nb_set)[source]
          +angn(nb_set)[source]

          Power angle weight.

          Parameters
          @@ -1315,7 +1315,7 @@
          -angninvdist(nb_set)[source]
          +angninvdist(nb_set)[source]

          Power angle/distance weight.

          Parameters
          @@ -1329,7 +1329,7 @@
          -angninvndist(nb_set)[source]
          +angninvndist(nb_set)[source]

          Power angle/power distance weight.

          Parameters
          @@ -1343,13 +1343,13 @@
          -as_dict()[source]
          +as_dict()[source]

          MSONable dict

          -static aweight(fda_list)[source]
          +static aweight(fda_list)[source]

          Standard mean of the weights.

          Parameters
          @@ -1363,7 +1363,7 @@
          -classmethod from_dict(dd)[source]
          +classmethod from_dict(dd)[source]

          Initialize from dict.

          Parameters
          @@ -1377,7 +1377,7 @@
          -static gweight(fda_list)[source]
          +static gweight(fda_list)[source]

          Geometric mean of the weights.

          Parameters
          @@ -1391,7 +1391,7 @@
          -static invdist(nb_set)[source]
          +static invdist(nb_set)[source]

          Inverse distance weight.

          Parameters
          @@ -1405,7 +1405,7 @@
          -invndist(nb_set)[source]
          +invndist(nb_set)[source]

          Inverse power distance weight.

          Parameters
          @@ -1419,7 +1419,7 @@
          -weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]
          +weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]

          Get the weight of a given neighbors set.

          Parameters
          @@ -1440,7 +1440,7 @@
          -class SelfCSMNbSetWeight(effective_csm_estimator={'function': 'power2_inverse_decreasing', 'options': {'max_csm': 8.0}}, weight_estimator={'function': 'power2_decreasing_exp', 'options': {'alpha': 1.0, 'max_csm': 8.0}}, symmetry_measure_type='csm_wcs_ctwcc')[source]
          +class SelfCSMNbSetWeight(effective_csm_estimator={'function': 'power2_inverse_decreasing', 'options': {'max_csm': 8.0}}, weight_estimator={'function': 'power2_decreasing_exp', 'options': {'alpha': 1.0, 'max_csm': 8.0}}, symmetry_measure_type='csm_wcs_ctwcc')[source]

          Bases: pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.NbSetWeight

          Weight of neighbors set based on the Self CSM.

          Initialize SelfCSMNbSetWeight.

          @@ -1455,33 +1455,33 @@
          -DEFAULT_EFFECTIVE_CSM_ESTIMATOR = {'function': 'power2_inverse_decreasing', 'options': {'max_csm': 8.0}}[source]
          +DEFAULT_EFFECTIVE_CSM_ESTIMATOR = {'function': 'power2_inverse_decreasing', 'options': {'max_csm': 8.0}}[source]
          -DEFAULT_SYMMETRY_MEASURE_TYPE = 'csm_wcs_ctwcc'[source]
          +DEFAULT_SYMMETRY_MEASURE_TYPE = 'csm_wcs_ctwcc'[source]
          -DEFAULT_WEIGHT_ESTIMATOR = {'function': 'power2_decreasing_exp', 'options': {'alpha': 1.0, 'max_csm': 8.0}}[source]
          +DEFAULT_WEIGHT_ESTIMATOR = {'function': 'power2_decreasing_exp', 'options': {'alpha': 1.0, 'max_csm': 8.0}}[source]
          -SHORT_NAME = 'SelfCSMWeight'[source]
          +SHORT_NAME = 'SelfCSMWeight'[source]
          -as_dict()[source]
          +as_dict()[source]

          MSONable dict

          -classmethod from_dict(dd)[source]
          +classmethod from_dict(dd)[source]

          Initialize from dict.

          Parameters
          @@ -1495,7 +1495,7 @@
          -weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]
          +weight(nb_set, structure_environments, cn_map=None, additional_info=None)[source]

          Get the weight of a given neighbors set.

          Parameters
          @@ -1516,7 +1516,7 @@
          -class SimpleAbundanceChemenvStrategy(structure_environments=None, additional_condition=1, symmetry_measure_type='csm_wcs_ctwcc')[source]
          +class SimpleAbundanceChemenvStrategy(structure_environments=None, additional_condition=1, symmetry_measure_type='csm_wcs_ctwcc')[source]

          Bases: pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy

          Simple ChemenvStrategy using the neighbors that are the most “abundant” in the grid of angle and distance parameters for the definition of neighbors in the Voronoi approach. @@ -1528,34 +1528,34 @@

          -DEFAULT_ADDITIONAL_CONDITION = 1[source]
          +DEFAULT_ADDITIONAL_CONDITION = 1[source]
          -DEFAULT_MAX_DIST = 2.0[source]
          +DEFAULT_MAX_DIST = 2.0[source]
          -STRATEGY_DESCRIPTION: str = '    Simple Abundance ChemenvStrategy using the most "abundant" neighbors map \n    for the definition of neighbors in the Voronoi approach. \n    The coordination environment is then given as the one with the \n    lowest continuous symmetry measure.'[source]
          +STRATEGY_DESCRIPTION: str = '    Simple Abundance ChemenvStrategy using the most "abundant" neighbors map \n    for the definition of neighbors in the Voronoi approach. \n    The coordination environment is then given as the one with the \n    lowest continuous symmetry measure.'[source]
          -STRATEGY_OPTIONS: Dict[str, Dict] = {'additional_condition': {'default': 1, 'internal': '_additional_condition', 'type': <class 'pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AdditionalConditionInt'>}, 'surface_calculation_type': {}}[source]
          +STRATEGY_OPTIONS: Dict[str, Dict] = {'additional_condition': {'default': 1, 'internal': '_additional_condition', 'type': <class 'pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AdditionalConditionInt'>}, 'surface_calculation_type': {}}[source]
          -as_dict()[source]
          +as_dict()[source]

          Bson-serializable dict representation of the SimpleAbundanceChemenvStrategy object. :return: Bson-serializable dict representation of the SimpleAbundanceChemenvStrategy object.

          -classmethod from_dict(d)[source]
          +classmethod from_dict(d)[source]

          Reconstructs the SimpleAbundanceChemenvStrategy object from a dict representation of the SimpleAbundanceChemenvStrategy object created using the as_dict method. :param d: dict representation of the SimpleAbundanceChemenvStrategy object @@ -1564,7 +1564,7 @@

          -get_site_coordination_environment(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_map=False)[source]
          +get_site_coordination_environment(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_map=False)[source]

          Get the coordination environment of a given site.

          Parameters
          @@ -1585,7 +1585,7 @@
          -get_site_coordination_environments(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_maps=False)[source]
          +get_site_coordination_environments(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_maps=False)[source]

          Get the coordination environments of a given site.

          Parameters
          @@ -1606,7 +1606,7 @@
          -get_site_neighbors(site)[source]
          +get_site_neighbors(site)[source]

          Get the neighbors of a given site with this strategy.

          Parameters
          @@ -1620,7 +1620,7 @@
          -property uniquely_determines_coordination_environments[source]
          +property uniquely_determines_coordination_environments[source]

          Whether this strategy uniquely determines coordination environments.

          @@ -1628,7 +1628,7 @@
          -class SimplestChemenvStrategy(structure_environments=None, distance_cutoff=1.4, angle_cutoff=0.3, additional_condition=1, continuous_symmetry_measure_cutoff=10.0, symmetry_measure_type='csm_wcs_ctwcc')[source]
          +class SimplestChemenvStrategy(structure_environments=None, distance_cutoff=1.4, angle_cutoff=0.3, additional_condition=1, continuous_symmetry_measure_cutoff=10.0, symmetry_measure_type='csm_wcs_ctwcc')[source]

          Bases: pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy

          Simplest ChemenvStrategy using fixed angle and distance parameters for the definition of neighbors in the Voronoi approach. The coordination environment is then given as the one with the lowest continuous symmetry measure

          @@ -1637,37 +1637,37 @@ :param angle_cutoff: Angle cutoff used

          -DEFAULT_ADDITIONAL_CONDITION = 1[source]
          +DEFAULT_ADDITIONAL_CONDITION = 1[source]
          -DEFAULT_ANGLE_CUTOFF = 0.3[source]
          +DEFAULT_ANGLE_CUTOFF = 0.3[source]
          -DEFAULT_CONTINUOUS_SYMMETRY_MEASURE_CUTOFF = 10.0[source]
          +DEFAULT_CONTINUOUS_SYMMETRY_MEASURE_CUTOFF = 10.0[source]
          -DEFAULT_DISTANCE_CUTOFF = 1.4[source]
          +DEFAULT_DISTANCE_CUTOFF = 1.4[source]
          -STRATEGY_DESCRIPTION: str = '    Simplest ChemenvStrategy using fixed angle and distance parameters \n    for the definition of neighbors in the Voronoi approach. \n    The coordination environment is then given as the one with the \n    lowest continuous symmetry measure.'[source]
          +STRATEGY_DESCRIPTION: str = '    Simplest ChemenvStrategy using fixed angle and distance parameters \n    for the definition of neighbors in the Voronoi approach. \n    The coordination environment is then given as the one with the \n    lowest continuous symmetry measure.'[source]
          -STRATEGY_OPTIONS: Dict[str, Dict] = {'additional_condition': {'default': 1, 'internal': '_additional_condition', 'type': <class 'pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AdditionalConditionInt'>}, 'angle_cutoff': {'default': 0.3, 'internal': '_angle_cutoff', 'type': <class 'pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleCutoffFloat'>}, 'continuous_symmetry_measure_cutoff': {'default': 10.0, 'internal': '_continuous_symmetry_measure_cutoff', 'type': <class 'pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CSMFloat'>}, 'distance_cutoff': {'default': 1.4, 'internal': '_distance_cutoff', 'type': <class 'pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.DistanceCutoffFloat'>}}[source]
          +STRATEGY_OPTIONS: Dict[str, Dict] = {'additional_condition': {'default': 1, 'internal': '_additional_condition', 'type': <class 'pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AdditionalConditionInt'>}, 'angle_cutoff': {'default': 0.3, 'internal': '_angle_cutoff', 'type': <class 'pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleCutoffFloat'>}, 'continuous_symmetry_measure_cutoff': {'default': 10.0, 'internal': '_continuous_symmetry_measure_cutoff', 'type': <class 'pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CSMFloat'>}, 'distance_cutoff': {'default': 1.4, 'internal': '_distance_cutoff', 'type': <class 'pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.DistanceCutoffFloat'>}}[source]
          -add_strategy_visualization_to_subplot(subplot, visualization_options=None, plot_type=None)[source]
          +add_strategy_visualization_to_subplot(subplot, visualization_options=None, plot_type=None)[source]

          Add a visual of the strategy on a distance-angle plot.

          Parameters
          @@ -1685,38 +1685,38 @@
          -property additional_condition[source]
          +property additional_condition[source]

          Additional condition for this strategy.

          -property angle_cutoff[source]
          +property angle_cutoff[source]

          Angle cutoff used.

          -as_dict()[source]
          +as_dict()[source]

          Bson-serializable dict representation of the SimplestChemenvStrategy object. :return: Bson-serializable dict representation of the SimplestChemenvStrategy object.

          -property continuous_symmetry_measure_cutoff[source]
          +property continuous_symmetry_measure_cutoff[source]

          CSM cutoff used

          -property distance_cutoff[source]
          +property distance_cutoff[source]

          Distance cutoff used.

          -classmethod from_dict(d)[source]
          +classmethod from_dict(d)[source]

          Reconstructs the SimplestChemenvStrategy object from a dict representation of the SimplestChemenvStrategy object created using the as_dict method. :param d: dict representation of the SimplestChemenvStrategy object @@ -1725,7 +1725,7 @@

          -get_site_coordination_environment(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_map=False)[source]
          +get_site_coordination_environment(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_map=False)[source]

          Get the coordination environment of a given site.

          Parameters
          @@ -1746,7 +1746,7 @@
          -get_site_coordination_environments(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_maps=False)[source]
          +get_site_coordination_environments(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_maps=False)[source]

          Get the coordination environments of a given site.

          Parameters
          @@ -1767,7 +1767,7 @@
          -get_site_coordination_environments_fractions(site, isite=None, dequivsite=None, dthissite=None, mysym=None, ordered=True, min_fraction=0.0, return_maps=True, return_strategy_dict_info=False)[source]
          +get_site_coordination_environments_fractions(site, isite=None, dequivsite=None, dthissite=None, mysym=None, ordered=True, min_fraction=0.0, return_maps=True, return_strategy_dict_info=False)[source]

          Get the coordination environments of a given site and additional information.

          Parameters
          @@ -1791,7 +1791,7 @@
          -get_site_neighbors(site, isite=None, dequivsite=None, dthissite=None, mysym=None)[source]
          +get_site_neighbors(site, isite=None, dequivsite=None, dthissite=None, mysym=None)[source]

          Get the neighbors of a given site.

          Parameters
          @@ -1811,7 +1811,7 @@
          -property uniquely_determines_coordination_environments[source]
          +property uniquely_determines_coordination_environments[source]

          Whether this strategy uniquely determines coordination environments.

          @@ -1819,17 +1819,17 @@
          -class StrategyOption[source]
          +class StrategyOption[source]

          Bases: monty.json.MSONable

          Abstract class for the options of the chemenv strategies.

          -allowed_values: Optional[str] = None[source]
          +allowed_values: Optional[str] = None[source]
          -abstract as_dict()[source]
          +abstract as_dict()[source]

          A JSON-serializable dict representation of this strategy option.

          @@ -1837,7 +1837,7 @@
          -class TargettedPenaltiedAbundanceChemenvStrategy(structure_environments=None, truncate_dist_ang=True, additional_condition=1, max_nabundant=5, target_environments=['O:6'], target_penalty_type='max_csm', max_csm=5.0, symmetry_measure_type='csm_wcs_ctwcc')[source]
          +class TargettedPenaltiedAbundanceChemenvStrategy(structure_environments=None, truncate_dist_ang=True, additional_condition=1, max_nabundant=5, target_environments=['O:6'], target_penalty_type='max_csm', max_csm=5.0, symmetry_measure_type='csm_wcs_ctwcc')[source]

          Bases: pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimpleAbundanceChemenvStrategy

          Simple ChemenvStrategy using the neighbors that are the most “abundant” in the grid of angle and distance parameters for the definition of neighbors in the Voronoi approach, with a bias for a given list of target @@ -1855,19 +1855,19 @@ :param symmetry_measure_type:

          -DEFAULT_TARGET_ENVIRONMENTS = ['O:6'][source]
          +DEFAULT_TARGET_ENVIRONMENTS = ['O:6'][source]
          -as_dict()[source]
          +as_dict()[source]

          Bson-serializable dict representation of the TargettedPenaltiedAbundanceChemenvStrategy object. :return: Bson-serializable dict representation of the TargettedPenaltiedAbundanceChemenvStrategy object.

          -classmethod from_dict(d)[source]
          +classmethod from_dict(d)[source]

          Reconstructs the TargettedPenaltiedAbundanceChemenvStrategy object from a dict representation of the TargettedPenaltiedAbundanceChemenvStrategy object created using the as_dict method. :param d: dict representation of the TargettedPenaltiedAbundanceChemenvStrategy object @@ -1876,7 +1876,7 @@

          -get_site_coordination_environment(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_map=False)[source]
          +get_site_coordination_environment(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_map=False)[source]

          Get the coordination environment of a given site.

          Parameters
          @@ -1897,7 +1897,7 @@
          -property uniquely_determines_coordination_environments[source]
          +property uniquely_determines_coordination_environments[source]

          Whether this strategy uniquely determines coordination environments.

          @@ -1905,7 +1905,7 @@
          -class WeightedNbSetChemenvStrategy(structure_environments=None, additional_condition=1, symmetry_measure_type='csm_wcs_ctwcc', nb_set_weights=None, ce_estimator={'function': 'power2_inverse_power2_decreasing', 'options': {'max_csm': 8.0}})[source]
          +class WeightedNbSetChemenvStrategy(structure_environments=None, additional_condition=1, symmetry_measure_type='csm_wcs_ctwcc', nb_set_weights=None, ce_estimator={'function': 'power2_inverse_power2_decreasing', 'options': {'max_csm': 8.0}})[source]

          Bases: pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy

          Constructor for the WeightedNbSetChemenvStrategy. :param structure_environments: StructureEnvironments object containing all the information on the

          @@ -1914,24 +1914,24 @@
          -DEFAULT_CE_ESTIMATOR = {'function': 'power2_inverse_power2_decreasing', 'options': {'max_csm': 8.0}}[source]
          +DEFAULT_CE_ESTIMATOR = {'function': 'power2_inverse_power2_decreasing', 'options': {'max_csm': 8.0}}[source]
          -STRATEGY_DESCRIPTION: str = '    WeightedNbSetChemenvStrategy'[source]
          +STRATEGY_DESCRIPTION: str = '    WeightedNbSetChemenvStrategy'[source]
          -as_dict()[source]
          +as_dict()[source]

          Bson-serializable dict representation of the WeightedNbSetChemenvStrategy object. :return: Bson-serializable dict representation of the WeightedNbSetChemenvStrategy object.

          -classmethod from_dict(d)[source]
          +classmethod from_dict(d)[source]

          Reconstructs the WeightedNbSetChemenvStrategy object from a dict representation of the WeightedNbSetChemenvStrategy object created using the as_dict method. :param d: dict representation of the WeightedNbSetChemenvStrategy object @@ -1940,14 +1940,14 @@

          -get_site_coordination_environment(site)[source]
          +get_site_coordination_environment(site)[source]

          Get the coordination environment of a given site.

          Not implemented for this strategy

          -get_site_coordination_environments(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_maps=False)[source]
          +get_site_coordination_environments(site, isite=None, dequivsite=None, dthissite=None, mysym=None, return_maps=False)[source]

          Get the coordination environments of a given site.

          Parameters
          @@ -1968,7 +1968,7 @@
          -get_site_coordination_environments_fractions(site, isite=None, dequivsite=None, dthissite=None, mysym=None, ordered=True, min_fraction=0.0, return_maps=True, return_strategy_dict_info=False, return_all=False)[source]
          +get_site_coordination_environments_fractions(site, isite=None, dequivsite=None, dthissite=None, mysym=None, ordered=True, min_fraction=0.0, return_maps=True, return_strategy_dict_info=False, return_all=False)[source]

          Get the coordination environments of a given site and additional information.

          Parameters
          @@ -1992,14 +1992,14 @@
          -get_site_neighbors(site)[source]
          +get_site_neighbors(site)[source]

          Get the neighbors of a given site.

          Not implemented for this strategy.

          -property uniquely_determines_coordination_environments[source]
          +property uniquely_determines_coordination_environments[source]

          Whether this strategy uniquely determines coordination environments.

          @@ -2007,7 +2007,7 @@
          -get_effective_csm(nb_set, cn_map, structure_environments, additional_info, symmetry_measure_type, max_effective_csm, effective_csm_estimator_ratio_function)[source]
          +get_effective_csm(nb_set, cn_map, structure_environments, additional_info, symmetry_measure_type, max_effective_csm, effective_csm_estimator_ratio_function)[source]

          Get the effective continuous symmetry measure of a given neighbors set.

          Parameters
          @@ -2029,7 +2029,7 @@
          -set_info(additional_info, field, isite, cn_map, value)[source]
          +set_info(additional_info, field, isite, cn_map, value)[source]

          Set additional information for the weights.

          Parameters
          diff --git a/docs/pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.html b/docs/pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.html index cb0e6c2c44b..a0c42aaec89 100644 --- a/docs/pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.html +++ b/docs/pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.coordination_environments.coordination_geometries module — pymatgen 2022.5.18 documentation + pymatgen.analysis.chemenv.coordination_environments.coordination_geometries module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
          - 2022.5.18 + 2022.5.18.1
          @@ -129,7 +129,7 @@ identification algorithms.

          -class AbstractChemenvAlgorithm(algorithm_type)[source]
          +class AbstractChemenvAlgorithm(algorithm_type)[source]

          Bases: monty.json.MSONable

          Base class used to define a Chemenv algorithm used to identify the correct permutation for the computation of the Continuous Symmetry Measure.

          @@ -141,14 +141,14 @@
          -property algorithm_type[source]
          +property algorithm_type[source]

          Return the type of algorithm.

          Returns: Type of the algorithm

          -abstract as_dict()[source]
          +abstract as_dict()[source]

          A JSON-serializable dict representation of the algorithm

          @@ -156,7 +156,7 @@
          -class AllCoordinationGeometries(permutations_safe_override=False, only_symbols=None)[source]
          +class AllCoordinationGeometries(permutations_safe_override=False, only_symbols=None)[source]

          Bases: dict

          Class used to store all the reference “coordination geometries” (list with instances of the CoordinationGeometry classes)

          @@ -171,7 +171,7 @@
          -get_geometries(coordination=None, returned='cg')[source]
          +get_geometries(coordination=None, returned='cg')[source]

          Returns a list of coordination geometries with the given coordination number.

          Parameters
          @@ -185,7 +185,7 @@
          -get_geometry_from_IUCr_symbol(IUCr_symbol)[source]
          +get_geometry_from_IUCr_symbol(IUCr_symbol)[source]

          Returns the coordination geometry of the given IUCr symbol.

          Parameters
          @@ -196,7 +196,7 @@
          -get_geometry_from_IUPAC_symbol(IUPAC_symbol)[source]
          +get_geometry_from_IUPAC_symbol(IUPAC_symbol)[source]

          Returns the coordination geometry of the given IUPAC symbol.

          Parameters
          @@ -207,7 +207,7 @@
          -get_geometry_from_mp_symbol(mp_symbol)[source]
          +get_geometry_from_mp_symbol(mp_symbol)[source]

          Returns the coordination geometry of the given mp_symbol.

          Parameters
          @@ -218,7 +218,7 @@
          -get_geometry_from_name(name)[source]
          +get_geometry_from_name(name)[source]

          Returns the coordination geometry of the given name.

          Parameters
          @@ -229,7 +229,7 @@
          -get_implemented_geometries(coordination=None, returned='cg', include_deactivated=False)[source]
          +get_implemented_geometries(coordination=None, returned='cg', include_deactivated=False)[source]

          Returns a list of the implemented coordination geometries with the given coordination number.

          Parameters
          @@ -245,7 +245,7 @@
          -get_not_implemented_geometries(coordination=None, returned='mp_symbol')[source]
          +get_not_implemented_geometries(coordination=None, returned='mp_symbol')[source]

          Returns a list of the implemented coordination geometries with the given coordination number.

          Parameters
          @@ -260,7 +260,7 @@
          -get_symbol_cn_mapping(coordination=None)[source]
          +get_symbol_cn_mapping(coordination=None)[source]

          Return a dictionary mapping the symbol of a CoordinationGeometry to its coordination.

          Parameters
          @@ -272,7 +272,7 @@
          -get_symbol_name_mapping(coordination=None)[source]
          +get_symbol_name_mapping(coordination=None)[source]

          Return a dictionary mapping the symbol of a CoordinationGeometry to its name.

          Parameters
          @@ -284,7 +284,7 @@
          -is_a_valid_coordination_geometry(mp_symbol=None, IUPAC_symbol=None, IUCr_symbol=None, name=None, cn=None)[source]
          +is_a_valid_coordination_geometry(mp_symbol=None, IUPAC_symbol=None, IUCr_symbol=None, name=None, cn=None)[source]

          Checks whether a given coordination geometry is valid (exists) and whether the parameters are coherent with each other.

          @@ -302,7 +302,7 @@
          -pretty_print(type='implemented_geometries', maxcn=8, additional_info=None)[source]
          +pretty_print(type='implemented_geometries', maxcn=8, additional_info=None)[source]

          Return a string with a list of the Coordination Geometries.

          Parameters
          @@ -321,7 +321,7 @@
          -class CoordinationGeometry(mp_symbol, name, alternative_names=None, IUPAC_symbol=None, IUCr_symbol=None, coordination=None, central_site=array([0., 0., 0.]), points=None, solid_angles=None, permutations_safe_override=False, deactivate=False, faces=None, edges=None, algorithms=None, equivalent_indices=None, neighbors_sets_hints=None)[source]
          +class CoordinationGeometry(mp_symbol, name, alternative_names=None, IUPAC_symbol=None, IUCr_symbol=None, coordination=None, central_site=array([0., 0., 0.]), points=None, solid_angles=None, permutations_safe_override=False, deactivate=False, faces=None, edges=None, algorithms=None, equivalent_indices=None, neighbors_sets_hints=None)[source]

          Bases: object

          Class used to store the ideal representation of a chemical environment or “coordination geometry”.

          Initializes one “coordination geometry” according to [Pure Appl. Chem., Vol. 79, No. 10, pp. 1779–1799, 2007] @@ -353,36 +353,36 @@

          -CSM_SKIP_SEPARATION_PLANE_ALGO = 10.0[source]
          +CSM_SKIP_SEPARATION_PLANE_ALGO = 10.0[source]
          -property IUCr_symbol[source]
          +property IUCr_symbol[source]

          Returns the IUCr symbol of this coordination geometry.

          -property IUCr_symbol_str[source]
          +property IUCr_symbol_str[source]

          Returns a string representation of the IUCr symbol of this coordination geometry.

          -property IUPAC_symbol[source]
          +property IUPAC_symbol[source]

          Returns the IUPAC symbol of this coordination geometry.

          -property IUPAC_symbol_str[source]
          +property IUPAC_symbol_str[source]

          Returns a string representation of the IUPAC symbol of this coordination geometry.

          -class NeighborsSetsHints(hints_type, options)[source]
          +class NeighborsSetsHints(hints_type, options)[source]

          Bases: object

          Class used to describe neighbors sets hints.

          This allows to possibly get a lower coordination from a capped-like model polyhedron.

          @@ -398,18 +398,18 @@
          -ALLOWED_HINTS_TYPES = ['single_cap', 'double_cap', 'triple_cap'][source]
          +ALLOWED_HINTS_TYPES = ['single_cap', 'double_cap', 'triple_cap'][source]
          -as_dict()[source]
          +as_dict()[source]

          A JSON-serializable dict representation of this NeighborsSetsHints

          -double_cap_hints(hints_info)[source]
          +double_cap_hints(hints_info)[source]

          Return hints for an additional neighbors set, i.e. the voronoi indices that constitute this new neighbors set, in case of a “Double cap” hint.

          @@ -422,7 +422,7 @@
          -classmethod from_dict(dd)[source]
          +classmethod from_dict(dd)[source]

          Reconstructs the NeighborsSetsHints from its JSON-serializable dict representation.

          Parameters
          @@ -434,7 +434,7 @@
          -hints(hints_info)[source]
          +hints(hints_info)[source]

          Return hints for an additional neighbors set, i.e. the voronoi indices that constitute this new neighbors set.

          @@ -447,7 +447,7 @@
          -single_cap_hints(hints_info)[source]
          +single_cap_hints(hints_info)[source]

          Return hints for an additional neighbors set, i.e. the voronoi indices that constitute this new neighbors set, in case of a “Single cap” hint.

          @@ -460,7 +460,7 @@
          -triple_cap_hints(hints_info)[source]
          +triple_cap_hints(hints_info)[source]

          Return hints for an additional neighbors set, i.e. the voronoi indices that constitute this new neighbors set, in case of a “Triple cap” hint.

          @@ -475,52 +475,52 @@
          -property algorithms[source]
          +property algorithms[source]

          Returns the list of algorithms that are used to identify this coordination geometry.

          -as_dict()[source]
          +as_dict()[source]

          A JSON-serializable dict representation of this CoordinationGeometry.

          -property ce_symbol[source]
          +property ce_symbol[source]

          Returns the symbol of this coordination geometry.

          -property coordination_number[source]
          +property coordination_number[source]

          Returns the coordination number of this coordination geometry.

          -property distfactor_max[source]
          +property distfactor_max[source]

          The maximum distfactor for the perfect CoordinationGeometry.

          Returns: Maximum distfactor for the perfect CoordinationGeometry (usually 1.0 for symmetric polyhedrons).

          -edges(sites, permutation=None, input='sites')[source]
          +edges(sites, permutation=None, input='sites')[source]

          Returns the list of edges of this coordination geometry. Each edge is given as a list of its end vertices coordinates.

          -faces(sites, permutation=None)[source]
          +faces(sites, permutation=None)[source]

          Returns the list of faces of this coordination geometry. Each face is given as a list of its vertices coordinates.

          -classmethod from_dict(dd)[source]
          +classmethod from_dict(dd)[source]

          Reconstructs the CoordinationGeometry from its JSON-serializable dict representation.

          Parameters
          @@ -532,55 +532,55 @@
          -get_central_site()[source]
          +get_central_site()[source]

          Returns the central site of this coordination geometry.

          -get_coordination_number()[source]
          +get_coordination_number()[source]

          Returns the coordination number of this coordination geometry.

          -get_name()[source]
          +get_name()[source]

          Returns the name of this coordination geometry.

          -get_pmeshes(sites, permutation=None)[source]
          +get_pmeshes(sites, permutation=None)[source]

          Returns the pmesh strings used for jmol to show this geometry.

          -is_implemented()[source]
          +is_implemented()[source]

          Returns True if this coordination geometry is implemented.

          -property mp_symbol[source]
          +property mp_symbol[source]

          Returns the MP symbol of this coordination geometry.

          -property number_of_permutations[source]
          +property number_of_permutations[source]

          Returns the number of permutations of this coordination geometry.

          -property pauling_stability_ratio[source]
          +property pauling_stability_ratio[source]

          Returns the theoretical Pauling stability ratio (rC/rA) for this environment.

          -ref_permutation(permutation)[source]
          +ref_permutation(permutation)[source]

          Returns the reference permutation for a set of equivalent permutations.

          Can be useful to skip permutations that have already been performed.

          @@ -593,7 +593,7 @@
          -set_permutations_safe_override(permutations_safe_override)[source]
          +set_permutations_safe_override(permutations_safe_override)[source]

          Setup ChemEnv so that a safe set of permutations are used.

          Parameters
          @@ -604,7 +604,7 @@
          -solid_angles(permutation=None)[source]
          +solid_angles(permutation=None)[source]

          Returns the list of “perfect” solid angles Each edge is given as a list of its end vertices coordinates.

          @@ -613,7 +613,7 @@
          -class ExplicitPermutationsAlgorithm(permutations)[source]
          +class ExplicitPermutationsAlgorithm(permutations)[source]

          Bases: pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.AbstractChemenvAlgorithm

          Class representing the algorithm doing the explicit permutations for the calculation of the Continuous Symmetry Measure.

          @@ -627,14 +627,14 @@
          -property as_dict[source]
          +property as_dict[source]

          Return the JSON-serializable dict representation of this ExplicitPermutationsAlgorithm algorithm.

          Returns: a JSON-serializable dict representation of this ExplicitPermutationsAlgorithm algorithm.

          -classmethod from_dict(dd)[source]
          +classmethod from_dict(dd)[source]

          Reconstructs the ExplicitPermutationsAlgorithm algorithm from its JSON-serializable dict representation.

          Parameters
          @@ -646,7 +646,7 @@
          -property permutations[source]
          +property permutations[source]

          Return the permutations to be performed for this algorithm.

          Returns: Permutations to be performed.

          @@ -655,7 +655,7 @@
          -class SeparationPlane(plane_points, mirror_plane=False, ordered_plane=False, point_groups=None, ordered_point_groups=None, explicit_permutations=None, minimum_number_of_points=None, explicit_optimized_permutations=None, multiplicity=None, other_plane_points=None)[source]
          +class SeparationPlane(plane_points, mirror_plane=False, ordered_plane=False, point_groups=None, ordered_point_groups=None, explicit_permutations=None, minimum_number_of_points=None, explicit_optimized_permutations=None, multiplicity=None, other_plane_points=None)[source]

          Bases: pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.AbstractChemenvAlgorithm

          Class representing the algorithm using separation planes for the calculation of the Continuous Symmetry Measure.

          @@ -688,7 +688,7 @@
          -property argsorted_ref_separation_perm[source]
          +property argsorted_ref_separation_perm[source]

          “Arg sorted” ordered indices of the separation plane.

          This is used in the identification of the final permutation to be used.

          Returns: list of the “arg sorted” ordered indices of the separation plane.

          @@ -696,14 +696,14 @@
          -property as_dict[source]
          +property as_dict[source]

          Return the JSON-serializable dict representation of this SeparationPlane algorithm.

          Returns: a JSON-serializable dict representation of this SeparationPlane algorithm.

          -classmethod from_dict(dd)[source]
          +classmethod from_dict(dd)[source]

          Reconstructs the SeparationPlane algorithm from its JSON-serializable dict representation.

          Parameters
          @@ -715,14 +715,14 @@
          -property permutations[source]
          +property permutations[source]

          Permutations used for this separation plane algorithm.

          Returns: List of permutations to be performed.

          -property ref_separation_perm[source]
          +property ref_separation_perm[source]

          Ordered indices of the separation plane.

          Examples

          For a separation plane of type 2|4|3, with plane_points indices [0, 3, 5, 8] and @@ -733,7 +733,7 @@

          -safe_separation_permutations(ordered_plane=False, ordered_point_groups=None, add_opposite=False)[source]
          +safe_separation_permutations(ordered_plane=False, ordered_point_groups=None, add_opposite=False)[source]

          Simple and safe permutations for this separation plane.

          This is not meant to be used in production. Default configuration for ChemEnv does not use this method. :param ordered_plane: Whether the order of the points in the plane can be used to reduce the

          diff --git a/docs/pymatgen.analysis.chemenv.coordination_environments.coordination_geometries_files.html b/docs/pymatgen.analysis.chemenv.coordination_environments.coordination_geometries_files.html index 5f275f86a17..8d84c18c0a4 100644 --- a/docs/pymatgen.analysis.chemenv.coordination_environments.coordination_geometries_files.html +++ b/docs/pymatgen.analysis.chemenv.coordination_environments.coordination_geometries_files.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.coordination_environments.coordination_geometries_files package — pymatgen 2022.5.18 documentation + pymatgen.analysis.chemenv.coordination_environments.coordination_geometries_files package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
          - 2022.5.18 + 2022.5.18.1
          diff --git a/docs/pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.html b/docs/pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.html index e7e761f42d4..4d96ddc3302 100644 --- a/docs/pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.html +++ b/docs/pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder module — pymatgen 2022.5.18 documentation + pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
          - 2022.5.18 + 2022.5.18.1
          @@ -130,7 +130,7 @@ DOI: 10.1107/S2052520620007994

          -class AbstractGeometry(central_site=None, bare_coords=None, centering_type='standard', include_central_site_in_centroid=False, optimization=None)[source]
          +class AbstractGeometry(central_site=None, bare_coords=None, centering_type='standard', include_central_site_in_centroid=False, optimization=None)[source]

          Bases: object

          Class used to describe a geometry (perfect or distorted)

          Constructor for the abstract geometry @@ -148,7 +148,7 @@

          -property cn[source]
          +property cn[source]

          Coordination number

          Type
          @@ -159,7 +159,7 @@
          -property coordination_number[source]
          +property coordination_number[source]

          Coordination number

          Type
          @@ -170,7 +170,7 @@
          -classmethod from_cg(cg, centering_type='standard', include_central_site_in_centroid=False)[source]
          +classmethod from_cg(cg, centering_type='standard', include_central_site_in_centroid=False)[source]
          Parameters
            @@ -187,7 +187,7 @@
            -points_wcs_csc(permutation=None)[source]
            +points_wcs_csc(permutation=None)[source]
            Parameters

            permutation –

            @@ -200,7 +200,7 @@
            -points_wcs_ctwcc(permutation=None)[source]
            +points_wcs_ctwcc(permutation=None)[source]
            Parameters

            permutation –

            @@ -213,7 +213,7 @@
            -points_wcs_ctwocc(permutation=None)[source]
            +points_wcs_ctwocc(permutation=None)[source]
            Parameters

            permutation –

            @@ -226,7 +226,7 @@
            -points_wocs_csc(permutation=None)[source]
            +points_wocs_csc(permutation=None)[source]
            Parameters

            permutation –

            @@ -239,7 +239,7 @@
            -points_wocs_ctwcc(permutation=None)[source]
            +points_wocs_ctwcc(permutation=None)[source]
            Parameters

            permutation –

            @@ -252,7 +252,7 @@
            -points_wocs_ctwocc(permutation=None)[source]
            +points_wocs_ctwocc(permutation=None)[source]
            Parameters

            permutation –

            @@ -267,7 +267,7 @@
            -class LocalGeometryFinder(permutations_safe_override=False, plane_ordering_override=True, debug_level=None, plane_safe_permutations=False, only_symbols=None, print_citation=False)[source]
            +class LocalGeometryFinder(permutations_safe_override=False, plane_ordering_override=True, debug_level=None, plane_safe_permutations=False, only_symbols=None, print_citation=False)[source]

            Bases: object

            Main class used to find the local environments in a structure

            @@ -285,47 +285,47 @@
            -BVA_DISTANCE_SCALE_FACTORS = {'GGA_relaxed': 1.015, 'LDA_relaxed': 0.995, 'experimental': 1.0}[source]
            +BVA_DISTANCE_SCALE_FACTORS = {'GGA_relaxed': 1.015, 'LDA_relaxed': 0.995, 'experimental': 1.0}[source]
            -DEFAULT_BVA_DISTANCE_SCALE_FACTOR = 1.0[source]
            +DEFAULT_BVA_DISTANCE_SCALE_FACTOR = 1.0[source]
            -DEFAULT_SPG_ANALYZER_OPTIONS = {'angle_tolerance': 5, 'symprec': 0.001}[source]
            +DEFAULT_SPG_ANALYZER_OPTIONS = {'angle_tolerance': 5, 'symprec': 0.001}[source]
            -DEFAULT_STRATEGY = <pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.MultiWeightsChemenvStrategy object>[source]
            +DEFAULT_STRATEGY = <pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.MultiWeightsChemenvStrategy object>[source]
            -PRESETS = {'DEFAULT': {'maximum_distance_factor': 2.0, 'minimum_angle_factor': 0.05, 'optimization': 2, 'voronoi_normalized_angle_tolerance': 0.03, 'voronoi_normalized_distance_tolerance': 0.05}}[source]
            +PRESETS = {'DEFAULT': {'maximum_distance_factor': 2.0, 'minimum_angle_factor': 0.05, 'optimization': 2, 'voronoi_normalized_angle_tolerance': 0.03, 'voronoi_normalized_distance_tolerance': 0.05}}[source]
            -STRUCTURE_REFINEMENT_NONE = 'none'[source]
            +STRUCTURE_REFINEMENT_NONE = 'none'[source]
            -STRUCTURE_REFINEMENT_REFINED = 'refined'[source]
            +STRUCTURE_REFINEMENT_REFINED = 'refined'[source]
            -STRUCTURE_REFINEMENT_SYMMETRIZED = 'symmetrized'[source]
            +STRUCTURE_REFINEMENT_SYMMETRIZED = 'symmetrized'[source]
            -compute_coordination_environments(structure, indices=None, only_cations=True, strategy=<pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.MultiWeightsChemenvStrategy object>, valences='bond-valence-analysis', initial_structure_environments=None)[source]
            +compute_coordination_environments(structure, indices=None, only_cations=True, strategy=<pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.MultiWeightsChemenvStrategy object>, valences='bond-valence-analysis', initial_structure_environments=None)[source]
            Parameters
              @@ -345,7 +345,7 @@
              -compute_structure_environments(excluded_atoms=None, only_atoms=None, only_cations=True, only_indices=None, maximum_distance_factor=2.0, minimum_angle_factor=0.05, max_cn=None, min_cn=None, only_symbols=None, valences='undefined', additional_conditions=None, info=None, timelimit=None, initial_structure_environments=None, get_from_hints=False, voronoi_normalized_distance_tolerance=0.05, voronoi_normalized_angle_tolerance=0.03, recompute=None, optimization=2)[source]
              +compute_structure_environments(excluded_atoms=None, only_atoms=None, only_cations=True, only_indices=None, maximum_distance_factor=2.0, minimum_angle_factor=0.05, max_cn=None, min_cn=None, only_symbols=None, valences='undefined', additional_conditions=None, info=None, timelimit=None, initial_structure_environments=None, get_from_hints=False, voronoi_normalized_distance_tolerance=0.05, voronoi_normalized_angle_tolerance=0.03, recompute=None, optimization=2)[source]

              Computes and returns the StructureEnvironments object containing all the information about the coordination environments in the structure :param excluded_atoms: Atoms for which the coordination geometries does not have to be identified @@ -390,7 +390,7 @@

              -coordination_geometry_symmetry_measures(coordination_geometry, tested_permutations=False, points_perfect=None, optimization=None)[source]
              +coordination_geometry_symmetry_measures(coordination_geometry, tested_permutations=False, points_perfect=None, optimization=None)[source]

              Returns the symmetry measures of a given coordination_geometry for a set of permutations depending on the permutation setup. Depending on the parameters of the LocalGeometryFinder and on the coordination

              @@ -411,7 +411,7 @@
              -coordination_geometry_symmetry_measures_fallback_random(coordination_geometry, NRANDOM=10, points_perfect=None)[source]
              +coordination_geometry_symmetry_measures_fallback_random(coordination_geometry, NRANDOM=10, points_perfect=None)[source]

              Returns the symmetry measures for a random set of permutations for the coordination geometry “coordination_geometry”. Fallback implementation for the plane separation algorithms measures of each permutation @@ -422,7 +422,7 @@

              -coordination_geometry_symmetry_measures_separation_plane(coordination_geometry, separation_plane_algo, testing=False, tested_permutations=False, points_perfect=None)[source]
              +coordination_geometry_symmetry_measures_separation_plane(coordination_geometry, separation_plane_algo, testing=False, tested_permutations=False, points_perfect=None)[source]

              Returns the symmetry measures of the given coordination geometry “coordination_geometry” using separation facets to reduce the complexity of the system. Caller to the refined 2POINTS, 3POINTS and other … :param coordination_geometry: The coordination geometry to be investigated @@ -431,7 +431,7 @@

              -coordination_geometry_symmetry_measures_separation_plane_optim(coordination_geometry, separation_plane_algo, points_perfect=None, nb_set=None, optimization=None)[source]
              +coordination_geometry_symmetry_measures_separation_plane_optim(coordination_geometry, separation_plane_algo, points_perfect=None, nb_set=None, optimization=None)[source]

              Returns the symmetry measures of the given coordination geometry “coordination_geometry” using separation facets to reduce the complexity of the system. Caller to the refined 2POINTS, 3POINTS and other … :param coordination_geometry: The coordination geometry to be investigated. @@ -457,7 +457,7 @@

              -coordination_geometry_symmetry_measures_sepplane_optim(coordination_geometry, points_perfect=None, nb_set=None, optimization=None)[source]
              +coordination_geometry_symmetry_measures_sepplane_optim(coordination_geometry, points_perfect=None, nb_set=None, optimization=None)[source]

              Returns the symmetry measures of a given coordination_geometry for a set of permutations depending on the permutation setup. Depending on the parameters of the LocalGeometryFinder and on the coordination

              @@ -478,7 +478,7 @@
              -coordination_geometry_symmetry_measures_standard(coordination_geometry, algo, points_perfect=None, optimization=None)[source]
              +coordination_geometry_symmetry_measures_standard(coordination_geometry, algo, points_perfect=None, optimization=None)[source]

              Returns the symmetry measures for a set of permutations (whose setup depends on the coordination geometry) for the coordination geometry “coordination_geometry”. Standard implementation looking for the symmetry measures of each permutation @@ -488,21 +488,21 @@

              -get_coordination_symmetry_measures(only_minimum=True, all_csms=True, optimization=None)[source]
              +get_coordination_symmetry_measures(only_minimum=True, all_csms=True, optimization=None)[source]

              Returns the continuous symmetry measures of the current local geometry in a dictionary. :return: the continuous symmetry measures of the current local geometry in a dictionary.

              -get_coordination_symmetry_measures_optim(only_minimum=True, all_csms=True, nb_set=None, optimization=None)[source]
              +get_coordination_symmetry_measures_optim(only_minimum=True, all_csms=True, nb_set=None, optimization=None)[source]

              Returns the continuous symmetry measures of the current local geometry in a dictionary. :return: the continuous symmetry measures of the current local geometry in a dictionary.

              -get_structure()[source]
              +get_structure()[source]

              Returns the pymatgen Structure that has been setup for the identification of geometries (the initial one might have been refined/symmetrized using the SpaceGroupAnalyzer). :return: The pymatgen Structure that has been setup for the identification of geometries (the initial one @@ -511,7 +511,7 @@

              -set_structure(lattice, species, coords, coords_are_cartesian)[source]
              +set_structure(lattice, species, coords, coords_are_cartesian)[source]

              Sets up the pymatgen structure for which the coordination geometries have to be identified starting from the lattice, the species and the coordinates :param lattice: The lattice of the structure @@ -522,7 +522,7 @@

              -setup_explicit_indices_local_geometry(explicit_indices)[source]
              +setup_explicit_indices_local_geometry(explicit_indices)[source]

              Sets up explicit indices for the local geometry, for testing purposes :param explicit_indices: explicit indices for the neighbors (set of numbers from 0 to CN-1 in a given order)

              @@ -530,7 +530,7 @@
              -setup_local_geometry(isite, coords, optimization=None)[source]
              +setup_local_geometry(isite, coords, optimization=None)[source]

              Sets up the AbstractGeometry for the local geometry of site with index isite. :param isite: Index of the site for which the local geometry has to be set up :param coords: The coordinates of the (local) neighbors

              @@ -538,14 +538,14 @@
              -setup_ordered_indices_local_geometry(coordination)[source]
              +setup_ordered_indices_local_geometry(coordination)[source]

              Sets up ordered indices for the local geometry, for testing purposes :param coordination: coordination of the local geometry

              -setup_parameter(parameter, value)[source]
              +setup_parameter(parameter, value)[source]

              Setup of one specific parameter to the given value. The other parameters are unchanged. See setup_parameters method for the list of possible parameters :param parameter: Parameter to setup/update @@ -554,7 +554,7 @@

              -setup_parameters(centering_type='standard', include_central_site_in_centroid=False, bva_distance_scale_factor=None, structure_refinement='refined', spg_analyzer_options=None)[source]
              +setup_parameters(centering_type='standard', include_central_site_in_centroid=False, bva_distance_scale_factor=None, structure_refinement='refined', spg_analyzer_options=None)[source]

              Setup of the parameters for the coordination geometry finder. A reference point for the geometries has to be chosen. This can be the centroid of the structure (including or excluding the atom for which the coordination geometry is looked for) or the atom itself. In the ‘standard’ centering_type, the reference point is the central @@ -580,21 +580,21 @@

              -setup_random_indices_local_geometry(coordination)[source]
              +setup_random_indices_local_geometry(coordination)[source]

              Sets up random indices for the local geometry, for testing purposes :param coordination: coordination of the local geometry

              -setup_random_structure(coordination)[source]
              +setup_random_structure(coordination)[source]

              Sets up a purely random structure with a given coordination. :param coordination: coordination number for the random structure

              -setup_structure(structure)[source]
              +setup_structure(structure)[source]

              Sets up the structure for which the coordination geometries have to be identified. The structure is analyzed with the space group analyzer and a refined structure is used :param structure: A pymatgen Structure

              @@ -602,7 +602,7 @@
              -setup_test_perfect_environment(symbol, randomness=False, max_random_dist=0.1, symbol_type='mp_symbol', indices='RANDOM', random_translation='NONE', random_rotation='NONE', random_scale='NONE', points=None)[source]
              +setup_test_perfect_environment(symbol, randomness=False, max_random_dist=0.1, symbol_type='mp_symbol', indices='RANDOM', random_translation='NONE', random_rotation='NONE', random_scale='NONE', points=None)[source]
              Parameters
                @@ -625,7 +625,7 @@
                -update_nb_set_environments(se, isite, cn, inb_set, nb_set, recompute=False, optimization=None)[source]
                +update_nb_set_environments(se, isite, cn, inb_set, nb_set, recompute=False, optimization=None)[source]
                Parameters
                  @@ -648,7 +648,7 @@
                  -find_rotation(points_distorted, points_perfect)[source]
                  +find_rotation(points_distorted, points_perfect)[source]

                  This finds the rotation matrix that aligns the (distorted) set of points “points_distorted” with respect to the (perfect) set of points “points_perfect” in a least-square sense. :param points_distorted: List of points describing a given (distorted) polyhedron for which the rotation that

                  @@ -667,7 +667,7 @@
                  -find_scaling_factor(points_distorted, points_perfect, rot)[source]
                  +find_scaling_factor(points_distorted, points_perfect, rot)[source]

                  This finds the scaling factor between the (distorted) set of points “points_distorted” and the (perfect) set of points “points_perfect” in a least-square sense. :param points_distorted: List of points describing a given (distorted) polyhedron for which the scaling factor has

                  @@ -689,7 +689,7 @@
                  -symmetry_measure(points_distorted, points_perfect)[source]
                  +symmetry_measure(points_distorted, points_perfect)[source]

                  Computes the continuous symmetry measure of the (distorted) set of points “points_distorted” with respect to the (perfect) set of points “points_perfect”. :param points_distorted: List of points describing a given (distorted) polyhedron for which the symmetry measure

                  diff --git a/docs/pymatgen.analysis.chemenv.coordination_environments.html b/docs/pymatgen.analysis.chemenv.coordination_environments.html index dd15765ca99..f995ae31d7a 100644 --- a/docs/pymatgen.analysis.chemenv.coordination_environments.html +++ b/docs/pymatgen.analysis.chemenv.coordination_environments.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.coordination_environments package — pymatgen 2022.5.18 documentation + pymatgen.analysis.chemenv.coordination_environments package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                  - 2022.5.18 + 2022.5.18.1
                  diff --git a/docs/pymatgen.analysis.chemenv.coordination_environments.structure_environments.html b/docs/pymatgen.analysis.chemenv.coordination_environments.structure_environments.html index e3a699d266b..99d8f5e37d8 100644 --- a/docs/pymatgen.analysis.chemenv.coordination_environments.structure_environments.html +++ b/docs/pymatgen.analysis.chemenv.coordination_environments.structure_environments.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.coordination_environments.structure_environments module — pymatgen 2022.5.18 documentation + pymatgen.analysis.chemenv.coordination_environments.structure_environments module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                  - 2022.5.18 + 2022.5.18.1
                  @@ -124,7 +124,7 @@ and possibly some fraction corresponding to these.

                  -class ChemicalEnvironments(coord_geoms=None)[source]
                  +class ChemicalEnvironments(coord_geoms=None)[source]

                  Bases: monty.json.MSONable

                  Class used to store all the information about the chemical environment of a given site for a given list of coordinated neighbours (internally called “cn_map”).

                  @@ -137,7 +137,7 @@
                  -add_coord_geom(mp_symbol, symmetry_measure, algo='UNKNOWN', permutation=None, override=False, local2perfect_map=None, perfect2local_map=None, detailed_voronoi_index=None, other_symmetry_measures=None, rotation_matrix=None, scaling_factor=None)[source]
                  +add_coord_geom(mp_symbol, symmetry_measure, algo='UNKNOWN', permutation=None, override=False, local2perfect_map=None, perfect2local_map=None, detailed_voronoi_index=None, other_symmetry_measures=None, rotation_matrix=None, scaling_factor=None)[source]

                  Adds a coordination geometry to the ChemicalEnvironments object.

                  Parameters
                  @@ -164,7 +164,7 @@
                  -as_dict()[source]
                  +as_dict()[source]

                  Returns a dictionary representation of the ChemicalEnvironments object.

                  Returns
                  @@ -175,7 +175,7 @@
                  -classmethod from_dict(d)[source]
                  +classmethod from_dict(d)[source]

                  Reconstructs the ChemicalEnvironments object from a dict representation of the ChemicalEnvironments created using the as_dict method.

                  @@ -190,7 +190,7 @@
                  -is_close_to(other, rtol=0.0, atol=1e-08)[source]
                  +is_close_to(other, rtol=0.0, atol=1e-08)[source]

                  Whether this ChemicalEnvironments object is close to another one.

                  Parameters
                  @@ -208,7 +208,7 @@
                  -minimum_geometries(n=None, symmetry_measure_type=None, max_csm=None)[source]
                  +minimum_geometries(n=None, symmetry_measure_type=None, max_csm=None)[source]

                  Returns a list of geometries with increasing continuous symmetry measure in this ChemicalEnvironments object.

                  Parameters
                  @@ -225,7 +225,7 @@
                  -minimum_geometry(symmetry_measure_type=None, max_csm=None)[source]
                  +minimum_geometry(symmetry_measure_type=None, max_csm=None)[source]

                  Returns the geometry with the minimum continuous symmetry measure of this ChemicalEnvironments.

                  Returns
                  @@ -242,7 +242,7 @@
                  -class LightStructureEnvironments(strategy, coordination_environments=None, all_nbs_sites=None, neighbors_sets=None, structure=None, valences=None, valences_origin=None)[source]
                  +class LightStructureEnvironments(strategy, coordination_environments=None, all_nbs_sites=None, neighbors_sets=None, structure=None, valences=None, valences_origin=None)[source]

                  Bases: monty.json.MSONable

                  Class used to store the chemical environments of a given structure obtained from a given ChemenvStrategy. Currently, only strategies leading to the determination of a unique environment for each site is allowed @@ -265,17 +265,17 @@

                  -DEFAULT_STATISTICS_FIELDS = ['anion_list', 'anion_atom_list', 'cation_list', 'cation_atom_list', 'neutral_list', 'neutral_atom_list', 'atom_coordination_environments_present', 'ion_coordination_environments_present', 'fraction_atom_coordination_environments_present', 'fraction_ion_coordination_environments_present', 'coordination_environments_atom_present', 'coordination_environments_ion_present'][source]
                  +DEFAULT_STATISTICS_FIELDS = ['anion_list', 'anion_atom_list', 'cation_list', 'cation_atom_list', 'neutral_list', 'neutral_atom_list', 'atom_coordination_environments_present', 'ion_coordination_environments_present', 'fraction_atom_coordination_environments_present', 'fraction_ion_coordination_environments_present', 'coordination_environments_atom_present', 'coordination_environments_ion_present'][source]
                  -DELTA_MAX_OXIDATION_STATE = 0.1[source]
                  +DELTA_MAX_OXIDATION_STATE = 0.1[source]
                  -class NeighborsSet(structure, isite, all_nbs_sites, all_nbs_sites_indices)[source]
                  +class NeighborsSet(structure, isite, all_nbs_sites, all_nbs_sites_indices)[source]

                  Bases: object

                  Class used to store a given set of neighbors of a given site (based on a list of sites, the voronoi container is not part of the LightStructureEnvironments object).

                  @@ -292,13 +292,13 @@
                  -as_dict()[source]
                  +as_dict()[source]

                  A JSON-serializable dict representation of the NeighborsSet.

                  -classmethod from_dict(dd, structure, all_nbs_sites)[source]
                  +classmethod from_dict(dd, structure, all_nbs_sites)[source]

                  Reconstructs the NeighborsSet algorithm from its JSON-serializable dict representation, together with the structure and all the possible neighbors sites.

                  As an inner (nested) class, the NeighborsSet is not supposed to be used anywhere else that inside the @@ -318,25 +318,25 @@

                  -property neighb_coords[source]
                  +property neighb_coords[source]

                  Coordinates of neighbors for this NeighborsSet.

                  -property neighb_indices_and_images: list[dict[str, int]][source]
                  +property neighb_indices_and_images: list[dict[str, int]][source]

                  List of indices and images with respect to the original unit cell sites for this NeighborsSet.

                  -property neighb_sites[source]
                  +property neighb_sites[source]

                  Neighbors for this NeighborsSet as pymatgen Sites.

                  -property neighb_sites_and_indices[source]
                  +property neighb_sites_and_indices[source]

                  List of neighbors for this NeighborsSet as pymatgen Sites and their index in the original structure.

                  @@ -344,14 +344,14 @@
                  -as_dict()[source]
                  +as_dict()[source]

                  Bson-serializable dict representation of the LightStructureEnvironments object. :returns: Bson-serializable dict representation of the LightStructureEnvironments object.

                  -clear_environments(conditions=None)[source]
                  +clear_environments(conditions=None)[source]

                  Get the clear environments in the structure.

                  Parameters
                  @@ -363,7 +363,7 @@
                  -contains_only_one_anion(anion)[source]
                  +contains_only_one_anion(anion)[source]

                  Whether this LightStructureEnvironments concerns a structure with only one given anion type.

                  Parameters
                  @@ -375,7 +375,7 @@
                  -contains_only_one_anion_atom(anion_atom)[source]
                  +contains_only_one_anion_atom(anion_atom)[source]

                  Whether this LightStructureEnvironments concerns a structure with only one given anion atom type.

                  Parameters
                  @@ -387,14 +387,14 @@
                  -environments_identified()[source]
                  +environments_identified()[source]

                  Return the set of environments identified in this structure.

                  Returns: Set of environments identified in this structure.

                  -classmethod from_dict(d)[source]
                  +classmethod from_dict(d)[source]

                  Reconstructs the LightStructureEnvironments object from a dict representation of the LightStructureEnvironments created using the as_dict method.

                  @@ -409,7 +409,7 @@
                  -classmethod from_structure_environments(strategy, structure_environments, valences=None, valences_origin=None)[source]
                  +classmethod from_structure_environments(strategy, structure_environments, valences=None, valences_origin=None)[source]

                  Construct a LightStructureEnvironments object from a strategy and a StructureEnvironments object.

                  Parameters
                  @@ -427,7 +427,7 @@
                  -get_site_info_for_specie_allces(specie, min_fraction=0.0)[source]
                  +get_site_info_for_specie_allces(specie, min_fraction=0.0)[source]

                  Get list of indices that have the given specie.

                  Parameters
                  @@ -442,7 +442,7 @@
                  -get_site_info_for_specie_ce(specie, ce_symbol)[source]
                  +get_site_info_for_specie_ce(specie, ce_symbol)[source]

                  Get list of indices that have the given specie with a given Coordination environment.

                  Parameters
                  @@ -460,7 +460,7 @@
                  -get_statistics(statistics_fields=['anion_list', 'anion_atom_list', 'cation_list', 'cation_atom_list', 'neutral_list', 'neutral_atom_list', 'atom_coordination_environments_present', 'ion_coordination_environments_present', 'fraction_atom_coordination_environments_present', 'fraction_ion_coordination_environments_present', 'coordination_environments_atom_present', 'coordination_environments_ion_present'], bson_compatible=False)[source]
                  +get_statistics(statistics_fields=['anion_list', 'anion_atom_list', 'cation_list', 'cation_atom_list', 'neutral_list', 'neutral_atom_list', 'atom_coordination_environments_present', 'ion_coordination_environments_present', 'fraction_atom_coordination_environments_present', 'fraction_ion_coordination_environments_present', 'coordination_environments_atom_present', 'coordination_environments_ion_present'], bson_compatible=False)[source]

                  Get the statistics of environments for this structure. :param statistics_fields: Which statistics to get. :param bson_compatible: Whether to make the dictionary BSON-compatible.

                  @@ -473,13 +473,13 @@
                  -setup_statistic_lists()[source]
                  +setup_statistic_lists()[source]

                  Set up the statistics of environments for this LightStructureEnvironments.

                  -site_contains_environment(isite, ce_symbol)[source]
                  +site_contains_environment(isite, ce_symbol)[source]

                  Whether a given site contains a given coordination environment.

                  Parameters
                  @@ -494,7 +494,7 @@
                  -site_has_clear_environment(isite, conditions=None)[source]
                  +site_has_clear_environment(isite, conditions=None)[source]

                  Whether a given site has a “clear” environments.

                  A “clear” environment is somewhat arbitrary. You can pass (multiple) conditions, e.g. the environment should have a continuous symmetry measure lower than this, a fraction higher than that, …

                  @@ -511,7 +511,7 @@
                  -structure_contains_atom_environment(atom_symbol, ce_symbol)[source]
                  +structure_contains_atom_environment(atom_symbol, ce_symbol)[source]

                  Checks whether the structure contains a given atom in a given environment.

                  Parameters
                  @@ -528,7 +528,7 @@
                  -structure_has_clear_environments(conditions=None, skip_none=True, skip_empty=False)[source]
                  +structure_has_clear_environments(conditions=None, skip_none=True, skip_empty=False)[source]

                  Whether all sites in a structure have “clear” environments. :param conditions: Conditions to be checked for an environment to be “clear”. :param skip_none: Whether to skip sites for which no environments have been computed. @@ -538,7 +538,7 @@

                  -property uniquely_determines_coordination_environments[source]
                  +property uniquely_determines_coordination_environments[source]

                  True if the coordination environments are uniquely determined.

                  @@ -546,7 +546,7 @@
                  -class StructureEnvironments(voronoi, valences, sites_map, equivalent_sites, ce_list, structure, neighbors_sets=None, info=None)[source]
                  +class StructureEnvironments(voronoi, valences, sites_map, equivalent_sites, ce_list, structure, neighbors_sets=None, info=None)[source]

                  Bases: monty.json.MSONable

                  Class used to store the chemical environments of a given structure.

                  Constructor for the StructureEnvironments object.

                  @@ -566,12 +566,12 @@
                  -AC = <pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions object>[source]
                  +AC = <pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions object>[source]
                  -class NeighborsSet(structure, isite, detailed_voronoi, site_voronoi_indices, sources=None)[source]
                  +class NeighborsSet(structure, isite, detailed_voronoi, site_voronoi_indices, sources=None)[source]

                  Bases: object

                  Class used to store a given set of neighbors of a given site (based on the detailed_voronoi).

                  Constructor for NeighborsSet.

                  @@ -590,7 +590,7 @@
                  -add_source(source)[source]
                  +add_source(source)[source]

                  Add a source to this NeighborsSet.

                  Parameters
                  @@ -601,43 +601,43 @@
                  -angle_plateau()[source]
                  +angle_plateau()[source]

                  Returns the angles plateau’s for this NeighborsSet.

                  -property angles[source]
                  +property angles[source]

                  Angles for each neighbor in this NeighborsSet.

                  -as_dict()[source]
                  +as_dict()[source]

                  A JSON-serializable dict representation of the NeighborsSet.

                  -property coords[source]
                  +property coords[source]

                  Coordinates of the current central atom and its neighbors for this NeighborsSet.

                  -distance_plateau()[source]
                  +distance_plateau()[source]

                  Returns the distances plateau’s for this NeighborsSet.

                  -property distances[source]
                  +property distances[source]

                  Distances to each neighbor in this NeighborsSet.

                  -classmethod from_dict(dd, structure, detailed_voronoi)[source]
                  +classmethod from_dict(dd, structure, detailed_voronoi)[source]

                  Reconstructs the NeighborsSet algorithm from its JSON-serializable dict representation, together with the structure and the DetailedVoronoiContainer.

                  As an inner (nested) class, the NeighborsSet is not supposed to be used anywhere else that inside the @@ -658,7 +658,7 @@

                  -get_neighb_voronoi_indices(permutation)[source]
                  +get_neighb_voronoi_indices(permutation)[source]

                  Return the indices in the detailed_voronoi corresponding to the current permutation.

                  Parameters
                  @@ -670,56 +670,56 @@
                  -property info[source]
                  +property info[source]

                  Summarized information about this NeighborsSet.

                  -property neighb_coords[source]
                  +property neighb_coords[source]

                  Coordinates of neighbors for this NeighborsSet.

                  -property neighb_coordsOpt[source]
                  +property neighb_coordsOpt[source]

                  Optimized access to the coordinates of neighbors for this NeighborsSet.

                  -property neighb_sites[source]
                  +property neighb_sites[source]

                  Neighbors for this NeighborsSet as pymatgen Sites.

                  -property neighb_sites_and_indices[source]
                  +property neighb_sites_and_indices[source]

                  List of neighbors for this NeighborsSet as pymatgen Sites and their index in the original structure.

                  -property normalized_angles[source]
                  +property normalized_angles[source]

                  Normalized angles for each neighbor in this NeighborsSet.

                  -property normalized_distances[source]
                  +property normalized_distances[source]

                  Normalized distances to each neighbor in this NeighborsSet.

                  -property source[source]
                  +property source[source]

                  Returns the source of this NeighborsSet (how it was generated, e.g. from which Voronoi cut-offs, or from hints).

                  -voronoi_grid_surface_points(additional_condition=1, other_origins='DO_NOTHING')[source]
                  +voronoi_grid_surface_points(additional_condition=1, other_origins='DO_NOTHING')[source]

                  Get the surface points in the Voronoi grid for this neighbor from the sources. The general shape of the points should look like a staircase such as in the following figure :

                  @@ -768,7 +768,7 @@
                  -add_neighbors_set(isite, nb_set)[source]
                  +add_neighbors_set(isite, nb_set)[source]

                  Adds a neighbor set to the list of neighbors sets for this site.

                  Parameters
                  @@ -782,7 +782,7 @@
                  -as_dict()[source]
                  +as_dict()[source]

                  Bson-serializable dict representation of the StructureEnvironments object.

                  Returns
                  @@ -793,7 +793,7 @@
                  -differences_wrt(other)[source]
                  +differences_wrt(other)[source]

                  Return differences found in the current StructureEnvironments with respect to another StructureEnvironments.

                  Parameters
                  @@ -807,7 +807,7 @@
                  -classmethod from_dict(d)[source]
                  +classmethod from_dict(d)[source]

                  Reconstructs the StructureEnvironments object from a dict representation of the StructureEnvironments created using the as_dict method.

                  @@ -822,7 +822,7 @@
                  -get_coordination_environments(isite, cn, nb_set)[source]
                  +get_coordination_environments(isite, cn, nb_set)[source]

                  Get the ChemicalEnvironments for a given site, coordination and neighbors set.

                  Parameters
                  @@ -838,7 +838,7 @@
                  -get_csm(isite, mp_symbol)[source]
                  +get_csm(isite, mp_symbol)[source]

                  Get the continuous symmetry measure for a given site in the given coordination environment.

                  Parameters
                  @@ -853,7 +853,7 @@
                  -get_csm_and_maps(isite, max_csm=8.0, figsize=None, symmetry_measure_type=None)[source]
                  +get_csm_and_maps(isite, max_csm=8.0, figsize=None, symmetry_measure_type=None)[source]

                  Plotting of the coordination numbers of a given site for all the distfactor/angfactor parameters. If the chemical environments are given, a color map is added to the plot, with the lowest continuous symmetry measure as the value for the color of that distfactor/angfactor set.

                  @@ -874,7 +874,7 @@
                  -get_csms(isite, mp_symbol)[source]
                  +get_csms(isite, mp_symbol)[source]
                  Returns the continuous symmetry measure(s) of site with index isite with respect to the

                  perfect coordination environment with mp_symbol. For some environments, a given mp_symbol might not be available (if there is no voronoi parameters leading to a number of neighbours corresponding to @@ -898,7 +898,7 @@

                  -get_environments_figure(isite, plot_type=None, title='Coordination numbers', max_dist=2.0, colormap=None, figsize=None, strategy=None)[source]
                  +get_environments_figure(isite, plot_type=None, title='Coordination numbers', max_dist=2.0, colormap=None, figsize=None, strategy=None)[source]

                  Plotting of the coordination environments of a given site for all the distfactor/angfactor regions. The chemical environments with the lowest continuous symmetry measure is shown for each distfactor/angfactor region as the value for the color of that distfactor/angfactor region (using a colormap).

                  @@ -925,7 +925,7 @@
                  -init_neighbors_sets(isite, additional_conditions=None, valences=None)[source]
                  +init_neighbors_sets(isite, additional_conditions=None, valences=None)[source]

                  Initialize the list of neighbors sets for the current site.

                  Parameters
                  @@ -942,7 +942,7 @@
                  -plot_csm_and_maps(isite, max_csm=8.0)[source]
                  +plot_csm_and_maps(isite, max_csm=8.0)[source]

                  Plotting of the coordination numbers of a given site for all the distfactor/angfactor parameters. If the chemical environments are given, a color map is added to the plot, with the lowest continuous symmetry measure as the value for the color of that distfactor/angfactor set.

                  @@ -958,7 +958,7 @@
                  -plot_environments(isite, plot_type=None, title='Coordination numbers', max_dist=2.0, figsize=None, strategy=None)[source]
                  +plot_environments(isite, plot_type=None, title='Coordination numbers', max_dist=2.0, figsize=None, strategy=None)[source]

                  Plotting of the coordination numbers of a given site for all the distfactor/angfactor parameters. If the chemical environments are given, a color map is added to the plot, with the lowest continuous symmetry measure as the value for the color of that distfactor/angfactor set.

                  @@ -981,7 +981,7 @@
                  -save_environments_figure(isite, imagename='image.png', plot_type=None, title='Coordination numbers', max_dist=2.0, figsize=None)[source]
                  +save_environments_figure(isite, imagename='image.png', plot_type=None, title='Coordination numbers', max_dist=2.0, figsize=None)[source]

                  Saves the environments figure to a given file.

                  Parameters
                  @@ -1002,7 +1002,7 @@
                  -update_coordination_environments(isite, cn, nb_set, ce)[source]
                  +update_coordination_environments(isite, cn, nb_set, ce)[source]

                  Updates the coordination environment for this site, coordination and neighbor set.

                  Parameters
                  @@ -1018,7 +1018,7 @@
                  -update_site_info(isite, info_dict)[source]
                  +update_site_info(isite, info_dict)[source]

                  Update information about this site.

                  Parameters
                  diff --git a/docs/pymatgen.analysis.chemenv.coordination_environments.voronoi.html b/docs/pymatgen.analysis.chemenv.coordination_environments.voronoi.html index e6b5938cf62..171a9195ef1 100644 --- a/docs/pymatgen.analysis.chemenv.coordination_environments.voronoi.html +++ b/docs/pymatgen.analysis.chemenv.coordination_environments.voronoi.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.coordination_environments.voronoi module — pymatgen 2022.5.18 documentation + pymatgen.analysis.chemenv.coordination_environments.voronoi module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                  - 2022.5.18 + 2022.5.18.1
                  @@ -120,7 +120,7 @@

                  This module contains the object used to describe the possible bonded atoms based on a Voronoi analysis.

                  -class DetailedVoronoiContainer(structure=None, voronoi_list2=None, voronoi_cutoff=10.0, isites=None, normalized_distance_tolerance=1e-05, normalized_angle_tolerance=0.001, additional_conditions=None, valences=None, maximum_distance_factor=None, minimum_angle_factor=None)[source]
                  +class DetailedVoronoiContainer(structure=None, voronoi_list2=None, voronoi_cutoff=10.0, isites=None, normalized_distance_tolerance=1e-05, normalized_angle_tolerance=0.001, additional_conditions=None, valences=None, maximum_distance_factor=None, minimum_angle_factor=None)[source]

                  Bases: monty.json.MSONable

                  Class used to store the full Voronoi of a given structure.

                  Constructor for the VoronoiContainer object. Either a structure is given, in which case the Voronoi is @@ -146,12 +146,12 @@

                  -AC = <pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions object>[source]
                  +AC = <pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions object>[source]
                  -as_dict()[source]
                  +as_dict()[source]

                  Bson-serializable dict representation of the VoronoiContainer.

                  Returns
                  @@ -162,22 +162,22 @@
                  -default_normalized_angle_tolerance = 0.001[source]
                  +default_normalized_angle_tolerance = 0.001[source]
                  -default_normalized_distance_tolerance = 1e-05[source]
                  +default_normalized_distance_tolerance = 1e-05[source]
                  -default_voronoi_cutoff = 10.0[source]
                  +default_voronoi_cutoff = 10.0[source]
                  -classmethod from_dict(d)[source]
                  +classmethod from_dict(d)[source]

                  Reconstructs the VoronoiContainer object from a dict representation of the VoronoiContainer created using the as_dict method.

                  @@ -192,7 +192,7 @@
                  -get_rdf_figure(isite, normalized=True, figsize=None, step_function=None)[source]
                  +get_rdf_figure(isite, normalized=True, figsize=None, step_function=None)[source]

                  Get the Radial Distribution Figure for a given site.

                  Parameters
                  @@ -211,7 +211,7 @@
                  -get_sadf_figure(isite, normalized=True, figsize=None, step_function=None)[source]
                  +get_sadf_figure(isite, normalized=True, figsize=None, step_function=None)[source]

                  Get the Solid Angle Distribution Figure for a given site. :param isite: Index of the site. :param normalized: Whether to normalize angles. @@ -226,7 +226,7 @@

                  -is_close_to(other, rtol=0.0, atol=1e-08)[source]
                  +is_close_to(other, rtol=0.0, atol=1e-08)[source]

                  Whether two DetailedVoronoiContainer objects are close to each other.

                  Parameters
                  @@ -244,7 +244,7 @@
                  -maps_and_surfaces(isite, surface_calculation_type=None, max_dist=2.0, additional_conditions=None)[source]
                  +maps_and_surfaces(isite, surface_calculation_type=None, max_dist=2.0, additional_conditions=None)[source]

                  Get the different surfaces and their cn_map corresponding to the different distance-angle cutoffs for a given site.

                  @@ -264,7 +264,7 @@
                  -maps_and_surfaces_bounded(isite, surface_calculation_options=None, additional_conditions=None)[source]
                  +maps_and_surfaces_bounded(isite, surface_calculation_options=None, additional_conditions=None)[source]

                  Get the different surfaces (using boundaries) and their cn_map corresponding to the different distance-angle cutoffs for a given site.

                  @@ -283,7 +283,7 @@
                  -neighbors(isite, distfactor, angfactor, additional_condition=None)[source]
                  +neighbors(isite, distfactor, angfactor, additional_condition=None)[source]

                  Get the neighbors of a given site corresponding to a given distance and angle factor.

                  Parameters
                  @@ -302,7 +302,7 @@
                  -neighbors_surfaces(isite, surface_calculation_type=None, max_dist=2.0)[source]
                  +neighbors_surfaces(isite, surface_calculation_type=None, max_dist=2.0)[source]

                  Get the different surfaces corresponding to the different distance-angle cutoffs for a given site.

                  Parameters
                  @@ -320,7 +320,7 @@
                  -neighbors_surfaces_bounded(isite, surface_calculation_options=None)[source]
                  +neighbors_surfaces_bounded(isite, surface_calculation_options=None)[source]

                  Get the different surfaces (using boundaries) corresponding to the different distance-angle cutoffs for a given site.

                  @@ -338,7 +338,7 @@
                  -setup_neighbors_distances_and_angles(indices)[source]
                  +setup_neighbors_distances_and_angles(indices)[source]

                  Initializes the angle and distance separations.

                  Parameters
                  @@ -349,7 +349,7 @@
                  -setup_voronoi_list(indices, voronoi_cutoff)[source]
                  +setup_voronoi_list(indices, voronoi_cutoff)[source]

                  Set up of the voronoi list of neighbours by calling qhull.

                  Parameters
                  @@ -366,7 +366,7 @@
                  -to_bson_voronoi_list2()[source]
                  +to_bson_voronoi_list2()[source]

                  Transforms the voronoi_list into a vlist + bson_nb_voro_list, that are BSON-encodable.

                  Returns
                  @@ -377,7 +377,7 @@
                  -voronoi_parameters_bounds_and_limits(isite, plot_type, max_dist)[source]
                  +voronoi_parameters_bounds_and_limits(isite, plot_type, max_dist)[source]

                  Get the different boundaries and limits of the distance and angle factors for the given site.

                  Parameters
                  @@ -397,7 +397,7 @@
                  -from_bson_voronoi_list2(bson_nb_voro_list2, structure)[source]
                  +from_bson_voronoi_list2(bson_nb_voro_list2, structure)[source]

                  Returns the voronoi_list needed for the VoronoiContainer object from a bson-encoded voronoi_list.

                  Parameters
                  diff --git a/docs/pymatgen.analysis.chemenv.html b/docs/pymatgen.analysis.chemenv.html index a249fa9c243..fb5610bd8bc 100644 --- a/docs/pymatgen.analysis.chemenv.html +++ b/docs/pymatgen.analysis.chemenv.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv package — pymatgen 2022.5.18 documentation + pymatgen.analysis.chemenv package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                  - 2022.5.18 + 2022.5.18.1
                  diff --git a/docs/pymatgen.analysis.chemenv.utils.chemenv_config.html b/docs/pymatgen.analysis.chemenv.utils.chemenv_config.html index 14b6e98e7b9..294bcd66903 100644 --- a/docs/pymatgen.analysis.chemenv.utils.chemenv_config.html +++ b/docs/pymatgen.analysis.chemenv.utils.chemenv_config.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.utils.chemenv_config module — pymatgen 2022.5.18 documentation + pymatgen.analysis.chemenv.utils.chemenv_config module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                  - 2022.5.18 + 2022.5.18.1
                  @@ -120,7 +120,7 @@

                  This module contains the classes for configuration of the chemenv package.

                  -class ChemEnvConfig(package_options=None)[source]
                  +class ChemEnvConfig(package_options=None)[source]

                  Bases: object

                  Class used to store the configuration of the chemenv package :
                    @@ -137,45 +137,45 @@
                  -DEFAULT_PACKAGE_OPTIONS = {'default_max_distance_factor': 1.5, 'default_strategy': {'strategy': 'SimplestChemenvStrategy', 'strategy_options': {'additional_condition': 1, 'angle_cutoff': 0.3, 'continuous_symmetry_measure_cutoff': 10.0, 'distance_cutoff': 1.4}}}[source]
                  +DEFAULT_PACKAGE_OPTIONS = {'default_max_distance_factor': 1.5, 'default_strategy': {'strategy': 'SimplestChemenvStrategy', 'strategy_options': {'additional_condition': 1, 'angle_cutoff': 0.3, 'continuous_symmetry_measure_cutoff': 10.0, 'distance_cutoff': 1.4}}}[source]
                  -classmethod auto_load(root_dir=None)[source]
                  +classmethod auto_load(root_dir=None)[source]

                  Autoload options. :param root_dir:

                  -property has_materials_project_access[source]
                  +property has_materials_project_access[source]

                  Whether MP access is enabled. :return:

                  -package_options_description()[source]
                  +package_options_description()[source]

                  Describe package options.

                  -save(root_dir=None)[source]
                  +save(root_dir=None)[source]

                  Save the options. :param root_dir:

                  -setup()[source]
                  +setup()[source]

                  Setup the class.

                  -setup_package_options()[source]
                  +setup_package_options()[source]

                  Setup the package options.

                  diff --git a/docs/pymatgen.analysis.chemenv.utils.chemenv_errors.html b/docs/pymatgen.analysis.chemenv.utils.chemenv_errors.html index 9ec6265c6cf..0a39484fd13 100644 --- a/docs/pymatgen.analysis.chemenv.utils.chemenv_errors.html +++ b/docs/pymatgen.analysis.chemenv.utils.chemenv_errors.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.utils.chemenv_errors module — pymatgen 2022.5.18 documentation + pymatgen.analysis.chemenv.utils.chemenv_errors module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                  - 2022.5.18 + 2022.5.18.1
                  @@ -120,7 +120,7 @@

                  This module contains the error classes for the chemenv package.

                  -exception AbstractChemenvError(cls, method, msg)[source]
                  +exception AbstractChemenvError(cls, method, msg)[source]

                  Bases: Exception

                  Abstract class for Chemenv errors.

                  @@ -136,7 +136,7 @@
                  -exception ChemenvError(cls, method, msg)[source]
                  +exception ChemenvError(cls, method, msg)[source]

                  Bases: Exception

                  Chemenv error.

                  @@ -152,7 +152,7 @@
                  -exception EquivalentSiteSearchError(site)[source]
                  +exception EquivalentSiteSearchError(site)[source]

                  Bases: pymatgen.analysis.chemenv.utils.chemenv_errors.AbstractChemenvError

                  Equivalent site search error.

                  @@ -164,7 +164,7 @@
                  -exception NeighborsNotComputedChemenvError(site)[source]
                  +exception NeighborsNotComputedChemenvError(site)[source]

                  Bases: pymatgen.analysis.chemenv.utils.chemenv_errors.AbstractChemenvError

                  Neighbors not computed error.

                  @@ -176,7 +176,7 @@
                  -exception SolidAngleError(cosinus)[source]
                  +exception SolidAngleError(cosinus)[source]

                  Bases: pymatgen.analysis.chemenv.utils.chemenv_errors.AbstractChemenvError

                  Solid angle error.

                  diff --git a/docs/pymatgen.analysis.chemenv.utils.coordination_geometry_utils.html b/docs/pymatgen.analysis.chemenv.utils.coordination_geometry_utils.html index 3575401b817..56f18dc90db 100644 --- a/docs/pymatgen.analysis.chemenv.utils.coordination_geometry_utils.html +++ b/docs/pymatgen.analysis.chemenv.utils.coordination_geometry_utils.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.utils.coordination_geometry_utils module — pymatgen 2022.5.18 documentation + pymatgen.analysis.chemenv.utils.coordination_geometry_utils module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                  - 2022.5.18 + 2022.5.18.1
                  @@ -120,25 +120,25 @@

                  This module contains some utility functions and classes that are used in the chemenv package.

                  -class Plane(coefficients, p1=None, p2=None, p3=None)[source]
                  +class Plane(coefficients, p1=None, p2=None, p3=None)[source]

                  Bases: object

                  Class used to describe a plane

                  Initializes a plane from the 4 coefficients a, b, c and d of ax + by + cz + d = 0 :param coefficients: abcd coefficients of the plane

                  -TEST_2D_POINTS = [array([0., 0.]), array([1., 0.]), array([0., 1.]), array([-1.,  0.]), array([ 0., -1.]), array([0., 2.]), array([2., 0.]), array([ 0., -2.]), array([-2.,  0.]), array([1., 1.]), array([2., 2.]), array([-1., -1.]), array([-2., -2.]), array([1., 2.]), array([ 1., -2.]), array([-1.,  2.]), array([-1., -2.]), array([2., 1.]), array([ 2., -1.]), array([-2.,  1.]), array([-2., -1.])][source]
                  +TEST_2D_POINTS = [array([0., 0.]), array([1., 0.]), array([0., 1.]), array([-1.,  0.]), array([ 0., -1.]), array([0., 2.]), array([2., 0.]), array([ 0., -2.]), array([-2.,  0.]), array([1., 1.]), array([2., 2.]), array([-1., -1.]), array([-2., -2.]), array([1., 2.]), array([ 1., -2.]), array([-1.,  2.]), array([-1., -2.]), array([2., 1.]), array([ 2., -1.]), array([-2.,  1.]), array([-2., -1.])][source]
                  -property a[source]
                  +property a[source]

                  Coefficient a of the plane.

                  -property abcd[source]
                  +property abcd[source]

                  Return a tuple with the plane coefficients.

                  Returns
                  @@ -149,19 +149,19 @@
                  -property b[source]
                  +property b[source]

                  Coefficient b of the plane.

                  -property c[source]
                  +property c[source]

                  Coefficient c of the plane.

                  -property coefficients[source]
                  +property coefficients[source]

                  Return a copy of the plane coefficients.

                  Returns
                  @@ -172,25 +172,25 @@
                  -property crosses_origin[source]
                  +property crosses_origin[source]

                  Whether this plane crosses the origin (i.e. coefficient d is 0.0).

                  -property d[source]
                  +property d[source]

                  Coefficient d of the plane.

                  -property distance_to_origin[source]
                  +property distance_to_origin[source]

                  Distance of the plane to the origin.

                  -distance_to_point(point)[source]
                  +distance_to_point(point)[source]

                  Computes the absolute distance from the plane to the point :param point: Point for which distance is computed :return: Distance between the plane and the point

                  @@ -198,7 +198,7 @@
                  -distances(points)[source]
                  +distances(points)[source]

                  Computes the distances from the plane to each of the points. Positive distances are on the side of the normal of the plane while negative distances are on the other side :param points: Points for which distances are computed @@ -210,7 +210,7 @@

                  -distances_indices_groups(points, delta=None, delta_factor=0.05, sign=False)[source]
                  +distances_indices_groups(points, delta=None, delta_factor=0.05, sign=False)[source]

                  Computes the distances from the plane to each of the points. Positive distances are on the side of the normal of the plane while negative distances are on the other side. Indices sorting the points from closest to furthest is also computed. Grouped indices are also given, for which indices of the distances that are @@ -237,7 +237,7 @@

                  -distances_indices_sorted(points, sign=False)[source]
                  +distances_indices_sorted(points, sign=False)[source]

                  Computes the distances from the plane to each of the points. Positive distances are on the side of the normal of the plane while negative distances are on the other side. Indices sorting the points from closest to furthest is also computed. @@ -252,7 +252,7 @@

                  -fit_error(points, fit='least_square_distance')[source]
                  +fit_error(points, fit='least_square_distance')[source]

                  Evaluate the error for a list of points with respect to this plane.

                  Parameters
                  @@ -269,7 +269,7 @@
                  -fit_least_square_distance_error(points)[source]
                  +fit_least_square_distance_error(points)[source]

                  Evaluate the sum of squared distances error for a list of points with respect to this plane.

                  Parameters
                  @@ -283,7 +283,7 @@
                  -fit_maximum_distance_error(points)[source]
                  +fit_maximum_distance_error(points)[source]

                  Evaluate the max distance error for a list of points with respect to this plane.

                  Parameters
                  @@ -297,7 +297,7 @@
                  -classmethod from_2points_and_origin(p1, p2)[source]
                  +classmethod from_2points_and_origin(p1, p2)[source]

                  Initializes plane from two points and the origin.

                  Parameters
                  @@ -314,7 +314,7 @@
                  -classmethod from_3points(p1, p2, p3)[source]
                  +classmethod from_3points(p1, p2, p3)[source]

                  Initializes plane from three points.

                  Parameters
                  @@ -332,7 +332,7 @@
                  -classmethod from_coefficients(a, b, c, d)[source]
                  +classmethod from_coefficients(a, b, c, d)[source]

                  Initialize plane from its coefficients.

                  Parameters
                  @@ -351,7 +351,7 @@
                  -classmethod from_npoints(points, best_fit='least_square_distance')[source]
                  +classmethod from_npoints(points, best_fit='least_square_distance')[source]

                  Initializes plane from a list of points.

                  If the number of points is larger than 3, will use a least square fitting or max distance fitting.

                  @@ -369,7 +369,7 @@
                  -classmethod from_npoints_least_square_distance(points)[source]
                  +classmethod from_npoints_least_square_distance(points)[source]

                  Initializes plane from a list of points using a least square fitting procedure.

                  Parameters
                  @@ -383,7 +383,7 @@
                  -classmethod from_npoints_maximum_distance(points)[source]
                  +classmethod from_npoints_maximum_distance(points)[source]

                  Initializes plane from a list of points using a max distance fitting procedure.

                  Parameters
                  @@ -397,7 +397,7 @@
                  -indices_separate(points, dist_tolerance)[source]
                  +indices_separate(points, dist_tolerance)[source]

                  Returns three lists containing the indices of the points lying on one side of the plane, on the plane and on the other side of the plane. The dist_tolerance parameter controls the tolerance to which a point is considered to lie on the plane or not (distance to the plane) @@ -416,7 +416,7 @@

                  -init_3points(nonzeros, zeros)[source]
                  +init_3points(nonzeros, zeros)[source]

                  Initialize three random points on this plane.

                  Parameters
                  @@ -433,7 +433,7 @@
                  -is_in_list(plane_list)[source]
                  +is_in_list(plane_list)[source]

                  Checks whether the plane is identical to one of the Planes in the plane_list list of Planes :param plane_list: List of Planes to be compared to :return: True if the plane is in the list, False otherwise

                  @@ -441,7 +441,7 @@
                  -is_in_plane(pp, dist_tolerance)[source]
                  +is_in_plane(pp, dist_tolerance)[source]

                  Determines if point pp is in the plane within the tolerance dist_tolerance :param pp: point to be tested :param dist_tolerance: tolerance on the distance to the plane within which point pp is considered in the plane @@ -450,7 +450,7 @@

                  -is_same_plane_as(plane)[source]
                  +is_same_plane_as(plane)[source]

                  Checks whether the plane is identical to another Plane “plane” :param plane: Plane to be compared to :return: True if the two facets are identical, False otherwise

                  @@ -458,7 +458,7 @@
                  -orthonormal_vectors()[source]
                  +orthonormal_vectors()[source]

                  Returns a list of three orthogonal vectors, the two first being parallel to the plane and the third one is the normal vector of the plane :return: List of orthogonal vectors @@ -467,7 +467,7 @@

                  -classmethod perpendicular_bisector(p1, p2)[source]
                  +classmethod perpendicular_bisector(p1, p2)[source]

                  Initialize a plane from the perpendicular bisector of two points.

                  The perpendicular bisector of two points is the plane perpendicular to the vector joining these two points and passing through the middle of the segment joining the two points.

                  @@ -486,7 +486,7 @@
                  -project_and_to2dim(pps, plane_center)[source]
                  +project_and_to2dim(pps, plane_center)[source]

                  Projects the list of points pps to the plane and changes the basis from 3D to the 2D basis of the plane :param pps: List of points to be projected :return: :raise:

                  @@ -494,7 +494,7 @@
                  -project_and_to2dim_ordered_indices(pps, plane_center='mean')[source]
                  +project_and_to2dim_ordered_indices(pps, plane_center='mean')[source]

                  Projects each points in the point list pps on plane and returns the indices that would sort the list of projected points in anticlockwise order :param pps: List of points to project on plane @@ -503,7 +503,7 @@

                  -projectionpoints(pps)[source]
                  +projectionpoints(pps)[source]

                  Projects each points in the point list pps on plane and returns the list of projected points :param pps: List of points to project on plane :return: List of projected point on plane

                  @@ -513,7 +513,7 @@
                  -anticlockwise_sort(pps)[source]
                  +anticlockwise_sort(pps)[source]

                  Sort a list of 2D points in anticlockwise order :param pps: List of points to be sorted :return: Sorted list of points

                  @@ -521,7 +521,7 @@
                  -anticlockwise_sort_indices(pps)[source]
                  +anticlockwise_sort_indices(pps)[source]

                  Returns the indices that would sort a list of 2D points in anticlockwise order :param pps: List of points to be sorted :return: Indices of the sorted list of points

                  @@ -529,7 +529,7 @@
                  -changebasis(uu, vv, nn, pps)[source]
                  +changebasis(uu, vv, nn, pps)[source]

                  For a list of points given in standard coordinates (in terms of e1, e2 and e3), returns the same list expressed in the basis (uu, vv, nn), which is supposed to be orthonormal. :param uu: First vector of the basis @@ -541,7 +541,7 @@

                  -collinear(p1, p2, p3=None, tolerance=0.25)[source]
                  +collinear(p1, p2, p3=None, tolerance=0.25)[source]

                  Checks if the three points p1, p2 and p3 are collinear or not within a given tolerance. The collinearity is checked by computing the area of the triangle defined by the three points p1, p2 and p3. If the area of this triangle is less than (tolerance x largest_triangle), then the three points are considered collinear. The @@ -566,7 +566,7 @@

                  -diamond_functions(xx, yy, y_x0, x_y0)[source]
                  +diamond_functions(xx, yy, y_x0, x_y0)[source]

                  Method that creates two upper and lower functions based on points xx and yy as well as intercepts defined by y_x0 and x_y0. The resulting functions form kind of a distorted diamond-like structure aligned from @@ -616,7 +616,7 @@

                  -function_comparison(f1, f2, x1, x2, numpoints_check=500)[source]
                  +function_comparison(f1, f2, x1, x2, numpoints_check=500)[source]

                  Method that compares two functions

                  Parameters
                  @@ -642,7 +642,7 @@
                  -get_lower_and_upper_f(surface_calculation_options)[source]
                  +get_lower_and_upper_f(surface_calculation_options)[source]

                  Get the lower and upper functions defining a surface in the distance-angle space of neighbors.

                  Parameters
                  @@ -656,7 +656,7 @@
                  -is_anion_cation_bond(valences, ii, jj)[source]
                  +is_anion_cation_bond(valences, ii, jj)[source]

                  Checks if two given sites are an anion and a cation. :param valences: list of site valences :param ii: index of a site @@ -666,7 +666,7 @@

                  -matrixTimesVector(MM, aa)[source]
                  +matrixTimesVector(MM, aa)[source]
                  Parameters
                    @@ -682,7 +682,7 @@
                    -my_solid_angle(center, coords)[source]
                    +my_solid_angle(center, coords)[source]

                    Helper method to calculate the solid angle of a set of coords from the center.

                    @@ -700,7 +700,7 @@
                    -quarter_ellipsis_functions(xx, yy)[source]
                    +quarter_ellipsis_functions(xx, yy)[source]

                    Method that creates two quarter-ellipse functions based on points xx and yy. The ellipsis is supposed to be aligned with the axes. The two ellipsis pass through the two points xx and yy.

                    @@ -718,7 +718,7 @@
                    -rectangle_surface_intersection(rectangle, f_lower, f_upper, bounds_lower=None, bounds_upper=None, check=True, numpoints_check=500)[source]
                    +rectangle_surface_intersection(rectangle, f_lower, f_upper, bounds_lower=None, bounds_upper=None, check=True, numpoints_check=500)[source]

                    Method to calculate the surface of the intersection of a rectangle (aligned with axes) and another surface defined by two functions f_lower and f_upper.

                    @@ -741,7 +741,7 @@
                    -rotateCoords(coords, R)[source]
                    +rotateCoords(coords, R)[source]

                    Rotate the list of points using rotation matrix R :param coords: List of points to be rotated :param R: Rotation matrix @@ -750,7 +750,7 @@

                    -rotateCoordsOpt(coords, R)[source]
                    +rotateCoordsOpt(coords, R)[source]

                    Rotate the list of points using rotation matrix R :param coords: List of points to be rotated :param R: Rotation matrix @@ -759,7 +759,7 @@

                    -separation_in_list(separation_indices, separation_indices_list)[source]
                    +separation_in_list(separation_indices, separation_indices_list)[source]

                    Checks if the separation indices of a plane are already in the list :param separation_indices: list of separation indices (three arrays of integers) :param separation_indices_list: list of the list of separation indices to be compared to @@ -768,7 +768,7 @@

                    -sort_separation(separation)[source]
                    +sort_separation(separation)[source]

                    Sort a separation.

                    Parameters
                    @@ -782,7 +782,7 @@
                    -sort_separation_tuple(separation)[source]
                    +sort_separation_tuple(separation)[source]

                    Sort a separation

                    Parameters
                    @@ -796,7 +796,7 @@
                    -spline_functions(lower_points, upper_points, degree=3)[source]
                    +spline_functions(lower_points, upper_points, degree=3)[source]

                    Method that creates two (upper and lower) spline functions based on points lower_points and upper_points.

                    Parameters
                    @@ -814,7 +814,7 @@
                    -vectorsToMatrix(aa, bb)[source]
                    +vectorsToMatrix(aa, bb)[source]

                    Performs the vector multiplication of the elements of two vectors, constructing the 3x3 matrix. :param aa: One vector of size 3 :param bb: Another vector of size 3 diff --git a/docs/pymatgen.analysis.chemenv.utils.defs_utils.html b/docs/pymatgen.analysis.chemenv.utils.defs_utils.html index 506ababd5fc..09324d04def 100644 --- a/docs/pymatgen.analysis.chemenv.utils.defs_utils.html +++ b/docs/pymatgen.analysis.chemenv.utils.defs_utils.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.utils.defs_utils module — pymatgen 2022.5.18 documentation + pymatgen.analysis.chemenv.utils.defs_utils module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                    - 2022.5.18 + 2022.5.18.1
                    @@ -120,77 +120,77 @@

                    This module contains the definition of some objects used in the chemenv package.

                    -class AdditionalConditions[source]
                    +class AdditionalConditions[source]

                    Bases: object

                    Class for additional conditions.

                    -ALL = [0, 1, 2, 3, 4][source]
                    +ALL = [0, 1, 2, 3, 4][source]
                    -CONDITION_DESCRIPTION = {0: 'No additional condition', 1: 'Only anion-cation bonds', 2: 'No element-element bonds (same elements)', 3: 'Only anion-cation bonds and no element-element bonds (same elements)', 4: 'Only element-oxygen bonds'}[source]
                    +CONDITION_DESCRIPTION = {0: 'No additional condition', 1: 'Only anion-cation bonds', 2: 'No element-element bonds (same elements)', 3: 'Only anion-cation bonds and no element-element bonds (same elements)', 4: 'Only element-oxygen bonds'}[source]
                    -NONE = 0[source]
                    +NONE = 0[source]
                    -NO_AC = 0[source]
                    +NO_AC = 0[source]
                    -NO_ADDITIONAL_CONDITION = 0[source]
                    +NO_ADDITIONAL_CONDITION = 0[source]
                    -NO_E2SEB = 2[source]
                    +NO_E2SEB = 2[source]
                    -NO_ELEMENT_TO_SAME_ELEMENT_BONDS = 2[source]
                    +NO_ELEMENT_TO_SAME_ELEMENT_BONDS = 2[source]
                    -ONLY_ACB = 1[source]
                    +ONLY_ACB = 1[source]
                    -ONLY_ACB_AND_NO_E2SEB = 3[source]
                    +ONLY_ACB_AND_NO_E2SEB = 3[source]
                    -ONLY_ANION_CATION_BONDS = 1[source]
                    +ONLY_ANION_CATION_BONDS = 1[source]
                    -ONLY_ANION_CATION_BONDS_AND_NO_ELEMENT_TO_SAME_ELEMENT_BONDS = 3[source]
                    +ONLY_ANION_CATION_BONDS_AND_NO_ELEMENT_TO_SAME_ELEMENT_BONDS = 3[source]
                    -ONLY_E2OB = 4[source]
                    +ONLY_E2OB = 4[source]
                    -ONLY_ELEMENT_TO_OXYGEN_BONDS = 4[source]
                    +ONLY_ELEMENT_TO_OXYGEN_BONDS = 4[source]
                    -check_condition(condition, structure, parameters)[source]
                    +check_condition(condition, structure, parameters)[source]
                    Parameters
                      @@ -209,7 +209,7 @@
                      -chemenv_citations()[source]
                      +chemenv_citations()[source]
                      Returns

                      diff --git a/docs/pymatgen.analysis.chemenv.utils.func_utils.html b/docs/pymatgen.analysis.chemenv.utils.func_utils.html index f99e02c80cd..23778618094 100644 --- a/docs/pymatgen.analysis.chemenv.utils.func_utils.html +++ b/docs/pymatgen.analysis.chemenv.utils.func_utils.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.utils.func_utils module — pymatgen 2022.5.18 documentation + pymatgen.analysis.chemenv.utils.func_utils module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                      - 2022.5.18 + 2022.5.18.1
                      @@ -120,7 +120,7 @@

                      This module contains some utility functions and classes that are used in the chemenv package.

                      -class AbstractRatioFunction(function, options_dict=None)[source]
                      +class AbstractRatioFunction(function, options_dict=None)[source]

                      Bases: object

                      Abstract class for all ratio functions

                      Constructor for AbstractRatioFunction

                      @@ -134,12 +134,12 @@
                      -ALLOWED_FUNCTIONS: Dict[str, list] = {}[source]
                      +ALLOWED_FUNCTIONS: Dict[str, list] = {}[source]
                      -evaluate(value)[source]
                      +evaluate(value)[source]

                      Evaluate the ratio function for the given value.

                      Parameters
                      @@ -153,7 +153,7 @@
                      -classmethod from_dict(dd)[source]
                      +classmethod from_dict(dd)[source]

                      Construct ratio function from dict.

                      Parameters
                      @@ -167,7 +167,7 @@
                      -setup_parameters(options_dict)[source]
                      +setup_parameters(options_dict)[source]

                      Set up the parameters for this ratio function.

                      Parameters
                      @@ -183,7 +183,7 @@
                      -class CSMFiniteRatioFunction(function, options_dict=None)[source]
                      +class CSMFiniteRatioFunction(function, options_dict=None)[source]

                      Bases: pymatgen.analysis.chemenv.utils.func_utils.AbstractRatioFunction

                      Concrete implementation of a series of ratio functions applied to the continuous symmetry measure (CSM).

                      Uses “finite” ratio functions.

                      @@ -201,12 +201,12 @@
                      -ALLOWED_FUNCTIONS: Dict[str, list] = {'power2_decreasing_exp': ['max_csm', 'alpha'], 'smootherstep': ['lower_csm', 'upper_csm'], 'smoothstep': ['lower_csm', 'upper_csm']}[source]
                      +ALLOWED_FUNCTIONS: Dict[str, list] = {'power2_decreasing_exp': ['max_csm', 'alpha'], 'smootherstep': ['lower_csm', 'upper_csm'], 'smoothstep': ['lower_csm', 'upper_csm']}[source]
                      -fractions(data)[source]
                      +fractions(data)[source]

                      Get the fractions from the CSM ratio function applied to the data.

                      Parameters
                      @@ -220,7 +220,7 @@
                      -mean_estimator(data)[source]
                      +mean_estimator(data)[source]

                      Get the weighted CSM using this CSM ratio function applied to the data.

                      Parameters
                      @@ -234,7 +234,7 @@
                      -power2_decreasing_exp(vals)[source]
                      +power2_decreasing_exp(vals)[source]

                      Get the evaluation of the ratio function f(x)=exp(-a*x)*(x-1)^2.

                      The CSM values (i.e. “x”), are scaled to the “max_csm” parameter. The “a” constant correspond to the “alpha” parameter.

                      @@ -250,7 +250,7 @@
                      -ratios(data)[source]
                      +ratios(data)[source]

                      Get the fractions from the CSM ratio function applied to the data.

                      Parameters
                      @@ -264,7 +264,7 @@
                      -smootherstep(vals)[source]
                      +smootherstep(vals)[source]

                      Get the evaluation of the smootherstep ratio function: f(x)=6*x^5-15*x^4+10*x^3.

                      The CSM values (i.e. “x”), are scaled between the “lower_csm” and “upper_csm” parameters.

                      @@ -279,7 +279,7 @@
                      -smoothstep(vals)[source]
                      +smoothstep(vals)[source]

                      Get the evaluation of the smoothstep ratio function: f(x)=3*x^2-2*x^3.

                      The CSM values (i.e. “x”), are scaled between the “lower_csm” and “upper_csm” parameters.

                      @@ -296,7 +296,7 @@
                      -class CSMInfiniteRatioFunction(function, options_dict=None)[source]
                      +class CSMInfiniteRatioFunction(function, options_dict=None)[source]

                      Bases: pymatgen.analysis.chemenv.utils.func_utils.AbstractRatioFunction

                      Concrete implementation of a series of ratio functions applied to the continuous symmetry measure (CSM).

                      Uses “infinite” ratio functions.

                      @@ -314,12 +314,12 @@
                      -ALLOWED_FUNCTIONS: Dict[str, list] = {'power2_inverse_decreasing': ['max_csm'], 'power2_inverse_power2_decreasing': ['max_csm']}[source]
                      +ALLOWED_FUNCTIONS: Dict[str, list] = {'power2_inverse_decreasing': ['max_csm'], 'power2_inverse_power2_decreasing': ['max_csm']}[source]
                      -fractions(data)[source]
                      +fractions(data)[source]

                      Get the fractions from the CSM ratio function applied to the data.

                      Parameters
                      @@ -333,7 +333,7 @@
                      -mean_estimator(data)[source]
                      +mean_estimator(data)[source]

                      Get the weighted CSM using this CSM ratio function applied to the data.

                      Parameters
                      @@ -347,7 +347,7 @@
                      -power2_inverse_decreasing(vals)[source]
                      +power2_inverse_decreasing(vals)[source]

                      Get the evaluation of the ratio function f(x)=(x-1)^2 / x.

                      The CSM values (i.e. “x”), are scaled to the “max_csm” parameter. The “a” constant correspond to the “alpha” parameter.

                      @@ -363,7 +363,7 @@
                      -power2_inverse_power2_decreasing(vals)[source]
                      +power2_inverse_power2_decreasing(vals)[source]

                      Get the evaluation of the ratio function f(x)=(x-1)^2 / x^2.

                      The CSM values (i.e. “x”), are scaled to the “max_csm” parameter. The “a” constant correspond to the “alpha” parameter.

                      @@ -379,7 +379,7 @@
                      -ratios(data)[source]
                      +ratios(data)[source]

                      Get the fractions from the CSM ratio function applied to the data.

                      Parameters
                      @@ -395,7 +395,7 @@
                      -class DeltaCSMRatioFunction(function, options_dict=None)[source]
                      +class DeltaCSMRatioFunction(function, options_dict=None)[source]

                      Bases: pymatgen.analysis.chemenv.utils.func_utils.AbstractRatioFunction

                      Concrete implementation of a series of ratio functions applied to differences of continuous symmetry measures (DeltaCSM).

                      @@ -414,12 +414,12 @@
                      -ALLOWED_FUNCTIONS: Dict[str, list] = {'smootherstep': ['delta_csm_min', 'delta_csm_max']}[source]
                      +ALLOWED_FUNCTIONS: Dict[str, list] = {'smootherstep': ['delta_csm_min', 'delta_csm_max']}[source]
                      -smootherstep(vals)[source]
                      +smootherstep(vals)[source]

                      Get the evaluation of the smootherstep ratio function: f(x)=6*x^5-15*x^4+10*x^3.

                      The DeltaCSM values (i.e. “x”), are scaled between the “delta_csm_min” and “delta_csm_max” parameters.

                      @@ -436,7 +436,7 @@
                      -class RatioFunction(function, options_dict=None)[source]
                      +class RatioFunction(function, options_dict=None)[source]

                      Bases: pymatgen.analysis.chemenv.utils.func_utils.AbstractRatioFunction

                      Concrete implementation of a series of ratio functions.

                      Constructor for AbstractRatioFunction

                      @@ -450,12 +450,12 @@
                      -ALLOWED_FUNCTIONS: Dict[str, list] = {'inverse_smootherstep': ['lower', 'upper'], 'inverse_smoothstep': ['lower', 'upper'], 'power2_decreasing_exp': ['max', 'alpha'], 'power2_inverse_decreasing': ['max'], 'power2_inverse_power2_decreasing': ['max'], 'smootherstep': ['lower', 'upper'], 'smoothstep': ['lower', 'upper']}[source]
                      +ALLOWED_FUNCTIONS: Dict[str, list] = {'inverse_smootherstep': ['lower', 'upper'], 'inverse_smoothstep': ['lower', 'upper'], 'power2_decreasing_exp': ['max', 'alpha'], 'power2_inverse_decreasing': ['max'], 'power2_inverse_power2_decreasing': ['max'], 'smootherstep': ['lower', 'upper'], 'smoothstep': ['lower', 'upper']}[source]
                      -inverse_smootherstep(vals)[source]
                      +inverse_smootherstep(vals)[source]

                      Get the evaluation of the “inverse” smootherstep ratio function: f(x)=1-(6*x^5-15*x^4+10*x^3).

                      The values (i.e. “x”), are scaled between the “lower” and “upper” parameters.

                      @@ -470,7 +470,7 @@
                      -inverse_smoothstep(vals)[source]
                      +inverse_smoothstep(vals)[source]

                      Get the evaluation of the “inverse” smoothstep ratio function: f(x)=1-(3*x^2-2*x^3).

                      The values (i.e. “x”), are scaled between the “lower” and “upper” parameters.

                      @@ -485,7 +485,7 @@
                      -power2_decreasing_exp(vals)[source]
                      +power2_decreasing_exp(vals)[source]

                      Get the evaluation of the ratio function f(x)=exp(-a*x)*(x-1)^2.

                      The values (i.e. “x”), are scaled to the “max” parameter. The “a” constant correspond to the “alpha” parameter.

                      @@ -501,7 +501,7 @@
                      -power2_inverse_decreasing(vals)[source]
                      +power2_inverse_decreasing(vals)[source]

                      Get the evaluation of the ratio function f(x)=(x-1)^2 / x.

                      The values (i.e. “x”), are scaled to the “max” parameter.

                      @@ -516,7 +516,7 @@
                      -power2_inverse_power2_decreasing(vals)[source]
                      +power2_inverse_power2_decreasing(vals)[source]

                      Get the evaluation of the ratio function f(x)=(x-1)^2 / x^2.

                      The values (i.e. “x”), are scaled to the “max” parameter.

                      @@ -531,7 +531,7 @@
                      -smootherstep(vals)[source]
                      +smootherstep(vals)[source]

                      Get the evaluation of the smootherstep ratio function: f(x)=6*x^5-15*x^4+10*x^3.

                      The values (i.e. “x”), are scaled between the “lower” and “upper” parameters.

                      @@ -546,7 +546,7 @@
                      -smoothstep(vals)[source]
                      +smoothstep(vals)[source]

                      Get the evaluation of the smoothstep ratio function: f(x)=3*x^2-2*x^3.

                      The values (i.e. “x”), are scaled between the “lower” and “upper” parameters.

                      diff --git a/docs/pymatgen.analysis.chemenv.utils.graph_utils.html b/docs/pymatgen.analysis.chemenv.utils.graph_utils.html index 3cf451c4a60..c7b3345f1fc 100644 --- a/docs/pymatgen.analysis.chemenv.utils.graph_utils.html +++ b/docs/pymatgen.analysis.chemenv.utils.graph_utils.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.utils.graph_utils module — pymatgen 2022.5.18 documentation + pymatgen.analysis.chemenv.utils.graph_utils module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                      - 2022.5.18 + 2022.5.18.1
                      @@ -120,7 +120,7 @@

                      This module contains some graph utils that are used in the chemenv package.

                      -class MultiGraphCycle(nodes, edge_indices, validate=True, ordered=None)[source]
                      +class MultiGraphCycle(nodes, edge_indices, validate=True, ordered=None)[source]

                      Bases: monty.json.MSONable

                      Class used to describe a cycle in a multigraph.

                      nodes are the nodes of the cycle and edge_indices are the indices of the edges in the cycle. @@ -144,7 +144,7 @@

                      -order(raise_on_fail=True)[source]
                      +order(raise_on_fail=True)[source]

                      Orders the SimpleGraphCycle.

                      The ordering is performed such that the first node is the “lowest” one and the second node is the lowest one of the two neighbor nodes of the @@ -163,7 +163,7 @@

                      -validate(check_strict_ordering=False)[source]
                      +validate(check_strict_ordering=False)[source]
                      Parameters

                      check_strict_ordering –

                      @@ -178,7 +178,7 @@
                      -class SimpleGraphCycle(nodes, validate=True, ordered=None)[source]
                      +class SimpleGraphCycle(nodes, validate=True, ordered=None)[source]

                      Bases: monty.json.MSONable

                      Class used to describe a cycle in a simple graph (graph without multiple edges).

                      Note that the convention used here is the networkx convention for which simple graphs allow @@ -198,7 +198,7 @@

                      -as_dict()[source]
                      +as_dict()[source]
                      Returns

                      MSONAble dict

                      @@ -208,7 +208,7 @@
                      -classmethod from_dict(d, validate=False)[source]
                      +classmethod from_dict(d, validate=False)[source]

                      Serialize from dict. :param d: :param validate: @@ -217,7 +217,7 @@

                      -classmethod from_edges(edges, edges_are_ordered=True)[source]
                      +classmethod from_edges(edges, edges_are_ordered=True)[source]

                      Constructs SimpleGraphCycle from a list edges.

                      By default, the edges list is supposed to be ordered as it will be much faster to construct the cycle. If edges_are_ordered is set to @@ -227,7 +227,7 @@

                      -order(raise_on_fail=True)[source]
                      +order(raise_on_fail=True)[source]

                      Orders the SimpleGraphCycle.

                      The ordering is performed such that the first node is the “lowest” one and the second node is the lowest one of the two neighbor nodes of the @@ -246,7 +246,7 @@

                      -validate(check_strict_ordering=False)[source]
                      +validate(check_strict_ordering=False)[source]
                      Parameters

                      check_strict_ordering –

                      @@ -261,7 +261,7 @@
                      -get_all_elementary_cycles(graph)[source]
                      +get_all_elementary_cycles(graph)[source]
                      Parameters

                      graph –

                      @@ -274,7 +274,7 @@
                      -get_all_simple_paths_edges(graph, source, target, cutoff=None, data=True)[source]
                      +get_all_simple_paths_edges(graph, source, target, cutoff=None, data=True)[source]

                      Get all the simple path and edges. :param graph: :param source: @@ -286,7 +286,7 @@

                      -get_delta(node1, node2, edge_data)[source]
                      +get_delta(node1, node2, edge_data)[source]

                      Get the delta. :param node1: :param node2: diff --git a/docs/pymatgen.analysis.chemenv.utils.html b/docs/pymatgen.analysis.chemenv.utils.html index 3cf325c5766..5f0210097c2 100644 --- a/docs/pymatgen.analysis.chemenv.utils.html +++ b/docs/pymatgen.analysis.chemenv.utils.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.utils package — pymatgen 2022.5.18 documentation + pymatgen.analysis.chemenv.utils package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                      - 2022.5.18 + 2022.5.18.1
                      diff --git a/docs/pymatgen.analysis.chemenv.utils.math_utils.html b/docs/pymatgen.analysis.chemenv.utils.math_utils.html index f64fb786abb..64d108c81c9 100644 --- a/docs/pymatgen.analysis.chemenv.utils.math_utils.html +++ b/docs/pymatgen.analysis.chemenv.utils.math_utils.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.utils.math_utils module — pymatgen 2022.5.18 documentation + pymatgen.analysis.chemenv.utils.math_utils module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                      - 2022.5.18 + 2022.5.18.1
                      @@ -120,7 +120,7 @@

                      This module contains some math utils that are used in the chemenv package.

                      -cosinus_step(xx, edges=None, inverse=False)[source]
                      +cosinus_step(xx, edges=None, inverse=False)[source]
                      Parameters
                        @@ -137,7 +137,7 @@
                        -divisors(n)[source]
                        +divisors(n)[source]

                        From a given natural integer, returns the list of divisors in ascending order :param n: Natural integer :return: List of divisors of n in ascending order

                        @@ -145,7 +145,7 @@
                        -get_center_of_arc(p1, p2, radius)[source]
                        +get_center_of_arc(p1, p2, radius)[source]
                        Parameters
                          @@ -162,7 +162,7 @@
                          -get_linearly_independent_vectors(vectors_list)[source]
                          +get_linearly_independent_vectors(vectors_list)[source]
                          Parameters

                          vectors_list –

                          @@ -175,7 +175,7 @@
                          -normal_cdf_step(xx, mean, scale)[source]
                          +normal_cdf_step(xx, mean, scale)[source]
                          Parameters
                            @@ -192,7 +192,7 @@
                            -power2_decreasing_exp(xx, edges=None, alpha=1.0)[source]
                            +power2_decreasing_exp(xx, edges=None, alpha=1.0)[source]
                            Parameters
                              @@ -209,7 +209,7 @@
                              -power2_inverse_decreasing(xx, edges=None, prefactor=None)[source]
                              +power2_inverse_decreasing(xx, edges=None, prefactor=None)[source]
                              Parameters
                                @@ -226,7 +226,7 @@
                                -power2_inverse_power2_decreasing(xx, edges=None, prefactor=None)[source]
                                +power2_inverse_power2_decreasing(xx, edges=None, prefactor=None)[source]
                                Parameters
                                  @@ -243,7 +243,7 @@
                                  -power2_inverse_powern_decreasing(xx, edges=None, prefactor=None, powern=2.0)[source]
                                  +power2_inverse_powern_decreasing(xx, edges=None, prefactor=None, powern=2.0)[source]
                                  Parameters
                                    @@ -261,7 +261,7 @@
                                    -power2_tangent_decreasing(xx, edges=None, prefactor=None)[source]
                                    +power2_tangent_decreasing(xx, edges=None, prefactor=None)[source]
                                    Parameters
                                      @@ -278,7 +278,7 @@
                                      -power3_step(xx, edges=None, inverse=False)[source]
                                      +power3_step(xx, edges=None, inverse=False)[source]
                                      Parameters
                                        @@ -295,7 +295,7 @@
                                        -powern_decreasing(xx, edges=None, nn=2)[source]
                                        +powern_decreasing(xx, edges=None, nn=2)[source]
                                        Parameters
                                          @@ -312,7 +312,7 @@
                                          -powern_parts_step(xx, edges=None, inverse=False, nn=2)[source]
                                          +powern_parts_step(xx, edges=None, inverse=False, nn=2)[source]
                                          Parameters
                                            @@ -330,7 +330,7 @@
                                            -prime_factors(n)[source]
                                            +prime_factors(n)[source]

                                            Lists prime factors of a given natural integer, from greatest to smallest :param n: Natural integer :rtype : list of all prime factors of the given natural n

                                            @@ -338,7 +338,7 @@
                                            -scale_and_clamp(xx, edge0, edge1, clamp0, clamp1)[source]
                                            +scale_and_clamp(xx, edge0, edge1, clamp0, clamp1)[source]
                                            Parameters
                                              @@ -357,7 +357,7 @@
                                              -smootherstep(xx, edges=None, inverse=False)[source]
                                              +smootherstep(xx, edges=None, inverse=False)[source]
                                              Parameters
                                                @@ -374,7 +374,7 @@
                                                -smoothstep(xx, edges=None, inverse=False)[source]
                                                +smoothstep(xx, edges=None, inverse=False)[source]
                                                Parameters
                                                  diff --git a/docs/pymatgen.analysis.chemenv.utils.scripts_utils.html b/docs/pymatgen.analysis.chemenv.utils.scripts_utils.html index 98ae9db660d..59e7bb9ef45 100644 --- a/docs/pymatgen.analysis.chemenv.utils.scripts_utils.html +++ b/docs/pymatgen.analysis.chemenv.utils.scripts_utils.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chemenv.utils.scripts_utils module — pymatgen 2022.5.18 documentation + pymatgen.analysis.chemenv.utils.scripts_utils module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                  - 2022.5.18 + 2022.5.18.1
                                                  @@ -120,7 +120,7 @@

                                                  This module contains some script utils that are used in the chemenv package.

                                                  -compute_environments(chemenv_configuration)[source]
                                                  +compute_environments(chemenv_configuration)[source]

                                                  Compute the environments.

                                                  Parameters
                                                  @@ -134,7 +134,7 @@
                                                  -draw_cg(vis, site, neighbors, cg=None, perm=None, perfect2local_map=None, show_perfect=False, csm_info=None, symmetry_measure_type='csm_wcs_ctwcc', perfect_radius=0.1, show_distorted=True, faces_color_override=None)[source]
                                                  +draw_cg(vis, site, neighbors, cg=None, perm=None, perfect2local_map=None, show_perfect=False, csm_info=None, symmetry_measure_type='csm_wcs_ctwcc', perfect_radius=0.1, show_distorted=True, faces_color_override=None)[source]

                                                  Draw cg.

                                                  Parameters
                                                  @@ -161,14 +161,14 @@
                                                  -thankyou()[source]
                                                  +thankyou()[source]

                                                  Show thank you message. :return:

                                                  -visualize(cg, zoom=None, vis=None, myfactor=1.0, view_index=True, faces_color_override=None)[source]
                                                  +visualize(cg, zoom=None, vis=None, myfactor=1.0, view_index=True, faces_color_override=None)[source]

                                                  Visualizing a coordination geometry :param cg: :param zoom: @@ -181,7 +181,7 @@

                                                  -welcome(chemenv_config)[source]
                                                  +welcome(chemenv_config)[source]

                                                  Show welcome message. :param chemenv_config: :return:

                                                  diff --git a/docs/pymatgen.analysis.chempot_diagram.html b/docs/pymatgen.analysis.chempot_diagram.html index f77d45f08c8..c50cbda367e 100644 --- a/docs/pymatgen.analysis.chempot_diagram.html +++ b/docs/pymatgen.analysis.chempot_diagram.html @@ -4,7 +4,7 @@ - pymatgen.analysis.chempot_diagram module — pymatgen 2022.5.18 documentation + pymatgen.analysis.chempot_diagram module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                  - 2022.5.18 + 2022.5.18.1
                                                  @@ -136,7 +136,7 @@
                  -class ChemicalPotentialDiagram(entries: list[PDEntry], limits: dict[Element, float] | None = None, default_min_limit: float = - 50.0)[source]
                  +class ChemicalPotentialDiagram(entries: list[PDEntry], limits: dict[Element, float] | None = None, default_min_limit: float = - 50.0)[source]

                  Bases: monty.json.MSONable

                  The chemical potential diagram is the mathematical dual to the compositional phase diagram. To create the diagram, convex minimization is @@ -172,37 +172,37 @@

                  -property border_hyperplanes: numpy.ndarray[source]
                  +property border_hyperplanes: numpy.ndarray[source]

                  Returns bordering hyperplanes

                  -property chemical_system: str[source]
                  +property chemical_system: str[source]

                  Returns the chemical system (A-B-C-…) of diagram object

                  -property domains: dict[str, numpy.ndarray][source]
                  +property domains: dict[str, numpy.ndarray][source]

                  Mapping of formulas to array of domain boundary points

                  -property el_refs: dict[pymatgen.core.periodic_table.Element, pymatgen.analysis.phase_diagram.PDEntry][source]
                  +property el_refs: dict[pymatgen.core.periodic_table.Element, pymatgen.analysis.phase_diagram.PDEntry][source]

                  Returns a dictionary of elements and reference entries

                  -property entry_dict: dict[str, pymatgen.entries.computed_entries.ComputedEntry][source]
                  +property entry_dict: dict[str, pymatgen.entries.computed_entries.ComputedEntry][source]

                  Mapping between reduced formula and ComputedEntry

                  -get_plot(elements: list[Element | str] | None = None, label_stable: bool | None = True, formulas_to_draw: list[str] | None = None, draw_formula_meshes: bool | None = True, draw_formula_lines: bool | None = True, formula_colors: list[str] = ['rgb(27,158,119)', 'rgb(217,95,2)', 'rgb(117,112,179)', 'rgb(231,41,138)', 'rgb(102,166,30)', 'rgb(230,171,2)', 'rgb(166,118,29)', 'rgb(102,102,102)'], element_padding: float | None = 1.0) → Figure[source]
                  +get_plot(elements: list[Element | str] | None = None, label_stable: bool | None = True, formulas_to_draw: list[str] | None = None, draw_formula_meshes: bool | None = True, draw_formula_lines: bool | None = True, formula_colors: list[str] = ['rgb(27,158,119)', 'rgb(217,95,2)', 'rgb(117,112,179)', 'rgb(231,41,138)', 'rgb(102,166,30)', 'rgb(230,171,2)', 'rgb(166,118,29)', 'rgb(102,102,102)'], element_padding: float | None = 1.0) → Figure[source]

                  Plot the 2-dimensional or 3-dimensional chemical potential diagram using an interactive Plotly interface.

                  Elemental axes can be specified; if none provided, will automatically default @@ -241,19 +241,19 @@

                  -property hyperplane_entries: list[pymatgen.analysis.phase_diagram.PDEntry][source]
                  +property hyperplane_entries: list[pymatgen.analysis.phase_diagram.PDEntry][source]

                  Returns list of entries corresponding to hyperplanes

                  -property hyperplanes: numpy.ndarray[source]
                  +property hyperplanes: numpy.ndarray[source]

                  Returns array of hyperplane data

                  -property lims: numpy.ndarray[source]
                  +property lims: numpy.ndarray[source]

                  Returns array of limits used in constructing hyperplanes

                  @@ -261,7 +261,7 @@
                  -get_2d_orthonormal_vector(line_pts: numpy.ndarray) → numpy.ndarray[source]
                  +get_2d_orthonormal_vector(line_pts: numpy.ndarray) → numpy.ndarray[source]

                  Calculates a vector that is orthonormal to a line given by a set of points. Used for determining the location of an annotation on a 2-d chemical potential diagram.

                  @@ -275,7 +275,7 @@
                  -get_centroid_2d(vertices: numpy.ndarray) → numpy.ndarray[source]
                  +get_centroid_2d(vertices: numpy.ndarray) → numpy.ndarray[source]

                  A barebones implementation of the formula for calculating the centroid of a 2D polygon. Useful for calculating the location of an annotation on a chemical potential domain within a 3D chemical potential diagram.

                  @@ -293,7 +293,7 @@
                  -simple_pca(data: numpy.ndarray, k: int = 2) → tuple[numpy.ndarray, numpy.ndarray, numpy.ndarray][source]
                  +simple_pca(data: numpy.ndarray, k: int = 2) → tuple[numpy.ndarray, numpy.ndarray, numpy.ndarray][source]

                  A barebones implementation of principal component analysis (PCA) used in the ChemicalPotentialDiagram class for plotting.

                  diff --git a/docs/pymatgen.analysis.cost.html b/docs/pymatgen.analysis.cost.html index 4c4d2f30e86..02b7db84563 100644 --- a/docs/pymatgen.analysis.cost.html +++ b/docs/pymatgen.analysis.cost.html @@ -4,7 +4,7 @@ - pymatgen.analysis.cost module — pymatgen 2022.5.18 documentation + pymatgen.analysis.cost module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                  - 2022.5.18 + 2022.5.18.1
                  @@ -122,7 +122,7 @@ to give the desired compound with lowest total cost.

                  -class CostAnalyzer(costdb)[source]
                  +class CostAnalyzer(costdb)[source]

                  Bases: object

                  Given a CostDB, figures out the minimum cost solutions via convex hull

                  @@ -132,7 +132,7 @@
                  -get_cost_per_kg(comp)[source]
                  +get_cost_per_kg(comp)[source]

                  Get best estimate of minimum cost/kg based on known data

                  Parameters
                  @@ -146,7 +146,7 @@
                  -get_cost_per_mol(comp)[source]
                  +get_cost_per_mol(comp)[source]

                  Get best estimate of minimum cost/mol based on known data

                  Parameters
                  @@ -160,7 +160,7 @@
                  -get_lowest_decomposition(composition)[source]
                  +get_lowest_decomposition(composition)[source]

                  Get the decomposition leading to lowest cost

                  Parameters
                  @@ -179,13 +179,13 @@
                  -class CostDB[source]
                  +class CostDB[source]

                  Bases: object

                  Abstract class for representing a Cost database. Can be extended, e.g. for file-based or REST-based databases

                  -abstract get_entries(chemsys)[source]
                  +abstract get_entries(chemsys)[source]

                  For a given chemical system, return an array of CostEntries

                  Parameters
                  @@ -201,7 +201,7 @@
                  -class CostDBCSV(filename)[source]
                  +class CostDBCSV(filename)[source]

                  Bases: pymatgen.analysis.cost.CostDB

                  Read a CSV file to get costs Format is formula,cost_per_kg,name,BibTeX

                  @@ -212,7 +212,7 @@
                  -get_entries(chemsys)[source]
                  +get_entries(chemsys)[source]

                  For a given chemical system, return an array of CostEntries

                  Parameters
                  @@ -228,7 +228,7 @@
                  -class CostEntry(composition, cost, name, reference)[source]
                  +class CostEntry(composition, cost, name, reference)[source]

                  Bases: pymatgen.analysis.phase_diagram.PDEntry

                  Extends PDEntry to include a BibTeX reference and include language about cost

                  diff --git a/docs/pymatgen.analysis.defects.core.html b/docs/pymatgen.analysis.defects.core.html index 249cd311d38..8caf99c5611 100644 --- a/docs/pymatgen.analysis.defects.core.html +++ b/docs/pymatgen.analysis.defects.core.html @@ -4,7 +4,7 @@ - pymatgen.analysis.defects.core module — pymatgen 2022.5.18 documentation + pymatgen.analysis.defects.core module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                  - 2022.5.18 + 2022.5.18.1
                  @@ -119,7 +119,7 @@

                  Base classes representing defects.

                  -class Defect(structure, defect_site, charge=0.0, multiplicity=None)[source]
                  +class Defect(structure, defect_site, charge=0.0, multiplicity=None)[source]

                  Bases: monty.json.MSONable

                  Abstract class for a single point defect

                  Initializes an abstract defect

                  @@ -141,19 +141,19 @@
                  -property bulk_structure[source]
                  +property bulk_structure[source]

                  Returns the structure without any defects.

                  -property charge[source]
                  +property charge[source]

                  Returns the charge of a defect

                  -copy()[source]
                  +copy()[source]

                  Convenience method to get a copy of the defect.

                  Returns
                  @@ -164,13 +164,13 @@
                  -abstract property defect_composition[source]
                  +abstract property defect_composition[source]

                  Returns the defect composition as a Composition object

                  -abstract generate_defect_structure(supercell=(1, 1, 1))[source]
                  +abstract generate_defect_structure(supercell=(1, 1, 1))[source]

                  Given structure and defect_site (and type of defect) should return a defect_structure that is charged :param supercell: supercell integer, vector, or scaling matrix :type supercell: int, [3x1], or [[]] (3x3)

                  @@ -178,26 +178,26 @@
                  -abstract get_multiplicity()[source]
                  +abstract get_multiplicity()[source]

                  Method to determine multiplicity. For non-Interstitial objects, also confirms that defect_site is a site in bulk_structure.

                  -property multiplicity[source]
                  +property multiplicity[source]

                  Returns the multiplicity of a defect site within the structure (needed for concentration analysis)

                  -abstract property name[source]
                  +abstract property name[source]

                  Returns a name for this defect

                  -set_charge(new_charge=0.0)[source]
                  +set_charge(new_charge=0.0)[source]

                  Sets the overall charge :param charge: new charge to set :type charge: float

                  @@ -205,7 +205,7 @@
                  -property site[source]
                  +property site[source]

                  Returns the defect position as a site object

                  @@ -213,12 +213,12 @@
                  -class DefectCorrection[source]
                  +class DefectCorrection[source]

                  Bases: monty.json.MSONable

                  A Correction class modeled off the computed entry correction format

                  -correct_entry(entry)[source]
                  +correct_entry(entry)[source]

                  Corrects a single entry.

                  Parameters
                  @@ -235,7 +235,7 @@
                  -abstract get_correction(entry)[source]
                  +abstract get_correction(entry)[source]

                  Returns correction for a single entry.

                  Parameters
                  @@ -255,7 +255,7 @@
                  -class DefectEntry(defect, uncorrected_energy, corrections=None, parameters=None, entry_id=None)[source]
                  +class DefectEntry(defect, uncorrected_energy, corrections=None, parameters=None, entry_id=None)[source]

                  Bases: monty.json.MSONable

                  An lightweight DefectEntry object containing key computed data for many defect analysis.

                  @@ -279,13 +279,13 @@
                  -as_dict()[source]
                  +as_dict()[source]

                  JSON-serializable dict representation of DefectEntry

                  -property bulk_structure[source]
                  +property bulk_structure[source]

                  Structure object of bulk.

                  Type
                  @@ -296,7 +296,7 @@
                  -property charge[source]
                  +property charge[source]

                  Charge of defect.

                  Type
                  @@ -307,7 +307,7 @@
                  -copy()[source]
                  +copy()[source]

                  Convenience method to get a copy of the DefectEntry.

                  Returns
                  @@ -318,7 +318,7 @@
                  -defect_concentration(chemical_potentials, temperature=300, fermi_level=0.0)[source]
                  +defect_concentration(chemical_potentials, temperature=300, fermi_level=0.0)[source]

                  Compute the defect concentration for a temperature and Fermi level. :param temperature: the temperature in K :param fermi_level: the fermi level in eV (with respect to the VBM)

                  @@ -331,7 +331,7 @@
                  -property energy[source]
                  +property energy[source]

                  Corrected energy of the entry

                  Type
                  @@ -342,7 +342,7 @@
                  -formation_energy(chemical_potentials=None, fermi_level=0)[source]
                  +formation_energy(chemical_potentials=None, fermi_level=0)[source]
                  Compute the formation energy for a defect taking into account a given chemical potential and fermi_level
                  Args:
                  @@ -372,7 +372,7 @@
                  -classmethod from_dict(d)[source]
                  +classmethod from_dict(d)[source]

                  Reconstitute a DefectEntry object from a dict representation created using as_dict().

                  @@ -387,7 +387,7 @@
                  -property multiplicity[source]
                  +property multiplicity[source]

                  Multiplicity of defect.

                  Type
                  @@ -398,7 +398,7 @@
                  -property name[source]
                  +property name[source]

                  Defect name

                  Type
                  @@ -409,7 +409,7 @@
                  -property site[source]
                  +property site[source]

                  Site of defect.

                  Type
                  @@ -422,7 +422,7 @@
                  -class Interstitial(structure, defect_site, charge=0.0, site_name='', multiplicity=None)[source]
                  +class Interstitial(structure, defect_site, charge=0.0, site_name='', multiplicity=None)[source]

                  Bases: pymatgen.analysis.defects.core.Defect

                  Subclass of Defect to capture essential information for a single Interstitial defect structure.

                  Initializes an interstial defect. @@ -458,7 +458,7 @@

                  -property defect_composition[source]
                  +property defect_composition[source]

                  Defect composition.

                  Type
                  @@ -469,7 +469,7 @@
                  -generate_defect_structure(supercell=(1, 1, 1))[source]
                  +generate_defect_structure(supercell=(1, 1, 1))[source]

                  Returns Defective Interstitial structure, decorated with charge If bulk structure had any site properties, all of these properties are removed in the resulting defect structure

                  @@ -482,13 +482,13 @@
                  -get_multiplicity()[source]
                  +get_multiplicity()[source]

                  Returns the multiplicity of a defect site within the structure (needed for concentration analysis)

                  -property name[source]
                  +property name[source]

                  Returns a name for this defect

                  @@ -496,7 +496,7 @@
                  -class Substitution(structure, defect_site, charge=0.0, multiplicity=None)[source]
                  +class Substitution(structure, defect_site, charge=0.0, multiplicity=None)[source]

                  Bases: pymatgen.analysis.defects.core.Defect

                  Subclass of Defect to capture essential information for a single Substitution defect structure.

                  Initializes an abstract defect

                  @@ -518,7 +518,7 @@
                  -property defect_composition[source]
                  +property defect_composition[source]

                  Composition of defect.

                  Type
                  @@ -529,7 +529,7 @@
                  -generate_defect_structure(supercell=(1, 1, 1))[source]
                  +generate_defect_structure(supercell=(1, 1, 1))[source]

                  Returns Defective Substitution structure, decorated with charge. If bulk structure had any site properties, all of these properties are removed in the resulting defect structure.

                  @@ -542,14 +542,14 @@
                  -get_multiplicity()[source]
                  +get_multiplicity()[source]

                  Returns the multiplicity of a defect site within the structure (needed for concentration analysis) and confirms that defect_site is a site in bulk_structure.

                  -property name[source]
                  +property name[source]

                  Returns a name for this defect

                  @@ -557,7 +557,7 @@
                  -class Vacancy(structure, defect_site, charge=0.0, multiplicity=None)[source]
                  +class Vacancy(structure, defect_site, charge=0.0, multiplicity=None)[source]

                  Bases: pymatgen.analysis.defects.core.Defect

                  Subclass of Defect to capture essential information for a single Vacancy defect structure.

                  Initializes an abstract defect

                  @@ -579,7 +579,7 @@
                  -property defect_composition[source]
                  +property defect_composition[source]

                  Composition of defect.

                  Type
                  @@ -590,7 +590,7 @@
                  -generate_defect_structure(supercell=(1, 1, 1))[source]
                  +generate_defect_structure(supercell=(1, 1, 1))[source]

                  Returns Defective Vacancy structure, decorated with charge :param supercell: supercell integer, vector, or scaling matrix :type supercell: int, [3x1], or [[]] (3x3)

                  @@ -598,14 +598,14 @@
                  -get_multiplicity()[source]
                  +get_multiplicity()[source]

                  Returns the multiplicity of a defect site within the structure (needed for concentration analysis) and confirms that defect_site is a site in bulk_structure.

                  -property name[source]
                  +property name[source]

                  Returns a name for this defect

                  @@ -613,7 +613,7 @@
                  -create_saturated_interstitial_structure(interstitial_def, dist_tol=0.1)[source]
                  +create_saturated_interstitial_structure(interstitial_def, dist_tol=0.1)[source]

                  this takes a Interstitial defect object and generates the sublattice for it based on the structure’s space group. Useful for understanding multiplicity of an interstitial diff --git a/docs/pymatgen.analysis.defects.corrections.html b/docs/pymatgen.analysis.defects.corrections.html index 01a6e5ecd8b..d3830864004 100644 --- a/docs/pymatgen.analysis.defects.corrections.html +++ b/docs/pymatgen.analysis.defects.corrections.html @@ -4,7 +4,7 @@ - pymatgen.analysis.defects.corrections module — pymatgen 2022.5.18 documentation + pymatgen.analysis.defects.corrections module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                  - 2022.5.18 + 2022.5.18.1
                  @@ -119,13 +119,13 @@

                  Implementation of defect correction methods.

                  -class BandEdgeShiftingCorrection[source]
                  +class BandEdgeShiftingCorrection[source]

                  Bases: pymatgen.analysis.defects.core.DefectCorrection

                  A class for BandEdgeShiftingCorrection class. Largely adapted from PyCDT code

                  Initializes the BandEdgeShiftingCorrection class

                  -get_correction(entry)[source]
                  +get_correction(entry)[source]

                  Gets the BandEdge correction for a defect entry :param entry: defect entry to compute BandFilling correction on.

                  @@ -158,7 +158,7 @@
                  -class BandFillingCorrection(resolution=0.01)[source]
                  +class BandFillingCorrection(resolution=0.01)[source]

                  Bases: pymatgen.analysis.defects.core.DefectCorrection

                  A class for BandFillingCorrection class. Largely adapted from PyCDT code

                  Initializes the Bandfilling correction

                  @@ -169,7 +169,7 @@
                  -get_correction(entry)[source]
                  +get_correction(entry)[source]

                  Gets the BandFilling correction for a defect entry :param entry: defect entry to compute BandFilling correction on.

                  @@ -210,7 +210,7 @@
                  -perform_bandfill_corr(eigenvalues, kpoint_weights, potalign, vbm, cbm, soc_calc=False)[source]
                  +perform_bandfill_corr(eigenvalues, kpoint_weights, potalign, vbm, cbm, soc_calc=False)[source]

                  This calculates the band filling correction based on excess of electrons/holes in CB/VB…

                  Note that the total free holes and electrons may also be used for a “shallow donor/acceptor”
                  @@ -225,7 +225,7 @@
                  -class FreysoldtCorrection(dielectric_const, q_model=None, energy_cutoff=520, madetol=0.0001, axis=None)[source]
                  +class FreysoldtCorrection(dielectric_const, q_model=None, energy_cutoff=520, madetol=0.0001, axis=None)[source]

                  Bases: pymatgen.analysis.defects.core.DefectCorrection

                  A class for FreysoldtCorrection class. Largely adapted from PyCDT code

                  If this correction is used, please reference Freysoldt’s original paper. @@ -250,7 +250,7 @@

                  -get_correction(entry)[source]
                  +get_correction(entry)[source]

                  Gets the Freysoldt correction for a defect entry :param entry: defect entry to compute Freysoldt correction on.

                  @@ -293,7 +293,7 @@
                  -perform_es_corr(lattice, q, step=0.0001)[source]
                  +perform_es_corr(lattice, q, step=0.0001)[source]

                  Perform Electrostatic Freysoldt Correction :param lattice: Pymatgen lattice object :param q: Charge of defect @@ -309,7 +309,7 @@

                  -perform_pot_corr(axis_grid, pureavg, defavg, lattice, q, defect_frac_position, axis, widthsample=1.0)[source]
                  +perform_pot_corr(axis_grid, pureavg, defavg, lattice, q, defect_frac_position, axis, widthsample=1.0)[source]

                  For performing planar averaging potential alignment :param axis_grid (1 x NGX where NGX is the length of the NGX grid:

                  @@ -351,7 +351,7 @@
                  -plot(axis, title=None, saved=False)[source]
                  +plot(axis, title=None, saved=False)[source]

                  Plots the planar average electrostatic potential against the Long range and short range models from Freysoldt. Must run perform_pot_corr or get_correction (to load metadata) before this can be used. @@ -371,7 +371,7 @@

                  -class KumagaiCorrection(dielectric_tensor, sampling_radius=None, gamma=None)[source]
                  +class KumagaiCorrection(dielectric_tensor, sampling_radius=None, gamma=None)[source]

                  Bases: pymatgen.analysis.defects.core.DefectCorrection

                  A class for KumagaiCorrection class. Largely adapted from PyCDT code

                  If this correction is used, please reference Kumagai and Oba’s original paper @@ -393,7 +393,7 @@

                  -get_correction(entry)[source]
                  +get_correction(entry)[source]

                  Gets the Kumagai correction for a defect entry :param entry: defect entry to compute Kumagai correction on.

                  @@ -425,7 +425,7 @@
                  -static get_potential_shift(gamma, volume)[source]
                  +static get_potential_shift(gamma, volume)[source]
                  Parameters
                    @@ -441,19 +441,19 @@
                    -get_real_summation(gamma, real_vectors)[source]
                    +get_real_summation(gamma, real_vectors)[source]

                    Get real summation term from list of real-space vectors

                    -get_recip_summation(gamma, recip_vectors, volume, r=[0.0, 0.0, 0.0])[source]
                    +get_recip_summation(gamma, recip_vectors, volume, r=[0.0, 0.0, 0.0])[source]

                    Get Reciprocal summation term from list of reciprocal-space vectors

                    -get_self_interaction(gamma)[source]
                    +get_self_interaction(gamma)[source]
                    Parameters

                    () (gamma) –

                    @@ -466,7 +466,7 @@
                    -perform_es_corr(gamma, prec, lattice, charge)[source]
                    +perform_es_corr(gamma, prec, lattice, charge)[source]

                    Perform Electrostatic Kumagai Correction :param gamma: Ewald parameter :type gamma: float @@ -484,7 +484,7 @@

                    -perform_pot_corr(defect_structure, defect_frac_coords, site_list, sampling_radius, q, r_vecs, g_vecs, gamma)[source]
                    +perform_pot_corr(defect_structure, defect_frac_coords, site_list, sampling_radius, q, r_vecs, g_vecs, gamma)[source]

                    For performing potential alignment in manner described by Kumagai et al. :param defect_structure: Pymatgen Structure object corresponding to the defect supercell :param defect_frac_coords: Defect Position in fractional coordinates of the supercell

                    @@ -514,7 +514,7 @@
                    -plot(title=None, saved=False)[source]
                    +plot(title=None, saved=False)[source]

                    Plots the AtomicSite electrostatic potential against the Long range and short range models from Kumagai and Oba (doi: 10.1103/PhysRevB.89.195205)

                    diff --git a/docs/pymatgen.analysis.defects.defect_compatibility.html b/docs/pymatgen.analysis.defects.defect_compatibility.html index e82fedb4fdc..b598b9d2120 100644 --- a/docs/pymatgen.analysis.defects.defect_compatibility.html +++ b/docs/pymatgen.analysis.defects.defect_compatibility.html @@ -4,7 +4,7 @@ - pymatgen.analysis.defects.defect_compatibility module — pymatgen 2022.5.18 documentation + pymatgen.analysis.defects.defect_compatibility module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                    - 2022.5.18 + 2022.5.18.1
                    @@ -120,7 +120,7 @@ defects

                    -class DefectCompatibility(plnr_avg_var_tol=0.0001, plnr_avg_minmax_tol=0.1, atomic_site_var_tol=0.005, atomic_site_minmax_tol=0.1, tot_relax_tol=1.0, perc_relax_tol=50.0, defect_tot_relax_tol=2.0, preferred_cc='freysoldt', free_chg_cutoff=2.1, use_bandfilling=True, use_bandedgeshift=True)[source]
                    +class DefectCompatibility(plnr_avg_var_tol=0.0001, plnr_avg_minmax_tol=0.1, atomic_site_var_tol=0.005, atomic_site_minmax_tol=0.1, tot_relax_tol=1.0, perc_relax_tol=50.0, defect_tot_relax_tol=2.0, preferred_cc='freysoldt', free_chg_cutoff=2.1, use_bandfilling=True, use_bandedgeshift=True)[source]

                    Bases: monty.json.MSONable

                    The DefectCompatibility class evaluates corrections and delocalization metrics on a DefectEntry. It can only parse based on the available @@ -180,7 +180,7 @@

                    -check_final_relaxed_structure_delocalized(defect_entry)[source]
                    +check_final_relaxed_structure_delocalized(defect_entry)[source]

                    NOTE this assumes initial and final structures have sites indexed in same way

                    Parameters
                    @@ -194,7 +194,7 @@
                    -check_freysoldt_delocalized(defect_entry)[source]
                    +check_freysoldt_delocalized(defect_entry)[source]

                    Check for Freysoldt delocalization.

                    Parameters
                    @@ -208,7 +208,7 @@
                    -check_kumagai_delocalized(defect_entry)[source]
                    +check_kumagai_delocalized(defect_entry)[source]

                    Check for Kumagai delocalization.

                    Parameters
                    @@ -222,7 +222,7 @@
                    -delocalization_analysis(defect_entry)[source]
                    +delocalization_analysis(defect_entry)[source]
                    Do delocalization analysis. To do this, one considers:

                    1. sampling region of planar averaged electrostatic potential (freysoldt approach)

                      2. @@ -245,7 +245,7 @@
                      -perform_all_corrections(defect_entry)[source]
                      +perform_all_corrections(defect_entry)[source]

                      Perform all corrections for a defect.

                      Parameters
                      @@ -259,7 +259,7 @@
                      -static perform_band_edge_shifting(defect_entry)[source]
                      +static perform_band_edge_shifting(defect_entry)[source]

                      Perform band edge shifting correction.

                      Parameters
                      @@ -273,7 +273,7 @@
                      -static perform_bandfilling(defect_entry)[source]
                      +static perform_bandfilling(defect_entry)[source]

                      Perform bandfilling correction.

                      Parameters
                      @@ -287,7 +287,7 @@
                      -static perform_freysoldt(defect_entry)[source]
                      +static perform_freysoldt(defect_entry)[source]

                      Perform Freysoldt correction.

                      Parameters
                      @@ -301,7 +301,7 @@
                      -static perform_kumagai(defect_entry)[source]
                      +static perform_kumagai(defect_entry)[source]

                      Perform Kumagai correction.

                      Parameters
                      @@ -315,7 +315,7 @@
                      -process_entry(defect_entry, perform_corrections=True)[source]
                      +process_entry(defect_entry, perform_corrections=True)[source]

                      Process a given DefectEntry with qualifiers given from initialization of class. Order of processing is:

                      diff --git a/docs/pymatgen.analysis.defects.dilute_solution_model.html b/docs/pymatgen.analysis.defects.dilute_solution_model.html index df58f29b474..afd171f82cf 100644 --- a/docs/pymatgen.analysis.defects.dilute_solution_model.html +++ b/docs/pymatgen.analysis.defects.dilute_solution_model.html @@ -4,7 +4,7 @@ - pymatgen.analysis.defects.dilute_solution_model module — pymatgen 2022.5.18 documentation + pymatgen.analysis.defects.dilute_solution_model module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                      - 2022.5.18 + 2022.5.18.1
                      @@ -124,7 +124,7 @@ Manual and citation for the code, DOI: 10.1016/j.cpc.2015.03.015

                      -compute_defect_density(structure, e0, vac_defs, antisite_defs, T=800, trial_chem_pot=None, plot_style='highcharts')[source]
                      +compute_defect_density(structure, e0, vac_defs, antisite_defs, T=800, trial_chem_pot=None, plot_style='highcharts')[source]

                      Wrapper for the dilute_solution_model. The computed plot data is prepared based on plot_style.

                      @@ -161,7 +161,7 @@
                      -solute_defect_density(structure, e0, vac_defs, antisite_defs, solute_defs, solute_concen=0.01, T=800, trial_chem_pot=None, plot_style='highchargs')[source]
                      +solute_defect_density(structure, e0, vac_defs, antisite_defs, solute_defs, solute_concen=0.01, T=800, trial_chem_pot=None, plot_style='highchargs')[source]

                      Wrapper for the solute_site_preference_finder. The computed plot data is prepared based on plot_style.

                      @@ -202,7 +202,7 @@
                      -solute_site_preference_finder(structure, e0, T, vac_defs, antisite_defs, solute_defs, solute_concen=0.01, trial_chem_pot=None)[source]
                      +solute_site_preference_finder(structure, e0, T, vac_defs, antisite_defs, solute_defs, solute_concen=0.01, trial_chem_pot=None)[source]

                      Compute the solute defect densities using dilute solution model. :param structure: pymatgen.core.structure.Structure object representing the

                      diff --git a/docs/pymatgen.analysis.defects.generators.html b/docs/pymatgen.analysis.defects.generators.html index a148af631bc..701ac279913 100644 --- a/docs/pymatgen.analysis.defects.generators.html +++ b/docs/pymatgen.analysis.defects.generators.html @@ -4,7 +4,7 @@ - pymatgen.analysis.defects.generators module — pymatgen 2022.5.18 documentation + pymatgen.analysis.defects.generators module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                      - 2022.5.18 + 2022.5.18.1
                      @@ -119,7 +119,7 @@

                      This module defines classes to generate point defect structures

                      -class DefectGenerator[source]
                      +class DefectGenerator[source]

                      Bases: monty.json.MSONable

                      Abstract class for point defects Implements generator pattern

                      @@ -127,7 +127,7 @@
                      -class InterstitialGenerator(structure, element)[source]
                      +class InterstitialGenerator(structure, element)[source]

                      Bases: pymatgen.analysis.defects.generators.DefectGenerator

                      Generator for interstitials at positions where the interstitialcy is coordinated by nearest neighbors @@ -147,7 +147,7 @@

                      -class SimpleChargeGenerator(defect)[source]
                      +class SimpleChargeGenerator(defect)[source]

                      Bases: pymatgen.analysis.defects.generators.DefectGenerator

                      Does an extremely simple/limited charge generation scheme (only one charge generated)

                      @@ -167,7 +167,7 @@
                      -class SubstitutionGenerator(structure, element)[source]
                      +class SubstitutionGenerator(structure, element)[source]

                      Bases: pymatgen.analysis.defects.generators.DefectGenerator

                      Simple generator for substitution based on periodically equivalent sites

                      @@ -181,7 +181,7 @@
                      -class VacancyGenerator(structure, include_bv_charge=False)[source]
                      +class VacancyGenerator(structure, include_bv_charge=False)[source]

                      Bases: pymatgen.analysis.defects.generators.DefectGenerator

                      Simple generator for vacancies based on periodically equivalent sites

                      @@ -192,7 +192,7 @@
                      -class VoronoiInterstitialGenerator(structure, element)[source]
                      +class VoronoiInterstitialGenerator(structure, element)[source]

                      Bases: pymatgen.analysis.defects.generators.DefectGenerator

                      Generator for interstitials based on a simple Voronoi analysis

                      Initializes an Interstitial generator using Voronoi sites diff --git a/docs/pymatgen.analysis.defects.html b/docs/pymatgen.analysis.defects.html index 7bd11c5e5e6..8dede0a59f2 100644 --- a/docs/pymatgen.analysis.defects.html +++ b/docs/pymatgen.analysis.defects.html @@ -4,7 +4,7 @@ - pymatgen.analysis.defects package — pymatgen 2022.5.18 documentation + pymatgen.analysis.defects package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                      - 2022.5.18 + 2022.5.18.1
                      diff --git a/docs/pymatgen.analysis.defects.thermodynamics.html b/docs/pymatgen.analysis.defects.thermodynamics.html index f36b5cdbede..43e2a61f865 100644 --- a/docs/pymatgen.analysis.defects.thermodynamics.html +++ b/docs/pymatgen.analysis.defects.thermodynamics.html @@ -4,7 +4,7 @@ - pymatgen.analysis.defects.thermodynamics module — pymatgen 2022.5.18 documentation + pymatgen.analysis.defects.thermodynamics module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                      - 2022.5.18 + 2022.5.18.1
                      @@ -119,7 +119,7 @@

                      Defect thermodynamics, such as defect phase diagrams, etc.

                      -class DefectPhaseDiagram(entries, vbm, band_gap, filter_compatible=True, metadata=None)[source]
                      +class DefectPhaseDiagram(entries, vbm, band_gap, filter_compatible=True, metadata=None)[source]

                      Bases: monty.json.MSONable

                      This is similar to a PhaseDiagram object in pymatgen, but has ability to do quick analysis of defect formation energies @@ -160,19 +160,19 @@

                      -property all_stable_entries[source]
                      +property all_stable_entries[source]

                      List all stable entries (defect+charge) in the DefectPhaseDiagram

                      -property all_unstable_entries[source]
                      +property all_unstable_entries[source]

                      List all unstable entries (defect+charge) in the DefectPhaseDiagram

                      -as_dict()[source]
                      +as_dict()[source]
                      Returns

                      JSON-serializable dict representation of DefectPhaseDiagram

                      @@ -182,7 +182,7 @@
                      -defect_concentrations(chemical_potentials, temperature=300, fermi_level=0.0)[source]
                      +defect_concentrations(chemical_potentials, temperature=300, fermi_level=0.0)[source]

                      Give list of all concentrations at specified efermi in the DefectPhaseDiagram :param chemical_potentials = {Element: number} is dict of chemical potentials to provide formation energies for :param temperature = temperature to produce concentrations from: @@ -199,13 +199,13 @@

                      -property defect_types[source]
                      +property defect_types[source]

                      List types of defects existing in the DefectPhaseDiagram

                      -find_stable_charges()[source]
                      +find_stable_charges()[source]

                      Sets the stable charges and transition states for a series of defect entries. This function uses scipy’s HalfspaceInterection to oncstruct the polygons corresponding to defect stability as @@ -224,7 +224,7 @@

                      -classmethod from_dict(d)[source]
                      +classmethod from_dict(d)[source]

                      Reconstitute a DefectPhaseDiagram object from a dict representation created using as_dict().

                      @@ -239,7 +239,7 @@
                      -get_dopability_limits(chemical_potentials)[source]
                      +get_dopability_limits(chemical_potentials)[source]

                      Find Dopability limits for a given chemical potential. This is defined by the defect formation energies which first cross zero in formation energies. @@ -264,7 +264,7 @@

                      -plot(mu_elts=None, xlim=None, ylim=None, ax_fontsize=1.3, lg_fontsize=1.0, lg_position=None, fermi_level=None, title=None, saved=False)[source]
                      +plot(mu_elts=None, xlim=None, ylim=None, ax_fontsize=1.3, lg_fontsize=1.0, lg_position=None, fermi_level=None, title=None, saved=False)[source]

                      Produce defect Formation energy vs Fermi energy plot :param mu_elts: a dictionary of {Element:value} giving the chemical

                      @@ -291,7 +291,7 @@
                      -solve_for_fermi_energy(temperature, chemical_potentials, bulk_dos)[source]
                      +solve_for_fermi_energy(temperature, chemical_potentials, bulk_dos)[source]

                      Solve for the Fermi energy self-consistently as a function of T Observations are Defect concentrations, electron and hole conc :param temperature: Temperature to equilibrate fermi energies for @@ -306,7 +306,7 @@

                      -solve_for_non_equilibrium_fermi_energy(temperature, quench_temperature, chemical_potentials, bulk_dos)[source]
                      +solve_for_non_equilibrium_fermi_energy(temperature, quench_temperature, chemical_potentials, bulk_dos)[source]

                      Solve for the Fermi energy after quenching in the defect concentrations at a higher temperature (the quench temperature), as outlined in P. Canepa et al (2017) Chemistry of Materials (doi: 10.1021/acs.chemmater.7b02909)

                      @@ -327,7 +327,7 @@
                      -suggest_charges(tolerance=0.1)[source]
                      +suggest_charges(tolerance=0.1)[source]

                      Suggest possible charges for defects to compute based on proximity of known transitions from entries to VBM and CBM

                      @@ -340,7 +340,7 @@
                      -suggest_larger_supercells(tolerance=0.1)[source]
                      +suggest_larger_supercells(tolerance=0.1)[source]

                      Suggest larger supercells for different defect+chg combinations based on use of compatibility analysis. Does this for any charged defects which have is_compatible = False, and the defect+chg formation energy is stable at fermi levels within the band gap.

                      diff --git a/docs/pymatgen.analysis.defects.utils.html b/docs/pymatgen.analysis.defects.utils.html index ed65a3ca811..17f925a563f 100644 --- a/docs/pymatgen.analysis.defects.utils.html +++ b/docs/pymatgen.analysis.defects.utils.html @@ -4,7 +4,7 @@ - pymatgen.analysis.defects.utils module — pymatgen 2022.5.18 documentation + pymatgen.analysis.defects.utils module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                      - 2022.5.18 + 2022.5.18.1
                      @@ -119,7 +119,7 @@

                      Utilities for defects module.

                      -class ChargeDensityAnalyzer(chgcar)[source]
                      +class ChargeDensityAnalyzer(chgcar)[source]

                      Bases: monty.json.MSONable

                      Analyzer to find potential interstitial sites based on charge density. The total charge density is used.

                      @@ -131,7 +131,7 @@
                      -property charge_distribution_df[source]
                      +property charge_distribution_df[source]

                      Charge distribution.

                      Type
                      @@ -142,7 +142,7 @@
                      -cluster_nodes(tol=0.2)[source]
                      +cluster_nodes(tol=0.2)[source]

                      Cluster nodes that are too close together using a tol.

                      Parameters
                      @@ -153,7 +153,7 @@
                      -property extrema_df[source]
                      +property extrema_df[source]

                      The extrema in charge density.

                      Type
                      @@ -164,7 +164,7 @@
                      -classmethod from_file(chgcar_filename)[source]
                      +classmethod from_file(chgcar_filename)[source]

                      Init from a CHGCAR.

                      Parameters
                      @@ -178,7 +178,7 @@
                      -get_local_extrema(find_min=True, threshold_frac=None, threshold_abs=None)[source]
                      +get_local_extrema(find_min=True, threshold_frac=None, threshold_abs=None)[source]

                      Get all local extrema fractional coordinates in charge density, searching for local minimum by default. Note that sites are NOT grouped symmetrically.

                      @@ -218,7 +218,7 @@
                      -get_structure_with_nodes(find_min=True, min_dist=0.5, tol=0.2, threshold_frac=None, threshold_abs=None)[source]
                      +get_structure_with_nodes(find_min=True, min_dist=0.5, tol=0.2, threshold_frac=None, threshold_abs=None)[source]

                      Get the modified structure with the possible interstitial sites added. The species is set as a DummySpecies X.

                      @@ -257,7 +257,7 @@
                      -remove_collisions(min_dist=0.5)[source]
                      +remove_collisions(min_dist=0.5)[source]

                      Remove predicted sites that are too close to existing atoms in the structure.

                      @@ -271,7 +271,7 @@
                      -sort_sites_by_integrated_chg(r=0.4)[source]
                      +sort_sites_by_integrated_chg(r=0.4)[source]

                      Get the average charge density around each local minima in the charge density and store the result in _extrema_df :param r: radius of sphere around each site to evaluate the average @@ -282,7 +282,7 @@

                      -class ChargeInsertionAnalyzer(chgcar, working_ion='Li', avg_radius=0.4, max_avg_charge=1.0, clustering_tol=0.6, ltol=0.2, stol=0.3, angle_tol=5)[source]
                      +class ChargeInsertionAnalyzer(chgcar, working_ion='Li', avg_radius=0.4, max_avg_charge=1.0, clustering_tol=0.6, ltol=0.2, stol=0.3, angle_tol=5)[source]

                      Bases: pymatgen.analysis.defects.utils.ChargeDensityAnalyzer

                      Analyze the charge density and create new candidate structures by inserting at each charge minima The similar inserterd structures are given the same uniqueness label. @@ -307,7 +307,7 @@

                      -get_labels()[source]
                      +get_labels()[source]

                      Populate the extrema dataframe (self._extrema_df) with the insertion structure. Then, group the sites by structure similarity. Finally store a full list of the insertion sites, with their labels as a Structure Object

                      @@ -317,7 +317,7 @@
                      -class QModel(beta=1.0, expnorm=0.0, gamma=1.0)[source]
                      +class QModel(beta=1.0, expnorm=0.0, gamma=1.0)[source]

                      Bases: monty.json.MSONable

                      Model for the defect charge distribution. A combination of exponential tail and gaussian distribution is used @@ -342,7 +342,7 @@

                      -rho_rec(g2)[source]
                      +rho_rec(g2)[source]

                      Reciprocal space model charge value for input squared reciprocal vector. :param g2: Square of reciprocal vector

                      @@ -355,7 +355,7 @@
                      -property rho_rec_limit0[source]
                      +property rho_rec_limit0[source]

                      Reciprocal space model charge value close to reciprocal vector 0 . rho_rec(g->0) -> 1 + rho_rec_limit0 * g^2

                      @@ -365,7 +365,7 @@
                      -class StructureMotifInterstitial(struct, inter_elem, motif_types=('tetrahedral', 'octahedral'), op_threshs=(0.3, 0.5), dl=0.2, doverlap=1, facmaxdl=1.01, verbose=False)[source]
                      +class StructureMotifInterstitial(struct, inter_elem, motif_types=('tetrahedral', 'octahedral'), op_threshs=(0.3, 0.5), dl=0.2, doverlap=1, facmaxdl=1.01, verbose=False)[source]

                      Bases: object

                      Generate interstitial sites at positions where the interstitialcy is coordinated by nearest neighbors @@ -412,7 +412,7 @@

                      -enumerate_defectsites()[source]
                      +enumerate_defectsites()[source]

                      Get all defect sites.

                      Returns
                      @@ -430,7 +430,7 @@
                      -get_coordinating_elements_cns(i)[source]
                      +get_coordinating_elements_cns(i)[source]

                      Get element-specific coordination numbers of defect with index i.

                      Returns
                      @@ -449,13 +449,13 @@
                      -get_defectsite_multiplicity(n)[source]
                      +get_defectsite_multiplicity(n)[source]

                      Returns the symmtric multiplicity of the defect site at the index.

                      -get_motif_type(i)[source]
                      +get_motif_type(i)[source]

                      Get the motif type of defect with index i (e.g., “tet”).

                      Returns
                      @@ -469,7 +469,7 @@
                      -get_op_value(i)[source]
                      +get_op_value(i)[source]

                      Get order-parameter value of defect with index i.

                      Returns
                      @@ -483,7 +483,7 @@
                      -make_supercells_with_defects(scaling_matrix)[source]
                      +make_supercells_with_defects(scaling_matrix)[source]

                      Generate a sequence of supercells in which each supercell contains a single interstitial, except for the first supercell in the sequence @@ -506,7 +506,7 @@

                      -class TopographyAnalyzer(structure, framework_ions, cations, tol=0.0001, max_cell_range=1, check_volume=True, constrained_c_frac=0.5, thickness=0.5)[source]
                      +class TopographyAnalyzer(structure, framework_ions, cations, tol=0.0001, max_cell_range=1, check_volume=True, constrained_c_frac=0.5, thickness=0.5)[source]

                      Bases: object

                      This is a generalized module to perform topological analyses of a crystal structure using Voronoi tessellations. It can be used for finding potential @@ -560,7 +560,7 @@

                      -analyze_symmetry(tol)[source]
                      +analyze_symmetry(tol)[source]
                      Parameters

                      tol – Tolerance for SpaceGroupAnalyzer

                      @@ -573,14 +573,14 @@
                      -check_volume()[source]
                      +check_volume()[source]

                      Basic check for volume of all voronoi poly sum to unit cell volume Note that this does not apply after poly combination.

                      -cluster_nodes(tol=0.2)[source]
                      +cluster_nodes(tol=0.2)[source]

                      Cluster nodes that are too close together using a tol.

                      Parameters
                      @@ -591,20 +591,20 @@
                      -get_structure_with_nodes()[source]
                      +get_structure_with_nodes()[source]

                      Get the modified structure with the voronoi nodes inserted. The species is set as a DummySpecies X.

                      -print_stats()[source]
                      +print_stats()[source]

                      Print stats such as the MSE dist.

                      -remove_collisions(min_dist=0.5)[source]
                      +remove_collisions(min_dist=0.5)[source]

                      Remove vnodes that are too close to existing atoms in the structure

                      Parameters
                      @@ -616,13 +616,13 @@
                      -vtk()[source]
                      +vtk()[source]

                      Show VTK visualization.

                      -write_topology(fname='Topo.cif')[source]
                      +write_topology(fname='Topo.cif')[source]

                      Write topology to a file.

                      Parameters
                      @@ -635,7 +635,7 @@
                      -class VoronoiPolyhedron(lattice, frac_coords, polyhedron_indices, all_coords, name=None)[source]
                      +class VoronoiPolyhedron(lattice, frac_coords, polyhedron_indices, all_coords, name=None)[source]

                      Bases: object

                      Convenience container for a voronoi point in PBC and its associated polyhedron.

                      @@ -651,7 +651,7 @@
                      -property coordination[source]
                      +property coordination[source]

                      Coordination number

                      Type
                      @@ -662,7 +662,7 @@
                      -is_image(poly, tol)[source]
                      +is_image(poly, tol)[source]
                      Parameters
                        @@ -678,7 +678,7 @@
                        -property volume[source]
                        +property volume[source]

                        Volume

                        Type
                        @@ -691,7 +691,7 @@
                        -calculate_vol(coords)[source]
                        +calculate_vol(coords)[source]

                        Calculate volume given a set of coords.

                        Parameters
                        @@ -705,7 +705,7 @@
                        -closestsites(struct_blk, struct_def, pos)[source]
                        +closestsites(struct_blk, struct_def, pos)[source]

                        Returns closest site to the input position for both bulk and defect structures :param struct_blk: Bulk structure @@ -716,13 +716,13 @@

                        -converge(f, step, tol, max_h)[source]
                        +converge(f, step, tol, max_h)[source]

                        simple newton iteration based convergence function

                        -eV_to_k(energy)[source]
                        +eV_to_k(energy)[source]

                        Convert energy to reciprocal vector magnitude k via hbar*k^2/2m :param a: Energy in eV.

                        @@ -734,7 +734,7 @@
                        -generate_R_and_G_vecs(gamma, prec_set, lattice, epsilon)[source]
                        +generate_R_and_G_vecs(gamma, prec_set, lattice, epsilon)[source]

                        This returns a set of real and reciprocal lattice vectors (and real/recip summation values) based on a list of precision values (prec_set)

                        @@ -745,7 +745,7 @@
                        -generate_reciprocal_vectors_squared(a1, a2, a3, encut)[source]
                        +generate_reciprocal_vectors_squared(a1, a2, a3, encut)[source]

                        Generate reciprocal vector magnitudes within the cutoff along the specified lattice vectors. :param a1: Lattice vector a (in Bohrs) @@ -762,7 +762,7 @@

                        -generic_groupby(list_in, comp=<built-in function eq>)[source]
                        +generic_groupby(list_in, comp=<built-in function eq>)[source]

                        Group a list of unsortable objects :param list_in: A list of generic objects :param comp: (Default value = operator.eq) The comparator

                        @@ -775,7 +775,7 @@
                        -genrecip(a1, a2, a3, encut)[source]
                        +genrecip(a1, a2, a3, encut)[source]
                        Parameters
                          @@ -793,7 +793,7 @@
                          -tune_for_gamma(lattice, epsilon)[source]
                          +tune_for_gamma(lattice, epsilon)[source]

                          This tunes the gamma parameter for Kumagai anisotropic Ewald calculation. Method is to find a gamma parameter which generates a similar number of reciprocal and real lattice vectors, diff --git a/docs/pymatgen.analysis.diffraction.core.html b/docs/pymatgen.analysis.diffraction.core.html index 1c350eb769a..4e553a5d6c2 100644 --- a/docs/pymatgen.analysis.diffraction.core.html +++ b/docs/pymatgen.analysis.diffraction.core.html @@ -4,7 +4,7 @@ - pymatgen.analysis.diffraction.core module — pymatgen 2022.5.18 documentation + pymatgen.analysis.diffraction.core module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                          - 2022.5.18 + 2022.5.18.1
                          @@ -119,22 +119,22 @@

                          This module implements core classes for calculation of diffraction patterns.

                          -class AbstractDiffractionPatternCalculator[source]
                          +class AbstractDiffractionPatternCalculator[source]

                          Bases: abc.ABC

                          Abstract base class for computing the diffraction pattern of a crystal.

                          -SCALED_INTENSITY_TOL = 0.001[source]
                          +SCALED_INTENSITY_TOL = 0.001[source]
                          -TWO_THETA_TOL = 1e-05[source]
                          +TWO_THETA_TOL = 1e-05[source]
                          -abstract get_pattern(structure, scaled=True, two_theta_range=(0, 90))[source]
                          +abstract get_pattern(structure, scaled=True, two_theta_range=(0, 90))[source]

                          Calculates the diffraction pattern for a structure.

                          Parameters
                          @@ -157,7 +157,7 @@
                          -get_plot(structure, two_theta_range=(0, 90), annotate_peaks='compact', ax=None, with_labels=True, fontsize=16)[source]
                          +get_plot(structure, two_theta_range=(0, 90), annotate_peaks='compact', ax=None, with_labels=True, fontsize=16)[source]

                          Returns the diffraction plot as a matplotlib.pyplot.

                          Parameters
                          @@ -185,7 +185,7 @@
                          -plot_structures(structures, fontsize=6, **kwargs)[source]
                          +plot_structures(structures, fontsize=6, **kwargs)[source]

                          Plot diffraction patterns for multiple structures on the same figure.

                          Parameters
                          @@ -248,7 +248,7 @@
                          -show_plot(structure, **kwargs)[source]
                          +show_plot(structure, **kwargs)[source]

                          Shows the diffraction plot.

                          Parameters
                          @@ -271,7 +271,7 @@
                          -class DiffractionPattern(x, y, hkls, d_hkls)[source]
                          +class DiffractionPattern(x, y, hkls, d_hkls)[source]

                          Bases: pymatgen.core.spectrum.Spectrum

                          A representation of a diffraction pattern

                          @@ -290,19 +290,19 @@
                          -XLABEL = '$2\\Theta$'[source]
                          +XLABEL = '$2\\Theta$'[source]
                          -YLABEL = 'Intensity'[source]
                          +YLABEL = 'Intensity'[source]
                          -get_unique_families(hkls)[source]
                          +get_unique_families(hkls)[source]

                          Returns unique families of Miller indices. Families must be permutations of each other.

                          diff --git a/docs/pymatgen.analysis.diffraction.html b/docs/pymatgen.analysis.diffraction.html index 4eb17b97a20..7ade9902532 100644 --- a/docs/pymatgen.analysis.diffraction.html +++ b/docs/pymatgen.analysis.diffraction.html @@ -4,7 +4,7 @@ - pymatgen.analysis.diffraction package — pymatgen 2022.5.18 documentation + pymatgen.analysis.diffraction package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                          - 2022.5.18 + 2022.5.18.1
                          diff --git a/docs/pymatgen.analysis.diffraction.neutron.html b/docs/pymatgen.analysis.diffraction.neutron.html index c0d9794a448..0b917debe2d 100644 --- a/docs/pymatgen.analysis.diffraction.neutron.html +++ b/docs/pymatgen.analysis.diffraction.neutron.html @@ -4,7 +4,7 @@ - pymatgen.analysis.diffraction.neutron module — pymatgen 2022.5.18 documentation + pymatgen.analysis.diffraction.neutron module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                          - 2022.5.18 + 2022.5.18.1
                          @@ -119,7 +119,7 @@

                          This module implements a neutron diffraction (ND) pattern calculator.

                          -class NDCalculator(wavelength=1.54184, symprec=0, debye_waller_factors=None)[source]
                          +class NDCalculator(wavelength=1.54184, symprec=0, debye_waller_factors=None)[source]

                          Bases: pymatgen.analysis.diffraction.core.AbstractDiffractionPatternCalculator

                          Computes the powder neutron diffraction pattern of a crystal structure. This code is a slight modification of XRDCalculator in @@ -149,7 +149,7 @@

                          -get_pattern(structure, scaled=True, two_theta_range=(0, 90))[source]
                          +get_pattern(structure, scaled=True, two_theta_range=(0, 90))[source]

                          Calculates the powder neutron diffraction pattern for a structure.

                          Parameters
                          diff --git a/docs/pymatgen.analysis.diffraction.tem.html b/docs/pymatgen.analysis.diffraction.tem.html index 4d7d0e85e6e..0e80018b7be 100644 --- a/docs/pymatgen.analysis.diffraction.tem.html +++ b/docs/pymatgen.analysis.diffraction.tem.html @@ -4,7 +4,7 @@ - pymatgen.analysis.diffraction.tem module — pymatgen 2022.5.18 documentation + pymatgen.analysis.diffraction.tem module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                          - 2022.5.18 + 2022.5.18.1
                          @@ -119,7 +119,7 @@

                          This module implements a TEM pattern calculator.

                          -class TEMCalculator(symprec: Optional[float] = None, voltage: float = 200, beam_direction: tuple[int, int, int] = (0, 0, 1), camera_length: int = 160, debye_waller_factors: Optional[dict[str, float]] = None, cs: float = 1)[source]
                          +class TEMCalculator(symprec: Optional[float] = None, voltage: float = 200, beam_direction: tuple[int, int, int] = (0, 0, 1), camera_length: int = 160, debye_waller_factors: Optional[dict[str, float]] = None, cs: float = 1)[source]

                          Bases: pymatgen.analysis.diffraction.core.AbstractDiffractionPatternCalculator

                          Computes the TEM pattern of a crystal structure for multiple Laue zones. Code partially inspired from XRD calculation implementation. X-ray factor to electron factor

                          @@ -152,7 +152,7 @@
                          -bragg_angles(interplanar_spacings: dict[tuple[int, int, int], float]) → dict[tuple[int, int, int], float][source]
                          +bragg_angles(interplanar_spacings: dict[tuple[int, int, int], float]) → dict[tuple[int, int, int], float][source]

                          Gets the Bragg angles for every hkl point passed in (where n = 1). :param interplanar_spacings: dictionary of hkl to interplanar spacing :type interplanar_spacings: dict

                          @@ -165,7 +165,7 @@
                          -cell_intensity(structure: pymatgen.core.structure.Structure, bragg_angles: dict[tuple[int, int, int], float]) → dict[tuple[int, int, int], float][source]
                          +cell_intensity(structure: pymatgen.core.structure.Structure, bragg_angles: dict[tuple[int, int, int], float]) → dict[tuple[int, int, int], float][source]

                          Calculates cell intensity for each hkl plane. For simplicity’s sake, take I = |F|**2. :param structure: The input structure. :type structure: Structure @@ -180,7 +180,7 @@

                          -cell_scattering_factors(structure: pymatgen.core.structure.Structure, bragg_angles: dict[tuple[int, int, int], float]) → dict[tuple[int, int, int], int][source]
                          +cell_scattering_factors(structure: pymatgen.core.structure.Structure, bragg_angles: dict[tuple[int, int, int], float]) → dict[tuple[int, int, int], int][source]

                          Calculates the scattering factor for the whole cell. :param structure: The input structure. :type structure: Structure @@ -195,7 +195,7 @@

                          -electron_scattering_factors(structure: pymatgen.core.structure.Structure, bragg_angles: dict[tuple[int, int, int], float]) → dict[str, dict[tuple[int, int, int], float]][source]
                          +electron_scattering_factors(structure: pymatgen.core.structure.Structure, bragg_angles: dict[tuple[int, int, int], float]) → dict[str, dict[tuple[int, int, int], float]][source]

                          Calculates atomic scattering factors for electrons using the Mott-Bethe formula (1st order Born approximation). :param structure: The input structure. :type structure: Structure @@ -210,7 +210,7 @@

                          -static generate_points(coord_left: int = - 10, coord_right: int = 10) → numpy.ndarray[source]
                          +static generate_points(coord_left: int = - 10, coord_right: int = 10) → numpy.ndarray[source]

                          Generates a bunch of 3D points that span a cube. :param coord_left: The minimum coordinate value. :type coord_left: int @@ -225,7 +225,7 @@

                          -get_first_point(structure: pymatgen.core.structure.Structure, points: list) → dict[tuple[int, int, int], float][source]
                          +get_first_point(structure: pymatgen.core.structure.Structure, points: list) → dict[tuple[int, int, int], float][source]

                          Gets the first point to be plotted in the 2D DP, corresponding to maximum d/minimum R. :param structure: The input structure. :type structure: Structure @@ -240,7 +240,7 @@

                          -static get_interplanar_angle(structure: pymatgen.core.structure.Structure, p1: tuple[int, int, int], p2: tuple[int, int, int]) → float[source]
                          +static get_interplanar_angle(structure: pymatgen.core.structure.Structure, p1: tuple[int, int, int], p2: tuple[int, int, int]) → float[source]

                          Returns the interplanar angle (in degrees) between the normal of two crystal planes. Formulas from International Tables for Crystallography Volume C pp. 2-9. :param structure: The input structure. @@ -258,7 +258,7 @@

                          -get_interplanar_spacings(structure: Structure, points: list[tuple[int, int, int]] | np.ndarray) → dict[tuple[int, int, int], float][source]
                          +get_interplanar_spacings(structure: Structure, points: list[tuple[int, int, int]] | np.ndarray) → dict[tuple[int, int, int], float][source]
                          Parameters
                            @@ -274,7 +274,7 @@
                            -get_pattern(structure: pymatgen.core.structure.Structure, scaled: Optional[bool] = None, two_theta_range: Optional[tuple[float, float]] = None) → pandas.core.frame.DataFrame[source]
                            +get_pattern(structure: pymatgen.core.structure.Structure, scaled: Optional[bool] = None, two_theta_range: Optional[tuple[float, float]] = None) → pandas.core.frame.DataFrame[source]

                            Returns all relevant TEM DP info in a pandas dataframe. :param structure: The input structure. :type structure: Structure @@ -291,7 +291,7 @@

                            -get_plot_2d(structure: pymatgen.core.structure.Structure) → plotly.graph_objs._figure.Figure[source]
                            +get_plot_2d(structure: pymatgen.core.structure.Structure) → plotly.graph_objs._figure.Figure[source]

                            Generates the 2D diffraction pattern of the input structure. :param structure: The input structure. :type structure: Structure

                            @@ -304,7 +304,7 @@
                            -get_plot_2d_concise(structure: pymatgen.core.structure.Structure) → plotly.graph_objs._figure.Figure[source]
                            +get_plot_2d_concise(structure: pymatgen.core.structure.Structure) → plotly.graph_objs._figure.Figure[source]

                            Generates the concise 2D diffraction pattern of the input structure of a smaller size and without layout. Does not display. :param structure: The input structure. @@ -318,7 +318,7 @@

                            -static get_plot_coeffs(p1: tuple[int, int, int], p2: tuple[int, int, int], p3: tuple[int, int, int]) → numpy.ndarray[source]
                            +static get_plot_coeffs(p1: tuple[int, int, int], p2: tuple[int, int, int], p3: tuple[int, int, int]) → numpy.ndarray[source]

                            Calculates coefficients of the vector addition required to generate positions for each DP point by the Moore-Penrose inverse method. :param p1: The first point. Fixed. @@ -336,7 +336,7 @@

                            -get_positions(structure: pymatgen.core.structure.Structure, points: list) → dict[tuple[int, int, int], numpy.ndarray][source]
                            +get_positions(structure: pymatgen.core.structure.Structure, points: list) → dict[tuple[int, int, int], numpy.ndarray][source]

                            Calculates all the positions of each hkl point in the 2D diffraction pattern by vector addition. Distance in centimeters. :param structure: The input structure. @@ -352,7 +352,7 @@

                            -get_s2(bragg_angles: dict[tuple[int, int, int], float]) → dict[tuple[int, int, int], float][source]
                            +get_s2(bragg_angles: dict[tuple[int, int, int], float]) → dict[tuple[int, int, int], float][source]

                            Calculates the s squared parameter (= square of sin theta over lambda) for each hkl plane. :param bragg_angles: The bragg angles for each hkl plane. :type bragg_angles: Dict

                            @@ -369,7 +369,7 @@
                            -is_parallel(structure: pymatgen.core.structure.Structure, plane: tuple[int, int, int], other_plane: tuple[int, int, int]) → bool[source]
                            +is_parallel(structure: pymatgen.core.structure.Structure, plane: tuple[int, int, int], other_plane: tuple[int, int, int]) → bool[source]

                            Checks if two hkl planes are parallel in reciprocal space. :param structure: The input structure. :type structure: Structure @@ -386,7 +386,7 @@

                            -normalized_cell_intensity(structure: pymatgen.core.structure.Structure, bragg_angles: dict[tuple[int, int, int], float]) → dict[tuple[int, int, int], float][source]
                            +normalized_cell_intensity(structure: pymatgen.core.structure.Structure, bragg_angles: dict[tuple[int, int, int], float]) → dict[tuple[int, int, int], float][source]

                            Normalizes the cell_intensity dict to 1, for use in plotting. :param structure: The input structure. :type structure: Structure @@ -401,7 +401,7 @@

                            -tem_dots(structure: pymatgen.core.structure.Structure, points) → list[source]
                            +tem_dots(structure: pymatgen.core.structure.Structure, points) → list[source]

                            Generates all TEM_dot as named tuples that will appear on the 2D diffraction pattern. :param structure: The input structure. :type structure: Structure @@ -416,7 +416,7 @@

                            -wavelength_rel() → float[source]
                            +wavelength_rel() → float[source]
                            Calculates the wavelength of the electron beam with relativistic kinematic effects taken

                            into account.

                            @@ -433,7 +433,7 @@
                            -x_ray_factors(structure: pymatgen.core.structure.Structure, bragg_angles: dict[tuple[int, int, int], float]) → dict[str, dict[tuple[int, int, int], float]][source]
                            +x_ray_factors(structure: pymatgen.core.structure.Structure, bragg_angles: dict[tuple[int, int, int], float]) → dict[str, dict[tuple[int, int, int], float]][source]

                            Calculates x-ray factors, which are required to calculate atomic scattering factors. Method partially inspired by the equivalent process in the xrd module. :param structure: The input structure. @@ -449,7 +449,7 @@

                            -zone_axis_filter(points: list[tuple[int, int, int]] | np.ndarray, laue_zone: int = 0) → list[tuple[int, int, int]][source]
                            +zone_axis_filter(points: list[tuple[int, int, int]] | np.ndarray, laue_zone: int = 0) → list[tuple[int, int, int]][source]

                            Filters out all points that exist within the specified Laue zone according to the zone axis rule. :param points: The list of points to be filtered. :type points: np.ndarray diff --git a/docs/pymatgen.analysis.diffraction.xrd.html b/docs/pymatgen.analysis.diffraction.xrd.html index 7dc2c617988..12db9afdc35 100644 --- a/docs/pymatgen.analysis.diffraction.xrd.html +++ b/docs/pymatgen.analysis.diffraction.xrd.html @@ -4,7 +4,7 @@ - pymatgen.analysis.diffraction.xrd module — pymatgen 2022.5.18 documentation + pymatgen.analysis.diffraction.xrd module — pymatgen 2022.5.18.1 documentation @@ -40,7 +40,7 @@ pymatgen

                            - 2022.5.18 + 2022.5.18.1
                            @@ -120,7 +120,7 @@

                            This module implements an XRD pattern calculator.

                            -class XRDCalculator(wavelength='CuKa', symprec=0, debye_waller_factors=None)[source]
                            +class XRDCalculator(wavelength='CuKa', symprec=0, debye_waller_factors=None)[source]

                            Bases: pymatgen.analysis.diffraction.core.AbstractDiffractionPatternCalculator

                            Computes the XRD pattern of a crystal structure.

                            This code is implemented by Shyue Ping Ong as part of UCSD’s NANO106 - @@ -184,12 +184,12 @@

                            -AVAILABLE_RADIATION = ('CuKa', 'CuKa2', 'CuKa1', 'CuKb1', 'MoKa', 'MoKa2', 'MoKa1', 'MoKb1', 'CrKa', 'CrKa2', 'CrKa1', 'CrKb1', 'FeKa', 'FeKa2', 'FeKa1', 'FeKb1', 'CoKa', 'CoKa2', 'CoKa1', 'CoKb1', 'AgKa', 'AgKa2', 'AgKa1', 'AgKb1')[source]
                            +AVAILABLE_RADIATION = ('CuKa', 'CuKa2', 'CuKa1', 'CuKb1', 'MoKa', 'MoKa2', 'MoKa1', 'MoKb1', 'CrKa', 'CrKa2', 'CrKa1', 'CrKb1', 'FeKa', 'FeKa2', 'FeKa1', 'FeKb1', 'CoKa', 'CoKa2', 'CoKa1', 'CoKb1', 'AgKa', 'AgKa2', 'AgKa1', 'AgKb1')[source]
                            -get_pattern(structure, scaled=True, two_theta_range=(0, 90))[source]
                            +get_pattern(structure, scaled=True, two_theta_range=(0, 90))[source]

                            Calculates the diffraction pattern for a structure.

                            Parameters
                            diff --git a/docs/pymatgen.analysis.diffusion_analyzer.html b/docs/pymatgen.analysis.diffusion_analyzer.html index e885b46c6b7..ec87eebb16c 100644 --- a/docs/pymatgen.analysis.diffusion_analyzer.html +++ b/docs/pymatgen.analysis.diffusion_analyzer.html @@ -4,7 +4,7 @@ - pymatgen.analysis.diffusion_analyzer module — pymatgen 2022.5.18 documentation + pymatgen.analysis.diffusion_analyzer module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                            - 2022.5.18 + 2022.5.18.1
                            @@ -131,7 +131,7 @@
                            -class DiffusionAnalyzer(structure, displacements, specie, temperature, time_step, step_skip, smoothed='max', min_obs=30, avg_nsteps=1000, lattices=None)[source]
                            +class DiffusionAnalyzer(structure, displacements, specie, temperature, time_step, step_skip, smoothed='max', min_obs=30, avg_nsteps=1000, lattices=None)[source]

                            Bases: monty.json.MSONable

                            Class for performing diffusion analysis.

                            This constructor is meant to be used with pre-processed data. @@ -193,13 +193,13 @@

                            -as_dict()[source]
                            +as_dict()[source]

                            Returns: MSONable dict

                            -export_msdt(filename)[source]
                            +export_msdt(filename)[source]

                            Writes MSD data to a csv file that can be easily plotted in other software.

                            @@ -213,7 +213,7 @@
                            -classmethod from_dict(d)[source]
                            +classmethod from_dict(d)[source]
                            Parameters

                            d (dict) – Dict representation

                            @@ -224,7 +224,7 @@
                            -classmethod from_files(filepaths, specie, step_skip=10, ncores=None, initial_disp=None, initial_structure=None, **kwargs)[source]
                            +classmethod from_files(filepaths, specie, step_skip=10, ncores=None, initial_disp=None, initial_structure=None, **kwargs)[source]

                            Convenient constructor that takes in a list of vasprun.xml paths to perform diffusion analysis.

                            @@ -266,7 +266,7 @@
                            -classmethod from_structures(structures, specie, temperature, time_step, step_skip, initial_disp=None, initial_structure=None, **kwargs)[source]
                            +classmethod from_structures(structures, specie, temperature, time_step, step_skip, initial_disp=None, initial_structure=None, **kwargs)[source]

                            Convenient constructor that takes in a list of Structure objects to perform diffusion analysis.

                            @@ -301,7 +301,7 @@
                            -classmethod from_vaspruns(vaspruns, specie, initial_disp=None, initial_structure=None, **kwargs)[source]
                            +classmethod from_vaspruns(vaspruns, specie, initial_disp=None, initial_structure=None, **kwargs)[source]

                            Convenient constructor that takes in a list of Vasprun objects to perform diffusion analysis.

                            @@ -331,7 +331,7 @@
                            -get_drift_corrected_structures(start=None, stop=None, step=None)[source]
                            +get_drift_corrected_structures(start=None, stop=None, step=None)[source]

                            Returns an iterator for the drift-corrected structures. Use of iterator is to reduce memory usage as # of structures in MD can be huge. You don’t often need all the structures all at once.

                            @@ -354,7 +354,7 @@
                            -get_framework_rms_plot(plt=None, granularity=200, matching_s=None)[source]
                            +get_framework_rms_plot(plt=None, granularity=200, matching_s=None)[source]

                            Get the plot of rms framework displacement vs time. Useful for checking for melting, especially if framework atoms can move via paddle-wheel or similar mechanism (which would show up in max framework displacement @@ -377,7 +377,7 @@

                            -get_msd_plot(plt=None, mode='specie')[source]
                            +get_msd_plot(plt=None, mode='specie')[source]

                            Get the plot of the smoothed msd vs time graph. Useful for checking convergence. This can be written to an image file.

                            @@ -395,7 +395,7 @@
                            -get_summary_dict(include_msd_t=False, include_mscd_t=False)[source]
                            +get_summary_dict(include_msd_t=False, include_mscd_t=False)[source]

                            Provides a summary of diffusion information.

                            Parameters
                            @@ -414,7 +414,7 @@
                            -plot_msd(mode='default')[source]
                            +plot_msd(mode='default')[source]

                            Plot the smoothed msd vs time graph. Useful for checking convergence.

                            Parameters
                            @@ -431,7 +431,7 @@
                            -fit_arrhenius(temps, diffusivities)[source]
                            +fit_arrhenius(temps, diffusivities)[source]
                            Returns Ea, c, standard error of Ea from the Arrhenius fit:

                            D = c * exp(-Ea/kT)

                            @@ -449,7 +449,7 @@
                            -get_arrhenius_plot(temps, diffusivities, diffusivity_errors=None, **kwargs)[source]
                            +get_arrhenius_plot(temps, diffusivities, diffusivity_errors=None, **kwargs)[source]

                            Returns an Arrhenius plot.

                            Parameters
                            @@ -470,7 +470,7 @@
                            -get_conversion_factor(structure, species, temperature)[source]
                            +get_conversion_factor(structure, species, temperature)[source]

                            Conversion factor to convert between cm^2/s diffusivity measurements and mS/cm conductivity measurements based on number of atoms of diffusing species. Note that the charge is based on the oxidation state of the @@ -493,7 +493,7 @@

                            -get_extrapolated_conductivity(temps, diffusivities, new_temp, structure, species)[source]
                            +get_extrapolated_conductivity(temps, diffusivities, new_temp, structure, species)[source]

                            Returns extrapolated mS/cm conductivity.

                            Parameters
                            @@ -514,7 +514,7 @@
                            -get_extrapolated_diffusivity(temps, diffusivities, new_temp)[source]
                            +get_extrapolated_diffusivity(temps, diffusivities, new_temp)[source]

                            Returns (Arrhenius) extrapolated diffusivity at new_temp

                            Parameters
                            diff --git a/docs/pymatgen.analysis.dimensionality.html b/docs/pymatgen.analysis.dimensionality.html index 833cd1e382f..138ae583338 100644 --- a/docs/pymatgen.analysis.dimensionality.html +++ b/docs/pymatgen.analysis.dimensionality.html @@ -4,7 +4,7 @@ - pymatgen.analysis.dimensionality module — pymatgen 2022.5.18 documentation + pymatgen.analysis.dimensionality module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                            - 2022.5.18 + 2022.5.18.1
                            @@ -140,7 +140,7 @@
                            -calculate_dimensionality_of_site(bonded_structure, site_index, inc_vertices=False)[source]
                            +calculate_dimensionality_of_site(bonded_structure, site_index, inc_vertices=False)[source]

                            Calculates the dimensionality of the component containing the given site.

                            Implements directly the modified breadth-first-search algorithm described in Algorithm 1 of:

                            @@ -172,7 +172,7 @@
                            -find_clusters(struct, connected_matrix)[source]
                            +find_clusters(struct, connected_matrix)[source]

                            Finds bonded clusters of atoms in the structure with periodic boundary conditions.

                            If there are atoms that are not bonded to anything, returns [0,1,0]. (For @@ -201,7 +201,7 @@

                            -find_connected_atoms(struct, tolerance=0.45, ldict={'Ac': 1.88, 'Ag': 1.59, 'Al': 1.35, 'Am': 1.51, 'Ar': 1.57, 'As': 1.21, 'At': 1.7, 'Au': 1.5, 'B': 0.83, 'Ba': 1.34, 'Be': 0.35, 'Bh': 1.6, 'Bi': 1.54, 'Bk': 1.5, 'Br': 1.21, 'C': 0.68, 'Ca': 0.99, 'Cd': 1.69, 'Ce': 1.83, 'Cf': 1.5, 'Cl': 0.99, 'Cm': 1.5, 'Co': 1.33, 'Cr': 1.35, 'Cs': 1.67, 'Cu': 1.52, 'Db': 1.6, 'Dy': 1.75, 'Er': 1.73, 'Es': 1.5, 'Eu': 1.99, 'F': 0.64, 'Fe': 1.34, 'Fm': 1.5, 'Fr': 2, 'Ga': 1.22, 'Gd': 1.79, 'Ge': 1.17, 'H': 0.23, 'He': 0.93, 'Hf': 1.57, 'Hg': 1.7, 'Ho': 1.74, 'Hs': 1.6, 'I': 1.4, 'In': 1.63, 'Ir': 1.32, 'K': 1.33, 'Kr': 1.91, 'La': 1.87, 'Li': 0.68, 'Lr': 1.5, 'Lu': 1.72, 'Md': 1.5, 'Mg': 1.1, 'Mn': 1.35, 'Mo': 1.47, 'Mt': 1.6, 'N': 0.68, 'Na': 0.97, 'Nb': 1.48, 'Nd': 1.81, 'Ne': 1.12, 'Ni': 1.5, 'No': 1.5, 'Np': 1.55, 'O': 0.68, 'Os': 1.37, 'P': 0.75, 'Pa': 1.61, 'Pb': 1.54, 'Pd': 1.5, 'Pm': 1.8, 'Po': 1.68, 'Pr': 1.82, 'Pt': 1.5, 'Pu': 1.53, 'Ra': 1.9, 'Rb': 1.47, 'Re': 1.35, 'Rf': 1.6, 'Rh': 1.45, 'Rn': 2.4, 'Ru': 1.4, 'S': 1.02, 'Sb': 1.46, 'Sc': 1.44, 'Se': 1.22, 'Sg': 1.6, 'Si': 1.2, 'Sm': 1.8, 'Sn': 1.46, 'Sr': 1.12, 'Ta': 1.43, 'Tb': 1.76, 'Tc': 1.35, 'Te': 1.47, 'Th': 1.79, 'Ti': 1.47, 'Tl': 1.55, 'Tm': 1.72, 'U': 1.58, 'V': 1.33, 'W': 1.37, 'Xe': 1.98, 'Y': 1.78, 'Yb': 1.94, 'Zn': 1.45, 'Zr': 1.56})[source]
                            +find_connected_atoms(struct, tolerance=0.45, ldict={'Ac': 1.88, 'Ag': 1.59, 'Al': 1.35, 'Am': 1.51, 'Ar': 1.57, 'As': 1.21, 'At': 1.7, 'Au': 1.5, 'B': 0.83, 'Ba': 1.34, 'Be': 0.35, 'Bh': 1.6, 'Bi': 1.54, 'Bk': 1.5, 'Br': 1.21, 'C': 0.68, 'Ca': 0.99, 'Cd': 1.69, 'Ce': 1.83, 'Cf': 1.5, 'Cl': 0.99, 'Cm': 1.5, 'Co': 1.33, 'Cr': 1.35, 'Cs': 1.67, 'Cu': 1.52, 'Db': 1.6, 'Dy': 1.75, 'Er': 1.73, 'Es': 1.5, 'Eu': 1.99, 'F': 0.64, 'Fe': 1.34, 'Fm': 1.5, 'Fr': 2, 'Ga': 1.22, 'Gd': 1.79, 'Ge': 1.17, 'H': 0.23, 'He': 0.93, 'Hf': 1.57, 'Hg': 1.7, 'Ho': 1.74, 'Hs': 1.6, 'I': 1.4, 'In': 1.63, 'Ir': 1.32, 'K': 1.33, 'Kr': 1.91, 'La': 1.87, 'Li': 0.68, 'Lr': 1.5, 'Lu': 1.72, 'Md': 1.5, 'Mg': 1.1, 'Mn': 1.35, 'Mo': 1.47, 'Mt': 1.6, 'N': 0.68, 'Na': 0.97, 'Nb': 1.48, 'Nd': 1.81, 'Ne': 1.12, 'Ni': 1.5, 'No': 1.5, 'Np': 1.55, 'O': 0.68, 'Os': 1.37, 'P': 0.75, 'Pa': 1.61, 'Pb': 1.54, 'Pd': 1.5, 'Pm': 1.8, 'Po': 1.68, 'Pr': 1.82, 'Pt': 1.5, 'Pu': 1.53, 'Ra': 1.9, 'Rb': 1.47, 'Re': 1.35, 'Rf': 1.6, 'Rh': 1.45, 'Rn': 2.4, 'Ru': 1.4, 'S': 1.02, 'Sb': 1.46, 'Sc': 1.44, 'Se': 1.22, 'Sg': 1.6, 'Si': 1.2, 'Sm': 1.8, 'Sn': 1.46, 'Sr': 1.12, 'Ta': 1.43, 'Tb': 1.76, 'Tc': 1.35, 'Te': 1.47, 'Th': 1.79, 'Ti': 1.47, 'Tl': 1.55, 'Tm': 1.72, 'U': 1.58, 'V': 1.33, 'W': 1.37, 'Xe': 1.98, 'Y': 1.78, 'Yb': 1.94, 'Zn': 1.45, 'Zr': 1.56})[source]

                            Finds bonded atoms and returns a adjacency matrix of bonded atoms.

                            Author: “Gowoon Cheon” Email: “gcheon@stanford.edu”

                            @@ -230,7 +230,7 @@
                            -get_dimensionality_cheon(structure_raw, tolerance=0.45, ldict={'Ac': 1.88, 'Ag': 1.59, 'Al': 1.35, 'Am': 1.51, 'Ar': 1.57, 'As': 1.21, 'At': 1.7, 'Au': 1.5, 'B': 0.83, 'Ba': 1.34, 'Be': 0.35, 'Bh': 1.6, 'Bi': 1.54, 'Bk': 1.5, 'Br': 1.21, 'C': 0.68, 'Ca': 0.99, 'Cd': 1.69, 'Ce': 1.83, 'Cf': 1.5, 'Cl': 0.99, 'Cm': 1.5, 'Co': 1.33, 'Cr': 1.35, 'Cs': 1.67, 'Cu': 1.52, 'Db': 1.6, 'Dy': 1.75, 'Er': 1.73, 'Es': 1.5, 'Eu': 1.99, 'F': 0.64, 'Fe': 1.34, 'Fm': 1.5, 'Fr': 2, 'Ga': 1.22, 'Gd': 1.79, 'Ge': 1.17, 'H': 0.23, 'He': 0.93, 'Hf': 1.57, 'Hg': 1.7, 'Ho': 1.74, 'Hs': 1.6, 'I': 1.4, 'In': 1.63, 'Ir': 1.32, 'K': 1.33, 'Kr': 1.91, 'La': 1.87, 'Li': 0.68, 'Lr': 1.5, 'Lu': 1.72, 'Md': 1.5, 'Mg': 1.1, 'Mn': 1.35, 'Mo': 1.47, 'Mt': 1.6, 'N': 0.68, 'Na': 0.97, 'Nb': 1.48, 'Nd': 1.81, 'Ne': 1.12, 'Ni': 1.5, 'No': 1.5, 'Np': 1.55, 'O': 0.68, 'Os': 1.37, 'P': 0.75, 'Pa': 1.61, 'Pb': 1.54, 'Pd': 1.5, 'Pm': 1.8, 'Po': 1.68, 'Pr': 1.82, 'Pt': 1.5, 'Pu': 1.53, 'Ra': 1.9, 'Rb': 1.47, 'Re': 1.35, 'Rf': 1.6, 'Rh': 1.45, 'Rn': 2.4, 'Ru': 1.4, 'S': 1.02, 'Sb': 1.46, 'Sc': 1.44, 'Se': 1.22, 'Sg': 1.6, 'Si': 1.2, 'Sm': 1.8, 'Sn': 1.46, 'Sr': 1.12, 'Ta': 1.43, 'Tb': 1.76, 'Tc': 1.35, 'Te': 1.47, 'Th': 1.79, 'Ti': 1.47, 'Tl': 1.55, 'Tm': 1.72, 'U': 1.58, 'V': 1.33, 'W': 1.37, 'Xe': 1.98, 'Y': 1.78, 'Yb': 1.94, 'Zn': 1.45, 'Zr': 1.56}, standardize=True, larger_cell=False)[source]
                            +get_dimensionality_cheon(structure_raw, tolerance=0.45, ldict={'Ac': 1.88, 'Ag': 1.59, 'Al': 1.35, 'Am': 1.51, 'Ar': 1.57, 'As': 1.21, 'At': 1.7, 'Au': 1.5, 'B': 0.83, 'Ba': 1.34, 'Be': 0.35, 'Bh': 1.6, 'Bi': 1.54, 'Bk': 1.5, 'Br': 1.21, 'C': 0.68, 'Ca': 0.99, 'Cd': 1.69, 'Ce': 1.83, 'Cf': 1.5, 'Cl': 0.99, 'Cm': 1.5, 'Co': 1.33, 'Cr': 1.35, 'Cs': 1.67, 'Cu': 1.52, 'Db': 1.6, 'Dy': 1.75, 'Er': 1.73, 'Es': 1.5, 'Eu': 1.99, 'F': 0.64, 'Fe': 1.34, 'Fm': 1.5, 'Fr': 2, 'Ga': 1.22, 'Gd': 1.79, 'Ge': 1.17, 'H': 0.23, 'He': 0.93, 'Hf': 1.57, 'Hg': 1.7, 'Ho': 1.74, 'Hs': 1.6, 'I': 1.4, 'In': 1.63, 'Ir': 1.32, 'K': 1.33, 'Kr': 1.91, 'La': 1.87, 'Li': 0.68, 'Lr': 1.5, 'Lu': 1.72, 'Md': 1.5, 'Mg': 1.1, 'Mn': 1.35, 'Mo': 1.47, 'Mt': 1.6, 'N': 0.68, 'Na': 0.97, 'Nb': 1.48, 'Nd': 1.81, 'Ne': 1.12, 'Ni': 1.5, 'No': 1.5, 'Np': 1.55, 'O': 0.68, 'Os': 1.37, 'P': 0.75, 'Pa': 1.61, 'Pb': 1.54, 'Pd': 1.5, 'Pm': 1.8, 'Po': 1.68, 'Pr': 1.82, 'Pt': 1.5, 'Pu': 1.53, 'Ra': 1.9, 'Rb': 1.47, 'Re': 1.35, 'Rf': 1.6, 'Rh': 1.45, 'Rn': 2.4, 'Ru': 1.4, 'S': 1.02, 'Sb': 1.46, 'Sc': 1.44, 'Se': 1.22, 'Sg': 1.6, 'Si': 1.2, 'Sm': 1.8, 'Sn': 1.46, 'Sr': 1.12, 'Ta': 1.43, 'Tb': 1.76, 'Tc': 1.35, 'Te': 1.47, 'Th': 1.79, 'Ti': 1.47, 'Tl': 1.55, 'Tm': 1.72, 'U': 1.58, 'V': 1.33, 'W': 1.37, 'Xe': 1.98, 'Y': 1.78, 'Yb': 1.94, 'Zn': 1.45, 'Zr': 1.56}, standardize=True, larger_cell=False)[source]

                            Algorithm for finding the dimensions of connected subunits in a structure. This method finds the dimensionality of the material even when the material is not layered along low-index planes, or does not have flat @@ -273,7 +273,7 @@

                            -get_dimensionality_gorai(structure, max_hkl=2, el_radius_updates=None, min_slab_size=5, min_vacuum_size=5, standardize=True, bonds=None)[source]
                            +get_dimensionality_gorai(structure, max_hkl=2, el_radius_updates=None, min_slab_size=5, min_vacuum_size=5, standardize=True, bonds=None)[source]

                            This method returns whether a structure is 3D, 2D (layered), or 1D (linear chains or molecules) according to the algorithm published in Gorai, P., Toberer, E. & Stevanovic, V. Computational Identification of Promising @@ -311,7 +311,7 @@

                            -get_dimensionality_larsen(bonded_structure)[source]
                            +get_dimensionality_larsen(bonded_structure)[source]

                            Gets the dimensionality of a bonded structure.

                            The dimensionality of the structure is the highest dimensionality of all structure components. This method is very robust and can handle @@ -343,7 +343,7 @@

                            -get_structure_components(bonded_structure, inc_orientation=False, inc_site_ids=False, inc_molecule_graph=False)[source]
                            +get_structure_components(bonded_structure, inc_orientation=False, inc_site_ids=False, inc_molecule_graph=False)[source]

                            Gets information on the components in a bonded structure.

                            Correctly determines the dimensionality of all structures, regardless of structure type or improper connections due to periodic boundary conditions.

                            @@ -411,7 +411,7 @@
                            -zero_d_graph_to_molecule_graph(bonded_structure, graph)[source]
                            +zero_d_graph_to_molecule_graph(bonded_structure, graph)[source]

                            Converts a zero-dimensional networkx Graph object into a MoleculeGraph.

                            Implements a similar breadth-first search to that in calculate_dimensionality_of_site().

                            diff --git a/docs/pymatgen.analysis.elasticity.elastic.html b/docs/pymatgen.analysis.elasticity.elastic.html index af1c8bfe4f7..8b783943482 100644 --- a/docs/pymatgen.analysis.elasticity.elastic.html +++ b/docs/pymatgen.analysis.elasticity.elastic.html @@ -4,7 +4,7 @@ - pymatgen.analysis.elasticity.elastic module — pymatgen 2022.5.18 documentation + pymatgen.analysis.elasticity.elastic module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                            - 2022.5.18 + 2022.5.18.1
                            @@ -121,7 +121,7 @@ stress-strain data

                            -class ComplianceTensor(s_array)[source]
                            +class ComplianceTensor(s_array)[source]

                            Bases: pymatgen.core.tensors.Tensor

                            This class represents the compliance tensor, and exists primarily to keep the voigt-conversion scheme consistent @@ -135,7 +135,7 @@

                            -class ElasticTensor(input_array, tol=0.0001)[source]
                            +class ElasticTensor(input_array, tol=0.0001)[source]

                            Bases: pymatgen.analysis.elasticity.elastic.NthOrderElasticTensor

                            This class extends Tensor to describe the 3x3x3x3 second-order elastic tensor, C_{ijkl}, with various @@ -158,7 +158,7 @@

                            -cahill_thermalcond(*args, **kwargs)[source]
                            +cahill_thermalcond(*args, **kwargs)[source]
                            Parameters
                              @@ -173,7 +173,7 @@
                              -clarke_thermalcond(*args, **kwargs)[source]
                              +clarke_thermalcond(*args, **kwargs)[source]
                              Parameters
                                @@ -188,7 +188,7 @@
                                -property compliance_tensor[source]
                                +property compliance_tensor[source]

                                returns the Voigt-notation compliance tensor, which is the matrix inverse of the Voigt-notation elastic tensor

                                @@ -196,7 +196,7 @@
                                -debye_temperature(*args, **kwargs)[source]
                                +debye_temperature(*args, **kwargs)[source]
                                Parameters
                                  @@ -211,13 +211,13 @@
                                  -directional_elastic_mod(n)[source]
                                  +directional_elastic_mod(n)[source]

                                  Calculates directional elastic modulus for a specific vector

                                  -directional_poisson_ratio(n, m, tol=1e-08)[source]
                                  +directional_poisson_ratio(n, m, tol=1e-08)[source]

                                  Calculates the poisson ratio for a specific direction relative to a second, orthogonal direction

                                  @@ -233,7 +233,7 @@
                                  -classmethod from_independent_strains(strains, stresses, eq_stress=None, vasp=False, tol=1e-10)[source]
                                  +classmethod from_independent_strains(strains, stresses, eq_stress=None, vasp=False, tol=1e-10)[source]

                                  Constructs the elastic tensor least-squares fit of independent strains :param strains: list of strain objects to fit :type strains: list of Strains @@ -256,7 +256,7 @@

                                  -classmethod from_pseudoinverse(strains, stresses)[source]
                                  +classmethod from_pseudoinverse(strains, stresses)[source]

                                  Class method to fit an elastic tensor from stress/strain data. Method uses Moore-Penrose pseudoinverse to invert the s = C*e equation with elastic tensor, stress, and @@ -273,25 +273,25 @@

                                  -property g_reuss[source]
                                  +property g_reuss[source]

                                  returns the G_r shear modulus

                                  -property g_voigt[source]
                                  +property g_voigt[source]

                                  returns the G_v shear modulus

                                  -property g_vrh[source]
                                  +property g_vrh[source]

                                  returns the G_vrh (Voigt-Reuss-Hill) average shear modulus

                                  -get_structure_property_dict(structure, include_base_props=True, ignore_errors=False)[source]
                                  +get_structure_property_dict(structure, include_base_props=True, ignore_errors=False)[source]

                                  returns a dictionary of properties derived from the elastic tensor and an associated structure

                                  @@ -310,37 +310,37 @@
                                  -green_kristoffel(u)[source]
                                  +green_kristoffel(u)[source]

                                  Returns the Green-Kristoffel tensor for a second-order tensor

                                  -property homogeneous_poisson[source]
                                  +property homogeneous_poisson[source]

                                  returns the homogeneous poisson ratio

                                  -property k_reuss[source]
                                  +property k_reuss[source]

                                  returns the K_r bulk modulus

                                  -property k_voigt[source]
                                  +property k_voigt[source]

                                  returns the K_v bulk modulus

                                  -property k_vrh[source]
                                  +property k_vrh[source]

                                  returns the K_vrh (Voigt-Reuss-Hill) average bulk modulus

                                  -long_v(*args, **kwargs)[source]
                                  +long_v(*args, **kwargs)[source]
                                  Parameters
                                    @@ -355,13 +355,13 @@
                                    -property property_dict[source]
                                    +property property_dict[source]

                                    returns a dictionary of properties derived from the elastic tensor

                                    -snyder_ac(*args, **kwargs)[source]
                                    +snyder_ac(*args, **kwargs)[source]
                                    Parameters
                                      @@ -376,7 +376,7 @@
                                      -snyder_opt(*args, **kwargs)[source]
                                      +snyder_opt(*args, **kwargs)[source]
                                      Parameters
                                        @@ -391,7 +391,7 @@
                                        -snyder_total(*args, **kwargs)[source]
                                        +snyder_total(*args, **kwargs)[source]
                                        Parameters
                                          @@ -406,7 +406,7 @@
                                          -trans_v(*args, **kwargs)[source]
                                          +trans_v(*args, **kwargs)[source]
                                          Parameters
                                            @@ -421,13 +421,13 @@
                                            -property universal_anisotropy[source]
                                            +property universal_anisotropy[source]

                                            returns the universal anisotropy value

                                            -property y_mod[source]
                                            +property y_mod[source]

                                            Calculates Young’s modulus (in SI units) using the Voigt-Reuss-Hill averages of bulk and shear moduli

                                            @@ -436,7 +436,7 @@
                                            -class ElasticTensorExpansion(c_list)[source]
                                            +class ElasticTensorExpansion(c_list)[source]

                                            Bases: pymatgen.core.tensors.TensorCollection

                                            This class is a sequence of elastic tensors corresponding to an elastic tensor expansion, which can be used to @@ -453,34 +453,34 @@

                                            -calculate_stress(strain)[source]
                                            +calculate_stress(strain)[source]

                                            Calculate’s a given elastic tensor’s contribution to the stress using Einstein summation

                                            -energy_density(strain, convert_GPa_to_eV=True)[source]
                                            +energy_density(strain, convert_GPa_to_eV=True)[source]

                                            Calculates the elastic energy density due to a strain

                                            -classmethod from_diff_fit(strains, stresses, eq_stress=None, tol=1e-10, order=3)[source]
                                            +classmethod from_diff_fit(strains, stresses, eq_stress=None, tol=1e-10, order=3)[source]

                                            Generates an elastic tensor expansion via the fitting function defined below in diff_fit

                                            -get_compliance_expansion()[source]
                                            +get_compliance_expansion()[source]

                                            Gets a compliance tensor expansion from the elastic tensor expansion.

                                            -get_effective_ecs(strain, order=2)[source]
                                            +get_effective_ecs(strain, order=2)[source]

                                            Returns the effective elastic constants from the elastic tensor expansion.

                                            @@ -496,7 +496,7 @@
                                            -get_ggt(n, u)[source]
                                            +get_ggt(n, u)[source]

                                            Gets the Generalized Gruneisen tensor for a given third-order elastic tensor expansion.

                                            @@ -511,7 +511,7 @@
                                            -get_gruneisen_parameter(temperature=None, structure=None, quad=None)[source]
                                            +get_gruneisen_parameter(temperature=None, structure=None, quad=None)[source]

                                            Gets the single average gruneisen parameter from the TGT.

                                            Parameters
                                            @@ -531,7 +531,7 @@
                                            -get_heat_capacity(temperature, structure, n, u, cutoff=100.0)[source]
                                            +get_heat_capacity(temperature, structure, n, u, cutoff=100.0)[source]

                                            Gets the directional heat capacity for a higher order tensor expansion as a function of direction and polarization.

                                            @@ -552,7 +552,7 @@
                                            -get_stability_criteria(s, n)[source]
                                            +get_stability_criteria(s, n)[source]

                                            Gets the stability criteria from the symmetric Wallace tensor from an input vector and stress value.

                                            @@ -570,7 +570,7 @@
                                            -get_strain_from_stress(stress)[source]
                                            +get_strain_from_stress(stress)[source]

                                            Gets the strain from a stress state according to the compliance expansion corresponding to the tensor expansion.

                                            @@ -578,7 +578,7 @@
                                            -get_symmetric_wallace_tensor(tau)[source]
                                            +get_symmetric_wallace_tensor(tau)[source]

                                            Gets the symmetrized wallace tensor for determining yield strength criteria.

                                            @@ -591,7 +591,7 @@
                                            -get_tgt(temperature=None, structure=None, quad=None)[source]
                                            +get_tgt(temperature=None, structure=None, quad=None)[source]

                                            Gets the thermodynamic Gruneisen tensor (TGT) by via an integration of the GGT weighted by the directional heat capacity.

                                            @@ -618,7 +618,7 @@
                                            -get_wallace_tensor(tau)[source]
                                            +get_wallace_tensor(tau)[source]

                                            Gets the Wallace Tensor for determining yield strength criteria.

                                            @@ -631,7 +631,7 @@
                                            -get_yield_stress(n)[source]
                                            +get_yield_stress(n)[source]

                                            Gets the yield stress for a given direction

                                            Parameters
                                            @@ -643,7 +643,7 @@
                                            -omega(structure, n, u)[source]
                                            +omega(structure, n, u)[source]

                                            Finds directional frequency contribution to the heat capacity from direction and polarization

                                            @@ -661,14 +661,14 @@
                                            -property order[source]
                                            +property order[source]

                                            Order of the elastic tensor expansion, i. e. the order of the highest included set of elastic constants

                                            -thermal_expansion_coeff(structure, temperature, mode='debye')[source]
                                            +thermal_expansion_coeff(structure, temperature, mode='debye')[source]

                                            Gets thermal expansion coefficient from third-order constants.

                                            Parameters
                                            @@ -689,7 +689,7 @@
                                            -class NthOrderElasticTensor(input_array, check_rank=None, tol=0.0001)[source]
                                            +class NthOrderElasticTensor(input_array, check_rank=None, tol=0.0001)[source]

                                            Bases: pymatgen.core.tensors.Tensor

                                            An object representing an nth-order tensor expansion of the stress-strain constitutive equations

                                            @@ -704,12 +704,12 @@
                                            -GPa_to_eV_A3 = 0.006241509074460764[source]
                                            +GPa_to_eV_A3 = 0.006241509074460764[source]
                                            -calculate_stress(strain)[source]
                                            +calculate_stress(strain)[source]

                                            Calculate’s a given elastic tensor’s contribution to the stress using Einstein summation

                                            @@ -721,13 +721,13 @@
                                            -energy_density(strain, convert_GPa_to_eV=True)[source]
                                            +energy_density(strain, convert_GPa_to_eV=True)[source]

                                            Calculates the elastic energy density due to a strain

                                            -classmethod from_diff_fit(strains, stresses, eq_stress=None, order=2, tol=1e-10)[source]
                                            +classmethod from_diff_fit(strains, stresses, eq_stress=None, order=2, tol=1e-10)[source]
                                            Parameters
                                            -diff_fit(strains, stresses, eq_stress=None, order=2, tol=1e-10)[source]
                                            +diff_fit(strains, stresses, eq_stress=None, order=2, tol=1e-10)[source]

                                            nth order elastic constant fitting function based on central-difference derivatives with respect to distinct strain states. The algorithm is summarized as follows:

                                            @@ -804,7 +804,7 @@
                                            -find_eq_stress(strains, stresses, tol=1e-10)[source]
                                            +find_eq_stress(strains, stresses, tol=1e-10)[source]

                                            Finds stress corresponding to zero strain state in stress-strain list

                                            Parameters
                                            @@ -819,7 +819,7 @@
                                            -generate_pseudo(strain_states, order=3)[source]
                                            +generate_pseudo(strain_states, order=3)[source]

                                            Generates the pseudoinverse for a given set of strains.

                                            Parameters
                                            @@ -848,7 +848,7 @@
                                            -get_diff_coeff(hvec, n=1)[source]
                                            +get_diff_coeff(hvec, n=1)[source]

                                            Helper function to find difference coefficients of an derivative on an arbitrary mesh.

                                            @@ -863,7 +863,7 @@
                                            -get_strain_state_dict(strains, stresses, eq_stress=None, tol=1e-10, add_eq=True, sort=True)[source]
                                            +get_strain_state_dict(strains, stresses, eq_stress=None, tol=1e-10, add_eq=True, sort=True)[source]

                                            Creates a dictionary of voigt-notation stress-strain sets keyed by “strain state”, i. e. a tuple corresponding to the non-zero entries in ratios to the lowest nonzero value, @@ -893,7 +893,7 @@

                                            -get_symbol_list(rank, dim=6)[source]
                                            +get_symbol_list(rank, dim=6)[source]

                                            Returns a symbolic representation of the voigt-notation tensor that places identical symbols for entries related by index transposition, i. e. C_1121 = C_1211 etc.

                                            @@ -921,14 +921,14 @@
                                            -raise_error_if_unphysical(f)[source]
                                            +raise_error_if_unphysical(f)[source]

                                            Wrapper for functions or properties that should raise an error if tensor is unphysical.

                                            -subs(entry, cmap)[source]
                                            +subs(entry, cmap)[source]

                                            Sympy substitution function, primarily for the purposes of numpy vectorization

                                            diff --git a/docs/pymatgen.analysis.elasticity.html b/docs/pymatgen.analysis.elasticity.html index ca1eb598a42..42962daeb4d 100644 --- a/docs/pymatgen.analysis.elasticity.html +++ b/docs/pymatgen.analysis.elasticity.html @@ -4,7 +4,7 @@ - pymatgen.analysis.elasticity package — pymatgen 2022.5.18 documentation + pymatgen.analysis.elasticity package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                            - 2022.5.18 + 2022.5.18.1
                                            diff --git a/docs/pymatgen.analysis.elasticity.strain.html b/docs/pymatgen.analysis.elasticity.strain.html index 9f1c4c84fdb..4d9daff6d54 100644 --- a/docs/pymatgen.analysis.elasticity.strain.html +++ b/docs/pymatgen.analysis.elasticity.strain.html @@ -4,7 +4,7 @@ - pymatgen.analysis.elasticity.strain module — pymatgen 2022.5.18 documentation + pymatgen.analysis.elasticity.strain module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                            - 2022.5.18 + 2022.5.18.1
                                            @@ -121,7 +121,7 @@ generating deformed structure sets for further calculations.

                                            -class Deformation(deformation_gradient)[source]
                                            +class Deformation(deformation_gradient)[source]

                                            Bases: pymatgen.core.tensors.SquareTensor

                                            Subclass of SquareTensor that describes the deformation gradient tensor

                                            Create a Deformation object. Note that the constructor uses __new__ @@ -135,7 +135,7 @@

                                            -apply_to_structure(structure)[source]
                                            +apply_to_structure(structure)[source]

                                            Apply the deformation gradient to a structure.

                                            Parameters
                                            @@ -147,7 +147,7 @@
                                            -classmethod from_index_amount(matrixpos, amt)[source]
                                            +classmethod from_index_amount(matrixpos, amt)[source]

                                            Factory method for constructing a Deformation object from a matrix position and amount

                                            @@ -164,34 +164,34 @@
                                            -get_perturbed_indices(tol=1e-08)[source]
                                            +get_perturbed_indices(tol=1e-08)[source]

                                            Gets indices of perturbed elements of the deformation gradient, i. e. those that differ from the identity

                                            -property green_lagrange_strain[source]
                                            +property green_lagrange_strain[source]

                                            calculates the euler-lagrange strain from the deformation gradient

                                            -is_independent(tol=1e-08)[source]
                                            +is_independent(tol=1e-08)[source]

                                            checks to determine whether the deformation is independent

                                            -symbol = 'd'[source]
                                            +symbol = 'd'[source]
                                            -class DeformedStructureSet(structure, norm_strains=None, shear_strains=None, symmetry=False)[source]
                                            +class DeformedStructureSet(structure, norm_strains=None, shear_strains=None, symmetry=False)[source]

                                            Bases: collections.abc.Sequence

                                            class that generates a set of independently deformed structures that can be used to calculate linear stress-strain response

                                            @@ -213,7 +213,7 @@
                                            -class Strain(strain_matrix)[source]
                                            +class Strain(strain_matrix)[source]

                                            Bases: pymatgen.core.tensors.SquareTensor

                                            Subclass of SquareTensor that describes the Green-Lagrange strain tensor.

                                            Create a Strain object. Note that the constructor uses __new__ @@ -228,7 +228,7 @@

                                            -classmethod from_deformation(deformation)[source]
                                            +classmethod from_deformation(deformation)[source]

                                            Factory method that returns a Strain object from a deformation gradient

                                            @@ -240,7 +240,7 @@
                                            -classmethod from_index_amount(idx, amount)[source]
                                            +classmethod from_index_amount(idx, amount)[source]

                                            Like Deformation.from_index_amount, except generates a strain from the zero 3x3 tensor or voigt vector with the amount specified in the index location. Ensures @@ -258,18 +258,18 @@

                                            -get_deformation_matrix(shape='upper')[source]
                                            +get_deformation_matrix(shape='upper')[source]

                                            returns the deformation matrix

                                            -symbol = 'e'[source]
                                            +symbol = 'e'[source]
                                            -property von_mises_strain[source]
                                            +property von_mises_strain[source]

                                            Equivalent strain to Von Mises Stress

                                            @@ -277,7 +277,7 @@
                                            -convert_strain_to_deformation(strain, shape='upper')[source]
                                            +convert_strain_to_deformation(strain, shape='upper')[source]

                                            This function converts a strain to a deformation gradient that will produce that strain. Supports three methods:

                                            diff --git a/docs/pymatgen.analysis.elasticity.stress.html b/docs/pymatgen.analysis.elasticity.stress.html index dabad06865c..f595b10ee63 100644 --- a/docs/pymatgen.analysis.elasticity.stress.html +++ b/docs/pymatgen.analysis.elasticity.stress.html @@ -4,7 +4,7 @@ - pymatgen.analysis.elasticity.stress module — pymatgen 2022.5.18 documentation + pymatgen.analysis.elasticity.stress module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                            - 2022.5.18 + 2022.5.18.1
                                            @@ -120,7 +120,7 @@ calculate relevant properties of the stress tensor.

                                            -class Stress(stress_matrix)[source]
                                            +class Stress(stress_matrix)[source]

                                            Bases: pymatgen.core.tensors.SquareTensor

                                            This class extends SquareTensor as a representation of the stress

                                            @@ -135,7 +135,7 @@
                                            -property dev_principal_invariants[source]
                                            +property dev_principal_invariants[source]

                                            returns the principal invariants of the deviatoric stress tensor, which is calculated by finding the coefficients of the characteristic polynomial of the stress tensor minus the identity times the mean @@ -144,19 +144,19 @@

                                            -property deviator_stress[source]
                                            +property deviator_stress[source]

                                            returns the deviatoric component of the stress

                                            -property mean_stress[source]
                                            +property mean_stress[source]

                                            returns the mean stress

                                            -piola_kirchoff_1(def_grad)[source]
                                            +piola_kirchoff_1(def_grad)[source]

                                            calculates the first Piola-Kirchoff stress

                                            Parameters
                                            @@ -167,7 +167,7 @@
                                            -piola_kirchoff_2(def_grad)[source]
                                            +piola_kirchoff_2(def_grad)[source]

                                            calculates the second Piola-Kirchoff stress

                                            Parameters
                                            @@ -178,12 +178,12 @@
                                            -symbol = 's'[source]
                                            +symbol = 's'[source]
                                            -property von_mises[source]
                                            +property von_mises[source]

                                            returns the von mises stress

                                            diff --git a/docs/pymatgen.analysis.energy_models.html b/docs/pymatgen.analysis.energy_models.html index 1321c242703..abb47b291f0 100644 --- a/docs/pymatgen.analysis.energy_models.html +++ b/docs/pymatgen.analysis.energy_models.html @@ -4,7 +4,7 @@ - pymatgen.analysis.energy_models module — pymatgen 2022.5.18 documentation + pymatgen.analysis.energy_models module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                            - 2022.5.18 + 2022.5.18.1
                                            @@ -120,12 +120,12 @@ “energy” for any given structure.

                                            -class EnergyModel[source]
                                            +class EnergyModel[source]

                                            Bases: monty.json.MSONable

                                            Abstract structure filter class.

                                            -classmethod from_dict(d)[source]
                                            +classmethod from_dict(d)[source]
                                            Parameters

                                            d – Dict representation

                                            @@ -138,7 +138,7 @@
                                            -abstract get_energy(structure) → float[source]
                                            +abstract get_energy(structure) → float[source]
                                            Parameters

                                            structure – Structure

                                            @@ -153,7 +153,7 @@
                                            -class EwaldElectrostaticModel(real_space_cut=None, recip_space_cut=None, eta=None, acc_factor=8.0)[source]
                                            +class EwaldElectrostaticModel(real_space_cut=None, recip_space_cut=None, eta=None, acc_factor=8.0)[source]

                                            Bases: pymatgen.analysis.energy_models.EnergyModel

                                            Wrapper around EwaldSum to calculate the electrostatic energy.

                                            Initializes the model. Args have the same definitions as in @@ -177,7 +177,7 @@

                                            -as_dict()[source]
                                            +as_dict()[source]
                                            Returns

                                            MSONable dict

                                            @@ -187,7 +187,7 @@
                                            -get_energy(structure)[source]
                                            +get_energy(structure)[source]
                                            Parameters

                                            structure – Structure

                                            @@ -202,7 +202,7 @@
                                            -class IsingModel(j, max_radius)[source]
                                            +class IsingModel(j, max_radius)[source]

                                            Bases: pymatgen.analysis.energy_models.EnergyModel

                                            A very simple Ising model, with r^2 decay.

                                            @@ -215,7 +215,7 @@
                                            -as_dict()[source]
                                            +as_dict()[source]
                                            Returns

                                            MSONable dict

                                            @@ -225,7 +225,7 @@
                                            -get_energy(structure)[source]
                                            +get_energy(structure)[source]
                                            Parameters

                                            structure – Structure

                                            @@ -240,14 +240,14 @@
                                            -class NsitesModel[source]
                                            +class NsitesModel[source]

                                            Bases: pymatgen.analysis.energy_models.EnergyModel

                                            Sets the energy to the number of sites. More sites => higher “energy”. Used to rank structures from smallest number of sites to largest number of sites after enumeration.

                                            -as_dict()[source]
                                            +as_dict()[source]
                                            Returns

                                            MSONable dict

                                            @@ -257,7 +257,7 @@
                                            -get_energy(structure)[source]
                                            +get_energy(structure)[source]
                                            Parameters

                                            structure – Structure

                                            @@ -272,7 +272,7 @@
                                            -class SymmetryModel(symprec=0.1, angle_tolerance=5)[source]
                                            +class SymmetryModel(symprec=0.1, angle_tolerance=5)[source]

                                            Bases: pymatgen.analysis.energy_models.EnergyModel

                                            Sets the energy to the -ve of the spacegroup number. Higher symmetry => lower “energy”.

                                            @@ -288,7 +288,7 @@
                                            -as_dict()[source]
                                            +as_dict()[source]
                                            Returns

                                            MSONable dict

                                            @@ -298,7 +298,7 @@
                                            -get_energy(structure)[source]
                                            +get_energy(structure)[source]
                                            Parameters

                                            structure – Structure

                                            diff --git a/docs/pymatgen.analysis.eos.html b/docs/pymatgen.analysis.eos.html index fdfe711f985..beb0c7d4397 100644 --- a/docs/pymatgen.analysis.eos.html +++ b/docs/pymatgen.analysis.eos.html @@ -4,7 +4,7 @@ - pymatgen.analysis.eos module — pymatgen 2022.5.18 documentation + pymatgen.analysis.eos module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                            - 2022.5.18 + 2022.5.18.1
                                            @@ -120,7 +120,7 @@ @gmatteo but has since undergone major refactoring.

                                            -class Birch(volumes, energies)[source]
                                            +class Birch(volumes, energies)[source]

                                            Bases: pymatgen.analysis.eos.EOSBase

                                            Birch EOS.

                                            @@ -135,7 +135,7 @@
                                            -class BirchMurnaghan(volumes, energies)[source]
                                            +class BirchMurnaghan(volumes, energies)[source]

                                            Bases: pymatgen.analysis.eos.EOSBase

                                            BirchMurnaghan EOS

                                            @@ -150,7 +150,7 @@
                                            -class DeltaFactor(volumes, energies)[source]
                                            +class DeltaFactor(volumes, energies)[source]

                                            Bases: pymatgen.analysis.eos.PolynomialEOS

                                            Fitting a polynomial EOS using delta factor.

                                            @@ -163,7 +163,7 @@
                                            -fit(order=3)[source]
                                            +fit(order=3)[source]

                                            Overridden since this eos works with volume**(2/3) instead of volume.

                                            @@ -171,7 +171,7 @@
                                            -class EOS(eos_name='murnaghan')[source]
                                            +class EOS(eos_name='murnaghan')[source]

                                            Bases: object

                                            Convenient wrapper. Retained in its original state to ensure backward compatibility.

                                            @@ -206,12 +206,12 @@
                                            -MODELS = {'birch': <class 'pymatgen.analysis.eos.Birch'>, 'birch_murnaghan': <class 'pymatgen.analysis.eos.BirchMurnaghan'>, 'deltafactor': <class 'pymatgen.analysis.eos.DeltaFactor'>, 'murnaghan': <class 'pymatgen.analysis.eos.Murnaghan'>, 'numerical_eos': <class 'pymatgen.analysis.eos.NumericalEOS'>, 'pourier_tarantola': <class 'pymatgen.analysis.eos.PourierTarantola'>, 'vinet': <class 'pymatgen.analysis.eos.Vinet'>}[source]
                                            +MODELS = {'birch': <class 'pymatgen.analysis.eos.Birch'>, 'birch_murnaghan': <class 'pymatgen.analysis.eos.BirchMurnaghan'>, 'deltafactor': <class 'pymatgen.analysis.eos.DeltaFactor'>, 'murnaghan': <class 'pymatgen.analysis.eos.Murnaghan'>, 'numerical_eos': <class 'pymatgen.analysis.eos.NumericalEOS'>, 'pourier_tarantola': <class 'pymatgen.analysis.eos.PourierTarantola'>, 'vinet': <class 'pymatgen.analysis.eos.Vinet'>}[source]
                                            -fit(volumes, energies)[source]
                                            +fit(volumes, energies)[source]

                                            Fit energies as function of volumes.

                                            Parameters
                                            @@ -233,7 +233,7 @@
                                            -class EOSBase(volumes, energies)[source]
                                            +class EOSBase(volumes, energies)[source]

                                            Bases: object

                                            Abstract class that must be subcalssed by all equation of state implementations.

                                            @@ -247,14 +247,14 @@
                                            -property b0[source]
                                            +property b0[source]

                                            Returns the bulk modulus. Note: the units for the bulk modulus: unit of energy/unit of volume^3.

                                            -property b0_GPa[source]
                                            +property b0_GPa[source]

                                            Returns the bulk modulus in GPa. Note: This assumes that the energy and volumes are in eV and Ang^3

                                            @@ -264,26 +264,26 @@
                                            -property b1[source]
                                            +property b1[source]

                                            Returns the derivative of bulk modulus wrt pressure(dimensionless)

                                            -property e0[source]
                                            +property e0[source]

                                            Returns the min energy.

                                            -fit()[source]
                                            +fit()[source]

                                            Do the fitting. Does least square fitting. If you want to use custom fitting, must override this.

                                            -func(volume)[source]
                                            +func(volume)[source]

                                            The equation of state function with the parameters other than volume set to the ones obtained from fitting.

                                            @@ -298,7 +298,7 @@
                                            -plot(width=8, height=None, plt=None, dpi=None, **kwargs)[source]
                                            +plot(width=8, height=None, plt=None, dpi=None, **kwargs)[source]

                                            Plot the equation of state.

                                            Parameters
                                            @@ -321,7 +321,7 @@
                                            -plot_ax(ax=None, fontsize=12, **kwargs)[source]
                                            +plot_ax(ax=None, fontsize=12, **kwargs)[source]

                                            Plot the equation of state on axis ax

                                            Parameters
                                            @@ -382,7 +382,7 @@
                                            -property results[source]
                                            +property results[source]

                                            Returns a summary dict.

                                            Returns
                                            @@ -393,7 +393,7 @@
                                            -property v0[source]
                                            +property v0[source]

                                            Returns the minimum or the reference volume in Ang^3.

                                            @@ -401,14 +401,14 @@
                                            -exception EOSError[source]
                                            +exception EOSError[source]

                                            Bases: Exception

                                            Error class for EOS fitting.

                                            -class Murnaghan(volumes, energies)[source]
                                            +class Murnaghan(volumes, energies)[source]

                                            Bases: pymatgen.analysis.eos.EOSBase

                                            Murnaghan EOS.

                                            @@ -423,7 +423,7 @@
                                            -class NumericalEOS(volumes, energies)[source]
                                            +class NumericalEOS(volumes, energies)[source]

                                            Bases: pymatgen.analysis.eos.PolynomialEOS

                                            A numerical EOS.

                                            @@ -436,7 +436,7 @@
                                            -fit(min_ndata_factor=3, max_poly_order_factor=5, min_poly_order=2)[source]
                                            +fit(min_ndata_factor=3, max_poly_order_factor=5, min_poly_order=2)[source]

                                            Fit the input data to the ‘numerical eos’, the equation of state employed in the quasiharmonic Debye model described in the paper: 10.1103/PhysRevB.90.174107.

                                            @@ -469,7 +469,7 @@
                                            -class PolynomialEOS(volumes, energies)[source]
                                            +class PolynomialEOS(volumes, energies)[source]

                                            Bases: pymatgen.analysis.eos.EOSBase

                                            Derives from EOSBase. Polynomial based equations of states must subclass this.

                                            @@ -483,7 +483,7 @@
                                            -fit(order)[source]
                                            +fit(order)[source]

                                            Do polynomial fitting and set the parameters. Uses numpy polyfit.

                                            Parameters
                                            @@ -496,7 +496,7 @@
                                            -class PourierTarantola(volumes, energies)[source]
                                            +class PourierTarantola(volumes, energies)[source]

                                            Bases: pymatgen.analysis.eos.EOSBase

                                            PourierTarantola EOS

                                            @@ -511,7 +511,7 @@
                                            -class Vinet(volumes, energies)[source]
                                            +class Vinet(volumes, energies)[source]

                                            Bases: pymatgen.analysis.eos.EOSBase

                                            Vinet EOS.

                                            diff --git a/docs/pymatgen.analysis.ewald.html b/docs/pymatgen.analysis.ewald.html index 8bffc0afb71..1aab3ef90ad 100644 --- a/docs/pymatgen.analysis.ewald.html +++ b/docs/pymatgen.analysis.ewald.html @@ -4,7 +4,7 @@ - pymatgen.analysis.ewald module — pymatgen 2022.5.18 documentation + pymatgen.analysis.ewald module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                            - 2022.5.18 + 2022.5.18.1
                                            @@ -118,7 +118,7 @@

                                            This module provides classes for calculating the ewald sum of a structure.

                                            -class EwaldMinimizer(matrix, m_list, num_to_return=1, algo=0)[source]
                                            +class EwaldMinimizer(matrix, m_list, num_to_return=1, algo=0)[source]

                                            Bases: object

                                            This class determines the manipulations that will minimize an ewald matrix, given a list of possible manipulations. This class does not perform the @@ -153,7 +153,7 @@

                                            -ALGO_BEST_FIRST = 2[source]
                                            +ALGO_BEST_FIRST = 2[source]

                                            Slowly increases the speed (with the cost of decreasing accuracy) as the minimizer runs. Attempts to limit the run time to approximately 30 minutes.

                                            @@ -166,29 +166,29 @@
                                            -ALGO_COMPLETE = 1[source]
                                            +ALGO_COMPLETE = 1[source]
                                            -ALGO_FAST = 0[source]
                                            +ALGO_FAST = 0[source]
                                            -ALGO_TIME_LIMIT = 3[source]
                                            +ALGO_TIME_LIMIT = 3[source]
                                            -add_m_list(matrix_sum, m_list)[source]
                                            +add_m_list(matrix_sum, m_list)[source]

                                            This adds an m_list to the output_lists and updates the current minimum if the list is full.

                                            -best_case(matrix, m_list, indices_left)[source]
                                            +best_case(matrix, m_list, indices_left)[source]

                                            Computes a best case given a matrix and manipulation list.

                                            Parameters
                                            @@ -206,7 +206,7 @@
                                            -property best_m_list[source]
                                            +property best_m_list[source]

                                            Best m_list found.

                                            Type
                                            @@ -217,21 +217,21 @@
                                            -classmethod get_next_index(matrix, manipulation, indices_left)[source]
                                            +classmethod get_next_index(matrix, manipulation, indices_left)[source]

                                            Returns an index that should have the most negative effect on the matrix sum

                                            -minimize_matrix()[source]
                                            +minimize_matrix()[source]

                                            This method finds and returns the permutations that produce the lowest ewald sum calls recursive function to iterate through permutations

                                            -property minimized_sum[source]
                                            +property minimized_sum[source]

                                            Minimized sum

                                            Type
                                            @@ -242,7 +242,7 @@
                                            -property output_lists[source]
                                            +property output_lists[source]

                                            output lists.

                                            Type
                                            @@ -255,7 +255,7 @@
                                            -class EwaldSummation(structure, real_space_cut=None, recip_space_cut=None, eta=None, acc_factor=12.0, w=0.7071067811865475, compute_forces=False)[source]
                                            +class EwaldSummation(structure, real_space_cut=None, recip_space_cut=None, eta=None, acc_factor=12.0, w=0.7071067811865475, compute_forces=False)[source]

                                            Bases: monty.json.MSONable

                                            Calculates the electrostatic energy of a periodic array of charges using the Ewald technique.

                                            @@ -301,12 +301,12 @@
                                            -CONV_FACT = 14.39964547842567[source]
                                            +CONV_FACT = 14.39964547842567[source]
                                            -as_dict(verbosity: int = 0) → dict[source]
                                            +as_dict(verbosity: int = 0) → dict[source]

                                            Json-serialization dict representation of EwaldSummation.

                                            Parameters
                                            @@ -318,14 +318,14 @@
                                            -compute_partial_energy(removed_indices)[source]
                                            +compute_partial_energy(removed_indices)[source]

                                            Gives total ewald energy for certain sites being removed, i.e. zeroed out.

                                            -compute_sub_structure(sub_structure, tol=0.001)[source]
                                            +compute_sub_structure(sub_structure, tol=0.001)[source]

                                            Gives total ewald energy for an sub structure in the same lattice. The sub_structure must be a subset of the original structure, with possible different charges.

                                            @@ -344,7 +344,7 @@
                                            -property eta[source]
                                            +property eta[source]

                                            eta value used in Ewald summation.

                                            Type
                                            @@ -355,14 +355,14 @@
                                            -property forces[source]
                                            +property forces[source]

                                            The forces on each site as a Nx3 matrix. Each row corresponds to a site.

                                            -classmethod from_dict(d: dict, fmt: Optional[str] = None, **kwargs) → pymatgen.analysis.ewald.EwaldSummation[source]
                                            +classmethod from_dict(d: dict, fmt: Optional[str] = None, **kwargs) → pymatgen.analysis.ewald.EwaldSummation[source]

                                            Create an EwaldSummation instance from JSON-serialized dictionary.

                                            Parameters
                                            @@ -382,7 +382,7 @@
                                            -get_site_energy(site_index)[source]
                                            +get_site_energy(site_index)[source]

                                            Compute the energy for a single site in the structure

                                            Parameters
                                            @@ -396,39 +396,39 @@
                                            -property point_energy[source]
                                            +property point_energy[source]

                                            The point energy.

                                            -property point_energy_matrix[source]
                                            +property point_energy_matrix[source]

                                            The point space matrix. A diagonal matrix with the point terms for each site in the diagonal elements.

                                            -property real_space_energy[source]
                                            +property real_space_energy[source]

                                            The real space space energy.

                                            -property real_space_energy_matrix[source]
                                            +property real_space_energy_matrix[source]

                                            The real space energy matrix. Each matrix element (i, j) corresponds to the interaction energy between site i and site j in real space.

                                            -property reciprocal_space_energy[source]
                                            +property reciprocal_space_energy[source]

                                            The reciprocal space energy.

                                            -property reciprocal_space_energy_matrix[source]
                                            +property reciprocal_space_energy_matrix[source]

                                            The reciprocal space energy matrix. Each matrix element (i, j) corresponds to the interaction energy between site i and site j in reciprocal space.

                                            @@ -436,13 +436,13 @@
                                            -property total_energy[source]
                                            +property total_energy[source]

                                            The total energy.

                                            -property total_energy_matrix[source]
                                            +property total_energy_matrix[source]

                                            The total energy matrix. Each matrix element (i, j) corresponds to the total interaction energy between site i and site j.

                                            Note that this does not include the charged-cell energy, which is only important @@ -453,7 +453,7 @@

                                            -compute_average_oxidation_state(site)[source]
                                            +compute_average_oxidation_state(site)[source]

                                            Calculates the average oxidation state of a site

                                            Parameters
                                            diff --git a/docs/pymatgen.analysis.excitation.html b/docs/pymatgen.analysis.excitation.html index 9d183bdb85b..8b72e66bf26 100644 --- a/docs/pymatgen.analysis.excitation.html +++ b/docs/pymatgen.analysis.excitation.html @@ -4,7 +4,7 @@ - pymatgen.analysis.excitation module — pymatgen 2022.5.18 documentation + pymatgen.analysis.excitation module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                            - 2022.5.18 + 2022.5.18.1
                                            @@ -118,7 +118,7 @@

                                            This module defines an excitation spectrum class.

                                            -class ExcitationSpectrum(x, y)[source]
                                            +class ExcitationSpectrum(x, y)[source]

                                            Bases: pymatgen.core.spectrum.Spectrum

                                            Basic excitation spectrum object.

                                            @@ -131,12 +131,12 @@
                                            -XLABEL = 'Energy (eV)'[source]
                                            +XLABEL = 'Energy (eV)'[source]
                                            -YLABEL = 'Intensity'[source]
                                            +YLABEL = 'Intensity'[source]
                                            diff --git a/docs/pymatgen.analysis.ferroelectricity.html b/docs/pymatgen.analysis.ferroelectricity.html index 4194de34b55..621c3750fbb 100644 --- a/docs/pymatgen.analysis.ferroelectricity.html +++ b/docs/pymatgen.analysis.ferroelectricity.html @@ -4,7 +4,7 @@ - pymatgen.analysis.ferroelectricity package — pymatgen 2022.5.18 documentation + pymatgen.analysis.ferroelectricity package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                            - 2022.5.18 + 2022.5.18.1
                                            diff --git a/docs/pymatgen.analysis.ferroelectricity.polarization.html b/docs/pymatgen.analysis.ferroelectricity.polarization.html index 42c14cd3e34..6a05dc21c1e 100644 --- a/docs/pymatgen.analysis.ferroelectricity.polarization.html +++ b/docs/pymatgen.analysis.ferroelectricity.polarization.html @@ -4,7 +4,7 @@ - pymatgen.analysis.ferroelectricity.polarization module — pymatgen 2022.5.18 documentation + pymatgen.analysis.ferroelectricity.polarization module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                            - 2022.5.18 + 2022.5.18.1
                                            @@ -155,7 +155,7 @@ determine the spontaneous polarization because it serves as a reference point.

                                            -class EnergyTrend(energies)[source]
                                            +class EnergyTrend(energies)[source]

                                            Bases: object

                                            Class for fitting trends to energies.

                                            @@ -165,25 +165,25 @@
                                            -endpoints_minima(slope_cutoff=0.005)[source]
                                            +endpoints_minima(slope_cutoff=0.005)[source]

                                            Test if spline endpoints are at minima for a given slope cutoff.

                                            -max_spline_jump()[source]
                                            +max_spline_jump()[source]

                                            Get maximum difference between spline and energy trend.

                                            -smoothness()[source]
                                            +smoothness()[source]

                                            Get rms average difference between spline and energy trend.

                                            -spline()[source]
                                            +spline()[source]

                                            Fit spline to energy trend data.

                                            @@ -191,7 +191,7 @@
                                            -class Polarization(p_elecs, p_ions, structures, p_elecs_in_cartesian=True, p_ions_in_cartesian=False)[source]
                                            +class Polarization(p_elecs, p_ions, structures, p_elecs_in_cartesian=True, p_ions_in_cartesian=False)[source]

                                            Bases: object

                                            Class for recovering the same branch polarization for a set of polarization calculations along the nonpolar - polar distortion @@ -218,7 +218,7 @@

                                            -classmethod from_outcars_and_structures(outcars, structures, calc_ionic_from_zval=False)[source]
                                            +classmethod from_outcars_and_structures(outcars, structures, calc_ionic_from_zval=False)[source]

                                            Create Polarization object from list of Outcars and Structures in order of nonpolar to polar.

                                            Note, we recommend calculating the ionic dipole moment using calc_ionic @@ -228,14 +228,14 @@

                                            -get_lattice_quanta(convert_to_muC_per_cm2=True, all_in_polar=True)[source]
                                            +get_lattice_quanta(convert_to_muC_per_cm2=True, all_in_polar=True)[source]

                                            Returns the dipole / polarization quanta along a, b, and c for all structures.

                                            -get_pelecs_and_pions(convert_to_muC_per_cm2=False)[source]
                                            +get_pelecs_and_pions(convert_to_muC_per_cm2=False)[source]

                                            Get the electronic and ionic dipole moments / polarizations.

                                            convert_to_muC_per_cm2: Convert from electron * Angstroms to microCoulomb

                                            per centimeter**2

                                            @@ -245,20 +245,20 @@
                                            -get_polarization_change(convert_to_muC_per_cm2=True, all_in_polar=True)[source]
                                            +get_polarization_change(convert_to_muC_per_cm2=True, all_in_polar=True)[source]

                                            Get difference between nonpolar and polar same branch polarization.

                                            -get_polarization_change_norm(convert_to_muC_per_cm2=True, all_in_polar=True)[source]
                                            +get_polarization_change_norm(convert_to_muC_per_cm2=True, all_in_polar=True)[source]

                                            Get magnitude of difference between nonpolar and polar same branch polarization.

                                            -get_same_branch_polarization_data(convert_to_muC_per_cm2=True, all_in_polar=True)[source]
                                            +get_same_branch_polarization_data(convert_to_muC_per_cm2=True, all_in_polar=True)[source]

                                            Get same branch dipole moment (convert_to_muC_per_cm2=False) or polarization for given polarization data (convert_to_muC_per_cm2=True).

                                            Polarization is a lattice vector, meaning it is only defined modulo the @@ -295,20 +295,20 @@

                                            -max_spline_jumps(convert_to_muC_per_cm2=True, all_in_polar=True)[source]
                                            +max_spline_jumps(convert_to_muC_per_cm2=True, all_in_polar=True)[source]

                                            Get maximum difference between spline and same branch polarization data.

                                            -same_branch_splines(convert_to_muC_per_cm2=True, all_in_polar=True)[source]
                                            +same_branch_splines(convert_to_muC_per_cm2=True, all_in_polar=True)[source]

                                            Fit splines to same branch polarization. This is used to assess any jumps in the same branch polarizaiton.

                                            -smoothness(convert_to_muC_per_cm2=True, all_in_polar=True)[source]
                                            +smoothness(convert_to_muC_per_cm2=True, all_in_polar=True)[source]

                                            Get rms average difference between spline and same branch polarization data.

                                            @@ -316,7 +316,7 @@
                                            -class PolarizationLattice(lattice: ArrayLike | Lattice, species: Sequence[CompositionLike], coords: Sequence[ArrayLike], charge: float = None, validate_proximity: bool = False, to_unit_cell: bool = False, coords_are_cartesian: bool = False, site_properties: dict = None)[source]
                                            +class PolarizationLattice(lattice: ArrayLike | Lattice, species: Sequence[CompositionLike], coords: Sequence[ArrayLike], charge: float = None, validate_proximity: bool = False, to_unit_cell: bool = False, coords_are_cartesian: bool = False, site_properties: dict = None)[source]

                                            Bases: pymatgen.core.structure.Structure

                                            Why is a Lattice inheriting a structure? This is ridiculous.

                                            Create a periodic structure.

                                            @@ -358,7 +358,7 @@
                                            -get_nearest_site(coords, site, r=None)[source]
                                            +get_nearest_site(coords, site, r=None)[source]

                                            Given coords and a site, find closet site to coords. :param coords: Cartesian coords of center of sphere :type coords: 3x1 array @@ -375,7 +375,7 @@

                                            -calc_ionic(site, structure, zval)[source]
                                            +calc_ionic(site, structure, zval)[source]

                                            Calculate the ionic dipole moment using ZVAL from pseudopotential

                                            site: PeriodicSite structure: Structure @@ -385,7 +385,7 @@

                                            -get_total_ionic_dipole(structure, zval_dict)[source]
                                            +get_total_ionic_dipole(structure, zval_dict)[source]

                                            Get the total ionic dipole moment for a structure.

                                            structure: pymatgen Structure zval_dict: specie, zval dictionary pairs @@ -395,7 +395,7 @@

                                            -zval_dict_from_potcar(potcar)[source]
                                            +zval_dict_from_potcar(potcar)[source]

                                            Creates zval_dictionary for calculating the ionic polarization from Potcar object

                                            potcar: Potcar object

                                            diff --git a/docs/pymatgen.analysis.fragmenter.html b/docs/pymatgen.analysis.fragmenter.html index 71d919b40df..4ae599a1e58 100644 --- a/docs/pymatgen.analysis.fragmenter.html +++ b/docs/pymatgen.analysis.fragmenter.html @@ -4,7 +4,7 @@ - pymatgen.analysis.fragmenter module — pymatgen 2022.5.18 documentation + pymatgen.analysis.fragmenter module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                            - 2022.5.18 + 2022.5.18.1
                                            @@ -118,7 +118,7 @@

                                            Perform fragmentation of molecules.

                                            -class Fragmenter(molecule, edges=None, depth=1, open_rings=False, use_metal_edge_extender=False, opt_steps=10000, prev_unique_frag_dict=None, assume_previous_thoroughness=True)[source]
                                            +class Fragmenter(molecule, edges=None, depth=1, open_rings=False, use_metal_edge_extender=False, opt_steps=10000, prev_unique_frag_dict=None, assume_previous_thoroughness=True)[source]

                                            Bases: monty.json.MSONable

                                            Molecule fragmenter class.

                                            Standard constructor for molecule fragmentation

                                            @@ -162,7 +162,7 @@
                                            -open_ring(mol_graph, bond, opt_steps)[source]
                                            +open_ring(mol_graph, bond, opt_steps)[source]

                                            Function to actually open a ring using OpenBabel’s local opt. Given a molecule graph and a bond, convert the molecule graph into an OpenBabel molecule, remove the given bond, perform the local opt with the number of steps determined by diff --git a/docs/pymatgen.analysis.functional_groups.html b/docs/pymatgen.analysis.functional_groups.html index 03c4f4aab5f..2378b059279 100644 --- a/docs/pymatgen.analysis.functional_groups.html +++ b/docs/pymatgen.analysis.functional_groups.html @@ -4,7 +4,7 @@ - pymatgen.analysis.functional_groups module — pymatgen 2022.5.18 documentation + pymatgen.analysis.functional_groups module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                            - 2022.5.18 + 2022.5.18.1
                                            @@ -118,7 +118,7 @@

                                            Determine functional groups present in a Molecule.

                                            -class FunctionalGroupExtractor(molecule, optimize=False)[source]
                                            +class FunctionalGroupExtractor(molecule, optimize=False)[source]

                                            Bases: object

                                            This class is used to algorithmically parse a molecule (represented by an instance of pymatgen.analysis.graphs.MoleculeGraph) and determine arbitrary @@ -137,7 +137,7 @@

                                            -categorize_functional_groups(groups)[source]
                                            +categorize_functional_groups(groups)[source]

                                            Determine classes of functional groups present in a set.

                                            Parameters
                                            @@ -153,7 +153,7 @@
                                            -get_all_functional_groups(elements=None, func_groups=None, catch_basic=True)[source]
                                            +get_all_functional_groups(elements=None, func_groups=None, catch_basic=True)[source]

                                            Identify all functional groups (or all within a certain subset) in the molecule, combining the methods described above.

                                            @@ -177,7 +177,7 @@
                                            -get_basic_functional_groups(func_groups=None)[source]
                                            +get_basic_functional_groups(func_groups=None)[source]

                                            Identify functional groups that cannot be identified by the Ertl method of get_special_carbon and get_heteroatoms, such as benzene rings, methyl groups, and ethyl groups.

                                            @@ -197,7 +197,7 @@
                                            -get_heteroatoms(elements=None)[source]
                                            +get_heteroatoms(elements=None)[source]

                                            Identify non-H, non-C atoms in the MoleculeGraph, returning a list of their node indices.

                                            @@ -213,7 +213,7 @@
                                            -get_special_carbon(elements=None)[source]
                                            +get_special_carbon(elements=None)[source]

                                            Identify Carbon atoms in the MoleculeGraph that fit the characteristics defined Ertl (2017), returning a list of their node indices.

                                            @@ -239,7 +239,7 @@
                                            +link_marked_atoms(atoms)[source]

                                            Take a list of marked “interesting” atoms (heteroatoms, special carbons) and attempt to connect them, returning a list of disjoint groups of special atoms (and their connected hydrogens).

                                            diff --git a/docs/pymatgen.analysis.gb.grain.html b/docs/pymatgen.analysis.gb.grain.html index 0525775db2f..8f53501fea0 100644 --- a/docs/pymatgen.analysis.gb.grain.html +++ b/docs/pymatgen.analysis.gb.grain.html @@ -4,7 +4,7 @@ - pymatgen.analysis.gb.grain module — pymatgen 2022.5.18 documentation + pymatgen.analysis.gb.grain module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                            - 2022.5.18 + 2022.5.18.1
                                            @@ -119,7 +119,7 @@

                                            Module containing classes to generate grain boundaries.

                                            -class GrainBoundary(lattice, species, coords, rotation_axis, rotation_angle, gb_plane, join_plane, init_cell, vacuum_thickness, ab_shift, site_properties, oriented_unit_cell, validate_proximity=False, coords_are_cartesian=False)[source]
                                            +class GrainBoundary(lattice, species, coords, rotation_axis, rotation_angle, gb_plane, join_plane, init_cell, vacuum_thickness, ab_shift, site_properties, oriented_unit_cell, validate_proximity=False, coords_are_cartesian=False)[source]

                                            Bases: pymatgen.core.structure.Structure

                                            Subclass of Structure representing a GrainBoundary (gb) object. Implements additional attributes pertaining to gbs, but the @@ -185,7 +185,7 @@

                                            -as_dict()[source]
                                            +as_dict()[source]
                                            Returns

                                            Dictionary representation of GrainBoundary object

                                            @@ -195,19 +195,19 @@
                                            -property bottom_grain[source]
                                            +property bottom_grain[source]

                                            return the bottom grain (Structure) of the GB.

                                            -property coincidents[source]
                                            +property coincidents[source]

                                            return the a list of coincident sites.

                                            -copy()[source]
                                            +copy()[source]

                                            Convenience method to get a copy of the structure, with options to add site properties.

                                            @@ -220,7 +220,7 @@
                                            -classmethod from_dict(d)[source]
                                            +classmethod from_dict(d)[source]

                                            Generates a GrainBoundary object from a dictionary created by as_dict().

                                            Parameters
                                            @@ -234,7 +234,7 @@
                                            -get_sorted_structure(key=None, reverse=False)[source]
                                            +get_sorted_structure(key=None, reverse=False)[source]

                                            Get a sorted copy of the structure. The parameters have the same meaning as in list.sort. By default, sites are sorted by the electronegativity of the species. Note that Slab has to override this @@ -254,14 +254,14 @@

                                            -property sigma[source]
                                            +property sigma[source]

                                            This method returns the sigma value of the gb. If using ‘quick_gen’ to generate GB, this value is not valid.

                                            -property sigma_from_site_prop[source]
                                            +property sigma_from_site_prop[source]

                                            This method returns the sigma value of the gb from site properties. If the GB structure merge some atoms due to the atoms too closer with each other, this property will not work.

                                            @@ -269,7 +269,7 @@
                                            -property top_grain[source]
                                            +property top_grain[source]

                                            return the top grain (Structure) of the GB.

                                            @@ -277,7 +277,7 @@
                                            -class GrainBoundaryGenerator(initial_structure, symprec=0.1, angle_tolerance=1)[source]
                                            +class GrainBoundaryGenerator(initial_structure, symprec=0.1, angle_tolerance=1)[source]

                                            Bases: object

                                            This class is to generate grain boundaries (GBs) from bulk conventional cell (fcc, bcc can from the primitive cell), and works for Cubic, @@ -311,7 +311,7 @@

                                            angle_tolerance (float): Angle tolerance for symmetry finding.

                                            -static enum_possible_plane_cubic(plane_cutoff, r_axis, r_angle)[source]
                                            +static enum_possible_plane_cubic(plane_cutoff, r_axis, r_angle)[source]

                                            Find all possible plane combinations for GBs given a rotation axis and angle for cubic system, and classify them to different categories, including ‘Twist’, ‘Symmetric tilt’, ‘Normal tilt’, ‘Mixed’ GBs.

                                            @@ -339,7 +339,7 @@
                                            -static enum_sigma_cubic(cutoff, r_axis)[source]
                                            +static enum_sigma_cubic(cutoff, r_axis)[source]

                                            Find all possible sigma values and corresponding rotation angles within a sigma value cutoff with known rotation axis in cubic system. The algorithm for this code is from reference, Acta Cryst, A40,108(1984) @@ -368,7 +368,7 @@

                                            -static enum_sigma_hex(cutoff, r_axis, c2_a2_ratio)[source]
                                            +static enum_sigma_hex(cutoff, r_axis, c2_a2_ratio)[source]

                                            Find all possible sigma values and corresponding rotation angles within a sigma value cutoff with known rotation axis in hexagonal system. The algorithm for this code is from reference, Acta Cryst, A38,550(1982)

                                            @@ -408,7 +408,7 @@
                                            -static enum_sigma_ort(cutoff, r_axis, c2_b2_a2_ratio)[source]
                                            +static enum_sigma_ort(cutoff, r_axis, c2_b2_a2_ratio)[source]

                                            Find all possible sigma values and corresponding rotation angles within a sigma value cutoff with known rotation axis in orthorhombic system. The algorithm for this code is from reference, Scipta Metallurgica 27, 291(1992)

                                            @@ -442,7 +442,7 @@
                                            -static enum_sigma_rho(cutoff, r_axis, ratio_alpha)[source]
                                            +static enum_sigma_rho(cutoff, r_axis, ratio_alpha)[source]

                                            Find all possible sigma values and corresponding rotation angles within a sigma value cutoff with known rotation axis in rhombohedral system. The algorithm for this code is from reference, Acta Cryst, A45,505(1989).

                                            @@ -486,7 +486,7 @@
                                            -static enum_sigma_tet(cutoff, r_axis, c2_a2_ratio)[source]
                                            +static enum_sigma_tet(cutoff, r_axis, c2_a2_ratio)[source]

                                            Find all possible sigma values and corresponding rotation angles within a sigma value cutoff with known rotation axis in tetragonal system. The algorithm for this code is from reference, Acta Cryst, B46,117(1990)

                                            @@ -519,7 +519,7 @@
                                            -gb_from_parameters(rotation_axis, rotation_angle, expand_times=4, vacuum_thickness=0.0, ab_shift=[0, 0], normal=False, ratio=None, plane=None, max_search=20, tol_coi=1e-08, rm_ratio=0.7, quick_gen=False)[source]
                                            +gb_from_parameters(rotation_axis, rotation_angle, expand_times=4, vacuum_thickness=0.0, ab_shift=[0, 0], normal=False, ratio=None, plane=None, max_search=20, tol_coi=1e-08, rm_ratio=0.7, quick_gen=False)[source]
                                            Parameters
                                              @@ -584,7 +584,7 @@
                                              -get_ratio(max_denominator=5, index_none=None)[source]
                                              +get_ratio(max_denominator=5, index_none=None)[source]

                                              find the axial ratio needed for GB generator input. :param max_denominator: the maximum denominator for

                                              @@ -603,7 +603,7 @@
                                              -static get_rotation_angle_from_sigma(sigma, r_axis, lat_type='C', ratio=None)[source]
                                              +static get_rotation_angle_from_sigma(sigma, r_axis, lat_type='C', ratio=None)[source]

                                              Find all possible rotation angle for the given sigma value.

                                              Parameters
                                              @@ -650,7 +650,7 @@
                                              -static get_trans_mat(r_axis, angle, normal=False, trans_cry=array([[1., 0., 0.], [0., 1., 0.], [0., 0., 1.]]), lat_type='c', ratio=None, surface=None, max_search=20, quick_gen=False)[source]
                                              +static get_trans_mat(r_axis, angle, normal=False, trans_cry=array([[1., 0., 0.], [0., 1., 0.], [0., 0., 1.]]), lat_type='c', ratio=None, surface=None, max_search=20, quick_gen=False)[source]

                                              Find the two transformation matrix for each grain from given rotation axis, GB plane, rotation angle and corresponding ratio (see explanation for ratio below). @@ -735,7 +735,7 @@

                                              -static reduce_mat(mat, mag, r_matrix)[source]
                                              +static reduce_mat(mat, mag, r_matrix)[source]

                                              Reduce integer array mat’s determinant mag times by linear combination of its row vectors, so that the new array after rotation (r_matrix) is still an integer array

                                              @@ -755,7 +755,7 @@
                                              -static slab_from_csl(csl, surface, normal, trans_cry, max_search=20, quick_gen=False)[source]
                                              +static slab_from_csl(csl, surface, normal, trans_cry, max_search=20, quick_gen=False)[source]

                                              By linear operation of csl lattice vectors to get the best corresponding slab lattice. That is the area of a,b vectors (within the surface plane) is the smallest, the c vector first, has shortest length perpendicular @@ -785,7 +785,7 @@

                                              -static vec_to_surface(vec)[source]
                                              +static vec_to_surface(vec)[source]

                                              Transform a float vector to a surface miller index with integers.

                                              Parameters
                                              @@ -801,7 +801,7 @@
                                              -factors(n)[source]
                                              +factors(n)[source]

                                              Compute the factors of a integer. :param n: the input integer

                                              @@ -813,7 +813,7 @@
                                              -fix_pbc(structure, matrix=None)[source]
                                              +fix_pbc(structure, matrix=None)[source]

                                              Set all frac_coords of the input structure within [0,1].

                                              Parameters
                                              @@ -831,7 +831,7 @@
                                              -symm_group_cubic(mat)[source]
                                              +symm_group_cubic(mat)[source]

                                              obtain cubic symmetric equivalents of the list of vectors.

                                              diff --git a/docs/pymatgen.analysis.gb.html b/docs/pymatgen.analysis.gb.html index 733c916cab0..b2f657cd399 100644 --- a/docs/pymatgen.analysis.gb.html +++ b/docs/pymatgen.analysis.gb.html @@ -4,7 +4,7 @@ - pymatgen.analysis.gb package — pymatgen 2022.5.18 documentation + pymatgen.analysis.gb package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                              - 2022.5.18 + 2022.5.18.1
                                              diff --git a/docs/pymatgen.analysis.graphs.html b/docs/pymatgen.analysis.graphs.html index fe9f5ff7e38..ce3322f7469 100644 --- a/docs/pymatgen.analysis.graphs.html +++ b/docs/pymatgen.analysis.graphs.html @@ -4,7 +4,7 @@ - pymatgen.analysis.graphs module — pymatgen 2022.5.18 documentation + pymatgen.analysis.graphs module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                              - 2022.5.18 + 2022.5.18.1
                                              @@ -118,36 +118,36 @@

                                              Module for graph representations of crystals and molecules.

                                              -class ConnectedSite(site, jimage, index, weight, dist)[source]
                                              +class ConnectedSite(site, jimage, index, weight, dist)[source]

                                              Bases: tuple

                                              Create new instance of ConnectedSite(site, jimage, index, weight, dist)

                                              -dist[source]
                                              +dist[source]

                                              Alias for field number 4

                                              -index[source]
                                              +index[source]

                                              Alias for field number 2

                                              -jimage[source]
                                              +jimage[source]

                                              Alias for field number 1

                                              -site[source]
                                              +site[source]

                                              Alias for field number 0

                                              -weight[source]
                                              +weight[source]

                                              Alias for field number 3

                                              @@ -155,7 +155,7 @@
                                              -exception MolGraphSplitError[source]
                                              +exception MolGraphSplitError[source]

                                              Bases: Exception

                                              Raised when a molecule graph is failed to split into two disconnected subgraphs

                                              @@ -163,7 +163,7 @@
                                              -class MoleculeGraph(molecule, graph_data=None)[source]
                                              +class MoleculeGraph(molecule, graph_data=None)[source]

                                              Bases: monty.json.MSONable

                                              This is a class for annotating a Molecule with bond information, stored in the form of a graph. A “bond” does @@ -192,7 +192,7 @@

                                              -add_edge(from_index, to_index, weight=None, warn_duplicates=True, edge_properties=None)[source]
                                              +add_edge(from_index, to_index, weight=None, warn_duplicates=True, edge_properties=None)[source]

                                              Add edge to graph.

                                              Since physically a ‘bond’ (or other connection between sites) doesn’t have a direction, from_index, @@ -220,7 +220,7 @@

                                              -alter_edge(from_index, to_index, new_weight=None, new_edge_properties=None)[source]
                                              +alter_edge(from_index, to_index, new_weight=None, new_edge_properties=None)[source]

                                              Alters either the weight or the edge_properties of an edge in the MoleculeGraph.

                                              @@ -246,7 +246,7 @@
                                              -as_dict()[source]
                                              +as_dict()[source]

                                              As in :Class: pymatgen.core.Molecule except with using to_dict_of_dicts from NetworkX to store graph information.

                                              @@ -254,7 +254,7 @@
                                              -break_edge(from_index, to_index, allow_reverse=False)[source]
                                              +break_edge(from_index, to_index, allow_reverse=False)[source]

                                              Remove an edge from the MoleculeGraph

                                              Parameters
                                              @@ -274,7 +274,7 @@
                                              -build_unique_fragments()[source]
                                              +build_unique_fragments()[source]

                                              Find all possible fragment combinations of the MoleculeGraphs (in other words, all connected induced subgraphs)

                                              @@ -286,7 +286,7 @@
                                              -diff(other, strict=True)[source]
                                              +diff(other, strict=True)[source]

                                              Compares two MoleculeGraphs. Returns dict with keys ‘self’, ‘other’, ‘both’ with edges that are present in only one MoleculeGraph (‘self’ and @@ -320,7 +320,7 @@

                                              -draw_graph_to_file(filename='graph', diff=None, hide_unconnected_nodes=False, hide_image_edges=True, edge_colors=False, node_labels=False, weight_labels=False, image_labels=False, color_scheme='VESTA', keep_dot=False, algo='fdp')[source]
                                              +draw_graph_to_file(filename='graph', diff=None, hide_unconnected_nodes=False, hide_image_edges=True, edge_colors=False, node_labels=False, weight_labels=False, image_labels=False, color_scheme='VESTA', keep_dot=False, algo='fdp')[source]

                                              Draws graph using GraphViz.

                                              The networkx graph object itself can also be drawn with networkx’s in-built graph drawing methods, but @@ -367,7 +367,7 @@

                                              -property edge_weight_name[source]
                                              +property edge_weight_name[source]

                                              Name of the edge weight property of graph

                                              Type
                                              @@ -378,7 +378,7 @@
                                              -property edge_weight_unit[source]
                                              +property edge_weight_unit[source]

                                              Units of the edge weight property of graph

                                              Type
                                              @@ -389,7 +389,7 @@
                                              -find_rings(including=None)[source]
                                              +find_rings(including=None)[source]

                                              Find ring structures in the MoleculeGraph.

                                              Parameters
                                              @@ -410,7 +410,7 @@
                                              -classmethod from_dict(d)[source]
                                              +classmethod from_dict(d)[source]

                                              As in :Class: pymatgen.core.Molecule except restoring graphs using from_dict_of_dicts from NetworkX to restore graph information.

                                              @@ -418,7 +418,7 @@
                                              -get_connected_sites(n)[source]
                                              +get_connected_sites(n)[source]

                                              Returns a named tuple of neighbors of site n: periodic_site, jimage, index, weight. Index is the index of the corresponding site @@ -434,7 +434,7 @@

                                              -get_coordination_of_site(n)[source]
                                              +get_coordination_of_site(n)[source]

                                              Returns the number of neighbors of site n. In graph terms, simply returns degree of node corresponding to site n. @@ -444,7 +444,7 @@

                                              -get_disconnected_fragments()[source]
                                              +get_disconnected_fragments()[source]

                                              Determine if the MoleculeGraph is connected. If it is not, separate the MoleculeGraph into different MoleculeGraphs, where each resulting MoleculeGraph is a disconnected subgraph of the original. @@ -460,7 +460,7 @@

                                              -insert_node(i, species, coords, validate_proximity=False, site_properties=None, edges=None)[source]
                                              +insert_node(i, species, coords, validate_proximity=False, site_properties=None, edges=None)[source]

                                              A wrapper around Molecule.insert(), which also incorporates the new site into the MoleculeGraph.

                                              @@ -489,7 +489,7 @@
                                              -isomorphic_to(other)[source]
                                              +isomorphic_to(other)[source]

                                              Checks if the graphs of two MoleculeGraphs are isomorphic to one another. In order to prevent problems with misdirected edges, both graphs are converted into undirected nx.Graph objects.

                                              @@ -505,7 +505,7 @@
                                              -property name[source]
                                              +property name[source]

                                              Name of graph

                                              Type
                                              @@ -516,7 +516,7 @@
                                              -remove_nodes(indices)[source]
                                              +remove_nodes(indices)[source]

                                              A wrapper for Molecule.remove_sites().

                                              Parameters
                                              @@ -531,7 +531,7 @@
                                              -replace_group(index, func_grp, strategy, bond_order=1, graph_dict=None, strategy_params=None)[source]
                                              +replace_group(index, func_grp, strategy, bond_order=1, graph_dict=None, strategy_params=None)[source]

                                              Builds off of Molecule.substitute and MoleculeGraph.substitute_group to replace a functional group in self.molecule with a functional group. This method also amends self.graph to incorporate the new functional @@ -578,7 +578,7 @@

                                              -set_node_attributes()[source]
                                              +set_node_attributes()[source]

                                              Replicates molecule site properties (specie, coords, etc.) in the MoleculeGraph.

                                              @@ -590,7 +590,7 @@
                                              -sort(key: Optional[Callable[[pymatgen.core.structure.Molecule], float]] = None, reverse: bool = False) → None[source]
                                              +sort(key: Optional[Callable[[pymatgen.core.structure.Molecule], float]] = None, reverse: bool = False) → None[source]

                                              Same as Molecule.sort(), also remaps nodes in graph.

                                              Parameters
                                              @@ -604,7 +604,7 @@
                                              -split_molecule_subgraphs(bonds, allow_reverse=False, alterations=None)[source]
                                              +split_molecule_subgraphs(bonds, allow_reverse=False, alterations=None)[source]

                                              Split MoleculeGraph into two or more MoleculeGraphs by breaking a set of bonds. This function uses MoleculeGraph.break_edge repeatedly to create @@ -645,7 +645,7 @@

                                              -substitute_group(index, func_grp, strategy, bond_order=1, graph_dict=None, strategy_params=None)[source]
                                              +substitute_group(index, func_grp, strategy, bond_order=1, graph_dict=None, strategy_params=None)[source]

                                              Builds off of Molecule.substitute to replace an atom in self.molecule with a functional group. This method also amends self.graph to incorporate the new functional group.

                                              @@ -698,7 +698,7 @@
                                              -static with_edges(molecule, edges)[source]
                                              +static with_edges(molecule, edges)[source]

                                              Constructor for MoleculeGraph, using pre-existing or pre-defined edges with optional edge parameters.

                                              @@ -719,7 +719,7 @@
                                              -classmethod with_empty_graph(molecule, name='bonds', edge_weight_name=None, edge_weight_units=None)[source]
                                              +classmethod with_empty_graph(molecule, name='bonds', edge_weight_name=None, edge_weight_units=None)[source]

                                              Constructor for MoleculeGraph, returns a MoleculeGraph object with an empty graph (no edges, only nodes defined that correspond to Sites in Molecule).

                                              @@ -741,7 +741,7 @@
                                              -static with_local_env_strategy(molecule, strategy)[source]
                                              +static with_local_env_strategy(molecule, strategy)[source]

                                              Constructor for MoleculeGraph, using a strategy from :Class: pymatgen.analysis.local_env.

                                              @@ -762,7 +762,7 @@
                                              -class StructureGraph(structure, graph_data=None)[source]
                                              +class StructureGraph(structure, graph_data=None)[source]

                                              Bases: monty.json.MSONable

                                              This is a class for annotating a Structure with bond information, stored in the form of a graph. A “bond” does @@ -794,7 +794,7 @@

                                              see as_dict method for format)

                                              -add_edge(from_index, to_index, from_jimage=(0, 0, 0), to_jimage=None, weight=None, warn_duplicates=True, edge_properties=None)[source]
                                              +add_edge(from_index, to_index, from_jimage=(0, 0, 0), to_jimage=None, weight=None, warn_duplicates=True, edge_properties=None)[source]

                                              Add edge to graph.

                                              Since physically a ‘bond’ (or other connection between sites) doesn’t have a direction, from_index, @@ -825,7 +825,7 @@

                                              -alter_edge(from_index, to_index, to_jimage=None, new_weight=None, new_edge_properties=None)[source]
                                              +alter_edge(from_index, to_index, to_jimage=None, new_weight=None, new_edge_properties=None)[source]

                                              Alters either the weight or the edge_properties of an edge in the StructureGraph.

                                              @@ -852,7 +852,7 @@
                                              -as_dict()[source]
                                              +as_dict()[source]

                                              As in :Class: pymatgen.core.Structure except with using to_dict_of_dicts from NetworkX to store graph information.

                                              @@ -860,7 +860,7 @@
                                              -break_edge(from_index, to_index, to_jimage=None, allow_reverse=False)[source]
                                              +break_edge(from_index, to_index, to_jimage=None, allow_reverse=False)[source]

                                              Remove an edge from the StructureGraph. If no image is given, this method will fail.

                                              Parameters
                                              @@ -881,7 +881,7 @@
                                              -diff(other, strict=True)[source]
                                              +diff(other, strict=True)[source]

                                              Compares two StructureGraphs. Returns dict with keys ‘self’, ‘other’, ‘both’ with edges that are present in only one StructureGraph (‘self’ and @@ -915,7 +915,7 @@

                                              -draw_graph_to_file(filename='graph', diff=None, hide_unconnected_nodes=False, hide_image_edges=True, edge_colors=False, node_labels=False, weight_labels=False, image_labels=False, color_scheme='VESTA', keep_dot=False, algo='fdp')[source]
                                              +draw_graph_to_file(filename='graph', diff=None, hide_unconnected_nodes=False, hide_image_edges=True, edge_colors=False, node_labels=False, weight_labels=False, image_labels=False, color_scheme='VESTA', keep_dot=False, algo='fdp')[source]

                                              Draws graph using GraphViz.

                                              The networkx graph object itself can also be drawn with networkx’s in-built graph drawing methods, but @@ -962,7 +962,7 @@

                                              -property edge_weight_name[source]
                                              +property edge_weight_name[source]

                                              Name of the edge weight property of graph

                                              Type
                                              @@ -973,7 +973,7 @@
                                              -property edge_weight_unit[source]
                                              +property edge_weight_unit[source]

                                              Units of the edge weight property of graph

                                              Type
                                              @@ -984,7 +984,7 @@
                                              -classmethod from_dict(d)[source]
                                              +classmethod from_dict(d)[source]

                                              As in :Class: pymatgen.core.Structure except restoring graphs using from_dict_of_dicts from NetworkX to restore graph information.

                                              @@ -992,7 +992,7 @@
                                              -get_connected_sites(n, jimage=(0, 0, 0))[source]
                                              +get_connected_sites(n, jimage=(0, 0, 0))[source]

                                              Returns a named tuple of neighbors of site n: periodic_site, jimage, index, weight. Index is the index of the corresponding site @@ -1008,7 +1008,7 @@

                                              -get_coordination_of_site(n)[source]
                                              +get_coordination_of_site(n)[source]

                                              Returns the number of neighbors of site n. In graph terms, simply returns degree of node corresponding to site n. @@ -1018,7 +1018,7 @@

                                              -get_subgraphs_as_molecules(use_weights=False)[source]
                                              +get_subgraphs_as_molecules(use_weights=False)[source]

                                              Retrieve subgraphs as molecules, useful for extracting molecules from periodic crystals.

                                              Will only return unique molecules, not any duplicates @@ -1041,7 +1041,7 @@

                                              -insert_node(i, species, coords, coords_are_cartesian=False, validate_proximity=False, site_properties=None, edges=None)[source]
                                              +insert_node(i, species, coords, coords_are_cartesian=False, validate_proximity=False, site_properties=None, edges=None)[source]

                                              A wrapper around Molecule.insert(), which also incorporates the new site into the MoleculeGraph.

                                              @@ -1072,7 +1072,7 @@
                                              -property name[source]
                                              +property name[source]

                                              Name of graph

                                              Type
                                              @@ -1083,7 +1083,7 @@
                                              -remove_nodes(indices)[source]
                                              +remove_nodes(indices)[source]

                                              A wrapper for Molecule.remove_sites().

                                              Parameters
                                              @@ -1098,7 +1098,7 @@
                                              -set_node_attributes()[source]
                                              +set_node_attributes()[source]

                                              Gives each node a “specie” and a “coords” attribute, updated with the current species and coordinates.

                                              @@ -1110,7 +1110,7 @@
                                              -sort(key=None, reverse=False)[source]
                                              +sort(key=None, reverse=False)[source]

                                              Same as Structure.sort(), also remaps nodes in graph. :param key: :param reverse: @@ -1119,7 +1119,7 @@

                                              -substitute_group(index, func_grp, strategy, bond_order=1, graph_dict=None, strategy_params=None)[source]
                                              +substitute_group(index, func_grp, strategy, bond_order=1, graph_dict=None, strategy_params=None)[source]

                                              Builds off of Structure.substitute to replace an atom in self.structure with a functional group. This method also amends self.graph to incorporate the new functional group.

                                              @@ -1172,7 +1172,7 @@
                                              -property types_and_weights_of_connections[source]
                                              +property types_and_weights_of_connections[source]

                                              Extract a dictionary summarizing the types and weights of edges in the graph.

                                              @@ -1187,7 +1187,7 @@
                                              -types_of_coordination_environments(anonymous=False)[source]
                                              +types_of_coordination_environments(anonymous=False)[source]

                                              Extract information on the different co-ordination environments present in the graph.

                                              @@ -1204,7 +1204,7 @@
                                              -property weight_statistics[source]
                                              +property weight_statistics[source]

                                              Extract a statistical summary of edge weights present in the graph.

                                              @@ -1217,7 +1217,7 @@
                                              -static with_edges(structure, edges)[source]
                                              +static with_edges(structure, edges)[source]

                                              Constructor for MoleculeGraph, using pre-existing or pre-defined edges with optional edge parameters.

                                              @@ -1239,7 +1239,7 @@
                                              -classmethod with_empty_graph(structure, name='bonds', edge_weight_name=None, edge_weight_units=None)[source]
                                              +classmethod with_empty_graph(structure, name='bonds', edge_weight_name=None, edge_weight_units=None)[source]

                                              Constructor for StructureGraph, returns a StructureGraph object with an empty graph (no edges, only nodes defined that correspond to Sites in Structure).

                                              @@ -1261,7 +1261,7 @@
                                              -static with_local_env_strategy(structure, strategy, weights=False)[source]
                                              +static with_local_env_strategy(structure, strategy, weights=False)[source]

                                              Constructor for StructureGraph, using a strategy from :Class: pymatgen.analysis.local_env.

                                              diff --git a/docs/pymatgen.analysis.hhi.html b/docs/pymatgen.analysis.hhi.html index 4bf38e75040..ab877387119 100644 --- a/docs/pymatgen.analysis.hhi.html +++ b/docs/pymatgen.analysis.hhi.html @@ -4,7 +4,7 @@ - pymatgen.analysis.hhi module — pymatgen 2022.5.18 documentation + pymatgen.analysis.hhi module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                              - 2022.5.18 + 2022.5.18.1
                                              diff --git a/docs/pymatgen.analysis.html b/docs/pymatgen.analysis.html index f6333d47f6e..f7bcf3e9f72 100644 --- a/docs/pymatgen.analysis.html +++ b/docs/pymatgen.analysis.html @@ -4,7 +4,7 @@ - pymatgen.analysis namespace — pymatgen 2022.5.18 documentation + pymatgen.analysis namespace — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                              - 2022.5.18 + 2022.5.18.1
                                              diff --git a/docs/pymatgen.analysis.interface.html b/docs/pymatgen.analysis.interface.html index ba7e67a90a8..e4dca74e103 100644 --- a/docs/pymatgen.analysis.interface.html +++ b/docs/pymatgen.analysis.interface.html @@ -4,7 +4,7 @@ - pymatgen.analysis.interface module — pymatgen 2022.5.18 documentation + pymatgen.analysis.interface module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                              - 2022.5.18 + 2022.5.18.1
                                              diff --git a/docs/pymatgen.analysis.interface_reactions.html b/docs/pymatgen.analysis.interface_reactions.html index 45b21ca41bd..ef373401138 100644 --- a/docs/pymatgen.analysis.interface_reactions.html +++ b/docs/pymatgen.analysis.interface_reactions.html @@ -4,7 +4,7 @@ - pymatgen.analysis.interface_reactions module — pymatgen 2022.5.18 documentation + pymatgen.analysis.interface_reactions module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                              - 2022.5.18 + 2022.5.18.1
                                              @@ -128,7 +128,7 @@ Nature Reviews Materials, 5(2), 105–126. https://doi.org/10.1038/s41578-019-0157-5

                                              -class GrandPotentialInterfacialReactivity(c1: pymatgen.core.composition.Composition, c2: pymatgen.core.composition.Composition, grand_pd: pymatgen.analysis.phase_diagram.GrandPotentialPhaseDiagram, pd_non_grand: pymatgen.analysis.phase_diagram.PhaseDiagram, include_no_mixing_energy: bool = False, norm: bool = True, use_hull_energy: bool = True)[source]
                                              +class GrandPotentialInterfacialReactivity(c1: pymatgen.core.composition.Composition, c2: pymatgen.core.composition.Composition, grand_pd: pymatgen.analysis.phase_diagram.GrandPotentialPhaseDiagram, pd_non_grand: pymatgen.analysis.phase_diagram.PhaseDiagram, include_no_mixing_energy: bool = False, norm: bool = True, use_hull_energy: bool = True)[source]

                                              Bases: pymatgen.analysis.interface_reactions.InterfacialReactivity

                                              Extends upon InterfacialReactivity to allow for modelling possible reactions at the interface between two solids in the presence of an open element. The @@ -162,7 +162,7 @@

                                              -get_no_mixing_energy()[source]
                                              +get_no_mixing_energy()[source]

                                              Generates the opposite number of energy above grand potential convex hull for both reactants.

                                              @@ -176,7 +176,7 @@
                                              -class InterfacialReactivity(c1: pymatgen.core.composition.Composition, c2: pymatgen.core.composition.Composition, pd: pymatgen.analysis.phase_diagram.PhaseDiagram, norm: bool = True, use_hull_energy: bool = False, **kwargs)[source]
                                              +class InterfacialReactivity(c1: pymatgen.core.composition.Composition, c2: pymatgen.core.composition.Composition, pd: pymatgen.analysis.phase_diagram.PhaseDiagram, norm: bool = True, use_hull_energy: bool = False, **kwargs)[source]

                                              Bases: monty.json.MSONable

                                              Class for modeling an interface between two solids and its possible reactions. The two reactants are provided as Composition objects (c1 and c2), along with the @@ -212,12 +212,12 @@

                                              -EV_TO_KJ_PER_MOL = 96.4853[source]
                                              +EV_TO_KJ_PER_MOL = 96.4853[source]
                                              -classmethod get_chempot_correction(element: str, temp: float, pres: float)[source]
                                              +classmethod get_chempot_correction(element: str, temp: float, pres: float)[source]

                                              Get the normalized correction term Δμ for chemical potential of a gas phase consisting of element at given temperature and pressure, referenced to that in the standard state (T_std = 298.15 K, @@ -241,7 +241,7 @@

                                              -get_critical_original_kink_ratio()[source]
                                              +get_critical_original_kink_ratio()[source]

                                              Returns a list of molar mixing ratio for each kink between ORIGINAL (instead of processed) reactant compositions. This is the same list as mixing ratio obtained from get_kinks method @@ -256,14 +256,14 @@

                                              -get_dataframe() → pandas.core.frame.DataFrame[source]
                                              +get_dataframe() → pandas.core.frame.DataFrame[source]

                                              Returns a pandas DataFrame representation of the data produced by the get_kinks() method.

                                              -get_kinks() → list[tuple[int, float, float, pymatgen.analysis.reaction_calculator.Reaction, float]][source]
                                              +get_kinks() → list[tuple[int, float, float, pymatgen.analysis.reaction_calculator.Reaction, float]][source]

                                              Finds all the kinks in mixing ratio where reaction products changes along the tie-line of composition self.c1 and composition self.c2.

                                              @@ -279,7 +279,7 @@
                                              -property labels[source]
                                              +property labels[source]

                                              Returns a dictionary containing kink information: {index: ‘x= mixing_ratio energy= reaction_energy reaction_equation’}. E.g., {1: ‘x= 0.0 energy = 0.0 Mn -> Mn’,

                                              @@ -291,7 +291,7 @@
                                              -property minimum[source]
                                              +property minimum[source]

                                              Finds the minimum reaction energy E_min and corresponding mixing ratio x_min.

                                              @@ -303,7 +303,7 @@
                                              -plot(backend: Literal['plotly', 'matplotlib'] = 'plotly') → Figure | plt.Figure[source]
                                              +plot(backend: Literal['plotly', 'matplotlib'] = 'plotly') → Figure | plt.Figure[source]

                                              Plots reaction energy as a function of mixing ratio x in self.c1 - self.c2 tie line.

                                              @@ -319,7 +319,7 @@
                                              -property products[source]
                                              +property products[source]

                                              List of formulas of potential products. E.g., [‘Li’,’O2’,’Mn’].

                                              diff --git a/docs/pymatgen.analysis.interfaces.coherent_interfaces.html b/docs/pymatgen.analysis.interfaces.coherent_interfaces.html index f3ddd3b2d0b..c9a0c472e5d 100644 --- a/docs/pymatgen.analysis.interfaces.coherent_interfaces.html +++ b/docs/pymatgen.analysis.interfaces.coherent_interfaces.html @@ -4,7 +4,7 @@ - pymatgen.analysis.interfaces.coherent_interfaces module — pymatgen 2022.5.18 documentation + pymatgen.analysis.interfaces.coherent_interfaces module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                              - 2022.5.18 + 2022.5.18.1
                                              @@ -119,7 +119,7 @@

                                              This module provides classes to store, generate, and manipulate material interfaces.

                                              -class CoherentInterfaceBuilder(substrate_structure: Structure, film_structure: Structure, film_miller: tuple[int, int, int], substrate_miller: tuple[int, int, int], zslgen: ZSLGenerator | None = None)[source]
                                              +class CoherentInterfaceBuilder(substrate_structure: Structure, film_structure: Structure, film_miller: tuple[int, int, int], substrate_miller: tuple[int, int, int], zslgen: ZSLGenerator | None = None)[source]

                                              Bases: object

                                              This class constructs the coherent interfaces between two crystalline slabs Coherency is defined by matching lattices not sub-planes.

                                              @@ -136,7 +136,7 @@
                                              -get_interfaces(termination: tuple[str, str], gap: float = 2.0, vacuum_over_film: float = 20.0, film_thickness: float | int = 1, substrate_thickness: float | int = 1, in_layers: bool = True) → Iterator[Interface][source]
                                              +get_interfaces(termination: tuple[str, str], gap: float = 2.0, vacuum_over_film: float = 20.0, film_thickness: float | int = 1, substrate_thickness: float | int = 1, in_layers: bool = True) → Iterator[Interface][source]

                                              Generates interface structures given the film and substrate structure as well as the desired terminations

                                              @@ -157,20 +157,20 @@
                                              -from_2d_to_3d(mat: numpy.ndarray) → numpy.ndarray[source]
                                              +from_2d_to_3d(mat: numpy.ndarray) → numpy.ndarray[source]

                                              Converts a 2D matrix to a 3D matrix

                                              -get_2d_transform(start: numpy.ndarray, end: numpy.ndarray) → numpy.ndarray[source]
                                              +get_2d_transform(start: numpy.ndarray, end: numpy.ndarray) → numpy.ndarray[source]

                                              Gets a 2d transformation matrix that converts start to end

                                              -get_rot_3d_for_2d(film_matrix, sub_matrix) → numpy.ndarray[source]
                                              +get_rot_3d_for_2d(film_matrix, sub_matrix) → numpy.ndarray[source]

                                              Finds a trasnformation matrix that will rotate and strain the film to the subtrate while preserving the c-axis

                                              diff --git a/docs/pymatgen.analysis.interfaces.html b/docs/pymatgen.analysis.interfaces.html index d283b03258e..8bf71d2c3ae 100644 --- a/docs/pymatgen.analysis.interfaces.html +++ b/docs/pymatgen.analysis.interfaces.html @@ -4,7 +4,7 @@ - pymatgen.analysis.interfaces package — pymatgen 2022.5.18 documentation + pymatgen.analysis.interfaces package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                              - 2022.5.18 + 2022.5.18.1
                                              diff --git a/docs/pymatgen.analysis.interfaces.substrate_analyzer.html b/docs/pymatgen.analysis.interfaces.substrate_analyzer.html index 6f7dbba679d..97f59a76e9c 100644 --- a/docs/pymatgen.analysis.interfaces.substrate_analyzer.html +++ b/docs/pymatgen.analysis.interfaces.substrate_analyzer.html @@ -4,7 +4,7 @@ - pymatgen.analysis.interfaces.substrate_analyzer module — pymatgen 2022.5.18 documentation + pymatgen.analysis.interfaces.substrate_analyzer module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                              - 2022.5.18 + 2022.5.18.1
                                              @@ -119,7 +119,7 @@

                                              This module provides classes to identify optimal substrates for film growth

                                              -class SubstrateAnalyzer(film_max_miller=1, substrate_max_miller=1, **kwargs)[source]
                                              +class SubstrateAnalyzer(film_max_miller=1, substrate_max_miller=1, **kwargs)[source]

                                              Bases: pymatgen.analysis.interfaces.zsl.ZSLGenerator

                                              This class applies a set of search criteria to identify suitable substrates for film growth. It first uses a topoplogical search by Zur @@ -144,7 +144,7 @@

                                              -calculate(film, substrate, elasticity_tensor=None, film_millers=None, substrate_millers=None, ground_state_energy=0, lowest=False)[source]
                                              +calculate(film, substrate, elasticity_tensor=None, film_millers=None, substrate_millers=None, ground_state_energy=0, lowest=False)[source]

                                              Finds all topological matches for the substrate and calculates elastic strain energy and total energy for the film if elasticity tensor and ground state energy are provided:

                                              @@ -169,7 +169,7 @@
                                              -generate_surface_vectors(film_millers, substrate_millers)[source]
                                              +generate_surface_vectors(film_millers, substrate_millers)[source]

                                              Generates the film/substrate slab combinations for a set of given miller indices

                                              @@ -188,51 +188,51 @@
                                              -class SubstrateMatch(film_sl_vectors: list, substrate_sl_vectors: list, film_vectors: list, substrate_vectors: list, film_transformation: list, substrate_transformation: list, film_miller: tuple[int, int, int], substrate_miller: tuple[int, int, int], strain: pymatgen.analysis.elasticity.strain.Strain, von_mises_strain: float, ground_state_energy: float, elastic_energy: float)[source]
                                              +class SubstrateMatch(film_sl_vectors: list, substrate_sl_vectors: list, film_vectors: list, substrate_vectors: list, film_transformation: list, substrate_transformation: list, film_miller: tuple[int, int, int], substrate_miller: tuple[int, int, int], strain: pymatgen.analysis.elasticity.strain.Strain, von_mises_strain: float, ground_state_energy: float, elastic_energy: float)[source]

                                              Bases: pymatgen.analysis.interfaces.zsl.ZSLMatch

                                              A substrate match building on the Zur and McGill algorithm. This match class includes the miller planes of the film and substrate the full strain tensor, the Von Mises strain, the ground state energy if provided, and the elastic energy

                                              -elastic_energy: float[source]
                                              +elastic_energy: float[source]
                                              -film_miller: tuple[int, int, int][source]
                                              +film_miller: tuple[int, int, int][source]
                                              -classmethod from_zsl(match: pymatgen.analysis.interfaces.zsl.ZSLMatch, film: pymatgen.core.structure.Structure, film_miller, substrate_miller, elasticity_tensor=None, ground_state_energy=0)[source]
                                              +classmethod from_zsl(match: pymatgen.analysis.interfaces.zsl.ZSLMatch, film: pymatgen.core.structure.Structure, film_miller, substrate_miller, elasticity_tensor=None, ground_state_energy=0)[source]

                                              Generate a substrate match from a ZSL match plus metadata

                                              -ground_state_energy: float[source]
                                              +ground_state_energy: float[source]
                                              -strain: pymatgen.analysis.elasticity.strain.Strain[source]
                                              +strain: pymatgen.analysis.elasticity.strain.Strain[source]
                                              -substrate_miller: tuple[int, int, int][source]
                                              +substrate_miller: tuple[int, int, int][source]
                                              -property total_energy[source]
                                              +property total_energy[source]

                                              Total energy of this match

                                              -von_mises_strain: float[source]
                                              +von_mises_strain: float[source]
                                              diff --git a/docs/pymatgen.analysis.interfaces.zsl.html b/docs/pymatgen.analysis.interfaces.zsl.html index 1644ec7bb8c..d26a4f463d0 100644 --- a/docs/pymatgen.analysis.interfaces.zsl.html +++ b/docs/pymatgen.analysis.interfaces.zsl.html @@ -4,7 +4,7 @@ - pymatgen.analysis.interfaces.zsl module — pymatgen 2022.5.18 documentation + pymatgen.analysis.interfaces.zsl module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                              - 2022.5.18 + 2022.5.18.1
                                              @@ -119,7 +119,7 @@

                                              This module implements the Zur and McGill lattice matching algorithm

                                              -class ZSLGenerator(max_area_ratio_tol=0.09, max_area=400, max_length_tol=0.03, max_angle_tol=0.01, bidirectional=False)[source]
                                              +class ZSLGenerator(max_area_ratio_tol=0.09, max_area=400, max_length_tol=0.03, max_angle_tol=0.01, bidirectional=False)[source]

                                              Bases: monty.json.MSONable

                                              This class generate matching interface super lattices based on the methodology of lattice vector matching for heterostructural interfaces proposed by @@ -158,7 +158,7 @@

                                              -generate_sl_transformation_sets(film_area, substrate_area)[source]
                                              +generate_sl_transformation_sets(film_area, substrate_area)[source]

                                              Generates transformation sets for film/substrate pair given the area of the unit cell area for the film and substrate. The transformation sets map the film and substrate unit cells to super @@ -186,7 +186,7 @@

                                              -get_equiv_transformations(transformation_sets, film_vectors, substrate_vectors)[source]
                                              +get_equiv_transformations(transformation_sets, film_vectors, substrate_vectors)[source]

                                              Applies the transformation_sets to the film and substrate vectors to generate super-lattices and checks if they matches. Returns all matching vectors sets. @@ -211,7 +211,7 @@

                                              -is_same_vectors(vec_set1, vec_set2)[source]
                                              +is_same_vectors(vec_set1, vec_set2)[source]

                                              Determine if two sets of vectors are the same within length and angle tolerances :param vec_set1: an array of two vectors @@ -224,7 +224,7 @@

                                              -class ZSLMatch(film_sl_vectors: list, substrate_sl_vectors: list, film_vectors: list, substrate_vectors: list, film_transformation: list, substrate_transformation: list)[source]
                                              +class ZSLMatch(film_sl_vectors: list, substrate_sl_vectors: list, film_vectors: list, substrate_vectors: list, film_transformation: list, substrate_transformation: list)[source]

                                              Bases: monty.json.MSONable

                                              A match from the Zur and McGill Algorithm. The super_lattice vectors are listed as _sl_vectors. These are reduced according to the algorithm in the paper which @@ -232,57 +232,57 @@ the appropriate transformation matrix

                                              -film_sl_vectors: list[source]
                                              +film_sl_vectors: list[source]
                                              -film_transformation: list[source]
                                              +film_transformation: list[source]
                                              -film_vectors: list[source]
                                              +film_vectors: list[source]
                                              -property match_area[source]
                                              +property match_area[source]

                                              The area of the match between the substrate and film super lattice vectors

                                              -property match_transformation[source]
                                              +property match_transformation[source]

                                              The transformation matrix to convert the film super lattice vectors to the substrate

                                              -substrate_sl_vectors: list[source]
                                              +substrate_sl_vectors: list[source]
                                              -substrate_transformation: list[source]
                                              +substrate_transformation: list[source]
                                              -substrate_vectors: list[source]
                                              +substrate_vectors: list[source]
                                              -fast_norm(a)[source]
                                              +fast_norm(a)[source]

                                              Much faster variant of numpy linalg norm

                                              -gen_sl_transform_matricies(area_multiple)[source]
                                              +gen_sl_transform_matricies(area_multiple)[source]

                                              Generates the transformation matricies that convert a set of 2D vectors into a super lattice of integer area multiple as proven in Cassels:

                                              @@ -307,20 +307,20 @@
                                              -get_factors(n)[source]
                                              +get_factors(n)[source]

                                              Generate all factors of n

                                              -reduce_vectors(a, b)[source]
                                              +reduce_vectors(a, b)[source]

                                              Generate independent and unique basis vectors based on the methodology of Zur and McGill

                                              -rel_angle(vec_set1, vec_set2)[source]
                                              +rel_angle(vec_set1, vec_set2)[source]

                                              Calculate the relative angle between two vector sets

                                              Parameters
                                              @@ -334,19 +334,19 @@
                                              -rel_strain(vec1, vec2)[source]
                                              +rel_strain(vec1, vec2)[source]

                                              Calculate relative strain between two vectors

                                              -vec_angle(a, b)[source]
                                              +vec_angle(a, b)[source]

                                              Calculate angle between two vectors

                                              -vec_area(a, b)[source]
                                              +vec_area(a, b)[source]

                                              Area of lattice plane defined by two vectors

                                              diff --git a/docs/pymatgen.analysis.local_env.html b/docs/pymatgen.analysis.local_env.html index 046a545bd27..b4af51f6af0 100644 --- a/docs/pymatgen.analysis.local_env.html +++ b/docs/pymatgen.analysis.local_env.html @@ -4,7 +4,7 @@ - pymatgen.analysis.local_env module — pymatgen 2022.5.18 documentation + pymatgen.analysis.local_env module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                              - 2022.5.18 + 2022.5.18.1
                                              @@ -120,7 +120,7 @@ of single sites in molecules and structures.

                                              -class BrunnerNN_real(tol=0.0001, cutoff=8.0)[source]
                                              +class BrunnerNN_real(tol=0.0001, cutoff=8.0)[source]

                                              Bases: pymatgen.analysis.local_env.NearNeighbors

                                              Determine coordination number using Brunner’s algorithm which counts the atoms that are within the largest gap in differences in real space @@ -138,7 +138,7 @@

                                              -get_nn_info(structure, n)[source]
                                              +get_nn_info(structure, n)[source]

                                              Get all near-neighbor sites as well as the associated image locations and weights of the site with index n in structure.

                                              @@ -165,7 +165,7 @@
                                              -property molecules_allowed[source]
                                              +property molecules_allowed[source]

                                              can this NearNeighbors class be used with Molecule objects?

                                              @@ -177,7 +177,7 @@
                                              -property structures_allowed[source]
                                              +property structures_allowed[source]

                                              can this NearNeighbors class be used with Structure objects?

                                              @@ -191,7 +191,7 @@
                                              -class BrunnerNN_reciprocal(tol=0.0001, cutoff=8.0)[source]
                                              +class BrunnerNN_reciprocal(tol=0.0001, cutoff=8.0)[source]

                                              Bases: pymatgen.analysis.local_env.NearNeighbors

                                              Determine coordination number using Brunner’s algorithm which counts the atoms that are within the largest gap in differences in real space @@ -209,7 +209,7 @@

                                              -get_nn_info(structure, n)[source]
                                              +get_nn_info(structure, n)[source]

                                              Get all near-neighbor sites as well as the associated image locations and weights of the site with index n in structure.

                                              @@ -236,7 +236,7 @@
                                              -property molecules_allowed[source]
                                              +property molecules_allowed[source]

                                              can this NearNeighbors class be used with Molecule objects?

                                              @@ -248,7 +248,7 @@
                                              -property structures_allowed[source]
                                              +property structures_allowed[source]

                                              can this NearNeighbors class be used with Structure objects?

                                              @@ -262,7 +262,7 @@
                                              -class BrunnerNN_relative(tol=0.0001, cutoff=8.0)[source]
                                              +class BrunnerNN_relative(tol=0.0001, cutoff=8.0)[source]

                                              Bases: pymatgen.analysis.local_env.NearNeighbors

                                              Determine coordination number using Brunner’s algorithm which counts the atoms that are within the largest gap in differences in real space @@ -280,7 +280,7 @@

                                              -get_nn_info(structure, n)[source]
                                              +get_nn_info(structure, n)[source]

                                              Get all near-neighbor sites as well as the associated image locations and weights of the site with index n in structure.

                                              @@ -307,7 +307,7 @@
                                              -property molecules_allowed[source]
                                              +property molecules_allowed[source]

                                              can this NearNeighbors class be used with Molecule objects?

                                              @@ -319,7 +319,7 @@
                                              -property structures_allowed[source]
                                              +property structures_allowed[source]

                                              can this NearNeighbors class be used with Structure objects?

                                              @@ -333,7 +333,7 @@
                                              -class CovalentBondNN(tol=0.2, order=True)[source]
                                              +class CovalentBondNN(tol=0.2, order=True)[source]

                                              Bases: pymatgen.analysis.local_env.NearNeighbors

                                              Determine near-neighbor sites and bond orders using built-in pymatgen.Molecule CovalentBond functionality.

                                              @@ -350,7 +350,7 @@
                                              -property extend_structure_molecules[source]
                                              +property extend_structure_molecules[source]

                                              Do Molecules need to be converted to Structures to use this NearNeighbors class? Note: this property is not defined for classes for which molecules_allowed == False.

                                              @@ -363,7 +363,7 @@
                                              -get_bonded_structure(structure, decorate=False)[source]
                                              +get_bonded_structure(structure, decorate=False)[source]

                                              Obtain a MoleculeGraph object using this NearNeighbor class.

                                              @@ -381,7 +381,7 @@
                                              -get_nn_info(structure, n)[source]
                                              +get_nn_info(structure, n)[source]

                                              Get all near-neighbor sites and weights (orders) of bonds for a given atom.

                                              @@ -400,7 +400,7 @@
                                              -get_nn_shell_info(structure, site_idx, shell)[source]
                                              +get_nn_shell_info(structure, site_idx, shell)[source]

                                              Get a certain nearest neighbor shell for a certain site.

                                              Determines all non-backtracking paths through the neighbor network computed by get_nn_info. The weight is determined by multiplying @@ -435,7 +435,7 @@

                                              -property molecules_allowed[source]
                                              +property molecules_allowed[source]

                                              can this NearNeighbors class be used with Molecule objects?

                                              @@ -447,7 +447,7 @@
                                              -property structures_allowed[source]
                                              +property structures_allowed[source]

                                              can this NearNeighbors class be used with Structure objects?

                                              @@ -461,7 +461,7 @@
                                              -class Critic2NN[source]
                                              +class Critic2NN[source]

                                              Bases: pymatgen.analysis.local_env.NearNeighbors

                                              Performs a topological analysis using critic2 to obtain neighbor information, using a sum of atomic charge @@ -471,7 +471,7 @@

                                              Init for Critic2NN.

                                              -property extend_structure_molecules[source]
                                              +property extend_structure_molecules[source]

                                              Do Molecules need to be converted to Structures to use this NearNeighbors class? Note: this property is not defined for classes for which molecules_allowed == False.

                                              @@ -484,7 +484,7 @@
                                              -get_bonded_structure(structure, decorate=False)[source]
                                              +get_bonded_structure(structure, decorate=False)[source]
                                              Parameters
                                                @@ -500,7 +500,7 @@
                                                -get_nn_info(structure, n)[source]
                                                +get_nn_info(structure, n)[source]

                                                Get all near-neighbor sites as well as the associated image locations and weights of the site with index n in structure.

                                                @@ -527,7 +527,7 @@
                                                -property molecules_allowed[source]
                                                +property molecules_allowed[source]

                                                can this NearNeighbors class be used with Molecule objects?

                                                @@ -539,7 +539,7 @@
                                                -property structures_allowed[source]
                                                +property structures_allowed[source]

                                                can this NearNeighbors class be used with Structure objects?

                                                @@ -553,7 +553,7 @@
                                                -class CrystalNN(weighted_cn=False, cation_anion=False, distance_cutoffs=(0.5, 1), x_diff_weight=3.0, porous_adjustment=True, search_cutoff=7, fingerprint_length=None)[source]
                                                +class CrystalNN(weighted_cn=False, cation_anion=False, distance_cutoffs=(0.5, 1), x_diff_weight=3.0, porous_adjustment=True, search_cutoff=7, fingerprint_length=None)[source]

                                                Bases: pymatgen.analysis.local_env.NearNeighbors

                                                This is custom near neighbor method intended for use in all kinds of periodic structures (metals, minerals, porous structures, etc). It is based @@ -594,24 +594,24 @@

                                                -class NNData(all_nninfo, cn_weights, cn_nninfo)[source]
                                                +class NNData(all_nninfo, cn_weights, cn_nninfo)[source]

                                                Bases: tuple

                                                Create new instance of NNData(all_nninfo, cn_weights, cn_nninfo)

                                                -all_nninfo[source]
                                                +all_nninfo[source]

                                                Alias for field number 0

                                                -cn_nninfo[source]
                                                +cn_nninfo[source]

                                                Alias for field number 2

                                                -cn_weights[source]
                                                +cn_weights[source]

                                                Alias for field number 1

                                                @@ -619,7 +619,7 @@
                                                -get_cn(structure, n, use_weights=False)[source]
                                                +get_cn(structure, n, use_weights=False)[source]

                                                Get coordination number, CN, of site with index n in structure.

                                                Parameters
                                                @@ -643,7 +643,7 @@
                                                -get_cn_dict(structure, n, use_weights=False)[source]
                                                +get_cn_dict(structure, n, use_weights=False)[source]

                                                Get coordination number, CN, of each element bonded to site with index n in structure

                                                Parameters
                                                @@ -667,7 +667,7 @@
                                                -get_nn_data(structure, n, length=None)[source]
                                                +get_nn_data(structure, n, length=None)[source]

                                                The main logic of the method to compute near neighbor.

                                                Parameters
                                                @@ -693,7 +693,7 @@
                                                -get_nn_info(structure, n)[source]
                                                +get_nn_info(structure, n)[source]

                                                Get all near-neighbor information. :param structure: (Structure) pymatgen Structure :param n: (int) index of target site

                                                @@ -719,7 +719,7 @@
                                                -property molecules_allowed[source]
                                                +property molecules_allowed[source]

                                                can this NearNeighbors class be used with Molecule objects?

                                                @@ -731,7 +731,7 @@
                                                -property structures_allowed[source]
                                                +property structures_allowed[source]

                                                can this NearNeighbors class be used with Structure objects?

                                                @@ -743,7 +743,7 @@
                                                -static transform_to_length(nndata, length)[source]
                                                +static transform_to_length(nndata, length)[source]

                                                Given NNData, transforms data to the specified fingerprint length :param nndata: (NNData) :param length: (int) desired length of NNData

                                                @@ -753,7 +753,7 @@
                                                -class CutOffDictNN(cut_off_dict=None)[source]
                                                +class CutOffDictNN(cut_off_dict=None)[source]

                                                Bases: pymatgen.analysis.local_env.NearNeighbors

                                                A basic NN class using a dictionary of fixed cut-off distances. Only pairs of elements listed in the cut-off dictionary are considered @@ -780,7 +780,7 @@ :type e.g. {: ‘Fe2+’, ‘O2-’

                                                -property extend_structure_molecules[source]
                                                +property extend_structure_molecules[source]

                                                Do Molecules need to be converted to Structures to use this NearNeighbors class? Note: this property is not defined for classes for which molecules_allowed == False.

                                                @@ -793,7 +793,7 @@
                                                -static from_preset(preset)[source]
                                                +static from_preset(preset)[source]

                                                Initialise a CutOffDictNN according to a preset set of cut-offs.

                                                Parameters
                                                @@ -812,7 +812,7 @@
                                                -get_nn_info(structure, n)[source]
                                                +get_nn_info(structure, n)[source]

                                                Get all near-neighbor sites as well as the associated image locations and weights of the site with index n in structure.

                                                @@ -839,7 +839,7 @@
                                                -property molecules_allowed[source]
                                                +property molecules_allowed[source]

                                                can this NearNeighbors class be used with Molecule objects?

                                                @@ -851,7 +851,7 @@
                                                -property structures_allowed[source]
                                                +property structures_allowed[source]

                                                can this NearNeighbors class be used with Structure objects?

                                                @@ -865,7 +865,7 @@
                                                -class EconNN(tol: float = 0.2, cutoff: float = 10.0, cation_anion: bool = False, use_fictive_radius: bool = False)[source]
                                                +class EconNN(tol: float = 0.2, cutoff: float = 10.0, cation_anion: bool = False, use_fictive_radius: bool = False)[source]

                                                Bases: pymatgen.analysis.local_env.NearNeighbors

                                                Determines the average effective coordination number for each cation in a given structure using Hoppe’s algorithm.

                                                @@ -888,7 +888,7 @@
                                                -property extend_structure_molecules[source]
                                                +property extend_structure_molecules[source]

                                                Do Molecules need to be converted to Structures to use this NearNeighbors class? Note: this property is not defined for classes for which molecules_allowed == False.

                                                @@ -901,7 +901,7 @@
                                                -get_nn_info(structure, n)[source]
                                                +get_nn_info(structure, n)[source]

                                                Get all near-neighbor sites as well as the associated image locations and weights of the site with index n in structure.

                                                @@ -928,7 +928,7 @@
                                                -property molecules_allowed[source]
                                                +property molecules_allowed[source]

                                                can this NearNeighbors class be used with Molecule objects?

                                                @@ -940,7 +940,7 @@
                                                -property structures_allowed[source]
                                                +property structures_allowed[source]

                                                can this NearNeighbors class be used with Structure objects?

                                                @@ -954,7 +954,7 @@
                                                -class IsayevNN(tol: float = 0.25, targets: Element | list[Element] | None = None, cutoff: float = 13.0, allow_pathological: bool = False, extra_nn_info: bool = True, compute_adj_neighbors: bool = True)[source]
                                                +class IsayevNN(tol: float = 0.25, targets: Element | list[Element] | None = None, cutoff: float = 13.0, allow_pathological: bool = False, extra_nn_info: bool = True, compute_adj_neighbors: bool = True)[source]

                                                Bases: pymatgen.analysis.local_env.VoronoiNN

                                                Uses the algorithm defined in 10.1038/ncomms15679

                                                Sites are considered neighbors if (i) they share a Voronoi facet and (ii) the @@ -975,7 +975,7 @@

                                                -get_all_nn_info(structure: pymatgen.core.structure.Structure) → list[list[dict[str, Any]]][source]
                                                +get_all_nn_info(structure: pymatgen.core.structure.Structure) → list[list[dict[str, Any]]][source]
                                                Parameters

                                                structure (Structure) – input structure.

                                                @@ -989,7 +989,7 @@
                                                -get_nn_info(structure: pymatgen.core.structure.Structure, n: int) → list[dict[str, Any]][source]
                                                +get_nn_info(structure: pymatgen.core.structure.Structure, n: int) → list[dict[str, Any]][source]

                                                Get all near-neighbor site information.

                                                Gets the the associated image locations and weights of the site with index n in structure using Voronoi decomposition and distance cutoff.

                                                @@ -1019,7 +1019,7 @@
                                                -class JmolNN(tol=0.45, min_bond_distance=0.4, el_radius_updates=None)[source]
                                                +class JmolNN(tol=0.45, min_bond_distance=0.4, el_radius_updates=None)[source]

                                                Bases: pymatgen.analysis.local_env.NearNeighbors

                                                Determine near-neighbor sites and coordination number using an emulation of Jmol’s default autoBond() algorithm. This version of the algorithm @@ -1037,7 +1037,7 @@

                                                -property extend_structure_molecules[source]
                                                +property extend_structure_molecules[source]

                                                Do Molecules need to be converted to Structures to use this NearNeighbors class? Note: this property is not defined for classes for which molecules_allowed == False.

                                                @@ -1050,7 +1050,7 @@
                                                -get_max_bond_distance(el1_sym, el2_sym)[source]
                                                +get_max_bond_distance(el1_sym, el2_sym)[source]

                                                Use Jmol algorithm to determine bond length from atomic parameters :param el1_sym: (str) symbol of atom 1 :param el2_sym: (str) symbol of atom 2

                                                @@ -1059,7 +1059,7 @@
                                                -get_nn_info(structure, n)[source]
                                                +get_nn_info(structure, n)[source]

                                                Get all near-neighbor sites as well as the associated image locations and weights of the site with index n using the bond identification algorithm underlying Jmol.

                                                @@ -1087,7 +1087,7 @@
                                                -property molecules_allowed[source]
                                                +property molecules_allowed[source]

                                                can this NearNeighbors class be used with Molecule objects?

                                                @@ -1099,7 +1099,7 @@
                                                -property structures_allowed[source]
                                                +property structures_allowed[source]

                                                can this NearNeighbors class be used with Structure objects?

                                                @@ -1113,7 +1113,7 @@
                                                -class LocalStructOrderParams(types, parameters=None, cutoff=- 10.0)[source]
                                                +class LocalStructOrderParams(types, parameters=None, cutoff=- 10.0)[source]

                                                Bases: object

                                                This class permits the calculation of various types of local structure order parameters.

                                                @@ -1250,7 +1250,7 @@
                                                -compute_trigonometric_terms(thetas, phis)[source]
                                                +compute_trigonometric_terms(thetas, phis)[source]

                                                Computes trigonometric terms that are required to calculate bond orientational order parameters using internal variables.

                                                @@ -1275,7 +1275,7 @@
                                                -get_order_parameters(structure, n, indices_neighs=None, tol=0.0, target_spec=None)[source]
                                                +get_order_parameters(structure, n, indices_neighs=None, tol=0.0, target_spec=None)[source]

                                                Compute all order parameters of site n.

                                                Parameters
                                                @@ -1331,7 +1331,7 @@
                                                -get_parameters(index)[source]
                                                +get_parameters(index)[source]

                                                Returns list of floats that represents the parameters associated with calculation of the order @@ -1354,7 +1354,7 @@

                                                -get_q2(thetas=None, phis=None)[source]
                                                +get_q2(thetas=None, phis=None)[source]

                                                Calculates the value of the bond orientational order parameter of weight l=2. If the function is called with non-empty lists of polar and azimuthal angles the corresponding trigonometric terms @@ -1382,7 +1382,7 @@

                                                -get_q4(thetas=None, phis=None)[source]
                                                +get_q4(thetas=None, phis=None)[source]

                                                Calculates the value of the bond orientational order parameter of weight l=4. If the function is called with non-empty lists of polar and azimuthal angles the corresponding trigonometric terms @@ -1410,7 +1410,7 @@

                                                -get_q6(thetas=None, phis=None)[source]
                                                +get_q6(thetas=None, phis=None)[source]

                                                Calculates the value of the bond orientational order parameter of weight l=6. If the function is called with non-empty lists of polar and azimuthal angles the corresponding trigonometric terms @@ -1438,7 +1438,7 @@

                                                -get_type(index)[source]
                                                +get_type(index)[source]

                                                Return type of order parameter at the index provided and represented by a short string.

                                                @@ -1457,7 +1457,7 @@
                                                -property last_nneigh[source]
                                                +property last_nneigh[source]

                                                Returns: int: the number of neighbors encountered during the most

                                                @@ -1469,7 +1469,7 @@
                                                -property num_ops[source]
                                                +property num_ops[source]

                                                Returns: int: the number of different order parameters that are targeted

                                                @@ -1481,7 +1481,7 @@
                                                -class MinimumDistanceNN(tol=0.1, cutoff=10.0, get_all_sites=False)[source]
                                                +class MinimumDistanceNN(tol=0.1, cutoff=10.0, get_all_sites=False)[source]

                                                Bases: pymatgen.analysis.local_env.NearNeighbors

                                                Determine near-neighbor sites and coordination number using the nearest neighbor(s) at distance, d_min, plus all neighbors @@ -1501,7 +1501,7 @@

                                                -property extend_structure_molecules[source]
                                                +property extend_structure_molecules[source]

                                                Do Molecules need to be converted to Structures to use this NearNeighbors class? Note: this property is not defined for classes for which molecules_allowed == False.

                                                @@ -1514,7 +1514,7 @@
                                                -get_nn_info(structure, n)[source]
                                                +get_nn_info(structure, n)[source]

                                                Get all near-neighbor sites as well as the associated image locations and weights of the site with index n using the closest neighbor distance-based method.

                                                @@ -1542,7 +1542,7 @@
                                                -property molecules_allowed[source]
                                                +property molecules_allowed[source]

                                                can this NearNeighbors class be used with Molecule objects?

                                                @@ -1554,7 +1554,7 @@
                                                -property structures_allowed[source]
                                                +property structures_allowed[source]

                                                can this NearNeighbors class be used with Structure objects?

                                                @@ -1568,7 +1568,7 @@
                                                -class MinimumOKeeffeNN(tol=0.1, cutoff=10.0)[source]
                                                +class MinimumOKeeffeNN(tol=0.1, cutoff=10.0)[source]

                                                Bases: pymatgen.analysis.local_env.NearNeighbors

                                                Determine near-neighbor sites and coordination number using the neighbor(s) at closest relative distance, d_min_OKeffee, plus some @@ -1587,7 +1587,7 @@

                                                -property extend_structure_molecules[source]
                                                +property extend_structure_molecules[source]

                                                Do Molecules need to be converted to Structures to use this NearNeighbors class? Note: this property is not defined for classes for which molecules_allowed == False.

                                                @@ -1600,7 +1600,7 @@
                                                -get_nn_info(structure, n)[source]
                                                +get_nn_info(structure, n)[source]

                                                Get all near-neighbor sites as well as the associated image locations and weights of the site with index n using the closest relative neighbor distance-based method with O’Keeffe parameters.

                                                @@ -1628,7 +1628,7 @@
                                                -property molecules_allowed[source]
                                                +property molecules_allowed[source]

                                                can this NearNeighbors class be used with Molecule objects?

                                                @@ -1640,7 +1640,7 @@
                                                -property structures_allowed[source]
                                                +property structures_allowed[source]

                                                can this NearNeighbors class be used with Structure objects?

                                                @@ -1654,7 +1654,7 @@
                                                -class MinimumVIRENN(tol=0.1, cutoff=10.0)[source]
                                                +class MinimumVIRENN(tol=0.1, cutoff=10.0)[source]

                                                Bases: pymatgen.analysis.local_env.NearNeighbors

                                                Determine near-neighbor sites and coordination number using the neighbor(s) at closest relative distance, d_min_VIRE, plus some @@ -1673,7 +1673,7 @@

                                                -get_nn_info(structure, n)[source]
                                                +get_nn_info(structure, n)[source]

                                                Get all near-neighbor sites as well as the associated image locations and weights of the site with index n using the closest relative neighbor distance-based method with VIRE atomic/ionic radii.

                                                @@ -1701,7 +1701,7 @@
                                                -property molecules_allowed[source]
                                                +property molecules_allowed[source]

                                                can this NearNeighbors class be used with Molecule objects?

                                                @@ -1713,7 +1713,7 @@
                                                -property structures_allowed[source]
                                                +property structures_allowed[source]

                                                can this NearNeighbors class be used with Structure objects?

                                                @@ -1727,13 +1727,13 @@
                                                -class NearNeighbors[source]
                                                +class NearNeighbors[source]

                                                Bases: object

                                                Base class to determine near neighbors that typically include nearest neighbors and others that are within some tolerable distance.

                                                -property extend_structure_molecules[source]
                                                +property extend_structure_molecules[source]

                                                Do Molecules need to be converted to Structures to use this NearNeighbors class? Note: this property is not defined for classes for which molecules_allowed == False.

                                                @@ -1746,7 +1746,7 @@
                                                -get_all_nn_info(structure)[source]
                                                +get_all_nn_info(structure)[source]

                                                Get a listing of all neighbors for all sites in a structure

                                                Parameters
                                                @@ -1764,7 +1764,7 @@
                                                -get_bonded_structure(structure, decorate=False, weights=True)[source]
                                                +get_bonded_structure(structure, decorate=False, weights=True)[source]

                                                Obtain a StructureGraph object using this NearNeighbor class. Requires the optional dependency networkx (pip install networkx).

                                                @@ -1785,7 +1785,7 @@
                                                -get_cn(structure, n, use_weights=False)[source]
                                                +get_cn(structure, n, use_weights=False)[source]

                                                Get coordination number, CN, of site with index n in structure.

                                                Parameters
                                                @@ -1809,7 +1809,7 @@
                                                -get_cn_dict(structure, n, use_weights=False)[source]
                                                +get_cn_dict(structure, n, use_weights=False)[source]

                                                Get coordination number, CN, of each element bonded to site with index n in structure

                                                Parameters
                                                @@ -1833,7 +1833,7 @@
                                                -get_local_order_parameters(structure, n)[source]
                                                +get_local_order_parameters(structure, n)[source]

                                                Calculate those local structure order parameters for the given site whose ideal CN corresponds to the underlying motif (e.g., CN=4, then calculate the @@ -1856,7 +1856,7 @@

                                                -get_nn(structure, n)[source]
                                                +get_nn(structure, n)[source]

                                                Get near neighbors of site with index n in structure.

                                                Parameters
                                                @@ -1877,7 +1877,7 @@
                                                -get_nn_images(structure, n)[source]
                                                +get_nn_images(structure, n)[source]

                                                Get image location of all near neighbors of site with index n in structure.

                                                @@ -1903,7 +1903,7 @@
                                                -get_nn_info(structure, n)[source]
                                                +get_nn_info(structure, n)[source]

                                                Get all near-neighbor sites as well as the associated image locations and weights of the site with index n.

                                                @@ -1935,7 +1935,7 @@
                                                -get_nn_shell_info(structure, site_idx, shell)[source]
                                                +get_nn_shell_info(structure, site_idx, shell)[source]

                                                Get a certain nearest neighbor shell for a certain site.

                                                Determines all non-backtracking paths through the neighbor network computed by get_nn_info. The weight is determined by multiplying @@ -1970,7 +1970,7 @@

                                                -get_weights_of_nn_sites(structure, n)[source]
                                                +get_weights_of_nn_sites(structure, n)[source]

                                                Get weight associated with each near neighbor of site with index n in structure.

                                                @@ -1991,7 +1991,7 @@
                                                -property molecules_allowed[source]
                                                +property molecules_allowed[source]

                                                can this NearNeighbors class be used with Molecule objects?

                                                @@ -2003,7 +2003,7 @@
                                                -property structures_allowed[source]
                                                +property structures_allowed[source]

                                                can this NearNeighbors class be used with Structure objects?

                                                @@ -2017,7 +2017,7 @@
                                                -class OpenBabelNN(order=True)[source]
                                                +class OpenBabelNN(order=True)[source]

                                                Bases: pymatgen.analysis.local_env.NearNeighbors

                                                Determine near-neighbor sites and bond orders using OpenBabel API.

                                                NOTE: This strategy is only appropriate for molecules, and not for @@ -2032,7 +2032,7 @@

                                                -property extend_structure_molecules[source]
                                                +property extend_structure_molecules[source]

                                                Do Molecules need to be converted to Structures to use this NearNeighbors class? Note: this property is not defined for classes for which molecules_allowed == False.

                                                @@ -2045,7 +2045,7 @@
                                                -get_bonded_structure(structure, decorate=False)[source]
                                                +get_bonded_structure(structure, decorate=False)[source]

                                                Obtain a MoleculeGraph object using this NearNeighbor class. Requires the optional dependency networkx (pip install networkx).

                                                @@ -2064,7 +2064,7 @@
                                                -get_nn_info(structure, n)[source]
                                                +get_nn_info(structure, n)[source]

                                                Get all near-neighbor sites and weights (orders) of bonds for a given atom.

                                                @@ -2086,7 +2086,7 @@
                                                -get_nn_shell_info(structure, site_idx, shell)[source]
                                                +get_nn_shell_info(structure, site_idx, shell)[source]

                                                Get a certain nearest neighbor shell for a certain site.

                                                Determines all non-backtracking paths through the neighbor network computed by get_nn_info. The weight is determined by multiplying @@ -2121,7 +2121,7 @@

                                                -property molecules_allowed[source]
                                                +property molecules_allowed[source]

                                                can this NearNeighbors class be used with Molecule objects?

                                                @@ -2133,7 +2133,7 @@
                                                -property structures_allowed[source]
                                                +property structures_allowed[source]

                                                can this NearNeighbors class be used with Structure objects?

                                                @@ -2147,7 +2147,7 @@
                                                -class ValenceIonicRadiusEvaluator(structure)[source]
                                                +class ValenceIonicRadiusEvaluator(structure)[source]

                                                Bases: object

                                                Computes site valences and ionic radii for a structure using bond valence analyzer

                                                @@ -2158,19 +2158,19 @@
                                                -property radii[source]
                                                +property radii[source]

                                                List of ionic radii of elements in the order of sites.

                                                -property structure[source]
                                                +property structure[source]

                                                Returns oxidation state decorated structure.

                                                -property valences[source]
                                                +property valences[source]

                                                List of oxidation states of elements in the order of sites.

                                                @@ -2178,7 +2178,7 @@
                                                -class VoronoiNN(tol=0, targets=None, cutoff=13.0, allow_pathological=False, weight='solid_angle', extra_nn_info=True, compute_adj_neighbors=True)[source]
                                                +class VoronoiNN(tol=0, targets=None, cutoff=13.0, allow_pathological=False, weight='solid_angle', extra_nn_info=True, compute_adj_neighbors=True)[source]

                                                Bases: pymatgen.analysis.local_env.NearNeighbors

                                                Uses a Voronoi algorithm to determine near neighbors for each site in a structure.

                                                @@ -2201,7 +2201,7 @@
                                                -get_all_nn_info(structure)[source]
                                                +get_all_nn_info(structure)[source]
                                                Parameters

                                                structure (Structure) – input structure.

                                                @@ -2214,7 +2214,7 @@
                                                -get_all_voronoi_polyhedra(structure)[source]
                                                +get_all_voronoi_polyhedra(structure)[source]

                                                Get the Voronoi polyhedra for all site in a simulation cell

                                                Parameters
                                                @@ -2244,7 +2244,7 @@
                                                -get_nn_info(structure, n)[source]
                                                +get_nn_info(structure, n)[source]

                                                Get all near-neighbor sites as well as the associated image locations and weights of the site with index n in structure using Voronoi decomposition.

                                                @@ -2272,7 +2272,7 @@
                                                -get_voronoi_polyhedra(structure, n)[source]
                                                +get_voronoi_polyhedra(structure, n)[source]

                                                Gives a weighted polyhedra around a site.

                                                See ref: A Proposed Rigorous Definition of Coordination Number, M. O’Keeffe, Acta Cryst. (1979). A35, 772-775

                                                @@ -2308,7 +2308,7 @@
                                                -property molecules_allowed[source]
                                                +property molecules_allowed[source]

                                                can this NearNeighbors class be used with Molecule objects?

                                                @@ -2320,7 +2320,7 @@
                                                -property structures_allowed[source]
                                                +property structures_allowed[source]

                                                can this NearNeighbors class be used with Structure objects?

                                                @@ -2334,7 +2334,7 @@
                                                -get_neighbors_of_site_with_index(struct, n, approach='min_dist', delta=0.1, cutoff=10.0)[source]
                                                +get_neighbors_of_site_with_index(struct, n, approach='min_dist', delta=0.1, cutoff=10.0)[source]

                                                Returns the neighbors of a given site using a specific neighbor-finding method.

                                                @@ -2357,7 +2357,7 @@
                                                -get_okeeffe_distance_prediction(el1, el2)[source]
                                                +get_okeeffe_distance_prediction(el1, el2)[source]

                                                Returns an estimate of the bond valence parameter (bond length) using the derived parameters from ‘Atoms Sizes and Bond Lengths in Molecules and Crystals’ (O’Keeffe & Brese, 1991). The estimate is based on two @@ -2380,7 +2380,7 @@

                                                -get_okeeffe_params(el_symbol)[source]
                                                +get_okeeffe_params(el_symbol)[source]

                                                Returns the elemental parameters related to atom size and electronegativity which are used for estimating bond-valence parameters (bond length) of pairs of atoms on the basis of data @@ -2405,7 +2405,7 @@

                                                -gramschmidt(vin, uin)[source]
                                                +gramschmidt(vin, uin)[source]

                                                Returns that part of the first input vector that is orthogonal to the second input vector. The output vector is not normalized.

                                                @@ -2421,7 +2421,7 @@
                                                -metal_edge_extender(mol_graph)[source]
                                                +metal_edge_extender(mol_graph)[source]

                                                Function to identify and add missed coordinate bond edges for metals

                                                Parameters
                                                @@ -2442,7 +2442,7 @@
                                                -site_is_of_motif_type(struct, n, approach='min_dist', delta=0.1, cutoff=10.0, thresh=None)[source]
                                                +site_is_of_motif_type(struct, n, approach='min_dist', delta=0.1, cutoff=10.0, thresh=None)[source]

                                                Returns the motif type of the site with index n in structure struct; currently featuring “tetrahedral”, “octahedral”, “bcc”, and “cp” (close-packed: fcc and hcp) as well as “square pyramidal” and @@ -2472,7 +2472,7 @@

                                                -solid_angle(center, coords)[source]
                                                +solid_angle(center, coords)[source]

                                                Helper method to calculate the solid angle of a set of coords from the center.

                                                @@ -2490,7 +2490,7 @@
                                                -vol_tetra(vt1, vt2, vt3, vt4)[source]
                                                +vol_tetra(vt1, vt2, vt3, vt4)[source]

                                                Calculate the volume of a tetrahedron, given the four vertices of vt1, vt2, vt3 and vt4. :param vt1: coordinates of vertex 1. diff --git a/docs/pymatgen.analysis.magnetism.analyzer.html b/docs/pymatgen.analysis.magnetism.analyzer.html index 36a9309c2f0..ba5a031c9c6 100644 --- a/docs/pymatgen.analysis.magnetism.analyzer.html +++ b/docs/pymatgen.analysis.magnetism.analyzer.html @@ -4,7 +4,7 @@ - pymatgen.analysis.magnetism.analyzer module — pymatgen 2022.5.18 documentation + pymatgen.analysis.magnetism.analyzer module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                                - 2022.5.18 + 2022.5.18.1
                                                @@ -120,7 +120,7 @@ (e.g. Structures with associated magmom tags).

                                                -class CollinearMagneticStructureAnalyzer(structure: Structure, overwrite_magmom_mode: OverwriteMagmomMode | str = 'none', round_magmoms: bool = False, detect_valences: bool = False, make_primitive: bool = True, default_magmoms: dict = None, set_net_positive: bool = True, threshold: float = 0.0, threshold_nonmag: float = 0.1)[source]
                                                +class CollinearMagneticStructureAnalyzer(structure: Structure, overwrite_magmom_mode: OverwriteMagmomMode | str = 'none', round_magmoms: bool = False, detect_valences: bool = False, make_primitive: bool = True, default_magmoms: dict = None, set_net_positive: bool = True, threshold: float = 0.0, threshold_nonmag: float = 0.1)[source]

                                                Bases: object

                                                A class which provides a few helpful methods to analyze collinear magnetic structures.

                                                @@ -178,7 +178,7 @@
                                                -get_exchange_group_info(symprec: float = 0.01, angle_tolerance: float = 5.0) → tuple[str, int][source]
                                                +get_exchange_group_info(symprec: float = 0.01, angle_tolerance: float = 5.0) → tuple[str, int][source]

                                                Returns the information on the symmetry of the Hamiltonian describing the exchange energy of the system, taking into account relative direction of magnetic moments but not their @@ -202,7 +202,7 @@

                                                -get_ferromagnetic_structure(make_primitive: bool = True) → pymatgen.core.structure.Structure[source]
                                                +get_ferromagnetic_structure(make_primitive: bool = True) → pymatgen.core.structure.Structure[source]

                                                Returns a Structure with all magnetic moments positive or zero.

                                                @@ -218,7 +218,7 @@
                                                -get_nonmagnetic_structure(make_primitive: bool = True) → pymatgen.core.structure.Structure[source]
                                                +get_nonmagnetic_structure(make_primitive: bool = True) → pymatgen.core.structure.Structure[source]

                                                Returns a Structure without magnetic moments defined.

                                                Parameters
                                                @@ -233,7 +233,7 @@
                                                -get_structure_with_only_magnetic_atoms(make_primitive: bool = True) → pymatgen.core.structure.Structure[source]
                                                +get_structure_with_only_magnetic_atoms(make_primitive: bool = True) → pymatgen.core.structure.Structure[source]

                                                Returns a Structure with only magnetic atoms present.

                                                Parameters
                                                @@ -246,26 +246,26 @@
                                                -get_structure_with_spin() → pymatgen.core.structure.Structure[source]
                                                +get_structure_with_spin() → pymatgen.core.structure.Structure[source]

                                                Returns a Structure with species decorated with spin values instead of using magmom site properties.

                                                -property is_magnetic: bool[source]
                                                +property is_magnetic: bool[source]

                                                Convenience property, returns True if any non-zero magmoms present.

                                                -property magmoms: numpy.ndarray[source]
                                                +property magmoms: numpy.ndarray[source]

                                                Convenience property, returns magmoms as a numpy array.

                                                -property magnetic_species_and_magmoms: dict[str, Any][source]
                                                +property magnetic_species_and_magmoms: dict[str, Any][source]

                                                Returns a dict of magnetic species and the magnitude of their associated magmoms. Will return a list if there are multiple magmoms per species.

                                                @@ -274,7 +274,7 @@
                                                -matches_ordering(other: pymatgen.core.structure.Structure) → bool[source]
                                                +matches_ordering(other: pymatgen.core.structure.Structure) → bool[source]

                                                Compares the magnetic orderings of one structure with another.

                                                Parameters
                                                @@ -286,13 +286,13 @@
                                                -property number_of_magnetic_sites: int[source]
                                                +property number_of_magnetic_sites: int[source]

                                                Number of magnetic sites present in structure.

                                                -number_of_unique_magnetic_sites(symprec: float = 0.001, angle_tolerance: float = 5) → int[source]
                                                +number_of_unique_magnetic_sites(symprec: float = 0.001, angle_tolerance: float = 5) → int[source]
                                                Parameters
                                                  @@ -307,7 +307,7 @@
                                                  -property ordering: pymatgen.analysis.magnetism.analyzer.Ordering[source]
                                                  +property ordering: pymatgen.analysis.magnetism.analyzer.Ordering[source]

                                                  Applies heuristics to return a magnetic ordering for a collinear magnetic structure. Result is not guaranteed for correctness.

                                                  Returns: Ordering Enum (‘FiM’ is used as the abbreviation for @@ -316,13 +316,13 @@

                                                  -property types_of_magnetic_specie: tuple[Element | Species | DummySpecies, ...][source]
                                                  +property types_of_magnetic_specie: tuple[Element | Species | DummySpecies, ...][source]

                                                  Specie->Species rename. Used to maintain backwards compatibility.

                                                  -property types_of_magnetic_species: tuple[Element | Species | DummySpecies, ...][source]
                                                  +property types_of_magnetic_species: tuple[Element | Species | DummySpecies, ...][source]

                                                  Equivalent to Structure.types_of_specie but only returns magnetic species.

                                                  Returns: types of Species as a list

                                                  @@ -332,18 +332,18 @@
                                                  -class MagneticDeformation(type, deformation)[source]
                                                  +class MagneticDeformation(type, deformation)[source]

                                                  Bases: tuple

                                                  Create new instance of MagneticDeformation(type, deformation)

                                                  -deformation[source]
                                                  +deformation[source]

                                                  Alias for field number 1

                                                  -type[source]
                                                  +type[source]

                                                  Alias for field number 0

                                                  @@ -351,7 +351,7 @@
                                                  -class MagneticStructureEnumerator(structure: Structure, default_magmoms: dict[str, float] | None = None, strategies: list[str] | tuple[str, ...] = ('ferromagnetic', 'antiferromagnetic'), automatic: bool = True, truncate_by_symmetry: bool = True, transformation_kwargs: dict | None = None)[source]
                                                  +class MagneticStructureEnumerator(structure: Structure, default_magmoms: dict[str, float] | None = None, strategies: list[str] | tuple[str, ...] = ('ferromagnetic', 'antiferromagnetic'), automatic: bool = True, truncate_by_symmetry: bool = True, transformation_kwargs: dict | None = None)[source]

                                                  Bases: object

                                                  Combines MagneticStructureAnalyzer and MagOrderingTransformation to automatically generate a set of transformations for a given structure @@ -385,78 +385,78 @@

                                                  -available_strategies = ('ferromagnetic', 'antiferromagnetic', 'ferrimagnetic_by_motif', 'ferrimagnetic_by_species', 'antiferromagnetic_by_motif', 'nonmagnetic')[source]
                                                  +available_strategies = ('ferromagnetic', 'antiferromagnetic', 'ferrimagnetic_by_motif', 'ferrimagnetic_by_species', 'antiferromagnetic_by_motif', 'nonmagnetic')[source]
                                                  -class Ordering(value)[source]
                                                  +class Ordering(value)[source]

                                                  Bases: enum.Enum

                                                  Enumeration defining possible magnetic orderings.

                                                  -AFM = 'AFM'[source]
                                                  +AFM = 'AFM'[source]
                                                  -FM = 'FM'[source]
                                                  +FM = 'FM'[source]
                                                  -FiM = 'FiM'[source]
                                                  +FiM = 'FiM'[source]
                                                  -NM = 'NM'[source]
                                                  +NM = 'NM'[source]
                                                  -Unknown = 'Unknown'[source]
                                                  +Unknown = 'Unknown'[source]
                                                  -class OverwriteMagmomMode(value)[source]
                                                  +class OverwriteMagmomMode(value)[source]

                                                  Bases: enum.Enum

                                                  Enumeration defining different modes for analyzer.

                                                  -none = 'none'[source]
                                                  +none = 'none'[source]
                                                  -normalize = 'normalize'[source]
                                                  +normalize = 'normalize'[source]
                                                  -replace_all = 'replace_all'[source]
                                                  +replace_all = 'replace_all'[source]
                                                  -respect_sign = 'respect_sign'[source]
                                                  +respect_sign = 'respect_sign'[source]
                                                  -respect_zero = 'respect_zeros'[source]
                                                  +respect_zero = 'respect_zeros'[source]
                                                  -magnetic_deformation(structure_A: pymatgen.core.structure.Structure, structure_B: pymatgen.core.structure.Structure) → pymatgen.analysis.magnetism.analyzer.MagneticDeformation[source]
                                                  +magnetic_deformation(structure_A: pymatgen.core.structure.Structure, structure_B: pymatgen.core.structure.Structure) → pymatgen.analysis.magnetism.analyzer.MagneticDeformation[source]

                                                  Calculates ‘magnetic deformation proxy’, a measure of deformation (norm of finite strain) between ‘non-magnetic’ (non-spin-polarized) and diff --git a/docs/pymatgen.analysis.magnetism.heisenberg.html b/docs/pymatgen.analysis.magnetism.heisenberg.html index 8aa51a81f09..8ada252f4b0 100644 --- a/docs/pymatgen.analysis.magnetism.heisenberg.html +++ b/docs/pymatgen.analysis.magnetism.heisenberg.html @@ -4,7 +4,7 @@ - pymatgen.analysis.magnetism.heisenberg module — pymatgen 2022.5.18 documentation + pymatgen.analysis.magnetism.heisenberg module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                                  - 2022.5.18 + 2022.5.18.1
                                                  @@ -121,7 +121,7 @@ model.

                                                  -class HeisenbergMapper(ordered_structures, energies, cutoff=0.0, tol=0.02)[source]
                                                  +class HeisenbergMapper(ordered_structures, energies, cutoff=0.0, tol=0.02)[source]

                                                  Bases: object

                                                  Class to compute exchange parameters from low energy magnetic orderings.

                                                  Exchange parameters are computed by mapping to a classical Heisenberg @@ -161,7 +161,7 @@

                                                  -estimate_exchange(fm_struct=None, afm_struct=None, fm_e=None, afm_e=None)[source]
                                                  +estimate_exchange(fm_struct=None, afm_struct=None, fm_e=None, afm_e=None)[source]

                                                  Estimate <J> for a structure based on low energy FM and AFM orderings.

                                                  Parameters
                                                  @@ -183,7 +183,7 @@
                                                  -get_exchange()[source]
                                                  +get_exchange()[source]

                                                  Take Heisenberg Hamiltonian and corresponding energy for each row and solve for the exchange parameters.

                                                  @@ -198,7 +198,7 @@
                                                  -get_heisenberg_model()[source]
                                                  +get_heisenberg_model()[source]

                                                  Save results of mapping to a HeisenbergModel object.

                                                  Returns
                                                  @@ -212,7 +212,7 @@
                                                  -get_interaction_graph(filename=None)[source]
                                                  +get_interaction_graph(filename=None)[source]

                                                  Get a StructureGraph with edges and weights that correspond to exchange interactions and J_ij values, respectively.

                                                  @@ -230,7 +230,7 @@
                                                  -get_low_energy_orderings()[source]
                                                  +get_low_energy_orderings()[source]

                                                  Find lowest energy FM and AFM orderings to compute E_AFM - E_FM.

                                                  Returns
                                                  @@ -247,7 +247,7 @@
                                                  -get_mft_temperature(j_avg)[source]
                                                  +get_mft_temperature(j_avg)[source]

                                                  Crude mean field estimate of critical temperature based on <J> for one sublattice, or solving the coupled equations for a multisublattice material.

                                                  @@ -268,7 +268,7 @@
                                                  -class HeisenbergModel(formula=None, structures=None, energies=None, cutoff=None, tol=None, sgraphs=None, unique_site_ids=None, wyckoff_ids=None, nn_interactions=None, dists=None, ex_mat=None, ex_params=None, javg=None, igraph=None)[source]
                                                  +class HeisenbergModel(formula=None, structures=None, energies=None, cutoff=None, tol=None, sgraphs=None, unique_site_ids=None, wyckoff_ids=None, nn_interactions=None, dists=None, ex_mat=None, ex_params=None, javg=None, igraph=None)[source]

                                                  Bases: monty.json.MSONable

                                                  Store a Heisenberg model fit to low-energy magnetic orderings. Intended to be generated by HeisenbergMapper.get_heisenberg_model().

                                                  @@ -298,13 +298,13 @@
                                                  -as_dict()[source]
                                                  +as_dict()[source]

                                                  Because some dicts have tuple keys, some sanitization is required for json compatibility.

                                                  -classmethod from_dict(d)[source]
                                                  +classmethod from_dict(d)[source]

                                                  Create a HeisenbergModel from a dict.

                                                  @@ -312,7 +312,7 @@
                                                  -class HeisenbergScreener(structures, energies, screen=False)[source]
                                                  +class HeisenbergScreener(structures, energies, screen=False)[source]

                                                  Bases: object

                                                  Class to clean and screen magnetic orderings.

                                                  This class pre-processes magnetic orderings and energies for @@ -329,7 +329,7 @@

                                                  -screened_structures[source]
                                                  +screened_structures[source]

                                                  Sorted structures.

                                                  Type
                                                  @@ -340,7 +340,7 @@
                                                  -screened_energies[source]
                                                  +screened_energies[source]

                                                  Sorted energies.

                                                  Type
                                                  diff --git a/docs/pymatgen.analysis.magnetism.html b/docs/pymatgen.analysis.magnetism.html index bf691261c73..f4c78e07c02 100644 --- a/docs/pymatgen.analysis.magnetism.html +++ b/docs/pymatgen.analysis.magnetism.html @@ -4,7 +4,7 @@ - pymatgen.analysis.magnetism package — pymatgen 2022.5.18 documentation + pymatgen.analysis.magnetism package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                  - 2022.5.18 + 2022.5.18.1
                                                  diff --git a/docs/pymatgen.analysis.magnetism.jahnteller.html b/docs/pymatgen.analysis.magnetism.jahnteller.html index e5857148a78..1ee2804cd79 100644 --- a/docs/pymatgen.analysis.magnetism.jahnteller.html +++ b/docs/pymatgen.analysis.magnetism.jahnteller.html @@ -4,7 +4,7 @@ - pymatgen.analysis.magnetism.jahnteller module — pymatgen 2022.5.18 documentation + pymatgen.analysis.magnetism.jahnteller module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                  - 2022.5.18 + 2022.5.18.1
                                                  @@ -119,7 +119,7 @@

                                                  JahnTeller distortion analysis.

                                                  -class JahnTellerAnalyzer[source]
                                                  +class JahnTellerAnalyzer[source]

                                                  Bases: object

                                                  Will attempt to classify if structure may be Jahn-Teller active. Class currently uses datafile of hard-coded common Jahn-Teller @@ -130,7 +130,7 @@

                                                  Init for JahnTellerAnalyzer.

                                                  -get_analysis(structure: pymatgen.core.structure.Structure, calculate_valences: bool = True, guesstimate_spin: bool = False, op_threshold: float = 0.1) → dict[source]
                                                  +get_analysis(structure: pymatgen.core.structure.Structure, calculate_valences: bool = True, guesstimate_spin: bool = False, op_threshold: float = 0.1) → dict[source]

                                                  Convenience method, uses get_analysis_and_structure method.

                                                  Obtain an analysis of a given structure and if it may be Jahn-Teller active or not. This is a heuristic, and may give false positives and @@ -158,7 +158,7 @@

                                                  -get_analysis_and_structure(structure: pymatgen.core.structure.Structure, calculate_valences: bool = True, guesstimate_spin: bool = False, op_threshold: float = 0.1) → tuple[dict, pymatgen.core.structure.Structure][source]
                                                  +get_analysis_and_structure(structure: pymatgen.core.structure.Structure, calculate_valences: bool = True, guesstimate_spin: bool = False, op_threshold: float = 0.1) → tuple[dict, pymatgen.core.structure.Structure][source]

                                                  Obtain an analysis of a given structure and if it may be Jahn-Teller active or not. This is a heuristic, and may give false positives and false negatives (false positives are preferred).

                                                  @@ -185,7 +185,7 @@
                                                  -get_magnitude_of_effect_from_species(species: str | Species, spin_state: str, motif: str) → str[source]
                                                  +get_magnitude_of_effect_from_species(species: str | Species, spin_state: str, motif: str) → str[source]

                                                  Get magnitude of Jahn-Teller effect from provided species, spin state and motif.

                                                  Parameters
                                                  @@ -201,7 +201,7 @@
                                                  -static get_magnitude_of_effect_from_spin_config(motif: str, spin_config: dict[str, float]) → str[source]
                                                  +static get_magnitude_of_effect_from_spin_config(motif: str, spin_config: dict[str, float]) → str[source]

                                                  Roughly, the magnitude of Jahn-Teller distortion will be: * in octahedral environments, strong if e_g orbitals unevenly occupied but weak if t_2g orbitals unevenly @@ -221,7 +221,7 @@

                                                  -is_jahn_teller_active(structure: pymatgen.core.structure.Structure, calculate_valences: bool = True, guesstimate_spin: bool = False, op_threshold: float = 0.1) → bool[source]
                                                  +is_jahn_teller_active(structure: pymatgen.core.structure.Structure, calculate_valences: bool = True, guesstimate_spin: bool = False, op_threshold: float = 0.1) → bool[source]

                                                  Convenience method, uses get_analysis_and_structure method. Check if a given structure and if it may be Jahn-Teller active or not. This is a heuristic, and may give false positives and @@ -248,7 +248,7 @@

                                                  -static mu_so(species: str | Species, motif: Literal['oct', 'tet'], spin_state: Literal['high', 'low']) → float | None[source]
                                                  +static mu_so(species: str | Species, motif: Literal['oct', 'tet'], spin_state: Literal['high', 'low']) → float | None[source]

                                                  Calculates the spin-only magnetic moment for a given species. Only supports transition metals.

                                                  @@ -274,7 +274,7 @@
                                                  -tag_structure(structure: pymatgen.core.structure.Structure, calculate_valences: bool = True, guesstimate_spin: bool = False, op_threshold: float = 0.1) → pymatgen.core.structure.Structure[source]
                                                  +tag_structure(structure: pymatgen.core.structure.Structure, calculate_valences: bool = True, guesstimate_spin: bool = False, op_threshold: float = 0.1) → pymatgen.core.structure.Structure[source]

                                                  Convenience method, uses get_analysis_and_structure method. Add a “possible_jt_active” site property on Structure.

                                                  diff --git a/docs/pymatgen.analysis.molecule_matcher.html b/docs/pymatgen.analysis.molecule_matcher.html index 1484a2fad2b..463b324bf34 100644 --- a/docs/pymatgen.analysis.molecule_matcher.html +++ b/docs/pymatgen.analysis.molecule_matcher.html @@ -4,7 +4,7 @@ - pymatgen.analysis.molecule_matcher module — pymatgen 2022.5.18 documentation + pymatgen.analysis.molecule_matcher module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                  - 2022.5.18 + 2022.5.18.1
                                                  @@ -124,14 +124,14 @@ you can find at https://github.com/charnley/rmsd.

                                                  -class AbstractMolAtomMapper[source]
                                                  +class AbstractMolAtomMapper[source]

                                                  Bases: monty.json.MSONable

                                                  Abstract molecular atom order mapping class. A mapping will be able to find the uniform atom order of two molecules that can pair the geometrically equivalent atoms.

                                                  -classmethod from_dict(d)[source]
                                                  +classmethod from_dict(d)[source]
                                                  Parameters

                                                  () (d) – Dict

                                                  @@ -144,7 +144,7 @@
                                                  -abstract get_molecule_hash(mol)[source]
                                                  +abstract get_molecule_hash(mol)[source]

                                                  Defines a hash for molecules. This allows molecules to be grouped efficiently for comparison.

                                                  @@ -159,7 +159,7 @@
                                                  -abstract uniform_labels(mol1, mol2)[source]
                                                  +abstract uniform_labels(mol1, mol2)[source]

                                                  Pair the geometrically equivalent atoms of the molecules.

                                                  Parameters
                                                  @@ -184,7 +184,7 @@
                                                  -class BruteForceOrderMatcher(target: pymatgen.core.structure.Molecule)[source]
                                                  +class BruteForceOrderMatcher(target: pymatgen.core.structure.Molecule)[source]

                                                  Bases: pymatgen.analysis.molecule_matcher.KabschMatcher

                                                  Finding the best match between molecules by selecting molecule order with the smallest RMSD from all the possible order combinations.

                                                  @@ -199,7 +199,7 @@
                                                  -fit(p: pymatgen.core.structure.Molecule, ignore_warning=False)[source]
                                                  +fit(p: pymatgen.core.structure.Molecule, ignore_warning=False)[source]

                                                  Order, rotate and transform p molecule according to the best match.

                                                  A ValueError will be raised when the total number of possible combinations become unfeasible (more than a million combinations).

                                                  @@ -222,7 +222,7 @@
                                                  -match(p: pymatgen.core.structure.Molecule, ignore_warning=False)[source]
                                                  +match(p: pymatgen.core.structure.Molecule, ignore_warning=False)[source]

                                                  Similar as KabschMatcher.match but this method also finds the order of atoms which belongs to the best match.

                                                  A ValueError will be raised when the total number of possible combinations @@ -248,7 +248,7 @@

                                                  -static permutations(atoms)[source]
                                                  +static permutations(atoms)[source]

                                                  Generates all the possible permutations of atom order. To achieve better performance all the cases where the atoms are different has been ignored.

                                                  @@ -257,7 +257,7 @@
                                                  -class GeneticOrderMatcher(target: pymatgen.core.structure.Molecule, threshold: float)[source]
                                                  +class GeneticOrderMatcher(target: pymatgen.core.structure.Molecule, threshold: float)[source]

                                                  Bases: pymatgen.analysis.molecule_matcher.KabschMatcher

                                                  This method was inspired by genetic algorithms and tries to match molecules based on their already matched fragments.

                                                  @@ -286,7 +286,7 @@
                                                  -fit(p: pymatgen.core.structure.Molecule)[source]
                                                  +fit(p: pymatgen.core.structure.Molecule)[source]

                                                  Order, rotate and transform all of the matched p molecule according to the given threshold.

                                                  @@ -305,7 +305,7 @@
                                                  -match(p: pymatgen.core.structure.Molecule)[source]
                                                  +match(p: pymatgen.core.structure.Molecule)[source]

                                                  Similar as KabschMatcher.match but this method also finds all of the possible atomic orders according to the threshold.

                                                  @@ -326,7 +326,7 @@
                                                  -permutations(p: pymatgen.core.structure.Molecule)[source]
                                                  +permutations(p: pymatgen.core.structure.Molecule)[source]

                                                  Generates all of possible permutations of atom order according the threshold.

                                                  Parameters
                                                  @@ -342,7 +342,7 @@
                                                  -class HungarianOrderMatcher(target: pymatgen.core.structure.Molecule)[source]
                                                  +class HungarianOrderMatcher(target: pymatgen.core.structure.Molecule)[source]

                                                  Bases: pymatgen.analysis.molecule_matcher.KabschMatcher

                                                  This method pre-aligns the molecules based on their principal inertia axis and then re-orders the input atom list using the Hungarian method.

                                                  @@ -358,7 +358,7 @@
                                                  -fit(p: pymatgen.core.structure.Molecule)[source]
                                                  +fit(p: pymatgen.core.structure.Molecule)[source]

                                                  Order, rotate and transform p molecule according to the best match.

                                                  Parameters
                                                  @@ -376,7 +376,7 @@
                                                  -static get_principal_axis(coords, weights)[source]
                                                  +static get_principal_axis(coords, weights)[source]

                                                  Get the molecule’s principal axis.

                                                  Parameters
                                                  @@ -393,7 +393,7 @@
                                                  -match(p: pymatgen.core.structure.Molecule)[source]
                                                  +match(p: pymatgen.core.structure.Molecule)[source]

                                                  Similar as KabschMatcher.match but this method also finds the order of atoms which belongs to the best match.

                                                  @@ -414,7 +414,7 @@
                                                  -static permutations(p_atoms, p_centroid, p_weights, q_atoms, q_centroid, q_weights)[source]
                                                  +static permutations(p_atoms, p_centroid, p_weights, q_atoms, q_centroid, q_weights)[source]

                                                  Generates two possible permutations of atom order. This method uses the principle component of the inertia tensor to prealign the molecules and hungarian method to determine the order. There are always two possible permutation depending on the way to pre-aligning the molecules.

                                                  @@ -437,7 +437,7 @@
                                                  -static rotation_matrix_vectors(v1, v2)[source]
                                                  +static rotation_matrix_vectors(v1, v2)[source]

                                                  Returns the rotation matrix that rotates v1 onto v2 using Rodrigues’ rotation formula.

                                                  See more: https://math.stackexchange.com/a/476311

                                                  @@ -458,7 +458,7 @@
                                                  -class InchiMolAtomMapper(angle_tolerance=10.0)[source]
                                                  +class InchiMolAtomMapper(angle_tolerance=10.0)[source]

                                                  Bases: pymatgen.analysis.molecule_matcher.AbstractMolAtomMapper

                                                  Pair atoms by inchi labels.

                                                  @@ -468,7 +468,7 @@
                                                  -as_dict()[source]
                                                  +as_dict()[source]
                                                  Returns

                                                  MSONAble dict.

                                                  @@ -478,7 +478,7 @@
                                                  -classmethod from_dict(d)[source]
                                                  +classmethod from_dict(d)[source]
                                                  Parameters

                                                  d (dict) – Dict Representation

                                                  @@ -491,13 +491,13 @@
                                                  -get_molecule_hash(mol)[source]
                                                  +get_molecule_hash(mol)[source]

                                                  Return inchi as molecular hash

                                                  -uniform_labels(mol1, mol2)[source]
                                                  +uniform_labels(mol1, mol2)[source]
                                                  Parameters
                                                    @@ -515,12 +515,12 @@
                                                    -class IsomorphismMolAtomMapper[source]
                                                    +class IsomorphismMolAtomMapper[source]

                                                    Bases: pymatgen.analysis.molecule_matcher.AbstractMolAtomMapper

                                                    Pair atoms by isomorphism permutations in the OpenBabel::OBAlign class

                                                    -as_dict()[source]
                                                    +as_dict()[source]
                                                    Returns

                                                    Jsonable dict.

                                                    @@ -530,7 +530,7 @@
                                                    -classmethod from_dict(d)[source]
                                                    +classmethod from_dict(d)[source]
                                                    Parameters

                                                    d (dict) – Dict representation

                                                    @@ -543,13 +543,13 @@
                                                    -get_molecule_hash(mol)[source]
                                                    +get_molecule_hash(mol)[source]

                                                    Return inchi as molecular hash

                                                    -uniform_labels(mol1, mol2)[source]
                                                    +uniform_labels(mol1, mol2)[source]

                                                    Pair the geometrically equivalent atoms of the molecules. Calculate RMSD on all possible isomorphism mappings and return mapping with the least RMSD

                                                    @@ -576,7 +576,7 @@
                                                    -class KabschMatcher(target: pymatgen.core.structure.Molecule)[source]
                                                    +class KabschMatcher(target: pymatgen.core.structure.Molecule)[source]

                                                    Bases: monty.json.MSONable

                                                    Molecule matcher using Kabsch algorithm

                                                    The Kabsch algorithm capable aligning two molecules by finding the parameters @@ -593,7 +593,7 @@

                                                    -fit(p: pymatgen.core.structure.Molecule)[source]
                                                    +fit(p: pymatgen.core.structure.Molecule)[source]

                                                    Rotate and transform p molecule according to the best match.

                                                    Parameters
                                                    @@ -611,7 +611,7 @@
                                                    -static kabsch(P: numpy.ndarray, Q: numpy.ndarray)[source]
                                                    +static kabsch(P: numpy.ndarray, Q: numpy.ndarray)[source]

                                                    The Kabsch algorithm is a method for calculating the optimal rotation matrix that minimizes the root mean squared deviation (RMSD) between two paired sets of points P and Q, centered around the their centroid.

                                                    @@ -636,7 +636,7 @@
                                                    -match(p: pymatgen.core.structure.Molecule)[source]
                                                    +match(p: pymatgen.core.structure.Molecule)[source]

                                                    Using the Kabsch algorithm the alignment of two molecules (P, Q) happens in three steps: - translate the P and Q into their centroid @@ -666,7 +666,7 @@

                                                    -class MoleculeMatcher(tolerance=0.01, mapper=<pymatgen.analysis.molecule_matcher.InchiMolAtomMapper object>)[source]
                                                    +class MoleculeMatcher(tolerance=0.01, mapper=<pymatgen.analysis.molecule_matcher.InchiMolAtomMapper object>)[source]

                                                    Bases: monty.json.MSONable

                                                    Class to match molecules and identify whether molecules are the same.

                                                    @@ -681,7 +681,7 @@
                                                    -as_dict()[source]
                                                    +as_dict()[source]
                                                    Returns

                                                    MSONAble dict.

                                                    @@ -691,7 +691,7 @@
                                                    -fit(mol1, mol2)[source]
                                                    +fit(mol1, mol2)[source]

                                                    Fit two molecules.

                                                    Parameters
                                                    @@ -708,7 +708,7 @@
                                                    -classmethod from_dict(d)[source]
                                                    +classmethod from_dict(d)[source]
                                                    Parameters

                                                    d (dict) – Dict representation

                                                    @@ -721,7 +721,7 @@
                                                    -get_rmsd(mol1, mol2)[source]
                                                    +get_rmsd(mol1, mol2)[source]

                                                    Get RMSD between two molecule with arbitrary atom order.

                                                    Returns
                                                    @@ -733,7 +733,7 @@
                                                    -group_molecules(mol_list)[source]
                                                    +group_molecules(mol_list)[source]

                                                    Group molecules by structural equality.

                                                    Parameters
                                                    diff --git a/docs/pymatgen.analysis.molecule_structure_comparator.html b/docs/pymatgen.analysis.molecule_structure_comparator.html index 2c9de894d4c..14bea8f17b9 100644 --- a/docs/pymatgen.analysis.molecule_structure_comparator.html +++ b/docs/pymatgen.analysis.molecule_structure_comparator.html @@ -4,7 +4,7 @@ - pymatgen.analysis.molecule_structure_comparator module — pymatgen 2022.5.18 documentation + pymatgen.analysis.molecule_structure_comparator module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                    - 2022.5.18 + 2022.5.18.1
                                                    @@ -124,20 +124,20 @@ comparisons without the atom order correspondence prerequisite.

                                                    -class CovalentRadius[source]
                                                    +class CovalentRadius[source]

                                                    Bases: object

                                                    Covalent Radius of the elements.

                                                    Beatriz C. et al. Dalton Trans. 2008, 2832-2838. DOI: 10.1039/b801115j

                                                    -radius = {'Ac': 2.15, 'Ag': 1.45, 'Al': 1.21, 'Am': 1.8, 'Ar': 1.06, 'As': 1.19, 'At': 1.5, 'Au': 1.36, 'B': 0.84, 'Ba': 2.15, 'Be': 0.96, 'Bi': 1.48, 'Br': 1.2, 'C': 0.73, 'Ca': 1.76, 'Cd': 1.44, 'Ce': 2.04, 'Cl': 1.02, 'Cm': 1.69, 'Co': 1.38, 'Cr': 1.39, 'Cs': 2.44, 'Cu': 1.32, 'Dy': 1.92, 'Er': 1.89, 'Eu': 1.98, 'F': 0.57, 'Fe': 1.42, 'Fr': 2.6, 'Ga': 1.22, 'Gd': 1.96, 'Ge': 1.2, 'H': 0.31, 'He': 0.28, 'Hf': 1.75, 'Hg': 1.32, 'Ho': 1.92, 'I': 1.39, 'In': 1.42, 'Ir': 1.41, 'K': 2.03, 'Kr': 1.16, 'La': 2.07, 'Li': 1.28, 'Lu': 1.87, 'Mg': 1.41, 'Mn': 1.5, 'Mo': 1.54, 'N': 0.71, 'Na': 1.66, 'Nb': 1.64, 'Nd': 2.01, 'Ne': 0.58, 'Ni': 1.24, 'Np': 1.9, 'O': 0.66, 'Os': 1.44, 'P': 1.07, 'Pa': 2.0, 'Pb': 1.46, 'Pd': 1.39, 'Pm': 1.99, 'Po': 1.4, 'Pr': 2.03, 'Pt': 1.36, 'Pu': 1.87, 'Ra': 2.21, 'Rb': 2.2, 'Re': 1.51, 'Rh': 1.42, 'Rn': 1.5, 'Ru': 1.46, 'S': 1.05, 'Sb': 1.39, 'Sc': 1.7, 'Se': 1.2, 'Si': 1.11, 'Sm': 1.98, 'Sn': 1.39, 'Sr': 1.95, 'Ta': 1.7, 'Tb': 1.94, 'Tc': 1.47, 'Te': 1.38, 'Th': 2.06, 'Ti': 1.6, 'Tl': 1.45, 'Tm': 1.9, 'U': 1.96, 'V': 1.53, 'W': 1.62, 'Xe': 1.4, 'Y': 1.9, 'Yb': 1.87, 'Zn': 1.22, 'Zr': 1.75}[source]
                                                    +radius = {'Ac': 2.15, 'Ag': 1.45, 'Al': 1.21, 'Am': 1.8, 'Ar': 1.06, 'As': 1.19, 'At': 1.5, 'Au': 1.36, 'B': 0.84, 'Ba': 2.15, 'Be': 0.96, 'Bi': 1.48, 'Br': 1.2, 'C': 0.73, 'Ca': 1.76, 'Cd': 1.44, 'Ce': 2.04, 'Cl': 1.02, 'Cm': 1.69, 'Co': 1.38, 'Cr': 1.39, 'Cs': 2.44, 'Cu': 1.32, 'Dy': 1.92, 'Er': 1.89, 'Eu': 1.98, 'F': 0.57, 'Fe': 1.42, 'Fr': 2.6, 'Ga': 1.22, 'Gd': 1.96, 'Ge': 1.2, 'H': 0.31, 'He': 0.28, 'Hf': 1.75, 'Hg': 1.32, 'Ho': 1.92, 'I': 1.39, 'In': 1.42, 'Ir': 1.41, 'K': 2.03, 'Kr': 1.16, 'La': 2.07, 'Li': 1.28, 'Lu': 1.87, 'Mg': 1.41, 'Mn': 1.5, 'Mo': 1.54, 'N': 0.71, 'Na': 1.66, 'Nb': 1.64, 'Nd': 2.01, 'Ne': 0.58, 'Ni': 1.24, 'Np': 1.9, 'O': 0.66, 'Os': 1.44, 'P': 1.07, 'Pa': 2.0, 'Pb': 1.46, 'Pd': 1.39, 'Pm': 1.99, 'Po': 1.4, 'Pr': 2.03, 'Pt': 1.36, 'Pu': 1.87, 'Ra': 2.21, 'Rb': 2.2, 'Re': 1.51, 'Rh': 1.42, 'Rn': 1.5, 'Ru': 1.46, 'S': 1.05, 'Sb': 1.39, 'Sc': 1.7, 'Se': 1.2, 'Si': 1.11, 'Sm': 1.98, 'Sn': 1.39, 'Sr': 1.95, 'Ta': 1.7, 'Tb': 1.94, 'Tc': 1.47, 'Te': 1.38, 'Th': 2.06, 'Ti': 1.6, 'Tl': 1.45, 'Tm': 1.9, 'U': 1.96, 'V': 1.53, 'W': 1.62, 'Xe': 1.4, 'Y': 1.9, 'Yb': 1.87, 'Zn': 1.22, 'Zr': 1.75}[source]
                                                    -class MoleculeStructureComparator(bond_length_cap=0.3, covalent_radius={'Ac': 2.15, 'Ag': 1.45, 'Al': 1.21, 'Am': 1.8, 'Ar': 1.06, 'As': 1.19, 'At': 1.5, 'Au': 1.36, 'B': 0.84, 'Ba': 2.15, 'Be': 0.96, 'Bi': 1.48, 'Br': 1.2, 'C': 0.73, 'Ca': 1.76, 'Cd': 1.44, 'Ce': 2.04, 'Cl': 1.02, 'Cm': 1.69, 'Co': 1.38, 'Cr': 1.39, 'Cs': 2.44, 'Cu': 1.32, 'Dy': 1.92, 'Er': 1.89, 'Eu': 1.98, 'F': 0.57, 'Fe': 1.42, 'Fr': 2.6, 'Ga': 1.22, 'Gd': 1.96, 'Ge': 1.2, 'H': 0.31, 'He': 0.28, 'Hf': 1.75, 'Hg': 1.32, 'Ho': 1.92, 'I': 1.39, 'In': 1.42, 'Ir': 1.41, 'K': 2.03, 'Kr': 1.16, 'La': 2.07, 'Li': 1.28, 'Lu': 1.87, 'Mg': 1.41, 'Mn': 1.5, 'Mo': 1.54, 'N': 0.71, 'Na': 1.66, 'Nb': 1.64, 'Nd': 2.01, 'Ne': 0.58, 'Ni': 1.24, 'Np': 1.9, 'O': 0.66, 'Os': 1.44, 'P': 1.07, 'Pa': 2.0, 'Pb': 1.46, 'Pd': 1.39, 'Pm': 1.99, 'Po': 1.4, 'Pr': 2.03, 'Pt': 1.36, 'Pu': 1.87, 'Ra': 2.21, 'Rb': 2.2, 'Re': 1.51, 'Rh': 1.42, 'Rn': 1.5, 'Ru': 1.46, 'S': 1.05, 'Sb': 1.39, 'Sc': 1.7, 'Se': 1.2, 'Si': 1.11, 'Sm': 1.98, 'Sn': 1.39, 'Sr': 1.95, 'Ta': 1.7, 'Tb': 1.94, 'Tc': 1.47, 'Te': 1.38, 'Th': 2.06, 'Ti': 1.6, 'Tl': 1.45, 'Tm': 1.9, 'U': 1.96, 'V': 1.53, 'W': 1.62, 'Xe': 1.4, 'Y': 1.9, 'Yb': 1.87, 'Zn': 1.22, 'Zr': 1.75}, priority_bonds=(), priority_cap=0.8, ignore_ionic_bond=True, bond_13_cap=0.05)[source]
                                                    +class MoleculeStructureComparator(bond_length_cap=0.3, covalent_radius={'Ac': 2.15, 'Ag': 1.45, 'Al': 1.21, 'Am': 1.8, 'Ar': 1.06, 'As': 1.19, 'At': 1.5, 'Au': 1.36, 'B': 0.84, 'Ba': 2.15, 'Be': 0.96, 'Bi': 1.48, 'Br': 1.2, 'C': 0.73, 'Ca': 1.76, 'Cd': 1.44, 'Ce': 2.04, 'Cl': 1.02, 'Cm': 1.69, 'Co': 1.38, 'Cr': 1.39, 'Cs': 2.44, 'Cu': 1.32, 'Dy': 1.92, 'Er': 1.89, 'Eu': 1.98, 'F': 0.57, 'Fe': 1.42, 'Fr': 2.6, 'Ga': 1.22, 'Gd': 1.96, 'Ge': 1.2, 'H': 0.31, 'He': 0.28, 'Hf': 1.75, 'Hg': 1.32, 'Ho': 1.92, 'I': 1.39, 'In': 1.42, 'Ir': 1.41, 'K': 2.03, 'Kr': 1.16, 'La': 2.07, 'Li': 1.28, 'Lu': 1.87, 'Mg': 1.41, 'Mn': 1.5, 'Mo': 1.54, 'N': 0.71, 'Na': 1.66, 'Nb': 1.64, 'Nd': 2.01, 'Ne': 0.58, 'Ni': 1.24, 'Np': 1.9, 'O': 0.66, 'Os': 1.44, 'P': 1.07, 'Pa': 2.0, 'Pb': 1.46, 'Pd': 1.39, 'Pm': 1.99, 'Po': 1.4, 'Pr': 2.03, 'Pt': 1.36, 'Pu': 1.87, 'Ra': 2.21, 'Rb': 2.2, 'Re': 1.51, 'Rh': 1.42, 'Rn': 1.5, 'Ru': 1.46, 'S': 1.05, 'Sb': 1.39, 'Sc': 1.7, 'Se': 1.2, 'Si': 1.11, 'Sm': 1.98, 'Sn': 1.39, 'Sr': 1.95, 'Ta': 1.7, 'Tb': 1.94, 'Tc': 1.47, 'Te': 1.38, 'Th': 2.06, 'Ti': 1.6, 'Tl': 1.45, 'Tm': 1.9, 'U': 1.96, 'V': 1.53, 'W': 1.62, 'Xe': 1.4, 'Y': 1.9, 'Yb': 1.87, 'Zn': 1.22, 'Zr': 1.75}, priority_bonds=(), priority_cap=0.8, ignore_ionic_bond=True, bond_13_cap=0.05)[source]

                                                    Bases: monty.json.MSONable

                                                    Class to check whether the connection tables of the two molecules are the same. The atom in the two molecule must be paired accordingly.

                                                    @@ -160,7 +160,7 @@
                                                    -are_equal(mol1, mol2)[source]
                                                    +are_equal(mol1, mol2)[source]

                                                    Compare the bond table of the two molecules.

                                                    Parameters
                                                    @@ -174,13 +174,13 @@
                                                    -as_dict()[source]
                                                    +as_dict()[source]

                                                    Returns: MSONable dict

                                                    -classmethod from_dict(d)[source]
                                                    +classmethod from_dict(d)[source]
                                                    Parameters

                                                    d (dict) – Dict representation

                                                    @@ -193,7 +193,7 @@
                                                    -static get_13_bonds(priority_bonds)[source]
                                                    +static get_13_bonds(priority_bonds)[source]
                                                    Parameters

                                                    () (priority_bonds) –

                                                    @@ -204,12 +204,12 @@
                                                    -halogen_list = ['F', 'Cl', 'Br', 'I'][source]
                                                    +halogen_list = ['F', 'Cl', 'Br', 'I'][source]
                                                    -ionic_element_list = ['Na', 'Mg', 'Al', 'Sc', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Rb', 'Sr'][source]
                                                    +ionic_element_list = ['Na', 'Mg', 'Al', 'Sc', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Rb', 'Sr'][source]
                                                    diff --git a/docs/pymatgen.analysis.nmr.html b/docs/pymatgen.analysis.nmr.html index 2ff8cce201c..6c09a908b05 100644 --- a/docs/pymatgen.analysis.nmr.html +++ b/docs/pymatgen.analysis.nmr.html @@ -4,7 +4,7 @@ - pymatgen.analysis.nmr module — pymatgen 2022.5.18 documentation + pymatgen.analysis.nmr module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                    - 2022.5.18 + 2022.5.18.1
                                                    @@ -118,7 +118,7 @@

                                                    A module for NMR analysis

                                                    -class ChemicalShielding(cs_matrix, vscale=None)[source]
                                                    +class ChemicalShielding(cs_matrix, vscale=None)[source]

                                                    Bases: pymatgen.core.tensors.SquareTensor

                                                    This class extends the SquareTensor to perform extra analysis unique to NMR Chemical shielding tensors

                                                    @@ -143,30 +143,30 @@
                                                    -class HaeberlenNotation(sigma_iso, delta_sigma_iso, zeta, eta)[source]
                                                    +class HaeberlenNotation(sigma_iso, delta_sigma_iso, zeta, eta)[source]

                                                    Bases: tuple

                                                    Create new instance of HaeberlenNotation(sigma_iso, delta_sigma_iso, zeta, eta)

                                                    -delta_sigma_iso[source]
                                                    +delta_sigma_iso[source]

                                                    Alias for field number 1

                                                    -eta[source]
                                                    +eta[source]

                                                    Alias for field number 3

                                                    -sigma_iso[source]
                                                    +sigma_iso[source]

                                                    Alias for field number 0

                                                    -zeta[source]
                                                    +zeta[source]

                                                    Alias for field number 2

                                                    @@ -174,24 +174,24 @@
                                                    -class MarylandNotation(sigma_iso, omega, kappa)[source]
                                                    +class MarylandNotation(sigma_iso, omega, kappa)[source]

                                                    Bases: tuple

                                                    Create new instance of MarylandNotation(sigma_iso, omega, kappa)

                                                    -kappa[source]
                                                    +kappa[source]

                                                    Alias for field number 2

                                                    -omega[source]
                                                    +omega[source]

                                                    Alias for field number 1

                                                    -sigma_iso[source]
                                                    +sigma_iso[source]

                                                    Alias for field number 0

                                                    @@ -199,30 +199,30 @@
                                                    -class MehringNotation(sigma_iso, sigma_11, sigma_22, sigma_33)[source]
                                                    +class MehringNotation(sigma_iso, sigma_11, sigma_22, sigma_33)[source]

                                                    Bases: tuple

                                                    Create new instance of MehringNotation(sigma_iso, sigma_11, sigma_22, sigma_33)

                                                    -sigma_11[source]
                                                    +sigma_11[source]

                                                    Alias for field number 1

                                                    -sigma_22[source]
                                                    +sigma_22[source]

                                                    Alias for field number 2

                                                    -sigma_33[source]
                                                    +sigma_33[source]

                                                    Alias for field number 3

                                                    -sigma_iso[source]
                                                    +sigma_iso[source]

                                                    Alias for field number 0

                                                    @@ -230,7 +230,7 @@
                                                    -classmethod from_maryland_notation(sigma_iso, omega, kappa)[source]
                                                    +classmethod from_maryland_notation(sigma_iso, omega, kappa)[source]

                                                    Initialize from Maryland notation.

                                                    Parameters
                                                    @@ -248,7 +248,7 @@
                                                    -property haeberlen_values[source]
                                                    +property haeberlen_values[source]

                                                    the Chemical shielding tensor in Haeberlen Notation

                                                    Type
                                                    @@ -259,7 +259,7 @@
                                                    -property maryland_values[source]
                                                    +property maryland_values[source]

                                                    the Chemical shielding tensor in Maryland Notation

                                                    Type
                                                    @@ -270,7 +270,7 @@
                                                    -property mehring_values[source]
                                                    +property mehring_values[source]

                                                    the Chemical shielding tensor in Mehring Notation

                                                    Type
                                                    @@ -281,7 +281,7 @@
                                                    -property principal_axis_system[source]
                                                    +property principal_axis_system[source]

                                                    Returns a chemical shielding tensor aligned to the principle axis system so that only the 3 diagonal components are non-zero

                                                    @@ -290,7 +290,7 @@
                                                    -class ElectricFieldGradient(efg_matrix, vscale=None)[source]
                                                    +class ElectricFieldGradient(efg_matrix, vscale=None)[source]

                                                    Bases: pymatgen.core.tensors.SquareTensor

                                                    This class extends the SquareTensor to perform extra analysis unique to NMR Electric Field Gradient tensors in units of V/Angstrom^2

                                                    @@ -313,7 +313,7 @@
                                                    -property V_xx[source]
                                                    +property V_xx[source]

                                                    First diagonal element

                                                    Type
                                                    @@ -324,7 +324,7 @@
                                                    -property V_yy[source]
                                                    +property V_yy[source]

                                                    Second diagonal element

                                                    Type
                                                    @@ -335,7 +335,7 @@
                                                    -property V_zz[source]
                                                    +property V_zz[source]

                                                    Third diagonal element

                                                    Type
                                                    @@ -346,14 +346,14 @@
                                                    -property asymmetry[source]
                                                    +property asymmetry[source]

                                                    Asymmetry of the electric field tensor defined as: (V_yy - V_xx)/V_zz

                                                    -coupling_constant(specie)[source]
                                                    +coupling_constant(specie)[source]
                                                    Computes the coupling constant C_q as defined in:

                                                    Wasylishen R E, Ashbrook S E, Wimperis S. NMR of quadrupolar nuclei in solid materials[M]. John Wiley & Sons, 2012. (Chapter 3.2)

                                                    @@ -380,7 +380,7 @@
                                                    -property principal_axis_system[source]
                                                    +property principal_axis_system[source]

                                                    Returns a electric field gradient tensor aligned to the principle axis system so that only the 3 diagonal components are non-zero

                                                    diff --git a/docs/pymatgen.analysis.path_finder.html b/docs/pymatgen.analysis.path_finder.html index 7e8dc87e6ec..1b9fa106a41 100644 --- a/docs/pymatgen.analysis.path_finder.html +++ b/docs/pymatgen.analysis.path_finder.html @@ -4,7 +4,7 @@ - pymatgen.analysis.path_finder module — pymatgen 2022.5.18 documentation + pymatgen.analysis.path_finder module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                    - 2022.5.18 + 2022.5.18.1
                                                    @@ -125,7 +125,7 @@
                                                    -class ChgcarPotential(chgcar, smear=False, normalize=True)[source]
                                                    +class ChgcarPotential(chgcar, smear=False, normalize=True)[source]

                                                    Bases: pymatgen.analysis.path_finder.StaticPotential

                                                    Implements a potential field based on the charge density output from VASP.

                                                    @@ -144,7 +144,7 @@
                                                    -class FreeVolumePotential(struct, dim, smear=False, normalize=True)[source]
                                                    +class FreeVolumePotential(struct, dim, smear=False, normalize=True)[source]

                                                    Bases: pymatgen.analysis.path_finder.StaticPotential

                                                    Implements a potential field based on geometric distances from atoms in the structure - basically, the potential @@ -165,7 +165,7 @@

                                                    -class MixedPotential(potentials, coefficients, smear=False, normalize=True)[source]
                                                    +class MixedPotential(potentials, coefficients, smear=False, normalize=True)[source]

                                                    Bases: pymatgen.analysis.path_finder.StaticPotential

                                                    Implements a potential that is a weighted sum of some other potentials

                                                    @@ -183,7 +183,7 @@
                                                    -class NEBPathfinder(start_struct, end_struct, relax_sites, v, n_images=20, mid_struct=None)[source]
                                                    +class NEBPathfinder(start_struct, end_struct, relax_sites, v, n_images=20, mid_struct=None)[source]

                                                    Bases: object

                                                    General pathfinder for interpolating between two structures, where the interpolating path is calculated with the elastic band method with @@ -204,14 +204,14 @@

                                                    -property images[source]
                                                    +property images[source]

                                                    Returns a list of structures interpolating between the start and endpoint structures.

                                                    -interpolate()[source]
                                                    +interpolate()[source]

                                                    Finds a set of n_images from self.s1 to self.s2, where all sites except for the ones given in relax_sites, the interpolation is linear (as in pymatgen.core.structure.interpolate), and for the site indices given @@ -223,14 +223,14 @@

                                                    -plot_images(outfile)[source]
                                                    +plot_images(outfile)[source]

                                                    Generates a POSCAR with the calculated diffusion path with respect to the first endpoint. :param outfile: Output file for the POSCAR

                                                    -static string_relax(start, end, V, n_images=25, dr=None, h=3.0, k=0.17, min_iter=100, max_iter=10000, max_tol=5e-06)[source]
                                                    +static string_relax(start, end, V, n_images=25, dr=None, h=3.0, k=0.17, min_iter=100, max_iter=10000, max_tol=5e-06)[source]

                                                    Implements path relaxation via the elastic band method. In general, the method is to define a path by a set of points (images) connected with bands with some elasticity constant k. The images then relax along the @@ -272,7 +272,7 @@

                                                    -class StaticPotential(struct, pot)[source]
                                                    +class StaticPotential(struct, pot)[source]

                                                    Bases: object

                                                    Defines a general static potential for diffusion calculations. Implements grid-rescaling and smearing for the potential grid. Also provides a @@ -287,7 +287,7 @@

                                                    -gaussian_smear(r)[source]
                                                    +gaussian_smear(r)[source]

                                                    Applies an isotropic Gaussian smear of width (standard deviation) r to the potential field. This is necessary to avoid finding paths through narrow minima or nodes that may exist in the field (although any @@ -302,19 +302,19 @@

                                                    -get_v()[source]
                                                    +get_v()[source]

                                                    Returns the potential

                                                    -normalize()[source]
                                                    +normalize()[source]

                                                    Sets the potential range 0 to 1.

                                                    -rescale_field(new_dim)[source]
                                                    +rescale_field(new_dim)[source]

                                                    Changes the discretization of the potential field by linear interpolation. This is necessary if the potential field obtained from DFT is strangely skewed, or is too fine or coarse. Obeys diff --git a/docs/pymatgen.analysis.phase_diagram.html b/docs/pymatgen.analysis.phase_diagram.html index 32e5d626b4f..1e2725fcbcb 100644 --- a/docs/pymatgen.analysis.phase_diagram.html +++ b/docs/pymatgen.analysis.phase_diagram.html @@ -4,7 +4,7 @@ - pymatgen.analysis.phase_diagram module — pymatgen 2022.5.18 documentation + pymatgen.analysis.phase_diagram module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                                    - 2022.5.18 + 2022.5.18.1
                                                    @@ -118,7 +118,7 @@

                                                    This module defines tools to generate and analyze phase diagrams.

                                                    -class CompoundPhaseDiagram(entries, terminal_compositions, normalize_terminal_compositions=True)[source]
                                                    +class CompoundPhaseDiagram(entries, terminal_compositions, normalize_terminal_compositions=True)[source]

                                                    Bases: pymatgen.analysis.phase_diagram.PhaseDiagram

                                                    Generates phase diagrams from compounds as terminations instead of elements.

                                                    @@ -142,12 +142,12 @@
                                                    -amount_tol = 1e-05[source]
                                                    +amount_tol = 1e-05[source]
                                                    -as_dict()[source]
                                                    +as_dict()[source]
                                                    Returns

                                                    MSONable dictionary representation of CompoundPhaseDiagram

                                                    @@ -157,7 +157,7 @@
                                                    -classmethod from_dict(d)[source]
                                                    +classmethod from_dict(d)[source]
                                                    Parameters

                                                    d (dict) – dictionary representation of CompoundPhaseDiagram

                                                    @@ -170,7 +170,7 @@
                                                    -transform_entries(entries, terminal_compositions)[source]
                                                    +transform_entries(entries, terminal_compositions)[source]

                                                    Method to transform all entries to the composition coordinate in the terminal compositions. If the entry does not fall within the space defined by the terminal compositions, they are excluded. For example, @@ -193,7 +193,7 @@

                                                    -class GrandPotPDEntry(entry, chempots, name=None)[source]
                                                    +class GrandPotPDEntry(entry, chempots, name=None)[source]

                                                    Bases: pymatgen.analysis.phase_diagram.PDEntry

                                                    A grand potential pd entry object encompassing all relevant data for phase diagrams. Chemical potentials are given as a element-chemical potential @@ -210,7 +210,7 @@

                                                    -as_dict()[source]
                                                    +as_dict()[source]
                                                    Returns

                                                    MSONable dictionary representation of GrandPotPDEntry

                                                    @@ -220,7 +220,7 @@
                                                    -property chemical_energy[source]
                                                    +property chemical_energy[source]

                                                    The chemical energy term mu*N in the grand potential

                                                    Returns
                                                    @@ -231,7 +231,7 @@
                                                    -property composition: pymatgen.core.composition.Composition[source]
                                                    +property composition: pymatgen.core.composition.Composition[source]

                                                    The composition after removing free species

                                                    Returns
                                                    @@ -242,14 +242,14 @@
                                                    -property energy[source]
                                                    +property energy[source]

                                                    Returns: The grand potential energy

                                                    -classmethod from_dict(d)[source]
                                                    +classmethod from_dict(d)[source]
                                                    Parameters

                                                    d (dict) – dictionary representation of GrandPotPDEntry

                                                    @@ -264,7 +264,7 @@
                                                    -class GrandPotentialPhaseDiagram(entries, chempots, elements=None, *, computed_data=None)[source]
                                                    +class GrandPotentialPhaseDiagram(entries, chempots, elements=None, *, computed_data=None)[source]

                                                    Bases: pymatgen.analysis.phase_diagram.PhaseDiagram

                                                    A class representing a Grand potential phase diagram. Grand potential phase diagrams are essentially phase diagrams that are open to one or more @@ -298,7 +298,7 @@

                                                    -as_dict()[source]
                                                    +as_dict()[source]
                                                    Returns

                                                    MSONable dict

                                                    @@ -308,7 +308,7 @@
                                                    -classmethod from_dict(d)[source]
                                                    +classmethod from_dict(d)[source]
                                                    Parameters

                                                    d – Dict representation

                                                    @@ -323,12 +323,12 @@
                                                    -class PDEntry(composition: pymatgen.core.composition.Composition, energy: float, name: Optional[str] = None, attribute: Optional[object] = None)[source]
                                                    +class PDEntry(composition: pymatgen.core.composition.Composition, energy: float, name: Optional[str] = None, attribute: Optional[object] = None)[source]

                                                    Bases: pymatgen.entries.Entry

                                                    An object encompassing all relevant data for phase diagrams.

                                                    -composition[source]
                                                    +composition[source]

                                                    The composition associated with the PDEntry.

                                                    Type
                                                    @@ -339,7 +339,7 @@
                                                    -energy[source]
                                                    +energy[source]

                                                    The energy associated with the entry.

                                                    Type
                                                    @@ -350,7 +350,7 @@
                                                    -name[source]
                                                    +name[source]

                                                    A name for the entry. This is the string shown in the phase diagrams. By default, this is the reduced formula for the composition, but can be set to some other string for display purposes.

                                                    @@ -363,7 +363,7 @@
                                                    -attribute[source]
                                                    +attribute[source]

                                                    A arbitrary attribute. Can be used to specify that the entry is a newly found compound, or to specify a particular label for the entry, etc. An attribute can be anything but must be MSONable.

                                                    @@ -387,7 +387,7 @@
                                                    -as_dict()[source]
                                                    +as_dict()[source]
                                                    Returns

                                                    the energy of the entry.

                                                    @@ -397,14 +397,14 @@
                                                    -property energy: float[source]
                                                    +property energy: float[source]

                                                    Returns: the energy of the entry.

                                                    -classmethod from_dict(d)[source]
                                                    +classmethod from_dict(d)[source]
                                                    Parameters

                                                    d (dict) – dictionary representation of PDEntry

                                                    @@ -419,7 +419,7 @@
                                                    -class PDPlotter(phasediagram: pymatgen.analysis.phase_diagram.PhaseDiagram, show_unstable: float = 0.2, backend: Literal['plotly', 'matplotlib'] = 'plotly', **plotkwargs)[source]
                                                    +class PDPlotter(phasediagram: pymatgen.analysis.phase_diagram.PhaseDiagram, show_unstable: float = 0.2, backend: Literal['plotly', 'matplotlib'] = 'plotly', **plotkwargs)[source]

                                                    Bases: object

                                                    A plotter class for compositional phase diagrams.

                                                    @@ -445,7 +445,7 @@
                                                    -get_chempot_range_map_plot(elements, referenced=True)[source]
                                                    +get_chempot_range_map_plot(elements, referenced=True)[source]

                                                    Returns a plot of the chemical potential range _map. Currently works only for 3-component PDs.

                                                    @@ -467,7 +467,7 @@
                                                    -get_contour_pd_plot()[source]
                                                    +get_contour_pd_plot()[source]

                                                    Plot a contour phase diagram plot, where phase triangles are colored according to degree of instability by interpolation. Currently only works for 3-component phase diagrams.

                                                    @@ -480,7 +480,7 @@
                                                    -get_plot(label_stable=True, label_unstable=True, ordering=None, energy_colormap=None, process_attributes=False, plt=None, label_uncertainties=False)[source]
                                                    +get_plot(label_stable=True, label_unstable=True, ordering=None, energy_colormap=None, process_attributes=False, plt=None, label_uncertainties=False)[source]
                                                    Parameters
                                                      @@ -505,7 +505,7 @@
                                                      -property pd_plot_data[source]
                                                      +property pd_plot_data[source]

                                                      Plotting data for phase diagram. Cached for repetitive calls. 2-comp - Full hull with energies 3/4-comp - Projection into 2D or 3D Gibbs triangle.

                                                      @@ -535,7 +535,7 @@
                                                      -plot_chempot_range_map(elements, referenced=True)[source]
                                                      +plot_chempot_range_map(elements, referenced=True)[source]

                                                      Plot the chemical potential range _map. Currently works only for 3-component PDs.

                                                      @@ -554,7 +554,7 @@
                                                      -plot_element_profile(element, comp, show_label_index=None, xlim=5)[source]
                                                      +plot_element_profile(element, comp, show_label_index=None, xlim=5)[source]

                                                      Draw the element profile plot for a composition varying different chemical potential of an element. X value is the negative value of the chemical potential reference to @@ -588,7 +588,7 @@

                                                      -show(*args, **kwargs)[source]
                                                      +show(*args, **kwargs)[source]

                                                      Draw the phase diagram using Plotly (or Matplotlib) and show it.

                                                      Parameters
                                                      @@ -602,7 +602,7 @@
                                                      -write_image(stream, image_format='svg', **kwargs)[source]
                                                      +write_image(stream, image_format='svg', **kwargs)[source]

                                                      Writes the phase diagram to an image in a stream.

                                                      Parameters
                                                      @@ -620,7 +620,7 @@
                                                      -class PhaseDiagram(entries, elements=None, *, computed_data=None)[source]
                                                      +class PhaseDiagram(entries, elements=None, *, computed_data=None)[source]

                                                      Bases: monty.json.MSONable

                                                      BasePhaseDiagram is not intended to be used directly, and PhaseDiagram should be preferred.

                                                      When constructing a PhaseDiagram, a lot of heavy processing is performed to calculate the @@ -658,7 +658,7 @@

                                                      -dim[source]
                                                      +dim[source]

                                                      The dimensionality of the phase diagram.

                                                      Type
                                                      @@ -669,13 +669,13 @@
                                                      -elements[source]
                                                      +elements[source]

                                                      Elements in the phase diagram.

                                                      -el_refs[source]
                                                      +el_refs[source]

                                                      List of elemental references for the phase diagrams. These are entries corresponding to the lowest energy element entries for simple compositional phase diagrams.

                                                      @@ -683,7 +683,7 @@
                                                      -all_entries[source]
                                                      +all_entries[source]

                                                      All entries provided for Phase Diagram construction. Note that this does not mean that all these entries are actually used in the phase diagram. For example, this includes the positive formation energy @@ -692,21 +692,21 @@

                                                      -qhull_entries[source]
                                                      +qhull_entries[source]

                                                      Actual entries used in convex hull. Excludes all positive formation energy entries.

                                                      -qhull_data[source]
                                                      +qhull_data[source]

                                                      Data used in the convex hull operation. This is essentially a matrix of composition data and energy per atom values created from qhull_entries.

                                                      -facets[source]
                                                      +facets[source]

                                                      Facets of the phase diagram in the form of [[1,2,3],[4,5,6]…]. For a ternary, it is the indices (references to qhull_entries and qhull_data) for the vertices of the phase triangles. Similarly @@ -715,21 +715,21 @@

                                                      -simplices[source]
                                                      +simplices[source]

                                                      The simplices of the phase diagram as a list of np.ndarray, i.e., the list of stable compositional coordinates in the phase diagram.

                                                      -property all_entries_hulldata[source]
                                                      +property all_entries_hulldata[source]

                                                      Returns: The actual ndarray used to construct the convex hull.

                                                      -as_dict()[source]
                                                      +as_dict()[source]
                                                      Returns

                                                      MSONAble dict

                                                      @@ -739,12 +739,12 @@
                                                      -formation_energy_tol = 1e-11[source]
                                                      +formation_energy_tol = 1e-11[source]
                                                      -classmethod from_dict(d)[source]
                                                      +classmethod from_dict(d)[source]
                                                      Parameters

                                                      d – Dict representation

                                                      @@ -757,7 +757,7 @@
                                                      -get_all_chempots(comp)[source]
                                                      +get_all_chempots(comp)[source]

                                                      Get chemical potentials at a given compositon.

                                                      Parameters
                                                      @@ -771,7 +771,7 @@
                                                      -get_chempot_range_map(elements, referenced=True, joggle=True)[source]
                                                      +get_chempot_range_map(elements, referenced=True, joggle=True)[source]

                                                      Returns a chemical potential range map for each stable entry.

                                                      Parameters
                                                      @@ -799,7 +799,7 @@
                                                      -get_chempot_range_stability_phase(target_comp, open_elt)[source]
                                                      +get_chempot_range_stability_phase(target_comp, open_elt)[source]

                                                      returns a set of chemical potentials corresponding to the max and min chemical potential of the open element for a given composition. It is quite common to have for instance a ternary oxide (e.g., ABO3) for @@ -825,7 +825,7 @@

                                                      -get_composition_chempots(comp)[source]
                                                      +get_composition_chempots(comp)[source]

                                                      Get the chemical potentials for all elements at a given composition.

                                                      Parameters
                                                      @@ -839,7 +839,7 @@
                                                      -get_critical_compositions(comp1, comp2)[source]
                                                      +get_critical_compositions(comp1, comp2)[source]

                                                      Get the critical compositions along the tieline between two compositions. I.e. where the decomposition products change. The endpoints are also returned.

                                                      @@ -865,7 +865,7 @@
                                                      -get_decomp_and_e_above_hull(entry, allow_negative=False, check_stable=True)[source]
                                                      +get_decomp_and_e_above_hull(entry, allow_negative=False, check_stable=True)[source]

                                                      Provides the decomposition and energy above convex hull for an entry. Due to caching, can be much faster if entries with the same composition are processed together.

                                                      @@ -896,7 +896,7 @@
                                                      -get_decomp_and_hull_energy_per_atom(comp)[source]
                                                      +get_decomp_and_hull_energy_per_atom(comp)[source]
                                                      Parameters

                                                      comp (Composition) – Input composition

                                                      @@ -909,7 +909,7 @@
                                                      -get_decomp_and_phase_separation_energy(entry, space_limit=200, stable_only=False, tols=[1e-08], maxiter=1000)[source]
                                                      +get_decomp_and_phase_separation_energy(entry, space_limit=200, stable_only=False, tols=[1e-08], maxiter=1000)[source]

                                                      Provides the combination of entries in the PhaseDiagram that gives the lowest formation enthalpy with the same composition as the given entry excluding entries with the same composition and the energy difference @@ -958,7 +958,7 @@

                                                      -get_decomposition(comp)[source]
                                                      +get_decomposition(comp)[source]

                                                      Provides the decomposition at a particular composition.

                                                      Parameters
                                                      @@ -976,7 +976,7 @@
                                                      -get_e_above_hull(entry, **kwargs)[source]
                                                      +get_e_above_hull(entry, **kwargs)[source]

                                                      Provides the energy above convex hull for an entry

                                                      Parameters
                                                      @@ -991,7 +991,7 @@
                                                      -get_element_profile(element, comp, comp_tol=1e-05)[source]
                                                      +get_element_profile(element, comp, comp_tol=1e-05)[source]

                                                      Provides the element evolution data for a composition. For example, can be used to analyze Li conversion voltages by varying uLi and looking at the phases formed. Also can be used to analyze O2 @@ -1018,7 +1018,7 @@

                                                      -get_equilibrium_reaction_energy(entry)[source]
                                                      +get_equilibrium_reaction_energy(entry)[source]

                                                      Provides the reaction energy of a stable entry from the neighboring equilibrium stable entries (also known as the inverse distance to hull).

                                                      @@ -1035,7 +1035,7 @@
                                                      -get_form_energy(entry)[source]
                                                      +get_form_energy(entry)[source]

                                                      Returns the formation energy for an entry (NOT normalized) from the elemental references.

                                                      @@ -1050,7 +1050,7 @@
                                                      -get_form_energy_per_atom(entry)[source]
                                                      +get_form_energy_per_atom(entry)[source]

                                                      Returns the formation energy per atom for an entry from the elemental references.

                                                      @@ -1065,7 +1065,7 @@
                                                      -get_hull_energy(comp)[source]
                                                      +get_hull_energy(comp)[source]
                                                      Parameters

                                                      comp (Composition) – Input composition

                                                      @@ -1082,7 +1082,7 @@
                                                      -get_hull_energy_per_atom(comp)[source]
                                                      +get_hull_energy_per_atom(comp)[source]
                                                      Parameters

                                                      comp (Composition) – Input composition

                                                      @@ -1095,7 +1095,7 @@
                                                      -get_phase_separation_energy(entry, **kwargs)[source]
                                                      +get_phase_separation_energy(entry, **kwargs)[source]

                                                      Provides the energy to the convex hull for the given entry. For stable entries already in the phase diagram the algorithm provides the phase separation energy which is referred to as the decomposition enthalpy in:

                                                      @@ -1137,7 +1137,7 @@
                                                      -get_reference_energy_per_atom(comp)[source]
                                                      +get_reference_energy_per_atom(comp)[source]
                                                      Parameters

                                                      comp (Composition) – Input composition

                                                      @@ -1150,7 +1150,7 @@
                                                      -get_transition_chempots(element)[source]
                                                      +get_transition_chempots(element)[source]

                                                      Get the critical chemical potentials for an element in the Phase Diagram.

                                                      @@ -1166,7 +1166,7 @@
                                                      -getmu_vertices_stability_phase(target_comp, dep_elt, tol_en=0.01)[source]
                                                      +getmu_vertices_stability_phase(target_comp, dep_elt, tol_en=0.01)[source]

                                                      returns a set of chemical potentials corresponding to the vertices of the simplex in the chemical potential phase diagram. The simplex is built using all elements in the target_composition @@ -1197,12 +1197,12 @@

                                                      -numerical_tol = 1e-08[source]
                                                      +numerical_tol = 1e-08[source]
                                                      -pd_coords(comp)[source]
                                                      +pd_coords(comp)[source]

                                                      The phase diagram is generated in a reduced dimensional space (n_elements - 1). This function returns the coordinates in that space. These coordinates are compatible with the stored simplex objects.

                                                      @@ -1218,7 +1218,7 @@
                                                      -property unstable_entries[source]
                                                      +property unstable_entries[source]

                                                      Returns: list of Entries that are unstable in the phase diagram.

                                                      @@ -1230,14 +1230,14 @@
                                                      -exception PhaseDiagramError[source]
                                                      +exception PhaseDiagramError[source]

                                                      Bases: Exception

                                                      An exception class for Phase Diagram generation.

                                                      -class ReactionDiagram(entry1, entry2, all_entries, tol=0.0001, float_fmt='%.4f')[source]
                                                      +class ReactionDiagram(entry1, entry2, all_entries, tol=0.0001, float_fmt='%.4f')[source]

                                                      Bases: object

                                                      Analyzes the possible reactions between a pair of compounds, e.g., an electrolyte and an electrode.

                                                      @@ -1265,7 +1265,7 @@
                                                      -get_compound_pd()[source]
                                                      +get_compound_pd()[source]

                                                      Get the CompoundPhaseDiagram object, which can then be used for plotting.

                                                      @@ -1279,7 +1279,7 @@
                                                      -class TransformedPDEntry(entry, sp_mapping, name=None)[source]
                                                      +class TransformedPDEntry(entry, sp_mapping, name=None)[source]

                                                      Bases: pymatgen.analysis.phase_diagram.PDEntry

                                                      This class represents a TransformedPDEntry, which allows for a PDEntry to be transformed to a different composition coordinate space. It is used in the @@ -1296,12 +1296,12 @@

                                                      -amount_tol = 1e-05[source]
                                                      +amount_tol = 1e-05[source]
                                                      -as_dict()[source]
                                                      +as_dict()[source]
                                                      Returns

                                                      MSONable dictionary representation of TransformedPDEntry

                                                      @@ -1311,7 +1311,7 @@
                                                      -property composition: pymatgen.core.composition.Composition[source]
                                                      +property composition: pymatgen.core.composition.Composition[source]

                                                      The composition in the dummy species space

                                                      Returns
                                                      @@ -1322,7 +1322,7 @@
                                                      -classmethod from_dict(d)[source]
                                                      +classmethod from_dict(d)[source]
                                                      Parameters

                                                      d (dict) – dictionary representation of TransformedPDEntry

                                                      @@ -1337,14 +1337,14 @@
                                                      -exception TransformedPDEntryError[source]
                                                      +exception TransformedPDEntryError[source]

                                                      Bases: Exception

                                                      An exception class for TransformedPDEntry.

                                                      -get_facets(qhull_data, joggle=False)[source]
                                                      +get_facets(qhull_data, joggle=False)[source]

                                                      Get the simplex facets for the Convex hull.

                                                      Parameters
                                                      @@ -1364,7 +1364,7 @@
                                                      -order_phase_diagram(lines, stable_entries, unstable_entries, ordering)[source]
                                                      +order_phase_diagram(lines, stable_entries, unstable_entries, ordering)[source]

                                                      Orders the entries (their coordinates) in a phase diagram plot according to the user specified ordering. Ordering should be given as [‘Up’, ‘Left’, ‘Right’], where Up, @@ -1401,7 +1401,7 @@

                                                      -tet_coord(coord)[source]
                                                      +tet_coord(coord)[source]

                                                      Convert a 3D coordinate into a tetrahedron based coordinate system for a prettier phase diagram.

                                                      @@ -1416,7 +1416,7 @@
                                                      -triangular_coord(coord)[source]
                                                      +triangular_coord(coord)[source]

                                                      Convert a 2D coordinate into a triangle-based coordinate system for a prettier phase diagram.

                                                      @@ -1431,7 +1431,7 @@
                                                      -uniquelines(q)[source]
                                                      +uniquelines(q)[source]

                                                      Given all the facets, convert it into a set of unique lines. Specifically used for converting convex hull facets into line pairs of coordinates.

                                                      diff --git a/docs/pymatgen.analysis.piezo.html b/docs/pymatgen.analysis.piezo.html index c2f42a600f1..eb83d0ca33c 100644 --- a/docs/pymatgen.analysis.piezo.html +++ b/docs/pymatgen.analysis.piezo.html @@ -4,7 +4,7 @@ - pymatgen.analysis.piezo module — pymatgen 2022.5.18 documentation + pymatgen.analysis.piezo module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                      - 2022.5.18 + 2022.5.18.1
                                                      @@ -118,7 +118,7 @@

                                                      This module provides classes for the Piezoelectric tensor

                                                      -class PiezoTensor(input_array, tol=0.001)[source]
                                                      +class PiezoTensor(input_array, tol=0.001)[source]

                                                      Bases: pymatgen.core.tensors.Tensor

                                                      This class describes the 3x6 piezo tensor in Voigt-notation

                                                      Create an PiezoTensor object. The constructor throws an error if @@ -134,7 +134,7 @@

                                                      -classmethod from_vasp_voigt(input_vasp_array)[source]
                                                      +classmethod from_vasp_voigt(input_vasp_array)[source]
                                                      Parameters

                                                      input_vasp_array (nd.array) – Voigt form of tensor.

                                                      diff --git a/docs/pymatgen.analysis.piezo_sensitivity.html b/docs/pymatgen.analysis.piezo_sensitivity.html index daad12314b6..285d9aba1de 100644 --- a/docs/pymatgen.analysis.piezo_sensitivity.html +++ b/docs/pymatgen.analysis.piezo_sensitivity.html @@ -4,7 +4,7 @@ - pymatgen.analysis.piezo_sensitivity module — pymatgen 2022.5.18 documentation + pymatgen.analysis.piezo_sensitivity module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                      - 2022.5.18 + 2022.5.18.1
                                                      @@ -118,7 +118,7 @@

                                                      Piezo sensitivity analysis module.

                                                      -class BornEffectiveCharge(structure, bec, pointops, tol=0.001)[source]
                                                      +class BornEffectiveCharge(structure, bec, pointops, tol=0.001)[source]

                                                      Bases: object

                                                      This class describes the Nx3x3 born effective charge tensor

                                                      Create an BornEffectiveChargeTensor object defined by a @@ -133,7 +133,7 @@

                                                      -get_BEC_operations(eigtol=1e-05, opstol=0.001)[source]
                                                      +get_BEC_operations(eigtol=1e-05, opstol=0.001)[source]

                                                      Returns the symmetry operations which maps the tensors belonging to equivalent sites onto each other in the form [site index 1, site index 2, [Symmops mapping from site @@ -156,7 +156,7 @@

                                                      -get_rand_BEC(max_charge=1)[source]
                                                      +get_rand_BEC(max_charge=1)[source]

                                                      Generate a random born effective charge tensor which obeys a structure’s symmetry and the acoustic sum rule

                                                      @@ -173,7 +173,7 @@
                                                      -class ForceConstantMatrix(structure, fcm, pointops, sharedops, tol=0.001)[source]
                                                      +class ForceConstantMatrix(structure, fcm, pointops, sharedops, tol=0.001)[source]

                                                      Bases: object

                                                      This class describes the NxNx3x3 force constant matrix defined by a structure, point operations of the structure’s atomic sites, and the @@ -187,7 +187,7 @@

                                                      -get_FCM_operations(eigtol=1e-05, opstol=1e-05)[source]
                                                      +get_FCM_operations(eigtol=1e-05, opstol=1e-05)[source]

                                                      Returns the symmetry operations which maps the tensors belonging to equivalent sites onto each other in the form [site index 1a, site index 1b, site index 2a, site index 2b, @@ -210,7 +210,7 @@

                                                      -get_asum_FCM(fcm, numiter=15)[source]
                                                      +get_asum_FCM(fcm, numiter=15)[source]

                                                      Generate a symmeterized force constant matrix that obeys the objects symmetry constraints and obeys the acoustic sum rule through an iterative procedure

                                                      @@ -229,7 +229,7 @@
                                                      -get_rand_FCM(asum=15, force=10)[source]
                                                      +get_rand_FCM(asum=15, force=10)[source]

                                                      Generate a symmeterized force constant matrix from an unsymmeterized matrix that has no unstable modes and also obeys the acoustic sum rule through an iterative procedure

                                                      @@ -249,7 +249,7 @@
                                                      -get_stable_FCM(fcm, fcmasum=10)[source]
                                                      +get_stable_FCM(fcm, fcmasum=10)[source]

                                                      Generate a symmeterized force constant matrix that obeys the objects symmetry constraints, has no unstable modes and also obeys the acoustic sum rule through an iterative procedure

                                                      @@ -269,7 +269,7 @@
                                                      -get_symmetrized_FCM(unsymmetrized_fcm, max_force=1)[source]
                                                      +get_symmetrized_FCM(unsymmetrized_fcm, max_force=1)[source]

                                                      Generate a symmeterized force constant matrix from an unsymmeterized matrix

                                                      Parameters
                                                      @@ -286,7 +286,7 @@
                                                      -get_unstable_FCM(max_force=1)[source]
                                                      +get_unstable_FCM(max_force=1)[source]

                                                      Generate an unsymmeterized force constant matrix

                                                      Parameters
                                                      @@ -302,7 +302,7 @@
                                                      -class InternalStrainTensor(structure, ist, pointops, tol=0.001)[source]
                                                      +class InternalStrainTensor(structure, ist, pointops, tol=0.001)[source]

                                                      Bases: object

                                                      This class describes the Nx3x3x3 internal tensor defined by a structure, point operations of the structure’s atomic sites.

                                                      @@ -315,7 +315,7 @@
                                                      -get_IST_operations(opstol=0.001)[source]
                                                      +get_IST_operations(opstol=0.001)[source]

                                                      Returns the symmetry operations which maps the tensors belonging to equivalent sites onto each other in the form [site index 1, site index 2, [Symmops mapping from site @@ -336,7 +336,7 @@

                                                      -get_rand_IST(max_force=1)[source]
                                                      +get_rand_IST(max_force=1)[source]

                                                      Generate a random internal strain tensor which obeys a structure’s symmetry and the acoustic sum rule

                                                      @@ -353,7 +353,7 @@
                                                      -get_piezo(BEC, IST, FCM, rcond=0.0001)[source]
                                                      +get_piezo(BEC, IST, FCM, rcond=0.0001)[source]

                                                      Generate a random piezoelectric tensor based on a structure and corresponding symmetry

                                                      @@ -373,7 +373,7 @@
                                                      -rand_piezo(struc, pointops, sharedops, BEC, IST, FCM, anumiter=10)[source]
                                                      +rand_piezo(struc, pointops, sharedops, BEC, IST, FCM, anumiter=10)[source]

                                                      Generate a random piezoelectric tensor based on a structure and corresponding symmetry

                                                      diff --git a/docs/pymatgen.analysis.pourbaix_diagram.html b/docs/pymatgen.analysis.pourbaix_diagram.html index 751718171e7..c5e03413637 100644 --- a/docs/pymatgen.analysis.pourbaix_diagram.html +++ b/docs/pymatgen.analysis.pourbaix_diagram.html @@ -4,7 +4,7 @@ - pymatgen.analysis.pourbaix_diagram module — pymatgen 2022.5.18 documentation + pymatgen.analysis.pourbaix_diagram module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                      - 2022.5.18 + 2022.5.18.1
                                                      @@ -128,13 +128,13 @@
                                                      -class IonEntry(ion, energy, name=None, attribute=None)[source]
                                                      +class IonEntry(ion, energy, name=None, attribute=None)[source]

                                                      Bases: pymatgen.analysis.phase_diagram.PDEntry

                                                      Object similar to PDEntry, but contains an Ion object instead of a Composition object.

                                                      -name[source]
                                                      +name[source]

                                                      A name for the entry. This is the string shown in the phase diagrams. By default, this is the reduced formula for the composition, but can be set to some other string for display purposes.

                                                      @@ -152,13 +152,13 @@
                                                      -as_dict()[source]
                                                      +as_dict()[source]

                                                      Creates a dict of composition, energy, and ion name

                                                      -classmethod from_dict(d)[source]
                                                      +classmethod from_dict(d)[source]

                                                      Returns an IonEntry object from a dict.

                                                      @@ -166,7 +166,7 @@
                                                      -class MultiEntry(entry_list, weights=None)[source]
                                                      +class MultiEntry(entry_list, weights=None)[source]

                                                      Bases: pymatgen.analysis.pourbaix_diagram.PourbaixEntry

                                                      PourbaixEntry-like object for constructing multi-elemental Pourbaix diagrams.

                                                      @@ -181,13 +181,13 @@
                                                      -as_dict()[source]
                                                      +as_dict()[source]

                                                      Returns: MSONable dict

                                                      -classmethod from_dict(d)[source]
                                                      +classmethod from_dict(d)[source]
                                                      Parameters

                                                      () (d) – Dict representation

                                                      @@ -200,7 +200,7 @@
                                                      -property name[source]
                                                      +property name[source]

                                                      MultiEntry name, i. e. the name of each entry joined by ‘ + ‘

                                                      @@ -208,7 +208,7 @@
                                                      -class PourbaixDiagram(entries: list[PourbaixEntry] | list[MultiEntry], comp_dict: dict[str, float] | None = None, conc_dict: dict[str, float] | None = None, filter_solids: bool = True, nproc: int | None = None)[source]
                                                      +class PourbaixDiagram(entries: list[PourbaixEntry] | list[MultiEntry], comp_dict: dict[str, float] | None = None, conc_dict: dict[str, float] | None = None, filter_solids: bool = True, nproc: int | None = None)[source]

                                                      Bases: monty.json.MSONable

                                                      Class to create a Pourbaix diagram from entries

                                                      @@ -236,13 +236,13 @@
                                                      -property all_entries[source]
                                                      +property all_entries[source]

                                                      Return all entries used to generate the Pourbaix diagram

                                                      -as_dict(include_unprocessed_entries=None)[source]
                                                      +as_dict(include_unprocessed_entries=None)[source]
                                                      Parameters

                                                      () (include_unprocessed_entries) – DEPRECATED. Whether to include unprocessed @@ -258,7 +258,7 @@

                                                      -find_stable_entry(pH, V)[source]
                                                      +find_stable_entry(pH, V)[source]

                                                      Finds stable entry at a pH,V condition :param pH: pH to find stable entry :type pH: float @@ -269,7 +269,7 @@

                                                      -classmethod from_dict(d)[source]
                                                      +classmethod from_dict(d)[source]
                                                      Parameters

                                                      () (d) – Dict representation.

                                                      @@ -282,7 +282,7 @@
                                                      -get_decomposition_energy(entry, pH, V)[source]
                                                      +get_decomposition_energy(entry, pH, V)[source]

                                                      Finds decomposition to most stable entries in eV/atom, supports vectorized inputs for pH and V

                                                      @@ -306,7 +306,7 @@
                                                      -get_hull_energy(pH, V)[source]
                                                      +get_hull_energy(pH, V)[source]

                                                      Gets the minimum energy of the Pourbaix “basin” that is formed from the stable Pourbaix planes. Vectorized.

                                                      @@ -324,7 +324,7 @@
                                                      -static get_pourbaix_domains(pourbaix_entries, limits=None)[source]
                                                      +static get_pourbaix_domains(pourbaix_entries, limits=None)[source]

                                                      Returns a set of Pourbaix stable domains (i. e. polygons) in pH-V space from a list of pourbaix_entries

                                                      This function works by using scipy’s HalfspaceIntersection @@ -357,7 +357,7 @@

                                                      -get_stable_entry(pH, V)[source]
                                                      +get_stable_entry(pH, V)[source]

                                                      Gets the stable entry at a given pH, V condition

                                                      Parameters
                                                      @@ -382,7 +382,7 @@
                                                      -static process_multientry(entry_list, prod_comp, coeff_threshold=0.0001)[source]
                                                      +static process_multientry(entry_list, prod_comp, coeff_threshold=0.0001)[source]

                                                      Static method for finding a multientry based on a list of entries and a product composition. Essentially checks to see if a valid aqueous @@ -406,19 +406,19 @@

                                                      -property stable_entries[source]
                                                      +property stable_entries[source]

                                                      Returns the stable entries in the Pourbaix diagram.

                                                      -property unprocessed_entries[source]
                                                      +property unprocessed_entries[source]

                                                      Return unprocessed entries

                                                      -property unstable_entries[source]
                                                      +property unstable_entries[source]

                                                      Returns all unstable entries in the Pourbaix diagram

                                                      @@ -426,7 +426,7 @@
                                                      -class PourbaixEntry(entry, entry_id=None, concentration=1e-06)[source]
                                                      +class PourbaixEntry(entry, entry_id=None, concentration=1e-06)[source]

                                                      Bases: monty.json.MSONable, pymatgen.util.string.Stringify

                                                      An object encompassing all data relevant to a solid or ion in a Pourbaix diagram. Each bulk solid/ion has an energy @@ -448,7 +448,7 @@

                                                      -as_dict()[source]
                                                      +as_dict()[source]

                                                      Returns dict which contains Pourbaix Entry data. Note that the pH, voltage, H2O factors are always calculated when constructing a PourbaixEntry object.

                                                      @@ -456,20 +456,20 @@
                                                      -property composition[source]
                                                      +property composition[source]

                                                      Returns composition

                                                      -property conc_term[source]
                                                      +property conc_term[source]

                                                      Returns the concentration contribution to the free energy, and should only be present when there are ions in the entry

                                                      -property energy[source]
                                                      +property energy[source]

                                                      returns energy

                                                      Returns (float): total energy of the Pourbaix

                                                      entry (at pH, V = 0 vs. SHE)

                                                      @@ -479,7 +479,7 @@
                                                      -energy_at_conditions(pH, V)[source]
                                                      +energy_at_conditions(pH, V)[source]

                                                      Get free energy for a given pH and V

                                                      Parameters
                                                      @@ -496,20 +496,20 @@
                                                      -property energy_per_atom[source]
                                                      +property energy_per_atom[source]

                                                      energy per atom of the Pourbaix entry

                                                      Returns (float): energy per atom

                                                      -classmethod from_dict(d)[source]
                                                      +classmethod from_dict(d)[source]

                                                      Invokes a PourbaixEntry from a dictionary

                                                      -get_element_fraction(element)[source]
                                                      +get_element_fraction(element)[source]

                                                      Gets the elemental fraction of a given non-OH element

                                                      Parameters
                                                      @@ -524,7 +524,7 @@
                                                      -property nH2O[source]
                                                      +property nH2O[source]

                                                      Number of H2O.

                                                      Type
                                                      @@ -535,7 +535,7 @@
                                                      -property nPhi[source]
                                                      +property nPhi[source]

                                                      Number of H2O.

                                                      Type
                                                      @@ -546,7 +546,7 @@
                                                      -property name[source]
                                                      +property name[source]

                                                      Name for entry

                                                      Type
                                                      @@ -557,13 +557,13 @@
                                                      -property normalization_factor[source]
                                                      +property normalization_factor[source]

                                                      Sum of number of atoms minus the number of H and O in composition

                                                      -property normalized_energy[source]
                                                      +property normalized_energy[source]

                                                      Returns: energy normalized by number of non H or O atoms, e. g. for Zn2O6, energy / 2 or for AgTe3(OH)3, energy / 4

                                                      @@ -571,7 +571,7 @@
                                                      -normalized_energy_at_conditions(pH, V)[source]
                                                      +normalized_energy_at_conditions(pH, V)[source]

                                                      Energy at an electrochemical condition, compatible with numpy arrays for pH/V input

                                                      @@ -589,19 +589,19 @@
                                                      -property npH[source]
                                                      +property npH[source]

                                                      Returns:

                                                      -property num_atoms[source]
                                                      +property num_atoms[source]

                                                      Return number of atoms in current formula. Useful for normalization

                                                      -to_pretty_string() → str[source]
                                                      +to_pretty_string() → str[source]
                                                      Returns

                                                      A pretty string representation.

                                                      @@ -613,7 +613,7 @@
                                                      -class PourbaixPlotter(pourbaix_diagram)[source]
                                                      +class PourbaixPlotter(pourbaix_diagram)[source]

                                                      Bases: object

                                                      A plotter class for phase diagrams.

                                                      @@ -623,7 +623,7 @@
                                                      -domain_vertices(entry)[source]
                                                      +domain_vertices(entry)[source]

                                                      Returns the vertices of the Pourbaix domain.

                                                      Parameters
                                                      @@ -637,7 +637,7 @@
                                                      -get_pourbaix_plot(limits=None, title='', label_domains=True, label_fontsize=20, show_water_lines=True, show_neutral_axes=True, plt=None)[source]
                                                      +get_pourbaix_plot(limits=None, title='', label_domains=True, label_fontsize=20, show_water_lines=True, show_neutral_axes=True, plt=None)[source]

                                                      Plot Pourbaix diagram.

                                                      Parameters
                                                      @@ -661,7 +661,7 @@
                                                      -plot_entry_stability(entry, pH_range=None, pH_resolution=100, V_range=None, V_resolution=100, e_hull_max=1, cmap='RdYlBu_r', **kwargs)[source]
                                                      +plot_entry_stability(entry, pH_range=None, pH_resolution=100, V_range=None, V_resolution=100, e_hull_max=1, cmap='RdYlBu_r', **kwargs)[source]
                                                      Parameters
                                                        @@ -681,7 +681,7 @@
                                                        -show(*args, **kwargs)[source]
                                                        +show(*args, **kwargs)[source]

                                                        Shows the Pourbaix plot

                                                        Parameters
                                                        @@ -700,7 +700,7 @@
                                                        -generate_entry_label(entry)[source]
                                                        +generate_entry_label(entry)[source]

                                                        Generates a label for the Pourbaix plotter

                                                        Parameters
                                                        @@ -711,7 +711,7 @@
                                                        -ion_or_solid_comp_object(formula)[source]
                                                        +ion_or_solid_comp_object(formula)[source]

                                                        Returns either an ion object or composition object given a formula.

                                                        diff --git a/docs/pymatgen.analysis.prototypes.html b/docs/pymatgen.analysis.prototypes.html index 52b59bcdb0d..e3a963ea6b7 100644 --- a/docs/pymatgen.analysis.prototypes.html +++ b/docs/pymatgen.analysis.prototypes.html @@ -4,7 +4,7 @@ - pymatgen.analysis.prototypes module — pymatgen 2022.5.18 documentation + pymatgen.analysis.prototypes module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                        - 2022.5.18 + 2022.5.18.1
                                                        @@ -125,7 +125,7 @@ https://doi.org/10.1016/j.commatsci.2017.01.017

                                                        -class AflowPrototypeMatcher(initial_ltol=0.2, initial_stol=0.3, initial_angle_tol=5)[source]
                                                        +class AflowPrototypeMatcher(initial_ltol=0.2, initial_stol=0.3, initial_angle_tol=5)[source]

                                                        Bases: object

                                                        This class will match structures to their crystal prototypes, and will attempt to group species together to match structures derived from @@ -150,7 +150,7 @@

                                                        -get_prototypes(structure)[source]
                                                        +get_prototypes(structure)[source]

                                                        Get prototype(s) structures for a given input structure. If you use this method in your work, please cite the appropriate diff --git a/docs/pymatgen.analysis.quasiharmonic.html b/docs/pymatgen.analysis.quasiharmonic.html index 64f1b28c9d9..ce5a0df6ae1 100644 --- a/docs/pymatgen.analysis.quasiharmonic.html +++ b/docs/pymatgen.analysis.quasiharmonic.html @@ -4,7 +4,7 @@ - pymatgen.analysis.quasiharmonic module — pymatgen 2022.5.18 documentation + pymatgen.analysis.quasiharmonic module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                                        - 2022.5.18 + 2022.5.18.1
                                                        @@ -124,7 +124,7 @@
                                                      -class QuasiharmonicDebyeApprox(energies, volumes, structure, t_min=300.0, t_step=100, t_max=300.0, eos='vinet', pressure=0.0, poisson=0.25, use_mie_gruneisen=False, anharmonic_contribution=False)[source]
                                                      +class QuasiharmonicDebyeApprox(energies, volumes, structure, t_min=300.0, t_step=100, t_max=300.0, eos='vinet', pressure=0.0, poisson=0.25, use_mie_gruneisen=False, anharmonic_contribution=False)[source]

                                                      Bases: object

                                                      Quasiharmonic approximation.

                                                      @@ -157,7 +157,7 @@
                                                      -static debye_integral(y)[source]
                                                      +static debye_integral(y)[source]

                                                      Debye integral. Eq(5) in doi.org/10.1016/j.comphy.2003.12.001

                                                      Parameters
                                                      @@ -174,7 +174,7 @@
                                                      -debye_temperature(volume)[source]
                                                      +debye_temperature(volume)[source]

                                                      Calculates the debye temperature. Eq(6) in doi.org/10.1016/j.comphy.2003.12.001. Thanks to Joey.

                                                      Eq(6) above is equivalent to Eq(3) in doi.org/10.1103/PhysRevB.37.790 @@ -199,13 +199,13 @@

                                                      -get_summary_dict()[source]
                                                      +get_summary_dict()[source]

                                                      Returns a dict with a summary of the computed properties.

                                                      -gruneisen_parameter(temperature, volume)[source]
                                                      +gruneisen_parameter(temperature, volume)[source]
                                                      Slater-gamma formulation(the default):
                                                      gruneisen parameter = - d log(theta)/ d log(V)

                                                      = - ( 1/6 + 0.5 d log(B)/ d log(V) ) @@ -246,7 +246,7 @@

                                                      -optimize_gibbs_free_energy()[source]
                                                      +optimize_gibbs_free_energy()[source]

                                                      Evaluate the Gibbs free energy as a function of V, T and P i.e G(V, T, P), minimize G(V, T, P) wrt V for each T and store the optimum values.

                                                      @@ -258,7 +258,7 @@
                                                      -optimizer(temperature)[source]
                                                      +optimizer(temperature)[source]

                                                      Evaluate G(V, T, P) at the given temperature(and pressure) and minimize it wrt V.

                                                        @@ -290,7 +290,7 @@
                                                        -thermal_conductivity(temperature, volume)[source]
                                                        +thermal_conductivity(temperature, volume)[source]

                                                        Eq(17) in 10.1103/PhysRevB.90.174107

                                                        Parameters
                                                        @@ -310,7 +310,7 @@
                                                        -vibrational_free_energy(temperature, volume)[source]
                                                        +vibrational_free_energy(temperature, volume)[source]

                                                        Vibrational Helmholtz free energy, A_vib(V, T). Eq(4) in doi.org/10.1016/j.comphy.2003.12.001

                                                        @@ -331,7 +331,7 @@
                                                        -vibrational_internal_energy(temperature, volume)[source]
                                                        +vibrational_internal_energy(temperature, volume)[source]

                                                        Vibrational internal energy, U_vib(V, T). Eq(4) in doi.org/10.1016/j.comphy.2003.12.001

                                                        diff --git a/docs/pymatgen.analysis.reaction_calculator.html b/docs/pymatgen.analysis.reaction_calculator.html index 03400170d93..92467106ffb 100644 --- a/docs/pymatgen.analysis.reaction_calculator.html +++ b/docs/pymatgen.analysis.reaction_calculator.html @@ -4,7 +4,7 @@ - pymatgen.analysis.reaction_calculator module — pymatgen 2022.5.18 documentation + pymatgen.analysis.reaction_calculator module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                        - 2022.5.18 + 2022.5.18.1
                                                        @@ -118,7 +118,7 @@

                                                        This module provides classes that define a chemical reaction.

                                                        -class BalancedReaction(reactants_coeffs, products_coeffs)[source]
                                                        +class BalancedReaction(reactants_coeffs, products_coeffs)[source]

                                                        Bases: monty.json.MSONable

                                                        An object representing a complete chemical reaction.

                                                        Reactants and products to be specified as dict of {Composition: coeff}.

                                                        @@ -134,18 +134,18 @@
                                                        -TOLERANCE = 1e-06[source]
                                                        +TOLERANCE = 1e-06[source]
                                                        -property all_comp[source]
                                                        +property all_comp[source]

                                                        List of all compositions in the reaction.

                                                        -as_dict()[source]
                                                        +as_dict()[source]
                                                        Returns

                                                        A dictionary representation of BalancedReaction.

                                                        @@ -155,14 +155,14 @@
                                                        -as_entry(energies)[source]
                                                        +as_entry(energies)[source]

                                                        Returns a ComputedEntry representation of the reaction. :return:

                                                        -calculate_energy(energies)[source]
                                                        +calculate_energy(energies)[source]

                                                        Calculates the energy of the reaction.

                                                        Parameters
                                                        @@ -177,19 +177,19 @@
                                                        -property coeffs[source]
                                                        +property coeffs[source]

                                                        Final coefficients of the calculated reaction

                                                        -property elements[source]
                                                        +property elements[source]

                                                        List of elements in the reaction

                                                        -classmethod from_dict(d)[source]
                                                        +classmethod from_dict(d)[source]
                                                        Parameters

                                                        d (dict) – from as_dict()

                                                        @@ -202,7 +202,7 @@
                                                        -static from_string(rxn_string)[source]
                                                        +static from_string(rxn_string)[source]

                                                        Generates a balanced reaction from a string. The reaction must already be balanced.

                                                        @@ -217,13 +217,13 @@
                                                        -get_coeff(comp)[source]
                                                        +get_coeff(comp)[source]

                                                        Returns coefficient for a particular composition

                                                        -get_el_amount(element)[source]
                                                        +get_el_amount(element)[source]

                                                        Returns the amount of the element in the reaction.

                                                        Parameters
                                                        @@ -237,7 +237,7 @@
                                                        -normalize_to(comp, factor=1)[source]
                                                        +normalize_to(comp, factor=1)[source]

                                                        Normalizes the reaction to one of the compositions. By default, normalizes such that the composition given has a coefficient of 1. Another factor can be specified.

                                                        @@ -253,7 +253,7 @@
                                                        -normalize_to_element(element, factor=1)[source]
                                                        +normalize_to_element(element, factor=1)[source]

                                                        Normalizes the reaction to one of the elements. By default, normalizes such that the amount of the element is 1. Another factor can be specified.

                                                        @@ -269,27 +269,27 @@
                                                        -property normalized_repr[source]
                                                        +property normalized_repr[source]

                                                        A normalized representation of the reaction. All factors are converted to lowest common factors.

                                                        -normalized_repr_and_factor()[source]
                                                        +normalized_repr_and_factor()[source]

                                                        Normalized representation for a reaction For example, 4 Li + 2 O -> 2Li2O becomes 2 Li + O -> Li2O

                                                        -property products[source]
                                                        +property products[source]

                                                        List of products

                                                        -property reactants[source]
                                                        +property reactants[source]

                                                        List of reactants

                                                        @@ -297,7 +297,7 @@
                                                        -class ComputedReaction(reactant_entries, product_entries)[source]
                                                        +class ComputedReaction(reactant_entries, product_entries)[source]

                                                        Bases: pymatgen.analysis.reaction_calculator.Reaction

                                                        Convenience class to generate a reaction from ComputedEntry objects, with some additional attributes, such as a reaction energy based on computed @@ -312,14 +312,14 @@

                                                        -property all_entries[source]
                                                        +property all_entries[source]

                                                        Equivalent of all_comp but returns entries, in the same order as the coefficients.

                                                        -as_dict()[source]
                                                        +as_dict()[source]
                                                        Returns

                                                        A dictionary representation of ComputedReaction.

                                                        @@ -329,21 +329,21 @@
                                                        -property calculated_reaction_energy[source]
                                                        +property calculated_reaction_energy[source]

                                                        Returns (float): The calculated reaction energy.

                                                        -property calculated_reaction_energy_uncertainty[source]
                                                        +property calculated_reaction_energy_uncertainty[source]

                                                        Calculates the uncertainty in the reaction energy based on the uncertainty in the energies of the products and reactants

                                                        -classmethod from_dict(d)[source]
                                                        +classmethod from_dict(d)[source]
                                                        Parameters

                                                        d (dict) – from as_dict()

                                                        @@ -358,7 +358,7 @@
                                                        -class Reaction(reactants, products)[source]
                                                        +class Reaction(reactants, products)[source]

                                                        Bases: pymatgen.analysis.reaction_calculator.BalancedReaction

                                                        A more flexible class representing a Reaction. The reaction amounts will be automatically balanced. Reactants and products can swap sides so that @@ -377,7 +377,7 @@

                                                        -as_dict()[source]
                                                        +as_dict()[source]
                                                        Returns

                                                        A dictionary representation of Reaction.

                                                        @@ -387,13 +387,13 @@
                                                        -copy()[source]
                                                        +copy()[source]

                                                        Returns a copy of the Reaction object.

                                                        -classmethod from_dict(d)[source]
                                                        +classmethod from_dict(d)[source]
                                                        Parameters

                                                        d (dict) – from as_dict()

                                                        @@ -408,7 +408,7 @@
                                                        -exception ReactionError(msg)[source]
                                                        +exception ReactionError(msg)[source]

                                                        Bases: Exception

                                                        Exception class for Reactions. Allows more information in exception messages to cover situations not covered by standard exception classes.

                                                        diff --git a/docs/pymatgen.analysis.solar.html b/docs/pymatgen.analysis.solar.html index 3c4b1d97b42..20371acdf32 100644 --- a/docs/pymatgen.analysis.solar.html +++ b/docs/pymatgen.analysis.solar.html @@ -4,7 +4,7 @@ - pymatgen.analysis.solar package — pymatgen 2022.5.18 documentation + pymatgen.analysis.solar package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                        - 2022.5.18 + 2022.5.18.1
                                                        diff --git a/docs/pymatgen.analysis.solar.slme.html b/docs/pymatgen.analysis.solar.slme.html index 8bf541d4743..d5626255640 100644 --- a/docs/pymatgen.analysis.solar.slme.html +++ b/docs/pymatgen.analysis.solar.slme.html @@ -4,7 +4,7 @@ - pymatgen.analysis.solar.slme module — pymatgen 2022.5.18 documentation + pymatgen.analysis.solar.slme module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                        - 2022.5.18 + 2022.5.18.1
                                                        @@ -127,7 +127,7 @@
                                                        -absorption_coefficient(dielectric)[source]
                                                        +absorption_coefficient(dielectric)[source]

                                                        Calculate the optical absorption coefficient from an input set of pymatgen vasprun dielectric constant data. :param dielectric: A list containing the dielectric response function

                                                        @@ -149,13 +149,13 @@
                                                        -get_dir_indir_gap(run='')[source]
                                                        +get_dir_indir_gap(run='')[source]

                                                        Get direct and indirect bandgaps for a vasprun.xml

                                                        -matrix_eigvals(matrix)[source]
                                                        +matrix_eigvals(matrix)[source]

                                                        Calculate the eigenvalues of a matrix. :param matrix: The matrix to diagonalise. :type matrix: np.array

                                                        @@ -171,13 +171,13 @@
                                                        -optics(path='')[source]
                                                        +optics(path='')[source]

                                                        Helper function to calculate optical absorption coefficient

                                                        -parse_dielectric_data(data)[source]
                                                        +parse_dielectric_data(data)[source]

                                                        Convert a set of 2D vasprun formatted dielectric data to the eigenvalues of each corresponding 3x3 symmetric numpy matrices. :param data: length N list of dielectric data. Each entry should be

                                                        @@ -201,7 +201,7 @@
                                                        -slme(material_energy_for_absorbance_data, material_absorbance_data, material_direct_allowed_gap, material_indirect_gap, thickness=5e-05, temperature=293.15, absorbance_in_inverse_centimeters=False, cut_off_absorbance_below_direct_allowed_gap=True, plot_current_voltage=False)[source]
                                                        +slme(material_energy_for_absorbance_data, material_absorbance_data, material_direct_allowed_gap, material_indirect_gap, thickness=5e-05, temperature=293.15, absorbance_in_inverse_centimeters=False, cut_off_absorbance_below_direct_allowed_gap=True, plot_current_voltage=False)[source]

                                                        Calculate the SLME

                                                        Parameters
                                                        @@ -225,7 +225,7 @@
                                                        -to_matrix(xx, yy, zz, xy, yz, xz)[source]
                                                        +to_matrix(xx, yy, zz, xy, yz, xz)[source]

                                                        Convert a list of matrix components to a symmetric 3x3 matrix. Inputs should be in the order xx, yy, zz, xy, yz, xz. :param xx: xx component of the matrix. diff --git a/docs/pymatgen.analysis.structure_analyzer.html b/docs/pymatgen.analysis.structure_analyzer.html index 1dc432f4452..d8bd7003ed9 100644 --- a/docs/pymatgen.analysis.structure_analyzer.html +++ b/docs/pymatgen.analysis.structure_analyzer.html @@ -4,7 +4,7 @@ - pymatgen.analysis.structure_analyzer module — pymatgen 2022.5.18 documentation + pymatgen.analysis.structure_analyzer module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                                        - 2022.5.18 + 2022.5.18.1
                                                        @@ -118,7 +118,7 @@

                                                        This module provides classes to perform topological analyses of structures.

                                                        -class OxideType(structure, relative_cutoff=1.1)[source]
                                                        +class OxideType(structure, relative_cutoff=1.1)[source]

                                                        Bases: object

                                                        Separate class for determining oxide type.

                                                        @@ -134,7 +134,7 @@
                                                        -parse_oxide()[source]
                                                        +parse_oxide()[source]

                                                        Determines if an oxide is a peroxide/superoxide/ozonide/normal oxide.

                                                        Returns
                                                        @@ -153,7 +153,7 @@
                                                        -class RelaxationAnalyzer(initial_structure, final_structure)[source]
                                                        +class RelaxationAnalyzer(initial_structure, final_structure)[source]

                                                        Bases: object

                                                        This class analyzes the relaxation in a calculation.

                                                        Please note that the input and final structures should have the same @@ -171,7 +171,7 @@

                                                        -get_percentage_bond_dist_changes(max_radius=3.0)[source]
                                                        +get_percentage_bond_dist_changes(max_radius=3.0)[source]

                                                        Returns the percentage bond distance changes for each site up to a maximum radius for nearest neighbors.

                                                        @@ -192,7 +192,7 @@
                                                        -get_percentage_lattice_parameter_changes()[source]
                                                        +get_percentage_lattice_parameter_changes()[source]

                                                        Returns the percentage lattice parameter changes.

                                                        Returns
                                                        @@ -205,7 +205,7 @@
                                                        -get_percentage_volume_change()[source]
                                                        +get_percentage_volume_change()[source]

                                                        Returns the percentage volume change.

                                                        Returns
                                                        @@ -218,7 +218,7 @@
                                                        -class VoronoiAnalyzer(cutoff=5.0, qhull_options='Qbb Qc Qz')[source]
                                                        +class VoronoiAnalyzer(cutoff=5.0, qhull_options='Qbb Qc Qz')[source]

                                                        Bases: object

                                                        Performs a statistical analysis of Voronoi polyhedra around each site. Each Voronoi polyhedron is described using Schaefli notation. @@ -244,7 +244,7 @@

                                                        -analyze(structure, n=0)[source]
                                                        +analyze(structure, n=0)[source]

                                                        Performs Voronoi analysis and returns the polyhedra around atom n in Schlaefli notation.

                                                        @@ -269,7 +269,7 @@
                                                        -analyze_structures(structures, step_freq=10, most_frequent_polyhedra=15)[source]
                                                        +analyze_structures(structures, step_freq=10, most_frequent_polyhedra=15)[source]

                                                        Perform Voronoi analysis on a list of Structures. Note that this might take a significant amount of time depending on the size and number of structures.

                                                        @@ -293,7 +293,7 @@
                                                        -static plot_vor_analysis(voronoi_ensemble)[source]
                                                        +static plot_vor_analysis(voronoi_ensemble)[source]

                                                        Plot the Voronoi analysis.

                                                        Parameters
                                                        @@ -309,7 +309,7 @@
                                                        -class VoronoiConnectivity(structure, cutoff=10)[source]
                                                        +class VoronoiConnectivity(structure, cutoff=10)[source]

                                                        Bases: object

                                                        Computes the solid angles swept out by the shared face of the voronoi polyhedron between two sites.

                                                        @@ -323,7 +323,7 @@
                                                        -property connectivity_array[source]
                                                        +property connectivity_array[source]

                                                        Provides connectivity array.

                                                        Returns
                                                        @@ -341,14 +341,14 @@
                                                        -get_connections()[source]
                                                        +get_connections()[source]

                                                        Returns a list of site pairs that are Voronoi Neighbors, along with their real-space distances.

                                                        -get_sitej(site_index, image_index)[source]
                                                        +get_sitej(site_index, image_index)[source]

                                                        Assuming there is some value in the connectivity array at indices (1, 3, 12). sitei can be obtained directly from the input structure (structure[1]). sitej can be obtained by passing 3, 12 to this function

                                                        @@ -364,7 +364,7 @@
                                                        -property max_connectivity[source]
                                                        +property max_connectivity[source]

                                                        returns the 2d array [sitei, sitej] that represents the maximum connectivity of site i to any periodic image of site j

                                                        @@ -374,7 +374,7 @@
                                                        -average_coordination_number(structures, freq=10)[source]
                                                        +average_coordination_number(structures, freq=10)[source]

                                                        Calculates the ensemble averaged Voronoi coordination numbers of a list of Structures using VoronoiNN. Typically used for analyzing the output of a Molecular Dynamics run.

                                                        @@ -393,7 +393,7 @@
                                                        -contains_peroxide(structure, relative_cutoff=1.1)[source]
                                                        +contains_peroxide(structure, relative_cutoff=1.1)[source]

                                                        Determines if a structure contains peroxide anions.

                                                        Parameters
                                                        @@ -412,7 +412,7 @@
                                                        -get_max_bond_lengths(structure, el_radius_updates=None)[source]
                                                        +get_max_bond_lengths(structure, el_radius_updates=None)[source]

                                                        Provides max bond length estimates for a structure based on the JMol table and algorithms.

                                                        @@ -431,7 +431,7 @@
                                                        -oxide_type(structure, relative_cutoff=1.1, return_nbonds=False)[source]
                                                        +oxide_type(structure, relative_cutoff=1.1, return_nbonds=False)[source]

                                                        Determines if an oxide is a peroxide/superoxide/ozonide/normal oxide

                                                        Parameters
                                                        @@ -447,7 +447,7 @@
                                                        -solid_angle(center, coords)[source]
                                                        +solid_angle(center, coords)[source]

                                                        Helper method to calculate the solid angle of a set of coords from the center.

                                                        @@ -465,7 +465,7 @@
                                                        -sulfide_type(structure)[source]
                                                        +sulfide_type(structure)[source]

                                                        Determines if a structure is a sulfide/polysulfide/sulfate

                                                        Parameters
                                                        diff --git a/docs/pymatgen.analysis.structure_matcher.html b/docs/pymatgen.analysis.structure_matcher.html index 891f5f654d4..de30952f206 100644 --- a/docs/pymatgen.analysis.structure_matcher.html +++ b/docs/pymatgen.analysis.structure_matcher.html @@ -4,7 +4,7 @@ - pymatgen.analysis.structure_matcher module — pymatgen 2022.5.18 documentation + pymatgen.analysis.structure_matcher module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                        - 2022.5.18 + 2022.5.18.1
                                                        @@ -118,13 +118,13 @@

                                                        This module provides classes to perform fitting of structures.

                                                        -class AbstractComparator[source]
                                                        +class AbstractComparator[source]

                                                        Bases: monty.json.MSONable

                                                        Abstract Comparator class. A Comparator defines how sites are compared in a structure.

                                                        -abstract are_equal(sp1, sp2)[source]
                                                        +abstract are_equal(sp1, sp2)[source]

                                                        Defines how the species of two sites are considered equal. For example, one can consider sites to have the same species only when the species are exactly the same, i.e., Fe2+ matches Fe2+ but not @@ -147,7 +147,7 @@

                                                        -as_dict()[source]
                                                        +as_dict()[source]
                                                        Returns

                                                        MSONable dict

                                                        @@ -157,7 +157,7 @@
                                                        -classmethod from_dict(d)[source]
                                                        +classmethod from_dict(d)[source]
                                                        Parameters

                                                        d – Dict representation

                                                        @@ -170,7 +170,7 @@
                                                        -abstract get_hash(composition)[source]
                                                        +abstract get_hash(composition)[source]

                                                        Defines a hash to group structures. This allows structures to be grouped efficiently for comparison. The hash must be invariant under supercell creation. (e.g. composition is not a good hash, but @@ -193,13 +193,13 @@

                                                        -class ElementComparator[source]
                                                        +class ElementComparator[source]

                                                        Bases: pymatgen.analysis.structure_matcher.AbstractComparator

                                                        A Comparator that matches elements. i.e. oxidation states are ignored.

                                                        -are_equal(sp1, sp2)[source]
                                                        +are_equal(sp1, sp2)[source]

                                                        True if element:amounts are exactly the same, i.e., oxidation state is not considered.

                                                        @@ -220,7 +220,7 @@
                                                        -get_hash(composition)[source]
                                                        +get_hash(composition)[source]

                                                        Returns: Fractional element composition

                                                        @@ -228,12 +228,12 @@
                                                        -class FrameworkComparator[source]
                                                        +class FrameworkComparator[source]

                                                        Bases: pymatgen.analysis.structure_matcher.AbstractComparator

                                                        A Comparator that matches sites, regardless of species.

                                                        -are_equal(sp1, sp2)[source]
                                                        +are_equal(sp1, sp2)[source]

                                                        True if there are atoms on both sites.

                                                        Parameters
                                                        @@ -252,7 +252,7 @@
                                                        -get_hash(composition)[source]
                                                        +get_hash(composition)[source]

                                                        No hash possible

                                                        @@ -260,13 +260,13 @@
                                                        -class OccupancyComparator[source]
                                                        +class OccupancyComparator[source]

                                                        Bases: pymatgen.analysis.structure_matcher.AbstractComparator

                                                        A Comparator that matches occupancies on sites, irrespective of the species of those sites.

                                                        -are_equal(sp1, sp2)[source]
                                                        +are_equal(sp1, sp2)[source]
                                                        Parameters
                                                          @@ -284,7 +284,7 @@
                                                          -get_hash(composition)[source]
                                                          +get_hash(composition)[source]
                                                          Parameters

                                                          composition – Composition.

                                                          @@ -302,13 +302,13 @@
                                                          -class OrderDisorderElementComparator[source]
                                                          +class OrderDisorderElementComparator[source]

                                                          Bases: pymatgen.analysis.structure_matcher.AbstractComparator

                                                          A Comparator that matches sites, given some overlap in the element composition

                                                          -are_equal(sp1, sp2)[source]
                                                          +are_equal(sp1, sp2)[source]

                                                          True if there is some overlap in composition between the species

                                                          Parameters
                                                          @@ -327,7 +327,7 @@
                                                          -get_hash(composition)[source]
                                                          +get_hash(composition)[source]

                                                          Returns: Fractional composition

                                                          @@ -335,7 +335,7 @@
                                                          -class PointDefectComparator(check_charge=False, check_primitive_cell=False, check_lattice_scale=False)[source]
                                                          +class PointDefectComparator(check_charge=False, check_primitive_cell=False, check_lattice_scale=False)[source]

                                                          Bases: monty.json.MSONable

                                                          A class that matches pymatgen Point Defect objects even if their Cartesian coordinates are different (compares sublattices for the defect)

                                                          @@ -360,7 +360,7 @@
                                                          -are_equal(d1, d2)[source]
                                                          +are_equal(d1, d2)[source]
                                                          Parameters
                                                            @@ -378,13 +378,13 @@
                                                            -class SpeciesComparator[source]
                                                            +class SpeciesComparator[source]

                                                            Bases: pymatgen.analysis.structure_matcher.AbstractComparator

                                                            A Comparator that matches species exactly. The default used in StructureMatcher.

                                                            -are_equal(sp1, sp2)[source]
                                                            +are_equal(sp1, sp2)[source]

                                                            True if species are exactly the same, i.e., Fe2+ == Fe2+ but not Fe3+.

                                                            Parameters
                                                            @@ -403,7 +403,7 @@
                                                            -get_hash(composition)[source]
                                                            +get_hash(composition)[source]

                                                            Returns: Fractional composition

                                                            @@ -411,14 +411,14 @@
                                                            -class SpinComparator[source]
                                                            +class SpinComparator[source]

                                                            Bases: pymatgen.analysis.structure_matcher.AbstractComparator

                                                            A Comparator that matches magnetic structures to their inverse spins. This comparator is primarily used to filter magnetically ordered structures with opposite spins, which are equivalent.

                                                            -are_equal(sp1, sp2)[source]
                                                            +are_equal(sp1, sp2)[source]

                                                            True if species are exactly the same, i.e., Fe2+ == Fe2+ but not Fe3+. and the spins are reversed. i.e., spin up maps to spin down, and vice versa.

                                                            @@ -439,7 +439,7 @@
                                                            -get_hash(composition)[source]
                                                            +get_hash(composition)[source]

                                                            Returns: Fractional composition

                                                            @@ -447,7 +447,7 @@
                                                            -class StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5, primitive_cell=True, scale=True, attempt_supercell=False, allow_subset=False, comparator=<pymatgen.analysis.structure_matcher.SpeciesComparator object>, supercell_size='num_sites', ignored_species=None)[source]
                                                            +class StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5, primitive_cell=True, scale=True, attempt_supercell=False, allow_subset=False, comparator=<pymatgen.analysis.structure_matcher.SpeciesComparator object>, supercell_size='num_sites', ignored_species=None)[source]

                                                            Bases: monty.json.MSONable

                                                            Class to match structures by similarity.

                                                            Algorithm:

                                                            @@ -541,7 +541,7 @@
                                                            -as_dict()[source]
                                                            +as_dict()[source]
                                                            Returns

                                                            MSONable dict

                                                            @@ -551,7 +551,7 @@
                                                            -fit(struct1: pymatgen.core.structure.Structure, struct2: pymatgen.core.structure.Structure, symmetric: bool = False, skip_structure_reduction: bool = False) → bool[source]
                                                            +fit(struct1: pymatgen.core.structure.Structure, struct2: pymatgen.core.structure.Structure, symmetric: bool = False, skip_structure_reduction: bool = False) → bool[source]

                                                            Fit two structures.

                                                            Parameters
                                                            @@ -573,7 +573,7 @@
                                                            -fit_anonymous(struct1: pymatgen.core.structure.Structure, struct2: pymatgen.core.structure.Structure, niggli: bool = True, skip_structure_reduction: bool = False)[source]
                                                            +fit_anonymous(struct1: pymatgen.core.structure.Structure, struct2: pymatgen.core.structure.Structure, niggli: bool = True, skip_structure_reduction: bool = False)[source]

                                                            Performs an anonymous fitting, which allows distinct species in one structure to map to another. E.g., to compare if the Li2O and Na2O structures are similar.

                                                            @@ -598,7 +598,7 @@
                                                            -classmethod from_dict(d)[source]
                                                            +classmethod from_dict(d)[source]
                                                            Parameters

                                                            d – Dict representation

                                                            @@ -611,7 +611,7 @@
                                                            -get_all_anonymous_mappings(struct1, struct2, niggli=True, include_dist=False)[source]
                                                            +get_all_anonymous_mappings(struct1, struct2, niggli=True, include_dist=False)[source]

                                                            Performs an anonymous fitting, which allows distinct species in one structure to map to another. Returns a dictionary of species substitutions that are within tolerance

                                                            @@ -632,7 +632,7 @@
                                                            -get_best_electronegativity_anonymous_mapping(struct1, struct2)[source]
                                                            +get_best_electronegativity_anonymous_mapping(struct1, struct2)[source]

                                                            Performs an anonymous fitting, which allows distinct species in one structure to map to another. E.g., to compare if the Li2O and Na2O structures are similar. If multiple substitutions are within tolerance @@ -656,7 +656,7 @@

                                                            -get_mapping(superset, subset)[source]
                                                            +get_mapping(superset, subset)[source]

                                                            Calculate the mapping from superset to subset.

                                                            Parameters
                                                            @@ -676,7 +676,7 @@
                                                            -get_rms_anonymous(struct1, struct2)[source]
                                                            +get_rms_anonymous(struct1, struct2)[source]

                                                            Performs an anonymous fitting, which allows distinct species in one structure to map to another. E.g., to compare if the Li2O and Na2O structures are similar.

                                                            @@ -699,7 +699,7 @@
                                                            -get_rms_dist(struct1, struct2)[source]
                                                            +get_rms_dist(struct1, struct2)[source]

                                                            Calculate RMS displacement between two structures

                                                            Parameters
                                                            @@ -718,7 +718,7 @@
                                                            -get_s2_like_s1(struct1, struct2, include_ignored_species=True)[source]
                                                            +get_s2_like_s1(struct1, struct2, include_ignored_species=True)[source]

                                                            Performs transformations on struct2 to put it in a basis similar to struct1 (without changing any of the inter-site distances)

                                                            @@ -741,7 +741,7 @@
                                                            -get_supercell_matrix(supercell, struct)[source]
                                                            +get_supercell_matrix(supercell, struct)[source]

                                                            Returns the matrix for transforming struct to supercell. This can be used for very distorted ‘supercells’ where the primitive cell is impossible to find

                                                            @@ -749,7 +749,7 @@
                                                            -get_transformation(struct1, struct2)[source]
                                                            +get_transformation(struct1, struct2)[source]

                                                            Returns the supercell transformation, fractional translation vector, and a mapping to transform struct2 to be similar to struct1.

                                                            @@ -779,7 +779,7 @@
                                                            -group_structures(s_list, anonymous=False)[source]
                                                            +group_structures(s_list, anonymous=False)[source]

                                                            Given a list of structures, use fit to group them by structural equality.

                                                            diff --git a/docs/pymatgen.analysis.structure_prediction.dopant_predictor.html b/docs/pymatgen.analysis.structure_prediction.dopant_predictor.html index 10810e08036..5a8aef36f9a 100644 --- a/docs/pymatgen.analysis.structure_prediction.dopant_predictor.html +++ b/docs/pymatgen.analysis.structure_prediction.dopant_predictor.html @@ -4,7 +4,7 @@ - pymatgen.analysis.structure_prediction.dopant_predictor module — pymatgen 2022.5.18 documentation + pymatgen.analysis.structure_prediction.dopant_predictor module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                            - 2022.5.18 + 2022.5.18.1
                                                            @@ -119,7 +119,7 @@

                                                            Predicting potential dopants

                                                            -get_dopants_from_shannon_radii(bonded_structure, num_dopants=5, match_oxi_sign=False)[source]
                                                            +get_dopants_from_shannon_radii(bonded_structure, num_dopants=5, match_oxi_sign=False)[source]

                                                            Get dopant suggestions based on Shannon radii differences.

                                                            Parameters
                                                            @@ -154,7 +154,7 @@
                                                            -get_dopants_from_substitution_probabilities(structure, num_dopants=5, threshold=0.001, match_oxi_sign=False)[source]
                                                            +get_dopants_from_substitution_probabilities(structure, num_dopants=5, threshold=0.001, match_oxi_sign=False)[source]

                                                            Get dopant suggestions based on substitution probabilities.

                                                            Parameters
                                                            diff --git a/docs/pymatgen.analysis.structure_prediction.html b/docs/pymatgen.analysis.structure_prediction.html index 455f49bd277..0c94cedfd80 100644 --- a/docs/pymatgen.analysis.structure_prediction.html +++ b/docs/pymatgen.analysis.structure_prediction.html @@ -4,7 +4,7 @@ - pymatgen.analysis.structure_prediction package — pymatgen 2022.5.18 documentation + pymatgen.analysis.structure_prediction package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                            - 2022.5.18 + 2022.5.18.1
                                                            diff --git a/docs/pymatgen.analysis.structure_prediction.substitution_probability.html b/docs/pymatgen.analysis.structure_prediction.substitution_probability.html index ac2691480dc..524e01c574d 100644 --- a/docs/pymatgen.analysis.structure_prediction.substitution_probability.html +++ b/docs/pymatgen.analysis.structure_prediction.substitution_probability.html @@ -4,7 +4,7 @@ - pymatgen.analysis.structure_prediction.substitution_probability module — pymatgen 2022.5.18 documentation + pymatgen.analysis.structure_prediction.substitution_probability module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                            - 2022.5.18 + 2022.5.18.1
                                                            @@ -120,7 +120,7 @@ probabilities.

                                                            -class SubstitutionPredictor(lambda_table=None, alpha=- 5, threshold=0.001)[source]
                                                            +class SubstitutionPredictor(lambda_table=None, alpha=- 5, threshold=0.001)[source]

                                                            Bases: object

                                                            Predicts likely substitutions either to or from a given composition or species list using the SubstitutionProbability

                                                            @@ -135,7 +135,7 @@
                                                            -composition_prediction(composition, to_this_composition=True)[source]
                                                            +composition_prediction(composition, to_this_composition=True)[source]

                                                            Returns charged balanced substitutions from a starting or ending composition.

                                                            @@ -159,7 +159,7 @@
                                                            -list_prediction(species, to_this_composition=True)[source]
                                                            +list_prediction(species, to_this_composition=True)[source]
                                                            Parameters
                                                              @@ -183,7 +183,7 @@
                                                              -class SubstitutionProbability(*args, **kwargs)[source]
                                                              +class SubstitutionProbability(*args, **kwargs)[source]

                                                              Bases: pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability

                                                              This class finds substitution probabilities given lists of atoms to substitute. The inputs make more sense if you look through the diff --git a/docs/pymatgen.analysis.structure_prediction.substitutor.html b/docs/pymatgen.analysis.structure_prediction.substitutor.html index 9de157b5186..dda41fb4138 100644 --- a/docs/pymatgen.analysis.structure_prediction.substitutor.html +++ b/docs/pymatgen.analysis.structure_prediction.substitutor.html @@ -4,7 +4,7 @@ - pymatgen.analysis.structure_prediction.substitutor module — pymatgen 2022.5.18 documentation + pymatgen.analysis.structure_prediction.substitutor module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                                              - 2022.5.18 + 2022.5.18.1
                                                              @@ -119,7 +119,7 @@

                                                              This module provides classes for predicting new structures from existing ones.

                                                              -class Substitutor(threshold=0.001, symprec=0.1, **kwargs)[source]
                                                              +class Substitutor(threshold=0.001, symprec=0.1, **kwargs)[source]

                                                              Bases: monty.json.MSONable

                                                              This object uses a data mined ionic substitution approach to propose compounds likely to be stable. It relies on an algorithm presented in @@ -141,13 +141,13 @@

                                                              -as_dict()[source]
                                                              +as_dict()[source]

                                                              Returns: MSONable dict

                                                              -classmethod from_dict(d)[source]
                                                              +classmethod from_dict(d)[source]
                                                              Parameters

                                                              d (dict) – Dict representation

                                                              @@ -160,21 +160,21 @@
                                                              -get_allowed_species()[source]
                                                              +get_allowed_species()[source]

                                                              returns the species in the domain of the probability function any other specie will not work

                                                              -pred_from_comp(composition)[source]
                                                              +pred_from_comp(composition)[source]

                                                              Similar to pred_from_list except this method returns a list after checking that compositions are charge balanced.

                                                              -pred_from_list(species_list)[source]
                                                              +pred_from_list(species_list)[source]

                                                              There are an exceptionally large number of substitutions to look at (260^n), where n is the number of species in the list. We need a more efficient than brute force way of going @@ -202,7 +202,7 @@

                                                              -pred_from_structures(target_species, structures_list, remove_duplicates=True, remove_existing=False)[source]
                                                              +pred_from_structures(target_species, structures_list, remove_duplicates=True, remove_existing=False)[source]

                                                              performs a structure prediction targeting compounds containing all of the target_species, based on a list of structure (those structures can for instance come from a database like the ICSD). It will return diff --git a/docs/pymatgen.analysis.structure_prediction.volume_predictor.html b/docs/pymatgen.analysis.structure_prediction.volume_predictor.html index 779f067d5cf..d207c0f739c 100644 --- a/docs/pymatgen.analysis.structure_prediction.volume_predictor.html +++ b/docs/pymatgen.analysis.structure_prediction.volume_predictor.html @@ -4,7 +4,7 @@ - pymatgen.analysis.structure_prediction.volume_predictor module — pymatgen 2022.5.18 documentation + pymatgen.analysis.structure_prediction.volume_predictor module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                                              - 2022.5.18 + 2022.5.18.1
                                                              @@ -119,7 +119,7 @@

                                                              Predict volumes of crystal structures.

                                                              -class DLSVolumePredictor(cutoff=4.0, min_scaling=0.5, max_scaling=1.5)[source]
                                                              +class DLSVolumePredictor(cutoff=4.0, min_scaling=0.5, max_scaling=1.5)[source]

                                                              Bases: object

                                                              Data-mined lattice scaling (DLS) scheme that relies on data-mined bond lengths to predict the crystal volume of a given structure.

                                                              @@ -145,7 +145,7 @@
                                                              -get_predicted_structure(structure, icsd_vol=False)[source]
                                                              +get_predicted_structure(structure, icsd_vol=False)[source]

                                                              Given a structure, returns back the structure scaled to predicted volume. :param structure: structure w/unknown volume @@ -159,7 +159,7 @@

                                                              -predict(structure, icsd_vol=False)[source]
                                                              +predict(structure, icsd_vol=False)[source]

                                                              Given a structure, returns the predicted volume.

                                                              Parameters
                                                              @@ -179,7 +179,7 @@
                                                              -class RLSVolumePredictor(check_isostructural=True, radii_type='ionic-atomic', use_bv=True)[source]
                                                              +class RLSVolumePredictor(check_isostructural=True, radii_type='ionic-atomic', use_bv=True)[source]

                                                              Bases: object

                                                              Reference lattice scaling (RLS) scheme that predicts the volume of a structure based on a known crystal structure.

                                                              @@ -200,7 +200,7 @@
                                                              -get_predicted_structure(structure, ref_structure)[source]
                                                              +get_predicted_structure(structure, ref_structure)[source]

                                                              Given a structure, returns back the structure scaled to predicted volume. :param structure: structure w/unknown volume @@ -218,7 +218,7 @@

                                                              -predict(structure, ref_structure)[source]
                                                              +predict(structure, ref_structure)[source]

                                                              Given a structure, returns the predicted volume.

                                                              Parameters
                                                              diff --git a/docs/pymatgen.analysis.substrate_analyzer.html b/docs/pymatgen.analysis.substrate_analyzer.html index 07c6ee52093..4ebba649fa1 100644 --- a/docs/pymatgen.analysis.substrate_analyzer.html +++ b/docs/pymatgen.analysis.substrate_analyzer.html @@ -4,7 +4,7 @@ - pymatgen.analysis.substrate_analyzer module — pymatgen 2022.5.18 documentation + pymatgen.analysis.substrate_analyzer module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                              - 2022.5.18 + 2022.5.18.1
                                                              diff --git a/docs/pymatgen.analysis.surface_analysis.html b/docs/pymatgen.analysis.surface_analysis.html index 48d2d889993..0bee3d4e9be 100644 --- a/docs/pymatgen.analysis.surface_analysis.html +++ b/docs/pymatgen.analysis.surface_analysis.html @@ -4,7 +4,7 @@ - pymatgen.analysis.surface_analysis module — pymatgen 2022.5.18 documentation + pymatgen.analysis.surface_analysis module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                              - 2022.5.18 + 2022.5.18.1
                                                              @@ -138,7 +138,7 @@
                                                              -class NanoscaleStability(se_analyzers, symprec=1e-05)[source]
                                                              +class NanoscaleStability(se_analyzers, symprec=1e-05)[source]

                                                              Bases: object

                                                              A class for analyzing the stability of nanoparticles of different

                                                              polymorphs with respect to size. The Wulff shape will be the @@ -158,7 +158,7 @@

                                                              -se_analyzers[source]
                                                              +se_analyzers[source]
                                                              List of SurfaceEnergyPlotter objects. Each item corresponds to a

                                                              different polymorph.

                                                              @@ -167,14 +167,14 @@
                                                              -symprec[source]
                                                              +symprec[source]

                                                              See WulffShape.

                                                              Analyzes the nanoscale stability of different polymorphs.

                                                              -static bulk_gform(bulk_entry)[source]
                                                              +static bulk_gform(bulk_entry)[source]

                                                              Returns the formation energy of the bulk :param bulk_entry: Entry of the corresponding bulk. :type bulk_entry: ComputedStructureEntry

                                                              @@ -182,7 +182,7 @@
                                                              -plot_all_stability_map(max_r, increments=50, delu_dict=None, delu_default=0, plt=None, labels=None, from_sphere_area=False, e_units='keV', r_units='nanometers', normalize=False, scale_per_atom=False)[source]
                                                              +plot_all_stability_map(max_r, increments=50, delu_dict=None, delu_default=0, plt=None, labels=None, from_sphere_area=False, e_units='keV', r_units='nanometers', normalize=False, scale_per_atom=False)[source]
                                                              Returns the plot of the formation energy of a particles

                                                              of different polymorphs against its effect radius

                                                              @@ -209,7 +209,7 @@
                                                              -plot_one_stability_map(analyzer, max_r, delu_dict=None, label='', increments=50, delu_default=0, plt=None, from_sphere_area=False, e_units='keV', r_units='nanometers', normalize=False, scale_per_atom=False)[source]
                                                              +plot_one_stability_map(analyzer, max_r, delu_dict=None, label='', increments=50, delu_default=0, plt=None, from_sphere_area=False, e_units='keV', r_units='nanometers', normalize=False, scale_per_atom=False)[source]
                                                              Returns the plot of the formation energy of a particle against its

                                                              effect radius

                                                              @@ -240,7 +240,7 @@
                                                              -scaled_wulff(wulffshape, r)[source]
                                                              +scaled_wulff(wulffshape, r)[source]
                                                              Scales the Wulff shape with an effective radius r. Note that the resulting

                                                              Wulff does not necessarily have the same effective radius as the one provided. The Wulff shape is scaled by its surface energies where first @@ -263,7 +263,7 @@

                                                              -solve_equilibrium_point(analyzer1, analyzer2, delu_dict={}, delu_default=0, units='nanometers')[source]
                                                              +solve_equilibrium_point(analyzer1, analyzer2, delu_dict={}, delu_default=0, units='nanometers')[source]
                                                              Gives the radial size of two particles where equilibrium is reached

                                                              between both particles. NOTE: the solution here is not the same as the solution visualized in the plot because solving for r @@ -293,7 +293,7 @@

                                                              -wulff_gform_and_r(wulffshape, bulk_entry, r, from_sphere_area=False, r_units='nanometers', e_units='keV', normalize=False, scale_per_atom=False)[source]
                                                              +wulff_gform_and_r(wulffshape, bulk_entry, r, from_sphere_area=False, r_units='nanometers', e_units='keV', normalize=False, scale_per_atom=False)[source]

                                                              Calculates the formation energy of the particle with arbitrary radius r.

                                                              Parameters
                                                              @@ -321,7 +321,7 @@
                                                              -class SlabEntry(structure, energy, miller_index, correction=0.0, parameters=None, data=None, entry_id=None, label=None, adsorbates=None, clean_entry=None, marker=None, color=None)[source]
                                                              +class SlabEntry(structure, energy, miller_index, correction=0.0, parameters=None, data=None, entry_id=None, label=None, adsorbates=None, clean_entry=None, marker=None, color=None)[source]

                                                              Bases: pymatgen.entries.computed_entries.ComputedStructureEntry

                                                              A ComputedStructureEntry object encompassing all data relevant to a

                                                              slab for analyzing surface thermodynamics.

                                                              @@ -329,19 +329,19 @@
                                                              -miller_index[source]
                                                              +miller_index[source]

                                                              Miller index of plane parallel to surface.

                                                              -label[source]
                                                              +label[source]

                                                              Brief description for this slab.

                                                              -adsorbates[source]
                                                              +adsorbates[source]

                                                              List of ComputedStructureEntry for the types of adsorbates

                                                              @@ -386,64 +386,64 @@
                                                              -property Nads_in_slab[source]
                                                              +property Nads_in_slab[source]

                                                              Returns the TOTAL number of adsorbates in the slab on BOTH sides

                                                              -property Nsurfs_ads_in_slab[source]
                                                              +property Nsurfs_ads_in_slab[source]

                                                              Returns the TOTAL number of adsorbed surfaces in the slab

                                                              -as_dict()[source]
                                                              +as_dict()[source]

                                                              Returns dict which contains Slab Entry data.

                                                              -property cleaned_up_slab[source]
                                                              +property cleaned_up_slab[source]

                                                              Returns a slab with the adsorbates removed

                                                              -property create_slab_label[source]
                                                              +property create_slab_label[source]

                                                              Returns a label (str) for this particular slab based on composition, coverage and Miller index.

                                                              -static from_computed_structure_entry(entry, miller_index, label=None, adsorbates=None, clean_entry=None, **kwargs)[source]
                                                              +static from_computed_structure_entry(entry, miller_index, label=None, adsorbates=None, clean_entry=None, **kwargs)[source]

                                                              Returns SlabEntry from a ComputedStructureEntry

                                                              -classmethod from_dict(d)[source]
                                                              +classmethod from_dict(d)[source]

                                                              Returns a SlabEntry by reading in an dictionary

                                                              -property get_monolayer[source]
                                                              +property get_monolayer[source]

                                                              Returns the primitive unit surface area density of the adsorbate.

                                                              -property get_unit_primitive_area[source]
                                                              +property get_unit_primitive_area[source]

                                                              Returns the surface area of the adsorbed system per unit area of the primitive slab system.

                                                              -gibbs_binding_energy(eads=False)[source]
                                                              +gibbs_binding_energy(eads=False)[source]
                                                              Returns the adsorption energy or Gibb’s binding energy

                                                              of an adsorbate on a surface

                                                              @@ -459,13 +459,13 @@
                                                              -property surface_area[source]
                                                              +property surface_area[source]

                                                              Calculates the surface area of the slab

                                                              -surface_energy(ucell_entry, ref_entries=None)[source]
                                                              +surface_energy(ucell_entry, ref_entries=None)[source]

                                                              Calculates the surface energy of this SlabEntry. :param ucell_entry: An entry object for the bulk :type ucell_entry: entry @@ -484,7 +484,7 @@

                                                              -class SurfaceEnergyPlotter(all_slab_entries, ucell_entry, ref_entries=None)[source]
                                                              +class SurfaceEnergyPlotter(all_slab_entries, ucell_entry, ref_entries=None)[source]

                                                              Bases: object

                                                              A class used for generating plots to analyze the thermodynamics of surfaces

                                                              of a material. Produces stability maps of different slab configurations, @@ -494,7 +494,7 @@

                                                              -all_slab_entries[source]
                                                              +all_slab_entries[source]
                                                              Either a list of SlabEntry objects (note for a list, the SlabEntry must

                                                              have the adsorbates and clean_entry parameter pulgged in) or a Nested dictionary containing a list of entries for slab calculations as @@ -532,19 +532,19 @@

                                                -ucell_entry[source]
                                                +ucell_entry[source]

                                                ComputedStructureEntry of the bulk reference for this particular material.

                                                -ref_entries[source]
                                                +ref_entries[source]

                                                List of ComputedStructureEntries to be used for calculating chemical potential.

                                                -color_dict[source]
                                                +color_dict[source]

                                                Randomly generated dictionary of colors associated with each facet.

                                                @@ -576,7 +576,7 @@
                                                -BE_vs_clean_SE(delu_dict, delu_default=0, plot_eads=False, annotate_monolayer=True, JPERM2=False)[source]
                                                +BE_vs_clean_SE(delu_dict, delu_default=0, plot_eads=False, annotate_monolayer=True, JPERM2=False)[source]
                                                For each facet, plot the clean surface energy against the most

                                                stable binding energy.

                                                @@ -611,7 +611,7 @@
                                                -area_frac_vs_chempot_plot(ref_delu, chempot_range, delu_dict=None, delu_default=0, increments=10, no_clean=False, no_doped=False)[source]
                                                +area_frac_vs_chempot_plot(ref_delu, chempot_range, delu_dict=None, delu_default=0, increments=10, no_clean=False, no_doped=False)[source]

                                                1D plot. Plots the change in the area contribution of each facet as a function of chemical potential.

                                                @@ -643,7 +643,7 @@
                                                -static chempot_plot_addons(plt, xrange, ref_el, axes, pad=2.4, rect=[- 0.047, 0, 0.84, 1], ylim=[])[source]
                                                +static chempot_plot_addons(plt, xrange, ref_el, axes, pad=2.4, rect=[- 0.047, 0, 0.84, 1], ylim=[])[source]

                                                Helper function to a chempot plot look nicer.

                                                Parameters
                                                @@ -664,7 +664,7 @@
                                                -chempot_vs_gamma(ref_delu, chempot_range, miller_index=(), delu_dict={}, delu_default=0, JPERM2=False, show_unstable=False, ylim=[], plt=None, no_clean=False, no_doped=False, use_entry_labels=False, no_label=False)[source]
                                                +chempot_vs_gamma(ref_delu, chempot_range, miller_index=(), delu_dict={}, delu_default=0, JPERM2=False, show_unstable=False, ylim=[], plt=None, no_clean=False, no_doped=False, use_entry_labels=False, no_label=False)[source]
                                                Plots the surface energy as a function of chemical potential.

                                                Each facet will be associated with its own distinct colors. Dashed lines will represent stoichiometries different from that @@ -709,7 +709,7 @@

                                                -chempot_vs_gamma_plot_one(plt, entry, ref_delu, chempot_range, delu_dict={}, delu_default=0, label='', JPERM2=False)[source]
                                                +chempot_vs_gamma_plot_one(plt, entry, ref_delu, chempot_range, delu_dict={}, delu_default=0, label='', JPERM2=False)[source]

                                                Helper function to help plot the surface energy of a single SlabEntry as a function of chemical potential.

                                                @@ -744,7 +744,7 @@
                                                -color_palette_dict(alpha=0.35)[source]
                                                +color_palette_dict(alpha=0.35)[source]

                                                Helper function to assign each facet a unique color using a dictionary.

                                                Parameters
                                                @@ -761,7 +761,7 @@
                                                -get_stable_entry_at_u(miller_index, delu_dict=None, delu_default=0, no_doped=False, no_clean=False)[source]
                                                +get_stable_entry_at_u(miller_index, delu_dict=None, delu_default=0, no_doped=False, no_clean=False)[source]
                                                Returns the entry corresponding to the most stable slab for a particular

                                                facet at a specific chempot. We assume that surface energy is constant so all free variables must be set with delu_dict, otherwise they are @@ -788,7 +788,7 @@

                                                -get_surface_equilibrium(slab_entries, delu_dict=None)[source]
                                                +get_surface_equilibrium(slab_entries, delu_dict=None)[source]
                                                Takes in a list of SlabEntries and calculates the chemical potentials

                                                at which all slabs in the list coexists simultaneously. Useful for building surface phase diagrams. Note that to solve for x equations @@ -820,7 +820,7 @@

                                                -monolayer_vs_BE(plot_eads=False)[source]
                                                +monolayer_vs_BE(plot_eads=False)[source]
                                                Plots the binding energy energy as a function of monolayers (ML), i.e.

                                                the fractional area adsorbate density for all facets. For each facet at a specific monlayer, only plot the lowest binding energy.

                                                @@ -842,7 +842,7 @@
                                                -set_all_variables(delu_dict, delu_default)[source]
                                                +set_all_variables(delu_dict, delu_default)[source]
                                                Sets all chemical potential values and returns a dictionary where

                                                the key is a sympy Symbol and the value is a float (chempot).

                                                @@ -865,7 +865,7 @@
                                                -stable_u_range_dict(chempot_range, ref_delu, no_doped=True, no_clean=False, delu_dict={}, miller_index=(), dmu_at_0=False, return_se_dict=False)[source]
                                                +stable_u_range_dict(chempot_range, ref_delu, no_doped=True, no_clean=False, delu_dict={}, miller_index=(), dmu_at_0=False, return_se_dict=False)[source]

                                                Creates a dictionary where each entry is a key pointing to a chemical potential range where the surface of that entry is stable. Does so by enumerating through all possible solutions (intersect) @@ -901,7 +901,7 @@

                                                -surface_chempot_range_map(elements, miller_index, ranges, incr=50, no_doped=False, no_clean=False, delu_dict=None, plt=None, annotate=True, show_unphyiscal_only=False, fontsize=10)[source]
                                                +surface_chempot_range_map(elements, miller_index, ranges, incr=50, no_doped=False, no_clean=False, delu_dict=None, plt=None, annotate=True, show_unphyiscal_only=False, fontsize=10)[source]
                                                Adapted from the get_chempot_range_map() method in the PhaseDiagram

                                                class. Plot the chemical potential range map based on surface energy stability. Currently works only for 2-component PDs. At @@ -939,7 +939,7 @@

                                                -wulff_from_chempot(delu_dict=None, delu_default=0, symprec=1e-05, no_clean=False, no_doped=False)[source]
                                                +wulff_from_chempot(delu_dict=None, delu_default=0, symprec=1e-05, no_clean=False, no_doped=False)[source]

                                                Method to get the Wulff shape at a specific chemical potential.

                                                Parameters
                                                @@ -966,7 +966,7 @@
                                                -class WorkFunctionAnalyzer(structure, locpot_along_c, efermi, shift=0, blength=3.5)[source]
                                                +class WorkFunctionAnalyzer(structure, locpot_along_c, efermi, shift=0, blength=3.5)[source]

                                                Bases: object

                                                A class used for calculating the work function

                                                from a slab model and visualizing the behavior @@ -975,19 +975,19 @@

                                                -efermi[source]
                                                +efermi[source]

                                                The Fermi energy

                                                -locpot_along_c[source]
                                                +locpot_along_c[source]

                                                Local potential in eV along points along the axis

                                                -vacuum_locpot[source]
                                                +vacuum_locpot[source]
                                                The maximum local potential along the c direction for

                                                the slab model, ie the potential at the vacuum

                                                @@ -996,7 +996,7 @@
                                                -work_function[source]
                                                +work_function[source]
                                                The minimum energy needed to move an electron from the

                                                surface to infinity. Defined as the difference between the potential at the vacuum and the Fermi energy.

                                                @@ -1006,13 +1006,13 @@
                                                -slab[source]
                                                +slab[source]

                                                The slab structure model

                                                -along_c[source]
                                                +along_c[source]
                                                Points along the c direction with same

                                                increments as the locpot in the c axis

                                                @@ -1021,19 +1021,19 @@
                                                -ave_locpot[source]
                                                +ave_locpot[source]

                                                Mean of the minimum and maximmum (vacuum) locpot along c

                                                -sorted_sites[source]
                                                +sorted_sites[source]

                                                List of sites from the slab sorted along the c direction

                                                -ave_bulk_p[source]
                                                +ave_bulk_p[source]

                                                The average locpot of the slab region along the c direction

                                                @@ -1054,7 +1054,7 @@
                                                -static from_files(poscar_filename, locpot_filename, outcar_filename, shift=0, blength=3.5)[source]
                                                +static from_files(poscar_filename, locpot_filename, outcar_filename, shift=0, blength=3.5)[source]
                                                Parameters
                                                  @@ -1074,7 +1074,7 @@
                                                  -get_labels(plt, label_fontsize=10)[source]
                                                  +get_labels(plt, label_fontsize=10)[source]

                                                  Handles the optional labelling of the plot with relevant quantities :param plt: Plot of the locpot vs c axis :type plt: plt @@ -1085,7 +1085,7 @@

                                                  -get_locpot_along_slab_plot(label_energies=True, plt=None, label_fontsize=10)[source]
                                                  +get_locpot_along_slab_plot(label_energies=True, plt=None, label_fontsize=10)[source]
                                                  Returns a plot of the local potential (eV) vs the

                                                  position along the c axis of the slab model (Ang)

                                                  @@ -1106,7 +1106,7 @@
                                                  -is_converged(min_points_frac=0.015, tol=0.0025)[source]
                                                  +is_converged(min_points_frac=0.015, tol=0.0025)[source]
                                                  A well converged work function should have a flat electrostatic

                                                  potential within some distance (min_point) about where the peak electrostatic potential is found along the c direction of the @@ -1131,7 +1131,7 @@

                                                  -entry_dict_from_list(all_slab_entries)[source]
                                                  +entry_dict_from_list(all_slab_entries)[source]

                                                  Converts a list of SlabEntry to an appropriate dictionary. It is assumed that if there is no adsorbate, then it is a clean SlabEntry and that adsorbed SlabEntry has the clean_entry parameter set.

                                                  @@ -1155,7 +1155,7 @@
                                                  -sub_chempots(gamma_dict, chempots)[source]
                                                  +sub_chempots(gamma_dict, chempots)[source]
                                                  Uses dot product of numpy array to sub chemical potentials

                                                  into the surface grand potential. This is much faster than using the subs function in sympy.

                                                  diff --git a/docs/pymatgen.analysis.thermochemistry.html b/docs/pymatgen.analysis.thermochemistry.html index cc46d031ea0..188552a126a 100644 --- a/docs/pymatgen.analysis.thermochemistry.html +++ b/docs/pymatgen.analysis.thermochemistry.html @@ -4,7 +4,7 @@ - pymatgen.analysis.thermochemistry module — pymatgen 2022.5.18 documentation + pymatgen.analysis.thermochemistry module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                  - 2022.5.18 + 2022.5.18.1
                                                  @@ -118,7 +118,7 @@

                                                  A module to perform experimental thermochemical data analysis.

                                                  -class ThermoData(data_type, cpdname, phaseinfo, formula, value, ref='', method='', temp_range=(298, 298), uncertainty=None)[source]
                                                  +class ThermoData(data_type, cpdname, phaseinfo, formula, value, ref='', method='', temp_range=(298, 298), uncertainty=None)[source]

                                                  Bases: object

                                                  A object container for an experimental Thermochemical Data.

                                                  @@ -146,13 +146,13 @@
                                                  -as_dict()[source]
                                                  +as_dict()[source]

                                                  Returns: MSONable dict

                                                  -classmethod from_dict(d)[source]
                                                  +classmethod from_dict(d)[source]
                                                  Parameters

                                                  d (dict) – Dict representation

                                                  diff --git a/docs/pymatgen.analysis.topological.html b/docs/pymatgen.analysis.topological.html index 81fe4a679ec..3d1cc3be263 100644 --- a/docs/pymatgen.analysis.topological.html +++ b/docs/pymatgen.analysis.topological.html @@ -4,7 +4,7 @@ - pymatgen.analysis.topological package — pymatgen 2022.5.18 documentation + pymatgen.analysis.topological package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                  - 2022.5.18 + 2022.5.18.1
                                                  diff --git a/docs/pymatgen.analysis.topological.spillage.html b/docs/pymatgen.analysis.topological.spillage.html index b6631b7be03..df4ab8359e6 100644 --- a/docs/pymatgen.analysis.topological.spillage.html +++ b/docs/pymatgen.analysis.topological.spillage.html @@ -4,7 +4,7 @@ - pymatgen.analysis.topological.spillage module — pymatgen 2022.5.18 documentation + pymatgen.analysis.topological.spillage module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                  - 2022.5.18 + 2022.5.18.1
                                                  @@ -122,7 +122,7 @@ https://www.nature.com/articles/s41524-020-0319-4

                                                  -class SOCSpillage(wf_noso='', wf_so='')[source]
                                                  +class SOCSpillage(wf_noso='', wf_so='')[source]

                                                  Bases: object

                                                  Spin-orbit spillage criteria to predict whether a material is topologically non-trival. The spillage criteria physically signifies number of band-inverted electrons. @@ -132,19 +132,19 @@ :param wf_so: WAVECAR with spin-orbit coupling

                                                  -static isclose(n1, n2, rel_tol=1e-07)[source]
                                                  +static isclose(n1, n2, rel_tol=1e-07)[source]

                                                  Checking if the numbers are close enough

                                                  -static orth(A)[source]
                                                  +static orth(A)[source]

                                                  Helper function to create orthonormal basis

                                                  -overlap_so_spinpol()[source]
                                                  +overlap_so_spinpol()[source]

                                                  Main function to calculate SOC spillage

                                                  diff --git a/docs/pymatgen.analysis.transition_state.html b/docs/pymatgen.analysis.transition_state.html index 9bdf0ed8e24..7228672260d 100644 --- a/docs/pymatgen.analysis.transition_state.html +++ b/docs/pymatgen.analysis.transition_state.html @@ -4,7 +4,7 @@ - pymatgen.analysis.transition_state module — pymatgen 2022.5.18 documentation + pymatgen.analysis.transition_state module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                  - 2022.5.18 + 2022.5.18.1
                                                  @@ -121,7 +121,7 @@

                                                  This allows the usage and customization in Python.

                                                  -class NEBAnalysis(r, energies, forces, structures, spline_options=None)[source]
                                                  +class NEBAnalysis(r, energies, forces, structures, spline_options=None)[source]

                                                  Bases: monty.json.MSONable

                                                  An NEBAnalysis class.

                                                  Initializes an NEBAnalysis from the cumulative root mean squared distances @@ -143,7 +143,7 @@

                                                  -as_dict()[source]
                                                  +as_dict()[source]

                                                  Dict representation of NEBAnalysis.

                                                  Returns
                                                  @@ -154,7 +154,7 @@
                                                  -classmethod from_dir(root_dir, relaxation_dirs=None, **kwargs)[source]
                                                  +classmethod from_dir(root_dir, relaxation_dirs=None, **kwargs)[source]

                                                  Initializes a NEBAnalysis object from a directory of a NEB run. Note that OUTCARs must be present in all image directories. For the terminal OUTCARs from relaxation calculations, you can specify the @@ -195,7 +195,7 @@

                                                  -classmethod from_outcars(outcars, structures, **kwargs)[source]
                                                  +classmethod from_outcars(outcars, structures, **kwargs)[source]

                                                  Initializes an NEBAnalysis from Outcar and Structure objects. Use the static constructors, e.g., from_dir instead if you prefer to have these automatically generated from a directory of NEB @@ -217,7 +217,7 @@

                                                  -get_extrema(normalize_rxn_coordinate=True)[source]
                                                  +get_extrema(normalize_rxn_coordinate=True)[source]

                                                  Returns the positions of the extrema along the MEP. Both local minimums and maximums are returned.

                                                  @@ -234,7 +234,7 @@
                                                  -get_plot(normalize_rxn_coordinate=True, label_barrier=True)[source]
                                                  +get_plot(normalize_rxn_coordinate=True, label_barrier=True)[source]

                                                  Returns the NEB plot. Uses Henkelman’s approach of spline fitting each section of the reaction path based on tangent force and energies.

                                                  @@ -253,7 +253,7 @@
                                                  -setup_spline(spline_options=None)[source]
                                                  +setup_spline(spline_options=None)[source]

                                                  Setup of the options for the spline interpolation

                                                  Parameters
                                                  @@ -268,7 +268,7 @@
                                                  -combine_neb_plots(neb_analyses, arranged_neb_analyses=False, reverse_plot=False)[source]
                                                  +combine_neb_plots(neb_analyses, arranged_neb_analyses=False, reverse_plot=False)[source]

                                                  neb_analyses: a list of NEBAnalysis objects

                                                  arranged_neb_analyses: The code connects two end points with the smallest-energy difference. If all end points have very close energies, it’s diff --git a/docs/pymatgen.analysis.wulff.html b/docs/pymatgen.analysis.wulff.html index ff707f613e2..621a101f0ab 100644 --- a/docs/pymatgen.analysis.wulff.html +++ b/docs/pymatgen.analysis.wulff.html @@ -4,7 +4,7 @@ - pymatgen.analysis.wulff module — pymatgen 2022.5.18 documentation + pymatgen.analysis.wulff module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                                  - 2022.5.18 + 2022.5.18.1
                                                  @@ -127,7 +127,7 @@ (2016). Surface energies of elemental crystals. Scientific Data.

                                                  -class WulffFacet(normal, e_surf, normal_pt, dual_pt, index, m_ind_orig, miller)[source]
                                                  +class WulffFacet(normal, e_surf, normal_pt, dual_pt, index, m_ind_orig, miller)[source]

                                                  Bases: object

                                                  Helper container for each Wulff plane.

                                                  @@ -147,7 +147,7 @@
                                                  -class WulffShape(lattice, miller_list, e_surf_list, symprec=1e-05)[source]
                                                  +class WulffShape(lattice, miller_list, e_surf_list, symprec=1e-05)[source]

                                                  Bases: object

                                                  Generate Wulff Shape from list of miller index and surface energies, with given conventional unit cell. @@ -165,121 +165,121 @@

                                                  -debug(bool)[source]
                                                  +debug(bool)[source]
                                                  -alpha[source]
                                                  +alpha[source]
                                                  transparency
                                                  -color_set[source]
                                                  +color_set[source]
                                                  -grid_off(bool)[source]
                                                  +grid_off(bool)[source]
                                                  -axis_off(bool)[source]
                                                  +axis_off(bool)[source]
                                                  -show_area[source]
                                                  +show_area[source]
                                                  -off_color[source]
                                                  +off_color[source]
                                                  color of facets off wulff
                                                  -structure[source]
                                                  +structure[source]
                                                  Structure object, input conventional unit cell (with H ) from lattice
                                                  -miller_list[source]
                                                  +miller_list[source]
                                                  list of input miller index, for hcp in the form of hkil
                                                  -hkl_list[source]
                                                  +hkl_list[source]
                                                  modify hkill to hkl, in the same order with input_miller
                                                  -e_surf_list[source]
                                                  +e_surf_list[source]
                                                  list of input surface energies, in the same order with input_miller
                                                  -lattice[source]
                                                  +lattice[source]
                                                  Lattice object, the input lattice for the conventional unit cell
                                                  -facets[source]
                                                  +facets[source]
                                                  [WulffFacet] for all facets considering symm
                                                  -dual_cv_simp[source]
                                                  +dual_cv_simp[source]
                                                  simplices from the dual convex hull (dual_pt)
                                                  -wulff_pt_list[source]
                                                  +wulff_pt_list[source]
                                                  -wulff_cv_simp[source]
                                                  +wulff_cv_simp[source]
                                                  simplices from the convex hull of wulff_pt_list
                                                  -on_wulff[source]
                                                  +on_wulff[source]
                                                  list for all input_miller, True is on wulff.
                                                  -color_area[source]
                                                  +color_area[source]
                                                  list for all input_miller, total area on wulff, off_wulff = 0.
                                                  -miller_area[source]
                                                  +miller_area[source]
                                                  ($hkl$): area for all input_miller
                                                  @@ -296,7 +296,7 @@
                                                  -property anisotropy[source]
                                                  +property anisotropy[source]

                                                  Returns: (float) Coefficient of Variation from weighted surface energy The ideal sphere is 0.

                                                  @@ -304,14 +304,14 @@
                                                  -property area_fraction_dict[source]
                                                  +property area_fraction_dict[source]

                                                  Returns: (dict): {hkl: area_hkl/total area on wulff}

                                                  -property effective_radius[source]
                                                  +property effective_radius[source]

                                                  Radius of the Wulffshape when the Wulffshape is approximated as a sphere.

                                                  @@ -323,13 +323,13 @@
                                                  -get_line_in_facet(facet)[source]
                                                  +get_line_in_facet(facet)[source]

                                                  Returns the sorted pts in a facet used to draw a line

                                                  -get_plot(color_set='PuBu', grid_off=True, axis_off=True, show_area=False, alpha=1, off_color='red', direction=None, bar_pos=(0.75, 0.15, 0.05, 0.65), bar_on=False, units_in_JPERM2=True, legend_on=True, aspect_ratio=(8, 8), custom_colors={})[source]
                                                  +get_plot(color_set='PuBu', grid_off=True, axis_off=True, show_area=False, alpha=1, off_color='red', direction=None, bar_pos=(0.75, 0.15, 0.05, 0.65), bar_on=False, units_in_JPERM2=True, legend_on=True, aspect_ratio=(8, 8), custom_colors={})[source]

                                                  Get the Wulff shape plot.

                                                  Parameters
                                                  @@ -372,7 +372,7 @@
                                                  -get_plotly(color_set='PuBu', off_color='red', alpha=1, custom_colors={}, units_in_JPERM2=True)[source]
                                                  +get_plotly(color_set='PuBu', off_color='red', alpha=1, custom_colors={}, units_in_JPERM2=True)[source]

                                                  Get the Wulff shape as a plotly Figure object.

                                                  Parameters
                                                  @@ -407,7 +407,7 @@
                                                  -property miller_area_dict[source]
                                                  +property miller_area_dict[source]

                                                  area_hkl on wulff}

                                                  Type
                                                  @@ -418,7 +418,7 @@
                                                  -property miller_energy_dict[source]
                                                  +property miller_energy_dict[source]

                                                  surface energy_hkl}

                                                  Type
                                                  @@ -429,7 +429,7 @@
                                                  -property shape_factor[source]
                                                  +property shape_factor[source]

                                                  This is useful for determining the critical nucleus size. A large shape factor indicates great anisotropy. See Ballufi, R. W., Allen, S. M. & Carter, W. C. Kinetics

                                                  @@ -445,7 +445,7 @@
                                                  -show(*args, **kwargs)[source]
                                                  +show(*args, **kwargs)[source]

                                                  Show the Wulff plot.

                                                  Parameters
                                                  @@ -459,27 +459,27 @@
                                                  -property surface_area[source]
                                                  +property surface_area[source]

                                                  Total surface area of Wulff shape.

                                                  -property tot_corner_sites[source]
                                                  +property tot_corner_sites[source]

                                                  Returns the number of vertices in the convex hull. Useful for identifying catalytically active sites.

                                                  -property tot_edges[source]
                                                  +property tot_edges[source]

                                                  Returns the number of edges in the convex hull. Useful for identifying catalytically active sites.

                                                  -property total_surface_energy[source]
                                                  +property total_surface_energy[source]

                                                  Total surface energy of the Wulff shape.

                                                  Returns
                                                  @@ -490,13 +490,13 @@
                                                  -property volume[source]
                                                  +property volume[source]

                                                  Volume of the Wulff shape

                                                  -property weighted_surface_energy[source]
                                                  +property weighted_surface_energy[source]

                                                  Returns: sum(surface_energy_hkl * area_hkl)/ sum(area_hkl)

                                                  @@ -505,7 +505,7 @@
                                                  -get_tri_area(pts)[source]
                                                  +get_tri_area(pts)[source]

                                                  Given a list of coords for 3 points, Compute the area of this triangle.

                                                  @@ -517,7 +517,7 @@
                                                  -hkl_tuple_to_str(hkl)[source]
                                                  +hkl_tuple_to_str(hkl)[source]

                                                  Prepare for display on plots “(hkl)” for surfaces Agrs:

                                                  diff --git a/docs/pymatgen.analysis.xas.html b/docs/pymatgen.analysis.xas.html index 3a0132ce0bf..3fd5373a2f4 100644 --- a/docs/pymatgen.analysis.xas.html +++ b/docs/pymatgen.analysis.xas.html @@ -4,7 +4,7 @@ - pymatgen.analysis.xas package — pymatgen 2022.5.18 documentation + pymatgen.analysis.xas package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                  - 2022.5.18 + 2022.5.18.1
                                                  diff --git a/docs/pymatgen.analysis.xas.spectrum.html b/docs/pymatgen.analysis.xas.spectrum.html index d6c3d7043ca..31134ca50cc 100644 --- a/docs/pymatgen.analysis.xas.spectrum.html +++ b/docs/pymatgen.analysis.xas.spectrum.html @@ -4,7 +4,7 @@ - pymatgen.analysis.xas.spectrum module — pymatgen 2022.5.18 documentation + pymatgen.analysis.xas.spectrum module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                  - 2022.5.18 + 2022.5.18.1
                                                  @@ -119,7 +119,7 @@

                                                  This module defines classes to represent all xas and stitching methods

                                                  -class XAS(x, y, structure, absorbing_element, edge='K', spectrum_type='XANES', absorbing_index=None)[source]
                                                  +class XAS(x, y, structure, absorbing_element, edge='K', spectrum_type='XANES', absorbing_index=None)[source]

                                                  Bases: pymatgen.core.spectrum.Spectrum

                                                  Basic XAS object.

                                                  @@ -140,17 +140,17 @@

                                                  Initializes a spectrum object.

                                                  -XLABEL = 'Energy'[source]
                                                  +XLABEL = 'Energy'[source]
                                                  -YLABEL = 'Intensity'[source]
                                                  +YLABEL = 'Intensity'[source]
                                                  -stitch(other: pymatgen.analysis.xas.spectrum.XAS, num_samples: int = 500, mode: Literal['XAFS', 'L23'] = 'XAFS') → pymatgen.analysis.xas.spectrum.XAS[source]
                                                  +stitch(other: pymatgen.analysis.xas.spectrum.XAS, num_samples: int = 500, mode: Literal['XAFS', 'L23'] = 'XAFS') → pymatgen.analysis.xas.spectrum.XAS[source]

                                                  Stitch XAS objects to get the full XAFS spectrum or L23 edge XANES spectrum depending on the mode.

                                                    @@ -194,7 +194,7 @@
                                                    -site_weighted_spectrum(xas_list: list[pymatgen.analysis.xas.spectrum.XAS], num_samples: int = 500) → pymatgen.analysis.xas.spectrum.XAS[source]
                                                    +site_weighted_spectrum(xas_list: list[pymatgen.analysis.xas.spectrum.XAS], num_samples: int = 500) → pymatgen.analysis.xas.spectrum.XAS[source]

                                                    Obtain site-weighted XAS object based on site multiplicity for each absorbing index and its corresponding site-wise spectrum.

                                                    diff --git a/docs/pymatgen.analysis.xps.html b/docs/pymatgen.analysis.xps.html index fc23adbaab4..0f54e388a60 100644 --- a/docs/pymatgen.analysis.xps.html +++ b/docs/pymatgen.analysis.xps.html @@ -4,7 +4,7 @@ - pymatgen.analysis.xps module — pymatgen 2022.5.18 documentation + pymatgen.analysis.xps module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                    - 2022.5.18 + 2022.5.18.1
                                                    @@ -132,7 +132,7 @@

                                                    This version contains all detailed information for all orbitals.

                                                    -class XPS(x: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], y: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], *args, **kwargs)[source]
                                                    +class XPS(x: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], y: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], *args, **kwargs)[source]

                                                    Bases: pymatgen.core.spectrum.Spectrum

                                                    Class representing an X-ray photoelectron spectra.

                                                    @@ -151,17 +151,17 @@
                                                    -XLABEL = 'Binding Energy (eV)'[source]
                                                    +XLABEL = 'Binding Energy (eV)'[source]
                                                    -YLABEL = 'Intensity'[source]
                                                    +YLABEL = 'Intensity'[source]
                                                    -classmethod from_dos(dos: pymatgen.electronic_structure.dos.CompleteDos)[source]
                                                    +classmethod from_dos(dos: pymatgen.electronic_structure.dos.CompleteDos)[source]
                                                    Parameters
                                                      diff --git a/docs/pymatgen.apps.battery.analyzer.html b/docs/pymatgen.apps.battery.analyzer.html index 71299bbb9dc..19702f1c37f 100644 --- a/docs/pymatgen.apps.battery.analyzer.html +++ b/docs/pymatgen.apps.battery.analyzer.html @@ -4,7 +4,7 @@ - pymatgen.apps.battery.analyzer module — pymatgen 2022.5.18 documentation + pymatgen.apps.battery.analyzer module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                      - 2022.5.18 + 2022.5.18.1
                                                      @@ -119,7 +119,7 @@

                                                      Analysis classes for batteries

                                                      -class BatteryAnalyzer(struc_oxid, working_ion='Li', oxi_override={})[source]
                                                      +class BatteryAnalyzer(struc_oxid, working_ion='Li', oxi_override={})[source]

                                                      Bases: object

                                                      A suite of methods for starting with an oxidized structure and determining its potential as a battery

                                                      Pass in a structure for analysis

                                                      @@ -136,7 +136,7 @@
                                                      -get_max_capgrav(remove=True, insert=True)[source]
                                                      +get_max_capgrav(remove=True, insert=True)[source]

                                                      Give max capacity in mAh/g for inserting and removing a charged ion Note that the weight is normalized to the most ion-packed state, thus removal of 1 Li from LiFePO4 gives the same capacity as insertion of 1 Li into FePO4.

                                                      @@ -155,7 +155,7 @@
                                                      -get_max_capvol(remove=True, insert=True, volume=None)[source]
                                                      +get_max_capvol(remove=True, insert=True, volume=None)[source]

                                                      Give max capacity in mAh/cc for inserting and removing a charged ion into base structure.

                                                      Parameters
                                                      @@ -173,7 +173,7 @@
                                                      -get_removals_int_oxid()[source]
                                                      +get_removals_int_oxid()[source]

                                                      Returns a set of ion removal steps, e.g. set([1.0 2.0 4.0]) etc. in order to produce integer oxidation states of the redox metals. If multiple redox metals are present, all combinations of reduction/oxidation are tested. @@ -191,7 +191,7 @@

                                                      -property max_ion_insertion[source]
                                                      +property max_ion_insertion[source]

                                                      Maximum number of ion A that can be inserted while maintaining charge-balance. No consideration is given to whether there (geometrically speaking) are ion sites to actually accommodate the extra ions.

                                                      @@ -204,7 +204,7 @@
                                                      -property max_ion_removal[source]
                                                      +property max_ion_removal[source]

                                                      Maximum number of ion A that can be removed while maintaining charge-balance.

                                                      Returns
                                                      @@ -217,7 +217,7 @@
                                                      -is_redox_active_intercalation(element)[source]
                                                      +is_redox_active_intercalation(element)[source]

                                                      True if element is redox active and interesting for intercalation materials

                                                      Parameters
                                                      diff --git a/docs/pymatgen.apps.battery.battery_abc.html b/docs/pymatgen.apps.battery.battery_abc.html index f7759585ef1..c7bab9443ac 100644 --- a/docs/pymatgen.apps.battery.battery_abc.html +++ b/docs/pymatgen.apps.battery.battery_abc.html @@ -4,7 +4,7 @@ - pymatgen.apps.battery.battery_abc module — pymatgen 2022.5.18 documentation + pymatgen.apps.battery.battery_abc module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                      - 2022.5.18 + 2022.5.18.1
                                                      @@ -123,7 +123,7 @@ these common definitions to allow sharing of common logic between them.

                                                      -class AbstractElectrode(voltage_pairs: Tuple[pymatgen.apps.battery.battery_abc.AbstractVoltagePair, ...], working_ion_entry: pymatgen.entries.computed_entries.ComputedEntry, framework_formula: str)[source]
                                                      +class AbstractElectrode(voltage_pairs: Tuple[pymatgen.apps.battery.battery_abc.AbstractVoltagePair, ...], working_ion_entry: pymatgen.entries.computed_entries.ComputedEntry, framework_formula: str)[source]

                                                      Bases: collections.abc.Sequence, monty.json.MSONable

                                                      An Abstract Base Class representing an Electrode. It is essentially a sequence of VoltagePairs. Generally, subclasses only need to implement @@ -165,13 +165,13 @@

                                                -working_ion[source]
                                                +working_ion[source]

                                                Representation of the working ion that only contains element type

                                                -working_ion_entry[source]
                                                +working_ion_entry[source]

                                                Representation of the working_ion that contains the energy

                                                Type
                                                @@ -182,7 +182,7 @@
                                                -framework_formula[source]
                                                +framework_formula[source]

                                                The compositions of one formula unit of the host material

                                                Type
                                                @@ -193,18 +193,18 @@
                                                -property framework[source]
                                                +property framework[source]

                                                The composition object representing the framework

                                                -framework_formula: str[source]
                                                +framework_formula: str[source]
                                                -get_average_voltage(min_voltage=None, max_voltage=None)[source]
                                                +get_average_voltage(min_voltage=None, max_voltage=None)[source]

                                                Average voltage for path satisfying between a min and max voltage.

                                                Parameters
                                                @@ -224,7 +224,7 @@
                                                -get_capacity_grav(min_voltage=None, max_voltage=None, use_overall_normalization=True)[source]
                                                +get_capacity_grav(min_voltage=None, max_voltage=None, use_overall_normalization=True)[source]

                                                Get the gravimetric capacity of the electrode.

                                                Parameters
                                                @@ -248,7 +248,7 @@
                                                -get_capacity_vol(min_voltage=None, max_voltage=None, use_overall_normalization=True)[source]
                                                +get_capacity_vol(min_voltage=None, max_voltage=None, use_overall_normalization=True)[source]

                                                Get the volumetric capacity of the electrode.

                                                Parameters
                                                @@ -272,7 +272,7 @@
                                                -get_energy_density(min_voltage=None, max_voltage=None, use_overall_normalization=True)[source]
                                                +get_energy_density(min_voltage=None, max_voltage=None, use_overall_normalization=True)[source]
                                                Parameters
                                              -voltage[source]
                                              +voltage[source]

                                              Voltage for the step

                                              Type
                                              @@ -268,7 +268,7 @@
                                              -mAh[source]
                                              +mAh[source]

                                              Capacity of the step

                                              Type
                                              @@ -279,7 +279,7 @@
                                              -vol_charge[source]
                                              +vol_charge[source]

                                              Volume of charged state

                                              Type
                                              @@ -290,7 +290,7 @@
                                              -vol_discharge[source]
                                              +vol_discharge[source]

                                              Volume of discharged state

                                              Type
                                              @@ -301,7 +301,7 @@
                                              -mass_charge[source]
                                              +mass_charge[source]

                                              Mass of charged state

                                              Type
                                              @@ -312,7 +312,7 @@
                                              -mass_discharge[source]
                                              +mass_discharge[source]

                                              Mass of discharged state

                                              Type
                                              @@ -323,7 +323,7 @@
                                              -frac_charge[source]
                                              +frac_charge[source]

                                              Fraction of working ion in the charged state

                                              Type
                                              @@ -334,7 +334,7 @@
                                              -frac_discharge[source]
                                              +frac_discharge[source]

                                              Fraction of working ion in the discharged state

                                              Type
                                              @@ -345,7 +345,7 @@
                                              -entries_charge[source]
                                              +entries_charge[source]

                                              Entries in the charged state

                                              Type
                                              @@ -356,7 +356,7 @@
                                              -entries_discharge[source]
                                              +entries_discharge[source]

                                              Entries in discharged state

                                              Type
                                              @@ -367,7 +367,7 @@
                                              -working_ion_entry[source]
                                              +working_ion_entry[source]

                                              Entry of the working ion.

                                              Type
                                              @@ -378,17 +378,17 @@
                                              -entries_charge: Iterable[pymatgen.entries.computed_entries.ComputedEntry][source]
                                              +entries_charge: Iterable[pymatgen.entries.computed_entries.ComputedEntry][source]
                                              -entries_discharge: Iterable[pymatgen.entries.computed_entries.ComputedEntry][source]
                                              +entries_discharge: Iterable[pymatgen.entries.computed_entries.ComputedEntry][source]
                                              -classmethod from_steps(step1, step2, normalization_els, framework_formula=None)[source]
                                              +classmethod from_steps(step1, step2, normalization_els, framework_formula=None)[source]

                                              Creates a ConversionVoltagePair from two steps in the element profile from a PD analysis.

                                              @@ -405,7 +405,7 @@
                                              -rxn: pymatgen.analysis.reaction_calculator.BalancedReaction[source]
                                              +rxn: pymatgen.analysis.reaction_calculator.BalancedReaction[source]
                                              diff --git a/docs/pymatgen.apps.battery.html b/docs/pymatgen.apps.battery.html index 82b68d6c7c5..71820edc94e 100644 --- a/docs/pymatgen.apps.battery.html +++ b/docs/pymatgen.apps.battery.html @@ -4,7 +4,7 @@ - pymatgen.apps.battery package — pymatgen 2022.5.18 documentation + pymatgen.apps.battery package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                              - 2022.5.18 + 2022.5.18.1
                                              diff --git a/docs/pymatgen.apps.battery.insertion_battery.html b/docs/pymatgen.apps.battery.insertion_battery.html index 419bd0b47af..d69f87e32d3 100644 --- a/docs/pymatgen.apps.battery.insertion_battery.html +++ b/docs/pymatgen.apps.battery.insertion_battery.html @@ -4,7 +4,7 @@ - pymatgen.apps.battery.insertion_battery module — pymatgen 2022.5.18 documentation + pymatgen.apps.battery.insertion_battery module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                              - 2022.5.18 + 2022.5.18.1
                                              @@ -120,20 +120,20 @@ intercalation batteries.

                                              -class InsertionElectrode(voltage_pairs: Tuple[pymatgen.apps.battery.battery_abc.AbstractVoltagePair, ...], working_ion_entry: pymatgen.entries.computed_entries.ComputedEntry, framework_formula: str, stable_entries: Iterable[pymatgen.entries.computed_entries.ComputedEntry], unstable_entries: Iterable[pymatgen.entries.computed_entries.ComputedEntry])[source]
                                              +class InsertionElectrode(voltage_pairs: Tuple[pymatgen.apps.battery.battery_abc.AbstractVoltagePair, ...], working_ion_entry: pymatgen.entries.computed_entries.ComputedEntry, framework_formula: str, stable_entries: Iterable[pymatgen.entries.computed_entries.ComputedEntry], unstable_entries: Iterable[pymatgen.entries.computed_entries.ComputedEntry])[source]

                                              Bases: pymatgen.apps.battery.battery_abc.AbstractElectrode

                                              A set of topotactically related compounds, with different amounts of a single element, e.g. TiO2 and LiTiO2, that can be used to define an insertion battery electrode.

                                              -as_dict_legacy()[source]
                                              +as_dict_legacy()[source]

                                              Returns: MSONAble dict

                                              -classmethod from_dict_legacy(d)[source]
                                              +classmethod from_dict_legacy(d)[source]
                                              Parameters

                                              d (dict) – Dict representation

                                              @@ -146,7 +146,7 @@
                                              -classmethod from_entries(entries: Iterable[ComputedEntry | ComputedStructureEntry], working_ion_entry: ComputedEntry | ComputedStructureEntry | PDEntry, strip_structures: bool = False)[source]
                                              +classmethod from_entries(entries: Iterable[ComputedEntry | ComputedStructureEntry], working_ion_entry: ComputedEntry | ComputedStructureEntry | PDEntry, strip_structures: bool = False)[source]

                                              Create a new InsertionElectrode.

                                              Parameters
                                              @@ -170,19 +170,19 @@
                                              -property fully_charged_entry[source]
                                              +property fully_charged_entry[source]

                                              The most charged entry along the topotactic path.

                                              -property fully_discharged_entry[source]
                                              +property fully_discharged_entry[source]

                                              The most discharged entry along the topotactic path.

                                              -get_all_entries(charge_to_discharge=True)[source]
                                              +get_all_entries(charge_to_discharge=True)[source]

                                              Return all entries input for the electrode.

                                              Parameters
                                              @@ -198,7 +198,7 @@
                                              -get_max_instability(min_voltage=None, max_voltage=None)[source]
                                              +get_max_instability(min_voltage=None, max_voltage=None)[source]

                                              The maximum instability along a path for a specific voltage range.

                                              Parameters
                                              @@ -216,7 +216,7 @@
                                              -get_max_muO2(min_voltage=None, max_voltage=None)[source]
                                              +get_max_muO2(min_voltage=None, max_voltage=None)[source]

                                              Maximum critical oxygen chemical potential along path.

                                              Parameters
                                              @@ -235,7 +235,7 @@
                                              -get_min_instability(min_voltage=None, max_voltage=None)[source]
                                              +get_min_instability(min_voltage=None, max_voltage=None)[source]

                                              The minimum instability along a path for a specific voltage range.

                                              Parameters
                                              @@ -253,7 +253,7 @@
                                              -get_min_muO2(min_voltage=None, max_voltage=None)[source]
                                              +get_min_muO2(min_voltage=None, max_voltage=None)[source]

                                              Minimum critical oxygen chemical potential along path.

                                              Parameters
                                              @@ -273,7 +273,7 @@
                                              -get_stable_entries(charge_to_discharge=True)[source]
                                              +get_stable_entries(charge_to_discharge=True)[source]

                                              Get the stable entries.

                                              Parameters
                                              @@ -289,7 +289,7 @@
                                              -get_sub_electrodes(adjacent_only=True, include_myself=True)[source]
                                              +get_sub_electrodes(adjacent_only=True, include_myself=True)[source]

                                              If this electrode contains multiple voltage steps, then it is possible to use only a subset of the voltage steps to define other electrodes. For example, an LiTiO2 electrode might contain three subelectrodes: @@ -314,7 +314,7 @@

                                              -get_summary_dict(print_subelectrodes=True) → dict[source]
                                              +get_summary_dict(print_subelectrodes=True) → dict[source]

                                              Generate a summary dict. Populates the summary dict with the basic information from the parent method then populates more information. Since the parent method calls self.get_summary_dict(print_subelectrodes=True) for the subelectrodes. @@ -332,7 +332,7 @@

                                              -get_unstable_entries(charge_to_discharge=True)[source]
                                              +get_unstable_entries(charge_to_discharge=True)[source]

                                              Returns the unstable entries for the electrode.

                                              Parameters
                                              @@ -348,34 +348,34 @@
                                              -stable_entries: Iterable[ComputedEntry][source]
                                              +stable_entries: Iterable[ComputedEntry][source]
                                              -unstable_entries: Iterable[ComputedEntry][source]
                                              +unstable_entries: Iterable[ComputedEntry][source]
                                              -class InsertionVoltagePair(voltage: float, mAh: float, mass_charge: float, mass_discharge: float, vol_charge: float, vol_discharge: float, frac_charge: float, frac_discharge: float, working_ion_entry: pymatgen.entries.computed_entries.ComputedEntry, framework_formula: str, entry_charge: pymatgen.entries.computed_entries.ComputedEntry, entry_discharge: pymatgen.entries.computed_entries.ComputedEntry)[source]
                                              +class InsertionVoltagePair(voltage: float, mAh: float, mass_charge: float, mass_discharge: float, vol_charge: float, vol_discharge: float, frac_charge: float, frac_discharge: float, working_ion_entry: pymatgen.entries.computed_entries.ComputedEntry, framework_formula: str, entry_charge: pymatgen.entries.computed_entries.ComputedEntry, entry_discharge: pymatgen.entries.computed_entries.ComputedEntry)[source]

                                              Bases: pymatgen.apps.battery.battery_abc.AbstractVoltagePair

                                              Defines an Insertion Voltage Pair.

                                              -entry_charge: pymatgen.entries.computed_entries.ComputedEntry[source]
                                              +entry_charge: pymatgen.entries.computed_entries.ComputedEntry[source]
                                              -entry_discharge: pymatgen.entries.computed_entries.ComputedEntry[source]
                                              +entry_discharge: pymatgen.entries.computed_entries.ComputedEntry[source]
                                              -classmethod from_entries(entry1, entry2, working_ion_entry)[source]
                                              +classmethod from_entries(entry1, entry2, working_ion_entry)[source]
                                              Parameters
                                                diff --git a/docs/pymatgen.apps.battery.plotter.html b/docs/pymatgen.apps.battery.plotter.html index b1f55564e12..7de5a072528 100644 --- a/docs/pymatgen.apps.battery.plotter.html +++ b/docs/pymatgen.apps.battery.plotter.html @@ -4,7 +4,7 @@ - pymatgen.apps.battery.plotter module — pymatgen 2022.5.18 documentation + pymatgen.apps.battery.plotter module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                - 2022.5.18 + 2022.5.18.1
                                                @@ -119,7 +119,7 @@

                                                This module provides plotting capabilities for battery related applications.

                                                -class VoltageProfilePlotter(xaxis='capacity', hide_negative=False)[source]
                                                +class VoltageProfilePlotter(xaxis='capacity', hide_negative=False)[source]

                                                Bases: object

                                                A plotter to make voltage profile plots for batteries.

                                                @@ -136,7 +136,7 @@
                                                -add_electrode(electrode, label=None)[source]
                                                +add_electrode(electrode, label=None)[source]

                                                Add an electrode to the plot.

                                                Parameters
                                                @@ -152,7 +152,7 @@
                                                -get_plot(width=8, height=8, term_zero=True)[source]
                                                +get_plot(width=8, height=8, term_zero=True)[source]

                                                Returns a plot object.

                                                Parameters
                                                @@ -170,7 +170,7 @@
                                                -get_plot_data(electrode, term_zero=True)[source]
                                                +get_plot_data(electrode, term_zero=True)[source]
                                                Parameters
                                                  @@ -186,7 +186,7 @@
                                                  -get_plotly_figure(width=800, height=600, font_dict=None, term_zero=True, **kwargs)[source]
                                                  +get_plotly_figure(width=800, height=600, font_dict=None, term_zero=True, **kwargs)[source]

                                                  Return plotly Figure object :param width: Width of the plot. Defaults to 800 px. :param height: Height of the plot. Defaults to 600 px. @@ -198,7 +198,7 @@

                                                  -save(filename, image_format='eps', width=8, height=6)[source]
                                                  +save(filename, image_format='eps', width=8, height=6)[source]

                                                  Save the plot to an image file.

                                                  Parameters
                                                  @@ -212,7 +212,7 @@
                                                  -show(width=8, height=6)[source]
                                                  +show(width=8, height=6)[source]

                                                  Show the voltage profile plot.

                                                  Parameters
                                                  diff --git a/docs/pymatgen.apps.borg.hive.html b/docs/pymatgen.apps.borg.hive.html index aa9ca810434..5e72255aff7 100644 --- a/docs/pymatgen.apps.borg.hive.html +++ b/docs/pymatgen.apps.borg.hive.html @@ -4,7 +4,7 @@ - pymatgen.apps.borg.hive module — pymatgen 2022.5.18 documentation + pymatgen.apps.borg.hive module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                  - 2022.5.18 + 2022.5.18.1
                                                  @@ -119,7 +119,7 @@

                                                  This module define the various drones used to assimilate data.

                                                  -class AbstractDrone[source]
                                                  +class AbstractDrone[source]

                                                  Bases: monty.json.MSONable

                                                  Abstract drone class that defines the various methods that must be implemented by drones. Because of the quirky nature of Python”s @@ -129,7 +129,7 @@ from_dict API.

                                                  -abstract assimilate(path)[source]
                                                  +abstract assimilate(path)[source]

                                                  Assimilate data in a directory path into a pymatgen object. Because of the quirky nature of Python”s multiprocessing, the object must support pymatgen’s as_dict() for parallel processing.

                                                  @@ -145,7 +145,7 @@
                                                  -abstract get_valid_paths(path)[source]
                                                  +abstract get_valid_paths(path)[source]

                                                  Checks if path contains valid data for assimilation, and then returns the valid paths. The paths returned can be a list of directory or file paths, depending on what kind of data you are assimilating. For @@ -168,7 +168,7 @@

                                                  -class GaussianToComputedEntryDrone(inc_structure=False, parameters=None, data=None, file_extensions=('.log',))[source]
                                                  +class GaussianToComputedEntryDrone(inc_structure=False, parameters=None, data=None, file_extensions=('.log',))[source]

                                                  Bases: pymatgen.apps.borg.hive.AbstractDrone

                                                  GaussianToEntryDrone assimilates directories containing Gaussian output to ComputedEntry/ComputedStructureEntry objects. By default, it is assumed @@ -200,13 +200,13 @@

                                                  -as_dict()[source]
                                                  +as_dict()[source]

                                                  Returns: MSONable dict

                                                  -assimilate(path)[source]
                                                  +assimilate(path)[source]

                                                  Assimilate data in a directory path into a ComputedEntry object.

                                                  Parameters
                                                  @@ -220,7 +220,7 @@
                                                  -classmethod from_dict(d)[source]
                                                  +classmethod from_dict(d)[source]
                                                  Parameters

                                                  d (dict) – Dict Representation

                                                  @@ -233,7 +233,7 @@
                                                  -get_valid_paths(path)[source]
                                                  +get_valid_paths(path)[source]

                                                  Checks if path contains files with define extensions.

                                                  Parameters
                                                  @@ -250,7 +250,7 @@
                                                  -class SimpleVaspToComputedEntryDrone(inc_structure=False)[source]
                                                  +class SimpleVaspToComputedEntryDrone(inc_structure=False)[source]

                                                  Bases: pymatgen.apps.borg.hive.VaspToComputedEntryDrone

                                                  A simpler VaspToComputedEntryDrone. Instead of parsing vasprun.xml, it parses only the INCAR, POTCAR, OSZICAR and KPOINTS files, which are much @@ -265,13 +265,13 @@

                                                  -as_dict()[source]
                                                  +as_dict()[source]

                                                  Returns: MSONAble dict

                                                  -assimilate(path)[source]
                                                  +assimilate(path)[source]

                                                  Assimilate data in a directory path into a ComputedEntry object.

                                                  Parameters
                                                  @@ -285,7 +285,7 @@
                                                  -classmethod from_dict(d)[source]
                                                  +classmethod from_dict(d)[source]
                                                  Parameters

                                                  d (dict) – Dict Representation

                                                  @@ -300,7 +300,7 @@
                                                  -class VaspToComputedEntryDrone(inc_structure=False, parameters=None, data=None)[source]
                                                  +class VaspToComputedEntryDrone(inc_structure=False, parameters=None, data=None)[source]

                                                  Bases: pymatgen.apps.borg.hive.AbstractDrone

                                                  VaspToEntryDrone assimilates directories containing vasp output to ComputedEntry/ComputedStructureEntry objects. There are some restrictions @@ -329,13 +329,13 @@

                                                  -as_dict()[source]
                                                  +as_dict()[source]

                                                  Returns: MSONABle dict

                                                  -assimilate(path)[source]
                                                  +assimilate(path)[source]

                                                  Assimilate data in a directory path into a ComputedEntry object.

                                                  Parameters
                                                  @@ -349,7 +349,7 @@
                                                  -classmethod from_dict(d)[source]
                                                  +classmethod from_dict(d)[source]
                                                  Parameters

                                                  d (dict) – Dict Representation

                                                  @@ -362,7 +362,7 @@
                                                  -get_valid_paths(path)[source]
                                                  +get_valid_paths(path)[source]

                                                  Checks if paths contains vasprun.xml or (POSCAR+OSZICAR)

                                                  Parameters
                                                  diff --git a/docs/pymatgen.apps.borg.html b/docs/pymatgen.apps.borg.html index f9426c819b6..637a4a7f57c 100644 --- a/docs/pymatgen.apps.borg.html +++ b/docs/pymatgen.apps.borg.html @@ -4,7 +4,7 @@ - pymatgen.apps.borg package — pymatgen 2022.5.18 documentation + pymatgen.apps.borg package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                  - 2022.5.18 + 2022.5.18.1
                                                  diff --git a/docs/pymatgen.apps.borg.queen.html b/docs/pymatgen.apps.borg.queen.html index ed5821d2d20..0e1ff02682d 100644 --- a/docs/pymatgen.apps.borg.queen.html +++ b/docs/pymatgen.apps.borg.queen.html @@ -4,7 +4,7 @@ - pymatgen.apps.borg.queen module — pymatgen 2022.5.18 documentation + pymatgen.apps.borg.queen module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                  - 2022.5.18 + 2022.5.18.1
                                                  @@ -120,7 +120,7 @@ data using Python’s multiprocessing.

                                                  -class BorgQueen(drone, rootpath=None, number_of_drones=1)[source]
                                                  +class BorgQueen(drone, rootpath=None, number_of_drones=1)[source]

                                                  Bases: object

                                                  The Borg Queen controls the drones to assimilate data in an entire directory tree. Uses multiprocessing to speed up things considerably. It @@ -145,25 +145,25 @@

                                                  -get_data()[source]
                                                  +get_data()[source]

                                                  Returns an list of assimilated objects

                                                  -load_data(filename)[source]
                                                  +load_data(filename)[source]

                                                  Load assimilated data from a file

                                                  -parallel_assimilate(rootpath)[source]
                                                  +parallel_assimilate(rootpath)[source]

                                                  Assimilate the entire subdirectory structure in rootpath.

                                                  -save_data(filename)[source]
                                                  +save_data(filename)[source]

                                                  Save the assimilated data to a file.

                                                  Parameters
                                                  @@ -176,7 +176,7 @@
                                                  -serial_assimilate(rootpath)[source]
                                                  +serial_assimilate(rootpath)[source]

                                                  Assimilate the entire subdirectory structure in rootpath serially.

                                                  @@ -184,7 +184,7 @@
                                                  -order_assimilation(args)[source]
                                                  +order_assimilation(args)[source]

                                                  Internal helper method for BorgQueen to process assimilation

                                                  diff --git a/docs/pymatgen.apps.html b/docs/pymatgen.apps.html index c41a52995e0..a11b7ba05a2 100644 --- a/docs/pymatgen.apps.html +++ b/docs/pymatgen.apps.html @@ -4,7 +4,7 @@ - pymatgen.apps package — pymatgen 2022.5.18 documentation + pymatgen.apps package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                  - 2022.5.18 + 2022.5.18.1
                                                  diff --git a/docs/pymatgen.cli.feff_plot_cross_section.html b/docs/pymatgen.cli.feff_plot_cross_section.html index c18231a69cb..cdb56052a47 100644 --- a/docs/pymatgen.cli.feff_plot_cross_section.html +++ b/docs/pymatgen.cli.feff_plot_cross_section.html @@ -4,7 +4,7 @@ - pymatgen.cli.feff_plot_cross_section module — pymatgen 2022.5.18 documentation + pymatgen.cli.feff_plot_cross_section module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                  - 2022.5.18 + 2022.5.18.1
                                                  @@ -118,7 +118,7 @@

                                                  Script for plotting cross sections generated by FEFF found in xmu.dat files.

                                                  -main()[source]
                                                  +main()[source]

                                                  Main function.

                                                  diff --git a/docs/pymatgen.cli.feff_plot_dos.html b/docs/pymatgen.cli.feff_plot_dos.html index 25fa265adf8..b69f4c4cec4 100644 --- a/docs/pymatgen.cli.feff_plot_dos.html +++ b/docs/pymatgen.cli.feff_plot_dos.html @@ -4,7 +4,7 @@ - pymatgen.cli.feff_plot_dos module — pymatgen 2022.5.18 documentation + pymatgen.cli.feff_plot_dos module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                  - 2022.5.18 + 2022.5.18.1
                                                  @@ -119,7 +119,7 @@ either by site, element, or orbital

                                                  -main()[source]
                                                  +main()[source]

                                                  Main function.

                                                  diff --git a/docs/pymatgen.cli.gaussian_analyzer.html b/docs/pymatgen.cli.gaussian_analyzer.html index d0f162dd3c2..397bb7bb19d 100644 --- a/docs/pymatgen.cli.gaussian_analyzer.html +++ b/docs/pymatgen.cli.gaussian_analyzer.html @@ -4,7 +4,7 @@ - pymatgen.cli.gaussian_analyzer module — pymatgen 2022.5.18 documentation + pymatgen.cli.gaussian_analyzer module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                  - 2022.5.18 + 2022.5.18.1
                                                  @@ -118,7 +118,7 @@

                                                  A convenience script engine to read Gaussian output in a directory tree.

                                                  -get_energies(rootdir, reanalyze, verbose)[source]
                                                  +get_energies(rootdir, reanalyze, verbose)[source]
                                                  Parameters
                                                    @@ -135,7 +135,7 @@
                                                    -main()[source]
                                                    +main()[source]

                                                    Main function

                                                    diff --git a/docs/pymatgen.cli.get_environment.html b/docs/pymatgen.cli.get_environment.html index ba243a104a1..f5612da209a 100644 --- a/docs/pymatgen.cli.get_environment.html +++ b/docs/pymatgen.cli.get_environment.html @@ -4,7 +4,7 @@ - pymatgen.cli.get_environment module — pymatgen 2022.5.18 documentation + pymatgen.cli.get_environment module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                    - 2022.5.18 + 2022.5.18.1
                                                    @@ -118,7 +118,7 @@

                                                    Implementation for get_environment CLI.

                                                    -main()[source]
                                                    +main()[source]

                                                    Main function.

                                                    diff --git a/docs/pymatgen.cli.html b/docs/pymatgen.cli.html index 2e93dc52356..6deb329096d 100644 --- a/docs/pymatgen.cli.html +++ b/docs/pymatgen.cli.html @@ -4,7 +4,7 @@ - pymatgen.cli package — pymatgen 2022.5.18 documentation + pymatgen.cli package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                    - 2022.5.18 + 2022.5.18.1
                                                    diff --git a/docs/pymatgen.cli.pmg.html b/docs/pymatgen.cli.pmg.html index b9dc6d54d1a..a641fdafa70 100644 --- a/docs/pymatgen.cli.pmg.html +++ b/docs/pymatgen.cli.pmg.html @@ -4,7 +4,7 @@ - pymatgen.cli.pmg module — pymatgen 2022.5.18 documentation + pymatgen.cli.pmg module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                    - 2022.5.18 + 2022.5.18.1
                                                    @@ -118,7 +118,7 @@

                                                    A master convenience script with many tools for vasp and structure analysis.

                                                    -diff_incar(args)[source]
                                                    +diff_incar(args)[source]

                                                    Handle diff commands.

                                                    Parameters
                                                    @@ -129,13 +129,13 @@
                                                    -main()[source]
                                                    +main()[source]

                                                    Handle main.

                                                    -parse_view(args)[source]
                                                    +parse_view(args)[source]

                                                    Handle view commands.

                                                    Parameters
                                                    diff --git a/docs/pymatgen.cli.pmg_analyze.html b/docs/pymatgen.cli.pmg_analyze.html index 10c6a95500b..da71da5b175 100644 --- a/docs/pymatgen.cli.pmg_analyze.html +++ b/docs/pymatgen.cli.pmg_analyze.html @@ -4,7 +4,7 @@ - pymatgen.cli.pmg_analyze module — pymatgen 2022.5.18 documentation + pymatgen.cli.pmg_analyze module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                    - 2022.5.18 + 2022.5.18.1
                                                    @@ -118,7 +118,7 @@

                                                    Implementation for pmg analyze CLI.

                                                    -analyze(args)[source]
                                                    +analyze(args)[source]

                                                    Master function controlling which analysis to call.

                                                    Parameters
                                                    @@ -129,7 +129,7 @@
                                                    -get_energies(rootdir, reanalyze, verbose, quick, sort, fmt)[source]
                                                    +get_energies(rootdir, reanalyze, verbose, quick, sort, fmt)[source]

                                                    Get energies of all vaspruns in directory (nested). :param rootdir: Root directory. :type rootdir: str @@ -153,7 +153,7 @@

                                                    -get_magnetizations(mydir, ion_list)[source]
                                                    +get_magnetizations(mydir, ion_list)[source]

                                                    Get magnetization info from OUTCARs.

                                                    Parameters
                                                    diff --git a/docs/pymatgen.cli.pmg_config.html b/docs/pymatgen.cli.pmg_config.html index eff9d504726..ae063edefcc 100644 --- a/docs/pymatgen.cli.pmg_config.html +++ b/docs/pymatgen.cli.pmg_config.html @@ -4,7 +4,7 @@ - pymatgen.cli.pmg_config module — pymatgen 2022.5.18 documentation + pymatgen.cli.pmg_config module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                    - 2022.5.18 + 2022.5.18.1
                                                    @@ -118,13 +118,13 @@

                                                    Implementation for pmg config CLI.

                                                    -add_config_var(tokens: list[str], backup_suffix: str) → None[source]
                                                    +add_config_var(tokens: list[str], backup_suffix: str) → None[source]

                                                    Add/update keys in .pmgrc.yaml config file.

                                                    -build_bader(fortran_command='gfortran')[source]
                                                    +build_bader(fortran_command='gfortran')[source]

                                                    Build bader package.

                                                    Parameters
                                                    @@ -135,7 +135,7 @@
                                                    -build_enum(fortran_command: str = 'gfortran') → bool[source]
                                                    +build_enum(fortran_command: str = 'gfortran') → bool[source]

                                                    Build enum.

                                                    Parameters
                                                    @@ -146,19 +146,19 @@
                                                    -configure_pmg(args: argparse.Namespace)[source]
                                                    +configure_pmg(args: argparse.Namespace)[source]

                                                    Handle configure command.

                                                    -install_software(install: Literal['enumlib', 'bader'])[source]
                                                    +install_software(install: Literal['enumlib', 'bader'])[source]

                                                    Install all optional external software.

                                                    -setup_potcars(potcar_dirs: list[str])[source]
                                                    +setup_potcars(potcar_dirs: list[str])[source]

                                                    Setup POTCAR directories.

                                                    diff --git a/docs/pymatgen.cli.pmg_plot.html b/docs/pymatgen.cli.pmg_plot.html index 1730de8389f..323c5b79a00 100644 --- a/docs/pymatgen.cli.pmg_plot.html +++ b/docs/pymatgen.cli.pmg_plot.html @@ -4,7 +4,7 @@ - pymatgen.cli.pmg_plot module — pymatgen 2022.5.18 documentation + pymatgen.cli.pmg_plot module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                    - 2022.5.18 + 2022.5.18.1
                                                    @@ -118,7 +118,7 @@

                                                    Implementation for pmg plot CLI.

                                                    -get_chgint_plot(args)[source]
                                                    +get_chgint_plot(args)[source]

                                                    Plot integrated charge.

                                                    Parameters
                                                    @@ -129,7 +129,7 @@
                                                    -get_dos_plot(args)[source]
                                                    +get_dos_plot(args)[source]

                                                    Plot DOS.

                                                    Parameters
                                                    @@ -140,7 +140,7 @@
                                                    -get_xrd_plot(args)[source]
                                                    +get_xrd_plot(args)[source]

                                                    Plot XRD

                                                    Parameters
                                                    @@ -151,7 +151,7 @@
                                                    -plot(args)[source]
                                                    +plot(args)[source]

                                                    Master control method calling other plot methods based on args.

                                                    Parameters
                                                    diff --git a/docs/pymatgen.cli.pmg_potcar.html b/docs/pymatgen.cli.pmg_potcar.html index 559de7ed5e9..117f33cd95b 100644 --- a/docs/pymatgen.cli.pmg_potcar.html +++ b/docs/pymatgen.cli.pmg_potcar.html @@ -4,7 +4,7 @@ - pymatgen.cli.pmg_potcar module — pymatgen 2022.5.18 documentation + pymatgen.cli.pmg_potcar module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                    - 2022.5.18 + 2022.5.18.1
                                                    @@ -118,7 +118,7 @@

                                                    Implementation for pmg potcar CLI.

                                                    -gen_potcar(dirname, filename)[source]
                                                    +gen_potcar(dirname, filename)[source]

                                                    Generate POTCAR from POTCAR.spec in directories.

                                                    Parameters
                                                    @@ -132,7 +132,7 @@
                                                    -generate_potcar(args)[source]
                                                    +generate_potcar(args)[source]

                                                    Generate POTCAR.

                                                    Parameters
                                                    @@ -143,7 +143,7 @@
                                                    -proc_dir(dirname, procfilefunction)[source]
                                                    +proc_dir(dirname, procfilefunction)[source]

                                                    Process a directory.

                                                    Parameters
                                                    diff --git a/docs/pymatgen.cli.pmg_query.html b/docs/pymatgen.cli.pmg_query.html index 238ecaec089..1357198195e 100644 --- a/docs/pymatgen.cli.pmg_query.html +++ b/docs/pymatgen.cli.pmg_query.html @@ -4,7 +4,7 @@ - pymatgen.cli.pmg_query module — pymatgen 2022.5.18 documentation + pymatgen.cli.pmg_query module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                    - 2022.5.18 + 2022.5.18.1
                                                    @@ -118,7 +118,7 @@

                                                    Implementation for pmg query CLI.

                                                    -do_query(args)[source]
                                                    +do_query(args)[source]

                                                    Perform query to the Materials Project

                                                    Parameters
                                                    diff --git a/docs/pymatgen.cli.pmg_structure.html b/docs/pymatgen.cli.pmg_structure.html index ae1b4aefcb8..1b9e00f5977 100644 --- a/docs/pymatgen.cli.pmg_structure.html +++ b/docs/pymatgen.cli.pmg_structure.html @@ -4,7 +4,7 @@ - pymatgen.cli.pmg_structure module — pymatgen 2022.5.18 documentation + pymatgen.cli.pmg_structure module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                    - 2022.5.18 + 2022.5.18.1
                                                    @@ -118,7 +118,7 @@

                                                    Implementation for pmg structure CLI.

                                                    -analyze_localenv(args)[source]
                                                    +analyze_localenv(args)[source]

                                                    Analyze local env of structures in files.

                                                    Parameters
                                                    @@ -129,7 +129,7 @@
                                                    -analyze_structures(args)[source]
                                                    +analyze_structures(args)[source]

                                                    Master function to handle which operation to perform.

                                                    Parameters
                                                    @@ -140,7 +140,7 @@
                                                    -analyze_symmetry(args)[source]
                                                    +analyze_symmetry(args)[source]

                                                    Analyze symmetry of structures in files.

                                                    Parameters
                                                    @@ -151,7 +151,7 @@
                                                    -compare_structures(args)[source]
                                                    +compare_structures(args)[source]

                                                    Compare structures in files for similarity using structure matcher.

                                                    Parameters
                                                    @@ -162,7 +162,7 @@
                                                    -convert_fmt(args)[source]
                                                    +convert_fmt(args)[source]

                                                    Convert files from one format to another

                                                    Parameters
                                                    diff --git a/docs/pymatgen.command_line.bader_caller.html b/docs/pymatgen.command_line.bader_caller.html index 8e90a1729c1..083351bb502 100644 --- a/docs/pymatgen.command_line.bader_caller.html +++ b/docs/pymatgen.command_line.bader_caller.html @@ -4,7 +4,7 @@ - pymatgen.command_line.bader_caller module — pymatgen 2022.5.18 documentation + pymatgen.command_line.bader_caller module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                    - 2022.5.18 + 2022.5.18.1
                                                    @@ -125,7 +125,7 @@ Bader decomposition of charge density”, Comput. Mater. Sci. 36, 254-360 (2006).

                                                    -class BaderAnalysis(chgcar_filename=None, potcar_filename=None, chgref_filename=None, parse_atomic_densities=False, cube_filename=None)[source]
                                                    +class BaderAnalysis(chgcar_filename=None, potcar_filename=None, chgref_filename=None, parse_atomic_densities=False, cube_filename=None)[source]

                                                    Bases: object

                                                    Bader analysis for Cube files and VASP outputs.

                                                    Initializes the Bader caller.

                                                    @@ -143,7 +143,7 @@
                                                    -classmethod from_path(path, suffix='')[source]
                                                    +classmethod from_path(path, suffix='')[source]

                                                    Convenient constructor that takes in the path name of VASP run to perform Bader analysis.

                                                    @@ -160,7 +160,7 @@
                                                    -get_charge(atom_index)[source]
                                                    +get_charge(atom_index)[source]

                                                    Convenience method to get the charge on a particular atom. This is the “raw” charge generated by the Bader program, not a partial atomic charge. If the cube file is a spin-density file, then this will return the spin density per atom with @@ -177,7 +177,7 @@

                                                    -get_charge_decorated_structure()[source]
                                                    +get_charge_decorated_structure()[source]

                                                    Returns a charge decorated structure

                                                    Note, this assumes that the Bader analysis was correctly performed on a file with electron densities

                                                    @@ -185,7 +185,7 @@
                                                    -get_charge_transfer(atom_index, nelect=None)[source]
                                                    +get_charge_transfer(atom_index, nelect=None)[source]

                                                    Returns the charge transferred for a particular atom. A positive value means that the site has gained electron density (i.e. exhibits anionic character) whereas a negative value means the site has lost electron density (i.e. exhibits @@ -209,7 +209,7 @@

                                                    -get_decorated_structure(property_name, average=False)[source]
                                                    +get_decorated_structure(property_name, average=False)[source]

                                                    Get a property-decorated structure from the Bader analysis.

                                                    This is distinct from getting charge decorated structure, which assumes the “standard” Bader analysis of electron densities followed by converting @@ -240,7 +240,7 @@

                                                    -get_oxidation_state_decorated_structure(nelects=None)[source]
                                                    +get_oxidation_state_decorated_structure(nelects=None)[source]

                                                    Returns an oxidation state decorated structure based on bader analysis results. Each site is assigned a charge based on the computed partial atomic charge from bader.

                                                    Note, this assumes that the Bader analysis was correctly performed on a file @@ -249,7 +249,7 @@

                                                    -get_partial_charge(atom_index, nelect=None)[source]
                                                    +get_partial_charge(atom_index, nelect=None)[source]

                                                    Convenience method to get the partial charge on a particular atom. This is simply the negative value of the charge transferred. A positive value indicates that the atom has cationic character, whereas a negative value indicates the @@ -271,7 +271,7 @@

                                                    -property summary[source]
                                                    +property summary[source]

                                                    Dict summary of key analysis, e.g., atomic volume, charge, etc.

                                                    Type
                                                    @@ -284,7 +284,7 @@
                                                    -bader_analysis_from_objects(chgcar, potcar=None, aeccar0=None, aeccar2=None)[source]
                                                    +bader_analysis_from_objects(chgcar, potcar=None, aeccar0=None, aeccar2=None)[source]

                                                    Convenience method to run Bader analysis from a set of pymatgen Chgcar and Potcar objects.

                                                    This method will:

                                                    @@ -309,7 +309,7 @@
                                                    -bader_analysis_from_path(path, suffix='')[source]
                                                    +bader_analysis_from_path(path, suffix='')[source]

                                                    Convenience method to run Bader analysis on a folder containing typical VASP output files.

                                                    This method will:

                                                    diff --git a/docs/pymatgen.command_line.chargemol_caller.html b/docs/pymatgen.command_line.chargemol_caller.html index 7c48f601abd..6ea8a61985b 100644 --- a/docs/pymatgen.command_line.chargemol_caller.html +++ b/docs/pymatgen.command_line.chargemol_caller.html @@ -4,7 +4,7 @@ - pymatgen.command_line.chargemol_caller module — pymatgen 2022.5.18 documentation + pymatgen.command_line.chargemol_caller module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                    - 2022.5.18 + 2022.5.18.1
                                                    @@ -151,7 +151,7 @@ (2010) 2455-2468.

                                                    -class ChargemolAnalysis(path=None, atomic_densities_path=None, run_chargemol=True)[source]
                                                    +class ChargemolAnalysis(path=None, atomic_densities_path=None, run_chargemol=True)[source]

                                                    Bases: object

                                                    Chargemol analysis for DDEC3, DDEC6, and/or CM5 population analyses, including the calculation of partial atomic charges, atomic spin moments, @@ -174,7 +174,7 @@

                                                    -get_bond_order(index_from, index_to)[source]
                                                    +get_bond_order(index_from, index_to)[source]

                                                    Convenience method to get the bond order between two atoms.

                                                    Parameters
                                                    @@ -194,7 +194,7 @@
                                                    -get_charge(atom_index, nelect=None, charge_type='ddec')[source]
                                                    +get_charge(atom_index, nelect=None, charge_type='ddec')[source]

                                                    Convenience method to get the charge on a particular atom using the same sign convention as the BaderAnalysis. Note that this is not the partial atomic charge. This value is nelect (e.g. ZVAL from the POTCAR) + the @@ -223,7 +223,7 @@

                                                    -get_charge_transfer(atom_index, charge_type='ddec')[source]
                                                    +get_charge_transfer(atom_index, charge_type='ddec')[source]

                                                    Returns the charge transferred for a particular atom. A positive value means that the site has gained electron density (i.e. exhibits anionic character) whereas a negative value means the site has lost electron density (i.e. exhibits @@ -247,7 +247,7 @@

                                                    -get_partial_charge(atom_index, charge_type='ddec')[source]
                                                    +get_partial_charge(atom_index, charge_type='ddec')[source]

                                                    Convenience method to get the partial atomic charge on a particular atom. This is the value printed in the Chargemol analysis.

                                                    @@ -262,7 +262,7 @@
                                                    -get_property_decorated_structure()[source]
                                                    +get_property_decorated_structure()[source]

                                                    Takes CHGCAR’s structure object and updates it with properties from the Chargemol analysis.

                                                    @@ -273,7 +273,7 @@
                                                    -property summary[source]
                                                    +property summary[source]

                                                    Returns a dictionary summary of the Chargemol analysis {

                                                    diff --git a/docs/pymatgen.command_line.critic2_caller.html b/docs/pymatgen.command_line.critic2_caller.html index 971561c1e27..feaeffeac71 100644 --- a/docs/pymatgen.command_line.critic2_caller.html +++ b/docs/pymatgen.command_line.critic2_caller.html @@ -4,7 +4,7 @@ - pymatgen.command_line.critic2_caller module — pymatgen 2022.5.18 documentation + pymatgen.command_line.critic2_caller module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                    - 2022.5.18 + 2022.5.18.1
                                                    @@ -150,7 +150,7 @@ (https://doi.org/10.1016/j.cpc.2008.07.018)

                                                    -class Critic2Analysis(structure, stdout=None, stderr=None, cpreport=None, yt=None, zpsp=None)[source]
                                                    +class Critic2Analysis(structure, stdout=None, stderr=None, cpreport=None, yt=None, zpsp=None)[source]

                                                    Bases: monty.json.MSONable

                                                    Class to process the standard output from critic2 into pymatgen-compatible objects.

                                                    This class is used to store results from the Critic2Caller.

                                                    @@ -190,7 +190,7 @@ Optional.

                                                    -get_critical_point_for_site(n)[source]
                                                    +get_critical_point_for_site(n)[source]
                                                    Parameters

                                                    n – Site index n

                                                    @@ -201,7 +201,7 @@
                                                    -get_volume_and_charge_for_site(n)[source]
                                                    +get_volume_and_charge_for_site(n)[source]
                                                    Parameters

                                                    n – Site index n

                                                    @@ -213,7 +213,7 @@
                                                    -structure_graph(include_critical_points=('bond', 'ring', 'cage'))[source]
                                                    +structure_graph(include_critical_points=('bond', 'ring', 'cage'))[source]

                                                    A StructureGraph object describing bonding information in the crystal. :param include_critical_points: add DummySpecies for @@ -232,7 +232,7 @@

                                                    -class Critic2Caller(input_script)[source]
                                                    +class Critic2Caller(input_script)[source]

                                                    Bases: object

                                                    Class to call critic2 and store standard output for further processing.

                                                    Run Critic2 on a given input script

                                                    @@ -243,7 +243,7 @@
                                                    -classmethod from_chgcar(structure, chgcar=None, chgcar_ref=None, user_input_settings=None, write_cml=False, write_json=True, zpsp=None)[source]
                                                    +classmethod from_chgcar(structure, chgcar=None, chgcar_ref=None, user_input_settings=None, write_cml=False, write_json=True, zpsp=None)[source]

                                                    Run Critic2 in automatic mode on a supplied structure, charge density (chgcar) and reference charge density (chgcar_ref).

                                                    The reason for a separate reference field is that in @@ -305,7 +305,7 @@

                                                    -classmethod from_path(path, suffix='', zpsp=None)[source]
                                                    +classmethod from_path(path, suffix='', zpsp=None)[source]

                                                    Convenience method to run critic2 analysis on a folder containing typical VASP output files. This method will:

                                                    @@ -334,7 +334,7 @@
                                                    -class CriticalPoint(index, type, frac_coords, point_group, multiplicity, field, field_gradient, coords=None, field_hessian=None)[source]
                                                    +class CriticalPoint(index, type, frac_coords, point_group, multiplicity, field, field_gradient, coords=None, field_hessian=None)[source]

                                                    Bases: monty.json.MSONable

                                                    Access information about a critical point and the field values at that point.

                                                    Class to characterise a critical point from a topological @@ -358,7 +358,7 @@

                                                    -property ellipticity[source]
                                                    +property ellipticity[source]

                                                    Most meaningful for bond critical points, can be physically interpreted as e.g. degree of pi-bonding in organic molecules. Consult @@ -368,7 +368,7 @@

                                                    -property laplacian[source]
                                                    +property laplacian[source]

                                                    The Laplacian of the field at the critical point

                                                    Type
                                                    @@ -379,7 +379,7 @@
                                                    -property type[source]
                                                    +property type[source]

                                                    Instance of CriticalPointType

                                                    Type
                                                    @@ -392,39 +392,39 @@
                                                    -class CriticalPointType(value)[source]
                                                    +class CriticalPointType(value)[source]

                                                    Bases: enum.Enum

                                                    Enum type for the different varieties of critical point.

                                                    -bond = 'bond'[source]
                                                    +bond = 'bond'[source]
                                                    -cage = 'cage'[source]
                                                    +cage = 'cage'[source]
                                                    -nnattr = 'nnattr'[source]
                                                    +nnattr = 'nnattr'[source]
                                                    -nucleus = 'nucleus'[source]
                                                    +nucleus = 'nucleus'[source]
                                                    -ring = 'ring'[source]
                                                    +ring = 'ring'[source]
                                                    -get_filepath(filename, warning, path, suffix)[source]
                                                    +get_filepath(filename, warning, path, suffix)[source]
                                                    Parameters
                                                      diff --git a/docs/pymatgen.command_line.enumlib_caller.html b/docs/pymatgen.command_line.enumlib_caller.html index a98f30a9f1b..f458c130958 100644 --- a/docs/pymatgen.command_line.enumlib_caller.html +++ b/docs/pymatgen.command_line.enumlib_caller.html @@ -4,7 +4,7 @@ - pymatgen.command_line.enumlib_caller module — pymatgen 2022.5.18 documentation + pymatgen.command_line.enumlib_caller module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                      - 2022.5.18 + 2022.5.18.1
                                                      @@ -134,7 +134,7 @@ Sci. 136 144-149 (May 2017)

                                                      -exception EnumError[source]
                                                      +exception EnumError[source]

                                                      Bases: BaseException

                                                      Error subclass for enumeration errors.

                                                      diff --git a/docs/pymatgen.command_line.gulp_caller.html b/docs/pymatgen.command_line.gulp_caller.html index e2d49b526b8..814fedee44c 100644 --- a/docs/pymatgen.command_line.gulp_caller.html +++ b/docs/pymatgen.command_line.gulp_caller.html @@ -4,7 +4,7 @@ - pymatgen.command_line.gulp_caller module — pymatgen 2022.5.18 documentation + pymatgen.command_line.gulp_caller module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                      - 2022.5.18 + 2022.5.18.1
                                                      @@ -120,7 +120,7 @@ WARNING: you need to have GULP installed on your system.

                                                      -class BuckinghamPotential(bush_lewis_flag)[source]
                                                      +class BuckinghamPotential(bush_lewis_flag)[source]

                                                      Bases: object

                                                      Generate the Buckingham Potential Table from the bush.lib and lewis.lib.

                                                      Ref: @@ -137,7 +137,7 @@

                                                      -class GulpCaller(cmd='gulp')[source]
                                                      +class GulpCaller(cmd='gulp')[source]

                                                      Bases: object

                                                      Class to run gulp from commandline

                                                      Initialize with the executable if not in the standard path

                                                      @@ -148,7 +148,7 @@
                                                      -run(gin)[source]
                                                      +run(gin)[source]

                                                      Run GULP using the gin as input

                                                      Parameters
                                                      @@ -167,7 +167,7 @@
                                                      -exception GulpConvergenceError(msg='')[source]
                                                      +exception GulpConvergenceError(msg='')[source]

                                                      Bases: Exception

                                                      Exception class for GULP. Raised when proper convergence is not reached in Mott-Littleton @@ -181,7 +181,7 @@

                                                      -exception GulpError(msg)[source]
                                                      +exception GulpError(msg)[source]

                                                      Bases: Exception

                                                      Exception class for GULP. Raised when the GULP gives an error

                                                      @@ -194,12 +194,12 @@
                                                      -class GulpIO[source]
                                                      +class GulpIO[source]

                                                      Bases: object

                                                      To generate GULP input and process output

                                                      -buckingham_input(structure, keywords, library=None, uc=True, valence_dict=None)[source]
                                                      +buckingham_input(structure, keywords, library=None, uc=True, valence_dict=None)[source]

                                                      Gets a GULP input for an oxide structure and buckingham potential from library.

                                                      @@ -217,7 +217,7 @@
                                                      -static buckingham_potential(structure, val_dict=None)[source]
                                                      +static buckingham_potential(structure, val_dict=None)[source]

                                                      Generate species, buckingham, and spring options for an oxide structure using the parameters in default libraries.

                                                      @@ -242,7 +242,7 @@
                                                      -static get_energy(gout)[source]
                                                      +static get_energy(gout)[source]
                                                      Parameters

                                                      () (gout) –

                                                      @@ -255,7 +255,7 @@
                                                      -static get_relaxed_structure(gout)[source]
                                                      +static get_relaxed_structure(gout)[source]
                                                      Parameters

                                                      () (gout) –

                                                      @@ -268,7 +268,7 @@
                                                      -static keyword_line(*args)[source]
                                                      +static keyword_line(*args)[source]

                                                      Checks if the input args are proper gulp keywords and generates the 1st line of gulp input. Full keywords are expected.

                                                      @@ -280,7 +280,7 @@
                                                      -static library_line(file_name)[source]
                                                      +static library_line(file_name)[source]

                                                      Specifies GULP library file to read species and potential parameters. If using library don’t specify species and potential in the input file and vice versa. Make sure the elements of @@ -297,7 +297,7 @@

                                                      -static specie_potential_lines(structure, potential, **kwargs)[source]
                                                      +static specie_potential_lines(structure, potential, **kwargs)[source]

                                                      Generates GULP input specie and potential string for pymatgen structure.

                                                      @@ -326,7 +326,7 @@
                                                      -static structure_lines(structure, cell_flg=True, frac_flg=True, anion_shell_flg=True, cation_shell_flg=False, symm_flg=True)[source]
                                                      +static structure_lines(structure, cell_flg=True, frac_flg=True, anion_shell_flg=True, cation_shell_flg=False, symm_flg=True)[source]

                                                      Generates GULP input string corresponding to pymatgen structure.

                                                      Parameters
                                                      @@ -356,7 +356,7 @@
                                                      -tersoff_input(structure, periodic=False, uc=True, *keywords)[source]
                                                      +tersoff_input(structure, periodic=False, uc=True, *keywords)[source]

                                                      Gets a GULP input with Tersoff potential for an oxide structure

                                                      Parameters
                                                      @@ -374,7 +374,7 @@
                                                      -static tersoff_potential(structure)[source]
                                                      +static tersoff_potential(structure)[source]

                                                      Generate the species, tersoff potential lines for an oxide structure

                                                      Parameters
                                                      @@ -387,7 +387,7 @@
                                                      -class TersoffPotential[source]
                                                      +class TersoffPotential[source]

                                                      Bases: object

                                                      Generate Tersoff Potential Table from “OxideTersoffPotentialentials” file

                                                      Init TersoffPotential

                                                      @@ -395,7 +395,7 @@
                                                      -get_energy_buckingham(structure, gulp_cmd='gulp', keywords=('optimise', 'conp', 'qok'), valence_dict=None)[source]
                                                      +get_energy_buckingham(structure, gulp_cmd='gulp', keywords=('optimise', 'conp', 'qok'), valence_dict=None)[source]

                                                      Compute the energy of a structure using Buckingham potential.

                                                      Parameters
                                                      @@ -412,7 +412,7 @@
                                                      -get_energy_relax_structure_buckingham(structure, gulp_cmd='gulp', keywords=('optimise', 'conp'), valence_dict=None)[source]
                                                      +get_energy_relax_structure_buckingham(structure, gulp_cmd='gulp', keywords=('optimise', 'conp'), valence_dict=None)[source]

                                                      Relax a structure and compute the energy using Buckingham potential.

                                                      Parameters
                                                      @@ -429,7 +429,7 @@
                                                      -get_energy_tersoff(structure, gulp_cmd='gulp')[source]
                                                      +get_energy_tersoff(structure, gulp_cmd='gulp')[source]

                                                      Compute the energy of a structure using Tersoff potential.

                                                      Parameters
                                                      diff --git a/docs/pymatgen.command_line.html b/docs/pymatgen.command_line.html index 9718d8723ff..3215b97e54b 100644 --- a/docs/pymatgen.command_line.html +++ b/docs/pymatgen.command_line.html @@ -4,7 +4,7 @@ - pymatgen.command_line package — pymatgen 2022.5.18 documentation + pymatgen.command_line package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                      - 2022.5.18 + 2022.5.18.1
                                                      diff --git a/docs/pymatgen.command_line.mcsqs_caller.html b/docs/pymatgen.command_line.mcsqs_caller.html index 06056039314..80425400ff1 100644 --- a/docs/pymatgen.command_line.mcsqs_caller.html +++ b/docs/pymatgen.command_line.mcsqs_caller.html @@ -4,7 +4,7 @@ - pymatgen.command_line.mcsqs_caller module — pymatgen 2022.5.18 documentation + pymatgen.command_line.mcsqs_caller module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                      - 2022.5.18 + 2022.5.18.1
                                                      @@ -119,7 +119,7 @@ https://www.brown.edu/Departments/Engineering/Labs/avdw/atat/

                                                      -class Sqs(bestsqs, objective_function, allsqs, clusters, directory)[source]
                                                      +class Sqs(bestsqs, objective_function, allsqs, clusters, directory)[source]

                                                      Bases: tuple

                                                      Return type for run_mcsqs. bestsqs: Structure @@ -129,31 +129,31 @@ directory: str

                                                      -allsqs[source]
                                                      +allsqs[source]

                                                      Alias for field number 2

                                                      -bestsqs[source]
                                                      +bestsqs[source]

                                                      Alias for field number 0

                                                      -clusters[source]
                                                      +clusters[source]

                                                      Alias for field number 3

                                                      -directory[source]
                                                      +directory[source]

                                                      Alias for field number 4

                                                      -objective_function[source]
                                                      +objective_function[source]

                                                      Alias for field number 1

                                                      @@ -161,7 +161,7 @@
                                                      -run_mcsqs(structure: Structure, clusters: dict[int, float], scaling: int | list[int] = 1, search_time: float = 60, directory: str | None = None, instances: int | None = None, temperature: int | float = 1, wr: float = 1, wn: float = 1, wd: float = 0.5, tol: float = 0.001) → Sqs[source]
                                                      +run_mcsqs(structure: Structure, clusters: dict[int, float], scaling: int | list[int] = 1, search_time: float = 60, directory: str | None = None, instances: int | None = None, temperature: int | float = 1, wr: float = 1, wn: float = 1, wd: float = 0.5, tol: float = 0.001) → Sqs[source]

                                                      Helper function for calling mcsqs with different arguments :param structure: Disordered pymatgen Structure object :type structure: Structure diff --git a/docs/pymatgen.command_line.vampire_caller.html b/docs/pymatgen.command_line.vampire_caller.html index 1103bb4b2f0..57b0005b96a 100644 --- a/docs/pymatgen.command_line.vampire_caller.html +++ b/docs/pymatgen.command_line.vampire_caller.html @@ -4,7 +4,7 @@ - pymatgen.command_line.vampire_caller module — pymatgen 2022.5.18 documentation + pymatgen.command_line.vampire_caller module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                                      - 2022.5.18 + 2022.5.18.1
                                                      @@ -126,7 +126,7 @@ and R. W. Chantrell. J. Phys.: Condens. Matter 26, 103202 (2014)

                                                      -class VampireCaller(ordered_structures=None, energies=None, mc_box_size=4.0, equil_timesteps=2000, mc_timesteps=4000, save_inputs=False, hm=None, avg=True, user_input_settings=None)[source]
                                                      +class VampireCaller(ordered_structures=None, energies=None, mc_box_size=4.0, equil_timesteps=2000, mc_timesteps=4000, save_inputs=False, hm=None, avg=True, user_input_settings=None)[source]

                                                      Bases: object

                                                      Run Vampire on a material with magnetic ordering and exchange parameter information to compute the critical temperature with classical Monte Carlo.

                                                      @@ -162,7 +162,7 @@
                                                      -static parse_stdout(vamp_stdout, nmats)[source]
                                                      +static parse_stdout(vamp_stdout, nmats)[source]

                                                      Parse stdout from Vampire.

                                                      Parameters
                                                      @@ -185,7 +185,7 @@
                                                      -class VampireOutput(parsed_out=None, nmats=None, critical_temp=None)[source]
                                                      +class VampireOutput(parsed_out=None, nmats=None, critical_temp=None)[source]

                                                      Bases: monty.json.MSONable

                                                      This class processes results from a Vampire Monte Carlo simulation and returns the critical temperature.

                                                      diff --git a/docs/pymatgen.core.bonds.html b/docs/pymatgen.core.bonds.html index bbe3a4fa0a0..d92225a9a41 100644 --- a/docs/pymatgen.core.bonds.html +++ b/docs/pymatgen.core.bonds.html @@ -4,7 +4,7 @@ - pymatgen.core.bonds module — pymatgen 2022.5.18 documentation + pymatgen.core.bonds module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                      - 2022.5.18 + 2022.5.18.1
                                                      @@ -119,7 +119,7 @@ Molecule analysis.

                                                      -class CovalentBond(site1: pymatgen.core.sites.Site, site2: pymatgen.core.sites.Site)[source]
                                                      +class CovalentBond(site1: pymatgen.core.sites.Site, site2: pymatgen.core.sites.Site)[source]

                                                      Bases: object

                                                      Defines a covalent bond between two sites.

                                                      Initializes a covalent bond between two sites.

                                                      @@ -133,7 +133,7 @@
                                                      -get_bond_order(tol: float = 0.2, default_bl: float | None = None) → float[source]
                                                      +get_bond_order(tol: float = 0.2, default_bl: float | None = None) → float[source]

                                                      The bond order according the distance between the two sites :param tol: Relative tolerance to test.

                                                      @@ -158,7 +158,7 @@
                                                      -static is_bonded(site1, site2, tol: float = 0.2, bond_order: float | None = None, default_bl: float | None = None)[source]
                                                      +static is_bonded(site1, site2, tol: float = 0.2, bond_order: float | None = None, default_bl: float | None = None)[source]

                                                      Test if two sites are bonded, up to a certain limit. :param site1: First site :type site1: Site @@ -187,7 +187,7 @@

                                                      -property length: float[source]
                                                      +property length: float[source]

                                                      Length of the bond.

                                                      @@ -195,7 +195,7 @@
                                                      -get_bond_length(sp1: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies], sp2: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies], bond_order: float = 1) → float[source]
                                                      +get_bond_length(sp1: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies], sp2: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies], bond_order: float = 1) → float[source]

                                                      Get the bond length between two species.

                                                      Parameters
                                                      @@ -217,7 +217,7 @@
                                                      -get_bond_order(sp1, sp2, dist: float, tol: float = 0.2, default_bl: float | None = None)[source]
                                                      +get_bond_order(sp1, sp2, dist: float, tol: float = 0.2, default_bl: float | None = None)[source]

                                                      Calculate the bond order given the distance of 2 species

                                                      Parameters
                                                      @@ -244,7 +244,7 @@
                                                      -obtain_all_bond_lengths(sp1, sp2, default_bl: float | None = None)[source]
                                                      +obtain_all_bond_lengths(sp1, sp2, default_bl: float | None = None)[source]

                                                      Obtain bond lengths for all bond orders from bond length database

                                                      Parameters
                                                      diff --git a/docs/pymatgen.core.composition.html b/docs/pymatgen.core.composition.html index e313b90eec7..4e3600c34fe 100644 --- a/docs/pymatgen.core.composition.html +++ b/docs/pymatgen.core.composition.html @@ -4,7 +4,7 @@ - pymatgen.core.composition module — pymatgen 2022.5.18 documentation + pymatgen.core.composition module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                      - 2022.5.18 + 2022.5.18.1
                                                      @@ -119,7 +119,7 @@ and a ChemicalPotential class to represent potentials.

                                                      -class ChemicalPotential(*args, **kwargs)[source]
                                                      +class ChemicalPotential(*args, **kwargs)[source]

                                                      Bases: dict, monty.json.MSONable

                                                      Class to represent set of chemical potentials. Can be: multiplied/divided by a Number multiplied by a Composition (returns an energy) added/subtracted with other ChemicalPotentials.

                                                      @@ -134,7 +134,7 @@
                                                      -get_energy(composition: pymatgen.core.composition.Composition, strict: bool = True) → float[source]
                                                      +get_energy(composition: pymatgen.core.composition.Composition, strict: bool = True) → float[source]

                                                      Calculates the energy of a composition.

                                                      Parameters
                                                      @@ -150,7 +150,7 @@
                                                      -class Composition(*args, strict: bool = False, **kwargs)[source]
                                                      +class Composition(*args, strict: bool = False, **kwargs)[source]

                                                      Bases: collections.abc.Hashable, collections.abc.Mapping, monty.json.MSONable, pymatgen.util.string.Stringify

                                                      Represents a Composition, which is essentially a {element:amount} mapping type. Composition is written to be immutable and hashable, @@ -216,7 +216,7 @@

                                                      -add_charges_from_oxi_state_guesses(oxi_states_override: Optional[dict] = None, target_charge: float = 0, all_oxi_states: bool = False, max_sites: Optional[int] = None) → pymatgen.core.composition.Composition[source]
                                                      +add_charges_from_oxi_state_guesses(oxi_states_override: Optional[dict] = None, target_charge: float = 0, all_oxi_states: bool = False, max_sites: Optional[int] = None) → pymatgen.core.composition.Composition[source]

                                                      Assign oxidation states based on guessed oxidation states.

                                                      See oxi_state_guesses for an explanation of how oxidation states are guessed. This operation uses the set of oxidation states for each site @@ -253,7 +253,7 @@

                                                      -almost_equals(other: pymatgen.core.composition.Composition, rtol: float = 0.1, atol: float = 1e-08) → bool[source]
                                                      +almost_equals(other: pymatgen.core.composition.Composition, rtol: float = 0.1, atol: float = 1e-08) → bool[source]

                                                      Returns true if compositions are equal within a tolerance.

                                                      Parameters
                                                      @@ -268,19 +268,19 @@
                                                      -property alphabetical_formula: str[source]
                                                      +property alphabetical_formula: str[source]

                                                      Returns a formula string, with elements sorted by alphabetically e.g., Fe4 Li4 O16 P4.

                                                      -amount_tolerance = 1e-08[source]
                                                      +amount_tolerance = 1e-08[source]
                                                      -property anonymized_formula: str[source]
                                                      +property anonymized_formula: str[source]

                                                      An anonymized formula. Unique species are arranged in ordering of increasing amounts and assigned ascending alphabets. Useful for prototyping formulas. For example, all stoichiometric perovskites have @@ -289,7 +289,7 @@

                                                      -as_dict() → dict[str, float][source]
                                                      +as_dict() → dict[str, float][source]
                                                      Returns

                                                      dict with species symbol and (unreduced) amount e.g., @@ -300,7 +300,7 @@

                                                      -property average_electroneg: float[source]
                                                      +property average_electroneg: float[source]

                                                      Average electronegativity of the composition.

                                                      Type
                                                      @@ -311,7 +311,7 @@
                                                      -property chemical_system: str[source]
                                                      +property chemical_system: str[source]

                                                      Get the chemical system of a Composition, for example “O-Si” for SiO2. Chemical system is a string of a list of elements sorted alphabetically and joined by dashes, by convention for use @@ -320,7 +320,7 @@

                                                      -contains_element_type(category: str) → bool[source]
                                                      +contains_element_type(category: str) → bool[source]

                                                      Check if Composition contains any elements matching a given category.

                                                      Parameters
                                                      @@ -337,7 +337,7 @@
                                                      -copy() → pymatgen.core.composition.Composition[source]
                                                      +copy() → pymatgen.core.composition.Composition[source]
                                                      Returns

                                                      A copy of the composition.

                                                      @@ -347,27 +347,27 @@
                                                      -property element_composition: pymatgen.core.composition.Composition[source]
                                                      +property element_composition: pymatgen.core.composition.Composition[source]

                                                      Returns the composition replacing any species by the corresponding element.

                                                      -property elements: list[Element | Species | DummySpecies][source]
                                                      +property elements: list[Element | Species | DummySpecies][source]

                                                      Returns view of elements in Composition.

                                                      -property formula: str[source]
                                                      +property formula: str[source]

                                                      Returns a formula string, with elements sorted by electronegativity, e.g., Li4 Fe4 P4 O16.

                                                      -property fractional_composition: pymatgen.core.composition.Composition[source]
                                                      +property fractional_composition: pymatgen.core.composition.Composition[source]

                                                      Returns the normalized composition in which the amounts of each species sum to 1. E.g. “Fe2 O3”.fractional_composition = “Fe0.4 O0.6”.

                                                      @@ -375,7 +375,7 @@
                                                      -classmethod from_dict(d) → pymatgen.core.composition.Composition[source]
                                                      +classmethod from_dict(d) → pymatgen.core.composition.Composition[source]

                                                      Creates a composition from a dict generated by as_dict(). Strictly not necessary given that the standard constructor already takes in such an input, but this method preserves the standard pymatgen API of having @@ -390,7 +390,7 @@

                                                      -get_atomic_fraction(el: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]) → float[source]
                                                      +get_atomic_fraction(el: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]) → float[source]

                                                      Calculate atomic fraction of an Element or Species.

                                                      Parameters
                                                      @@ -404,7 +404,7 @@
                                                      -get_el_amt_dict() → dict[str, float][source]
                                                      +get_el_amt_dict() → dict[str, float][source]
                                                      Returns

                                                      element symbol and (unreduced) amount. E.g. @@ -418,7 +418,7 @@

                                                      -get_integer_formula_and_factor(max_denominator: int = 10000, iupac_ordering: bool = False) → tuple[str, float][source]
                                                      +get_integer_formula_and_factor(max_denominator: int = 10000, iupac_ordering: bool = False) → tuple[str, float][source]

                                                      Calculates an integer formula and factor.

                                                      Parameters
                                                      @@ -444,7 +444,7 @@
                                                      -get_reduced_composition_and_factor() → tuple[pymatgen.core.composition.Composition, float][source]
                                                      +get_reduced_composition_and_factor() → tuple[pymatgen.core.composition.Composition, float][source]

                                                      Calculates a reduced composition and factor.

                                                      Returns
                                                      @@ -456,7 +456,7 @@
                                                      -get_reduced_formula_and_factor(iupac_ordering: bool = False) → tuple[str, float][source]
                                                      +get_reduced_formula_and_factor(iupac_ordering: bool = False) → tuple[str, float][source]

                                                      Calculates a reduced formula and factor.

                                                      Parameters
                                                      @@ -478,7 +478,7 @@
                                                      -get_wt_fraction(el: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]) → float[source]
                                                      +get_wt_fraction(el: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]) → float[source]

                                                      Calculate weight fraction of an Element or Species.

                                                      Parameters
                                                      @@ -495,7 +495,7 @@
                                                      -property hill_formula: str[source]
                                                      +property hill_formula: str[source]

                                                      Hill formula. The Hill system (or Hill notation) is a system of writing empirical chemical formulas, molecular chemical formulas and components of a condensed formula such that the number of carbon atoms @@ -513,13 +513,13 @@

                                                      -property is_element: bool[source]
                                                      +property is_element: bool[source]

                                                      True if composition is for an element.

                                                      -property iupac_formula: str[source]
                                                      +property iupac_formula: str[source]

                                                      Returns a formula string, with elements sorted by the iupac electronegativity ordering defined in Table VI of “Nomenclature of Inorganic Chemistry (IUPAC Recommendations 2005)”. This ordering @@ -531,19 +531,19 @@

                                                      -property num_atoms: float[source]
                                                      +property num_atoms: float[source]

                                                      Total number of atoms in Composition. For negative amounts, sum of absolute values

                                                      -oxi_prob = None[source]
                                                      +oxi_prob = None[source]
                                                      -oxi_state_guesses(oxi_states_override: Optional[dict] = None, target_charge: float = 0, all_oxi_states: bool = False, max_sites: Optional[int] = None) → list[dict[str, float]][source]
                                                      +oxi_state_guesses(oxi_states_override: Optional[dict] = None, target_charge: float = 0, all_oxi_states: bool = False, max_sites: Optional[int] = None) → list[dict[str, float]][source]

                                                      Checks if the composition is charge-balanced and returns back all charge-balanced oxidation state combinations. Composition must have integer values. Note that more num_atoms in the composition gives @@ -585,7 +585,7 @@

                                                      -static ranked_compositions_from_indeterminate_formula(fuzzy_formula: str, lock_if_strict: bool = True) → list[pymatgen.core.composition.Composition][source]
                                                      +static ranked_compositions_from_indeterminate_formula(fuzzy_formula: str, lock_if_strict: bool = True) → list[pymatgen.core.composition.Composition][source]

                                                      Takes in a formula where capitalization might not be correctly entered, and suggests a ranked list of potential Composition matches. Author: Anubhav Jain

                                                      @@ -608,21 +608,21 @@
                                                      -property reduced_composition: pymatgen.core.composition.Composition[source]
                                                      +property reduced_composition: pymatgen.core.composition.Composition[source]

                                                      Returns the reduced composition, i.e. amounts normalized by greatest common denominator. E.g. “Fe4 P4 O16”.reduced_composition = “Fe P O4”.

                                                      -property reduced_formula: str[source]
                                                      +property reduced_formula: str[source]

                                                      Returns a pretty normalized formula, i.e., LiFePO4 instead of Li4Fe4P4O16.

                                                      -remove_charges() → pymatgen.core.composition.Composition[source]
                                                      +remove_charges() → pymatgen.core.composition.Composition[source]

                                                      Removes the charges from any species in a Composition object.

                                                      Returns
                                                      @@ -634,7 +634,7 @@
                                                      -replace(elem_map: dict[str, str | dict[str, int | float]]) → Composition[source]
                                                      +replace(elem_map: dict[str, str | dict[str, int | float]]) → Composition[source]

                                                      Replace elements in a composition. Returns a new Composition, leaving the old one unchanged.

                                                      Parameters
                                                      @@ -653,12 +653,12 @@
                                                      -special_formulas = {'Cl': 'Cl2', 'CsO': 'Cs2O2', 'F': 'F2', 'H': 'H2', 'HO': 'H2O2', 'KO': 'K2O2', 'LiO': 'Li2O2', 'N': 'N2', 'NaO': 'Na2O2', 'O': 'O2', 'RbO': 'Rb2O2'}[source]
                                                      +special_formulas = {'Cl': 'Cl2', 'CsO': 'Cs2O2', 'F': 'F2', 'H': 'H2', 'HO': 'H2O2', 'KO': 'K2O2', 'LiO': 'Li2O2', 'N': 'N2', 'NaO': 'Na2O2', 'O': 'O2', 'RbO': 'Rb2O2'}[source]
                                                      -property to_data_dict: dict[source]
                                                      +property to_data_dict: dict[source]

                                                      Returns: A dict with many keys and values relating to Composition/Formula, including reduced_cell_composition, unit_cell_composition, @@ -667,7 +667,7 @@

                                                      -to_pretty_string() → str[source]
                                                      +to_pretty_string() → str[source]
                                                      Returns

                                                      Same as output __str__() but without spaces.

                                                      @@ -680,7 +680,7 @@
                                                      -property to_reduced_dict: dict[source]
                                                      +property to_reduced_dict: dict[source]

                                                      Returns: Dict with element symbol and reduced amount e.g., {“Fe”: 2.0, “O”:3.0}

                                                      @@ -688,7 +688,7 @@
                                                      -property total_electrons: float[source]
                                                      +property total_electrons: float[source]

                                                      Total number of electrons in composition.

                                                      Type
                                                      @@ -699,14 +699,14 @@
                                                      -property valid: bool[source]
                                                      +property valid: bool[source]

                                                      Returns True if Composition contains valid elements or species and False if the Composition contains any dummy species.

                                                      -property weight: float[source]
                                                      +property weight: float[source]

                                                      Total molecular weight of Composition

                                                      @@ -714,14 +714,14 @@
                                                      -exception CompositionError[source]
                                                      +exception CompositionError[source]

                                                      Bases: Exception

                                                      Exception class for composition errors

                                                      -reduce_formula(sym_amt, iupac_ordering: bool = False) → tuple[str, float][source]
                                                      +reduce_formula(sym_amt, iupac_ordering: bool = False) → tuple[str, float][source]

                                                      Helper method to reduce a sym_amt dict to a reduced formula and factor.

                                                      Parameters
                                                      diff --git a/docs/pymatgen.core.html b/docs/pymatgen.core.html index fa74a8384a8..9a6ed7335ea 100644 --- a/docs/pymatgen.core.html +++ b/docs/pymatgen.core.html @@ -4,7 +4,7 @@ - pymatgen.core package — pymatgen 2022.5.18 documentation + pymatgen.core package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                      - 2022.5.18 + 2022.5.18.1
                                                      diff --git a/docs/pymatgen.core.interface.html b/docs/pymatgen.core.interface.html index 4658c9ab503..dc10a04973b 100644 --- a/docs/pymatgen.core.interface.html +++ b/docs/pymatgen.core.interface.html @@ -4,7 +4,7 @@ - pymatgen.core.interface module — pymatgen 2022.5.18 documentation + pymatgen.core.interface module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                      - 2022.5.18 + 2022.5.18.1
                                                      @@ -118,7 +118,7 @@

                                                      This module provides classes to store, generate, and manipulate material interfaces.

                                                      -class Interface(lattice, species, coords, site_properties, validate_proximity=False, to_unit_cell=False, coords_are_cartesian=False, in_plane_offset: tuple[float, float] = (0, 0), gap: float = 0, vacuum_over_film: float = 0.0, interface_properties: dict | None = None)[source]
                                                      +class Interface(lattice, species, coords, site_properties, validate_proximity=False, to_unit_cell=False, coords_are_cartesian=False, in_plane_offset: tuple[float, float] = (0, 0), gap: float = 0, vacuum_over_film: float = 0.0, interface_properties: dict | None = None)[source]

                                                      Bases: pymatgen.core.structure.Structure

                                                      This class stores data for defining an interface between two structures. It is a subclass of pymatgen.core.structure.Structure.

                                                      @@ -163,7 +163,7 @@
                                                      -as_dict()[source]
                                                      +as_dict()[source]
                                                      Returns

                                                      MSONAble dict

                                                      @@ -173,7 +173,7 @@
                                                      -copy()[source]
                                                      +copy()[source]
                                                      Returns

                                                      A copy of the Interface.

                                                      @@ -186,37 +186,37 @@
                                                      -property film: pymatgen.core.structure.Structure[source]
                                                      +property film: pymatgen.core.structure.Structure[source]

                                                      A pymatgen Structure for just the film

                                                      -property film_indices: list[int][source]
                                                      +property film_indices: list[int][source]

                                                      Site indices of the film sites

                                                      -property film_layers: int[source]
                                                      +property film_layers: int[source]

                                                      Number of layers of the minimum element in the film composition

                                                      -property film_sites: list[pymatgen.core.sites.Site][source]
                                                      +property film_sites: list[pymatgen.core.sites.Site][source]

                                                      Return the film sites of the interface.

                                                      -property film_termination: str[source]
                                                      +property film_termination: str[source]

                                                      Label for the film termination chemistry

                                                      -classmethod from_dict(d)[source]
                                                      +classmethod from_dict(d)[source]
                                                      Parameters

                                                      d – dict

                                                      @@ -229,7 +229,7 @@
                                                      -classmethod from_slabs(substrate_slab: Slab, film_slab: Slab, in_plane_offset: tuple[float, float] = (0, 0), gap: float = 1.6, vacuum_over_film: float = 0.0, interface_properties: dict | None = None, center_slab: bool = True) → Interface[source]
                                                      +classmethod from_slabs(substrate_slab: Slab, film_slab: Slab, in_plane_offset: tuple[float, float] = (0, 0), gap: float = 1.6, vacuum_over_film: float = 0.0, interface_properties: dict | None = None, center_slab: bool = True) → Interface[source]

                                                      Makes an interface structure by merging a substrate and film slabs The film a- and b-vectors will be forced to be the substrate slab’s a- and b-vectors.

                                                      @@ -253,13 +253,13 @@
                                                      -property gap: float[source]
                                                      +property gap: float[source]

                                                      The gap in Cartesian units between the film and the substrate

                                                      -get_shifts_based_on_adsorbate_sites(tolerance: float = 0.1) → list[tuple[float, float]][source]
                                                      +get_shifts_based_on_adsorbate_sites(tolerance: float = 0.1) → list[tuple[float, float]][source]

                                                      Computes possible in-plane shifts based on an adsorbate site algorithm

                                                      Parameters
                                                      @@ -271,7 +271,7 @@
                                                      -get_sorted_structure(key=None, reverse=False) → pymatgen.core.structure.Structure[source]
                                                      +get_sorted_structure(key=None, reverse=False) → pymatgen.core.structure.Structure[source]

                                                      Get a sorted structure for the interface. The parameters have the same meaning as in list.sort. By default, sites are sorted by the electronegativity of the species.

                                                      @@ -290,44 +290,44 @@
                                                      -property in_plane_offset: numpy.ndarray[source]
                                                      +property in_plane_offset: numpy.ndarray[source]

                                                      The shift between the film and substrate in fractional coordinates

                                                      -property substrate: pymatgen.core.structure.Structure[source]
                                                      +property substrate: pymatgen.core.structure.Structure[source]

                                                      A pymatgen Structure for just the substrate

                                                      -property substrate_indices: list[int][source]
                                                      +property substrate_indices: list[int][source]

                                                      Site indices for the substrate atoms

                                                      -property substrate_layers: int[source]
                                                      +property substrate_layers: int[source]

                                                      Number of layers of the minimum element in the substrate composition

                                                      -property substrate_sites: list[pymatgen.core.sites.Site][source]
                                                      +property substrate_sites: list[pymatgen.core.sites.Site][source]

                                                      The site objects in the substrate

                                                      -property substrate_termination: str[source]
                                                      +property substrate_termination: str[source]

                                                      Label for the substrate termination chemistry

                                                      -property vacuum_over_film: float[source]
                                                      +property vacuum_over_film: float[source]

                                                      The vacuum space over the film in Cartesian units

                                                      @@ -335,13 +335,13 @@
                                                      -count_layers(struc: pymatgen.core.structure.Structure, el=None) → int[source]
                                                      +count_layers(struc: pymatgen.core.structure.Structure, el=None) → int[source]

                                                      Counts the number of ‘layers’ along the c-axis

                                                      -label_termination(slab: pymatgen.core.structure.Structure) → str[source]
                                                      +label_termination(slab: pymatgen.core.structure.Structure) → str[source]

                                                      Labels the slab surface termination

                                                      diff --git a/docs/pymatgen.core.ion.html b/docs/pymatgen.core.ion.html index 8aea06feb8e..f2d4d9467d1 100644 --- a/docs/pymatgen.core.ion.html +++ b/docs/pymatgen.core.ion.html @@ -4,7 +4,7 @@ - pymatgen.core.ion module — pymatgen 2022.5.18 documentation + pymatgen.core.ion module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                      - 2022.5.18 + 2022.5.18.1
                                                      @@ -118,7 +118,7 @@

                                                      Module containing class to create an ion

                                                      -class Ion(composition, charge=0.0, properties=None)[source]
                                                      +class Ion(composition, charge=0.0, properties=None)[source]

                                                      Bases: pymatgen.core.composition.Composition, monty.json.MSONable, pymatgen.util.string.Stringify

                                                      Ion object. Just a Composition object with an additional variable to store charge.

                                                      @@ -128,21 +128,21 @@ For more information, please see pymatgen.core.Composition

                                                      -property alphabetical_formula: str[source]
                                                      +property alphabetical_formula: str[source]

                                                      Returns a formula string, with elements sorted by alphabetically and appended charge

                                                      -property anonymized_formula: str[source]
                                                      +property anonymized_formula: str[source]

                                                      An anonymized formula. Appends charge to the end of anonymized composition

                                                      -as_dict() → dict[str, float][source]
                                                      +as_dict() → dict[str, float][source]
                                                      Returns

                                                      dict with composition, as well as charge

                                                      @@ -152,26 +152,26 @@
                                                      -property charge: float[source]
                                                      +property charge: float[source]

                                                      Charge of the ion

                                                      -property composition: pymatgen.core.composition.Composition[source]
                                                      +property composition: pymatgen.core.composition.Composition[source]

                                                      Composition of ion.

                                                      -property formula: str[source]
                                                      +property formula: str[source]

                                                      Returns a formula string, with elements sorted by electronegativity, e.g., Li4 Fe4 P4 O16.

                                                      -classmethod from_dict(d) → pymatgen.core.ion.Ion[source]
                                                      +classmethod from_dict(d) → pymatgen.core.ion.Ion[source]

                                                      Generates an ion object from a dict created by as_dict().

                                                      Parameters
                                                      @@ -182,7 +182,7 @@
                                                      -classmethod from_formula(formula: str) → pymatgen.core.ion.Ion[source]
                                                      +classmethod from_formula(formula: str) → pymatgen.core.ion.Ion[source]

                                                      Creates Ion from formula. The net charge can either be represented as Mn++, Mn+2, Mn[2+], Mn[++], or Mn[+2]. Note the order of the sign and magnitude in each representation.

                                                      @@ -199,7 +199,7 @@
                                                      -get_reduced_formula_and_factor(iupac_ordering: bool = False, hydrates: bool = True) → tuple[str, float][source]
                                                      +get_reduced_formula_and_factor(iupac_ordering: bool = False, hydrates: bool = True) → tuple[str, float][source]

                                                      Calculates a reduced formula and factor.

                                                      Similar to Composition.get_reduced_formula_and_factor except that O-H formulas receive special handling to differentiate between hydrogen peroxide and OH-. @@ -234,7 +234,7 @@

                                                      -property reduced_formula: str[source]
                                                      +property reduced_formula: str[source]

                                                      Returns a reduced formula string with appended charge. The charge is placed in brackets with the sign preceding the magnitude, e.g., ‘Ca[+2]’.

                                                      @@ -242,7 +242,7 @@
                                                      -to_pretty_string() → str[source]
                                                      +to_pretty_string() → str[source]
                                                      Returns

                                                      Pretty string with proper superscripts.

                                                      @@ -252,7 +252,7 @@
                                                      -property to_reduced_dict: dict[source]
                                                      +property to_reduced_dict: dict[source]

                                                      Returns: dict with element symbol and reduced amount e.g., {“Fe”: 2.0, “O”:3.0}.

                                                      diff --git a/docs/pymatgen.core.lattice.html b/docs/pymatgen.core.lattice.html index 8735b73a163..017b12dda44 100644 --- a/docs/pymatgen.core.lattice.html +++ b/docs/pymatgen.core.lattice.html @@ -4,7 +4,7 @@ - pymatgen.core.lattice module — pymatgen 2022.5.18 documentation + pymatgen.core.lattice module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                      - 2022.5.18 + 2022.5.18.1
                                                      @@ -118,7 +118,7 @@

                                                      Defines the classes relating to 3D lattices.

                                                      -class Lattice(matrix: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]])[source]
                                                      +class Lattice(matrix: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]])[source]

                                                      Bases: monty.json.MSONable

                                                      A lattice object. Essentially a matrix with conversion matrices. In general, it is assumed that length units are in Angstroms and angles are in @@ -141,31 +141,31 @@

                                                      -property a: float[source]
                                                      +property a: float[source]

                                                      a lattice parameter.

                                                      -property abc: tuple[float, float, float][source]
                                                      +property abc: tuple[float, float, float][source]

                                                      Lengths of the lattice vectors, i.e. (a, b, c)

                                                      -property alpha: float[source]
                                                      +property alpha: float[source]

                                                      Angle alpha of lattice in degrees.

                                                      -property angles: tuple[float, float, float][source]
                                                      +property angles: tuple[float, float, float][source]

                                                      Returns the angles (alpha, beta, gamma) of the lattice.

                                                      -as_dict(verbosity: int = 0) → dict[source]
                                                      +as_dict(verbosity: int = 0) → dict[source]

                                                      Json-serialization dict representation of the Lattice.

                                                      Parameters
                                                      @@ -177,31 +177,31 @@
                                                      -property b: float[source]
                                                      +property b: float[source]

                                                      b lattice parameter.

                                                      -property beta: float[source]
                                                      +property beta: float[source]

                                                      Angle beta of lattice in degrees.

                                                      -property c: float[source]
                                                      +property c: float[source]

                                                      c lattice parameter.

                                                      -copy()[source]
                                                      +copy()[source]

                                                      Deep copy of self.

                                                      -static cubic(a: float) → pymatgen.core.lattice.Lattice[source]
                                                      +static cubic(a: float) → pymatgen.core.lattice.Lattice[source]

                                                      Convenience constructor for a cubic lattice.

                                                      Parameters
                                                      @@ -215,7 +215,7 @@
                                                      -d_hkl(miller_index: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]) → float[source]
                                                      +d_hkl(miller_index: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]) → float[source]

                                                      Returns the distance between the hkl plane and the origin

                                                      Parameters
                                                      @@ -229,7 +229,7 @@
                                                      -dot(coords_a: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], coords_b: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], frac_coords: bool = False) → numpy.ndarray[source]
                                                      +dot(coords_a: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], coords_b: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], frac_coords: bool = False) → numpy.ndarray[source]

                                                      Compute the scalar product of vector(s).

                                                      Parameters
                                                      @@ -248,7 +248,7 @@
                                                      -find_all_mappings(other_lattice: Lattice, ltol: float = 1e-05, atol: float = 1, skip_rotation_matrix: bool = False) → Iterator[tuple[Lattice, np.ndarray | None, np.ndarray]][source]
                                                      +find_all_mappings(other_lattice: Lattice, ltol: float = 1e-05, atol: float = 1, skip_rotation_matrix: bool = False) → Iterator[tuple[Lattice, np.ndarray | None, np.ndarray]][source]

                                                      Finds all mappings between current lattice and another lattice.

                                                      Parameters
                                                      @@ -281,7 +281,7 @@
                                                      -find_mapping(other_lattice: Lattice, ltol: float = 1e-05, atol: float = 1, skip_rotation_matrix: bool = False) → tuple[Lattice, np.ndarray | None, np.ndarray] | None[source]
                                                      +find_mapping(other_lattice: Lattice, ltol: float = 1e-05, atol: float = 1, skip_rotation_matrix: bool = False) → tuple[Lattice, np.ndarray | None, np.ndarray] | None[source]

                                                      Finds a mapping between current lattice and another lattice. There are an infinite number of choices of basis vectors for two entirely equivalent lattices. This method returns a mapping that maps @@ -316,7 +316,7 @@

                                                      -classmethod from_dict(d: dict, fmt: Optional[str] = None, **kwargs)[source]
                                                      +classmethod from_dict(d: dict, fmt: Optional[str] = None, **kwargs)[source]

                                                      Create a Lattice from a dictionary containing the a, b, c, alpha, beta, and gamma parameters if fmt is None.

                                                      If fmt == “abivars”, the function build a Lattice object from a @@ -328,7 +328,7 @@

                                                      -classmethod from_parameters(a: float, b: float, c: float, alpha: float, beta: float, gamma: float, vesta: bool = False)[source]
                                                      +classmethod from_parameters(a: float, b: float, c: float, alpha: float, beta: float, gamma: float, vesta: bool = False)[source]

                                                      Create a Lattice using unit cell lengths and angles (in degrees).

                                                      Parameters
                                                      @@ -350,13 +350,13 @@
                                                      -property gamma: float[source]
                                                      +property gamma: float[source]

                                                      Angle gamma of lattice in degrees.

                                                      -get_all_distances(fcoords1: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], fcoords2: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]) → numpy.ndarray[source]
                                                      +get_all_distances(fcoords1: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], fcoords2: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]) → numpy.ndarray[source]

                                                      Returns the distances between two lists of coordinates taking into account periodic boundary conditions and the lattice. Note that this computes an MxN array of distances (i.e. the distance between each @@ -380,7 +380,7 @@

                                                      -get_brillouin_zone() → list[list[numpy.ndarray]][source]
                                                      +get_brillouin_zone() → list[list[numpy.ndarray]][source]

                                                      Returns the Wigner-Seitz cell for the reciprocal lattice, aka the Brillouin Zone.

                                                      @@ -395,7 +395,7 @@
                                                      -get_cartesian_coords(fractional_coords: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]) → numpy.ndarray[source]
                                                      +get_cartesian_coords(fractional_coords: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]) → numpy.ndarray[source]

                                                      Returns the Cartesian coordinates given fractional coordinates.

                                                      Parameters
                                                      @@ -409,7 +409,7 @@
                                                      -get_distance_and_image(frac_coords1: ArrayLike, frac_coords2: ArrayLike, jimage: ArrayLike | None = None) → tuple[float, np.ndarray][source]
                                                      +get_distance_and_image(frac_coords1: ArrayLike, frac_coords2: ArrayLike, jimage: ArrayLike | None = None) → tuple[float, np.ndarray][source]

                                                      Gets distance between two frac_coords assuming periodic boundary conditions. If the index jimage is not specified it selects the j image nearest to the i atom and returns the distance and jimage @@ -442,14 +442,14 @@

                                                      -get_frac_coords_from_lll(lll_frac_coords: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]) → numpy.ndarray[source]
                                                      +get_frac_coords_from_lll(lll_frac_coords: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]) → numpy.ndarray[source]

                                                      Given fractional coordinates in the lll basis, returns corresponding fractional coordinates in the lattice basis.

                                                      -get_fractional_coords(cart_coords: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]) → numpy.ndarray[source]
                                                      +get_fractional_coords(cart_coords: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]) → numpy.ndarray[source]

                                                      Returns the fractional coordinates given Cartesian coordinates.

                                                      Parameters
                                                      @@ -463,14 +463,14 @@
                                                      -get_lll_frac_coords(frac_coords: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]) → numpy.ndarray[source]
                                                      +get_lll_frac_coords(frac_coords: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]) → numpy.ndarray[source]

                                                      Given fractional coordinates in the lattice basis, returns corresponding fractional coordinates in the lll basis.

                                                      -get_lll_reduced_lattice(delta: float = 0.75) → pymatgen.core.lattice.Lattice[source]
                                                      +get_lll_reduced_lattice(delta: float = 0.75) → pymatgen.core.lattice.Lattice[source]
                                                      Parameters

                                                      delta – Delta parameter.

                                                      @@ -483,7 +483,7 @@
                                                      -get_miller_index_from_coords(coords: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], coords_are_cartesian: bool = True, round_dp: int = 4, verbose: bool = True) → tuple[int, int, int][source]
                                                      +get_miller_index_from_coords(coords: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], coords_are_cartesian: bool = True, round_dp: int = 4, verbose: bool = True) → tuple[int, int, int][source]

                                                      Get the Miller index of a plane from a list of site coordinates.

                                                      A minimum of 3 sets of coordinates are required. If more than 3 sets of coordinates are given, the best plane that minimises the distance to all @@ -514,7 +514,7 @@

                                                      -get_niggli_reduced_lattice(tol: float = 1e-05) → pymatgen.core.lattice.Lattice[source]
                                                      +get_niggli_reduced_lattice(tol: float = 1e-05) → pymatgen.core.lattice.Lattice[source]

                                                      Get the Niggli reduced lattice using the numerically stable algo proposed by R. W. Grosse-Kunstleve, N. K. Sauter, & P. D. Adams, Acta Crystallographica Section A Foundations of Crystallography, 2003, @@ -532,7 +532,7 @@

                                                      -get_points_in_sphere(frac_points: ArrayLike, center: ArrayLike, r: float, zip_results=True) → list[tuple[np.ndarray, float, int, np.ndarray]] | list[np.ndarray] | list[source]
                                                      +get_points_in_sphere(frac_points: ArrayLike, center: ArrayLike, r: float, zip_results=True) → list[tuple[np.ndarray, float, int, np.ndarray]] | list[np.ndarray] | list[source]

                                                      Find all points within a sphere from the point taking into account periodic boundary conditions. This includes sites in other periodic images.

                                                      @@ -574,12 +574,12 @@
                                                      -get_points_in_sphere_old(**kwargs)[source]
                                                      +get_points_in_sphere_old(**kwargs)[source]
                                                      -get_points_in_sphere_py(frac_points: ArrayLike, center: ArrayLike, r: float, zip_results=True) → list[tuple[np.ndarray, float, int, np.ndarray]] | list[np.ndarray][source]
                                                      +get_points_in_sphere_py(frac_points: ArrayLike, center: ArrayLike, r: float, zip_results=True) → list[tuple[np.ndarray, float, int, np.ndarray]] | list[np.ndarray][source]

                                                      Find all points within a sphere from the point taking into account periodic boundary conditions. This includes sites in other periodic images.

                                                      @@ -621,7 +621,7 @@
                                                      -get_recp_symmetry_operation(symprec: float = 0.01) → list[source]
                                                      +get_recp_symmetry_operation(symprec: float = 0.01) → list[source]

                                                      Find the symmetric operations of the reciprocal lattice, to be used for hkl transformations :param symprec: default is 0.001

                                                      @@ -629,7 +629,7 @@
                                                      -get_vector_along_lattice_directions(cart_coords: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]) → numpy.ndarray[source]
                                                      +get_vector_along_lattice_directions(cart_coords: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]) → numpy.ndarray[source]

                                                      Returns the coordinates along lattice directions given Cartesian coordinates.

                                                      Note, this is different than a projection of the Cartesian vector along the lattice parameters. It is simply the fractional coordinates multiplied by the @@ -649,7 +649,7 @@

                                                      -get_wigner_seitz_cell() → list[list[numpy.ndarray]][source]
                                                      +get_wigner_seitz_cell() → list[list[numpy.ndarray]][source]

                                                      Returns the Wigner-Seitz cell for the given lattice.

                                                      Returns
                                                      @@ -663,7 +663,7 @@
                                                      -static hexagonal(a: float, c: float) → pymatgen.core.lattice.Lattice[source]
                                                      +static hexagonal(a: float, c: float) → pymatgen.core.lattice.Lattice[source]

                                                      Convenience constructor for a hexagonal lattice.

                                                      Parameters
                                                      @@ -680,13 +680,13 @@
                                                      -property inv_matrix: numpy.ndarray[source]
                                                      +property inv_matrix: numpy.ndarray[source]

                                                      Inverse of lattice matrix.

                                                      -is_hexagonal(hex_angle_tol: float = 5, hex_length_tol: float = 0.01) → bool[source]
                                                      +is_hexagonal(hex_angle_tol: float = 5, hex_length_tol: float = 0.01) → bool[source]
                                                      Parameters
                                                        @@ -702,7 +702,7 @@
                                                        -property is_orthogonal: bool[source]
                                                        +property is_orthogonal: bool[source]

                                                        Whether all angles are 90 degrees.

                                                        Type
                                                        @@ -713,7 +713,7 @@
                                                        -property lengths: tuple[float, float, float][source]
                                                        +property lengths: tuple[float, float, float][source]

                                                        The lengths (a, b, c) of the lattice.

                                                        Type
                                                        @@ -724,7 +724,7 @@
                                                        -property lll_inverse: numpy.ndarray[source]
                                                        +property lll_inverse: numpy.ndarray[source]

                                                        Inverse of self.lll_mapping.

                                                        Type
                                                        @@ -735,7 +735,7 @@
                                                        -property lll_mapping: numpy.ndarray[source]
                                                        +property lll_mapping: numpy.ndarray[source]

                                                        The mapping between the LLL reduced lattice and the original lattice.

                                                        @@ -747,7 +747,7 @@
                                                        -property lll_matrix: numpy.ndarray[source]
                                                        +property lll_matrix: numpy.ndarray[source]

                                                        The matrix for LLL reduction

                                                        Type
                                                        @@ -758,19 +758,19 @@
                                                        -property matrix: numpy.ndarray[source]
                                                        +property matrix: numpy.ndarray[source]

                                                        Copy of matrix representing the Lattice

                                                        -property metric_tensor: numpy.ndarray[source]
                                                        +property metric_tensor: numpy.ndarray[source]

                                                        The metric tensor of the lattice.

                                                        -static monoclinic(a: float, b: float, c: float, beta: float) → pymatgen.core.lattice.Lattice[source]
                                                        +static monoclinic(a: float, b: float, c: float, beta: float) → pymatgen.core.lattice.Lattice[source]

                                                        Convenience constructor for a monoclinic lattice.

                                                        Parameters
                                                        @@ -791,7 +791,7 @@
                                                        -norm(coords: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], frac_coords: bool = True) → float[source]
                                                        +norm(coords: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], frac_coords: bool = True) → float[source]

                                                        Compute the norm of vector(s).

                                                        Parameters
                                                        @@ -809,7 +809,7 @@
                                                        -static orthorhombic(a: float, b: float, c: float) → pymatgen.core.lattice.Lattice[source]
                                                        +static orthorhombic(a: float, b: float, c: float) → pymatgen.core.lattice.Lattice[source]

                                                        Convenience constructor for an orthorhombic lattice.

                                                        Parameters
                                                        @@ -827,7 +827,7 @@
                                                        -property parameters: tuple[float, float, float, float, float, float][source]
                                                        +property parameters: tuple[float, float, float, float, float, float][source]

                                                        (a, b, c, alpha, beta, gamma).

                                                        Type
                                                        @@ -838,7 +838,7 @@
                                                        -property reciprocal_lattice: pymatgen.core.lattice.Lattice[source]
                                                        +property reciprocal_lattice: pymatgen.core.lattice.Lattice[source]

                                                        Return the reciprocal lattice. Note that this is the standard reciprocal lattice used for solid state physics with a factor of 2 * pi. If you are looking for the crystallographic reciprocal lattice, @@ -848,14 +848,14 @@

                                                        -property reciprocal_lattice_crystallographic: pymatgen.core.lattice.Lattice[source]
                                                        +property reciprocal_lattice_crystallographic: pymatgen.core.lattice.Lattice[source]

                                                        Returns the crystallographic reciprocal lattice, i.e., no factor of 2 * pi.

                                                        -static rhombohedral(a: float, alpha: float) → pymatgen.core.lattice.Lattice[source]
                                                        +static rhombohedral(a: float, alpha: float) → pymatgen.core.lattice.Lattice[source]

                                                        Convenience constructor for a rhombohedral lattice.

                                                        Parameters
                                                        @@ -872,7 +872,7 @@
                                                        -scale(new_volume: float) → pymatgen.core.lattice.Lattice[source]
                                                        +scale(new_volume: float) → pymatgen.core.lattice.Lattice[source]

                                                        Return a new Lattice with volume new_volume by performing a scaling of the lattice vectors so that length proportions and angles are preserved.

                                                        @@ -888,19 +888,19 @@
                                                        -selling_dist(other)[source]
                                                        +selling_dist(other)[source]

                                                        Returns the minimum Selling distance between two lattices.

                                                        -property selling_vector: numpy.ndarray[source]
                                                        +property selling_vector: numpy.ndarray[source]

                                                        Returns the (1,6) array of Selling Scalars.

                                                        -static tetragonal(a: float, c: float) → pymatgen.core.lattice.Lattice[source]
                                                        +static tetragonal(a: float, c: float) → pymatgen.core.lattice.Lattice[source]

                                                        Convenience constructor for a tetragonal lattice.

                                                        Parameters
                                                        @@ -917,7 +917,7 @@
                                                        -property volume: float[source]
                                                        +property volume: float[source]

                                                        Volume of the unit cell.

                                                        @@ -925,7 +925,7 @@
                                                        -find_neighbors(label: numpy.ndarray, nx: int, ny: int, nz: int) → list[numpy.ndarray][source]
                                                        +find_neighbors(label: numpy.ndarray, nx: int, ny: int, nz: int) → list[numpy.ndarray][source]

                                                        Given a cube index, find the neighbor cube indices

                                                        Parameters
                                                        @@ -942,7 +942,7 @@
                                                        -get_integer_index(miller_index: Sequence[float], round_dp: int = 4, verbose: bool = True) → tuple[int, int, int][source]
                                                        +get_integer_index(miller_index: Sequence[float], round_dp: int = 4, verbose: bool = True) → tuple[int, int, int][source]

                                                        Attempt to convert a vector of floats to whole numbers.

                                                        Parameters
                                                        @@ -964,7 +964,7 @@
                                                        -get_points_in_spheres(all_coords: np.ndarray, center_coords: np.ndarray, r: float, pbc: bool | list[bool] = True, numerical_tol: float = 1e-08, lattice: Lattice = None, return_fcoords: bool = False) → list[list[tuple[np.ndarray, float, int, np.ndarray]]][source]
                                                        +get_points_in_spheres(all_coords: np.ndarray, center_coords: np.ndarray, r: float, pbc: bool | list[bool] = True, numerical_tol: float = 1e-08, lattice: Lattice = None, return_fcoords: bool = False) → list[list[tuple[np.ndarray, float, int, np.ndarray]]][source]

                                                        For each point in center_coords, get all the neighboring points in all_coords that are within the cutoff radius r.

                                                        diff --git a/docs/pymatgen.core.libxcfunc.html b/docs/pymatgen.core.libxcfunc.html index 0fa0183e786..5fcb37a722c 100644 --- a/docs/pymatgen.core.libxcfunc.html +++ b/docs/pymatgen.core.libxcfunc.html @@ -4,7 +4,7 @@ - pymatgen.core.libxcfunc module — pymatgen 2022.5.18 documentation + pymatgen.core.libxcfunc module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                        - 2022.5.18 + 2022.5.18.1
                                                        @@ -122,7 +122,7 @@ Use the script ~pymatgen/dev_scripts/regen_libxcfunc.py to regenerate the enum values.

                                                        -class LibxcFunc(value)[source]
                                                        +class LibxcFunc(value)[source]

                                                        Bases: enum.Enum

                                                        Enumerator with the identifiers. This object is used by Xcfunc declared in xcfunc.py to create an internal representation of the XC functional. @@ -136,1824 +136,1824 @@

                                                        -GGA_C_AM05 = 135[source]
                                                        +GGA_C_AM05 = 135[source]
                                                        -GGA_C_APBE = 186[source]
                                                        +GGA_C_APBE = 186[source]
                                                        -GGA_C_BGCP = 39[source]
                                                        +GGA_C_BGCP = 39[source]
                                                        -GGA_C_FT97 = 88[source]
                                                        +GGA_C_FT97 = 88[source]
                                                        -GGA_C_GAM = 33[source]
                                                        +GGA_C_GAM = 33[source]
                                                        -GGA_C_HCTH_A = 97[source]
                                                        +GGA_C_HCTH_A = 97[source]
                                                        -GGA_C_LM = 137[source]
                                                        +GGA_C_LM = 137[source]
                                                        -GGA_C_LYP = 131[source]
                                                        +GGA_C_LYP = 131[source]
                                                        -GGA_C_N12 = 80[source]
                                                        +GGA_C_N12 = 80[source]
                                                        -GGA_C_N12_SX = 79[source]
                                                        +GGA_C_N12_SX = 79[source]
                                                        -GGA_C_OPTC = 200[source]
                                                        +GGA_C_OPTC = 200[source]
                                                        -GGA_C_OP_B88 = 87[source]
                                                        +GGA_C_OP_B88 = 87[source]
                                                        -GGA_C_OP_G96 = 85[source]
                                                        +GGA_C_OP_G96 = 85[source]
                                                        -GGA_C_OP_PBE = 86[source]
                                                        +GGA_C_OP_PBE = 86[source]
                                                        -GGA_C_OP_PW91 = 262[source]
                                                        +GGA_C_OP_PW91 = 262[source]
                                                        -GGA_C_OP_XALPHA = 84[source]
                                                        +GGA_C_OP_XALPHA = 84[source]
                                                        -GGA_C_P86 = 132[source]
                                                        +GGA_C_P86 = 132[source]
                                                        -GGA_C_PBE = 130[source]
                                                        +GGA_C_PBE = 130[source]
                                                        -GGA_C_PBEFE = 258[source]
                                                        +GGA_C_PBEFE = 258[source]
                                                        -GGA_C_PBEINT = 62[source]
                                                        +GGA_C_PBEINT = 62[source]
                                                        -GGA_C_PBELOC = 246[source]
                                                        +GGA_C_PBELOC = 246[source]
                                                        -GGA_C_PBE_JRGX = 138[source]
                                                        +GGA_C_PBE_JRGX = 138[source]
                                                        -GGA_C_PBE_SOL = 133[source]
                                                        +GGA_C_PBE_SOL = 133[source]
                                                        -GGA_C_PW91 = 134[source]
                                                        +GGA_C_PW91 = 134[source]
                                                        -GGA_C_Q2D = 47[source]
                                                        +GGA_C_Q2D = 47[source]
                                                        -GGA_C_REGTPSS = 83[source]
                                                        +GGA_C_REGTPSS = 83[source]
                                                        -GGA_C_REVTCA = 99[source]
                                                        +GGA_C_REVTCA = 99[source]
                                                        -GGA_C_RGE2 = 143[source]
                                                        +GGA_C_RGE2 = 143[source]
                                                        -GGA_C_SOGGA11 = 152[source]
                                                        +GGA_C_SOGGA11 = 152[source]
                                                        -GGA_C_SOGGA11_X = 159[source]
                                                        +GGA_C_SOGGA11_X = 159[source]
                                                        -GGA_C_SPBE = 89[source]
                                                        +GGA_C_SPBE = 89[source]
                                                        -GGA_C_TCA = 100[source]
                                                        +GGA_C_TCA = 100[source]
                                                        -GGA_C_WI = 148[source]
                                                        +GGA_C_WI = 148[source]
                                                        -GGA_C_WI0 = 153[source]
                                                        +GGA_C_WI0 = 153[source]
                                                        -GGA_C_WL = 147[source]
                                                        +GGA_C_WL = 147[source]
                                                        -GGA_C_XPBE = 136[source]
                                                        +GGA_C_XPBE = 136[source]
                                                        -GGA_C_ZPBEINT = 61[source]
                                                        +GGA_C_ZPBEINT = 61[source]
                                                        -GGA_C_ZPBESOL = 63[source]
                                                        +GGA_C_ZPBESOL = 63[source]
                                                        -GGA_K_ABSP1 = 506[source]
                                                        +GGA_K_ABSP1 = 506[source]
                                                        -GGA_K_ABSP2 = 507[source]
                                                        +GGA_K_ABSP2 = 507[source]
                                                        -GGA_K_APBE = 185[source]
                                                        +GGA_K_APBE = 185[source]
                                                        -GGA_K_APBEINT = 54[source]
                                                        +GGA_K_APBEINT = 54[source]
                                                        -GGA_K_BALTIN = 504[source]
                                                        +GGA_K_BALTIN = 504[source]
                                                        -GGA_K_DK = 516[source]
                                                        +GGA_K_DK = 516[source]
                                                        -GGA_K_ERNZERHOF = 520[source]
                                                        +GGA_K_ERNZERHOF = 520[source]
                                                        -GGA_K_FR_B88 = 514[source]
                                                        +GGA_K_FR_B88 = 514[source]
                                                        -GGA_K_FR_PW86 = 515[source]
                                                        +GGA_K_FR_PW86 = 515[source]
                                                        -GGA_K_GE2 = 501[source]
                                                        +GGA_K_GE2 = 501[source]
                                                        -GGA_K_GOLDEN = 502[source]
                                                        +GGA_K_GOLDEN = 502[source]
                                                        -GGA_K_GP85 = 510[source]
                                                        +GGA_K_GP85 = 510[source]
                                                        -GGA_K_GR = 508[source]
                                                        +GGA_K_GR = 508[source]
                                                        -GGA_K_LC94 = 521[source]
                                                        +GGA_K_LC94 = 521[source]
                                                        -GGA_K_LIEB = 505[source]
                                                        +GGA_K_LIEB = 505[source]
                                                        -GGA_K_LLP = 522[source]
                                                        +GGA_K_LLP = 522[source]
                                                        -GGA_K_LUDENA = 509[source]
                                                        +GGA_K_LUDENA = 509[source]
                                                        -GGA_K_MEYER = 57[source]
                                                        +GGA_K_MEYER = 57[source]
                                                        -GGA_K_OL1 = 512[source]
                                                        +GGA_K_OL1 = 512[source]
                                                        -GGA_K_OL2 = 513[source]
                                                        +GGA_K_OL2 = 513[source]
                                                        -GGA_K_PEARSON = 511[source]
                                                        +GGA_K_PEARSON = 511[source]
                                                        -GGA_K_PERDEW = 517[source]
                                                        +GGA_K_PERDEW = 517[source]
                                                        -GGA_K_REVAPBE = 55[source]
                                                        +GGA_K_REVAPBE = 55[source]
                                                        -GGA_K_REVAPBEINT = 53[source]
                                                        +GGA_K_REVAPBEINT = 53[source]
                                                        -GGA_K_TFVW = 52[source]
                                                        +GGA_K_TFVW = 52[source]
                                                        -GGA_K_THAKKAR = 523[source]
                                                        +GGA_K_THAKKAR = 523[source]
                                                        -GGA_K_TW1 = 187[source]
                                                        +GGA_K_TW1 = 187[source]
                                                        -GGA_K_TW2 = 188[source]
                                                        +GGA_K_TW2 = 188[source]
                                                        -GGA_K_TW3 = 189[source]
                                                        +GGA_K_TW3 = 189[source]
                                                        -GGA_K_TW4 = 190[source]
                                                        +GGA_K_TW4 = 190[source]
                                                        -GGA_K_VJKS = 519[source]
                                                        +GGA_K_VJKS = 519[source]
                                                        -GGA_K_VSK = 518[source]
                                                        +GGA_K_VSK = 518[source]
                                                        -GGA_K_VW = 500[source]
                                                        +GGA_K_VW = 500[source]
                                                        -GGA_K_YT65 = 503[source]
                                                        +GGA_K_YT65 = 503[source]
                                                        -GGA_XC_B97_D = 170[source]
                                                        +GGA_XC_B97_D = 170[source]
                                                        -GGA_XC_B97_GGA1 = 96[source]
                                                        +GGA_XC_B97_GGA1 = 96[source]
                                                        -GGA_XC_EDF1 = 165[source]
                                                        +GGA_XC_EDF1 = 165[source]
                                                        -GGA_XC_HCTH_120 = 162[source]
                                                        +GGA_XC_HCTH_120 = 162[source]
                                                        -GGA_XC_HCTH_147 = 163[source]
                                                        +GGA_XC_HCTH_147 = 163[source]
                                                        -GGA_XC_HCTH_407 = 164[source]
                                                        +GGA_XC_HCTH_407 = 164[source]
                                                        -GGA_XC_HCTH_407P = 93[source]
                                                        +GGA_XC_HCTH_407P = 93[source]
                                                        -GGA_XC_HCTH_93 = 161[source]
                                                        +GGA_XC_HCTH_93 = 161[source]
                                                        -GGA_XC_HCTH_P14 = 95[source]
                                                        +GGA_XC_HCTH_P14 = 95[source]
                                                        -GGA_XC_HCTH_P76 = 94[source]
                                                        +GGA_XC_HCTH_P76 = 94[source]
                                                        -GGA_XC_KT2 = 146[source]
                                                        +GGA_XC_KT2 = 146[source]
                                                        -GGA_XC_MOHLYP = 194[source]
                                                        +GGA_XC_MOHLYP = 194[source]
                                                        -GGA_XC_MOHLYP2 = 195[source]
                                                        +GGA_XC_MOHLYP2 = 195[source]
                                                        -GGA_XC_MPWLYP1W = 174[source]
                                                        +GGA_XC_MPWLYP1W = 174[source]
                                                        -GGA_XC_OBLYP_D = 67[source]
                                                        +GGA_XC_OBLYP_D = 67[source]
                                                        -GGA_XC_OPBE_D = 65[source]
                                                        +GGA_XC_OPBE_D = 65[source]
                                                        -GGA_XC_OPWLYP_D = 66[source]
                                                        +GGA_XC_OPWLYP_D = 66[source]
                                                        -GGA_XC_PBE1W = 173[source]
                                                        +GGA_XC_PBE1W = 173[source]
                                                        -GGA_XC_PBELYP1W = 175[source]
                                                        +GGA_XC_PBELYP1W = 175[source]
                                                        -GGA_XC_TH1 = 154[source]
                                                        +GGA_XC_TH1 = 154[source]
                                                        -GGA_XC_TH2 = 155[source]
                                                        +GGA_XC_TH2 = 155[source]
                                                        -GGA_XC_TH3 = 156[source]
                                                        +GGA_XC_TH3 = 156[source]
                                                        -GGA_XC_TH4 = 157[source]
                                                        +GGA_XC_TH4 = 157[source]
                                                        -GGA_XC_TH_FC = 197[source]
                                                        +GGA_XC_TH_FC = 197[source]
                                                        -GGA_XC_TH_FCFO = 198[source]
                                                        +GGA_XC_TH_FCFO = 198[source]
                                                        -GGA_XC_TH_FCO = 199[source]
                                                        +GGA_XC_TH_FCO = 199[source]
                                                        -GGA_XC_TH_FL = 196[source]
                                                        +GGA_XC_TH_FL = 196[source]
                                                        -GGA_XC_VV10 = 255[source]
                                                        +GGA_XC_VV10 = 255[source]
                                                        -GGA_XC_XLYP = 166[source]
                                                        +GGA_XC_XLYP = 166[source]
                                                        -GGA_X_2D_B86 = 128[source]
                                                        +GGA_X_2D_B86 = 128[source]
                                                        -GGA_X_2D_B86_MGC = 124[source]
                                                        +GGA_X_2D_B86_MGC = 124[source]
                                                        -GGA_X_2D_B88 = 127[source]
                                                        +GGA_X_2D_B88 = 127[source]
                                                        -GGA_X_2D_PBE = 129[source]
                                                        +GGA_X_2D_PBE = 129[source]
                                                        -GGA_X_AIRY = 192[source]
                                                        +GGA_X_AIRY = 192[source]
                                                        -GGA_X_AK13 = 56[source]
                                                        +GGA_X_AK13 = 56[source]
                                                        -GGA_X_AM05 = 120[source]
                                                        +GGA_X_AM05 = 120[source]
                                                        -GGA_X_APBE = 184[source]
                                                        +GGA_X_APBE = 184[source]
                                                        -GGA_X_B86 = 103[source]
                                                        +GGA_X_B86 = 103[source]
                                                        -GGA_X_B86_MGC = 105[source]
                                                        +GGA_X_B86_MGC = 105[source]
                                                        -GGA_X_B86_R = 41[source]
                                                        +GGA_X_B86_R = 41[source]
                                                        -GGA_X_B88 = 106[source]
                                                        +GGA_X_B88 = 106[source]
                                                        -GGA_X_BAYESIAN = 125[source]
                                                        +GGA_X_BAYESIAN = 125[source]
                                                        -GGA_X_BGCP = 38[source]
                                                        +GGA_X_BGCP = 38[source]
                                                        -GGA_X_BPCCAC = 98[source]
                                                        +GGA_X_BPCCAC = 98[source]
                                                        -GGA_X_C09X = 158[source]
                                                        +GGA_X_C09X = 158[source]
                                                        -GGA_X_CAP = 270[source]
                                                        +GGA_X_CAP = 270[source]
                                                        -GGA_X_DK87_R1 = 111[source]
                                                        +GGA_X_DK87_R1 = 111[source]
                                                        -GGA_X_DK87_R2 = 112[source]
                                                        +GGA_X_DK87_R2 = 112[source]
                                                        -GGA_X_EV93 = 35[source]
                                                        +GGA_X_EV93 = 35[source]
                                                        -GGA_X_FT97_A = 114[source]
                                                        +GGA_X_FT97_A = 114[source]
                                                        -GGA_X_FT97_B = 115[source]
                                                        +GGA_X_FT97_B = 115[source]
                                                        -GGA_X_G96 = 107[source]
                                                        +GGA_X_G96 = 107[source]
                                                        -GGA_X_GAM = 32[source]
                                                        +GGA_X_GAM = 32[source]
                                                        -GGA_X_HCTH_A = 34[source]
                                                        +GGA_X_HCTH_A = 34[source]
                                                        -GGA_X_HERMAN = 104[source]
                                                        +GGA_X_HERMAN = 104[source]
                                                        -GGA_X_HJS_B88 = 527[source]
                                                        +GGA_X_HJS_B88 = 527[source]
                                                        -GGA_X_HJS_B88_V2 = 46[source]
                                                        +GGA_X_HJS_B88_V2 = 46[source]
                                                        -GGA_X_HJS_B97X = 528[source]
                                                        +GGA_X_HJS_B97X = 528[source]
                                                        -GGA_X_HJS_PBE = 525[source]
                                                        +GGA_X_HJS_PBE = 525[source]
                                                        -GGA_X_HJS_PBE_SOL = 526[source]
                                                        +GGA_X_HJS_PBE_SOL = 526[source]
                                                        -GGA_X_HTBS = 191[source]
                                                        +GGA_X_HTBS = 191[source]
                                                        -GGA_X_ITYH = 529[source]
                                                        +GGA_X_ITYH = 529[source]
                                                        -GGA_X_KT1 = 145[source]
                                                        +GGA_X_KT1 = 145[source]
                                                        -GGA_X_LAG = 193[source]
                                                        +GGA_X_LAG = 193[source]
                                                        -GGA_X_LAMBDA_CH_N = 44[source]
                                                        +GGA_X_LAMBDA_CH_N = 44[source]
                                                        -GGA_X_LAMBDA_LO_N = 45[source]
                                                        +GGA_X_LAMBDA_LO_N = 45[source]
                                                        -GGA_X_LAMBDA_OC2_N = 40[source]
                                                        +GGA_X_LAMBDA_OC2_N = 40[source]
                                                        -GGA_X_LB = 160[source]
                                                        +GGA_X_LB = 160[source]
                                                        -GGA_X_LBM = 182[source]
                                                        +GGA_X_LBM = 182[source]
                                                        -GGA_X_LG93 = 113[source]
                                                        +GGA_X_LG93 = 113[source]
                                                        -GGA_X_LV_RPW86 = 58[source]
                                                        +GGA_X_LV_RPW86 = 58[source]
                                                        -GGA_X_MB88 = 149[source]
                                                        +GGA_X_MB88 = 149[source]
                                                        -GGA_X_MPBE = 122[source]
                                                        +GGA_X_MPBE = 122[source]
                                                        -GGA_X_MPW91 = 119[source]
                                                        +GGA_X_MPW91 = 119[source]
                                                        -GGA_X_N12 = 82[source]
                                                        +GGA_X_N12 = 82[source]
                                                        -GGA_X_OL2 = 183[source]
                                                        +GGA_X_OL2 = 183[source]
                                                        -GGA_X_OPTB88_VDW = 139[source]
                                                        +GGA_X_OPTB88_VDW = 139[source]
                                                        -GGA_X_OPTPBE_VDW = 141[source]
                                                        +GGA_X_OPTPBE_VDW = 141[source]
                                                        -GGA_X_OPTX = 110[source]
                                                        +GGA_X_OPTX = 110[source]
                                                        -GGA_X_PBE = 101[source]
                                                        +GGA_X_PBE = 101[source]
                                                        -GGA_X_PBEA = 121[source]
                                                        +GGA_X_PBEA = 121[source]
                                                        -GGA_X_PBEFE = 265[source]
                                                        +GGA_X_PBEFE = 265[source]
                                                        -GGA_X_PBEINT = 60[source]
                                                        +GGA_X_PBEINT = 60[source]
                                                        -GGA_X_PBEK1_VDW = 140[source]
                                                        +GGA_X_PBEK1_VDW = 140[source]
                                                        -GGA_X_PBE_JSJR = 126[source]
                                                        +GGA_X_PBE_JSJR = 126[source]
                                                        -GGA_X_PBE_MOL = 49[source]
                                                        +GGA_X_PBE_MOL = 49[source]
                                                        -GGA_X_PBE_R = 102[source]
                                                        +GGA_X_PBE_R = 102[source]
                                                        -GGA_X_PBE_SOL = 116[source]
                                                        +GGA_X_PBE_SOL = 116[source]
                                                        -GGA_X_PBE_TCA = 59[source]
                                                        +GGA_X_PBE_TCA = 59[source]
                                                        -GGA_X_PW86 = 108[source]
                                                        +GGA_X_PW86 = 108[source]
                                                        -GGA_X_PW91 = 109[source]
                                                        +GGA_X_PW91 = 109[source]
                                                        -GGA_X_Q2D = 48[source]
                                                        +GGA_X_Q2D = 48[source]
                                                        -GGA_X_RGE2 = 142[source]
                                                        +GGA_X_RGE2 = 142[source]
                                                        -GGA_X_RPBE = 117[source]
                                                        +GGA_X_RPBE = 117[source]
                                                        -GGA_X_RPW86 = 144[source]
                                                        +GGA_X_RPW86 = 144[source]
                                                        -GGA_X_SFAT = 530[source]
                                                        +GGA_X_SFAT = 530[source]
                                                        -GGA_X_SOGGA = 150[source]
                                                        +GGA_X_SOGGA = 150[source]
                                                        -GGA_X_SOGGA11 = 151[source]
                                                        +GGA_X_SOGGA11 = 151[source]
                                                        -GGA_X_SSB = 91[source]
                                                        +GGA_X_SSB = 91[source]
                                                        -GGA_X_SSB_D = 92[source]
                                                        +GGA_X_SSB_D = 92[source]
                                                        -GGA_X_SSB_SW = 90[source]
                                                        +GGA_X_SSB_SW = 90[source]
                                                        -GGA_X_VMT84_GE = 68[source]
                                                        +GGA_X_VMT84_GE = 68[source]
                                                        -GGA_X_VMT84_PBE = 69[source]
                                                        +GGA_X_VMT84_PBE = 69[source]
                                                        -GGA_X_VMT_GE = 70[source]
                                                        +GGA_X_VMT_GE = 70[source]
                                                        -GGA_X_VMT_PBE = 71[source]
                                                        +GGA_X_VMT_PBE = 71[source]
                                                        -GGA_X_WC = 118[source]
                                                        +GGA_X_WC = 118[source]
                                                        -GGA_X_WPBEH = 524[source]
                                                        +GGA_X_WPBEH = 524[source]
                                                        -GGA_X_XPBE = 123[source]
                                                        +GGA_X_XPBE = 123[source]
                                                        -HYB_GGA_XC_B1LYP = 416[source]
                                                        +HYB_GGA_XC_B1LYP = 416[source]
                                                        -HYB_GGA_XC_B1PW91 = 417[source]
                                                        +HYB_GGA_XC_B1PW91 = 417[source]
                                                        -HYB_GGA_XC_B1WC = 412[source]
                                                        +HYB_GGA_XC_B1WC = 412[source]
                                                        -HYB_GGA_XC_B3LYP = 402[source]
                                                        +HYB_GGA_XC_B3LYP = 402[source]
                                                        -HYB_GGA_XC_B3LYP5 = 475[source]
                                                        +HYB_GGA_XC_B3LYP5 = 475[source]
                                                        -HYB_GGA_XC_B3LYPs = 459[source]
                                                        +HYB_GGA_XC_B3LYPs = 459[source]
                                                        -HYB_GGA_XC_B3P86 = 403[source]
                                                        +HYB_GGA_XC_B3P86 = 403[source]
                                                        -HYB_GGA_XC_B3PW91 = 401[source]
                                                        +HYB_GGA_XC_B3PW91 = 401[source]
                                                        -HYB_GGA_XC_B97 = 407[source]
                                                        +HYB_GGA_XC_B97 = 407[source]
                                                        -HYB_GGA_XC_B97_1 = 408[source]
                                                        +HYB_GGA_XC_B97_1 = 408[source]
                                                        -HYB_GGA_XC_B97_1p = 266[source]
                                                        +HYB_GGA_XC_B97_1p = 266[source]
                                                        -HYB_GGA_XC_B97_2 = 410[source]
                                                        +HYB_GGA_XC_B97_2 = 410[source]
                                                        -HYB_GGA_XC_B97_3 = 414[source]
                                                        +HYB_GGA_XC_B97_3 = 414[source]
                                                        -HYB_GGA_XC_B97_K = 413[source]
                                                        +HYB_GGA_XC_B97_K = 413[source]
                                                        -HYB_GGA_XC_BHANDH = 435[source]
                                                        +HYB_GGA_XC_BHANDH = 435[source]
                                                        -HYB_GGA_XC_BHANDHLYP = 436[source]
                                                        +HYB_GGA_XC_BHANDHLYP = 436[source]
                                                        -HYB_GGA_XC_CAMY_B3LYP = 470[source]
                                                        +HYB_GGA_XC_CAMY_B3LYP = 470[source]
                                                        -HYB_GGA_XC_CAMY_BLYP = 455[source]
                                                        +HYB_GGA_XC_CAMY_BLYP = 455[source]
                                                        -HYB_GGA_XC_CAM_B3LYP = 433[source]
                                                        +HYB_GGA_XC_CAM_B3LYP = 433[source]
                                                        -HYB_GGA_XC_CAP0 = 477[source]
                                                        +HYB_GGA_XC_CAP0 = 477[source]
                                                        -HYB_GGA_XC_EDF2 = 476[source]
                                                        +HYB_GGA_XC_EDF2 = 476[source]
                                                        -HYB_GGA_XC_HJS_B88 = 431[source]
                                                        +HYB_GGA_XC_HJS_B88 = 431[source]
                                                        -HYB_GGA_XC_HJS_B97X = 432[source]
                                                        +HYB_GGA_XC_HJS_B97X = 432[source]
                                                        -HYB_GGA_XC_HJS_PBE = 429[source]
                                                        +HYB_GGA_XC_HJS_PBE = 429[source]
                                                        -HYB_GGA_XC_HJS_PBE_SOL = 430[source]
                                                        +HYB_GGA_XC_HJS_PBE_SOL = 430[source]
                                                        -HYB_GGA_XC_HPBEINT = 472[source]
                                                        +HYB_GGA_XC_HPBEINT = 472[source]
                                                        -HYB_GGA_XC_HSE03 = 427[source]
                                                        +HYB_GGA_XC_HSE03 = 427[source]
                                                        -HYB_GGA_XC_HSE06 = 428[source]
                                                        +HYB_GGA_XC_HSE06 = 428[source]
                                                        -HYB_GGA_XC_LCY_BLYP = 468[source]
                                                        +HYB_GGA_XC_LCY_BLYP = 468[source]
                                                        -HYB_GGA_XC_LCY_PBE = 467[source]
                                                        +HYB_GGA_XC_LCY_PBE = 467[source]
                                                        -HYB_GGA_XC_LC_VV10 = 469[source]
                                                        +HYB_GGA_XC_LC_VV10 = 469[source]
                                                        -HYB_GGA_XC_LRC_WPBE = 473[source]
                                                        +HYB_GGA_XC_LRC_WPBE = 473[source]
                                                        -HYB_GGA_XC_LRC_WPBEH = 465[source]
                                                        +HYB_GGA_XC_LRC_WPBEH = 465[source]
                                                        -HYB_GGA_XC_MB3LYP_RC04 = 437[source]
                                                        +HYB_GGA_XC_MB3LYP_RC04 = 437[source]
                                                        -HYB_GGA_XC_MPW3LYP = 419[source]
                                                        +HYB_GGA_XC_MPW3LYP = 419[source]
                                                        -HYB_GGA_XC_MPW3PW = 415[source]
                                                        +HYB_GGA_XC_MPW3PW = 415[source]
                                                        -HYB_GGA_XC_MPWLYP1M = 453[source]
                                                        +HYB_GGA_XC_MPWLYP1M = 453[source]
                                                        -HYB_GGA_XC_O3LYP = 404[source]
                                                        +HYB_GGA_XC_O3LYP = 404[source]
                                                        -HYB_GGA_XC_PBE0_13 = 456[source]
                                                        +HYB_GGA_XC_PBE0_13 = 456[source]
                                                        -HYB_GGA_XC_PBEH = 406[source]
                                                        +HYB_GGA_XC_PBEH = 406[source]
                                                        -HYB_GGA_XC_REVB3LYP = 454[source]
                                                        +HYB_GGA_XC_REVB3LYP = 454[source]
                                                        -HYB_GGA_XC_SB98_1a = 420[source]
                                                        +HYB_GGA_XC_SB98_1a = 420[source]
                                                        -HYB_GGA_XC_SB98_1b = 421[source]
                                                        +HYB_GGA_XC_SB98_1b = 421[source]
                                                        -HYB_GGA_XC_SB98_1c = 422[source]
                                                        +HYB_GGA_XC_SB98_1c = 422[source]
                                                        -HYB_GGA_XC_SB98_2a = 423[source]
                                                        +HYB_GGA_XC_SB98_2a = 423[source]
                                                        -HYB_GGA_XC_SB98_2b = 424[source]
                                                        +HYB_GGA_XC_SB98_2b = 424[source]
                                                        -HYB_GGA_XC_SB98_2c = 425[source]
                                                        +HYB_GGA_XC_SB98_2c = 425[source]
                                                        -HYB_GGA_XC_TUNED_CAM_B3LYP = 434[source]
                                                        +HYB_GGA_XC_TUNED_CAM_B3LYP = 434[source]
                                                        -HYB_GGA_XC_WB97 = 463[source]
                                                        +HYB_GGA_XC_WB97 = 463[source]
                                                        -HYB_GGA_XC_WB97X = 464[source]
                                                        +HYB_GGA_XC_WB97X = 464[source]
                                                        -HYB_GGA_XC_WB97X_D = 471[source]
                                                        +HYB_GGA_XC_WB97X_D = 471[source]
                                                        -HYB_GGA_XC_WB97X_V = 466[source]
                                                        +HYB_GGA_XC_WB97X_V = 466[source]
                                                        -HYB_GGA_XC_X3LYP = 411[source]
                                                        +HYB_GGA_XC_X3LYP = 411[source]
                                                        -HYB_GGA_XC_mPW1K = 405[source]
                                                        +HYB_GGA_XC_mPW1K = 405[source]
                                                        -HYB_GGA_XC_mPW1PW = 418[source]
                                                        +HYB_GGA_XC_mPW1PW = 418[source]
                                                        -HYB_GGA_X_N12_SX = 81[source]
                                                        +HYB_GGA_X_N12_SX = 81[source]
                                                        -HYB_GGA_X_SOGGA11_X = 426[source]
                                                        +HYB_GGA_X_SOGGA11_X = 426[source]
                                                        -HYB_MGGA_XC_B86B95 = 441[source]
                                                        +HYB_MGGA_XC_B86B95 = 441[source]
                                                        -HYB_MGGA_XC_B88B95 = 440[source]
                                                        +HYB_MGGA_XC_B88B95 = 440[source]
                                                        -HYB_MGGA_XC_BB1K = 443[source]
                                                        +HYB_MGGA_XC_BB1K = 443[source]
                                                        -HYB_MGGA_XC_M05 = 438[source]
                                                        +HYB_MGGA_XC_M05 = 438[source]
                                                        -HYB_MGGA_XC_M05_2X = 439[source]
                                                        +HYB_MGGA_XC_M05_2X = 439[source]
                                                        -HYB_MGGA_XC_M06 = 449[source]
                                                        +HYB_MGGA_XC_M06 = 449[source]
                                                        -HYB_MGGA_XC_M06_2X = 450[source]
                                                        +HYB_MGGA_XC_M06_2X = 450[source]
                                                        -HYB_MGGA_XC_M06_HF = 444[source]
                                                        +HYB_MGGA_XC_M06_HF = 444[source]
                                                        -HYB_MGGA_XC_M08_HX = 460[source]
                                                        +HYB_MGGA_XC_M08_HX = 460[source]
                                                        -HYB_MGGA_XC_M08_SO = 461[source]
                                                        +HYB_MGGA_XC_M08_SO = 461[source]
                                                        -HYB_MGGA_XC_M11 = 462[source]
                                                        +HYB_MGGA_XC_M11 = 462[source]
                                                        -HYB_MGGA_XC_MPW1B95 = 445[source]
                                                        +HYB_MGGA_XC_MPW1B95 = 445[source]
                                                        -HYB_MGGA_XC_MPWB1K = 446[source]
                                                        +HYB_MGGA_XC_MPWB1K = 446[source]
                                                        -HYB_MGGA_XC_PW6B95 = 451[source]
                                                        +HYB_MGGA_XC_PW6B95 = 451[source]
                                                        -HYB_MGGA_XC_PW86B95 = 442[source]
                                                        +HYB_MGGA_XC_PW86B95 = 442[source]
                                                        -HYB_MGGA_XC_PWB6K = 452[source]
                                                        +HYB_MGGA_XC_PWB6K = 452[source]
                                                        -HYB_MGGA_XC_REVTPSSH = 458[source]
                                                        +HYB_MGGA_XC_REVTPSSH = 458[source]
                                                        -HYB_MGGA_XC_TPSSH = 457[source]
                                                        +HYB_MGGA_XC_TPSSH = 457[source]
                                                        -HYB_MGGA_XC_WB97M_V = 531[source]
                                                        +HYB_MGGA_XC_WB97M_V = 531[source]
                                                        -HYB_MGGA_XC_X1B95 = 447[source]
                                                        +HYB_MGGA_XC_X1B95 = 447[source]
                                                        -HYB_MGGA_XC_XB1K = 448[source]
                                                        +HYB_MGGA_XC_XB1K = 448[source]
                                                        -HYB_MGGA_X_DLDF = 36[source]
                                                        +HYB_MGGA_X_DLDF = 36[source]
                                                        -HYB_MGGA_X_MN12_SX = 248[source]
                                                        +HYB_MGGA_X_MN12_SX = 248[source]
                                                        -HYB_MGGA_X_MN15 = 268[source]
                                                        +HYB_MGGA_X_MN15 = 268[source]
                                                        -HYB_MGGA_X_MS2H = 224[source]
                                                        +HYB_MGGA_X_MS2H = 224[source]
                                                        -HYB_MGGA_X_MVSH = 474[source]
                                                        +HYB_MGGA_X_MVSH = 474[source]
                                                        -HYB_MGGA_X_SCAN0 = 264[source]
                                                        +HYB_MGGA_X_SCAN0 = 264[source]
                                                        -LDA_C_1D_CSC = 18[source]
                                                        +LDA_C_1D_CSC = 18[source]
                                                        -LDA_C_1D_LOOS = 26[source]
                                                        +LDA_C_1D_LOOS = 26[source]
                                                        -LDA_C_2D_AMGB = 15[source]
                                                        +LDA_C_2D_AMGB = 15[source]
                                                        -LDA_C_2D_PRM = 16[source]
                                                        +LDA_C_2D_PRM = 16[source]
                                                        -LDA_C_GL = 5[source]
                                                        +LDA_C_GL = 5[source]
                                                        -LDA_C_GOMBAS = 24[source]
                                                        +LDA_C_GOMBAS = 24[source]
                                                        -LDA_C_HL = 4[source]
                                                        +LDA_C_HL = 4[source]
                                                        -LDA_C_ML1 = 22[source]
                                                        +LDA_C_ML1 = 22[source]
                                                        -LDA_C_ML2 = 23[source]
                                                        +LDA_C_ML2 = 23[source]
                                                        -LDA_C_OB_PW = 14[source]
                                                        +LDA_C_OB_PW = 14[source]
                                                        -LDA_C_OB_PZ = 11[source]
                                                        +LDA_C_OB_PZ = 11[source]
                                                        -LDA_C_PW = 12[source]
                                                        +LDA_C_PW = 12[source]
                                                        -LDA_C_PW_MOD = 13[source]
                                                        +LDA_C_PW_MOD = 13[source]
                                                        -LDA_C_PW_RPA = 25[source]
                                                        +LDA_C_PW_RPA = 25[source]
                                                        -LDA_C_PZ = 9[source]
                                                        +LDA_C_PZ = 9[source]
                                                        -LDA_C_PZ_MOD = 10[source]
                                                        +LDA_C_PZ_MOD = 10[source]
                                                        -LDA_C_RC04 = 27[source]
                                                        +LDA_C_RC04 = 27[source]
                                                        -LDA_C_RPA = 3[source]
                                                        +LDA_C_RPA = 3[source]
                                                        -LDA_C_VWN = 7[source]
                                                        +LDA_C_VWN = 7[source]
                                                        -LDA_C_VWN_1 = 28[source]
                                                        +LDA_C_VWN_1 = 28[source]
                                                        -LDA_C_VWN_2 = 29[source]
                                                        +LDA_C_VWN_2 = 29[source]
                                                        -LDA_C_VWN_3 = 30[source]
                                                        +LDA_C_VWN_3 = 30[source]
                                                        -LDA_C_VWN_4 = 31[source]
                                                        +LDA_C_VWN_4 = 31[source]
                                                        -LDA_C_VWN_RPA = 8[source]
                                                        +LDA_C_VWN_RPA = 8[source]
                                                        -LDA_C_WIGNER = 2[source]
                                                        +LDA_C_WIGNER = 2[source]
                                                        -LDA_C_XALPHA = 6[source]
                                                        +LDA_C_XALPHA = 6[source]
                                                        -LDA_C_vBH = 17[source]
                                                        +LDA_C_vBH = 17[source]
                                                        -LDA_K_LP = 51[source]
                                                        +LDA_K_LP = 51[source]
                                                        -LDA_K_TF = 50[source]
                                                        +LDA_K_TF = 50[source]
                                                        -LDA_X = 1[source]
                                                        +LDA_X = 1[source]
                                                        -LDA_XC_KSDT = 259[source]
                                                        +LDA_XC_KSDT = 259[source]
                                                        -LDA_XC_TETER93 = 20[source]
                                                        +LDA_XC_TETER93 = 20[source]
                                                        -LDA_XC_ZLP = 43[source]
                                                        +LDA_XC_ZLP = 43[source]
                                                        -LDA_X_1D = 21[source]
                                                        +LDA_X_1D = 21[source]
                                                        -LDA_X_2D = 19[source]
                                                        +LDA_X_2D = 19[source]
                                                        -MGGA_C_BC95 = 240[source]
                                                        +MGGA_C_BC95 = 240[source]
                                                        -MGGA_C_CC06 = 229[source]
                                                        +MGGA_C_CC06 = 229[source]
                                                        -MGGA_C_CS = 72[source]
                                                        +MGGA_C_CS = 72[source]
                                                        -MGGA_C_DLDF = 37[source]
                                                        +MGGA_C_DLDF = 37[source]
                                                        -MGGA_C_M05 = 237[source]
                                                        +MGGA_C_M05 = 237[source]
                                                        -MGGA_C_M05_2X = 238[source]
                                                        +MGGA_C_M05_2X = 238[source]
                                                        -MGGA_C_M06 = 235[source]
                                                        +MGGA_C_M06 = 235[source]
                                                        -MGGA_C_M06_2X = 236[source]
                                                        +MGGA_C_M06_2X = 236[source]
                                                        -MGGA_C_M06_HF = 234[source]
                                                        +MGGA_C_M06_HF = 234[source]
                                                        -MGGA_C_M06_L = 233[source]
                                                        +MGGA_C_M06_L = 233[source]
                                                        -MGGA_C_M08_HX = 78[source]
                                                        +MGGA_C_M08_HX = 78[source]
                                                        -MGGA_C_M08_SO = 77[source]
                                                        +MGGA_C_M08_SO = 77[source]
                                                        -MGGA_C_M11 = 76[source]
                                                        +MGGA_C_M11 = 76[source]
                                                        -MGGA_C_M11_L = 75[source]
                                                        +MGGA_C_M11_L = 75[source]
                                                        -MGGA_C_MN12_L = 74[source]
                                                        +MGGA_C_MN12_L = 74[source]
                                                        -MGGA_C_MN12_SX = 73[source]
                                                        +MGGA_C_MN12_SX = 73[source]
                                                        -MGGA_C_MN15 = 269[source]
                                                        +MGGA_C_MN15 = 269[source]
                                                        -MGGA_C_MN15_L = 261[source]
                                                        +MGGA_C_MN15_L = 261[source]
                                                        -MGGA_C_PKZB = 239[source]
                                                        +MGGA_C_PKZB = 239[source]
                                                        -MGGA_C_REVTPSS = 241[source]
                                                        +MGGA_C_REVTPSS = 241[source]
                                                        -MGGA_C_SCAN = 267[source]
                                                        +MGGA_C_SCAN = 267[source]
                                                        -MGGA_C_TPSS = 231[source]
                                                        +MGGA_C_TPSS = 231[source]
                                                        -MGGA_C_TPSSLOC = 247[source]
                                                        +MGGA_C_TPSSLOC = 247[source]
                                                        -MGGA_C_VSXC = 232[source]
                                                        +MGGA_C_VSXC = 232[source]
                                                        -MGGA_XC_B97M_V = 254[source]
                                                        +MGGA_XC_B97M_V = 254[source]
                                                        -MGGA_XC_OTPSS_D = 64[source]
                                                        +MGGA_XC_OTPSS_D = 64[source]
                                                        -MGGA_XC_TPSSLYP1W = 242[source]
                                                        +MGGA_XC_TPSSLYP1W = 242[source]
                                                        -MGGA_XC_ZLP = 42[source]
                                                        +MGGA_XC_ZLP = 42[source]
                                                        -MGGA_X_2D_PRHG07 = 210[source]
                                                        +MGGA_X_2D_PRHG07 = 210[source]
                                                        -MGGA_X_2D_PRHG07_PRP10 = 211[source]
                                                        +MGGA_X_2D_PRHG07_PRP10 = 211[source]
                                                        -MGGA_X_BJ06 = 207[source]
                                                        +MGGA_X_BJ06 = 207[source]
                                                        -MGGA_X_BLOC = 244[source]
                                                        +MGGA_X_BLOC = 244[source]
                                                        -MGGA_X_BR89 = 206[source]
                                                        +MGGA_X_BR89 = 206[source]
                                                        -MGGA_X_GVT4 = 204[source]
                                                        +MGGA_X_GVT4 = 204[source]
                                                        -MGGA_X_LTA = 201[source]
                                                        +MGGA_X_LTA = 201[source]
                                                        -MGGA_X_M05 = 214[source]
                                                        +MGGA_X_M05 = 214[source]
                                                        -MGGA_X_M05_2X = 215[source]
                                                        +MGGA_X_M05_2X = 215[source]
                                                        -MGGA_X_M06 = 217[source]
                                                        +MGGA_X_M06 = 217[source]
                                                        -MGGA_X_M06_2X = 218[source]
                                                        +MGGA_X_M06_2X = 218[source]
                                                        -MGGA_X_M06_HF = 216[source]
                                                        +MGGA_X_M06_HF = 216[source]
                                                        -MGGA_X_M06_L = 203[source]
                                                        +MGGA_X_M06_L = 203[source]
                                                        -MGGA_X_M08_HX = 219[source]
                                                        +MGGA_X_M08_HX = 219[source]
                                                        -MGGA_X_M08_SO = 220[source]
                                                        +MGGA_X_M08_SO = 220[source]
                                                        -MGGA_X_M11 = 225[source]
                                                        +MGGA_X_M11 = 225[source]
                                                        -MGGA_X_M11_L = 226[source]
                                                        +MGGA_X_M11_L = 226[source]
                                                        -MGGA_X_MBEEF = 249[source]
                                                        +MGGA_X_MBEEF = 249[source]
                                                        -MGGA_X_MBEEFVDW = 250[source]
                                                        +MGGA_X_MBEEFVDW = 250[source]
                                                        -MGGA_X_MK00 = 230[source]
                                                        +MGGA_X_MK00 = 230[source]
                                                        -MGGA_X_MK00B = 243[source]
                                                        +MGGA_X_MK00B = 243[source]
                                                        -MGGA_X_MN12_L = 227[source]
                                                        +MGGA_X_MN12_L = 227[source]
                                                        -MGGA_X_MN15_L = 260[source]
                                                        +MGGA_X_MN15_L = 260[source]
                                                        -MGGA_X_MODTPSS = 245[source]
                                                        +MGGA_X_MODTPSS = 245[source]
                                                        -MGGA_X_MS0 = 221[source]
                                                        +MGGA_X_MS0 = 221[source]
                                                        -MGGA_X_MS1 = 222[source]
                                                        +MGGA_X_MS1 = 222[source]
                                                        -MGGA_X_MS2 = 223[source]
                                                        +MGGA_X_MS2 = 223[source]
                                                        -MGGA_X_MVS = 257[source]
                                                        +MGGA_X_MVS = 257[source]
                                                        -MGGA_X_PKZB = 213[source]
                                                        +MGGA_X_PKZB = 213[source]
                                                        -MGGA_X_REVTPSS = 212[source]
                                                        +MGGA_X_REVTPSS = 212[source]
                                                        -MGGA_X_RPP09 = 209[source]
                                                        +MGGA_X_RPP09 = 209[source]
                                                        -MGGA_X_SCAN = 263[source]
                                                        +MGGA_X_SCAN = 263[source]
                                                        -MGGA_X_TAU_HCTH = 205[source]
                                                        +MGGA_X_TAU_HCTH = 205[source]
                                                        -MGGA_X_TB09 = 208[source]
                                                        +MGGA_X_TB09 = 208[source]
                                                        -MGGA_X_TPSS = 202[source]
                                                        +MGGA_X_TPSS = 202[source]
                                                        -static all_families()[source]
                                                        +static all_families()[source]

                                                        List of strings with the libxc families. Note that XC_FAMILY if removed from the string e.g. XC_FAMILY_LDA becomes LDA

                                                        -static all_kinds()[source]
                                                        +static all_kinds()[source]

                                                        List of strings with the libxc kinds. Also in this case, the string is obtained by remove the XC_ prefix. XC_CORRELATION –> CORRELATION

                                                        @@ -1961,81 +1961,81 @@
                                                        -as_dict()[source]
                                                        +as_dict()[source]

                                                        Makes LibxcFunc obey the general json interface used in pymatgen for easier serialization.

                                                        -static from_dict(d)[source]
                                                        +static from_dict(d)[source]

                                                        Makes LibxcFunc obey the general json interface used in pymatgen for easier serialization.

                                                        -property info_dict[source]
                                                        +property info_dict[source]

                                                        Dictionary with metadata. see libxc_docs.json

                                                        -property is_c_kind[source]
                                                        +property is_c_kind[source]

                                                        True if this is a correlation-only functional

                                                        -property is_gga_family[source]
                                                        +property is_gga_family[source]

                                                        True if this functional belongs to the GGA family.

                                                        -property is_hyb_gga_family[source]
                                                        +property is_hyb_gga_family[source]

                                                        True if this functional belongs to the hybrid + GGA family.

                                                        -property is_hyb_mgga_family[source]
                                                        +property is_hyb_mgga_family[source]

                                                        True if this functional belongs to the hybrid + meta-GGA family.

                                                        -property is_k_kind[source]
                                                        +property is_k_kind[source]

                                                        True if this is a kinetic functional

                                                        -property is_lda_family[source]
                                                        +property is_lda_family[source]

                                                        True if this functional belongs to the LDA family.

                                                        -property is_mgga_family[source]
                                                        +property is_mgga_family[source]

                                                        True if this functional belongs to the meta-GGA family.

                                                        -property is_x_kind[source]
                                                        +property is_x_kind[source]

                                                        True if this is an exchange-only functional

                                                        -property is_xc_kind[source]
                                                        +property is_xc_kind[source]

                                                        True if this is a exchange+correlation functional

                                                        -to_json()[source]
                                                        +to_json()[source]

                                                        Returns a json string representation of the MSONable object.

                                                        diff --git a/docs/pymatgen.core.molecular_orbitals.html b/docs/pymatgen.core.molecular_orbitals.html index ad89b938ad0..37712373ec8 100644 --- a/docs/pymatgen.core.molecular_orbitals.html +++ b/docs/pymatgen.core.molecular_orbitals.html @@ -4,7 +4,7 @@ - pymatgen.core.molecular_orbitals module — pymatgen 2022.5.18 documentation + pymatgen.core.molecular_orbitals module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                        - 2022.5.18 + 2022.5.18.1
                                                        @@ -119,7 +119,7 @@ solids. Useful for predicting PDOS character from structural information.

                                                        -class MolecularOrbitals(formula)[source]
                                                        +class MolecularOrbitals(formula)[source]

                                                        Bases: object

                                                        Represents the character of bands in a solid. The input is a chemical formula, since no structural characteristics are taken into account.

                                                        @@ -145,33 +145,33 @@
                                                        -composition[source]
                                                        +composition[source]

                                                        the composition as a dictionary. Ex: {‘Sr’: 1, ‘Ti’: 1, ‘O’, 3}

                                                        -elements[source]
                                                        +elements[source]

                                                        the dictionary keys for the composition

                                                        -elec_neg[source]
                                                        +elec_neg[source]

                                                        the maximum pairwise electronegativity difference

                                                        -aos[source]
                                                        +aos[source]

                                                        the consituant atomic orbitals for each element as a dictionary

                                                        -band_edges[source]
                                                        +band_edges[source]

                                                        dictionary containing the highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), and whether the material is predicted to be a @@ -180,7 +180,7 @@

                                                        -aos_as_list()[source]
                                                        +aos_as_list()[source]
                                                        Returns

                                                        A list of atomic orbitals, sorted from lowest to highest energy.

                                                        @@ -197,7 +197,7 @@
                                                        -max_electronegativity()[source]
                                                        +max_electronegativity()[source]
                                                        Returns

                                                        The maximum pairwise electronegativity difference.

                                                        @@ -207,7 +207,7 @@
                                                        -obtain_band_edges()[source]
                                                        +obtain_band_edges()[source]

                                                        Fill up the atomic orbitals with available electrons. :returns: HOMO, LUMO, and whether it’s a metal.

                                                        diff --git a/docs/pymatgen.core.operations.html b/docs/pymatgen.core.operations.html index 2f9d17b8b62..a9ae500a273 100644 --- a/docs/pymatgen.core.operations.html +++ b/docs/pymatgen.core.operations.html @@ -4,7 +4,7 @@ - pymatgen.core.operations module — pymatgen 2022.5.18 documentation + pymatgen.core.operations module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                        - 2022.5.18 + 2022.5.18.1
                                                        @@ -118,7 +118,7 @@

                                                        This module provides classes that operate on points or vectors in 3D space.

                                                        -class MagSymmOp(affine_transformation_matrix: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], time_reversal: int, tol: float = 0.01)[source]
                                                        +class MagSymmOp(affine_transformation_matrix: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], time_reversal: int, tol: float = 0.01)[source]

                                                        Bases: pymatgen.core.operations.SymmOp

                                                        Thin wrapper around SymmOp to extend it to support magnetic symmetry by including a time reversal operator. Magnetic symmetry is similar @@ -142,7 +142,7 @@

                                                        -as_dict() → dict[source]
                                                        +as_dict() → dict[source]
                                                        Returns

                                                        MSONABle dict

                                                        @@ -152,14 +152,14 @@
                                                        -as_xyzt_string() → str[source]
                                                        +as_xyzt_string() → str[source]

                                                        Returns a string of the form ‘x, y, z, +1’, ‘-x, -y, z, -1’, ‘-y+1/2, x+1/2, z+1/2, +1’, etc. Only works for integer rotation matrices

                                                        -classmethod from_dict(d: dict) → pymatgen.core.operations.MagSymmOp[source]
                                                        +classmethod from_dict(d: dict) → pymatgen.core.operations.MagSymmOp[source]
                                                        Parameters

                                                        d – dict

                                                        @@ -172,7 +172,7 @@
                                                        -static from_rotation_and_translation_and_time_reversal(rotation_matrix: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]] = ((1, 0, 0), (0, 1, 0), (0, 0, 1)), translation_vec: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]] = (0, 0, 0), time_reversal: int = 1, tol: float = 0.1) → pymatgen.core.operations.MagSymmOp[source]
                                                        +static from_rotation_and_translation_and_time_reversal(rotation_matrix: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]] = ((1, 0, 0), (0, 1, 0), (0, 0, 1)), translation_vec: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]] = (0, 0, 0), time_reversal: int = 1, tol: float = 0.1) → pymatgen.core.operations.MagSymmOp[source]

                                                        Creates a symmetry operation from a rotation matrix, translation vector and time reversal operator.

                                                        @@ -192,7 +192,7 @@
                                                        -classmethod from_symmop(symmop, time_reversal) → pymatgen.core.operations.MagSymmOp[source]
                                                        +classmethod from_symmop(symmop, time_reversal) → pymatgen.core.operations.MagSymmOp[source]

                                                        Initialize a MagSymmOp from a SymmOp and time reversal operator.

                                                        Parameters
                                                        @@ -209,7 +209,7 @@
                                                        -static from_xyzt_string(xyzt_string: str) → pymatgen.core.operations.MagSymmOp[source]
                                                        +static from_xyzt_string(xyzt_string: str) → pymatgen.core.operations.MagSymmOp[source]
                                                        Parameters

                                                        xyz_string – string of the form ‘x, y, z, +1’, ‘-x, -y, z, -1’, @@ -223,7 +223,7 @@

                                                        -operate_magmom(magmom)[source]
                                                        +operate_magmom(magmom)[source]

                                                        Apply time reversal operator on the magnetic moment. Note that magnetic moments transform as axial vectors, not polar vectors.

                                                        See ‘Symmetry and magnetic structures’, Rodríguez-Carvajal and @@ -245,14 +245,14 @@

                                                        -class SymmOp(affine_transformation_matrix: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], tol=0.01)[source]
                                                        +class SymmOp(affine_transformation_matrix: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], tol=0.01)[source]

                                                        Bases: monty.json.MSONable

                                                        A symmetry operation in Cartesian space. Consists of a rotation plus a translation. Implementation is as an affine transformation matrix of rank 4 for efficiency. Read: http://en.wikipedia.org/wiki/Affine_transformation.

                                                        -affine_matrix[source]
                                                        +affine_matrix[source]

                                                        A 4x4 numpy.array representing the symmetry operation.

                                                        @@ -271,7 +271,7 @@
                                                        -apply_rotation_only(vector: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]])[source]
                                                        +apply_rotation_only(vector: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]])[source]

                                                        Vectors should only be operated by the rotation matrix and not the translation vector.

                                                        @@ -283,7 +283,7 @@
                                                        +are_symmetrically_related(point_a: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], point_b: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], tol: float = 0.001) → bool[source]

                                                        Checks if two points are symmetrically related.

                                                        Parameters
                                                        @@ -301,7 +301,7 @@
                                                        +are_symmetrically_related_vectors(from_a: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], to_a: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], r_a: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], from_b: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], to_b: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], r_b: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], tol: float = 0.001) → tuple[bool, bool][source]

                                                        Checks if two vectors, or rather two vectors that connect two points each are symmetrically related. r_a and r_b give the change of unit cells. Two vectors are also considered symmetrically equivalent if starting @@ -326,7 +326,7 @@

                                                        -as_dict() → dict[source]
                                                        +as_dict() → dict[source]
                                                        Returns

                                                        MSONAble dict.

                                                        @@ -336,14 +336,14 @@
                                                        -as_xyz_string() → str[source]
                                                        +as_xyz_string() → str[source]

                                                        Returns a string of the form ‘x, y, z’, ‘-x, -y, z’, ‘-y+1/2, x+1/2, z+1/2’, etc. Only works for integer rotation matrices

                                                        -static from_axis_angle_and_translation(axis: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], angle: float, angle_in_radians: bool = False, translation_vec: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]] = (0, 0, 0)) → pymatgen.core.operations.SymmOp[source]
                                                        +static from_axis_angle_and_translation(axis: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], angle: float, angle_in_radians: bool = False, translation_vec: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]] = (0, 0, 0)) → pymatgen.core.operations.SymmOp[source]

                                                        Generates a SymmOp for a rotation about a given axis plus translation.

                                                        Parameters
                                                        @@ -364,7 +364,7 @@
                                                        -classmethod from_dict(d) → pymatgen.core.operations.SymmOp[source]
                                                        +classmethod from_dict(d) → pymatgen.core.operations.SymmOp[source]
                                                        Parameters

                                                        d – dict

                                                        @@ -377,7 +377,7 @@
                                                        -static from_origin_axis_angle(origin: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], axis: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], angle: float, angle_in_radians: bool = False) → pymatgen.core.operations.SymmOp[source]
                                                        +static from_origin_axis_angle(origin: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], axis: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], angle: float, angle_in_radians: bool = False) → pymatgen.core.operations.SymmOp[source]

                                                        Generates a SymmOp for a rotation about a given axis through an origin.

                                                        @@ -399,7 +399,7 @@
                                                        -static from_rotation_and_translation(rotation_matrix: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]] = ((1, 0, 0), (0, 1, 0), (0, 0, 1)), translation_vec: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]] = (0, 0, 0), tol=0.1)[source]
                                                        +static from_rotation_and_translation(rotation_matrix: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]] = ((1, 0, 0), (0, 1, 0), (0, 0, 1)), translation_vec: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]] = (0, 0, 0), tol=0.1)[source]

                                                        Creates a symmetry operation from a rotation matrix and a translation vector.

                                                        @@ -418,7 +418,7 @@
                                                        -static from_xyz_string(xyz_string: str) → pymatgen.core.operations.SymmOp[source]
                                                        +static from_xyz_string(xyz_string: str) → pymatgen.core.operations.SymmOp[source]
                                                        Parameters

                                                        xyz_string – string of the form ‘x, y, z’, ‘-x, -y, z’, @@ -432,13 +432,13 @@

                                                        -property inverse: pymatgen.core.operations.SymmOp[source]
                                                        +property inverse: pymatgen.core.operations.SymmOp[source]

                                                        Returns inverse of transformation.

                                                        -static inversion(origin: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]] = (0, 0, 0)) → pymatgen.core.operations.SymmOp[source]
                                                        +static inversion(origin: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]] = (0, 0, 0)) → pymatgen.core.operations.SymmOp[source]

                                                        Inversion symmetry operation about axis.

                                                        Parameters
                                                        @@ -453,7 +453,7 @@
                                                        -operate(point)[source]
                                                        +operate(point)[source]

                                                        Apply the operation on a point.

                                                        Parameters
                                                        @@ -467,7 +467,7 @@
                                                        -operate_multi(points)[source]
                                                        +operate_multi(points)[source]

                                                        Apply the operation on a list of points.

                                                        Parameters
                                                        @@ -481,7 +481,7 @@
                                                        -static reflection(normal: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], origin: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]] = (0, 0, 0)) → pymatgen.core.operations.SymmOp[source]
                                                        +static reflection(normal: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], origin: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]] = (0, 0, 0)) → pymatgen.core.operations.SymmOp[source]

                                                        Returns reflection symmetry operation.

                                                        Parameters
                                                        @@ -500,13 +500,13 @@
                                                        -property rotation_matrix: numpy.ndarray[source]
                                                        +property rotation_matrix: numpy.ndarray[source]

                                                        A 3x3 numpy.array representing the rotation matrix.

                                                        -static rotoreflection(axis: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], angle: float, origin: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]] = (0, 0, 0)) → pymatgen.core.operations.SymmOp[source]
                                                        +static rotoreflection(axis: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], angle: float, origin: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]] = (0, 0, 0)) → pymatgen.core.operations.SymmOp[source]

                                                        Returns a roto-reflection symmetry operation

                                                        Parameters
                                                        @@ -525,7 +525,7 @@
                                                        -transform_tensor(tensor: numpy.ndarray)[source]
                                                        +transform_tensor(tensor: numpy.ndarray)[source]

                                                        Applies rotation portion to a tensor. Note that tensor has to be in full form, not the Voigt form.

                                                        @@ -540,7 +540,7 @@
                                                        -property translation_vector: numpy.ndarray[source]
                                                        +property translation_vector: numpy.ndarray[source]

                                                        A rank 1 numpy.array of dim 3 representing the translation vector.

                                                        diff --git a/docs/pymatgen.core.periodic_table.html b/docs/pymatgen.core.periodic_table.html index 2e970b29719..81fb5f524f3 100644 --- a/docs/pymatgen.core.periodic_table.html +++ b/docs/pymatgen.core.periodic_table.html @@ -4,7 +4,7 @@ - pymatgen.core.periodic_table module — pymatgen 2022.5.18 documentation + pymatgen.core.periodic_table module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                        - 2022.5.18 + 2022.5.18.1
                                                        @@ -118,7 +118,7 @@

                                                        Module contains classes presenting Element and Species (Element + oxidation state) and PeriodicTable.

                                                        -class DummySpecie(symbol: str = 'X', oxidation_state: float | None = 0, properties: dict | None = None)[source]
                                                        +class DummySpecie(symbol: str = 'X', oxidation_state: float | None = 0, properties: dict | None = None)[source]

                                                        Bases: pymatgen.core.periodic_table.DummySpecies

                                                        This maps the historical grammatically inaccurate DummySpecie to DummySpecies to maintain backwards compatibility.

                                                        @@ -140,20 +140,20 @@
                                                        -class DummySpecies(symbol: str = 'X', oxidation_state: float | None = 0, properties: dict | None = None)[source]
                                                        +class DummySpecies(symbol: str = 'X', oxidation_state: float | None = 0, properties: dict | None = None)[source]

                                                        Bases: pymatgen.core.periodic_table.Species

                                                        A special specie for representing non-traditional elements or species. For example, representation of vacancies (charged or otherwise), or special sites, etc.

                                                        -oxi_state[source]
                                                        +oxi_state[source]

                                                        Oxidation state associated with Species.

                                                        -Z[source]
                                                        +Z[source]

                                                        DummySpecies is always assigned an atomic number equal to the hash number of the symbol. Obviously, it makes no sense whatsoever to use the atomic number of a Dummy specie for anything scientific. The purpose @@ -163,7 +163,7 @@

                                                        -X[source]
                                                        +X[source]

                                                        DummySpecies is always assigned an electronegativity of 0.

                                                        @@ -183,14 +183,14 @@
                                                        -property X: float[source]
                                                        +property X: float[source]

                                                        DummySpecies is always assigned an electronegativity of 0. The effect of this is that DummySpecies are always sorted in front of actual Species.

                                                        -property Z: int[source]
                                                        +property Z: int[source]

                                                        DummySpecies is always assigned an atomic number equal to the hash of the symbol. The expectation is that someone would be an actual dummy to use atomic numbers for a Dummy specie.

                                                        @@ -198,7 +198,7 @@
                                                        -as_dict() → dict[source]
                                                        +as_dict() → dict[source]
                                                        Returns

                                                        MSONAble dict representation.

                                                        @@ -208,7 +208,7 @@
                                                        -classmethod from_dict(d) → pymatgen.core.periodic_table.DummySpecies[source]
                                                        +classmethod from_dict(d) → pymatgen.core.periodic_table.DummySpecies[source]
                                                        Parameters

                                                        d – Dict representation

                                                        @@ -221,7 +221,7 @@
                                                        -static from_string(species_string: str) → pymatgen.core.periodic_table.DummySpecies[source]
                                                        +static from_string(species_string: str) → pymatgen.core.periodic_table.DummySpecies[source]

                                                        Returns a Dummy from a string representation.

                                                        Parameters
                                                        @@ -239,13 +239,13 @@
                                                        -property oxi_state: float | None[source]
                                                        +property oxi_state: float | None[source]

                                                        Oxidation state associated with DummySpecies

                                                        -property symbol: str[source]
                                                        +property symbol: str[source]

                                                        Symbol for DummySpecies.

                                                        Type
                                                        @@ -258,7 +258,7 @@
                                                        -class Element(value)[source]
                                                        +class Element(value)[source]

                                                        Bases: pymatgen.core.periodic_table.ElementBase

                                                        Enum representing an element in the periodic table.

                                                        Basic immutable element object with all relevant properties.

                                                        @@ -273,25 +273,25 @@
                                                        -Z[source]
                                                        +Z[source]

                                                        Atomic number

                                                        -symbol[source]
                                                        +symbol[source]

                                                        Element symbol

                                                        -long_name[source]
                                                        +long_name[source]

                                                        Long name for element. E.g., “Hydrogen”.

                                                        -atomic_radius_calculated[source]
                                                        +atomic_radius_calculated[source]

                                                        Calculated atomic radius for the element. This is the empirical value. Data is obtained from http://en.wikipedia.org/wiki/Atomic_radii_of_the_elements_(data_page).

                                                        @@ -299,7 +299,7 @@
                                                        -van_der_waals_radius[source]
                                                        +van_der_waals_radius[source]

                                                        Van der Waals radius for the element. This is the empirical value determined from critical reviews of X-ray diffraction, gas kinetic collision cross-section, and other experimental data by Bondi and later @@ -313,7 +313,7 @@

                                                        -mendeleev_no[source]
                                                        +mendeleev_no[source]

                                                        Mendeleev number from definition given by Pettifor, D. G. (1984). A chemical scale for crystal-structure maps. Solid State Communications, 51 (1), 31-34

                                                        @@ -321,43 +321,43 @@
                                                        -electrical_resistivity[source]
                                                        +electrical_resistivity[source]

                                                        Electrical resistivity

                                                        -velocity_of_sound[source]
                                                        +velocity_of_sound[source]

                                                        Velocity of sound

                                                        -reflectivity[source]
                                                        +reflectivity[source]

                                                        Reflectivity

                                                        -refractive_index[source]
                                                        +refractive_index[source]

                                                        Refractice index

                                                        -poissons_ratio[source]
                                                        +poissons_ratio[source]

                                                        Poisson’s ratio

                                                        -molar_volume[source]
                                                        +molar_volume[source]

                                                        Molar volume

                                                        -electronic_structure[source]
                                                        +electronic_structure[source]

                                                        Electronic structure. E.g., The electronic structure for Fe is represented as [Ar].3d6.4s2

                                                        @@ -365,7 +365,7 @@
                                                        -atomic_orbitals[source]
                                                        +atomic_orbitals[source]

                                                        Atomic Orbitals. Energy of the atomic orbitals as a dict. E.g., The orbitals energies in eV are represented as {‘1s’: -1.0, ‘2s’: -0.1} @@ -376,97 +376,97 @@

                                                        -thermal_conductivity[source]
                                                        +thermal_conductivity[source]

                                                        Thermal conductivity

                                                        -boiling_point[source]
                                                        +boiling_point[source]

                                                        Boiling point

                                                        -melting_point[source]
                                                        +melting_point[source]

                                                        Melting point

                                                        -critical_temperature[source]
                                                        +critical_temperature[source]

                                                        Critical temperature

                                                        -superconduction_temperature[source]
                                                        +superconduction_temperature[source]

                                                        Superconduction temperature

                                                        -liquid_range[source]
                                                        +liquid_range[source]

                                                        Liquid range

                                                        -bulk_modulus[source]
                                                        +bulk_modulus[source]

                                                        Bulk modulus

                                                        -youngs_modulus[source]
                                                        +youngs_modulus[source]

                                                        Young’s modulus

                                                        -brinell_hardness[source]
                                                        +brinell_hardness[source]

                                                        Brinell hardness

                                                        -rigidity_modulus[source]
                                                        +rigidity_modulus[source]

                                                        Rigidity modulus

                                                        -mineral_hardness[source]
                                                        +mineral_hardness[source]

                                                        Mineral hardness

                                                        -vickers_hardness[source]
                                                        +vickers_hardness[source]

                                                        Vicker’s hardness

                                                        -density_of_solid[source]
                                                        +density_of_solid[source]

                                                        Density of solid phase

                                                        -coefficient_of_linear_thermal_expansion[source]
                                                        +coefficient_of_linear_thermal_expansion[source]

                                                        Coefficient of linear thermal expansion

                                                        -ground_level[source]
                                                        +ground_level[source]

                                                        Ground level for element

                                                        -ionization_energies[source]
                                                        +ionization_energies[source]

                                                        List of ionization energies. First value is the first ionization energy, second is the second ionization energy, etc. Note that this is zero-based indexing! So Element.ionization_energies[0] refer to the 1st ionization energy. Values are from the NIST Atomic Spectra Database. Missing values are None.

                                                        @@ -474,599 +474,599 @@
                                                        -Ac = 'Ac'[source]
                                                        +Ac = 'Ac'[source]
                                                        -Ag = 'Ag'[source]
                                                        +Ag = 'Ag'[source]
                                                        -Al = 'Al'[source]
                                                        +Al = 'Al'[source]
                                                        -Am = 'Am'[source]
                                                        +Am = 'Am'[source]
                                                        -Ar = 'Ar'[source]
                                                        +Ar = 'Ar'[source]
                                                        -As = 'As'[source]
                                                        +As = 'As'[source]
                                                        -At = 'At'[source]
                                                        +At = 'At'[source]
                                                        -Au = 'Au'[source]
                                                        +Au = 'Au'[source]
                                                        -B = 'B'[source]
                                                        +B = 'B'[source]
                                                        -Ba = 'Ba'[source]
                                                        +Ba = 'Ba'[source]
                                                        -Be = 'Be'[source]
                                                        +Be = 'Be'[source]
                                                        -Bh = 'Bh'[source]
                                                        +Bh = 'Bh'[source]
                                                        -Bi = 'Bi'[source]
                                                        +Bi = 'Bi'[source]
                                                        -Bk = 'Bk'[source]
                                                        +Bk = 'Bk'[source]
                                                        -Br = 'Br'[source]
                                                        +Br = 'Br'[source]
                                                        -C = 'C'[source]
                                                        +C = 'C'[source]
                                                        -Ca = 'Ca'[source]
                                                        +Ca = 'Ca'[source]
                                                        -Cd = 'Cd'[source]
                                                        +Cd = 'Cd'[source]
                                                        -Ce = 'Ce'[source]
                                                        +Ce = 'Ce'[source]
                                                        -Cf = 'Cf'[source]
                                                        +Cf = 'Cf'[source]
                                                        -Cl = 'Cl'[source]
                                                        +Cl = 'Cl'[source]
                                                        -Cm = 'Cm'[source]
                                                        +Cm = 'Cm'[source]
                                                        -Cn = 'Cn'[source]
                                                        +Cn = 'Cn'[source]
                                                        -Co = 'Co'[source]
                                                        +Co = 'Co'[source]
                                                        -Cr = 'Cr'[source]
                                                        +Cr = 'Cr'[source]
                                                        -Cs = 'Cs'[source]
                                                        +Cs = 'Cs'[source]
                                                        -Cu = 'Cu'[source]
                                                        +Cu = 'Cu'[source]
                                                        -Db = 'Db'[source]
                                                        +Db = 'Db'[source]
                                                        -Ds = 'Ds'[source]
                                                        +Ds = 'Ds'[source]
                                                        -Dy = 'Dy'[source]
                                                        +Dy = 'Dy'[source]
                                                        -Er = 'Er'[source]
                                                        +Er = 'Er'[source]
                                                        -Es = 'Es'[source]
                                                        +Es = 'Es'[source]
                                                        -Eu = 'Eu'[source]
                                                        +Eu = 'Eu'[source]
                                                        -F = 'F'[source]
                                                        +F = 'F'[source]
                                                        -Fe = 'Fe'[source]
                                                        +Fe = 'Fe'[source]
                                                        -Fl = 'Fl'[source]
                                                        +Fl = 'Fl'[source]
                                                        -Fm = 'Fm'[source]
                                                        +Fm = 'Fm'[source]
                                                        -Fr = 'Fr'[source]
                                                        +Fr = 'Fr'[source]
                                                        -Ga = 'Ga'[source]
                                                        +Ga = 'Ga'[source]
                                                        -Gd = 'Gd'[source]
                                                        +Gd = 'Gd'[source]
                                                        -Ge = 'Ge'[source]
                                                        +Ge = 'Ge'[source]
                                                        -H = 'H'[source]
                                                        +H = 'H'[source]
                                                        -He = 'He'[source]
                                                        +He = 'He'[source]
                                                        -Hf = 'Hf'[source]
                                                        +Hf = 'Hf'[source]
                                                        -Hg = 'Hg'[source]
                                                        +Hg = 'Hg'[source]
                                                        -Ho = 'Ho'[source]
                                                        +Ho = 'Ho'[source]
                                                        -Hs = 'Hs'[source]
                                                        +Hs = 'Hs'[source]
                                                        -I = 'I'[source]
                                                        +I = 'I'[source]
                                                        -In = 'In'[source]
                                                        +In = 'In'[source]
                                                        -Ir = 'Ir'[source]
                                                        +Ir = 'Ir'[source]
                                                        -K = 'K'[source]
                                                        +K = 'K'[source]
                                                        -Kr = 'Kr'[source]
                                                        +Kr = 'Kr'[source]
                                                        -La = 'La'[source]
                                                        +La = 'La'[source]
                                                        -Li = 'Li'[source]
                                                        +Li = 'Li'[source]
                                                        -Lr = 'Lr'[source]
                                                        +Lr = 'Lr'[source]
                                                        -Lu = 'Lu'[source]
                                                        +Lu = 'Lu'[source]
                                                        -Lv = 'Lv'[source]
                                                        +Lv = 'Lv'[source]
                                                        -Mc = 'Mc'[source]
                                                        +Mc = 'Mc'[source]
                                                        -Md = 'Md'[source]
                                                        +Md = 'Md'[source]
                                                        -Mg = 'Mg'[source]
                                                        +Mg = 'Mg'[source]
                                                        -Mn = 'Mn'[source]
                                                        +Mn = 'Mn'[source]
                                                        -Mo = 'Mo'[source]
                                                        +Mo = 'Mo'[source]
                                                        -Mt = 'Mt'[source]
                                                        +Mt = 'Mt'[source]
                                                        -N = 'N'[source]
                                                        +N = 'N'[source]
                                                        -Na = 'Na'[source]
                                                        +Na = 'Na'[source]
                                                        -Nb = 'Nb'[source]
                                                        +Nb = 'Nb'[source]
                                                        -Nd = 'Nd'[source]
                                                        +Nd = 'Nd'[source]
                                                        -Ne = 'Ne'[source]
                                                        +Ne = 'Ne'[source]
                                                        -Nh = 'Nh'[source]
                                                        +Nh = 'Nh'[source]
                                                        -Ni = 'Ni'[source]
                                                        +Ni = 'Ni'[source]
                                                        -No = 'No'[source]
                                                        +No = 'No'[source]
                                                        -Np = 'Np'[source]
                                                        +Np = 'Np'[source]
                                                        -O = 'O'[source]
                                                        +O = 'O'[source]
                                                        -Og = 'Og'[source]
                                                        +Og = 'Og'[source]
                                                        -Os = 'Os'[source]
                                                        +Os = 'Os'[source]
                                                        -P = 'P'[source]
                                                        +P = 'P'[source]
                                                        -Pa = 'Pa'[source]
                                                        +Pa = 'Pa'[source]
                                                        -Pb = 'Pb'[source]
                                                        +Pb = 'Pb'[source]
                                                        -Pd = 'Pd'[source]
                                                        +Pd = 'Pd'[source]
                                                        -Pm = 'Pm'[source]
                                                        +Pm = 'Pm'[source]
                                                        -Po = 'Po'[source]
                                                        +Po = 'Po'[source]
                                                        -Pr = 'Pr'[source]
                                                        +Pr = 'Pr'[source]
                                                        -Pt = 'Pt'[source]
                                                        +Pt = 'Pt'[source]
                                                        -Pu = 'Pu'[source]
                                                        +Pu = 'Pu'[source]
                                                        -Ra = 'Ra'[source]
                                                        +Ra = 'Ra'[source]
                                                        -Rb = 'Rb'[source]
                                                        +Rb = 'Rb'[source]
                                                        -Re = 'Re'[source]
                                                        +Re = 'Re'[source]
                                                        -Rf = 'Rf'[source]
                                                        +Rf = 'Rf'[source]
                                                        -Rg = 'Rg'[source]
                                                        +Rg = 'Rg'[source]
                                                        -Rh = 'Rh'[source]
                                                        +Rh = 'Rh'[source]
                                                        -Rn = 'Rn'[source]
                                                        +Rn = 'Rn'[source]
                                                        -Ru = 'Ru'[source]
                                                        +Ru = 'Ru'[source]
                                                        -S = 'S'[source]
                                                        +S = 'S'[source]
                                                        -Sb = 'Sb'[source]
                                                        +Sb = 'Sb'[source]
                                                        -Sc = 'Sc'[source]
                                                        +Sc = 'Sc'[source]
                                                        -Se = 'Se'[source]
                                                        +Se = 'Se'[source]
                                                        -Sg = 'Sg'[source]
                                                        +Sg = 'Sg'[source]
                                                        -Si = 'Si'[source]
                                                        +Si = 'Si'[source]
                                                        -Sm = 'Sm'[source]
                                                        +Sm = 'Sm'[source]
                                                        -Sn = 'Sn'[source]
                                                        +Sn = 'Sn'[source]
                                                        -Sr = 'Sr'[source]
                                                        +Sr = 'Sr'[source]
                                                        -Ta = 'Ta'[source]
                                                        +Ta = 'Ta'[source]
                                                        -Tb = 'Tb'[source]
                                                        +Tb = 'Tb'[source]
                                                        -Tc = 'Tc'[source]
                                                        +Tc = 'Tc'[source]
                                                        -Te = 'Te'[source]
                                                        +Te = 'Te'[source]
                                                        -Th = 'Th'[source]
                                                        +Th = 'Th'[source]
                                                        -Ti = 'Ti'[source]
                                                        +Ti = 'Ti'[source]
                                                        -Tl = 'Tl'[source]
                                                        +Tl = 'Tl'[source]
                                                        -Tm = 'Tm'[source]
                                                        +Tm = 'Tm'[source]
                                                        -Ts = 'Ts'[source]
                                                        +Ts = 'Ts'[source]
                                                        -U = 'U'[source]
                                                        +U = 'U'[source]
                                                        -V = 'V'[source]
                                                        +V = 'V'[source]
                                                        -W = 'W'[source]
                                                        +W = 'W'[source]
                                                        -Xe = 'Xe'[source]
                                                        +Xe = 'Xe'[source]
                                                        -Y = 'Y'[source]
                                                        +Y = 'Y'[source]
                                                        -Yb = 'Yb'[source]
                                                        +Yb = 'Yb'[source]
                                                        -Zn = 'Zn'[source]
                                                        +Zn = 'Zn'[source]
                                                        -Zr = 'Zr'[source]
                                                        +Zr = 'Zr'[source]
                                                        -class ElementBase(value)[source]
                                                        +class ElementBase(value)[source]

                                                        Bases: enum.Enum

                                                        Element class defined without any enum values so it can be subclassed.

                                                        Basic immutable element object with all relevant properties.

                                                        @@ -1081,25 +1081,25 @@
                                                        -Z[source]
                                                        +Z[source]

                                                        Atomic number

                                                        -symbol[source]
                                                        +symbol[source]

                                                        Element symbol

                                                        -long_name[source]
                                                        +long_name[source]

                                                        Long name for element. E.g., “Hydrogen”.

                                                        -atomic_radius_calculated[source]
                                                        +atomic_radius_calculated[source]

                                                        Calculated atomic radius for the element. This is the empirical value. Data is obtained from http://en.wikipedia.org/wiki/Atomic_radii_of_the_elements_(data_page).

                                                        @@ -1107,7 +1107,7 @@
                                                        -van_der_waals_radius[source]
                                                        +van_der_waals_radius[source]

                                                        Van der Waals radius for the element. This is the empirical value determined from critical reviews of X-ray diffraction, gas kinetic collision cross-section, and other experimental data by Bondi and later @@ -1121,7 +1121,7 @@

                                                        -mendeleev_no[source]
                                                        +mendeleev_no[source]

                                                        Mendeleev number from definition given by Pettifor, D. G. (1984). A chemical scale for crystal-structure maps. Solid State Communications, 51 (1), 31-34

                                                        @@ -1129,43 +1129,43 @@
                                                        -electrical_resistivity[source]
                                                        +electrical_resistivity[source]

                                                        Electrical resistivity

                                                        -velocity_of_sound[source]
                                                        +velocity_of_sound[source]

                                                        Velocity of sound

                                                        -reflectivity[source]
                                                        +reflectivity[source]

                                                        Reflectivity

                                                        -refractive_index[source]
                                                        +refractive_index[source]

                                                        Refractice index

                                                        -poissons_ratio[source]
                                                        +poissons_ratio[source]

                                                        Poisson’s ratio

                                                        -molar_volume[source]
                                                        +molar_volume[source]

                                                        Molar volume

                                                        -electronic_structure[source]
                                                        +electronic_structure[source]

                                                        Electronic structure. E.g., The electronic structure for Fe is represented as [Ar].3d6.4s2

                                                        @@ -1173,7 +1173,7 @@
                                                        -atomic_orbitals[source]
                                                        +atomic_orbitals[source]

                                                        Atomic Orbitals. Energy of the atomic orbitals as a dict. E.g., The orbitals energies in eV are represented as {‘1s’: -1.0, ‘2s’: -0.1} @@ -1184,97 +1184,97 @@

                                                        -thermal_conductivity[source]
                                                        +thermal_conductivity[source]

                                                        Thermal conductivity

                                                        -boiling_point[source]
                                                        +boiling_point[source]

                                                        Boiling point

                                                        -melting_point[source]
                                                        +melting_point[source]

                                                        Melting point

                                                        -critical_temperature[source]
                                                        +critical_temperature[source]

                                                        Critical temperature

                                                        -superconduction_temperature[source]
                                                        +superconduction_temperature[source]

                                                        Superconduction temperature

                                                        -liquid_range[source]
                                                        +liquid_range[source]

                                                        Liquid range

                                                        -bulk_modulus[source]
                                                        +bulk_modulus[source]

                                                        Bulk modulus

                                                        -youngs_modulus[source]
                                                        +youngs_modulus[source]

                                                        Young’s modulus

                                                        -brinell_hardness[source]
                                                        +brinell_hardness[source]

                                                        Brinell hardness

                                                        -rigidity_modulus[source]
                                                        +rigidity_modulus[source]

                                                        Rigidity modulus

                                                        -mineral_hardness[source]
                                                        +mineral_hardness[source]

                                                        Mineral hardness

                                                        -vickers_hardness[source]
                                                        +vickers_hardness[source]

                                                        Vicker’s hardness

                                                        -density_of_solid[source]
                                                        +density_of_solid[source]

                                                        Density of solid phase

                                                        -coefficient_of_linear_thermal_expansion[source]
                                                        +coefficient_of_linear_thermal_expansion[source]

                                                        Coefficient of linear thermal expansion

                                                        -ground_level[source]
                                                        +ground_level[source]

                                                        Ground level for element

                                                        -ionization_energies[source]
                                                        +ionization_energies[source]

                                                        List of ionization energies. First value is the first ionization energy, second is the second ionization energy, etc. Note that this is zero-based indexing! So Element.ionization_energies[0] refer to the 1st ionization energy. Values are from the NIST Atomic Spectra Database. Missing values are None.

                                                        @@ -1282,7 +1282,7 @@
                                                        -property X: float[source]
                                                        +property X: float[source]

                                                        Electronegativity of element. Note that if an element does not have an electronegativity, a NaN float is returned.

                                                        @@ -1294,21 +1294,21 @@
                                                        -as_dict() → dict[Literal['element', '@module', '@class'], str][source]
                                                        +as_dict() → dict[Literal['element', '@module', '@class'], str][source]

                                                        Makes Element obey the general json interface used in pymatgen for easier serialization.

                                                        -property atomic_mass: pymatgen.core.units.FloatWithUnit[source]
                                                        +property atomic_mass: pymatgen.core.units.FloatWithUnit[source]

                                                        Returns: float: The atomic mass of the element in amu.

                                                        -property atomic_radius: FloatWithUnit | None[source]
                                                        +property atomic_radius: FloatWithUnit | None[source]

                                                        Returns: float | None: The atomic radius of the element in Ångstroms. Can be None for

                                                        @@ -1318,7 +1318,7 @@
                                                        -property average_anionic_radius: float[source]
                                                        +property average_anionic_radius: float[source]

                                                        Average anionic radius for element (with units). The average is taken over all negative oxidation states of the element for which data is present.

                                                        @@ -1326,7 +1326,7 @@
                                                        -property average_cationic_radius: pymatgen.core.units.FloatWithUnit[source]
                                                        +property average_cationic_radius: pymatgen.core.units.FloatWithUnit[source]

                                                        Average cationic radius for element (with units). The average is taken over all positive oxidation states of the element for which data is present.

                                                        @@ -1334,45 +1334,45 @@
                                                        -property average_ionic_radius: pymatgen.core.units.FloatWithUnit[source]
                                                        +property average_ionic_radius: pymatgen.core.units.FloatWithUnit[source]

                                                        Average ionic radius for element (with units). The average is taken over all oxidation states of the element for which data is present.

                                                        -property block: str[source]
                                                        +property block: str[source]

                                                        Return the block character “s,p,d,f”

                                                        -property common_oxidation_states: tuple[int, ...][source]
                                                        +property common_oxidation_states: tuple[int, ...][source]

                                                        Tuple of common oxidation states

                                                        -property data: dict[str, Any][source]
                                                        +property data: dict[str, Any][source]

                                                        Returns dict of data for element.

                                                        -property electron_affinity: float[source]
                                                        +property electron_affinity: float[source]

                                                        First ionization energy of element.

                                                        -property electronic_structure: str[source]
                                                        +property electronic_structure: str[source]

                                                        Electronic structure as string, with only valence electrons. E.g., The electronic structure for Fe is represented as ‘[Ar].3d6.4s2’

                                                        -static from_Z(z: int) → pymatgen.core.periodic_table.Element[source]
                                                        +static from_Z(z: int) → pymatgen.core.periodic_table.Element[source]

                                                        Get an element from an atomic number.

                                                        Parameters
                                                        @@ -1386,14 +1386,14 @@
                                                        -static from_dict(d) → pymatgen.core.periodic_table.Element[source]
                                                        +static from_dict(d) → pymatgen.core.periodic_table.Element[source]

                                                        Makes Element obey the general json interface used in pymatgen for easier serialization.

                                                        -static from_row_and_group(row: int, group: int) → pymatgen.core.periodic_table.Element[source]
                                                        +static from_row_and_group(row: int, group: int) → pymatgen.core.periodic_table.Element[source]

                                                        Returns an element from a row and group number. Important Note: For lanthanoids and actinoids, the row number must be 8 and 9, respectively, and the group number must be @@ -1420,7 +1420,7 @@

                                                        -property full_electronic_structure: list[tuple[int, str, int]][source]
                                                        +property full_electronic_structure: list[tuple[int, str, int]][source]

                                                        Full electronic structure as tuple. E.g., The electronic structure for Fe is represented as: [(1, “s”, 2), (2, “s”, 2), (2, “p”, 6), (3, “s”, 2), (3, “p”, 6), @@ -1429,119 +1429,119 @@

                                                        -property ground_state_term_symbol[source]
                                                        +property ground_state_term_symbol[source]

                                                        Ground state term symbol Selected based on Hund’s Rule

                                                        -property group: int[source]
                                                        +property group: int[source]

                                                        Returns the periodic table group of the element. Note: For lanthanoids and actinoids, the group is always 3.

                                                        -property icsd_oxidation_states: tuple[int, ...][source]
                                                        +property icsd_oxidation_states: tuple[int, ...][source]

                                                        Tuple of all oxidation states with at least 10 instances in ICSD database AND at least 1% of entries for that element

                                                        -property ionic_radii: dict[int, float][source]
                                                        +property ionic_radii: dict[int, float][source]

                                                        All ionic radii of the element as a dict of {oxidation state: ionic radii}. Radii are given in angstrom.

                                                        -property ionization_energy: float[source]
                                                        +property ionization_energy: float[source]

                                                        First ionization energy of element.

                                                        -property is_actinoid: bool[source]
                                                        +property is_actinoid: bool[source]

                                                        True if element is a actinoid.

                                                        -property is_alkali: bool[source]
                                                        +property is_alkali: bool[source]

                                                        True if element is an alkali metal.

                                                        -property is_alkaline: bool[source]
                                                        +property is_alkaline: bool[source]

                                                        True if element is an alkaline earth metal (group II).

                                                        -property is_chalcogen: bool[source]
                                                        +property is_chalcogen: bool[source]

                                                        True if element is a chalcogen.

                                                        -property is_halogen: bool[source]
                                                        +property is_halogen: bool[source]

                                                        True if element is a halogen.

                                                        -property is_lanthanoid: bool[source]
                                                        +property is_lanthanoid: bool[source]

                                                        True if element is a lanthanoid.

                                                        -property is_metal: bool[source]
                                                        +property is_metal: bool[source]

                                                        True if is a metal.

                                                        -property is_metalloid: bool[source]
                                                        +property is_metalloid: bool[source]

                                                        True if element is a metalloid.

                                                        -property is_noble_gas: bool[source]
                                                        +property is_noble_gas: bool[source]

                                                        True if element is noble gas.

                                                        -property is_post_transition_metal: bool[source]
                                                        +property is_post_transition_metal: bool[source]

                                                        True if element is a post-transition or poor metal.

                                                        -property is_quadrupolar: bool[source]
                                                        +property is_quadrupolar: bool[source]

                                                        Checks if this element can be quadrupolar.

                                                        -property is_rare_earth_metal: bool[source]
                                                        +property is_rare_earth_metal: bool[source]

                                                        True if element is a rare earth metal.

                                                        -property is_transition_metal: bool[source]
                                                        +property is_transition_metal: bool[source]

                                                        True if element is a transition metal.

                                                        -static is_valid_symbol(symbol: str) → bool[source]
                                                        +static is_valid_symbol(symbol: str) → bool[source]

                                                        Returns true if symbol is a valid element symbol.

                                                        Parameters
                                                        @@ -1556,7 +1556,7 @@
                                                        -property iupac_ordering[source]
                                                        +property iupac_ordering[source]

                                                        Ordering according to Table VI of “Nomenclature of Inorganic Chemistry (IUPAC Recommendations 2005)”. This ordering effectively follows the groups and rows of the periodic table, except the Lanthanides, Actinides @@ -1565,44 +1565,44 @@

                                                        -property max_oxidation_state: float[source]
                                                        +property max_oxidation_state: float[source]

                                                        Maximum oxidation state for element

                                                        -property metallic_radius: float[source]
                                                        +property metallic_radius: float[source]

                                                        Metallic radius of the element. Radius is given in ang.

                                                        -property min_oxidation_state: float[source]
                                                        +property min_oxidation_state: float[source]

                                                        Minimum oxidation state for element

                                                        -property nmr_quadrupole_moment: dict[str, pymatgen.core.units.FloatWithUnit][source]
                                                        +property nmr_quadrupole_moment: dict[str, pymatgen.core.units.FloatWithUnit][source]

                                                        Get a dictionary the nuclear electric quadrupole moment in units of e*millibarns for various isotopes

                                                        -property number: int[source]
                                                        +property number: int[source]

                                                        Alternative attribute for atomic number Z

                                                        -property oxidation_states: tuple[int, ...][source]
                                                        +property oxidation_states: tuple[int, ...][source]

                                                        Tuple of all known oxidation states

                                                        -static print_periodic_table(filter_function: Callable | None = None)[source]
                                                        +static print_periodic_table(filter_function: Callable | None = None)[source]

                                                        A pretty ASCII printer for the periodic table, based on some filter_function.

                                                        @@ -1617,7 +1617,7 @@
                                                        -property row: int[source]
                                                        +property row: int[source]

                                                        Returns the periodic table row of the element. Note: For lanthanoids and actinoids, the row is always 6 or 7, respectively.

                                                        @@ -1625,14 +1625,14 @@
                                                        -property term_symbols: list[list[str]][source]
                                                        +property term_symbols: list[list[str]][source]

                                                        All possible Russell-Saunders term symbol of the Element. eg. L = 1, n_e = 2 (s2) returns [[‘1D2’], [‘3P0’, ‘3P1’, ‘3P2’], [‘1S0’]]

                                                        -property valence[source]
                                                        +property valence[source]

                                                        From full electron config obtain valence subshell angular moment (L) and number of valence e- (v_e)

                                                        @@ -1640,7 +1640,7 @@
                                                        -class Specie(symbol: str, oxidation_state: float | None = 0.0, properties: dict | None = None)[source]
                                                        +class Specie(symbol: str, oxidation_state: float | None = 0.0, properties: dict | None = None)[source]

                                                        Bases: pymatgen.core.periodic_table.Species

                                                        This maps the historical grammatically inaccurate Specie to Species to maintain backwards compatibility.

                                                        @@ -1658,13 +1658,13 @@
                                                        -oxi_state[source]
                                                        +oxi_state[source]

                                                        Oxidation state associated with Species

                                                        -ionic_radius[source]
                                                        +ionic_radius[source]

                                                        Ionic radius of Species (with specific oxidation state).

                                                        @@ -1675,7 +1675,7 @@
                                                        -class Species(symbol: str, oxidation_state: float | None = 0.0, properties: dict | None = None)[source]
                                                        +class Species(symbol: str, oxidation_state: float | None = 0.0, properties: dict | None = None)[source]

                                                        Bases: monty.json.MSONable, pymatgen.util.string.Stringify

                                                        An extension of Element with an oxidation state and other optional properties. Properties associated with Species should be “idealized” @@ -1697,13 +1697,13 @@

                                                        -oxi_state[source]
                                                        +oxi_state[source]

                                                        Oxidation state associated with Species

                                                        -ionic_radius[source]
                                                        +ionic_radius[source]

                                                        Ionic radius of Species (with specific oxidation state).

                                                        @@ -1712,12 +1712,12 @@
                                                        -STRING_MODE = 'SUPERSCRIPT'[source]
                                                        +STRING_MODE = 'SUPERSCRIPT'[source]
                                                        -as_dict() → dict[source]
                                                        +as_dict() → dict[source]
                                                        Returns

                                                        Json-able dictionary representation.

                                                        @@ -1727,13 +1727,13 @@
                                                        -property element[source]
                                                        +property element[source]

                                                        Underlying element object

                                                        -classmethod from_dict(d) → pymatgen.core.periodic_table.Species[source]
                                                        +classmethod from_dict(d) → pymatgen.core.periodic_table.Species[source]
                                                        Parameters

                                                        d – Dict representation.

                                                        @@ -1746,7 +1746,7 @@
                                                        -static from_string(species_string: str) → pymatgen.core.periodic_table.Species[source]
                                                        +static from_string(species_string: str) → pymatgen.core.periodic_table.Species[source]

                                                        Returns a Species from a string representation.

                                                        Parameters
                                                        @@ -1764,7 +1764,7 @@
                                                        -get_crystal_field_spin(coordination: Literal['oct', 'tet'] = 'oct', spin_config: Literal['low', 'high'] = 'high') → float[source]
                                                        +get_crystal_field_spin(coordination: Literal['oct', 'tet'] = 'oct', spin_config: Literal['low', 'high'] = 'high') → float[source]

                                                        Calculate the crystal field spin based on coordination and spin configuration. Only works for transition metal species.

                                                        @@ -1788,7 +1788,7 @@
                                                        -get_nmr_quadrupole_moment(isotope: str | None = None) → float[source]
                                                        +get_nmr_quadrupole_moment(isotope: str | None = None) → float[source]

                                                        Gets the nuclear electric quadrupole moment in units of e*millibarns

                                                        @@ -1801,7 +1801,7 @@
                                                        -get_shannon_radius(cn: str, spin: Literal['', 'Low Spin', 'High Spin'] = '', radius_type: Literal['ionic', 'crystal'] = 'ionic') → float[source]
                                                        +get_shannon_radius(cn: str, spin: Literal['', 'Low Spin', 'High Spin'] = '', radius_type: Literal['ionic', 'crystal'] = 'ionic') → float[source]

                                                        Get the local environment specific ionic radius for species.

                                                        Parameters
                                                        @@ -1824,24 +1824,24 @@
                                                        -property ionic_radius: float | None[source]
                                                        +property ionic_radius: float | None[source]

                                                        Ionic radius of specie. Returns None if data is not present.

                                                        -property oxi_state: float | None[source]
                                                        +property oxi_state: float | None[source]

                                                        Oxidation state of Species.

                                                        -supported_properties = ('spin',)[source]
                                                        +supported_properties = ('spin',)[source]
                                                        -to_pretty_string() → str[source]
                                                        +to_pretty_string() → str[source]
                                                        Returns

                                                        String without properties.

                                                        @@ -1853,7 +1853,7 @@
                                                        -get_el_sp(obj) → Element | Species | DummySpecies[source]
                                                        +get_el_sp(obj) → Element | Species | DummySpecies[source]

                                                        Utility method to get an Element or Species from an input obj. If obj is in itself an element or a specie, it is returned automatically. If obj is an int or a string representing an integer, the Element diff --git a/docs/pymatgen.core.sites.html b/docs/pymatgen.core.sites.html index 2a83d445400..f01d70cfee0 100644 --- a/docs/pymatgen.core.sites.html +++ b/docs/pymatgen.core.sites.html @@ -4,7 +4,7 @@ - pymatgen.core.sites module — pymatgen 2022.5.18 documentation + pymatgen.core.sites module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                                        - 2022.5.18 + 2022.5.18.1
                                                        @@ -118,7 +118,7 @@

                                                        This module defines classes representing non-periodic and periodic sites.

                                                        -class PeriodicSite(species: SpeciesLike | CompositionLike, coords: ArrayLike, lattice: Lattice, to_unit_cell: bool = False, coords_are_cartesian: bool = False, properties: dict = None, skip_checks: bool = False)[source]
                                                        +class PeriodicSite(species: SpeciesLike | CompositionLike, coords: ArrayLike, lattice: Lattice, to_unit_cell: bool = False, coords_are_cartesian: bool = False, properties: dict = None, skip_checks: bool = False)[source]

                                                        Bases: pymatgen.core.sites.Site, monty.json.MSONable

                                                        Extension of generic Site object to periodic systems. PeriodicSite includes a lattice system.

                                                        @@ -156,13 +156,13 @@
                                                        -property a: float[source]
                                                        +property a: float[source]

                                                        Fractional a coordinate

                                                        -as_dict(verbosity: int = 0) → dict[source]
                                                        +as_dict(verbosity: int = 0) → dict[source]

                                                        JSON-serializable dict representation of PeriodicSite.

                                                        Parameters
                                                        @@ -175,25 +175,25 @@
                                                        -property b: float[source]
                                                        +property b: float[source]

                                                        Fractional b coordinate

                                                        -property c: float[source]
                                                        +property c: float[source]

                                                        Fractional c coordinate

                                                        -property coords: numpy.ndarray[source]
                                                        +property coords: numpy.ndarray[source]

                                                        Cartesian coordinates

                                                        -distance(other: PeriodicSite, jimage: ArrayLike | None = None)[source]
                                                        +distance(other: PeriodicSite, jimage: ArrayLike | None = None)[source]

                                                        Get distance between two sites assuming periodic boundary conditions.

                                                        Parameters
                                                        @@ -216,7 +216,7 @@
                                                        -distance_and_image(other: PeriodicSite, jimage: ArrayLike | None = None) → tuple[float, np.ndarray][source]
                                                        +distance_and_image(other: PeriodicSite, jimage: ArrayLike | None = None) → tuple[float, np.ndarray][source]

                                                        Gets distance and instance between two sites assuming periodic boundary conditions. If the index jimage of two sites atom j is not specified it selects the j image nearest to the i atom and returns the distance and @@ -245,7 +245,7 @@

                                                        -distance_and_image_from_frac_coords(fcoords: ArrayLike, jimage: ArrayLike | None = None) → tuple[float, np.ndarray][source]
                                                        +distance_and_image_from_frac_coords(fcoords: ArrayLike, jimage: ArrayLike | None = None) → tuple[float, np.ndarray][source]

                                                        Gets distance between site and a fractional coordinate assuming periodic boundary conditions. If the index jimage of two sites atom j is not specified it selects the j image nearest to the i atom and @@ -275,13 +275,13 @@

                                                        -property frac_coords: numpy.ndarray[source]
                                                        +property frac_coords: numpy.ndarray[source]

                                                        Fractional coordinates

                                                        -classmethod from_dict(d, lattice=None) → pymatgen.core.sites.PeriodicSite[source]
                                                        +classmethod from_dict(d, lattice=None) → pymatgen.core.sites.PeriodicSite[source]

                                                        Create PeriodicSite from dict representation.

                                                        Parameters
                                                        @@ -300,7 +300,7 @@
                                                        -is_periodic_image(other: pymatgen.core.sites.PeriodicSite, tolerance: float = 1e-08, check_lattice: bool = True) → bool[source]
                                                        +is_periodic_image(other: pymatgen.core.sites.PeriodicSite, tolerance: float = 1e-08, check_lattice: bool = True) → bool[source]

                                                        Returns True if sites are periodic images of each other.

                                                        Parameters
                                                        @@ -322,31 +322,31 @@
                                                        -property lattice: pymatgen.core.lattice.Lattice[source]
                                                        +property lattice: pymatgen.core.lattice.Lattice[source]

                                                        Lattice associated with PeriodicSite

                                                        -to_unit_cell(in_place=False) → PeriodicSite | None[source]
                                                        +to_unit_cell(in_place=False) → PeriodicSite | None[source]

                                                        Move frac coords to within the unit cell cell.

                                                        -property x: float[source]
                                                        +property x: float[source]

                                                        Cartesian x coordinate

                                                        -property y: float[source]
                                                        +property y: float[source]

                                                        Cartesian y coordinate

                                                        -property z: float[source]
                                                        +property z: float[source]

                                                        Cartesian z coordinate

                                                        @@ -354,7 +354,7 @@
                                                        -class Site(species: SpeciesLike | CompositionLike, coords: ArrayLike, properties: dict = None, skip_checks: bool = False)[source]
                                                        +class Site(species: SpeciesLike | CompositionLike, coords: ArrayLike, properties: dict = None, skip_checks: bool = False)[source]

                                                        Bases: collections.abc.Hashable, monty.json.MSONable

                                                        A generalized non-periodic site. This is essentially a composition at a point in space, with some optional properties associated with it. A @@ -389,13 +389,13 @@

                                                        -as_dict() → dict[source]
                                                        +as_dict() → dict[source]

                                                        JSON-serializable dict representation for Site.

                                                        -distance(other) → float[source]
                                                        +distance(other) → float[source]

                                                        Get distance between two sites.

                                                        Parameters
                                                        @@ -409,7 +409,7 @@
                                                        -distance_from_point(pt) → float[source]
                                                        +distance_from_point(pt) → float[source]

                                                        Returns distance between the site and a point in space.

                                                        Parameters
                                                        @@ -423,25 +423,25 @@
                                                        -classmethod from_dict(d: dict) → pymatgen.core.sites.Site[source]
                                                        +classmethod from_dict(d: dict) → pymatgen.core.sites.Site[source]

                                                        Create Site from dict representation

                                                        -property is_ordered: bool[source]
                                                        +property is_ordered: bool[source]

                                                        True if site is an ordered site, i.e., with a single species with occupancy 1.

                                                        -position_atol = 1e-05[source]
                                                        +position_atol = 1e-05[source]
                                                        -property specie: Element | Species | DummySpecies[source]
                                                        +property specie: Element | Species | DummySpecies[source]

                                                        The Species/Element at the site. Only works for ordered sites. Otherwise an AttributeError is raised. Use this property sparingly. Robust design should make use of the property species instead. Note that the @@ -456,7 +456,7 @@

                                                        -property species: pymatgen.core.composition.Composition[source]
                                                        +property species: pymatgen.core.composition.Composition[source]

                                                        The species on the site as a composition, e.g., Fe0.5Mn0.5.

                                                        Type
                                                        @@ -467,25 +467,25 @@
                                                        -property species_string: str[source]
                                                        +property species_string: str[source]

                                                        String representation of species on the site.

                                                        -property x: float[source]
                                                        +property x: float[source]

                                                        Cartesian x coordinate

                                                        -property y: float[source]
                                                        +property y: float[source]

                                                        Cartesian y coordinate

                                                        -property z: float[source]
                                                        +property z: float[source]

                                                        Cartesian z coordinate

                                                        diff --git a/docs/pymatgen.core.spectrum.html b/docs/pymatgen.core.spectrum.html index 3d749973be4..ff2aa0946c1 100644 --- a/docs/pymatgen.core.spectrum.html +++ b/docs/pymatgen.core.spectrum.html @@ -4,7 +4,7 @@ - pymatgen.core.spectrum module — pymatgen 2022.5.18 documentation + pymatgen.core.spectrum module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                        - 2022.5.18 + 2022.5.18.1
                                                        @@ -119,7 +119,7 @@ x y value pairs.

                                                        -class Spectrum(x: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], y: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], *args, **kwargs)[source]
                                                        +class Spectrum(x: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], y: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], *args, **kwargs)[source]

                                                        Bases: monty.json.MSONable

                                                        Base class for any type of xas, essentially just x, y values. Examples include XRD patterns, XANES, EXAFS, NMR, DOS, etc.

                                                        @@ -144,17 +144,17 @@
                                                        -XLABEL = 'x'[source]
                                                        +XLABEL = 'x'[source]
                                                        -YLABEL = 'y'[source]
                                                        +YLABEL = 'y'[source]
                                                        -copy()[source]
                                                        +copy()[source]
                                                        Returns

                                                        Copy of Spectrum object.

                                                        @@ -164,7 +164,7 @@
                                                        -get_interpolated_value(x: float) → list[float][source]
                                                        +get_interpolated_value(x: float) → list[float][source]

                                                        Returns an interpolated y value for a particular x value.

                                                        Parameters
                                                        @@ -178,7 +178,7 @@
                                                        -normalize(mode: Literal['max', 'sum'] = 'max', value: float = 1.0)[source]
                                                        +normalize(mode: Literal['max', 'sum'] = 'max', value: float = 1.0)[source]

                                                        Normalize the spectrum with respect to the sum of intensity

                                                        Parameters
                                                        @@ -194,7 +194,7 @@
                                                        -smear(sigma: float = 0.0, func: str | Callable = 'gaussian')[source]
                                                        +smear(sigma: float = 0.0, func: str | Callable = 'gaussian')[source]

                                                        Apply Gaussian/Lorentzian smearing to spectrum y value.

                                                        Parameters
                                                        @@ -211,7 +211,7 @@
                                                        -lorentzian(x, x_0: float = 0, sigma: float = 1.0)[source]
                                                        +lorentzian(x, x_0: float = 0, sigma: float = 1.0)[source]
                                                        Parameters
                                                          diff --git a/docs/pymatgen.core.structure.html b/docs/pymatgen.core.structure.html index d92598c34ab..9e23eeeeef3 100644 --- a/docs/pymatgen.core.structure.html +++ b/docs/pymatgen.core.structure.html @@ -4,7 +4,7 @@ - pymatgen.core.structure module — pymatgen 2022.5.18 documentation + pymatgen.core.structure module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                          - 2022.5.18 + 2022.5.18.1
                                                          @@ -119,7 +119,7 @@ periodic structure.

                                                          -class IMolecule(species: Sequence[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies, dict, pymatgen.core.composition.Composition]], coords: Sequence[Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]], charge: float = 0.0, spin_multiplicity: Optional[int] = None, validate_proximity: bool = False, site_properties: Optional[dict] = None, charge_spin_check: bool = True)[source]
                                                          +class IMolecule(species: Sequence[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies, dict, pymatgen.core.composition.Composition]], coords: Sequence[Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]], charge: float = 0.0, spin_multiplicity: Optional[int] = None, validate_proximity: bool = False, site_properties: Optional[dict] = None, charge_spin_check: bool = True)[source]

                                                          Bases: pymatgen.core.structure.SiteCollection, monty.json.MSONable

                                                          Basic immutable Molecule object without periodicity. Essentially a sequence of sites. IMolecule is made to be immutable so that they can @@ -156,13 +156,13 @@

                                                          -as_dict()[source]
                                                          +as_dict()[source]

                                                          JSON-serializable dict representation of Molecule

                                                          -break_bond(ind1: int, ind2: int, tol: float = 0.2) → tuple[IMolecule | Molecule, ...][source]
                                                          +break_bond(ind1: int, ind2: int, tol: float = 0.2) → tuple[IMolecule | Molecule, ...][source]

                                                          Returns two molecules based on breaking the bond between atoms at index ind1 and ind2.

                                                          @@ -185,19 +185,19 @@
                                                          -property center_of_mass: numpy.ndarray[source]
                                                          +property center_of_mass: numpy.ndarray[source]

                                                          Center of mass of molecule.

                                                          -property charge: float[source]
                                                          +property charge: float[source]

                                                          Charge of molecule

                                                          -classmethod from_dict(d) → dict[source]
                                                          +classmethod from_dict(d) → dict[source]

                                                          Reconstitute a Molecule object from a dict representation created using as_dict().

                                                          @@ -212,7 +212,7 @@
                                                          -classmethod from_file(filename)[source]
                                                          +classmethod from_file(filename)[source]

                                                          Reads a molecule from a file. Supported formats include xyz, gaussian input (gjf|g03|g09|com|inp), Gaussian output (.out|and pymatgen’s JSON-serialized molecules. Using openbabel, @@ -230,7 +230,7 @@

                                                          -classmethod from_sites(sites: Sequence[Site], charge: float = 0, spin_multiplicity: int = None, validate_proximity: bool = False, charge_spin_check: bool = True) → IMolecule | Molecule[source]
                                                          +classmethod from_sites(sites: Sequence[Site], charge: float = 0, spin_multiplicity: int = None, validate_proximity: bool = False, charge_spin_check: bool = True) → IMolecule | Molecule[source]

                                                          Convenience constructor to make a Molecule from a list of sites.

                                                          Parameters
                                                          @@ -251,7 +251,7 @@
                                                          -classmethod from_str(input_string: str, fmt: str)[source]
                                                          +classmethod from_str(input_string: str, fmt: str)[source]

                                                          Reads the molecule from a string.

                                                          Parameters
                                                          @@ -272,7 +272,7 @@
                                                          -get_boxed_structure(a: float, b: float, c: float, images: ArrayLike = (1, 1, 1), random_rotation: bool = False, min_dist: float = 1.0, cls=None, offset: ArrayLike = None, no_cross: bool = False, reorder: bool = True) → IStructure | Structure[source]
                                                          +get_boxed_structure(a: float, b: float, c: float, images: ArrayLike = (1, 1, 1), random_rotation: bool = False, min_dist: float = 1.0, cls=None, offset: ArrayLike = None, no_cross: bool = False, reorder: bool = True) → IStructure | Structure[source]

                                                          Creates a Structure from a Molecule by putting the Molecule in the center of a orthorhombic box. Useful for creating Structure for calculating molecules using periodic codes.

                                                          @@ -309,7 +309,7 @@
                                                          -get_centered_molecule() → IMolecule | Molecule[source]
                                                          +get_centered_molecule() → IMolecule | Molecule[source]

                                                          Returns a Molecule centered at the center of mass.

                                                          Returns
                                                          @@ -320,7 +320,7 @@
                                                          -get_covalent_bonds(tol: float = 0.2) → list[pymatgen.core.bonds.CovalentBond][source]
                                                          +get_covalent_bonds(tol: float = 0.2) → list[pymatgen.core.bonds.CovalentBond][source]

                                                          Determines the covalent bonds in a molecule.

                                                          Parameters
                                                          @@ -335,7 +335,7 @@
                                                          -get_distance(i: int, j: int) → float[source]
                                                          +get_distance(i: int, j: int) → float[source]

                                                          Get distance between site i and j.

                                                          Parameters
                                                          @@ -352,7 +352,7 @@
                                                          -get_neighbors(site: pymatgen.core.sites.Site, r: float) → list[pymatgen.core.structure.Neighbor][source]
                                                          +get_neighbors(site: pymatgen.core.sites.Site, r: float) → list[pymatgen.core.structure.Neighbor][source]

                                                          Get all neighbors to a site within a sphere of radius r. Excludes the site itself.

                                                          @@ -370,7 +370,7 @@
                                                          -get_neighbors_in_shell(origin: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], r: float, dr: float) → list[pymatgen.core.structure.Neighbor][source]
                                                          +get_neighbors_in_shell(origin: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], r: float, dr: float) → list[pymatgen.core.structure.Neighbor][source]

                                                          Returns all sites in a shell centered on origin (coords) between radii r-dr and r+dr.

                                                          @@ -389,7 +389,7 @@
                                                          -get_sites_in_sphere(pt: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], r: float) → list[pymatgen.core.structure.Neighbor][source]
                                                          +get_sites_in_sphere(pt: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], r: float) → list[pymatgen.core.structure.Neighbor][source]

                                                          Find all sites within a sphere from a point.

                                                          Parameters
                                                          @@ -406,25 +406,25 @@
                                                          -property nelectrons: float[source]
                                                          +property nelectrons: float[source]

                                                          Number of electrons in the molecule.

                                                          -property sites: tuple[pymatgen.core.sites.Site, ...][source]
                                                          +property sites: tuple[pymatgen.core.sites.Site, ...][source]

                                                          Returns a tuple of sites in the Molecule.

                                                          -property spin_multiplicity: float[source]
                                                          +property spin_multiplicity: float[source]

                                                          Spin multiplicity of molecule.

                                                          -to(fmt=None, filename=None)[source]
                                                          +to(fmt=None, filename=None)[source]

                                                          Outputs the molecule to a file or string.

                                                          Parameters
                                                          @@ -449,7 +449,7 @@
                                                          -class IStructure(lattice: ArrayLike | Lattice, species: Sequence[CompositionLike], coords: Sequence[ArrayLike], charge: float = None, validate_proximity: bool = False, to_unit_cell: bool = False, coords_are_cartesian: bool = False, site_properties: dict = None)[source]
                                                          +class IStructure(lattice: ArrayLike | Lattice, species: Sequence[CompositionLike], coords: Sequence[ArrayLike], charge: float = None, validate_proximity: bool = False, to_unit_cell: bool = False, coords_are_cartesian: bool = False, site_properties: dict = None)[source]

                                                          Bases: pymatgen.core.structure.SiteCollection, monty.json.MSONable

                                                          Basic immutable Structure object with periodicity. Essentially a sequence of PeriodicSites having a common lattice. IStructure is made to be @@ -498,7 +498,7 @@

                                                          -as_dataframe()[source]
                                                          +as_dataframe()[source]

                                                          Returns a Pandas dataframe of the sites. Structure level attributes are stored in DataFrame.attrs. Example:

                                                          Species a b c x y z magmom 0 (Si) 0.0 0.0 0.000000e+00 0.0 0.000000e+00 0.000000e+00 5 @@ -507,7 +507,7 @@

                                                          -as_dict(verbosity=1, fmt=None, **kwargs)[source]
                                                          +as_dict(verbosity=1, fmt=None, **kwargs)[source]

                                                          Dict representation of Structure.

                                                          Parameters
                                                          @@ -535,13 +535,13 @@
                                                          -property charge: float[source]
                                                          +property charge: float[source]

                                                          Overall charge of the structure

                                                          -copy(site_properties=None, sanitize=False)[source]
                                                          +copy(site_properties=None, sanitize=False)[source]

                                                          Convenience method to get a copy of the structure, with options to add site properties.

                                                          @@ -569,26 +569,26 @@
                                                          -property density: float[source]
                                                          +property density: float[source]

                                                          Returns the density in units of g/cc

                                                          -property distance_matrix: numpy.ndarray[source]
                                                          +property distance_matrix: numpy.ndarray[source]

                                                          Returns the distance matrix between all sites in the structure. For periodic structures, this should return the nearest image distance.

                                                          -property frac_coords[source]
                                                          +property frac_coords[source]

                                                          Fractional coordinates as a Nx3 numpy array.

                                                          -classmethod from_dict(d, fmt=None)[source]
                                                          +classmethod from_dict(d, fmt=None)[source]

                                                          Reconstitute a Structure object from a dict representation of Structure created using as_dict().

                                                          @@ -603,7 +603,7 @@
                                                          -classmethod from_file(filename, primitive=False, sort=False, merge_tol=0.0)[source]
                                                          +classmethod from_file(filename, primitive=False, sort=False, merge_tol=0.0)[source]

                                                          Reads a structure from a file. For example, anything ending in a “cif” is assumed to be a Crystallographic Information Format file. Supported formats include CIF, POSCAR/CONTCAR, CHGCAR, LOCPOT, @@ -628,7 +628,7 @@

                                                          -classmethod from_magnetic_spacegroup(msg: str | MagneticSpaceGroup, lattice: list | np.ndarray | Lattice, species: Sequence[str | Element | Species | DummySpecies | Composition], coords: Sequence[Sequence[float]], site_properties: dict[str, Sequence], coords_are_cartesian: bool = False, tol: float = 1e-05) → IStructure | Structure[source]
                                                          +classmethod from_magnetic_spacegroup(msg: str | MagneticSpaceGroup, lattice: list | np.ndarray | Lattice, species: Sequence[str | Element | Species | DummySpecies | Composition], coords: Sequence[Sequence[float]], site_properties: dict[str, Sequence], coords_are_cartesian: bool = False, tol: float = 1e-05) → IStructure | Structure[source]

                                                          Generate a structure using a magnetic spacegroup. Note that only symmetrically distinct species, coords and magmoms should be provided.] All equivalent sites are generated from the spacegroup operations.

                                                          @@ -680,7 +680,7 @@
                                                          -classmethod from_sites(sites: list[PeriodicSite], charge: float = None, validate_proximity: bool = False, to_unit_cell: bool = False) → IStructure | Structure[source]
                                                          +classmethod from_sites(sites: list[PeriodicSite], charge: float = None, validate_proximity: bool = False, to_unit_cell: bool = False) → IStructure | Structure[source]

                                                          Convenience constructor to make a Structure from a list of sites.

                                                          Parameters
                                                          @@ -702,7 +702,7 @@
                                                          -classmethod from_spacegroup(sg: str, lattice: list | np.ndarray | Lattice, species: Sequence[str | Element | Species | DummySpecies | Composition], coords: Sequence[Sequence[float]], site_properties: dict[str, Sequence] = None, coords_are_cartesian: bool = False, tol: float = 1e-05) → IStructure | Structure[source]
                                                          +classmethod from_spacegroup(sg: str, lattice: list | np.ndarray | Lattice, species: Sequence[str | Element | Species | DummySpecies | Composition], coords: Sequence[Sequence[float]], site_properties: dict[str, Sequence] = None, coords_are_cartesian: bool = False, tol: float = 1e-05) → IStructure | Structure[source]

                                                          Generate a structure using a spacegroup. Note that only symmetrically distinct species and coords should be provided. All equivalent sites are generated from the spacegroup operations.

                                                          @@ -749,7 +749,7 @@
                                                          -classmethod from_str(input_string: str, fmt: Literal['cif', 'poscar', 'cssr', 'json', 'yaml', 'xsf', 'mcsqs'], primitive=False, sort=False, merge_tol=0.0)[source]
                                                          +classmethod from_str(input_string: str, fmt: Literal['cif', 'poscar', 'cssr', 'json', 'yaml', 'xsf', 'mcsqs'], primitive=False, sort=False, merge_tol=0.0)[source]

                                                          Reads a structure from a string.

                                                          Parameters
                                                          @@ -774,7 +774,7 @@
                                                          -get_all_neighbors(r: float, include_index: bool = False, include_image: bool = False, sites: Optional[Sequence[pymatgen.core.sites.PeriodicSite]] = None, numerical_tol: float = 1e-08) → list[list[pymatgen.core.structure.PeriodicNeighbor]][source]
                                                          +get_all_neighbors(r: float, include_index: bool = False, include_image: bool = False, sites: Optional[Sequence[pymatgen.core.sites.PeriodicSite]] = None, numerical_tol: float = 1e-08) → list[list[pymatgen.core.structure.PeriodicNeighbor]][source]

                                                          Get neighbors for each atom in the unit cell, out to a distance r Returns a list of list of neighbors for each site in structure. Use this method if you are planning on looping over all sites in the @@ -817,12 +817,12 @@

                                                          -get_all_neighbors_old(**kwargs)[source]
                                                          +get_all_neighbors_old(**kwargs)[source]
                                                          -get_all_neighbors_py(r: float, include_index: bool = False, include_image: bool = False, sites: Optional[Sequence[pymatgen.core.sites.PeriodicSite]] = None, numerical_tol: float = 1e-08) → list[list[pymatgen.core.structure.PeriodicNeighbor]][source]
                                                          +get_all_neighbors_py(r: float, include_index: bool = False, include_image: bool = False, sites: Optional[Sequence[pymatgen.core.sites.PeriodicSite]] = None, numerical_tol: float = 1e-08) → list[list[pymatgen.core.structure.PeriodicNeighbor]][source]

                                                          Get neighbors for each atom in the unit cell, out to a distance r Returns a list of list of neighbors for each site in structure. Use this method if you are planning on looping over all sites in the @@ -865,7 +865,7 @@

                                                          -get_distance(i: int, j: int, jimage=None) → float[source]
                                                          +get_distance(i: int, j: int, jimage=None) → float[source]

                                                          Get distance between site i and j assuming periodic boundary conditions. If the index jimage of two sites atom j is not specified it selects the jimage nearest to the i atom and returns the distance and @@ -889,7 +889,7 @@

                                                          -get_miller_index_from_site_indexes(site_ids, round_dp=4, verbose=True)[source]
                                                          +get_miller_index_from_site_indexes(site_ids, round_dp=4, verbose=True)[source]

                                                          Get the Miller index of a plane from a set of sites indexes.

                                                          A minimum of 3 sites are required. If more than 3 sites are given the best plane that minimises the distance to all points will be @@ -917,7 +917,7 @@

                                                          -get_neighbor_list(r: float, sites: Optional[Sequence[pymatgen.core.sites.PeriodicSite]] = None, numerical_tol: float = 1e-08, exclude_self: bool = True) → tuple[numpy.ndarray, ...][source]
                                                          +get_neighbor_list(r: float, sites: Optional[Sequence[pymatgen.core.sites.PeriodicSite]] = None, numerical_tol: float = 1e-08, exclude_self: bool = True) → tuple[numpy.ndarray, ...][source]

                                                          Get neighbor lists using numpy array representations without constructing Neighbor objects. If the cython extension is installed, this method will be orders of magnitude faster than get_all_neighbors_old and 2-3x faster @@ -950,7 +950,7 @@

                                                          -get_neighbors(site: pymatgen.core.sites.PeriodicSite, r: float, include_index: bool = False, include_image: bool = False) → list[pymatgen.core.structure.PeriodicNeighbor][source]
                                                          +get_neighbors(site: pymatgen.core.sites.PeriodicSite, r: float, include_index: bool = False, include_image: bool = False) → list[pymatgen.core.structure.PeriodicNeighbor][source]

                                                          Get all neighbors to a site within a sphere of radius r. Excludes the site itself.

                                                          @@ -972,7 +972,7 @@
                                                          -get_neighbors_in_shell(origin: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], r: float, dr: float, include_index: bool = False, include_image: bool = False) → list[pymatgen.core.structure.PeriodicNeighbor][source]
                                                          +get_neighbors_in_shell(origin: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], r: float, dr: float, include_index: bool = False, include_image: bool = False) → list[pymatgen.core.structure.PeriodicNeighbor][source]

                                                          Returns all sites in a shell centered on origin (coords) between radii r-dr and r+dr.

                                                          @@ -996,12 +996,12 @@
                                                          -get_neighbors_old(**kwargs)[source]
                                                          +get_neighbors_old(**kwargs)[source]
                                                          -get_orderings(mode: Literal['enum', 'sqs'] = 'enum', **kwargs) → list[pymatgen.core.structure.Structure][source]
                                                          +get_orderings(mode: Literal['enum', 'sqs'] = 'enum', **kwargs) → list[pymatgen.core.structure.Structure][source]

                                                          Returns list of orderings for a disordered structure. If structure does not contain disorder, the default structure is returned.

                                                          @@ -1027,7 +1027,7 @@
                                                          -get_primitive_structure(tolerance: float = 0.25, use_site_props: bool = False, constrain_latt: list | dict | None = None)[source]
                                                          +get_primitive_structure(tolerance: float = 0.25, use_site_props: bool = False, constrain_latt: list | dict | None = None)[source]

                                                          This finds a smaller unit cell than the input. Sometimes it doesn”t find the smallest possible one, so this method is recursively called until it is unable to find a smaller cell.

                                                          @@ -1056,7 +1056,7 @@
                                                          -get_reduced_structure(reduction_algo: Literal['niggli', 'LLL'] = 'niggli') → IStructure | Structure[source]
                                                          +get_reduced_structure(reduction_algo: Literal['niggli', 'LLL'] = 'niggli') → IStructure | Structure[source]

                                                          Get a reduced structure.

                                                          Parameters
                                                          @@ -1068,7 +1068,7 @@
                                                          -get_sites_in_sphere(pt: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], r: float, include_index: bool = False, include_image: bool = False) → list[pymatgen.core.structure.PeriodicNeighbor][source]
                                                          +get_sites_in_sphere(pt: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], r: float, include_index: bool = False, include_image: bool = False) → list[pymatgen.core.structure.PeriodicNeighbor][source]

                                                          Find all sites within a sphere from the point, including a site (if any) sitting on the point itself. This includes sites in other periodic images.

                                                          @@ -1102,7 +1102,7 @@
                                                          -get_sorted_structure(key: Callable | None = None, reverse: bool = False) → IStructure | Structure[source]
                                                          +get_sorted_structure(key: Callable | None = None, reverse: bool = False) → IStructure | Structure[source]

                                                          Get a sorted copy of the structure. The parameters have the same meaning as in list.sort. By default, sites are sorted by the electronegativity of the species.

                                                          @@ -1121,7 +1121,7 @@
                                                          -get_space_group_info(symprec=0.01, angle_tolerance=5.0) → tuple[str, int][source]
                                                          +get_space_group_info(symprec=0.01, angle_tolerance=5.0) → tuple[str, int][source]

                                                          Convenience method to quickly get the spacegroup of a structure.

                                                          Parameters
                                                          @@ -1140,7 +1140,7 @@
                                                          -get_symmetric_neighbor_list(r: float, sg: str, unique: bool = False, numerical_tol: float = 1e-08, exclude_self: bool = True) → tuple[numpy.ndarray, ...][source]
                                                          +get_symmetric_neighbor_list(r: float, sg: str, unique: bool = False, numerical_tol: float = 1e-08, exclude_self: bool = True) → tuple[numpy.ndarray, ...][source]

                                                          Similar to ‘get_neighbor_list’ with sites=None, but the neighbors are grouped by symmetry. The returned values are a tuple of numpy arrays (center_indices, points_indices, offset_vectors, distances,

                                                          @@ -1189,7 +1189,7 @@
                                                          -interpolate(end_structure: IStructure | Structure, nimages: int | Iterable = 10, interpolate_lattices: bool = False, pbc: bool = True, autosort_tol: float = 0) → list[IStructure | Structure][source]
                                                          +interpolate(end_structure: IStructure | Structure, nimages: int | Iterable = 10, interpolate_lattices: bool = False, pbc: bool = True, autosort_tol: float = 0) → list[IStructure | Structure][source]

                                                          Interpolate between this structure and end_structure. Useful for construction of NEB inputs.

                                                          @@ -1221,13 +1221,13 @@
                                                          -property lattice: pymatgen.core.lattice.Lattice[source]
                                                          +property lattice: pymatgen.core.lattice.Lattice[source]

                                                          Lattice of the structure.

                                                          -matches(other, anonymous=False, **kwargs) → bool[source]
                                                          +matches(other, anonymous=False, **kwargs) → bool[source]

                                                          Check whether this structure is similar to another structure. Basically a convenience method to call structure matching.

                                                          @@ -1247,13 +1247,13 @@
                                                          -property sites: tuple[pymatgen.core.sites.PeriodicSite, ...][source]
                                                          +property sites: tuple[pymatgen.core.sites.PeriodicSite, ...][source]

                                                          Returns an iterator for the sites in the Structure.

                                                          -to(fmt: str = None, filename=None, **kwargs) → str | None[source]
                                                          +to(fmt: str = None, filename=None, **kwargs) → str | None[source]

                                                          Outputs the structure to a file or string.

                                                          Parameters
                                                          @@ -1278,7 +1278,7 @@
                                                          -property volume: float[source]
                                                          +property volume: float[source]

                                                          Returns the volume of the structure.

                                                          @@ -1286,7 +1286,7 @@
                                                          -class Molecule(species: Sequence[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]], coords: Sequence[Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]], charge: float = 0.0, spin_multiplicity: Optional[int] = None, validate_proximity: bool = False, site_properties: Optional[dict] = None, charge_spin_check: bool = True)[source]
                                                          +class Molecule(species: Sequence[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]], coords: Sequence[Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]], charge: float = 0.0, spin_multiplicity: Optional[int] = None, validate_proximity: bool = False, site_properties: Optional[dict] = None, charge_spin_check: bool = True)[source]

                                                          Bases: pymatgen.core.structure.IMolecule, collections.abc.MutableSequence

                                                          Mutable Molecule. It has all the methods in IMolecule, but in addition, it allows a user to perform edits on the molecule.

                                                          @@ -1318,7 +1318,7 @@
                                                          -append(species: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies, dict, pymatgen.core.composition.Composition], coords: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], validate_proximity: bool = False, properties: Optional[dict] = None)[source]
                                                          +append(species: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies, dict, pymatgen.core.composition.Composition], coords: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], validate_proximity: bool = False, properties: Optional[dict] = None)[source]

                                                          Appends a site to the molecule.

                                                          Parameters
                                                          @@ -1338,7 +1338,7 @@
                                                          -apply_operation(symmop: pymatgen.core.operations.SymmOp)[source]
                                                          +apply_operation(symmop: pymatgen.core.operations.SymmOp)[source]

                                                          Apply a symmetry operation to the molecule.

                                                          Parameters
                                                          @@ -1349,7 +1349,7 @@
                                                          -copy()[source]
                                                          +copy()[source]

                                                          Convenience method to get a copy of the molecule.

                                                          Returns
                                                          @@ -1360,7 +1360,7 @@
                                                          -insert(i: int, species: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies, dict, pymatgen.core.composition.Composition], coords: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], validate_proximity: bool = False, properties: Optional[dict] = None)[source]
                                                          +insert(i: int, species: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies, dict, pymatgen.core.composition.Composition], coords: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], validate_proximity: bool = False, properties: Optional[dict] = None)[source]

                                                          Insert a site to the molecule.

                                                          Parameters
                                                          @@ -1381,7 +1381,7 @@
                                                          -perturb(distance: float)[source]
                                                          +perturb(distance: float)[source]

                                                          Performs a random perturbation of the sites in a structure to break symmetries.

                                                          @@ -1394,7 +1394,7 @@
                                                          -remove_sites(indices: Sequence[int])[source]
                                                          +remove_sites(indices: Sequence[int])[source]

                                                          Delete sites with at indices.

                                                          Parameters
                                                          @@ -1405,7 +1405,7 @@
                                                          -remove_species(species: Sequence[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]])[source]
                                                          +remove_species(species: Sequence[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]])[source]

                                                          Remove all occurrences of a species from a molecule.

                                                          Parameters
                                                          @@ -1416,7 +1416,7 @@
                                                          -rotate_sites(indices: Optional[Sequence[int]] = None, theta: float = 0.0, axis: Optional[Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]] = None, anchor: Optional[Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]] = None)[source]
                                                          +rotate_sites(indices: Optional[Sequence[int]] = None, theta: float = 0.0, axis: Optional[Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]] = None, anchor: Optional[Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]] = None)[source]

                                                          Rotate specific sites by some angle around vector at anchor.

                                                          Parameters
                                                          @@ -1433,7 +1433,7 @@
                                                          -set_charge_and_spin(charge: float, spin_multiplicity: int | None = None)[source]
                                                          +set_charge_and_spin(charge: float, spin_multiplicity: int | None = None)[source]

                                                          Set the charge and spin multiplicity.

                                                          Parameters
                                                          @@ -1450,7 +1450,7 @@
                                                          -substitute(index: int, func_group: IMolecule | Molecule | str, bond_order: int = 1)[source]
                                                          +substitute(index: int, func_group: IMolecule | Molecule | str, bond_order: int = 1)[source]

                                                          Substitute atom at index with a functional group.

                                                          Parameters
                                                          @@ -1481,7 +1481,7 @@
                                                          -translate_sites(indices: Optional[Sequence[int]] = None, vector: Optional[Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]] = None)[source]
                                                          +translate_sites(indices: Optional[Sequence[int]] = None, vector: Optional[Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]] = None)[source]

                                                          Translate specific sites by some vector, keeping the sites within the unit cell.

                                                          @@ -1499,7 +1499,7 @@
                                                          -class Neighbor(species: pymatgen.core.composition.Composition, coords: numpy.ndarray, properties: Optional[dict] = None, nn_distance: float = 0.0, index: int = 0)[source]
                                                          +class Neighbor(species: pymatgen.core.composition.Composition, coords: numpy.ndarray, properties: Optional[dict] = None, nn_distance: float = 0.0, index: int = 0)[source]

                                                          Bases: pymatgen.core.sites.Site

                                                          Simple Site subclass to contain a neighboring atom that skips all the unnecessary checks for speed. Can be used as a fixed-length tuple of size 3 to retain backwards compatibility with past use cases.

                                                          @@ -1520,19 +1520,19 @@
                                                          -coords: numpy.ndarray[source]
                                                          +coords: numpy.ndarray[source]
                                                          -properties: dict[source]
                                                          +properties: dict[source]
                                                          -class PeriodicNeighbor(species: pymatgen.core.composition.Composition, coords: numpy.ndarray, lattice: pymatgen.core.lattice.Lattice, properties: Optional[dict] = None, nn_distance: float = 0.0, index: int = 0, image: tuple = (0, 0, 0))[source]
                                                          +class PeriodicNeighbor(species: pymatgen.core.composition.Composition, coords: numpy.ndarray, lattice: pymatgen.core.lattice.Lattice, properties: Optional[dict] = None, nn_distance: float = 0.0, index: int = 0, image: tuple = (0, 0, 0))[source]

                                                          Bases: pymatgen.core.sites.PeriodicSite

                                                          Simple PeriodicSite subclass to contain a neighboring atom that skips all the unnecessary checks for speed. Can be used as a fixed-length tuple of @@ -1557,7 +1557,7 @@

                                                          -property coords: numpy.ndarray[source]
                                                          +property coords: numpy.ndarray[source]

                                                          Cartesian coords.

                                                          Type
                                                          @@ -1568,14 +1568,14 @@
                                                          -properties: dict[source]
                                                          +properties: dict[source]
                                                          -class SiteCollection[source]
                                                          +class SiteCollection[source]

                                                          Bases: collections.abc.Sequence

                                                          Basic SiteCollection. Essentially a sequence of Sites or PeriodicSites. This serves as a base class for Molecule (a collection of Site, i.e., no @@ -1583,12 +1583,12 @@ periodicity). Not meant to be instantiated directly.

                                                          -DISTANCE_TOLERANCE = 0.5[source]
                                                          +DISTANCE_TOLERANCE = 0.5[source]
                                                          -add_oxidation_state_by_element(oxidation_states: dict[str, float])[source]
                                                          +add_oxidation_state_by_element(oxidation_states: dict[str, float])[source]

                                                          Add oxidation states.

                                                          Parameters
                                                          @@ -1600,7 +1600,7 @@
                                                          -add_oxidation_state_by_guess(**kwargs)[source]
                                                          +add_oxidation_state_by_guess(**kwargs)[source]

                                                          Decorates the structure with oxidation state, guessing using Composition.oxi_state_guesses()

                                                          @@ -1612,7 +1612,7 @@
                                                          -add_oxidation_state_by_site(oxidation_states: list[float])[source]
                                                          +add_oxidation_state_by_site(oxidation_states: list[float])[source]

                                                          Add oxidation states to a structure by site.

                                                          Parameters
                                                          @@ -1624,7 +1624,7 @@
                                                          -add_site_property(property_name: str, values: list)[source]
                                                          +add_site_property(property_name: str, values: list)[source]

                                                          Adds a property to a site. Note: This is the preferred method for adding magnetic moments, selective dynamics, and related site-specific properties to a structure/molecule object. @@ -1644,7 +1644,7 @@

                                                          -add_spin_by_element(spins: dict[str, float])[source]
                                                          +add_spin_by_element(spins: dict[str, float])[source]

                                                          Add spin states to a structure.

                                                          Parameters
                                                          @@ -1656,7 +1656,7 @@
                                                          -add_spin_by_site(spins: list[float])[source]
                                                          +add_spin_by_site(spins: list[float])[source]

                                                          Add spin states to a structure by site.

                                                          Parameters
                                                          @@ -1668,33 +1668,33 @@
                                                          -property atomic_numbers: tuple[int, ...][source]
                                                          +property atomic_numbers: tuple[int, ...][source]

                                                          List of atomic numbers.

                                                          -property cart_coords: numpy.ndarray[source]
                                                          +property cart_coords: numpy.ndarray[source]

                                                          Returns an np.array of the Cartesian coordinates of sites in the structure.

                                                          -property charge: float[source]
                                                          +property charge: float[source]

                                                          Returns the net charge of the structure based on oxidation states. If Elements are found, a charge of 0 is assumed.

                                                          -property composition: pymatgen.core.composition.Composition[source]
                                                          +property composition: pymatgen.core.composition.Composition[source]

                                                          (Composition) Returns the composition

                                                          -property distance_matrix: numpy.ndarray[source]
                                                          +property distance_matrix: numpy.ndarray[source]

                                                          Returns the distance matrix between all sites in the structure. For periodic structures, this is overwritten to return the nearest image distance.

                                                          @@ -1702,7 +1702,7 @@
                                                          -extract_cluster(target_sites: list[pymatgen.core.sites.Site], **kwargs)[source]
                                                          +extract_cluster(target_sites: list[pymatgen.core.sites.Site], **kwargs)[source]

                                                          Extracts a cluster of atoms based on bond lengths

                                                          Parameters
                                                          @@ -1719,25 +1719,25 @@
                                                          -property formula: str[source]
                                                          +property formula: str[source]

                                                          (str) Returns the formula.

                                                          -abstract classmethod from_file(filename: str)[source]
                                                          +abstract classmethod from_file(filename: str)[source]

                                                          Reads in SiteCollection from a filename.

                                                          -abstract classmethod from_str(input_string: str, fmt: Any)[source]
                                                          +abstract classmethod from_str(input_string: str, fmt: Any)[source]

                                                          Reads in SiteCollection from a string.

                                                          -get_angle(i: int, j: int, k: int) → float[source]
                                                          +get_angle(i: int, j: int, k: int) → float[source]

                                                          Returns angle specified by three sites.

                                                          Parameters
                                                          @@ -1755,7 +1755,7 @@
                                                          -get_dihedral(i: int, j: int, k: int, l: int) → float[source]
                                                          +get_dihedral(i: int, j: int, k: int, l: int) → float[source]

                                                          Returns dihedral angle specified by four sites.

                                                          Parameters
                                                          @@ -1774,7 +1774,7 @@
                                                          -abstract get_distance(i: int, j: int) → float[source]
                                                          +abstract get_distance(i: int, j: int) → float[source]

                                                          Returns distance between sites at index i and j.

                                                          Parameters
                                                          @@ -1791,27 +1791,27 @@
                                                          -group_by_types() → Iterator[Site | PeriodicSite][source]
                                                          +group_by_types() → Iterator[Site | PeriodicSite][source]

                                                          Iterate over species grouped by type

                                                          -indices_from_symbol(symbol: str) → tuple[int, ...][source]
                                                          +indices_from_symbol(symbol: str) → tuple[int, ...][source]

                                                          Returns a tuple with the sequential indices of the sites that contain an element with the given chemical symbol.

                                                          -property is_ordered: bool[source]
                                                          +property is_ordered: bool[source]

                                                          Checks if structure is ordered, meaning no partial occupancies in any of the sites.

                                                          -is_valid(tol: float = 0.5) → bool[source]
                                                          +is_valid(tol: float = 0.5) → bool[source]

                                                          True if SiteCollection does not contain atoms that are too close together. Note that the distance definition is based on type of SiteCollection. Cartesian distances are used for non-periodic @@ -1829,25 +1829,25 @@

                                                          -property ntypesp: int[source]
                                                          +property ntypesp: int[source]

                                                          Number of types of atoms.

                                                          -property num_sites: int[source]
                                                          +property num_sites: int[source]

                                                          Number of sites.

                                                          -remove_oxidation_states()[source]
                                                          +remove_oxidation_states()[source]

                                                          Removes oxidation states from a structure.

                                                          -remove_site_property(property_name: str)[source]
                                                          +remove_site_property(property_name: str)[source]

                                                          Removes a property to a site.

                                                          Parameters
                                                          @@ -1858,13 +1858,13 @@
                                                          -remove_spin()[source]
                                                          +remove_spin()[source]

                                                          Removes spin states from a structure.

                                                          -replace_species(species_mapping: dict[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies], Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]]) → None[source]
                                                          +replace_species(species_mapping: dict[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies], Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]]) → None[source]

                                                          Swap species. Note that this method modifies the structure in place.

                                                          Parameters
                                                          @@ -1880,20 +1880,20 @@
                                                          -property site_properties: dict[str, list][source]
                                                          +property site_properties: dict[str, list][source]

                                                          Returns the site properties as a dict of sequences. E.g., {“magmom”: (5,-5), “charge”: (-4,4)}.

                                                          -abstract property sites: tuple[pymatgen.core.sites.Site, ...][source]
                                                          +abstract property sites: tuple[pymatgen.core.sites.Site, ...][source]

                                                          Returns a tuple of sites.

                                                          -property species: list[Element | Species][source]
                                                          +property species: list[Element | Species][source]

                                                          Only works for ordered structures. Disordered structures will raise an AttributeError.

                                                          @@ -1905,33 +1905,33 @@
                                                          -property species_and_occu: list[pymatgen.core.composition.Composition][source]
                                                          +property species_and_occu: list[pymatgen.core.composition.Composition][source]

                                                          List of species and occupancies at each site of the structure.

                                                          -property symbol_set: tuple[str, ...][source]
                                                          +property symbol_set: tuple[str, ...][source]

                                                          Tuple with the set of chemical symbols. Note that len(symbol_set) == len(types_of_specie)

                                                          -abstract to(fmt: Optional[str] = None, filename: Optional[str] = None)[source]
                                                          +abstract to(fmt: Optional[str] = None, filename: Optional[str] = None)[source]

                                                          Generates well-known string representations of SiteCollections (e.g., molecules / structures). Should return a string type or write to a file.

                                                          -property types_of_specie: tuple[Element | Species | DummySpecies][source]
                                                          +property types_of_specie: tuple[Element | Species | DummySpecies][source]

                                                          Specie->Species rename. Maintained for backwards compatibility.

                                                          -property types_of_species: tuple[Element | Species | DummySpecies][source]
                                                          +property types_of_species: tuple[Element | Species | DummySpecies][source]

                                                          List of types of specie.

                                                          @@ -1939,7 +1939,7 @@
                                                          -class Structure(lattice: ArrayLike | Lattice, species: Sequence[CompositionLike], coords: Sequence[ArrayLike], charge: float = None, validate_proximity: bool = False, to_unit_cell: bool = False, coords_are_cartesian: bool = False, site_properties: dict = None)[source]
                                                          +class Structure(lattice: ArrayLike | Lattice, species: Sequence[CompositionLike], coords: Sequence[ArrayLike], charge: float = None, validate_proximity: bool = False, to_unit_cell: bool = False, coords_are_cartesian: bool = False, site_properties: dict = None)[source]

                                                          Bases: pymatgen.core.structure.IStructure, collections.abc.MutableSequence

                                                          Mutable version of structure.

                                                          Create a periodic structure.

                                                          @@ -1981,7 +1981,7 @@
                                                          -append(species: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies, dict, pymatgen.core.composition.Composition], coords: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], coords_are_cartesian: bool = False, validate_proximity: bool = False, properties: Optional[dict] = None)[source]
                                                          +append(species: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies, dict, pymatgen.core.composition.Composition], coords: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], coords_are_cartesian: bool = False, validate_proximity: bool = False, properties: Optional[dict] = None)[source]

                                                          Append a site to the structure.

                                                          Parameters
                                                          @@ -2003,7 +2003,7 @@
                                                          -apply_operation(symmop: pymatgen.core.operations.SymmOp, fractional: bool = False) → pymatgen.core.structure.Structure[source]
                                                          +apply_operation(symmop: pymatgen.core.operations.SymmOp, fractional: bool = False) → pymatgen.core.structure.Structure[source]

                                                          Apply a symmetry operation to the structure in place and return the modified structure. The lattice is operated on by the rotation matrix only. Coords are operated in full and then transformed to the new lattice.

                                                          @@ -2027,7 +2027,7 @@
                                                          -apply_strain(strain: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]) → None[source]
                                                          +apply_strain(strain: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]) → None[source]

                                                          Apply a strain to the lattice.

                                                          Parameters
                                                          @@ -2042,7 +2042,7 @@
                                                          -insert(i: int, species: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies, dict, pymatgen.core.composition.Composition], coords: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], coords_are_cartesian: bool = False, validate_proximity: bool = False, properties: Optional[dict] = None)[source]
                                                          +insert(i: int, species: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies, dict, pymatgen.core.composition.Composition], coords: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], coords_are_cartesian: bool = False, validate_proximity: bool = False, properties: Optional[dict] = None)[source]

                                                          Insert a site to the structure.

                                                          Parameters
                                                          @@ -2065,7 +2065,7 @@
                                                          -property lattice: pymatgen.core.lattice.Lattice[source]
                                                          +property lattice: pymatgen.core.lattice.Lattice[source]

                                                          Lattice associated with structure.

                                                          Type
                                                          @@ -2076,7 +2076,7 @@
                                                          -make_supercell(scaling_matrix: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], to_unit_cell: bool = True) → None[source]
                                                          +make_supercell(scaling_matrix: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], to_unit_cell: bool = True) → None[source]

                                                          Create a supercell.

                                                          Parameters
                                                          @@ -2104,7 +2104,7 @@
                                                          -merge_sites(tol: float = 0.01, mode: Literal['sum', 'delete', 'average'] = 'sum') → None[source]
                                                          +merge_sites(tol: float = 0.01, mode: Literal['sum', 'delete', 'average'] = 'sum') → None[source]

                                                          Merges sites (adding occupancies) within tol of each other. Removes site properties.

                                                          @@ -2122,7 +2122,7 @@
                                                          -perturb(distance: float, min_distance: Optional[float] = None) → None[source]
                                                          +perturb(distance: float, min_distance: Optional[float] = None) → None[source]

                                                          Performs a random perturbation of the sites in a structure to break symmetries.

                                                          @@ -2141,7 +2141,7 @@
                                                          -remove_sites(indices: Sequence[int]) → None[source]
                                                          +remove_sites(indices: Sequence[int]) → None[source]

                                                          Delete sites with at indices.

                                                          Parameters
                                                          @@ -2152,7 +2152,7 @@
                                                          -remove_species(species: Sequence[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]])[source]
                                                          +remove_species(species: Sequence[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]])[source]

                                                          Remove all occurrences of several species from a structure.

                                                          Parameters
                                                          @@ -2163,7 +2163,7 @@
                                                          -replace(i: int, species: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies, dict, pymatgen.core.composition.Composition], coords: Optional[Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]] = None, coords_are_cartesian: bool = False, properties: Optional[dict] = None)[source]
                                                          +replace(i: int, species: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies, dict, pymatgen.core.composition.Composition], coords: Optional[Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]] = None, coords_are_cartesian: bool = False, properties: Optional[dict] = None)[source]

                                                          Replace a single site. Takes either a species or a dict of species and occupations.

                                                          @@ -2183,7 +2183,7 @@
                                                          -rotate_sites(indices: Optional[list[int]] = None, theta: float = 0.0, axis: Optional[Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]] = None, anchor: Optional[Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]] = None, to_unit_cell: bool = True) → None[source]
                                                          +rotate_sites(indices: Optional[list[int]] = None, theta: float = 0.0, axis: Optional[Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]] = None, anchor: Optional[Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]] = None, to_unit_cell: bool = True) → None[source]

                                                          Rotate specific sites by some angle around vector at anchor.

                                                          Parameters
                                                          @@ -2202,7 +2202,7 @@
                                                          -scale_lattice(volume: float) → None[source]
                                                          +scale_lattice(volume: float) → None[source]

                                                          Performs a scaling of the lattice vectors so that length proportions and angles are preserved.

                                                          @@ -2214,7 +2214,7 @@
                                                          -set_charge(new_charge: float = 0.0) → None[source]
                                                          +set_charge(new_charge: float = 0.0) → None[source]

                                                          Sets the overall structure charge

                                                          Parameters
                                                          @@ -2225,7 +2225,7 @@
                                                          -sort(key: Optional[Callable] = None, reverse: bool = False) → None[source]
                                                          +sort(key: Optional[Callable] = None, reverse: bool = False) → None[source]

                                                          Sort a structure in place. The parameters have the same meaning as in list.sort. By default, sites are sorted by the electronegativity of the species. The difference between this method and @@ -2247,7 +2247,7 @@

                                                          -substitute(index: int, func_group: IMolecule | Molecule | str, bond_order: int = 1)[source]
                                                          +substitute(index: int, func_group: IMolecule | Molecule | str, bond_order: int = 1)[source]

                                                          Substitute atom at index with a functional group.

                                                          Parameters
                                                          @@ -2278,7 +2278,7 @@
                                                          -translate_sites(indices: int | Sequence[int], vector: ArrayLike, frac_coords: bool = True, to_unit_cell: bool = True) → None[source]
                                                          +translate_sites(indices: int | Sequence[int], vector: ArrayLike, frac_coords: bool = True, to_unit_cell: bool = True) → None[source]

                                                          Translate specific sites by some vector, keeping the sites within the unit cell.

                                                          @@ -2300,7 +2300,7 @@
                                                          -exception StructureError[source]
                                                          +exception StructureError[source]

                                                          Bases: Exception

                                                          Exception class for Structure. Raised when the structure has problems, e.g., atoms that are too close.

                                                          diff --git a/docs/pymatgen.core.surface.html b/docs/pymatgen.core.surface.html index 06b82b4424b..85190db63fa 100644 --- a/docs/pymatgen.core.surface.html +++ b/docs/pymatgen.core.surface.html @@ -4,7 +4,7 @@ - pymatgen.core.surface module — pymatgen 2022.5.18 documentation + pymatgen.core.surface module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                          - 2022.5.18 + 2022.5.18.1
                                                          @@ -130,7 +130,7 @@
                                                          -class ReconstructionGenerator(initial_structure, min_slab_size, min_vacuum_size, reconstruction_name)[source]
                                                          +class ReconstructionGenerator(initial_structure, min_slab_size, min_vacuum_size, reconstruction_name)[source]

                                                          Bases: object

                                                          This class takes in a pre-defined dictionary specifying the parameters need to build a reconstructed slab such as the SlabGenerator parameters, @@ -139,7 +139,7 @@ the desired reconstructed slab from the initial structure.

                                                          -slabgen_params[source]
                                                          +slabgen_params[source]

                                                          Parameters for the SlabGenerator

                                                          @@ -250,7 +250,7 @@
                                                          -build_slabs()[source]
                                                          +build_slabs()[source]
                                                          Builds the reconstructed slab by:

                                                          1. Obtaining the unreconstructed slab using the specified @@ -274,7 +274,7 @@

                                                            -get_unreconstructed_slabs()[source]
                                                            +get_unreconstructed_slabs()[source]

                                                            Generates the unreconstructed or pristine super slab.

                                                            @@ -282,7 +282,7 @@
                                                            -class Slab(lattice, species, coords, miller_index, oriented_unit_cell, shift, scale_factor, reorient_lattice=True, validate_proximity=False, to_unit_cell=False, reconstruction=None, coords_are_cartesian=False, site_properties=None, energy=None)[source]
                                                            +class Slab(lattice, species, coords, miller_index, oriented_unit_cell, shift, scale_factor, reorient_lattice=True, validate_proximity=False, to_unit_cell=False, reconstruction=None, coords_are_cartesian=False, site_properties=None, energy=None)[source]

                                                            Bases: pymatgen.core.structure.Structure

                                                            Subclass of Structure representing a Slab. Implements additional attributes pertaining to slabs, but the init method does not @@ -296,20 +296,20 @@ necessarily perpendicular to the surface).

                                                            -miller_index[source]
                                                            +miller_index[source]

                                                            Miller index of plane parallel to surface.

                                                            -scale_factor[source]
                                                            +scale_factor[source]

                                                            Final computed scale factor that brings the parent cell to the surface cell.

                                                            -shift[source]
                                                            +shift[source]

                                                            The shift value in Angstrom that indicates how much this slab has been shifted.

                                                            @@ -365,7 +365,7 @@
                                                            -add_adsorbate_atom(indices, specie, distance)[source]
                                                            +add_adsorbate_atom(indices, specie, distance)[source]

                                                            Gets the structure of single atom adsorption. slab structure from the Slab class(in [0, 0, 1])

                                                            @@ -384,7 +384,7 @@
                                                            -as_dict()[source]
                                                            +as_dict()[source]
                                                            Returns

                                                            MSONAble dict

                                                            @@ -394,13 +394,13 @@
                                                            -property center_of_mass[source]
                                                            +property center_of_mass[source]

                                                            Calculates the center of mass of the slab

                                                            -copy(site_properties=None, sanitize=False)[source]
                                                            +copy(site_properties=None, sanitize=False)[source]

                                                            Convenience method to get a copy of the structure, with options to add site properties.

                                                            @@ -428,7 +428,7 @@
                                                            -property dipole[source]
                                                            +property dipole[source]

                                                            Calculates the dipole of the Slab in the direction of the surface normal. Note that the Slab must be oxidation state-decorated for this to work properly. Otherwise, the Slab will always have a dipole of 0.

                                                            @@ -436,7 +436,7 @@
                                                            -classmethod from_dict(d)[source]
                                                            +classmethod from_dict(d)[source]
                                                            Parameters

                                                            d – dict

                                                            @@ -449,7 +449,7 @@
                                                            -get_orthogonal_c_slab()[source]
                                                            +get_orthogonal_c_slab()[source]

                                                            This method returns a Slab where the normal (c lattice vector) is “forced” to be exactly orthogonal to the surface a and b lattice vectors. Note that this breaks inherent symmetries in the slab. @@ -461,7 +461,7 @@

                                                            -get_sorted_structure(key=None, reverse=False)[source]
                                                            +get_sorted_structure(key=None, reverse=False)[source]

                                                            Get a sorted copy of the structure. The parameters have the same meaning as in list.sort. By default, sites are sorted by the electronegativity of the species. Note that Slab has to override this @@ -481,7 +481,7 @@

                                                            -get_surface_sites(tag=False)[source]
                                                            +get_surface_sites(tag=False)[source]

                                                            Returns the surface sites and their indices in a dictionary. The oriented unit cell of the slab will determine the coordination number of a typical site. We use VoronoiNN to determine the @@ -507,7 +507,7 @@

                                                            -get_symmetric_site(point, cartesian=False)[source]
                                                            +get_symmetric_site(point, cartesian=False)[source]
                                                            This method uses symmetry operations to find equivalent sites on

                                                            both sides of the slab. Works mainly for slabs with Laue symmetry. This is useful for retaining the non-polar and @@ -533,7 +533,7 @@

                                                            -get_tasker2_slabs(tol=0.01, same_species_only=True)[source]
                                                            +get_tasker2_slabs(tol=0.01, same_species_only=True)[source]

                                                            Get a list of slabs that have been Tasker 2 corrected.

                                                            Parameters
                                                            @@ -555,7 +555,7 @@
                                                            -is_polar(tol_dipole_per_unit_area=0.001)[source]
                                                            +is_polar(tol_dipole_per_unit_area=0.001)[source]

                                                            Checks whether the surface is polar by computing the dipole per unit area. Note that the Slab must be oxidation state-decorated for this to work properly. Otherwise, the Slab will always be non-polar.

                                                            @@ -573,7 +573,7 @@
                                                            -is_symmetric(symprec=0.1)[source]
                                                            +is_symmetric(symprec=0.1)[source]
                                                            Checks if surfaces are symmetric, i.e., contains inversion, mirror on (hkl) plane,

                                                            or screw axis (rotation and translation) about [hkl].

                                                            @@ -590,19 +590,19 @@
                                                            -property normal[source]
                                                            +property normal[source]

                                                            Calculates the surface normal vector of the slab

                                                            -property surface_area[source]
                                                            +property surface_area[source]

                                                            Calculates the surface area of the slab

                                                            -symmetrically_add_atom(specie, point, coords_are_cartesian=False)[source]
                                                            +symmetrically_add_atom(specie, point, coords_are_cartesian=False)[source]
                                                            Class method for adding a site at a specified point in a slab.

                                                            Will add the corresponding site on the other side of the slab to maintain equivalent surfaces.

                                                            @@ -624,7 +624,7 @@
                                                            -symmetrically_remove_atoms(indices)[source]
                                                            +symmetrically_remove_atoms(indices)[source]
                                                            Class method for removing sites corresponding to a list of indices.

                                                            Will remove the corresponding site on the other side of the slab to maintain equivalent surfaces.

                                                            @@ -641,7 +641,7 @@
                                                            -class SlabGenerator(initial_structure, miller_index, min_slab_size, min_vacuum_size, lll_reduce=False, center_slab=False, in_unit_planes=False, primitive=True, max_normal_search=None, reorient_lattice=True)[source]
                                                            +class SlabGenerator(initial_structure, miller_index, min_slab_size, min_vacuum_size, lll_reduce=False, center_slab=False, in_unit_planes=False, primitive=True, max_normal_search=None, reorient_lattice=True)[source]

                                                            Bases: object

                                                            This class generates different slabs using shift values determined by where a unique termination can be found along with other criteria such as where a @@ -649,52 +649,52 @@ where the slab layer will begin and terminate in the slab-vacuum system.

                                                            -oriented_unit_cell[source]
                                                            +oriented_unit_cell[source]

                                                            A unit cell of the parent structure with the miller index of plane parallel to surface

                                                            -parent[source]
                                                            +parent[source]

                                                            Parent structure from which Slab was derived.

                                                            -lll_reduce[source]
                                                            +lll_reduce[source]

                                                            Whether or not the slabs will be orthogonalized

                                                            -center_slab[source]
                                                            +center_slab[source]

                                                            Whether or not the slabs will be centered between the vacuum layer

                                                            -slab_scale_factor[source]
                                                            +slab_scale_factor[source]

                                                            Final computed scale factor that brings the parent cell to the surface cell.

                                                            -miller_index[source]
                                                            +miller_index[source]

                                                            Miller index of plane parallel to surface.

                                                            -min_slab_size[source]
                                                            +min_slab_size[source]

                                                            Minimum size in angstroms of layers containing atoms

                                                            -min_vac_size[source]
                                                            +min_vac_size[source]

                                                            Minimize size in angstroms of layers containing vacuum

                                                            @@ -752,7 +752,7 @@
                                                            -get_slab(shift=0, tol=0.1, energy=None)[source]
                                                            +get_slab(shift=0, tol=0.1, energy=None)[source]

                                                            This method takes in shift value for the c lattice direction and generates a slab based on the given shift. You should rarely use this method. Instead, it is used by other generation algorithms to obtain @@ -775,7 +775,7 @@

                                                            -get_slabs(bonds=None, ftol=0.1, tol=0.1, max_broken_bonds=0, symmetrize=False, repair=False)[source]
                                                            +get_slabs(bonds=None, ftol=0.1, tol=0.1, max_broken_bonds=0, symmetrize=False, repair=False)[source]

                                                            This method returns a list of slabs that are generated using the list of shift values from the method, _calculate_possible_shifts(). Before the shifts are used to create the slabs however, if the user decides to take @@ -814,7 +814,7 @@

                                                            -move_to_other_side(init_slab, index_of_sites)[source]
                                                            +move_to_other_side(init_slab, index_of_sites)[source]

                                                            This method will Move a set of sites to the other side of the slab (opposite surface).

                                                            @@ -834,7 +834,7 @@
                                                            -nonstoichiometric_symmetrized_slab(init_slab)[source]
                                                            +nonstoichiometric_symmetrized_slab(init_slab)[source]

                                                            This method checks whether or not the two surfaces of the slab are equivalent. If the point group of the slab has an inversion symmetry ( ie. belong to one of the Laue groups), then it is assumed that the @@ -858,7 +858,7 @@

                                                            -repair_broken_bonds(slab, bonds)[source]
                                                            +repair_broken_bonds(slab, bonds)[source]

                                                            This method will find undercoordinated atoms due to slab cleaving specified by the bonds parameter and move them to the other surface to make sure the bond is kept intact. @@ -885,7 +885,7 @@

                                                            -center_slab(slab)[source]
                                                            +center_slab(slab)[source]
                                                            The goal here is to ensure the center of the slab region

                                                            is centered close to c=0.5. This makes it easier to find the surface sites and apply operations like doping.

                                                            @@ -915,7 +915,7 @@
                                                            -generate_all_slabs(structure, max_index, min_slab_size, min_vacuum_size, bonds=None, tol=0.1, ftol=0.1, max_broken_bonds=0, lll_reduce=False, center_slab=False, primitive=True, max_normal_search=None, symmetrize=False, repair=False, include_reconstructions=False, in_unit_planes=False)[source]
                                                            +generate_all_slabs(structure, max_index, min_slab_size, min_vacuum_size, bonds=None, tol=0.1, ftol=0.1, max_broken_bonds=0, lll_reduce=False, center_slab=False, primitive=True, max_normal_search=None, symmetrize=False, repair=False, include_reconstructions=False, in_unit_planes=False)[source]

                                                            A function that finds all different slabs up to a certain miller index. Slabs oriented under certain Miller indices that are equivalent to other slabs in other Miller indices are filtered out using symmetry operations @@ -978,14 +978,14 @@

                                                            -get_d(slab)[source]
                                                            +get_d(slab)[source]

                                                            Determine the distance of space between each layer of atoms along c

                                                            -get_slab_regions(slab, blength=3.5)[source]
                                                            +get_slab_regions(slab, blength=3.5)[source]

                                                            Function to get the ranges of the slab regions. Useful for discerning where the slab ends and vacuum begins if the slab is not fully within the cell :param slab: Structure object modelling the surface @@ -1001,7 +1001,7 @@

                                                            -get_symmetrically_distinct_miller_indices(structure, max_index, return_hkil=False)[source]
                                                            +get_symmetrically_distinct_miller_indices(structure, max_index, return_hkil=False)[source]

                                                            Returns all symmetrically distinct indices below a certain max-index for a given structure. Analysis is based on the symmetry of the reciprocal lattice of the structure. @@ -1022,7 +1022,7 @@

                                                            -get_symmetrically_equivalent_miller_indices(structure, miller_index, return_hkil=True)[source]
                                                            +get_symmetrically_equivalent_miller_indices(structure, miller_index, return_hkil=True)[source]

                                                            Returns all symmetrically equivalent indices for a given structure. Analysis is based on the symmetry of the reciprocal lattice of the structure.

                                                            @@ -1039,7 +1039,7 @@
                                                            -hkl_transformation(transf, miller_index)[source]
                                                            +hkl_transformation(transf, miller_index)[source]

                                                            Returns the Miller index from setting A to B using a transformation matrix :param transf: The transformation matrix

                                                            @@ -1055,7 +1055,7 @@
                                                            -is_already_analyzed(miller_index: tuple, miller_list: list, symm_ops: list) → bool[source]
                                                            +is_already_analyzed(miller_index: tuple, miller_list: list, symm_ops: list) → bool[source]

                                                            Helper function to check if a given Miller index is part of the family of indices of any index in a list

                                                            @@ -1074,7 +1074,7 @@
                                                            -miller_index_from_sites(lattice, coords, coords_are_cartesian=True, round_dp=4, verbose=True)[source]
                                                            +miller_index_from_sites(lattice, coords, coords_are_cartesian=True, round_dp=4, verbose=True)[source]

                                                            Get the Miller index of a plane from a list of site coordinates.

                                                            A minimum of 3 sets of coordinates are required. If more than 3 sets of coordinates are given, the best plane that minimises the distance to all diff --git a/docs/pymatgen.core.tensors.html b/docs/pymatgen.core.tensors.html index e72ea899b53..99df01c0739 100644 --- a/docs/pymatgen.core.tensors.html +++ b/docs/pymatgen.core.tensors.html @@ -4,7 +4,7 @@ - pymatgen.core.tensors module — pymatgen 2022.5.18 documentation + pymatgen.core.tensors module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                                            - 2022.5.18 + 2022.5.18.1
                                                            @@ -120,7 +120,7 @@ that provides basic methods for creating and manipulating rank 2 tensors

                                                            -class SquareTensor(input_array, vscale=None)[source]
                                                            +class SquareTensor(input_array, vscale=None)[source]

                                                            Bases: pymatgen.core.tensors.Tensor

                                                            Base class for doing useful general operations on second rank tensors (stress, strain etc.).

                                                            @@ -140,13 +140,13 @@
                                                            -property det[source]
                                                            +property det[source]

                                                            shorthand for the determinant of the SquareTensor

                                                            -get_scaled(scale_factor)[source]
                                                            +get_scaled(scale_factor)[source]

                                                            Scales the tensor by a certain multiplicative scale factor

                                                            Parameters
                                                            @@ -158,13 +158,13 @@
                                                            -property inv[source]
                                                            +property inv[source]

                                                            shorthand for matrix inverse on SquareTensor

                                                            -is_rotation(tol=0.001, include_improper=True)[source]
                                                            +is_rotation(tol=0.001, include_improper=True)[source]

                                                            Test to see if tensor is a valid rotation matrix, performs a test to check whether the inverse is equal to the transpose and if the determinant is equal to one within the specified @@ -184,13 +184,13 @@

                                                            -polar_decomposition(side='right')[source]
                                                            +polar_decomposition(side='right')[source]

                                                            calculates matrices for polar decomposition

                                                            -property principal_invariants[source]
                                                            +property principal_invariants[source]

                                                            Returns a list of principal invariants for the tensor, which are the values of the coefficients of the characteristic polynomial for the matrix

                                                            @@ -198,7 +198,7 @@
                                                            -refine_rotation()[source]
                                                            +refine_rotation()[source]

                                                            Helper method for refining rotation matrix by ensuring that second and third rows are perpendicular to the first. Gets new y vector from an orthogonal projection of x onto y @@ -215,7 +215,7 @@

                                                            -property trans[source]
                                                            +property trans[source]

                                                            shorthand for transpose on SquareTensor

                                                            @@ -223,7 +223,7 @@
                                                            -class Tensor(input_array, vscale=None, check_rank=None)[source]
                                                            +class Tensor(input_array, vscale=None, check_rank=None)[source]

                                                            Bases: numpy.ndarray, monty.json.MSONable

                                                            Base class for doing useful general operations on Nth order tensors, without restrictions on the type (stress, elastic, strain, piezo, etc.)

                                                            @@ -242,7 +242,7 @@
                                                            -as_dict(voigt: bool = False) → dict[source]
                                                            +as_dict(voigt: bool = False) → dict[source]

                                                            Serializes the tensor object

                                                            Parameters
                                                            @@ -259,7 +259,7 @@
                                                            -average_over_unit_sphere(quad=None)[source]
                                                            +average_over_unit_sphere(quad=None)[source]

                                                            Method for averaging the tensor projection over the unit with option for custom quadrature.

                                                            @@ -276,7 +276,7 @@
                                                            -convert_to_ieee(structure, initial_fit=True, refine_rotation=True)[source]
                                                            +convert_to_ieee(structure, initial_fit=True, refine_rotation=True)[source]

                                                            Given a structure associated with a tensor, attempts a calculation of the tensor in IEEE format according to the 1987 IEEE standards.

                                                            @@ -300,13 +300,13 @@
                                                            -einsum_sequence(other_arrays, einsum_string=None)[source]
                                                            +einsum_sequence(other_arrays, einsum_string=None)[source]

                                                            Calculates the result of an einstein summation expression

                                                            -fit_to_structure(structure, symprec=0.1)[source]
                                                            +fit_to_structure(structure, symprec=0.1)[source]

                                                            Returns a tensor that is invariant with respect to symmetry operations corresponding to a structure

                                                            @@ -323,13 +323,13 @@
                                                            -classmethod from_dict(d)[source]
                                                            +classmethod from_dict(d)[source]

                                                            MSONAble from_dict implementation.

                                                            -classmethod from_values_indices(values, indices, populate=False, structure=None, voigt_rank=None, vsym=True, verbose=False)[source]
                                                            +classmethod from_values_indices(values, indices, populate=False, structure=None, voigt_rank=None, vsym=True, verbose=False)[source]

                                                            Creates a tensor from values and indices, with options for populating the remainder of the tensor.

                                                            @@ -355,7 +355,7 @@
                                                            -classmethod from_voigt(voigt_input)[source]
                                                            +classmethod from_voigt(voigt_input)[source]

                                                            Constructor based on the voigt notation vector or matrix.

                                                            Parameters
                                                            @@ -366,7 +366,7 @@
                                                            -get_grouped_indices(voigt=False, **kwargs)[source]
                                                            +get_grouped_indices(voigt=False, **kwargs)[source]

                                                            Gets index sets for equivalent tensor values

                                                            Parameters
                                                            @@ -395,7 +395,7 @@
                                                            -static get_ieee_rotation(structure, refine_rotation=True)[source]
                                                            +static get_ieee_rotation(structure, refine_rotation=True)[source]

                                                            Given a structure associated with a tensor, determines the rotation matrix for IEEE conversion according to the 1987 IEEE standards.

                                                            @@ -413,7 +413,7 @@
                                                            -get_symbol_dict(voigt=True, zero_index=False, **kwargs)[source]
                                                            +get_symbol_dict(voigt=True, zero_index=False, **kwargs)[source]

                                                            Creates a summary dict for tensor with associated symbol

                                                            Parameters
                                                            @@ -446,7 +446,7 @@
                                                            -static get_voigt_dict(rank)[source]
                                                            +static get_voigt_dict(rank)[source]

                                                            Returns a dictionary that maps indices in the tensor to those in a voigt representation based on input rank

                                                            @@ -458,7 +458,7 @@
                                                            -is_fit_to_structure(structure, tol=0.01)[source]
                                                            +is_fit_to_structure(structure, tol=0.01)[source]

                                                            Tests whether a tensor is invariant with respect to the symmetry operations of a particular structure by testing whether the residual of the symmetric portion is below a @@ -475,7 +475,7 @@

                                                            -is_symmetric(tol=1e-05)[source]
                                                            +is_symmetric(tol=1e-05)[source]

                                                            Tests whether a tensor is symmetric or not based on the residual with its symmetric part, from self.symmetrized

                                                            @@ -487,7 +487,7 @@
                                                            -is_voigt_symmetric(tol=1e-06)[source]
                                                            +is_voigt_symmetric(tol=1e-06)[source]

                                                            Tests symmetry of tensor to that necessary for voigt-conversion by grouping indices into pairs and constructing a sequence of possible permutations to be used in a tensor transpose

                                                            @@ -495,7 +495,7 @@
                                                            -populate(structure, prec=1e-05, maxiter=200, verbose=False, precond=True, vsym=True)[source]
                                                            +populate(structure, prec=1e-05, maxiter=200, verbose=False, precond=True, vsym=True)[source]

                                                            Takes a partially populated tensor, and populates the non-zero entries according to the following procedure, iterated until the desired convergence (specified via prec) is achieved.

                                                            @@ -523,7 +523,7 @@
                                                            -project(n)[source]
                                                            +project(n)[source]

                                                            Convenience method for projection of a tensor into a vector. Returns the tensor dotted into a unit vector along the input n.

                                                            @@ -541,7 +541,7 @@
                                                            -rotate(matrix, tol=0.001)[source]
                                                            +rotate(matrix, tol=0.001)[source]

                                                            Applies a rotation directly, and tests input matrix to ensure a valid rotation.

                                                            @@ -556,7 +556,7 @@
                                                            -round(decimals=0)[source]
                                                            +round(decimals=0)[source]

                                                            Wrapper around numpy.round to ensure object of same type is returned

                                                            @@ -574,7 +574,7 @@
                                                            -structure_transform(original_structure, new_structure, refine_rotation=True)[source]
                                                            +structure_transform(original_structure, new_structure, refine_rotation=True)[source]

                                                            Transforms a tensor from one basis for an original structure into a new basis defined by a new structure.

                                                            @@ -597,12 +597,12 @@
                                                            -symbol = 'T'[source]
                                                            +symbol = 'T'[source]
                                                            -property symmetrized[source]
                                                            +property symmetrized[source]

                                                            Returns a generally symmetrized tensor, calculated by taking the sum of the tensor and its transpose with respect to all possible permutations of indices

                                                            @@ -610,7 +610,7 @@
                                                            -transform(symm_op)[source]
                                                            +transform(symm_op)[source]

                                                            Applies a transformation (via a symmetry operation) to a tensor.

                                                            Parameters
                                                            @@ -621,20 +621,20 @@
                                                            -property voigt[source]
                                                            +property voigt[source]

                                                            Returns the tensor in Voigt notation

                                                            -property voigt_symmetrized[source]
                                                            +property voigt_symmetrized[source]

                                                            Returns a “voigt”-symmetrized tensor, i. e. a voigt-notation tensor such that it is invariant wrt permutation of indices

                                                            -zeroed(tol=0.001)[source]
                                                            +zeroed(tol=0.001)[source]

                                                            returns the matrix with all entries below a certain threshold (i.e. tol) set to zero

                                                            @@ -643,7 +643,7 @@
                                                            -class TensorCollection(tensor_list, base_class=<class 'pymatgen.core.tensors.Tensor'>)[source]
                                                            +class TensorCollection(tensor_list, base_class=<class 'pymatgen.core.tensors.Tensor'>)[source]

                                                            Bases: collections.abc.Sequence, monty.json.MSONable

                                                            A sequence of tensors that can be used for fitting data or for having a tensor expansion

                                                            @@ -657,7 +657,7 @@
                                                            -as_dict(voigt=False)[source]
                                                            +as_dict(voigt=False)[source]
                                                            Parameters

                                                            voigt – Whether to use voight form.

                                                            @@ -670,7 +670,7 @@
                                                            -convert_to_ieee(structure, initial_fit=True, refine_rotation=True)[source]
                                                            +convert_to_ieee(structure, initial_fit=True, refine_rotation=True)[source]

                                                            Convert all tensors to IEEE.

                                                            Parameters
                                                            @@ -688,7 +688,7 @@
                                                            -fit_to_structure(structure, symprec=0.1)[source]
                                                            +fit_to_structure(structure, symprec=0.1)[source]

                                                            Fits all tensors to a Structure.

                                                            Parameters
                                                            @@ -705,7 +705,7 @@
                                                            -classmethod from_dict(d)[source]
                                                            +classmethod from_dict(d)[source]

                                                            Creates TensorCollection from dict.

                                                            Parameters
                                                            @@ -719,7 +719,7 @@
                                                            -classmethod from_voigt(voigt_input_list, base_class=<class 'pymatgen.core.tensors.Tensor'>)[source]
                                                            +classmethod from_voigt(voigt_input_list, base_class=<class 'pymatgen.core.tensors.Tensor'>)[source]

                                                            Creates TensorCollection from voigt form.

                                                            Parameters
                                                            @@ -736,7 +736,7 @@
                                                            -is_fit_to_structure(structure, tol=0.01)[source]
                                                            +is_fit_to_structure(structure, tol=0.01)[source]
                                                            Parameters
                                                              @@ -752,7 +752,7 @@
                                                              -is_symmetric(tol=1e-05)[source]
                                                              +is_symmetric(tol=1e-05)[source]
                                                              Parameters

                                                              tol – tolerance

                                                              @@ -765,7 +765,7 @@
                                                              -is_voigt_symmetric(tol=1e-06)[source]
                                                              +is_voigt_symmetric(tol=1e-06)[source]
                                                              Parameters

                                                              tol – tolerance

                                                              @@ -778,7 +778,7 @@
                                                              -property ranks[source]
                                                              +property ranks[source]

                                                              Ranks for all tensors.

                                                              Type
                                                              @@ -789,7 +789,7 @@
                                                              -rotate(matrix, tol=0.001)[source]
                                                              +rotate(matrix, tol=0.001)[source]

                                                              Rotates TensorCollection.

                                                              Parameters
                                                              @@ -806,7 +806,7 @@
                                                              -round(*args, **kwargs)[source]
                                                              +round(*args, **kwargs)[source]

                                                              Round all tensors.

                                                              Parameters
                                                              @@ -823,7 +823,7 @@
                                                              -property symmetrized[source]
                                                              +property symmetrized[source]

                                                              TensorCollection where all tensors are symmetrized.

                                                              Type
                                                              @@ -834,7 +834,7 @@
                                                              -transform(symm_op)[source]
                                                              +transform(symm_op)[source]

                                                              Transforms TensorCollection with a symmetry operation.

                                                              Parameters
                                                              @@ -848,7 +848,7 @@
                                                              -property voigt[source]
                                                              +property voigt[source]

                                                              TensorCollection where all tensors are in voight form.

                                                              Type
                                                              @@ -859,7 +859,7 @@
                                                              -property voigt_symmetrized[source]
                                                              +property voigt_symmetrized[source]

                                                              TensorCollection where all tensors are voigt symmetrized.

                                                              Type
                                                              @@ -870,7 +870,7 @@
                                                              -zeroed(tol=0.001)[source]
                                                              +zeroed(tol=0.001)[source]
                                                              Parameters

                                                              tol – Tolerance

                                                              @@ -885,7 +885,7 @@
                                                              -class TensorMapping(tensors=None, values=None, tol=1e-05)[source]
                                                              +class TensorMapping(tensors=None, values=None, tol=1e-05)[source]

                                                              Bases: collections.abc.MutableMapping

                                                              Base class for tensor mappings, which function much like a dictionary, but use numpy routines to determine approximate @@ -907,7 +907,7 @@

                                                              -items()[source]
                                                              +items()[source]
                                                              Returns

                                                              Items in mapping.

                                                              @@ -917,7 +917,7 @@
                                                              -values()[source]
                                                              +values()[source]
                                                              Returns

                                                              Values in mapping.

                                                              @@ -929,13 +929,13 @@
                                                              -get_uvec(vec)[source]
                                                              +get_uvec(vec)[source]

                                                              Gets a unit vector parallel to input vector

                                                              -symmetry_reduce(tensors, structure, tol=1e-08, **kwargs)[source]
                                                              +symmetry_reduce(tensors, structure, tol=1e-08, **kwargs)[source]

                                                              Function that converts a list of tensors corresponding to a structure and returns a dictionary consisting of unique tensor keys with symmop values corresponding to transformations that will result in derivative diff --git a/docs/pymatgen.core.trajectory.html b/docs/pymatgen.core.trajectory.html index 0001e827f10..36214e017f9 100644 --- a/docs/pymatgen.core.trajectory.html +++ b/docs/pymatgen.core.trajectory.html @@ -4,7 +4,7 @@ - pymatgen.core.trajectory module — pymatgen 2022.5.18 documentation + pymatgen.core.trajectory module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                                              - 2022.5.18 + 2022.5.18.1
                                                              @@ -118,7 +118,7 @@

                                                              This module provides classes used to define a MD trajectory.

                                                              -class Trajectory(lattice: Sequence[float] | Sequence[Sequence[float]] | np.ndarray | Lattice, species: list[str | Element | Species | DummySpecies | Composition], frac_coords: list[Sequence[Sequence[float]]] | np.ndarray, time_step: float = 2, site_properties: dict = None, frame_properties: dict = None, constant_lattice: bool = True, coords_are_displacement: bool = False, base_positions: Sequence[Sequence[float]] = None)[source]
                                                              +class Trajectory(lattice: Sequence[float] | Sequence[Sequence[float]] | np.ndarray | Lattice, species: list[str | Element | Species | DummySpecies | Composition], frac_coords: list[Sequence[Sequence[float]]] | np.ndarray, time_step: float = 2, site_properties: dict = None, frame_properties: dict = None, constant_lattice: bool = True, coords_are_displacement: bool = False, base_positions: Sequence[Sequence[float]] = None)[source]

                                                              Bases: monty.json.MSONable

                                                              Trajectory object that stores structural information related to a MD simulation. Provides basic functions such as slicing trajectory or obtaining displacements.

                                                              @@ -165,7 +165,7 @@
                                                              -as_dict()[source]
                                                              +as_dict()[source]
                                                              Returns

                                                              MSONAble dict.

                                                              @@ -175,7 +175,7 @@
                                                              -copy()[source]
                                                              +copy()[source]
                                                              Returns

                                                              Copy of Trajectory.

                                                              @@ -185,7 +185,7 @@
                                                              -extend(trajectory)[source]
                                                              +extend(trajectory)[source]

                                                              Concatenate another trajectory :param trajectory: Trajectory to add :type trajectory: Trajectory

                                                              @@ -193,7 +193,7 @@
                                                              -classmethod from_file(filename, constant_lattice=True, **kwargs)[source]
                                                              +classmethod from_file(filename, constant_lattice=True, **kwargs)[source]

                                                              Convenience constructor to obtain trajectory from XDATCAR or vasprun.xml file :param filename: The filename to read from. :type filename: str @@ -210,7 +210,7 @@

                                                              -classmethod from_structures(structures, constant_lattice=True, **kwargs)[source]
                                                              +classmethod from_structures(structures, constant_lattice=True, **kwargs)[source]

                                                              Convenience constructor to obtain trajectory from a list of structures. Note: Assumes no atoms removed during simulation

                                                              @@ -229,7 +229,7 @@
                                                              -get_structure(i)[source]
                                                              +get_structure(i)[source]

                                                              Returns structure at specified index :param i: Index of structure :type i: int

                                                              @@ -242,19 +242,19 @@
                                                              -to_displacements()[source]
                                                              +to_displacements()[source]

                                                              Converts position coordinates of trajectory into displacements between consecutive frames

                                                              -to_positions()[source]
                                                              +to_positions()[source]

                                                              Converts fractional coordinates of trajectory into positions

                                                              -write_Xdatcar(filename='XDATCAR', system=None, significant_figures=6)[source]
                                                              +write_Xdatcar(filename='XDATCAR', system=None, significant_figures=6)[source]

                                                              Writes Xdatcar to a file. The supported kwargs are the same as those for the Xdatcar_from_structs.get_string method and are passed through directly.

                                                              diff --git a/docs/pymatgen.core.units.html b/docs/pymatgen.core.units.html index 0d223a06104..64af752d5e4 100644 --- a/docs/pymatgen.core.units.html +++ b/docs/pymatgen.core.units.html @@ -4,7 +4,7 @@ - pymatgen.core.units module — pymatgen 2022.5.18 documentation + pymatgen.core.units module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                              - 2022.5.18 + 2022.5.18.1
                                                              @@ -123,7 +123,7 @@ of numpy’s ndarray with similar unit features.

                                                              -class ArrayWithUnit(input_array, unit, unit_type=None)[source]
                                                              +class ArrayWithUnit(input_array, unit, unit_type=None)[source]

                                                              Bases: numpy.ndarray

                                                              Subclasses numpy.ndarray to attach a unit type. Typically, you should use the pre-defined unit type subclasses such as EnergyArray, @@ -143,13 +143,13 @@

                                                              Override __new__.

                                                              -Error[source]
                                                              +Error[source]

                                                              alias of pymatgen.core.units.UnitError

                                                              -property as_base_units[source]
                                                              +property as_base_units[source]

                                                              Returns this ArrayWithUnit in base SI units, including derived units.

                                                              Returns
                                                              @@ -160,20 +160,20 @@
                                                              -conversions()[source]
                                                              +conversions()[source]

                                                              Returns a string showing the available conversions. Useful tool in interactive mode.

                                                              -property supported_units[source]
                                                              +property supported_units[source]

                                                              Supported units for specific unit type.

                                                              -to(new_unit)[source]
                                                              +to(new_unit)[source]

                                                              Conversion to a new_unit.

                                                              Parameters
                                                              @@ -191,7 +191,7 @@
                                                              -property unit: str[source]
                                                              +property unit: str[source]

                                                              The unit, e.g., “eV”.

                                                              Type
                                                              @@ -202,7 +202,7 @@
                                                              -property unit_type: str[source]
                                                              +property unit_type: str[source]

                                                              The type of unit. Energy, Charge, etc.

                                                              Type
                                                              @@ -215,7 +215,7 @@
                                                              -Charge = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='charge')[source]
                                                              +Charge = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='charge')[source]

                                                              A float with a charge unit.

                                                              Parameters
                                                              @@ -230,7 +230,7 @@
                                                              -Energy = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='energy')[source]
                                                              +Energy = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='energy')[source]

                                                              A float with an energy unit.

                                                              Parameters
                                                              @@ -244,7 +244,7 @@
                                                              -class FloatWithUnit(val, unit, unit_type=None)[source]
                                                              +class FloatWithUnit(val, unit, unit_type=None)[source]

                                                              Bases: float

                                                              Subclasses float to attach a unit type. Typically, you should use the pre-defined unit type subclasses such as Energy, Length, etc. instead of @@ -277,13 +277,13 @@

                                                              -Error[source]
                                                              +Error[source]

                                                              alias of pymatgen.core.units.UnitError

                                                              -property as_base_units[source]
                                                              +property as_base_units[source]

                                                              Returns this FloatWithUnit in base SI units, including derived units.

                                                              Returns
                                                              @@ -294,19 +294,19 @@
                                                              -classmethod from_string(s)[source]
                                                              +classmethod from_string(s)[source]

                                                              Initialize a FloatWithUnit from a string. Example Memory.from_string(“1. Mb”)

                                                              -property supported_units[source]
                                                              +property supported_units[source]

                                                              Supported units for specific unit type.

                                                              -to(new_unit)[source]
                                                              +to(new_unit)[source]

                                                              Conversion to a new_unit. Right now, only supports 1 to 1 mapping of units of each type.

                                                              @@ -326,7 +326,7 @@
                                                              -property unit: str[source]
                                                              +property unit: str[source]

                                                              The unit, e.g., “eV”.

                                                              Type
                                                              @@ -337,7 +337,7 @@
                                                              -property unit_type: str[source]
                                                              +property unit_type: str[source]

                                                              The type of unit. Energy, Charge, etc.

                                                              Type
                                                              @@ -350,7 +350,7 @@
                                                              -Length = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='length')[source]
                                                              +Length = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='length')[source]

                                                              A float with a length unit.

                                                              Parameters
                                                              @@ -365,7 +365,7 @@
                                                              -Mass = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='mass')[source]
                                                              +Mass = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='mass')[source]

                                                              A float with a mass unit.

                                                              Parameters
                                                              @@ -380,7 +380,7 @@
                                                              -Memory = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='memory')[source]
                                                              +Memory = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='memory')[source]

                                                              A float with a memory unit.

                                                              Parameters
                                                              @@ -395,7 +395,7 @@
                                                              -Temp = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='temperature')[source]
                                                              +Temp = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='temperature')[source]

                                                              A float with a temperature unit.

                                                              Parameters
                                                              @@ -409,7 +409,7 @@
                                                              -Time = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='time')[source]
                                                              +Time = functools.partial(<class 'pymatgen.core.units.FloatWithUnit'>, unit_type='time')[source]

                                                              A float with a time unit.

                                                              Parameters
                                                              @@ -424,7 +424,7 @@
                                                              -class Unit(unit_def)[source]
                                                              +class Unit(unit_def)[source]

                                                              Bases: collections.abc.Mapping

                                                              Represents a unit, e.g., “m” for meters, etc. Supports compound units. Only integer powers are supported for units.

                                                              @@ -440,13 +440,13 @@
                                                              -Error[source]
                                                              +Error[source]

                                                              alias of pymatgen.core.units.UnitError

                                                              -property as_base_units[source]
                                                              +property as_base_units[source]

                                                              Converts all units to base SI units, including derived units.

                                                              Returns
                                                              @@ -458,7 +458,7 @@
                                                              -get_conversion_factor(new_unit)[source]
                                                              +get_conversion_factor(new_unit)[source]

                                                              Returns a conversion factor between this unit and a new unit. Compound units are supported, but must have the same powers in each unit type.

                                                              @@ -473,14 +473,14 @@
                                                              -exception UnitError[source]
                                                              +exception UnitError[source]

                                                              Bases: BaseException

                                                              Exception class for unit errors.

                                                              -kb = 8.617333262e-05[source]
                                                              +kb = 8.617333262e-05[source]

                                                              Definitions of supported units. Values below are essentially scaling and conversion factors. What matters is the relative values, not the absolute. The SI units must have factor 1.

                                                              @@ -488,7 +488,7 @@
                                                              -obj_with_unit(obj, unit)[source]
                                                              +obj_with_unit(obj, unit)[source]

                                                              Returns a FloatWithUnit instance if obj is scalar, a dictionary of objects with units if obj is a dict, else an instance of ArrayWithFloatWithUnit.

                                                              @@ -501,7 +501,7 @@
                                                              -unitized(unit)[source]
                                                              +unitized(unit)[source]

                                                              Useful decorator to assign units to the output of a function. You can also use it to standardize the output units of a function that already returns a FloatWithUnit or ArrayWithUnit. For sequences, all values in the sequences diff --git a/docs/pymatgen.core.xcfunc.html b/docs/pymatgen.core.xcfunc.html index 5b70c8524c1..ff64bfe0b55 100644 --- a/docs/pymatgen.core.xcfunc.html +++ b/docs/pymatgen.core.xcfunc.html @@ -4,7 +4,7 @@ - pymatgen.core.xcfunc module — pymatgen 2022.5.18 documentation + pymatgen.core.xcfunc module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                                              - 2022.5.18 + 2022.5.18.1
                                                              @@ -118,7 +118,7 @@

                                                              This module provides

                                                              -class XcFunc(xc=None, x=None, c=None)[source]
                                                              +class XcFunc(xc=None, x=None, c=None)[source]

                                                              Bases: monty.json.MSONable

                                                              This object stores information about the XC correlation functional. Client code usually creates the object by calling the class methods:

                                                              @@ -175,66 +175,66 @@
                                                              -abinitixc_to_libxc = {1: {'xc': LibxcFunc.LDA_XC_TETER93}, 2: {'c': LibxcFunc.LDA_C_PZ, 'x': LibxcFunc.LDA_X}, 4: {'c': LibxcFunc.LDA_C_WIGNER, 'x': LibxcFunc.LDA_X}, 5: {'c': LibxcFunc.LDA_C_HL, 'x': LibxcFunc.LDA_X}, 7: {'c': LibxcFunc.LDA_C_PW, 'x': LibxcFunc.LDA_X}, 11: {'c': LibxcFunc.GGA_C_PBE, 'x': LibxcFunc.GGA_X_PBE}, 14: {'c': LibxcFunc.GGA_C_PBE, 'x': LibxcFunc.GGA_X_PBE_R}, 15: {'c': LibxcFunc.GGA_C_PBE, 'x': LibxcFunc.GGA_X_RPBE}}[source]
                                                              +abinitixc_to_libxc = {1: {'xc': LibxcFunc.LDA_XC_TETER93}, 2: {'c': LibxcFunc.LDA_C_PZ, 'x': LibxcFunc.LDA_X}, 4: {'c': LibxcFunc.LDA_C_WIGNER, 'x': LibxcFunc.LDA_X}, 5: {'c': LibxcFunc.LDA_C_HL, 'x': LibxcFunc.LDA_X}, 7: {'c': LibxcFunc.LDA_C_PW, 'x': LibxcFunc.LDA_X}, 11: {'c': LibxcFunc.GGA_C_PBE, 'x': LibxcFunc.GGA_X_PBE}, 14: {'c': LibxcFunc.GGA_C_PBE, 'x': LibxcFunc.GGA_X_PBE_R}, 15: {'c': LibxcFunc.GGA_C_PBE, 'x': LibxcFunc.GGA_X_RPBE}}[source]
                                                              -classmethod aliases()[source]
                                                              +classmethod aliases()[source]

                                                              List of registered names.

                                                              -as_dict()[source]
                                                              +as_dict()[source]

                                                              Makes XcFunc obey the general json interface used in pymatgen for easier serialization.

                                                              -classmethod asxc(obj)[source]
                                                              +classmethod asxc(obj)[source]

                                                              Convert object into Xcfunc.

                                                              -defined_aliases = {(<LibxcFunc.LDA_X: 1>, <LibxcFunc.LDA_C_PW: 12>): type_name(type='LDA', name='PW'), (<LibxcFunc.LDA_X: 1>, <LibxcFunc.LDA_C_PW_MOD: 13>): type_name(type='LDA', name='PW_MOD'), (<LibxcFunc.LDA_X: 1>, <LibxcFunc.LDA_C_PZ: 9>): type_name(type='LDA', name='PZ'), (<LibxcFunc.LDA_X: 1>, <LibxcFunc.LDA_C_WIGNER: 2>): type_name(type='LDA', name='W'), (<LibxcFunc.LDA_X: 1>, <LibxcFunc.LDA_C_HL: 4>): type_name(type='LDA', name='HL'), (<LibxcFunc.LDA_X: 1>, <LibxcFunc.LDA_C_GL: 5>): type_name(type='LDA', name='GL'), (<LibxcFunc.LDA_X: 1>, <LibxcFunc.LDA_C_VWN: 7>): type_name(type='LDA', name='VWN'), (<LibxcFunc.GGA_X_PW91: 109>, <LibxcFunc.GGA_C_PW91: 134>): type_name(type='GGA', name='PW91'), (<LibxcFunc.GGA_X_PBE: 101>, <LibxcFunc.GGA_C_PBE: 130>): type_name(type='GGA', name='PBE'), (<LibxcFunc.GGA_X_RPBE: 117>, <LibxcFunc.GGA_C_PBE: 130>): type_name(type='GGA', name='RPBE'), (<LibxcFunc.GGA_X_PBE_R: 102>, <LibxcFunc.GGA_C_PBE: 130>): type_name(type='GGA', name='revPBE'), (<LibxcFunc.GGA_X_PBE_SOL: 116>, <LibxcFunc.GGA_C_PBE_SOL: 133>): type_name(type='GGA', name='PBEsol'), (<LibxcFunc.GGA_X_AM05: 120>, <LibxcFunc.GGA_C_AM05: 135>): type_name(type='GGA', name='AM05'), (<LibxcFunc.GGA_X_B88: 106>, <LibxcFunc.GGA_C_LYP: 131>): type_name(type='GGA', name='BLYP')}[source]
                                                              +defined_aliases = {(<LibxcFunc.LDA_X: 1>, <LibxcFunc.LDA_C_PW: 12>): type_name(type='LDA', name='PW'), (<LibxcFunc.LDA_X: 1>, <LibxcFunc.LDA_C_PW_MOD: 13>): type_name(type='LDA', name='PW_MOD'), (<LibxcFunc.LDA_X: 1>, <LibxcFunc.LDA_C_PZ: 9>): type_name(type='LDA', name='PZ'), (<LibxcFunc.LDA_X: 1>, <LibxcFunc.LDA_C_WIGNER: 2>): type_name(type='LDA', name='W'), (<LibxcFunc.LDA_X: 1>, <LibxcFunc.LDA_C_HL: 4>): type_name(type='LDA', name='HL'), (<LibxcFunc.LDA_X: 1>, <LibxcFunc.LDA_C_GL: 5>): type_name(type='LDA', name='GL'), (<LibxcFunc.LDA_X: 1>, <LibxcFunc.LDA_C_VWN: 7>): type_name(type='LDA', name='VWN'), (<LibxcFunc.GGA_X_PW91: 109>, <LibxcFunc.GGA_C_PW91: 134>): type_name(type='GGA', name='PW91'), (<LibxcFunc.GGA_X_PBE: 101>, <LibxcFunc.GGA_C_PBE: 130>): type_name(type='GGA', name='PBE'), (<LibxcFunc.GGA_X_RPBE: 117>, <LibxcFunc.GGA_C_PBE: 130>): type_name(type='GGA', name='RPBE'), (<LibxcFunc.GGA_X_PBE_R: 102>, <LibxcFunc.GGA_C_PBE: 130>): type_name(type='GGA', name='revPBE'), (<LibxcFunc.GGA_X_PBE_SOL: 116>, <LibxcFunc.GGA_C_PBE_SOL: 133>): type_name(type='GGA', name='PBEsol'), (<LibxcFunc.GGA_X_AM05: 120>, <LibxcFunc.GGA_C_AM05: 135>): type_name(type='GGA', name='AM05'), (<LibxcFunc.GGA_X_B88: 106>, <LibxcFunc.GGA_C_LYP: 131>): type_name(type='GGA', name='BLYP')}[source]
                                                              -classmethod from_abinit_ixc(ixc)[source]
                                                              +classmethod from_abinit_ixc(ixc)[source]

                                                              Build the object from Abinit ixc (integer)

                                                              -classmethod from_dict(d)[source]
                                                              +classmethod from_dict(d)[source]

                                                              Makes XcFunc obey the general json interface used in pymatgen for easier serialization.

                                                              -classmethod from_name(name)[source]
                                                              +classmethod from_name(name)[source]

                                                              Build the object from one of the registered names

                                                              -classmethod from_type_name(typ, name)[source]
                                                              +classmethod from_type_name(typ, name)[source]

                                                              Build the object from (type, name).

                                                              -name()[source]
                                                              +name()[source]

                                                              The name of the functional. If the functional is not found in the aliases, the string has the form X_NAME+C_NAME

                                                              -type()[source]
                                                              +type()[source]

                                                              The type of the functional.

                                                              diff --git a/docs/pymatgen.dao.html b/docs/pymatgen.dao.html index ba2cfe77664..8bb8d69eeda 100644 --- a/docs/pymatgen.dao.html +++ b/docs/pymatgen.dao.html @@ -4,7 +4,7 @@ - pymatgen.dao module — pymatgen 2022.5.18 documentation + pymatgen.dao module — pymatgen 2022.5.18.1 documentation @@ -38,7 +38,7 @@ pymatgen
                                                              - 2022.5.18 + 2022.5.18.1
                                                              diff --git a/docs/pymatgen.electronic_structure.bandstructure.html b/docs/pymatgen.electronic_structure.bandstructure.html index a3b446e3453..0bbdc9aa42b 100644 --- a/docs/pymatgen.electronic_structure.bandstructure.html +++ b/docs/pymatgen.electronic_structure.bandstructure.html @@ -4,7 +4,7 @@ - pymatgen.electronic_structure.bandstructure module — pymatgen 2022.5.18 documentation + pymatgen.electronic_structure.bandstructure module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                              - 2022.5.18 + 2022.5.18.1
                                                              @@ -118,7 +118,7 @@

                                                              This module provides classes to define everything related to band structures.

                                                              -class BandStructure(kpoints: numpy.ndarray, eigenvals: dict[pymatgen.electronic_structure.core.Spin, numpy.ndarray], lattice: pymatgen.core.lattice.Lattice, efermi: float, labels_dict=None, coords_are_cartesian: bool = False, structure: Optional[pymatgen.core.structure.Structure] = None, projections: Optional[dict[pymatgen.electronic_structure.core.Spin, numpy.ndarray]] = None)[source]
                                                              +class BandStructure(kpoints: numpy.ndarray, eigenvals: dict[pymatgen.electronic_structure.core.Spin, numpy.ndarray], lattice: pymatgen.core.lattice.Lattice, efermi: float, labels_dict=None, coords_are_cartesian: bool = False, structure: Optional[pymatgen.core.structure.Structure] = None, projections: Optional[dict[pymatgen.electronic_structure.core.Spin, numpy.ndarray]] = None)[source]

                                                              Bases: object

                                                              This is the most generic band structure data possible it’s defined by a list of kpoints + energies for each of them

                                                              @@ -131,25 +131,25 @@
                                                              -lattice_rec[source]
                                                              +lattice_rec[source]

                                                              the reciprocal lattice of the band structure.

                                                              -efermi[source]
                                                              +efermi[source]

                                                              the fermi energy

                                                              -is_spin_polarized[source]
                                                              +is_spin_polarized[source]

                                                              True if the band structure is spin-polarized, False otherwise

                                                              -bands[source]
                                                              +bands[source]

                                                              The energy eigenvalues as a {spin: ndarray}. Note that the use of an ndarray is necessary for computational as well as memory efficiency due to the large amount of numerical data. The indices of the ndarray @@ -158,19 +158,19 @@

                                                              -nb_bands[source]
                                                              +nb_bands[source]

                                                              returns the number of bands in the band structure

                                                              -structure[source]
                                                              +structure[source]

                                                              returns the structure

                                                              -projections[source]
                                                              +projections[source]

                                                              The projections as a {spin: ndarray}. Note that the use of an ndarray is necessary for computational as well as memory efficiency due to the large amount of numerical data. The indices of the ndarray @@ -207,13 +207,13 @@

                                                              -as_dict()[source]
                                                              +as_dict()[source]

                                                              JSON-serializable dict representation of BandStructure.

                                                              -classmethod from_dict(d)[source]
                                                              +classmethod from_dict(d)[source]

                                                              Create from dict.

                                                              Parameters
                                                              @@ -227,7 +227,7 @@
                                                              -classmethod from_old_dict(d)[source]
                                                              +classmethod from_old_dict(d)[source]
                                                              Parameters

                                                              d (dict) – A dict with all data for a band structure symm line @@ -241,7 +241,7 @@

                                                              -get_band_gap()[source]
                                                              +get_band_gap()[source]

                                                              Returns band gap data.

                                                              Returns
                                                              @@ -257,7 +257,7 @@
                                                              -get_cbm()[source]
                                                              +get_cbm()[source]

                                                              Returns data about the CBM.

                                                              Returns
                                                              @@ -283,7 +283,7 @@
                                                              -get_direct_band_gap()[source]
                                                              +get_direct_band_gap()[source]

                                                              Returns the direct band gap.

                                                              Returns
                                                              @@ -294,7 +294,7 @@
                                                              -get_direct_band_gap_dict()[source]
                                                              +get_direct_band_gap_dict()[source]

                                                              Returns a dictionary of information about the direct band gap

                                                              @@ -307,7 +307,7 @@
                                                              -get_kpoint_degeneracy(kpoint, cartesian=False, tol=0.01)[source]
                                                              +get_kpoint_degeneracy(kpoint, cartesian=False, tol=0.01)[source]

                                                              Returns degeneracy of a given k-point based on structure symmetry :param kpoint: coordinate of the k-point :type kpoint: 1x3 array @@ -327,7 +327,7 @@

                                                              -get_projection_on_elements()[source]
                                                              +get_projection_on_elements()[source]

                                                              Method returning a dictionary of projections on elements.

                                                              Returns
                                                              @@ -344,7 +344,7 @@
                                                              -get_projections_on_elements_and_orbitals(el_orb_spec)[source]
                                                              +get_projections_on_elements_and_orbitals(el_orb_spec)[source]

                                                              Method returning a dictionary of projections on elements and specific orbitals

                                                              @@ -365,7 +365,7 @@
                                                              -get_sym_eq_kpoints(kpoint, cartesian=False, tol=0.01)[source]
                                                              +get_sym_eq_kpoints(kpoint, cartesian=False, tol=0.01)[source]

                                                              Returns a list of unique symmetrically equivalent k-points.

                                                              Parameters
                                                              @@ -386,7 +386,7 @@
                                                              -get_vbm()[source]
                                                              +get_vbm()[source]

                                                              Returns data about the VBM.

                                                              Returns
                                                              @@ -412,7 +412,7 @@
                                                              -is_metal(efermi_tol=0.0001)[source]
                                                              +is_metal(efermi_tol=0.0001)[source]

                                                              Check if the band structure indicates a metal by looking if the fermi level crosses a band.

                                                              @@ -426,7 +426,7 @@
                                                              -class BandStructureSymmLine(kpoints, eigenvals, lattice, efermi, labels_dict, coords_are_cartesian=False, structure=None, projections=None)[source]
                                                              +class BandStructureSymmLine(kpoints, eigenvals, lattice, efermi, labels_dict, coords_are_cartesian=False, structure=None, projections=None)[source]

                                                              Bases: pymatgen.electronic_structure.bandstructure.BandStructure, monty.json.MSONable

                                                              This object stores band structures along selected (symmetry) lines in the Brillouin zone. We call the different symmetry lines (ex: \Gamma to Z) @@ -461,7 +461,7 @@

                                                              -apply_scissor(new_band_gap)[source]
                                                              +apply_scissor(new_band_gap)[source]

                                                              Apply a scissor operator (shift of the CBM) to fit the given band gap. If it’s a metal. We look for the band crossing the fermi level and shift this one up. This will not work all the time for metals!

                                                              @@ -477,13 +477,13 @@
                                                              -as_dict()[source]
                                                              +as_dict()[source]

                                                              JSON-serializable dict representation of BandStructureSymmLine.

                                                              -get_branch(index)[source]
                                                              +get_branch(index)[source]

                                                              Returns in what branch(es) is the kpoint. There can be several branches.

                                                              @@ -501,7 +501,7 @@
                                                              -get_equivalent_kpoints(index)[source]
                                                              +get_equivalent_kpoints(index)[source]

                                                              Returns the list of kpoint indices equivalent (meaning they are the same frac coords) to the given one.

                                                              @@ -520,7 +520,7 @@
                                                              -class Kpoint(coords, lattice, to_unit_cell=False, coords_are_cartesian=False, label=None)[source]
                                                              +class Kpoint(coords, lattice, to_unit_cell=False, coords_are_cartesian=False, label=None)[source]

                                                              Bases: monty.json.MSONable

                                                              Class to store kpoint objects. A kpoint is defined with a lattice and frac or Cartesian coordinates syntax similar than the site object in @@ -542,43 +542,43 @@

                                                              -property a[source]
                                                              +property a[source]

                                                              Fractional a coordinate of the kpoint

                                                              -as_dict()[source]
                                                              +as_dict()[source]

                                                              JSON-serializable dict representation of a kpoint

                                                              -property b[source]
                                                              +property b[source]

                                                              Fractional b coordinate of the kpoint

                                                              -property c[source]
                                                              +property c[source]

                                                              Fractional c coordinate of the kpoint

                                                              -property cart_coords[source]
                                                              +property cart_coords[source]

                                                              The Cartesian coordinates of the kpoint as a numpy array

                                                              -property frac_coords[source]
                                                              +property frac_coords[source]

                                                              The fractional coordinates of the kpoint as a numpy array

                                                              -classmethod from_dict(d)[source]
                                                              +classmethod from_dict(d)[source]

                                                              Create from dict.

                                                              Parameters
                                                              @@ -592,13 +592,13 @@
                                                              -property label[source]
                                                              +property label[source]

                                                              The label associated with the kpoint

                                                              -property lattice[source]
                                                              +property lattice[source]

                                                              The lattice associated with the kpoint. It’s a pymatgen.core.lattice.Lattice object

                                                              @@ -607,7 +607,7 @@
                                                              -class LobsterBandStructureSymmLine(kpoints, eigenvals, lattice, efermi, labels_dict, coords_are_cartesian=False, structure=None, projections=None)[source]
                                                              +class LobsterBandStructureSymmLine(kpoints, eigenvals, lattice, efermi, labels_dict, coords_are_cartesian=False, structure=None, projections=None)[source]

                                                              Bases: pymatgen.electronic_structure.bandstructure.BandStructureSymmLine

                                                              Lobster subclass of BandStructure with customized functions.

                                                              @@ -640,13 +640,13 @@
                                                              -as_dict()[source]
                                                              +as_dict()[source]

                                                              JSON-serializable dict representation of BandStructureSymmLine.

                                                              -classmethod from_dict(d)[source]
                                                              +classmethod from_dict(d)[source]
                                                              Parameters

                                                              d (dict) – A dict with all data for a band structure symm line @@ -660,7 +660,7 @@

                                                              -classmethod from_old_dict(d)[source]
                                                              +classmethod from_old_dict(d)[source]
                                                              Parameters

                                                              d (dict) – A dict with all data for a band structure symm line @@ -674,7 +674,7 @@

                                                              -get_projection_on_elements()[source]
                                                              +get_projection_on_elements()[source]

                                                              Method returning a dictionary of projections on elements. It sums over all available orbitals for each element.

                                                              @@ -692,7 +692,7 @@
                                                              -get_projections_on_elements_and_orbitals(el_orb_spec)[source]
                                                              +get_projections_on_elements_and_orbitals(el_orb_spec)[source]

                                                              Method returning a dictionary of projections on elements and specific orbitals

                                                              @@ -715,7 +715,7 @@
                                                              -get_reconstructed_band_structure(list_bs, efermi=None)[source]
                                                              +get_reconstructed_band_structure(list_bs, efermi=None)[source]

                                                              This method takes a list of band structures and reconstructs one band structure object from all of them.

                                                              This is typically very useful when you split non self consistent diff --git a/docs/pymatgen.electronic_structure.boltztrap.html b/docs/pymatgen.electronic_structure.boltztrap.html index fa1eb4ea08c..a6545d5598b 100644 --- a/docs/pymatgen.electronic_structure.boltztrap.html +++ b/docs/pymatgen.electronic_structure.boltztrap.html @@ -4,7 +4,7 @@ - pymatgen.electronic_structure.boltztrap module — pymatgen 2022.5.18 documentation + pymatgen.electronic_structure.boltztrap module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                                              - 2022.5.18 + 2022.5.18.1
                                                              @@ -130,7 +130,7 @@
                                                              -class BoltztrapAnalyzer(gap=None, mu_steps=None, cond=None, seebeck=None, kappa=None, hall=None, doping=None, mu_doping=None, seebeck_doping=None, cond_doping=None, kappa_doping=None, hall_doping=None, intrans=None, dos=None, dos_partial=None, carrier_conc=None, vol=None, warning=None, bz_bands=None, bz_kpoints=None, fermi_surface_data=None)[source]
                                                              +class BoltztrapAnalyzer(gap=None, mu_steps=None, cond=None, seebeck=None, kappa=None, hall=None, doping=None, mu_doping=None, seebeck_doping=None, cond_doping=None, kappa_doping=None, hall_doping=None, intrans=None, dos=None, dos_partial=None, carrier_conc=None, vol=None, warning=None, bz_bands=None, bz_kpoints=None, fermi_surface_data=None)[source]

                                                              Bases: object

                                                              Class used to store all the data from a boltztrap run

                                                              Constructor taking directly all the data generated by Boltztrap. You @@ -218,7 +218,7 @@

                                                              -as_dict()[source]
                                                              +as_dict()[source]
                                                              Returns

                                                              MSONable dict.

                                                              @@ -228,7 +228,7 @@
                                                              -static check_acc_bzt_bands(sbs_bz, sbs_ref, warn_thr=(0.03, 0.03))[source]
                                                              +static check_acc_bzt_bands(sbs_bz, sbs_ref, warn_thr=(0.03, 0.03))[source]

                                                              Compare sbs_bz BandStructureSymmLine calculated with boltztrap with the sbs_ref BandStructureSymmLine as reference (from MP for instance), computing correlation and energy difference for eight bands @@ -265,7 +265,7 @@

                                                              -static from_dict(data)[source]
                                                              +static from_dict(data)[source]
                                                              Parameters

                                                              data – Dict representation.

                                                              @@ -278,7 +278,7 @@
                                                              -static from_files(path_dir, dos_spin=1)[source]
                                                              +static from_files(path_dir, dos_spin=1)[source]

                                                              get a BoltztrapAnalyzer object from a set of files

                                                              Parameters
                                                              @@ -295,7 +295,7 @@
                                                              -get_average_eff_mass(output='eigs', doping_levels=True)[source]
                                                              +get_average_eff_mass(output='eigs', doping_levels=True)[source]

                                                              Gives the average effective mass tensor. We call it average because it takes into account all the bands and regions in the Brillouin zone. This is different than the standard @@ -349,7 +349,7 @@

                                                              -get_carrier_concentration()[source]
                                                              +get_carrier_concentration()[source]

                                                              gives the carrier concentration (in cm^-3)

                                                              Returns

                                                              a dictionary {temp:[]} with an array of carrier concentration @@ -361,7 +361,7 @@

                                                              -get_complete_dos(structure, analyzer_for_second_spin=None)[source]
                                                              +get_complete_dos(structure, analyzer_for_second_spin=None)[source]

                                                              Gives a CompleteDos object with the DOS from the interpolated projected band structure :param the structure: @@ -385,7 +385,7 @@

                                                              -get_complexity_factor(output='average', temp=300, doping_levels=False, Lambda=0.5)[source]
                                                              +get_complexity_factor(output='average', temp=300, doping_levels=False, Lambda=0.5)[source]

                                                              Fermi surface complexity factor respect to calculated as explained in Ref. Gibbs, Z. M. et al., Effective mass and fermi surface complexity factor from ab initio band structure calculations. @@ -419,7 +419,7 @@

                                                              -get_conductivity(output='eigs', doping_levels=True, relaxation_time=1e-14)[source]
                                                              +get_conductivity(output='eigs', doping_levels=True, relaxation_time=1e-14)[source]

                                                              Gives the conductivity (1/Ohm*m) in either a full 3x3 tensor form, as 3 eigenvalues, or as the average value (trace/3.0) If doping_levels=True, the results are given at @@ -462,7 +462,7 @@

                                                              -get_extreme(target_prop, maximize=True, min_temp=None, max_temp=None, min_doping=None, max_doping=None, isotropy_tolerance=0.05, use_average=True)[source]
                                                              +get_extreme(target_prop, maximize=True, min_temp=None, max_temp=None, min_doping=None, max_doping=None, isotropy_tolerance=0.05, use_average=True)[source]

                                                              This method takes in eigenvalues over a range of carriers, temperatures, and doping levels, and tells you what is the “best” value that can be achieved for the given target_property. Note that @@ -492,7 +492,7 @@

                                                              -get_hall_carrier_concentration()[source]
                                                              +get_hall_carrier_concentration()[source]

                                                              gives the Hall carrier concentration (in cm^-3). This is the trace of the Hall tensor (see Boltztrap source code) Hall carrier concentration are not always exactly the same than carrier concentration.

                                                              @@ -506,7 +506,7 @@
                                                              -get_mu_bounds(temp=300)[source]
                                                              +get_mu_bounds(temp=300)[source]
                                                              Parameters

                                                              temp – Temperature.

                                                              @@ -519,7 +519,7 @@
                                                              -get_power_factor(output='eigs', doping_levels=True, relaxation_time=1e-14)[source]
                                                              +get_power_factor(output='eigs', doping_levels=True, relaxation_time=1e-14)[source]

                                                              Gives the power factor (Seebeck^2 * conductivity) in units microW/(m*K^2) in either a full 3x3 tensor form, as 3 eigenvalues, or as the average value (trace/3.0) If @@ -563,7 +563,7 @@

                                                              -get_seebeck(output='eigs', doping_levels=True)[source]
                                                              +get_seebeck(output='eigs', doping_levels=True)[source]

                                                              Gives the seebeck coefficient (microV/K) in either a full 3x3 tensor form, as 3 eigenvalues, or as the average value (trace/3.0) If doping_levels=True, the results are given at @@ -604,7 +604,7 @@

                                                              -get_seebeck_eff_mass(output='average', temp=300, doping_levels=False, Lambda=0.5)[source]
                                                              +get_seebeck_eff_mass(output='average', temp=300, doping_levels=False, Lambda=0.5)[source]

                                                              Seebeck effective mass calculated as explained in Ref. Gibbs, Z. M. et al., Effective mass and fermi surface complexity factor from ab initio band structure calculations. @@ -638,7 +638,7 @@

                                                              -get_symm_bands(structure, efermi, kpt_line=None, labels_dict=None)[source]
                                                              +get_symm_bands(structure, efermi, kpt_line=None, labels_dict=None)[source]

                                                              Function useful to read bands from Boltztrap output and get a BandStructureSymmLine object comparable with that one from a DFT calculation (if the same kpt_line is provided). Default kpt_line @@ -651,7 +651,7 @@

                                                              -get_thermal_conductivity(output='eigs', doping_levels=True, k_el=True, relaxation_time=1e-14)[source]
                                                              +get_thermal_conductivity(output='eigs', doping_levels=True, k_el=True, relaxation_time=1e-14)[source]

                                                              Gives the electronic part of the thermal conductivity in either a full 3x3 tensor form, as 3 eigenvalues, or as the average value (trace/3.0) If @@ -696,7 +696,7 @@

                                                              -get_zt(output='eigs', doping_levels=True, relaxation_time=1e-14, kl=1.0)[source]
                                                              +get_zt(output='eigs', doping_levels=True, relaxation_time=1e-14, kl=1.0)[source]

                                                              Gives the ZT coefficient (S^2*cond*T/thermal cond) in either a full 3x3 tensor form, as 3 eigenvalues, or as the average value (trace/3.0) If @@ -741,7 +741,7 @@

                                                              -static parse_cond_and_hall(path_dir, doping_levels=None)[source]
                                                              +static parse_cond_and_hall(path_dir, doping_levels=None)[source]

                                                              Parses the conductivity and Hall tensors :param path_dir: Path containing .condtens / .halltens files :param doping_levels: ([float]) - doping lvls, parse outtrans to get this

                                                              @@ -756,7 +756,7 @@
                                                              -static parse_intrans(path_dir)[source]
                                                              +static parse_intrans(path_dir)[source]

                                                              Parses boltztrap.intrans mainly to extract the value of scissor applied to the bands or some other inputs

                                                              @@ -778,7 +778,7 @@
                                                              -static parse_outputtrans(path_dir)[source]
                                                              +static parse_outputtrans(path_dir)[source]

                                                              Parses .outputtrans file

                                                              Parameters
                                                              @@ -792,7 +792,7 @@
                                                              -static parse_struct(path_dir)[source]
                                                              +static parse_struct(path_dir)[source]

                                                              Parses boltztrap.struct file (only the volume) :param path_dir: (str) dir containing the boltztrap.struct file

                                                              @@ -804,7 +804,7 @@
                                                              -static parse_transdos(path_dir, efermi, dos_spin=1, trim_dos=False)[source]
                                                              +static parse_transdos(path_dir, efermi, dos_spin=1, trim_dos=False)[source]

                                                              Parses .transdos (total DOS) and .transdos_x_y (partial DOS) files :param path_dir: (str) dir containing DOS files :param efermi: (float) Fermi energy @@ -821,7 +821,7 @@

                                                              -exception BoltztrapError[source]
                                                              +exception BoltztrapError[source]

                                                              Bases: Exception

                                                              Exception class for boltztrap. Raised when the boltztrap gives an error

                                                              @@ -829,7 +829,7 @@
                                                              -class BoltztrapRunner(bs, nelec, dos_type='HISTO', energy_grid=0.005, lpfac=10, run_type='BOLTZ', band_nb=None, tauref=0, tauexp=0, tauen=0, soc=False, doping=None, energy_span_around_fermi=1.5, scissor=0.0, kpt_line=None, spin=None, cond_band=False, tmax=1300, tgrid=50, symprec=0.001, cb_cut=10, timeout=7200)[source]
                                                              +class BoltztrapRunner(bs, nelec, dos_type='HISTO', energy_grid=0.005, lpfac=10, run_type='BOLTZ', band_nb=None, tauref=0, tauexp=0, tauen=0, soc=False, doping=None, energy_span_around_fermi=1.5, scissor=0.0, kpt_line=None, spin=None, cond_band=False, tmax=1300, tgrid=50, symprec=0.001, cb_cut=10, timeout=7200)[source]

                                                              Bases: monty.json.MSONable

                                                              This class is used to run Boltztrap on a band structure object.

                                                              @@ -904,7 +904,7 @@
                                                              -as_dict()[source]
                                                              +as_dict()[source]
                                                              Returns

                                                              MSONable dict

                                                              @@ -914,7 +914,7 @@
                                                              -property bs[source]
                                                              +property bs[source]

                                                              The BandStructure

                                                              Type
                                                              @@ -925,7 +925,7 @@
                                                              -property nelec[source]
                                                              +property nelec[source]

                                                              Number of electrons

                                                              Type
                                                              @@ -936,7 +936,7 @@
                                                              -run(path_dir=None, convergence=True, write_input=True, clear_dir=False, max_lpfac=150, min_egrid=5e-05)[source]
                                                              +run(path_dir=None, convergence=True, write_input=True, clear_dir=False, max_lpfac=150, min_egrid=5e-05)[source]

                                                              Write inputs (optional), run BoltzTraP, and ensure convergence (optional) :param path_dir: directory in which to run BoltzTraP @@ -964,7 +964,7 @@

                                                              -write_def(output_file)[source]
                                                              +write_def(output_file)[source]

                                                              Writes the def to an output file.

                                                              Parameters
                                                              @@ -975,7 +975,7 @@
                                                              -write_energy(output_file)[source]
                                                              +write_energy(output_file)[source]

                                                              Writes the energy to an output file.

                                                              Parameters
                                                              @@ -986,7 +986,7 @@
                                                              -write_input(output_dir)[source]
                                                              +write_input(output_dir)[source]

                                                              Writes the input files.

                                                              Parameters
                                                              @@ -997,7 +997,7 @@
                                                              -write_intrans(output_file)[source]
                                                              +write_intrans(output_file)[source]

                                                              Writes the intrans to an output file.

                                                              Parameters
                                                              @@ -1008,7 +1008,7 @@
                                                              -write_proj(output_file_proj, output_file_def)[source]
                                                              +write_proj(output_file_proj, output_file_def)[source]

                                                              Writes the projections to an output file.

                                                              Parameters
                                                              @@ -1019,7 +1019,7 @@
                                                              -write_struct(output_file)[source]
                                                              +write_struct(output_file)[source]

                                                              Writes the structure to an output file.

                                                              Parameters
                                                              @@ -1032,7 +1032,7 @@
                                                              -compare_sym_bands(bands_obj, bands_ref_obj, nb=None)[source]
                                                              +compare_sym_bands(bands_obj, bands_ref_obj, nb=None)[source]

                                                              Compute the mean of correlation between bzt and vasp bandstructure on sym line, for all bands and locally (for each branches) the difference squared (%) if nb is specified.

                                                              @@ -1040,7 +1040,7 @@
                                                              -eta_from_seebeck(seeb, Lambda)[source]
                                                              +eta_from_seebeck(seeb, Lambda)[source]

                                                              It takes a value of seebeck and adjusts the analytic seebeck until it’s equal Returns: eta where the two seebeck coefficients are equal (reduced chemical potential)

                                                              @@ -1048,7 +1048,7 @@
                                                              -read_cube_file(filename)[source]
                                                              +read_cube_file(filename)[source]
                                                              Parameters

                                                              filename – Cube filename

                                                              @@ -1061,14 +1061,14 @@
                                                              -seebeck_eff_mass_from_carr(eta, n, T, Lambda)[source]
                                                              +seebeck_eff_mass_from_carr(eta, n, T, Lambda)[source]

                                                              Calculate seebeck effective mass at a certain carrier concentration eta in kB*T units, n in cm-3, T in K, returns mass in m0 units

                                                              -seebeck_eff_mass_from_seebeck_carr(seeb, n, T, Lambda)[source]
                                                              +seebeck_eff_mass_from_seebeck_carr(seeb, n, T, Lambda)[source]

                                                              Find the chemical potential where analytic and calculated seebeck are identical and then calculate the seebeck effective mass at that chemical potential and a certain carrier concentration n

                                                              @@ -1076,7 +1076,7 @@
                                                              -seebeck_spb(eta, Lambda=0.5)[source]
                                                              +seebeck_spb(eta, Lambda=0.5)[source]

                                                              Seebeck analytic formula in the single parabolic model

                                                              diff --git a/docs/pymatgen.electronic_structure.boltztrap2.html b/docs/pymatgen.electronic_structure.boltztrap2.html index c87af6661b8..58f99ac9077 100644 --- a/docs/pymatgen.electronic_structure.boltztrap2.html +++ b/docs/pymatgen.electronic_structure.boltztrap2.html @@ -4,7 +4,7 @@ - pymatgen.electronic_structure.boltztrap2 module — pymatgen 2022.5.18 documentation + pymatgen.electronic_structure.boltztrap2 module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                              - 2022.5.18 + 2022.5.18.1
                                                              diff --git a/docs/pymatgen.electronic_structure.cohp.html b/docs/pymatgen.electronic_structure.cohp.html index 7d540564167..39e55597c5e 100644 --- a/docs/pymatgen.electronic_structure.cohp.html +++ b/docs/pymatgen.electronic_structure.cohp.html @@ -4,7 +4,7 @@ - pymatgen.electronic_structure.cohp module — pymatgen 2022.5.18 documentation + pymatgen.electronic_structure.cohp module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                              - 2022.5.18 + 2022.5.18.1
                                                              @@ -120,7 +120,7 @@ for crystal orbital overlap populations (COOP).

                                                              -class Cohp(efermi, energies, cohp, are_coops=False, are_cobis=False, icohp=None)[source]
                                                              +class Cohp(efermi, energies, cohp, are_coops=False, are_cobis=False, icohp=None)[source]

                                                              Bases: monty.json.MSONable

                                                              Basic COHP object.

                                                              @@ -137,19 +137,19 @@
                                                              -as_dict()[source]
                                                              +as_dict()[source]

                                                              JSON-serializable dict representation of COHP.

                                                              -classmethod from_dict(d)[source]
                                                              +classmethod from_dict(d)[source]

                                                              Returns a COHP object from a dict representation of the COHP.

                                                              -get_cohp(spin=None, integrated=False)[source]
                                                              +get_cohp(spin=None, integrated=False)[source]

                                                              Returns the COHP or ICOHP for a particular spin.

                                                              Parameters
                                                              @@ -169,13 +169,13 @@
                                                              -get_icohp(spin=None)[source]
                                                              +get_icohp(spin=None)[source]

                                                              Convenient alternative to get the ICOHP for a particular spin.

                                                              -get_interpolated_value(energy, integrated=False)[source]
                                                              +get_interpolated_value(energy, integrated=False)[source]

                                                              Returns the COHP for a particular energy.

                                                              Parameters
                                                              @@ -186,7 +186,7 @@
                                                              -has_antibnd_states_below_efermi(spin=None, limit=0.01)[source]
                                                              +has_antibnd_states_below_efermi(spin=None, limit=0.01)[source]
                                                              Returns dict indicating if there are antibonding states below the Fermi level depending on the spin

                                                              spin: Spin limit: -COHP smaller -limit will be considered.

                                                              @@ -198,7 +198,7 @@
                                                              -class CompleteCohp(structure, avg_cohp, cohp_dict, bonds=None, are_coops=False, are_cobis=False, orb_res_cohp=None)[source]
                                                              +class CompleteCohp(structure, avg_cohp, cohp_dict, bonds=None, are_coops=False, are_cobis=False, orb_res_cohp=None)[source]

                                                              Bases: pymatgen.electronic_structure.cohp.Cohp

                                                              A wrapper class that defines an average COHP, and individual COHPs.

                                                              @@ -223,19 +223,19 @@
                                                              -as_dict()[source]
                                                              +as_dict()[source]

                                                              JSON-serializable dict representation of CompleteCohp.

                                                              -classmethod from_dict(d)[source]
                                                              +classmethod from_dict(d)[source]

                                                              Returns CompleteCohp object from dict representation.

                                                              -classmethod from_file(fmt, filename=None, structure_file=None, are_coops=False, are_cobis=False)[source]
                                                              +classmethod from_file(fmt, filename=None, structure_file=None, are_coops=False, are_cobis=False)[source]

                                                              Creates a CompleteCohp object from an output file of a COHP calculation. Valid formats are either LMTO (for the Stuttgart LMTO-ASA code) or LOBSTER (for the LOBSTER code).

                                                              @@ -264,7 +264,7 @@
                                                              -get_cohp_by_label(label, summed_spin_channels=False)[source]
                                                              +get_cohp_by_label(label, summed_spin_channels=False)[source]

                                                              Get specific COHP object.

                                                              Parameters
                                                              @@ -281,7 +281,7 @@
                                                              -get_orbital_resolved_cohp(label, orbitals, summed_spin_channels=False)[source]
                                                              +get_orbital_resolved_cohp(label, orbitals, summed_spin_channels=False)[source]

                                                              Get orbital-resolved COHP.

                                                              Parameters
                                                              @@ -307,7 +307,7 @@
                                                              -get_summed_cohp_by_label_and_orbital_list(label_list, orbital_list, divisor=1, summed_spin_channels=False)[source]
                                                              +get_summed_cohp_by_label_and_orbital_list(label_list, orbital_list, divisor=1, summed_spin_channels=False)[source]

                                                              Returns a COHP object that includes a summed COHP divided by divisor

                                                              Parameters
                                                              @@ -327,7 +327,7 @@
                                                              -get_summed_cohp_by_label_list(label_list, divisor=1, summed_spin_channels=False)[source]
                                                              +get_summed_cohp_by_label_list(label_list, divisor=1, summed_spin_channels=False)[source]

                                                              Returns a COHP object that includes a summed COHP divided by divisor

                                                              Parameters
                                                              @@ -347,26 +347,26 @@
                                                              -class IcohpCollection(list_labels, list_atom1, list_atom2, list_length, list_translation, list_num, list_icohp, is_spin_polarized, are_coops=False, are_cobis=False)[source]
                                                              +class IcohpCollection(list_labels, list_atom1, list_atom2, list_length, list_translation, list_num, list_icohp, is_spin_polarized, are_coops=False, are_cobis=False)[source]

                                                              Bases: monty.json.MSONable

                                                              Class to store IcohpValues

                                                              -are_coops[source]
                                                              +are_coops[source]
                                                              Boolean to indicate if this are ICOOPs
                                                              -are_cobis[source]
                                                              +are_cobis[source]
                                                              Boolean to indicate if this are ICOOPs
                                                              -is_spin_polarized[source]
                                                              +is_spin_polarized[source]
                                                              Boolean to indicate if the Lobster calculation was done spin polarized or not
                                                              @@ -390,7 +390,7 @@
                                                              -property are_cobis[source]
                                                              +property are_cobis[source]

                                                              Whether this a cobi.

                                                              Type
                                                              @@ -401,7 +401,7 @@
                                                              -property are_coops[source]
                                                              +property are_coops[source]

                                                              Whether this is a coop.

                                                              Type
                                                              @@ -412,7 +412,7 @@
                                                              -extremum_icohpvalue(summed_spin_channels=True, spin=Spin.up)[source]
                                                              +extremum_icohpvalue(summed_spin_channels=True, spin=Spin.up)[source]

                                                              get ICOHP/ICOOP of strongest bond :param summed_spin_channels: Boolean to indicate whether the ICOHPs/ICOOPs of both spin channels should be summed :param spin: if summed_spin_channels is equal to False, this spin indicates which spin channel should be returned

                                                              @@ -425,7 +425,7 @@
                                                              -get_icohp_by_label(label, summed_spin_channels=True, spin=Spin.up)[source]
                                                              +get_icohp_by_label(label, summed_spin_channels=True, spin=Spin.up)[source]

                                                              get an icohp value for a certain bond as indicated by the label (bond labels starting by “1” as in ICOHPLIST/ICOOPLIST)

                                                              @@ -444,7 +444,7 @@
                                                              -get_icohp_dict_by_bondlengths(minbondlength=0.0, maxbondlength=8.0)[source]
                                                              +get_icohp_dict_by_bondlengths(minbondlength=0.0, maxbondlength=8.0)[source]

                                                              get a dict of IcohpValues corresponding to certain bond lengths :param minbondlength: defines the minimum of the bond lengths of the bonds :param maxbondlength: defines the maximum of the bond lengths of the bonds

                                                              @@ -457,7 +457,7 @@
                                                              -get_icohp_dict_of_site(site, minsummedicohp=None, maxsummedicohp=None, minbondlength=0.0, maxbondlength=8.0, only_bonds_to=None)[source]
                                                              +get_icohp_dict_of_site(site, minsummedicohp=None, maxsummedicohp=None, minbondlength=0.0, maxbondlength=8.0, only_bonds_to=None)[source]

                                                              get a dict of IcohpValue for a certain site (indicated by integer) :param site: integer describing the site of interest, order as in Icohplist.lobster/Icooplist.lobster, starts at 0 :param minsummedicohp: float, minimal icohp/icoop of the bonds that are considered. It is the summed ICOHP value

                                                              @@ -482,7 +482,7 @@
                                                              -get_summed_icohp_by_label_list(label_list, divisor=1.0, summed_spin_channels=True, spin=Spin.up)[source]
                                                              +get_summed_icohp_by_label_list(label_list, divisor=1.0, summed_spin_channels=True, spin=Spin.up)[source]

                                                              get the sum of several ICOHP values that are indicated by a list of labels (labels of the bonds are the same as in ICOHPLIST/ICOOPLIST)

                                                              @@ -502,7 +502,7 @@
                                                              -property is_spin_polarized[source]
                                                              +property is_spin_polarized[source]

                                                              Whether it is spin polarized.

                                                              Type
                                                              @@ -515,33 +515,33 @@
                                                              -class IcohpValue(label, atom1, atom2, length, translation, num, icohp, are_coops=False, are_cobis=False)[source]
                                                              +class IcohpValue(label, atom1, atom2, length, translation, num, icohp, are_coops=False, are_cobis=False)[source]

                                                              Bases: monty.json.MSONable

                                                              Class to store information on an ICOHP or ICOOP value

                                                              -num_bonds[source]
                                                              +num_bonds[source]
                                                              number of bonds used for the average cohp (relevant for Lobster versions <3.0) (int)
                                                              -are_coops[source]
                                                              +are_coops[source]
                                                              Boolean to indicates ICOOPs
                                                              -are_cobis[source]
                                                              +are_cobis[source]
                                                              Boolean to indicates ICOBIs
                                                              -icohp[source]
                                                              +icohp[source]
                                                              dict={Spin.up: icohpvalue for spin.up, Spin.down: icohpvalue for spin.down}
                                                              @@ -570,21 +570,21 @@
                                                              -property are_cobis[source]
                                                              +property are_cobis[source]

                                                              tells if ICOBIs or not :returns: Boolean

                                                              -property are_coops[source]
                                                              +property are_coops[source]

                                                              tells if ICOOPs or not :returns: Boolean

                                                              -property icohp[source]
                                                              +property icohp[source]

                                                              dict with icohps for spinup and spindown :returns: icohpvalue for spin.up, Spin.down: icohpvalue for spin.down} :rtype: dict={Spin.up

                                                              @@ -592,7 +592,7 @@
                                                              -icohpvalue(spin=Spin.up)[source]
                                                              +icohpvalue(spin=Spin.up)[source]
                                                              Parameters

                                                              spin – Spin.up or Spin.down

                                                              @@ -605,21 +605,21 @@
                                                              -property is_spin_polarized[source]
                                                              +property is_spin_polarized[source]

                                                              tells if spin polarized calculation or not :returns: Boolean

                                                              -property num_bonds[source]
                                                              +property num_bonds[source]

                                                              tells the number of bonds for which the ICOHP value is an average :returns: Int

                                                              -property summed_icohp[source]
                                                              +property summed_icohp[source]

                                                              Adds ICOHPs of both spin channels for spin polarized compounds :returns: icohp value in eV

                                                              @@ -628,7 +628,7 @@
                                                              -get_integrated_cohp_in_energy_range(cohp, label, orbital=None, energy_range=None, relative_E_Fermi=True, summed_spin_channels=True)[source]
                                                              +get_integrated_cohp_in_energy_range(cohp, label, orbital=None, energy_range=None, relative_E_Fermi=True, summed_spin_channels=True)[source]

                                                              Method that can integrate completecohp objects which include data on integrated COHPs :param cohp: CompleteCOHP object :param label: label of the COHP data diff --git a/docs/pymatgen.electronic_structure.core.html b/docs/pymatgen.electronic_structure.core.html index baa0cc10f84..d119f2b048c 100644 --- a/docs/pymatgen.electronic_structure.core.html +++ b/docs/pymatgen.electronic_structure.core.html @@ -4,7 +4,7 @@ - pymatgen.electronic_structure.core module — pymatgen 2022.5.18 documentation + pymatgen.electronic_structure.core module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                                              - 2022.5.18 + 2022.5.18.1
                                                              @@ -119,7 +119,7 @@ such as the Spin, Orbital, etc.

                                                              -class Magmom(moment, saxis=(0, 0, 1))[source]
                                                              +class Magmom(moment, saxis=(0, 0, 1))[source]

                                                              Bases: monty.json.MSONable

                                                              New class in active development. Use with caution, feedback is appreciated.

                                                              @@ -170,7 +170,7 @@
                                                              -static are_collinear(magmoms)[source]
                                                              +static are_collinear(magmoms)[source]

                                                              Method checks to see if a set of magnetic moments are collinear with each other. :param magmoms: list of magmoms (Magmoms, scalars or vectors) @@ -179,7 +179,7 @@

                                                              -classmethod from_global_moment_and_saxis(global_moment, saxis)[source]
                                                              +classmethod from_global_moment_and_saxis(global_moment, saxis)[source]

                                                              Convenience method to initialize Magmom from a given global magnetic moment, i.e. magnetic moment with saxis=(0,0,1), and provided saxis.

                                                              @@ -200,7 +200,7 @@
                                                              -classmethod from_moment_relative_to_crystal_axes(moment, lattice)[source]
                                                              +classmethod from_moment_relative_to_crystal_axes(moment, lattice)[source]

                                                              Obtaining a Magmom object from a magnetic moment provided relative to crystal axes.

                                                              Used for obtaining moments from magCIF file. @@ -211,7 +211,7 @@

                                                              -get_00t_magmom_with_xyz_saxis()[source]
                                                              +get_00t_magmom_with_xyz_saxis()[source]

                                                              For internal implementation reasons, in non-collinear calculations VASP prefers:

                                                              MAGMOM = 0 0 total_magnetic_moment @@ -234,7 +234,7 @@

                                                              -static get_consistent_set_and_saxis(magmoms, saxis=None)[source]
                                                              +static get_consistent_set_and_saxis(magmoms, saxis=None)[source]

                                                              Method to ensure a list of magmoms use the same spin axis. Returns a tuple of a list of Magmoms and their global spin axis.

                                                              @@ -252,7 +252,7 @@
                                                              -get_moment(saxis=(0, 0, 1))[source]
                                                              +get_moment(saxis=(0, 0, 1))[source]

                                                              Get magnetic moment relative to a given spin quantization axis. If no axis is provided, moment will be given relative to the Magmom’s internal spin quantization axis, i.e. equivalent to @@ -269,7 +269,7 @@

                                                              -get_moment_relative_to_crystal_axes(lattice)[source]
                                                              +get_moment_relative_to_crystal_axes(lattice)[source]

                                                              If scalar magmoms, moments will be given arbitrarily along z. Used for writing moments to magCIF file.

                                                              @@ -284,7 +284,7 @@
                                                              -static get_suggested_saxis(magmoms)[source]
                                                              +static get_suggested_saxis(magmoms)[source]

                                                              This method returns a suggested spin axis for a set of magmoms, taking the largest magnetic moment as the reference. For calculations with collinear spins, this would give a sensible saxis for a ncl @@ -301,7 +301,7 @@

                                                              -get_xyz_magmom_with_001_saxis()[source]
                                                              +get_xyz_magmom_with_001_saxis()[source]

                                                              Returns a Magmom in the default setting of saxis = [0, 0, 1] and the magnetic moment rotated as required.

                                                              @@ -313,7 +313,7 @@
                                                              -property global_moment[source]
                                                              +property global_moment[source]

                                                              Get the magnetic moment defined in an arbitrary global reference frame.

                                                              Returns
                                                              @@ -324,7 +324,7 @@
                                                              -static have_consistent_saxis(magmoms)[source]
                                                              +static have_consistent_saxis(magmoms)[source]

                                                              This method checks that all Magmom objects in a list have a consistent spin quantization axis. To write MAGMOM tags to a VASP INCAR, a global SAXIS value for all magmoms has to be used. @@ -342,7 +342,7 @@

                                                              -property projection[source]
                                                              +property projection[source]

                                                              Projects moment along spin quantisation axis. Useful for obtaining collinear approximation for slightly non-collinear magmoms.

                                                              @@ -356,140 +356,140 @@
                                                              -class Orbital(value)[source]
                                                              +class Orbital(value)[source]

                                                              Bases: enum.Enum

                                                              Enum type for specific orbitals. The indices are basically the order in which the orbitals are reported in VASP and has no special meaning.

                                                              -dx2 = 8[source]
                                                              +dx2 = 8[source]
                                                              -dxy = 4[source]
                                                              +dxy = 4[source]
                                                              -dxz = 7[source]
                                                              +dxz = 7[source]
                                                              -dyz = 5[source]
                                                              +dyz = 5[source]
                                                              -dz2 = 6[source]
                                                              +dz2 = 6[source]
                                                              -f0 = 12[source]
                                                              +f0 = 12[source]
                                                              -f1 = 13[source]
                                                              +f1 = 13[source]
                                                              -f2 = 14[source]
                                                              +f2 = 14[source]
                                                              -f3 = 15[source]
                                                              +f3 = 15[source]
                                                              -f_1 = 11[source]
                                                              +f_1 = 11[source]
                                                              -f_2 = 10[source]
                                                              +f_2 = 10[source]
                                                              -f_3 = 9[source]
                                                              +f_3 = 9[source]
                                                              -property orbital_type[source]
                                                              +property orbital_type[source]

                                                              Returns OrbitalType of an orbital.

                                                              -px = 3[source]
                                                              +px = 3[source]
                                                              -py = 1[source]
                                                              +py = 1[source]
                                                              -pz = 2[source]
                                                              +pz = 2[source]
                                                              -s = 0[source]
                                                              +s = 0[source]
                                                              -class OrbitalType(value)[source]
                                                              +class OrbitalType(value)[source]

                                                              Bases: enum.Enum

                                                              Enum type for orbital type. Indices are basically the azimuthal quantum number, l.

                                                              -d = 2[source]
                                                              +d = 2[source]
                                                              -f = 3[source]
                                                              +f = 3[source]
                                                              -p = 1[source]
                                                              +p = 1[source]
                                                              -s = 0[source]
                                                              +s = 0[source]
                                                              -class Spin(value)[source]
                                                              +class Spin(value)[source]

                                                              Bases: enum.Enum

                                                              Enum type for Spin. Only up and down. Usage: Spin.up, Spin.down.

                                                              -down = -1[source]
                                                              +down = -1[source]
                                                              -up = 1[source]
                                                              +up = 1[source]
                                                              diff --git a/docs/pymatgen.electronic_structure.dos.html b/docs/pymatgen.electronic_structure.dos.html index 3e53f207539..2a038af8428 100644 --- a/docs/pymatgen.electronic_structure.dos.html +++ b/docs/pymatgen.electronic_structure.dos.html @@ -4,7 +4,7 @@ - pymatgen.electronic_structure.dos module — pymatgen 2022.5.18 documentation + pymatgen.electronic_structure.dos module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                              - 2022.5.18 + 2022.5.18.1
                                                              @@ -118,7 +118,7 @@

                                                              This module defines classes to represent the density of states, etc.

                                                              -class CompleteDos(structure: pymatgen.core.structure.Structure, total_dos: pymatgen.electronic_structure.dos.Dos, pdoss: dict[pymatgen.core.sites.PeriodicSite, dict[pymatgen.electronic_structure.core.Orbital, dict[pymatgen.electronic_structure.core.Spin, Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]]]])[source]
                                                              +class CompleteDos(structure: pymatgen.core.structure.Structure, total_dos: pymatgen.electronic_structure.dos.Dos, pdoss: dict[pymatgen.core.sites.PeriodicSite, dict[pymatgen.electronic_structure.core.Orbital, dict[pymatgen.electronic_structure.core.Spin, Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]]]])[source]

                                                              Bases: pymatgen.electronic_structure.dos.Dos

                                                              This wrapper class defines a total dos, and also provides a list of PDos. Mainly used by pymatgen.io.vasp.Vasprun to create a complete Dos from @@ -126,13 +126,13 @@ manually.

                                                              -structure[source]
                                                              +structure[source]

                                                              Structure associated with the CompleteDos.

                                                              -pdos[source]
                                                              +pdos[source]

                                                              Dict of partial densities of the form {Site:{Orbital:{Spin:Densities}}}

                                                              @@ -148,19 +148,19 @@
                                                              -as_dict() → dict[source]
                                                              +as_dict() → dict[source]

                                                              JSON-serializable dict representation of CompleteDos.

                                                              -classmethod from_dict(d) → pymatgen.electronic_structure.dos.CompleteDos[source]
                                                              +classmethod from_dict(d) → pymatgen.electronic_structure.dos.CompleteDos[source]

                                                              Returns CompleteDos object from dict representation.

                                                              -get_band_center(band: pymatgen.electronic_structure.core.OrbitalType = OrbitalType.d, elements: Optional[list[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]]] = None, sites: Optional[list[pymatgen.core.sites.PeriodicSite]] = None, spin: Optional[pymatgen.electronic_structure.core.Spin] = None, erange: Optional[list[float]] = None) → float[source]
                                                              +get_band_center(band: pymatgen.electronic_structure.core.OrbitalType = OrbitalType.d, elements: Optional[list[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]]] = None, sites: Optional[list[pymatgen.core.sites.PeriodicSite]] = None, spin: Optional[pymatgen.electronic_structure.core.Spin] = None, erange: Optional[list[float]] = None) → float[source]

                                                              Computes the orbital-projected band center, defined as the first moment relative to the Fermi level

                                                              @@ -189,7 +189,7 @@
                                                              -get_band_filling(band: pymatgen.electronic_structure.core.OrbitalType = OrbitalType.d, elements: Optional[list[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]]] = None, sites: Optional[list[pymatgen.core.sites.PeriodicSite]] = None, spin: Optional[pymatgen.electronic_structure.core.Spin] = None) → float[source]
                                                              +get_band_filling(band: pymatgen.electronic_structure.core.OrbitalType = OrbitalType.d, elements: Optional[list[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]]] = None, sites: Optional[list[pymatgen.core.sites.PeriodicSite]] = None, spin: Optional[pymatgen.electronic_structure.core.Spin] = None) → float[source]

                                                              Computes the orbital-projected band filling, defined as the zeroth moment up to the Fermi level

                                                              @@ -209,7 +209,7 @@
                                                              -get_band_kurtosis(band: pymatgen.electronic_structure.core.OrbitalType = OrbitalType.d, elements: Optional[list[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]]] = None, sites: Optional[list[pymatgen.core.sites.PeriodicSite]] = None, spin: Optional[pymatgen.electronic_structure.core.Spin] = None, erange: Optional[list[float]] = None) → float[source]
                                                              +get_band_kurtosis(band: pymatgen.electronic_structure.core.OrbitalType = OrbitalType.d, elements: Optional[list[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]]] = None, sites: Optional[list[pymatgen.core.sites.PeriodicSite]] = None, spin: Optional[pymatgen.electronic_structure.core.Spin] = None, erange: Optional[list[float]] = None) → float[source]
                                                              Get the orbital-projected kurtosis, defined as the fourth standardized moment

                                                              int_{-inf}^{+inf} rho(E)*(E-E_center)^4 dE/int_{-inf}^{+inf} rho(E) dE) / @@ -238,7 +238,7 @@

                                                              -get_band_skewness(band: pymatgen.electronic_structure.core.OrbitalType = OrbitalType.d, elements: Optional[list[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]]] = None, sites: Optional[list[pymatgen.core.sites.PeriodicSite]] = None, spin: Optional[pymatgen.electronic_structure.core.Spin] = None, erange: Optional[list[float]] = None) → float[source]
                                                              +get_band_skewness(band: pymatgen.electronic_structure.core.OrbitalType = OrbitalType.d, elements: Optional[list[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]]] = None, sites: Optional[list[pymatgen.core.sites.PeriodicSite]] = None, spin: Optional[pymatgen.electronic_structure.core.Spin] = None, erange: Optional[list[float]] = None) → float[source]
                                                              Get the orbital-projected skewness, defined as the third standardized moment

                                                              int_{-inf}^{+inf} rho(E)*(E-E_center)^3 dE/int_{-inf}^{+inf} rho(E) dE) / @@ -267,7 +267,7 @@

                                                              -get_band_width(band: pymatgen.electronic_structure.core.OrbitalType = OrbitalType.d, elements: Optional[list[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]]] = None, sites: Optional[list[pymatgen.core.sites.PeriodicSite]] = None, spin: Optional[pymatgen.electronic_structure.core.Spin] = None, erange: Optional[list[float]] = None) → float[source]
                                                              +get_band_width(band: pymatgen.electronic_structure.core.OrbitalType = OrbitalType.d, elements: Optional[list[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]]] = None, sites: Optional[list[pymatgen.core.sites.PeriodicSite]] = None, spin: Optional[pymatgen.electronic_structure.core.Spin] = None, erange: Optional[list[float]] = None) → float[source]
                                                              Get the orbital-projected band width, defined as the square root of the second moment

                                                              sqrt(int_{-inf}^{+inf} rho(E)*(E-E_center)^2 dE/int_{-inf}^{+inf} rho(E) dE)

                                                              @@ -294,7 +294,7 @@
                                                              -get_element_dos() → dict[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies], pymatgen.electronic_structure.dos.Dos][source]
                                                              +get_element_dos() → dict[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies], pymatgen.electronic_structure.dos.Dos][source]

                                                              Get element projected Dos.

                                                              Returns
                                                              @@ -308,7 +308,7 @@
                                                              -get_element_spd_dos(el: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]) → dict[pymatgen.electronic_structure.core.OrbitalType, pymatgen.electronic_structure.dos.Dos][source]
                                                              +get_element_spd_dos(el: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]) → dict[pymatgen.electronic_structure.core.OrbitalType, pymatgen.electronic_structure.dos.Dos][source]

                                                              Get element and spd projected Dos

                                                              Parameters
                                                              @@ -325,7 +325,7 @@
                                                              -get_hilbert_transform(band: pymatgen.electronic_structure.core.OrbitalType = OrbitalType.d, elements: Optional[list[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]]] = None, sites: Optional[list[pymatgen.core.sites.PeriodicSite]] = None) → pymatgen.electronic_structure.dos.Dos[source]
                                                              +get_hilbert_transform(band: pymatgen.electronic_structure.core.OrbitalType = OrbitalType.d, elements: Optional[list[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]]] = None, sites: Optional[list[pymatgen.core.sites.PeriodicSite]] = None) → pymatgen.electronic_structure.dos.Dos[source]

                                                              Returns the Hilbert transform of the orbital-projected density of states, often plotted for a Newns-Anderson analysis.

                                                              @@ -344,7 +344,7 @@
                                                              -get_n_moment(n: int, band: pymatgen.electronic_structure.core.OrbitalType = OrbitalType.d, elements: Optional[list[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]]] = None, sites: Optional[list[pymatgen.core.sites.PeriodicSite]] = None, spin: Optional[pymatgen.electronic_structure.core.Spin] = None, erange: Optional[list[float]] = None, center: bool = True) → float[source]
                                                              +get_n_moment(n: int, band: pymatgen.electronic_structure.core.OrbitalType = OrbitalType.d, elements: Optional[list[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]]] = None, sites: Optional[list[pymatgen.core.sites.PeriodicSite]] = None, spin: Optional[pymatgen.electronic_structure.core.Spin] = None, erange: Optional[list[float]] = None, center: bool = True) → float[source]
                                                              Get the nth moment of the DOS centered around the orbital-projected band center, defined as

                                                              int_{-inf}^{+inf} rho(E)*(E-E_center)^n dE/int_{-inf}^{+inf} rho(E) dE

                                                              @@ -373,7 +373,7 @@
                                                              -get_site_dos(site: pymatgen.core.sites.PeriodicSite) → pymatgen.electronic_structure.dos.Dos[source]
                                                              +get_site_dos(site: pymatgen.core.sites.PeriodicSite) → pymatgen.electronic_structure.dos.Dos[source]

                                                              Get the total Dos for a site (all orbitals).

                                                              Parameters
                                                              @@ -387,7 +387,7 @@
                                                              -get_site_orbital_dos(site: pymatgen.core.sites.PeriodicSite, orbital: pymatgen.electronic_structure.core.Orbital) → pymatgen.electronic_structure.dos.Dos[source]
                                                              +get_site_orbital_dos(site: pymatgen.core.sites.PeriodicSite, orbital: pymatgen.electronic_structure.core.Orbital) → pymatgen.electronic_structure.dos.Dos[source]

                                                              Get the Dos for a particular orbital of a particular site.

                                                              Parameters
                                                              @@ -404,7 +404,7 @@
                                                              -get_site_spd_dos(site: pymatgen.core.sites.PeriodicSite) → dict[pymatgen.electronic_structure.core.OrbitalType, pymatgen.electronic_structure.dos.Dos][source]
                                                              +get_site_spd_dos(site: pymatgen.core.sites.PeriodicSite) → dict[pymatgen.electronic_structure.core.OrbitalType, pymatgen.electronic_structure.dos.Dos][source]

                                                              Get orbital projected Dos of a particular site

                                                              Parameters
                                                              @@ -421,7 +421,7 @@
                                                              -get_site_t2g_eg_resolved_dos(site: pymatgen.core.sites.PeriodicSite) → dict[str, pymatgen.electronic_structure.dos.Dos][source]
                                                              +get_site_t2g_eg_resolved_dos(site: pymatgen.core.sites.PeriodicSite) → dict[str, pymatgen.electronic_structure.dos.Dos][source]

                                                              Get the t2g, eg projected DOS for a particular site.

                                                              Parameters
                                                              @@ -439,7 +439,7 @@
                                                              -get_spd_dos() → dict[pymatgen.electronic_structure.core.OrbitalType, pymatgen.electronic_structure.dos.Dos][source]
                                                              +get_spd_dos() → dict[pymatgen.electronic_structure.core.OrbitalType, pymatgen.electronic_structure.dos.Dos][source]

                                                              Get orbital projected Dos.

                                                              Returns
                                                              @@ -453,7 +453,7 @@
                                                              -get_upper_band_edge(band: pymatgen.electronic_structure.core.OrbitalType = OrbitalType.d, elements: Optional[list[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]]] = None, sites: Optional[list[pymatgen.core.sites.PeriodicSite]] = None, spin: Optional[pymatgen.electronic_structure.core.Spin] = None, erange: Optional[list[float]] = None) → float[source]
                                                              +get_upper_band_edge(band: pymatgen.electronic_structure.core.OrbitalType = OrbitalType.d, elements: Optional[list[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]]] = None, sites: Optional[list[pymatgen.core.sites.PeriodicSite]] = None, spin: Optional[pymatgen.electronic_structure.core.Spin] = None, erange: Optional[list[float]] = None) → float[source]

                                                              Get the orbital-projected upper band edge. The definition by Xin et al. Phys. Rev. B, 89, 115114 (2014) is used, which is the highest peak position of the Hilbert transform of the orbital-projected DOS.

                                                              @@ -476,7 +476,7 @@
                                                              -property spin_polarization: float | None[source]
                                                              +property spin_polarization: float | None[source]

                                                              Calculates spin polarization at Fermi level. If the calculation is not spin-polarized, None will be returned.

                                                              @@ -495,7 +495,7 @@
                                                              -class DOS(energies: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], densities: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], efermi: float)[source]
                                                              +class DOS(energies: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], densities: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], efermi: float)[source]

                                                              Bases: pymatgen.core.spectrum.Spectrum

                                                              Replacement basic DOS object. All other DOS objects are extended versions of this object. Work in progress.

                                                              @@ -512,17 +512,17 @@
                                                              -XLABEL = 'Energy'[source]
                                                              +XLABEL = 'Energy'[source]
                                                              -YLABEL = 'Density'[source]
                                                              +YLABEL = 'Density'[source]
                                                              -get_cbm_vbm(tol: float = 0.001, abs_tol: bool = False, spin=None)[source]
                                                              +get_cbm_vbm(tol: float = 0.001, abs_tol: bool = False, spin=None)[source]

                                                              Expects a DOS object and finds the cbm and vbm.

                                                              Parameters
                                                              @@ -545,7 +545,7 @@
                                                              -get_gap(tol: float = 0.001, abs_tol: bool = False, spin: Optional[pymatgen.electronic_structure.core.Spin] = None)[source]
                                                              +get_gap(tol: float = 0.001, abs_tol: bool = False, spin: Optional[pymatgen.electronic_structure.core.Spin] = None)[source]

                                                              Expects a DOS object and finds the gap.

                                                              Parameters
                                                              @@ -565,7 +565,7 @@
                                                              -get_interpolated_gap(tol: float = 0.001, abs_tol: bool = False, spin: Optional[pymatgen.electronic_structure.core.Spin] = None)[source]
                                                              +get_interpolated_gap(tol: float = 0.001, abs_tol: bool = False, spin: Optional[pymatgen.electronic_structure.core.Spin] = None)[source]

                                                              Expects a DOS object and finds the gap

                                                              Parameters
                                                              @@ -591,7 +591,7 @@
                                                              -class Dos(efermi: float, energies: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], densities: dict[pymatgen.electronic_structure.core.Spin, Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]])[source]
                                                              +class Dos(efermi: float, energies: Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]], densities: dict[pymatgen.electronic_structure.core.Spin, Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]])[source]

                                                              Bases: monty.json.MSONable

                                                              Basic DOS object. All other DOS objects are extended versions of this object.

                                                              @@ -607,19 +607,19 @@
                                                              -as_dict() → dict[source]
                                                              +as_dict() → dict[source]

                                                              JSON-serializable dict representation of Dos.

                                                              -classmethod from_dict(d) → pymatgen.electronic_structure.dos.Dos[source]
                                                              +classmethod from_dict(d) → pymatgen.electronic_structure.dos.Dos[source]

                                                              Returns Dos object from dict representation of Dos.

                                                              -get_cbm_vbm(tol: float = 0.001, abs_tol: bool = False, spin: Optional[pymatgen.electronic_structure.core.Spin] = None)[source]
                                                              +get_cbm_vbm(tol: float = 0.001, abs_tol: bool = False, spin: Optional[pymatgen.electronic_structure.core.Spin] = None)[source]

                                                              Expects a DOS object and finds the cbm and vbm.

                                                              Parameters
                                                              @@ -642,7 +642,7 @@
                                                              -get_densities(spin: Optional[pymatgen.electronic_structure.core.Spin] = None)[source]
                                                              +get_densities(spin: Optional[pymatgen.electronic_structure.core.Spin] = None)[source]

                                                              Returns the density of states for a particular spin.

                                                              Parameters
                                                              @@ -657,7 +657,7 @@
                                                              -get_gap(tol: float = 0.001, abs_tol: bool = False, spin: Optional[pymatgen.electronic_structure.core.Spin] = None)[source]
                                                              +get_gap(tol: float = 0.001, abs_tol: bool = False, spin: Optional[pymatgen.electronic_structure.core.Spin] = None)[source]

                                                              Expects a DOS object and finds the gap.

                                                              Parameters
                                                              @@ -677,7 +677,7 @@
                                                              -get_interpolated_gap(tol: float = 0.001, abs_tol: bool = False, spin: Optional[pymatgen.electronic_structure.core.Spin] = None)[source]
                                                              +get_interpolated_gap(tol: float = 0.001, abs_tol: bool = False, spin: Optional[pymatgen.electronic_structure.core.Spin] = None)[source]

                                                              Expects a DOS object and finds the gap

                                                              Parameters
                                                              @@ -701,7 +701,7 @@
                                                              -get_interpolated_value(energy: float)[source]
                                                              +get_interpolated_value(energy: float)[source]

                                                              Returns interpolated density for a particular energy.

                                                              Parameters
                                                              @@ -712,7 +712,7 @@
                                                              -get_smeared_densities(sigma: float)[source]
                                                              +get_smeared_densities(sigma: float)[source]

                                                              Returns the Dict representation of the densities, {Spin: densities}, but with a Gaussian smearing of std dev sigma

                                                              @@ -729,7 +729,7 @@
                                                              -class FermiDos(dos: pymatgen.electronic_structure.dos.Dos, structure: Optional[pymatgen.core.structure.Structure] = None, nelecs: Optional[float] = None, bandgap: Optional[float] = None)[source]
                                                              +class FermiDos(dos: pymatgen.electronic_structure.dos.Dos, structure: Optional[pymatgen.core.structure.Structure] = None, nelecs: Optional[float] = None, bandgap: Optional[float] = None)[source]

                                                              Bases: pymatgen.electronic_structure.dos.Dos, monty.json.MSONable

                                                              This wrapper class helps relate the density of states, doping levels (i.e. carrier concentrations) and corresponding fermi levels. A negative @@ -753,19 +753,19 @@

                                                              -as_dict() → dict[source]
                                                              +as_dict() → dict[source]

                                                              JSON-serializable dict representation of Dos.

                                                              -classmethod from_dict(d) → pymatgen.electronic_structure.dos.FermiDos[source]
                                                              +classmethod from_dict(d) → pymatgen.electronic_structure.dos.FermiDos[source]

                                                              Returns Dos object from dict representation of Dos.

                                                              -get_doping(fermi_level: float, temperature: float) → float[source]
                                                              +get_doping(fermi_level: float, temperature: float) → float[source]

                                                              Calculate the doping (majority carrier concentration) at a given fermi level and temperature. A simple Left Riemann sum is used for integrating the density of states over energy & equilibrium Fermi-Dirac @@ -788,7 +788,7 @@

                                                              -get_fermi(concentration: float, temperature: float, rtol: float = 0.01, nstep: int = 50, step: float = 0.1, precision: int = 8)[source]
                                                              +get_fermi(concentration: float, temperature: float, rtol: float = 0.01, nstep: int = 50, step: float = 0.1, precision: int = 8)[source]

                                                              Finds the fermi level at which the doping concentration at the given temperature (T) is equal to concentration. A greedy algorithm is used where the relative error is minimized by calculating the doping at a @@ -815,7 +815,7 @@

                                                              -get_fermi_interextrapolated(concentration: float, temperature: float, warn: bool = True, c_ref: float = 10000000000.0, **kwargs) → float[source]
                                                              +get_fermi_interextrapolated(concentration: float, temperature: float, warn: bool = True, c_ref: float = 10000000000.0, **kwargs) → float[source]

                                                              Similar to get_fermi except that when get_fermi fails to converge, an interpolated or extrapolated fermi is returned with the assumption that the fermi level changes linearly with log(abs(concentration)).

                                                              @@ -844,7 +844,7 @@
                                                              -class LobsterCompleteDos(structure: pymatgen.core.structure.Structure, total_dos: pymatgen.electronic_structure.dos.Dos, pdoss: dict[pymatgen.core.sites.PeriodicSite, dict[pymatgen.electronic_structure.core.Orbital, dict[pymatgen.electronic_structure.core.Spin, Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]]]])[source]
                                                              +class LobsterCompleteDos(structure: pymatgen.core.structure.Structure, total_dos: pymatgen.electronic_structure.dos.Dos, pdoss: dict[pymatgen.core.sites.PeriodicSite, dict[pymatgen.electronic_structure.core.Orbital, dict[pymatgen.electronic_structure.core.Spin, Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]]]])[source]

                                                              Bases: pymatgen.electronic_structure.dos.CompleteDos

                                                              Extended CompleteDOS for Lobster

                                                              @@ -859,13 +859,13 @@
                                                              -classmethod from_dict(d) → pymatgen.electronic_structure.dos.LobsterCompleteDos[source]
                                                              +classmethod from_dict(d) → pymatgen.electronic_structure.dos.LobsterCompleteDos[source]

                                                              Returns: CompleteDos object from dict representation.

                                                              -get_element_spd_dos(el: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]) → dict[str, pymatgen.electronic_structure.dos.Dos][source]
                                                              +get_element_spd_dos(el: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]) → dict[str, pymatgen.electronic_structure.dos.Dos][source]

                                                              Get element and spd projected Dos

                                                              Parameters
                                                              @@ -882,7 +882,7 @@
                                                              -get_site_orbital_dos(site: pymatgen.core.sites.PeriodicSite, orbital: str) → pymatgen.electronic_structure.dos.Dos[source]
                                                              +get_site_orbital_dos(site: pymatgen.core.sites.PeriodicSite, orbital: str) → pymatgen.electronic_structure.dos.Dos[source]

                                                              Get the Dos for a particular orbital of a particular site.

                                                              Parameters
                                                              @@ -903,7 +903,7 @@
                                                              -get_site_t2g_eg_resolved_dos(site: pymatgen.core.sites.PeriodicSite) → dict[str, pymatgen.electronic_structure.dos.Dos][source]
                                                              +get_site_t2g_eg_resolved_dos(site: pymatgen.core.sites.PeriodicSite) → dict[str, pymatgen.electronic_structure.dos.Dos][source]

                                                              Get the t2g, eg projected DOS for a particular site. :param site: Site in Structure associated with CompleteDos.

                                                              @@ -919,7 +919,7 @@
                                                              -get_spd_dos() → dict[str, pymatgen.electronic_structure.dos.Dos][source]
                                                              +get_spd_dos() → dict[str, pymatgen.electronic_structure.dos.Dos][source]

                                                              Get orbital projected Dos. For example, if 3s and 4s are included in the basis of some element, they will be both summed in the orbital projected DOS

                                                              @@ -937,7 +937,7 @@
                                                              -add_densities(density1: dict[pymatgen.electronic_structure.core.Spin, Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]], density2: dict[pymatgen.electronic_structure.core.Spin, Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]]) → dict[pymatgen.electronic_structure.core.Spin, Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]][source]
                                                              +add_densities(density1: dict[pymatgen.electronic_structure.core.Spin, Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]], density2: dict[pymatgen.electronic_structure.core.Spin, Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]]) → dict[pymatgen.electronic_structure.core.Spin, Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]][source]

                                                              Method to sum two densities.

                                                              Parameters
                                                              @@ -957,7 +957,7 @@
                                                              -f0(E, fermi, T)[source]
                                                              +f0(E, fermi, T)[source]

                                                              Returns the equilibrium fermi-dirac. :param E: energy in eV :type E: float diff --git a/docs/pymatgen.electronic_structure.html b/docs/pymatgen.electronic_structure.html index b4782fea703..bc7ea4a2e1c 100644 --- a/docs/pymatgen.electronic_structure.html +++ b/docs/pymatgen.electronic_structure.html @@ -4,7 +4,7 @@ - pymatgen.electronic_structure package — pymatgen 2022.5.18 documentation + pymatgen.electronic_structure package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                                              - 2022.5.18 + 2022.5.18.1
                                                              diff --git a/docs/pymatgen.electronic_structure.plotter.html b/docs/pymatgen.electronic_structure.plotter.html index 6684ef84976..bfe7f5cf835 100644 --- a/docs/pymatgen.electronic_structure.plotter.html +++ b/docs/pymatgen.electronic_structure.plotter.html @@ -4,7 +4,7 @@ - pymatgen.electronic_structure.plotter module — pymatgen 2022.5.18 documentation + pymatgen.electronic_structure.plotter module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                              - 2022.5.18 + 2022.5.18.1
                                                              @@ -118,7 +118,7 @@

                                                              This module implements plotter for DOS and band structure.

                                                              -class BSDOSPlotter(bs_projection: Literal['elements'] | None = 'elements', dos_projection: str = 'elements', vb_energy_range: float = 4, cb_energy_range: float = 4, fixed_cb_energy: bool = False, egrid_interval: float = 1, font: str = 'Times New Roman', axis_fontsize: float = 20, tick_fontsize: float = 15, legend_fontsize: float = 14, bs_legend: str = 'best', dos_legend: str = 'best', rgb_legend: bool = True, fig_size: tuple[float, float] = (11, 8.5))[source]
                                                              +class BSDOSPlotter(bs_projection: Literal['elements'] | None = 'elements', dos_projection: str = 'elements', vb_energy_range: float = 4, cb_energy_range: float = 4, fixed_cb_energy: bool = False, egrid_interval: float = 1, font: str = 'Times New Roman', axis_fontsize: float = 20, tick_fontsize: float = 15, legend_fontsize: float = 14, bs_legend: str = 'best', dos_legend: str = 'best', rgb_legend: bool = True, fig_size: tuple[float, float] = (11, 8.5))[source]

                                                              Bases: object

                                                              A joint, aligned band structure and density of states plot. Contributions from Jan Pohls as well as the online example from Germain Salvato-Vallverdu: @@ -147,7 +147,7 @@

                                                              -get_plot(bs: BandStructureSymmLine, dos: Dos | CompleteDos | None = None)[source]
                                                              +get_plot(bs: BandStructureSymmLine, dos: Dos | CompleteDos | None = None)[source]

                                                              Get a matplotlib plot object. :param bs: the bandstructure to plot. Projection

                                                              @@ -169,7 +169,7 @@
                                                              -class BSPlotter(bs: pymatgen.electronic_structure.bandstructure.BandStructureSymmLine)[source]
                                                              +class BSPlotter(bs: pymatgen.electronic_structure.bandstructure.BandStructureSymmLine)[source]

                                                              Bases: object

                                                              Class to plot or get data to facilitate the plot of band structure objects.

                                                              @@ -179,13 +179,13 @@
                                                              -add_bs(bs: BandStructureSymmLine | list[BandStructureSymmLine]) → None[source]
                                                              +add_bs(bs: BandStructureSymmLine | list[BandStructureSymmLine]) → None[source]

                                                              Method to add bands objects to the BSPlotter

                                                              -bs_plot_data(zero_to_efermi=True, bs=None, bs_ref=None, split_branches=True)[source]
                                                              +bs_plot_data(zero_to_efermi=True, bs=None, bs_ref=None, split_branches=True)[source]

                                                              Get the data nicely formatted for a plot

                                                              Parameters
                                                              @@ -229,7 +229,7 @@
                                                              -get_plot(zero_to_efermi=True, ylim=None, smooth=False, vbm_cbm_marker=False, smooth_tol=0, smooth_k=3, smooth_np=100, bs_labels=[])[source]
                                                              +get_plot(zero_to_efermi=True, ylim=None, smooth=False, vbm_cbm_marker=False, smooth_tol=0, smooth_k=3, smooth_np=100, bs_labels=[])[source]

                                                              Get a matplotlib object for the bandstructures plot. Multiple bandstructure objs are plotted together if they have the same high symm path.

                                                              @@ -256,7 +256,7 @@
                                                              -get_ticks()[source]
                                                              +get_ticks()[source]

                                                              Get all ticks and labels for a band structure plot.

                                                              Returns
                                                              @@ -272,7 +272,7 @@
                                                              -get_ticks_old()[source]
                                                              +get_ticks_old()[source]

                                                              Get all ticks and labels for a band structure plot.

                                                              Returns
                                                              @@ -288,13 +288,13 @@
                                                              -plot_brillouin()[source]
                                                              +plot_brillouin()[source]

                                                              plot the Brillouin zone

                                                              -plot_compare(other_plotter, legend=True)[source]
                                                              +plot_compare(other_plotter, legend=True)[source]

                                                              plot two band structure for comparison. One is in red the other in blue (no difference in spins). The two band structures need to be defined on the same symmetry lines! and the distance between symmetry lines is @@ -311,7 +311,7 @@

                                                              -save_plot(filename, img_format='eps', ylim=None, zero_to_efermi=True, smooth=False)[source]
                                                              +save_plot(filename, img_format='eps', ylim=None, zero_to_efermi=True, smooth=False)[source]

                                                              Save matplotlib plot to a file.

                                                              Parameters
                                                              @@ -326,7 +326,7 @@
                                                              -show(zero_to_efermi=True, ylim=None, smooth=False, smooth_tol=None)[source]
                                                              +show(zero_to_efermi=True, ylim=None, smooth=False, smooth_tol=None)[source]

                                                              Show the plot using matplotlib.

                                                              Parameters
                                                              @@ -348,7 +348,7 @@
                                                              -class BSPlotterProjected(bs)[source]
                                                              +class BSPlotterProjected(bs)[source]

                                                              Bases: pymatgen.electronic_structure.plotter.BSPlotter

                                                              Class to plot or get data to facilitate the plot of band structure objects projected along orbitals, elements or sites.

                                                              @@ -359,7 +359,7 @@
                                                              -get_elt_projected_plots(zero_to_efermi=True, ylim=None, vbm_cbm_marker=False)[source]
                                                              +get_elt_projected_plots(zero_to_efermi=True, ylim=None, vbm_cbm_marker=False)[source]

                                                              Method returning a plot composed of subplots along different elements

                                                              Returns
                                                              @@ -373,7 +373,7 @@
                                                              -get_elt_projected_plots_color(zero_to_efermi=True, elt_ordered=None)[source]
                                                              +get_elt_projected_plots_color(zero_to_efermi=True, elt_ordered=None)[source]

                                                              returns a pylab plot object with one plot where the band structure line color depends on the character of the band (along different elements). Each element is associated with red, green or blue @@ -393,7 +393,7 @@

                                                              -get_projected_plots_dots(dictio, zero_to_efermi=True, ylim=None, vbm_cbm_marker=False)[source]
                                                              +get_projected_plots_dots(dictio, zero_to_efermi=True, ylim=None, vbm_cbm_marker=False)[source]

                                                              Method returning a plot composed of subplots along different elements and orbitals.

                                                              @@ -417,7 +417,7 @@
                                                              -get_projected_plots_dots_patom_pmorb(dictio, dictpa, sum_atoms=None, sum_morbs=None, zero_to_efermi=True, ylim=None, vbm_cbm_marker=False, selected_branches=None, w_h_size=(12, 8), num_column=None)[source]
                                                              +get_projected_plots_dots_patom_pmorb(dictio, dictpa, sum_atoms=None, sum_morbs=None, zero_to_efermi=True, ylim=None, vbm_cbm_marker=False, selected_branches=None, w_h_size=(12, 8), num_column=None)[source]

                                                              Method returns a plot composed of subplots for different atoms and orbitals (subshell orbitals such as ‘s’, ‘p’, ‘d’ and ‘f’ defined by azimuthal quantum numbers l = 0, 1, 2 and 3, respectively or @@ -509,7 +509,7 @@

                                                              -class BoltztrapPlotter(bz)[source]
                                                              +class BoltztrapPlotter(bz)[source]

                                                              Bases: object

                                                              class containing methods to plot the data from Boltztrap.

                                                              @@ -519,7 +519,7 @@
                                                              -plot_carriers(temp=300)[source]
                                                              +plot_carriers(temp=300)[source]

                                                              Plot the carrier concentration in function of Fermi level

                                                              Parameters
                                                              @@ -533,7 +533,7 @@
                                                              -plot_complexity_factor_mu(temps=[300], output='average', Lambda=0.5)[source]
                                                              +plot_complexity_factor_mu(temps=[300], output='average', Lambda=0.5)[source]

                                                              Plot respect to the chemical potential of the Fermi surface complexity factor calculated as explained in Ref. Gibbs, Z. M. et al., Effective mass and fermi surface complexity factor @@ -559,7 +559,7 @@

                                                              -plot_conductivity_dop(temps='all', output='average', relaxation_time=1e-14)[source]
                                                              +plot_conductivity_dop(temps='all', output='average', relaxation_time=1e-14)[source]

                                                              Plot the conductivity in function of doping levels for different temperatures.

                                                              @@ -580,7 +580,7 @@
                                                              -plot_conductivity_mu(temp=600, output='eig', relaxation_time=1e-14, xlim=None)[source]
                                                              +plot_conductivity_mu(temp=600, output='eig', relaxation_time=1e-14, xlim=None)[source]

                                                              Plot the conductivity in function of Fermi level. Semi-log plot

                                                              Parameters
                                                              @@ -600,7 +600,7 @@
                                                              -plot_conductivity_temp(doping='all', output='average', relaxation_time=1e-14)[source]
                                                              +plot_conductivity_temp(doping='all', output='average', relaxation_time=1e-14)[source]

                                                              Plot the conductivity in function of temperature for different doping levels.

                                                              Parameters
                                                              @@ -620,7 +620,7 @@
                                                              -plot_dos(sigma=0.05)[source]
                                                              +plot_dos(sigma=0.05)[source]

                                                              plot dos

                                                              Parameters
                                                              @@ -634,7 +634,7 @@
                                                              -plot_eff_mass_dop(temps='all', output='average')[source]
                                                              +plot_eff_mass_dop(temps='all', output='average')[source]

                                                              Plot the average effective mass in function of doping levels for different temperatures.

                                                              @@ -655,7 +655,7 @@
                                                              -plot_eff_mass_temp(doping='all', output='average')[source]
                                                              +plot_eff_mass_temp(doping='all', output='average')[source]

                                                              Plot the average effective mass in function of temperature for different doping levels.

                                                              @@ -675,7 +675,7 @@
                                                              -plot_hall_carriers(temp=300)[source]
                                                              +plot_hall_carriers(temp=300)[source]

                                                              Plot the Hall carrier concentration in function of Fermi level

                                                              Parameters
                                                              @@ -689,7 +689,7 @@
                                                              -plot_power_factor_dop(temps='all', output='average', relaxation_time=1e-14)[source]
                                                              +plot_power_factor_dop(temps='all', output='average', relaxation_time=1e-14)[source]

                                                              Plot the Power Factor in function of doping levels for different temperatures.

                                                              Parameters
                                                              @@ -709,7 +709,7 @@
                                                              -plot_power_factor_mu(temp=600, output='eig', relaxation_time=1e-14, xlim=None)[source]
                                                              +plot_power_factor_mu(temp=600, output='eig', relaxation_time=1e-14, xlim=None)[source]

                                                              Plot the power factor in function of Fermi level. Semi-log plot

                                                              Parameters
                                                              @@ -729,7 +729,7 @@
                                                              -plot_power_factor_temp(doping='all', output='average', relaxation_time=1e-14)[source]
                                                              +plot_power_factor_temp(doping='all', output='average', relaxation_time=1e-14)[source]

                                                              Plot the Power Factor in function of temperature for different doping levels.

                                                              Parameters
                                                              @@ -749,7 +749,7 @@
                                                              -plot_seebeck_dop(temps='all', output='average')[source]
                                                              +plot_seebeck_dop(temps='all', output='average')[source]

                                                              Plot the Seebeck in function of doping levels for different temperatures.

                                                              Parameters
                                                              @@ -768,7 +768,7 @@
                                                              -plot_seebeck_eff_mass_mu(temps=[300], output='average', Lambda=0.5)[source]
                                                              +plot_seebeck_eff_mass_mu(temps=[300], output='average', Lambda=0.5)[source]

                                                              Plot respect to the chemical potential of the Seebeck effective mass calculated as explained in Ref. Gibbs, Z. M. et al., Effective mass and fermi surface complexity factor @@ -794,7 +794,7 @@

                                                              -plot_seebeck_mu(temp=600, output='eig', xlim=None)[source]
                                                              +plot_seebeck_mu(temp=600, output='eig', xlim=None)[source]

                                                              Plot the seebeck coefficient in function of Fermi level

                                                              Parameters
                                                              @@ -811,7 +811,7 @@
                                                              -plot_seebeck_temp(doping='all', output='average')[source]
                                                              +plot_seebeck_temp(doping='all', output='average')[source]

                                                              Plot the Seebeck coefficient in function of temperature for different doping levels.

                                                              @@ -831,7 +831,7 @@
                                                              -plot_zt_dop(temps='all', output='average', relaxation_time=1e-14)[source]
                                                              +plot_zt_dop(temps='all', output='average', relaxation_time=1e-14)[source]

                                                              Plot the figure of merit zT in function of doping levels for different temperatures.

                                                              @@ -852,7 +852,7 @@
                                                              -plot_zt_mu(temp=600, output='eig', relaxation_time=1e-14, xlim=None)[source]
                                                              +plot_zt_mu(temp=600, output='eig', relaxation_time=1e-14, xlim=None)[source]

                                                              Plot the ZT in function of Fermi level.

                                                              Parameters
                                                              @@ -872,7 +872,7 @@
                                                              -plot_zt_temp(doping='all', output='average', relaxation_time=1e-14)[source]
                                                              +plot_zt_temp(doping='all', output='average', relaxation_time=1e-14)[source]

                                                              Plot the figure of merit zT in function of temperature for different doping levels.

                                                              Parameters
                                                              @@ -894,7 +894,7 @@
                                                              -class CohpPlotter(zero_at_efermi=True, are_coops=False, are_cobis=False)[source]
                                                              +class CohpPlotter(zero_at_efermi=True, are_coops=False, are_cobis=False)[source]

                                                              Bases: object

                                                              Class for plotting crystal orbital Hamilton populations (COHPs) or crystal orbital overlap populations (COOPs). It is modeled after the @@ -913,7 +913,7 @@

                                                              -add_cohp(label, cohp)[source]
                                                              +add_cohp(label, cohp)[source]

                                                              Adds a COHP for plotting.

                                                              Parameters
                                                              @@ -927,7 +927,7 @@
                                                              -add_cohp_dict(cohp_dict, key_sort_func=None)[source]
                                                              +add_cohp_dict(cohp_dict, key_sort_func=None)[source]

                                                              Adds a dictionary of COHPs with an optional sorting function for the keys.

                                                              @@ -942,7 +942,7 @@
                                                              -get_cohp_dict()[source]
                                                              +get_cohp_dict()[source]

                                                              Returns the added COHPs as a json-serializable dict. Note that if you have specified smearing for the COHP plot, the populations returned will be the smeared and not the original populations.

                                                              @@ -959,7 +959,7 @@
                                                              -get_plot(xlim=None, ylim=None, plot_negative=None, integrated=False, invert_axes=True)[source]
                                                              +get_plot(xlim=None, ylim=None, plot_negative=None, integrated=False, invert_axes=True)[source]

                                                              Get a matplotlib plot showing the COHP.

                                                              Parameters
                                                              @@ -985,7 +985,7 @@
                                                              -save_plot(filename, img_format='eps', xlim=None, ylim=None)[source]
                                                              +save_plot(filename, img_format='eps', xlim=None, ylim=None)[source]

                                                              Save matplotlib plot to a file.

                                                              Parameters
                                                              @@ -1003,7 +1003,7 @@
                                                              -show(xlim=None, ylim=None)[source]
                                                              +show(xlim=None, ylim=None)[source]

                                                              Show the plot using matplotlib.

                                                              Parameters
                                                              @@ -1021,7 +1021,7 @@
                                                              -class DosPlotter(zero_at_efermi: bool = True, stack: bool = False, sigma: Optional[float] = None)[source]
                                                              +class DosPlotter(zero_at_efermi: bool = True, stack: bool = False, sigma: Optional[float] = None)[source]

                                                              Bases: object

                                                              Class for plotting DOSs. Note that the interface is extremely flexible given that there are many different ways in which people want to view @@ -1053,7 +1053,7 @@

                                                              -add_dos(label: str, dos: pymatgen.electronic_structure.dos.Dos) → None[source]
                                                              +add_dos(label: str, dos: pymatgen.electronic_structure.dos.Dos) → None[source]

                                                              Adds a dos for plotting.

                                                              Parameters
                                                              @@ -1067,7 +1067,7 @@
                                                              -add_dos_dict(dos_dict, key_sort_func=None)[source]
                                                              +add_dos_dict(dos_dict, key_sort_func=None)[source]

                                                              Add a dictionary of doses, with an optional sorting function for the keys.

                                                              @@ -1082,7 +1082,7 @@
                                                              -get_dos_dict()[source]
                                                              +get_dos_dict()[source]

                                                              Returns the added doses as a json-serializable dict. Note that if you have specified smearing for the DOS plot, the densities returned will be the smeared densities, not the original densities.

                                                              @@ -1099,7 +1099,7 @@
                                                              -get_plot(xlim=None, ylim=None)[source]
                                                              +get_plot(xlim=None, ylim=None)[source]

                                                              Get a matplotlib plot showing the DOS.

                                                              Parameters
                                                              @@ -1114,7 +1114,7 @@
                                                              -save_plot(filename, img_format='eps', xlim=None, ylim=None)[source]
                                                              +save_plot(filename, img_format='eps', xlim=None, ylim=None)[source]

                                                              Save matplotlib plot to a file.

                                                              Parameters
                                                              @@ -1131,7 +1131,7 @@
                                                              -show(xlim=None, ylim=None)[source]
                                                              +show(xlim=None, ylim=None)[source]

                                                              Show the plot using matplotlib.

                                                              Parameters
                                                              @@ -1148,7 +1148,7 @@
                                                              -fold_point(p, lattice, coords_are_cartesian=False)[source]
                                                              +fold_point(p, lattice, coords_are_cartesian=False)[source]

                                                              Folds a point with coordinates p inside the first Brillouin zone of the lattice.

                                                              Parameters
                                                              @@ -1167,7 +1167,7 @@
                                                              -plot_brillouin_zone(bz_lattice, lines=None, labels=None, kpoints=None, fold=False, coords_are_cartesian=False, ax=None, **kwargs)[source]
                                                              +plot_brillouin_zone(bz_lattice, lines=None, labels=None, kpoints=None, fold=False, coords_are_cartesian=False, ax=None, **kwargs)[source]

                                                              Plots a 3D representation of the Brillouin zone of the structure. Can add to the plot paths, labels and kpoints

                                                              @@ -1235,7 +1235,7 @@
                                                              -plot_brillouin_zone_from_kpath(kpath, ax=None, **kwargs)[source]
                                                              +plot_brillouin_zone_from_kpath(kpath, ax=None, **kwargs)[source]
                                                              Gives the plot (as a matplotlib object) of the symmetry line path in

                                                              the Brillouin Zone.

                                                              @@ -1298,7 +1298,7 @@
                                                              -plot_ellipsoid(hessian, center, lattice=None, rescale=1.0, ax=None, coords_are_cartesian=False, arrows=False, **kwargs)[source]
                                                              +plot_ellipsoid(hessian, center, lattice=None, rescale=1.0, ax=None, coords_are_cartesian=False, arrows=False, **kwargs)[source]

                                                              Plots a 3D ellipsoid rappresenting the Hessian matrix in input. Useful to get a graphical visualization of the effective mass of a band in a single k-point.

                                                              @@ -1330,7 +1330,7 @@
                                                              -plot_fermi_surface(data, structure, cbm, energy_levels=None, multiple_figure=True, mlab_figure=None, kpoints_dict=None, colors=None, transparency_factor=None, labels_scale_factor=0.05, points_scale_factor=0.02, interactive=True)[source]
                                                              +plot_fermi_surface(data, structure, cbm, energy_levels=None, multiple_figure=True, mlab_figure=None, kpoints_dict=None, colors=None, transparency_factor=None, labels_scale_factor=0.05, points_scale_factor=0.02, interactive=True)[source]

                                                              Plot the Fermi surface at specific energy value using Boltztrap 1 FERMI mode.

                                                              The easiest way to use this plotter is:

                                                              @@ -1400,7 +1400,7 @@
                                                              -plot_labels(labels, lattice=None, coords_are_cartesian=False, ax=None, **kwargs)[source]
                                                              +plot_labels(labels, lattice=None, coords_are_cartesian=False, ax=None, **kwargs)[source]

                                                              Adds labels to a matplotlib Axes

                                                              Parameters
                                                              @@ -1423,7 +1423,7 @@
                                                              -plot_lattice_vectors(lattice, ax=None, **kwargs)[source]
                                                              +plot_lattice_vectors(lattice, ax=None, **kwargs)[source]

                                                              Adds the basis vectors of the lattice provided to a matplotlib Axes

                                                              Parameters
                                                              @@ -1442,7 +1442,7 @@
                                                              -plot_path(line, lattice=None, coords_are_cartesian=False, ax=None, **kwargs)[source]
                                                              +plot_path(line, lattice=None, coords_are_cartesian=False, ax=None, **kwargs)[source]

                                                              Adds a line passing through the coordinates listed in ‘line’ to a matplotlib Axes

                                                              Parameters
                                                              @@ -1465,7 +1465,7 @@
                                                              -plot_points(points, lattice=None, coords_are_cartesian=False, fold=False, ax=None, **kwargs)[source]
                                                              +plot_points(points, lattice=None, coords_are_cartesian=False, fold=False, ax=None, **kwargs)[source]

                                                              Adds Points to a matplotlib Axes

                                                              Parameters
                                                              @@ -1489,7 +1489,7 @@
                                                              -plot_wigner_seitz(lattice, ax=None, **kwargs)[source]
                                                              +plot_wigner_seitz(lattice, ax=None, **kwargs)[source]

                                                              Adds the skeleton of the Wigner-Seitz cell of the lattice to a matplotlib Axes

                                                              Parameters
                                                              diff --git a/docs/pymatgen.entries.compatibility.html b/docs/pymatgen.entries.compatibility.html index e060f3fedac..84a82a9b7dd 100644 --- a/docs/pymatgen.entries.compatibility.html +++ b/docs/pymatgen.entries.compatibility.html @@ -4,7 +4,7 @@ - pymatgen.entries.compatibility module — pymatgen 2022.5.18 documentation + pymatgen.entries.compatibility module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                              - 2022.5.18 + 2022.5.18.1
                                                              @@ -119,7 +119,7 @@ functionals.

                                                              -class AnionCorrection(*args, **kwargs)[source]
                                                              +class AnionCorrection(*args, **kwargs)[source]

                                                              Bases: pymatgen.entries.compatibility.AnionCorrection

                                                              Correct anion energies to obtain the right formation energies. Note that this depends on calculations being run within the same input set.

                                                              @@ -137,7 +137,7 @@
                                                              -class AqueousCorrection(*args, **kwargs)[source]
                                                              +class AqueousCorrection(*args, **kwargs)[source]

                                                              Bases: pymatgen.entries.compatibility.AqueousCorrection

                                                              This class implements aqueous phase compound corrections for elements and H2O.

                                                              @@ -154,14 +154,14 @@
                                                              -class Compatibility[source]
                                                              +class Compatibility[source]

                                                              Bases: monty.json.MSONable

                                                              Abstract Compatibility class, not intended for direct use. Compatibility classes are used to correct the energies of an entry or a set of entries. All Compatibility classes must implement .get_adjustments method.

                                                              -static explain(entry)[source]
                                                              +static explain(entry)[source]

                                                              Prints an explanation of the energy adjustments applied by the Compatibility class. Inspired by the “explain” methods in many database methodologies.

                                                              @@ -174,7 +174,7 @@
                                                              -abstract get_adjustments(entry: Union[pymatgen.entries.computed_entries.ComputedEntry, pymatgen.entries.computed_entries.ComputedStructureEntry]) → list[pymatgen.entries.computed_entries.EnergyAdjustment][source]
                                                              +abstract get_adjustments(entry: Union[pymatgen.entries.computed_entries.ComputedEntry, pymatgen.entries.computed_entries.ComputedStructureEntry]) → list[pymatgen.entries.computed_entries.EnergyAdjustment][source]

                                                              Get the energy adjustments for a ComputedEntry.

                                                              This method must generate a list of EnergyAdjustment objects of the appropriate type (constant, composition-based, or temperature-based) @@ -202,7 +202,7 @@

                                                              -process_entries(entries: AnyCompEntry | list[AnyCompEntry], clean: bool = True, verbose: bool = False) → list[ComputedEntry][source]
                                                              +process_entries(entries: AnyCompEntry | list[AnyCompEntry], clean: bool = True, verbose: bool = False) → list[ComputedEntry][source]

                                                              Process a sequence of entries with the chosen Compatibility scheme. Note that this method will change the data of the original entries.

                                                              @@ -225,7 +225,7 @@
                                                              -process_entry(entry: ComputedEntry) → ComputedEntry | None[source]
                                                              +process_entry(entry: ComputedEntry) → ComputedEntry | None[source]

                                                              Process a single entry with the chosen Corrections. Note that this method will change the data of the original entry.

                                                              @@ -243,7 +243,7 @@
                                                              -exception CompatibilityError[source]
                                                              +exception CompatibilityError[source]

                                                              Bases: Exception

                                                              Exception class for Compatibility. Raised by attempting correction on incompatible calculation

                                                              @@ -251,7 +251,7 @@
                                                              -class Correction[source]
                                                              +class Correction[source]

                                                              Bases: object

                                                              A Correction class is a pre-defined scheme for correction a computed entry based on the type and chemistry of the structure and the @@ -259,7 +259,7 @@ correct_entry method.

                                                              -correct_entry(entry)[source]
                                                              +correct_entry(entry)[source]

                                                              Corrects a single entry.

                                                              Parameters
                                                              @@ -276,7 +276,7 @@
                                                              -abstract get_correction(entry)[source]
                                                              +abstract get_correction(entry)[source]

                                                              Returns correction and uncertainty for a single entry.

                                                              Parameters
                                                              @@ -295,7 +295,7 @@
                                                              -class CorrectionsList(corrections: Sequence)[source]
                                                              +class CorrectionsList(corrections: Sequence)[source]

                                                              Bases: pymatgen.entries.compatibility.Compatibility

                                                              The CorrectionsList class combines a list of corrections to be applied to an entry or a set of entries. Note that some of the Corrections have @@ -311,7 +311,7 @@

                                                              -explain(entry)[source]
                                                              +explain(entry)[source]

                                                              Prints an explanation of the corrections that are being applied for a given compatibility scheme. Inspired by the “explain” methods in many database methodologies.

                                                              @@ -324,13 +324,13 @@
                                                              -get_adjustments(entry)[source]
                                                              +get_adjustments(entry)[source]

                                                              Get the list of energy adjustments to be applied to an entry.

                                                              -get_corrections_dict(entry)[source]
                                                              +get_corrections_dict(entry)[source]

                                                              Returns the corrections applied to a particular entry.

                                                              Parameters
                                                              @@ -347,7 +347,7 @@
                                                              -get_explanation_dict(entry)[source]
                                                              +get_explanation_dict(entry)[source]

                                                              Provides an explanation dict of the corrections that are being applied for a given compatibility scheme. Inspired by the “explain” methods in many database methodologies.

                                                              @@ -371,7 +371,7 @@
                                                              -class GasCorrection(*args, **kwargs)[source]
                                                              +class GasCorrection(*args, **kwargs)[source]

                                                              Bases: pymatgen.entries.compatibility.GasCorrection

                                                              Correct gas energies to obtain the right formation energies. Note that this depends on calculations being run within the same input set. @@ -385,7 +385,7 @@

                                                              -class MITAqueousCompatibility(compat_type='Advanced', correct_peroxide=True, check_potcar_hash=False)[source]
                                                              +class MITAqueousCompatibility(compat_type='Advanced', correct_peroxide=True, check_potcar_hash=False)[source]

                                                              Bases: pymatgen.entries.compatibility.CorrectionsList

                                                              This class implements the GGA/GGA+U mixing scheme, which allows mixing of entries. Note that this should only be used for VASP calculations using the @@ -411,7 +411,7 @@

                                                              -class MITCompatibility(compat_type='Advanced', correct_peroxide=True, check_potcar_hash=False)[source]
                                                              +class MITCompatibility(compat_type='Advanced', correct_peroxide=True, check_potcar_hash=False)[source]

                                                              Bases: pymatgen.entries.compatibility.CorrectionsList

                                                              This class implements the GGA/GGA+U mixing scheme, which allows mixing of entries. Note that this should only be used for VASP calculations using the @@ -437,7 +437,7 @@

                                                              -class MaterialsProject2020Compatibility(*args, **kwargs)[source]
                                                              +class MaterialsProject2020Compatibility(*args, **kwargs)[source]

                                                              Bases: pymatgen.entries.compatibility.MaterialsProject2020Compatibility

                                                              This class implements the Materials Project 2020 energy correction scheme, which incorporates uncertainty quantification and allows for mixing of GGA @@ -492,7 +492,7 @@

                                                              -class MaterialsProjectAqueousCompatibility(*args, **kwargs)[source]
                                                              +class MaterialsProjectAqueousCompatibility(*args, **kwargs)[source]

                                                              Bases: pymatgen.entries.compatibility.MaterialsProjectAqueousCompatibility

                                                              This class implements the Aqueous energy referencing scheme for constructing Pourbaix diagrams from DFT energies, as described in Persson et al.

                                                              @@ -545,7 +545,7 @@
                                                              -class MaterialsProjectCompatibility(compat_type='Advanced', correct_peroxide=True, check_potcar_hash=False)[source]
                                                              +class MaterialsProjectCompatibility(compat_type='Advanced', correct_peroxide=True, check_potcar_hash=False)[source]

                                                              Bases: pymatgen.entries.compatibility.CorrectionsList

                                                              This class implements the GGA/GGA+U mixing scheme, which allows mixing of entries. Note that this should only be used for VASP calculations using the @@ -572,7 +572,7 @@

                                                              -class PotcarCorrection(input_set, check_hash=False)[source]
                                                              +class PotcarCorrection(input_set, check_hash=False)[source]

                                                              Bases: pymatgen.entries.compatibility.Correction

                                                              Checks that POTCARs are valid within a pre-defined input set. This ensures that calculations performed using different InputSets are not @@ -601,7 +601,7 @@

                                                              -get_correction(entry) → uncertainties.core.ufloat[source]
                                                              +get_correction(entry) → uncertainties.core.ufloat[source]
                                                              Parameters

                                                              entry – A ComputedEntry/ComputedStructureEntry

                                                              @@ -616,7 +616,7 @@
                                                              -class UCorrection(*args, **kwargs)[source]
                                                              +class UCorrection(*args, **kwargs)[source]

                                                              Bases: pymatgen.entries.compatibility.UCorrection

                                                              This class implements the GGA/GGA+U mixing scheme, which allows mixing of entries. Entry.parameters must contain a “hubbards” key which is a dict diff --git a/docs/pymatgen.entries.computed_entries.html b/docs/pymatgen.entries.computed_entries.html index c93ed87c1ff..724ae4b1912 100644 --- a/docs/pymatgen.entries.computed_entries.html +++ b/docs/pymatgen.entries.computed_entries.html @@ -4,7 +4,7 @@ - pymatgen.entries.computed_entries module — pymatgen 2022.5.18 documentation + pymatgen.entries.computed_entries module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                                              - 2022.5.18 + 2022.5.18.1
                                                              @@ -122,7 +122,7 @@ diagram analysis.

                                                              -class CompositionEnergyAdjustment(adj_per_atom, n_atoms, uncertainty_per_atom=nan, name='', cls=None, description='Composition-based energy adjustment')[source]
                                                              +class CompositionEnergyAdjustment(adj_per_atom, n_atoms, uncertainty_per_atom=nan, name='', cls=None, description='Composition-based energy adjustment')[source]

                                                              Bases: pymatgen.entries.computed_entries.EnergyAdjustment

                                                              An energy adjustment applied to a ComputedEntry based on the atomic composition. Used in various DFT energy correction schemes.

                                                              @@ -143,13 +143,13 @@
                                                              -property explain[source]
                                                              +property explain[source]

                                                              Return an explanaion of how the energy adjustment is calculated.

                                                              -normalize(factor)[source]
                                                              +normalize(factor)[source]

                                                              Normalize energy adjustment (in place), dividing value/uncertainty by a factor. :param factor: factor to divide by

                                                              @@ -157,13 +157,13 @@
                                                              -property uncertainty[source]
                                                              +property uncertainty[source]

                                                              Return the value of the energy adjustment in eV.

                                                              -property value[source]
                                                              +property value[source]

                                                              Return the value of the energy adjustment in eV.

                                                              @@ -171,7 +171,7 @@
                                                              -class ComputedEntry(composition: Composition | str | dict[str, float], energy: float, correction: float = 0.0, energy_adjustments: list = None, parameters: dict = None, data: dict = None, entry_id: object = None)[source]
                                                              +class ComputedEntry(composition: Composition | str | dict[str, float], energy: float, correction: float = 0.0, energy_adjustments: list = None, parameters: dict = None, data: dict = None, entry_id: object = None)[source]

                                                              Bases: pymatgen.entries.Entry

                                                              Lightweight Entry object for computed data. Contains facilities for applying corrections to the energy attribute and for storing @@ -201,7 +201,7 @@

                                                              -as_dict() → dict[source]
                                                              +as_dict() → dict[source]
                                                              Returns

                                                              MSONable dict.

                                                              @@ -211,7 +211,7 @@
                                                              -property correction: float[source]
                                                              +property correction: float[source]

                                                              Returns: float: the total energy correction / adjustment applied to the entry,

                                                              @@ -221,7 +221,7 @@
                                                              -property correction_per_atom: float[source]
                                                              +property correction_per_atom: float[source]

                                                              Returns: float: the total energy correction / adjustment applied to the entry,

                                                              @@ -231,14 +231,14 @@
                                                              -property correction_uncertainty: float[source]
                                                              +property correction_uncertainty: float[source]

                                                              Returns: float: the uncertainty of the energy adjustments applied to the entry, in eV

                                                              -property correction_uncertainty_per_atom: float[source]
                                                              +property correction_uncertainty_per_atom: float[source]

                                                              Returns: float: the uncertainty of the energy adjustments applied to the entry,

                                                              @@ -248,7 +248,7 @@
                                                              -property energy: float[source]
                                                              +property energy: float[source]

                                                              the corrected energy of the entry.

                                                              Type
                                                              @@ -259,7 +259,7 @@
                                                              -classmethod from_dict(d) → pymatgen.entries.computed_entries.ComputedEntry[source]
                                                              +classmethod from_dict(d) → pymatgen.entries.computed_entries.ComputedEntry[source]
                                                              Parameters

                                                              d – Dict representation.

                                                              @@ -272,7 +272,7 @@
                                                              -normalize(mode: Literal['formula_unit', 'atom'] = 'formula_unit') → pymatgen.entries.computed_entries.ComputedEntry[source]
                                                              +normalize(mode: Literal['formula_unit', 'atom'] = 'formula_unit') → pymatgen.entries.computed_entries.ComputedEntry[source]

                                                              Normalize the entry’s composition and energy.

                                                              Parameters
                                                              @@ -284,14 +284,14 @@
                                                              -property uncorrected_energy: float[source]
                                                              +property uncorrected_energy: float[source]

                                                              Returns: float: the uncorrected energy of the entry

                                                              -property uncorrected_energy_per_atom: float[source]
                                                              +property uncorrected_energy_per_atom: float[source]

                                                              Returns: float: the uncorrected energy of the entry, normalized by atoms

                                                              @@ -303,7 +303,7 @@
                                                              -class ComputedStructureEntry(structure: Structure, energy: float, correction: float = 0.0, composition: Composition | str | dict[str, float] | None = None, energy_adjustments: list = None, parameters: dict = None, data: dict = None, entry_id: object = None)[source]
                                                              +class ComputedStructureEntry(structure: Structure, energy: float, correction: float = 0.0, composition: Composition | str | dict[str, float] | None = None, energy_adjustments: list = None, parameters: dict = None, data: dict = None, entry_id: object = None)[source]

                                                              Bases: pymatgen.entries.computed_entries.ComputedEntry

                                                              A heavier version of ComputedEntry which contains a structure as well. The structure is needed for some analyses.

                                                              @@ -331,7 +331,7 @@
                                                              -as_dict() → dict[source]
                                                              +as_dict() → dict[source]
                                                              Returns

                                                              MSONAble dict.

                                                              @@ -341,7 +341,7 @@
                                                              -classmethod from_dict(d) → pymatgen.entries.computed_entries.ComputedStructureEntry[source]
                                                              +classmethod from_dict(d) → pymatgen.entries.computed_entries.ComputedStructureEntry[source]
                                                              Parameters

                                                              d – Dict representation.

                                                              @@ -354,7 +354,7 @@
                                                              -normalize(mode: Literal['formula_unit', 'atom'] = 'formula_unit') → pymatgen.entries.computed_entries.ComputedStructureEntry[source]
                                                              +normalize(mode: Literal['formula_unit', 'atom'] = 'formula_unit') → pymatgen.entries.computed_entries.ComputedStructureEntry[source]

                                                              Normalize the entry’s composition and energy. The structure remains unchanged. :param mode: “formula_unit” (the default) normalizes to composition.reduced_formula.

                                                              @@ -367,7 +367,7 @@
                                                              -property structure: pymatgen.core.structure.Structure[source]
                                                              +property structure: pymatgen.core.structure.Structure[source]

                                                              the structure of the entry.

                                                              Type
                                                              @@ -380,7 +380,7 @@
                                                              -class ConstantEnergyAdjustment(value, uncertainty=nan, name='Constant energy adjustment', cls=None, description='Constant energy adjustment')[source]
                                                              +class ConstantEnergyAdjustment(value, uncertainty=nan, name='Constant energy adjustment', cls=None, description='Constant energy adjustment')[source]

                                                              Bases: pymatgen.entries.computed_entries.EnergyAdjustment

                                                              A constant energy adjustment applied to a ComputedEntry. Useful in energy referencing schemes such as the Aqueous energy referencing scheme.

                                                              @@ -399,13 +399,13 @@
                                                              -property explain[source]
                                                              +property explain[source]

                                                              Return an explanaion of how the energy adjustment is calculated.

                                                              -normalize(factor)[source]
                                                              +normalize(factor)[source]

                                                              Normalize energy adjustment (in place), dividing value/uncertainty by a factor. :param factor: factor to divide by

                                                              @@ -415,7 +415,7 @@
                                                              -class EnergyAdjustment(value, uncertainty=nan, name='Manual adjustment', cls=None, description='')[source]
                                                              +class EnergyAdjustment(value, uncertainty=nan, name='Manual adjustment', cls=None, description='')[source]

                                                              Bases: monty.json.MSONable

                                                              Lightweight class to contain information about an energy adjustment or energy correction.

                                                              @@ -433,13 +433,13 @@
                                                              -abstract property explain[source]
                                                              +abstract property explain[source]

                                                              Return an explanaion of how the energy adjustment is calculated.

                                                              -abstract normalize(factor)[source]
                                                              +abstract normalize(factor)[source]

                                                              Scale the value of the current energy adjustment by factor in-place.

                                                              This method is utilized in ComputedEntry.normalize() to scale the energies to a formula unit basis (e.g. E_Fe6O9 = 3 x E_Fe2O3).

                                                              @@ -447,13 +447,13 @@
                                                              -property uncertainty[source]
                                                              +property uncertainty[source]

                                                              Return the uncertainty in the value of the energy adjustment in eV

                                                              -property value[source]
                                                              +property value[source]

                                                              Return the value of the energy correction in eV.

                                                              @@ -461,7 +461,7 @@
                                                              -class GibbsComputedStructureEntry(structure: pymatgen.core.structure.Structure, formation_enthalpy_per_atom: float, temp: float = 300, gibbs_model: Literal['SISSO'] = 'SISSO', composition: Optional[pymatgen.core.composition.Composition] = None, correction: float = 0.0, energy_adjustments: Optional[list] = None, parameters: Optional[dict] = None, data: Optional[dict] = None, entry_id: Optional[object] = None)[source]
                                                              +class GibbsComputedStructureEntry(structure: pymatgen.core.structure.Structure, formation_enthalpy_per_atom: float, temp: float = 300, gibbs_model: Literal['SISSO'] = 'SISSO', composition: Optional[pymatgen.core.composition.Composition] = None, correction: float = 0.0, energy_adjustments: Optional[list] = None, parameters: Optional[dict] = None, data: Optional[dict] = None, entry_id: Optional[object] = None)[source]

                                                              Bases: pymatgen.entries.computed_entries.ComputedStructureEntry

                                                              An extension to ComputedStructureEntry which includes the estimated Gibbs free energy of formation via a machine-learned model.

                                                              @@ -488,7 +488,7 @@
                                                              -as_dict() → dict[source]
                                                              +as_dict() → dict[source]
                                                              Returns

                                                              MSONAble dict.

                                                              @@ -498,7 +498,7 @@
                                                              -classmethod from_dict(d) → pymatgen.entries.computed_entries.GibbsComputedStructureEntry[source]
                                                              +classmethod from_dict(d) → pymatgen.entries.computed_entries.GibbsComputedStructureEntry[source]
                                                              Parameters

                                                              d – Dict representation.

                                                              @@ -511,7 +511,7 @@
                                                              -classmethod from_entries(entries, temp=300, gibbs_model='SISSO') → list[pymatgen.entries.computed_entries.GibbsComputedStructureEntry][source]
                                                              +classmethod from_entries(entries, temp=300, gibbs_model='SISSO') → list[pymatgen.entries.computed_entries.GibbsComputedStructureEntry][source]

                                                              Constructor method for initializing GibbsComputedStructureEntry objects from T = 0 K ComputedStructureEntry objects, as acquired from a thermochemical database e.g. The Materials Project.

                                                              @@ -540,7 +540,7 @@
                                                              -classmethod from_pd(pd, temp=300, gibbs_model='SISSO') → list[pymatgen.entries.computed_entries.GibbsComputedStructureEntry][source]
                                                              +classmethod from_pd(pd, temp=300, gibbs_model='SISSO') → list[pymatgen.entries.computed_entries.GibbsComputedStructureEntry][source]

                                                              Constructor method for initializing a list of GibbsComputedStructureEntry objects from an existing T = 0 K phase diagram composed of ComputedStructureEntry objects, as acquired from a thermochemical database; @@ -570,7 +570,7 @@

                                                              -gf_sisso() → float[source]
                                                              +gf_sisso() → float[source]

                                                              Gibbs Free Energy of formation as calculated by SISSO descriptor from Bartel et al. (2018). Units: eV (not normalized)

                                                              WARNING: This descriptor only applies to solids. The implementation here @@ -598,7 +598,7 @@

                                                              -class ManualEnergyAdjustment(value)[source]
                                                              +class ManualEnergyAdjustment(value)[source]

                                                              Bases: pymatgen.entries.computed_entries.ConstantEnergyAdjustment

                                                              A manual energy adjustment applied to a ComputedEntry.

                                                              @@ -610,7 +610,7 @@
                                                              -class TemperatureEnergyAdjustment(adj_per_deg, temp, n_atoms, uncertainty_per_deg=nan, name='', cls=None, description='Temperature-based energy adjustment')[source]
                                                              +class TemperatureEnergyAdjustment(adj_per_deg, temp, n_atoms, uncertainty_per_deg=nan, name='', cls=None, description='Temperature-based energy adjustment')[source]

                                                              Bases: pymatgen.entries.computed_entries.EnergyAdjustment

                                                              An energy adjustment applied to a ComputedEntry based on the temperature. Used, for example, to add entropy to DFT energies.

                                                              @@ -632,13 +632,13 @@
                                                              -property explain[source]
                                                              +property explain[source]

                                                              Return an explanaion of how the energy adjustment is calculated.

                                                              -normalize(factor)[source]
                                                              +normalize(factor)[source]

                                                              Normalize energy adjustment (in place), dividing value/uncertainty by a factor. :param factor: factor to divide by

                                                              @@ -646,13 +646,13 @@
                                                              -property uncertainty[source]
                                                              +property uncertainty[source]

                                                              Return the value of the energy adjustment in eV.

                                                              -property value[source]
                                                              +property value[source]

                                                              Return the value of the energy correction in eV.

                                                              diff --git a/docs/pymatgen.entries.correction_calculator.html b/docs/pymatgen.entries.correction_calculator.html index 0d67f087710..26dca12611f 100644 --- a/docs/pymatgen.entries.correction_calculator.html +++ b/docs/pymatgen.entries.correction_calculator.html @@ -4,7 +4,7 @@ - pymatgen.entries.correction_calculator module — pymatgen 2022.5.18 documentation + pymatgen.entries.correction_calculator module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                              - 2022.5.18 + 2022.5.18.1
                                                              @@ -119,44 +119,44 @@ entries given to the CorrectionCalculator constructor.

                                                              -class CorrectionCalculator(species: list[str] = ['oxide', 'peroxide', 'superoxide', 'S', 'F', 'Cl', 'Br', 'I', 'N', 'Se', 'Si', 'Sb', 'Te', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'W', 'Mo', 'H'], max_error: float = 0.1, allow_unstable: float | bool = 0.1, exclude_polyanions: list[str] = ['SO4', 'SO3', 'CO3', 'NO3', 'NO2', 'OCl3', 'ClO3', 'ClO4', 'HO', 'ClO', 'SeO3', 'TiO3', 'TiO4', 'WO4', 'SiO3', 'SiO4', 'Si2O5', 'PO3', 'PO4', 'P2O7'])[source]
                                                              +class CorrectionCalculator(species: list[str] = ['oxide', 'peroxide', 'superoxide', 'S', 'F', 'Cl', 'Br', 'I', 'N', 'Se', 'Si', 'Sb', 'Te', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'W', 'Mo', 'H'], max_error: float = 0.1, allow_unstable: float | bool = 0.1, exclude_polyanions: list[str] = ['SO4', 'SO3', 'CO3', 'NO3', 'NO2', 'OCl3', 'ClO3', 'ClO4', 'HO', 'ClO', 'SeO3', 'TiO3', 'TiO4', 'WO4', 'SiO3', 'SiO4', 'Si2O5', 'PO3', 'PO4', 'P2O7'])[source]

                                                              Bases: object

                                                              A CorrectionCalculator contains experimental and computed entries which it uses to compute corrections.

                                                              It graphs residual errors after applying the computed corrections and creates the MPCompatibility.yaml file the Correction classes use.

                                                              -species[source]
                                                              +species[source]

                                                              list of species that corrections are being calculated for

                                                              -exp_compounds[source]
                                                              +exp_compounds[source]

                                                              list of dictionaries which each contain a compound’s formula and experimental data

                                                              -calc_compounds[source]
                                                              +calc_compounds[source]

                                                              dictionary of ComputedEntry objects

                                                              -corrections[source]
                                                              +corrections[source]

                                                              list of corrections in same order as species list

                                                              -corrections_std_error[source]
                                                              +corrections_std_error[source]

                                                              list of the variances of the corrections in same order as species list

                                                              -corrections_dict[source]
                                                              +corrections_dict[source]

                                                              dictionary of format {‘species’: (value, uncertainty)} for easier correction lookup

                                                              @@ -179,7 +179,7 @@
                                                              -compute_corrections(exp_entries: list, calc_entries: dict) → dict[source]
                                                              +compute_corrections(exp_entries: list, calc_entries: dict) → dict[source]

                                                              Computes the corrections and fills in correction, corrections_std_error, and corrections_dict.

                                                              Parameters
                                                              @@ -198,7 +198,7 @@
                                                              -compute_from_files(exp_gz: str, comp_gz: str)[source]
                                                              +compute_from_files(exp_gz: str, comp_gz: str)[source]
                                                              Parameters
                                                                @@ -215,13 +215,13 @@
                                                                -graph_residual_error() → plotly.graph_objs._figure.Figure[source]
                                                                +graph_residual_error() → plotly.graph_objs._figure.Figure[source]

                                                                Graphs the residual errors for all compounds after applying computed corrections.

                                                                -graph_residual_error_per_species(specie: str) → plotly.graph_objs._figure.Figure[source]
                                                                +graph_residual_error_per_species(specie: str) → plotly.graph_objs._figure.Figure[source]

                                                                Graphs the residual errors for each compound that contains specie after applying computed corrections.

                                                                Parameters
                                                                @@ -235,7 +235,7 @@
                                                                -make_yaml(name: str = 'MP2020', dir: str | None = None) → None[source]
                                                                +make_yaml(name: str = 'MP2020', dir: str | None = None) → None[source]

                                                                Creates the _name_Compatibility.yaml that stores corrections as well as _name_CompatibilityUncertainties.yaml for correction uncertainties.

                                                                diff --git a/docs/pymatgen.entries.entry_tools.html b/docs/pymatgen.entries.entry_tools.html index 3e8c58826fc..c6fb02bb405 100644 --- a/docs/pymatgen.entries.entry_tools.html +++ b/docs/pymatgen.entries.entry_tools.html @@ -4,7 +4,7 @@ - pymatgen.entries.entry_tools module — pymatgen 2022.5.18 documentation + pymatgen.entries.entry_tools module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                - 2022.5.18 + 2022.5.18.1
                                                                @@ -119,7 +119,7 @@ entries, such as grouping entries by structure.

                                                                -class EntrySet(entries: Iterable[PDEntry | ComputedEntry | ComputedStructureEntry])[source]
                                                                +class EntrySet(entries: Iterable[PDEntry | ComputedEntry | ComputedStructureEntry])[source]

                                                                Bases: collections.abc.MutableSet, monty.json.MSONable

                                                                A convenient container for manipulating entries. Allows for generating subsets, dumping into files, etc.

                                                                @@ -130,7 +130,7 @@
                                                                -add(element)[source]
                                                                +add(element)[source]

                                                                Add an entry.

                                                                Parameters
                                                                @@ -141,20 +141,20 @@
                                                                -as_dict() → dict[Literal['entries'], list[pymatgen.entries.Entry]][source]
                                                                +as_dict() → dict[Literal['entries'], list[pymatgen.entries.Entry]][source]

                                                                Returns MSONable dict.

                                                                -property chemsys: set[source]
                                                                +property chemsys: set[source]

                                                                Returns: set representing the chemical system, e.g., {“Li”, “Fe”, “P”, “O”}

                                                                -discard(element)[source]
                                                                +discard(element)[source]

                                                                Discard an entry.

                                                                Parameters
                                                                @@ -165,7 +165,7 @@
                                                                -classmethod from_csv(filename: str)[source]
                                                                +classmethod from_csv(filename: str)[source]

                                                                Imports PDEntries from a csv.

                                                                Parameters
                                                                @@ -179,7 +179,7 @@
                                                                -get_subset_in_chemsys(chemsys: list[str])[source]
                                                                +get_subset_in_chemsys(chemsys: list[str])[source]

                                                                Returns an EntrySet containing only the set of entries belonging to a particular chemical system (in this definition, it includes all sub systems). For example, if the entries are from the @@ -198,27 +198,27 @@

                                                                -property ground_states: set[source]
                                                                +property ground_states: set[source]

                                                                A set containing only the entries that are ground states, i.e., the lowest energy per atom entry at each composition.

                                                                -is_ground_state(entry) → bool[source]
                                                                +is_ground_state(entry) → bool[source]

                                                                Boolean indicating whether a given Entry is a ground state

                                                                -remove_non_ground_states()[source]
                                                                +remove_non_ground_states()[source]

                                                                Removes all non-ground state entries, i.e., only keep the lowest energy per atom entry at each composition.

                                                                -to_csv(filename: str, latexify_names: bool = False) → None[source]
                                                                +to_csv(filename: str, latexify_names: bool = False) → None[source]

                                                                Exports PDEntries to a csv

                                                                Parameters
                                                                @@ -236,7 +236,7 @@
                                                                -group_entries_by_composition(entries, sort_by_e_per_atom=True)[source]
                                                                +group_entries_by_composition(entries, sort_by_e_per_atom=True)[source]
                                                                Given a sequence of Entry-like objects, group them by composition and

                                                                optionally sort by energy above hull.

                                                                @@ -258,7 +258,7 @@
                                                                -group_entries_by_structure(entries, species_to_remove=None, ltol=0.2, stol=0.4, angle_tol=5, primitive_cell=True, scale=True, comparator=<pymatgen.analysis.structure_matcher.SpeciesComparator object>, ncpus=None)[source]
                                                                +group_entries_by_structure(entries, species_to_remove=None, ltol=0.2, stol=0.4, angle_tol=5, primitive_cell=True, scale=True, comparator=<pymatgen.analysis.structure_matcher.SpeciesComparator object>, ncpus=None)[source]

                                                                Given a sequence of ComputedStructureEntries, use structure fitter to group them by structural similarity.

                                                                diff --git a/docs/pymatgen.entries.exp_entries.html b/docs/pymatgen.entries.exp_entries.html index b1fa1fbaf62..d1198cec317 100644 --- a/docs/pymatgen.entries.exp_entries.html +++ b/docs/pymatgen.entries.exp_entries.html @@ -4,7 +4,7 @@ - pymatgen.entries.exp_entries module — pymatgen 2022.5.18 documentation + pymatgen.entries.exp_entries module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                - 2022.5.18 + 2022.5.18.1
                                                                @@ -118,7 +118,7 @@

                                                                This module defines Entry classes for containing experimental data.

                                                                -class ExpEntry(composition, thermodata, temperature=298)[source]
                                                                +class ExpEntry(composition, thermodata, temperature=298)[source]

                                                                Bases: pymatgen.analysis.phase_diagram.PDEntry, monty.json.MSONable

                                                                An lightweight ExpEntry object containing experimental data for a composition for many purposes. Extends a PDEntry so that it can be used for @@ -138,7 +138,7 @@

                                                                -as_dict()[source]
                                                                +as_dict()[source]
                                                                Returns

                                                                MSONable dict

                                                                @@ -148,7 +148,7 @@
                                                                -classmethod from_dict(d)[source]
                                                                +classmethod from_dict(d)[source]
                                                                Parameters

                                                                d – Dict representation.

                                                                diff --git a/docs/pymatgen.entries.html b/docs/pymatgen.entries.html index b4172b4c027..3af9d0de9db 100644 --- a/docs/pymatgen.entries.html +++ b/docs/pymatgen.entries.html @@ -4,7 +4,7 @@ - pymatgen.entries package — pymatgen 2022.5.18 documentation + pymatgen.entries package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                - 2022.5.18 + 2022.5.18.1
                                                                @@ -141,7 +141,7 @@

                                                                Submodules
                                                                -class Entry(composition: Composition | str | dict[str, float], energy: float)[source]
                                                                +class Entry(composition: Composition | str | dict[str, float], energy: float)[source]

                                                                Bases: monty.json.MSONable

                                                                A lightweight object containing the energy associated with a specific chemical composition. This base class is not @@ -161,7 +161,7 @@

                                                                Submodules
                                                                -as_dict() → dict[source]
                                                                +as_dict() → dict[source]
                                                                Returns

                                                                MSONable dict.

                                                                @@ -171,7 +171,7 @@

                                                                Submodules
                                                                -property composition: pymatgen.core.composition.Composition[source]
                                                                +property composition: pymatgen.core.composition.Composition[source]

                                                                the composition of the entry.

                                                                Type
                                                                @@ -182,7 +182,7 @@

                                                                Submodules
                                                                -abstract property energy: float[source]
                                                                +abstract property energy: float[source]

                                                                the energy of the entry.

                                                                Type
                                                                @@ -193,7 +193,7 @@

                                                                Submodules
                                                                -property energy_per_atom: float[source]
                                                                +property energy_per_atom: float[source]

                                                                the energy per atom of the entry.

                                                                Type
                                                                @@ -204,7 +204,7 @@

                                                                Submodules
                                                                -property is_element: bool[source]
                                                                +property is_element: bool[source]

                                                                Whether composition of entry is an element.

                                                                Type
                                                                @@ -215,7 +215,7 @@

                                                                Submodules
                                                                -normalize(mode: Literal['formula_unit', 'atom'] = 'formula_unit') → pymatgen.entries.Entry[source]
                                                                +normalize(mode: Literal['formula_unit', 'atom'] = 'formula_unit') → pymatgen.entries.Entry[source]

                                                                Normalize the entry’s composition and energy.

                                                                Parameters
                                                                diff --git a/docs/pymatgen.entries.mixing_scheme.html b/docs/pymatgen.entries.mixing_scheme.html index 037b26a7ffb..4efbc0d49ee 100644 --- a/docs/pymatgen.entries.mixing_scheme.html +++ b/docs/pymatgen.entries.mixing_scheme.html @@ -4,7 +4,7 @@ - pymatgen.entries.mixing_scheme module — pymatgen 2022.5.18 documentation + pymatgen.entries.mixing_scheme module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                - 2022.5.18 + 2022.5.18.1
                                                                @@ -119,7 +119,7 @@ functionals.

                                                                -class MaterialsProjectDFTMixingScheme(structure_matcher: StructureMatcher = <pymatgen.analysis.structure_matcher.StructureMatcher object>, run_type_1: str = 'GGA(+U)', run_type_2: str = 'R2SCAN', compat_1: Compatibility | None = <pymatgen.entries.compatibility.cached_class.<locals>._decorated object>, compat_2: Compatibility | None = None, fuzzy_matching: bool = True)[source]
                                                                +class MaterialsProjectDFTMixingScheme(structure_matcher: StructureMatcher = <pymatgen.analysis.structure_matcher.StructureMatcher object>, run_type_1: str = 'GGA(+U)', run_type_2: str = 'R2SCAN', compat_1: Compatibility | None = <pymatgen.entries.compatibility.cached_class.<locals>._decorated object>, compat_2: Compatibility | None = None, fuzzy_matching: bool = True)[source]

                                                                Bases: pymatgen.entries.compatibility.Compatibility

                                                                This class implements the Materials Project mixing scheme, which allows mixing of energies from different DFT functionals. Note that this should only be used for @@ -171,13 +171,13 @@

                                                                -static display_entries(entries)[source]
                                                                +static display_entries(entries)[source]

                                                                Generate a pretty printout of key properties of a list of ComputedEntry

                                                                -get_adjustments(entry, mixing_state_data: Optional[pandas.core.frame.DataFrame] = None)[source]
                                                                +get_adjustments(entry, mixing_state_data: Optional[pandas.core.frame.DataFrame] = None)[source]

                                                                Returns the corrections applied to a particular entry. Note that get_adjustments is not intended to be called directly in the R2SCAN mixing scheme. Call process_entries instead, and it will pass the required arguments to get_adjustments.

                                                                @@ -210,7 +210,7 @@
                                                                -get_mixing_state_data(entries: list[pymatgen.entries.computed_entries.ComputedStructureEntry], verbose: bool = False)[source]
                                                                +get_mixing_state_data(entries: list[pymatgen.entries.computed_entries.ComputedStructureEntry], verbose: bool = False)[source]

                                                                Generate internal state data to be passed to get_adjustments.

                                                                Parameters
                                                                @@ -251,7 +251,7 @@
                                                                -process_entries(entries: ComputedStructureEntry | ComputedEntry | list, clean: bool = True, verbose: bool = True, mixing_state_data=None)[source]
                                                                +process_entries(entries: ComputedStructureEntry | ComputedEntry | list, clean: bool = True, verbose: bool = True, mixing_state_data=None)[source]

                                                                Process a sequence of entries with the DFT mixing scheme. Note that this method will change the data of the original entries.

                                                                diff --git a/docs/pymatgen.ext.cod.html b/docs/pymatgen.ext.cod.html index 1a53a787aae..417453ef789 100644 --- a/docs/pymatgen.ext.cod.html +++ b/docs/pymatgen.ext.cod.html @@ -4,7 +4,7 @@ - pymatgen.ext.cod module — pymatgen 2022.5.18 documentation + pymatgen.ext.cod module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                - 2022.5.18 + 2022.5.18.1
                                                                @@ -143,13 +143,13 @@
                                                                -class COD[source]
                                                                +class COD[source]

                                                                Bases: object

                                                                An interface to the Crystallography Open Database.

                                                                Blank __init__. No args required.

                                                                -get_cod_ids(formula)[source]
                                                                +get_cod_ids(formula)[source]

                                                                Queries the COD for all cod ids associated with a formula. Requires mysql executable to be in the path.

                                                                @@ -164,7 +164,7 @@
                                                                -get_structure_by_formula(formula, **kwargs)[source]
                                                                +get_structure_by_formula(formula, **kwargs)[source]

                                                                Queries the COD for structures by formula. Requires mysql executable to be in the path.

                                                                @@ -184,7 +184,7 @@
                                                                -get_structure_by_id(cod_id, **kwargs)[source]
                                                                +get_structure_by_id(cod_id, **kwargs)[source]

                                                                Queries the COD for a structure by id.

                                                                Parameters
                                                                @@ -202,7 +202,7 @@
                                                                -query(sql: str) → str[source]
                                                                +query(sql: str) → str[source]

                                                                Perform a query.

                                                                Parameters
                                                                diff --git a/docs/pymatgen.ext.crystalsai.html b/docs/pymatgen.ext.crystalsai.html index 9cb04aa3756..9d4638a2dd3 100644 --- a/docs/pymatgen.ext.crystalsai.html +++ b/docs/pymatgen.ext.crystalsai.html @@ -4,7 +4,7 @@ - pymatgen.ext.crystalsai module — pymatgen 2022.5.18 documentation + pymatgen.ext.crystalsai module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                - 2022.5.18 + 2022.5.18.1
                                                                @@ -119,7 +119,7 @@ for rapid property prediction.

                                                                -class CrystalAIRester[source]
                                                                +class CrystalAIRester[source]

                                                                Bases: object

                                                                This is a high-level interface to the REST API for http://megnet.crystals.ai for property prediction. Using this API, you can use MatErials Graph @@ -139,7 +139,7 @@

                                                                Init for Rester.

                                                                -get_available_models()[source]
                                                                +get_available_models()[source]
                                                                Returns

                                                                Available model names. It should be noted that model names starting @@ -150,7 +150,7 @@

                                                                -predict_mp(model_name, mp_id)[source]
                                                                +predict_mp(model_name, mp_id)[source]

                                                                Predict using the http://megnet.crystals.ai API.

                                                                Parameters
                                                                @@ -171,7 +171,7 @@
                                                                -predict_structure(model_name, structure)[source]
                                                                +predict_structure(model_name, structure)[source]

                                                                Predict using the http://megnet.crystals.ai API.

                                                                Parameters
                                                                diff --git a/docs/pymatgen.ext.html b/docs/pymatgen.ext.html index 51863b8212e..717d75dd1e2 100644 --- a/docs/pymatgen.ext.html +++ b/docs/pymatgen.ext.html @@ -4,7 +4,7 @@ - pymatgen.ext namespace — pymatgen 2022.5.18 documentation + pymatgen.ext namespace — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                - 2022.5.18 + 2022.5.18.1
                                                                diff --git a/docs/pymatgen.ext.jhu.html b/docs/pymatgen.ext.jhu.html index 9400e329077..5c2f053d705 100644 --- a/docs/pymatgen.ext.jhu.html +++ b/docs/pymatgen.ext.jhu.html @@ -4,7 +4,7 @@ - pymatgen.ext.jhu module — pymatgen 2022.5.18 documentation + pymatgen.ext.jhu module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                - 2022.5.18 + 2022.5.18.1
                                                                @@ -119,7 +119,7 @@ see http://muellergroup.jhu.edu/K-Points.html.

                                                                -get_kpoints(structure, min_distance=0, min_total_kpoints=1, kppra=None, gap_distance=7, remove_symmetry=None, include_gamma='auto', header='simple', incar=None)[source]
                                                                +get_kpoints(structure, min_distance=0, min_total_kpoints=1, kppra=None, gap_distance=7, remove_symmetry=None, include_gamma='auto', header='simple', incar=None)[source]

                                                                Get kpoints object from JHU servlet, per Wisesa-McGill-Mueller methodology. Refer to http://muellergroup.jhu.edu/K-Points.html and P. Wisesa, K. A. McGill, T. Mueller, Phys. Rev. B 93, diff --git a/docs/pymatgen.ext.matproj.html b/docs/pymatgen.ext.matproj.html index 9252c1c61c7..983e762fded 100644 --- a/docs/pymatgen.ext.matproj.html +++ b/docs/pymatgen.ext.matproj.html @@ -4,7 +4,7 @@ - pymatgen.ext.matproj module — pymatgen 2022.5.18 documentation + pymatgen.ext.matproj module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                                                - 2022.5.18 + 2022.5.18.1
                                                                @@ -123,7 +123,7 @@ https://www.materialsproject.org/dashboard.

                                                                -exception MPRestError[source]
                                                                +exception MPRestError[source]

                                                                Bases: Exception

                                                                Exception class for MPRestAdaptor. Raised when the query has problems, e.g., bad query format.

                                                                @@ -131,7 +131,7 @@
                                                                -class MPRester(api_key=None, endpoint=None, notify_db_version=True, include_user_agent=True)[source]
                                                                +class MPRester(api_key=None, endpoint=None, notify_db_version=True, include_user_agent=True)[source]

                                                                Bases: object

                                                                A class to conveniently interface with the Materials Project REST interface. The recommended way to use MPRester is with the “with” context @@ -175,7 +175,7 @@

                                                                -delete_snl(snl_ids)[source]
                                                                +delete_snl(snl_ids)[source]

                                                                Delete earlier submitted SNLs.

                                                                Note

                                                                @@ -195,7 +195,7 @@
                                                                -find_structure(filename_or_structure)[source]
                                                                +find_structure(filename_or_structure)[source]

                                                                Finds matching structures on the Materials Project site.

                                                                Parameters
                                                                @@ -212,7 +212,7 @@
                                                                -get_all_substrates()[source]
                                                                +get_all_substrates()[source]

                                                                Gets the list of all possible substrates considered in the Materials Project substrate database

                                                                @@ -224,7 +224,7 @@
                                                                -get_bandstructure_by_material_id(material_id, line_mode=True)[source]
                                                                +get_bandstructure_by_material_id(material_id, line_mode=True)[source]

                                                                Get a BandStructure corresponding to a material_id.

                                                                REST Endpoint: https://www.materialsproject.org/rest/v2/materials/<mp-id>/vasp/bandstructure or https://www.materialsproject.org/rest/v2/materials/<mp-id>/vasp/bandstructure_uniform

                                                                @@ -244,7 +244,7 @@
                                                                -get_cohesive_energy(material_id, per_atom=False)[source]
                                                                +get_cohesive_energy(material_id, per_atom=False)[source]
                                                                Gets the cohesive for a material (eV per formula unit). Cohesive energy

                                                                is defined as the difference between the bulk energy and the sum of total DFT energy of isolated atoms for atom elements in the bulk.

                                                                @@ -265,7 +265,7 @@
                                                                -get_data(chemsys_formula_id, data_type='vasp', prop='')[source]
                                                                +get_data(chemsys_formula_id, data_type='vasp', prop='')[source]

                                                                Flexible method to get any data using the Materials Project REST interface. Generally used by other methods for more specific queries.

                                                                Format of REST return is always a list of dict (regardless of the @@ -291,7 +291,7 @@

                                                                -get_database_version()[source]
                                                                +get_database_version()[source]

                                                                The Materials Project database is periodically updated and has a database version associated with it. When the database is updated, consolidated data (information about “a material”) may and does @@ -305,7 +305,7 @@

                                                                -get_doc(materials_id)[source]
                                                                +get_doc(materials_id)[source]

                                                                Get the entire data document for one materials id. Use this judiciously.

                                                                REST Endpoint: https://www.materialsproject.org/materials/<mp-id>/doc.

                                                                @@ -321,7 +321,7 @@
                                                                -get_dos_by_material_id(material_id)[source]
                                                                +get_dos_by_material_id(material_id)[source]

                                                                Get a Dos corresponding to a material_id.

                                                                REST Endpoint: https://www.materialsproject.org/rest/v2/materials/<mp-id>/vasp/dos

                                                                @@ -337,7 +337,7 @@
                                                                -get_download_info(material_ids, task_types=None, file_patterns=None)[source]
                                                                +get_download_info(material_ids, task_types=None, file_patterns=None)[source]

                                                                get a list of URLs to retrieve raw VASP output files from the NoMaD repository

                                                                Parameters
                                                                @@ -358,7 +358,7 @@
                                                                -get_entries(chemsys_formula_id_criteria, compatible_only=True, inc_structure=None, property_data=None, conventional_unit_cell=False, sort_by_e_above_hull=False)[source]
                                                                +get_entries(chemsys_formula_id_criteria, compatible_only=True, inc_structure=None, property_data=None, conventional_unit_cell=False, sort_by_e_above_hull=False)[source]

                                                                Get a list of ComputedEntries or ComputedStructureEntries corresponding to a chemical system, formula, or materials_id or full criteria.

                                                                @@ -395,7 +395,7 @@
                                                                -get_entries_in_chemsys(elements, compatible_only=True, inc_structure=None, property_data=None, conventional_unit_cell=False)[source]
                                                                +get_entries_in_chemsys(elements, compatible_only=True, inc_structure=None, property_data=None, conventional_unit_cell=False)[source]

                                                                Helper method to get a list of ComputedEntries in a chemical system. For example, elements = [“Li”, “Fe”, “O”] will return a list of all entries in the Li-Fe-O chemical system, i.e., all LixOy, @@ -433,7 +433,7 @@

                                                                -get_entry_by_material_id(material_id, compatible_only=True, inc_structure=None, property_data=None, conventional_unit_cell=False)[source]
                                                                +get_entry_by_material_id(material_id, compatible_only=True, inc_structure=None, property_data=None, conventional_unit_cell=False)[source]

                                                                Get a ComputedEntry corresponding to a material_id.

                                                                Parameters
                                                                @@ -466,7 +466,7 @@
                                                                -get_exp_entry(formula)[source]
                                                                +get_exp_entry(formula)[source]

                                                                Returns an ExpEntry object, which is the experimental equivalent of a ComputedEntry and can be used for analyses using experimental data.

                                                                @@ -481,7 +481,7 @@
                                                                -get_exp_thermo_data(formula)[source]
                                                                +get_exp_thermo_data(formula)[source]

                                                                Get a list of ThermoData objects associated with a formula using the Materials Project REST interface.

                                                                @@ -496,7 +496,7 @@
                                                                -get_gb_data(material_id=None, pretty_formula=None, chemsys=None, sigma=None, gb_plane=None, rotation_axis=None, include_work_of_separation=False)[source]
                                                                +get_gb_data(material_id=None, pretty_formula=None, chemsys=None, sigma=None, gb_plane=None, rotation_axis=None, include_work_of_separation=False)[source]

                                                                Gets grain boundary data for a material.

                                                                Parameters
                                                                @@ -538,7 +538,7 @@
                                                                -get_interface_reactions(reactant1, reactant2, open_el=None, relative_mu=None, use_hull_energy=False)[source]
                                                                +get_interface_reactions(reactant1, reactant2, open_el=None, relative_mu=None, use_hull_energy=False)[source]

                                                                Gets critical reactions between two reactants.

                                                                Get critical reactions (“kinks” in the mixing ratio where reaction products change) between two reactants. See the @@ -579,7 +579,7 @@

                                                                -get_materials_id_from_task_id(task_id)[source]
                                                                +get_materials_id_from_task_id(task_id)[source]

                                                                Returns a new MP materials id from a task id (which can be equivalent to an old materials id)

                                                                @@ -594,7 +594,7 @@
                                                                -get_materials_id_references(material_id)[source]
                                                                +get_materials_id_references(material_id)[source]

                                                                Returns all references for a materials id.

                                                                Parameters
                                                                @@ -608,7 +608,7 @@
                                                                -get_materials_ids(chemsys_formula)[source]
                                                                +get_materials_ids(chemsys_formula)[source]

                                                                Get all materials ids for a formula or chemsys.

                                                                Parameters
                                                                @@ -623,7 +623,7 @@
                                                                -get_phonon_bandstructure_by_material_id(material_id)[source]
                                                                +get_phonon_bandstructure_by_material_id(material_id)[source]

                                                                Get phonon dispersion data corresponding to a material_id.

                                                                Parameters
                                                                @@ -640,7 +640,7 @@
                                                                -get_phonon_ddb_by_material_id(material_id)[source]
                                                                +get_phonon_ddb_by_material_id(material_id)[source]

                                                                Get ABINIT Derivative Data Base (DDB) output for phonon calculations.

                                                                Parameters
                                                                @@ -657,7 +657,7 @@
                                                                -get_phonon_dos_by_material_id(material_id)[source]
                                                                +get_phonon_dos_by_material_id(material_id)[source]

                                                                Get phonon density of states data corresponding to a material_id.

                                                                Parameters
                                                                @@ -674,7 +674,7 @@
                                                                -get_pourbaix_entries(chemsys, solid_compat='MaterialsProject2020Compatibility')[source]
                                                                +get_pourbaix_entries(chemsys, solid_compat='MaterialsProject2020Compatibility')[source]

                                                                A helper function to get all entries necessary to generate a Pourbaix diagram from the rest interface.

                                                                @@ -694,7 +694,7 @@
                                                                -get_reaction(reactants, products)[source]
                                                                +get_reaction(reactants, products)[source]

                                                                Gets a reaction from the Materials Project.

                                                                Parameters
                                                                @@ -711,13 +711,13 @@
                                                                -get_stability(entries)[source]
                                                                +get_stability(entries)[source]

                                                                Returns the stability of all entries.

                                                                -get_structure_by_material_id(material_id, final=True, conventional_unit_cell=False)[source]
                                                                +get_structure_by_material_id(material_id, final=True, conventional_unit_cell=False)[source]

                                                                Get a Structure corresponding to a material_id.

                                                                Parameters
                                                                @@ -738,7 +738,7 @@
                                                                -get_structures(chemsys_formula_id, final=True)[source]
                                                                +get_structures(chemsys_formula_id, final=True)[source]

                                                                Get a list of Structures corresponding to a chemical system, formula, or materials_id.

                                                                @@ -758,7 +758,7 @@
                                                                -get_substrates(material_id, number=50, orient=None)[source]
                                                                +get_substrates(material_id, number=50, orient=None)[source]

                                                                Get a substrate list for a material id. The list is in order of increasing elastic energy if a elastic tensor is available for the material_id. Otherwise the list is in order of increasing @@ -780,7 +780,7 @@

                                                                -get_surface_data(material_id, miller_index=None, inc_structures=False)[source]
                                                                +get_surface_data(material_id, miller_index=None, inc_structures=False)[source]

                                                                Gets surface data for a material. Useful for Wulff shapes.

                                                                Reference for surface data:

                                                                Tran, R., Xu, Z., Radhakrishnan, B., Winston, D., Sun, W., Persson, K. @@ -810,7 +810,7 @@

                                                                -get_task_data(chemsys_formula_id, prop='')[source]
                                                                +get_task_data(chemsys_formula_id, prop='')[source]

                                                                Flexible method to get any data using the Materials Project REST interface. Generally used by other methods for more specific queries. Unlike the :func:`get_data`_, this method queries the task collection @@ -833,7 +833,7 @@

                                                                -get_wulff_shape(material_id)[source]
                                                                +get_wulff_shape(material_id)[source]

                                                                Constructs a Wulff shape for a material.

                                                                Parameters
                                                                @@ -847,7 +847,7 @@
                                                                -get_xas_data(material_id, absorbing_element)[source]
                                                                +get_xas_data(material_id, absorbing_element)[source]

                                                                Get X-ray absorption spectroscopy data for absorbing element in the structure corresponding to a material_id. Only X-ray Absorption Near Edge Structure (XANES) for K-edge is supported.

                                                                @@ -866,7 +866,7 @@
                                                                -static parse_criteria(criteria_string)[source]
                                                                +static parse_criteria(criteria_string)[source]

                                                                Parses a powerful and simple string criteria and generates a proper mongo syntax criteria.

                                                                @@ -894,7 +894,7 @@
                                                                -query(criteria, properties, chunk_size: int = 500, max_tries_per_chunk: int = 5, mp_decode: bool = True, show_progress_bar: bool = True)[source]
                                                                +query(criteria, properties, chunk_size: int = 500, max_tries_per_chunk: int = 5, mp_decode: bool = True, show_progress_bar: bool = True)[source]

                                                                Performs an advanced query using MongoDB-like syntax for directly querying the Materials Project database. This allows one to perform queries which are otherwise too cumbersome to perform using the standard @@ -963,7 +963,7 @@

                                                                -query_snl(criteria)[source]
                                                                +query_snl(criteria)[source]

                                                                Query for submitted SNLs.

                                                                Note

                                                                @@ -986,7 +986,7 @@
                                                                -submit_snl(snl)[source]
                                                                +submit_snl(snl)[source]

                                                                Submits a list of StructureNL to the Materials Project site.

                                                                Note

                                                                @@ -1012,7 +1012,7 @@
                                                                -submit_structures(structures, authors, projects=None, references='', remarks=None, data=None, histories=None, created_at=None)[source]
                                                                +submit_structures(structures, authors, projects=None, references='', remarks=None, data=None, histories=None, created_at=None)[source]

                                                                Submits a list of structures to the Materials Project as SNL files. The argument list mirrors the arguments for the StructureNL object, except that a list of structures with the same metadata is used as an @@ -1053,7 +1053,7 @@

                                                                -submit_vasp_directory(rootdir, authors, projects=None, references='', remarks=None, master_data=None, master_history=None, created_at=None, ncpus=None)[source]
                                                                +submit_vasp_directory(rootdir, authors, projects=None, references='', remarks=None, master_data=None, master_history=None, created_at=None, ncpus=None)[source]

                                                                Assimilates all vasp run directories beneath a particular directory using BorgQueen to obtain structures, and then submits thhem to the Materials Project as SNL files. VASP related meta data like @@ -1093,96 +1093,96 @@

                                                                -supported_properties = ('energy', 'energy_per_atom', 'volume', 'formation_energy_per_atom', 'nsites', 'unit_cell_formula', 'pretty_formula', 'is_hubbard', 'elements', 'nelements', 'e_above_hull', 'hubbards', 'is_compatible', 'spacegroup', 'task_ids', 'band_gap', 'density', 'icsd_id', 'icsd_ids', 'cif', 'total_magnetization', 'material_id', 'oxide_type', 'tags', 'elasticity')[source]
                                                                +supported_properties = ('energy', 'energy_per_atom', 'volume', 'formation_energy_per_atom', 'nsites', 'unit_cell_formula', 'pretty_formula', 'is_hubbard', 'elements', 'nelements', 'e_above_hull', 'hubbards', 'is_compatible', 'spacegroup', 'task_ids', 'band_gap', 'density', 'icsd_id', 'icsd_ids', 'cif', 'total_magnetization', 'material_id', 'oxide_type', 'tags', 'elasticity')[source]
                                                                -supported_task_properties = ('energy', 'energy_per_atom', 'volume', 'formation_energy_per_atom', 'nsites', 'unit_cell_formula', 'pretty_formula', 'is_hubbard', 'elements', 'nelements', 'e_above_hull', 'hubbards', 'is_compatible', 'spacegroup', 'band_gap', 'density', 'icsd_id', 'cif')[source]
                                                                +supported_task_properties = ('energy', 'energy_per_atom', 'volume', 'formation_energy_per_atom', 'nsites', 'unit_cell_formula', 'pretty_formula', 'is_hubbard', 'elements', 'nelements', 'e_above_hull', 'hubbards', 'is_compatible', 'spacegroup', 'band_gap', 'density', 'icsd_id', 'cif')[source]
                                                                -class TaskType(value)[source]
                                                                +class TaskType(value)[source]

                                                                Bases: enum.Enum

                                                                task types available in MP

                                                                -GGAU_DEF = 'GGA+U Deformation'[source]
                                                                +GGAU_DEF = 'GGA+U Deformation'[source]
                                                                -GGAU_LINE = 'GGA+U NSCF Line'[source]
                                                                +GGAU_LINE = 'GGA+U NSCF Line'[source]
                                                                -GGAU_OPT = 'GGA+U Structure Optimization'[source]
                                                                +GGAU_OPT = 'GGA+U Structure Optimization'[source]
                                                                -GGAU_STATIC = 'GGA+U Static'[source]
                                                                +GGAU_STATIC = 'GGA+U Static'[source]
                                                                -GGAU_STATIC_DIEL = 'GGA+U Static Dielectric'[source]
                                                                +GGAU_STATIC_DIEL = 'GGA+U Static Dielectric'[source]
                                                                -GGAU_UNIFORM = 'GGA+U NSCF Uniform'[source]
                                                                +GGAU_UNIFORM = 'GGA+U NSCF Uniform'[source]
                                                                -GGA_DEF = 'GGA Deformation'[source]
                                                                +GGA_DEF = 'GGA Deformation'[source]
                                                                -GGA_LINE = 'GGA NSCF Line'[source]
                                                                +GGA_LINE = 'GGA NSCF Line'[source]
                                                                -GGA_OPT = 'GGA Structure Optimization'[source]
                                                                +GGA_OPT = 'GGA Structure Optimization'[source]
                                                                -GGA_STATIC = 'GGA Static'[source]
                                                                +GGA_STATIC = 'GGA Static'[source]
                                                                -GGA_STATIC_DIEL = 'GGA Static Dielectric'[source]
                                                                +GGA_STATIC_DIEL = 'GGA Static Dielectric'[source]
                                                                -GGA_UNIFORM = 'GGA NSCF Uniform'[source]
                                                                +GGA_UNIFORM = 'GGA NSCF Uniform'[source]
                                                                -LDA_STATIC_DIEL = 'LDA Static Dielectric'[source]
                                                                +LDA_STATIC_DIEL = 'LDA Static Dielectric'[source]
                                                                -SCAN_OPT = 'SCAN Structure Optimization'[source]
                                                                +SCAN_OPT = 'SCAN Structure Optimization'[source]
                                                                -get_chunks(sequence, size=1)[source]
                                                                +get_chunks(sequence, size=1)[source]
                                                                Parameters
                                                                  diff --git a/docs/pymatgen.ext.optimade.html b/docs/pymatgen.ext.optimade.html index c227340ffe1..205079226a3 100644 --- a/docs/pymatgen.ext.optimade.html +++ b/docs/pymatgen.ext.optimade.html @@ -4,7 +4,7 @@ - pymatgen.ext.optimade module — pymatgen 2022.5.18 documentation + pymatgen.ext.optimade module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                  - 2022.5.18 + 2022.5.18.1
                                                                  @@ -118,7 +118,7 @@

                                                                  Optimade support.

                                                                  -class OptimadeRester(aliases_or_resource_urls: str | list[str] | None = None, timeout: int = 5)[source]
                                                                  +class OptimadeRester(aliases_or_resource_urls: str | list[str] | None = None, timeout: int = 5)[source]

                                                                  Bases: object

                                                                  Class to call OPTIMADE-compliant APIs, see https://optimade.org and [1].

                                                                  This class is ready to use but considered in-development and subject to change.

                                                                  @@ -159,18 +159,18 @@
                                                                  -aliases: dict[str, str] = {'aflow': 'http://aflow.org/API/optimade/', 'cod': 'https://www.crystallography.net/cod/optimade', 'mcloud.2dstructures': 'https://aiida.materialscloud.org/2dstructures/optimade', 'mcloud.2dtopo': 'https://aiida.materialscloud.org/2dtopo/optimade', 'mcloud.curated-cofs': 'https://aiida.materialscloud.org/curated-cofs/optimade', 'mcloud.li-ion-conductors': 'https://aiida.materialscloud.org/li-ion-conductors/optimade', 'mcloud.optimade-sample': 'https://aiida.materialscloud.org/optimade-sample/optimade', 'mcloud.pyrene-mofs': 'https://aiida.materialscloud.org/pyrene-mofs/optimade', 'mcloud.scdm': 'https://aiida.materialscloud.org/autowannier/optimade', 'mcloud.sssp': 'https://aiida.materialscloud.org/sssplibrary/optimade', 'mcloud.stoceriaitf': 'https://aiida.materialscloud.org/stoceriaitf/optimade', 'mcloud.tc-applicability': 'https://aiida.materialscloud.org/tc-applicability/optimade', 'mcloud.threedd': 'https://aiida.materialscloud.org/3dd/optimade', 'mp': 'https://optimade.materialsproject.org', 'mpds': 'https://api.mpds.io', 'nmd': 'https://nomad-lab.eu/prod/rae/optimade/', 'odbx': 'https://optimade.odbx.science', 'omdb.omdb_production': 'http://optimade.openmaterialsdb.se', 'oqmd': 'http://oqmd.org/optimade/', 'tcod': 'https://www.crystallography.net/tcod/optimade'}[source]
                                                                  +aliases: dict[str, str] = {'aflow': 'http://aflow.org/API/optimade/', 'cod': 'https://www.crystallography.net/cod/optimade', 'mcloud.2dstructures': 'https://aiida.materialscloud.org/2dstructures/optimade', 'mcloud.2dtopo': 'https://aiida.materialscloud.org/2dtopo/optimade', 'mcloud.curated-cofs': 'https://aiida.materialscloud.org/curated-cofs/optimade', 'mcloud.li-ion-conductors': 'https://aiida.materialscloud.org/li-ion-conductors/optimade', 'mcloud.optimade-sample': 'https://aiida.materialscloud.org/optimade-sample/optimade', 'mcloud.pyrene-mofs': 'https://aiida.materialscloud.org/pyrene-mofs/optimade', 'mcloud.scdm': 'https://aiida.materialscloud.org/autowannier/optimade', 'mcloud.sssp': 'https://aiida.materialscloud.org/sssplibrary/optimade', 'mcloud.stoceriaitf': 'https://aiida.materialscloud.org/stoceriaitf/optimade', 'mcloud.tc-applicability': 'https://aiida.materialscloud.org/tc-applicability/optimade', 'mcloud.threedd': 'https://aiida.materialscloud.org/3dd/optimade', 'mp': 'https://optimade.materialsproject.org', 'mpds': 'https://api.mpds.io', 'nmd': 'https://nomad-lab.eu/prod/rae/optimade/', 'odbx': 'https://optimade.odbx.science', 'omdb.omdb_production': 'http://optimade.openmaterialsdb.se', 'oqmd': 'http://oqmd.org/optimade/', 'tcod': 'https://www.crystallography.net/tcod/optimade'}[source]
                                                                  -describe()[source]
                                                                  +describe()[source]

                                                                  Provides human-readable information about the resources being searched by the OptimadeRester.

                                                                  -get_snls(elements: list[str] | str | None = None, nelements: int = None, nsites: int = None, chemical_formula_anonymous: str = None, chemical_formula_hill: str = None, additional_response_fields: str | list[str] | set[str] | None = None) → dict[str, dict[str, StructureNL]][source]
                                                                  +get_snls(elements: list[str] | str | None = None, nelements: int = None, nsites: int = None, chemical_formula_anonymous: str = None, chemical_formula_hill: str = None, additional_response_fields: str | list[str] | set[str] | None = None) → dict[str, dict[str, StructureNL]][source]

                                                                  Retrieve StructureNL from OPTIMADE providers.

                                                                  A StructureNL is an object provided by pymatgen which combines Structure with associated metadata, such as the URL is was downloaded from and any additional namespaced @@ -195,7 +195,7 @@

                                                                  -get_snls_with_filter(optimade_filter: str, additional_response_fields: str | list[str] | set[str] | None = None) → dict[str, dict[str, StructureNL]][source]
                                                                  +get_snls_with_filter(optimade_filter: str, additional_response_fields: str | list[str] | set[str] | None = None) → dict[str, dict[str, StructureNL]][source]

                                                                  Get structures satisfying a given OPTIMADE filter.

                                                                  Parameters
                                                                  @@ -207,7 +207,7 @@
                                                                  -get_structures(elements: list[str] | str | None = None, nelements: int = None, nsites: int = None, chemical_formula_anonymous: str = None, chemical_formula_hill: str = None) → dict[str, dict[str, Structure]][source]
                                                                  +get_structures(elements: list[str] | str | None = None, nelements: int = None, nsites: int = None, chemical_formula_anonymous: str = None, chemical_formula_hill: str = None) → dict[str, dict[str, Structure]][source]

                                                                  Retrieve Structures from OPTIMADE providers.

                                                                  Not all functionality of OPTIMADE is currently exposed in this convenience method. To use a custom filter, call get_structures_with_filter().

                                                                  @@ -227,7 +227,7 @@
                                                                  -get_structures_with_filter(optimade_filter: str) → dict[str, dict[str, pymatgen.core.structure.Structure]][source]
                                                                  +get_structures_with_filter(optimade_filter: str) → dict[str, dict[str, pymatgen.core.structure.Structure]][source]

                                                                  Get structures satisfying a given OPTIMADE filter.

                                                                  Parameters
                                                                  @@ -239,12 +239,12 @@
                                                                  -mandatory_response_fields: set[str] = {'cartesian_site_positions', 'lattice_vectors', 'species', 'species_at_sites'}[source]
                                                                  +mandatory_response_fields: set[str] = {'cartesian_site_positions', 'lattice_vectors', 'species', 'species_at_sites'}[source]
                                                                  -refresh_aliases(providers_url='https://providers.optimade.org/providers.json')[source]
                                                                  +refresh_aliases(providers_url='https://providers.optimade.org/providers.json')[source]

                                                                  Updates available OPTIMADE structure resources based on the current list of OPTIMADE providers.

                                                                  @@ -253,36 +253,36 @@
                                                                  -class Provider(name, base_url, description, homepage, prefix)[source]
                                                                  +class Provider(name, base_url, description, homepage, prefix)[source]

                                                                  Bases: tuple

                                                                  Create new instance of Provider(name, base_url, description, homepage, prefix)

                                                                  -base_url[source]
                                                                  +base_url[source]

                                                                  Alias for field number 1

                                                                  -description[source]
                                                                  +description[source]

                                                                  Alias for field number 2

                                                                  -homepage[source]
                                                                  +homepage[source]

                                                                  Alias for field number 3

                                                                  -name[source]
                                                                  +name[source]

                                                                  Alias for field number 0

                                                                  -prefix[source]
                                                                  +prefix[source]

                                                                  Alias for field number 4

                                                                  diff --git a/docs/pymatgen.html b/docs/pymatgen.html index 7d0928747f4..27f66c6033c 100644 --- a/docs/pymatgen.html +++ b/docs/pymatgen.html @@ -4,7 +4,7 @@ - pymatgen namespace — pymatgen 2022.5.18 documentation + pymatgen namespace — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                  - 2022.5.18 + 2022.5.18.1
                                                                  diff --git a/docs/pymatgen.io.abinit.abiobjects.html b/docs/pymatgen.io.abinit.abiobjects.html index 5ca32bc1f46..ee245560106 100644 --- a/docs/pymatgen.io.abinit.abiobjects.html +++ b/docs/pymatgen.io.abinit.abiobjects.html @@ -4,7 +4,7 @@ - pymatgen.io.abinit.abiobjects module — pymatgen 2022.5.18 documentation + pymatgen.io.abinit.abiobjects module — pymatgen 2022.5.18.1 documentation @@ -40,7 +40,7 @@ pymatgen
                                                                  - 2022.5.18 + 2022.5.18.1
                                                                  @@ -120,13 +120,13 @@

                                                                  Low-level objects providing an abstraction for the objects involved in the calculation.

                                                                  -class AbivarAble[source]
                                                                  +class AbivarAble[source]

                                                                  Bases: object

                                                                  An AbivarAble object provides a method to_abivars that returns a dictionary with the abinit variables.

                                                                  -abstract to_abivars()[source]
                                                                  +abstract to_abivars()[source]

                                                                  Returns a dictionary with the abinit variables.

                                                                  @@ -134,12 +134,12 @@
                                                                  -class Constraints[source]
                                                                  +class Constraints[source]

                                                                  Bases: pymatgen.io.abinit.abiobjects.AbivarAble

                                                                  This object defines the constraints for structural relaxation

                                                                  -to_abivars()[source]
                                                                  +to_abivars()[source]

                                                                  Dictionary with Abinit variables.

                                                                  @@ -147,7 +147,7 @@
                                                                  -class Electrons(spin_mode='polarized', smearing='fermi_dirac:0.1 eV', algorithm=None, nband=None, fband=None, charge=0.0, comment=None)[source]
                                                                  +class Electrons(spin_mode='polarized', smearing='fermi_dirac:0.1 eV', algorithm=None, nband=None, fband=None, charge=0.0, comment=None)[source]

                                                                  Bases: pymatgen.io.abinit.abiobjects.AbivarAble, monty.json.MSONable

                                                                  The electronic degrees of freedom

                                                                  Constructor for Electrons object.

                                                                  @@ -161,37 +161,37 @@
                                                                  -as_dict()[source]
                                                                  +as_dict()[source]

                                                                  json friendly dict representation

                                                                  -classmethod from_dict(d)[source]
                                                                  +classmethod from_dict(d)[source]

                                                                  Build object from dictionary.

                                                                  -property nspden[source]
                                                                  +property nspden[source]

                                                                  Number of independent density components.

                                                                  -property nspinor[source]
                                                                  +property nspinor[source]

                                                                  Number of independent spinor components.

                                                                  -property nsppol[source]
                                                                  +property nsppol[source]

                                                                  Number of independent spin polarizations.

                                                                  -to_abivars()[source]
                                                                  +to_abivars()[source]

                                                                  Return dictionary with Abinit variables.

                                                                  @@ -199,25 +199,25 @@
                                                                  -class ElectronsAlgorithm(*args, **kwargs)[source]
                                                                  +class ElectronsAlgorithm(*args, **kwargs)[source]

                                                                  Bases: dict, pymatgen.io.abinit.abiobjects.AbivarAble, monty.json.MSONable

                                                                  Variables controlling the SCF/NSCF algorithm.

                                                                  Initialize object.

                                                                  -as_dict()[source]
                                                                  +as_dict()[source]

                                                                  Convert object to dict.

                                                                  -classmethod from_dict(d)[source]
                                                                  +classmethod from_dict(d)[source]

                                                                  Build object from dict.

                                                                  -to_abivars()[source]
                                                                  +to_abivars()[source]

                                                                  Dictionary with Abinit input variables.

                                                                  @@ -225,7 +225,7 @@
                                                                  -class ExcHamiltonian(bs_loband, nband, mbpt_sciss, coulomb_mode, ecuteps, spin_mode='polarized', mdf_epsinf=None, exc_type='TDA', algo='haydock', with_lf=True, bs_freq_mesh=None, zcut=None, **kwargs)[source]
                                                                  +class ExcHamiltonian(bs_loband, nband, mbpt_sciss, coulomb_mode, ecuteps, spin_mode='polarized', mdf_epsinf=None, exc_type='TDA', algo='haydock', with_lf=True, bs_freq_mesh=None, zcut=None, **kwargs)[source]

                                                                  Bases: pymatgen.io.abinit.abiobjects.AbivarAble

                                                                  This object contains the parameters for the solution of the Bethe-Salpeter equation.

                                                                  @@ -249,31 +249,31 @@
                                                                  -property inclvkb[source]
                                                                  +property inclvkb[source]

                                                                  Treatment of the dipole matrix element (NC pseudos, default is 2)

                                                                  -to_abivars()[source]
                                                                  +to_abivars()[source]

                                                                  Returns a dictionary with the abinit variables.

                                                                  -property use_cg[source]
                                                                  +property use_cg[source]

                                                                  True if we are using the conjugate gradient method.

                                                                  -property use_direct_diago[source]
                                                                  +property use_direct_diago[source]

                                                                  True if we are performing the direct diagonalization of the BSE Hamiltonian.

                                                                  -property use_haydock[source]
                                                                  +property use_haydock[source]

                                                                  True if we are using the Haydock iterative technique.

                                                                  @@ -281,7 +281,7 @@
                                                                  -class HilbertTransform(nomegasf, domegasf=None, spmeth=1, nfreqre=None, freqremax=None, nfreqim=None, freqremin=None)[source]
                                                                  +class HilbertTransform(nomegasf, domegasf=None, spmeth=1, nfreqre=None, freqremax=None, nfreqim=None, freqremin=None)[source]

                                                                  Bases: pymatgen.io.abinit.abiobjects.AbivarAble

                                                                  Parameters for the Hilbert-transform method (Screening code) i.e. the parameters defining the frequency mesh used for the spectral function @@ -301,7 +301,7 @@

                                                                  -to_abivars()[source]
                                                                  +to_abivars()[source]

                                                                  Returns a dictionary with the abinit variables

                                                                  @@ -309,7 +309,7 @@
                                                                  -class KSampling(mode=KSamplingModes.monkhorst, num_kpts=0, kpts=((1, 1, 1),), kpt_shifts=(0.5, 0.5, 0.5), kpts_weights=None, use_symmetries=True, use_time_reversal=True, chksymbreak=None, comment=None)[source]
                                                                  +class KSampling(mode=KSamplingModes.monkhorst, num_kpts=0, kpts=((1, 1, 1),), kpt_shifts=(0.5, 0.5, 0.5), kpts_weights=None, use_symmetries=True, use_time_reversal=True, chksymbreak=None, comment=None)[source]

                                                                  Bases: pymatgen.io.abinit.abiobjects.AbivarAble, monty.json.MSONable

                                                                  Input variables defining the K-point sampling.

                                                                  Highly flexible constructor for KSampling objects. The flexibility comes @@ -354,13 +354,13 @@

                                                                  -as_dict()[source]
                                                                  +as_dict()[source]

                                                                  Convert object to dict.

                                                                  -classmethod automatic_density(structure, kppa, chksymbreak=None, use_symmetries=True, use_time_reversal=True, shifts=(0.5, 0.5, 0.5))[source]
                                                                  +classmethod automatic_density(structure, kppa, chksymbreak=None, use_symmetries=True, use_time_reversal=True, shifts=(0.5, 0.5, 0.5))[source]

                                                                  Returns an automatic Kpoint object based on a structure and a kpoint density. Uses Gamma centered meshes for hexagonal cells and Monkhorst-Pack grids otherwise.

                                                                  @@ -380,19 +380,19 @@
                                                                  -classmethod explicit_path(ndivsm, kpath_bounds)[source]
                                                                  +classmethod explicit_path(ndivsm, kpath_bounds)[source]

                                                                  See _path for the meaning of the variables

                                                                  -classmethod from_dict(d)[source]
                                                                  +classmethod from_dict(d)[source]

                                                                  Build object from dict.

                                                                  -classmethod gamma_centered(kpts=(1, 1, 1), use_symmetries=True, use_time_reversal=True)[source]
                                                                  +classmethod gamma_centered(kpts=(1, 1, 1), use_symmetries=True, use_time_reversal=True)[source]

                                                                  Convenient static constructor for an automatic Gamma centered Kpoint grid.

                                                                  Parameters
                                                                  @@ -412,19 +412,19 @@
                                                                  -classmethod gamma_only()[source]
                                                                  +classmethod gamma_only()[source]

                                                                  Gamma-only sampling

                                                                  -property is_homogeneous[source]
                                                                  +property is_homogeneous[source]

                                                                  Homogeneous sampling.

                                                                  -classmethod monkhorst(ngkpt, shiftk=(0.5, 0.5, 0.5), chksymbreak=None, use_symmetries=True, use_time_reversal=True, comment=None)[source]
                                                                  +classmethod monkhorst(ngkpt, shiftk=(0.5, 0.5, 0.5), chksymbreak=None, use_symmetries=True, use_time_reversal=True, comment=None)[source]

                                                                  Convenient static constructor for a Monkhorst-Pack mesh.

                                                                  Parameters
                                                                  @@ -443,7 +443,7 @@
                                                                  -classmethod monkhorst_automatic(structure, ngkpt, use_symmetries=True, use_time_reversal=True, chksymbreak=None, comment=None)[source]
                                                                  +classmethod monkhorst_automatic(structure, ngkpt, use_symmetries=True, use_time_reversal=True, chksymbreak=None, comment=None)[source]

                                                                  Convenient static constructor for an automatic Monkhorst-Pack mesh.

                                                                  Parameters
                                                                  @@ -462,13 +462,13 @@
                                                                  -classmethod path_from_structure(ndivsm, structure)[source]
                                                                  +classmethod path_from_structure(ndivsm, structure)[source]

                                                                  See _path for the meaning of the variables

                                                                  -to_abivars()[source]
                                                                  +to_abivars()[source]

                                                                  Dictionary with Abinit variables.

                                                                  @@ -476,29 +476,29 @@
                                                                  -class KSamplingModes(value)[source]
                                                                  +class KSamplingModes(value)[source]

                                                                  Bases: enum.Enum

                                                                  Enum if the different samplings of the BZ.

                                                                  -automatic = 3[source]
                                                                  +automatic = 3[source]
                                                                  -monkhorst = 1[source]
                                                                  +monkhorst = 1[source]
                                                                  -path = 2[source]
                                                                  +path = 2[source]
                                                                  -class ModelDielectricFunction(mdf_epsinf)[source]
                                                                  +class ModelDielectricFunction(mdf_epsinf)[source]

                                                                  Bases: pymatgen.io.abinit.abiobjects.AbivarAble

                                                                  Model dielectric function used for BSE calculation

                                                                  @@ -508,7 +508,7 @@
                                                                  -to_abivars()[source]
                                                                  +to_abivars()[source]

                                                                  Return dictionary with abinit variables.

                                                                  @@ -516,7 +516,7 @@
                                                                  -class PPModel(mode='godby', plasmon_freq=None)[source]
                                                                  +class PPModel(mode='godby', plasmon_freq=None)[source]

                                                                  Bases: pymatgen.io.abinit.abiobjects.AbivarAble, monty.json.MSONable

                                                                  Parameters defining the plasmon-pole technique. The common way to instantiate a PPModel object is via the class method PPModel.as_ppmodel(string)

                                                                  @@ -530,13 +530,13 @@
                                                                  -as_dict()[source]
                                                                  +as_dict()[source]

                                                                  Convert object to dictionary.

                                                                  -classmethod as_ppmodel(obj)[source]
                                                                  +classmethod as_ppmodel(obj)[source]

                                                                  Constructs an instance of PPModel from obj.

                                                                  Accepts obj in the form:
                                                                    @@ -549,19 +549,19 @@
                                                                    -static from_dict(d)[source]
                                                                    +static from_dict(d)[source]

                                                                    Build object from dictionary.

                                                                    -classmethod get_noppmodel()[source]
                                                                    +classmethod get_noppmodel()[source]

                                                                    Calculation without plasmon-pole model.

                                                                    -to_abivars()[source]
                                                                    +to_abivars()[source]

                                                                    Return dictionary with Abinit variables.

                                                                    @@ -569,39 +569,39 @@
                                                                    -class PPModelModes(value)[source]
                                                                    +class PPModelModes(value)[source]

                                                                    Bases: enum.Enum

                                                                    Different kind of plasmon-pole models.

                                                                    -farid = 4[source]
                                                                    +farid = 4[source]
                                                                    -godby = 1[source]
                                                                    +godby = 1[source]
                                                                    -hybersten = 2[source]
                                                                    +hybersten = 2[source]
                                                                    -linden = 3[source]
                                                                    +linden = 3[source]
                                                                    -noppmodel = 0[source]
                                                                    +noppmodel = 0[source]
                                                                    -class RelaxationMethod(*args, **kwargs)[source]
                                                                    +class RelaxationMethod(*args, **kwargs)[source]

                                                                    Bases: pymatgen.io.abinit.abiobjects.AbivarAble, monty.json.MSONable

                                                                    This object stores the variables for the (constrained) structural optimization ionmov and optcell specify the type of relaxation. @@ -612,53 +612,53 @@

                                                                    Initialize object.

                                                                    -IONMOV_DEFAULT = 3[source]
                                                                    +IONMOV_DEFAULT = 3[source]
                                                                    -OPTCELL_DEFAULT = 2[source]
                                                                    +OPTCELL_DEFAULT = 2[source]
                                                                    -as_dict()[source]
                                                                    +as_dict()[source]

                                                                    Convert object to dict.

                                                                    -classmethod atoms_and_cell(atoms_constraints=None)[source]
                                                                    +classmethod atoms_and_cell(atoms_constraints=None)[source]

                                                                    Relax atomic positions as well as unit cell

                                                                    -classmethod atoms_only(atoms_constraints=None)[source]
                                                                    +classmethod atoms_only(atoms_constraints=None)[source]

                                                                    Relax atomic positions, keep unit cell fixed.

                                                                    -classmethod from_dict(d)[source]
                                                                    +classmethod from_dict(d)[source]

                                                                    Build object from dictionary.

                                                                    -property move_atoms[source]
                                                                    +property move_atoms[source]

                                                                    True if atoms must be moved.

                                                                    -property move_cell[source]
                                                                    +property move_cell[source]

                                                                    True if lattice parameters must be optimized.

                                                                    -to_abivars()[source]
                                                                    +to_abivars()[source]

                                                                    Returns a dictionary with the abinit variables

                                                                    @@ -666,7 +666,7 @@
                                                                    -class Screening(ecuteps, nband, w_type='RPA', sc_mode='one_shot', hilbert=None, ecutwfn=None, inclvkb=2)[source]
                                                                    +class Screening(ecuteps, nband, w_type='RPA', sc_mode='one_shot', hilbert=None, ecutwfn=None, inclvkb=2)[source]

                                                                    Bases: pymatgen.io.abinit.abiobjects.AbivarAble

                                                                    This object defines the parameters used for the computation of the screening function.

                                                                    @@ -685,13 +685,13 @@
                                                                    -to_abivars()[source]
                                                                    +to_abivars()[source]

                                                                    Returns a dictionary with the abinit variables

                                                                    -property use_hilbert[source]
                                                                    +property use_hilbert[source]

                                                                    True if we are using the Hilbert transform method.

                                                                    @@ -699,7 +699,7 @@
                                                                    -class SelfEnergy(se_type, sc_mode, nband, ecutsigx, screening, gw_qprange=1, ppmodel=None, ecuteps=None, ecutwfn=None, gwpara=2)[source]
                                                                    +class SelfEnergy(se_type, sc_mode, nband, ecutsigx, screening, gw_qprange=1, ppmodel=None, ecuteps=None, ecutwfn=None, gwpara=2)[source]

                                                                    Bases: pymatgen.io.abinit.abiobjects.AbivarAble

                                                                    This object defines the parameters used for the computation of the self-energy.

                                                                    @@ -721,25 +721,25 @@
                                                                    -property gwcalctyp[source]
                                                                    +property gwcalctyp[source]

                                                                    Returns the value of the gwcalctyp input variable.

                                                                    -property symsigma[source]
                                                                    +property symsigma[source]

                                                                    1 if symmetries can be used to reduce the number of q-points.

                                                                    -to_abivars()[source]
                                                                    +to_abivars()[source]

                                                                    Returns a dictionary with the abinit variables.

                                                                    -property use_ppmodel[source]
                                                                    +property use_ppmodel[source]

                                                                    True if we are using the plasmon-pole approximation.

                                                                    @@ -747,20 +747,20 @@
                                                                    -class Smearing(occopt, tsmear)[source]
                                                                    +class Smearing(occopt, tsmear)[source]

                                                                    Bases: pymatgen.io.abinit.abiobjects.AbivarAble, monty.json.MSONable

                                                                    Variables defining the smearing technique. The preferred way to instantiate a Smearing object is via the class method Smearing.as_smearing(string)

                                                                    Build object with occopt and tsmear

                                                                    -as_dict()[source]
                                                                    +as_dict()[source]

                                                                    json friendly dict representation of Smearing

                                                                    -classmethod as_smearing(obj)[source]
                                                                    +classmethod as_smearing(obj)[source]

                                                                    Constructs an instance of Smearing from obj. Accepts obj in the form:

                                                                      @@ -774,25 +774,25 @@
                                                                      -static from_dict(d)[source]
                                                                      +static from_dict(d)[source]

                                                                      Build object from dict.

                                                                      -property mode[source]
                                                                      +property mode[source]

                                                                      String with smearing technique.

                                                                      -static nosmearing()[source]
                                                                      +static nosmearing()[source]

                                                                      Build object for calculations without smearing.

                                                                      -to_abivars()[source]
                                                                      +to_abivars()[source]

                                                                      Return dictionary with Abinit variables.

                                                                      @@ -800,7 +800,7 @@
                                                                      -class SpinMode(mode, nsppol, nspinor, nspden)[source]
                                                                      +class SpinMode(mode, nsppol, nspinor, nspden)[source]

                                                                      Bases: pymatgen.io.abinit.abiobjects.SpinMode, pymatgen.io.abinit.abiobjects.AbivarAble, monty.json.MSONable

                                                                      Different configurations of the electron density as implemented in abinit: One can use as_spinmode to construct the object via SpinMode.as_spinmode @@ -817,25 +817,25 @@

                                                                      Create new instance of SpinMode(mode, nsppol, nspinor, nspden)

                                                                      -as_dict()[source]
                                                                      +as_dict()[source]

                                                                      Convert object to dict.

                                                                      -classmethod as_spinmode(obj)[source]
                                                                      +classmethod as_spinmode(obj)[source]

                                                                      Converts obj into a SpinMode instance

                                                                      -classmethod from_dict(d)[source]
                                                                      +classmethod from_dict(d)[source]

                                                                      Build object from dict.

                                                                      -to_abivars()[source]
                                                                      +to_abivars()[source]

                                                                      Dictionary with Abinit input variables.

                                                                      @@ -843,7 +843,7 @@
                                                                      -contract(s)[source]
                                                                      +contract(s)[source] 
                                                                      >>> assert contract("1 1 1 2 2 3") == "3*1 2*2 1*3"
 >>> assert contract("1 1 3 2 3") == "2*1 1*3 1*2 1*3"
                                                                      @@ -852,7 +852,7 @@
                                                                      -lattice_from_abivars(cls=None, *args, **kwargs)[source]
                                                                      +lattice_from_abivars(cls=None, *args, **kwargs)[source]

                                                                      Returns a Lattice object from a dictionary with the Abinit variables acell and either rprim in Bohr or angdeg If acell is not given, the Abinit default is used i.e. [1,1,1] Bohr

                                                                      @@ -867,7 +867,7 @@
                                                                      -species_by_znucl(structure)[source]
                                                                      +species_by_znucl(structure)[source]

                                                                      Return list of unique specie found in structure ordered according to sites.

                                                                      Example

                                                                      Site0: 0.5 0 0 O @@ -877,7 +877,7 @@

                                                                      -structure_from_abivars(cls=None, *args, **kwargs)[source]
                                                                      +structure_from_abivars(cls=None, *args, **kwargs)[source]

                                                                      Build a Structure object from a dictionary with ABINIT variables.

                                                                      Parameters
                                                                      @@ -904,7 +904,7 @@
                                                                      -structure_to_abivars(structure, enforce_znucl=None, enforce_typat=None, **kwargs)[source]
                                                                      +structure_to_abivars(structure, enforce_znucl=None, enforce_typat=None, **kwargs)[source]

                                                                      Receives a structure and returns a dictionary with ABINIT variables.

                                                                      Parameters
                                                                      diff --git a/docs/pymatgen.io.abinit.abitimer.html b/docs/pymatgen.io.abinit.abitimer.html index 837c8ca4636..24234c3c58a 100644 --- a/docs/pymatgen.io.abinit.abitimer.html +++ b/docs/pymatgen.io.abinit.abitimer.html @@ -4,7 +4,7 @@ - pymatgen.io.abinit.abitimer module — pymatgen 2022.5.18 documentation + pymatgen.io.abinit.abitimer module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                      - 2022.5.18 + 2022.5.18.1
                                                                      @@ -120,7 +120,7 @@ It also provides tools to analyze and to visualize the parallel efficiency.

                                                                      -class AbinitTimer(sections, info, cpu_time, wall_time)[source]
                                                                      +class AbinitTimer(sections, info, cpu_time, wall_time)[source]

                                                                      Bases: object

                                                                      Container class storing the timing results.

                                                                      @@ -135,7 +135,7 @@
                                                                      -cpuwall_histogram(ax=None, **kwargs)[source]
                                                                      +cpuwall_histogram(ax=None, **kwargs)[source]

                                                                      Plot histogram with cpu- and wall-time on axis ax.

                                                                      Parameters
                                                                      @@ -188,44 +188,44 @@
                                                                      -get_dataframe(sort_key='wall_time', **kwargs)[source]
                                                                      +get_dataframe(sort_key='wall_time', **kwargs)[source]

                                                                      Return a pandas DataFrame with entries sorted according to sort_key.

                                                                      -get_section(section_name)[source]
                                                                      +get_section(section_name)[source]

                                                                      Return section associated to section_name.

                                                                      -get_values(keys)[source]
                                                                      +get_values(keys)[source]

                                                                      Return a list of values associated to a particular list of keys.

                                                                      -names_and_values(key, minval=None, minfract=None, sorted=True)[source]
                                                                      +names_and_values(key, minval=None, minfract=None, sorted=True)[source]

                                                                      Select the entries whose value[key] is >= minval or whose fraction[key] is >= minfract Return the names of the sections and the corresponding values.

                                                                      -property ncpus[source]
                                                                      +property ncpus[source]

                                                                      Total number of CPUs employed.

                                                                      -order_sections(key, reverse=True)[source]
                                                                      +order_sections(key, reverse=True)[source]

                                                                      Sort sections according to the value of key.

                                                                      -pie(key='wall_time', minfract=0.05, ax=None, **kwargs)[source]
                                                                      +pie(key='wall_time', minfract=0.05, ax=None, **kwargs)[source]

                                                                      Plot pie chart for this timer.

                                                                      Parameters
                                                                      @@ -282,7 +282,7 @@
                                                                      -scatter_hist(ax=None, **kwargs)[source]
                                                                      +scatter_hist(ax=None, **kwargs)[source]

                                                                      Scatter plot + histogram.

                                                                      Parameters
                                                                      @@ -335,25 +335,25 @@
                                                                      -sum_sections(keys)[source]
                                                                      +sum_sections(keys)[source]

                                                                      Sum value of keys.

                                                                      -to_csv(fileobj=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)[source]
                                                                      +to_csv(fileobj=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)[source]

                                                                      Write data on file fileobj using CSV format.

                                                                      -to_table(sort_key='wall_time', stop=None)[source]
                                                                      +to_table(sort_key='wall_time', stop=None)[source]

                                                                      Return a table (list of lists) with timer data

                                                                      -totable(sort_key='wall_time', stop=None)[source]
                                                                      +totable(sort_key='wall_time', stop=None)[source]

                                                                      Return a table (list of lists) with timer data

                                                                      @@ -361,7 +361,7 @@
                                                                      -class AbinitTimerParser[source]
                                                                      +class AbinitTimerParser[source]

                                                                      Bases: collections.abc.Iterable

                                                                      Responsible for parsing a list of output files, extracting the timing results and analyzing the results. @@ -376,36 +376,36 @@

                                                                      Initialize object.

                                                                      -BEGIN_TAG = '-<BEGIN_TIMER'[source]
                                                                      +BEGIN_TAG = '-<BEGIN_TIMER'[source]
                                                                      -END_TAG = '-<END_TIMER>'[source]
                                                                      +END_TAG = '-<END_TIMER>'[source]
                                                                      -Error[source]
                                                                      +Error[source]

                                                                      alias of pymatgen.io.abinit.abitimer.AbinitTimerParserError

                                                                      -property filenames[source]
                                                                      +property filenames[source]

                                                                      List of files that have been parsed successfully.

                                                                      -get_sections(section_name)[source]
                                                                      +get_sections(section_name)[source]

                                                                      Return the list of sections stored in self.timers() given section_name A fake section is returned if the timer does not have section_name.

                                                                      -parse(filenames)[source]
                                                                      +parse(filenames)[source]

                                                                      Read and parse a filename or a list of filenames. Files that cannot be opened are ignored. A single filename may also be given.

                                                                      Return: list of successfully read files.

                                                                      @@ -413,20 +413,20 @@
                                                                      -pefficiency()[source]
                                                                      +pefficiency()[source]

                                                                      Analyze the parallel efficiency.

                                                                      Return: ParallelEfficiency object.

                                                                      -plot_all(show=True, **kwargs)[source]
                                                                      +plot_all(show=True, **kwargs)[source]

                                                                      Call all plot methods provided by the parser.

                                                                      -plot_efficiency(key='wall_time', what='good+bad', nmax=5, ax=None, **kwargs)[source]
                                                                      +plot_efficiency(key='wall_time', what='good+bad', nmax=5, ax=None, **kwargs)[source]

                                                                      Plot the parallel efficiency

                                                                      Parameters
                                                                      @@ -508,7 +508,7 @@
                                                                      -plot_pie(key='wall_time', minfract=0.05, **kwargs)[source]
                                                                      +plot_pie(key='wall_time', minfract=0.05, **kwargs)[source]

                                                                      Plot pie charts of the different timers.

                                                                      Parameters
                                                                      @@ -566,7 +566,7 @@
                                                                      -plot_stacked_hist(key='wall_time', nmax=5, ax=None, **kwargs)[source]
                                                                      +plot_stacked_hist(key='wall_time', nmax=5, ax=None, **kwargs)[source]

                                                                      Plot stacked histogram of the different timers.

                                                                      Parameters
                                                                      @@ -627,26 +627,26 @@
                                                                      -section_names(ordkey='wall_time')[source]
                                                                      +section_names(ordkey='wall_time')[source]

                                                                      Return the names of sections ordered by ordkey. For the time being, the values are taken from the first timer.

                                                                      -summarize(**kwargs)[source]
                                                                      +summarize(**kwargs)[source]

                                                                      Return pandas DataFrame with the most important results stored in the timers.

                                                                      -timers(filename=None, mpi_rank='0')[source]
                                                                      +timers(filename=None, mpi_rank='0')[source]

                                                                      Return the list of timers associated to the given filename and MPI rank mpi_rank.

                                                                      -classmethod walk(top='.', ext='.abo')[source]
                                                                      +classmethod walk(top='.', ext='.abo')[source]

                                                                      Scan directory tree starting from top, look for files with extension ext and parse timing data.

                                                                      @@ -661,14 +661,14 @@
                                                                      -exception AbinitTimerParserError[source]
                                                                      +exception AbinitTimerParserError[source]

                                                                      Bases: Exception

                                                                      Errors raised by AbinitTimerParser

                                                                      -class AbinitTimerSection(name, cpu_time, cpu_fract, wall_time, wall_fract, ncalls, gflops)[source]
                                                                      +class AbinitTimerSection(name, cpu_time, cpu_fract, wall_time, wall_fract, ncalls, gflops)[source]

                                                                      Bases: object

                                                                      Record with the timing results associated to a section of code.

                                                                      @@ -686,40 +686,40 @@
                                                                      -FIELDS = ('name', 'wall_time', 'wall_fract', 'cpu_time', 'cpu_fract', 'ncalls', 'gflops')[source]
                                                                      +FIELDS = ('name', 'wall_time', 'wall_fract', 'cpu_time', 'cpu_fract', 'ncalls', 'gflops')[source]
                                                                      -NUMERIC_FIELDS = ['wall_time', 'wall_fract', 'cpu_time', 'cpu_fract', 'ncalls', 'gflops'][source]
                                                                      +NUMERIC_FIELDS = ['wall_time', 'wall_fract', 'cpu_time', 'cpu_fract', 'ncalls', 'gflops'][source]
                                                                      -STR_FIELDS = ['name'][source]
                                                                      +STR_FIELDS = ['name'][source]
                                                                      -classmethod fake()[source]
                                                                      +classmethod fake()[source]

                                                                      Return a fake section. Mainly used to fill missing entries if needed.

                                                                      -to_csvline(with_header=False)[source]
                                                                      +to_csvline(with_header=False)[source]

                                                                      Return a string with data in CSV format. Add header if with_header

                                                                      -to_dict()[source]
                                                                      +to_dict()[source]

                                                                      Convert object to dictionary.

                                                                      -to_tuple()[source]
                                                                      +to_tuple()[source]

                                                                      Convert object to tuple.

                                                                      @@ -727,7 +727,7 @@
                                                                      -class ParallelEfficiency(filenames, ref_idx, *args, **kwargs)[source]
                                                                      +class ParallelEfficiency(filenames, ref_idx, *args, **kwargs)[source]

                                                                      Bases: dict

                                                                      Store results concerning the parallel efficiency of the job.

                                                                      @@ -740,19 +740,19 @@
                                                                      -bad_sections(key='wall_time', criterion='mean', nmax=5)[source]
                                                                      +bad_sections(key='wall_time', criterion='mean', nmax=5)[source]

                                                                      Return first nmax sections with worst value of key key using criterion criterion.

                                                                      -good_sections(key='wall_time', criterion='mean', nmax=5)[source]
                                                                      +good_sections(key='wall_time', criterion='mean', nmax=5)[source]

                                                                      Return first nmax sections with best value of key key using criterion criterion.

                                                                      -totable(stop=None, reverse=True)[source]
                                                                      +totable(stop=None, reverse=True)[source]

                                                                      Return table (list of lists) with timing results.

                                                                      Parameters
                                                                      @@ -768,7 +768,7 @@
                                                                      -alternate(*iterables)[source]
                                                                      +alternate(*iterables)[source]

                                                                      [a[0], b[0], … , a[1], b[1], …, a[n], b[n] …] >>> alternate([1,4], [2,5], [3,6]) [1, 2, 3, 4, 5, 6]

                                                                      diff --git a/docs/pymatgen.io.abinit.html b/docs/pymatgen.io.abinit.html index 178e869b9ef..8ecfcdb1a93 100644 --- a/docs/pymatgen.io.abinit.html +++ b/docs/pymatgen.io.abinit.html @@ -4,7 +4,7 @@ - pymatgen.io.abinit package — pymatgen 2022.5.18 documentation + pymatgen.io.abinit package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                      - 2022.5.18 + 2022.5.18.1
                                                                      diff --git a/docs/pymatgen.io.abinit.inputs.html b/docs/pymatgen.io.abinit.inputs.html index 105f2278121..55301b73997 100644 --- a/docs/pymatgen.io.abinit.inputs.html +++ b/docs/pymatgen.io.abinit.inputs.html @@ -4,7 +4,7 @@ - pymatgen.io.abinit.inputs module — pymatgen 2022.5.18 documentation + pymatgen.io.abinit.inputs module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                      - 2022.5.18 + 2022.5.18.1
                                                                      @@ -121,18 +121,18 @@ For a more comprehensive implementation, use the AbinitInput object provided by AbiPy.

                                                                      -class AbstractInput[source]
                                                                      +class AbstractInput[source]

                                                                      Bases: collections.abc.MutableMapping

                                                                      Abstract class defining the methods that must be implemented by Input objects.

                                                                      -deepcopy()[source]
                                                                      +deepcopy()[source]

                                                                      Deep copy of the input.

                                                                      -pop_vars(keys)[source]
                                                                      +pop_vars(keys)[source]

                                                                      Remove the variables listed in keys. Return dictionary with the variables that have been removed. Unlike remove_vars, no exception is raised if the variables are not in the input.

                                                                      @@ -147,7 +147,7 @@
                                                                      -remove_vars(keys, strict=True)[source]
                                                                      +remove_vars(keys, strict=True)[source]

                                                                      Remove the variables listed in keys. Return dictionary with the variables that have been removed.

                                                                      @@ -162,7 +162,7 @@
                                                                      -set_vars(*args, **kwargs)[source]
                                                                      +set_vars(*args, **kwargs)[source]

                                                                      Set the value of the variables. Return dict with the variables added to the input.

                                                                      Example

                                                                      @@ -171,7 +171,7 @@
                                                                      -set_vars_ifnotin(*args, **kwargs)[source]
                                                                      +set_vars_ifnotin(*args, **kwargs)[source]

                                                                      Set the value of the variables but only if the variable is not already present. Return dict with the variables added to the input.

                                                                      Example

                                                                      @@ -180,19 +180,19 @@
                                                                      -abstract to_string()[source]
                                                                      +abstract to_string()[source]

                                                                      Returns a string with the input.

                                                                      -abstract property vars[source]
                                                                      +abstract property vars[source]

                                                                      Dictionary with the input variables. Used to implement dict-like interface.

                                                                      -write(filepath='run.abi')[source]
                                                                      +write(filepath='run.abi')[source]

                                                                      Write the input file to file to filepath.

                                                                      @@ -200,7 +200,7 @@
                                                                      -class BasicAbinitInput(structure, pseudos, pseudo_dir=None, comment=None, abi_args=None, abi_kwargs=None)[source]
                                                                      +class BasicAbinitInput(structure, pseudos, pseudo_dir=None, comment=None, abi_args=None, abi_kwargs=None)[source]

                                                                      Bases: pymatgen.io.abinit.inputs.AbstractInput, monty.json.MSONable

                                                                      This object stores the ABINIT variables for a single dataset.

                                                                      @@ -221,50 +221,50 @@
                                                                      -Error[source]
                                                                      +Error[source]

                                                                      alias of pymatgen.io.abinit.inputs.BasicAbinitInputError

                                                                      -add_abiobjects(*abi_objects)[source]
                                                                      +add_abiobjects(*abi_objects)[source]

                                                                      This function receive a list of AbiVarable objects and add the corresponding variables to the input.

                                                                      -as_dict()[source]
                                                                      +as_dict()[source]

                                                                      JSON interface used in pymatgen for easier serialization.

                                                                      -property comment[source]
                                                                      +property comment[source]

                                                                      Optional string with comment. None if comment is not set.

                                                                      -classmethod from_dict(d)[source]
                                                                      +classmethod from_dict(d)[source]

                                                                      JSON interface used in pymatgen for easier serialization.

                                                                      -property isnc[source]
                                                                      +property isnc[source]

                                                                      True if norm-conserving calculation.

                                                                      -property ispaw[source]
                                                                      +property ispaw[source]

                                                                      True if PAW calculation.

                                                                      -new_with_vars(*args, **kwargs)[source]
                                                                      +new_with_vars(*args, **kwargs)[source]

                                                                      Return a new input with the given variables.

                                                                      Example

                                                                      new = input.new_with_vars(ecut=20)

                                                                      @@ -272,39 +272,39 @@
                                                                      -pop_irdvars()[source]
                                                                      +pop_irdvars()[source]

                                                                      Remove all the ird* variables present in self. Return dictionary with the variables that have been removed.

                                                                      -pop_tolerances()[source]
                                                                      +pop_tolerances()[source]

                                                                      Remove all the tolerance variables present in self. Return dictionary with the variables that have been removed.

                                                                      -property pseudos[source]
                                                                      +property pseudos[source]

                                                                      List of |Pseudo| objects.

                                                                      -set_comment(comment)[source]
                                                                      +set_comment(comment)[source]

                                                                      Set a comment to be included at the top of the file.

                                                                      -set_gamma_sampling()[source]
                                                                      +set_gamma_sampling()[source]

                                                                      Gamma-only sampling of the BZ.

                                                                      -set_kmesh(ngkpt, shiftk, kptopt=1)[source]
                                                                      +set_kmesh(ngkpt, shiftk, kptopt=1)[source]

                                                                      Set the variables for the sampling of the BZ.

                                                                      Parameters
                                                                      @@ -319,7 +319,7 @@
                                                                      -set_kpath(ndivsm, kptbounds=None, iscf=- 2)[source]
                                                                      +set_kpath(ndivsm, kptbounds=None, iscf=- 2)[source]

                                                                      Set the variables for the computation of the electronic band structure.

                                                                      Parameters
                                                                      @@ -334,7 +334,7 @@
                                                                      -set_spin_mode(spin_mode)[source]
                                                                      +set_spin_mode(spin_mode)[source]

                                                                      Set the variables used to the treat the spin degree of freedom. Return dictionary with the variables that have been removed.

                                                                      @@ -353,19 +353,19 @@
                                                                      -set_structure(structure)[source]
                                                                      +set_structure(structure)[source]

                                                                      Set structure.

                                                                      -property structure[source]
                                                                      +property structure[source]

                                                                      The |Structure| object associated to this input.

                                                                      -to_string(post=None, with_structure=True, with_pseudos=True, exclude=None)[source]
                                                                      +to_string(post=None, with_structure=True, with_pseudos=True, exclude=None)[source]

                                                                      String representation.

                                                                      Parameters
                                                                      @@ -387,7 +387,7 @@
                                                                      -property vars[source]
                                                                      +property vars[source]

                                                                      Dictionary with variables.

                                                                      @@ -395,14 +395,14 @@
                                                                      -exception BasicAbinitInputError[source]
                                                                      +exception BasicAbinitInputError[source]

                                                                      Bases: Exception

                                                                      Base error class for exceptions raised by BasicAbinitInput.

                                                                      -class BasicMultiDataset(structure, pseudos, pseudo_dir='', ndtset=1)[source]
                                                                      +class BasicMultiDataset(structure, pseudos, pseudo_dir='', ndtset=1)[source]

                                                                      Bases: object

                                                                      This object is essentially a list of BasicAbinitInput objects. that provides an easy-to-use interface to apply global changes to the @@ -455,85 +455,85 @@

                                                                      -Error[source]
                                                                      +Error[source]

                                                                      alias of pymatgen.io.abinit.inputs.BasicAbinitInputError

                                                                      -addnew_from(dtindex)[source]
                                                                      +addnew_from(dtindex)[source]

                                                                      Add a new entry in the multidataset by copying the input with index dtindex.

                                                                      -append(abinit_input)[source]
                                                                      +append(abinit_input)[source]

                                                                      Add a |BasicAbinitInput| to the list.

                                                                      -deepcopy()[source]
                                                                      +deepcopy()[source]

                                                                      Deep copy of the BasicMultiDataset.

                                                                      -extend(abinit_inputs)[source]
                                                                      +extend(abinit_inputs)[source]

                                                                      Extends self with a list of |BasicAbinitInput| objects.

                                                                      -classmethod from_inputs(inputs)[source]
                                                                      +classmethod from_inputs(inputs)[source]

                                                                      Build object from a list of BasicAbinitInput objects.

                                                                      -property has_same_structures[source]
                                                                      +property has_same_structures[source]

                                                                      True if all inputs in BasicMultiDataset are equal.

                                                                      -property isnc[source]
                                                                      +property isnc[source]

                                                                      True if norm-conserving calculation.

                                                                      -property ispaw[source]
                                                                      +property ispaw[source]

                                                                      True if PAW calculation.

                                                                      -property ndtset[source]
                                                                      +property ndtset[source]

                                                                      Number of inputs in self.

                                                                      -property pseudos[source]
                                                                      +property pseudos[source]

                                                                      Pseudopotential objects.

                                                                      -classmethod replicate_input(input, ndtset)[source]
                                                                      +classmethod replicate_input(input, ndtset)[source]

                                                                      Construct a multidataset with ndtset from the BasicAbinitInput input.

                                                                      -split_datasets()[source]
                                                                      +split_datasets()[source]

                                                                      Return list of |BasicAbinitInput| objects..

                                                                      -to_string(with_pseudos=True)[source]
                                                                      +to_string(with_pseudos=True)[source]

                                                                      String representation i.e. the input file read by Abinit.

                                                                      Parameters
                                                                      @@ -544,7 +544,7 @@
                                                                      -write(filepath='run.abi')[source]
                                                                      +write(filepath='run.abi')[source]

                                                                      Write ndset input files to disk. The name of the file is constructed from the dataset index e.g. run0.abi

                                                                      @@ -553,7 +553,7 @@
                                                                      -class ShiftMode(value)[source]
                                                                      +class ShiftMode(value)[source]

                                                                      Bases: enum.Enum

                                                                      Class defining the mode to be used for the shifts. G: Gamma centered @@ -565,27 +565,27 @@

                                                                    -GammaCentered = 'G'[source]
                                                                    +GammaCentered = 'G'[source]
                                                                    -MonkhorstPack = 'M'[source]
                                                                    +MonkhorstPack = 'M'[source]
                                                                    -OneSymmetric = 'O'[source]
                                                                    +OneSymmetric = 'O'[source]
                                                                    -Symmetric = 'S'[source]
                                                                    +Symmetric = 'S'[source]
                                                                    -classmethod from_object(obj)[source]
                                                                    +classmethod from_object(obj)[source]

                                                                    Returns an instance of ShiftMode based on the type of object passed. Converts strings to ShiftMode depending on the iniital letter of the string. G for GammaCenterd, M for MonkhorstPack, S for Symmetric, O for OneSymmetric. @@ -596,7 +596,7 @@

                                                                    -as_structure(obj)[source]
                                                                    +as_structure(obj)[source]

                                                                    Convert obj into a Structure. Accepts:

                                                                      @@ -609,7 +609,7 @@
                                                                      -calc_shiftk(structure, symprec=0.01, angle_tolerance=5)[source]
                                                                      +calc_shiftk(structure, symprec=0.01, angle_tolerance=5)[source]

                                                                      Find the values of shiftk and nshiftk appropriated for the sampling of the Brillouin zone.

                                                                      When the primitive vectors of the lattice do NOT form a FCC or a BCC lattice, the usual (shifted) Monkhorst-Pack grids are formed by using nshiftk=1 and shiftk 0.5 0.5 0.5 . @@ -658,7 +658,7 @@

                                                                      -ebands_input(structure, pseudos, kppa=None, nscf_nband=None, ndivsm=15, ecut=None, pawecutdg=None, scf_nband=None, accuracy='normal', spin_mode='polarized', smearing='fermi_dirac:0.1 eV', charge=0.0, scf_algorithm=None, dos_kppa=None)[source]
                                                                      +ebands_input(structure, pseudos, kppa=None, nscf_nband=None, ndivsm=15, ecut=None, pawecutdg=None, scf_nband=None, accuracy='normal', spin_mode='polarized', smearing='fermi_dirac:0.1 eV', charge=0.0, scf_algorithm=None, dos_kppa=None)[source]

                                                                      Returns a |BasicMultiDataset| object for band structure calculations.

                                                                      Parameters
                                                                      @@ -688,7 +688,7 @@
                                                                      -gs_input(structure, pseudos, kppa=None, ecut=None, pawecutdg=None, scf_nband=None, accuracy='normal', spin_mode='polarized', smearing='fermi_dirac:0.1 eV', charge=0.0, scf_algorithm=None)[source]
                                                                      +gs_input(structure, pseudos, kppa=None, ecut=None, pawecutdg=None, scf_nband=None, accuracy='normal', spin_mode='polarized', smearing='fermi_dirac:0.1 eV', charge=0.0, scf_algorithm=None)[source]

                                                                      Returns a |BasicAbinitInput| for ground-state calculation.

                                                                      Parameters
                                                                      @@ -713,7 +713,7 @@
                                                                      -ion_ioncell_relax_input(structure, pseudos, kppa=None, nband=None, ecut=None, pawecutdg=None, accuracy='normal', spin_mode='polarized', smearing='fermi_dirac:0.1 eV', charge=0.0, scf_algorithm=None, shift_mode='Monkhorst-pack')[source]
                                                                      +ion_ioncell_relax_input(structure, pseudos, kppa=None, nband=None, ecut=None, pawecutdg=None, accuracy='normal', spin_mode='polarized', smearing='fermi_dirac:0.1 eV', charge=0.0, scf_algorithm=None, shift_mode='Monkhorst-pack')[source]

                                                                      Returns a |BasicMultiDataset| for a structural relaxation. The first dataset optmizes the atomic positions at fixed unit cell. The second datasets optimizes both ions and unit cell parameters.

                                                                      @@ -735,7 +735,7 @@
                                                                      -num_valence_electrons(structure, pseudos)[source]
                                                                      +num_valence_electrons(structure, pseudos)[source]

                                                                      Returns the number of valence electrons.

                                                                      Parameters
                                                                      diff --git a/docs/pymatgen.io.abinit.netcdf.html b/docs/pymatgen.io.abinit.netcdf.html index db526148c8f..173a37c4fc0 100644 --- a/docs/pymatgen.io.abinit.netcdf.html +++ b/docs/pymatgen.io.abinit.netcdf.html @@ -4,7 +4,7 @@ - pymatgen.io.abinit.netcdf module — pymatgen 2022.5.18 documentation + pymatgen.io.abinit.netcdf module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                      - 2022.5.18 + 2022.5.18.1
                                                                      @@ -119,39 +119,39 @@

                                                                      Wrapper for netCDF readers.

                                                                      -class ETSF_Reader(path)[source]
                                                                      +class ETSF_Reader(path)[source]

                                                                      Bases: pymatgen.io.abinit.netcdf.NetcdfReader

                                                                      This object reads data from a file written according to the ETSF-IO specifications.

                                                                      We assume that the netcdf file contains at least the crystallographic section.

                                                                      Open the Netcdf file specified by path (read mode).

                                                                      -chemical_symbols()[source]
                                                                      +chemical_symbols()[source]

                                                                      Chemical symbols char [number of atom species][symbol length].

                                                                      -read_abinit_hdr()[source]
                                                                      +read_abinit_hdr()[source]

                                                                      Read the variables associated to the Abinit header.

                                                                      Return AbinitHeader

                                                                      -read_abinit_xcfunc()[source]
                                                                      +read_abinit_xcfunc()[source]

                                                                      Read ixc from an Abinit file. Return XcFunc object.

                                                                      -read_structure(cls=<class 'pymatgen.core.structure.Structure'>)[source]
                                                                      +read_structure(cls=<class 'pymatgen.core.structure.Structure'>)[source]

                                                                      Returns the crystalline structure stored in the rootgrp.

                                                                      -typeidx_from_symbol(symbol)[source]
                                                                      +typeidx_from_symbol(symbol)[source]

                                                                      Returns the type index from the chemical symbol. Note python convention.

                                                                      @@ -159,14 +159,14 @@
                                                                      -class NO_DEFAULT[source]
                                                                      +class NO_DEFAULT[source]

                                                                      Bases: object

                                                                      Signal that read_value should raise an Error

                                                                      -class NetcdfReader(path)[source]
                                                                      +class NetcdfReader(path)[source]

                                                                      Bases: object

                                                                      Wraps and extends netCDF4.Dataset. Read only mode. Supports with statements.

                                                                      @@ -176,25 +176,25 @@

                                                                      Open the Netcdf file specified by path (read mode).

                                                                      -Error[source]
                                                                      +Error[source]

                                                                      alias of pymatgen.io.abinit.netcdf.NetcdfReaderError

                                                                      -close()[source]
                                                                      +close()[source]

                                                                      Close the file.

                                                                      -print_tree()[source]
                                                                      +print_tree()[source]

                                                                      Print all the groups in the file.

                                                                      -read_dimvalue(dimname, path='/', default=<class 'pymatgen.io.abinit.netcdf.NO_DEFAULT'>)[source]
                                                                      +read_dimvalue(dimname, path='/', default=<class 'pymatgen.io.abinit.netcdf.NO_DEFAULT'>)[source]

                                                                      Returns the value of a dimension.

                                                                      Parameters
                                                                      @@ -210,14 +210,14 @@
                                                                      -read_keys(keys, dict_cls=<class 'monty.collections.AttrDict'>, path='/')[source]
                                                                      +read_keys(keys, dict_cls=<class 'monty.collections.AttrDict'>, path='/')[source]

                                                                      Read a list of variables/dimensions from file. If a key is not present the corresponding entry in the output dictionary is set to None.

                                                                      -read_value(varname, path='/', cmode=None, default=<class 'pymatgen.io.abinit.netcdf.NO_DEFAULT'>)[source]
                                                                      +read_value(varname, path='/', cmode=None, default=<class 'pymatgen.io.abinit.netcdf.NO_DEFAULT'>)[source]

                                                                      Returns the values of variable with name varname in the group specified by path.

                                                                      Parameters
                                                                      @@ -238,19 +238,19 @@
                                                                      -read_variable(varname, path='/')[source]
                                                                      +read_variable(varname, path='/')[source]

                                                                      Returns the variable with name varname in the group specified by path.

                                                                      -read_varnames(path='/')[source]
                                                                      +read_varnames(path='/')[source]

                                                                      List of variable names stored in the group specified by path.

                                                                      -walk_tree(top=None)[source]
                                                                      +walk_tree(top=None)[source]

                                                                      Navigate all the groups in the file starting from top. If top is None, the root group is used.

                                                                      @@ -259,13 +259,13 @@
                                                                      -as_etsfreader(file)[source]
                                                                      +as_etsfreader(file)[source]

                                                                      Return an ETSF_Reader. Accepts filename or ETSF_Reader.

                                                                      -as_ncreader(file)[source]
                                                                      +as_ncreader(file)[source]

                                                                      Convert file into a NetcdfReader instance. Returns reader, closeit where closeit is set to True if we have to close the file before leaving the procedure.

                                                                      @@ -273,7 +273,7 @@
                                                                      -structure_from_ncdata(ncdata, site_properties=None, cls=<class 'pymatgen.core.structure.Structure'>)[source]
                                                                      +structure_from_ncdata(ncdata, site_properties=None, cls=<class 'pymatgen.core.structure.Structure'>)[source]

                                                                      Reads and returns a pymatgen structure from a NetCDF file containing crystallographic data in the ETSF-IO format.

                                                                      diff --git a/docs/pymatgen.io.abinit.pseudos.html b/docs/pymatgen.io.abinit.pseudos.html index 412e395629e..d9a437a5992 100644 --- a/docs/pymatgen.io.abinit.pseudos.html +++ b/docs/pymatgen.io.abinit.pseudos.html @@ -4,7 +4,7 @@ - pymatgen.io.abinit.pseudos module — pymatgen 2022.5.18 documentation + pymatgen.io.abinit.pseudos module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                      - 2022.5.18 + 2022.5.18.1
                                                                      @@ -120,31 +120,31 @@ pseudopotentials used in Abinit, and a parser to instantiate pseudopotential objects..

                                                                      -class Pseudo[source]
                                                                      +class Pseudo[source]

                                                                      Bases: monty.json.MSONable

                                                                      Abstract base class defining the methods that must be implemented by the concrete pseudopotential sub-classes.

                                                                      -abstract property Z[source]
                                                                      +abstract property Z[source]

                                                                      The atomic number of the atom.

                                                                      -abstract property Z_val[source]
                                                                      +abstract property Z_val[source]

                                                                      Valence charge.

                                                                      -as_dict(**kwargs)[source]
                                                                      +as_dict(**kwargs)[source]

                                                                      Return dictionary for MSONable protocol.

                                                                      -classmethod as_pseudo(obj)[source]
                                                                      +classmethod as_pseudo(obj)[source]

                                                                      Convert obj into a pseudo. Accepts:

                                                                        @@ -156,7 +156,7 @@
                                                                        -as_tmpfile(tmpdir=None)[source]
                                                                        +as_tmpfile(tmpdir=None)[source]

                                                                        Copy the pseudopotential to a temporary a file and returns a new pseudopotential object. Useful for unit tests in which we have to change the content of the file.

                                                                        @@ -169,43 +169,43 @@
                                                                        -property basename[source]
                                                                        +property basename[source]

                                                                        File basename.

                                                                        -compute_md5()[source]
                                                                        +compute_md5()[source]

                                                                        Compute and erturn MD5 hash value.

                                                                        -property djrepo_path[source]
                                                                        +property djrepo_path[source]

                                                                        The path of the djrepo file. None if file does not exist.

                                                                        -property element[source]
                                                                        +property element[source]

                                                                        Pymatgen Element.

                                                                        -property filepath[source]
                                                                        +property filepath[source]

                                                                        Absolute path to pseudopotential file.

                                                                        -classmethod from_dict(d)[source]
                                                                        +classmethod from_dict(d)[source]

                                                                        Build instance from dictionary (MSONable protocol).

                                                                        -static from_file(filename)[source]
                                                                        +static from_file(filename)[source]

                                                                        Build an instance of a concrete Pseudo subclass from filename. Note: the parser knows the concrete class that should be instantiated Client code should rely on the abstract interface provided by Pseudo.

                                                                        @@ -213,19 +213,19 @@
                                                                        -property has_dojo_report[source]
                                                                        +property has_dojo_report[source]

                                                                        True if the pseudo has an associated DOJO_REPORT section.

                                                                        -property has_hints[source]
                                                                        +property has_hints[source]

                                                                        True if self provides hints on the cutoff energy.

                                                                        -hint_for_accuracy(accuracy='normal')[source]
                                                                        +hint_for_accuracy(accuracy='normal')[source]

                                                                        Returns a Hint object with the suggested value of ecut [Ha] and pawecutdg [Ha] for the given accuracy. ecut and pawecutdg are set to zero if no hint is available.

                                                                        @@ -238,37 +238,37 @@
                                                                        -property isnc[source]
                                                                        +property isnc[source]

                                                                        True if norm-conserving pseudopotential.

                                                                        -property ispaw[source]
                                                                        +property ispaw[source]

                                                                        True if PAW pseudopotential.

                                                                        -abstract property l_local[source]
                                                                        +abstract property l_local[source]

                                                                        Angular momentum used for the local part.

                                                                        -abstract property l_max[source]
                                                                        +abstract property l_max[source]

                                                                        Maximum angular momentum.

                                                                        -md5()[source]
                                                                        +md5()[source]

                                                                        MD5 hash value.

                                                                        -open_pspsfile(ecut=20, pawecutdg=None)[source]
                                                                        +open_pspsfile(ecut=20, pawecutdg=None)[source]

                                                                        Calls Abinit to compute the internal tables for the application of the pseudopotential part. Returns PspsFile object providing methods to plot and analyze the data or None if file is not found or it’s not readable.

                                                                        @@ -284,32 +284,32 @@
                                                                        -abstract property summary[source]
                                                                        +abstract property summary[source]

                                                                        String summarizing the most important properties.

                                                                        -abstract property supports_soc[source]
                                                                        +abstract property supports_soc[source]

                                                                        True if the pseudo can be used in a calculation with spin-orbit coupling. Base classes should provide a concrete implementation that computes this value.

                                                                        -property symbol[source]
                                                                        +property symbol[source]

                                                                        Element symbol.

                                                                        -to_string(verbose=0)[source]
                                                                        +to_string(verbose=0)[source]

                                                                        String representation.

                                                                        -property type[source]
                                                                        +property type[source]

                                                                        Type of pseudo.

                                                                        @@ -317,7 +317,7 @@
                                                                        -class PseudoTable(pseudos)[source]
                                                                        +class PseudoTable(pseudos)[source]

                                                                        Bases: collections.abc.Sequence, monty.json.MSONable

                                                                        Define the pseudopotentials from the element table. Individidual elements are accessed by name, symbol or atomic number.

                                                                        @@ -339,7 +339,7 @@
                                                                        -all_combinations_for_elements(element_symbols)[source]
                                                                        +all_combinations_for_elements(element_symbols)[source]

                                                                        Return a list with all the the possible combination of pseudos for the given list of element_symbols. Each item is a list of pseudopotential objects.

                                                                        @@ -351,37 +351,37 @@
                                                                        -property allnc[source]
                                                                        +property allnc[source]

                                                                        True if all pseudos are norm-conserving.

                                                                        -property allpaw[source]
                                                                        +property allpaw[source]

                                                                        True if all pseudos are PAW.

                                                                        -as_dict(**kwargs)[source]
                                                                        +as_dict(**kwargs)[source]

                                                                        Return dictionary for MSONable protocol.

                                                                        -classmethod as_table(items)[source]
                                                                        +classmethod as_table(items)[source]

                                                                        Return an instance of PseudoTable from the iterable items.

                                                                        -classmethod from_dict(d)[source]
                                                                        +classmethod from_dict(d)[source]

                                                                        Build instance from dictionary (MSONable protocol).

                                                                        -classmethod from_dir(top, exts=None, exclude_dirs='_*')[source]
                                                                        +classmethod from_dir(top, exts=None, exclude_dirs='_*')[source]

                                                                        Find all pseudos in the directory tree starting from top.

                                                                        Parameters
                                                                        @@ -398,7 +398,7 @@
                                                                        -get_pseudos_for_structure(structure)[source]
                                                                        +get_pseudos_for_structure(structure)[source]

                                                                        Return the list of Pseudo objects to be used for this Structure.

                                                                        Parameters
                                                                        @@ -415,13 +415,13 @@
                                                                        -is_complete(zmax=118)[source]
                                                                        +is_complete(zmax=118)[source]

                                                                        True if table is complete i.e. all elements with Z < zmax have at least on pseudopotential

                                                                        -print_table(stream=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, filter_function=None)[source]
                                                                        +print_table(stream=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, filter_function=None)[source]

                                                                        A pretty ASCII printer for the periodic table, based on some filter_function.

                                                                        Parameters
                                                                        @@ -437,7 +437,7 @@
                                                                        -pseudo_with_symbol(symbol, allow_multi=False)[source]
                                                                        +pseudo_with_symbol(symbol, allow_multi=False)[source]

                                                                        Return the pseudo with the given chemical symbol.

                                                                        Parameters
                                                                        @@ -455,7 +455,7 @@
                                                                        -pseudos_with_symbols(symbols)[source]
                                                                        +pseudos_with_symbols(symbols)[source]

                                                                        Return the pseudos with the given chemical symbols.

                                                                        Raises
                                                                        @@ -466,7 +466,7 @@
                                                                        -select(condition)[source]
                                                                        +select(condition)[source]

                                                                        Select only those pseudopotentials for which condition is True. Return new class:PseudoTable object.

                                                                        @@ -478,20 +478,20 @@
                                                                        -select_family(family)[source]
                                                                        +select_family(family)[source]

                                                                        Return PseudoTable with element belonging to the specified family, e.g. family=”alkaline”

                                                                        -select_rows(rows)[source]
                                                                        +select_rows(rows)[source]

                                                                        Return new class:PseudoTable object with pseudos in the given rows of the periodic table. rows can be either a int or a list of integers.

                                                                        -select_symbols(symbols, ret_list=False)[source]
                                                                        +select_symbols(symbols, ret_list=False)[source]

                                                                        Return a PseudoTable with the pseudopotentials with the given list of chemical symbols.

                                                                        Parameters
                                                                        @@ -506,13 +506,13 @@
                                                                        -sort_by_z()[source]
                                                                        +sort_by_z()[source]

                                                                        Return a new PseudoTable with pseudos sorted by Z

                                                                        -sorted(attrname, reverse=False)[source]
                                                                        +sorted(attrname, reverse=False)[source]

                                                                        Sort the table according to the value of attribute attrname.

                                                                        Returns
                                                                        @@ -526,19 +526,19 @@
                                                                        -to_table(filter_function=None)[source]
                                                                        +to_table(filter_function=None)[source]

                                                                        Return string with data in tabular form.

                                                                        -with_dojo_report()[source]
                                                                        +with_dojo_report()[source]

                                                                        Select pseudos containing the DOJO_REPORT section. Return new class:PseudoTable object.

                                                                        -property zlist[source]
                                                                        +property zlist[source]

                                                                        Ordered list with the atomic numbers available in the table.

                                                                        diff --git a/docs/pymatgen.io.abinit.variable.html b/docs/pymatgen.io.abinit.variable.html index 5e909168d2b..c09352ef697 100644 --- a/docs/pymatgen.io.abinit.variable.html +++ b/docs/pymatgen.io.abinit.variable.html @@ -4,7 +4,7 @@ - pymatgen.io.abinit.variable module — pymatgen 2022.5.18 documentation + pymatgen.io.abinit.variable module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                        - 2022.5.18 + 2022.5.18.1
                                                                        @@ -119,7 +119,7 @@

                                                                        Support for Abinit input variables.

                                                                        -class InputVariable(name, value, units='', valperline=3)[source]
                                                                        +class InputVariable(name, value, units='', valperline=3)[source]

                                                                        Bases: object

                                                                        An Abinit input variable.

                                                                        @@ -134,51 +134,51 @@
                                                                        -property basename[source]
                                                                        +property basename[source]

                                                                        Return the name trimmed of any dataset index.

                                                                        -property dataset[source]
                                                                        +property dataset[source]

                                                                        Return the dataset index in string form.

                                                                        -format_list(values, floatdecimal=0)[source]
                                                                        +format_list(values, floatdecimal=0)[source]

                                                                        Format a list of values into a string. The result might be spread among several lines.

                                                                        -static format_list2d(values, floatdecimal=0)[source]
                                                                        +static format_list2d(values, floatdecimal=0)[source]

                                                                        Format a list of lists.

                                                                        -static format_scalar(val, floatdecimal=0)[source]
                                                                        +static format_scalar(val, floatdecimal=0)[source]

                                                                        Format a single numerical value into a string with the appropriate number of decimal.

                                                                        -get_value()[source]
                                                                        +get_value()[source]

                                                                        Return the value.

                                                                        -property name[source]
                                                                        +property name[source]

                                                                        Name of the variable.

                                                                        -property units[source]
                                                                        +property units[source]

                                                                        Return the units.

                                                                        diff --git a/docs/pymatgen.io.adf.html b/docs/pymatgen.io.adf.html index 1181703910f..27c6294e609 100644 --- a/docs/pymatgen.io.adf.html +++ b/docs/pymatgen.io.adf.html @@ -4,7 +4,7 @@ - pymatgen.io.adf module — pymatgen 2022.5.18 documentation + pymatgen.io.adf module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                        - 2022.5.18 + 2022.5.18.1
                                                                        @@ -118,7 +118,7 @@

                                                                        IO for ADF files.

                                                                        -class AdfInput(task)[source]
                                                                        +class AdfInput(task)[source]

                                                                        Bases: object

                                                                        A basic ADF input file writer.

                                                                        Initialization method.

                                                                        @@ -129,7 +129,7 @@
                                                                        -write_file(molecule, inpfile)[source]
                                                                        +write_file(molecule, inpfile)[source]

                                                                        Write an ADF input file.

                                                                        Parameters
                                                                        @@ -145,14 +145,14 @@
                                                                        -exception AdfInputError[source]
                                                                        +exception AdfInputError[source]

                                                                        Bases: Exception

                                                                        The default error class for ADF.

                                                                        -class AdfKey(name, options=None, subkeys=None)[source]
                                                                        +class AdfKey(name, options=None, subkeys=None)[source]

                                                                        Bases: monty.json.MSONable

                                                                        The basic input unit for ADF. A key is a string of characters that does not contain a delimiter (blank, comma or equal sign). A key may have multiple @@ -174,7 +174,7 @@

                                                                        -add_option(option)[source]
                                                                        +add_option(option)[source]

                                                                        Add a new option to this key.

                                                                        Parameters
                                                                        @@ -189,7 +189,7 @@
                                                                        -add_subkey(subkey)[source]
                                                                        +add_subkey(subkey)[source]

                                                                        Add a new subkey to this key.

                                                                        Parameters
                                                                        @@ -202,18 +202,18 @@
                                                                        -as_dict()[source]
                                                                        +as_dict()[source]

                                                                        A JSON-serializable dict representation of self.

                                                                        -block_keys = {'A1FIT', 'ANALYTICALFREQ', 'ATOMS', 'BASIS', 'CHARGE', 'EXACTDENSITY', 'GEOMETRY', 'INTEGRATION', 'OCCUPATIONS', 'RELATIVISTIC', 'SAVE', 'SCF', 'SYMMETRY', 'TITLE', 'TOTALENERGY', 'UNITS', 'UNRESTRICTED', 'XC', 'ZLMFIT'}[source]
                                                                        +block_keys = {'A1FIT', 'ANALYTICALFREQ', 'ATOMS', 'BASIS', 'CHARGE', 'EXACTDENSITY', 'GEOMETRY', 'INTEGRATION', 'OCCUPATIONS', 'RELATIVISTIC', 'SAVE', 'SCF', 'SYMMETRY', 'TITLE', 'TOTALENERGY', 'UNITS', 'UNRESTRICTED', 'XC', 'ZLMFIT'}[source]
                                                                        -classmethod from_dict(d)[source]
                                                                        +classmethod from_dict(d)[source]

                                                                        Construct a MSONable AdfKey object from the JSON dict.

                                                                        Parameters
                                                                        @@ -230,7 +230,7 @@
                                                                        -static from_string(string)[source]
                                                                        +static from_string(string)[source]

                                                                        Construct an AdfKey object from the string.

                                                                        Parameters
                                                                        @@ -253,7 +253,7 @@
                                                                        -has_option(option)[source]
                                                                        +has_option(option)[source]

                                                                        Return True if the option is included in this key.

                                                                        Parameters
                                                                        @@ -270,7 +270,7 @@
                                                                        -has_subkey(subkey)[source]
                                                                        +has_subkey(subkey)[source]

                                                                        Return True if this AdfKey contains the given subkey.

                                                                        Parameters
                                                                        @@ -287,20 +287,20 @@
                                                                        -is_block_key()[source]
                                                                        +is_block_key()[source]

                                                                        Return True if this key is a block key.

                                                                        -property key[source]
                                                                        +property key[source]

                                                                        Return the name of this key. If this is a block key, the name will be converted to upper cases.

                                                                        -remove_option(option)[source]
                                                                        +remove_option(option)[source]

                                                                        Remove an option.

                                                                        Parameters
                                                                        @@ -314,7 +314,7 @@
                                                                        -remove_subkey(subkey)[source]
                                                                        +remove_subkey(subkey)[source]

                                                                        Remove the given subkey, if existed, from this AdfKey.

                                                                        Parameters
                                                                        @@ -325,12 +325,12 @@
                                                                        -sub_keys = {'AtomDepQuality'}[source]
                                                                        +sub_keys = {'AtomDepQuality'}[source]
                                                                        -to_json()[source]
                                                                        +to_json()[source]

                                                                        Return a json string representation of the MSONable AdfKey object.

                                                                        @@ -338,12 +338,12 @@
                                                                        -class AdfOutput(filename)[source]
                                                                        +class AdfOutput(filename)[source]

                                                                        Bases: object

                                                                        A basic ADF output file parser.

                                                                        -is_failed[source]
                                                                        +is_failed[source]

                                                                        True is the ADF job is terminated without success. Otherwise False.

                                                                        Type
                                                                        @@ -354,7 +354,7 @@
                                                                        -is_internal_crash[source]
                                                                        +is_internal_crash[source]

                                                                        True if the job is terminated with internal crash. Please read ‘TAPE13’ of the ADF manual for more detail.

                                                                        @@ -366,7 +366,7 @@
                                                                        -error[source]
                                                                        +error[source]

                                                                        The error description.

                                                                        Type
                                                                        @@ -377,7 +377,7 @@
                                                                        -run_type[source]
                                                                        +run_type[source]

                                                                        The RunType of this ADF job. Possible options are: ‘SinglePoint’, ‘GeometryOptimization’, ‘AnalyticalFreq’ and ‘NUmericalFreq’.

                                                                        @@ -389,7 +389,7 @@
                                                                        -final_energy[source]
                                                                        +final_energy[source]

                                                                        The final molecule energy (a.u).

                                                                        Type
                                                                        @@ -400,7 +400,7 @@
                                                                        -final_structure[source]
                                                                        +final_structure[source]

                                                                        The final structure of the molecule.

                                                                        Type
                                                                        @@ -411,7 +411,7 @@
                                                                        -energies[source]
                                                                        +energies[source]

                                                                        The energy of each cycle.

                                                                        Type
                                                                        @@ -422,7 +422,7 @@
                                                                        -structures[source]
                                                                        +structures[source]

                                                                        The structure of each cycle If geometry optimization is performed.

                                                                        Type
                                                                        @@ -433,7 +433,7 @@
                                                                        -frequencies[source]
                                                                        +frequencies[source]

                                                                        The frequencies of the molecule.

                                                                        Type
                                                                        @@ -444,7 +444,7 @@
                                                                        -normal_modes[source]
                                                                        +normal_modes[source]

                                                                        The normal modes of the molecule.

                                                                        Type
                                                                        @@ -455,7 +455,7 @@
                                                                        -freq_type[source]
                                                                        +freq_type[source]

                                                                        Either ‘Analytical’ or ‘Numerical’.

                                                                        Type
                                                                        @@ -474,14 +474,14 @@
                                                                        -exception AdfOutputError[source]
                                                                        +exception AdfOutputError[source]

                                                                        Bases: Exception

                                                                        The default error class for errors raised by AdfOutput.

                                                                        -class AdfTask(operation='energy', basis_set=None, xc=None, title='ADF_RUN', units=None, geo_subkeys=None, scf=None, other_directives=None)[source]
                                                                        +class AdfTask(operation='energy', basis_set=None, xc=None, title='ADF_RUN', units=None, geo_subkeys=None, scf=None, other_directives=None)[source]

                                                                        Bases: monty.json.MSONable

                                                                        Basic task for ADF. All settings in this class are independent of molecules.

                                                                        Notes

                                                                        @@ -504,13 +504,13 @@
                                                                        -as_dict()[source]
                                                                        +as_dict()[source]

                                                                        A JSON-serializable dict representation of self.

                                                                        -classmethod from_dict(d)[source]
                                                                        +classmethod from_dict(d)[source]

                                                                        Construct a MSONable AdfTask object from the JSON dict.

                                                                        Parameters
                                                                        @@ -527,42 +527,42 @@
                                                                        -static get_default_basis_set()[source]
                                                                        +static get_default_basis_set()[source]

                                                                        Returns: Default basis set

                                                                        -static get_default_geo()[source]
                                                                        +static get_default_geo()[source]

                                                                        Returns: ADFKey using default geometry.

                                                                        -static get_default_scf()[source]
                                                                        +static get_default_scf()[source]

                                                                        Returns: ADF using default SCF.

                                                                        -static get_default_units()[source]
                                                                        +static get_default_units()[source]

                                                                        Returns: Default units.

                                                                        -static get_default_xc()[source]
                                                                        +static get_default_xc()[source]

                                                                        Returns: ADFKey using default XC.

                                                                        -operations = {'energy': 'Evaluate the single point energy.', 'freq': 'Same as frequencies.', 'frequencies': 'Compute second derivatives and print out an analysis of molecular vibrations.', 'numerical_frequencies': 'Compute molecular frequencies using numerical method.', 'optimize': 'Minimize the energy by varying the molecular structure.'}[source]
                                                                        +operations = {'energy': 'Evaluate the single point energy.', 'freq': 'Same as frequencies.', 'frequencies': 'Compute second derivatives and print out an analysis of molecular vibrations.', 'numerical_frequencies': 'Compute molecular frequencies using numerical method.', 'optimize': 'Minimize the energy by varying the molecular structure.'}[source]
                                                                        -to_json()[source]
                                                                        +to_json()[source]

                                                                        Return a json string representation of the MSONable AdfTask object.

                                                                        @@ -570,7 +570,7 @@
                                                                        -is_numeric(s)[source]
                                                                        +is_numeric(s)[source]

                                                                        Return True is the string s is a numeric string.

                                                                        Parameters
                                                                        @@ -588,7 +588,7 @@
                                                                        -iterlines(s: str) → Generator[str, None, None][source]
                                                                        +iterlines(s: str) → Generator[str, None, None][source]

                                                                        A generator form of s.split(’n’) for reducing memory overhead.

                                                                        Parameters
                                                                        diff --git a/docs/pymatgen.io.ase.html b/docs/pymatgen.io.ase.html index 6127446b5ea..e975d1fb31d 100644 --- a/docs/pymatgen.io.ase.html +++ b/docs/pymatgen.io.ase.html @@ -4,7 +4,7 @@ - pymatgen.io.ase module — pymatgen 2022.5.18 documentation + pymatgen.io.ase module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                        - 2022.5.18 + 2022.5.18.1
                                                                        @@ -119,12 +119,12 @@ Atoms object and pymatgen Structure objects.

                                                                        -class AseAtomsAdaptor[source]
                                                                        +class AseAtomsAdaptor[source]

                                                                        Bases: object

                                                                        Adaptor serves as a bridge between ASE Atoms and pymatgen objects.

                                                                        -static get_atoms(structure, **kwargs)[source]
                                                                        +static get_atoms(structure, **kwargs)[source]

                                                                        Returns ASE Atoms object from pymatgen structure or molecule.

                                                                        Parameters
                                                                        @@ -141,7 +141,7 @@
                                                                        -static get_molecule(atoms, cls=None, **cls_kwargs)[source]
                                                                        +static get_molecule(atoms, cls=None, **cls_kwargs)[source]

                                                                        Returns pymatgen molecule from ASE Atoms.

                                                                        Parameters
                                                                        @@ -159,7 +159,7 @@
                                                                        -static get_structure(atoms, cls=None, **cls_kwargs)[source]
                                                                        +static get_structure(atoms, cls=None, **cls_kwargs)[source]

                                                                        Returns pymatgen structure from ASE Atoms.

                                                                        Parameters
                                                                        diff --git a/docs/pymatgen.io.atat.html b/docs/pymatgen.io.atat.html index 80f78bfb4a1..5e8fee05eab 100644 --- a/docs/pymatgen.io.atat.html +++ b/docs/pymatgen.io.atat.html @@ -4,7 +4,7 @@ - pymatgen.io.atat module — pymatgen 2022.5.18 documentation + pymatgen.io.atat module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                        - 2022.5.18 + 2022.5.18.1
                                                                        @@ -118,7 +118,7 @@

                                                                        Classes for reading/writing mcsqs files following the rndstr.in format.

                                                                        -class Mcsqs(structure)[source]
                                                                        +class Mcsqs(structure)[source]

                                                                        Bases: object

                                                                        Handle input/output for the crystal definition format used by mcsqs and other ATAT codes.

                                                                        @@ -129,7 +129,7 @@
                                                                        -static structure_from_string(data)[source]
                                                                        +static structure_from_string(data)[source]

                                                                        Parses a rndstr.in, lat.in or bestsqs.out file into pymatgen’s Structure format.

                                                                        @@ -144,7 +144,7 @@
                                                                        -to_string()[source]
                                                                        +to_string()[source]

                                                                        Returns a structure in mcsqs rndstr.in format. :return (str):

                                                                        diff --git a/docs/pymatgen.io.babel.html b/docs/pymatgen.io.babel.html index 96561042edb..45573dfe0d7 100644 --- a/docs/pymatgen.io.babel.html +++ b/docs/pymatgen.io.babel.html @@ -4,7 +4,7 @@ - pymatgen.io.babel module — pymatgen 2022.5.18 documentation + pymatgen.io.babel module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                        - 2022.5.18 + 2022.5.18.1
                                                                        @@ -121,7 +121,7 @@ openbabel documentation.

                                                                        -class BabelMolAdaptor(mol)[source]
                                                                        +class BabelMolAdaptor(mol)[source]

                                                                        Bases: object

                                                                        Adaptor serves as a bridge between OpenBabel’s Molecule and pymatgen’s Molecule.

                                                                        @@ -133,13 +133,13 @@
                                                                        -add_hydrogen()[source]
                                                                        +add_hydrogen()[source]

                                                                        Add hydrogens (make all hydrogen explicit).

                                                                        -confab_conformers(forcefield='mmff94', freeze_atoms=None, rmsd_cutoff=0.5, energy_cutoff=50.0, conf_cutoff=100000, verbose=False)[source]
                                                                        +confab_conformers(forcefield='mmff94', freeze_atoms=None, rmsd_cutoff=0.5, energy_cutoff=50.0, conf_cutoff=100000, verbose=False)[source]

                                                                        Conformer generation based on Confab to generate all diverse low-energy conformers for molecules. This is different from rotor_conformer or gen3d_conformer as it aims to not simply to find a low energy @@ -170,7 +170,7 @@

                                                                        -static from_file(filename, file_format='xyz', return_all_molecules=False)[source]
                                                                        +static from_file(filename, file_format='xyz', return_all_molecules=False)[source]

                                                                        Uses OpenBabel to read a molecule from a file in all supported formats.

                                                                        Parameters
                                                                        @@ -190,7 +190,7 @@
                                                                        -static from_molecule_graph(mol)[source]
                                                                        +static from_molecule_graph(mol)[source]

                                                                        Read a molecule from a pymatgen MoleculeGraph object.

                                                                        Parameters
                                                                        @@ -204,7 +204,7 @@
                                                                        -static from_string(string_data, file_format='xyz')[source]
                                                                        +static from_string(string_data, file_format='xyz')[source]

                                                                        Uses OpenBabel to read a molecule from a string in all supported formats.

                                                                        @@ -222,7 +222,7 @@
                                                                        -gen3d_conformer()[source]
                                                                        +gen3d_conformer()[source]

                                                                        A combined method to first generate 3D structures from 0D or 2D structures and then find the minimum energy conformer:

                                                                          @@ -244,7 +244,7 @@
                                                                          -localopt(forcefield='mmff94', steps=500)[source]
                                                                          +localopt(forcefield='mmff94', steps=500)[source]

                                                                          A wrapper to pybel’s localopt method to optimize a Molecule.

                                                                          Parameters
                                                                          @@ -259,7 +259,7 @@
                                                                          -make3d(forcefield='mmff94', steps=50)[source]
                                                                          +make3d(forcefield='mmff94', steps=50)[source]

                                                                          A wrapper to pybel’s make3D method generate a 3D structure from a 2D or 0D structure. The 3D structure is made very quickly using a combination of rules @@ -283,25 +283,25 @@

                                                                          -property openbabel_mol[source]
                                                                          +property openbabel_mol[source]

                                                                          Returns OpenBabel’s OBMol.

                                                                          -property pybel_mol[source]
                                                                          +property pybel_mol[source]

                                                                          Returns Pybel’s Molecule object.

                                                                          -property pymatgen_mol[source]
                                                                          +property pymatgen_mol[source]

                                                                          Returns pymatgen Molecule object.

                                                                          -remove_bond(idx1, idx2)[source]
                                                                          +remove_bond(idx1, idx2)[source]

                                                                          Remove a bond from an openbabel molecule

                                                                          Parameters
                                                                          @@ -315,7 +315,7 @@
                                                                          -rotor_conformer(*rotor_args, algo='WeightedRotorSearch', forcefield='mmff94')[source]
                                                                          +rotor_conformer(*rotor_args, algo='WeightedRotorSearch', forcefield='mmff94')[source]

                                                                          Conformer search based on several Rotor Search algorithms of openbabel. If the input molecule is not 3D, make3d will be called (generate 3D structure, add hydrogen, a quick localopt). All hydrogen atoms need @@ -342,7 +342,7 @@

                                                                          -write_file(filename, file_format='xyz')[source]
                                                                          +write_file(filename, file_format='xyz')[source]

                                                                          Uses OpenBabel to output all supported formats.

                                                                          Parameters
                                                                          diff --git a/docs/pymatgen.io.cif.html b/docs/pymatgen.io.cif.html index 87677f11d80..1f0cf7e2da4 100644 --- a/docs/pymatgen.io.cif.html +++ b/docs/pymatgen.io.cif.html @@ -4,7 +4,7 @@ - pymatgen.io.cif module — pymatgen 2022.5.18 documentation + pymatgen.io.cif module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                          - 2022.5.18 + 2022.5.18.1
                                                                          @@ -118,7 +118,7 @@

                                                                          Wrapper classes for Cif input and output from Structures.

                                                                          -class CifBlock(data, loops, header)[source]
                                                                          +class CifBlock(data, loops, header)[source]

                                                                          Bases: object

                                                                          Object for storing cif data. All data is stored in a single dictionary. Data inside loops are stored in lists in the data dictionary, and @@ -136,7 +136,7 @@

                                                                          -classmethod from_string(string)[source]
                                                                          +classmethod from_string(string)[source]

                                                                          Reads CifBlock from string.

                                                                          Parameters
                                                                          @@ -150,14 +150,14 @@
                                                                          -maxlen = 70[source]
                                                                          +maxlen = 70[source]
                                                                          -class CifFile(data, orig_string=None, comment=None)[source]
                                                                          +class CifFile(data, orig_string=None, comment=None)[source]

                                                                          Bases: object

                                                                          Reads and parses CifBlocks from a .cif file or string

                                                                          @@ -171,7 +171,7 @@
                                                                          -classmethod from_file(filename)[source]
                                                                          +classmethod from_file(filename)[source]

                                                                          Reads CifFile from a filename.

                                                                          Parameters
                                                                          @@ -185,7 +185,7 @@
                                                                          -classmethod from_string(string)[source]
                                                                          +classmethod from_string(string)[source]

                                                                          Reads CifFile from a string.

                                                                          Parameters
                                                                          @@ -201,7 +201,7 @@
                                                                          -class CifParser(filename, occupancy_tolerance=1.0, site_tolerance=0.0001)[source]
                                                                          +class CifParser(filename, occupancy_tolerance=1.0, site_tolerance=0.0001)[source]

                                                                          Bases: object

                                                                          Parses a CIF file. Attempts to fix CIFs that are out-of-spec, but will issue warnings if corrections applied. These are also stored in the @@ -220,7 +220,7 @@

                                                                          -as_dict()[source]
                                                                          +as_dict()[source]
                                                                          Returns

                                                                          MSONable dict

                                                                          @@ -230,7 +230,7 @@
                                                                          -static from_string(cif_string, occupancy_tolerance=1.0)[source]
                                                                          +static from_string(cif_string, occupancy_tolerance=1.0)[source]

                                                                          Creates a CifParser from a string.

                                                                          Parameters
                                                                          @@ -249,7 +249,7 @@
                                                                          -get_bibtex_string()[source]
                                                                          +get_bibtex_string()[source]

                                                                          Get BibTeX reference from CIF file. :param data: :return: BibTeX string

                                                                          @@ -257,7 +257,7 @@
                                                                          -get_lattice(data, length_strings=('a', 'b', 'c'), angle_strings=('alpha', 'beta', 'gamma'), lattice_type=None)[source]
                                                                          +get_lattice(data, length_strings=('a', 'b', 'c'), angle_strings=('alpha', 'beta', 'gamma'), lattice_type=None)[source]

                                                                          Generate the lattice from the provided lattice parameters. In the absence of all six lattice parameters, the crystal system and necessary parameters are parsed

                                                                          @@ -265,7 +265,7 @@
                                                                          -get_magsymops(data)[source]
                                                                          +get_magsymops(data)[source]

                                                                          Equivalent to get_symops except for magnetic symmetry groups. Separate function since additional operation for time reversal symmetry (which changes magnetic moments on sites) needs to be returned.

                                                                          @@ -273,7 +273,7 @@
                                                                          -get_structures(primitive=True, symmetrized=False)[source]
                                                                          +get_structures(primitive=True, symmetrized=False)[source]

                                                                          Return list of structures in CIF file. primitive boolean sets whether a conventional cell structure or primitive cell structure is returned.

                                                                          @@ -300,7 +300,7 @@
                                                                          -get_symops(data)[source]
                                                                          +get_symops(data)[source]

                                                                          In order to generate symmetry equivalent positions, the symmetry operations are parsed. If the symops are not present, the space group symbol is parsed, and symops are generated.

                                                                          @@ -308,7 +308,7 @@
                                                                          -property has_errors[source]
                                                                          +property has_errors[source]

                                                                          Whether there are errors/warnings detected in CIF parsing.

                                                                          Type
                                                                          @@ -319,13 +319,13 @@
                                                                          -static parse_magmoms(data, lattice=None)[source]
                                                                          +static parse_magmoms(data, lattice=None)[source]

                                                                          Parse atomic magnetic moments from data dictionary

                                                                          -static parse_oxi_states(data)[source]
                                                                          +static parse_oxi_states(data)[source]

                                                                          Parse oxidation states from data dictionary

                                                                          @@ -333,7 +333,7 @@
                                                                          -class CifWriter(struct, symprec=None, write_magmoms=False, significant_figures=8, angle_tolerance=5.0, refine_struct=True)[source]
                                                                          +class CifWriter(struct, symprec=None, write_magmoms=False, significant_figures=8, angle_tolerance=5.0, refine_struct=True)[source]

                                                                          Bases: object

                                                                          A wrapper around CifFile to write CIF files from pymatgen structures.

                                                                          @@ -357,7 +357,7 @@
                                                                          -property ciffile[source]
                                                                          +property ciffile[source]

                                                                          CifFile associated with the CifWriter.

                                                                          Type
                                                                          @@ -368,7 +368,7 @@
                                                                          -write_file(filename)[source]
                                                                          +write_file(filename)[source]

                                                                          Write the cif file.

                                                                          @@ -376,7 +376,7 @@
                                                                          -str2float(text)[source]
                                                                          +str2float(text)[source]

                                                                          Remove uncertainty brackets from strings and return the float.

                                                                          diff --git a/docs/pymatgen.io.core.html b/docs/pymatgen.io.core.html index 1cf1a550a97..336edd14a0b 100644 --- a/docs/pymatgen.io.core.html +++ b/docs/pymatgen.io.core.html @@ -4,7 +4,7 @@ - pymatgen.io.core module — pymatgen 2022.5.18 documentation + pymatgen.io.core module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                          - 2022.5.18 + 2022.5.18.1
                                                                          @@ -140,7 +140,7 @@
                                                                        -class InputFile[source]
                                                                        +class InputFile[source]

                                                                        Bases: monty.json.MSONable

                                                                        Abstract base class to represent a single input file. Note that use of this class is optional; it is possible create an InputSet that @@ -149,7 +149,7 @@ is called by write_file.

                                                                        -classmethod from_file(path: Union[str, pathlib.Path])[source]
                                                                        +classmethod from_file(path: Union[str, pathlib.Path])[source]

                                                                        Creates an InputFile object from a file.

                                                                        Parameters
                                                                        @@ -163,7 +163,7 @@
                                                                        -abstract classmethod from_string(contents: str)[source]
                                                                        +abstract classmethod from_string(contents: str)[source]

                                                                        Create an InputFile object from a string

                                                                        Parameters
                                                                        @@ -177,13 +177,13 @@
                                                                        -abstract get_string() → str[source]
                                                                        +abstract get_string() → str[source]

                                                                        Return a string representation of an entire input file.

                                                                        -write_file(filename: Union[str, pathlib.Path]) → None[source]
                                                                        +write_file(filename: Union[str, pathlib.Path]) → None[source]

                                                                        Write the input file.

                                                                        Parameters
                                                                        @@ -199,14 +199,14 @@
                                                                        -class InputGenerator[source]
                                                                        +class InputGenerator[source]

                                                                        Bases: monty.json.MSONable

                                                                        InputGenerator classes serve as generators for Input objects. They contain settings or sets of instructions for how to create Input from a set of coordinates or a previous calculation directory.

                                                                        -abstract get_input_set() → pymatgen.io.core.InputSet[source]
                                                                        +abstract get_input_set() → pymatgen.io.core.InputSet[source]

                                                                        Generate an InputSet object. Typically the first argument to this method will be a Structure or other form of atomic coordinates.

                                                                        @@ -215,7 +215,7 @@
                                                                        -class InputSet(inputs: Dict[Union[str, pathlib.Path], Union[str, pymatgen.io.core.InputFile]] = {}, **kwargs)[source]
                                                                        +class InputSet(inputs: Dict[Union[str, pathlib.Path], Union[str, pymatgen.io.core.InputFile]] = {}, **kwargs)[source]

                                                                        Bases: monty.json.MSONable, collections.abc.MutableMapping

                                                                        Abstract base class for all InputSet classes. InputSet are dict-like containers for all calculation input data.

                                                                        @@ -242,7 +242,7 @@
                                                                        -classmethod from_directory(directory: Union[str, pathlib.Path])[source]
                                                                        +classmethod from_directory(directory: Union[str, pathlib.Path])[source]

                                                                        Construct an InputSet from a directory of one or more files.

                                                                        Parameters
                                                                        @@ -253,7 +253,7 @@
                                                                        -validate() → bool[source]
                                                                        +validate() → bool[source]

                                                                        A place to implement basic checks to verify the validity of an input set. Can be as simple or as complex as desired.

                                                                        Will raise a NotImplementedError unless overloaded by the inheriting class.

                                                                        @@ -261,7 +261,7 @@
                                                                        -write_input(directory: Union[str, pathlib.Path], make_dir: bool = True, overwrite: bool = True, zip_inputs: bool = False)[source]
                                                                        +write_input(directory: Union[str, pathlib.Path], make_dir: bool = True, overwrite: bool = True, zip_inputs: bool = False)[source]

                                                                        Write Inputs to one or more files

                                                                        Parameters
                                                                        diff --git a/docs/pymatgen.io.cp2k.html b/docs/pymatgen.io.cp2k.html index c865c7b4a6a..d852f1eafd9 100644 --- a/docs/pymatgen.io.cp2k.html +++ b/docs/pymatgen.io.cp2k.html @@ -4,7 +4,7 @@ - pymatgen.io.cp2k package — pymatgen 2022.5.18 documentation + pymatgen.io.cp2k package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                        - 2022.5.18 + 2022.5.18.1
                                                                        diff --git a/docs/pymatgen.io.cp2k.inputs.html b/docs/pymatgen.io.cp2k.inputs.html index e517e1fe254..4ae3915162b 100644 --- a/docs/pymatgen.io.cp2k.inputs.html +++ b/docs/pymatgen.io.cp2k.inputs.html @@ -4,7 +4,7 @@ - pymatgen.io.cp2k.inputs module — pymatgen 2022.5.18 documentation + pymatgen.io.cp2k.inputs module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                        - 2022.5.18 + 2022.5.18.1
                                                                        @@ -137,7 +137,7 @@
                                                                        -class BrokenSymmetry(l_alpha: Sequence = (- 1,), n_alpha: Sequence = (0,), nel_alpha: Sequence = (- 1,), l_beta: Sequence = (- 1,), n_beta: Sequence = (0,), nel_beta: Sequence = (- 1,))[source]
                                                                        +class BrokenSymmetry(l_alpha: Sequence = (- 1,), n_alpha: Sequence = (0,), nel_alpha: Sequence = (- 1,), l_beta: Sequence = (- 1,), n_beta: Sequence = (0,), nel_beta: Sequence = (- 1,))[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Define the required atomic orbital occupation assigned in initialization of the density matrix, by adding or subtracting electrons from specific @@ -159,7 +159,7 @@

                                                                        -classmethod from_el(el, oxi_state=0, spin=0)[source]
                                                                        +classmethod from_el(el, oxi_state=0, spin=0)[source]

                                                                        Create section from element, oxidation state, and spin.

                                                                        @@ -167,7 +167,7 @@
                                                                        -class Cell(lattice: pymatgen.core.lattice.Lattice, **kwargs)[source]
                                                                        +class Cell(lattice: pymatgen.core.lattice.Lattice, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Defines the simulation cell (lattice)

                                                                        Initialize the cell section.

                                                                        @@ -180,7 +180,7 @@
                                                                        -class Coord(structure: Structure | Molecule, aliases: dict | None = None, subsections: dict = None, **kwargs)[source]
                                                                        +class Coord(structure: Structure | Molecule, aliases: dict | None = None, subsections: dict = None, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Specifies the coordinates of the atoms using a pymatgen structure object.

                                                                        @@ -196,7 +196,7 @@
                                                                        -class Cp2kInput(name: str = 'CP2K_INPUT', subsections: Optional[dict] = None, **kwargs)[source]
                                                                        +class Cp2kInput(name: str = 'CP2K_INPUT', subsections: Optional[dict] = None, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Special instance of ‘Section’ class that is meant to represent the overall cp2k input. Distinguishes itself from Section by overriding get_string() to not print this section’s @@ -204,31 +204,31 @@

                                                                        Initialize Cp2kInput by calling the super

                                                                        -static from_file(file: str)[source]
                                                                        +static from_file(file: str)[source]

                                                                        Initialize from a file

                                                                        -classmethod from_lines(lines: list | tuple)[source]
                                                                        +classmethod from_lines(lines: list | tuple)[source]

                                                                        Helper method to read lines of file

                                                                        -static from_string(s: str)[source]
                                                                        +static from_string(s: str)[source]

                                                                        Initialize from a string

                                                                        -get_string()[source]
                                                                        +get_string()[source]

                                                                        Get string representation of the Cp2kInput

                                                                        -write_file(input_filename: str = 'cp2k.inp', output_dir: str = '.', make_dir_if_not_present: bool = True)[source]
                                                                        +write_file(input_filename: str = 'cp2k.inp', output_dir: str = '.', make_dir_if_not_present: bool = True)[source]

                                                                        Write input to a file.

                                                                        Parameters
                                                                        @@ -245,7 +245,7 @@
                                                                        -class Davidson(new_prec_each: int = 20, preconditioner: str = 'FULL_SINGLE_INVERSE', **kwargs)[source]
                                                                        +class Davidson(new_prec_each: int = 20, preconditioner: str = 'FULL_SINGLE_INVERSE', **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Parameters for davidson diagonalization

                                                                        @@ -279,7 +279,7 @@
                                                                        -class Dft(basis_set_filenames='BASIS_MOLOPT', potential_filename='GTH_POTENTIALS', uks: bool = True, wfn_restart_file_name: Optional[str] = None, subsections: Optional[dict] = None, **kwargs)[source]
                                                                        +class Dft(basis_set_filenames='BASIS_MOLOPT', potential_filename='GTH_POTENTIALS', uks: bool = True, wfn_restart_file_name: Optional[str] = None, subsections: Optional[dict] = None, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Controls the DFT parameters in Cp2k

                                                                        Initialize the DFT section.

                                                                        @@ -301,7 +301,7 @@
                                                                        -class DftPlusU(eps_u_ramping=1e-05, init_u_ramping_each_scf=False, l=- 1, u_minus_j=0, u_ramping=0)[source]
                                                                        +class DftPlusU(eps_u_ramping=1e-05, init_u_ramping_each_scf=False, l=- 1, u_minus_j=0, u_ramping=0)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Controls DFT+U for an atom kind

                                                                        Initialize the DftPlusU section.

                                                                        @@ -320,7 +320,7 @@
                                                                        -class Diagonalization(eps_adapt: float = 0, eps_iter: float = 1e-08, eps_jacobi: float = 0, jacobi_threshold: float = 1e-07, subsections: Optional[dict] = None, **kwargs)[source]
                                                                        +class Diagonalization(eps_adapt: float = 0, eps_iter: float = 1e-08, eps_jacobi: float = 0, jacobi_threshold: float = 1e-07, subsections: Optional[dict] = None, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Controls diagonalization settings (if using traditional diagonalization).

                                                                        Initialize the diagronalization section

                                                                        @@ -328,7 +328,7 @@
                                                                        -class E_Density_Cube(keywords=None, **kwargs)[source]
                                                                        +class E_Density_Cube(keywords=None, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Controls printing of the electron density cube file

                                                                        Initialize the E_DENSITY_CUBE Section

                                                                        @@ -336,7 +336,7 @@
                                                                        -class ForceEval(subsections: Optional[dict] = None, **kwargs)[source]
                                                                        +class ForceEval(subsections: Optional[dict] = None, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Controls the calculation of energy and forces in Cp2k

                                                                        Initialize the ForceEval section

                                                                        @@ -349,7 +349,7 @@
                                                                        -class Global(project_name: str = 'CP2K', run_type: str = 'ENERGY_FORCE', **kwargs)[source]
                                                                        +class Global(project_name: str = 'CP2K', run_type: str = 'ENERGY_FORCE', **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Controls ‘global’ settings for cp2k execution such as RUN_TYPE and PROJECT_NAME

                                                                        Initialize the global section

                                                                        @@ -365,7 +365,7 @@
                                                                        -class Keyword(name: str, *values, description: Optional[str] = None, units: Optional[str] = None, verbose: bool = True, repeats: bool = False)[source]
                                                                        +class Keyword(name: str, *values, description: Optional[str] = None, units: Optional[str] = None, verbose: bool = True, repeats: bool = False)[source]

                                                                        Bases: monty.json.MSONable

                                                                        Class representing a keyword argument in CP2K. Within CP2K Sections, which activate features of the CP2K code, the keywords are arguments that control the functionality of that feature. @@ -392,19 +392,19 @@

                                                                        -as_dict()[source]
                                                                        +as_dict()[source]

                                                                        Get a dictionary representation of the Keyword

                                                                        -classmethod from_dict(d)[source]
                                                                        +classmethod from_dict(d)[source]

                                                                        Initialise from dictionary

                                                                        -static from_string(s)[source]
                                                                        +static from_string(s)[source]

                                                                        Initialise from a string.

                                                                        Keywords must be labeled with strings. If the postprocessor finds that the keywords is a number, then None is return (used by @@ -418,13 +418,13 @@

                                                                        -get_string()[source]
                                                                        +get_string()[source]

                                                                        String representation of Keyword

                                                                        -verbosity(v)[source]
                                                                        +verbosity(v)[source]

                                                                        Change the printing of this keyword’s description.

                                                                        @@ -432,7 +432,7 @@
                                                                        -class KeywordList(keywords: Sequence[pymatgen.io.cp2k.inputs.Keyword])[source]
                                                                        +class KeywordList(keywords: Sequence[pymatgen.io.cp2k.inputs.Keyword])[source]

                                                                        Bases: monty.json.MSONable

                                                                        Some keywords can be repeated, which makes accessing them via the normal dictionary methods a little unnatural. This class deals with this by defining a collection @@ -445,25 +445,25 @@

                                                                        -append(item)[source]
                                                                        +append(item)[source]

                                                                        append the keyword list

                                                                        -extend(l)[source]
                                                                        +extend(l)[source]

                                                                        extend the keyword list

                                                                        -get_string(indent=0)[source]
                                                                        +get_string(indent=0)[source]

                                                                        String representation of Keyword

                                                                        -verbosity(verbosity)[source]
                                                                        +verbosity(verbosity)[source]

                                                                        Silence all keywords in keyword list

                                                                        @@ -471,7 +471,7 @@
                                                                        -class Kind(specie: str, alias: str | None = None, magnetization: float = 0.0, subsections: dict = None, basis_set: str = 'GTH_BASIS', potential: str = 'GTH_POTENTIALS', ghost: bool = False, aux_basis: str | None = None, **kwargs)[source]
                                                                        +class Kind(specie: str, alias: str | None = None, magnetization: float = 0.0, subsections: dict = None, basis_set: str = 'GTH_BASIS', potential: str = 'GTH_POTENTIALS', ghost: bool = False, aux_basis: str | None = None, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Specifies the information for the different atom types being simulated.

                                                                        Initialize a KIND section

                                                                        @@ -497,7 +497,7 @@
                                                                        -class Kpoints(kpts: Sequence | Sequence[Sequence[int]], weights: Sequence | None = None, eps_geo: float = 1e-06, full_grid: bool = False, parallel_group_size: int = - 1, scheme: str = 'MONKHORST-PACK', symmetry: bool = False, units: str = 'B_VECTOR', verbose: bool = False, wavefunctions: str = 'COMPLEX')[source]
                                                                        +class Kpoints(kpts: Sequence | Sequence[Sequence[int]], weights: Sequence | None = None, eps_geo: float = 1e-06, full_grid: bool = False, parallel_group_size: int = - 1, scheme: str = 'MONKHORST-PACK', symmetry: bool = False, units: str = 'B_VECTOR', verbose: bool = False, wavefunctions: str = 'COMPLEX')[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Description of the k-points to use for the calculation.

                                                                        @@ -531,7 +531,7 @@
                                                                        -classmethod from_kpoints(kpoints, structure=None, reduce=True)[source]
                                                                        +classmethod from_kpoints(kpoints, structure=None, reduce=True)[source]

                                                                        Initialize the section from a Kpoints object (pymatgen.io.vasp.inputs). CP2K does not have an automatic gamma-point constructor, so this is generally used to get the number of divisions from a kpoint static constructor and then @@ -554,7 +554,7 @@

                                                                        -class LDOS(index: int = 1, alias: str | None = None, **kwargs)[source]
                                                                        +class LDOS(index: int = 1, alias: str | None = None, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Controls printing of the LDOS (List-Density of states). i.e. projects onto specific atoms.

                                                                        Initialize the LDOS section

                                                                        @@ -567,7 +567,7 @@
                                                                        -class MO_Cubes(write_cube: bool = False, nhomo: int = 1, nlumo: int = 1, **kwargs)[source]
                                                                        +class MO_Cubes(write_cube: bool = False, nhomo: int = 1, nlumo: int = 1, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Controls printing of the molecular orbital eigenvalues

                                                                        Initialize the MO_CUBES section

                                                                        @@ -575,7 +575,7 @@
                                                                        -class Mgrid(cutoff: int | float = 1200, rel_cutoff: int | float = 80, ngrids: int = 5, progression_factor: int = 3, subsections: dict = None, **kwargs)[source]
                                                                        +class Mgrid(cutoff: int | float = 1200, rel_cutoff: int | float = 80, ngrids: int = 5, progression_factor: int = 3, subsections: dict = None, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Controls the multigrid for numerical integration

                                                                        Initialize the MGRID section

                                                                        @@ -597,7 +597,7 @@
                                                                        -class OrbitalTransformation(minimizer: str = 'CG', preconditioner: str = 'FULL_ALL', algorithm: str = 'STRICT', rotation: bool = False, occupation_preconditioner: bool = False, energy_gap: float = - 1, linesearch: str = '2PNT', subsections: Optional[dict] = None, **kwargs)[source]
                                                                        +class OrbitalTransformation(minimizer: str = 'CG', preconditioner: str = 'FULL_ALL', algorithm: str = 'STRICT', rotation: bool = False, occupation_preconditioner: bool = False, energy_gap: float = - 1, linesearch: str = '2PNT', subsections: Optional[dict] = None, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Turns on the Orbital Transformation scheme for diagonalizing the Hamiltonian. Much faster and with guaranteed convergence compared to normal diagonalization, but requires the system @@ -635,7 +635,7 @@

                                                                        -class PBE(parameterization: str = 'ORIG', scale_c: float | int = 1, scale_x: float | int = 1)[source]
                                                                        +class PBE(parameterization: str = 'ORIG', scale_c: float | int = 1, scale_x: float | int = 1)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Info about the PBE functional.

                                                                        @@ -653,7 +653,7 @@
                                                                        -class PDOS(nlumo: int = - 1, **kwargs)[source]
                                                                        +class PDOS(nlumo: int = - 1, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Controls printing of projected density of states onto the different atom KINDS (elemental decomposed DOS).

                                                                        @@ -667,7 +667,7 @@
                                                                        -class QS(method: str = 'GPW', eps_default: float = 1e-10, extrapolation: str = 'ASPC', subsections: Optional[dict] = None, **kwargs)[source]
                                                                        +class QS(method: str = 'GPW', eps_default: float = 1e-10, extrapolation: str = 'ASPC', subsections: Optional[dict] = None, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Controls the quickstep settings (DFT driver)

                                                                        Initialize the QS Section

                                                                        @@ -692,7 +692,7 @@
                                                                        -class Scf(max_scf: int = 50, eps_scf: float = 1e-06, scf_guess: str = 'RESTART', subsections: Optional[dict] = None, **kwargs)[source]
                                                                        +class Scf(max_scf: int = 50, eps_scf: float = 1e-06, scf_guess: str = 'RESTART', subsections: Optional[dict] = None, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Controls the self consistent field loop

                                                                        Initialize the Scf section

                                                                        @@ -724,7 +724,7 @@
                                                                        -class Section(name: str, subsections: dict = None, repeats: bool = False, description: str | None = None, keywords: dict = {}, section_parameters: list | tuple = [], location: str = None, verbose: bool = True, alias: str = None, **kwargs)[source]
                                                                        +class Section(name: str, subsections: dict = None, repeats: bool = False, description: str | None = None, keywords: dict = {}, section_parameters: list | tuple = [], location: str = None, verbose: bool = True, alias: str = None, **kwargs)[source]

                                                                        Bases: monty.json.MSONable

                                                                        Basic input representation of input to Cp2k. Activates functionality inside of the Cp2k executable.

                                                                        @@ -765,13 +765,13 @@
                                                                        -add(other)[source]
                                                                        +add(other)[source]

                                                                        Add another keyword to the current section

                                                                        -by_path(path: str)[source]
                                                                        +by_path(path: str)[source]

                                                                        Access a sub-section using a path. Used by the file parser.

                                                                        Parameters
                                                                        @@ -782,7 +782,7 @@
                                                                        -check(path: str)[source]
                                                                        +check(path: str)[source]

                                                                        Check if section exists within the current using a path. Can be useful for cross-checking whether or not required dependencies have been satisfied, which CP2K does not enforce.

                                                                        @@ -794,7 +794,7 @@
                                                                        -get(d, default=None)[source]
                                                                        +get(d, default=None)[source]

                                                                        Similar to get for dictionaries. This will attempt to retrieve the section or keyword matching d. Will not raise an error if d does not exist.

                                                                        @@ -810,7 +810,7 @@
                                                                        -get_keyword(d, default=None)[source]
                                                                        +get_keyword(d, default=None)[source]

                                                                        Get function, only for subsections

                                                                        Parameters
                                                                        @@ -824,7 +824,7 @@
                                                                        -get_section(d, default=None)[source]
                                                                        +get_section(d, default=None)[source]

                                                                        Get function, only for subsections

                                                                        Parameters
                                                                        @@ -838,59 +838,59 @@
                                                                        -get_string()[source]
                                                                        +get_string()[source]

                                                                        Get string representation of Section

                                                                        -inc(d: dict)[source]
                                                                        +inc(d: dict)[source]

                                                                        Mongo style dict modification. Include.

                                                                        -insert(d)[source]
                                                                        +insert(d)[source]

                                                                        Insert a new section as a subsection of the current one

                                                                        -required_keywords: tuple = ()[source]
                                                                        +required_keywords: tuple = ()[source]
                                                                        -required_sections: tuple = ()[source]
                                                                        +required_sections: tuple = ()[source]
                                                                        -safeset(d: dict)[source]
                                                                        +safeset(d: dict)[source]

                                                                        Alias for update with strict (no insertions). Used by custodian.

                                                                        -set(d: dict)[source]
                                                                        +set(d: dict)[source]

                                                                        Alias for update. Used by custodian.

                                                                        -silence()[source]
                                                                        +silence()[source]

                                                                        Recursively delete all print sections so that only defaults are printed out.

                                                                        -unset(d: dict)[source]
                                                                        +unset(d: dict)[source]

                                                                        Dict based deletion. Used by custodian.

                                                                        -update(d: dict, strict=False)[source]
                                                                        +update(d: dict, strict=False)[source]

                                                                        Update the Section according to a dictionary argument. This is most useful for providing user-override settings to default parameters. As you pass a dictionary the class variables like “description”, “location”, or “repeats” @@ -924,7 +924,7 @@

                                                                        -verbosity(verbosity)[source]
                                                                        +verbosity(verbosity)[source]

                                                                        Change the section verbossity recursively by turning on/off the printing of descriptions. Turning off descriptions may reduce the appealing documentation of input files, but also helps de-clutter them.

                                                                        @@ -934,7 +934,7 @@
                                                                        -class SectionList(sections: Sequence[pymatgen.io.cp2k.inputs.Section])[source]
                                                                        +class SectionList(sections: Sequence[pymatgen.io.cp2k.inputs.Section])[source]

                                                                        Bases: monty.json.MSONable

                                                                        Section list

                                                                        Initializes a SectionList object using a sequence of sections.

                                                                        @@ -945,32 +945,32 @@
                                                                        -append(item)[source]
                                                                        +append(item)[source]

                                                                        append the keyword list

                                                                        -extend(l)[source]
                                                                        +extend(l)[source]

                                                                        extend the keyword list

                                                                        -get(d, index=- 1)[source]
                                                                        +get(d, index=- 1)[source]

                                                                        Get for section list. If index is specified, return the section at that index. Otherwise, return a get on the last section.

                                                                        -get_string()[source]
                                                                        +get_string()[source]

                                                                        Return string representation of section list

                                                                        -verbosity(verbosity)[source]
                                                                        +verbosity(verbosity)[source]

                                                                        Silence all keywords in keyword list

                                                                        @@ -978,7 +978,7 @@
                                                                        -class Smear(elec_temp: int | float = 300, method: str = 'FERMI_DIRAC', fixed_magnetic_moment: float = - 100.0, **kwargs)[source]
                                                                        +class Smear(elec_temp: int | float = 300, method: str = 'FERMI_DIRAC', fixed_magnetic_moment: float = - 100.0, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Control electron smearing

                                                                        Initialize the SMEAR section

                                                                        @@ -986,7 +986,7 @@
                                                                        -class Subsys(subsections: Optional[dict] = None, **kwargs)[source]
                                                                        +class Subsys(subsections: Optional[dict] = None, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Controls the definition of the system to be simulated

                                                                        Initialize the subsys section

                                                                        @@ -994,7 +994,7 @@
                                                                        -class V_Hartree_Cube(keywords=None, **kwargs)[source]
                                                                        +class V_Hartree_Cube(keywords=None, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Controls printing of the hartree potential as a cube file.

                                                                        Initialize the V_HARTREE_CUBE section

                                                                        @@ -1002,7 +1002,7 @@
                                                                        -class Xc_Functional(functionals: Iterable = [], subsections: Optional[dict] = None, **kwargs)[source]
                                                                        +class Xc_Functional(functionals: Iterable = [], subsections: Optional[dict] = None, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Section

                                                                        Defines the XC functional(s) to use.

                                                                        Initialize the XC_FUNCTIONAL class

                                                                        diff --git a/docs/pymatgen.io.cp2k.outputs.html b/docs/pymatgen.io.cp2k.outputs.html index 22fb8adf27d..18f5756e32c 100644 --- a/docs/pymatgen.io.cp2k.outputs.html +++ b/docs/pymatgen.io.cp2k.outputs.html @@ -4,7 +4,7 @@ - pymatgen.io.cp2k.outputs module — pymatgen 2022.5.18 documentation + pymatgen.io.cp2k.outputs module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                        - 2022.5.18 + 2022.5.18.1
                                                                        @@ -120,7 +120,7 @@ outputs.

                                                                        -class Cp2kOutput(filename, verbose=False, auto_load=False)[source]
                                                                        +class Cp2kOutput(filename, verbose=False, auto_load=False)[source]

                                                                        Bases: object

                                                                        Class for parsing output file from CP2K. The CP2K output file is very flexible in the way that it is returned. This class will automatically parse parameters that should always be present, but other parsing features may be @@ -137,86 +137,86 @@

                                                                        -as_dict()[source]
                                                                        +as_dict()[source]

                                                                        Return dictionary representation of the output

                                                                        -property calculation_type[source]
                                                                        +property calculation_type[source]

                                                                        Returns the calculation type (what io.vasp.outputs calls run_type)

                                                                        -property completed[source]
                                                                        +property completed[source]

                                                                        Did the calculation complete

                                                                        -convergence()[source]
                                                                        +convergence()[source]

                                                                        Check whether or not the SCF and geometry optimization cycles converged.

                                                                        -property cp2k_version[source]
                                                                        +property cp2k_version[source]

                                                                        The cp2k version used in the calculation

                                                                        -property is_hubbard[source]
                                                                        +property is_hubbard[source]

                                                                        returns True if hubbard +U correction was used

                                                                        -property is_metal[source]
                                                                        +property is_metal[source]

                                                                        Was a band gap found? i.e. is it a metal

                                                                        -property is_molecule[source]
                                                                        +property is_molecule[source]

                                                                        Returns True if the cp2k output was generated for a molecule (i.e. no periodicity in the cell). Returns false otherwise.

                                                                        -property num_warnings[source]
                                                                        +property num_warnings[source]

                                                                        How many warnings showed up during the run

                                                                        -parse_atomic_kind_info()[source]
                                                                        +parse_atomic_kind_info()[source]

                                                                        Parse info on what atomic kinds are present and what basis/pseudopotential is describing each of them.

                                                                        -parse_cell_params()[source]
                                                                        +parse_cell_params()[source]

                                                                        Parse the lattice parameters (initial) from the output file

                                                                        -parse_cp2k_params()[source]
                                                                        +parse_cp2k_params()[source]

                                                                        Parse the CP2K general parameters from CP2K output file into a dictionary.

                                                                        -parse_dft_params()[source]
                                                                        +parse_dft_params()[source]

                                                                        Parse the DFT parameters (as well as functional, HF, vdW params)

                                                                        -parse_dos(pdos_files=None, ldos_files=None, sigma=0)[source]
                                                                        +parse_dos(pdos_files=None, ldos_files=None, sigma=0)[source]

                                                                        Parse the pdos_ALPHA files created by cp2k, and assimilate them into a CompleteDos object. Either provide a list of PDOS file paths, or use glob to find the .pdos_ALPHA extension in the calculation directory.

                                                                        @@ -235,7 +235,7 @@
                                                                        -parse_energies()[source]
                                                                        +parse_energies()[source]

                                                                        Get the total energy from a CP2K calculation. Presently, the energy reported in the trajectory (pos.xyz) file takes presidence over the energy reported in the main output file. This is because the trajectory file keeps track of energies in between restarts, while the main output file may or may not depending on whether @@ -244,56 +244,56 @@

                                                                        -parse_files()[source]
                                                                        +parse_files()[source]

                                                                        Identify files present in the directory with the cp2k output file. Looks for trajectories, dos, and cubes

                                                                        -parse_forces()[source]
                                                                        +parse_forces()[source]

                                                                        Get the forces from the output file

                                                                        -parse_global_params()[source]
                                                                        +parse_global_params()[source]

                                                                        Parse the GLOBAL section parameters from CP2K output file into a dictionary.

                                                                        -parse_hirshfeld()[source]
                                                                        +parse_hirshfeld()[source]

                                                                        parse the hirshfeld population analysis for each step

                                                                        -parse_homo_lumo()[source]
                                                                        +parse_homo_lumo()[source]

                                                                        Find the HOMO - LUMO gap in [eV]. Returns the last value. For gaps/eigenvalues decomposed by spin up/spin down channel and over many ionic steps, see parse_mo_eigenvalues()

                                                                        -parse_initial_structure()[source]
                                                                        +parse_initial_structure()[source]

                                                                        Parse the initial structure from the main cp2k output file

                                                                        -parse_input()[source]
                                                                        +parse_input()[source]

                                                                        Load in the input set from the input file (if it can be found)

                                                                        -parse_ionic_steps()[source]
                                                                        +parse_ionic_steps()[source]

                                                                        Parse the ionic step info. If already parsed, this will just assimilate.

                                                                        -parse_mo_eigenvalues()[source]
                                                                        +parse_mo_eigenvalues()[source]

                                                                        Parse the MO eigenvalues from the cp2k output file. Will get the eigenvalues (and band gap) at each ionic step (if more than one exist).

                                                                        Everything is decomposed by spin channel. If calculation was performed without spin polarization, @@ -302,45 +302,45 @@

                                                                        -parse_mulliken()[source]
                                                                        +parse_mulliken()[source]

                                                                        Parse the mulliken population analysis info for each step :return:

                                                                        -parse_opt_steps()[source]
                                                                        +parse_opt_steps()[source]

                                                                        Parse the geometry optimization information

                                                                        -parse_overlap_condition()[source]
                                                                        +parse_overlap_condition()[source]

                                                                        Retrieve the overlap condition number :return:

                                                                        -parse_plus_u_params()[source]
                                                                        +parse_plus_u_params()[source]

                                                                        Parse the DFT+U params

                                                                        -parse_qs_params()[source]
                                                                        +parse_qs_params()[source]

                                                                        Parse the DFT parameters (as well as functional, HF, vdW params)

                                                                        -parse_scf_opt()[source]
                                                                        +parse_scf_opt()[source]

                                                                        Parse the SCF cycles (not usually important)

                                                                        -parse_scf_params()[source]
                                                                        +parse_scf_params()[source]

                                                                        Retrieve the most import SCF parameters: the max number of scf cycles (max_scf), the convergence cutoff for scf (eps_scf), :return:

                                                                        @@ -348,13 +348,13 @@
                                                                        -parse_stresses()[source]
                                                                        +parse_stresses()[source]

                                                                        Get the stresses from the output file.

                                                                        -parse_structures(trajectory_file=None, lattice_file=None)[source]
                                                                        +parse_structures(trajectory_file=None, lattice_file=None)[source]

                                                                        Parses the structures from a cp2k calculation. Static calculations simply use the initial structure. For calculations with ionic motion, the function will look for the appropriate trajectory and lattice files based on naming convention. If no file is given, and no file is found, it is assumed @@ -365,25 +365,25 @@

                                                                        -parse_timing()[source]
                                                                        +parse_timing()[source]

                                                                        Parse the timing info (how long did the run take).

                                                                        -parse_total_numbers()[source]
                                                                        +parse_total_numbers()[source]

                                                                        Parse total numbers (not usually important)

                                                                        -property project_name[source]
                                                                        +property project_name[source]

                                                                        What project name was used for this calculation

                                                                        -ran_successfully()[source]
                                                                        +ran_successfully()[source]

                                                                        Sanity checks that the program ran successfully. Looks at the bottom of the CP2K output file for the “PROGRAM ENDED” line, which is printed when successfully ran. Also grabs the number of warnings issued.

                                                                        @@ -391,7 +391,7 @@
                                                                        -read_pattern(patterns, reverse=False, terminate_on_match=False, postprocess=<class 'str'>)[source]
                                                                        +read_pattern(patterns, reverse=False, terminate_on_match=False, postprocess=<class 'str'>)[source]

                                                                        This function originally comes from pymatgen.io.vasp.outputs Outcar class

                                                                        General pattern reading. Uses monty’s regrep method. Takes the same arguments.

                                                                        @@ -422,7 +422,7 @@
                                                                        -read_table_pattern(header_pattern, row_pattern, footer_pattern, postprocess=<class 'str'>, attribute_name=None, last_one_only=True, strip=None)[source]
                                                                        +read_table_pattern(header_pattern, row_pattern, footer_pattern, postprocess=<class 'str'>, attribute_name=None, last_one_only=True, strip=None)[source]

                                                                        This function originally comes from pymatgen.io.vasp.outputs Outcar class

                                                                        Parse table-like data. A table composes of three parts: header, main body, footer. All the data matches “row pattern” in the main body @@ -467,13 +467,13 @@

                                                                        -property run_type[source]
                                                                        +property run_type[source]

                                                                        What type of run (Energy, MD, etc.) was performed

                                                                        -property spin_polarized[source]
                                                                        +property spin_polarized[source]

                                                                        Was the calculation spin polarized

                                                                        @@ -481,7 +481,7 @@
                                                                        -parse_dos(dos_file=None, spin_channel=None, total=False, sigma=0)[source]
                                                                        +parse_dos(dos_file=None, spin_channel=None, total=False, sigma=0)[source]

                                                                        Parse a single DOS file created by cp2k. Must contain one PDOS snapshot. i.e. you cannot use this cannot deal with multiple concatenated dos files.

                                                                        @@ -516,7 +516,7 @@
                                                                        -parse_energy_file(energy_file)[source]
                                                                        +parse_energy_file(energy_file)[source]

                                                                        Parses energy file for calculations with multiple ionic steps.

                                                                        diff --git a/docs/pymatgen.io.cp2k.sets.html b/docs/pymatgen.io.cp2k.sets.html index ef95af3e791..09ca14ac9ef 100644 --- a/docs/pymatgen.io.cp2k.sets.html +++ b/docs/pymatgen.io.cp2k.sets.html @@ -4,7 +4,7 @@ - pymatgen.io.cp2k.sets module — pymatgen 2022.5.18 documentation + pymatgen.io.cp2k.sets module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                        - 2022.5.18 + 2022.5.18.1
                                                                        @@ -136,7 +136,7 @@
                                                                        -class CellOptSet(structure: Structure | Molecule, project_name: str = 'CellOpt', override_default_params: dict = {}, **kwargs)[source]
                                                                        +class CellOptSet(structure: Structure | Molecule, project_name: str = 'CellOpt', override_default_params: dict = {}, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.sets.DftSet

                                                                        CP2K input set containing the basic settings for performing geometry optimization. Values are all cp2k defaults, and should be good for most systems of interest.

                                                                        @@ -170,7 +170,7 @@
                                                                        -class Cp2kInputSet(structure: Structure | Molecule, basis_and_potential: dict | str = 'preferred', multiplicity: int = 0, project_name: str = 'CP2K', override_default_params: dict = {}, **kwargs)[source]
                                                                        +class Cp2kInputSet(structure: Structure | Molecule, basis_and_potential: dict | str = 'preferred', multiplicity: int = 0, project_name: str = 'CP2K', override_default_params: dict = {}, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.inputs.Cp2kInput

                                                                        The basic representation of a CP2K input set as a collection of “sections” defining the simulation connected to a structure object. At the most basis level, CP2K requires a &GLOBAL section and @@ -219,13 +219,13 @@

                                                                        -create_subsys(structure: Structure | Molecule)[source]
                                                                        +create_subsys(structure: Structure | Molecule)[source]

                                                                        Create the structure for the input

                                                                        -print_forces()[source]
                                                                        +print_forces()[source]

                                                                        Print out the forces and stress during calculation

                                                                        @@ -233,7 +233,7 @@
                                                                        -class DftSet(structure: Structure | Molecule, ot: bool = True, energy_gap: float = - 1, eps_default: float = 1e-12, eps_scf: float = 1e-06, max_scf: int | None = None, minimizer: str = 'DIIS', preconditioner: str = 'FULL_SINGLE_INVERSE', algorithm: str = 'IRAC', linesearch: str = '2PNT', rotation: bool = True, occupation_preconditioner: bool = False, cutoff: int = 0, rel_cutoff: int = 50, ngrids: int = 5, progression_factor: int = 3, override_default_params: dict = {}, wfn_restart_file_name: str = None, kpoints: Kpoints | None = None, smearing: bool = False, **kwargs)[source]
                                                                        +class DftSet(structure: Structure | Molecule, ot: bool = True, energy_gap: float = - 1, eps_default: float = 1e-12, eps_scf: float = 1e-06, max_scf: int | None = None, minimizer: str = 'DIIS', preconditioner: str = 'FULL_SINGLE_INVERSE', algorithm: str = 'IRAC', linesearch: str = '2PNT', rotation: bool = True, occupation_preconditioner: bool = False, cutoff: int = 0, rel_cutoff: int = 50, ngrids: int = 5, progression_factor: int = 3, override_default_params: dict = {}, wfn_restart_file_name: str = None, kpoints: Kpoints | None = None, smearing: bool = False, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.sets.Cp2kInputSet

                                                                        Base for an input set using the Quickstep module (i.e. a DFT calculation). The DFT section is pretty vast in CP2K, so this set hopes to make the DFT setup fairly simple. The provided parameters are pretty conservative, @@ -307,13 +307,13 @@

                                                                        -activate_fast_minimization(on)[source]
                                                                        +activate_fast_minimization(on)[source]

                                                                        Method to modify the set to use fast SCF minimization.

                                                                        -activate_hybrid(hybrid_functional: str = 'PBE0', hf_fraction: float = 0.25, gga_x_fraction: float = 0.75, gga_c_fraction: float = 1, max_memory: int = 2000, cutoff_radius: float = 8.0, potential_type: str = None, scale_coulomb: float = 1, scale_gaussian: float = 1, scale_longrange: float = 1, omega: float = 0.11, aux_basis: dict | None = None, admm: bool = True, eps_schwarz: float = 1e-07, eps_schwarz_forces: float = 1e-06, screen_on_initial_p: bool = True, screen_p_forces: bool = True)[source]
                                                                        +activate_hybrid(hybrid_functional: str = 'PBE0', hf_fraction: float = 0.25, gga_x_fraction: float = 0.75, gga_c_fraction: float = 1, max_memory: int = 2000, cutoff_radius: float = 8.0, potential_type: str = None, scale_coulomb: float = 1, scale_gaussian: float = 1, scale_longrange: float = 1, omega: float = 0.11, aux_basis: dict | None = None, admm: bool = True, eps_schwarz: float = 1e-07, eps_schwarz_forces: float = 1e-06, screen_on_initial_p: bool = True, screen_p_forces: bool = True)[source]

                                                                        Basic set for activating hybrid DFT calculation using Auxiliary Density Matrix Method.

                                                                        Note 1: When running ADMM with cp2k, memory is very important. If the memory requirements exceed what is available (see max_memory), then CP2K will have to calculate the 4-electron integrals @@ -373,7 +373,7 @@

                                                                        -activate_motion()[source]
                                                                        +activate_motion()[source]

                                                                        Turns on the motion section for GEO_OPT, CELL_OPT, etc. calculations. Will turn on the printing subsections and also bind any constraints to their respective atoms.

                                                                        @@ -381,27 +381,27 @@
                                                                        -activate_nonperiodic(solver='MT')[source]
                                                                        +activate_nonperiodic(solver='MT')[source]

                                                                        Activates a calculation with non-periodic calculations by turning of PBC and changing the poisson solver. Still requires a CELL to put the atoms

                                                                        -activate_robust_minimization()[source]
                                                                        +activate_robust_minimization()[source]

                                                                        Method to modify the set to use more robust SCF minimization technique

                                                                        -activate_very_strict_minimization()[source]
                                                                        +activate_very_strict_minimization()[source]

                                                                        Method to modify the set to use very strict SCF minimization scheme :return:

                                                                        -modify_dft_print_iters(iters, add_last='no')[source]
                                                                        +modify_dft_print_iters(iters, add_last='no')[source]

                                                                        Modify all DFT print iterations at once. Common use is to set iters to the max number of iterations + 1 and then set add_last to numeric. This would have the effect of printing only the first and last iteration, which might be useful for @@ -421,13 +421,13 @@

                                                                        -print_e_density(stride=(2, 2, 2))[source]
                                                                        +print_e_density(stride=(2, 2, 2))[source]

                                                                        Controls the printing of cube files with the electronic density and, for LSD calculations, the spin density

                                                                        -print_hartree_potential(stride=(2, 2, 2))[source]
                                                                        +print_hartree_potential(stride=(2, 2, 2))[source]

                                                                        Controls the printing of a cube file with eletrostatic potential generated by the total density (electrons+ions). It is valid only for QS with GPW formalism. Note that by convention the potential has opposite sign than the expected physical one.

                                                                        @@ -435,7 +435,7 @@
                                                                        -print_ldos(nlumo=- 1)[source]
                                                                        +print_ldos(nlumo=- 1)[source]

                                                                        Activate the printing of LDOS files, printing one for each atom kind by default

                                                                        Parameters
                                                                        @@ -447,13 +447,13 @@
                                                                        -print_mo()[source]
                                                                        +print_mo()[source]

                                                                        Print molecular orbitals when running non-OT diagonalization

                                                                        -print_mo_cubes(write_cube=False, nlumo=- 1, nhomo=- 1)[source]
                                                                        +print_mo_cubes(write_cube=False, nlumo=- 1, nhomo=- 1)[source]

                                                                        Activate printing of molecular orbitals.

                                                                        Parameters
                                                                        @@ -468,7 +468,7 @@
                                                                        -print_pdos(nlumo=- 1)[source]
                                                                        +print_pdos(nlumo=- 1)[source]

                                                                        Activate creation of the PDOS file.

                                                                        Parameters
                                                                        @@ -480,7 +480,7 @@
                                                                        -set_charge(charge: int)[source]
                                                                        +set_charge(charge: int)[source]

                                                                        Set the overall charge of the simulation cell

                                                                        @@ -488,7 +488,7 @@
                                                                        -class HybridCellOptSet(structure: Structure | Molecule, hybrid_functional: str = 'PBE0', hf_fraction: float = 0.25, project_name: str = 'Hybrid-Static', potential_type: str = None, gga_x_fraction: float = 0.75, gga_c_fraction: float = 1, scale_coulomb: float = 1, scale_gaussian: float = 1, scale_longrange: float = 1, override_default_params: dict = {}, max_memory: int = 2000, cutoff_radius: float = 8.0, omega: float = 0.2, aux_basis: dict | None = None, admm: bool = True, eps_schwarz: float = 1e-06, eps_schwarz_forces: float = 1e-06, screen_on_initial_p: bool = True, screen_p_forces: bool = True, **kwargs)[source]
                                                                        +class HybridCellOptSet(structure: Structure | Molecule, hybrid_functional: str = 'PBE0', hf_fraction: float = 0.25, project_name: str = 'Hybrid-Static', potential_type: str = None, gga_x_fraction: float = 0.75, gga_c_fraction: float = 1, scale_coulomb: float = 1, scale_gaussian: float = 1, scale_longrange: float = 1, override_default_params: dict = {}, max_memory: int = 2000, cutoff_radius: float = 8.0, omega: float = 0.2, aux_basis: dict | None = None, admm: bool = True, eps_schwarz: float = 1e-06, eps_schwarz_forces: float = 1e-06, screen_on_initial_p: bool = True, screen_p_forces: bool = True, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.sets.CellOptSet

                                                                        Static calculation using hybrid DFT with the ADMM formalism in Cp2k.

                                                                        @@ -508,7 +508,7 @@
                                                                        -class HybridRelaxSet(structure: Structure | Molecule, hybrid_functional: str = 'PBE0', hf_fraction: float = 0.25, project_name: str = 'Hybrid-Static', potential_type: str = None, gga_x_fraction: float = 0.75, gga_c_fraction: float = 1, scale_coulomb: float = 1, scale_gaussian: float = 1, scale_longrange: float = 1, override_default_params: dict = {}, max_memory: int = 2000, cutoff_radius: float = 8.0, omega: float = 0.2, aux_basis: dict | None = None, admm: bool = True, eps_schwarz: float = 1e-06, eps_schwarz_forces: float = 1e-06, screen_on_initial_p: bool = True, screen_p_forces: bool = True, **kwargs)[source]
                                                                        +class HybridRelaxSet(structure: Structure | Molecule, hybrid_functional: str = 'PBE0', hf_fraction: float = 0.25, project_name: str = 'Hybrid-Static', potential_type: str = None, gga_x_fraction: float = 0.75, gga_c_fraction: float = 1, scale_coulomb: float = 1, scale_gaussian: float = 1, scale_longrange: float = 1, override_default_params: dict = {}, max_memory: int = 2000, cutoff_radius: float = 8.0, omega: float = 0.2, aux_basis: dict | None = None, admm: bool = True, eps_schwarz: float = 1e-06, eps_schwarz_forces: float = 1e-06, screen_on_initial_p: bool = True, screen_p_forces: bool = True, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.sets.RelaxSet

                                                                        Static calculation using hybrid DFT with the ADMM formalism in Cp2k.

                                                                        @@ -528,7 +528,7 @@
                                                                        -class HybridStaticSet(structure: Structure | Molecule, hybrid_functional: str = 'PBE0', hf_fraction: float = 0.25, project_name: str = 'Hybrid-Static', gga_x_fraction: float = 0.75, gga_c_fraction: float = 1, potential_type: str = None, scale_coulomb: float = 1, scale_gaussian: float = 1, scale_longrange: float = 1, override_default_params: dict = {}, max_memory: int = 2000, cutoff_radius: float = 8.0, omega: float = 0.2, aux_basis: dict | None = None, admm: bool = True, eps_schwarz: float = 1e-06, eps_schwarz_forces: float = 1e-06, screen_on_initial_p: bool = True, screen_p_forces: bool = True, **kwargs)[source]
                                                                        +class HybridStaticSet(structure: Structure | Molecule, hybrid_functional: str = 'PBE0', hf_fraction: float = 0.25, project_name: str = 'Hybrid-Static', gga_x_fraction: float = 0.75, gga_c_fraction: float = 1, potential_type: str = None, scale_coulomb: float = 1, scale_gaussian: float = 1, scale_longrange: float = 1, override_default_params: dict = {}, max_memory: int = 2000, cutoff_radius: float = 8.0, omega: float = 0.2, aux_basis: dict | None = None, admm: bool = True, eps_schwarz: float = 1e-06, eps_schwarz_forces: float = 1e-06, screen_on_initial_p: bool = True, screen_p_forces: bool = True, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.sets.StaticSet

                                                                        Static calculation using hybrid DFT with the ADMM formalism in Cp2k.

                                                                        @@ -548,7 +548,7 @@
                                                                        -class RelaxSet(structure: Structure | Molecule, max_drift: float = 0.003, rms_drift: float = 0.0015, max_force: float = 0.00045, rms_force: float = 0.0003, max_iter: int = 200, project_name: str = 'Relax', optimizer: str = 'BFGS', override_default_params: dict = {}, **kwargs)[source]
                                                                        +class RelaxSet(structure: Structure | Molecule, max_drift: float = 0.003, rms_drift: float = 0.0015, max_force: float = 0.00045, rms_force: float = 0.0003, max_iter: int = 200, project_name: str = 'Relax', optimizer: str = 'BFGS', override_default_params: dict = {}, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.sets.DftSet

                                                                        CP2K input set containing the basic settings for performing geometry optimization. Values are all cp2k defaults, and should be good for most systems of interest.

                                                                        @@ -590,7 +590,7 @@
                                                                        -class StaticSet(structure: Structure | Molecule, project_name: str = 'Static', run_type: str = 'ENERGY_FORCE', override_default_params: dict = {}, **kwargs)[source]
                                                                        +class StaticSet(structure: Structure | Molecule, project_name: str = 'Static', run_type: str = 'ENERGY_FORCE', override_default_params: dict = {}, **kwargs)[source]

                                                                        Bases: pymatgen.io.cp2k.sets.DftSet

                                                                        Basic static energy calculation. Turns on Quickstep module, sets the run_type in global, and uses structure object to build the subsystem.

                                                                        diff --git a/docs/pymatgen.io.cp2k.utils.html b/docs/pymatgen.io.cp2k.utils.html index 21679ff9181..061f34a474b 100644 --- a/docs/pymatgen.io.cp2k.utils.html +++ b/docs/pymatgen.io.cp2k.utils.html @@ -4,7 +4,7 @@ - pymatgen.io.cp2k.utils module — pymatgen 2022.5.18 documentation + pymatgen.io.cp2k.utils module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                        - 2022.5.18 + 2022.5.18.1
                                                                        @@ -119,7 +119,7 @@

                                                                        Utility functions for assisting with cp2k IO

                                                                        -get_aux_basis(basis_type, default_basis_type='cpFIT')[source]
                                                                        +get_aux_basis(basis_type, default_basis_type='cpFIT')[source]

                                                                        Get auxiliary basis info for a list of species.

                                                                        Parameters
                                                                        @@ -145,7 +145,7 @@
                                                                        -get_basis_and_potential(species, basis_and_potential_map, functional='PBE')[source]
                                                                        +get_basis_and_potential(species, basis_and_potential_map, functional='PBE')[source]

                                                                        Retrieve basis/potential dictionary

                                                                        Parameters
                                                                        @@ -167,7 +167,7 @@
                                                                        -get_cutoff_from_basis(els, bases, rel_cutoff=50)[source]
                                                                        +get_cutoff_from_basis(els, bases, rel_cutoff=50)[source]

                                                                        Gets the appropriate cutoff for the calculation given the elements/basis sets being used and the desired relative cutoff.

                                                                        @@ -186,13 +186,13 @@
                                                                        -get_truncated_coulomb_cutoff(inp_struct)[source]
                                                                        +get_truncated_coulomb_cutoff(inp_struct)[source]

                                                                        Get the truncated Coulomb cutoff for a given structure.

                                                                        -get_unique_site_indices(structure)[source]
                                                                        +get_unique_site_indices(structure)[source]

                                                                        Get unique site indices for a structure according to site properties. Whatever site-property has the most unique values is used for indexing.

                                                                        For example, if you have magnetic CoO with half Co atoms having a positive moment, and the other @@ -206,7 +206,7 @@

                                                                        -get_xc_functionals(name)[source]
                                                                        +get_xc_functionals(name)[source]

                                                                        Get the XC functionals for a given functional name. This utility does not deal with defining hybrid functionals since those may or may not require ADMM, which is not supported by LibXC and so needs to be manually @@ -220,7 +220,7 @@

                                                                        -natural_keys(text)[source]
                                                                        +natural_keys(text)[source]

                                                                        Sort text by numbers coming after an underscore with natural number convention, Ex: [file_1, file_12, file_2] becomes [file_1, file_2, file_12]

                                                                        diff --git a/docs/pymatgen.io.cssr.html b/docs/pymatgen.io.cssr.html index f565232bab4..86ad1bc935f 100644 --- a/docs/pymatgen.io.cssr.html +++ b/docs/pymatgen.io.cssr.html @@ -4,7 +4,7 @@ - pymatgen.io.cssr module — pymatgen 2022.5.18 documentation + pymatgen.io.cssr module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                        - 2022.5.18 + 2022.5.18.1
                                                                        @@ -118,7 +118,7 @@

                                                                        This module provides input and output from the CSSR file format.

                                                                        -class Cssr(structure)[source]
                                                                        +class Cssr(structure)[source]

                                                                        Bases: object

                                                                        Basic object for working with Cssr file. Right now, only conversion from a Structure to a Cssr file is supported.

                                                                        @@ -129,7 +129,7 @@
                                                                        -static from_file(filename)[source]
                                                                        +static from_file(filename)[source]

                                                                        Reads a CSSR file to a Cssr object.

                                                                        Parameters
                                                                        @@ -143,7 +143,7 @@
                                                                        -static from_string(string)[source]
                                                                        +static from_string(string)[source]

                                                                        Reads a string representation to a Cssr object.

                                                                        Parameters
                                                                        @@ -157,7 +157,7 @@
                                                                        -write_file(filename)[source]
                                                                        +write_file(filename)[source]

                                                                        Write out a CSSR file.

                                                                        Parameters
                                                                        diff --git a/docs/pymatgen.io.cube.html b/docs/pymatgen.io.cube.html index 2bf03e07ca7..5d9fb26676a 100644 --- a/docs/pymatgen.io.cube.html +++ b/docs/pymatgen.io.cube.html @@ -4,7 +4,7 @@ - pymatgen.io.cube module — pymatgen 2022.5.18 documentation + pymatgen.io.cube module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                        - 2022.5.18 + 2022.5.18.1
                                                                        @@ -162,7 +162,7 @@
                                                                      -class Cube(fname)[source]
                                                                      +class Cube(fname)[source]

                                                                      Bases: object

                                                                      Class to read Gaussian cube file formats for volumetric data.

                                                                      Cube files are, by default, written in atomic units, and this @@ -175,7 +175,7 @@

                                                                      -get_atomic_site_averages(atomic_site_radii)[source]
                                                                      +get_atomic_site_averages(atomic_site_radii)[source]

                                                                      Get the average value around each atomic site.

                                                                      Parameters
                                                                      @@ -191,7 +191,7 @@
                                                                      -get_atomic_site_totals(atomic_site_radii)[source]
                                                                      +get_atomic_site_totals(atomic_site_radii)[source]

                                                                      Get the integrated total in a sphere around each atomic site.

                                                                      Parameters
                                                                      @@ -207,7 +207,7 @@
                                                                      -get_average_along_axis(ind)[source]
                                                                      +get_average_along_axis(ind)[source]

                                                                      Modified from pymatgen.io.vasp.outputs

                                                                      Get the averaged total of the volumetric data a certain axis direction. For example, useful for visualizing Hartree Potentials.

                                                                      @@ -223,7 +223,7 @@
                                                                      -get_axis_grid(ind)[source]
                                                                      +get_axis_grid(ind)[source]

                                                                      Modified from pymatgen.io.vasp.outputs

                                                                      Returns the grid for a particular axis.

                                                                      @@ -235,7 +235,7 @@
                                                                      -mask_sphere(radius, cx, cy, cz)[source]
                                                                      +mask_sphere(radius, cx, cy, cz)[source]

                                                                      Create a mask for a sphere with radius=radius, centered at cx, cy, cz.

                                                                      Parameters
                                                                      diff --git a/docs/pymatgen.io.exciting.html b/docs/pymatgen.io.exciting.html index 5c28a6553a3..aefdad5d838 100644 --- a/docs/pymatgen.io.exciting.html +++ b/docs/pymatgen.io.exciting.html @@ -4,7 +4,7 @@ - pymatgen.io.exciting package — pymatgen 2022.5.18 documentation + pymatgen.io.exciting package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                      - 2022.5.18 + 2022.5.18.1
                                                                      diff --git a/docs/pymatgen.io.exciting.inputs.html b/docs/pymatgen.io.exciting.inputs.html index 80fc3445c46..3952ee748ec 100644 --- a/docs/pymatgen.io.exciting.inputs.html +++ b/docs/pymatgen.io.exciting.inputs.html @@ -4,7 +4,7 @@ - pymatgen.io.exciting.inputs module — pymatgen 2022.5.18 documentation + pymatgen.io.exciting.inputs module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                      - 2022.5.18 + 2022.5.18.1
                                                                      @@ -119,25 +119,25 @@

                                                                      Classes for reading/manipulating/writing exciting input files.

                                                                      -class ExcitingInput(structure, title=None, lockxyz=None)[source]
                                                                      +class ExcitingInput(structure, title=None, lockxyz=None)[source]

                                                                      Bases: monty.json.MSONable

                                                                      Object for representing the data stored in the structure part of the exciting input.

                                                                      -structure[source]
                                                                      +structure[source]

                                                                      Associated Structure.

                                                                      -title[source]
                                                                      +title[source]

                                                                      Optional title string.

                                                                      -lockxyz[source]
                                                                      +lockxyz[source]

                                                                      Lockxyz attribute for each site if available. A Nx3 array of booleans.

                                                                      @@ -155,12 +155,12 @@
                                                                      -bohr2ang = 0.5291692998219677[source]
                                                                      +bohr2ang = 0.5291692998219677[source]
                                                                      -static from_file(filename)[source]
                                                                      +static from_file(filename)[source]
                                                                      Parameters

                                                                      filename – Filename

                                                                      @@ -173,13 +173,13 @@
                                                                      -static from_string(data)[source]
                                                                      +static from_string(data)[source]

                                                                      Reads the exciting input from a string

                                                                      -property lockxyz[source]
                                                                      +property lockxyz[source]

                                                                      Selective dynamics site properties.

                                                                      Type
                                                                      @@ -190,7 +190,7 @@
                                                                      -write_etree(celltype, cartesian=False, bandstr=False, symprec=0.4, angle_tolerance=5, **kwargs)[source]
                                                                      +write_etree(celltype, cartesian=False, bandstr=False, symprec=0.4, angle_tolerance=5, **kwargs)[source]

                                                                      Writes the exciting input parameters to an xml object.

                                                                      Parameters
                                                                      @@ -218,7 +218,7 @@
                                                                      -write_file(celltype, filename, cartesian=False, bandstr=False, symprec=0.4, angle_tolerance=5, **kwargs)[source]
                                                                      +write_file(celltype, filename, cartesian=False, bandstr=False, symprec=0.4, angle_tolerance=5, **kwargs)[source]

                                                                      Writes exciting input file.

                                                                      Parameters
                                                                      @@ -244,7 +244,7 @@
                                                                      -write_string(celltype, cartesian=False, bandstr=False, symprec=0.4, angle_tolerance=5, **kwargs)[source]
                                                                      +write_string(celltype, cartesian=False, bandstr=False, symprec=0.4, angle_tolerance=5, **kwargs)[source]

                                                                      Writes exciting input.xml as a string.

                                                                      Parameters
                                                                      diff --git a/docs/pymatgen.io.feff.html b/docs/pymatgen.io.feff.html index 68343f44bfc..a0fe7509e5d 100644 --- a/docs/pymatgen.io.feff.html +++ b/docs/pymatgen.io.feff.html @@ -4,7 +4,7 @@ - pymatgen.io.feff package — pymatgen 2022.5.18 documentation + pymatgen.io.feff package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                      - 2022.5.18 + 2022.5.18.1
                                                                      diff --git a/docs/pymatgen.io.feff.inputs.html b/docs/pymatgen.io.feff.inputs.html index a76612db33b..4bdc7469b2a 100644 --- a/docs/pymatgen.io.feff.inputs.html +++ b/docs/pymatgen.io.feff.inputs.html @@ -4,7 +4,7 @@ - pymatgen.io.feff.inputs module — pymatgen 2022.5.18 documentation + pymatgen.io.feff.inputs module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                      - 2022.5.18 + 2022.5.18.1
                                                                      @@ -122,7 +122,7 @@

                                                                      XANES and EXAFS input files, are available, for non-spin case at this time.

                                                                      -class Atoms(struct, absorbing_atom, radius)[source]
                                                                      +class Atoms(struct, absorbing_atom, radius)[source]

                                                                      Bases: monty.json.MSONable

                                                                      Atomic cluster centered around the absorbing atom.

                                                                      @@ -136,7 +136,7 @@
                                                                      -static atoms_string_from_file(filename)[source]
                                                                      +static atoms_string_from_file(filename)[source]

                                                                      Reads atomic shells from file such as feff.inp or ATOMS file The lines are arranged as follows:

                                                                      x y z ipot Atom Symbol Distance Number

                                                                      @@ -154,13 +154,13 @@
                                                                      -property cluster[source]
                                                                      +property cluster[source]

                                                                      Returns the atomic cluster as a Molecule object.

                                                                      -static cluster_from_file(filename)[source]
                                                                      +static cluster_from_file(filename)[source]

                                                                      Parse the feff input file and return the atomic cluster as a Molecule object.

                                                                      @@ -182,7 +182,7 @@
                                                                      -get_lines()[source]
                                                                      +get_lines()[source]

                                                                      Returns a list of string representations of the atomic configuration information(x, y, z, ipot, atom_symbol, distance, id).

                                                                      @@ -201,7 +201,7 @@
                                                                      -write_file(filename='ATOMS')[source]
                                                                      +write_file(filename='ATOMS')[source]

                                                                      Write Atoms list to file.

                                                                      Parameters
                                                                      @@ -214,7 +214,7 @@
                                                                      -exception FeffParserError[source]
                                                                      +exception FeffParserError[source]

                                                                      Bases: Exception

                                                                      Exception class for Structure. Raised when the structure has problems, e.g., atoms that are too close.

                                                                      @@ -222,7 +222,7 @@
                                                                      -class Header(struct, source='', comment='')[source]
                                                                      +class Header(struct, source='', comment='')[source]

                                                                      Bases: monty.json.MSONable

                                                                      Creates Header for the FEFF input file.

                                                                      Has the following format:

                                                                      @@ -253,13 +253,13 @@
                                                                      -property formula[source]
                                                                      +property formula[source]

                                                                      Formula of structure

                                                                      -static from_cif_file(cif_file, source='', comment='')[source]
                                                                      +static from_cif_file(cif_file, source='', comment='')[source]

                                                                      Static method to create Header object from cif_file

                                                                      Parameters
                                                                      @@ -278,13 +278,13 @@
                                                                      -static from_file(filename)[source]
                                                                      +static from_file(filename)[source]

                                                                      Returns Header object from file

                                                                      -static from_string(header_str)[source]
                                                                      +static from_string(header_str)[source]

                                                                      Reads Header string and returns Header object if header was generated by pymatgen. Note: Checks to see if generated by pymatgen, if not it is impossible

                                                                      @@ -304,7 +304,7 @@
                                                                      -static header_string_from_file(filename='feff.inp')[source]
                                                                      +static header_string_from_file(filename='feff.inp')[source]

                                                                      Reads Header string from either a HEADER file or feff.inp file Will also read a header from a non-pymatgen generated feff.inp file

                                                                      @@ -319,7 +319,7 @@
                                                                      -property structure_symmetry[source]
                                                                      +property structure_symmetry[source]

                                                                      Returns space number and space group

                                                                      Returns
                                                                      @@ -330,7 +330,7 @@
                                                                      -write_file(filename='HEADER')[source]
                                                                      +write_file(filename='HEADER')[source]

                                                                      Writes Header into filename on disk.

                                                                      Parameters
                                                                      @@ -343,7 +343,7 @@
                                                                      -class Paths(atoms, paths, degeneracies=None)[source]
                                                                      +class Paths(atoms, paths, degeneracies=None)[source]

                                                                      Bases: monty.json.MSONable

                                                                      Set FEFF scattering paths(‘paths.dat’ file used by the ‘genfmt’ module).

                                                                      @@ -359,7 +359,7 @@
                                                                      -write_file(filename='paths.dat')[source]
                                                                      +write_file(filename='paths.dat')[source]

                                                                      Write paths.dat.

                                                                      @@ -367,7 +367,7 @@
                                                                      -class Potential(struct, absorbing_atom)[source]
                                                                      +class Potential(struct, absorbing_atom)[source]

                                                                      Bases: monty.json.MSONable

                                                                      FEFF atomic potential.

                                                                      @@ -380,7 +380,7 @@
                                                                      -static pot_dict_from_string(pot_data)[source]
                                                                      +static pot_dict_from_string(pot_data)[source]

                                                                      Creates atomic symbol/potential number dictionary forward and reverse

                                                                      @@ -396,7 +396,7 @@
                                                                      -static pot_string_from_file(filename='feff.inp')[source]
                                                                      +static pot_string_from_file(filename='feff.inp')[source]

                                                                      Reads Potential parameters from a feff.inp or FEFFPOT file. The lines are arranged as follows:

                                                                      @@ -414,7 +414,7 @@
                                                                      -write_file(filename='POTENTIALS')[source]
                                                                      +write_file(filename='POTENTIALS')[source]

                                                                      Write to file.

                                                                      Parameters
                                                                      @@ -427,7 +427,7 @@
                                                                      -class Tags(params=None)[source]
                                                                      +class Tags(params=None)[source]

                                                                      Bases: dict

                                                                      FEFF control parameters.

                                                                      @@ -437,7 +437,7 @@
                                                                      -as_dict()[source]
                                                                      +as_dict()[source]

                                                                      Dict representation.

                                                                      Returns
                                                                      @@ -448,7 +448,7 @@
                                                                      -diff(other)[source]
                                                                      +diff(other)[source]

                                                                      Diff function. Compares two PARAMETER files and indicates which parameters are the same and which are not. Useful for checking whether two runs were done using the same parameters.

                                                                      @@ -469,7 +469,7 @@
                                                                      -static from_dict(d)[source]
                                                                      +static from_dict(d)[source]

                                                                      Creates Tags object from a dictionary.

                                                                      Parameters
                                                                      @@ -483,7 +483,7 @@
                                                                      -static from_file(filename='feff.inp')[source]
                                                                      +static from_file(filename='feff.inp')[source]

                                                                      Creates a Feff_tag dictionary from a PARAMETER or feff.inp file.

                                                                      Parameters
                                                                      @@ -497,7 +497,7 @@
                                                                      -get_string(sort_keys=False, pretty=False)[source]
                                                                      +get_string(sort_keys=False, pretty=False)[source]

                                                                      Returns a string representation of the Tags. The reason why this method is different from the __str__ method is to provide options for pretty printing.

                                                                      @@ -517,7 +517,7 @@
                                                                      -static proc_val(key, val)[source]
                                                                      +static proc_val(key, val)[source]

                                                                      Static helper method to convert Feff parameters to proper types, e.g. integers, floats, lists, etc.

                                                                      @@ -532,7 +532,7 @@
                                                                      -write_file(filename='PARAMETERS')[source]
                                                                      +write_file(filename='PARAMETERS')[source]

                                                                      Write Tags to a Feff parameter tag file.

                                                                      Parameters
                                                                      @@ -545,7 +545,7 @@
                                                                      -get_absorbing_atom_symbol_index(absorbing_atom, structure)[source]
                                                                      +get_absorbing_atom_symbol_index(absorbing_atom, structure)[source]

                                                                      Return the absorbing atom symbol and site index in the given structure.

                                                                      Parameters
                                                                      @@ -565,7 +565,7 @@
                                                                      -get_atom_map(structure)[source]
                                                                      +get_atom_map(structure)[source]

                                                                      Returns a dict that maps each atomic symbol to a unique integer starting from 1.

                                                                      diff --git a/docs/pymatgen.io.feff.outputs.html b/docs/pymatgen.io.feff.outputs.html index 5c12ff93c86..b9f0e399b87 100644 --- a/docs/pymatgen.io.feff.outputs.html +++ b/docs/pymatgen.io.feff.outputs.html @@ -4,7 +4,7 @@ - pymatgen.io.feff.outputs module — pymatgen 2022.5.18 documentation + pymatgen.io.feff.outputs module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                      - 2022.5.18 + 2022.5.18.1
                                                                      @@ -120,7 +120,7 @@

                                                                      Currently supports the xmu.dat, ldos.dat output files are for non-spin case.

                                                                      -class Eels(data)[source]
                                                                      +class Eels(data)[source]

                                                                      Bases: monty.json.MSONable

                                                                      Parse’eels.dat’ file.

                                                                      @@ -130,13 +130,13 @@
                                                                      -as_dict()[source]
                                                                      +as_dict()[source]

                                                                      Returns dict representations of Xmu object

                                                                      -property atomic_background[source]
                                                                      +property atomic_background[source]

                                                                      atomic background.

                                                                      Type
                                                                      @@ -147,13 +147,13 @@
                                                                      -property energies[source]
                                                                      +property energies[source]

                                                                      Returns the energies in eV.

                                                                      -property fine_structure[source]
                                                                      +property fine_structure[source]

                                                                      Fine structure of EELS.

                                                                      Type
                                                                      @@ -164,7 +164,7 @@
                                                                      -static from_file(eels_dat_file='eels.dat')[source]
                                                                      +static from_file(eels_dat_file='eels.dat')[source]

                                                                      Parse eels spectrum.

                                                                      Parameters
                                                                      @@ -178,7 +178,7 @@
                                                                      -property total_spectrum[source]
                                                                      +property total_spectrum[source]

                                                                      Returns the total eels spectrum.

                                                                      @@ -186,7 +186,7 @@
                                                                      -class LDos(complete_dos, charge_transfer)[source]
                                                                      +class LDos(complete_dos, charge_transfer)[source]

                                                                      Bases: monty.json.MSONable

                                                                      Parser for ldos files ldos01, ldos02, …..

                                                                      @@ -200,7 +200,7 @@
                                                                      -static charge_transfer_from_file(feff_inp_file, ldos_file)[source]
                                                                      +static charge_transfer_from_file(feff_inp_file, ldos_file)[source]

                                                                      Get charge transfer from file.

                                                                      Parameters
                                                                      @@ -219,13 +219,13 @@
                                                                      -charge_transfer_to_string()[source]
                                                                      +charge_transfer_to_string()[source]

                                                                      returns shrage transfer as string

                                                                      -static from_file(feff_inp_file='feff.inp', ldos_file='ldos')[source]
                                                                      +static from_file(feff_inp_file='feff.inp', ldos_file='ldos')[source]

                                                                      Creates LDos object from raw Feff ldos files by by assuming they are numbered consecutively, i.e. ldos01.dat ldos02.dat…

                                                                      @@ -243,7 +243,7 @@
                                                                      -class Xmu(header, parameters, absorbing_atom, data)[source]
                                                                      +class Xmu(header, parameters, absorbing_atom, data)[source]

                                                                      Bases: monty.json.MSONable

                                                                      Parser for data in ‘xmu.dat’ file. The file ‘xmu.dat’ contains XANES, EXAFS or NRIXS data depending on the @@ -276,43 +276,43 @@

                                                                      -as_dict()[source]
                                                                      +as_dict()[source]

                                                                      Returns dict representations of Xmu object

                                                                      -property calc[source]
                                                                      +property calc[source]

                                                                      Returns type of Feff calculation, XANES or EXAFS

                                                                      -property chi[source]
                                                                      +property chi[source]

                                                                      Returns the normalized fine structure.

                                                                      -property e_fermi[source]
                                                                      +property e_fermi[source]

                                                                      Returns the fermi level in eV.

                                                                      -property edge[source]
                                                                      +property edge[source]

                                                                      Returns excitation edge.

                                                                      -property energies[source]
                                                                      +property energies[source]

                                                                      Returns the absolute energies in eV.

                                                                      -static from_file(xmu_dat_file='xmu.dat', feff_inp_file='feff.inp')[source]
                                                                      +static from_file(xmu_dat_file='xmu.dat', feff_inp_file='feff.inp')[source]

                                                                      Get Xmu from file.

                                                                      Parameters
                                                                      @@ -329,38 +329,38 @@
                                                                      -property material_formula[source]
                                                                      +property material_formula[source]

                                                                      Returns chemical formula of material from feff.inp file

                                                                      -property mu[source]
                                                                      +property mu[source]

                                                                      Returns the total absorption cross-section.

                                                                      -property mu0[source]
                                                                      +property mu0[source]

                                                                      Returns the embedded atomic background absorption.

                                                                      -property relative_energies[source]
                                                                      +property relative_energies[source]

                                                                      Returns energy with respect to the fermi level. E - E_f

                                                                      -property source[source]
                                                                      +property source[source]

                                                                      Returns source identification from Header file

                                                                      -property wavenumber[source]
                                                                      +property wavenumber[source]

                                                                      Returns The wave number in units of \AA^-1. k=\sqrt(E - E_f) where E is the energy and E_f is the Fermi level computed from electron gas theory at the average interstitial charge density.

                                                                      diff --git a/docs/pymatgen.io.feff.sets.html b/docs/pymatgen.io.feff.sets.html index ef2e4e9ba0f..37a18206bc2 100644 --- a/docs/pymatgen.io.feff.sets.html +++ b/docs/pymatgen.io.feff.sets.html @@ -4,7 +4,7 @@ - pymatgen.io.feff.sets module — pymatgen 2022.5.18 documentation + pymatgen.io.feff.sets module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                      - 2022.5.18 + 2022.5.18.1
                                                                      @@ -123,7 +123,7 @@ runs.

                                                                      -class AbstractFeffInputSet[source]
                                                                      +class AbstractFeffInputSet[source]

                                                                      Bases: monty.json.MSONable

                                                                      Abstract base class representing a set of Feff input parameters. The idea is that using a FeffInputSet, a complete set of input files @@ -131,13 +131,13 @@ can be generated in an automated fashion for any structure.

                                                                      -all_input()[source]
                                                                      +all_input()[source]

                                                                      Returns all input files as a dict of {filename: feffio object}

                                                                      -abstract property atoms[source]
                                                                      +abstract property atoms[source]

                                                                      Returns Atoms string from a structure that goes in feff.inp file.

                                                                      Returns
                                                                      @@ -148,25 +148,25 @@
                                                                      -abstract header()[source]
                                                                      +abstract header()[source]

                                                                      Returns header to be used in feff.inp file from a pymatgen structure

                                                                      -abstract property potential[source]
                                                                      +abstract property potential[source]

                                                                      Returns POTENTIAL section used in feff.inp from a structure.

                                                                      -abstract property tags[source]
                                                                      +abstract property tags[source]

                                                                      Returns standard calculation parameters.

                                                                      -write_input(output_dir='.', make_dir_if_not_present=True)[source]
                                                                      +write_input(output_dir='.', make_dir_if_not_present=True)[source]

                                                                      Writes a set of FEFF input to a directory.

                                                                      Parameters
                                                                      @@ -183,7 +183,7 @@
                                                                      -class FEFFDictSet(absorbing_atom, structure, radius, config_dict, edge='K', spectrum='EXAFS', nkpts=1000, user_tag_settings=None)[source]
                                                                      +class FEFFDictSet(absorbing_atom, structure, radius, config_dict, edge='K', spectrum='EXAFS', nkpts=1000, user_tag_settings=None)[source]

                                                                      Bases: pymatgen.io.feff.sets.AbstractFeffInputSet

                                                                      Standard implementation of FeffInputSet, which can be extended by specific implementations.

                                                                      @@ -208,7 +208,7 @@
                                                                      -property atoms[source]
                                                                      +property atoms[source]

                                                                      absorber + the rest

                                                                      Returns
                                                                      @@ -219,14 +219,14 @@
                                                                      -static from_directory(input_dir)[source]
                                                                      +static from_directory(input_dir)[source]

                                                                      Read in a set of FEFF input files from a directory, which is useful when existing FEFF input needs some adjustment.

                                                                      -header(source='', comment='')[source]
                                                                      +header(source='', comment='')[source]

                                                                      Creates header string from structure object

                                                                      Parameters
                                                                      @@ -245,7 +245,7 @@
                                                                      -property potential[source]
                                                                      +property potential[source]

                                                                      FEFF potential

                                                                      Returns
                                                                      @@ -256,7 +256,7 @@
                                                                      -property tags[source]
                                                                      +property tags[source]

                                                                      FEFF job parameters.

                                                                      Returns
                                                                      @@ -269,7 +269,7 @@
                                                                      -class MPEELSDictSet(absorbing_atom, structure, edge, spectrum, radius, beam_energy, beam_direction, collection_angle, convergence_angle, config_dict, user_eels_settings=None, nkpts=1000, user_tag_settings=None)[source]
                                                                      +class MPEELSDictSet(absorbing_atom, structure, edge, spectrum, radius, beam_energy, beam_direction, collection_angle, convergence_angle, config_dict, user_eels_settings=None, nkpts=1000, user_tag_settings=None)[source]

                                                                      Bases: pymatgen.io.feff.sets.FEFFDictSet

                                                                      FeffDictSet for ELNES spectroscopy.

                                                                      @@ -297,7 +297,7 @@
                                                                      -class MPELNESSet(absorbing_atom, structure, edge='K', radius=10.0, beam_energy=100, beam_direction=None, collection_angle=1, convergence_angle=1, user_eels_settings=None, nkpts=1000, user_tag_settings=None)[source]
                                                                      +class MPELNESSet(absorbing_atom, structure, edge='K', radius=10.0, beam_energy=100, beam_direction=None, collection_angle=1, convergence_angle=1, user_eels_settings=None, nkpts=1000, user_tag_settings=None)[source]

                                                                      Bases: pymatgen.io.feff.sets.MPEELSDictSet

                                                                      FeffDictSet for ELNES spectroscopy.

                                                                      @@ -322,14 +322,14 @@
                                                                      -CONFIG = {'CONTROL': '1 1 1 1 1 1', 'COREHOLE': 'FSR', 'EDGE': 'K', 'ELNES': {'ANGLES': '1 1', 'BEAM_DIRECTION': '0 1 0', 'BEAM_ENERGY': '100 0 1 1', 'ENERGY': '4 0.04 0.1', 'MESH': '50 1', 'POSITION': '0.0 0.0'}, 'EXCHANGE': '0 0.0 0.0 2', 'FMS': '7.5 0', 'LDOS': '-20.0 20.0 0.1', 'PRINT': '1 0 0 0 0 0', 'S02': 0.0, 'SCF': '6.0 0 30 0.2 1'}[source]
                                                                      +CONFIG = {'CONTROL': '1 1 1 1 1 1', 'COREHOLE': 'FSR', 'EDGE': 'K', 'ELNES': {'ANGLES': '1 1', 'BEAM_DIRECTION': '0 1 0', 'BEAM_ENERGY': '100 0 1 1', 'ENERGY': '4 0.04 0.1', 'MESH': '50 1', 'POSITION': '0.0 0.0'}, 'EXCHANGE': '0 0.0 0.0 2', 'FMS': '7.5 0', 'LDOS': '-20.0 20.0 0.1', 'PRINT': '1 0 0 0 0 0', 'S02': 0.0, 'SCF': '6.0 0 30 0.2 1'}[source]
                                                                      -class MPEXAFSSet(absorbing_atom, structure, edge='K', radius=10.0, nkpts=1000, user_tag_settings=None)[source]
                                                                      +class MPEXAFSSet(absorbing_atom, structure, edge='K', radius=10.0, nkpts=1000, user_tag_settings=None)[source]

                                                                      Bases: pymatgen.io.feff.sets.FEFFDictSet

                                                                      FeffDictSet for EXAFS spectroscopy.

                                                                      @@ -347,14 +347,14 @@
                                                                      -CONFIG = {'CONTROL': '1 1 1 1 1 1', 'COREHOLE': 'FSR', 'EDGE': 'K', 'EXAFS': 20, 'PRINT': '1 0 0 0 0 0', 'RPATH': 10, 'S02': 0.0, 'SCF': '4.5 0 30 .2 1'}[source]
                                                                      +CONFIG = {'CONTROL': '1 1 1 1 1 1', 'COREHOLE': 'FSR', 'EDGE': 'K', 'EXAFS': 20, 'PRINT': '1 0 0 0 0 0', 'RPATH': 10, 'S02': 0.0, 'SCF': '4.5 0 30 .2 1'}[source]
                                                                      -class MPEXELFSSet(absorbing_atom, structure, edge='K', radius=10.0, beam_energy=100, beam_direction=None, collection_angle=1, convergence_angle=1, user_eels_settings=None, nkpts=1000, user_tag_settings=None)[source]
                                                                      +class MPEXELFSSet(absorbing_atom, structure, edge='K', radius=10.0, beam_energy=100, beam_direction=None, collection_angle=1, convergence_angle=1, user_eels_settings=None, nkpts=1000, user_tag_settings=None)[source]

                                                                      Bases: pymatgen.io.feff.sets.MPEELSDictSet

                                                                      FeffDictSet for EXELFS spectroscopy.

                                                                      @@ -379,14 +379,14 @@
                                                                      -CONFIG = {'CONTROL': '1 1 1 1 1 1', 'COREHOLE': 'FSR', 'EDGE': 'K', 'EXCHANGE': '0 0.0 0.0 2', 'EXELFS': {'ANGLES': '1 1', 'BEAM_DIRECTION': '0 1 0', 'BEAM_ENERGY': '100 0 1 1', 'ENERGY': 20, 'MESH': '50 1', 'POSITION': '0.0 0.0'}, 'PRINT': '1 0 0 0 0 0', 'RPATH': 10, 'S02': 0.0, 'SCF': '5.0 0 30 0.2 1'}[source]
                                                                      +CONFIG = {'CONTROL': '1 1 1 1 1 1', 'COREHOLE': 'FSR', 'EDGE': 'K', 'EXCHANGE': '0 0.0 0.0 2', 'EXELFS': {'ANGLES': '1 1', 'BEAM_DIRECTION': '0 1 0', 'BEAM_ENERGY': '100 0 1 1', 'ENERGY': 20, 'MESH': '50 1', 'POSITION': '0.0 0.0'}, 'PRINT': '1 0 0 0 0 0', 'RPATH': 10, 'S02': 0.0, 'SCF': '5.0 0 30 0.2 1'}[source]
                                                                      -class MPXANESSet(absorbing_atom, structure, edge='K', radius=10.0, nkpts=1000, user_tag_settings=None)[source]
                                                                      +class MPXANESSet(absorbing_atom, structure, edge='K', radius=10.0, nkpts=1000, user_tag_settings=None)[source]

                                                                      Bases: pymatgen.io.feff.sets.FEFFDictSet

                                                                      FeffDictSet for XANES spectroscopy.

                                                                      @@ -404,7 +404,7 @@
                                                                      -CONFIG = {'CONTROL': '1 1 1 1 1 1', 'COREHOLE': 'FSR', 'EDGE': 'K', 'EXCHANGE': '0 0.0 0.0 2', 'FMS': '7.5 0', 'LDOS': '-30. 15. .1', 'PRINT': '1 0 0 0 0 0', 'S02': 0.0, 'SCF': '4.5 0 30 .2 1', 'XANES': '3.7 .04 .1'}[source]
                                                                      +CONFIG = {'CONTROL': '1 1 1 1 1 1', 'COREHOLE': 'FSR', 'EDGE': 'K', 'EXCHANGE': '0 0.0 0.0 2', 'FMS': '7.5 0', 'LDOS': '-30. 15. .1', 'PRINT': '1 0 0 0 0 0', 'S02': 0.0, 'SCF': '4.5 0 30 .2 1', 'XANES': '3.7 .04 .1'}[source]
                                                                      diff --git a/docs/pymatgen.io.fiesta.html b/docs/pymatgen.io.fiesta.html index 75df6f4b9dc..6f0e3fe8290 100644 --- a/docs/pymatgen.io.fiesta.html +++ b/docs/pymatgen.io.fiesta.html @@ -4,7 +4,7 @@ - pymatgen.io.fiesta module — pymatgen 2022.5.18 documentation + pymatgen.io.fiesta module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                      - 2022.5.18 + 2022.5.18.1
                                                                      @@ -122,7 +122,7 @@ -Localised Basis set reader

                                                                      -class BSEOutput(filename)[source]
                                                                      +class BSEOutput(filename)[source]

                                                                      Bases: object

                                                                      A bse output file parser. The start…

                                                                      All energies are in eV.

                                                                      @@ -135,7 +135,7 @@
                                                                      -class BasisSetReader(filename)[source]
                                                                      +class BasisSetReader(filename)[source]

                                                                      Bases: object

                                                                      A basis set reader. Basis set are stored in data as a dict: @@ -148,13 +148,13 @@

                                                                      -infos_on_basis_set()[source]
                                                                      +infos_on_basis_set()[source]

                                                                      infos on the basis set as in Fiesta log

                                                                      -set_n_nlmo()[source]
                                                                      +set_n_nlmo()[source]
                                                                      Returns

                                                                      the number of nlm orbitals for the basis set

                                                                      @@ -166,7 +166,7 @@
                                                                      -class FiestaInput(mol, correlation_grid={'dE_grid': '0.500', 'n_grid': '14'}, Exc_DFT_option={'rdVxcpsi': '1'}, COHSEX_options={'eigMethod': 'C', 'mix_cohsex': '0.500', 'nc_cohsex': '0', 'nit_cohsex': '0', 'nv_cohsex': '0', 'resMethod': 'V', 'scf_cohsex_wf': '0'}, GW_options={'nc_corr': '10', 'nit_gw': '3', 'nv_corr': '10'}, BSE_TDDFT_options={'do_bse': '1', 'do_tddft': '0', 'nc_bse': '382', 'nit_bse': '50', 'npsi_bse': '1', 'nv_bse': '21'})[source]
                                                                      +class FiestaInput(mol, correlation_grid={'dE_grid': '0.500', 'n_grid': '14'}, Exc_DFT_option={'rdVxcpsi': '1'}, COHSEX_options={'eigMethod': 'C', 'mix_cohsex': '0.500', 'nc_cohsex': '0', 'nit_cohsex': '0', 'nv_cohsex': '0', 'resMethod': 'V', 'scf_cohsex_wf': '0'}, GW_options={'nc_corr': '10', 'nit_gw': '3', 'nv_corr': '10'}, BSE_TDDFT_options={'do_bse': '1', 'do_tddft': '0', 'nc_bse': '382', 'nit_bse': '50', 'npsi_bse': '1', 'nv_bse': '21'})[source]

                                                                      Bases: monty.json.MSONable

                                                                      Input File for Fiesta called “cell.in” by default (mandatory in Fiesta for now)

                                                                      @@ -183,7 +183,7 @@
                                                                      -as_dict()[source]
                                                                      +as_dict()[source]
                                                                      Returns

                                                                      MSONable dict

                                                                      @@ -193,7 +193,7 @@
                                                                      -dump_BSE_data_in_GW_run(BSE_dump=True)[source]
                                                                      +dump_BSE_data_in_GW_run(BSE_dump=True)[source]
                                                                      Parameters

                                                                      BSE_dump – boolean

                                                                      @@ -206,7 +206,7 @@
                                                                      -dump_TDDFT_data_in_GW_run(TDDFT_dump=True)[source]
                                                                      +dump_TDDFT_data_in_GW_run(TDDFT_dump=True)[source]
                                                                      Parameters

                                                                      TDDFT_dump – boolean

                                                                      @@ -219,7 +219,7 @@
                                                                      -classmethod from_dict(d)[source]
                                                                      +classmethod from_dict(d)[source]
                                                                      Parameters

                                                                      d – Dict representation

                                                                      @@ -232,7 +232,7 @@
                                                                      -classmethod from_file(filename)[source]
                                                                      +classmethod from_file(filename)[source]

                                                                      Read an Fiesta input from a file. Currently tested to work with files generated from this class itself.

                                                                      @@ -247,7 +247,7 @@
                                                                      -classmethod from_string(string_input)[source]
                                                                      +classmethod from_string(string_input)[source]

                                                                      Read an FiestaInput from a string. Currently tested to work with files generated from this class itself.

                                                                      @@ -262,25 +262,25 @@
                                                                      -property infos_on_system[source]
                                                                      +property infos_on_system[source]

                                                                      Returns infos on initial parameters as in the log file of Fiesta

                                                                      -static make_FULL_BSE_Densities_folder(folder)[source]
                                                                      +static make_FULL_BSE_Densities_folder(folder)[source]

                                                                      mkdir “FULL_BSE_Densities” folder (needed for bse run) in the desired folder

                                                                      -property molecule[source]
                                                                      +property molecule[source]

                                                                      Returns molecule associated with this FiestaInput.

                                                                      -set_BSE_options(n_excitations=10, nit_bse=200)[source]
                                                                      +set_BSE_options(n_excitations=10, nit_bse=200)[source]

                                                                      Set parameters in cell.in for a BSE computation :param nv_bse: number of valence bands :param nc_bse: number of conduction bands @@ -290,7 +290,7 @@

                                                                      -set_GW_options(nv_band=10, nc_band=10, n_iteration=5, n_grid=6, dE_grid=0.5)[source]
                                                                      +set_GW_options(nv_band=10, nc_band=10, n_iteration=5, n_grid=6, dE_grid=0.5)[source]

                                                                      Set parameters in cell.in for a GW computation :param nv__band: number of valence bands to correct with GW :param nc_band: number of conduction bands to correct with GW @@ -300,7 +300,7 @@

                                                                      -set_auxiliary_basis_set(folder, auxiliary_folder, auxiliary_basis_set_type='aug_cc_pvtz')[source]
                                                                      +set_auxiliary_basis_set(folder, auxiliary_folder, auxiliary_basis_set_type='aug_cc_pvtz')[source]

                                                                      copy in the desired folder the needed auxiliary basis set “X2.ion” where X is a specie. :param auxiliary_folder: folder where the auxiliary basis sets are stored :param auxiliary_basis_set_type: type of basis set (string to be found in the extension of the file name; must

                                                                      @@ -311,7 +311,7 @@
                                                                      -write_file(filename)[source]
                                                                      +write_file(filename)[source]

                                                                      Write FiestaInput to a file :param filename: Filename

                                                                      @@ -320,7 +320,7 @@
                                                                      -class FiestaOutput(filename)[source]
                                                                      +class FiestaOutput(filename)[source]

                                                                      Bases: object

                                                                      A Fiesta output file parser.

                                                                      All energies are in eV.

                                                                      @@ -333,7 +333,7 @@
                                                                      -class FiestaRun(folder='/Users/shyue/repos/pymatgen/docs_rst', grid=[2, 2, 2], log_file='log')[source]
                                                                      +class FiestaRun(folder='/Users/shyue/repos/pymatgen/docs_rst', grid=[2, 2, 2], log_file='log')[source]

                                                                      Bases: monty.json.MSONable

                                                                      To run FIESTA inside python:

                                                                      if grid is [x,x] then bse runs @@ -352,7 +352,7 @@

                                                                      -as_dict()[source]
                                                                      +as_dict()[source]
                                                                      Returns

                                                                      MSONable dict

                                                                      @@ -362,13 +362,13 @@
                                                                      -bse_run()[source]
                                                                      +bse_run()[source]

                                                                      Performs BSE run

                                                                      -classmethod from_dict(d)[source]
                                                                      +classmethod from_dict(d)[source]
                                                                      Parameters

                                                                      d – Dict representation

                                                                      @@ -381,7 +381,7 @@
                                                                      -run()[source]
                                                                      +run()[source]

                                                                      Performs FIESTA (gw) run.

                                                                      @@ -389,7 +389,7 @@
                                                                      -class Nwchem2Fiesta(folder, filename='nwchem', log_file='log_n2f')[source]
                                                                      +class Nwchem2Fiesta(folder, filename='nwchem', log_file='log_n2f')[source]

                                                                      Bases: monty.json.MSONable

                                                                      To run NWCHEM2FIESTA inside python:

                                                                      If nwchem.nw is the input, nwchem.out the output, and structure.movecs the @@ -401,7 +401,7 @@

                                                                      the run method launches NWCHEM2FIESTA

                                                                      -as_dict()[source]
                                                                      +as_dict()[source]
                                                                      Returns

                                                                      MSONable dict

                                                                      @@ -411,7 +411,7 @@
                                                                      -classmethod from_dict(d)[source]
                                                                      +classmethod from_dict(d)[source]
                                                                      Parameters

                                                                      d – Dict representation.

                                                                      @@ -424,7 +424,7 @@
                                                                      -run()[source]
                                                                      +run()[source]

                                                                      Performs actual NWCHEM2FIESTA run

                                                                      diff --git a/docs/pymatgen.io.gaussian.html b/docs/pymatgen.io.gaussian.html index fc79fc84b52..472e86766c4 100644 --- a/docs/pymatgen.io.gaussian.html +++ b/docs/pymatgen.io.gaussian.html @@ -4,7 +4,7 @@ - pymatgen.io.gaussian module — pymatgen 2022.5.18 documentation + pymatgen.io.gaussian module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                      - 2022.5.18 + 2022.5.18.1
                                                                      @@ -118,7 +118,7 @@

                                                                      This module implements input and output processing from Gaussian.

                                                                      -class GaussianInput(mol, charge=None, spin_multiplicity=None, title=None, functional='HF', basis_set='6-31G(d)', route_parameters=None, input_parameters=None, link0_parameters=None, dieze_tag='#P', gen_basis=None)[source]
                                                                      +class GaussianInput(mol, charge=None, spin_multiplicity=None, title=None, functional='HF', basis_set='6-31G(d)', route_parameters=None, input_parameters=None, link0_parameters=None, dieze_tag='#P', gen_basis=None)[source]

                                                                      Bases: object

                                                                      An object representing a Gaussian input file.

                                                                      @@ -158,7 +158,7 @@
                                                                      -as_dict()[source]
                                                                      +as_dict()[source]
                                                                      Returns

                                                                      MSONable dict

                                                                      @@ -168,7 +168,7 @@
                                                                      -classmethod from_dict(d)[source]
                                                                      +classmethod from_dict(d)[source]
                                                                      Parameters

                                                                      d – dict

                                                                      @@ -181,7 +181,7 @@
                                                                      -static from_file(filename)[source]
                                                                      +static from_file(filename)[source]

                                                                      Creates GaussianInput from a file.

                                                                      Parameters
                                                                      @@ -195,7 +195,7 @@
                                                                      -static from_string(contents)[source]
                                                                      +static from_string(contents)[source]

                                                                      Creates GaussianInput from a string.

                                                                      Parameters
                                                                      @@ -209,25 +209,25 @@
                                                                      -get_cart_coords()[source]
                                                                      +get_cart_coords()[source]

                                                                      Return the Cartesian coordinates of the molecule

                                                                      -get_zmatrix()[source]
                                                                      +get_zmatrix()[source]

                                                                      Returns a z-matrix representation of the molecule.

                                                                      -property molecule[source]
                                                                      +property molecule[source]

                                                                      Returns molecule associated with this GaussianInput.

                                                                      -to_string(cart_coords=False)[source]
                                                                      +to_string(cart_coords=False)[source]

                                                                      Return GaussianInput string

                                                                      Option: when cart_coords is set to True return the Cartesian coordinates

                                                                      instead of the z-matrix

                                                                      @@ -237,7 +237,7 @@
                                                                      -write_file(filename, cart_coords=False)[source]
                                                                      +write_file(filename, cart_coords=False)[source]

                                                                      Write the input string into a file

                                                                      Option: see __str__ method

                                                                      @@ -246,7 +246,7 @@
                                                                      -class GaussianOutput(filename)[source]
                                                                      +class GaussianOutput(filename)[source]

                                                                      Bases: object

                                                                      Parser for Gaussian output files.

                                                                      @@ -256,7 +256,7 @@

                                                                      Attributes:

                                                                      -structures[source]
                                                                      +structures[source]

                                                                      All structures from the calculation in the standard orientation. If the symmetry is not considered, the standard orientation is not printed out and the input orientation is used instead. Check the standard_orientation @@ -265,14 +265,14 @@

                                                                      -structures_input_orientation[source]
                                                                      +structures_input_orientation[source]

                                                                      All structures from the calculation in the input orientation or the Z-matrix orientation (if an opt=z-matrix was requested).

                                                                      -opt_structures[source]
                                                                      +opt_structures[source]

                                                                      All optimized structures from the calculation in the standard orientation, if the attribute ‘standard_orientation’ is True, otherwise in the input or the Z-matrix orientation.

                                                                      @@ -280,31 +280,31 @@
                                                                      -energies[source]
                                                                      +energies[source]

                                                                      All energies from the calculation.

                                                                      -eigenvalues[source]
                                                                      +eigenvalues[source]

                                                                      List of eigenvalues for the last geometry

                                                                      -MO_coefficients[source]
                                                                      +MO_coefficients[source]

                                                                      Matrix of MO coefficients for the last geometry

                                                                      -cart_forces[source]
                                                                      +cart_forces[source]

                                                                      All Cartesian forces from the calculation.

                                                                      -frequencies[source]
                                                                      +frequencies[source]

                                                                      A list for each freq calculation and for each mode of a dict with {

                                                                      @@ -323,7 +323,7 @@
                                                                      -hessian[source]
                                                                      +hessian[source]

                                                                      Matrix of second derivatives of the energy with respect to cartesian coordinates in the input orientation frame. Need #P in the route section in order to be in the output.

                                                                      @@ -331,51 +331,51 @@
                                                                      -properly_terminated[source]
                                                                      +properly_terminated[source]

                                                                      True if run has properly terminated

                                                                      -is_pcm[source]
                                                                      +is_pcm[source]

                                                                      True if run is a PCM run.

                                                                      -is_spin[source]
                                                                      +is_spin[source]

                                                                      True if it is an unrestricted run

                                                                      -stationary_type[source]
                                                                      +stationary_type[source]

                                                                      If it is a relaxation run, indicates whether it is a minimum (Minimum) or a saddle point (“Saddle”).

                                                                      -corrections[source]
                                                                      +corrections[source]

                                                                      Thermochemical corrections if this run is a Freq run as a dict. Keys are “Zero-point”, “Thermal”, “Enthalpy” and “Gibbs Free Energy”

                                                                      -functional[source]
                                                                      +functional[source]

                                                                      Functional used in the run.

                                                                      -basis_set[source]
                                                                      +basis_set[source]

                                                                      Basis set used in the run

                                                                      -route[source]
                                                                      +route[source]
                                                                      Additional route parameters as a dict. For example,

                                                                      {‘SP’:””, “SCF”:”Tight”}

                                                                      @@ -384,61 +384,61 @@
                                                                      -dieze_tag[source]
                                                                      +dieze_tag[source]

                                                                      # preceding the route line, e.g. “#P”

                                                                      -link0[source]
                                                                      +link0[source]

                                                                      Link0 parameters as a dict. E.g., {“%mem”: “1000MW”}

                                                                      -charge[source]
                                                                      +charge[source]

                                                                      Charge for structure

                                                                      -spin_multiplicity[source]
                                                                      +spin_multiplicity[source]

                                                                      Spin multiplicity for structure

                                                                      -num_basis_func[source]
                                                                      +num_basis_func[source]

                                                                      Number of basis functions in the run.

                                                                      -electrons[source]
                                                                      +electrons[source]

                                                                      number of alpha and beta electrons as (N alpha, N beta)

                                                                      -pcm[source]
                                                                      +pcm[source]

                                                                      PCM parameters and output if available.

                                                                      -errors[source]
                                                                      +errors[source]

                                                                      error if not properly terminated (list to be completed in error_defs)

                                                                      -Mulliken_charges[source]
                                                                      +Mulliken_charges[source]

                                                                      Mulliken atomic charges

                                                                      -eigenvectors[source]
                                                                      +eigenvectors[source]

                                                                      Matrix of shape (num_basis_func, num_basis_func). Each column is an eigenvectors and contains AO coefficients of an MO.

                                                                      eigenvectors[Spin] = mat(num_basis_func, num_basis_func)

                                                                      @@ -446,7 +446,7 @@
                                                                      -molecular_orbital[source]
                                                                      +molecular_orbital[source]

                                                                      MO development coefficients on AO in a more convenient array dict for each atom and basis set label.

                                                                      mo[Spin][OM j][atom i] = {AO_k: coeff, AO_k: coeff … }

                                                                      @@ -454,7 +454,7 @@
                                                                      -atom_basis_labels[source]
                                                                      +atom_basis_labels[source]

                                                                      Labels of AO for each atoms. These labels are those used in the output of molecular orbital coefficients (POP=Full) and in the molecular_orbital array dict.

                                                                      @@ -463,27 +463,27 @@
                                                                      -resumes[source]
                                                                      +resumes[source]

                                                                      List of gaussian data resume given at the end of the output file before the quotation. The resumes are given as string.

                                                                      -title[source]
                                                                      +title[source]

                                                                      Title of the gaussian run.

                                                                      -standard_orientation[source]
                                                                      +standard_orientation[source]

                                                                      If True, the geometries stored in the structures are in the standard orientation. Else, the geometries are in the input orientation.

                                                                      -bond_orders[source]
                                                                      +bond_orders[source]

                                                                      Dict of bond order values read in the output file such as: {(0, 1): 0.8709, (1, 6): 1.234, …}

                                                                      The keys are the atom indexes and the values are the Wiberg bond indexes @@ -493,26 +493,26 @@

                                                                      Methods:

                                                                      -to_input()[source]
                                                                      +to_input()[source]

                                                                      Return a GaussianInput object using the last geometry and the same calculation parameters.

                                                                      -read_scan()[source]
                                                                      +read_scan()[source]

                                                                      Read a potential energy surface from a gaussian scan calculation.

                                                                      -get_scan_plot()[source]
                                                                      +get_scan_plot()[source]

                                                                      Get a matplotlib plot of the potential energy surface

                                                                      -save_scan_plot()[source]
                                                                      +save_scan_plot()[source]

                                                                      Save a matplotlib plot of the potential energy surface to a file

                                                                      @@ -523,13 +523,13 @@
                                                                      -as_dict()[source]
                                                                      +as_dict()[source]

                                                                      JSON-serializable dict representation.

                                                                      -property final_energy[source]
                                                                      +property final_energy[source]

                                                                      Final energy in Gaussian output.

                                                                      Type
                                                                      @@ -540,7 +540,7 @@
                                                                      -property final_structure[source]
                                                                      +property final_structure[source]

                                                                      Final structure in Gaussian output.

                                                                      Type
                                                                      @@ -551,7 +551,7 @@
                                                                      -get_scan_plot(coords=None)[source]
                                                                      +get_scan_plot(coords=None)[source]

                                                                      Get a matplotlib plot of the potential energy surface.

                                                                      Parameters
                                                                      @@ -562,7 +562,7 @@
                                                                      -get_spectre_plot(sigma=0.05, step=0.01)[source]
                                                                      +get_spectre_plot(sigma=0.05, step=0.01)[source]

                                                                      Get a matplotlib plot of the UV-visible xas. Transitions are plotted as vertical lines and as a sum of normal functions with sigma with. The broadening is applied in energy and the xas is plotted as a function @@ -591,7 +591,7 @@

                                                                      -read_excitation_energies()[source]
                                                                      +read_excitation_energies()[source]

                                                                      Read a excitation energies after a TD-DFT calculation.

                                                                      Returns
                                                                      @@ -609,7 +609,7 @@
                                                                      -read_scan()[source]
                                                                      +read_scan()[source]

                                                                      Read a potential energy surface from a gaussian scan calculation.

                                                                      Returns
                                                                      @@ -631,7 +631,7 @@
                                                                      -save_scan_plot(filename='scan.pdf', img_format='pdf', coords=None)[source]
                                                                      +save_scan_plot(filename='scan.pdf', img_format='pdf', coords=None)[source]

                                                                      Save matplotlib plot of the potential energy surface to a file.

                                                                      Parameters
                                                                      @@ -646,7 +646,7 @@
                                                                      -save_spectre_plot(filename='spectre.pdf', img_format='pdf', sigma=0.05, step=0.01)[source]
                                                                      +save_spectre_plot(filename='spectre.pdf', img_format='pdf', sigma=0.05, step=0.01)[source]

                                                                      Save matplotlib plot of the spectre to a file.

                                                                      Parameters
                                                                      @@ -662,7 +662,7 @@
                                                                      -to_input(mol=None, charge=None, spin_multiplicity=None, title=None, functional=None, basis_set=None, route_parameters=None, input_parameters=None, link0_parameters=None, dieze_tag=None, cart_coords=False)[source]
                                                                      +to_input(mol=None, charge=None, spin_multiplicity=None, title=None, functional=None, basis_set=None, route_parameters=None, input_parameters=None, link0_parameters=None, dieze_tag=None, cart_coords=False)[source]

                                                                      Create a new input object using by default the last geometry read in the output file and with the same calculation parameters. Arguments are the same as GaussianInput class.

                                                                      @@ -676,7 +676,7 @@
                                                                      -read_route_line(route)[source]
                                                                      +read_route_line(route)[source]

                                                                      read route line in gaussian input/output and return functional basis_set and a dictionary of other route parameters

                                                                      diff --git a/docs/pymatgen.io.html b/docs/pymatgen.io.html index 723242e2c2f..2d64b52f04e 100644 --- a/docs/pymatgen.io.html +++ b/docs/pymatgen.io.html @@ -4,7 +4,7 @@ - pymatgen.io namespace — pymatgen 2022.5.18 documentation + pymatgen.io namespace — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                      - 2022.5.18 + 2022.5.18.1
                                                                      diff --git a/docs/pymatgen.io.jarvis.html b/docs/pymatgen.io.jarvis.html index 3b51294a1f4..e873e6909f8 100644 --- a/docs/pymatgen.io.jarvis.html +++ b/docs/pymatgen.io.jarvis.html @@ -4,7 +4,7 @@ - pymatgen.io.jarvis module — pymatgen 2022.5.18 documentation + pymatgen.io.jarvis module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                      - 2022.5.18 + 2022.5.18.1
                                                                      @@ -119,12 +119,12 @@ Atoms object and pymatgen Structure objects.

                                                                      -class JarvisAtomsAdaptor[source]
                                                                      +class JarvisAtomsAdaptor[source]

                                                                      Bases: object

                                                                      Adaptor serves as a bridge between JARVIS Atoms and pymatgen objects.

                                                                      -static get_atoms(structure)[source]
                                                                      +static get_atoms(structure)[source]

                                                                      Returns JARVIS Atoms object from pymatgen structure.

                                                                      Parameters
                                                                      @@ -138,7 +138,7 @@
                                                                      -static get_structure(atoms)[source]
                                                                      +static get_structure(atoms)[source]

                                                                      Returns pymatgen structure from JARVIS Atoms.

                                                                      Parameters
                                                                      diff --git a/docs/pymatgen.io.lammps.data.html b/docs/pymatgen.io.lammps.data.html index 96a036fb37c..43fb9a262ae 100644 --- a/docs/pymatgen.io.lammps.data.html +++ b/docs/pymatgen.io.lammps.data.html @@ -4,7 +4,7 @@ - pymatgen.io.lammps.data module — pymatgen 2022.5.18 documentation + pymatgen.io.lammps.data module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                      - 2022.5.18 + 2022.5.18.1
                                                                      @@ -129,7 +129,7 @@
                                                                      -class CombinedData(list_of_molecules, list_of_names, list_of_numbers, coordinates, atom_style='full')[source]
                                                                      +class CombinedData(list_of_molecules, list_of_names, list_of_numbers, coordinates, atom_style='full')[source]

                                                                      Bases: pymatgen.io.lammps.data.LammpsData

                                                                      Object for a collective set of data for a series of LAMMPS data file. velocities not yet implemented.

                                                                      @@ -150,7 +150,7 @@
                                                                      -as_lammpsdata()[source]
                                                                      +as_lammpsdata()[source]

                                                                      Convert a CombinedData object to a LammpsData object. attributes are deepcopied.

                                                                      box (LammpsBox): Simulation box. force_field (dict): Data for force field sections. Optional

                                                                      @@ -168,7 +168,7 @@
                                                                      -disassemble(atom_labels=None, guess_element=True, ff_label='ff_map')[source]
                                                                      +disassemble(atom_labels=None, guess_element=True, ff_label='ff_map')[source]

                                                                      Breaks down each LammpsData in CombinedData to building blocks (LammpsBox, ForceField and a series of Topology). RESTRICTIONS APPLIED: @@ -211,13 +211,13 @@

                                                                      -classmethod from_ff_and_topologies()[source]
                                                                      +classmethod from_ff_and_topologies()[source]

                                                                      Unsupported constructor for CombinedData objects.

                                                                      -classmethod from_files(coordinate_file, list_of_numbers, *filenames)[source]
                                                                      +classmethod from_files(coordinate_file, list_of_numbers, *filenames)[source]

                                                                      Constructor that parse a series of data file.

                                                                      Parameters
                                                                      @@ -233,7 +233,7 @@
                                                                      -classmethod from_lammpsdata(mols, names, list_of_numbers, coordinates, atom_style=None)[source]
                                                                      +classmethod from_lammpsdata(mols, names, list_of_numbers, coordinates, atom_style=None)[source]

                                                                      Constructor that can infer atom_style. The input LammpsData objects are used non-destructively.

                                                                      @@ -253,13 +253,13 @@
                                                                      -classmethod from_structure()[source]
                                                                      +classmethod from_structure()[source]

                                                                      Unsupported constructor for CombinedData objects.

                                                                      -get_string(distance=6, velocity=8, charge=4, hybrid=True)[source]
                                                                      +get_string(distance=6, velocity=8, charge=4, hybrid=True)[source]

                                                                      Returns the string representation of CombinedData, essentially the string to be written to a file. Combination info is included as a comment. For single molecule ID data, the info format is:

                                                                      @@ -295,7 +295,7 @@
                                                                      -classmethod parse_xyz(filename)[source]
                                                                      +classmethod parse_xyz(filename)[source]

                                                                      load xyz file generated from packmol (for those who find it hard to install openbabel)

                                                                      Returns
                                                                      @@ -306,7 +306,7 @@
                                                                      -property structure[source]
                                                                      +property structure[source]

                                                                      Exports a periodic structure object representing the simulation box. :returns: Structure

                                                                      @@ -316,12 +316,12 @@
                                                                      -class ForceField(mass_info, nonbond_coeffs=None, topo_coeffs=None)[source]
                                                                      +class ForceField(mass_info, nonbond_coeffs=None, topo_coeffs=None)[source]

                                                                      Bases: monty.json.MSONable

                                                                      Class carrying most data in Masses and force field sections.

                                                                      -masses[source]
                                                                      +masses[source]

                                                                      DataFrame for Masses section.

                                                                      Type
                                                                      @@ -332,7 +332,7 @@
                                                                      -force_field[source]
                                                                      +force_field[source]

                                                                      Force field section keywords (keys) and data (values) as DataFrames.

                                                                      @@ -344,7 +344,7 @@
                                                                      -maps[source]
                                                                      +maps[source]

                                                                      Dict for labeling atoms and topologies.

                                                                      Type
                                                                      @@ -411,7 +411,7 @@
                                                                      -classmethod from_dict(d)[source]
                                                                      +classmethod from_dict(d)[source]

                                                                      Constructor that reads in a dictionary.

                                                                      Parameters
                                                                      @@ -422,7 +422,7 @@
                                                                      -classmethod from_file(filename)[source]
                                                                      +classmethod from_file(filename)[source]

                                                                      Constructor that reads in a file in YAML format.

                                                                      Parameters
                                                                      @@ -433,7 +433,7 @@
                                                                      -to_file(filename)[source]
                                                                      +to_file(filename)[source]

                                                                      Saves object to a file in YAML format.

                                                                      Parameters
                                                                      @@ -446,7 +446,7 @@
                                                                      -class LammpsBox(bounds, tilt=None)[source]
                                                                      +class LammpsBox(bounds, tilt=None)[source]

                                                                      Bases: monty.json.MSONable

                                                                      Object for representing a simulation box in LAMMPS settings.

                                                                      @@ -462,7 +462,7 @@
                                                                      -get_box_shift(i)[source]
                                                                      +get_box_shift(i)[source]

                                                                      Calculates the coordinate shift due to PBC.

                                                                      Parameters
                                                                      @@ -479,7 +479,7 @@
                                                                      -get_string(significant_figures=6)[source]
                                                                      +get_string(significant_figures=6)[source]

                                                                      Returns the string representation of simulation box in LAMMPS data file format.

                                                                      @@ -495,7 +495,7 @@
                                                                      -to_lattice()[source]
                                                                      +to_lattice()[source]

                                                                      Converts the simulation box to a more powerful Lattice backend. Note that Lattice is always periodic in 3D space while a simulation box is not necessarily periodic in all dimensions.

                                                                      @@ -508,7 +508,7 @@
                                                                      -property volume[source]
                                                                      +property volume[source]

                                                                      Volume of simulation box.

                                                                      @@ -516,7 +516,7 @@
                                                                      -class LammpsData(box, masses, atoms, velocities=None, force_field=None, topology=None, atom_style='full')[source]
                                                                      +class LammpsData(box, masses, atoms, velocities=None, force_field=None, topology=None, atom_style='full')[source]

                                                                      Bases: monty.json.MSONable

                                                                      Object for representing the data in a LAMMPS data file.

                                                                      This is a low level constructor designed to work with parsed @@ -547,7 +547,7 @@

                                                                      -disassemble(atom_labels=None, guess_element=True, ff_label='ff_map')[source]
                                                                      +disassemble(atom_labels=None, guess_element=True, ff_label='ff_map')[source]

                                                                      Breaks down LammpsData to building blocks (LammpsBox, ForceField and a series of Topology). RESTRICTIONS APPLIED:

                                                                      @@ -591,7 +591,7 @@
                                                                      -classmethod from_ff_and_topologies(box, ff, topologies, atom_style='full')[source]
                                                                      +classmethod from_ff_and_topologies(box, ff, topologies, atom_style='full')[source]

                                                                      Constructor building LammpsData from a ForceField object and a list of Topology objects. Do not support intermolecular topologies since a Topology object includes data for ONE @@ -612,7 +612,7 @@

                                                                      -classmethod from_file(filename, atom_style='full', sort_id=False)[source]
                                                                      +classmethod from_file(filename, atom_style='full', sort_id=False)[source]

                                                                      Constructor that parses a file.

                                                                      Parameters
                                                                      @@ -628,7 +628,7 @@
                                                                      -classmethod from_structure(structure, ff_elements=None, atom_style='charge', is_sort=False)[source]
                                                                      +classmethod from_structure(structure, ff_elements=None, atom_style='charge', is_sort=False)[source]

                                                                      Simple constructor building LammpsData from a structure without force field parameters and topologies.

                                                                      @@ -648,7 +648,7 @@
                                                                      -get_string(distance=6, velocity=8, charge=4, hybrid=True)[source]
                                                                      +get_string(distance=6, velocity=8, charge=4, hybrid=True)[source]

                                                                      Returns the string representation of LammpsData, essentially the string to be written to a file. Support hybrid style coeffs read and write.

                                                                      @@ -677,7 +677,7 @@
                                                                      -property structure[source]
                                                                      +property structure[source]

                                                                      Exports a periodic structure object representing the simulation box.

                                                                      @@ -689,7 +689,7 @@
                                                                      -write_file(filename, distance=6, velocity=8, charge=4)[source]
                                                                      +write_file(filename, distance=6, velocity=8, charge=4)[source]

                                                                      Writes LammpsData to file.

                                                                      Parameters
                                                                      @@ -711,7 +711,7 @@
                                                                      -class Topology(sites, ff_label=None, charges=None, velocities=None, topologies=None)[source]
                                                                      +class Topology(sites, ff_label=None, charges=None, velocities=None, topologies=None)[source]

                                                                      Bases: monty.json.MSONable

                                                                      Class carrying most data in Atoms, Velocities and molecular topology sections for ONE SINGLE Molecule or Structure @@ -749,7 +749,7 @@

                                                                      -classmethod from_bonding(molecule, bond=True, angle=True, dihedral=True, tol=0.1, **kwargs)[source]
                                                                      +classmethod from_bonding(molecule, bond=True, angle=True, dihedral=True, tol=0.1, **kwargs)[source]

                                                                      Another constructor that creates an instance from a molecule. Covalent bonds and other bond-based topologies (angles and dihedrals) can be automatically determined. Cannot be used for @@ -774,7 +774,7 @@

                                                                      -lattice_2_lmpbox(lattice, origin=(0, 0, 0))[source]
                                                                      +lattice_2_lmpbox(lattice, origin=(0, 0, 0))[source]

                                                                      Converts a lattice object to LammpsBox, and calculates the symmetry operation used.

                                                                      diff --git a/docs/pymatgen.io.lammps.html b/docs/pymatgen.io.lammps.html index 5934b2642b8..7f6d65dcf4c 100644 --- a/docs/pymatgen.io.lammps.html +++ b/docs/pymatgen.io.lammps.html @@ -4,7 +4,7 @@ - pymatgen.io.lammps package — pymatgen 2022.5.18 documentation + pymatgen.io.lammps package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                      - 2022.5.18 + 2022.5.18.1
                                                                      diff --git a/docs/pymatgen.io.lammps.inputs.html b/docs/pymatgen.io.lammps.inputs.html index 86f7bc717c2..9cf073e6bac 100644 --- a/docs/pymatgen.io.lammps.inputs.html +++ b/docs/pymatgen.io.lammps.inputs.html @@ -4,7 +4,7 @@ - pymatgen.io.lammps.inputs module — pymatgen 2022.5.18 documentation + pymatgen.io.lammps.inputs module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                      - 2022.5.18 + 2022.5.18.1
                                                                      @@ -119,7 +119,7 @@

                                                                      This module implements methods for writing LAMMPS input files.

                                                                      -class LammpsRun(script_template, settings, data, script_filename)[source]
                                                                      +class LammpsRun(script_template, settings, data, script_filename)[source]

                                                                      Bases: monty.json.MSONable

                                                                      Examples for various simple LAMMPS runs with given simulation box, force field and a few more settings. Experienced LAMMPS users should @@ -144,7 +144,7 @@

                                                                      -classmethod md(data, force_field, temperature, nsteps, other_settings=None)[source]
                                                                      +classmethod md(data, force_field, temperature, nsteps, other_settings=None)[source]

                                                                      Example for a simple MD run based on template md.txt.

                                                                      Parameters
                                                                      @@ -164,12 +164,12 @@
                                                                      -template_dir = '/Users/shyue/repos/pymatgen/pymatgen/io/lammps/templates'[source]
                                                                      +template_dir = '/Users/shyue/repos/pymatgen/pymatgen/io/lammps/templates'[source]
                                                                      -write_inputs(output_dir, **kwargs)[source]
                                                                      +write_inputs(output_dir, **kwargs)[source]

                                                                      Writes all input files (input script, and data if needed). Other supporting files are not handled at this moment.

                                                                      @@ -186,7 +186,7 @@
                                                                      -class LammpsTemplateGen[source]
                                                                      +class LammpsTemplateGen[source]

                                                                      Bases: pymatgen.io.template.TemplateInputGen

                                                                      Creates an InputSet object for a LAMMPS run based on a template file. The input script is constructed by substituting variables into placeholders @@ -199,7 +199,7 @@ See pymatgen.io.template.py for additional documentation of this method.

                                                                      -get_input_set(script_template: Union[str, pathlib.Path], settings: Optional[Dict] = None, script_filename: str = 'in.lammps', data: Optional[Union[pymatgen.io.lammps.data.LammpsData, pymatgen.io.lammps.data.CombinedData]] = None, data_filename: str = 'system.data')[source]
                                                                      +get_input_set(script_template: Union[str, pathlib.Path], settings: Optional[Dict] = None, script_filename: str = 'in.lammps', data: Optional[Union[pymatgen.io.lammps.data.LammpsData, pymatgen.io.lammps.data.CombinedData]] = None, data_filename: str = 'system.data')[source]
                                                                      Parameters
                                                                        diff --git a/docs/pymatgen.io.lammps.outputs.html b/docs/pymatgen.io.lammps.outputs.html index 7f612e1c470..c033b94af41 100644 --- a/docs/pymatgen.io.lammps.outputs.html +++ b/docs/pymatgen.io.lammps.outputs.html @@ -4,7 +4,7 @@ - pymatgen.io.lammps.outputs module — pymatgen 2022.5.18 documentation + pymatgen.io.lammps.outputs module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                        - 2022.5.18 + 2022.5.18.1
                                                                        @@ -120,7 +120,7 @@ files (log and dump).

                                                                        -class LammpsDump(timestep, natoms, box, data)[source]
                                                                        +class LammpsDump(timestep, natoms, box, data)[source]

                                                                        Bases: monty.json.MSONable

                                                                        Object for representing dump data for a single snapshot.

                                                                        Base constructor.

                                                                        @@ -136,13 +136,13 @@
                                                                        -as_dict()[source]
                                                                        +as_dict()[source]

                                                                        Returns: MSONable dict

                                                                        -classmethod from_dict(d)[source]
                                                                        +classmethod from_dict(d)[source]
                                                                        Parameters

                                                                        d (dict) – Dict representation

                                                                        @@ -155,7 +155,7 @@
                                                                        -classmethod from_string(string)[source]
                                                                        +classmethod from_string(string)[source]

                                                                        Constructor from string parsing.

                                                                        Parameters
                                                                        @@ -168,7 +168,7 @@
                                                                        -parse_lammps_dumps(file_pattern)[source]
                                                                        +parse_lammps_dumps(file_pattern)[source]

                                                                        Generator that parses dump file(s).

                                                                        Parameters
                                                                        @@ -184,7 +184,7 @@
                                                                        -parse_lammps_log(filename='log.lammps')[source]
                                                                        +parse_lammps_log(filename='log.lammps')[source]

                                                                        Parses log file with focus on thermo data. Both one and multi line formats are supported. Any incomplete runs (no “Loop time” marker) will not be parsed.

                                                                        diff --git a/docs/pymatgen.io.lammps.utils.html b/docs/pymatgen.io.lammps.utils.html index 35edc42f7e5..f007f875b59 100644 --- a/docs/pymatgen.io.lammps.utils.html +++ b/docs/pymatgen.io.lammps.utils.html @@ -4,7 +4,7 @@ - pymatgen.io.lammps.utils module — pymatgen 2022.5.18 documentation + pymatgen.io.lammps.utils module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                        - 2022.5.18 + 2022.5.18.1
                                                                        @@ -119,7 +119,7 @@

                                                                        This module defines utility classes and functions.

                                                                        -class LammpsRunner(input_filename='lammps.in', bin='lammps')[source]
                                                                        +class LammpsRunner(input_filename='lammps.in', bin='lammps')[source]

                                                                        Bases: object

                                                                        LAMMPS wrapper

                                                                        @@ -132,7 +132,7 @@
                                                                        -run()[source]
                                                                        +run()[source]

                                                                        Write the input/data files and run LAMMPS.

                                                                        @@ -140,7 +140,7 @@
                                                                        -class Polymer(start_monomer, s_head, s_tail, monomer, head, tail, end_monomer, e_head, e_tail, n_units, link_distance=1.0, linear_chain=False)[source]
                                                                        +class Polymer(start_monomer, s_head, s_tail, monomer, head, tail, end_monomer, e_head, e_tail, n_units, link_distance=1.0, linear_chain=False)[source]

                                                                        Bases: object

                                                                        Generate polymer chain via Random walk. At each position there are a total of 5 possible moves(excluding the previous direction).

                                                                        diff --git a/docs/pymatgen.io.lmto.html b/docs/pymatgen.io.lmto.html index b1c8e74c120..d60651b43db 100644 --- a/docs/pymatgen.io.lmto.html +++ b/docs/pymatgen.io.lmto.html @@ -4,7 +4,7 @@ - pymatgen.io.lmto module — pymatgen 2022.5.18 documentation + pymatgen.io.lmto module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                        - 2022.5.18 + 2022.5.18.1
                                                                        @@ -120,7 +120,7 @@ Structure object in the pymatgen.electronic_structure.cohp.py module.

                                                                        -class LMTOCopl(filename='COPL', to_eV=False)[source]
                                                                        +class LMTOCopl(filename='COPL', to_eV=False)[source]

                                                                        Bases: object

                                                                        Class for reading COPL files, which contain COHP data.

                                                                        @@ -136,7 +136,7 @@
                                                                        -class LMTOCtrl(structure, header=None, version='LMASA-47')[source]
                                                                        +class LMTOCtrl(structure, header=None, version='LMASA-47')[source]

                                                                        Bases: object

                                                                        Class for parsing CTRL files from the Stuttgart LMTO-ASA code. Currently, only HEADER, VERS and the structure can be used.

                                                                        @@ -153,7 +153,7 @@
                                                                        -as_dict()[source]
                                                                        +as_dict()[source]

                                                                        Returns the CTRL as a dictionary. “SITE” and “CLASS” are of the form {‘CATEGORY’: {‘TOKEN’: value}}, the rest is of the form ‘TOKEN’/’CATEGORY’: value. It gets the conventional standard @@ -164,7 +164,7 @@

                                                                        -classmethod from_dict(d)[source]
                                                                        +classmethod from_dict(d)[source]

                                                                        Creates a CTRL file object from a dictionary. The dictionary must contain the items “ALAT”, PLAT” and “SITE”.

                                                                        @@ -195,7 +195,7 @@
                                                                        -classmethod from_file(filename='CTRL', **kwargs)[source]
                                                                        +classmethod from_file(filename='CTRL', **kwargs)[source]

                                                                        Creates a CTRL file object from an existing file.

                                                                        Parameters
                                                                        @@ -209,7 +209,7 @@
                                                                        -classmethod from_string(data, sigfigs=8)[source]
                                                                        +classmethod from_string(data, sigfigs=8)[source]

                                                                        Creates a CTRL file object from a string. This will mostly be used to read an LMTOCtrl object from a CTRL file. Empty spheres are ignored.

                                                                        @@ -225,14 +225,14 @@
                                                                        -get_string(sigfigs=8)[source]
                                                                        +get_string(sigfigs=8)[source]

                                                                        Generates the string representation of the CTRL file. This is the mininmal CTRL file necessary to execute lmhart.run.

                                                                        -write_file(filename='CTRL', **kwargs)[source]
                                                                        +write_file(filename='CTRL', **kwargs)[source]

                                                                        Writes a CTRL file with structure, HEADER, and VERS that can be used as input for lmhart.run.

                                                                        diff --git a/docs/pymatgen.io.lobster.html b/docs/pymatgen.io.lobster.html index 47541122353..db39189ca8b 100644 --- a/docs/pymatgen.io.lobster.html +++ b/docs/pymatgen.io.lobster.html @@ -4,7 +4,7 @@ - pymatgen.io.lobster package — pymatgen 2022.5.18 documentation + pymatgen.io.lobster package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                        - 2022.5.18 + 2022.5.18.1
                                                                        diff --git a/docs/pymatgen.io.lobster.inputs.html b/docs/pymatgen.io.lobster.inputs.html index e3df1126664..c305ffd0354 100644 --- a/docs/pymatgen.io.lobster.inputs.html +++ b/docs/pymatgen.io.lobster.inputs.html @@ -4,7 +4,7 @@ - pymatgen.io.lobster.inputs module — pymatgen 2022.5.18 documentation + pymatgen.io.lobster.inputs module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                        - 2022.5.18 + 2022.5.18.1
                                                                        @@ -120,7 +120,7 @@ on LOBSTER see www.cohp.de.

                                                                        -class Lobsterin(settingsdict: dict)[source]
                                                                        +class Lobsterin(settingsdict: dict)[source]

                                                                        Bases: dict, monty.json.MSONable

                                                                        This class can handle and generate lobsterin files Furthermore, it can also modify INCAR files for lobster, generate KPOINT files for fatband calculations in Lobster, @@ -133,32 +133,32 @@

                                                                        -AVAILABLEKEYWORDS = ['COHPstartEnergy', 'COHPendEnergy', 'gaussianSmearingWidth', 'useDecimalPlaces', 'COHPSteps', 'basisSet', 'cohpGenerator', 'realspaceHamiltonian', 'realspaceOverlap', 'printPAWRealSpaceWavefunction', 'printLCAORealSpaceWavefunction', 'kSpaceCOHP', 'EwaldSum', 'saveProjectionToFile', 'skipdos', 'skipcohp', 'skipcoop', 'skipcobi', 'skipMadelungEnergy', 'loadProjectionFromFile', 'forceEnergyRange', 'DensityOfEnergy', 'BWDF', 'BWDFCOHP', 'skipPopulationAnalysis', 'skipGrossPopulation', 'userecommendedbasisfunctions', 'skipProjection', 'writeBasisFunctions', 'writeMatricesToFile', 'noFFTforVisualization', 'RMSp', 'onlyReadVasprun.xml', 'noMemoryMappedFiles', 'skipPAWOrthonormalityTest', 'doNotIgnoreExcessiveBands', 'doNotUseAbsoluteSpilling', 'skipReOrthonormalization', 'forceV1HMatrix', 'useOriginalTetrahedronMethod', 'forceEnergyRange', 'bandwiseSpilling', 'kpointwiseSpilling', 'basisfunctions', 'cohpbetween', 'createFatband'][source]
                                                                        +AVAILABLEKEYWORDS = ['COHPstartEnergy', 'COHPendEnergy', 'gaussianSmearingWidth', 'useDecimalPlaces', 'COHPSteps', 'basisSet', 'cohpGenerator', 'realspaceHamiltonian', 'realspaceOverlap', 'printPAWRealSpaceWavefunction', 'printLCAORealSpaceWavefunction', 'kSpaceCOHP', 'EwaldSum', 'saveProjectionToFile', 'skipdos', 'skipcohp', 'skipcoop', 'skipcobi', 'skipMadelungEnergy', 'loadProjectionFromFile', 'forceEnergyRange', 'DensityOfEnergy', 'BWDF', 'BWDFCOHP', 'skipPopulationAnalysis', 'skipGrossPopulation', 'userecommendedbasisfunctions', 'skipProjection', 'writeBasisFunctions', 'writeMatricesToFile', 'noFFTforVisualization', 'RMSp', 'onlyReadVasprun.xml', 'noMemoryMappedFiles', 'skipPAWOrthonormalityTest', 'doNotIgnoreExcessiveBands', 'doNotUseAbsoluteSpilling', 'skipReOrthonormalization', 'forceV1HMatrix', 'useOriginalTetrahedronMethod', 'forceEnergyRange', 'bandwiseSpilling', 'kpointwiseSpilling', 'basisfunctions', 'cohpbetween', 'createFatband'][source]
                                                                        -BOOLEANKEYWORDS = ['saveProjectionToFile', 'skipdos', 'skipcohp', 'skipcoop', 'skipcobi', 'skipMadelungEnergy', 'loadProjectionFromFile', 'forceEnergyRange', 'DensityOfEnergy', 'BWDF', 'BWDFCOHP', 'skipPopulationAnalysis', 'skipGrossPopulation', 'userecommendedbasisfunctions', 'skipProjection', 'writeBasisFunctions', 'writeMatricesToFile', 'noFFTforVisualization', 'RMSp', 'onlyReadVasprun.xml', 'noMemoryMappedFiles', 'skipPAWOrthonormalityTest', 'doNotIgnoreExcessiveBands', 'doNotUseAbsoluteSpilling', 'skipReOrthonormalization', 'forceV1HMatrix', 'useOriginalTetrahedronMethod', 'forceEnergyRange', 'bandwiseSpilling', 'kpointwiseSpilling'][source]
                                                                        +BOOLEANKEYWORDS = ['saveProjectionToFile', 'skipdos', 'skipcohp', 'skipcoop', 'skipcobi', 'skipMadelungEnergy', 'loadProjectionFromFile', 'forceEnergyRange', 'DensityOfEnergy', 'BWDF', 'BWDFCOHP', 'skipPopulationAnalysis', 'skipGrossPopulation', 'userecommendedbasisfunctions', 'skipProjection', 'writeBasisFunctions', 'writeMatricesToFile', 'noFFTforVisualization', 'RMSp', 'onlyReadVasprun.xml', 'noMemoryMappedFiles', 'skipPAWOrthonormalityTest', 'doNotIgnoreExcessiveBands', 'doNotUseAbsoluteSpilling', 'skipReOrthonormalization', 'forceV1HMatrix', 'useOriginalTetrahedronMethod', 'forceEnergyRange', 'bandwiseSpilling', 'kpointwiseSpilling'][source]
                                                                        -FLOATKEYWORDS = ['COHPstartEnergy', 'COHPendEnergy', 'gaussianSmearingWidth', 'useDecimalPlaces', 'COHPSteps'][source]
                                                                        +FLOATKEYWORDS = ['COHPstartEnergy', 'COHPendEnergy', 'gaussianSmearingWidth', 'useDecimalPlaces', 'COHPSteps'][source]
                                                                        -LISTKEYWORDS = ['basisfunctions', 'cohpbetween', 'createFatband'][source]
                                                                        +LISTKEYWORDS = ['basisfunctions', 'cohpbetween', 'createFatband'][source]
                                                                        -STRINGKEYWORDS = ['basisSet', 'cohpGenerator', 'realspaceHamiltonian', 'realspaceOverlap', 'printPAWRealSpaceWavefunction', 'printLCAORealSpaceWavefunction', 'kSpaceCOHP', 'EwaldSum'][source]
                                                                        +STRINGKEYWORDS = ['basisSet', 'cohpGenerator', 'realspaceHamiltonian', 'realspaceOverlap', 'printPAWRealSpaceWavefunction', 'printLCAORealSpaceWavefunction', 'kSpaceCOHP', 'EwaldSum'][source]
                                                                        -as_dict()[source]
                                                                        +as_dict()[source]
                                                                        Returns

                                                                        MSONable dict

                                                                        @@ -168,7 +168,7 @@
                                                                        -diff(other)[source]
                                                                        +diff(other)[source]

                                                                        Diff function for lobsterin. Compares two lobsterin and indicates which parameters are the same. Similar to the diff in INCAR. :param other: Lobsterin object to compare to @@ -182,7 +182,7 @@

                                                                        -classmethod from_dict(d)[source]
                                                                        +classmethod from_dict(d)[source]
                                                                        Parameters

                                                                        d – Dict representation

                                                                        @@ -195,7 +195,7 @@
                                                                        -classmethod from_file(lobsterin: str)[source]
                                                                        +classmethod from_file(lobsterin: str)[source]
                                                                        Parameters

                                                                        lobsterin (str) – path to lobsterin

                                                                        @@ -208,7 +208,7 @@
                                                                        -static get_all_possible_basis_functions(structure: pymatgen.core.structure.Structure, potcar_symbols: list, address_basis_file_min: str = '/Users/shyue/repos/pymatgen/pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_min.yaml', address_basis_file_max: str = '/Users/shyue/repos/pymatgen/pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_max.yaml')[source]
                                                                        +static get_all_possible_basis_functions(structure: pymatgen.core.structure.Structure, potcar_symbols: list, address_basis_file_min: str = '/Users/shyue/repos/pymatgen/pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_min.yaml', address_basis_file_max: str = '/Users/shyue/repos/pymatgen/pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_max.yaml')[source]
                                                                        Parameters
                                                                          @@ -225,7 +225,7 @@
                                                                          -static get_basis(structure: pymatgen.core.structure.Structure, potcar_symbols: list, address_basis_file: str = '/Users/shyue/repos/pymatgen/pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_standard.yaml')[source]
                                                                          +static get_basis(structure: pymatgen.core.structure.Structure, potcar_symbols: list, address_basis_file: str = '/Users/shyue/repos/pymatgen/pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_standard.yaml')[source]

                                                                          will get the basis from given potcar_symbols (e.g., [“Fe_pv”,”Si”] #include this in lobsterin class :param structure: Structure object @@ -240,7 +240,7 @@

                                                                          -classmethod standard_calculations_from_vasp_files(POSCAR_input: str = 'POSCAR', INCAR_input: str = 'INCAR', POTCAR_input: str | None = None, dict_for_basis: dict | None = None, option: str = 'standard')[source]
                                                                          +classmethod standard_calculations_from_vasp_files(POSCAR_input: str = 'POSCAR', INCAR_input: str = 'INCAR', POTCAR_input: str | None = None, dict_for_basis: dict | None = None, option: str = 'standard')[source]

                                                                          will generate Lobsterin with standard settings

                                                                          Parameters
                                                                          @@ -269,7 +269,7 @@
                                                                          -write_INCAR(incar_input: str = 'INCAR', incar_output: str = 'INCAR.lobster', poscar_input: str = 'POSCAR', isym: int = - 1, further_settings: Optional[dict] = None)[source]
                                                                          +write_INCAR(incar_input: str = 'INCAR', incar_output: str = 'INCAR.lobster', poscar_input: str = 'POSCAR', isym: int = - 1, further_settings: Optional[dict] = None)[source]

                                                                          Will only make the run static, insert nbands, make ISYM=-1, set LWAVE=True and write a new INCAR. You have to check for the rest. :param incar_input: path to input INCAR @@ -286,7 +286,7 @@

                                                                          -static write_KPOINTS(POSCAR_input: str = 'POSCAR', KPOINTS_output='KPOINTS.lobster', reciprocal_density: int = 100, isym: int = - 1, from_grid: bool = False, input_grid: list = [5, 5, 5], line_mode: bool = True, kpoints_line_density: int = 20, symprec: float = 0.01)[source]
                                                                          +static write_KPOINTS(POSCAR_input: str = 'POSCAR', KPOINTS_output='KPOINTS.lobster', reciprocal_density: int = 100, isym: int = - 1, from_grid: bool = False, input_grid: list = [5, 5, 5], line_mode: bool = True, kpoints_line_density: int = 20, symprec: float = 0.01)[source]

                                                                          writes a KPOINT file for lobster (only ISYM=-1 and ISYM=0 are possible), grids are gamma centered :param POSCAR_input: path to POSCAR :type POSCAR_input: str @@ -314,7 +314,7 @@

                                                                          -static write_POSCAR_with_standard_primitive(POSCAR_input='POSCAR', POSCAR_output='POSCAR.lobster', symprec=0.01)[source]
                                                                          +static write_POSCAR_with_standard_primitive(POSCAR_input='POSCAR', POSCAR_output='POSCAR.lobster', symprec=0.01)[source]

                                                                          writes a POSCAR with the standard primitive cell. This is needed to arrive at the correct kpath :param POSCAR_input: filename of input POSCAR :type POSCAR_input: str @@ -326,7 +326,7 @@

                                                                          -write_lobsterin(path='lobsterin', overwritedict=None)[source]
                                                                          +write_lobsterin(path='lobsterin', overwritedict=None)[source]

                                                                          writes a lobsterin file :param path: filename of the lobsterin file that will be written :type path: str @@ -338,7 +338,7 @@

                                                                          -get_all_possible_basis_combinations(min_basis: list, max_basis: list) → list[source]
                                                                          +get_all_possible_basis_combinations(min_basis: list, max_basis: list) → list[source]
                                                                          Parameters
                                                                            diff --git a/docs/pymatgen.io.lobster.lobsterenv.html b/docs/pymatgen.io.lobster.lobsterenv.html index f679ec6e4ff..35c4e2e9d7b 100644 --- a/docs/pymatgen.io.lobster.lobsterenv.html +++ b/docs/pymatgen.io.lobster.lobsterenv.html @@ -4,7 +4,7 @@ - pymatgen.io.lobster.lobsterenv module — pymatgen 2022.5.18 documentation + pymatgen.io.lobster.lobsterenv module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                            - 2022.5.18 + 2022.5.18.1
                                                                            @@ -122,7 +122,7 @@ bonding analysis with Lobster.

                                                                            -class LobsterLightStructureEnvironments(strategy, coordination_environments=None, all_nbs_sites=None, neighbors_sets=None, structure=None, valences=None, valences_origin=None)[source]
                                                                            +class LobsterLightStructureEnvironments(strategy, coordination_environments=None, all_nbs_sites=None, neighbors_sets=None, structure=None, valences=None, valences_origin=None)[source]

                                                                            Bases: pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments

                                                                            Class to store LightStructureEnvironments based on Lobster outputs

                                                                            Constructor for the LightStructureEnvironments object.

                                                                            @@ -142,14 +142,14 @@
                                                                            -as_dict()[source]
                                                                            +as_dict()[source]

                                                                            Bson-serializable dict representation of the LightStructureEnvironments object. :return: Bson-serializable dict representation of the LightStructureEnvironments object.

                                                                            -classmethod from_Lobster(list_ce_symbol, list_csm, list_permutation, list_neighsite, list_neighisite, structure, valences=None)[source]
                                                                            +classmethod from_Lobster(list_ce_symbol, list_csm, list_permutation, list_neighsite, list_neighisite, structure, valences=None)[source]

                                                                            will set up a LightStructureEnvironments from Lobster :param structure: Structure object :param list_ce_symbol: list of symbols for coordination environments @@ -163,7 +163,7 @@

                                                                            -property uniquely_determines_coordination_environments[source]
                                                                            +property uniquely_determines_coordination_environments[source]

                                                                            True if the coordination environments are uniquely determined.

                                                                            @@ -171,7 +171,7 @@
                                                                            -class LobsterNeighbors(are_coops=False, filename_ICOHP=None, valences=None, limits=None, structure=None, additional_condition=0, only_bonds_to=None, perc_strength_ICOHP=0.15, valences_from_charges=False, filename_CHARGE=None, which_charge='Mulliken', adapt_extremum_to_add_cond=False)[source]
                                                                            +class LobsterNeighbors(are_coops=False, filename_ICOHP=None, valences=None, limits=None, structure=None, additional_condition=0, only_bonds_to=None, perc_strength_ICOHP=0.15, valences_from_charges=False, filename_CHARGE=None, which_charge='Mulliken', adapt_extremum_to_add_cond=False)[source]

                                                                            Bases: pymatgen.analysis.local_env.NearNeighbors

                                                                            This class combines capabilities from LocalEnv and ChemEnv to determine coordination environments based on bonding analysis

                                                                            @@ -208,14 +208,14 @@
                                                                            -get_anion_types()[source]
                                                                            +get_anion_types()[source]

                                                                            will return the types of anions present in crystal structure Returns:

                                                                            -get_info_cohps_to_neighbors(path_to_COHPCAR='COHPCAR.lobster', isites=None, only_bonds_to=None, onlycation_isites=True, per_bond=True, summed_spin_channels=False)[source]
                                                                            +get_info_cohps_to_neighbors(path_to_COHPCAR='COHPCAR.lobster', isites=None, only_bonds_to=None, onlycation_isites=True, per_bond=True, summed_spin_channels=False)[source]

                                                                            will return info about the cohps from all sites mentioned in isites with neighbors :param path_to_COHPCAR: str, path to COHPCAR :param isites: list of int that indicate the number of the site @@ -229,7 +229,7 @@

                                                                            -get_info_icohps_between_neighbors(isites=None, onlycation_isites=True)[source]
                                                                            +get_info_icohps_between_neighbors(isites=None, onlycation_isites=True)[source]

                                                                            will return infos about interactions between neighbors of a certain atom :param isites: list of site ids, if isite==None, all isites will be used :param onlycation_isites: will only use cations, if isite==None

                                                                            @@ -238,7 +238,7 @@
                                                                            -get_info_icohps_to_neighbors(isites=None, onlycation_isites=True)[source]
                                                                            +get_info_icohps_to_neighbors(isites=None, onlycation_isites=True)[source]

                                                                            this method will return information of cohps of neighbors :param isites: list of site ids, if isite==None, all isites will be used to add the icohps of the neighbors :param onlycation_isites: will only use cations, if isite==[]

                                                                            @@ -255,7 +255,7 @@
                                                                            -get_light_structure_environment(only_cation_environments=False, only_indices=None)[source]
                                                                            +get_light_structure_environment(only_cation_environments=False, only_indices=None)[source]

                                                                            will return a LobsterLightStructureEnvironments object if the structure only contains coordination environments smaller 13 :param only_cation_environments: only data for cations will be returned @@ -265,7 +265,7 @@

                                                                            -get_nn_info(structure, n, use_weights=False)[source]
                                                                            +get_nn_info(structure, n, use_weights=False)[source]

                                                                            Get coordination number, CN, of site with index n in structure.

                                                                            Parameters
                                                                            @@ -290,7 +290,7 @@
                                                                            -property molecules_allowed[source]
                                                                            +property molecules_allowed[source]

                                                                            can this NearNeighbors class be used with Molecule objects?

                                                                            @@ -302,7 +302,7 @@
                                                                            -plot_cohps_of_neighbors(path_to_COHPCAR='COHPCAR.lobster', isites=[], onlycation_isites=True, only_bonds_to=None, per_bond=False, summed_spin_channels=False, xlim=None, ylim=[- 10, 6], integrated=False)[source]
                                                                            +plot_cohps_of_neighbors(path_to_COHPCAR='COHPCAR.lobster', isites=[], onlycation_isites=True, only_bonds_to=None, per_bond=False, summed_spin_channels=False, xlim=None, ylim=[- 10, 6], integrated=False)[source]

                                                                            will plot summed cohps (please be careful in the spin polarized case (plots might overlap (exactly!)) :param isites: list of site ids, if isite==[], all isites will be used to add the icohps of the neighbors :param onlycation_isites: bool, will only use cations, if isite==[] @@ -322,7 +322,7 @@

                                                                            -property structures_allowed[source]
                                                                            +property structures_allowed[source]

                                                                            can this NearNeighbors class be used with Structure objects?

                                                                            diff --git a/docs/pymatgen.io.lobster.outputs.html b/docs/pymatgen.io.lobster.outputs.html index 767ee8085ff..314bbc87e61 100644 --- a/docs/pymatgen.io.lobster.outputs.html +++ b/docs/pymatgen.io.lobster.outputs.html @@ -4,7 +4,7 @@ - pymatgen.io.lobster.outputs module — pymatgen 2022.5.18 documentation + pymatgen.io.lobster.outputs module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                            - 2022.5.18 + 2022.5.18.1
                                                                            @@ -120,7 +120,7 @@ on LOBSTER see www.cohp.de.

                                                                            -class Bandoverlaps(filename: str = 'bandOverlaps.lobster')[source]
                                                                            +class Bandoverlaps(filename: str = 'bandOverlaps.lobster')[source]

                                                                            Bases: object

                                                                            Class to read in bandOverlaps.lobster files. These files are not created during every Lobster run. .. attribute: bandoverlapsdict is a dict of the following form:

                                                                            @@ -135,7 +135,7 @@
                                                                            -has_good_quality_check_occupied_bands(number_occ_bands_spin_up: int, number_occ_bands_spin_down: int | None = None, spin_polarized: bool = False, limit_deviation: float = 0.1) → bool[source]
                                                                            +has_good_quality_check_occupied_bands(number_occ_bands_spin_up: int, number_occ_bands_spin_down: int | None = None, spin_polarized: bool = False, limit_deviation: float = 0.1) → bool[source]

                                                                            will check if the deviation from the ideal bandoverlap of all occupied bands is smaller or equal to limit_deviation

                                                                            Args: @@ -148,7 +148,7 @@

                                                                            -has_good_quality_maxDeviation(limit_maxDeviation: float = 0.1) → bool[source]
                                                                            +has_good_quality_maxDeviation(limit_maxDeviation: float = 0.1) → bool[source]

                                                                            will check if the maxDeviation from the ideal bandoverlap is smaller or equal to limit_maxDeviation :param limit_maxDeviation: limit of the maxDeviation

                                                                            @@ -162,7 +162,7 @@
                                                                            -class Charge(filename: str = 'CHARGE.lobster')[source]
                                                                            +class Charge(filename: str = 'CHARGE.lobster')[source]

                                                                            Bases: object

                                                                            Class to read CHARGE files generated by LOBSTER

                                                                            @@ -172,7 +172,7 @@
                                                                            -get_structure_with_charges(structure_filename)[source]
                                                                            +get_structure_with_charges(structure_filename)[source]

                                                                            get a Structure with Mulliken and Loewdin charges as site properties :param structure_filename: filename of POSCAR

                                                                            @@ -186,7 +186,7 @@
                                                                            -class Cohpcar(are_coops: bool = False, are_cobis: bool = False, filename: Optional[str] = None)[source]
                                                                            +class Cohpcar(are_coops: bool = False, are_cobis: bool = False, filename: Optional[str] = None)[source]

                                                                            Bases: object

                                                                            Class to read COHPCAR/COOPCAR files generated by LOBSTER.

                                                                            @@ -205,40 +205,40 @@
                                                                            -class Doscar(doscar: str = 'DOSCAR.lobster', structure_file: str = 'POSCAR', dftprogram: str = 'Vasp')[source]
                                                                            +class Doscar(doscar: str = 'DOSCAR.lobster', structure_file: str = 'POSCAR', dftprogram: str = 'Vasp')[source]

                                                                            Bases: object

                                                                            Class to deal with Lobster’s projected DOS and local projected DOS. The beforehand quantum-chemical calculation was performed with VASP

                                                                            -completedos[source]
                                                                            +completedos[source]

                                                                            LobsterCompleteDos Object

                                                                            -pdos[source]
                                                                            +pdos[source]
                                                                            List of Dict including numpy arrays with pdos. Access as pdos[atomindex]['orbitalstring']['Spin.up/Spin.down']
                                                                            -tdos[source]
                                                                            +tdos[source]
                                                                            Dos Object of the total density of states
                                                                            -energies[source]
                                                                            +energies[source]
                                                                            numpy array of the energies at which the DOS was calculated (in eV, relative to Efermi)
                                                                            -tdensities[source]
                                                                            +tdensities[source]
                                                                            tdensities[Spin.up]: numpy array of the total density of states for the Spin.up contribution at each of the
                                                                            @@ -257,7 +257,7 @@
                                                                            itdensities[Spin.up]: numpy array of the total density of states for the Spin.up contribution at each of the
                                                                            -energies[source]
                                                                            +energies[source]
                                                                            itdensities[Spin.down]: numpy array of the total density of states for the Spin.down contribution at each of the
                                                                            @@ -268,7 +268,7 @@
                                                                            -is_spin_polarized[source]
                                                                            +is_spin_polarized[source]
                                                                            Boolean. Tells if the system is spin polarized
                                                                            @@ -284,7 +284,7 @@
                                                                            -property completedos: pymatgen.electronic_structure.dos.LobsterCompleteDos[source]
                                                                            +property completedos: pymatgen.electronic_structure.dos.LobsterCompleteDos[source]

                                                                            CompleteDos

                                                                            Type
                                                                            @@ -295,7 +295,7 @@
                                                                            -property energies: numpy.ndarray[source]
                                                                            +property energies: numpy.ndarray[source]

                                                                            Energies

                                                                            Type
                                                                            @@ -306,7 +306,7 @@
                                                                            -property is_spin_polarized: bool[source]
                                                                            +property is_spin_polarized: bool[source]

                                                                            Whether run is spin polarized.

                                                                            Type
                                                                            @@ -317,7 +317,7 @@
                                                                            -property itdensities: numpy.ndarray[source]
                                                                            +property itdensities: numpy.ndarray[source]

                                                                            integrated total densities as a np.ndarray

                                                                            Type
                                                                            @@ -328,7 +328,7 @@
                                                                            -property pdos: list[source]
                                                                            +property pdos: list[source]

                                                                            Projected DOS

                                                                            Type
                                                                            @@ -339,7 +339,7 @@
                                                                            -property tdensities: numpy.ndarray[source]
                                                                            +property tdensities: numpy.ndarray[source]

                                                                            total densities as a np.ndarray

                                                                            Type
                                                                            @@ -350,7 +350,7 @@
                                                                            -property tdos: pymatgen.electronic_structure.dos.Dos[source]
                                                                            +property tdos: pymatgen.electronic_structure.dos.Dos[source]

                                                                            Total DOS

                                                                            Type
                                                                            @@ -363,7 +363,7 @@
                                                                            -class Fatband(filenames='.', vasprun='vasprun.xml', Kpointsfile='KPOINTS')[source]
                                                                            +class Fatband(filenames='.', vasprun='vasprun.xml', Kpointsfile='KPOINTS')[source]

                                                                            Bases: object

                                                                            Reads in FATBAND_x_y.lobster files

                                                                            @@ -378,7 +378,7 @@
                                                                            -get_bandstructure()[source]
                                                                            +get_bandstructure()[source]

                                                                            returns a LobsterBandStructureSymmLine object which can be plotted with a normal BSPlotter

                                                                            @@ -386,7 +386,7 @@
                                                                            -class Grosspop(filename: str = 'GROSSPOP.lobster')[source]
                                                                            +class Grosspop(filename: str = 'GROSSPOP.lobster')[source]

                                                                            Bases: object

                                                                            Class to read in GROSSPOP.lobster files.

                                                                            @@ -396,7 +396,7 @@
                                                                            -get_structure_with_total_grosspop(structure_filename: str) → pymatgen.core.structure.Structure[source]
                                                                            +get_structure_with_total_grosspop(structure_filename: str) → pymatgen.core.structure.Structure[source]

                                                                            get a Structure with Mulliken and Loewdin total grosspopulations as site properties :param structure_filename: filename of POSCAR :type structure_filename: str

                                                                            @@ -411,7 +411,7 @@
                                                                            -class Icohplist(are_coops: bool = False, are_cobis: bool = False, filename: Optional[str] = None)[source]
                                                                            +class Icohplist(are_coops: bool = False, are_cobis: bool = False, filename: Optional[str] = None)[source]

                                                                            Bases: object

                                                                            Class to read ICOHPLIST/ICOOPLIST files generated by LOBSTER.

                                                                            @@ -428,7 +428,7 @@
                                                                            -property icohpcollection[source]
                                                                            +property icohpcollection[source]

                                                                            IcohpCollection object

                                                                            Type
                                                                            @@ -439,7 +439,7 @@
                                                                            -property icohplist: dict[Any, dict[str, Any]][source]
                                                                            +property icohplist: dict[Any, dict[str, Any]][source]

                                                                            icohplist compatible with older version of this class

                                                                            Type
                                                                            @@ -452,7 +452,7 @@
                                                                            -class Lobsterout(filename='lobsterout')[source]
                                                                            +class Lobsterout(filename='lobsterout')[source]

                                                                            Bases: object

                                                                            Class to read in the lobsterout and evaluate the spilling, save the basis, save warnings, save infos

                                                                            @@ -464,7 +464,7 @@
                                                                            -get_doc()[source]
                                                                            +get_doc()[source]

                                                                            Returns: LobsterDict with all the information stored in lobsterout

                                                                            @@ -472,7 +472,7 @@
                                                                            -class MadelungEnergies(filename: str = 'MadelungEnergies.lobster')[source]
                                                                            +class MadelungEnergies(filename: str = 'MadelungEnergies.lobster')[source]

                                                                            Bases: object

                                                                            Class to read MadelungEnergies.lobster files generated by LOBSTER

                                                                            @@ -484,7 +484,7 @@
                                                                            -class SitePotential(filename: str = 'SitePotentials.lobster')[source]
                                                                            +class SitePotential(filename: str = 'SitePotentials.lobster')[source]

                                                                            Bases: object

                                                                            Class to read SitePotentials.lobster files generated by LOBSTER

                                                                            @@ -494,7 +494,7 @@
                                                                            -get_structure_with_site_potentials(structure_filename)[source]
                                                                            +get_structure_with_site_potentials(structure_filename)[source]

                                                                            get a Structure with Mulliken and Loewdin charges as site properties :param structure_filename: filename of POSCAR

                                                                            @@ -508,7 +508,7 @@
                                                                            -class Wavefunction(filename, structure)[source]
                                                                            +class Wavefunction(filename, structure)[source]

                                                                            Bases: object

                                                                            Class to read in wave function files from Lobster and transfer them into an object of the type VolumetricData

                                                                            @@ -521,28 +521,28 @@
                                                                            -get_volumetricdata_density()[source]
                                                                            +get_volumetricdata_density()[source]

                                                                            will return a VolumetricData object including the imaginary part of the wave function

                                                                            Returns: VolumetricData object

                                                                            -get_volumetricdata_imaginary()[source]
                                                                            +get_volumetricdata_imaginary()[source]

                                                                            will return a VolumetricData object including the imaginary part of the wave function

                                                                            Returns: VolumetricData object

                                                                            -get_volumetricdata_real()[source]
                                                                            +get_volumetricdata_real()[source]

                                                                            will return a VolumetricData object including the real part of the wave function

                                                                            Returns: VolumetricData object

                                                                            -set_volumetric_data(grid, structure)[source]
                                                                            +set_volumetric_data(grid, structure)[source]

                                                                            Will create the VolumetricData Objects

                                                                            Parameters
                                                                            @@ -557,7 +557,7 @@
                                                                            -write_file(filename='WAVECAR.vasp', part='real')[source]
                                                                            +write_file(filename='WAVECAR.vasp', part='real')[source]

                                                                            will save the wavefunction in a file format that can be read by VESTA This will only work if the wavefunction from lobster was constructed with: “printLCAORealSpaceWavefunction kpoint 1 coordinates 0.0 0.0 0.0 coordinates 1.0 1.0 1.0 box bandlist 1 2 3 4 diff --git a/docs/pymatgen.io.nwchem.html b/docs/pymatgen.io.nwchem.html index 200539daa5d..8e04ead352d 100644 --- a/docs/pymatgen.io.nwchem.html +++ b/docs/pymatgen.io.nwchem.html @@ -4,7 +4,7 @@ - pymatgen.io.nwchem module — pymatgen 2022.5.18 documentation + pymatgen.io.nwchem module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                                                            - 2022.5.18 + 2022.5.18.1
                                                                            @@ -140,7 +140,7 @@
                                                                            -class NwInput(mol, tasks, directives=None, geometry_options=('units', 'angstroms'), symmetry_options=None, memory_options=None)[source]
                                                                            +class NwInput(mol, tasks, directives=None, geometry_options=('units', 'angstroms'), symmetry_options=None, memory_options=None)[source]

                                                                            Bases: monty.json.MSONable

                                                                            An object representing a Nwchem input file, which is essentially a list of tasks on a particular molecule.

                                                                            @@ -165,13 +165,13 @@
                                                                            -as_dict()[source]
                                                                            +as_dict()[source]

                                                                            Returns: MSONable dict

                                                                            -classmethod from_dict(d)[source]
                                                                            +classmethod from_dict(d)[source]
                                                                            Parameters

                                                                            d (dict) – Dict representation

                                                                            @@ -184,7 +184,7 @@
                                                                            -classmethod from_file(filename)[source]
                                                                            +classmethod from_file(filename)[source]

                                                                            Read an NwInput from a file. Currently tested to work with files generated from this class itself.

                                                                            @@ -199,7 +199,7 @@
                                                                            -classmethod from_string(string_input)[source]
                                                                            +classmethod from_string(string_input)[source]

                                                                            Read an NwInput from a string. Currently tested to work with files generated from this class itself.

                                                                            @@ -214,13 +214,13 @@
                                                                            -property molecule[source]
                                                                            +property molecule[source]

                                                                            Returns molecule associated with this GaussianInput.

                                                                            -write_file(filename)[source]
                                                                            +write_file(filename)[source]
                                                                            Parameters

                                                                            filename (str) – Filename

                                                                            @@ -232,14 +232,14 @@
                                                                            -exception NwInputError[source]
                                                                            +exception NwInputError[source]

                                                                            Bases: Exception

                                                                            Error class for NwInput.

                                                                            -class NwOutput(filename)[source]
                                                                            +class NwOutput(filename)[source]

                                                                            Bases: object

                                                                            A Nwchem output file parser. Very basic for now - supports only dft and only parses energies and geometries. Please note that Nwchem typically @@ -252,7 +252,7 @@

                                                                            -get_excitation_spectrum(width=0.1, npoints=2000)[source]
                                                                            +get_excitation_spectrum(width=0.1, npoints=2000)[source]

                                                                            Generate an excitation spectra from the singlet roots of TDDFT calculations.

                                                                            @@ -275,7 +275,7 @@
                                                                            -parse_tddft()[source]
                                                                            +parse_tddft()[source]

                                                                            Parses TDDFT roots. Adapted from nw_spectrum.py script.

                                                                            Returns
                                                                            @@ -311,7 +311,7 @@
                                                                            -class NwTask(charge, spin_multiplicity, basis_set, basis_set_option='cartesian', title=None, theory='dft', operation='optimize', theory_directives=None, alternate_directives=None)[source]
                                                                            +class NwTask(charge, spin_multiplicity, basis_set, basis_set_option='cartesian', title=None, theory='dft', operation='optimize', theory_directives=None, alternate_directives=None)[source]

                                                                            Bases: monty.json.MSONable

                                                                            Base task for Nwchem.

                                                                            Very flexible arguments to support many types of potential setups. @@ -346,13 +346,13 @@

                                                                            -as_dict()[source]
                                                                            +as_dict()[source]

                                                                            Returns: MSONable dict.

                                                                            -classmethod dft_task(mol, xc='b3lyp', **kwargs)[source]
                                                                            +classmethod dft_task(mol, xc='b3lyp', **kwargs)[source]

                                                                            A class method for quickly creating DFT tasks with optional cosmo parameter .

                                                                            @@ -369,7 +369,7 @@
                                                                            -classmethod esp_task(mol, **kwargs)[source]
                                                                            +classmethod esp_task(mol, **kwargs)[source]

                                                                            A class method for quickly creating ESP tasks with RESP charge fitting.

                                                                            @@ -385,7 +385,7 @@
                                                                            -classmethod from_dict(d)[source]
                                                                            +classmethod from_dict(d)[source]
                                                                            Parameters

                                                                            d (dict) – Dict representation

                                                                            @@ -398,7 +398,7 @@
                                                                            -classmethod from_molecule(mol, theory, charge=None, spin_multiplicity=None, basis_set='6-31g', basis_set_option='cartesian', title=None, operation='optimize', theory_directives=None, alternate_directives=None)[source]
                                                                            +classmethod from_molecule(mol, theory, charge=None, spin_multiplicity=None, basis_set='6-31g', basis_set_option='cartesian', title=None, operation='optimize', theory_directives=None, alternate_directives=None)[source]

                                                                            Very flexible arguments to support many types of potential setups. Users should use more friendly static methods unless they need the flexibility.

                                                                            @@ -435,12 +435,12 @@
                                                                            -operations = {'': 'dummy', 'dynamics': 'Perform classical molecular dynamics.', 'energy': 'Evaluate the single point energy.', 'freq': 'Same as frequencies.', 'frequencies': 'Compute second derivatives and print out an analysis of molecular vibrations.', 'gradient': 'Evaluate the derivative of the energy with respect to nuclear coordinates.', 'hessian': 'Compute second derivatives.', 'optimize': 'Minimize the energy by varying the molecular structure.', 'property': 'Calculate the properties for the wave function.', 'saddle': 'Conduct a search for a transition state (or saddle point).', 'thermodynamics': 'Perform multi-configuration thermodynamic integration using classical MD.', 'vscf': 'Compute anharmonic contributions to the vibrational modes.'}[source]
                                                                            +operations = {'': 'dummy', 'dynamics': 'Perform classical molecular dynamics.', 'energy': 'Evaluate the single point energy.', 'freq': 'Same as frequencies.', 'frequencies': 'Compute second derivatives and print out an analysis of molecular vibrations.', 'gradient': 'Evaluate the derivative of the energy with respect to nuclear coordinates.', 'hessian': 'Compute second derivatives.', 'optimize': 'Minimize the energy by varying the molecular structure.', 'property': 'Calculate the properties for the wave function.', 'saddle': 'Conduct a search for a transition state (or saddle point).', 'thermodynamics': 'Perform multi-configuration thermodynamic integration using classical MD.', 'vscf': 'Compute anharmonic contributions to the vibrational modes.'}[source]
                                                                            -theories = {'band': 'Pseudopotential plane-wave DFT for solids using NWPW', 'ccsd': 'Coupled-cluster single and double excitations', 'ccsd(t)': 'Coupled-cluster linearized triples approximation', 'ccsd+t(ccsd)': 'Fourth order triples contribution', 'dft': 'DFT', 'direct_mp2': 'MP2 using a full-direct algorithm', 'esp': 'ESP', 'g3gn': 'some description', 'mcscf': 'Multiconfiguration SCF', 'md': 'Classical molecular dynamics simulation', 'mp2': 'MP2 using a semi-direct algorithm', 'pspw': 'Pseudopotential plane-wave DFT for molecules and insulating solids using NWPW', 'rimp2': 'MP2 using the RI approximation', 'scf': 'Hartree-Fock', 'selci': 'Selected CI with perturbation correction', 'sodft': 'Spin-Orbit DFT', 'tce': 'Tensor Contraction Engine', 'tddft': 'Time Dependent DFT'}[source]
                                                                            +theories = {'band': 'Pseudopotential plane-wave DFT for solids using NWPW', 'ccsd': 'Coupled-cluster single and double excitations', 'ccsd(t)': 'Coupled-cluster linearized triples approximation', 'ccsd+t(ccsd)': 'Fourth order triples contribution', 'dft': 'DFT', 'direct_mp2': 'MP2 using a full-direct algorithm', 'esp': 'ESP', 'g3gn': 'some description', 'mcscf': 'Multiconfiguration SCF', 'md': 'Classical molecular dynamics simulation', 'mp2': 'MP2 using a semi-direct algorithm', 'pspw': 'Pseudopotential plane-wave DFT for molecules and insulating solids using NWPW', 'rimp2': 'MP2 using the RI approximation', 'scf': 'Hartree-Fock', 'selci': 'Selected CI with perturbation correction', 'sodft': 'Spin-Orbit DFT', 'tce': 'Tensor Contraction Engine', 'tddft': 'Time Dependent DFT'}[source]
                                                                            diff --git a/docs/pymatgen.io.packmol.html b/docs/pymatgen.io.packmol.html index 93afb70327f..9958b48d760 100644 --- a/docs/pymatgen.io.packmol.html +++ b/docs/pymatgen.io.packmol.html @@ -4,7 +4,7 @@ - pymatgen.io.packmol module — pymatgen 2022.5.18 documentation + pymatgen.io.packmol module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                            - 2022.5.18 + 2022.5.18.1
                                                                            @@ -130,7 +130,7 @@ executable to the PATH environment variable.

                                                                            -class PackmolBoxGen(tolerance: float = 2.0, seed: int = 1, control_params: Optional[Dict] = None, inputfile: Union[str, pathlib.Path] = 'packmol.inp', outputfile: Union[str, pathlib.Path] = 'packmol_out.xyz', stdoutfile: Union[str, pathlib.Path] = 'packmol.stdout')[source]
                                                                            +class PackmolBoxGen(tolerance: float = 2.0, seed: int = 1, control_params: Optional[Dict] = None, inputfile: Union[str, pathlib.Path] = 'packmol.inp', outputfile: Union[str, pathlib.Path] = 'packmol_out.xyz', stdoutfile: Union[str, pathlib.Path] = 'packmol.stdout')[source]

                                                                            Bases: pymatgen.io.core.InputGenerator

                                                                            Generator for a Packmol InputSet that packs one or more molecules into a rectangular simulation box.

                                                                            @@ -150,7 +150,7 @@
                                                                            -get_input_set(molecules: List[Dict], box: Optional[List[float]] = None)[source]
                                                                            +get_input_set(molecules: List[Dict], box: Optional[List[float]] = None)[source]

                                                                            Generate a Packmol InputSet for a set of molecules.

                                                                            Parameters
                                                                            @@ -187,7 +187,7 @@
                                                                            -class PackmolSet(inputs: Dict[Union[str, pathlib.Path], Union[str, pymatgen.io.core.InputFile]] = {}, **kwargs)[source]
                                                                            +class PackmolSet(inputs: Dict[Union[str, pathlib.Path], Union[str, pymatgen.io.core.InputFile]] = {}, **kwargs)[source]

                                                                            Bases: pymatgen.io.core.InputSet

                                                                            InputSet for the Packmol software. This class defines several attributes related to

                                                                            @@ -208,7 +208,7 @@
                                                                            -classmethod from_directory(directory: Union[str, pathlib.Path])[source]
                                                                            +classmethod from_directory(directory: Union[str, pathlib.Path])[source]

                                                                            Construct an InputSet from a directory of one or more files.

                                                                            Parameters
                                                                            @@ -219,7 +219,7 @@
                                                                            -run(path: Union[str, pathlib.Path], timeout=30)[source]
                                                                            +run(path: Union[str, pathlib.Path], timeout=30)[source]

                                                                            Run packmol and write out the packed structure. :param path: The path in which packmol input files are located. :param timeout: Timeout in seconds.

                                                                            diff --git a/docs/pymatgen.io.phonopy.html b/docs/pymatgen.io.phonopy.html index bad18cadf41..4793d36130f 100644 --- a/docs/pymatgen.io.phonopy.html +++ b/docs/pymatgen.io.phonopy.html @@ -4,7 +4,7 @@ - pymatgen.io.phonopy module — pymatgen 2022.5.18 documentation + pymatgen.io.phonopy module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                            - 2022.5.18 + 2022.5.18.1
                                                                            @@ -118,7 +118,7 @@

                                                                            Module for interfacing with phonopy, see https://atztogo.github.io/phonopy/

                                                                            -eigvec_to_eigdispl(v, q, frac_coords, mass)[source]
                                                                            +eigvec_to_eigdispl(v, q, frac_coords, mass)[source]

                                                                            Converts a single eigenvector to an eigendisplacement in the primitive cell according to the formula:

                                                                            exp(2*pi*i*(frac_coords \\dot q) / sqrt(mass) * v
@@ -140,7 +140,7 @@
 
 
                                                                            
 
                                                                            
-get_complete_ph_dos(partial_dos_path, phonopy_yaml_path)[source]
                                                                            
+get_complete_ph_dos(partial_dos_path, phonopy_yaml_path)[source]
 
                                                                            Creates a pymatgen CompletePhononDos from a partial_dos.dat and
 phonopy.yaml files.
 The second is produced when generating a Dos and is needed to extract
@@ -157,7 +157,7 @@
 
 
                                                                            
 
                                                                            
-get_displaced_structures(pmg_structure, atom_disp=0.01, supercell_matrix=None, yaml_fname=None, **kwargs)[source]
                                                                            
+get_displaced_structures(pmg_structure, atom_disp=0.01, supercell_matrix=None, yaml_fname=None, **kwargs)[source]
 
                                                                            Generate a set of symmetrically inequivalent displaced structures for
 phonon calculations.
                                                                            
 
                                                                            
@@ -180,7 +180,7 @@
 
 
                                                                            
 
                                                                            
-get_gruneisen_ph_bs_symm_line(gruneisen_path, structure=None, structure_path=None, labels_dict=None, fit=False)[source]
                                                                            
+get_gruneisen_ph_bs_symm_line(gruneisen_path, structure=None, structure_path=None, labels_dict=None, fit=False)[source]
 
                                                                            Creates a pymatgen GruneisenPhononBandStructure from a band.yaml file.
 The labels will be extracted from the dictionary, if present.
 If the ‘eigenvector’ key is found the eigendisplacements will be
@@ -209,7 +209,7 @@
 
 
                                                                            
 
                                                                            
-get_gruneisenparameter(gruneisen_path, structure=None, structure_path=None) → pymatgen.phonon.gruneisen.GruneisenParameter[source]
                                                                            
+get_gruneisenparameter(gruneisen_path, structure=None, structure_path=None) → pymatgen.phonon.gruneisen.GruneisenParameter[source]
 
                                                                            Get Gruneisen object from gruneisen.yaml file, as obtained from phonopy (Frequencies in THz!).
 The order is structure > structure path > structure from gruneisen dict.
 Newer versions of phonopy include the structure in the yaml file,
@@ -228,7 +228,7 @@
 
 
                                                                            
 
                                                                            
-get_gs_ph_bs_symm_line_from_dict(gruneisen_dict, structure=None, structure_path=None, labels_dict=None, fit=False) → pymatgen.phonon.gruneisen.GruneisenPhononBandStructureSymmLine[source]
                                                                            
+get_gs_ph_bs_symm_line_from_dict(gruneisen_dict, structure=None, structure_path=None, labels_dict=None, fit=False) → pymatgen.phonon.gruneisen.GruneisenPhononBandStructureSymmLine[source]
 
                                                                            Creates a pymatgen GruneisenPhononBandStructure object from the dictionary
 extracted by the gruneisen.yaml file produced by phonopy. The labels
 will be extracted from the dictionary, if present. If the ‘eigenvector’
@@ -260,7 +260,7 @@
 
 
                                                                            
 
                                                                            
-get_ph_bs_symm_line(bands_path, has_nac=False, labels_dict=None)[source]
                                                                            
+get_ph_bs_symm_line(bands_path, has_nac=False, labels_dict=None)[source]
 
                                                                            Creates a pymatgen PhononBandStructure from a band.yaml file.
 The labels will be extracted from the dictionary, if present.
 If the ‘eigenvector’  key is found the eigendisplacements will be
@@ -283,7 +283,7 @@
 
 
                                                                            
 
                                                                            
-get_ph_bs_symm_line_from_dict(bands_dict, has_nac=False, labels_dict=None)[source]
                                                                            
+get_ph_bs_symm_line_from_dict(bands_dict, has_nac=False, labels_dict=None)[source]
 
                                                                            Creates a pymatgen PhononBandStructure object from the dictionary
 extracted by the band.yaml file produced by phonopy. The labels
 will be extracted from the dictionary, if present. If the ‘eigenvector’
@@ -308,7 +308,7 @@
 
 
                                                                            
 
                                                                            
-get_ph_dos(total_dos_path)[source]
                                                                            
+get_ph_dos(total_dos_path)[source]
 
                                                                            Creates a pymatgen PhononDos from a total_dos.dat file.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -319,7 +319,7 @@
 
 
                                                                            
 
                                                                            
-get_phonon_band_structure_from_fc(structure: pymatgen.core.structure.Structure, supercell_matrix: numpy.ndarray, force_constants: numpy.ndarray, mesh_density: float = 100.0, **kwargs) → pymatgen.phonon.bandstructure.PhononBandStructure[source]
                                                                            
+get_phonon_band_structure_from_fc(structure: pymatgen.core.structure.Structure, supercell_matrix: numpy.ndarray, force_constants: numpy.ndarray, mesh_density: float = 100.0, **kwargs) → pymatgen.phonon.bandstructure.PhononBandStructure[source]
 
                                                                            Get a uniform phonon band structure from phonopy force constants.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -341,7 +341,7 @@
 
 
                                                                            
 
                                                                            
-get_phonon_band_structure_symm_line_from_fc(structure: pymatgen.core.structure.Structure, supercell_matrix: numpy.ndarray, force_constants: numpy.ndarray, line_density: float = 20.0, symprec: float = 0.01, **kwargs) → pymatgen.phonon.bandstructure.PhononBandStructureSymmLine[source]
                                                                            
+get_phonon_band_structure_symm_line_from_fc(structure: pymatgen.core.structure.Structure, supercell_matrix: numpy.ndarray, force_constants: numpy.ndarray, line_density: float = 20.0, symprec: float = 0.01, **kwargs) → pymatgen.phonon.bandstructure.PhononBandStructureSymmLine[source]
 
                                                                            Get a phonon band structure along a high symmetry path from phonopy force
 constants.
                                                                            
 
                                                                            
@@ -365,7 +365,7 @@
 
 
                                                                            
 
                                                                            
-get_phonon_dos_from_fc(structure: pymatgen.core.structure.Structure, supercell_matrix: numpy.ndarray, force_constants: numpy.ndarray, mesh_density: float = 100.0, num_dos_steps: int = 200, **kwargs) → pymatgen.phonon.dos.CompletePhononDos[source]
                                                                            
+get_phonon_dos_from_fc(structure: pymatgen.core.structure.Structure, supercell_matrix: numpy.ndarray, force_constants: numpy.ndarray, mesh_density: float = 100.0, num_dos_steps: int = 200, **kwargs) → pymatgen.phonon.dos.CompletePhononDos[source]
 
                                                                            Get a projected phonon density of states from phonopy force constants.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -388,7 +388,7 @@
 
 
                                                                            
 
                                                                            
-get_phonopy_structure(pmg_structure)[source]
                                                                            
+get_phonopy_structure(pmg_structure)[source]
 
                                                                            Convert a pymatgen Structure object to a PhonopyAtoms object.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -399,7 +399,7 @@
 
 
                                                                            
 
                                                                            
-get_pmg_structure(phonopy_structure)[source]
                                                                            
+get_pmg_structure(phonopy_structure)[source]
 
                                                                            Convert a PhonopyAtoms object to pymatgen Structure object.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -410,7 +410,7 @@
 
 
                                                                            
 
                                                                            
-get_structure_from_dict(d)[source]
                                                                            
+get_structure_from_dict(d)[source]
 
                                                                            Extracts a structure from the dictionary extracted from the output
 files of phonopy like phonopy.yaml or band.yaml.
 Adds “phonopy_masses” in the site_properties of the structures.
diff --git a/docs/pymatgen.io.prismatic.html b/docs/pymatgen.io.prismatic.html
index b3efc2c1084..ffe832d366c 100644
--- a/docs/pymatgen.io.prismatic.html
+++ b/docs/pymatgen.io.prismatic.html
@@ -4,7 +4,7 @@
   
 
   
-  pymatgen.io.prismatic module — pymatgen 2022.5.18 documentation
+  pymatgen.io.prismatic module — pymatgen 2022.5.18.1 documentation
       
       
       
@@ -39,7 +39,7 @@
              pymatgen
           
               
                                                                            
-                2022.5.18
+                2022.5.18.1
               
                                                                            
 
                                                                            
   
@@ -118,7 +118,7 @@
 
                                                                            Write Prismatic (http://prism-em.com/) input files.
                                                                            
 
                                                                            
 
                                                                            
-class Prismatic(structure, comment='Generated by pymatgen')[source]
                                                                            
+class Prismatic(structure, comment='Generated by pymatgen')[source]
 
                                                                            Bases: object
                                                                            
 
                                                                            Class to write Prismatic  (http://prism-em.com/) input files.
 This is designed for STEM image simulation.
                                                                            
@@ -132,7 +132,7 @@
 
                                                                            
 
                                                                            
 
                                                                            
-to_string()[source]
                                                                            
+to_string()[source]
 
                                                                            Returns: Prismatic XYZ file. This is similar to XYZ format
 but has specific requirements for extra fields, headers, etc.
                                                                            
 
                                                                            
diff --git a/docs/pymatgen.io.pwscf.html b/docs/pymatgen.io.pwscf.html
index 40d9b6546f2..266af207083 100644
--- a/docs/pymatgen.io.pwscf.html
+++ b/docs/pymatgen.io.pwscf.html
@@ -4,7 +4,7 @@
   
 
   
-  pymatgen.io.pwscf module — pymatgen 2022.5.18 documentation
+  pymatgen.io.pwscf module — pymatgen 2022.5.18.1 documentation
       
       
       
@@ -39,7 +39,7 @@
              pymatgen
           
               
                                                                            
-                2022.5.18
+                2022.5.18.1
               
                                                                            
 
                                                                            
   
@@ -118,7 +118,7 @@
 
                                                                            This module implements input and output processing from PWSCF.
                                                                            
 
                                                                            
 
                                                                            
-class PWInput(structure, pseudo=None, control=None, system=None, electrons=None, ions=None, cell=None, kpoints_mode='automatic', kpoints_grid=(1, 1, 1), kpoints_shift=(0, 0, 0))[source]
                                                                            
+class PWInput(structure, pseudo=None, control=None, system=None, electrons=None, ions=None, cell=None, kpoints_mode='automatic', kpoints_grid=(1, 1, 1), kpoints_shift=(0, 0, 0))[source]
 
                                                                            Bases: object
                                                                            
 
                                                                            Base input file class. Right now, only supports no symmetry and is
 very basic.
                                                                            
@@ -150,7 +150,7 @@
 
                                                                            
 
                                                                            
 
                                                                            
-as_dict()[source]
                                                                            
+as_dict()[source]
 
                                                                            Create a dictionary representation of a PWInput object
                                                                            
 
                                                                            
 
                                                                            Returns
                                                                            
@@ -161,7 +161,7 @@
 
 
                                                                            
 
                                                                            
-classmethod from_dict(pwinput_dict)[source]
                                                                            
+classmethod from_dict(pwinput_dict)[source]
 
                                                                            Load a PWInput object from a dictionary.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -175,7 +175,7 @@
 
 
                                                                            
 
                                                                            
-static from_file(filename)[source]
                                                                            
+static from_file(filename)[source]
 
                                                                            Reads an PWInput object from a file.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -189,7 +189,7 @@
 
 
                                                                            
 
                                                                            
-static from_string(string)[source]
                                                                            
+static from_string(string)[source]
 
                                                                            Reads an PWInput object from a string.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -203,7 +203,7 @@
 
 
                                                                            
 
                                                                            
-static proc_val(key, val)[source]
                                                                            
+static proc_val(key, val)[source]
 
                                                                            Static helper method to convert PWINPUT parameters to proper type, e.g.,
 integers, floats, etc.
                                                                            
 
                                                                            
@@ -218,7 +218,7 @@
 
 
                                                                            
 
                                                                            
-write_file(filename)[source]
                                                                            
+write_file(filename)[source]
 
                                                                            Write the PWSCF input file.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -231,14 +231,14 @@
 
 
                                                                            
 
                                                                            
-exception PWInputError[source]
                                                                            
+exception PWInputError[source]
 
                                                                            Bases: BaseException
                                                                            
 
                                                                            Error for PWInput
                                                                            
 
                                                                            
 
 
                                                                            
 
                                                                            
-class PWOutput(filename)[source]
                                                                            
+class PWOutput(filename)[source]
 
                                                                            Bases: object
                                                                            
 
                                                                            Parser for PWSCF output file.
                                                                            
 
                                                                            
@@ -248,7 +248,7 @@
 
                                                                            
 
                                                                            
 
                                                                            
-property final_energy[source]
                                                                            
+property final_energy[source]
 
                                                                            Final energy
                                                                            
 
                                                                            
 
                                                                            Type
                                                                            
@@ -259,7 +259,7 @@
 
 
                                                                            
 
                                                                            
-get_celldm(idx: int)[source]
                                                                            
+get_celldm(idx: int)[source]
 
                                                                            
 
                                                                            Parameters
                                                                            
 
                                                                            idx (int) – index
                                                                            
@@ -272,7 +272,7 @@
 
 
                                                                            
 
                                                                            
-property lattice_type[source]
                                                                            
+property lattice_type[source]
 
                                                                            Lattice type.
                                                                            
 
                                                                            
 
                                                                            Type
                                                                            
@@ -283,12 +283,12 @@
 
 
                                                                            
 
                                                                            
-patterns = {'celldm1': 'celldm\\(1\\)=\\s+([\\d\\.]+)\\s', 'celldm2': 'celldm\\(2\\)=\\s+([\\d\\.]+)\\s', 'celldm3': 'celldm\\(3\\)=\\s+([\\d\\.]+)\\s', 'celldm4': 'celldm\\(4\\)=\\s+([\\d\\.]+)\\s', 'celldm5': 'celldm\\(5\\)=\\s+([\\d\\.]+)\\s', 'celldm6': 'celldm\\(6\\)=\\s+([\\d\\.]+)\\s', 'ecut': 'kinetic\\-energy cutoff\\s+=\\s+([\\d\\.\\-]+)\\s+Ry', 'energies': 'total energy\\s+=\\s+([\\d\\.\\-]+)\\sRy', 'lattice_type': 'bravais\\-lattice index\\s+=\\s+(\\d+)', 'nkpts': 'number of k points=\\s+([\\d]+)'}[source]
                                                                            
+patterns = {'celldm1': 'celldm\\(1\\)=\\s+([\\d\\.]+)\\s', 'celldm2': 'celldm\\(2\\)=\\s+([\\d\\.]+)\\s', 'celldm3': 'celldm\\(3\\)=\\s+([\\d\\.]+)\\s', 'celldm4': 'celldm\\(4\\)=\\s+([\\d\\.]+)\\s', 'celldm5': 'celldm\\(5\\)=\\s+([\\d\\.]+)\\s', 'celldm6': 'celldm\\(6\\)=\\s+([\\d\\.]+)\\s', 'ecut': 'kinetic\\-energy cutoff\\s+=\\s+([\\d\\.\\-]+)\\s+Ry', 'energies': 'total energy\\s+=\\s+([\\d\\.\\-]+)\\sRy', 'lattice_type': 'bravais\\-lattice index\\s+=\\s+(\\d+)', 'nkpts': 'number of k points=\\s+([\\d]+)'}[source]
 
                                                                            
 
 
                                                                            
 
                                                                            
-read_pattern(patterns, reverse=False, terminate_on_match=False, postprocess=<class 'str'>)[source]
                                                                            
+read_pattern(patterns, reverse=False, terminate_on_match=False, postprocess=<class 'str'>)[source]
 
                                                                            General pattern reading. Uses monty’s regrep method. Takes the same
 arguments.
                                                                            
 
                                                                            
diff --git a/docs/pymatgen.io.qchem.html b/docs/pymatgen.io.qchem.html
index 11edd6ca4fa..45fb8633417 100644
--- a/docs/pymatgen.io.qchem.html
+++ b/docs/pymatgen.io.qchem.html
@@ -4,7 +4,7 @@
   
 
   
-  pymatgen.io.qchem package — pymatgen 2022.5.18 documentation
+  pymatgen.io.qchem package — pymatgen 2022.5.18.1 documentation
       
       
       
@@ -39,7 +39,7 @@
              pymatgen
           
               
                                                                            
-                2022.5.18
+                2022.5.18.1
               
                                                                            
 
                                                                            
   
diff --git a/docs/pymatgen.io.qchem.inputs.html b/docs/pymatgen.io.qchem.inputs.html
index de226416a39..1ab9c050f80 100644
--- a/docs/pymatgen.io.qchem.inputs.html
+++ b/docs/pymatgen.io.qchem.inputs.html
@@ -4,7 +4,7 @@
   
 
   
-  pymatgen.io.qchem.inputs module — pymatgen 2022.5.18 documentation
+  pymatgen.io.qchem.inputs module — pymatgen 2022.5.18.1 documentation
       
       
       
@@ -39,7 +39,7 @@
              pymatgen
           
               
                                                                            
-                2022.5.18
+                2022.5.18.1
               
                                                                            
 
                                                                            
   
@@ -119,7 +119,7 @@
 
                                                                            Classes for reading/manipulating/writing QChem input files.
                                                                            
 
                                                                            
 
                                                                            
-class QCInput(molecule: Molecule | Literal['read'], rem: dict, opt: dict[str, list] | None = None, pcm: dict | None = None, solvent: dict | None = None, smx: dict | None = None, scan: dict[str, list] | None = None, van_der_waals: dict[str, float] | None = None, vdw_mode: str = 'atomic', plots: dict | None = None, nbo: dict | None = None)[source]
                                                                            
+class QCInput(molecule: Molecule | Literal['read'], rem: dict, opt: dict[str, list] | None = None, pcm: dict | None = None, solvent: dict | None = None, smx: dict | None = None, scan: dict[str, list] | None = None, van_der_waals: dict[str, float] | None = None, vdw_mode: str = 'atomic', plots: dict | None = None, nbo: dict | None = None)[source]
 
                                                                            Bases: pymatgen.io.core.InputFile
                                                                            
 
                                                                            An object representing a QChem input file. QCInput attributes represent different sections of a QChem input file.
 To add a new section one needs to modify __init__, __str__, from_sting and add staticmethods
@@ -165,7 +165,7 @@
 
                                                                            
 
                                                                            
 
                                                                            
-static find_sections(string: str) → list[source]
                                                                            
+static find_sections(string: str) → list[source]
 
                                                                            Find sections in the string.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -179,7 +179,7 @@
 
 
                                                                            
 
                                                                            
-static from_file(filename: str | Path) → QCInput[source]
                                                                            
+static from_file(filename: str | Path) → QCInput[source]
 
                                                                            Create QcInput from file.
 :param filename: Filename
 :type filename: str
                                                                            
@@ -192,7 +192,7 @@
 
 
                                                                            
 
                                                                            
-classmethod from_multi_jobs_file(filename: str) → list[pymatgen.io.qchem.inputs.QCInput][source]
                                                                            
+classmethod from_multi_jobs_file(filename: str) → list[pymatgen.io.qchem.inputs.QCInput][source]
 
                                                                            Create list of QcInput from a file.
 :param filename: Filename
 :type filename: str
                                                                            
@@ -205,7 +205,7 @@
 
 
                                                                            
 
                                                                            
-classmethod from_string(string: str) → pymatgen.io.qchem.inputs.QCInput[source]
                                                                            
+classmethod from_string(string: str) → pymatgen.io.qchem.inputs.QCInput[source]
 
                                                                            Read QcInput from string.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -219,13 +219,13 @@
 
 
                                                                            
 
                                                                            
-get_string()[source]
                                                                            
+get_string()[source]
 
                                                                            Return a string representation of an entire input file.
                                                                            
 
                                                                            
 
 
                                                                            
 
                                                                            
-static molecule_template(molecule: Molecule | Literal['read']) → str[source]
                                                                            
+static molecule_template(molecule: Molecule | Literal['read']) → str[source]
 
                                                                            
 
                                                                            Parameters
                                                                            
 
                                                                            molecule (Molecule) – molecule
                                                                            
@@ -238,7 +238,7 @@
 
 
                                                                            
 
                                                                            
-static multi_job_string(job_list: list[pymatgen.io.qchem.inputs.QCInput]) → str[source]
                                                                            
+static multi_job_string(job_list: list[pymatgen.io.qchem.inputs.QCInput]) → str[source]
 
                                                                            
 
                                                                            Parameters
                                                                            
 
                                                                            () (job_list) – List of jobs
                                                                            
@@ -251,7 +251,7 @@
 
 
                                                                            
 
                                                                            
-static nbo_template(nbo: dict) → str[source]
                                                                            
+static nbo_template(nbo: dict) → str[source]
 
                                                                            
 
                                                                            Parameters
                                                                            
 
                                                                            () (nbo) – 
                                                                            
@@ -264,7 +264,7 @@
 
 
                                                                            
 
                                                                            
-static opt_template(opt: dict[str, list]) → str[source]
                                                                            
+static opt_template(opt: dict[str, list]) → str[source]
 
                                                                            Optimization template.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -278,7 +278,7 @@
 
 
                                                                            
 
                                                                            
-static pcm_template(pcm: dict) → str[source]
                                                                            
+static pcm_template(pcm: dict) → str[source]
 
                                                                            Pcm run template.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -292,7 +292,7 @@
 
 
                                                                            
 
                                                                            
-static plots_template(plots: dict) → str[source]
                                                                            
+static plots_template(plots: dict) → str[source]
 
                                                                            
 
                                                                            Parameters
                                                                            
 
                                                                            () (plots) – 
                                                                            
@@ -305,7 +305,7 @@
 
 
                                                                            
 
                                                                            
-static read_molecule(string: str) → Molecule | Literal['read'][source]
                                                                            
+static read_molecule(string: str) → Molecule | Literal['read'][source]
 
                                                                            Read molecule from string.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -319,7 +319,7 @@
 
 
                                                                            
 
                                                                            
-static read_nbo(string: str) → dict[source]
                                                                            
+static read_nbo(string: str) → dict[source]
 
                                                                            Read nbo parameters from string.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -333,7 +333,7 @@
 
 
                                                                            
 
                                                                            
-static read_opt(string: str) → dict[str, list][source]
                                                                            
+static read_opt(string: str) → dict[str, list][source]
 
                                                                            Read opt section from string.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -347,7 +347,7 @@
 
 
                                                                            
 
                                                                            
-static read_pcm(string: str) → dict[source]
                                                                            
+static read_pcm(string: str) → dict[source]
 
                                                                            Read pcm parameters from string.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -361,7 +361,7 @@
 
 
                                                                            
 
                                                                            
-static read_plots(string: str) → dict[source]
                                                                            
+static read_plots(string: str) → dict[source]
 
                                                                            Read plots parameters from string.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -375,7 +375,7 @@
 
 
                                                                            
 
                                                                            
-static read_rem(string: str) → dict[source]
                                                                            
+static read_rem(string: str) → dict[source]
 
                                                                            Parse rem from string.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -389,7 +389,7 @@
 
 
                                                                            
 
                                                                            
-static read_scan(string: str) → dict[str, list][source]
                                                                            
+static read_scan(string: str) → dict[str, list][source]
 
                                                                            Read scan section from a string.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -403,7 +403,7 @@
 
 
                                                                            
 
                                                                            
-static read_smx(string: str) → dict[source]
                                                                            
+static read_smx(string: str) → dict[source]
 
                                                                            Read smx parameters from string.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -417,7 +417,7 @@
 
 
                                                                            
 
                                                                            
-static read_solvent(string: str) → dict[source]
                                                                            
+static read_solvent(string: str) → dict[source]
 
                                                                            Read solvent parameters from string.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -431,7 +431,7 @@
 
 
                                                                            
 
                                                                            
-static read_vdw(string: str) → tuple[str, dict][source]
                                                                            
+static read_vdw(string: str) → tuple[str, dict][source]
 
                                                                            Read van der Waals parameters from string.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -445,7 +445,7 @@
 
 
                                                                            
 
                                                                            
-static rem_template(rem: dict) → str[source]
                                                                            
+static rem_template(rem: dict) → str[source]
 
                                                                            
 
                                                                            Parameters
                                                                            
 
                                                                            () (rem) – 
                                                                            
@@ -458,7 +458,7 @@
 
 
                                                                            
 
                                                                            
-static scan_template(scan: dict[str, list]) → str[source]
                                                                            
+static scan_template(scan: dict[str, list]) → str[source]
 
                                                                            
 
                                                                            Parameters
                                                                            
 
                                                                            scan (dict) – Dictionary with scan section information.
@@ -472,7 +472,7 @@
 
 
                                                                            
 
                                                                            
-static smx_template(smx: dict) → str[source]
                                                                            
+static smx_template(smx: dict) → str[source]
 
                                                                            
 
                                                                            Parameters
                                                                            
 
                                                                            () (smx) – 
                                                                            
@@ -485,7 +485,7 @@
 
 
                                                                            
 
                                                                            
-static solvent_template(solvent: dict) → str[source]
                                                                            
+static solvent_template(solvent: dict) → str[source]
 
                                                                            Solvent template.
                                                                            
 
                                                                            
 
                                                                            Parameters
                                                                            
@@ -499,7 +499,7 @@
 
 
                                                                            
 
                                                                            
-static van_der_waals_template(radii: dict[str, float], mode: str = 'atomic') → str[source]
                                                                            
+static van_der_waals_template(radii: dict[str, float], mode: str = 'atomic') → str[source]
 
                                                                            
 
                                                                            Parameters
                                                                            
 
                                                                              
@@ -522,7 +522,7 @@
 
 
                                                                              
 
                                                                              
-static write_multi_job_file(job_list: list[pymatgen.io.qchem.inputs.QCInput], filename: str)[source]
                                                                              
+static write_multi_job_file(job_list: list[pymatgen.io.qchem.inputs.QCInput], filename: str)[source]
 
                                                                              Write a multijob file.
                                                                              
 
                                                                              
 
                                                                              Parameters
                                                                              
diff --git a/docs/pymatgen.io.qchem.outputs.html b/docs/pymatgen.io.qchem.outputs.html
index 700d196a046..708a719fe88 100644
--- a/docs/pymatgen.io.qchem.outputs.html
+++ b/docs/pymatgen.io.qchem.outputs.html
@@ -4,7 +4,7 @@
   
 
   
-  pymatgen.io.qchem.outputs module — pymatgen 2022.5.18 documentation
+  pymatgen.io.qchem.outputs module — pymatgen 2022.5.18.1 documentation
       
       
       
@@ -39,7 +39,7 @@
              pymatgen
           
               
                                                                              
-                2022.5.18
+                2022.5.18.1
               
                                                                              
 
                                                                              
   
@@ -119,7 +119,7 @@
 
                                                                              Parsers for Qchem output files.
                                                                              
 
                                                                              
 
                                                                              
-class QCOutput(filename: str)[source]
                                                                              
+class QCOutput(filename: str)[source]
 
                                                                              Bases: monty.json.MSONable
                                                                              
 
                                                                              Class to parse QChem output files.
                                                                              
 
                                                                              
@@ -129,7 +129,7 @@
 
                                                                              
 
                                                                              
 
                                                                              
-as_dict()[source]
                                                                              
+as_dict()[source]
 
                                                                              
 
                                                                              Returns
                                                                              
 
                                                                              MSONAble dict.
                                                                              
@@ -139,7 +139,7 @@
 
 
                                                                              
 
                                                                              
-static multiple_outputs_from_file(cls, filename, keep_sub_files=True)[source]
                                                                              
+static multiple_outputs_from_file(cls, filename, keep_sub_files=True)[source]
 
                                                                              Parses a QChem output file with multiple calculations
 # 1.) Separates the output into sub-files
                                                                              
 
                                                                              
@@ -154,7 +154,7 @@
 
 
                                                                              
 
                                                                              
-check_for_structure_changes(mol1: pymatgen.core.structure.Molecule, mol2: pymatgen.core.structure.Molecule) → str[source]
                                                                              
+check_for_structure_changes(mol1: pymatgen.core.structure.Molecule, mol2: pymatgen.core.structure.Molecule) → str[source]
 
                                                                              Compares connectivity of two molecules (using MoleculeGraph w/ OpenBabelNN).
 This function will work with two molecules with different atom orderings,
                                                                              
 
                                                                              
@@ -189,7 +189,7 @@
 
 
                                                                              
 
                                                                              
-get_percentage(line: str, orbital: str) → str[source]
                                                                              
+get_percentage(line: str, orbital: str) → str[source]
 
                                                                              Retrieve the percent character of an orbital.
                                                                              
 
                                                                              
 
                                                                              Parameters
                                                                              
@@ -209,7 +209,7 @@
 
 
                                                                              
 
                                                                              
-jump_to_header(lines: list[str], header: str) → list[str][source]
                                                                              
+jump_to_header(lines: list[str], header: str) → list[str][source]
 
                                                                              Given a list of lines, truncate the start of the list so that the first line
 of the new list contains the header.
                                                                              
 
                                                                              
@@ -230,7 +230,7 @@
 
 
                                                                              
 
                                                                              
-nbo_parser(filename: str) → dict[str, list[pandas.core.frame.DataFrame]][source]
                                                                              
+nbo_parser(filename: str) → dict[str, list[pandas.core.frame.DataFrame]][source]
 
                                                                              Parse all the important sections of NBO output.
                                                                              
 
                                                                              
 
                                                                              Parameters
                                                                              
@@ -247,7 +247,7 @@
 
 
                                                                              
 
                                                                              
-parse_hybridization_character(lines: list[str]) → list[pandas.core.frame.DataFrame][source]
                                                                              
+parse_hybridization_character(lines: list[str]) → list[pandas.core.frame.DataFrame][source]
 
                                                                              Parse the hybridization character section of NBO output.
                                                                              
 
                                                                              
 
                                                                              Parameters
                                                                              
@@ -264,7 +264,7 @@
 
 
                                                                              
 
                                                                              
-parse_natural_populations(lines: list[str]) → list[pandas.core.frame.DataFrame][source]
                                                                              
+parse_natural_populations(lines: list[str]) → list[pandas.core.frame.DataFrame][source]
 
                                                                              Parse the natural populations section of NBO output.
                                                                              
 
                                                                              
 
                                                                              Parameters
                                                                              
@@ -281,7 +281,7 @@
 
 
                                                                              
 
                                                                              
-parse_perturbation_energy(lines: list[str]) → list[pandas.core.frame.DataFrame][source]
                                                                              
+parse_perturbation_energy(lines: list[str]) → list[pandas.core.frame.DataFrame][source]
 
                                                                              Parse the perturbation energy section of NBO output.
                                                                              
 
                                                                              
 
                                                                              Parameters
                                                                              
@@ -298,7 +298,7 @@
 
 
                                                                              
 
                                                                              
-z_int(string: str) → int[source]
                                                                              
+z_int(string: str) → int[source]
 
                                                                              Convert string to integer.
 If string empty, return -1.
                                                                              
 
                                                                              
diff --git a/docs/pymatgen.io.qchem.sets.html b/docs/pymatgen.io.qchem.sets.html
index 18f08bf5754..910599605fb 100644
--- a/docs/pymatgen.io.qchem.sets.html
+++ b/docs/pymatgen.io.qchem.sets.html
@@ -4,7 +4,7 @@
   
 
   
-  pymatgen.io.qchem.sets module — pymatgen 2022.5.18 documentation
+  pymatgen.io.qchem.sets module — pymatgen 2022.5.18.1 documentation
       
       
       
@@ -39,7 +39,7 @@
              pymatgen
           
               
                                                                              
-                2022.5.18
+                2022.5.18.1
               
                                                                              
 
                                                                              
   
@@ -119,7 +119,7 @@
 
                                                                              Input sets for Qchem
                                                                              
 
                                                                              
 
                                                                              
-class ForceSet(molecule: Molecule, basis_set: str = 'def2-tzvppd', scf_algorithm: str = 'diis', dft_rung: int = 3, pcm_dielectric: float | None = None, smd_solvent: str | None = None, custom_smd: str | None = None, max_scf_cycles: int = 200, plot_cubes: bool = False, nbo_params: dict | None = None, overwrite_inputs: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic')[source]
                                                                              
+class ForceSet(molecule: Molecule, basis_set: str = 'def2-tzvppd', scf_algorithm: str = 'diis', dft_rung: int = 3, pcm_dielectric: float | None = None, smd_solvent: str | None = None, custom_smd: str | None = None, max_scf_cycles: int = 200, plot_cubes: bool = False, nbo_params: dict | None = None, overwrite_inputs: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic')[source]
 
                                                                              Bases: pymatgen.io.qchem.sets.QChemDictSet
                                                                              
 
                                                                              QChemDictSet for a force (gradient) calculation
                                                                              
 
                                                                              
@@ -178,7 +178,7 @@
 
 
                                                                              
 
                                                                              
-class FreqSet(molecule: Molecule, basis_set: str = 'def2-tzvppd', scf_algorithm: str = 'diis', dft_rung: int = 3, pcm_dielectric: float | None = None, smd_solvent: str | None = None, custom_smd: str | None = None, max_scf_cycles: int = 200, plot_cubes: bool = False, nbo_params: dict | None = None, overwrite_inputs: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic')[source]
                                                                              
+class FreqSet(molecule: Molecule, basis_set: str = 'def2-tzvppd', scf_algorithm: str = 'diis', dft_rung: int = 3, pcm_dielectric: float | None = None, smd_solvent: str | None = None, custom_smd: str | None = None, max_scf_cycles: int = 200, plot_cubes: bool = False, nbo_params: dict | None = None, overwrite_inputs: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic')[source]
 
                                                                              Bases: pymatgen.io.qchem.sets.QChemDictSet
                                                                              
 
                                                                              QChemDictSet for a frequency calculation
                                                                              
 
                                                                              
@@ -237,7 +237,7 @@
 
 
                                                                              
 
                                                                              
-class OptSet(molecule: Molecule, basis_set: str = 'def2-tzvppd', scf_algorithm: str = 'diis', dft_rung: int = 3, pcm_dielectric: float | None = None, smd_solvent: str | None = None, custom_smd: str | None = None, max_scf_cycles: int = 200, plot_cubes: bool = False, nbo_params: dict | None = None, opt_variables: dict[str, list] | None = None, geom_opt_max_cycles: int = 200, overwrite_inputs: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic')[source]
                                                                              
+class OptSet(molecule: Molecule, basis_set: str = 'def2-tzvppd', scf_algorithm: str = 'diis', dft_rung: int = 3, pcm_dielectric: float | None = None, smd_solvent: str | None = None, custom_smd: str | None = None, max_scf_cycles: int = 200, plot_cubes: bool = False, nbo_params: dict | None = None, opt_variables: dict[str, list] | None = None, geom_opt_max_cycles: int = 200, overwrite_inputs: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic')[source]
 
                                                                              Bases: pymatgen.io.qchem.sets.QChemDictSet
                                                                              
 
                                                                              QChemDictSet for a geometry optimization
                                                                              
 
                                                                              
@@ -299,7 +299,7 @@
 
 
                                                                              
 
                                                                              
-class PESScanSet(molecule: Molecule, basis_set: str = 'def2-tzvppd', scf_algorithm: str = 'diis', dft_rung: int = 3, pcm_dielectric: float | None = None, smd_solvent: str | None = None, custom_smd: str | None = None, max_scf_cycles: int = 200, plot_cubes: bool = False, nbo_params: dict | None = None, opt_variables: dict[str, list] | None = None, scan_variables: dict[str, list] | None = None, overwrite_inputs: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic')[source]
                                                                              
+class PESScanSet(molecule: Molecule, basis_set: str = 'def2-tzvppd', scf_algorithm: str = 'diis', dft_rung: int = 3, pcm_dielectric: float | None = None, smd_solvent: str | None = None, custom_smd: str | None = None, max_scf_cycles: int = 200, plot_cubes: bool = False, nbo_params: dict | None = None, opt_variables: dict[str, list] | None = None, scan_variables: dict[str, list] | None = None, overwrite_inputs: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic')[source]
 
                                                                              Bases: pymatgen.io.qchem.sets.QChemDictSet
                                                                              
 
                                                                              QChemDictSet for a potential energy surface scan (PES_SCAN) calculation,
 used primarily to identify possible transition states or to sample different
@@ -376,7 +376,7 @@
 
 
                                                                              
 
                                                                              
-class QChemDictSet(molecule: Molecule, job_type: str, basis_set: str, scf_algorithm: str, dft_rung: int = 4, pcm_dielectric: float | None = None, smd_solvent: str | None = None, custom_smd: str | None = None, opt_variables: dict[str, list] | None = None, scan_variables: dict[str, list] | None = None, max_scf_cycles: int = 200, geom_opt_max_cycles: int = 200, plot_cubes: bool = False, nbo_params: dict | None = None, overwrite_inputs: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic')[source]
                                                                              
+class QChemDictSet(molecule: Molecule, job_type: str, basis_set: str, scf_algorithm: str, dft_rung: int = 4, pcm_dielectric: float | None = None, smd_solvent: str | None = None, custom_smd: str | None = None, opt_variables: dict[str, list] | None = None, scan_variables: dict[str, list] | None = None, max_scf_cycles: int = 200, geom_opt_max_cycles: int = 200, plot_cubes: bool = False, nbo_params: dict | None = None, overwrite_inputs: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic')[source]
 
                                                                              Bases: pymatgen.io.qchem.inputs.QCInput
                                                                              
 
                                                                              Build a QCInput given all the various input parameters. Can be extended by standard implementations below.
                                                                              
 
                                                                              
@@ -449,7 +449,7 @@
 
                                                                              
 
                                                                              
 
                                                                              
-write(input_file: str)[source]
                                                                              
+write(input_file: str)[source]
 
                                                                              
 
                                                                              Parameters
                                                                              
 
                                                                              input_file (str) – Filename
                                                                              
@@ -461,7 +461,7 @@
 
 
                                                                              
 
                                                                              
-class SinglePointSet(molecule: Molecule, basis_set: str = 'def2-tzvppd', scf_algorithm: str = 'diis', dft_rung: int = 3, pcm_dielectric: float | None = None, smd_solvent: str | None = None, custom_smd: str | None = None, max_scf_cycles: int = 200, plot_cubes: bool = False, nbo_params: dict | None = None, overwrite_inputs: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic')[source]
                                                                              
+class SinglePointSet(molecule: Molecule, basis_set: str = 'def2-tzvppd', scf_algorithm: str = 'diis', dft_rung: int = 3, pcm_dielectric: float | None = None, smd_solvent: str | None = None, custom_smd: str | None = None, max_scf_cycles: int = 200, plot_cubes: bool = False, nbo_params: dict | None = None, overwrite_inputs: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic')[source]
 
                                                                              Bases: pymatgen.io.qchem.sets.QChemDictSet
                                                                              
 
                                                                              QChemDictSet for a single point calculation
                                                                              
 
                                                                              
@@ -522,7 +522,7 @@
 
 
                                                                              
 
                                                                              
-class TransitionStateSet(molecule: Molecule, basis_set: str = 'def2-tzvppd', scf_algorithm: str = 'diis', dft_rung: int = 3, pcm_dielectric: float | None = None, smd_solvent: str | None = None, custom_smd: str | None = None, max_scf_cycles: int = 200, plot_cubes: bool = False, nbo_params: dict | None = None, opt_variables: dict[str, list] | None = None, geom_opt_max_cycles: int = 200, overwrite_inputs: dict | None = None, vdw_mode='atomic')[source]
                                                                              
+class TransitionStateSet(molecule: Molecule, basis_set: str = 'def2-tzvppd', scf_algorithm: str = 'diis', dft_rung: int = 3, pcm_dielectric: float | None = None, smd_solvent: str | None = None, custom_smd: str | None = None, max_scf_cycles: int = 200, plot_cubes: bool = False, nbo_params: dict | None = None, opt_variables: dict[str, list] | None = None, geom_opt_max_cycles: int = 200, overwrite_inputs: dict | None = None, vdw_mode='atomic')[source]
 
                                                                              Bases: pymatgen.io.qchem.sets.QChemDictSet
                                                                              
 
                                                                              QChemDictSet for a transition-state search
                                                                              
 
                                                                              
diff --git a/docs/pymatgen.io.qchem.utils.html b/docs/pymatgen.io.qchem.utils.html
index 546af99a4c7..5bcd2728992 100644
--- a/docs/pymatgen.io.qchem.utils.html
+++ b/docs/pymatgen.io.qchem.utils.html
@@ -4,7 +4,7 @@
   
 
   
-  pymatgen.io.qchem.utils module — pymatgen 2022.5.18 documentation
+  pymatgen.io.qchem.utils module — pymatgen 2022.5.18.1 documentation
       
       
       
@@ -39,7 +39,7 @@
              pymatgen
           
               
                                                                              
-                2022.5.18
+                2022.5.18.1
               
                                                                              
 
                                                                              
   
@@ -119,7 +119,7 @@
 
                                                                              Utilities for Qchem io.
                                                                              
 
                                                                              
 
                                                                              
-lower_and_check_unique(dict_to_check)[source]
                                                                              
+lower_and_check_unique(dict_to_check)[source]
 
                                                                              Takes a dictionary and makes all the keys lower case. Also replaces
 “jobtype” with “job_type” just so that key specifically can be called
 elsewhere without ambiguity. Finally, ensures that multiple identical
@@ -144,14 +144,14 @@
 
 
                                                                              
 
                                                                              
-process_parsed_coords(coords)[source]
                                                                              
+process_parsed_coords(coords)[source]
 
                                                                              Takes a set of parsed coordinates, which come as an array of strings,
 and returns a numpy array of floats.
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-read_pattern(text_str, patterns, terminate_on_match=False, postprocess=<class 'str'>)[source]
                                                                              
+read_pattern(text_str, patterns, terminate_on_match=False, postprocess=<class 'str'>)[source]
 
                                                                              General pattern reading on an input string
                                                                              
 
                                                                              
 
                                                                              Parameters
                                                                              
@@ -178,7 +178,7 @@
 
 
                                                                              
 
                                                                              
-read_table_pattern(text_str, header_pattern, row_pattern, footer_pattern, postprocess=<class 'str'>, attribute_name=None, last_one_only=False)[source]
                                                                              
+read_table_pattern(text_str, header_pattern, row_pattern, footer_pattern, postprocess=<class 'str'>, attribute_name=None, last_one_only=False)[source]
 
                                                                              Parse table-like data. A table composes of three parts: header,
 main body, footer. All the data matches “row pattern” in the main body
 will be returned.
                                                                              
diff --git a/docs/pymatgen.io.shengbte.html b/docs/pymatgen.io.shengbte.html
index d2ae2749f1a..fc81034e5e5 100644
--- a/docs/pymatgen.io.shengbte.html
+++ b/docs/pymatgen.io.shengbte.html
@@ -4,7 +4,7 @@
   
 
   
-  pymatgen.io.shengbte module — pymatgen 2022.5.18 documentation
+  pymatgen.io.shengbte module — pymatgen 2022.5.18.1 documentation
       
       
       
@@ -39,7 +39,7 @@
              pymatgen
           
               
                                                                              
-                2022.5.18
+                2022.5.18.1
               
                                                                              
 
                                                                              
   
@@ -118,7 +118,7 @@
 
                                                                              This module implements reading and writing of ShengBTE CONTROL files.
                                                                              
 
                                                                              
 
                                                                              
-class Control(ngrid: list[int] | None = None, temperature: float | dict[str, float] = 300, **kwargs)[source]
                                                                              
+class Control(ngrid: list[int] | None = None, temperature: float | dict[str, float] = 300, **kwargs)[source]
 
                                                                              Bases: monty.json.MSONable, dict
                                                                              
 
                                                                              Class for reading, updating, and writing ShengBTE CONTROL files.
 See  https://bitbucket.org/sousaw/shengbte/src/master/ for more
@@ -157,28 +157,28 @@
 
                                                                              
 
                                                                              
 
                                                                              
-allocations_keys = ['nelements', 'natoms', 'ngrid', 'norientations'][source]
                                                                              
+allocations_keys = ['nelements', 'natoms', 'ngrid', 'norientations'][source]
 
                                                                              
 
 
                                                                              
 
                                                                              
-as_dict()[source]
                                                                              
+as_dict()[source]
 
                                                                              Returns: MSONAble dict
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-crystal_keys = ['lfactor', 'lattvec', 'types', 'elements', 'positions', 'masses', 'gfactors', 'epsilon', 'born', 'scell', 'orientations'][source]
                                                                              
+crystal_keys = ['lfactor', 'lattvec', 'types', 'elements', 'positions', 'masses', 'gfactors', 'epsilon', 'born', 'scell', 'orientations'][source]
 
                                                                              
 
 
                                                                              
 
                                                                              
-flags_keys = ['nonanalytic', 'convergence', 'isotopes', 'autoisotopes', 'nanowires', 'onlyharmonic', 'espresso'][source]
                                                                              
+flags_keys = ['nonanalytic', 'convergence', 'isotopes', 'autoisotopes', 'nanowires', 'onlyharmonic', 'espresso'][source]
 
                                                                              
 
 
                                                                              
 
                                                                              
-classmethod from_dict(control_dict: dict)[source]
                                                                              
+classmethod from_dict(control_dict: dict)[source]
 
                                                                              Write a CONTROL file from a Python dictionary. Description and default
 parameters can be found at
 https://bitbucket.org/sousaw/shengbte/src/master/.
@@ -193,7 +193,7 @@
 
 
                                                                              
 
                                                                              
-classmethod from_file(filepath: str)[source]
                                                                              
+classmethod from_file(filepath: str)[source]
 
                                                                              Read a CONTROL namelist file and output a ‘Control’ object
                                                                              
 
                                                                              
 
                                                                              Parameters
                                                                              
@@ -207,7 +207,7 @@
 
 
                                                                              
 
                                                                              
-classmethod from_structure(structure: Structure, reciprocal_density: int | None = 50000, **kwargs)[source]
                                                                              
+classmethod from_structure(structure: Structure, reciprocal_density: int | None = 50000, **kwargs)[source]
 
                                                                              Get a ShengBTE control object from a structure.
                                                                              
 
                                                                              
 
                                                                              Parameters
                                                                              
@@ -227,7 +227,7 @@
 
 
                                                                              
 
                                                                              
-get_structure() → pymatgen.core.structure.Structure[source]
                                                                              
+get_structure() → pymatgen.core.structure.Structure[source]
 
                                                                              Get a pymatgen Structure from a ShengBTE control object.
                                                                              
 
                                                                              The control object must have the “lattvec”, “types”, “elements”, and
 “positions” settings otherwise an error will be thrown.
                                                                              
@@ -240,17 +240,17 @@
 
 
                                                                              
 
                                                                              
-params_keys = ['t', 't_min', 't_max', 't_step', 'omega_max', 'scalebroad', 'rmin', 'rmax', 'dr', 'maxiter', 'nticks', 'eps'][source]
                                                                              
+params_keys = ['t', 't_min', 't_max', 't_step', 'omega_max', 'scalebroad', 'rmin', 'rmax', 'dr', 'maxiter', 'nticks', 'eps'][source]
 
                                                                              
 
 
                                                                              
 
                                                                              
-required_params = ['nelements', 'natoms', 'ngrid', 'lattvec', 'types', 'elements', 'positions', 'scell'][source]
                                                                              
+required_params = ['nelements', 'natoms', 'ngrid', 'lattvec', 'types', 'elements', 'positions', 'scell'][source]
 
                                                                              
 
 
                                                                              
 
                                                                              
-to_file(filename: str = 'CONTROL')[source]
                                                                              
+to_file(filename: str = 'CONTROL')[source]
 
                                                                              Writes ShengBTE CONTROL file from ‘Control’ object
                                                                              
 
                                                                              
 
                                                                              Parameters
                                                                              
diff --git a/docs/pymatgen.io.template.html b/docs/pymatgen.io.template.html
index 4843b54851f..0e5710ab7ca 100644
--- a/docs/pymatgen.io.template.html
+++ b/docs/pymatgen.io.template.html
@@ -4,7 +4,7 @@
   
 
   
-  pymatgen.io.template module — pymatgen 2022.5.18 documentation
+  pymatgen.io.template module — pymatgen 2022.5.18.1 documentation
       
       
       
@@ -39,7 +39,7 @@
              pymatgen
           
               
                                                                              
-                2022.5.18
+                2022.5.18.1
               
                                                                              
 
                                                                              
   
@@ -119,7 +119,7 @@
 used to facilitate writing large numbers of input files based on a template.
                                                                              
 
                                                                              
 
                                                                              
-class TemplateInputGen[source]
                                                                              
+class TemplateInputGen[source]
 
                                                                              Bases: pymatgen.io.core.InputGenerator
                                                                              
 
                                                                              Concrete implementation of InputGenerator that is based on a single template input
 file with variables.
                                                                              
@@ -128,7 +128,7 @@
 classes.
                                                                              
 
                                                                              
 
                                                                              
-get_input_set(template: Union[str, pathlib.Path], variables: Optional[Dict] = None, filename: str = 'input.txt')[source]
                                                                              
+get_input_set(template: Union[str, pathlib.Path], variables: Optional[Dict] = None, filename: str = 'input.txt')[source]
 
                                                                              
 
                                                                              Parameters
                                                                              
 
                                                                                
diff --git a/docs/pymatgen.io.vasp.help.html b/docs/pymatgen.io.vasp.help.html
index 9229d254f53..3d0200c818b 100644
--- a/docs/pymatgen.io.vasp.help.html
+++ b/docs/pymatgen.io.vasp.help.html
@@ -4,7 +4,7 @@
   
 
   
-  pymatgen.io.vasp.help module — pymatgen 2022.5.18 documentation
+  pymatgen.io.vasp.help module — pymatgen 2022.5.18.1 documentation
       
       
       
@@ -39,7 +39,7 @@
              pymatgen
           
               
                                                                                
-                2022.5.18
+                2022.5.18.1
               
                                                                                
 
                                                                                
   
@@ -119,13 +119,13 @@
 
                                                                                Get help with VASP parameters from VASP wiki.
                                                                                
 
                                                                                
 
                                                                                
-class VaspDoc[source]
                                                                                
+class VaspDoc[source]
 
                                                                                Bases: object
                                                                                
 
                                                                                A VASP documentation helper.
                                                                                
 
                                                                                Init for VaspDoc.
                                                                                
 
                                                                                
 
                                                                                
-classmethod get_help(tag, fmt='text')[source]
                                                                                
+classmethod get_help(tag, fmt='text')[source]
 
                                                                                Get help on a VASP tag.
                                                                                
 
                                                                                
 
                                                                                Parameters
                                                                                
@@ -139,13 +139,13 @@
 
 
                                                                                
 
                                                                                
-classmethod get_incar_tags()[source]
                                                                                
+classmethod get_incar_tags()[source]
 
                                                                                Returns: All incar tags
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-print_help(tag)[source]
                                                                                
+print_help(tag)[source]
 
                                                                                Print the help for a TAG.
                                                                                
 
                                                                                
 
                                                                                Parameters
                                                                                
@@ -156,7 +156,7 @@
 
 
                                                                                
 
                                                                                
-print_jupyter_help(tag)[source]
                                                                                
+print_jupyter_help(tag)[source]
 
                                                                                Display HTML help in ipython notebook.
                                                                                
 
                                                                                
 
                                                                                Parameters
                                                                                
diff --git a/docs/pymatgen.io.vasp.html b/docs/pymatgen.io.vasp.html
index ad919cf4466..e0dfd732558 100644
--- a/docs/pymatgen.io.vasp.html
+++ b/docs/pymatgen.io.vasp.html
@@ -4,7 +4,7 @@
   
 
   
-  pymatgen.io.vasp package — pymatgen 2022.5.18 documentation
+  pymatgen.io.vasp package — pymatgen 2022.5.18.1 documentation
       
       
       
@@ -39,7 +39,7 @@
              pymatgen
           
               
                                                                                
-                2022.5.18
+                2022.5.18.1
               
                                                                                
 
                                                                                
   
diff --git a/docs/pymatgen.io.vasp.inputs.html b/docs/pymatgen.io.vasp.inputs.html
index 4e0064dc351..e0655a62bde 100644
--- a/docs/pymatgen.io.vasp.inputs.html
+++ b/docs/pymatgen.io.vasp.inputs.html
@@ -4,7 +4,7 @@
   
 
   
-  pymatgen.io.vasp.inputs module — pymatgen 2022.5.18 documentation
+  pymatgen.io.vasp.inputs module — pymatgen 2022.5.18.1 documentation
       
       
       
@@ -39,7 +39,7 @@
              pymatgen
           
               
                                                                                
-                2022.5.18
+                2022.5.18.1
               
                                                                                
 
                                                                                
   
@@ -120,14 +120,14 @@
 files.
                                                                                
 
                                                                                
 
                                                                                
-exception BadIncarWarning[source]
                                                                                
+exception BadIncarWarning[source]
 
                                                                                Bases: UserWarning
                                                                                
 
                                                                                Warning class for bad Incar parameters.
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-class Incar(params: Optional[dict[str, Any]] = None)[source]
                                                                                
+class Incar(params: Optional[dict[str, Any]] = None)[source]
 
                                                                                Bases: dict, monty.json.MSONable
                                                                                
 
                                                                                INCAR object for reading and writing INCAR files. Essentially consists of
 a dictionary with some helper functions
                                                                                
@@ -139,7 +139,7 @@
 
                                                                                
 
                                                                                
 
                                                                                
-as_dict() → dict[source]
                                                                                
+as_dict() → dict[source]
 
                                                                                
 
                                                                                Returns
                                                                                
 
                                                                                MSONable dict.
                                                                                
@@ -149,7 +149,7 @@
 
 
                                                                                
 
                                                                                
-check_params()[source]
                                                                                
+check_params()[source]
 
                                                                                Raises a warning for nonsensical or non-existent INCAR tags and
 parameters. If a keyword doesn’t exist (e.g. there’s a typo in a
 keyword), your calculation will still run, however VASP will ignore the
@@ -158,7 +158,7 @@
 
 
                                                                                
 
                                                                                
-diff(other: pymatgen.io.vasp.inputs.Incar) → dict[str, dict[str, Any]][source]
                                                                                
+diff(other: pymatgen.io.vasp.inputs.Incar) → dict[str, dict[str, Any]][source]
 
                                                                                Diff function for Incar. Compares two Incars and indicates which
 parameters are the same and which are not. Useful for checking whether
 two runs were done using the same parameters.
                                                                                
@@ -180,7 +180,7 @@
 
 
                                                                                
 
                                                                                
-classmethod from_dict(d) → pymatgen.io.vasp.inputs.Incar[source]
                                                                                
+classmethod from_dict(d) → pymatgen.io.vasp.inputs.Incar[source]
 
                                                                                
 
                                                                                Parameters
                                                                                
 
                                                                                d – Dict representation.
                                                                                
@@ -193,7 +193,7 @@
 
 
                                                                                
 
                                                                                
-static from_file(filename: Union[str, pathlib.Path]) → pymatgen.io.vasp.inputs.Incar[source]
                                                                                
+static from_file(filename: Union[str, pathlib.Path]) → pymatgen.io.vasp.inputs.Incar[source]
 
                                                                                Reads an Incar object from a file.
                                                                                
 
                                                                                
 
                                                                                Parameters
                                                                                
@@ -207,7 +207,7 @@
 
 
                                                                                
 
                                                                                
-static from_string(string: str) → pymatgen.io.vasp.inputs.Incar[source]
                                                                                
+static from_string(string: str) → pymatgen.io.vasp.inputs.Incar[source]
 
                                                                                Reads an Incar object from a string.
                                                                                
 
                                                                                
 
                                                                                Parameters
                                                                                
@@ -221,7 +221,7 @@
 
 
                                                                                
 
                                                                                
-get_string(sort_keys: bool = False, pretty: bool = False) → str[source]
                                                                                
+get_string(sort_keys: bool = False, pretty: bool = False) → str[source]
 
                                                                                Returns a string representation of the INCAR. The reason why this
 method is different from the __str__ method is to provide options for
 pretty printing.
                                                                                
@@ -239,7 +239,7 @@
 
 
                                                                                
 
                                                                                
-static proc_val(key: str, val: Any)[source]
                                                                                
+static proc_val(key: str, val: Any)[source]
 
                                                                                Static helper method to convert INCAR parameters to proper types, e.g.,
 integers, floats, lists, etc.
                                                                                
 
                                                                                
@@ -254,7 +254,7 @@
 
 
                                                                                
 
                                                                                
-write_file(filename: Union[str, pathlib.Path])[source]
                                                                                
+write_file(filename: Union[str, pathlib.Path])[source]
 
                                                                                Write Incar to a file.
                                                                                
 
                                                                                
 
                                                                                Parameters
                                                                                
@@ -267,7 +267,7 @@
 
 
                                                                                
 
                                                                                
-class Kpoints(comment: str = 'Default gamma', num_kpts: int = 0, style: Kpoints_supported_modes = Kpoints_supported_modes.Gamma, kpts: Sequence[float | int | Sequence] = ((1, 1, 1),), kpts_shift: tuple[float, float, float] = (0, 0, 0), kpts_weights=None, coord_type=None, labels=None, tet_number: int = 0, tet_weight: float = 0, tet_connections=None)[source]
                                                                                
+class Kpoints(comment: str = 'Default gamma', num_kpts: int = 0, style: Kpoints_supported_modes = Kpoints_supported_modes.Gamma, kpts: Sequence[float | int | Sequence] = ((1, 1, 1),), kpts_shift: tuple[float, float, float] = (0, 0, 0), kpts_weights=None, coord_type=None, labels=None, tet_number: int = 0, tet_weight: float = 0, tet_connections=None)[source]
 
                                                                                Bases: monty.json.MSONable
                                                                                
 
                                                                                KPOINT reader/writer.
                                                                                
 
                                                                                Highly flexible constructor for Kpoints object. The flexibility comes
@@ -313,7 +313,7 @@
 1x1x1 KPOINTS with no shift.
                                                                                
 
                                                                                
 
                                                                                
-as_dict()[source]
                                                                                
+as_dict()[source]
 
                                                                                
 
                                                                                Returns
                                                                                
 
                                                                                MSONable dict.
                                                                                
@@ -323,7 +323,7 @@
 
 
                                                                                
 
                                                                                
-static automatic(subdivisions)[source]
                                                                                
+static automatic(subdivisions)[source]
 
                                                                                Convenient static constructor for a fully automatic Kpoint grid, with
 gamma centered Monkhorst-Pack grids and the number of subdivisions
 along each reciprocal lattice vector determined by the scheme in the
@@ -341,7 +341,7 @@
 
 
                                                                                
 
                                                                                
-static automatic_density(structure: pymatgen.core.structure.Structure, kppa: float, force_gamma: bool = False)[source]
                                                                                
+static automatic_density(structure: pymatgen.core.structure.Structure, kppa: float, force_gamma: bool = False)[source]
 
                                                                                Returns an automatic Kpoint object based on a structure and a kpoint
 density. Uses Gamma centered meshes for hexagonal cells and
 Monkhorst-Pack grids otherwise.
                                                                                
@@ -367,7 +367,7 @@
 
 
                                                                                
 
                                                                                
-static automatic_density_by_lengths(structure: pymatgen.core.structure.Structure, length_densities: Sequence[float], force_gamma: bool = False)[source]
                                                                                
+static automatic_density_by_lengths(structure: pymatgen.core.structure.Structure, length_densities: Sequence[float], force_gamma: bool = False)[source]
 
                                                                                Returns an automatic Kpoint object based on a structure and a k-point
 density normalized by lattice constants.
                                                                                
 
                                                                                
@@ -396,7 +396,7 @@
 
 
                                                                                
 
                                                                                
-static automatic_density_by_vol(structure: pymatgen.core.structure.Structure, kppvol: int, force_gamma: bool = False)[source]
                                                                                
+static automatic_density_by_vol(structure: pymatgen.core.structure.Structure, kppvol: int, force_gamma: bool = False)[source]
 
                                                                                Returns an automatic Kpoint object based on a structure and a kpoint
 density per inverse Angstrom^3 of reciprocal cell.
                                                                                
 
                                                                                
@@ -419,7 +419,7 @@
 
 
                                                                                
 
                                                                                
-static automatic_gamma_density(structure: pymatgen.core.structure.Structure, kppa: float)[source]
                                                                                
+static automatic_gamma_density(structure: pymatgen.core.structure.Structure, kppa: float)[source]
 
                                                                                Returns an automatic Kpoint object based on a structure and a kpoint
 density. Uses Gamma centered meshes always. For GW.
                                                                                
 
                                                                                
@@ -439,7 +439,7 @@
 
 
                                                                                
 
                                                                                
-static automatic_linemode(divisions, ibz)[source]
                                                                                
+static automatic_linemode(divisions, ibz)[source]
 
                                                                                Convenient static constructor for a KPOINTS in mode line_mode.
 gamma centered Monkhorst-Pack grids and the number of subdivisions
 along each reciprocal lattice vector determined by the scheme in the
@@ -459,7 +459,7 @@
 
 
                                                                                
 
                                                                                
-classmethod from_dict(d)[source]
                                                                                
+classmethod from_dict(d)[source]
 
                                                                                
 
                                                                                Parameters
                                                                                
 
                                                                                d – Dict representation.
                                                                                
@@ -472,7 +472,7 @@
 
 
                                                                                
 
                                                                                
-static from_file(filename)[source]
                                                                                
+static from_file(filename)[source]
 
                                                                                Reads a Kpoints object from a KPOINTS file.
                                                                                
 
                                                                                
 
                                                                                Parameters
                                                                                
@@ -486,7 +486,7 @@
 
 
                                                                                
 
                                                                                
-static from_string(string)[source]
                                                                                
+static from_string(string)[source]
 
                                                                                Reads a Kpoints object from a KPOINTS string.
                                                                                
 
                                                                                
 
                                                                                Parameters
                                                                                
@@ -500,7 +500,7 @@
 
 
                                                                                
 
                                                                                
-static gamma_automatic(kpts: tuple[int, int, int] = (1, 1, 1), shift: tuple[float, float, float] = (0, 0, 0))[source]
                                                                                
+static gamma_automatic(kpts: tuple[int, int, int] = (1, 1, 1), shift: tuple[float, float, float] = (0, 0, 0))[source]
 
                                                                                Convenient static constructor for an automatic Gamma centered Kpoint
 grid.
                                                                                
 
                                                                                
@@ -519,7 +519,7 @@
 
 
                                                                                
 
                                                                                
-static monkhorst_automatic(kpts: tuple[int, int, int] = (2, 2, 2), shift: tuple[float, float, float] = (0, 0, 0))[source]
                                                                                
+static monkhorst_automatic(kpts: tuple[int, int, int] = (2, 2, 2), shift: tuple[float, float, float] = (0, 0, 0))[source]
 
                                                                                Convenient static constructor for an automatic Monkhorst pack Kpoint
 grid.
                                                                                
 
                                                                                
@@ -538,7 +538,7 @@
 
 
                                                                                
 
                                                                                
-property style[source]
                                                                                
+property style[source]
 
                                                                                Style for kpoint generation. One of Kpoints_supported_modes
 enum.
                                                                                
 
                                                                                
@@ -550,13 +550,13 @@
 
 
                                                                                
 
                                                                                
-supported_modes[source]
                                                                                
+supported_modes[source]
 
                                                                                alias of pymatgen.io.vasp.inputs.Kpoints_supported_modes
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-write_file(filename)[source]
                                                                                
+write_file(filename)[source]
 
                                                                                Write Kpoints to a file.
                                                                                
 
                                                                                
 
                                                                                Parameters
                                                                                
@@ -569,42 +569,42 @@
 
 
                                                                                
 
                                                                                
-class Kpoints_supported_modes(value)[source]
                                                                                
+class Kpoints_supported_modes(value)[source]
 
                                                                                Bases: enum.Enum
                                                                                
 
                                                                                Enum type of all supported modes for Kpoint generation.
                                                                                
 
                                                                                
 
                                                                                
-Automatic = 0[source]
                                                                                
+Automatic = 0[source]
 
                                                                                
 
 
                                                                                
 
                                                                                
-Cartesian = 4[source]
                                                                                
+Cartesian = 4[source]
 
                                                                                
 
 
                                                                                
 
                                                                                
-Gamma = 1[source]
                                                                                
+Gamma = 1[source]
 
                                                                                
 
 
                                                                                
 
                                                                                
-Line_mode = 3[source]
                                                                                
+Line_mode = 3[source]
 
                                                                                
 
 
                                                                                
 
                                                                                
-Monkhorst = 2[source]
                                                                                
+Monkhorst = 2[source]
 
                                                                                
 
 
                                                                                
 
                                                                                
-Reciprocal = 5[source]
                                                                                
+Reciprocal = 5[source]
 
                                                                                
 
 
                                                                                
 
                                                                                
-static from_string(s: str) → pymatgen.io.vasp.inputs.Kpoints_supported_modes[source]
                                                                                
+static from_string(s: str) → pymatgen.io.vasp.inputs.Kpoints_supported_modes[source]
 
                                                                                
 
                                                                                Parameters
                                                                                
 
                                                                                s – String
                                                                                
@@ -619,36 +619,36 @@
 
 
                                                                                
 
                                                                                
-class Orbital(n, l, j, E, occ)[source]
                                                                                
+class Orbital(n, l, j, E, occ)[source]
 
                                                                                Bases: tuple
                                                                                
 
                                                                                Create new instance of Orbital(n, l, j, E, occ)
                                                                                
 
                                                                                
 
                                                                                
-E[source]
                                                                                
+E[source]
 
                                                                                Alias for field number 3
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-j[source]
                                                                                
+j[source]
 
                                                                                Alias for field number 2
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-l[source]
                                                                                
+l[source]
 
                                                                                Alias for field number 1
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-n[source]
                                                                                
+n[source]
 
                                                                                Alias for field number 0
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-occ[source]
                                                                                
+occ[source]
 
                                                                                Alias for field number 4
                                                                                
 
                                                                                
 
@@ -656,42 +656,42 @@
 
 
                                                                                
 
                                                                                
-class OrbitalDescription(l, E, Type, Rcut, Type2, Rcut2)[source]
                                                                                
+class OrbitalDescription(l, E, Type, Rcut, Type2, Rcut2)[source]
 
                                                                                Bases: tuple
                                                                                
 
                                                                                Create new instance of OrbitalDescription(l, E, Type, Rcut, Type2, Rcut2)
                                                                                
 
                                                                                
 
                                                                                
-E[source]
                                                                                
+E[source]
 
                                                                                Alias for field number 1
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-Rcut[source]
                                                                                
+Rcut[source]
 
                                                                                Alias for field number 3
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-Rcut2[source]
                                                                                
+Rcut2[source]
 
                                                                                Alias for field number 5
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-Type[source]
                                                                                
+Type[source]
 
                                                                                Alias for field number 2
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-Type2[source]
                                                                                
+Type2[source]
 
                                                                                Alias for field number 4
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-l[source]
                                                                                
+l[source]
 
                                                                                Alias for field number 0
                                                                                
 
                                                                                
 
@@ -699,47 +699,47 @@
 
 
                                                                                
 
                                                                                
-class Poscar(structure: pymatgen.core.structure.Structure, comment: Optional[str] = None, selective_dynamics=None, true_names: bool = True, velocities: Optional[Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]] = None, predictor_corrector: Optional[Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]] = None, predictor_corrector_preamble: Optional[str] = None, sort_structure: bool = False)[source]
                                                                                
+class Poscar(structure: pymatgen.core.structure.Structure, comment: Optional[str] = None, selective_dynamics=None, true_names: bool = True, velocities: Optional[Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]] = None, predictor_corrector: Optional[Union[numpy.typing._array_like._SupportsArray[numpy.dtype], numpy.typing._nested_sequence._NestedSequence[numpy.typing._array_like._SupportsArray[numpy.dtype]], bool, int, float, complex, str, bytes, numpy.typing._nested_sequence._NestedSequence[Union[bool, int, float, complex, str, bytes]]]] = None, predictor_corrector_preamble: Optional[str] = None, sort_structure: bool = False)[source]
 
                                                                                Bases: monty.json.MSONable
                                                                                
 
                                                                                Object for representing the data in a POSCAR or CONTCAR file.
 Please note that this current implementation. Most attributes can be set
 directly.
                                                                                
 
                                                                                
 
                                                                                
-structure[source]
                                                                                
+structure[source]
 
                                                                                Associated Structure.
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-comment[source]
                                                                                
+comment[source]
 
                                                                                Optional comment string.
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-true_names[source]
                                                                                
+true_names[source]
 
                                                                                Boolean indication whether Poscar contains actual real names parsed
 from either a POTCAR or the POSCAR itself.
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-selective_dynamics[source]
                                                                                
+selective_dynamics[source]
 
                                                                                Selective dynamics attribute for each site if available. A Nx3 array of
 booleans.
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-velocities[source]
                                                                                
+velocities[source]
 
                                                                                Velocities for each site (typically read in from a CONTCAR). A Nx3
 array of floats.
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-predictor_corrector[source]
                                                                                
+predictor_corrector[source]
 
                                                                                Predictor corrector coordinates and derivatives for each site; i.e.
 a list of three 1x3 arrays for each site (typically read in from a MD
 CONTCAR).
                                                                                
@@ -747,7 +747,7 @@
 
 
                                                                                
 
                                                                                
-predictor_corrector_preamble[source]
                                                                                
+predictor_corrector_preamble[source]
 
                                                                                Predictor corrector preamble contains the predictor-corrector key,
 POTIM, and thermostat parameters that precede the site-specic predictor
 corrector data in MD CONTCAR
                                                                                
@@ -755,7 +755,7 @@
 
 
                                                                                
 
                                                                                
-temperature[source]
                                                                                
+temperature[source]
 
                                                                                Temperature of velocity Maxwell-Boltzmann initialization. Initialized
 to -1 (MB hasn”t been performed).
                                                                                
 
                                                                                
@@ -785,7 +785,7 @@
 
                                                                                
 
                                                                                
 
                                                                                
-as_dict() → dict[source]
                                                                                
+as_dict() → dict[source]
 
                                                                                
 
                                                                                Returns
                                                                                
 
                                                                                MSONable dict.
                                                                                
@@ -795,7 +795,7 @@
 
 
                                                                                
 
                                                                                
-classmethod from_dict(d: dict) → pymatgen.io.vasp.inputs.Poscar[source]
                                                                                
+classmethod from_dict(d: dict) → pymatgen.io.vasp.inputs.Poscar[source]
 
                                                                                
 
                                                                                Parameters
                                                                                
 
                                                                                d – Dict representation.
                                                                                
@@ -808,7 +808,7 @@
 
 
                                                                                
 
                                                                                
-static from_file(filename, check_for_POTCAR=True, read_velocities=True)[source]
                                                                                
+static from_file(filename, check_for_POTCAR=True, read_velocities=True)[source]
 
                                                                                Reads a Poscar from a file.
                                                                                
 
                                                                                The code will try its best to determine the elements in the POSCAR in
 the following order:
                                                                                
@@ -843,7 +843,7 @@
 
 
                                                                                
 
                                                                                
-static from_string(data, default_names=None, read_velocities=True)[source]
                                                                                
+static from_string(data, default_names=None, read_velocities=True)[source]
 
                                                                                Reads a Poscar from a string.
                                                                                
 
                                                                                The code will try its best to determine the elements in the POSCAR in
 the following order:
                                                                                
@@ -877,7 +877,7 @@
 
 
                                                                                
 
                                                                                
-get_string(direct: bool = True, vasp4_compatible: bool = False, significant_figures: int = 6) → str[source]
                                                                                
+get_string(direct: bool = True, vasp4_compatible: bool = False, significant_figures: int = 6) → str[source]
 
                                                                                Returns a string to be written as a POSCAR file. By default, site
 symbols are written, which means compatibility is for vasp >= 5.
                                                                                
 
                                                                                
@@ -902,26 +902,26 @@
 
 
                                                                                
 
                                                                                
-property natoms[source]
                                                                                
+property natoms[source]
 
                                                                                Sequence of number of sites of each type associated with the Poscar.
 Similar to 7th line in vasp 5+ POSCAR or the 6th line in vasp 4 POSCAR.
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-property predictor_corrector[source]
                                                                                
+property predictor_corrector[source]
 
                                                                                Predictor corrector in Poscar
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-property selective_dynamics[source]
                                                                                
+property selective_dynamics[source]
 
                                                                                Selective dynamics in Poscar
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-set_temperature(temperature: float)[source]
                                                                                
+set_temperature(temperature: float)[source]
 
                                                                                Initializes the velocities based on Maxwell-Boltzmann distribution.
 Removes linear, but not angular drift (same as VASP)
                                                                                
 
                                                                                Scales the energies to the exact temperature (microcanonical ensemble)
@@ -938,20 +938,20 @@
 
 
                                                                                
 
                                                                                
-property site_symbols[source]
                                                                                
+property site_symbols[source]
 
                                                                                Sequence of symbols associated with the Poscar. Similar to 6th line in
 vasp 5+ POSCAR.
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-property velocities[source]
                                                                                
+property velocities[source]
 
                                                                                Velocities in Poscar
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-write_file(filename: Union[str, pathlib.Path], **kwargs)[source]
                                                                                
+write_file(filename: Union[str, pathlib.Path], **kwargs)[source]
 
                                                                                Writes POSCAR to a file. The supported kwargs are the same as those for
 the Poscar.get_string method and are passed through directly.
                                                                                
 
                                                                                
@@ -960,7 +960,7 @@
 
 
                                                                                
 
                                                                                
-class Potcar(symbols=None, functional=None, sym_potcar_map=None)[source]
                                                                                
+class Potcar(symbols=None, functional=None, sym_potcar_map=None)[source]
 
                                                                                Bases: list, monty.json.MSONable
                                                                                
 
                                                                                Object for reading and writing POTCAR files for calculations. Consists of a
 list of PotcarSingle.
                                                                                
@@ -984,12 +984,12 @@
 
                                                                                
 
                                                                                
 
                                                                                
-FUNCTIONAL_CHOICES = ['PBE', 'PBE_52', 'PBE_54', 'LDA', 'LDA_52', 'LDA_54', 'PW91', 'LDA_US', 'PW91_US', 'Perdew-Zunger81'][source]
                                                                                
+FUNCTIONAL_CHOICES = ['PBE', 'PBE_52', 'PBE_54', 'LDA', 'LDA_52', 'LDA_54', 'PW91', 'LDA_US', 'PW91_US', 'Perdew-Zunger81'][source]
 
                                                                                
 
 
                                                                                
 
                                                                                
-as_dict()[source]
                                                                                
+as_dict()[source]
 
                                                                                
 
                                                                                Returns
                                                                                
 
                                                                                MSONable dict representation
                                                                                
@@ -999,7 +999,7 @@
 
 
                                                                                
 
                                                                                
-classmethod from_dict(d)[source]
                                                                                
+classmethod from_dict(d)[source]
 
                                                                                
 
                                                                                Parameters
                                                                                
 
                                                                                d – Dict representation
                                                                                
@@ -1012,7 +1012,7 @@
 
 
                                                                                
 
                                                                                
-static from_file(filename: str)[source]
                                                                                
+static from_file(filename: str)[source]
 
                                                                                Reads Potcar from file.
                                                                                
 
                                                                                
 
                                                                                Parameters
                                                                                
@@ -1026,7 +1026,7 @@
 
 
                                                                                
 
                                                                                
-set_symbols(symbols, functional=None, sym_potcar_map=None)[source]
                                                                                
+set_symbols(symbols, functional=None, sym_potcar_map=None)[source]
 
                                                                                Initialize the POTCAR from a set of symbols. Currently, the POTCARs can
 be fetched from a location specified in .pmgrc.yaml. Use pmg config
 to add this setting.
                                                                                
@@ -1047,19 +1047,19 @@
 
 
                                                                                
 
                                                                                
-property spec[source]
                                                                                
+property spec[source]
 
                                                                                Get the atomic symbols and hash of all the atoms in the POTCAR file.
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-property symbols[source]
                                                                                
+property symbols[source]
 
                                                                                Get the atomic symbols of all the atoms in the POTCAR file.
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-write_file(filename)[source]
                                                                                
+write_file(filename)[source]
 
                                                                                Write Potcar to a file.
                                                                                
 
                                                                                
 
                                                                                Parameters
                                                                                
@@ -1072,19 +1072,19 @@
 
 
                                                                                
 
                                                                                
-class PotcarSingle(data, symbol=None)[source]
                                                                                
+class PotcarSingle(data, symbol=None)[source]
 
                                                                                Bases: object
                                                                                
 
                                                                                Object for a single POTCAR. The builder assumes the POTCAR contains
 the complete untouched data in “data” as a string and a dict of keywords.
                                                                                
 
                                                                                
 
                                                                                
-data[source]
                                                                                
+data[source]
 
                                                                                POTCAR data as a string.
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-keywords[source]
                                                                                
+keywords[source]
 
                                                                                Keywords parsed from the POTCAR as a dict. All keywords are also
 accessible as attributes in themselves. E.g., potcar.enmax,
 potcar.encut, etc.
                                                                                
@@ -1106,13 +1106,13 @@
 
                                                                                
 
                                                                                
 
                                                                                
-property atomic_no: int[source]
                                                                                
+property atomic_no: int[source]
 
                                                                                Attempt to return the atomic number based on the VRHFIN keyword.
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-property electron_configuration[source]
                                                                                
+property electron_configuration[source]
 
                                                                                Electronic configuration of the PotcarSingle.
                                                                                
 
                                                                                
 
                                                                                Type
                                                                                
@@ -1123,13 +1123,13 @@
 
 
                                                                                
 
                                                                                
-property element[source]
                                                                                
+property element[source]
 
                                                                                Attempt to return the atomic symbol based on the VRHFIN keyword.
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-static from_file(filename: str) → pymatgen.io.vasp.inputs.PotcarSingle[source]
                                                                                
+static from_file(filename: str) → pymatgen.io.vasp.inputs.PotcarSingle[source]
 
                                                                                Reads PotcarSingle from file.
                                                                                
 
                                                                                
 
                                                                                Parameters
                                                                                
@@ -1143,7 +1143,7 @@
 
 
                                                                                
 
                                                                                
-static from_symbol_and_functional(symbol: str, functional: Optional[str] = None)[source]
                                                                                
+static from_symbol_and_functional(symbol: str, functional: Optional[str] = None)[source]
 
                                                                                Makes a PotcarSingle from a symbol and functional.
                                                                                
 
                                                                                
 
                                                                                Parameters
                                                                                
@@ -1160,7 +1160,7 @@
 
 
                                                                                
 
                                                                                
-property functional[source]
                                                                                
+property functional[source]
 
                                                                                Functional associated with PotcarSingle.
                                                                                
 
                                                                                
 
                                                                                Type
                                                                                
@@ -1171,7 +1171,7 @@
 
 
                                                                                
 
                                                                                
-property functional_class[source]
                                                                                
+property functional_class[source]
 
                                                                                Functional class associated with PotcarSingle.
                                                                                
 
                                                                                
 
                                                                                Type
                                                                                
@@ -1182,17 +1182,17 @@
 
 
                                                                                
 
                                                                                
-functional_dir = {'LDA': 'POT_LDA_PAW', 'LDA_52': 'POT_LDA_PAW_52', 'LDA_54': 'POT_LDA_PAW_54', 'LDA_US': 'POT_LDA_US', 'PBE': 'POT_GGA_PAW_PBE', 'PBE_52': 'POT_GGA_PAW_PBE_52', 'PBE_54': 'POT_GGA_PAW_PBE_54', 'PW91': 'POT_GGA_PAW_PW91', 'PW91_US': 'POT_GGA_US_PW91', 'Perdew-Zunger81': 'POT_LDA_PAW'}[source]
                                                                                
+functional_dir = {'LDA': 'POT_LDA_PAW', 'LDA_52': 'POT_LDA_PAW_52', 'LDA_54': 'POT_LDA_PAW_54', 'LDA_US': 'POT_LDA_US', 'PBE': 'POT_GGA_PAW_PBE', 'PBE_52': 'POT_GGA_PAW_PBE_52', 'PBE_54': 'POT_GGA_PAW_PBE_54', 'PW91': 'POT_GGA_PAW_PW91', 'PW91_US': 'POT_GGA_US_PW91', 'Perdew-Zunger81': 'POT_LDA_PAW'}[source]
 
                                                                                
 
 
                                                                                
 
                                                                                
-functional_tags = {'91': {'class': 'GGA', 'name': 'PW91'}, 'am': {'class': 'GGA', 'name': 'AM05'}, 'ca': {'class': 'LDA', 'name': 'Perdew-Zunger81'}, 'hl': {'class': 'LDA', 'name': 'Hedin-Lundquist'}, 'lm': {'class': 'GGA', 'name': 'Langreth-Mehl-Hu'}, 'pb': {'class': 'GGA', 'name': 'Perdew-Becke'}, 'pe': {'class': 'GGA', 'name': 'PBE'}, 'ps': {'class': 'GGA', 'name': 'PBEsol'}, 'pw': {'class': 'GGA', 'name': 'PW86'}, 'rp': {'class': 'GGA', 'name': 'revPBE'}, 'wi': {'class': 'LDA', 'name': 'Wigner Interpoloation'}}[source]
                                                                                
+functional_tags = {'91': {'class': 'GGA', 'name': 'PW91'}, 'am': {'class': 'GGA', 'name': 'AM05'}, 'ca': {'class': 'LDA', 'name': 'Perdew-Zunger81'}, 'hl': {'class': 'LDA', 'name': 'Hedin-Lundquist'}, 'lm': {'class': 'GGA', 'name': 'Langreth-Mehl-Hu'}, 'pb': {'class': 'GGA', 'name': 'Perdew-Becke'}, 'pe': {'class': 'GGA', 'name': 'PBE'}, 'ps': {'class': 'GGA', 'name': 'PBEsol'}, 'pw': {'class': 'GGA', 'name': 'PW86'}, 'rp': {'class': 'GGA', 'name': 'revPBE'}, 'wi': {'class': 'LDA', 'name': 'Wigner Interpoloation'}}[source]
 
                                                                                
 
 
                                                                                
 
                                                                                
-get_potcar_file_hash()[source]
                                                                                
+get_potcar_file_hash()[source]
 
                                                                                Computes a hash of the entire PotcarSingle.
                                                                                
 
                                                                                This hash corresponds to the md5 hash of the POTCAR file itself.
                                                                                
 
                                                                                
@@ -1204,7 +1204,7 @@
 
 
                                                                                
 
                                                                                
-get_potcar_hash()[source]
                                                                                
+get_potcar_hash()[source]
 
                                                                                Computes a md5 hash of the data defining the PotcarSingle.
                                                                                
 
                                                                                
 
                                                                                Returns
                                                                                
@@ -1215,7 +1215,7 @@
 
 
                                                                                
 
                                                                                
-identify_potcar(mode: Literal['data', 'file'] = 'data')[source]
                                                                                
+identify_potcar(mode: Literal['data', 'file'] = 'data')[source]
 
                                                                                Identify the symbol and compatible functionals associated with this PotcarSingle.
                                                                                
 
                                                                                This method checks the md5 hash of either the POTCAR data (PotcarSingle.hash)
 or the entire POTCAR file (PotcarSingle.file_hash) against a database
@@ -1241,7 +1241,7 @@
 
 
                                                                                
 
                                                                                
-property nelectrons[source]
                                                                                
+property nelectrons[source]
 
                                                                                Number of electrons
                                                                                
 
                                                                                
 
                                                                                Type
                                                                                
@@ -1252,12 +1252,12 @@
 
 
                                                                                
 
                                                                                
-parse_functions = {'DEXC': <function _parse_float>, 'EATOM': <function _parse_float>, 'EAUG': <function _parse_float>, 'EMMIN': <function _parse_float>, 'ENMAX': <function _parse_float>, 'ENMIN': <function _parse_float>, 'GGA': <function _parse_list>, 'ICORE': <function _parse_int>, 'IUNSCR': <function _parse_int>, 'LCOR': <function _parse_bool>, 'LEXCH': <function _parse_string>, 'LPAW': <function _parse_bool>, 'LULTRA': <function _parse_bool>, 'LUNSCR': <function _parse_bool>, 'NDATA': <function _parse_int>, 'POMASS': <function _parse_float>, 'QCUT': <function _parse_float>, 'QGAM': <function _parse_float>, 'RAUG': <function _parse_float>, 'RCLOC': <function _parse_float>, 'RCORE': <function _parse_float>, 'RDEP': <function _parse_float>, 'RDEPT': <function _parse_float>, 'RMAX': <function _parse_float>, 'RPACOR': <function _parse_float>, 'RRKJ': <function _parse_list>, 'RWIGS': <function _parse_float>, 'STEP': <function _parse_list>, 'TITEL': <function _parse_string>, 'VRHFIN': <function _parse_string>, 'ZVAL': <function _parse_float>}[source]
                                                                                
+parse_functions = {'DEXC': <function _parse_float>, 'EATOM': <function _parse_float>, 'EAUG': <function _parse_float>, 'EMMIN': <function _parse_float>, 'ENMAX': <function _parse_float>, 'ENMIN': <function _parse_float>, 'GGA': <function _parse_list>, 'ICORE': <function _parse_int>, 'IUNSCR': <function _parse_int>, 'LCOR': <function _parse_bool>, 'LEXCH': <function _parse_string>, 'LPAW': <function _parse_bool>, 'LULTRA': <function _parse_bool>, 'LUNSCR': <function _parse_bool>, 'NDATA': <function _parse_int>, 'POMASS': <function _parse_float>, 'QCUT': <function _parse_float>, 'QGAM': <function _parse_float>, 'RAUG': <function _parse_float>, 'RCLOC': <function _parse_float>, 'RCORE': <function _parse_float>, 'RDEP': <function _parse_float>, 'RDEPT': <function _parse_float>, 'RMAX': <function _parse_float>, 'RPACOR': <function _parse_float>, 'RRKJ': <function _parse_list>, 'RWIGS': <function _parse_float>, 'STEP': <function _parse_list>, 'TITEL': <function _parse_string>, 'VRHFIN': <function _parse_string>, 'ZVAL': <function _parse_float>}[source]
 
                                                                                
 
 
                                                                                
 
                                                                                
-property potential_type: str[source]
                                                                                
+property potential_type: str[source]
 
                                                                                Type of PSP. E.g., US, PAW, etc.
                                                                                
 
                                                                                
 
                                                                                Type
                                                                                
@@ -1268,7 +1268,7 @@
 
 
                                                                                
 
                                                                                
-property symbol[source]
                                                                                
+property symbol[source]
 
                                                                                The POTCAR symbol, e.g. W_pv
                                                                                
 
                                                                                
 
                                                                                Type
                                                                                
@@ -1279,7 +1279,7 @@
 
 
                                                                                
 
                                                                                
-write_file(filename: str) → None[source]
                                                                                
+write_file(filename: str) → None[source]
 
                                                                                Writes PotcarSingle to a file.
 :param filename: Filename
                                                                                
 
                                                                                
@@ -1288,14 +1288,14 @@
 
 
                                                                                
 
                                                                                
-exception UnknownPotcarWarning[source]
                                                                                
+exception UnknownPotcarWarning[source]
 
                                                                                Bases: UserWarning
                                                                                
 
                                                                                Warning raised when POTCAR hashes do not pass validation
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-class VaspInput(incar, kpoints, poscar, potcar, optional_files=None, **kwargs)[source]
                                                                                
+class VaspInput(incar, kpoints, poscar, potcar, optional_files=None, **kwargs)[source]
 
                                                                                Bases: dict, monty.json.MSONable
                                                                                
 
                                                                                Class to contain a set of vasp input objects corresponding to a run.
                                                                                
 
                                                                                
@@ -1313,7 +1313,7 @@
 
                                                                                
 
                                                                                
 
                                                                                
-as_dict()[source]
                                                                                
+as_dict()[source]
 
                                                                                
 
                                                                                Returns
                                                                                
 
                                                                                MSONable dict.
                                                                                
@@ -1323,7 +1323,7 @@
 
 
                                                                                
 
                                                                                
-classmethod from_dict(d)[source]
                                                                                
+classmethod from_dict(d)[source]
 
                                                                                
 
                                                                                Parameters
                                                                                
 
                                                                                d – Dict representation.
                                                                                
@@ -1336,7 +1336,7 @@
 
 
                                                                                
 
                                                                                
-static from_directory(input_dir, optional_files=None)[source]
                                                                                
+static from_directory(input_dir, optional_files=None)[source]
 
                                                                                Read in a set of VASP input from a directory. Note that only the
 standard INCAR, POSCAR, POTCAR and KPOINTS files are read unless
 optional_filenames is specified.
                                                                                
@@ -1354,7 +1354,7 @@
 
 
                                                                                
 
                                                                                
-run_vasp(run_dir: Union[str, pathlib.Path] = '.', vasp_cmd: Optional[list] = None, output_file: Union[str, pathlib.Path] = 'vasp.out', err_file: Union[str, pathlib.Path] = 'vasp.err')[source]
                                                                                
+run_vasp(run_dir: Union[str, pathlib.Path] = '.', vasp_cmd: Optional[list] = None, output_file: Union[str, pathlib.Path] = 'vasp.out', err_file: Union[str, pathlib.Path] = 'vasp.err')[source]
 
                                                                                Write input files and run VASP.
                                                                                
 
                                                                                
 
                                                                                Parameters
                                                                                
@@ -1371,7 +1371,7 @@
 
 
                                                                                
 
                                                                                
-write_input(output_dir='.', make_dir_if_not_present=True)[source]
                                                                                
+write_input(output_dir='.', make_dir_if_not_present=True)[source]
 
                                                                                Write VASP input to a directory.
                                                                                
 
                                                                                
 
                                                                                Parameters
                                                                                
diff --git a/docs/pymatgen.io.vasp.outputs.html b/docs/pymatgen.io.vasp.outputs.html
index 876ac059298..194c3c94874 100644
--- a/docs/pymatgen.io.vasp.outputs.html
+++ b/docs/pymatgen.io.vasp.outputs.html
@@ -4,7 +4,7 @@
   
 
   
-  pymatgen.io.vasp.outputs module — pymatgen 2022.5.18 documentation
+  pymatgen.io.vasp.outputs module — pymatgen 2022.5.18.1 documentation
       
       
       
@@ -39,7 +39,7 @@
              pymatgen
           
               
                                                                                
-                2022.5.18
+                2022.5.18.1
               
                                                                                
 
                                                                                
   
@@ -119,7 +119,7 @@
 
                                                                                Classes for reading/manipulating/writing VASP output files.
                                                                                
 
                                                                                
 
                                                                                
-class BSVasprun(filename: str, parse_projected_eigen: bool | str = False, parse_potcar_file: bool | str = False, occu_tol: float = 1e-08, separate_spins: bool = False)[source]
                                                                                
+class BSVasprun(filename: str, parse_projected_eigen: bool | str = False, parse_potcar_file: bool | str = False, occu_tol: float = 1e-08, separate_spins: bool = False)[source]
 
                                                                                Bases: pymatgen.io.vasp.outputs.Vasprun
                                                                                
 
                                                                                A highly optimized version of Vasprun that parses only eigenvalues for
 bandstructures. All other properties like structures, parameters,
@@ -153,7 +153,7 @@
 
                                                                                
 
                                                                                
 
                                                                                
-as_dict()[source]
                                                                                
+as_dict()[source]
 
                                                                                JSON-serializable dict representation.
                                                                                
 
                                                                                
 
@@ -161,7 +161,7 @@
 
 
                                                                                
 
                                                                                
-class Chgcar(poscar, data, data_aug=None)[source]
                                                                                
+class Chgcar(poscar, data, data_aug=None)[source]
 
                                                                                Bases: pymatgen.io.vasp.outputs.VolumetricData
                                                                                
 
                                                                                Simple object for reading a CHGCAR file.
                                                                                
 
                                                                                
@@ -175,7 +175,7 @@
 
                                                                                
 
                                                                                
 
                                                                                
-static from_file(filename)[source]
                                                                                
+static from_file(filename)[source]
 
                                                                                Reads a CHGCAR file.
                                                                                
 
                                                                                
 
                                                                                Parameters
                                                                                
@@ -189,7 +189,7 @@
 
 
                                                                                
 
                                                                                
-property net_magnetization[source]
                                                                                
+property net_magnetization[source]
 
                                                                                Net magnetization from Chgcar
                                                                                
 
                                                                                
 
                                                                                Type
                                                                                
@@ -202,12 +202,12 @@
 
 
                                                                                
 
                                                                                
-class Dynmat(filename)[source]
                                                                                
+class Dynmat(filename)[source]
 
                                                                                Bases: object
                                                                                
 
                                                                                Object for reading a DYNMAT file.
                                                                                
 
                                                                                
 
                                                                                
-data[source]
                                                                                
+data[source]
 
                                                                                A nested dict containing the DYNMAT data of the form::
 [atom <int>][disp <int>][‘dispvec’] =
                                                                                
 
                                                                                
@@ -227,31 +227,31 @@
 
                                                                                
 
                                                                                
 
                                                                                
-get_phonon_frequencies()[source]
                                                                                
+get_phonon_frequencies()[source]
 
                                                                                calculate phonon frequencies
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-property masses[source]
                                                                                
+property masses[source]
 
                                                                                returns the list of atomic masses
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-property natoms[source]
                                                                                
+property natoms[source]
 
                                                                                returns the number of atoms
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-property ndisps[source]
                                                                                
+property ndisps[source]
 
                                                                                returns the number of displacements
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-property nspecs[source]
                                                                                
+property nspecs[source]
 
                                                                                returns the number of species
                                                                                
 
                                                                                
 
@@ -259,60 +259,60 @@
 
 
                                                                                
 
                                                                                
-class Eigenval(filename, occu_tol=1e-08, separate_spins=False)[source]
                                                                                
+class Eigenval(filename, occu_tol=1e-08, separate_spins=False)[source]
 
                                                                                Bases: object
                                                                                
 
                                                                                Object for reading EIGENVAL file.
                                                                                
 
                                                                                
 
                                                                                
-filename[source]
                                                                                
+filename[source]
 
                                                                                string containing input filename
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-occu_tol[source]
                                                                                
+occu_tol[source]
 
                                                                                tolerance for determining occupation in band properties
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-ispin[source]
                                                                                
+ispin[source]
 
                                                                                spin polarization tag (int)
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-nelect[source]
                                                                                
+nelect[source]
 
                                                                                number of electrons
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-nkpt[source]
                                                                                
+nkpt[source]
 
                                                                                number of kpoints
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-nbands[source]
                                                                                
+nbands[source]
 
                                                                                number of bands
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-kpoints[source]
                                                                                
+kpoints[source]
 
                                                                                list of kpoints
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-kpoints_weights[source]
                                                                                
+kpoints_weights[source]
 
                                                                                weights of each kpoint in the BZ, should sum to 1.
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-eigenvalues[source]
                                                                                
+eigenvalues[source]
 
                                                                                Eigenvalues as a dict of {(spin): np.ndarray(shape=(nkpt, nbands, 2))}.
 This representation is based on actual ordering in VASP and is meant as
 an intermediate representation to be converted into proper objects. The
@@ -337,7 +337,7 @@
 
                                                                                
 
                                                                                
 
                                                                                
-property eigenvalue_band_properties[source]
                                                                                
+property eigenvalue_band_properties[source]
 
                                                                                Band properties from the eigenvalues as a tuple,
 (band gap, cbm, vbm, is_band_gap_direct). In the case of separate_spins=True,
 the band gap, cbm, vbm, and is_band_gap_direct are each lists of length 2,
@@ -349,7 +349,7 @@
 
 
                                                                                
 
                                                                                
-class Elfcar(poscar, data)[source]
                                                                                
+class Elfcar(poscar, data)[source]
 
                                                                                Bases: pymatgen.io.vasp.outputs.VolumetricData
                                                                                
 
                                                                                Read an ELFCAR file which contains the Electron Localization Function (ELF)
 as calculated by VASP.
                                                                                
@@ -365,7 +365,7 @@
 
                                                                                
 
                                                                                
 
                                                                                
-classmethod from_file(filename)[source]
                                                                                
+classmethod from_file(filename)[source]
 
                                                                                Reads a ELFCAR file.
                                                                                
 
                                                                                
 
                                                                                Parameters
                                                                                
@@ -379,7 +379,7 @@
 
 
                                                                                
 
                                                                                
-get_alpha()[source]
                                                                                
+get_alpha()[source]
 
                                                                                Get the parameter alpha where ELF = 1/(1+alpha^2).
                                                                                
 
                                                                                
 
@@ -387,7 +387,7 @@
 
 
                                                                                
 
                                                                                
-class Locpot(poscar, data)[source]
                                                                                
+class Locpot(poscar, data)[source]
 
                                                                                Bases: pymatgen.io.vasp.outputs.VolumetricData
                                                                                
 
                                                                                Simple object for reading a LOCPOT file.
                                                                                
 
                                                                                
@@ -400,7 +400,7 @@
 
                                                                                
 
                                                                                
 
                                                                                
-classmethod from_file(filename, **kwargs)[source]
                                                                                
+classmethod from_file(filename, **kwargs)[source]
 
                                                                                Reads a LOCPOT file.
                                                                                
 
                                                                                
 
                                                                                Parameters
                                                                                
@@ -416,7 +416,7 @@
 
 
                                                                                
 
                                                                                
-class Oszicar(filename)[source]
                                                                                
+class Oszicar(filename)[source]
 
                                                                                Bases: object
                                                                                
 
                                                                                A basic parser for an OSZICAR output from VASP. In general, while the
 OSZICAR is useful for a quick look at the output from a VASP run, we
@@ -424,7 +424,7 @@
 information about a run.
                                                                                
 
                                                                                
 
                                                                                
-electronic_steps[source]
                                                                                
+electronic_steps[source]
 
                                                                                All electronic steps as a list of list of dict. e.g.,
 [[{“rms”: 160.0, “E”: 4507.24605593, “dE”: 4507.2, “N”: 1,
 “deps”: -17777.0, “ncg”: 16576}, …], [….]
@@ -451,7 +451,7 @@
 
                                                                                
 
                                                                                
 
                                                                                
-property all_energies[source]
                                                                                
+property all_energies[source]
 
                                                                                Compilation of all energies from all electronic steps and ionic steps
 as a tuple of list of energies, e.g.,
 ((4507.24605593, 143.824705755, -512.073149912, …), …)
                                                                                
@@ -459,7 +459,7 @@
 
 
                                                                                
 
                                                                                
-as_dict()[source]
                                                                                
+as_dict()[source]
 
                                                                                
 
                                                                                Returns
                                                                                
 
                                                                                MSONable dict
                                                                                
@@ -469,14 +469,14 @@
 
 
                                                                                
 
                                                                                
-property final_energy[source]
                                                                                
+property final_energy[source]
 
                                                                                
 
 
                                                                                
 
 
                                                                                
 
                                                                                
-class Outcar(filename)[source]
                                                                                
+class Outcar(filename)[source]
 
                                                                                Bases: object
                                                                                
 
                                                                                Parser for data in OUTCAR that is not available in Vasprun.xml
                                                                                
 
                                                                                Note, this class works a bit differently than most of the other
@@ -486,7 +486,7 @@
 are always present.
                                                                                
 
                                                                                
 
                                                                                
-magnetization[source]
                                                                                
+magnetization[source]
 
                                                                                Magnetization on each ion as a tuple of dict, e.g.,
 ({“d”: 0.0, “p”: 0.003, “s”: 0.002, “tot”: 0.005}, … )
 Note that this data is not always present. LORBIT must be set to some
@@ -495,13 +495,13 @@
 
 
                                                                                
 
                                                                                
-chemical_shielding[source]
                                                                                
+chemical_shielding[source]
 
                                                                                chemical shielding on each ion as a dictionary with core and valence contributions
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-unsym_cs_tensor[source]
                                                                                
+unsym_cs_tensor[source]
 
                                                                                Unsymmetrized chemical shielding tensor matrixes on each ion as a list.
 e.g.,
 [[[sigma11, sigma12, sigma13],
                                                                                
@@ -521,20 +521,20 @@
 
 
                                                                                
 
                                                                                
-cs_g0_contribution[source]
                                                                                
+cs_g0_contribution[source]
 
                                                                                G=0 contribution to chemical shielding. 2D rank 3 matrix
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-cs_core_contribution[source]
                                                                                
+cs_core_contribution[source]
 
                                                                                Core contribution to chemical shielding. dict. e.g.,
 {‘Mg’: -412.8, ‘C’: -200.5, ‘O’: -271.1}
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-efg[source]
                                                                                
+efg[source]
 
                                                                                Electric Field Gradient (EFG) tensor on each ion as a tuple of dict, e.g.,
 ({“cq”: 0.1, “eta”, 0.2, “nuclear_quadrupole_moment”: 0.3},
                                                                                
 
                                                                                
@@ -545,7 +545,7 @@
 
 
                                                                                
 
                                                                                
-charge[source]
                                                                                
+charge[source]
 
                                                                                Charge on each ion as a tuple of dict, e.g.,
 ({“p”: 0.154, “s”: 0.078, “d”: 0.0, “tot”: 0.232}, …)
 Note that this data is not always present. LORBIT must be set to some
@@ -554,13 +554,13 @@
 
 
                                                                                
 
                                                                                
-is_stopped[source]
                                                                                
+is_stopped[source]
 
                                                                                True if OUTCAR is from a stopped run (using STOPCAR, see Vasp Manual).
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-run_stats[source]
                                                                                
+run_stats[source]
 
                                                                                Various useful run stats as a dict including “System time (sec)”,
 “Total CPU time used (sec)”, “Elapsed time (sec)”,
 “Maximum memory used (kb)”, “Average memory used (kb)”,
@@ -569,19 +569,19 @@
 
 
                                                                                
 
                                                                                
-elastic_tensor[source]
                                                                                
+elastic_tensor[source]
 
                                                                                Total elastic moduli (Kbar) is given in a 6x6 array matrix.
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-drift[source]
                                                                                
+drift[source]
 
                                                                                Total drift for each step in eV/Atom
                                                                                
 
                                                                                
 
 
                                                                                
 
                                                                                
-ngf[source]
                                                                                
+ngf[source]
 
                                                                                Dimensions for the Augementation grid
                                                                                
 
                                                                                
 
@@ -596,19 +596,19 @@
 
                                                                              
 
                                                                              
 
                                                                              
-efermi[source]
                                                                              
+efermi[source]
 
                                                                              Fermi energy
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-filename[source]
                                                                              
+filename[source]
 
                                                                              
 
                                                                              Filename
                                                                              
 
                                                                              
 
                                                                              
 
                                                                              
-final_energy[source]
                                                                              
+final_energy[source]
 
                                                                              Final energy after extrapolation of sigma back to 0, i.e. energy(sigma->0).
                                                                              
 
                                                                              
 
@@ -616,49 +616,49 @@
 
 
                                                                              
 
                                                                              
-final_energy_wo_entrp[source]
                                                                              
+final_energy_wo_entrp[source]
 
                                                                              Final energy before extrapolation of sigma, i.e. energy without entropy.
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-final_fr_energy[source]
                                                                              
+final_fr_energy[source]
 
                                                                              Final “free energy”, i.e. free energy TOTEN
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-has_onsite_density_matrices[source]
                                                                              
+has_onsite_density_matrices[source]
 
                                                                              Boolean for if onsite density matrices have been set
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-lcalcpol[source]
                                                                              
+lcalcpol[source]
 
                                                                              If LCALCPOL has been set
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-lepsilon[source]
                                                                              
+lepsilon[source]
 
                                                                              If LEPSILON has been set
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-nelect[source]
                                                                              
+nelect[source]
 
                                                                              Returns the number of electrons in the calculation
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-spin[source]
                                                                              
+spin[source]
 
                                                                              If spin-polarization was enabled via ISPIN
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-total_mag[source]
                                                                              
+total_mag[source]
 
                                                                              Total magnetization (in terms of the number of unpaired electrons)
                                                                              
 
                                                                              
 
@@ -674,7 +674,7 @@
 
                                                                              
 
                                                                              
 
                                                                              
-as_dict()[source]
                                                                              
+as_dict()[source]
 
                                                                              
 
                                                                              Returns
                                                                              
 
                                                                              MSONAble dict.
                                                                              
@@ -684,12 +684,12 @@
 
 
                                                                              
 
                                                                              
-property frequencies[source]
                                                                              
+property frequencies[source]
 
                                                                              
 
 
                                                                              
 
                                                                              
-read_avg_core_poten()[source]
                                                                              
+read_avg_core_poten()[source]
 
                                                                              Read the core potential at each ionic step.
                                                                              
 
                                                                              
 
                                                                              Returns
                                                                              
@@ -704,7 +704,7 @@
 
 
                                                                              
 
                                                                              
-read_chemical_shielding()[source]
                                                                              
+read_chemical_shielding()[source]
 
                                                                              Parse the NMR chemical shieldings data. Only the second part “absolute, valence and core”
 will be parsed. And only the three right most field (ISO_SHIELDING, SPAN, SKEW) will be retrieved.
                                                                              
 
                                                                              
@@ -716,7 +716,7 @@
 
 
                                                                              
 
                                                                              
-read_core_state_eigen()[source]
                                                                              
+read_core_state_eigen()[source]
 
                                                                              Read the core state eigenenergies at each ionic step.
                                                                              
 
                                                                              
 
                                                                              Returns
                                                                              
@@ -735,7 +735,7 @@
 
 
                                                                              
 
                                                                              
-read_corrections(reverse=True, terminate_on_match=True)[source]
                                                                              
+read_corrections(reverse=True, terminate_on_match=True)[source]
 
                                                                              Reads the dipol qudropol corrections into the
 Outcar.data[“dipol_quadrupol_correction”].
                                                                              
 
                                                                              
@@ -750,7 +750,7 @@
 
 
                                                                              
 
                                                                              
-read_cs_core_contribution()[source]
                                                                              
+read_cs_core_contribution()[source]
 
                                                                              Parse the core contribution of NMR chemical shielding.
                                                                              
 
                                                                              Returns:
 G0 contribution matrix as list of list.
                                                                              
@@ -758,7 +758,7 @@
 
 
                                                                              
 
                                                                              
-read_cs_g0_contribution()[source]
                                                                              
+read_cs_g0_contribution()[source]
 
                                                                              Parse the  G0 contribution of NMR chemical shielding.
                                                                              
 
                                                                              
 
                                                                              Returns
                                                                              
@@ -769,7 +769,7 @@
 
 
                                                                              
 
                                                                              
-read_cs_raw_symmetrized_tensors()[source]
                                                                              
+read_cs_raw_symmetrized_tensors()[source]
 
                                                                              Parse the matrix form of NMR tensor before corrected to table.
                                                                              
 
                                                                              
 
                                                                              Returns
                                                                              
@@ -780,7 +780,7 @@
 
 
                                                                              
 
                                                                              
-read_elastic_tensor()[source]
                                                                              
+read_elastic_tensor()[source]
 
                                                                              Parse the elastic tensor data.
                                                                              
 
                                                                              
 
                                                                              Returns
                                                                              
@@ -791,13 +791,13 @@
 
 
                                                                              
 
                                                                              
-read_electrostatic_potential()[source]
                                                                              
+read_electrostatic_potential()[source]
 
                                                                              Parses the eletrostatic potential for the last ionic step
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-read_fermi_contact_shift()[source]
                                                                              
+read_fermi_contact_shift()[source]
 
                                                                              output example:
 Fermi contact (isotropic) hyperfine coupling parameter (MHz)
 ————————————————————-
@@ -818,7 +818,7 @@
 
 
                                                                              
 
                                                                              
-read_freq_dielectric()[source]
                                                                              
+read_freq_dielectric()[source]
 
                                                                              Parses the frequency dependent dielectric function (obtained with
 LOPTICS). Frequencies (in eV) are in self.frequencies, and dielectric
 tensor function is given as self.dielectric_tensor_function.
                                                                              
@@ -826,7 +826,7 @@
 
 
                                                                              
 
                                                                              
-read_igpar()[source]
                                                                              
+read_igpar()[source]
 
                                                                              
 
                                                                              Renders accessible:
                                                                              er_ev = e<r>_ev (dictionary with Spin.up/Spin.down as keys)
 er_bp = e<r>_bp (dictionary with Spin.up/Spin.down as keys)
@@ -842,7 +842,7 @@
 
 
                                                                              
 
                                                                              
-read_internal_strain_tensor()[source]
                                                                              
+read_internal_strain_tensor()[source]
 
                                                                              
 
                                                                              Reads the internal strain tensor and populates self.internal_strain_tensor with an array of voigt notation
                                                                              tensors for each site.
                                                                              
 
                                                                              
@@ -851,28 +851,28 @@
 
 
                                                                              
 
                                                                              
-read_lcalcpol()[source]
                                                                              
+read_lcalcpol()[source]
 
                                                                              Reads the lcalpol.
                                                                              
 
                                                                              # TODO: Document the actual variables.
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-read_lepsilon()[source]
                                                                              
+read_lepsilon()[source]
 
                                                                              Reads an LEPSILON run.
                                                                              
 
                                                                              # TODO: Document the actual variables.
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-read_lepsilon_ionic()[source]
                                                                              
+read_lepsilon_ionic()[source]
 
                                                                              Reads an LEPSILON run, the ionic component.
                                                                              
 
                                                                              # TODO: Document the actual variables.
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-read_neb(reverse=True, terminate_on_match=True)[source]
                                                                              
+read_neb(reverse=True, terminate_on_match=True)[source]
 
                                                                              Reads NEB data. This only works with OUTCARs from both normal
 VASP NEB calculations or from the CI NEB method implemented by
 Henkelman et al.
                                                                              
@@ -899,7 +899,7 @@
 
 
                                                                              
 
                                                                              
-read_nmr_efg()[source]
                                                                              
+read_nmr_efg()[source]
 
                                                                              Parse the NMR Electric Field Gradient interpreted values.
                                                                              
 
                                                                              
 
                                                                              Returns
                                                                              
@@ -911,7 +911,7 @@
 
 
                                                                              
 
                                                                              
-read_nmr_efg_tensor()[source]
                                                                              
+read_nmr_efg_tensor()[source]
 
                                                                              Parses the NMR Electric Field Gradient Raw Tensors
                                                                              
 
                                                                              
 
                                                                              Returns
                                                                              
@@ -922,14 +922,14 @@
 
 
                                                                              
 
                                                                              
-read_onsite_density_matrices()[source]
                                                                              
+read_onsite_density_matrices()[source]
 
                                                                              Parse the onsite density matrices, returns list with index corresponding
 to atom index in Structure.
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-read_pattern(patterns, reverse=False, terminate_on_match=False, postprocess=<class 'str'>)[source]
                                                                              
+read_pattern(patterns, reverse=False, terminate_on_match=False, postprocess=<class 'str'>)[source]
 
                                                                              General pattern reading. Uses monty’s regrep method. Takes the same
 arguments.
                                                                              
 
                                                                              
@@ -959,19 +959,19 @@
 
 
                                                                              
 
                                                                              
-read_piezo_tensor()[source]
                                                                              
+read_piezo_tensor()[source]
 
                                                                              Parse the piezo tensor data
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-read_pseudo_zval()[source]
                                                                              
+read_pseudo_zval()[source]
 
                                                                              Create pseudopotential ZVAL dictionary.
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-read_table_pattern(header_pattern, row_pattern, footer_pattern, postprocess=<class 'str'>, attribute_name=None, last_one_only=True)[source]
                                                                              
+read_table_pattern(header_pattern, row_pattern, footer_pattern, postprocess=<class 'str'>, attribute_name=None, last_one_only=True)[source]
 
                                                                              Parse table-like data. A table composes of three parts: header,
 main body, footer. All the data matches “row pattern” in the main body
 will be returned.
                                                                              
@@ -1013,12 +1013,12 @@
 
 
                                                                              
 
                                                                              
-class Procar(filename)[source]
                                                                              
+class Procar(filename)[source]
 
                                                                              Bases: object
                                                                              
 
                                                                              Object for reading a PROCAR file.
                                                                              
 
                                                                              
 
                                                                              
-data[source]
                                                                              
+data[source]
 
                                                                              The PROCAR data of the form below. It should VASP uses 1-based indexing,
 but all indices are converted to 0-based here.:
                                                                              
 
                                                                              {
@@ -1031,7 +1031,7 @@
 
 
                                                                              
 
                                                                              
-weights[source]
                                                                              
+weights[source]
 
                                                                              The weights associated with each k-point as an nd.array of length
 nkpoints.
                                                                              
 
                                                                              
@@ -1067,7 +1067,7 @@
 
                                                                              
 
                                                                              
 
                                                                              
-get_occupation(atom_index, orbital)[source]
                                                                              
+get_occupation(atom_index, orbital)[source]
 
                                                                              Returns the occupation for a particular orbital of a particular atom.
                                                                              
 
                                                                              
 
                                                                              Parameters
                                                                              
@@ -1091,7 +1091,7 @@
 
 
                                                                              
 
                                                                              
-get_projection_on_elements(structure)[source]
                                                                              
+get_projection_on_elements(structure)[source]
 
                                                                              Method returning a dictionary of projections on elements.
                                                                              
 
                                                                              
 
                                                                              Parameters
                                                                              
@@ -1110,21 +1110,21 @@
 
 
                                                                              
 
                                                                              
-exception UnconvergedVASPWarning[source]
                                                                              
+exception UnconvergedVASPWarning[source]
 
                                                                              Bases: Warning
                                                                              
 
                                                                              Warning for unconverged vasp run.
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-exception VaspParserError[source]
                                                                              
+exception VaspParserError[source]
 
                                                                              Bases: Exception
                                                                              
 
                                                                              Exception class for VASP parsing.
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-class Vasprun(filename, ionic_step_skip=None, ionic_step_offset=0, parse_dos=True, parse_eigen=True, parse_projected_eigen=False, parse_potcar_file=True, occu_tol=1e-08, separate_spins=False, exception_on_bad_xml=True)[source]
                                                                              
+class Vasprun(filename, ionic_step_skip=None, ionic_step_offset=0, parse_dos=True, parse_eigen=True, parse_projected_eigen=False, parse_potcar_file=True, occu_tol=1e-08, separate_spins=False, exception_on_bad_xml=True)[source]
 
                                                                              Bases: monty.json.MSONable
                                                                              
 
                                                                              Vastly improved cElementTree-based parser for vasprun.xml files. Uses
 iterparse to support incremental parsing of large files.
@@ -1133,7 +1133,7 @@
 
                                                                              Vasp results
                                                                              
 
                                                                              
 
                                                                              
-ionic_steps[source]
                                                                              
+ionic_steps[source]
 
                                                                              All ionic steps in the run as a list of
 {“structure”: structure at end of run,
 “electronic_steps”: {All electronic step data in vasprun file},
@@ -1142,31 +1142,31 @@
 
 
                                                                              
 
                                                                              
-tdos[source]
                                                                              
+tdos[source]
 
                                                                              Total dos calculated at the end of run.
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-idos[source]
                                                                              
+idos[source]
 
                                                                              Integrated dos calculated at the end of run.
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-pdos[source]
                                                                              
+pdos[source]
 
                                                                              List of list of PDos objects. Access as pdos[atomindex][orbitalindex]
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-efermi[source]
                                                                              
+efermi[source]
 
                                                                              Fermi energy
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-eigenvalues[source]
                                                                              
+eigenvalues[source]
 
                                                                              Available only if parse_eigen=True. Final eigenvalues as a dict of
 {(spin, kpoint index):[[eigenvalue, occu]]}.
 This representation is based on actual ordering in VASP and is meant as
@@ -1176,7 +1176,7 @@
 
 
                                                                              
 
                                                                              
-projected_eigenvalues[source]
                                                                              
+projected_eigenvalues[source]
 
                                                                              Final projected eigenvalues as a dict of {spin: nd-array}. To access
 a particular value, you need to do
 Vasprun.projected_eigenvalues[spin][kpoint index][band index][atom index][orbital_index]
@@ -1188,7 +1188,7 @@
 
 
                                                                              
 
                                                                              
-projected_magnetisation[source]
                                                                              
+projected_magnetisation[source]
 
                                                                              Final projected magnetisation as a numpy array with the shape (nkpoints, nbands,
 natoms, norbitals, 3). Where the last axis is the contribution in the 3
 Cartesian directions. This attribute is only set if spin-orbit coupling
@@ -1198,7 +1198,7 @@
 
 
                                                                              
 
                                                                              
-other_dielectric[source]
                                                                              
+other_dielectric[source]
 
                                                                              Dictionary, with the tag comment as key, containing other variants of
 the real and imaginary part of the dielectric constant (e.g., computed
 by RPA) in function of the energy (frequency). Optical properties (e.g.
@@ -1212,7 +1212,7 @@
 
 
                                                                              
 
                                                                              
-nionic_steps[source]
                                                                              
+nionic_steps[source]
 
                                                                              The total number of ionic steps. This number is always equal
 to the total number of steps in the actual run even if
 ionic_step_skip is used.
                                                                              
@@ -1220,48 +1220,77 @@
 
 
                                                                              
 
                                                                              
-force_constants[source]
                                                                              
+force_constants[source]
 
                                                                              Force constants computed in phonon DFPT run(IBRION = 8).
 The data is a 4D numpy array of shape (natoms, natoms, 3, 3).
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-normalmode_eigenvals[source]
                                                                              
+normalmode_eigenvals[source]
 
                                                                              Normal mode frequencies.
 1D numpy array of size 3*natoms.
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-normalmode_eigenvecs[source]
                                                                              
+normalmode_eigenvecs[source]
 
                                                                              Normal mode eigen vectors.
 3D numpy array of shape (3*natoms, natoms, 3).
                                                                              
 
                                                                              
 
+
                                                                              
+
                                                                              
+md_data[source]
                                                                              
+
                                                                              Available only for ML MD runs, i.e., INCAR with ML_LMLFF = .TRUE.
+md_data is a list of dict with the following format:
                                                                              
+
                                                                              
+
                                                                              [
                                                                              
+
                                                                              {
                                                                              
+
                                                                              ‘energy’: {
                                                                              ‘e_0_energy’: -525.07195568,
+‘e_fr_energy’: -525.07195568,
+‘e_wo_entrp’: -525.07195568,
+‘kinetic’: 3.17809233,
+‘lattice kinetic’: 0.0,
+‘nosekinetic’: 1.323e-05,
+‘nosepot’: 0.0,
+‘total’: -521.89385012
+},
                                                                              
+
                                                                              
+
                                                                              
+
                                                                              ‘forces’: [[0.17677989, 0.48309874, 1.85806696], …],
+‘structure’: Structure object
                                                                              
+
                                                                              
+
                                                                              
+
                                                                              }
                                                                              
+
                                                                              
+
                                                                              
+
                                                                              ]
                                                                              
+
                                                                              
+
 
                                                                              Vasp inputs
                                                                              
 
                                                                              
 
                                                                              
-incar[source]
                                                                              
+incar[source]
 
                                                                              Incar object for parameters specified in INCAR file.
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-parameters[source]
                                                                              
+parameters[source]
 
                                                                              Incar object with parameters that vasp actually used, including all
 defaults.
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-kpoints[source]
                                                                              
+kpoints[source]
 
                                                                              Kpoints object for KPOINTS specified in run.
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-actual_kpoints[source]
                                                                              
+actual_kpoints[source]
 
                                                                              List of actual kpoints, e.g.,
 [[0.25, 0.125, 0.08333333], [-0.25, 0.125, 0.08333333],
 [0.25, 0.375, 0.08333333], ….]
                                                                              
@@ -1269,20 +1298,20 @@
 
 
                                                                              
 
                                                                              
-actual_kpoints_weights[source]
                                                                              
+actual_kpoints_weights[source]
 
                                                                              List of kpoint weights, E.g.,
 [0.04166667, 0.04166667, 0.04166667, 0.04166667, 0.04166667, ….]
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-atomic_symbols[source]
                                                                              
+atomic_symbols[source]
 
                                                                              List of atomic symbols, e.g., [“Li”, “Fe”, “Fe”, “P”, “P”, “P”]
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-potcar_symbols[source]
                                                                              
+potcar_symbols[source]
 
                                                                              List of POTCAR symbols. e.g.,
 [“PAW_PBE Li 17Jan2003”, “PAW_PBE Fe 06Sep2000”, ..]
                                                                              
 
                                                                              
@@ -1342,13 +1371,13 @@
 
                                                                              
 
                                                                              
 
                                                                              
-as_dict()[source]
                                                                              
+as_dict()[source]
 
                                                                              JSON-serializable dict representation.
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-calculate_efermi(tol=0.001)[source]
                                                                              
+calculate_efermi(tol=0.001)[source]
 
                                                                              Calculate the Fermi level using a robust algorithm.
                                                                              
 
                                                                              Sometimes VASP can put the Fermi level just inside of a band due to issues in
 the way band occupancies are handled. This algorithm tries to detect and correct
@@ -1358,14 +1387,14 @@
 
 
                                                                              
 
                                                                              
-property complete_dos[source]
                                                                              
+property complete_dos[source]
 
                                                                              A complete dos object which incorporates the total dos and all
 projected dos.
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-property converged[source]
                                                                              
+property converged[source]
 
                                                                              Returns:
 True if a relaxation run is converged both ionically and
 electronically.
                                                                              
@@ -1373,7 +1402,7 @@
 
 
                                                                              
 
                                                                              
-property converged_electronic[source]
                                                                              
+property converged_electronic[source]
 
                                                                              Returns:
 True if electronic step convergence has been reached in the final
 ionic step
                                                                              
@@ -1381,7 +1410,7 @@
 
 
                                                                              
 
                                                                              
-property converged_ionic[source]
                                                                              
+property converged_ionic[source]
 
                                                                              Returns:
 True if ionic step convergence has been reached, i.e. that vasp
 exited before reaching the max ionic steps for a relaxation run
                                                                              
@@ -1389,7 +1418,7 @@
 
 
                                                                              
 
                                                                              
-property dielectric[source]
                                                                              
+property dielectric[source]
 
                                                                              Returns:
 The real and imaginary part of the dielectric constant (e.g., computed
 by RPA) in function of the energy (frequency). Optical properties (e.g.
@@ -1403,7 +1432,7 @@
 
 
                                                                              
 
                                                                              
-property eigenvalue_band_properties[source]
                                                                              
+property eigenvalue_band_properties[source]
 
                                                                              Band properties from the eigenvalues as a tuple,
 (band gap, cbm, vbm, is_band_gap_direct). In the case of separate_spins=True,
 the band gap, cbm, vbm, and is_band_gap_direct are each lists of length 2,
@@ -1413,7 +1442,7 @@
 
 
                                                                              
 
                                                                              
-property epsilon_ionic[source]
                                                                              
+property epsilon_ionic[source]
 
                                                                              Property only available for DFPT calculations and when IBRION=5, 6, 7 or 8.
                                                                              
 
                                                                              
 
                                                                              Returns
                                                                              
@@ -1425,7 +1454,7 @@
 
 
                                                                              
 
                                                                              
-property epsilon_static[source]
                                                                              
+property epsilon_static[source]
 
                                                                              Property only available for DFPT calculations.
                                                                              
 
                                                                              
 
                                                                              Returns
                                                                              
@@ -1437,7 +1466,7 @@
 
 
                                                                              
 
                                                                              
-property epsilon_static_wolfe[source]
                                                                              
+property epsilon_static_wolfe[source]
 
                                                                              Property only available for DFPT calculations.
                                                                              
 
                                                                              
 
                                                                              Returns
                                                                              
@@ -1449,12 +1478,12 @@
 
 
                                                                              
 
                                                                              
-property final_energy[source]
                                                                              
+property final_energy[source]
 
                                                                              
 
 
                                                                              
 
                                                                              
-get_band_structure(kpoints_filename: str | None = None, efermi: float | Literal['smart'] | None = None, line_mode: bool = False, force_hybrid_mode: bool = False)[source]
                                                                              
+get_band_structure(kpoints_filename: str | None = None, efermi: float | Literal['smart'] | None = None, line_mode: bool = False, force_hybrid_mode: bool = False)[source]
 
                                                                              Returns the band structure as a BandStructure object
                                                                              
 
                                                                              
 
                                                                              Parameters
                                                                              
@@ -1496,7 +1525,7 @@
 
 
                                                                              
 
                                                                              
-get_computed_entry(inc_structure=True, parameters=None, data=None, entry_id='vasprun-2022-05-18 10:14:03.656888')[source]
                                                                              
+get_computed_entry(inc_structure=True, parameters=None, data=None, entry_id='vasprun-2022-05-18 13:30:32.254329')[source]
 
                                                                              Returns a ComputedEntry or ComputedStructureEntry from the vasprun.
                                                                              
 
                                                                              
 
                                                                              Parameters
                                                                              
@@ -1522,7 +1551,7 @@
 
 
                                                                              
 
                                                                              
-get_potcars(path)[source]
                                                                              
+get_potcars(path)[source]
 
                                                                              
 
                                                                              Parameters
                                                                              
 
                                                                              path – Path to search for POTCARs
                                                                              
@@ -1535,7 +1564,7 @@
 
 
                                                                              
 
                                                                              
-get_trajectory()[source]
                                                                              
+get_trajectory()[source]
 
                                                                              This method returns a Trajectory object, which is an alternative
 representation of self.structures into a single object. Forces are
 added to the Trajectory as site properties.
                                                                              
@@ -1544,25 +1573,25 @@
 
 
                                                                              
 
                                                                              
-property hubbards[source]
                                                                              
+property hubbards[source]
 
                                                                              Hubbard U values used if a vasprun is a GGA+U run. {} otherwise.
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-property is_hubbard[source]
                                                                              
+property is_hubbard[source]
 
                                                                              True if run is a DFT+U run.
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-property is_spin[source]
                                                                              
+property is_spin[source]
 
                                                                              True if run is spin-polarized.
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-property optical_absorption_coeff[source]
                                                                              
+property optical_absorption_coeff[source]
 
                                                                              Calculate the optical absorption coefficient
 from the dielectric constants. Note that this method is only
 implemented for optical properties calculated with GGA and BSE.
@@ -1572,7 +1601,7 @@
 
 
                                                                              
 
                                                                              
-property run_type[source]
                                                                              
+property run_type[source]
 
                                                                              Returns the run type. Currently detects GGA, metaGGA, HF, HSE, B3LYP,
 and hybrid functionals based on relevant INCAR tags. LDA is assigned if
 PAW POTCARs are used and no other functional is detected.
                                                                              
@@ -1581,14 +1610,14 @@
 
 
                                                                              
 
                                                                              
-property structures[source]
                                                                              
+property structures[source]
 
                                                                              Returns:
 List of Structure objects for the structure at each ionic step.
                                                                              
 
                                                                              
 
 
                                                                              
 
                                                                              
-update_charge_from_potcar(path)[source]
                                                                              
+update_charge_from_potcar(path)[source]
 
                                                                              Sets the charge of a structure based on the POTCARs found.
                                                                              
 
                                                                              
 
                                                                              Parameters
                                                                              
@@ -1599,7 +1628,7 @@
 
 
                                                                              
 
                                                                              
-update_potcar_spec(path)[source]
                                                                              
+update_potcar_spec(path)[source]
 
                                                                              
 
                                                                              Parameters
                                                                              
 
                                                                              path – Path to search for POTCARs
                                                                              
@@ -1614,12 +1643,12 @@
 
 
                                                                              
 
                                                                              
-class VolumetricData(structure, data, distance_matrix=None, data_aug=None)[source]
                                                                              
+class VolumetricData(structure, data, distance_matrix=None, data_aug=None)[source]
 
                                                                              Bases: monty.json.MSONable
                                                                              
 
                                                                              Simple volumetric object for reading LOCPOT and CHGCAR type files.
                                                                              
 
                                                                              
 
                                                                              
-structure[source]
                                                                              
+structure[source]
 
                                                                              Structure associated with the Volumetric Data object
                                                                              
 
                                                                              
 
@@ -1640,7 +1669,7 @@
                                                                      -ngridpts[source]
                                                                      +ngridpts[source]

                                                                      Total number of grid points in volumetric data.

                                                                      @@ -1662,7 +1691,7 @@
                                                                      -copy()[source]
                                                                      +copy()[source]
                                                                      Returns

                                                                      Copy of Volumetric object

                                                                      @@ -1672,7 +1701,7 @@
                                                                      -classmethod from_hdf5(filename, **kwargs)[source]
                                                                      +classmethod from_hdf5(filename, **kwargs)[source]

                                                                      Reads VolumetricData from HDF5 file.

                                                                      Parameters
                                                                      @@ -1686,7 +1715,7 @@
                                                                      -get_average_along_axis(ind)[source]
                                                                      +get_average_along_axis(ind)[source]

                                                                      Get the averaged total of the volumetric data a certain axis direction. For example, useful for visualizing Hartree Potentials from a LOCPOT file.

                                                                      @@ -1702,7 +1731,7 @@
                                                                      -get_axis_grid(ind)[source]
                                                                      +get_axis_grid(ind)[source]

                                                                      Returns the grid for a particular axis.

                                                                      Parameters
                                                                      @@ -1713,7 +1742,7 @@
                                                                      -get_integrated_diff(ind, radius, nbins=1)[source]
                                                                      +get_integrated_diff(ind, radius, nbins=1)[source]

                                                                      Get integrated difference of atom index ind up to radius. This can be an extremely computationally intensive process, depending on how many grid points are in the VolumetricData.

                                                                      @@ -1738,7 +1767,7 @@
                                                                      -linear_add(other, scale_factor=1.0)[source]
                                                                      +linear_add(other, scale_factor=1.0)[source]

                                                                      Method to do a linear sum of volumetric objects. Used by + and - operators as well. Returns a VolumetricData object containing the linear sum.

                                                                      @@ -1757,7 +1786,7 @@
                                                                      -linear_slice(p1, p2, n=100)[source]
                                                                      +linear_slice(p1, p2, n=100)[source]

                                                                      Get a linear slice of the volumetric data with n data points from point p1 to point p2, in the form of a list.

                                                                      @@ -1777,7 +1806,7 @@
                                                                      -static parse_file(filename)[source]
                                                                      +static parse_file(filename)[source]

                                                                      Convenience method to parse a generic volumetric data file in the vasp like format. Used by subclasses for parsing file.

                                                                      @@ -1792,7 +1821,7 @@
                                                                      -property spin_data[source]
                                                                      +property spin_data[source]

                                                                      data}. Essentially, this provides the actual Spin.up and Spin.down data instead of the total and diff. Note that by definition, a @@ -1806,7 +1835,7 @@

                                                                      -to_hdf5(filename)[source]
                                                                      +to_hdf5(filename)[source]

                                                                      Writes the VolumetricData to a HDF5 format, which is a highly optimized format for reading storing large data. The mapping of the VolumetricData to this file format is as follows:

                                                                      @@ -1830,7 +1859,7 @@
                                                                      -value_at(x, y, z)[source]
                                                                      +value_at(x, y, z)[source]

                                                                      Get a data value from self.data at a given point (x, y, z) in terms of fractional lattice parameters. Will be interpolated using a RegularGridInterpolator on self.data if (x, y, z) is not in the original @@ -1852,7 +1881,7 @@

                                                                      -write_file(file_name, vasp4_compatible=False)[source]
                                                                      +write_file(file_name, vasp4_compatible=False)[source]

                                                                      Write the VolumetricData object to a vasp compatible file.

                                                                      Parameters
                                                                      @@ -1868,7 +1897,7 @@
                                                                      -class WSWQ(nspin: int, nkpoints: int, nbands: int, me_real: numpy.ndarray, me_imag: numpy.ndarray)[source]
                                                                      +class WSWQ(nspin: int, nkpoints: int, nbands: int, me_real: numpy.ndarray, me_imag: numpy.ndarray)[source]

                                                                      Bases: monty.json.MSONable

                                                                      Class for reading a WSWQ file. The WSWQ file is used to calculation the wave function overlaps betweeen

                                                                      @@ -1894,7 +1923,7 @@
                                                                      -nspin[source]
                                                                      +nspin[source]

                                                                      Number of spin channels

                                                                      Type
                                                                      @@ -1905,7 +1934,7 @@
                                                                      -nkpoints[source]
                                                                      +nkpoints[source]

                                                                      Number of k-points

                                                                      Type
                                                                      @@ -1916,7 +1945,7 @@
                                                                      -nbands[source]
                                                                      +nbands[source]

                                                                      Number of bands

                                                                      Type
                                                                      @@ -1927,7 +1956,7 @@
                                                                      -me_real[source]
                                                                      +me_real[source]

                                                                      Real part of the overlap matrix elements

                                                                      Type
                                                                      @@ -1938,7 +1967,7 @@
                                                                      -me_imag[source]
                                                                      +me_imag[source]

                                                                      Imaginary part of the overlap matrix elements

                                                                      Type
                                                                      @@ -1949,40 +1978,40 @@
                                                                      -classmethod from_file(filename)[source]
                                                                      +classmethod from_file(filename)[source]

                                                                      Search for lines containing “spin”

                                                                      -me_imag: numpy.ndarray[source]
                                                                      +me_imag: numpy.ndarray[source]
                                                                      -me_real: numpy.ndarray[source]
                                                                      +me_real: numpy.ndarray[source]
                                                                      -nbands: int[source]
                                                                      +nbands: int[source]
                                                                      -nkpoints: int[source]
                                                                      +nkpoints: int[source]
                                                                      -nspin: int[source]
                                                                      +nspin: int[source]
                                                                      -class Wavecar(filename='WAVECAR', verbose=False, precision='normal', vasp_type=None)[source]
                                                                      +class Wavecar(filename='WAVECAR', verbose=False, precision='normal', vasp_type=None)[source]

                                                                      Bases: object

                                                                      This is a class that contains the (pseudo-) wavefunctions from VASP.

                                                                      Coefficients are read from the given WAVECAR file and the corresponding @@ -1998,68 +2027,68 @@ (https://doi.org/10.1103/PhysRevMaterials.1.065001).

                                                                      -filename[source]
                                                                      +filename[source]

                                                                      String of the input file (usually WAVECAR)

                                                                      -vasp_type[source]
                                                                      +vasp_type[source]

                                                                      String that determines VASP type the WAVECAR was generated with (either ‘std’, ‘gam’, or ‘ncl’)

                                                                      -nk[source]
                                                                      +nk[source]

                                                                      Number of k-points from the WAVECAR

                                                                      -nb[source]
                                                                      +nb[source]

                                                                      Number of bands per k-point

                                                                      -encut[source]
                                                                      +encut[source]

                                                                      Energy cutoff (used to define G_{cut})

                                                                      -efermi[source]
                                                                      +efermi[source]

                                                                      Fermi energy

                                                                      -a[source]
                                                                      +a[source]

                                                                      Primitive lattice vectors of the cell (e.g. a_1 = self.a[0, :])

                                                                      -b[source]
                                                                      +b[source]

                                                                      Reciprocal lattice vectors of the cell (e.g. b_1 = self.b[0, :])

                                                                      -vol[source]
                                                                      +vol[source]

                                                                      The volume of the unit cell in real space

                                                                      -kpoints[source]
                                                                      +kpoints[source]

                                                                      The list of k-points read from the WAVECAR file

                                                                      -band_energy[source]
                                                                      +band_energy[source]

                                                                      The list of band eigenenergies (and corresponding occupancies) for each kpoint, where the first index corresponds to the index of the k-point (e.g. self.band_energy[kp])

                                                                      @@ -2067,7 +2096,7 @@
                                                                      -Gpoints[source]
                                                                      +Gpoints[source]

                                                                      The list of generated G-points for each k-point (a double list), which are used with the coefficients for each k-point and band to recreate the wavefunction (e.g. self.Gpoints[kp] is the list of G-points for @@ -2080,7 +2109,7 @@

                                                                      -coeffs[source]
                                                                      +coeffs[source]

                                                                      The list of coefficients for each k-point and band for reconstructing the wavefunction. For non-spin-polarized, the first index corresponds to the kpoint and the second corresponds to the band (e.g. @@ -2114,7 +2143,7 @@

                                                                      -evaluate_wavefunc(kpoint: int, band: int, r: numpy.ndarray, spin: int = 0, spinor: int = 0) → numpy.complex64[source]
                                                                      +evaluate_wavefunc(kpoint: int, band: int, r: numpy.ndarray, spin: int = 0, spinor: int = 0) → numpy.complex64[source]

                                                                      Evaluates the wavefunction for a given position, r.

                                                                      The wavefunction is given by the k-point and band. It is evaluated at the given position by summing over the components. Formally,

                                                                      @@ -2147,7 +2176,7 @@
                                                                      -fft_mesh(kpoint: int, band: int, spin: int = 0, spinor: int = 0, shift: bool = True) → numpy.ndarray[source]
                                                                      +fft_mesh(kpoint: int, band: int, spin: int = 0, spinor: int = 0, shift: bool = True) → numpy.ndarray[source]

                                                                      Places the coefficients of a wavefunction onto an fft mesh.

                                                                      Once the mesh has been obtained, a discrete fourier transform can be used to obtain real-space evaluation of the wavefunction. The output @@ -2178,7 +2207,7 @@

                                                                      -get_parchg(poscar: Poscar, kpoint: int, band: int, spin: int | None = None, spinor: int | None = None, phase: bool = False, scale: int = 2) → Chgcar[source]
                                                                      +get_parchg(poscar: Poscar, kpoint: int, band: int, spin: int | None = None, spinor: int | None = None, phase: bool = False, scale: int = 2) → Chgcar[source]

                                                                      Generates a Chgcar object, which is the charge density of the specified wavefunction.

                                                                      This function generates a Chgcar object with the charge density of the @@ -2220,7 +2249,7 @@

                                                                      -write_unks(directory: str) → None[source]
                                                                      +write_unks(directory: str) → None[source]

                                                                      Write the UNK files to the given directory.

                                                                      Writes the cell-periodic part of the bloch wavefunctions from the WAVECAR file to each of the UNK files. There will be one UNK file for @@ -2242,7 +2271,7 @@

                                                                      -class Waveder(filename, gamma_only=False)[source]
                                                                      +class Waveder(filename, gamma_only=False)[source]

                                                                      Bases: object

                                                                      Class for reading a WAVEDER file. The LOPTICS tag produces a WAVEDER file. @@ -2255,13 +2284,13 @@

                                                                      -property cder_data[source]
                                                                      +property cder_data[source]

                                                                      Returns the orbital derivative between states

                                                                      -get_orbital_derivative_between_states(band_i, band_j, kpoint, spin, cart_dir)[source]
                                                                      +get_orbital_derivative_between_states(band_i, band_j, kpoint, spin, cart_dir)[source]

                                                                      Method returning a value between bands band_i and band_j for k-point index, spin-channel and Cartesian direction. :param band_i: Index of band i @@ -2283,19 +2312,19 @@

                                                                      -property nbands[source]
                                                                      +property nbands[source]

                                                                      Returns the number of bands in the calculation

                                                                      -property nelect[source]
                                                                      +property nelect[source]

                                                                      Returns the number of electrons in the calculation

                                                                      -property nkpoints[source]
                                                                      +property nkpoints[source]

                                                                      Returns the number of k-points in the calculation

                                                                      @@ -2303,7 +2332,7 @@
                                                                      -class Wavederf(filename)[source]
                                                                      +class Wavederf(filename)[source]

                                                                      Bases: object

                                                                      Object for reading a WAVEDERF file.

                                                                      Note: This file is only produced when LOPTICS is true AND vasp has been @@ -2311,7 +2340,7 @@ WRT_CDER_BETWEEN_STATES_FORMATTED in linear_optics.F

                                                                      -data[source]
                                                                      +data[source]

                                                                      A numpy array containing the WAVEDERF data of the form below. It should be noted that VASP uses 1-based indexing for bands, but this is converted to 0-based numpy array indexing.

                                                                      @@ -2346,7 +2375,7 @@
                                                                      -get_elements_between_bands(band_i, band_j)[source]
                                                                      +get_elements_between_bands(band_i, band_j)[source]

                                                                      Method returning a numpy array with elements

                                                                      [cdum_x_real, cdum_x_imag, cdum_y_real, cdum_y_imag, cdum_z_real, cdum_z_imag]

                                                                      between bands band_i and band_j (vasp 1-based indexing) for all kpoints.

                                                                      @@ -2365,13 +2394,13 @@
                                                                      -property nb_bands[source]
                                                                      +property nb_bands[source]

                                                                      returns the number of bands in the band structure

                                                                      -property nb_kpoints[source]
                                                                      +property nb_kpoints[source]

                                                                      Returns the number of k-points in the band structure calculation

                                                                      @@ -2379,18 +2408,18 @@
                                                                      -class Xdatcar(filename, ionicstep_start=1, ionicstep_end=None, comment=None)[source]
                                                                      +class Xdatcar(filename, ionicstep_start=1, ionicstep_end=None, comment=None)[source]

                                                                      Bases: object

                                                                      Class representing an XDATCAR file. Only tested with VASP 5.x files.

                                                                      -structures[source]
                                                                      +structures[source]

                                                                      List of structures parsed from XDATCAR.

                                                                      -comment[source]
                                                                      +comment[source]

                                                                      Optional comment string.

                                                                      @@ -2407,7 +2436,7 @@
                                                                      -concatenate(filename, ionicstep_start=1, ionicstep_end=None)[source]
                                                                      +concatenate(filename, ionicstep_start=1, ionicstep_end=None)[source]

                                                                      Concatenate structures in file to Xdatcar.

                                                                      Parameters
                                                                      @@ -2427,7 +2456,7 @@
                                                                      -get_string(ionicstep_start=1, ionicstep_end=None, significant_figures=8)[source]
                                                                      +get_string(ionicstep_start=1, ionicstep_end=None, significant_figures=8)[source]

                                                                      Write Xdatcar class to a string.

                                                                      Parameters
                                                                      @@ -2442,21 +2471,21 @@
                                                                      -property natoms[source]
                                                                      +property natoms[source]

                                                                      Sequence of number of sites of each type associated with the Poscar. Similar to 7th line in vasp 5+ Xdatcar.

                                                                      -property site_symbols[source]
                                                                      +property site_symbols[source]

                                                                      Sequence of symbols associated with the Xdatcar. Similar to 6th line in vasp 5+ Xdatcar.

                                                                      -write_file(filename, **kwargs)[source]
                                                                      +write_file(filename, **kwargs)[source]

                                                                      Write Xdatcar class into a file.

                                                                      Parameters
                                                                      @@ -2473,7 +2502,7 @@
                                                                      -get_adjusted_fermi_level(efermi, cbm, band_structure)[source]
                                                                      +get_adjusted_fermi_level(efermi, cbm, band_structure)[source]

                                                                      When running a band structure computations the fermi level needs to be take from the static run that gave the charge density used for the non-self consistent band structure run. Sometimes this fermi level is however a @@ -2500,7 +2529,7 @@

                                                                      -get_band_structure_from_vasp_multiple_branches(dir_name, efermi=None, projections=False)[source]
                                                                      +get_band_structure_from_vasp_multiple_branches(dir_name, efermi=None, projections=False)[source]

                                                                      This method is used to get band structure info from a VASP directory. It takes into account that the run can be divided in several branches named “branch_x”. If the run has not been divided in branches the method will diff --git a/docs/pymatgen.io.vasp.sets.html b/docs/pymatgen.io.vasp.sets.html index 3bf977c8890..b1e6991b24d 100644 --- a/docs/pymatgen.io.vasp.sets.html +++ b/docs/pymatgen.io.vasp.sets.html @@ -4,7 +4,7 @@ - pymatgen.io.vasp.sets module — pymatgen 2022.5.18 documentation + pymatgen.io.vasp.sets module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                                                      - 2022.5.18 + 2022.5.18.1
                                                                      @@ -152,14 +152,14 @@

                                                          -exception BadInputSetWarning[source]
                                                          +exception BadInputSetWarning[source]

                                                          Bases: UserWarning

                                                          Warning class for bad but legal inputs.

                                                          -class DictSet(structure, config_dict, files_to_transfer=None, user_incar_settings=None, user_kpoints_settings=None, user_potcar_settings=None, constrain_total_magmom=False, sort_structure=True, potcar_functional=None, user_potcar_functional=None, force_gamma=False, reduce_structure=None, vdw=None, use_structure_charge=False, standardize=False, sym_prec=0.1, international_monoclinic=True, validate_magmom=True)[source]
                                                          +class DictSet(structure, config_dict, files_to_transfer=None, user_incar_settings=None, user_kpoints_settings=None, user_potcar_settings=None, constrain_total_magmom=False, sort_structure=True, potcar_functional=None, user_potcar_functional=None, force_gamma=False, reduce_structure=None, vdw=None, use_structure_charge=False, standardize=False, sym_prec=0.1, international_monoclinic=True, validate_magmom=True)[source]

                                                          Bases: pymatgen.io.vasp.sets.VaspInputSet

                                                          Concrete implementation of VaspInputSet that is initialized from a dict settings. This allows arbitrary settings to be input. In general, @@ -257,7 +257,7 @@

                                                          -calculate_ng(max_prime_factor: int = 7, must_inc_2: bool = True) → tuple[source]
                                                          +calculate_ng(max_prime_factor: int = 7, must_inc_2: bool = True) → tuple[source]

                                                          Calculates the NGX, NGY, and NGZ values using the information available in the INCAR and POTCAR This is meant to help with making initial guess for the FFT grid so we can interact with the Charge density API

                                                          @@ -271,7 +271,7 @@
                                                          -estimate_nbands() → int[source]
                                                          +estimate_nbands() → int[source]

                                                          Estimate the number of bands that VASP will initialize a calculation with by default. Note that in practice this can depend on # of cores (if not set explicitly)

                                                          @@ -279,7 +279,7 @@
                                                          -property incar: pymatgen.io.vasp.inputs.Incar[source]
                                                          +property incar: pymatgen.io.vasp.inputs.Incar[source]

                                                          Incar

                                                          Type
                                                          @@ -290,7 +290,7 @@
                                                          -property kpoints: Kpoints | None[source]
                                                          +property kpoints: Kpoints | None[source]

                                                          Returns a KPOINTS file using the fully automated grid method. Uses Gamma centered meshes for hexagonal cells and Monk grids otherwise.

                                                          If KSPACING is set in user_incar_settings (or the INCAR file), no @@ -304,13 +304,13 @@

                                                          -property nelect: float[source]
                                                          +property nelect: float[source]

                                                          Gets the default number of electrons for a given structure.

                                                          -property poscar: pymatgen.io.vasp.inputs.Poscar[source]
                                                          +property poscar: pymatgen.io.vasp.inputs.Poscar[source]

                                                          Poscar

                                                          Type
                                                          @@ -321,7 +321,7 @@
                                                          -property structure: pymatgen.core.structure.Structure[source]
                                                          +property structure: pymatgen.core.structure.Structure[source]

                                                          Structure

                                                          Type
                                                          @@ -332,7 +332,7 @@
                                                          -write_input(output_dir: str, make_dir_if_not_present: bool = True, include_cif: bool = False, potcar_spec: bool = False, zip_output: bool = False)[source]
                                                          +write_input(output_dir: str, make_dir_if_not_present: bool = True, include_cif: bool = False, potcar_spec: bool = False, zip_output: bool = False)[source]

                                                          Writes out all input to a directory.

                                                          Parameters
                                                          @@ -357,7 +357,7 @@
                                                          -class LobsterSet(structure: pymatgen.core.structure.Structure, isym: int = 0, ismear: int = - 5, reciprocal_density: Optional[int] = None, address_basis_file: Optional[str] = None, user_supplied_basis: Optional[dict] = None, user_potcar_settings: Optional[dict] = None, **kwargs)[source]
                                                          +class LobsterSet(structure: pymatgen.core.structure.Structure, isym: int = 0, ismear: int = - 5, reciprocal_density: Optional[int] = None, address_basis_file: Optional[str] = None, user_supplied_basis: Optional[dict] = None, user_potcar_settings: Optional[dict] = None, **kwargs)[source]

                                                          Bases: pymatgen.io.vasp.sets.MPRelaxSet

                                                          Input set to prepare VASP runs that can be digested by Lobster (See cohp.de)

                                                          @@ -377,14 +377,14 @@
                                                          -CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                          +CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                          -class MITMDSet(structure, start_temp, end_temp, nsteps, time_step=2, spin_polarized=False, **kwargs)[source]
                                                          +class MITMDSet(structure, start_temp, end_temp, nsteps, time_step=2, spin_polarized=False, **kwargs)[source]

                                                          Bases: pymatgen.io.vasp.sets.MITRelaxSet

                                                          Class for writing a vasp md run. This DOES NOT do multiple stage runs.

                                                          @@ -405,7 +405,7 @@
                                                          -property kpoints[source]
                                                          +property kpoints[source]

                                                          Kpoints

                                                          Type
                                                          @@ -418,7 +418,7 @@
                                                          -class MITNEBSet(structures, unset_encut=False, **kwargs)[source]
                                                          +class MITNEBSet(structures, unset_encut=False, **kwargs)[source]

                                                          Bases: pymatgen.io.vasp.sets.MITRelaxSet

                                                          Class for writing NEB inputs. Note that EDIFF is not on a per atom basis for this input set.

                                                          @@ -433,7 +433,7 @@
                                                          -property poscar[source]
                                                          +property poscar[source]

                                                          Poscar for structure of first end point.

                                                          Type
                                                          @@ -444,7 +444,7 @@
                                                          -property poscars[source]
                                                          +property poscars[source]

                                                          List of Poscars.

                                                          Type
                                                          @@ -455,7 +455,7 @@
                                                          -write_input(output_dir, make_dir_if_not_present=True, write_cif=False, write_path_cif=False, write_endpoint_inputs=False)[source]
                                                          +write_input(output_dir, make_dir_if_not_present=True, write_cif=False, write_path_cif=False, write_endpoint_inputs=False)[source]

                                                          NEB inputs has a special directory structure where inputs are in 00, 01, 02, ….

                                                          @@ -478,7 +478,7 @@
                                                          -class MITRelaxSet(structure, **kwargs)[source]
                                                          +class MITRelaxSet(structure, **kwargs)[source]

                                                          Bases: pymatgen.io.vasp.sets.DictSet

                                                          Standard implementation of VaspInputSet utilizing parameters in the MIT High-throughput project. @@ -501,14 +501,14 @@

                                                          -CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF': 1e-05, 'ENCUT': 520, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'ISYM': 0, 'LDAU': True, 'LDAUJ': {'F': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'O': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'S': {'Fe': 0, 'Mn': 0}}, 'LDAUL': {'F': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'O': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'S': {'Fe': 2, 'Mn': 2.5}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'O': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'S': {'Fe': 1.9, 'Mn': 2.5}}, 'LORBIT': '11', 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 200, 'NELMIN': 6, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'length': 25}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': {'hash': 'd6854224d20e3de6e6fd7399503791d1', 'symbol': 'Ac'}, 'Ag': {'hash': 'e8ffa02fe3f3a51338ac1ac91ae968b9', 'symbol': 'Ag'}, 'Al': {'hash': 'a6fd9a46aec185f4ad2acd0cbe4ae2fa', 'symbol': 'Al'}, 'Ar': {'hash': 'e782fc6292623b396091bf8b871c272f', 'symbol': 'Ar'}, 'As': {'hash': '8005364db225a254e52cba350bedd032', 'symbol': 'As'}, 'Au': {'hash': 'a9182d436a13194b744640ac940ab9b0', 'symbol': 'Au'}, 'B': {'hash': '18ed2875dfa6305324cec3d7d59273ae', 'symbol': 'B'}, 'Ba': {'hash': 'c0477913afb63dfae3439f3534fbf0ed', 'symbol': 'Ba_sv'}, 'Be': {'hash': 'fb974e44d56a8c62c6bbd1a1eb70c3a7', 'symbol': 'Be'}, 'Bi': {'hash': 'e29661c79d59abae3b3ba69eae24b1a5', 'symbol': 'Bi'}, 'Br': {'hash': '40f9594b4506684a69158c8975cfb9d6', 'symbol': 'Br'}, 'C': {'hash': 'c0a8167dbb174fe492a3db7f5006c0f8', 'symbol': 'C'}, 'Ca': {'hash': 'eb006721e214c04b3c13146e81b3a27d', 'symbol': 'Ca_sv'}, 'Cd': {'hash': '0506b2d0ac28d5fe2b5ced77a701aa86', 'symbol': 'Cd'}, 'Ce': {'hash': 'ff3a09f2ff91798e58eb4b9854e9be4a', 'symbol': 'Ce'}, 'Cl': {'hash': '779b9901046c78fe51c5d80224642aeb', 'symbol': 'Cl'}, 'Co': {'hash': 'b169bca4e137294d2ab3df8cbdd09083', 'symbol': 'Co'}, 'Cr': {'hash': '82c14307937c7509fda4e9bc023d243d', 'symbol': 'Cr'}, 'Cs': {'hash': '096b53a7d80cc0086976bcda50d536e5', 'symbol': 'Cs_sv'}, 'Cu': {'hash': '8ca4e43a30de0c397e51f16bbb20d678', 'symbol': 'Cu'}, 'Dy': {'hash': 'd4a05220ab0a2d4c03a76872ea724a1e', 'symbol': 'Dy_3'}, 'Er': {'hash': 'daa65a04877317f8c3c593ddeaa8a132', 'symbol': 'Er_3'}, 'Eu': {'hash': 'd466d046adf21f6146ee9644049ea268', 'symbol': 'Eu'}, 'F': {'hash': '180141c33d032bfbfff30b3bea9d23dd', 'symbol': 'F'}, 'Fe': {'hash': '9530da8244e4dac17580869b4adab115', 'symbol': 'Fe'}, 'Ga': {'hash': '6e0b9d58412b1bfcd7252aff13d476c2', 'symbol': 'Ga'}, 'Gd': {'hash': '1f0d42b1e5f6769d319d3f247992aeb9', 'symbol': 'Gd'}, 'Ge': {'hash': '79e788788c31e196a460553010512d3f', 'symbol': 'Ge'}, 'H': {'hash': 'bb43c666e3d36577264afe07669e9582', 'symbol': 'H'}, 'He': {'hash': '47f9434aa3db96c85d7c4b3e4c2df09b', 'symbol': 'He'}, 'Hf': {'hash': 'b113f150cbf9c736f8244a6c25b0482e', 'symbol': 'Hf'}, 'Hg': {'hash': 'c2f15dfb5fd53396c5427635e5019160', 'symbol': 'Hg'}, 'Ho': {'hash': '661891464a27e87cf7e1324dd1893b77', 'symbol': 'Ho_3'}, 'I': {'hash': 'f4ff16a495dd361ff5824ee61b418bb0', 'symbol': 'I'}, 'In': {'hash': '7df38c0cdb4e6d9a9b93f09d690bb3ae', 'symbol': 'In'}, 'Ir': {'hash': 'dbcf7dcc6f4fb40df7b3d26904f60a66', 'symbol': 'Ir'}, 'K': {'hash': '3e84f86d37f203a4fb01de36af57e430', 'symbol': 'K_sv'}, 'Kr': {'hash': '39b9b85ae3982e6c012fb549b2840ce5', 'symbol': 'Kr'}, 'La': {'hash': '9b3ce03d18f7c0b40471a817ff91b287', 'symbol': 'La'}, 'Li': {'hash': '65e83282d1707ec078c1012afbd05be8', 'symbol': 'Li'}, 'Lu': {'hash': 'd40a90babf1224b88ffb4c3273ac3848', 'symbol': 'Lu_3'}, 'Mg': {'hash': '1771eb72adbbfa6310d66e7517e49930', 'symbol': 'Mg'}, 'Mn': {'hash': 'd082dba29b57ab59b3165e605dbf71b8', 'symbol': 'Mn'}, 'Mo': {'hash': '84e18fd84a98e3d7fa8f055952410df0', 'symbol': 'Mo_pv'}, 'N': {'hash': 'b98fd027ddebc67da4063ff2cabbc04b', 'symbol': 'N'}, 'Na': {'hash': '1a89e79f7e21d99e8cf5788979f6a987', 'symbol': 'Na'}, 'Nb': {'hash': '7bcee99a4dc3094be0f9fd7961c02966', 'symbol': 'Nb_pv'}, 'Nd': {'hash': '0c64e63070cee837c967283fffa001df', 'symbol': 'Nd'}, 'Ne': {'hash': '52064eee378b9e37a295a674f1c278f0', 'symbol': 'Ne'}, 'Ni': {'hash': '653f5772e68b2c7fd87ffd1086c0d710', 'symbol': 'Ni'}, 'Np': {'hash': '20cb30b714200c4db870550b288ac4cd', 'symbol': 'Np'}, 'O': {'hash': '7a25bc5b9a5393f46600a4939d357982', 'symbol': 'O'}, 'Os': {'hash': '35c2cb48d48a9c38c40fb82bbe70626d', 'symbol': 'Os'}, 'P': {'hash': '7dc3393307131ae67785a0cdacb61d5f', 'symbol': 'P'}, 'Pa': {'hash': 'a1fdb1089d0727f415416ec8082246ba', 'symbol': 'Pa'}, 'Pb': {'hash': '704c2c967247d7f84090d2536c91877d', 'symbol': 'Pb'}, 'Pd': {'hash': 'a395eb3aaf2fcab12fac3030a1146f61', 'symbol': 'Pd'}, 'Pm': {'hash': 'a2c9485ea86b2a7cf175077e6e5c7b3e', 'symbol': 'Pm'}, 'Pr': {'hash': '92f191499bf5346ea652bb806350ad87', 'symbol': 'Pr'}, 'Pt': {'hash': 'a604ea3c6a9cc23c739b762f625cf449', 'symbol': 'Pt'}, 'Pu': {'hash': 'f1d01e845dccc52d448679911f301a73', 'symbol': 'Pu'}, 'Rb': {'hash': 'e447c648d870b066b3514e6b800727ab', 'symbol': 'Rb_pv'}, 'Re': {'hash': '72385e193c92a8acfe17ea49004c2be1', 'symbol': 'Re'}, 'Rh': {'hash': '2c3dba3fcc6058ca1b1cfa75e45084bc', 'symbol': 'Rh'}, 'Ru': {'hash': '7925f4d4b68076d70af7cd86eef9ba8d', 'symbol': 'Ru_pv'}, 'S': {'hash': 'd368db6899d8839859bbee4811a42a88', 'symbol': 'S'}, 'Sb': {'hash': 'd82c022b02fc5344e85bd1909f9ee3e7', 'symbol': 'Sb'}, 'Sc': {'hash': 'dc386f505ad0c43385a7715b4111cb75', 'symbol': 'Sc_sv'}, 'Se': {'hash': '67a8804ede9f1112726e3d136978ef19', 'symbol': 'Se'}, 'Si': {'hash': 'b2b0ea6feb62e7cde209616683b8f7f5', 'symbol': 'Si'}, 'Sm': {'hash': 'e5e274e7cd99602ca81d146155abdf88', 'symbol': 'Sm_3'}, 'Sn': {'hash': '849b0795e148f93113a06be8fd5f5001', 'symbol': 'Sn_d'}, 'Sr': {'hash': 'ca6a5429c120a0ab705824386a76fe5b', 'symbol': 'Sr_sv'}, 'Ta': {'hash': 'd4e2cfe9338ef80da592d5bb9dc782c7', 'symbol': 'Ta'}, 'Tb': {'hash': '0790955c547003956c0fd4f080f7f508', 'symbol': 'Tb_3'}, 'Tc': {'hash': '9592642886319309a39d55c5717c6f48', 'symbol': 'Tc'}, 'Te': {'hash': '72719856e22fb1d3032df6f96d98a0f2', 'symbol': 'Te'}, 'Th': {'hash': 'aea79f322180fa6f0bfa74cb2a156dcf', 'symbol': 'Th'}, 'Ti': {'hash': 'c617e8b539c3f44a0ab6e8da2a92d318', 'symbol': 'Ti'}, 'Tl': {'hash': '2aa0d5406aaab7ebfbc761da382f1352', 'symbol': 'Tl'}, 'Tm': {'hash': '94a07cb7949b01305cb161da0cbfb492', 'symbol': 'Tm_3'}, 'U': {'hash': '72702eabbb1bc02b4167590dc848ed5d', 'symbol': 'U'}, 'V': {'hash': '7f1297a2e1d963e2a4d81b61f85e4ded', 'symbol': 'V_pv'}, 'W': {'hash': '2a33e0d5c700640535f60ac0a12177ab', 'symbol': 'W_pv'}, 'Xe': {'hash': '338472e581f58b41d37c002a5e22353b', 'symbol': 'Xe'}, 'Y': {'hash': '4ed187e77cd54f198bb88020278b143d', 'symbol': 'Y_sv'}, 'Yb': {'hash': '9f472bd422f640710f7d93e2d9ce89f4', 'symbol': 'Yb'}, 'Zn': {'hash': 'e35ee27f8483a63bb68dbc236a343af3', 'symbol': 'Zn'}, 'Zr': {'hash': 'd221d2c0bac4f8e81af2f5c42a314274', 'symbol': 'Zr'}}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                          +CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF': 1e-05, 'ENCUT': 520, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'ISYM': 0, 'LDAU': True, 'LDAUJ': {'F': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'O': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'S': {'Fe': 0, 'Mn': 0}}, 'LDAUL': {'F': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'O': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'S': {'Fe': 2, 'Mn': 2.5}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'O': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'S': {'Fe': 1.9, 'Mn': 2.5}}, 'LORBIT': '11', 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 200, 'NELMIN': 6, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'length': 25}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': {'hash': 'd6854224d20e3de6e6fd7399503791d1', 'symbol': 'Ac'}, 'Ag': {'hash': 'e8ffa02fe3f3a51338ac1ac91ae968b9', 'symbol': 'Ag'}, 'Al': {'hash': 'a6fd9a46aec185f4ad2acd0cbe4ae2fa', 'symbol': 'Al'}, 'Ar': {'hash': 'e782fc6292623b396091bf8b871c272f', 'symbol': 'Ar'}, 'As': {'hash': '8005364db225a254e52cba350bedd032', 'symbol': 'As'}, 'Au': {'hash': 'a9182d436a13194b744640ac940ab9b0', 'symbol': 'Au'}, 'B': {'hash': '18ed2875dfa6305324cec3d7d59273ae', 'symbol': 'B'}, 'Ba': {'hash': 'c0477913afb63dfae3439f3534fbf0ed', 'symbol': 'Ba_sv'}, 'Be': {'hash': 'fb974e44d56a8c62c6bbd1a1eb70c3a7', 'symbol': 'Be'}, 'Bi': {'hash': 'e29661c79d59abae3b3ba69eae24b1a5', 'symbol': 'Bi'}, 'Br': {'hash': '40f9594b4506684a69158c8975cfb9d6', 'symbol': 'Br'}, 'C': {'hash': 'c0a8167dbb174fe492a3db7f5006c0f8', 'symbol': 'C'}, 'Ca': {'hash': 'eb006721e214c04b3c13146e81b3a27d', 'symbol': 'Ca_sv'}, 'Cd': {'hash': '0506b2d0ac28d5fe2b5ced77a701aa86', 'symbol': 'Cd'}, 'Ce': {'hash': 'ff3a09f2ff91798e58eb4b9854e9be4a', 'symbol': 'Ce'}, 'Cl': {'hash': '779b9901046c78fe51c5d80224642aeb', 'symbol': 'Cl'}, 'Co': {'hash': 'b169bca4e137294d2ab3df8cbdd09083', 'symbol': 'Co'}, 'Cr': {'hash': '82c14307937c7509fda4e9bc023d243d', 'symbol': 'Cr'}, 'Cs': {'hash': '096b53a7d80cc0086976bcda50d536e5', 'symbol': 'Cs_sv'}, 'Cu': {'hash': '8ca4e43a30de0c397e51f16bbb20d678', 'symbol': 'Cu'}, 'Dy': {'hash': 'd4a05220ab0a2d4c03a76872ea724a1e', 'symbol': 'Dy_3'}, 'Er': {'hash': 'daa65a04877317f8c3c593ddeaa8a132', 'symbol': 'Er_3'}, 'Eu': {'hash': 'd466d046adf21f6146ee9644049ea268', 'symbol': 'Eu'}, 'F': {'hash': '180141c33d032bfbfff30b3bea9d23dd', 'symbol': 'F'}, 'Fe': {'hash': '9530da8244e4dac17580869b4adab115', 'symbol': 'Fe'}, 'Ga': {'hash': '6e0b9d58412b1bfcd7252aff13d476c2', 'symbol': 'Ga'}, 'Gd': {'hash': '1f0d42b1e5f6769d319d3f247992aeb9', 'symbol': 'Gd'}, 'Ge': {'hash': '79e788788c31e196a460553010512d3f', 'symbol': 'Ge'}, 'H': {'hash': 'bb43c666e3d36577264afe07669e9582', 'symbol': 'H'}, 'He': {'hash': '47f9434aa3db96c85d7c4b3e4c2df09b', 'symbol': 'He'}, 'Hf': {'hash': 'b113f150cbf9c736f8244a6c25b0482e', 'symbol': 'Hf'}, 'Hg': {'hash': 'c2f15dfb5fd53396c5427635e5019160', 'symbol': 'Hg'}, 'Ho': {'hash': '661891464a27e87cf7e1324dd1893b77', 'symbol': 'Ho_3'}, 'I': {'hash': 'f4ff16a495dd361ff5824ee61b418bb0', 'symbol': 'I'}, 'In': {'hash': '7df38c0cdb4e6d9a9b93f09d690bb3ae', 'symbol': 'In'}, 'Ir': {'hash': 'dbcf7dcc6f4fb40df7b3d26904f60a66', 'symbol': 'Ir'}, 'K': {'hash': '3e84f86d37f203a4fb01de36af57e430', 'symbol': 'K_sv'}, 'Kr': {'hash': '39b9b85ae3982e6c012fb549b2840ce5', 'symbol': 'Kr'}, 'La': {'hash': '9b3ce03d18f7c0b40471a817ff91b287', 'symbol': 'La'}, 'Li': {'hash': '65e83282d1707ec078c1012afbd05be8', 'symbol': 'Li'}, 'Lu': {'hash': 'd40a90babf1224b88ffb4c3273ac3848', 'symbol': 'Lu_3'}, 'Mg': {'hash': '1771eb72adbbfa6310d66e7517e49930', 'symbol': 'Mg'}, 'Mn': {'hash': 'd082dba29b57ab59b3165e605dbf71b8', 'symbol': 'Mn'}, 'Mo': {'hash': '84e18fd84a98e3d7fa8f055952410df0', 'symbol': 'Mo_pv'}, 'N': {'hash': 'b98fd027ddebc67da4063ff2cabbc04b', 'symbol': 'N'}, 'Na': {'hash': '1a89e79f7e21d99e8cf5788979f6a987', 'symbol': 'Na'}, 'Nb': {'hash': '7bcee99a4dc3094be0f9fd7961c02966', 'symbol': 'Nb_pv'}, 'Nd': {'hash': '0c64e63070cee837c967283fffa001df', 'symbol': 'Nd'}, 'Ne': {'hash': '52064eee378b9e37a295a674f1c278f0', 'symbol': 'Ne'}, 'Ni': {'hash': '653f5772e68b2c7fd87ffd1086c0d710', 'symbol': 'Ni'}, 'Np': {'hash': '20cb30b714200c4db870550b288ac4cd', 'symbol': 'Np'}, 'O': {'hash': '7a25bc5b9a5393f46600a4939d357982', 'symbol': 'O'}, 'Os': {'hash': '35c2cb48d48a9c38c40fb82bbe70626d', 'symbol': 'Os'}, 'P': {'hash': '7dc3393307131ae67785a0cdacb61d5f', 'symbol': 'P'}, 'Pa': {'hash': 'a1fdb1089d0727f415416ec8082246ba', 'symbol': 'Pa'}, 'Pb': {'hash': '704c2c967247d7f84090d2536c91877d', 'symbol': 'Pb'}, 'Pd': {'hash': 'a395eb3aaf2fcab12fac3030a1146f61', 'symbol': 'Pd'}, 'Pm': {'hash': 'a2c9485ea86b2a7cf175077e6e5c7b3e', 'symbol': 'Pm'}, 'Pr': {'hash': '92f191499bf5346ea652bb806350ad87', 'symbol': 'Pr'}, 'Pt': {'hash': 'a604ea3c6a9cc23c739b762f625cf449', 'symbol': 'Pt'}, 'Pu': {'hash': 'f1d01e845dccc52d448679911f301a73', 'symbol': 'Pu'}, 'Rb': {'hash': 'e447c648d870b066b3514e6b800727ab', 'symbol': 'Rb_pv'}, 'Re': {'hash': '72385e193c92a8acfe17ea49004c2be1', 'symbol': 'Re'}, 'Rh': {'hash': '2c3dba3fcc6058ca1b1cfa75e45084bc', 'symbol': 'Rh'}, 'Ru': {'hash': '7925f4d4b68076d70af7cd86eef9ba8d', 'symbol': 'Ru_pv'}, 'S': {'hash': 'd368db6899d8839859bbee4811a42a88', 'symbol': 'S'}, 'Sb': {'hash': 'd82c022b02fc5344e85bd1909f9ee3e7', 'symbol': 'Sb'}, 'Sc': {'hash': 'dc386f505ad0c43385a7715b4111cb75', 'symbol': 'Sc_sv'}, 'Se': {'hash': '67a8804ede9f1112726e3d136978ef19', 'symbol': 'Se'}, 'Si': {'hash': 'b2b0ea6feb62e7cde209616683b8f7f5', 'symbol': 'Si'}, 'Sm': {'hash': 'e5e274e7cd99602ca81d146155abdf88', 'symbol': 'Sm_3'}, 'Sn': {'hash': '849b0795e148f93113a06be8fd5f5001', 'symbol': 'Sn_d'}, 'Sr': {'hash': 'ca6a5429c120a0ab705824386a76fe5b', 'symbol': 'Sr_sv'}, 'Ta': {'hash': 'd4e2cfe9338ef80da592d5bb9dc782c7', 'symbol': 'Ta'}, 'Tb': {'hash': '0790955c547003956c0fd4f080f7f508', 'symbol': 'Tb_3'}, 'Tc': {'hash': '9592642886319309a39d55c5717c6f48', 'symbol': 'Tc'}, 'Te': {'hash': '72719856e22fb1d3032df6f96d98a0f2', 'symbol': 'Te'}, 'Th': {'hash': 'aea79f322180fa6f0bfa74cb2a156dcf', 'symbol': 'Th'}, 'Ti': {'hash': 'c617e8b539c3f44a0ab6e8da2a92d318', 'symbol': 'Ti'}, 'Tl': {'hash': '2aa0d5406aaab7ebfbc761da382f1352', 'symbol': 'Tl'}, 'Tm': {'hash': '94a07cb7949b01305cb161da0cbfb492', 'symbol': 'Tm_3'}, 'U': {'hash': '72702eabbb1bc02b4167590dc848ed5d', 'symbol': 'U'}, 'V': {'hash': '7f1297a2e1d963e2a4d81b61f85e4ded', 'symbol': 'V_pv'}, 'W': {'hash': '2a33e0d5c700640535f60ac0a12177ab', 'symbol': 'W_pv'}, 'Xe': {'hash': '338472e581f58b41d37c002a5e22353b', 'symbol': 'Xe'}, 'Y': {'hash': '4ed187e77cd54f198bb88020278b143d', 'symbol': 'Y_sv'}, 'Yb': {'hash': '9f472bd422f640710f7d93e2d9ce89f4', 'symbol': 'Yb'}, 'Zn': {'hash': 'e35ee27f8483a63bb68dbc236a343af3', 'symbol': 'Zn'}, 'Zr': {'hash': 'd221d2c0bac4f8e81af2f5c42a314274', 'symbol': 'Zr'}}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                          -class MPHSEBSSet(structure, user_incar_settings=None, added_kpoints=None, mode='Gap', reciprocal_density=None, copy_chgcar=True, kpoints_line_density=20, **kwargs)[source]
                                                          +class MPHSEBSSet(structure, user_incar_settings=None, added_kpoints=None, mode='Gap', reciprocal_density=None, copy_chgcar=True, kpoints_line_density=20, **kwargs)[source]

                                                          Bases: pymatgen.io.vasp.sets.MPHSERelaxSet

                                                          Implementation of a VaspInputSet for HSE band structure computations. Remember that HSE band structures must be self-consistent in VASP. A @@ -541,7 +541,7 @@

                                                          -classmethod from_prev_calc(prev_calc_dir, **kwargs)[source]
                                                          +classmethod from_prev_calc(prev_calc_dir, **kwargs)[source]

                                                          Generate a set of Vasp input files for HSE calculations from a directory of previous Vasp run.

                                                          @@ -558,7 +558,7 @@
                                                          -property kpoints: pymatgen.io.vasp.inputs.Kpoints[source]
                                                          +property kpoints: pymatgen.io.vasp.inputs.Kpoints[source]

                                                          Kpoints

                                                          Type
                                                          @@ -569,7 +569,7 @@
                                                          -override_from_prev_calc(prev_calc_dir='.')[source]
                                                          +override_from_prev_calc(prev_calc_dir='.')[source]

                                                          Update the input set to include settings from a previous calculation.

                                                          Parameters
                                                          @@ -586,7 +586,7 @@
                                                          -class MPHSERelaxSet(structure, **kwargs)[source]
                                                          +class MPHSERelaxSet(structure, **kwargs)[source]

                                                          Bases: pymatgen.io.vasp.sets.DictSet

                                                          Same as the MPRelaxSet, but with HSE parameters.

                                                          @@ -599,14 +599,14 @@
                                                          -CONFIG = {'INCAR': {'ALGO': 'All', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'HFSCREEN': 0.2, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': 0, 'ISPIN': 2, 'LHFCALC': True, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'PRECFOCK': 'Fast', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 50}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE_52'}[source]
                                                          +CONFIG = {'INCAR': {'ALGO': 'All', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'HFSCREEN': 0.2, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': 0, 'ISPIN': 2, 'LHFCALC': True, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'PRECFOCK': 'Fast', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 50}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE_52'}[source]
                                                          -class MPMDSet(structure, start_temp, end_temp, nsteps, spin_polarized=False, **kwargs)[source]
                                                          +class MPMDSet(structure, start_temp, end_temp, nsteps, spin_polarized=False, **kwargs)[source]

                                                          Bases: pymatgen.io.vasp.sets.MPRelaxSet

                                                          This a modified version of the old MITMDSet pre 2018/03/12.

                                                          This set serves as the basis for the amorphous skyline paper.

                                                          @@ -634,7 +634,7 @@
                                                          -property kpoints[source]
                                                          +property kpoints[source]

                                                          Kpoints

                                                          Type
                                                          @@ -647,7 +647,7 @@
                                                          -class MPMetalRelaxSet(structure, **kwargs)[source]
                                                          +class MPMetalRelaxSet(structure, **kwargs)[source]

                                                          Bases: pymatgen.io.vasp.sets.MPRelaxSet

                                                          Implementation of VaspInputSet utilizing parameters in the public Materials Project, but with tuning for metals. Key things are a denser @@ -662,14 +662,14 @@

                                                          -CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                          +CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                          -class MPNMRSet(structure, mode='cs', isotopes=None, prev_incar=None, reciprocal_density=100, **kwargs)[source]
                                                          +class MPNMRSet(structure, mode='cs', isotopes=None, prev_incar=None, reciprocal_density=100, **kwargs)[source]

                                                          Bases: pymatgen.io.vasp.sets.MPStaticSet

                                                          Init a MPNMRSet.

                                                          @@ -689,7 +689,7 @@
                                                          -property incar[source]
                                                          +property incar[source]

                                                          Incar

                                                          Type
                                                          @@ -702,7 +702,7 @@
                                                          -class MPNonSCFSet(structure, prev_incar=None, mode='line', nedos=2001, dedos=0.005, reciprocal_density=100, sym_prec=0.1, kpoints_line_density=20, optics=False, copy_chgcar=True, nbands_factor=1.2, small_gap_multiply=None, **kwargs)[source]
                                                          +class MPNonSCFSet(structure, prev_incar=None, mode='line', nedos=2001, dedos=0.005, reciprocal_density=100, sym_prec=0.1, kpoints_line_density=20, optics=False, copy_chgcar=True, nbands_factor=1.2, small_gap_multiply=None, **kwargs)[source]

                                                          Bases: pymatgen.io.vasp.sets.MPRelaxSet

                                                          Init a MPNonSCFSet. Typically, you would use the classmethod from_prev_calc to initialize from a previous SCF run.

                                                          @@ -735,7 +735,7 @@
                                                          -classmethod from_prev_calc(prev_calc_dir, **kwargs)[source]
                                                          +classmethod from_prev_calc(prev_calc_dir, **kwargs)[source]

                                                          Generate a set of Vasp input files for NonSCF calculations from a directory of previous static Vasp run.

                                                          @@ -753,7 +753,7 @@
                                                          -property incar: pymatgen.io.vasp.inputs.Incar[source]
                                                          +property incar: pymatgen.io.vasp.inputs.Incar[source]

                                                          Incar

                                                          Type
                                                          @@ -764,7 +764,7 @@
                                                          -property kpoints: Kpoints | None[source]
                                                          +property kpoints: Kpoints | None[source]

                                                          Kpoints

                                                          Type
                                                          @@ -775,7 +775,7 @@
                                                          -override_from_prev_calc(prev_calc_dir='.')[source]
                                                          +override_from_prev_calc(prev_calc_dir='.')[source]

                                                          Update the input set to include settings from a previous calculation.

                                                          Parameters
                                                          @@ -792,7 +792,7 @@
                                                          -class MPRelaxSet(structure, **kwargs)[source]
                                                          +class MPRelaxSet(structure, **kwargs)[source]

                                                          Bases: pymatgen.io.vasp.sets.DictSet

                                                          Implementation of VaspInputSet utilizing parameters in the public Materials Project. Typically, the pseudopotentials chosen contain more @@ -809,14 +809,14 @@

                                                          -CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                          +CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
                                                          -class MPSOCSet(structure, saxis=(0, 0, 1), copy_chgcar=True, nbands_factor=1.2, reciprocal_density=100, small_gap_multiply=None, magmom=None, **kwargs)[source]
                                                          +class MPSOCSet(structure, saxis=(0, 0, 1), copy_chgcar=True, nbands_factor=1.2, reciprocal_density=100, small_gap_multiply=None, magmom=None, **kwargs)[source]

                                                          Bases: pymatgen.io.vasp.sets.MPStaticSet

                                                          An input set for running spin-orbit coupling (SOC) calculations.

                                                          @@ -840,7 +840,7 @@
                                                          -classmethod from_prev_calc(prev_calc_dir, **kwargs)[source]
                                                          +classmethod from_prev_calc(prev_calc_dir, **kwargs)[source]

                                                          Generate a set of Vasp input files for SOC calculations from a directory of previous static Vasp run. SOC calc requires all 3 components for MAGMOM for each atom in the structure.

                                                          @@ -859,7 +859,7 @@
                                                          -property incar: pymatgen.io.vasp.inputs.Incar[source]
                                                          +property incar: pymatgen.io.vasp.inputs.Incar[source]

                                                          Incar

                                                          Type
                                                          @@ -870,7 +870,7 @@
                                                          -override_from_prev_calc(prev_calc_dir='.')[source]
                                                          +override_from_prev_calc(prev_calc_dir='.')[source]

                                                          Update the input set to include settings from a previous calculation.

                                                          Parameters
                                                          @@ -887,7 +887,7 @@
                                                          -class MPScanRelaxSet(structure, bandgap=0, **kwargs)[source]
                                                          +class MPScanRelaxSet(structure, bandgap=0, **kwargs)[source]

                                                          Bases: pymatgen.io.vasp.sets.DictSet

                                                          Class for writing a relaxation input set using the accurate and numerically efficient r2SCAN variant of the Strongly Constrained and Appropriately Normed @@ -942,14 +942,14 @@ Phys. Rev. B. 93 (2016) 1–10. doi:10.1103/PhysRevB.93.155109.

                                                          -CONFIG = {'INCAR': {'ALGO': 'ALL', 'EDIFF': 1e-05, 'EDIFFG': -0.02, 'ENAUG': 1360, 'ENCUT': 680, 'IBRION': 2, 'ISIF': 3, 'ISPIN': 2, 'LAECHG': True, 'LASPH': True, 'LCHARG': True, 'LELF': True, 'LMIXTAU': True, 'LORBIT': 11, 'LREAL': 'Auto', 'LVTOT': True, 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'METAGGA': 'R2SCAN', 'NELM': 200, 'NSW': 99, 'PREC': 'Accurate'}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Am': 'Am', 'Ar': 'Ar', 'As': 'As', 'At': 'At', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cf': 'Cf', 'Cl': 'Cl', 'Cm': 'Cm', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Fr': 'Fr_sv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Po': 'Po_d', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Ra': 'Ra_sv', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Rn': 'Rn', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_sv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE_54'}[source]
                                                          +CONFIG = {'INCAR': {'ALGO': 'ALL', 'EDIFF': 1e-05, 'EDIFFG': -0.02, 'ENAUG': 1360, 'ENCUT': 680, 'IBRION': 2, 'ISIF': 3, 'ISPIN': 2, 'LAECHG': True, 'LASPH': True, 'LCHARG': True, 'LELF': True, 'LMIXTAU': True, 'LORBIT': 11, 'LREAL': 'Auto', 'LVTOT': True, 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'METAGGA': 'R2SCAN', 'NELM': 200, 'NSW': 99, 'PREC': 'Accurate'}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Am': 'Am', 'Ar': 'Ar', 'As': 'As', 'At': 'At', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cf': 'Cf', 'Cl': 'Cl', 'Cm': 'Cm', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Fr': 'Fr_sv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Po': 'Po_d', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Ra': 'Ra_sv', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Rn': 'Rn', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_sv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE_54'}[source]
                                                          -class MPScanStaticSet(structure, bandgap=0, prev_incar=None, lepsilon=False, lcalcpol=False, **kwargs)[source]
                                                          +class MPScanStaticSet(structure, bandgap=0, prev_incar=None, lepsilon=False, lcalcpol=False, **kwargs)[source]

                                                          Bases: pymatgen.io.vasp.sets.MPScanRelaxSet

                                                          Creates input files for a static calculation using the accurate and numerically efficient r2SCAN variant of the Strongly Constrainted and Appropriately Normed @@ -971,7 +971,7 @@

                                                          -classmethod from_prev_calc(prev_calc_dir, **kwargs)[source]
                                                          +classmethod from_prev_calc(prev_calc_dir, **kwargs)[source]

                                                          Generate a set of Vasp input files for static calculations from a directory of previous Vasp run.

                                                          @@ -988,7 +988,7 @@
                                                          -property incar[source]
                                                          +property incar[source]

                                                          Incar

                                                          Type
                                                          @@ -999,7 +999,7 @@
                                                          -override_from_prev_calc(prev_calc_dir='.')[source]
                                                          +override_from_prev_calc(prev_calc_dir='.')[source]

                                                          Update the input set to include settings from a previous calculation.

                                                          Parameters
                                                          @@ -1016,7 +1016,7 @@
                                                          -class MPStaticSet(structure, prev_incar=None, prev_kpoints=None, lepsilon=False, lcalcpol=False, reciprocal_density=100, small_gap_multiply=None, **kwargs)[source]
                                                          +class MPStaticSet(structure, prev_incar=None, prev_kpoints=None, lepsilon=False, lcalcpol=False, reciprocal_density=100, small_gap_multiply=None, **kwargs)[source]

                                                          Bases: pymatgen.io.vasp.sets.MPRelaxSet

                                                          Creates input files for a static calculation.

                                                          @@ -1041,7 +1041,7 @@
                                                          -classmethod from_prev_calc(prev_calc_dir, **kwargs)[source]
                                                          +classmethod from_prev_calc(prev_calc_dir, **kwargs)[source]

                                                          Generate a set of Vasp input files for static calculations from a directory of previous Vasp run.

                                                          @@ -1059,7 +1059,7 @@
                                                          -property incar[source]
                                                          +property incar[source]

                                                          Incar

                                                          Type
                                                          @@ -1070,7 +1070,7 @@
                                                          -property kpoints: Kpoints | None[source]
                                                          +property kpoints: Kpoints | None[source]

                                                          Kpoints

                                                          Type
                                                          @@ -1081,7 +1081,7 @@
                                                          -override_from_prev_calc(prev_calc_dir='.')[source]
                                                          +override_from_prev_calc(prev_calc_dir='.')[source]

                                                          Update the input set to include settings from a previous calculation.

                                                          Parameters
                                                          @@ -1098,7 +1098,7 @@
                                                          -class MVLElasticSet(structure, potim=0.015, **kwargs)[source]
                                                          +class MVLElasticSet(structure, potim=0.015, **kwargs)[source]

                                                          Bases: pymatgen.io.vasp.sets.MPRelaxSet

                                                          MVL denotes VASP input sets that are implemented by the Materials Virtual Lab (http://www.materialsvirtuallab.org) for various research.

                                                          @@ -1127,7 +1127,7 @@
                                                          -class MVLGBSet(structure, k_product=40, slab_mode=False, is_metal=True, **kwargs)[source]
                                                          +class MVLGBSet(structure, k_product=40, slab_mode=False, is_metal=True, **kwargs)[source]

                                                          Bases: pymatgen.io.vasp.sets.MPRelaxSet

                                                          Class for writing a vasp input files for grain boundary calculations, slab or bulk.

                                                          @@ -1151,7 +1151,7 @@
                                                          -property incar[source]
                                                          +property incar[source]

                                                          Incar

                                                          Type
                                                          @@ -1162,7 +1162,7 @@
                                                          -property kpoints[source]
                                                          +property kpoints[source]

                                                          k_product, default to 40, is kpoint number * length for a & b directions, also for c direction in bulk calculations Automatic mesh & Gamma is the default setting.

                                                          @@ -1172,7 +1172,7 @@
                                                          -class MVLGWSet(structure, prev_incar=None, nbands=None, reciprocal_density=100, mode='STATIC', copy_wavecar=True, nbands_factor=5, ncores=16, **kwargs)[source]
                                                          +class MVLGWSet(structure, prev_incar=None, nbands=None, reciprocal_density=100, mode='STATIC', copy_wavecar=True, nbands_factor=5, ncores=16, **kwargs)[source]

                                                          Bases: pymatgen.io.vasp.sets.DictSet

                                                          MVL denotes VASP input sets that are implemented by the Materials Virtual Lab (http://www.materialsvirtuallab.org) for various research. This is a @@ -1211,17 +1211,17 @@

                                                          -CONFIG = {'INCAR': {'ALGO': 'Normal', 'EDIFF': 1e-08, 'IBRION': -1, 'ICHARG': 1, 'ISMEAR': 0, 'ISPIN': 2, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': True, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'PREC': 'Accurate', 'SIGMA': 0.01}, 'KPOINTS': {'reciprocal_density': 100}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag_sv_GW', 'Al': 'Al_GW', 'Ar': 'Ar_GW', 'As': 'As_GW', 'At': 'At_d_GW', 'Au': 'Au_sv_GW', 'B': 'B_GW', 'Ba': 'Ba_sv_GW', 'Be': 'Be_sv_GW', 'Bi': 'Bi_d_GW', 'Br': 'Br_GW', 'C': 'C_GW', 'Ca': 'Ca_sv_GW', 'Cd': 'Cd_sv_GW', 'Ce': 'Ce_GW', 'Cl': 'Cl_GW', 'Co': 'Co_sv_GW', 'Cr': 'Cr_sv_GW', 'Cs': 'Cs_sv_GW', 'Cu': 'Cu_sv_GW', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F_GW', 'Fe': 'Fe_sv_GW', 'Ga': 'Ga_d_GW', 'Gd': 'Gd', 'Ge': 'Ge_d_GW', 'H': 'H_GW', 'He': 'He_GW', 'Hf': 'Hf_sv_GW', 'Hg': 'Hg_sv_GW', 'Ho': 'Ho_3', 'I': 'I_GW', 'In': 'In_d_GW', 'Ir': 'Ir_sv_GW', 'K': 'K_sv_GW', 'Kr': 'Kr_GW', 'La': 'La_GW', 'Li': 'Li_sv_GW', 'Lu': 'Lu_3', 'Mg': 'Mg_sv_GW', 'Mn': 'Mn_sv_GW', 'Mo': 'Mo_sv_GW', 'N': 'N_GW', 'Na': 'Na_sv_GW', 'Nb': 'Nb_sv_GW', 'Nd': 'Nd_3', 'Ne': 'Ne_GW', 'Ni': 'Ni_sv_GW', 'Np': 'Np', 'O': 'O_GW', 'Os': 'Os_sv_GW', 'P': 'P_GW', 'Pa': 'Pa', 'Pb': 'Pb_d_GW', 'Pd': 'Pd_sv_GW', 'Pm': 'Pm_3', 'Po': 'Po_d_GW', 'Pr': 'Pr_3', 'Pt': 'Pt_sv_GW', 'Pu': 'Pu', 'Rb': 'Rb_sv_GW', 'Re': 'Re_sv_GW', 'Rh': 'Rh_sv_GW', 'Rn': 'Rn_d_GW', 'Ru': 'Ru_sv_GW', 'S': 'S_GW', 'Sb': 'Sb_d_GW', 'Sc': 'Sc_sv_GW', 'Se': 'Se_GW', 'Si': 'Si_GW', 'Sm': 'Sm_3', 'Sn': 'Sn_d_GW', 'Sr': 'Sr_sv_GW', 'Ta': 'Ta_sv_GW', 'Tb': 'Tb_3', 'Tc': 'Tc_sv_GW', 'Te': 'Te_GW', 'Th': 'Th', 'Ti': 'Ti_sv_GW', 'Tl': 'Tl_d_GW', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_sv_GW', 'W': 'W_sv_GW', 'Xe': 'Xe_GW', 'Y': 'Y_sv_GW', 'Yb': 'Yb_2', 'Zn': 'Zn_sv_GW', 'Zr': 'Zr_sv_GW'}, 'POTCAR_FUNCTIONAL': 'PBE_54'}[source]
                                                          +CONFIG = {'INCAR': {'ALGO': 'Normal', 'EDIFF': 1e-08, 'IBRION': -1, 'ICHARG': 1, 'ISMEAR': 0, 'ISPIN': 2, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': True, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'PREC': 'Accurate', 'SIGMA': 0.01}, 'KPOINTS': {'reciprocal_density': 100}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag_sv_GW', 'Al': 'Al_GW', 'Ar': 'Ar_GW', 'As': 'As_GW', 'At': 'At_d_GW', 'Au': 'Au_sv_GW', 'B': 'B_GW', 'Ba': 'Ba_sv_GW', 'Be': 'Be_sv_GW', 'Bi': 'Bi_d_GW', 'Br': 'Br_GW', 'C': 'C_GW', 'Ca': 'Ca_sv_GW', 'Cd': 'Cd_sv_GW', 'Ce': 'Ce_GW', 'Cl': 'Cl_GW', 'Co': 'Co_sv_GW', 'Cr': 'Cr_sv_GW', 'Cs': 'Cs_sv_GW', 'Cu': 'Cu_sv_GW', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F_GW', 'Fe': 'Fe_sv_GW', 'Ga': 'Ga_d_GW', 'Gd': 'Gd', 'Ge': 'Ge_d_GW', 'H': 'H_GW', 'He': 'He_GW', 'Hf': 'Hf_sv_GW', 'Hg': 'Hg_sv_GW', 'Ho': 'Ho_3', 'I': 'I_GW', 'In': 'In_d_GW', 'Ir': 'Ir_sv_GW', 'K': 'K_sv_GW', 'Kr': 'Kr_GW', 'La': 'La_GW', 'Li': 'Li_sv_GW', 'Lu': 'Lu_3', 'Mg': 'Mg_sv_GW', 'Mn': 'Mn_sv_GW', 'Mo': 'Mo_sv_GW', 'N': 'N_GW', 'Na': 'Na_sv_GW', 'Nb': 'Nb_sv_GW', 'Nd': 'Nd_3', 'Ne': 'Ne_GW', 'Ni': 'Ni_sv_GW', 'Np': 'Np', 'O': 'O_GW', 'Os': 'Os_sv_GW', 'P': 'P_GW', 'Pa': 'Pa', 'Pb': 'Pb_d_GW', 'Pd': 'Pd_sv_GW', 'Pm': 'Pm_3', 'Po': 'Po_d_GW', 'Pr': 'Pr_3', 'Pt': 'Pt_sv_GW', 'Pu': 'Pu', 'Rb': 'Rb_sv_GW', 'Re': 'Re_sv_GW', 'Rh': 'Rh_sv_GW', 'Rn': 'Rn_d_GW', 'Ru': 'Ru_sv_GW', 'S': 'S_GW', 'Sb': 'Sb_d_GW', 'Sc': 'Sc_sv_GW', 'Se': 'Se_GW', 'Si': 'Si_GW', 'Sm': 'Sm_3', 'Sn': 'Sn_d_GW', 'Sr': 'Sr_sv_GW', 'Ta': 'Ta_sv_GW', 'Tb': 'Tb_3', 'Tc': 'Tc_sv_GW', 'Te': 'Te_GW', 'Th': 'Th', 'Ti': 'Ti_sv_GW', 'Tl': 'Tl_d_GW', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_sv_GW', 'W': 'W_sv_GW', 'Xe': 'Xe_GW', 'Y': 'Y_sv_GW', 'Yb': 'Yb_2', 'Zn': 'Zn_sv_GW', 'Zr': 'Zr_sv_GW'}, 'POTCAR_FUNCTIONAL': 'PBE_54'}[source]
                                                          -SUPPORTED_MODES = ('DIAG', 'GW', 'STATIC', 'BSE')[source]
                                                          +SUPPORTED_MODES = ('DIAG', 'GW', 'STATIC', 'BSE')[source]
                                                          -classmethod from_prev_calc(prev_calc_dir, mode='DIAG', **kwargs)[source]
                                                          +classmethod from_prev_calc(prev_calc_dir, mode='DIAG', **kwargs)[source]

                                                          Generate a set of Vasp input files for GW or BSE calculations from a directory of previous Exact Diag Vasp run.

                                                          @@ -1241,7 +1241,7 @@
                                                          -property incar[source]
                                                          +property incar[source]

                                                          Incar

                                                          Type
                                                          @@ -1252,14 +1252,14 @@
                                                          -property kpoints[source]
                                                          +property kpoints[source]

                                                          Generate gamma center k-points mesh grid for GW calc, which is requested by GW calculation.

                                                          -override_from_prev_calc(prev_calc_dir='.')[source]
                                                          +override_from_prev_calc(prev_calc_dir='.')[source]

                                                          Update the input set to include settings from a previous calculation.

                                                          Parameters
                                                          @@ -1276,7 +1276,7 @@
                                                          -class MVLNPTMDSet(structure, start_temp, end_temp, nsteps, time_step=2, spin_polarized=False, **kwargs)[source]
                                                          +class MVLNPTMDSet(structure, start_temp, end_temp, nsteps, time_step=2, spin_polarized=False, **kwargs)[source]

                                                          Bases: pymatgen.io.vasp.sets.MITMDSet

                                                          Class for writing a vasp md run in NPT ensemble.

                                                          Notes

                                                          @@ -1301,7 +1301,7 @@
                                                          -class MVLRelax52Set(structure, **kwargs)[source]
                                                          +class MVLRelax52Set(structure, **kwargs)[source]

                                                          Bases: pymatgen.io.vasp.sets.DictSet

                                                          Implementation of VaspInputSet utilizing the public Materials Project parameters for INCAR & KPOINTS and VASP’s recommended PAW potentials for @@ -1334,14 +1334,14 @@

                                                          -CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Am': 'Am', 'Ar': 'Ar', 'As': 'As', 'At': 'At_d', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be', 'Bi': 'Bi_d', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Cm': 'Cm', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu_2', 'F': 'F', 'Fe': 'Fe', 'Fr': 'Fr_sv', 'Ga': 'Ga_d', 'Gd': 'Gd_3', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg', 'Mn': 'Mn_pv', 'Mo': 'Mo_sv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_sv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni', 'Np': 'Np', 'O': 'O', 'Os': 'Os', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Po': 'Po_d', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Ra': 'Ra_sv', 'Rb': 'Rb_sv', 'Re': 'Re', 'Rh': 'Rh_pv', 'Rn': 'Rn', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_sv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_sv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE_52'}[source]
                                                          +CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Am': 'Am', 'Ar': 'Ar', 'As': 'As', 'At': 'At_d', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be', 'Bi': 'Bi_d', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Cm': 'Cm', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu_2', 'F': 'F', 'Fe': 'Fe', 'Fr': 'Fr_sv', 'Ga': 'Ga_d', 'Gd': 'Gd_3', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg', 'Mn': 'Mn_pv', 'Mo': 'Mo_sv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_sv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni', 'Np': 'Np', 'O': 'O', 'Os': 'Os', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Po': 'Po_d', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Ra': 'Ra_sv', 'Rb': 'Rb_sv', 'Re': 'Re', 'Rh': 'Rh_pv', 'Rn': 'Rn', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_sv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_sv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE_52'}[source]
                                                          -class MVLScanRelaxSet(structure, **kwargs)[source]
                                                          +class MVLScanRelaxSet(structure, **kwargs)[source]

                                                          Bases: pymatgen.io.vasp.sets.MPRelaxSet

                                                          Class for writing a relax input set using Strongly Constrained and Appropriately Normed (SCAN) semilocal density functional.

                                                          @@ -1374,7 +1374,7 @@
                                                          -class MVLSlabSet(structure, k_product=50, bulk=False, auto_dipole=False, set_mix=True, sort_structure=True, **kwargs)[source]
                                                          +class MVLSlabSet(structure, k_product=50, bulk=False, auto_dipole=False, set_mix=True, sort_structure=True, **kwargs)[source]

                                                          Bases: pymatgen.io.vasp.sets.MPRelaxSet

                                                          Class for writing a set of slab vasp runs, including both slabs (along the c direction) and orient unit cells (bulk), @@ -1395,7 +1395,7 @@

                                                          -as_dict(verbosity=2)[source]
                                                          +as_dict(verbosity=2)[source]
                                                          Parameters

                                                          verbosity – Verbosity of dict. E.g., whether to include Structure.

                                                          @@ -1408,7 +1408,7 @@
                                                          -property kpoints[source]
                                                          +property kpoints[source]
                                                          k_product, default to 50, is kpoint number * length for a & b

                                                          directions, also for c direction in bulk calculations

                                                          @@ -1420,14 +1420,14 @@
                                                          -class VaspInputSet[source]
                                                          +class VaspInputSet[source]

                                                          Bases: monty.json.MSONable

                                                          Base class representing a set of Vasp input parameters with a structure supplied as init parameters. Typically, you should not inherit from this class. Start from DictSet or MPRelaxSet or MITRelaxSet.

                                                          -as_dict(verbosity=2)[source]
                                                          +as_dict(verbosity=2)[source]
                                                          Parameters
                                                            @@ -1443,7 +1443,7 @@
                                                            -get_vasp_input() → pymatgen.io.vasp.inputs.VaspInput[source]
                                                            +get_vasp_input() → pymatgen.io.vasp.inputs.VaspInput[source]
                                                            Returns

                                                            VaspInput

                                                            @@ -1453,37 +1453,37 @@
                                                            -abstract property incar[source]
                                                            +abstract property incar[source]

                                                            Incar object

                                                            -abstract property kpoints[source]
                                                            +abstract property kpoints[source]

                                                            Kpoints object

                                                            -abstract property poscar[source]
                                                            +abstract property poscar[source]

                                                            Poscar object

                                                            -property potcar[source]
                                                            +property potcar[source]

                                                            Potcar object.

                                                            -property potcar_symbols[source]
                                                            +property potcar_symbols[source]

                                                            List of POTCAR symbols.

                                                            -write_input(output_dir, make_dir_if_not_present=True, include_cif=False, potcar_spec=False, zip_output=False)[source]
                                                            +write_input(output_dir, make_dir_if_not_present=True, include_cif=False, potcar_spec=False, zip_output=False)[source]

                                                            Writes a set of VASP input to a directory.

                                                            Parameters
                                                            @@ -1510,7 +1510,7 @@
                                                            -batch_write_input(structures, vasp_input_set=<class 'pymatgen.io.vasp.sets.MPRelaxSet'>, output_dir='.', make_dir_if_not_present=True, subfolder=None, sanitize=False, include_cif=False, potcar_spec=False, zip_output=False, **kwargs)[source]
                                                            +batch_write_input(structures, vasp_input_set=<class 'pymatgen.io.vasp.sets.MPRelaxSet'>, output_dir='.', make_dir_if_not_present=True, subfolder=None, sanitize=False, include_cif=False, potcar_spec=False, zip_output=False, **kwargs)[source]

                                                            Batch write vasp input for a sequence of structures to output_dir, following the format output_dir/{group}/{formula}_{number}.

                                                            @@ -1548,7 +1548,7 @@
                                                            -get_structure_from_prev_run(vasprun, outcar=None)[source]
                                                            +get_structure_from_prev_run(vasprun, outcar=None)[source]

                                                            Process structure from previous run.

                                                            Parameters
                                                            @@ -1568,7 +1568,7 @@
                                                            -get_valid_magmom_struct(structure, inplace=True, spin_mode='auto')[source]
                                                            +get_valid_magmom_struct(structure, inplace=True, spin_mode='auto')[source]

                                                            Make sure that the structure has valid magmoms based on the kind of calculation Fill in missing Magmom values

                                                            @@ -1595,7 +1595,7 @@
                                                            -get_vasprun_outcar(path, parse_dos=True, parse_eigen=True)[source]
                                                            +get_vasprun_outcar(path, parse_dos=True, parse_eigen=True)[source]
                                                            Parameters
                                                              @@ -1612,7 +1612,7 @@
                                                              -next_num_with_prime_factors(n: int, max_prime_factor: int, must_inc_2: bool = True) → int[source]
                                                              +next_num_with_prime_factors(n: int, max_prime_factor: int, must_inc_2: bool = True) → int[source]

                                                              Return the next number greater than or equal to n that only has the desired prime factors

                                                              Parameters
                                                              @@ -1633,13 +1633,13 @@
                                                              -primes_less_than(max_val: int) → list[int][source]
                                                              +primes_less_than(max_val: int) → list[int][source]

                                                              Get the primes less than or equal to the max value

                                                              -standardize_structure(structure, sym_prec=0.1, international_monoclinic=True)[source]
                                                              +standardize_structure(structure, sym_prec=0.1, international_monoclinic=True)[source]

                                                              Get the symmetrically standardized structure.

                                                              Parameters
                                                              diff --git a/docs/pymatgen.io.wannier90.html b/docs/pymatgen.io.wannier90.html index 5044e73e576..25436c443ae 100644 --- a/docs/pymatgen.io.wannier90.html +++ b/docs/pymatgen.io.wannier90.html @@ -4,7 +4,7 @@ - pymatgen.io.wannier90 module — pymatgen 2022.5.18 documentation + pymatgen.io.wannier90 module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                              - 2022.5.18 + 2022.5.18.1
                                                              @@ -118,18 +118,18 @@

                                                              Modules for working with wannier90 input and output.

                                                              -class Unk(ik: int, data: numpy.ndarray)[source]
                                                              +class Unk(ik: int, data: numpy.ndarray)[source]

                                                              Bases: object

                                                              Object representing the data in a UNK file.

                                                              -ik[source]
                                                              +ik[source]

                                                              int index of kpoint for this file

                                                              -data[source]
                                                              +data[source]

                                                              numpy.ndarray that contains the wavefunction data for in the UNK file. The shape should be (nbnd, ngx, ngy, ngz) for regular calculations and (nbnd, 2, ngx, ngy, ngz) for noncollinear calculations.

                                                              @@ -137,19 +137,19 @@
                                                              -is_noncollinear[source]
                                                              +is_noncollinear[source]

                                                              bool that specifies if data is from a noncollinear calculation

                                                              -nbnd[source]
                                                              +nbnd[source]

                                                              int number of bands in data

                                                              -ng[source]
                                                              +ng[source]

                                                              sequence of three integers that correspond to the grid size of the given data. The definition is ng = (ngx, ngy, ngz).

                                                              @@ -166,7 +166,7 @@
                                                              -property data: numpy.ndarray[source]
                                                              +property data: numpy.ndarray[source]

                                                              contains the wavefunction data for in the UNK file. The shape should be (nbnd, ngx, ngy, ngz) for regular calculations and (nbnd, 2, ngx, ngy, ngz) for noncollinear calculations.

                                                              @@ -179,7 +179,7 @@
                                                              -static from_file(filename: str) → object[source]
                                                              +static from_file(filename: str) → object[source]

                                                              Reads the UNK data from file.

                                                              Parameters
                                                              @@ -193,27 +193,27 @@
                                                              -ik: int[source]
                                                              +ik: int[source]
                                                              -is_noncollinear: bool[source]
                                                              +is_noncollinear: bool[source]
                                                              -nbnd: int[source]
                                                              +nbnd: int[source]
                                                              -ng: Sequence[int][source]
                                                              +ng: Sequence[int][source]
                                                              -write_file(filename: str) → None[source]
                                                              +write_file(filename: str) → None[source]

                                                              Write the UNK file.

                                                              Parameters
                                                              diff --git a/docs/pymatgen.io.xcrysden.html b/docs/pymatgen.io.xcrysden.html index f02547d530d..8a84e27e941 100644 --- a/docs/pymatgen.io.xcrysden.html +++ b/docs/pymatgen.io.xcrysden.html @@ -4,7 +4,7 @@ - pymatgen.io.xcrysden module — pymatgen 2022.5.18 documentation + pymatgen.io.xcrysden module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                              - 2022.5.18 + 2022.5.18.1
                                                              @@ -118,7 +118,7 @@

                                                              Support for reading XCrysDen files.

                                                              -class XSF(structure)[source]
                                                              +class XSF(structure)[source]

                                                              Bases: object

                                                              Class for parsing XCrysden files.

                                                              @@ -128,7 +128,7 @@
                                                              -classmethod from_string(input_string, cls_=None)[source]
                                                              +classmethod from_string(input_string, cls_=None)[source]

                                                              Initialize a Structure object from a string with data in XSF format.

                                                              Parameters
                                                              @@ -143,7 +143,7 @@
                                                              -to_string(atom_symbol=True)[source]
                                                              +to_string(atom_symbol=True)[source]

                                                              Returns a string with the structure in XSF format See http://www.xcrysden.org/doc/XSF.html

                                                              diff --git a/docs/pymatgen.io.xr.html b/docs/pymatgen.io.xr.html index 402931e3be0..802722b0708 100644 --- a/docs/pymatgen.io.xr.html +++ b/docs/pymatgen.io.xr.html @@ -4,7 +4,7 @@ - pymatgen.io.xr module — pymatgen 2022.5.18 documentation + pymatgen.io.xr module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                              - 2022.5.18 + 2022.5.18.1
                                                              @@ -123,7 +123,7 @@ that employed core-shell models.

                                                              -class Xr(structure)[source]
                                                              +class Xr(structure)[source]

                                                              Bases: object

                                                              Basic object for working with xr files.

                                                              @@ -134,7 +134,7 @@
                                                              -static from_file(filename, use_cores=True, thresh=0.0001)[source]
                                                              +static from_file(filename, use_cores=True, thresh=0.0001)[source]

                                                              Reads an xr-formatted file to create an Xr object.

                                                              Parameters
                                                              @@ -163,7 +163,7 @@
                                                              -static from_string(string, use_cores=True, thresh=0.0001)[source]
                                                              +static from_string(string, use_cores=True, thresh=0.0001)[source]

                                                              Creates an Xr object from a string representation.

                                                              Parameters
                                                              @@ -192,7 +192,7 @@
                                                              -write_file(filename)[source]
                                                              +write_file(filename)[source]

                                                              Write out an xr file.

                                                              Parameters
                                                              diff --git a/docs/pymatgen.io.xtb.html b/docs/pymatgen.io.xtb.html index 5d28437e82f..49177294def 100644 --- a/docs/pymatgen.io.xtb.html +++ b/docs/pymatgen.io.xtb.html @@ -4,7 +4,7 @@ - pymatgen.io.xtb package — pymatgen 2022.5.18 documentation + pymatgen.io.xtb package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                              - 2022.5.18 + 2022.5.18.1
                                                              diff --git a/docs/pymatgen.io.xtb.inputs.html b/docs/pymatgen.io.xtb.inputs.html index a1eadf3c359..1f0948c5603 100644 --- a/docs/pymatgen.io.xtb.inputs.html +++ b/docs/pymatgen.io.xtb.inputs.html @@ -4,7 +4,7 @@ - pymatgen.io.xtb.inputs module — pymatgen 2022.5.18 documentation + pymatgen.io.xtb.inputs module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                              - 2022.5.18 + 2022.5.18.1
                                                              @@ -119,7 +119,7 @@

                                                              Classes for writing XTB input files

                                                              -class CRESTInput(molecule: Molecule, working_dir: str = '.', coords_filename: str | None = 'crest_in.xyz', constraints: dict[str, list[int] | float] | None = None)[source]
                                                              +class CRESTInput(molecule: Molecule, working_dir: str = '.', coords_filename: str | None = 'crest_in.xyz', constraints: dict[str, list[int] | float] | None = None)[source]

                                                              Bases: monty.json.MSONable

                                                              An object representing CREST input files. Because CREST is controlled through command line flags and external @@ -139,7 +139,7 @@

                                                              -static constrains_template(molecule, reference_fnm, constraints) → str[source]
                                                              +static constrains_template(molecule, reference_fnm, constraints) → str[source]
                                                              Parameters
                                                                @@ -161,7 +161,7 @@
                                                                -write_input_files()[source]
                                                                +write_input_files()[source]

                                                                Write input files to working directory

                                                                diff --git a/docs/pymatgen.io.xtb.outputs.html b/docs/pymatgen.io.xtb.outputs.html index e7720edb1a4..793f881d3fa 100644 --- a/docs/pymatgen.io.xtb.outputs.html +++ b/docs/pymatgen.io.xtb.outputs.html @@ -4,7 +4,7 @@ - pymatgen.io.xtb.outputs module — pymatgen 2022.5.18 documentation + pymatgen.io.xtb.outputs module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                - 2022.5.18 + 2022.5.18.1
                                                                @@ -119,7 +119,7 @@

                                                                Parsers for XTB output files and directories

                                                                -class CRESTOutput(output_filename, path='.')[source]
                                                                +class CRESTOutput(output_filename, path='.')[source]

                                                                Bases: monty.json.MSONable

                                                                Class to parse CREST output files

                                                                Assumes runtype is iMTD-GC [default] diff --git a/docs/pymatgen.io.xyz.html b/docs/pymatgen.io.xyz.html index a37411c4da4..425ef03bbb6 100644 --- a/docs/pymatgen.io.xyz.html +++ b/docs/pymatgen.io.xyz.html @@ -4,7 +4,7 @@ - pymatgen.io.xyz module — pymatgen 2022.5.18 documentation + pymatgen.io.xyz module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                                                - 2022.5.18 + 2022.5.18.1
                                                                @@ -118,7 +118,7 @@

                                                                Module implementing an XYZ file object class.

                                                                -class XYZ(mol: pymatgen.core.structure.Molecule, coord_precision: int = 6)[source]
                                                                +class XYZ(mol: pymatgen.core.structure.Molecule, coord_precision: int = 6)[source]

                                                                Bases: object

                                                                Basic class for importing and exporting Molecules or Structures in XYZ format.

                                                                @@ -139,13 +139,13 @@
                                                                -property all_molecules[source]
                                                                +property all_molecules[source]

                                                                Returns all the frames of molecule associated with this XYZ.

                                                                -as_dataframe()[source]
                                                                +as_dataframe()[source]

                                                                Generates a coordinates data frame with columns: atom, x, y, and z In case of multiple frame XYZ, returns the last frame.

                                                                @@ -157,7 +157,7 @@
                                                                -static from_file(filename)[source]
                                                                +static from_file(filename)[source]

                                                                Creates XYZ object from a file.

                                                                Parameters
                                                                @@ -171,7 +171,7 @@
                                                                -static from_string(contents)[source]
                                                                +static from_string(contents)[source]

                                                                Creates XYZ object from a string.

                                                                Parameters
                                                                @@ -185,14 +185,14 @@
                                                                -property molecule: pymatgen.core.structure.Molecule[source]
                                                                +property molecule: pymatgen.core.structure.Molecule[source]

                                                                Returns molecule associated with this XYZ. In case multiple frame XYZ, returns the last frame.

                                                                -write_file(filename)[source]
                                                                +write_file(filename)[source]

                                                                Writes XYZ to file.

                                                                Parameters
                                                                diff --git a/docs/pymatgen.io.zeopp.html b/docs/pymatgen.io.zeopp.html index e2d1d5a266a..b0672c88e15 100644 --- a/docs/pymatgen.io.zeopp.html +++ b/docs/pymatgen.io.zeopp.html @@ -4,7 +4,7 @@ - pymatgen.io.zeopp module — pymatgen 2022.5.18 documentation + pymatgen.io.zeopp module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                - 2022.5.18 + 2022.5.18.1
                                                                @@ -140,7 +140,7 @@

                                                                Zeo++ Post-Installation Checking:
                                                                -class ZeoCssr(structure)[source]
                                                                +class ZeoCssr(structure)[source]

                                                                Bases: pymatgen.io.cssr.Cssr

                                                                ZeoCssr adds extra fields to CSSR sites to conform with Zeo++ input CSSR format. The coordinate system is rotated from xyz to zyx. @@ -153,7 +153,7 @@

                                                                Zeo++ Post-Installation Checking:
                                                                -static from_file(filename)[source]
                                                                +static from_file(filename)[source]

                                                                Reads a CSSR file to a ZeoCssr object.

                                                                Parameters
                                                                @@ -167,7 +167,7 @@

                                                                Zeo++ Post-Installation Checking:
                                                                -static from_string(string)[source]
                                                                +static from_string(string)[source]

                                                                Reads a string representation to a ZeoCssr object.

                                                                Parameters
                                                                @@ -183,7 +183,7 @@

                                                                Zeo++ Post-Installation Checking:
                                                                -class ZeoVoronoiXYZ(mol)[source]
                                                                +class ZeoVoronoiXYZ(mol)[source]

                                                                Bases: pymatgen.io.xyz.XYZ

                                                                Class to read Voronoi Nodes from XYZ file written by Zeo++. The sites have an additional column representing the voronoi node radius. @@ -195,7 +195,7 @@

                                                                Zeo++ Post-Installation Checking:
                                                                -static from_file(filename)[source]
                                                                +static from_file(filename)[source]

                                                                Creates XYZ object from a file.

                                                                Parameters
                                                                @@ -209,7 +209,7 @@

                                                                Zeo++ Post-Installation Checking:
                                                                -static from_string(contents)[source]
                                                                +static from_string(contents)[source]

                                                                Creates Zeo++ Voronoi XYZ object from a string. from_string method of XYZ class is being redefined.

                                                                @@ -226,7 +226,7 @@

                                                                Zeo++ Post-Installation Checking:
                                                                -get_free_sphere_params(structure, rad_dict=None, probe_rad=0.1)[source]
                                                                +get_free_sphere_params(structure, rad_dict=None, probe_rad=0.1)[source]

                                                                Analyze the void space in the input structure using voronoi decomposition Calls Zeo++ for Voronoi decomposition.

                                                                @@ -252,7 +252,7 @@

                                                                Zeo++ Post-Installation Checking:
                                                                -get_high_accuracy_voronoi_nodes(structure, rad_dict, probe_rad=0.1)[source]
                                                                +get_high_accuracy_voronoi_nodes(structure, rad_dict, probe_rad=0.1)[source]

                                                                Analyze the void space in the input structure using high accuracy voronoi decomposition. Calls Zeo++ for Voronoi decomposition.

                                                                @@ -279,7 +279,7 @@

                                                                Zeo++ Post-Installation Checking:
                                                                -get_void_volume_surfarea(structure, rad_dict=None, chan_rad=0.3, probe_rad=0.1)[source]
                                                                +get_void_volume_surfarea(structure, rad_dict=None, chan_rad=0.3, probe_rad=0.1)[source]

                                                                Computes the volume and surface area of isolated void using Zeo++. Useful to compute the volume and surface area of vacant site.

                                                                @@ -303,7 +303,7 @@

                                                                Zeo++ Post-Installation Checking:
                                                                -get_voronoi_nodes(structure, rad_dict=None, probe_rad=0.1)[source]
                                                                +get_voronoi_nodes(structure, rad_dict=None, probe_rad=0.1)[source]

                                                                Analyze the void space in the input structure using voronoi decomposition Calls Zeo++ for Voronoi decomposition.

                                                                diff --git a/docs/pymatgen.optimization.html b/docs/pymatgen.optimization.html index 70175a19e4e..76216181979 100644 --- a/docs/pymatgen.optimization.html +++ b/docs/pymatgen.optimization.html @@ -4,7 +4,7 @@ - pymatgen.optimization package — pymatgen 2022.5.18 documentation + pymatgen.optimization package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                - 2022.5.18 + 2022.5.18.1
                                                                diff --git a/docs/pymatgen.optimization.linear_assignment.html b/docs/pymatgen.optimization.linear_assignment.html index 44ff360705f..446c10047ea 100644 --- a/docs/pymatgen.optimization.linear_assignment.html +++ b/docs/pymatgen.optimization.linear_assignment.html @@ -4,7 +4,7 @@ - pymatgen.optimization.linear_assignment module — pymatgen 2022.5.18 documentation + pymatgen.optimization.linear_assignment module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                - 2022.5.18 + 2022.5.18.1
                                                                @@ -117,7 +117,7 @@

                                                                pymatgen.optimization.linear_assignment module

                                                                -class LinearAssignment(costs, epsilon=1e-13)[source]
                                                                +class LinearAssignment(costs, epsilon=1e-13)[source]

                                                                Bases: object

                                                                This class finds the solution to the Linear Assignment Problem. It finds a minimum cost matching between two sets, given a cost diff --git a/docs/pymatgen.optimization.linear_assignment_numpy.html b/docs/pymatgen.optimization.linear_assignment_numpy.html index 8b722ed8c15..17c7c9d3cd9 100644 --- a/docs/pymatgen.optimization.linear_assignment_numpy.html +++ b/docs/pymatgen.optimization.linear_assignment_numpy.html @@ -4,7 +4,7 @@ - pymatgen.optimization.linear_assignment_numpy module — pymatgen 2022.5.18 documentation + pymatgen.optimization.linear_assignment_numpy module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                                                - 2022.5.18 + 2022.5.18.1
                                                                @@ -120,7 +120,7 @@ as it is vectorized in numpy rather than cython

                                                                -class LinearAssignment(costs, epsilon=1e-06)[source]
                                                                +class LinearAssignment(costs, epsilon=1e-06)[source]

                                                                Bases: object

                                                                This class finds the solution to the Linear Assignment Problem. It finds a minimum cost matching between two sets, given a cost @@ -141,7 +141,7 @@

                                                                -property min_cost[source]
                                                                +property min_cost[source]

                                                                Returns the cost of the best assignment

                                                                diff --git a/docs/pymatgen.optimization.neighbors.html b/docs/pymatgen.optimization.neighbors.html index e6f15d78e95..704d17dd0e5 100644 --- a/docs/pymatgen.optimization.neighbors.html +++ b/docs/pymatgen.optimization.neighbors.html @@ -4,7 +4,7 @@ - pymatgen.optimization.neighbors module — pymatgen 2022.5.18 documentation + pymatgen.optimization.neighbors module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                - 2022.5.18 + 2022.5.18.1
                                                                @@ -117,12 +117,12 @@

                                                                pymatgen.optimization.neighbors module

                                                                -compute_offset_vectors()[source]
                                                                +compute_offset_vectors()[source]
                                                                -find_points_in_spheres()[source]
                                                                +find_points_in_spheres()[source]

                                                                For each point in center_coords, get all the neighboring points in all_coords that are within the cutoff radius r. All the coordinates should be in cartesian.

                                                                diff --git a/docs/pymatgen.phonon.bandstructure.html b/docs/pymatgen.phonon.bandstructure.html index 9573d2a64bc..f7a20bf4c50 100644 --- a/docs/pymatgen.phonon.bandstructure.html +++ b/docs/pymatgen.phonon.bandstructure.html @@ -4,7 +4,7 @@ - pymatgen.phonon.bandstructure module — pymatgen 2022.5.18 documentation + pymatgen.phonon.bandstructure module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                - 2022.5.18 + 2022.5.18.1
                                                                @@ -118,7 +118,7 @@

                                                                This module provides classes to define a phonon band structure.

                                                                -class PhononBandStructure(qpoints, frequencies, lattice, nac_frequencies=None, eigendisplacements=None, nac_eigendisplacements=None, labels_dict=None, coords_are_cartesian=False, structure=None)[source]
                                                                +class PhononBandStructure(qpoints, frequencies, lattice, nac_frequencies=None, eigendisplacements=None, nac_eigendisplacements=None, labels_dict=None, coords_are_cartesian=False, structure=None)[source]

                                                                Bases: monty.json.MSONable

                                                                This is the most generic phonon band structure data possible it’s defined by a list of qpoints + frequencies for each of them. @@ -162,7 +162,7 @@

                                                                -as_dict()[source]
                                                                +as_dict()[source]
                                                                Returns

                                                                MSONable dict

                                                                @@ -172,7 +172,7 @@
                                                                -asr_breaking(tol_eigendisplacements=1e-05)[source]
                                                                +asr_breaking(tol_eigendisplacements=1e-05)[source]

                                                                Returns the breaking of the acoustic sum rule for the three acoustic modes, if Gamma is present. None otherwise. If eigendisplacements are available they are used to determine the acoustic @@ -184,7 +184,7 @@

                                                                -classmethod from_dict(d)[source]
                                                                +classmethod from_dict(d)[source]
                                                                Parameters

                                                                d – Dict representation

                                                                @@ -197,7 +197,7 @@
                                                                -get_nac_eigendisplacements_along_dir(direction)[source]
                                                                +get_nac_eigendisplacements_along_dir(direction)[source]

                                                                Returns the nac_eigendisplacements for the given direction (not necessarily a versor). None if the direction is not present or nac_eigendisplacements has not been calculated.

                                                                @@ -213,7 +213,7 @@
                                                                -get_nac_frequencies_along_dir(direction)[source]
                                                                +get_nac_frequencies_along_dir(direction)[source]

                                                                Returns the nac_frequencies for the given direction (not necessarily a versor). None if the direction is not present or nac_frequencies has not been calculated.

                                                                @@ -229,25 +229,25 @@
                                                                -property has_eigendisplacements[source]
                                                                +property has_eigendisplacements[source]

                                                                True if eigendisplacements are present.

                                                                -has_imaginary_freq(tol=1e-05)[source]
                                                                +has_imaginary_freq(tol=1e-05)[source]

                                                                True if imaginary frequencies are present in the BS.

                                                                -property has_nac[source]
                                                                +property has_nac[source]

                                                                True if nac_frequencies are present.

                                                                -min_freq()[source]
                                                                +min_freq()[source]

                                                                Returns the point where the minimum frequency is reached and its value

                                                                @@ -255,7 +255,7 @@
                                                                -class PhononBandStructureSymmLine(qpoints, frequencies, lattice, has_nac=False, eigendisplacements=None, labels_dict=None, coords_are_cartesian=False, structure=None)[source]
                                                                +class PhononBandStructureSymmLine(qpoints, frequencies, lattice, has_nac=False, eigendisplacements=None, labels_dict=None, coords_are_cartesian=False, structure=None)[source]

                                                                Bases: pymatgen.phonon.bandstructure.PhononBandStructure

                                                                This object stores phonon band structures along selected (symmetry) lines in the Brillouin zone. We call the different symmetry lines (ex: \Gamma to Z) @@ -290,26 +290,26 @@

                                                                -as_dict()[source]
                                                                +as_dict()[source]

                                                                Returns: MSONable dict

                                                                -as_phononwebsite()[source]
                                                                +as_phononwebsite()[source]

                                                                Return a dictionary with the phononwebsite format: http://henriquemiranda.github.io/phononwebsite

                                                                -band_reorder()[source]
                                                                +band_reorder()[source]

                                                                Re-order the eigenvalues according to the similarity of the eigenvectors

                                                                -classmethod from_dict(d)[source]
                                                                +classmethod from_dict(d)[source]
                                                                Parameters

                                                                d – Dict representation

                                                                @@ -320,7 +320,7 @@
                                                                -get_branch(index)[source]
                                                                +get_branch(index)[source]

                                                                Returns in what branch(es) is the qpoint. There can be several branches.

                                                                @@ -338,7 +338,7 @@
                                                                -get_equivalent_qpoints(index)[source]
                                                                +get_equivalent_qpoints(index)[source]

                                                                Returns the list of qpoint indices equivalent (meaning they are the same frac coords) to the given one.

                                                                @@ -355,7 +355,7 @@
                                                                -write_phononwebsite(filename)[source]
                                                                +write_phononwebsite(filename)[source]

                                                                Write a json file for the phononwebsite: http://henriquemiranda.github.io/phononwebsite

                                                                @@ -364,19 +364,19 @@
                                                                -eigenvectors_from_displacements(disp, masses)[source]
                                                                +eigenvectors_from_displacements(disp, masses)[source]

                                                                Calculate the eigenvectors from the atomic displacements

                                                                -estimate_band_connection(prev_eigvecs, eigvecs, prev_band_order)[source]
                                                                +estimate_band_connection(prev_eigvecs, eigvecs, prev_band_order)[source]

                                                                A function to order the phonon eigenvectors taken from phonopy

                                                                -get_reasonable_repetitions(natoms)[source]
                                                                +get_reasonable_repetitions(natoms)[source]

                                                                Choose the number of repetitions according to the number of atoms in the system

                                                                diff --git a/docs/pymatgen.phonon.dos.html b/docs/pymatgen.phonon.dos.html index 6564d7fadd8..2ac134c282b 100644 --- a/docs/pymatgen.phonon.dos.html +++ b/docs/pymatgen.phonon.dos.html @@ -4,7 +4,7 @@ - pymatgen.phonon.dos module — pymatgen 2022.5.18 documentation + pymatgen.phonon.dos module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                - 2022.5.18 + 2022.5.18.1
                                                                @@ -118,12 +118,12 @@

                                                                This module defines classes to represent the phonon density of states, etc.

                                                                -class CompletePhononDos(structure, total_dos, pdoss)[source]
                                                                +class CompletePhononDos(structure, total_dos, pdoss)[source]

                                                                Bases: pymatgen.phonon.dos.PhononDos

                                                                This wrapper class defines a total dos, and also provides a list of PDos.

                                                                -pdos[source]
                                                                +pdos[source]

                                                                Dict of partial densities of the form {Site:Densities}

                                                                @@ -138,19 +138,19 @@
                                                                -as_dict()[source]
                                                                +as_dict()[source]

                                                                JSON-serializable dict representation of CompletePhononDos.

                                                                -classmethod from_dict(d)[source]
                                                                +classmethod from_dict(d)[source]

                                                                Returns CompleteDos object from dict representation.

                                                                -get_element_dos()[source]
                                                                +get_element_dos()[source]

                                                                Get element projected Dos.

                                                                Returns
                                                                @@ -164,7 +164,7 @@
                                                                -get_site_dos(site)[source]
                                                                +get_site_dos(site)[source]

                                                                Get the Dos for a site.

                                                                Parameters
                                                                @@ -180,7 +180,7 @@
                                                                -class PhononDos(frequencies, densities)[source]
                                                                +class PhononDos(frequencies, densities)[source]

                                                                Bases: monty.json.MSONable

                                                                Basic DOS object. All other DOS objects are extended versions of this object.

                                                                @@ -194,13 +194,13 @@
                                                                -as_dict()[source]
                                                                +as_dict()[source]

                                                                JSON-serializable dict representation of PhononDos.

                                                                -cv(t, structure=None)[source]
                                                                +cv(t, structure=None)[source]

                                                                Constant volume specific heat C_v at temperature T obtained from the integration of the DOS. Only positive frequencies will be used. Result in J/(K*mol-c). A mol-c is the abbreviation of a mole-cell, that is, the number @@ -223,7 +223,7 @@

                                                                -entropy(t, structure=None)[source]
                                                                +entropy(t, structure=None)[source]

                                                                Vibrational entropy at temperature T obtained from the integration of the DOS. Only positive frequencies will be used. Result in J/(K*mol-c). A mol-c is the abbreviation of a mole-cell, that is, the number @@ -246,13 +246,13 @@

                                                                -classmethod from_dict(d)[source]
                                                                +classmethod from_dict(d)[source]

                                                                Returns PhononDos object from dict representation of PhononDos.

                                                                -get_interpolated_value(frequency)[source]
                                                                +get_interpolated_value(frequency)[source]

                                                                Returns interpolated density for a particular frequency.

                                                                Parameters
                                                                @@ -263,7 +263,7 @@
                                                                -get_smeared_densities(sigma)[source]
                                                                +get_smeared_densities(sigma)[source]

                                                                Returns the densities, but with a Gaussian smearing of std dev sigma applied.

                                                                @@ -278,7 +278,7 @@
                                                                -helmholtz_free_energy(t, structure=None)[source]
                                                                +helmholtz_free_energy(t, structure=None)[source]

                                                                Phonon contribution to the Helmholtz free energy at temperature T obtained from the integration of the DOS. Only positive frequencies will be used. Result in J/mol-c. A mol-c is the abbreviation of a mole-cell, that is, the number @@ -301,13 +301,13 @@

                                                                -ind_zero_freq()[source]
                                                                +ind_zero_freq()[source]

                                                                Index of the first point for which the frequencies are equal or greater than zero.

                                                                -internal_energy(t, structure=None)[source]
                                                                +internal_energy(t, structure=None)[source]

                                                                Phonon contribution to the internal energy at temperature T obtained from the integration of the DOS. Only positive frequencies will be used. Result in J/mol-c. A mol-c is the abbreviation of a mole-cell, that is, the number @@ -330,7 +330,7 @@

                                                                -zero_point_energy(structure=None)[source]
                                                                +zero_point_energy(structure=None)[source]

                                                                Zero point energy energy of the system. Only positive frequencies will be used. Result in J/mol-c. A mol-c is the abbreviation of a mole-cell, that is, the number of Avogadro times the atoms in a unit cell. To compare with experimental data the result @@ -351,7 +351,7 @@

                                                                -coth(x)[source]
                                                                +coth(x)[source]

                                                                Coth function.

                                                                Parameters
                                                                diff --git a/docs/pymatgen.phonon.gruneisen.html b/docs/pymatgen.phonon.gruneisen.html index 6af6c559dea..ccb00ed4892 100644 --- a/docs/pymatgen.phonon.gruneisen.html +++ b/docs/pymatgen.phonon.gruneisen.html @@ -4,7 +4,7 @@ - pymatgen.phonon.gruneisen module — pymatgen 2022.5.18 documentation + pymatgen.phonon.gruneisen module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                - 2022.5.18 + 2022.5.18.1
                                                                @@ -118,7 +118,7 @@

                                                                This module provides classes to define a Grueneisen band structure.

                                                                -class GruneisenParameter(qpoints, gruneisen, frequencies, multiplicities=None, structure=None, lattice=None)[source]
                                                                +class GruneisenParameter(qpoints, gruneisen, frequencies, multiplicities=None, structure=None, lattice=None)[source]

                                                                Bases: monty.json.MSONable

                                                                Class for Grueneisen parameters on a regular grid.

                                                                @@ -136,14 +136,14 @@
                                                                -property acoustic_debye_temp[source]
                                                                +property acoustic_debye_temp[source]

                                                                Acoustic Debye temperature in K, i.e. the Debye temperature divided by nsites**(1/3). Adapted from abipy.

                                                                -average_gruneisen(t=None, squared=True, limit_frequencies=None)[source]
                                                                +average_gruneisen(t=None, squared=True, limit_frequencies=None)[source]

                                                                Calculates the average of the Gruneisen based on the values on the regular grid. If squared is True the average will use the squared value of the Gruneisen and a squared root is performed on the final result. @@ -169,13 +169,13 @@

                                                                -property debye_temp_limit[source]
                                                                +property debye_temp_limit[source]

                                                                Debye temperature in K. Adapted from apipy.

                                                                -debye_temp_phonopy(freq_max_fit=None)[source]
                                                                +debye_temp_phonopy(freq_max_fit=None)[source]

                                                                Get Debye temperature in K as implemented in phonopy. :param freq_max_fit: Maximum frequency to include for fitting.

                                                                @@ -190,7 +190,7 @@
                                                                -property phdos[source]
                                                                +property phdos[source]

                                                                PhononDos object

                                                                Type
                                                                @@ -201,13 +201,13 @@
                                                                -property tdos[source]
                                                                +property tdos[source]

                                                                The total DOS (re)constructed from the gruneisen.yaml file

                                                                -thermal_conductivity_slack(squared=True, limit_frequencies=None, theta_d=None, t=None)[source]
                                                                +thermal_conductivity_slack(squared=True, limit_frequencies=None, theta_d=None, t=None)[source]

                                                                Calculates the thermal conductivity at the acoustic Debye temperature with the Slack formula, using the average Gruneisen. Adapted from abipy.

                                                                @@ -237,7 +237,7 @@
                                                                -class GruneisenPhononBandStructure(qpoints, frequencies, gruneisenparameters, lattice, eigendisplacements=None, labels_dict=None, coords_are_cartesian=False, structure=None)[source]
                                                                +class GruneisenPhononBandStructure(qpoints, frequencies, gruneisenparameters, lattice, eigendisplacements=None, labels_dict=None, coords_are_cartesian=False, structure=None)[source]

                                                                Bases: pymatgen.phonon.bandstructure.PhononBandStructure

                                                                This is the most generic phonon band structure data possible it’s defined by a list of qpoints + frequencies for each of them. @@ -273,7 +273,7 @@

                                                                -as_dict()[source]
                                                                +as_dict()[source]
                                                                Returns

                                                                MSONable (dict)

                                                                @@ -283,7 +283,7 @@
                                                                -classmethod from_dict(d)[source]
                                                                +classmethod from_dict(d)[source]
                                                                Parameters

                                                                d (dict) – Dict representation

                                                                @@ -301,7 +301,7 @@
                                                                -class GruneisenPhononBandStructureSymmLine(qpoints, frequencies, gruneisenparameters, lattice, eigendisplacements=None, labels_dict=None, coords_are_cartesian=False, structure=None)[source]
                                                                +class GruneisenPhononBandStructureSymmLine(qpoints, frequencies, gruneisenparameters, lattice, eigendisplacements=None, labels_dict=None, coords_are_cartesian=False, structure=None)[source]

                                                                Bases: pymatgen.phonon.gruneisen.GruneisenPhononBandStructure, pymatgen.phonon.bandstructure.PhononBandStructureSymmLine

                                                                This object stores a GruneisenPhononBandStructureSymmLine together with Grueneisen parameters for every frequency.

                                                                @@ -334,7 +334,7 @@
                                                                -classmethod from_dict(d)[source]
                                                                +classmethod from_dict(d)[source]
                                                                Parameters

                                                                d – Dict representation

                                                                diff --git a/docs/pymatgen.phonon.html b/docs/pymatgen.phonon.html index a0f4a56d004..fc956a358e3 100644 --- a/docs/pymatgen.phonon.html +++ b/docs/pymatgen.phonon.html @@ -4,7 +4,7 @@ - pymatgen.phonon package — pymatgen 2022.5.18 documentation + pymatgen.phonon package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                - 2022.5.18 + 2022.5.18.1
                                                                diff --git a/docs/pymatgen.phonon.ir_spectra.html b/docs/pymatgen.phonon.ir_spectra.html index 08a3f637ccf..40a7ea7920d 100644 --- a/docs/pymatgen.phonon.ir_spectra.html +++ b/docs/pymatgen.phonon.ir_spectra.html @@ -4,7 +4,7 @@ - pymatgen.phonon.ir_spectra module — pymatgen 2022.5.18 documentation + pymatgen.phonon.ir_spectra module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                - 2022.5.18 + 2022.5.18.1
                                                                @@ -121,7 +121,7 @@ where it was originally done by Guido Petretto and Matteo Giantomassi

                                                                -class IRDielectricTensor(oscillator_strength, ph_freqs_gamma, epsilon_infinity, structure)[source]
                                                                +class IRDielectricTensor(oscillator_strength, ph_freqs_gamma, epsilon_infinity, structure)[source]

                                                                Bases: monty.json.MSONable

                                                                Class to handle the Ionic Dielectric Tensor The implementation is adapted from Abipy @@ -139,19 +139,19 @@

                                                                -as_dict()[source]
                                                                +as_dict()[source]

                                                                JSON-serializable dict representation of IRDielectricTensor.

                                                                -classmethod from_dict(d)[source]
                                                                +classmethod from_dict(d)[source]

                                                                Returns IRDielectricTensor from dict representation

                                                                -get_ir_spectra(broad=5e-05, emin=0, emax=None, divs=500)[source]
                                                                +get_ir_spectra(broad=5e-05, emin=0, emax=None, divs=500)[source]

                                                                The IR spectra is obtained for the different directions

                                                                Parameters
                                                                @@ -179,7 +179,7 @@
                                                                -get_plotter(components=('xx',), reim='reim', broad=5e-05, emin=0, emax=None, divs=500, **kwargs)[source]
                                                                +get_plotter(components=('xx',), reim='reim', broad=5e-05, emin=0, emax=None, divs=500, **kwargs)[source]

                                                                Return an instance of the Spectrum plotter containing the different requested components

                                                                Parameters
                                                                @@ -197,7 +197,7 @@
                                                                -get_spectrum(component, reim, broad=5e-05, emin=0, emax=None, divs=500, label=None)[source]
                                                                +get_spectrum(component, reim, broad=5e-05, emin=0, emax=None, divs=500, label=None)[source]

                                                                component: either two indexes or a string like ‘xx’ to plot the (0,0) component reim: only “re” or “im” broad: a list of broadenings or a single broadening for the phonon peaks

                                                                @@ -205,19 +205,19 @@
                                                                -property max_phfreq[source]
                                                                +property max_phfreq[source]

                                                                Maximum phonon frequency

                                                                -property nph_freqs[source]
                                                                +property nph_freqs[source]

                                                                Number of phonon frequencies

                                                                -plot(components=('xx',), reim='reim', show_phonon_frequencies=True, xlim=None, ylim=None, **kwargs)[source]
                                                                +plot(components=('xx',), reim='reim', show_phonon_frequencies=True, xlim=None, ylim=None, **kwargs)[source]

                                                                Helper function to generate the Spectrum plotter and directly plot the results

                                                                Parameters
                                                                @@ -274,7 +274,7 @@
                                                                -write_json(filename)[source]
                                                                +write_json(filename)[source]

                                                                Save a json file with this data

                                                                diff --git a/docs/pymatgen.phonon.plotter.html b/docs/pymatgen.phonon.plotter.html index 66d0ab5ec3e..63281c06400 100644 --- a/docs/pymatgen.phonon.plotter.html +++ b/docs/pymatgen.phonon.plotter.html @@ -4,7 +4,7 @@ - pymatgen.phonon.plotter module — pymatgen 2022.5.18 documentation + pymatgen.phonon.plotter module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                - 2022.5.18 + 2022.5.18.1
                                                                @@ -118,18 +118,18 @@

                                                                This module implements plotter for DOS and band structure.

                                                                -class FreqUnits(factor, label)[source]
                                                                +class FreqUnits(factor, label)[source]

                                                                Bases: tuple

                                                                Create new instance of FreqUnits(factor, label)

                                                                -factor[source]
                                                                +factor[source]

                                                                Alias for field number 0

                                                                -label[source]
                                                                +label[source]

                                                                Alias for field number 1

                                                                @@ -137,7 +137,7 @@
                                                                -class GruneisenPhononBSPlotter(bs)[source]
                                                                +class GruneisenPhononBSPlotter(bs)[source]

                                                                Bases: pymatgen.phonon.plotter.PhononBSPlotter

                                                                Class to plot or get data to facilitate the plot of band structure objects.

                                                                @@ -147,7 +147,7 @@
                                                                -bs_plot_data()[source]
                                                                +bs_plot_data()[source]

                                                                Get the data nicely formatted for a plot

                                                                Returns
                                                                @@ -167,7 +167,7 @@
                                                                -get_plot_gs(ylim=None)[source]
                                                                +get_plot_gs(ylim=None)[source]

                                                                Get a matplotlib object for the gruneisen bandstructure plot.

                                                                Parameters
                                                                @@ -179,7 +179,7 @@
                                                                -plot_compare_gs(other_plotter)[source]
                                                                +plot_compare_gs(other_plotter)[source]

                                                                plot two band structure for comparison. One is in red the other in blue. The two band structures need to be defined on the same symmetry lines! and the distance between symmetry lines is @@ -196,7 +196,7 @@

                                                                -save_plot_gs(filename, img_format='eps', ylim=None)[source]
                                                                +save_plot_gs(filename, img_format='eps', ylim=None)[source]

                                                                Save matplotlib plot to a file.

                                                                Parameters
                                                                @@ -211,7 +211,7 @@
                                                                -show_gs(ylim=None)[source]
                                                                +show_gs(ylim=None)[source]

                                                                Show the plot using matplotlib.

                                                                Parameters
                                                                @@ -224,14 +224,14 @@
                                                                -class GruneisenPlotter(gruneisen)[source]
                                                                +class GruneisenPlotter(gruneisen)[source]

                                                                Bases: object

                                                                Class to plot Gruneisenparameter Object

                                                                Class to plot information from Gruneisenparameter Object :param gruneisen: GruneisenParameter Object

                                                                -get_plot(marker='o', markersize=None, units='thz')[source]
                                                                +get_plot(marker='o', markersize=None, units='thz')[source]

                                                                will produce a plot :param marker: marker for the depiction :param markersize: size of the marker @@ -241,7 +241,7 @@

                                                                -save_plot(filename, img_format='pdf', units='thz')[source]
                                                                +save_plot(filename, img_format='pdf', units='thz')[source]

                                                                Will save the plot to a file :param filename: name of the filename :param img_format: format of the saved plot @@ -251,7 +251,7 @@

                                                                -show(units='thz')[source]
                                                                +show(units='thz')[source]

                                                                will show the plot :param units: units for the plot, accepted units: thz, ev, mev, ha, cm-1, cm^-1

                                                                Returns: plot

                                                                @@ -261,7 +261,7 @@
                                                                -class PhononBSPlotter(bs)[source]
                                                                +class PhononBSPlotter(bs)[source]

                                                                Bases: object

                                                                Class to plot or get data to facilitate the plot of band structure objects.

                                                                @@ -271,7 +271,7 @@
                                                                -bs_plot_data()[source]
                                                                +bs_plot_data()[source]

                                                                Get the data nicely formatted for a plot

                                                                Returns
                                                                @@ -290,7 +290,7 @@
                                                                -get_plot(ylim=None, units='thz')[source]
                                                                +get_plot(ylim=None, units='thz')[source]

                                                                Get a matplotlib object for the bandstructure plot.

                                                                Parameters
                                                                @@ -305,7 +305,7 @@
                                                                -get_ticks()[source]
                                                                +get_ticks()[source]

                                                                Get all ticks and labels for a band structure plot.

                                                                Returns
                                                                @@ -320,13 +320,13 @@
                                                                -plot_brillouin()[source]
                                                                +plot_brillouin()[source]

                                                                plot the Brillouin zone

                                                                -plot_compare(other_plotter, units='thz')[source]
                                                                +plot_compare(other_plotter, units='thz')[source]

                                                                plot two band structure for comparison. One is in red the other in blue. The two band structures need to be defined on the same symmetry lines! and the distance between symmetry lines is the one of the band structure @@ -346,7 +346,7 @@

                                                                -save_plot(filename, img_format='eps', ylim=None, units='thz')[source]
                                                                +save_plot(filename, img_format='eps', ylim=None, units='thz')[source]

                                                                Save matplotlib plot to a file.

                                                                Parameters
                                                                @@ -362,7 +362,7 @@
                                                                -show(ylim=None, units='thz')[source]
                                                                +show(ylim=None, units='thz')[source]

                                                                Show the plot using matplotlib.

                                                                Parameters
                                                                @@ -379,7 +379,7 @@
                                                                -class PhononDosPlotter(stack=False, sigma=None)[source]
                                                                +class PhononDosPlotter(stack=False, sigma=None)[source]

                                                                Bases: object

                                                                Class for plotting phonon DOSs. Note that the interface is extremely flexible given that there are many different ways in which people want to view @@ -407,7 +407,7 @@

                                                                -add_dos(label, dos)[source]
                                                                +add_dos(label, dos)[source]

                                                                Adds a dos for plotting.

                                                                Parameters
                                                                @@ -421,7 +421,7 @@
                                                                -add_dos_dict(dos_dict, key_sort_func=None)[source]
                                                                +add_dos_dict(dos_dict, key_sort_func=None)[source]

                                                                Add a dictionary of doses, with an optional sorting function for the keys.

                                                                @@ -436,7 +436,7 @@
                                                                -get_dos_dict()[source]
                                                                +get_dos_dict()[source]

                                                                Returns the added doses as a json-serializable dict. Note that if you have specified smearing for the DOS plot, the densities returned will be the smeared densities, not the original densities.

                                                                @@ -453,7 +453,7 @@
                                                                -get_plot(xlim=None, ylim=None, units='thz')[source]
                                                                +get_plot(xlim=None, ylim=None, units='thz')[source]

                                                                Get a matplotlib plot showing the DOS.

                                                                Parameters
                                                                @@ -469,7 +469,7 @@
                                                                -save_plot(filename, img_format='eps', xlim=None, ylim=None, units='thz')[source]
                                                                +save_plot(filename, img_format='eps', xlim=None, ylim=None, units='thz')[source]

                                                                Save matplotlib plot to a file.

                                                                Parameters
                                                                @@ -487,7 +487,7 @@
                                                                -show(xlim=None, ylim=None, units='thz')[source]
                                                                +show(xlim=None, ylim=None, units='thz')[source]

                                                                Show the plot using matplotlib.

                                                                Parameters
                                                                @@ -505,7 +505,7 @@
                                                                -class ThermoPlotter(dos, structure=None)[source]
                                                                +class ThermoPlotter(dos, structure=None)[source]

                                                                Bases: object

                                                                Plotter for thermodynamic properties obtained from phonon DOS. If the structure corresponding to the DOS, it will be used to extract the formula unit and provide @@ -520,7 +520,7 @@

                                                                -plot_cv(tmin, tmax, ntemp, ylim=None, **kwargs)[source]
                                                                +plot_cv(tmin, tmax, ntemp, ylim=None, **kwargs)[source]

                                                                Plots the constant volume specific heat C_v in a temperature range.

                                                                Parameters
                                                                @@ -581,7 +581,7 @@
                                                                -plot_entropy(tmin, tmax, ntemp, ylim=None, **kwargs)[source]
                                                                +plot_entropy(tmin, tmax, ntemp, ylim=None, **kwargs)[source]

                                                                Plots the vibrational entrpy in a temperature range.

                                                                Parameters
                                                                @@ -642,7 +642,7 @@
                                                                -plot_helmholtz_free_energy(tmin, tmax, ntemp, ylim=None, **kwargs)[source]
                                                                +plot_helmholtz_free_energy(tmin, tmax, ntemp, ylim=None, **kwargs)[source]

                                                                Plots the vibrational contribution to the Helmoltz free energy in a temperature range.

                                                                Parameters
                                                                @@ -703,7 +703,7 @@
                                                                -plot_internal_energy(tmin, tmax, ntemp, ylim=None, **kwargs)[source]
                                                                +plot_internal_energy(tmin, tmax, ntemp, ylim=None, **kwargs)[source]

                                                                Plots the vibrational internal energy in a temperature range.

                                                                Parameters
                                                                @@ -764,7 +764,7 @@
                                                                -plot_thermodynamic_properties(tmin, tmax, ntemp, ylim=None, **kwargs)[source]
                                                                +plot_thermodynamic_properties(tmin, tmax, ntemp, ylim=None, **kwargs)[source]

                                                                Plots all the thermodynamic properties in a temperature range.

                                                                Parameters
                                                                @@ -827,7 +827,7 @@
                                                                -freq_units(units)[source]
                                                                +freq_units(units)[source]
                                                                Parameters

                                                                units – str, accepted values: thz, ev, mev, ha, cm-1, cm^-1

                                                                diff --git a/docs/pymatgen.symmetry.analyzer.html b/docs/pymatgen.symmetry.analyzer.html index 29656725a57..178e2297d62 100644 --- a/docs/pymatgen.symmetry.analyzer.html +++ b/docs/pymatgen.symmetry.analyzer.html @@ -4,7 +4,7 @@ - pymatgen.symmetry.analyzer module — pymatgen 2022.5.18 documentation + pymatgen.symmetry.analyzer module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                                - 2022.5.18 + 2022.5.18.1
                                                                @@ -126,7 +126,7 @@
                                                                -class PointGroupAnalyzer(mol, tolerance=0.3, eigen_tolerance=0.01, matrix_tolerance=0.1)[source]
                                                                +class PointGroupAnalyzer(mol, tolerance=0.3, eigen_tolerance=0.01, matrix_tolerance=0.1)[source]

                                                                Bases: object

                                                                A class to analyze the point group of a molecule. The general outline of the algorithm is as follows:

                                                                @@ -151,7 +151,7 @@

                    -sch_symbol[source]
                    +sch_symbol[source]

                    Schoenflies symbol of the detected point group.

                    @@ -171,7 +171,7 @@
                    -get_equivalent_atoms()[source]
                    +get_equivalent_atoms()[source]

                    Returns sets of equivalent atoms with symmetry operations

                    Parameters
                    @@ -197,19 +197,19 @@
                    -get_pointgroup()[source]
                    +get_pointgroup()[source]

                    Returns a PointGroup object for the molecule.

                    -get_rotational_symmetry_number()[source]
                    +get_rotational_symmetry_number()[source]

                    Return the rotational symmetry number.

                    -get_symmetry_operations()[source]
                    +get_symmetry_operations()[source]

                    Return symmetry operations as a list of SymmOp objects. Returns Cartesian coord symmops.

                    @@ -224,12 +224,12 @@
                    -inversion_op = Rot: [[-1. -0. -0.]  [-0. -1. -0.]  [-0. -0. -1.]] tau [0. 0. 0.][source]
                    +inversion_op = Rot: [[-1. -0. -0.]  [-0. -1. -0.]  [-0. -0. -1.]] tau [0. 0. 0.][source]
                    -is_valid_op(symmop)[source]
                    +is_valid_op(symmop)[source]

                    Check if a particular symmetry operation is a valid symmetry operation for a molecule, i.e., the operation maps all atoms to another equivalent atom.

                    @@ -248,7 +248,7 @@
                    -symmetrize_molecule()[source]
                    +symmetrize_molecule()[source]

                    Returns a symmetrized molecule

                    The equivalent atoms obtained via get_equivalent_atoms() @@ -285,13 +285,13 @@

                    -class PointGroupOperations(sch_symbol, operations, tol=0.1)[source]
                    +class PointGroupOperations(sch_symbol, operations, tol=0.1)[source]

                    Bases: list

                    Defines a point group, which is essentially a sequence of symmetry operations.

                    -sch_symbol[source]
                    +sch_symbol[source]

                    Schoenflies symbol of the point group.

                    @@ -311,7 +311,7 @@
                    -class SpacegroupAnalyzer(structure, symprec=0.01, angle_tolerance=5.0)[source]
                    +class SpacegroupAnalyzer(structure, symprec=0.01, angle_tolerance=5.0)[source]

                    Bases: object

                    Takes a pymatgen.core.structure.Structure object and a symprec. Uses spglib to perform various symmetry finding operations.

                    @@ -332,7 +332,7 @@
                    -find_primitive(keep_site_properties=False)[source]
                    +find_primitive(keep_site_properties=False)[source]

                    Find a primitive version of the unit cell.

                    Parameters
                    @@ -355,7 +355,7 @@
                    -get_conventional_standard_structure(international_monoclinic=True, keep_site_properties=False)[source]
                    +get_conventional_standard_structure(international_monoclinic=True, keep_site_properties=False)[source]

                    Gives a structure with a conventional cell according to certain standards. The standards are defined in Setyawan, W., & Curtarolo, S. (2010). High-throughput electronic band structure calculations: @@ -388,7 +388,7 @@

                    -get_conventional_to_primitive_transformation_matrix(international_monoclinic=True)[source]
                    +get_conventional_to_primitive_transformation_matrix(international_monoclinic=True)[source]

                    Gives the transformation matrix to transform a conventional unit cell to a primitive cell according to certain standards the standards are defined in Setyawan, W., & Curtarolo, S. (2010). @@ -408,7 +408,7 @@

                    -get_crystal_system() → Literal['triclinic', 'monoclinic', 'orthorhombic', 'tetragonal', 'trigonal', 'hexagonal', 'cubic'][source]
                    +get_crystal_system() → Literal['triclinic', 'monoclinic', 'orthorhombic', 'tetragonal', 'trigonal', 'hexagonal', 'cubic'][source]

                    Get the crystal system for the structure, e.g., (triclinic, orthorhombic, cubic, etc.).

                    @@ -426,7 +426,7 @@
                    -get_hall()[source]
                    +get_hall()[source]

                    Returns Hall symbol for structure.

                    Returns
                    @@ -440,7 +440,7 @@
                    -get_ir_reciprocal_mesh(mesh=(10, 10, 10), is_shift=(0, 0, 0))[source]
                    +get_ir_reciprocal_mesh(mesh=(10, 10, 10), is_shift=(0, 0, 0))[source]

                    k-point mesh of the Brillouin zone generated taken into account symmetry.The method returns the irreducible kpoints of the mesh and their weights

                    @@ -465,7 +465,7 @@
                    -get_kpoint_weights(kpoints, atol=1e-05)[source]
                    +get_kpoint_weights(kpoints, atol=1e-05)[source]

                    Calculate the weights for a list of kpoints.

                    Parameters
                    @@ -484,7 +484,7 @@
                    -get_lattice_type() → Literal['triclinic', 'monoclinic', 'orthorhombic', 'tetragonal', 'rhombohedral', 'hexagonal', 'cubic'][source]
                    +get_lattice_type() → Literal['triclinic', 'monoclinic', 'orthorhombic', 'tetragonal', 'rhombohedral', 'hexagonal', 'cubic'][source]

                    Get the lattice for the structure, e.g., (triclinic, orthorhombic, cubic, etc.).This is the same as the crystal system with the exception of the hexagonal/rhombohedral lattice.

                    @@ -502,7 +502,7 @@
                    -get_point_group_operations(cartesian=False)[source]
                    +get_point_group_operations(cartesian=False)[source]

                    Return symmetry operations as a list of SymmOp objects. By default returns fractional coord symmops. But Cartesian can be returned too.

                    @@ -522,7 +522,7 @@
                    -get_point_group_symbol()[source]
                    +get_point_group_symbol()[source]

                    Get the point group associated with the structure.

                    Returns
                    @@ -536,7 +536,7 @@
                    -get_primitive_standard_structure(international_monoclinic=True, keep_site_properties=False)[source]
                    +get_primitive_standard_structure(international_monoclinic=True, keep_site_properties=False)[source]

                    Gives a structure with a primitive cell according to certain standards the standards are defined in Setyawan, W., & Curtarolo, S. (2010). High-throughput electronic band structure calculations: @@ -565,7 +565,7 @@

                    -get_refined_structure(keep_site_properties=False)[source]
                    +get_refined_structure(keep_site_properties=False)[source]

                    Get the refined structure based on detected symmetry. The refined structure is a conventional cell setting with atoms moved to the expected symmetry positions.

                    @@ -588,7 +588,7 @@
                    -get_space_group_number()[source]
                    +get_space_group_number()[source]

                    Get the international spacegroup number (e.g., 62) for structure.

                    Returns
                    @@ -602,7 +602,7 @@
                    -get_space_group_operations()[source]
                    +get_space_group_operations()[source]

                    Get the SpacegroupOperations for the Structure.

                    Returns
                    @@ -613,7 +613,7 @@
                    -get_space_group_symbol()[source]
                    +get_space_group_symbol()[source]

                    Get the spacegroup symbol (e.g., Pnma) for structure.

                    Returns
                    @@ -627,7 +627,7 @@
                    -get_symmetrized_structure()[source]
                    +get_symmetrized_structure()[source]

                    Get a symmetrized structure. A symmetrized structure is one where the sites have been grouped into symmetrically equivalent groups.

                    @@ -639,7 +639,7 @@
                    -get_symmetry_dataset()[source]
                    +get_symmetry_dataset()[source]

                    Returns the symmetry dataset as a dict.

                    Returns
                    @@ -666,7 +666,7 @@
                    -get_symmetry_operations(cartesian=False)[source]
                    +get_symmetry_operations(cartesian=False)[source]

                    Return symmetry operations as a list of SymmOp objects. By default returns fractional coord symmops. But Cartesian can be returned too.

                    @@ -682,7 +682,7 @@
                    -is_laue()[source]
                    +is_laue()[source]
                    Check if the point group of the structure

                    has Laue symmetry (centrosymmetry)

                    @@ -693,7 +693,7 @@
                    -class SpacegroupOperations(int_symbol, int_number, symmops)[source]
                    +class SpacegroupOperations(int_symbol, int_number, symmops)[source]

                    Bases: list

                    Represents a space group, which is a collection of symmetry operations.

                    @@ -708,7 +708,7 @@
                    -are_symmetrically_equivalent(sites1, sites2, symm_prec=0.001)[source]
                    +are_symmetrically_equivalent(sites1, sites2, symm_prec=0.001)[source]

                    Given two sets of PeriodicSites, test if they are actually symmetrically equivalent under this space group. Useful, for example, if you want to test if selecting atoms 1 and 2 out of a set of 4 atoms @@ -738,7 +738,7 @@

                    -cluster_sites(mol, tol, give_only_index=False)[source]
                    +cluster_sites(mol, tol, give_only_index=False)[source]

                    Cluster sites based on distance and species type.

                    Parameters
                    @@ -760,7 +760,7 @@
                    -generate_full_symmops(symmops, tol)[source]
                    +generate_full_symmops(symmops, tol)[source]

                    Recursive algorithm to permute through all possible combinations of the initially supplied symmetry operations to arrive at a complete set of operations mapping a single atom to all other equivalent atoms in the @@ -778,7 +778,7 @@

                    -iterative_symmetrize(mol, max_n=10, tolerance=0.3, epsilon=0.01)[source]
                    +iterative_symmetrize(mol, max_n=10, tolerance=0.3, epsilon=0.01)[source]

                    Returns a symmetrized molecule

                    The equivalent atoms obtained via get_equivalent_atoms() diff --git a/docs/pymatgen.symmetry.bandstructure.html b/docs/pymatgen.symmetry.bandstructure.html index 6e883817290..48926226546 100644 --- a/docs/pymatgen.symmetry.bandstructure.html +++ b/docs/pymatgen.symmetry.bandstructure.html @@ -4,7 +4,7 @@ - pymatgen.symmetry.bandstructure module — pymatgen 2022.5.18 documentation + pymatgen.symmetry.bandstructure module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                    - 2022.5.18 + 2022.5.18.1
                    @@ -119,7 +119,7 @@ generate high-symmetry k-paths using different conventions.

                    -class HighSymmKpath(structure, has_magmoms=False, magmom_axis=None, path_type='setyawan_curtarolo', symprec=0.01, angle_tolerance=5, atol=1e-05)[source]
                    +class HighSymmKpath(structure, has_magmoms=False, magmom_axis=None, path_type='setyawan_curtarolo', symprec=0.01, angle_tolerance=5, atol=1e-05)[source]

                    Bases: pymatgen.symmetry.kpath.KPathBase

                    This class generates path along high symmetry lines in the Brillouin zone according to different conventions. @@ -164,7 +164,7 @@

                    -property equiv_labels[source]
                    +property equiv_labels[source]

                    Returns: The correspondence between the kpoint symbols in the Latimer and Munro convention, Setyawan and Curtarolo, and Hinuma @@ -173,7 +173,7 @@

                    -static get_continuous_path(bandstructure)[source]
                    +static get_continuous_path(bandstructure)[source]

                    Obtain a continuous version of an inputted path using graph theory. This routine will attempt to add connections between nodes of odd-degree to ensure a Eulerian path can be formed. Initial @@ -188,7 +188,7 @@

                    -property label_index[source]
                    +property label_index[source]

                    Returns: The correspondence between numbers and kpoint symbols for the combined kpath generated when path_type = ‘all’. None otherwise.

                    @@ -196,7 +196,7 @@
                    -property path_lengths[source]
                    +property path_lengths[source]

                    Returns: List of lengths of the Latimer and Munro, Setyawan and Curtarolo, and Hinuma conventions in the combined HighSymmKpath object when path_type = ‘all’ respectively. @@ -205,7 +205,7 @@

                    -property path_type[source]
                    +property path_type[source]

                    Returns: The type of kpath chosen

                    diff --git a/docs/pymatgen.symmetry.groups.html b/docs/pymatgen.symmetry.groups.html index e1ae180c3eb..d0569161312 100644 --- a/docs/pymatgen.symmetry.groups.html +++ b/docs/pymatgen.symmetry.groups.html @@ -4,7 +4,7 @@ - pymatgen.symmetry.groups module — pymatgen 2022.5.18 documentation + pymatgen.symmetry.groups module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                    - 2022.5.18 + 2022.5.18.1
                    @@ -120,25 +120,25 @@ SpaceGroup data as published in his textbook “Structure of Materials”.

                    -class PointGroup(*args, **kwargs)[source]
                    +class PointGroup(*args, **kwargs)[source]

                    Bases: pymatgen.symmetry.groups.PointGroup

                    Class representing a Point Group, with generators and symmetry operations.

                    -symbol[source]
                    +symbol[source]

                    Full International or Hermann-Mauguin Symbol.

                    -generators[source]
                    +generators[source]

                    List of generator matrices. Note that 3x3 matrices are used for Point Groups.

                    -symmetry_ops[source]
                    +symmetry_ops[source]

                    Full set of symmetry operations as matrices.

                    @@ -152,31 +152,31 @@
                    -class SpaceGroup(*args, **kwargs)[source]
                    +class SpaceGroup(*args, **kwargs)[source]

                    Bases: pymatgen.symmetry.groups.SpaceGroup

                    Class representing a SpaceGroup.

                    -symbol[source]
                    +symbol[source]

                    Full International or Hermann-Mauguin Symbol.

                    -int_number[source]
                    +int_number[source]

                    International number

                    -generators[source]
                    +generators[source]

                    List of generator matrices. Note that 4x4 matrices are used for Space Groups.

                    -order[source]
                    +order[source]

                    Order of Space Group

                    @@ -200,12 +200,12 @@
                    -class SymmetryGroup[source]
                    +class SymmetryGroup[source]

                    Bases: collections.abc.Sequence, pymatgen.util.string.Stringify

                    Abstract class representing a symmetry group.

                    -is_subgroup(supergroup: pymatgen.symmetry.groups.SymmetryGroup) → bool[source]
                    +is_subgroup(supergroup: pymatgen.symmetry.groups.SymmetryGroup) → bool[source]

                    True if this group is a subgroup of the supplied group.

                    Parameters
                    @@ -219,7 +219,7 @@
                    -is_supergroup(subgroup: pymatgen.symmetry.groups.SymmetryGroup) → bool[source]
                    +is_supergroup(subgroup: pymatgen.symmetry.groups.SymmetryGroup) → bool[source]

                    True if this group is a supergroup of the supplied group.

                    Parameters
                    @@ -233,14 +233,14 @@
                    -abstract property symmetry_ops: set[SymmOp][source]
                    +abstract property symmetry_ops: set[SymmOp][source]

                    Returns: List of symmetry operations associated with the group.

                    -to_latex_string() → str[source]
                    +to_latex_string() → str[source]
                    Returns

                    A latex formatted group symbol with proper subscripts and overlines.

                    @@ -252,7 +252,7 @@
                    -in_array_list(array_list: list[ArrayLike], a: ArrayLike, tol: float = 1e-05) → bool[source]
                    +in_array_list(array_list: list[ArrayLike], a: ArrayLike, tol: float = 1e-05) → bool[source]

                    Extremely efficient nd-array comparison using numpy’s broadcasting. This function checks if a particular array a, is present in a list of arrays. It works for arrays of any size, e.g., even matrix searches.

                    @@ -273,7 +273,7 @@
                    -sg_symbol_from_int_number(int_number: int, hexagonal: bool = True) → str[source]
                    +sg_symbol_from_int_number(int_number: int, hexagonal: bool = True) → str[source]

                    Obtains a SpaceGroup name from its international number.

                    Parameters
                    diff --git a/docs/pymatgen.symmetry.html b/docs/pymatgen.symmetry.html index 838e2d2de09..903ec1c3256 100644 --- a/docs/pymatgen.symmetry.html +++ b/docs/pymatgen.symmetry.html @@ -4,7 +4,7 @@ - pymatgen.symmetry package — pymatgen 2022.5.18 documentation + pymatgen.symmetry package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                    - 2022.5.18 + 2022.5.18.1
                    diff --git a/docs/pymatgen.symmetry.kpath.html b/docs/pymatgen.symmetry.kpath.html index 8256de92e8e..fba7bf3da58 100644 --- a/docs/pymatgen.symmetry.kpath.html +++ b/docs/pymatgen.symmetry.kpath.html @@ -4,7 +4,7 @@ - pymatgen.symmetry.kpath module — pymatgen 2022.5.18 documentation + pymatgen.symmetry.kpath module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                    - 2022.5.18 + 2022.5.18.1
                    @@ -118,7 +118,7 @@

                    Provides classes for generating high-symmetry k-paths using different conventions.

                    -class KPathBase(structure, symprec=0.01, angle_tolerance=5, atol=1e-05, *args, **kwargs)[source]
                    +class KPathBase(structure, symprec=0.01, angle_tolerance=5, atol=1e-05, *args, **kwargs)[source]

                    Bases: object

                    This is the base class for classes used to generate high-symmetry paths in reciprocal space (k-paths) for band structure calculations.

                    @@ -133,7 +133,7 @@
                  -get_kpoints(line_density=20, coords_are_cartesian=True)[source]
                  +get_kpoints(line_density=20, coords_are_cartesian=True)[source]

                  Returns: the kpoints along the paths in Cartesian coordinates together with the labels for symmetry points -Wei.

                  @@ -141,28 +141,28 @@
                  -property kpath[source]
                  +property kpath[source]

                  Returns: The symmetry line path in reciprocal space

                  -property lattice[source]
                  +property lattice[source]

                  Returns: The real space lattice

                  -property rec_lattice[source]
                  +property rec_lattice[source]

                  Returns: The reciprocal space lattice

                  -property structure[source]
                  +property structure[source]

                  Returns: The input structure

                  @@ -171,7 +171,7 @@
                  -class KPathLatimerMunro(structure, has_magmoms=False, magmom_axis=None, symprec=0.01, angle_tolerance=5, atol=1e-05)[source]
                  +class KPathLatimerMunro(structure, has_magmoms=False, magmom_axis=None, symprec=0.01, angle_tolerance=5, atol=1e-05)[source]

                  Bases: pymatgen.symmetry.kpath.KPathBase

                  This class looks for a path along high symmetry lines in the Brillouin zone. It is based on the method outlined in:

                  @@ -213,19 +213,19 @@
                  -static LabelPoints(index)[source]
                  +static LabelPoints(index)[source]

                  Axes used in generating labels for Latimer-Munro convention

                  -static LabelSymbol(index)[source]
                  +static LabelSymbol(index)[source]

                  Letters used in generating labels for Latimer-Munro convention

                  -property mag_type[source]
                  +property mag_type[source]

                  Returns: The type of magnetic space group as a string. Current implementation does not distinguish @@ -237,7 +237,7 @@

                  -class KPathSeek(structure, symprec=0.01, angle_tolerance=5, atol=1e-05, system_is_tri=True)[source]
                  +class KPathSeek(structure, symprec=0.01, angle_tolerance=5, atol=1e-05, system_is_tri=True)[source]

                  Bases: pymatgen.symmetry.kpath.KPathBase

                  This class looks for path along high symmetry lines in the Brillouin Zone. @@ -267,7 +267,7 @@

                  -class KPathSetyawanCurtarolo(structure, symprec=0.01, angle_tolerance=5, atol=1e-05)[source]
                  +class KPathSetyawanCurtarolo(structure, symprec=0.01, angle_tolerance=5, atol=1e-05)[source]

                  Bases: pymatgen.symmetry.kpath.KPathBase

                  This class looks for path along high symmetry lines in the Brillouin Zone. @@ -295,160 +295,160 @@

              -bcc()[source]
              +bcc()[source]

              BCC Path

              -bctet1(c, a)[source]
              +bctet1(c, a)[source]

              BCT1 Path

              -bctet2(c, a)[source]
              +bctet2(c, a)[source]

              BCT2 Path

              -property conventional[source]
              +property conventional[source]

              Returns: The conventional cell structure

              -cubic()[source]
              +cubic()[source]

              CUB Path

              -fcc()[source]
              +fcc()[source]

              FCC Path

              -hex()[source]
              +hex()[source]

              HEX Path

              -mcl(b, c, beta)[source]
              +mcl(b, c, beta)[source]

              MCL Path

              -mclc1(a, b, c, alpha)[source]
              +mclc1(a, b, c, alpha)[source]

              MCLC1 Path

              -mclc2(a, b, c, alpha)[source]
              +mclc2(a, b, c, alpha)[source]

              MCLC2 Path

              -mclc3(a, b, c, alpha)[source]
              +mclc3(a, b, c, alpha)[source]

              MCLC3 Path

              -mclc4(a, b, c, alpha)[source]
              +mclc4(a, b, c, alpha)[source]

              MCLC4 Path

              -mclc5(a, b, c, alpha)[source]
              +mclc5(a, b, c, alpha)[source]

              MCLC5 Path

              -orc()[source]
              +orc()[source]

              ORC Path

              -orcc(a, b, c)[source]
              +orcc(a, b, c)[source]

              ORCC Path

              -orcf1(a, b, c)[source]
              +orcf1(a, b, c)[source]

              ORFC1 Path

              -orcf2(a, b, c)[source]
              +orcf2(a, b, c)[source]

              ORFC2 Path

              -orcf3(a, b, c)[source]
              +orcf3(a, b, c)[source]

              ORFC3 Path

              -orci(a, b, c)[source]
              +orci(a, b, c)[source]

              ORCI Path

              -property prim[source]
              +property prim[source]

              Returns: The primitive cell structure

              -property prim_rec[source]
              +property prim_rec[source]

              Returns: The primitive reciprocal cell structure

              -rhl1(alpha)[source]
              +rhl1(alpha)[source]

              RHL1 Path

              -rhl2(alpha)[source]
              +rhl2(alpha)[source]

              RHL2 Path

              -tet()[source]
              +tet()[source]

              TET Path

              -tria()[source]
              +tria()[source]

              TRI1a Path

              -trib()[source]
              +trib()[source]

              TRI1b Path

              diff --git a/docs/pymatgen.symmetry.maggroups.html b/docs/pymatgen.symmetry.maggroups.html index d5aa859e36b..83088eec200 100644 --- a/docs/pymatgen.symmetry.maggroups.html +++ b/docs/pymatgen.symmetry.maggroups.html @@ -4,7 +4,7 @@ - pymatgen.symmetry.maggroups module — pymatgen 2022.5.18 documentation + pymatgen.symmetry.maggroups module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
              - 2022.5.18 + 2022.5.18.1
              @@ -118,7 +118,7 @@

              Magnetic space groups.

              -class MagneticSpaceGroup(*args, **kwargs)[source]
              +class MagneticSpaceGroup(*args, **kwargs)[source]

              Bases: pymatgen.symmetry.maggroups.MagneticSpaceGroup

              Representation of a magnetic space group.

              Initializes a MagneticSpaceGroup from its Belov, Neronova and diff --git a/docs/pymatgen.symmetry.settings.html b/docs/pymatgen.symmetry.settings.html index c9211fa3eed..474c531f49f 100644 --- a/docs/pymatgen.symmetry.settings.html +++ b/docs/pymatgen.symmetry.settings.html @@ -4,7 +4,7 @@ - pymatgen.symmetry.settings module — pymatgen 2022.5.18 documentation + pymatgen.symmetry.settings module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

              - 2022.5.18 + 2022.5.18.1
              @@ -118,7 +118,7 @@

              This module provides classes for non-standard space-group settings

              -class JonesFaithfulTransformation(P, p)[source]
              +class JonesFaithfulTransformation(P, p)[source]

              Bases: object

              Transformation for space-groups defined in a non-standard setting

              Transform between settings using matrix P and origin shift vector p, @@ -144,7 +144,7 @@ Chapter 1.5, pp. 75–106.

              -property P: list[list[float]][source]
              +property P: list[list[float]][source]

              transformation matrix

              Type
              @@ -155,7 +155,7 @@
              -classmethod from_origin_shift(origin_shift='0,0,0')[source]
              +classmethod from_origin_shift(origin_shift='0,0,0')[source]

              Construct SpaceGroupTransformation from its origin shift string. :param p: origin shift vector :return:

              @@ -163,7 +163,7 @@
              -classmethod from_transformation_string(transformation_string='a,b,c;0,0,0')[source]
              +classmethod from_transformation_string(transformation_string='a,b,c;0,0,0')[source]

              Construct SpaceGroupTransformation from its transformation string. :param P: matrix :param p: origin shift vector @@ -172,7 +172,7 @@

              -property inverse: pymatgen.symmetry.settings.JonesFaithfulTransformation[source]
              +property inverse: pymatgen.symmetry.settings.JonesFaithfulTransformation[source]

              JonesFaithfulTransformation

              Type
              @@ -183,7 +183,7 @@
              -property p: list[float][source]
              +property p: list[float][source]

              translation vector

              Type
              @@ -194,7 +194,7 @@
              -static parse_transformation_string(transformation_string: str = 'a,b,c;0,0,0') → tuple[list[list[float]] | np.ndarray, list[float]][source]
              +static parse_transformation_string(transformation_string: str = 'a,b,c;0,0,0') → tuple[list[list[float]] | np.ndarray, list[float]][source]
              Parameters

              transformation_string (str, optional) – Defaults to “a,b,c;0,0,0”.

              @@ -213,7 +213,7 @@
              -transform_coords(coords: list[list[float]] | np.ndarray) → list[list[float]][source]
              +transform_coords(coords: list[list[float]] | np.ndarray) → list[list[float]][source]

              Takes a list of coordinates and transforms them. :param coords: List of coords :return:

              @@ -221,7 +221,7 @@
              -transform_lattice(lattice: pymatgen.core.lattice.Lattice) → pymatgen.core.lattice.Lattice[source]
              +transform_lattice(lattice: pymatgen.core.lattice.Lattice) → pymatgen.core.lattice.Lattice[source]

              Takes a Lattice object and transforms it. :param lattice: Lattice :return:

              @@ -229,7 +229,7 @@
              -transform_symmop(symmop: SymmOp | MagSymmOp) → SymmOp | MagSymmOp[source]
              +transform_symmop(symmop: SymmOp | MagSymmOp) → SymmOp | MagSymmOp[source]

              Takes a symmetry operation and transforms it. :param symmop: SymmOp or MagSymmOp :return:

              @@ -237,7 +237,7 @@
              -property transformation_string: str[source]
              +property transformation_string: str[source]

              transformation string

              Type
              diff --git a/docs/pymatgen.symmetry.site_symmetries.html b/docs/pymatgen.symmetry.site_symmetries.html index c85fb1e451a..a8b65cf4915 100644 --- a/docs/pymatgen.symmetry.site_symmetries.html +++ b/docs/pymatgen.symmetry.site_symmetries.html @@ -4,7 +4,7 @@ - pymatgen.symmetry.site_symmetries module — pymatgen 2022.5.18 documentation + pymatgen.symmetry.site_symmetries module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
              - 2022.5.18 + 2022.5.18.1
              @@ -118,7 +118,7 @@

              Provides analysis of site symmetries.

              -get_shared_symmetry_operations(struc, pointops, tol=0.1)[source]
              +get_shared_symmetry_operations(struc, pointops, tol=0.1)[source]

              Get all the point group operations shared by a pair of atomic sites in the form [[point operations of site index 1],[],…,[]]

              @@ -136,7 +136,7 @@
              -get_site_symmetries(struc, precision=0.1)[source]
              +get_site_symmetries(struc, precision=0.1)[source]

              Get all the point group operations centered on each atomic site in the form [[point operations of site index 1]…[[point operations of site index N]]]

              diff --git a/docs/pymatgen.symmetry.structure.html b/docs/pymatgen.symmetry.structure.html index d3813df08f1..54c20b34e4f 100644 --- a/docs/pymatgen.symmetry.structure.html +++ b/docs/pymatgen.symmetry.structure.html @@ -4,7 +4,7 @@ - pymatgen.symmetry.structure module — pymatgen 2022.5.18 documentation + pymatgen.symmetry.structure module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
              - 2022.5.18 + 2022.5.18.1
              @@ -118,7 +118,7 @@

              This module implements symmetry-related structure forms.

              -class SymmetrizedStructure(structure: pymatgen.core.structure.Structure, spacegroup, equivalent_positions: Sequence[int], wyckoff_letters: Sequence[str])[source]
              +class SymmetrizedStructure(structure: pymatgen.core.structure.Structure, spacegroup, equivalent_positions: Sequence[int], wyckoff_letters: Sequence[str])[source]

              Bases: pymatgen.core.structure.Structure

              This class represents a symmetrized structure, i.e. a structure where the spacegroup and symmetry operations are defined. This class is @@ -137,7 +137,7 @@

              -as_dict()[source]
              +as_dict()[source]
              Returns

              MSONAble dict

              @@ -147,7 +147,7 @@
              -copy()[source]
              +copy()[source]
              Returns

              Copy of structure.

              @@ -157,7 +157,7 @@
              -find_equivalent_sites(site) → list[pymatgen.core.sites.PeriodicSite][source]
              +find_equivalent_sites(site) → list[pymatgen.core.sites.PeriodicSite][source]

              Finds all symmetrically equivalent sites for a particular site

              Parameters
              @@ -174,7 +174,7 @@
              -classmethod from_dict(d)[source]
              +classmethod from_dict(d)[source]
              Parameters

              d – Dict representation

              diff --git a/docs/pymatgen.transformations.advanced_transformations.html b/docs/pymatgen.transformations.advanced_transformations.html index 10d1ea1c554..deb310acd5a 100644 --- a/docs/pymatgen.transformations.advanced_transformations.html +++ b/docs/pymatgen.transformations.advanced_transformations.html @@ -4,7 +4,7 @@ - pymatgen.transformations.advanced_transformations module — pymatgen 2022.5.18 documentation + pymatgen.transformations.advanced_transformations module — pymatgen 2022.5.18.1 documentation @@ -40,7 +40,7 @@ pymatgen
              - 2022.5.18 + 2022.5.18.1
              @@ -119,7 +119,7 @@

              This module implements more advanced transformations.

              -class AddAdsorbateTransformation(adsorbate, selective_dynamics=False, height=0.9, mi_vec=None, repeat=None, min_lw=5.0, translate=True, reorient=True, find_args=None)[source]
              +class AddAdsorbateTransformation(adsorbate, selective_dynamics=False, height=0.9, mi_vec=None, repeat=None, min_lw=5.0, translate=True, reorient=True, find_args=None)[source]

              Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

              Create absorbate structures.

              Use AdsorbateSiteFinder to add an absorbate to a slab.

              @@ -148,7 +148,7 @@
              -apply_transformation(structure, return_ranked_list=False)[source]
              +apply_transformation(structure, return_ranked_list=False)[source]
              Parameters
                @@ -164,7 +164,7 @@
                -property inverse[source]
                +property inverse[source]

                None

                Type
                @@ -175,7 +175,7 @@
                -property is_one_to_many[source]
                +property is_one_to_many[source]

                True

                Type
                @@ -188,7 +188,7 @@
                -class ChargeBalanceTransformation(charge_balance_sp)[source]
                +class ChargeBalanceTransformation(charge_balance_sp)[source]

                Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                This is a transformation that disorders a structure to make it charge balanced, given an oxidation state-decorated structure.

                @@ -200,7 +200,7 @@
                -apply_transformation(structure)[source]
                +apply_transformation(structure)[source]

                Applies the transformation.

                Parameters
                @@ -214,7 +214,7 @@
                -property inverse[source]
                +property inverse[source]

                None

                Type
                @@ -225,7 +225,7 @@
                -property is_one_to_many[source]
                +property is_one_to_many[source]

                False

                Type
                @@ -238,7 +238,7 @@
                -class CubicSupercellTransformation(min_atoms: int | None = None, max_atoms: int | None = None, min_length: float = 15.0, force_diagonal: bool = False)[source]
                +class CubicSupercellTransformation(min_atoms: int | None = None, max_atoms: int | None = None, min_length: float = 15.0, force_diagonal: bool = False)[source]

                Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                A transformation that aims to generate a nearly cubic supercell structure from a structure.

                @@ -264,7 +264,7 @@
                -apply_transformation(structure: pymatgen.core.structure.Structure) → pymatgen.core.structure.Structure[source]
                +apply_transformation(structure: pymatgen.core.structure.Structure) → pymatgen.core.structure.Structure[source]

                The algorithm solves for a transformation matrix that makes the supercell cubic. The matrix must have integer entries, so entries are rounded (in such a way that forces the matrix to be nonsingular). From @@ -287,14 +287,14 @@

                -property inverse[source]
                +property inverse[source]

                Returns: None

                -property is_one_to_many[source]
                +property is_one_to_many[source]

                Returns: False

                @@ -303,7 +303,7 @@
                -class DisorderOrderedTransformation(max_sites_to_merge=2)[source]
                +class DisorderOrderedTransformation(max_sites_to_merge=2)[source]

                Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                Not to be confused with OrderDisorderedTransformation, this transformation attempts to obtain a @@ -321,7 +321,7 @@

                -apply_transformation(structure, return_ranked_list=False)[source]
                +apply_transformation(structure, return_ranked_list=False)[source]
                Parameters
                  @@ -337,7 +337,7 @@
                  -property inverse[source]
                  +property inverse[source]

                  None

                  Type
                  @@ -348,7 +348,7 @@
                  -property is_one_to_many[source]
                  +property is_one_to_many[source]

                  True

                  Type
                  @@ -361,7 +361,7 @@
                  -class DopingTransformation(dopant, ionic_radius_tol=inf, min_length=10, alio_tol=0, codopant=False, max_structures_per_enum=100, allowed_doping_species=None, **kwargs)[source]
                  +class DopingTransformation(dopant, ionic_radius_tol=inf, min_length=10, alio_tol=0, codopant=False, max_structures_per_enum=100, allowed_doping_species=None, **kwargs)[source]

                  Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                  A transformation that performs doping of a structure.

                  @@ -394,7 +394,7 @@
                  -apply_transformation(structure, return_ranked_list=False)[source]
                  +apply_transformation(structure, return_ranked_list=False)[source]
                  Parameters

                  structure (Structure) – Input structure to dope

                  @@ -410,7 +410,7 @@
                  -property inverse[source]
                  +property inverse[source]

                  None

                  Type
                  @@ -421,7 +421,7 @@
                  -property is_one_to_many[source]
                  +property is_one_to_many[source]

                  True

                  Type
                  @@ -434,7 +434,7 @@
                  -class EnumerateStructureTransformation(min_cell_size=1, max_cell_size=1, symm_prec=0.1, refine_structure=False, enum_precision_parameter=0.001, check_ordered_symmetry=True, max_disordered_sites=None, sort_criteria='ewald', timeout=None)[source]
                  +class EnumerateStructureTransformation(min_cell_size=1, max_cell_size=1, symm_prec=0.1, refine_structure=False, enum_precision_parameter=0.001, check_ordered_symmetry=True, max_disordered_sites=None, sort_criteria='ewald', timeout=None)[source]

                  Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                  Order a disordered structure using enumlib. For complete orderings, this generally produces fewer structures that the OrderDisorderedStructure @@ -479,7 +479,7 @@

                  -apply_transformation(structure, return_ranked_list=False)[source]
                  +apply_transformation(structure, return_ranked_list=False)[source]

                  Returns either a single ordered structure or a sequence of all ordered structures.

                  @@ -506,7 +506,7 @@
                  -property inverse[source]
                  +property inverse[source]

                  None

                  Type
                  @@ -517,7 +517,7 @@
                  -property is_one_to_many[source]
                  +property is_one_to_many[source]

                  True

                  Type
                  @@ -530,7 +530,7 @@
                  -class GrainBoundaryTransformation(rotation_axis, rotation_angle, expand_times=4, vacuum_thickness=0.0, ab_shift=None, normal=False, ratio=True, plane=None, max_search=20, tol_coi=1e-08, rm_ratio=0.7, quick_gen=False)[source]
                  +class GrainBoundaryTransformation(rotation_axis, rotation_angle, expand_times=4, vacuum_thickness=0.0, ab_shift=None, normal=False, ratio=True, plane=None, max_search=20, tol_coi=1e-08, rm_ratio=0.7, quick_gen=False)[source]

                  Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                  A transformation that creates a gb from a bulk structure.

                  @@ -596,7 +596,7 @@
                  -apply_transformation(structure)[source]
                  +apply_transformation(structure)[source]

                  Applies the transformation.

                  Parameters
                  @@ -613,7 +613,7 @@
                  -property inverse[source]
                  +property inverse[source]

                  None

                  Type
                  @@ -624,7 +624,7 @@
                  -property is_one_to_many[source]
                  +property is_one_to_many[source]

                  False

                  Type
                  @@ -637,7 +637,7 @@
                  -class MagOrderParameterConstraint(order_parameter, species_constraints=None, site_constraint_name=None, site_constraints=None)[source]
                  +class MagOrderParameterConstraint(order_parameter, species_constraints=None, site_constraint_name=None, site_constraints=None)[source]

                  Bases: monty.json.MSONable

                  This class can be used to supply MagOrderingTransformation to just a specific subset of species or sites that satisfy the @@ -661,7 +661,7 @@

                  -satisfies_constraint(site)[source]
                  +satisfies_constraint(site)[source]

                  Checks if a periodic site satisfies the constraint.

                  @@ -669,7 +669,7 @@
                  -class MagOrderingTransformation(mag_species_spin, order_parameter=0.5, energy_model=<pymatgen.analysis.energy_models.SymmetryModel object>, **kwargs)[source]
                  +class MagOrderingTransformation(mag_species_spin, order_parameter=0.5, energy_model=<pymatgen.analysis.energy_models.SymmetryModel object>, **kwargs)[source]

                  Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                  This transformation takes a structure and returns a list of collinear magnetic orderings. For disordered structures, make an ordered @@ -698,7 +698,7 @@

                  EnumerateStructureTransformation such as min_cell_size etc.

                  -apply_transformation(structure, return_ranked_list=False)[source]
                  +apply_transformation(structure, return_ranked_list=False)[source]

                  Apply MagOrderTransformation to an input structure. :param structure: Any ordered structure. :param return_ranked_list: As in other Transformations. @@ -707,14 +707,14 @@

                  -static determine_min_cell(disordered_structure)[source]
                  +static determine_min_cell(disordered_structure)[source]

                  Determine the smallest supercell that is able to enumerate the provided structure with the given order parameter

                  -property inverse[source]
                  +property inverse[source]

                  None

                  Type
                  @@ -725,7 +725,7 @@
                  -property is_one_to_many[source]
                  +property is_one_to_many[source]

                  True

                  Type
                  @@ -738,7 +738,7 @@
                  -class MonteCarloRattleTransformation(rattle_std: float, min_distance: float, seed: int | None = None, **kwargs)[source]
                  +class MonteCarloRattleTransformation(rattle_std: float, min_distance: float, seed: int | None = None, **kwargs)[source]

                  Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                  Uses a Monte Carlo rattle procedure to randomly perturb the sites in a structure.

                  @@ -769,7 +769,7 @@
                  -apply_transformation(structure: pymatgen.core.structure.Structure) → pymatgen.core.structure.Structure[source]
                  +apply_transformation(structure: pymatgen.core.structure.Structure) → pymatgen.core.structure.Structure[source]

                  Apply the transformation.

                  Parameters
                  @@ -783,7 +783,7 @@
                  -property inverse[source]
                  +property inverse[source]

                  None

                  Type
                  @@ -794,7 +794,7 @@
                  -property is_one_to_many[source]
                  +property is_one_to_many[source]

                  False

                  Type
                  @@ -807,7 +807,7 @@
                  -class MultipleSubstitutionTransformation(sp_to_replace, r_fraction, substitution_dict, charge_balance_species=None, order=True)[source]
                  +class MultipleSubstitutionTransformation(sp_to_replace, r_fraction, substitution_dict, charge_balance_species=None, order=True)[source]

                  Bases: object

                  Performs multiple substitutions on a structure. For example, can do a fractional replacement of Ge in LiGePS with a list of species, creating one @@ -841,7 +841,7 @@

                  -apply_transformation(structure, return_ranked_list=False)[source]
                  +apply_transformation(structure, return_ranked_list=False)[source]

                  Applies the transformation.

                  Parameters
                  @@ -858,7 +858,7 @@
                  -property inverse[source]
                  +property inverse[source]

                  None

                  Type
                  @@ -869,7 +869,7 @@
                  -property is_one_to_many[source]
                  +property is_one_to_many[source]

                  True

                  Type
                  @@ -882,7 +882,7 @@
                  -class SQSTransformation(scaling, cluster_size_and_shell=None, search_time=60, directory=None, instances=None, temperature=1, wr=1, wn=1, wd=0.5, tol=0.001, best_only=True, remove_duplicate_structures=True, reduction_algo='LLL')[source]
                  +class SQSTransformation(scaling, cluster_size_and_shell=None, search_time=60, directory=None, instances=None, temperature=1, wr=1, wn=1, wd=0.5, tol=0.001, best_only=True, remove_duplicate_structures=True, reduction_algo='LLL')[source]

                  Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                  A transformation that creates a special quasirandom structure (SQS) from a structure with partial occupancies.

                  @@ -926,7 +926,7 @@
                  -apply_transformation(structure, return_ranked_list=False)[source]
                  +apply_transformation(structure, return_ranked_list=False)[source]

                  Applies SQS transformation :param structure: pymatgen Structure with partial occupancies :type structure: pymatgen Structure @@ -941,7 +941,7 @@

                  -property inverse[source]
                  +property inverse[source]

                  None

                  Type
                  @@ -952,7 +952,7 @@
                  -property is_one_to_many[source]
                  +property is_one_to_many[source]

                  True

                  Type
                  @@ -965,7 +965,7 @@
                  -class SlabTransformation(miller_index, min_slab_size, min_vacuum_size, lll_reduce=False, center_slab=False, in_unit_planes=False, primitive=True, max_normal_search=None, shift=0, tol=0.1)[source]
                  +class SlabTransformation(miller_index, min_slab_size, min_vacuum_size, lll_reduce=False, center_slab=False, in_unit_planes=False, primitive=True, max_normal_search=None, shift=0, tol=0.1)[source]

                  Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                  A transformation that creates a slab from a structure.

                  @@ -987,7 +987,7 @@
                  -apply_transformation(structure)[source]
                  +apply_transformation(structure)[source]

                  Applies the transformation.

                  Parameters
                  @@ -1001,7 +1001,7 @@
                  -property inverse[source]
                  +property inverse[source]

                  None

                  Type
                  @@ -1012,7 +1012,7 @@
                  -property is_one_to_many[source]
                  +property is_one_to_many[source]

                  False

                  Type
                  @@ -1025,7 +1025,7 @@
                  -class SubstituteSurfaceSiteTransformation(atom, selective_dynamics=False, height=0.9, mi_vec=None, target_species=None, sub_both_sides=False, range_tol=0.01, dist_from_surf=0)[source]
                  +class SubstituteSurfaceSiteTransformation(atom, selective_dynamics=False, height=0.9, mi_vec=None, target_species=None, sub_both_sides=False, range_tol=0.01, dist_from_surf=0)[source]

                  Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                  Use AdsorptionSiteFinder to perform substitution-type doping on the surface and returns all possible configurations where one dopant is substituted @@ -1053,7 +1053,7 @@

                  -apply_transformation(structure, return_ranked_list=False)[source]
                  +apply_transformation(structure, return_ranked_list=False)[source]
                  Parameters
                    @@ -1069,7 +1069,7 @@
                    -property inverse[source]
                    +property inverse[source]

                    None

                    Type
                    @@ -1080,7 +1080,7 @@
                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    True

                    Type
                    @@ -1093,7 +1093,7 @@
                    -class SubstitutionPredictorTransformation(threshold=0.01, scale_volumes=True, **kwargs)[source]
                    +class SubstitutionPredictorTransformation(threshold=0.01, scale_volumes=True, **kwargs)[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    This transformation takes a structure and uses the structure prediction module to find likely site substitutions.

                    @@ -1108,7 +1108,7 @@
                    -apply_transformation(structure, return_ranked_list=False)[source]
                    +apply_transformation(structure, return_ranked_list=False)[source]

                    Applies the transformation.

                    Parameters
                    @@ -1125,7 +1125,7 @@
                    -property inverse[source]
                    +property inverse[source]

                    None

                    Type
                    @@ -1136,7 +1136,7 @@
                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    True

                    Type
                    @@ -1149,7 +1149,7 @@
                    -class SuperTransformation(transformations, nstructures_per_trans=1)[source]
                    +class SuperTransformation(transformations, nstructures_per_trans=1)[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    This is a transformation that is inherently one-to-many. It is constructed from a list of transformations and returns one structure for each @@ -1169,7 +1169,7 @@

                    -apply_transformation(structure, return_ranked_list=False)[source]
                    +apply_transformation(structure, return_ranked_list=False)[source]

                    Applies the transformation.

                    Parameters
                    @@ -1186,7 +1186,7 @@
                    -property inverse[source]
                    +property inverse[source]

                    None

                    Type
                    @@ -1197,7 +1197,7 @@
                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    True

                    Type
                    diff --git a/docs/pymatgen.transformations.defect_transformations.html b/docs/pymatgen.transformations.defect_transformations.html index 986216a037d..f6317d3f818 100644 --- a/docs/pymatgen.transformations.defect_transformations.html +++ b/docs/pymatgen.transformations.defect_transformations.html @@ -4,7 +4,7 @@ - pymatgen.transformations.defect_transformations module — pymatgen 2022.5.18 documentation + pymatgen.transformations.defect_transformations module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                    - 2022.5.18 + 2022.5.18.1
                    @@ -118,7 +118,7 @@

                    This module defines classes for point defect transformations on structures

                    -class DefectTransformation(scaling_matrix, defect)[source]
                    +class DefectTransformation(scaling_matrix, defect)[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    Generates Defect structures based on pymatgen Defect Core classes

                    @@ -132,7 +132,7 @@
                    -apply_transformation(structure)[source]
                    +apply_transformation(structure)[source]
                    Parameters

                    structure – (bulk structure to be scaled up - typically conventional unit cell)

                    @@ -145,13 +145,13 @@
                    -property inverse[source]
                    +property inverse[source]

                    Not implemented

                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    False

                    Type
                    diff --git a/docs/pymatgen.transformations.html b/docs/pymatgen.transformations.html index 4122dff6493..8ac4e89c87e 100644 --- a/docs/pymatgen.transformations.html +++ b/docs/pymatgen.transformations.html @@ -4,7 +4,7 @@ - pymatgen.transformations package — pymatgen 2022.5.18 documentation + pymatgen.transformations package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                    - 2022.5.18 + 2022.5.18.1
                    diff --git a/docs/pymatgen.transformations.site_transformations.html b/docs/pymatgen.transformations.site_transformations.html index 572d0ed78d3..e4ca61f2afc 100644 --- a/docs/pymatgen.transformations.site_transformations.html +++ b/docs/pymatgen.transformations.site_transformations.html @@ -4,7 +4,7 @@ - pymatgen.transformations.site_transformations module — pymatgen 2022.5.18 documentation + pymatgen.transformations.site_transformations module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                    - 2022.5.18 + 2022.5.18.1
                    @@ -121,7 +121,7 @@ All transformations should inherit the AbstractTransformation ABC.

                    -class AddSitePropertyTransformation(site_properties)[source]
                    +class AddSitePropertyTransformation(site_properties)[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    Simple transformation to add site properties to a given structure

                    @@ -131,7 +131,7 @@
                    -apply_transformation(structure)[source]
                    +apply_transformation(structure)[source]

                    Apply the transformation.

                    Arg:
                    @@ -149,7 +149,7 @@
                    -property inverse[source]
                    +property inverse[source]

                    None

                    Type
                    @@ -160,7 +160,7 @@
                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    False

                    Type
                    @@ -173,7 +173,7 @@
                    -class InsertSitesTransformation(species, coords, coords_are_cartesian=False, validate_proximity=True)[source]
                    +class InsertSitesTransformation(species, coords, coords_are_cartesian=False, validate_proximity=True)[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    This transformation substitutes certain sites with certain species.

                    @@ -191,7 +191,7 @@
                    -apply_transformation(structure)[source]
                    +apply_transformation(structure)[source]

                    Apply the transformation.

                    Arg:
                    @@ -209,7 +209,7 @@
                    -property inverse[source]
                    +property inverse[source]

                    None

                    Type
                    @@ -220,7 +220,7 @@
                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    False

                    Type
                    @@ -233,7 +233,7 @@
                    -class PartialRemoveSitesTransformation(indices, fractions, algo=1)[source]
                    +class PartialRemoveSitesTransformation(indices, fractions, algo=1)[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    Remove fraction of specie from a structure. Requires an oxidation state decorated structure for ewald sum to be @@ -282,27 +282,27 @@

                    -ALGO_BEST_FIRST = 2[source]
                    +ALGO_BEST_FIRST = 2[source]
                    -ALGO_COMPLETE = 1[source]
                    +ALGO_COMPLETE = 1[source]
                    -ALGO_ENUMERATE = 3[source]
                    +ALGO_ENUMERATE = 3[source]
                    -ALGO_FAST = 0[source]
                    +ALGO_FAST = 0[source]
                    -apply_transformation(structure, return_ranked_list=False)[source]
                    +apply_transformation(structure, return_ranked_list=False)[source]

                    Apply the transformation.

                    Parameters
                    @@ -329,7 +329,7 @@
                    -property inverse[source]
                    +property inverse[source]

                    None

                    Type
                    @@ -340,7 +340,7 @@
                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    True

                    Type
                    @@ -353,7 +353,7 @@
                    -class RadialSiteDistortionTransformation(site_index, displacement=0.1, nn_only=False)[source]
                    +class RadialSiteDistortionTransformation(site_index, displacement=0.1, nn_only=False)[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    Radially perturbs atoms around a site. Can be used to create spherical distortion due to a point defect.

                    @@ -375,7 +375,7 @@
                    -apply_transformation(structure)[source]
                    +apply_transformation(structure)[source]

                    Apply the transformation.

                    Parameters
                    @@ -389,14 +389,14 @@
                    -property inverse[source]
                    +property inverse[source]

                    Returns the inverse transformation if available. Otherwise, should return None.

                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    Determines if a Transformation is a one-to-many transformation. If a Transformation is a one-to-many transformation, the apply_transformation method should have a keyword arg @@ -406,7 +406,7 @@

                    -property use_multiprocessing[source]
                    +property use_multiprocessing[source]

                    Indicates whether the transformation can be applied by a subprocessing pool. This should be overridden to return True for transformations that the transmuter can parallelize.

                    @@ -416,7 +416,7 @@
                    -class RemoveSitesTransformation(indices_to_remove)[source]
                    +class RemoveSitesTransformation(indices_to_remove)[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    Remove certain sites in a structure.

                    @@ -426,7 +426,7 @@
                    -apply_transformation(structure)[source]
                    +apply_transformation(structure)[source]

                    Apply the transformation.

                    Arg:
                    @@ -444,7 +444,7 @@
                    -property inverse[source]
                    +property inverse[source]

                    None

                    Type
                    @@ -455,7 +455,7 @@
                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    False

                    Type
                    @@ -468,7 +468,7 @@
                    -class ReplaceSiteSpeciesTransformation(indices_species_map)[source]
                    +class ReplaceSiteSpeciesTransformation(indices_species_map)[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    This transformation substitutes certain sites with certain species.

                    @@ -483,7 +483,7 @@
                    -apply_transformation(structure)[source]
                    +apply_transformation(structure)[source]

                    Apply the transformation.

                    Arg:
                    @@ -501,7 +501,7 @@
                    -property inverse[source]
                    +property inverse[source]

                    None

                    Type
                    @@ -512,7 +512,7 @@
                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    False

                    Type
                    @@ -525,7 +525,7 @@
                    -class TranslateSitesTransformation(indices_to_move, translation_vector, vector_in_frac_coords=True)[source]
                    +class TranslateSitesTransformation(indices_to_move, translation_vector, vector_in_frac_coords=True)[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    This class translates a set of sites by a certain vector.

                    @@ -544,7 +544,7 @@
                    -apply_transformation(structure)[source]
                    +apply_transformation(structure)[source]

                    Apply the transformation.

                    Arg:
                    @@ -562,20 +562,20 @@
                    -as_dict()[source]
                    +as_dict()[source]

                    JSON-serializable dict representation.

                    -property inverse[source]
                    +property inverse[source]

                    Returns: TranslateSitesTransformation with the reverse translation.

                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    False

                    Type
                    diff --git a/docs/pymatgen.transformations.standard_transformations.html b/docs/pymatgen.transformations.standard_transformations.html index 7755190fd44..debea5a7645 100644 --- a/docs/pymatgen.transformations.standard_transformations.html +++ b/docs/pymatgen.transformations.standard_transformations.html @@ -4,7 +4,7 @@ - pymatgen.transformations.standard_transformations module — pymatgen 2022.5.18 documentation + pymatgen.transformations.standard_transformations module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                    - 2022.5.18 + 2022.5.18.1
                    @@ -121,7 +121,7 @@ All transformations should inherit the AbstractTransformation ABC.

                    -class AutoOxiStateDecorationTransformation(symm_tol=0.1, max_radius=4, max_permutations=100000, distance_scale_factor=1.015)[source]
                    +class AutoOxiStateDecorationTransformation(symm_tol=0.1, max_radius=4, max_permutations=100000, distance_scale_factor=1.015)[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    This transformation automatically decorates a structure with oxidation states using a bond valence approach.

                    @@ -144,7 +144,7 @@
                    -apply_transformation(structure)[source]
                    +apply_transformation(structure)[source]

                    Apply the transformation.

                    Parameters
                    @@ -158,7 +158,7 @@
                    -property inverse[source]
                    +property inverse[source]

                    None

                    Type
                    @@ -169,7 +169,7 @@
                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    False

                    Type
                    @@ -182,7 +182,7 @@
                    -class ChargedCellTransformation(charge=0)[source]
                    +class ChargedCellTransformation(charge=0)[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    The ChargedCellTransformation applies a charge to a structure (or defect object).

                    @@ -194,7 +194,7 @@
                    -apply_transformation(structure)[source]
                    +apply_transformation(structure)[source]

                    Apply the transformation.

                    Parameters
                    @@ -208,7 +208,7 @@
                    -property inverse[source]
                    +property inverse[source]

                    NotImplementedError

                    Type
                    @@ -219,7 +219,7 @@
                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    False

                    Type
                    @@ -232,7 +232,7 @@
                    -class ConventionalCellTransformation(symprec=0.01, angle_tolerance=5, international_monoclinic=True)[source]
                    +class ConventionalCellTransformation(symprec=0.01, angle_tolerance=5, international_monoclinic=True)[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    This class finds the conventional cell of the input structure.

                    @@ -247,7 +247,7 @@

                    as the non-right-angle in the unit cell

                    -apply_transformation(structure)[source]
                    +apply_transformation(structure)[source]

                    Returns most primitive cell for structure.

                    Parameters
                    @@ -261,7 +261,7 @@
                    -property inverse[source]
                    +property inverse[source]

                    None

                    Type
                    @@ -272,7 +272,7 @@
                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    False

                    Type
                    @@ -285,7 +285,7 @@
                    -class DeformStructureTransformation(deformation=((1, 0, 0), (0, 1, 0), (0, 0, 1)))[source]
                    +class DeformStructureTransformation(deformation=((1, 0, 0), (0, 1, 0), (0, 0, 1)))[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    This transformation deforms a structure by a deformation gradient matrix

                    @@ -295,7 +295,7 @@
                    -apply_transformation(structure)[source]
                    +apply_transformation(structure)[source]

                    Apply the transformation.

                    Parameters
                    @@ -309,14 +309,14 @@
                    -property inverse[source]
                    +property inverse[source]

                    Returns: Inverse Transformation.

                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    False

                    Type
                    @@ -329,7 +329,7 @@
                    -class DiscretizeOccupanciesTransformation(max_denominator=5, tol=None, fix_denominator=False)[source]
                    +class DiscretizeOccupanciesTransformation(max_denominator=5, tol=None, fix_denominator=False)[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    Discretizes the site occupancies in a disordered structure; useful for grouping similar structures or as a pre-processing step for order-disorder @@ -351,7 +351,7 @@

                    -apply_transformation(structure)[source]
                    +apply_transformation(structure)[source]

                    Discretizes the site occupancies in the structure.

                    Parameters
                    @@ -365,7 +365,7 @@
                    -property inverse[source]
                    +property inverse[source]

                    None

                    Type
                    @@ -376,7 +376,7 @@
                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    False

                    Type
                    @@ -389,7 +389,7 @@
                    -class OrderDisorderedStructureTransformation(algo=0, symmetrized_structures=False, no_oxi_states=False)[source]
                    +class OrderDisorderedStructureTransformation(algo=0, symmetrized_structures=False, no_oxi_states=False)[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    Order a disordered structure. The disordered structure must be oxidation state decorated for ewald sum to be computed. No attempt is made to perform @@ -425,22 +425,22 @@

                    -ALGO_BEST_FIRST = 2[source]
                    +ALGO_BEST_FIRST = 2[source]
                    -ALGO_COMPLETE = 1[source]
                    +ALGO_COMPLETE = 1[source]
                    -ALGO_FAST = 0[source]
                    +ALGO_FAST = 0[source]
                    -apply_transformation(structure, return_ranked_list=False)[source]
                    +apply_transformation(structure, return_ranked_list=False)[source]

                    For this transformation, the apply_transformation method will return only the ordered structure with the lowest Ewald energy, to be consistent with the method signature of the other transformations. @@ -471,7 +471,7 @@

                    -property inverse[source]
                    +property inverse[source]

                    None

                    Type
                    @@ -482,7 +482,7 @@
                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    True

                    Type
                    @@ -493,7 +493,7 @@
                    -property lowest_energy_structure[source]
                    +property lowest_energy_structure[source]

                    Lowest energy structure found.

                    Type
                    @@ -506,7 +506,7 @@
                    -class OxidationStateDecorationTransformation(oxidation_states)[source]
                    +class OxidationStateDecorationTransformation(oxidation_states)[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    This transformation decorates a structure with oxidation states.

                    @@ -520,7 +520,7 @@
                    -apply_transformation(structure)[source]
                    +apply_transformation(structure)[source]

                    Apply the transformation.

                    Parameters
                    @@ -534,7 +534,7 @@
                    -property inverse[source]
                    +property inverse[source]

                    None

                    Type
                    @@ -545,7 +545,7 @@
                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    False

                    Type
                    @@ -558,13 +558,13 @@
                    -class OxidationStateRemovalTransformation[source]
                    +class OxidationStateRemovalTransformation[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    This transformation removes oxidation states from a structure.

                    No arg needed.

                    -apply_transformation(structure)[source]
                    +apply_transformation(structure)[source]

                    Apply the transformation.

                    Parameters
                    @@ -578,7 +578,7 @@
                    -property inverse[source]
                    +property inverse[source]

                    None

                    Type
                    @@ -589,7 +589,7 @@
                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    False

                    Type
                    @@ -602,7 +602,7 @@
                    -class PartialRemoveSpecieTransformation(specie_to_remove, fraction_to_remove, algo=0)[source]
                    +class PartialRemoveSpecieTransformation(specie_to_remove, fraction_to_remove, algo=0)[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    Remove fraction of specie from a structure.

                    Requires an oxidation state decorated structure for ewald sum to be @@ -625,27 +625,27 @@

                    -ALGO_BEST_FIRST = 2[source]
                    +ALGO_BEST_FIRST = 2[source]
                    -ALGO_COMPLETE = 1[source]
                    +ALGO_COMPLETE = 1[source]
                    -ALGO_ENUMERATE = 3[source]
                    +ALGO_ENUMERATE = 3[source]
                    -ALGO_FAST = 0[source]
                    +ALGO_FAST = 0[source]
                    -apply_transformation(structure, return_ranked_list=False)[source]
                    +apply_transformation(structure, return_ranked_list=False)[source]

                    Apply the transformation.

                    Parameters
                    @@ -672,7 +672,7 @@
                    -property inverse[source]
                    +property inverse[source]

                    None

                    Type
                    @@ -683,7 +683,7 @@
                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    True

                    Type
                    @@ -696,7 +696,7 @@
                    -class PerturbStructureTransformation(distance: float = 0.01, min_distance: Optional[Union[int, float]] = None)[source]
                    +class PerturbStructureTransformation(distance: float = 0.01, min_distance: Optional[Union[int, float]] = None)[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    This transformation perturbs a structure by a specified distance in random directions. Used for breaking symmetries.

                    @@ -714,7 +714,7 @@
                    -apply_transformation(structure: pymatgen.core.structure.Structure) → pymatgen.core.structure.Structure[source]
                    +apply_transformation(structure: pymatgen.core.structure.Structure) → pymatgen.core.structure.Structure[source]

                    Apply the transformation.

                    Parameters
                    @@ -728,7 +728,7 @@
                    -property inverse[source]
                    +property inverse[source]

                    None

                    Type
                    @@ -739,7 +739,7 @@
                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    False

                    Type
                    @@ -752,7 +752,7 @@
                    -class PrimitiveCellTransformation(tolerance=0.5)[source]
                    +class PrimitiveCellTransformation(tolerance=0.5)[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    This class finds the primitive cell of the input structure. It returns a structure that is not necessarily orthogonalized @@ -767,7 +767,7 @@

                    -apply_transformation(structure)[source]
                    +apply_transformation(structure)[source]

                    Returns most primitive cell for structure.

                    Parameters
                    @@ -782,7 +782,7 @@
                    -property inverse[source]
                    +property inverse[source]

                    None

                    Type
                    @@ -793,7 +793,7 @@
                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    False

                    Type
                    @@ -806,7 +806,7 @@
                    -class RemoveSpeciesTransformation(species_to_remove)[source]
                    +class RemoveSpeciesTransformation(species_to_remove)[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    Remove all occurrences of some species from a structure.

                    @@ -816,7 +816,7 @@
                    -apply_transformation(structure)[source]
                    +apply_transformation(structure)[source]

                    Apply the transformation.

                    Parameters
                    @@ -830,7 +830,7 @@
                    -property inverse[source]
                    +property inverse[source]

                    None

                    Type
                    @@ -841,7 +841,7 @@
                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    False

                    Type
                    @@ -854,7 +854,7 @@
                    -class RotationTransformation(axis, angle, angle_in_radians=False)[source]
                    +class RotationTransformation(axis, angle, angle_in_radians=False)[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    The RotationTransformation applies a rotation to a structure.

                    @@ -869,7 +869,7 @@
                    -apply_transformation(structure)[source]
                    +apply_transformation(structure)[source]

                    Apply the transformation.

                    Parameters
                    @@ -883,14 +883,14 @@
                    -property inverse[source]
                    +property inverse[source]

                    Returns: Inverse Transformation.

                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    False

                    Type
                    @@ -903,7 +903,7 @@
                    -class ScaleToRelaxedTransformation(unrelaxed_structure, relaxed_structure, species_map=None)[source]
                    +class ScaleToRelaxedTransformation(unrelaxed_structure, relaxed_structure, species_map=None)[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    Takes the unrelaxed and relaxed structure and applies its site and volume relaxation to a structurally similar structures (e.g. bulk: NaCl and PbTe @@ -928,7 +928,7 @@

                    -apply_transformation(structure)[source]
                    +apply_transformation(structure)[source]

                    Returns a copy of structure with lattice parameters and sites scaled to the same degree as the relaxed_structure.

                    @@ -942,7 +942,7 @@
                    -property inverse[source]
                    +property inverse[source]

                    None

                    Type
                    @@ -953,7 +953,7 @@
                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    False

                    Type
                    @@ -966,7 +966,7 @@
                    -class SubstitutionTransformation(species_map)[source]
                    +class SubstitutionTransformation(species_map)[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    This transformation substitutes species for one another.

                    @@ -981,7 +981,7 @@
                    -apply_transformation(structure)[source]
                    +apply_transformation(structure)[source]

                    Apply the transformation.

                    Parameters
                    @@ -995,14 +995,14 @@
                    -property inverse[source]
                    +property inverse[source]

                    Returns: Inverse Transformation.

                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    False

                    Type
                    @@ -1015,7 +1015,7 @@
                    -class SupercellTransformation(scaling_matrix=((1, 0, 0), (0, 1, 0), (0, 0, 1)))[source]
                    +class SupercellTransformation(scaling_matrix=((1, 0, 0), (0, 1, 0), (0, 0, 1)))[source]

                    Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

                    The RotationTransformation applies a rotation to a structure.

                    @@ -1029,7 +1029,7 @@
                    -apply_transformation(structure)[source]
                    +apply_transformation(structure)[source]

                    Apply the transformation.

                    Parameters
                    @@ -1043,7 +1043,7 @@
                    -static from_scaling_factors(scale_a=1, scale_b=1, scale_c=1)[source]
                    +static from_scaling_factors(scale_a=1, scale_b=1, scale_c=1)[source]

                    Convenience method to get a SupercellTransformation from a simple series of three numbers for scaling each lattice vector. Equivalent to calling the normal with [[scale_a, 0, 0], [0, scale_b, 0], @@ -1064,7 +1064,7 @@

                    -property inverse[source]
                    +property inverse[source]

                    NotImplementedError

                    Type
                    @@ -1075,7 +1075,7 @@
                    -property is_one_to_many[source]
                    +property is_one_to_many[source]

                    False

                    Type
                    diff --git a/docs/pymatgen.transformations.transformation_abc.html b/docs/pymatgen.transformations.transformation_abc.html index 6d70ecf9753..454154d1265 100644 --- a/docs/pymatgen.transformations.transformation_abc.html +++ b/docs/pymatgen.transformations.transformation_abc.html @@ -4,7 +4,7 @@ - pymatgen.transformations.transformation_abc module — pymatgen 2022.5.18 documentation + pymatgen.transformations.transformation_abc module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                    - 2022.5.18 + 2022.5.18.1
                    @@ -118,12 +118,12 @@

                    Defines an abstract base class contract for Transformation object.

                    -class AbstractTransformation[source]
                    +class AbstractTransformation[source]

                    Bases: monty.json.MSONable

                    Abstract transformation class.

                    -abstract apply_transformation(structure: pymatgen.core.structure.Structure)[source]
                    +abstract apply_transformation(structure: pymatgen.core.structure.Structure)[source]

                    Applies the transformation to a structure. Depending on whether a transformation is one-to-many, there may be an option to return a ranked list of structures.

                    @@ -153,14 +153,14 @@
                    -abstract property inverse: AbstractTransformation | None[source]
                    +abstract property inverse: AbstractTransformation | None[source]

                    Returns the inverse transformation if available. Otherwise, should return None.

                    -abstract property is_one_to_many: bool[source]
                    +abstract property is_one_to_many: bool[source]

                    Determines if a Transformation is a one-to-many transformation. If a Transformation is a one-to-many transformation, the apply_transformation method should have a keyword arg @@ -170,7 +170,7 @@

                    -property use_multiprocessing: bool[source]
                    +property use_multiprocessing: bool[source]

                    Indicates whether the transformation can be applied by a subprocessing pool. This should be overridden to return True for transformations that the transmuter can parallelize.

                    diff --git a/docs/pymatgen.util.convergence.html b/docs/pymatgen.util.convergence.html index 9412370b374..80af506f6cb 100644 --- a/docs/pymatgen.util.convergence.html +++ b/docs/pymatgen.util.convergence.html @@ -4,7 +4,7 @@ - pymatgen.util.convergence module — pymatgen 2022.5.18 documentation + pymatgen.util.convergence module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                    - 2022.5.18 + 2022.5.18.1
                    @@ -127,7 +127,7 @@ for the best fit a gnuplot line is printed plotting the data, the function and the assymthotic value

                    -exception SplineInputError(msg)[source]
                    +exception SplineInputError(msg)[source]

                    Bases: Exception

                    Error for Spline input

                    @@ -139,25 +139,25 @@
                    -determine_convergence(xs, ys, name, tol=0.0001, extra='', verbose=False, mode='extra', plots=True)[source]
                    +determine_convergence(xs, ys, name, tol=0.0001, extra='', verbose=False, mode='extra', plots=True)[source]

                    test it and at which x_value dy(x)/dx < tol for all x >= x_value, conv is true is such a x_value exists.

                    -exponential(x, a, b, n)[source]
                    +exponential(x, a, b, n)[source]

                    exponential function base n to fit convergence data

                    -extrapolate_reciprocal(xs, ys, n, noise)[source]
                    +extrapolate_reciprocal(xs, ys, n, noise)[source]

                    return the parameters such that a + b / x^n hits the last two data points

                    -extrapolate_simple_reciprocal(xs, ys)[source]
                    +extrapolate_simple_reciprocal(xs, ys)[source]
                    Parameters
                      @@ -171,7 +171,7 @@
                      -get_derivatives(xs, ys, fd=False)[source]
                      +get_derivatives(xs, ys, fd=False)[source]

                      return the derivatives of y(x) at the points x if scipy is available a spline is generated to calculate the derivatives if scipy is not available the left and right slopes are calculated, if both exist the average is returned @@ -180,7 +180,7 @@

                      -get_weights(xs, ys, mode=2)[source]
                      +get_weights(xs, ys, mode=2)[source]
                      Parameters
                        @@ -195,7 +195,7 @@
                        -id_generator(size=8, chars='ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789')[source]
                        +id_generator(size=8, chars='ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789')[source]
                        Parameters
                          @@ -209,19 +209,19 @@
                          -measure(function, xs, ys, popt, weights)[source]
                          +measure(function, xs, ys, popt, weights)[source]

                          measure the quality of a fit

                          -multi_curve_fit(xs, ys, verbose)[source]
                          +multi_curve_fit(xs, ys, verbose)[source]

                          fit multiple functions to the x, y data, return the best fit

                          -multi_reciprocal_extra(xs, ys, noise=False)[source]
                          +multi_reciprocal_extra(xs, ys, noise=False)[source]

                          Calculates for a series of powers ns the parameters for which the last two points are at the curve. With these parameters measure how well the other data points fit. return the best fit.

                          @@ -229,7 +229,7 @@
                          -p0_exponential(xs, ys)[source]
                          +p0_exponential(xs, ys)[source]
                          Parameters
                            @@ -243,13 +243,13 @@
                            -p0_reciprocal(xs, ys)[source]
                            +p0_reciprocal(xs, ys)[source]

                            predictor for first guess for reciprocal

                            -p0_simple_2reciprocal(xs, ys)[source]
                            +p0_simple_2reciprocal(xs, ys)[source]
                            Parameters
                              @@ -263,7 +263,7 @@
                              -p0_simple_4reciprocal(xs, ys)[source]
                              +p0_simple_4reciprocal(xs, ys)[source]
                              Parameters
                                @@ -277,7 +277,7 @@
                                -p0_simple_5reciprocal(xs, ys)[source]
                                +p0_simple_5reciprocal(xs, ys)[source]
                                Parameters
                                  @@ -291,7 +291,7 @@
                                  -p0_simple_reciprocal(xs, ys)[source]
                                  +p0_simple_reciprocal(xs, ys)[source]
                                  Parameters
                                    @@ -305,7 +305,7 @@
                                    -p0_single_reciprocal(xs, ys)[source]
                                    +p0_single_reciprocal(xs, ys)[source]
                                    Parameters
                                      @@ -319,7 +319,7 @@
                                      -print_and_raise_error(xs, ys, name)[source]
                                      +print_and_raise_error(xs, ys, name)[source]
                                      Parameters
                                        @@ -334,43 +334,43 @@
                                        -print_plot_line(function, popt, xs, ys, name, tol=0.05, extra='')[source]
                                        +print_plot_line(function, popt, xs, ys, name, tol=0.05, extra='')[source]

                                        print the gnuplot command line to plot the x, y data with the fitted function using the popt parameters

                                        -reciprocal(x, a, b, n)[source]
                                        +reciprocal(x, a, b, n)[source]

                                        reciprocal function to the power n to fit convergence data

                                        -simple_2reciprocal(x, a, b)[source]
                                        +simple_2reciprocal(x, a, b)[source]

                                        reciprocal function to fit convergence data

                                        -simple_4reciprocal(x, a, b)[source]
                                        +simple_4reciprocal(x, a, b)[source]

                                        reciprocal function to fit convergence data

                                        -simple_5reciprocal(x, a, b)[source]
                                        +simple_5reciprocal(x, a, b)[source]

                                        reciprocal function to fit convergence data

                                        -simple_reciprocal(x, a, b)[source]
                                        +simple_reciprocal(x, a, b)[source]

                                        reciprocal function to fit convergence data

                                        -single_reciprocal(x, a, b, c)[source]
                                        +single_reciprocal(x, a, b, c)[source]

                                        reciprocal function to fit convergence data

                                        diff --git a/docs/pymatgen.util.coord.html b/docs/pymatgen.util.coord.html index 7523822b0ca..228be61b11f 100644 --- a/docs/pymatgen.util.coord.html +++ b/docs/pymatgen.util.coord.html @@ -4,7 +4,7 @@ - pymatgen.util.coord module — pymatgen 2022.5.18 documentation + pymatgen.util.coord module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                        - 2022.5.18 + 2022.5.18.1
                                        @@ -120,7 +120,7 @@ numpy for performance.

                                        -class Simplex(coords)[source]
                                        +class Simplex(coords)[source]

                                        Bases: monty.json.MSONable

                                        A generalized simplex object. See http://en.wikipedia.org/wiki/Simplex.

                                        Initializes a Simplex from vertex coordinates.

                                        @@ -132,7 +132,7 @@
                                        -bary_coords(point)[source]
                                        +bary_coords(point)[source]
                                        Parameters

                                        () (point) – Point coordinates.

                                        @@ -145,13 +145,13 @@
                                        -property coords[source]
                                        +property coords[source]

                                        Returns a copy of the vertex coordinates in the simplex.

                                        -in_simplex(point, tolerance=1e-08)[source]
                                        +in_simplex(point, tolerance=1e-08)[source]

                                        Checks if a point is in the simplex using the standard barycentric coordinate system algorithm.

                                        Taking an arbitrary vertex as an origin, we compute the basis for the @@ -172,7 +172,7 @@

                                        -line_intersection(point1, point2, tolerance=1e-08)[source]
                                        +line_intersection(point1, point2, tolerance=1e-08)[source]

                                        Computes the intersection points of a line with a simplex :param point1: Points that determine the line :type point1: [float] @@ -187,7 +187,7 @@

                                        -point_from_bary_coords(bary_coords)[source]
                                        +point_from_bary_coords(bary_coords)[source]
                                        Parameters

                                        () (bary_coords) – Barycentric coordinates

                                        @@ -200,7 +200,7 @@
                                        -property volume[source]
                                        +property volume[source]

                                        Volume of the simplex.

                                        @@ -208,7 +208,7 @@
                                        -all_distances(coords1, coords2)[source]
                                        +all_distances(coords1, coords2)[source]

                                        Returns the distances between two lists of coordinates

                                        Parameters
                                        @@ -226,7 +226,7 @@
                                        -barycentric_coords(coords, simplex)[source]
                                        +barycentric_coords(coords, simplex)[source]

                                        Converts a list of coordinates to barycentric coordinates, given a simplex with d+1 points. Only works for d >= 2.

                                        @@ -245,7 +245,7 @@
                                        -coord_list_mapping(subset, superset, atol=1e-08)[source]
                                        +coord_list_mapping(subset, superset, atol=1e-08)[source]

                                        Gives the index mapping from a subset to a superset. Subset and superset cannot contain duplicate rows

                                        @@ -263,7 +263,7 @@
                                        -coord_list_mapping_pbc(subset, superset, atol=1e-08)[source]
                                        +coord_list_mapping_pbc(subset, superset, atol=1e-08)[source]

                                        Gives the index mapping from a subset to a superset. Superset cannot contain duplicate matching rows

                                        @@ -281,7 +281,7 @@
                                        -find_in_coord_list(coord_list, coord, atol=1e-08)[source]
                                        +find_in_coord_list(coord_list, coord, atol=1e-08)[source]

                                        Find the indices of matches of a particular coord in a coord_list.

                                        Parameters
                                        @@ -300,7 +300,7 @@
                                        -find_in_coord_list_pbc(fcoord_list, fcoord, atol=1e-08)[source]
                                        +find_in_coord_list_pbc(fcoord_list, fcoord, atol=1e-08)[source]

                                        Get the indices of all points in a fractional coord list that are equal to a fractional coord (with a tolerance), taking into account periodic boundary conditions.

                                        @@ -320,7 +320,7 @@
                                        -get_angle(v1, v2, units='degrees')[source]
                                        +get_angle(v1, v2, units='degrees')[source]

                                        Calculates the angle between two vectors.

                                        Parameters
                                        @@ -338,7 +338,7 @@
                                        -get_linear_interpolated_value(x_values, y_values, x)[source]
                                        +get_linear_interpolated_value(x_values, y_values, x)[source]

                                        Returns an interpolated value by linear interpolation between two values. This method is written to avoid dependency on scipy, which causes issues on threading servers.

                                        @@ -358,7 +358,7 @@
                                        -in_coord_list(coord_list, coord, atol=1e-08)[source]
                                        +in_coord_list(coord_list, coord, atol=1e-08)[source]

                                        Tests if a particular coord is within a coord_list.

                                        Parameters
                                        @@ -377,7 +377,7 @@
                                        -in_coord_list_pbc(fcoord_list, fcoord, atol=1e-08)[source]
                                        +in_coord_list_pbc(fcoord_list, fcoord, atol=1e-08)[source]

                                        Tests if a particular fractional coord is within a fractional coord_list.

                                        Parameters
                                        @@ -395,7 +395,7 @@
                                        -is_coord_subset(subset, superset, atol=1e-08)[source]
                                        +is_coord_subset(subset, superset, atol=1e-08)[source]

                                        Tests if all coords in subset are contained in superset. Doesn’t use periodic boundary conditions

                                        @@ -413,7 +413,7 @@
                                        -is_coord_subset_pbc(subset, superset, atol=1e-08, mask=None)[source]
                                        +is_coord_subset_pbc(subset, superset, atol=1e-08, mask=None)[source]

                                        Tests if all fractional coords in subset are contained in superset.

                                        Parameters
                                        @@ -434,7 +434,7 @@
                                        -lattice_points_in_supercell(supercell_matrix)[source]
                                        +lattice_points_in_supercell(supercell_matrix)[source]

                                        Returns the list of points on the original lattice contained in the supercell in fractional coordinates (with the supercell basis). e.g. [[2,0,0],[0,1,0],[0,0,1]] returns [[0,0,0],[0.5,0,0]]

                                        @@ -450,7 +450,7 @@
                                        -pbc_diff(fcoords1, fcoords2)[source]
                                        +pbc_diff(fcoords1, fcoords2)[source]

                                        Returns the ‘fractional distance’ between two coordinates taking into account periodic boundary conditions.

                                        @@ -473,7 +473,7 @@
                                        -pbc_shortest_vectors(lattice, fcoords1, fcoords2, mask=None, return_d2=False)[source]
                                        +pbc_shortest_vectors(lattice, fcoords1, fcoords2, mask=None, return_d2=False)[source]

                                        Returns the shortest vectors between two lists of coordinates taking into account periodic boundary conditions and the lattice.

                                        diff --git a/docs/pymatgen.util.coord_cython.html b/docs/pymatgen.util.coord_cython.html index 99f04239ee6..79f9b0c80d2 100644 --- a/docs/pymatgen.util.coord_cython.html +++ b/docs/pymatgen.util.coord_cython.html @@ -4,7 +4,7 @@ - pymatgen.util.coord_cython module — pymatgen 2022.5.18 documentation + pymatgen.util.coord_cython module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                        - 2022.5.18 + 2022.5.18.1
                                        @@ -119,7 +119,7 @@ boundary conditions or otherwise.

                                        -coord_list_mapping_pbc()[source]
                                        +coord_list_mapping_pbc()[source]

                                        Gives the index mapping from a subset to a superset. Superset cannot contain duplicate matching rows

                                        @@ -137,7 +137,7 @@
                                        -is_coord_subset_pbc()[source]
                                        +is_coord_subset_pbc()[source]

                                        Tests if all fractional coords in subset are contained in superset. Allows specification of a mask determining pairs that are not allowed to match to each other

                                        @@ -156,7 +156,7 @@
                                        -pbc_shortest_vectors()[source]
                                        +pbc_shortest_vectors()[source]

                                        Returns the shortest vectors between two lists of coordinates taking into account periodic boundary conditions and the lattice.

                                        diff --git a/docs/pymatgen.util.html b/docs/pymatgen.util.html index ed2e1b772bb..94c171c9e8e 100644 --- a/docs/pymatgen.util.html +++ b/docs/pymatgen.util.html @@ -4,7 +4,7 @@ - pymatgen.util package — pymatgen 2022.5.18 documentation + pymatgen.util package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                        - 2022.5.18 + 2022.5.18.1
                                        diff --git a/docs/pymatgen.util.io_utils.html b/docs/pymatgen.util.io_utils.html index 6b6c135474b..9356a4c3c04 100644 --- a/docs/pymatgen.util.io_utils.html +++ b/docs/pymatgen.util.io_utils.html @@ -4,7 +4,7 @@ - pymatgen.util.io_utils module — pymatgen 2022.5.18 documentation + pymatgen.util.io_utils module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                        - 2022.5.18 + 2022.5.18.1
                                        @@ -118,7 +118,7 @@

                                        This module provides utility classes for io operations.

                                        -class AtomicFile(name, mode='w+b', createmode=None, encoding=None)[source]
                                        +class AtomicFile(name, mode='w+b', createmode=None, encoding=None)[source]

                                        Bases: object

                                        This is a straight port of Alexander Saltanov’s atomicfile package.

                                        Writeable file object that atomically writes a file. @@ -141,13 +141,13 @@

                                        -close()[source]
                                        +close()[source]

                                        Close the file.

                                        -discard()[source]
                                        +discard()[source]

                                        Discard the file.

                                        @@ -155,7 +155,7 @@
                                        -ask_yesno(question, default=True)[source]
                                        +ask_yesno(question, default=True)[source]
                                        Parameters
                                          @@ -169,7 +169,7 @@
                                          -clean_lines(string_list, remove_empty_lines=True)[source]
                                          +clean_lines(string_list, remove_empty_lines=True)[source]

                                          Strips whitespace, carriage returns and empty lines from a list of strings.

                                          Parameters
                                          @@ -187,7 +187,7 @@
                                          -micro_pyawk(filename, search, results=None, debug=None, postdebug=None)[source]
                                          +micro_pyawk(filename, search, results=None, debug=None, postdebug=None)[source]

                                          Small awk-mimicking search routine.

                                          ‘file’ is file to search through. ‘search’ is the “search program”, a list of lists/tuples with 3 elements; diff --git a/docs/pymatgen.util.num.html b/docs/pymatgen.util.num.html index 7cfb75ae9a6..b0175d71e1a 100644 --- a/docs/pymatgen.util.num.html +++ b/docs/pymatgen.util.num.html @@ -4,7 +4,7 @@ - pymatgen.util.num module — pymatgen 2022.5.18 documentation + pymatgen.util.num module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                          - 2022.5.18 + 2022.5.18.1
                                          @@ -118,7 +118,7 @@

                                          This module provides utilities for basic math operations.

                                          -abs_cap(val, max_abs_val=1)[source]
                                          +abs_cap(val, max_abs_val=1)[source]

                                          Returns the value with its absolute value capped at max_abs_val. Particularly useful in passing values to trignometric functions where numerical errors may result in an argument > 1 being passed in.

                                          @@ -137,7 +137,7 @@
                                          -make_symmetric_matrix_from_upper_tri(val)[source]
                                          +make_symmetric_matrix_from_upper_tri(val)[source]

                                          Given a symmetric matrix in upper triangular matrix form as flat array indexes as: [A_xx,A_yy,A_zz,A_xy,A_xz,A_yz] This will generate the full matrix: @@ -146,7 +146,7 @@

                                          -maxloc(seq)[source]
                                          +maxloc(seq)[source]

                                          Return the index of the (first) maximum in seq

                                          >>> assert maxloc([1,3,2,3]) == 1
                                          @@ -155,14 +155,14 @@
                                          -min_max_indexes(seq)[source]
                                          +min_max_indexes(seq)[source]

                                          Uses enumerate, max, and min to return the indices of the values in a list with the maximum and minimum value:

                                          -minloc(seq)[source]
                                          +minloc(seq)[source]

                                          Return the index of the (first) minimum in seq

                                          >>> assert minloc(range(3)) == 0
                                          @@ -171,7 +171,7 @@
                                          -monotonic(values, mode='<', atol=1e-08)[source]
                                          +monotonic(values, mode='<', atol=1e-08)[source]

                                          Returns False if values are not monotonic (decreasing|increasing). mode is “<” for a decreasing sequence, “>” for an increasing sequence. Two numbers are considered equal if they differ less that atol.

                                          @@ -186,32 +186,32 @@
                                          -non_decreasing(values)[source]
                                          +non_decreasing(values)[source]

                                          True if values are not decreasing.

                                          -non_increasing(values)[source]
                                          +non_increasing(values)[source]

                                          True if values are not increasing.

                                          -round_to_sigfigs(num, sigfigs)[source]
                                          +round_to_sigfigs(num, sigfigs)[source]

                                          Rounds a number rounded to a specific number of significant figures instead of to a specific precision.

                                          -strictly_decreasing(values)[source]
                                          +strictly_decreasing(values)[source]

                                          True if values are strictly decreasing.

                                          -strictly_increasing(values)[source]
                                          +strictly_increasing(values)[source]

                                          True if values are strictly increasing.

                                          diff --git a/docs/pymatgen.util.plotting.html b/docs/pymatgen.util.plotting.html index dc8ccc0a7fb..b4ced8603ad 100644 --- a/docs/pymatgen.util.plotting.html +++ b/docs/pymatgen.util.plotting.html @@ -4,7 +4,7 @@ - pymatgen.util.plotting module — pymatgen 2022.5.18 documentation + pymatgen.util.plotting module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                          - 2022.5.18 + 2022.5.18.1
                                          @@ -118,7 +118,7 @@

                                          Utilities for generating nicer plots.

                                          -add_fig_kwargs(func)[source]
                                          +add_fig_kwargs(func)[source]

                                          Decorator that adds keyword arguments for functions returning matplotlib figures.

                                          The function should return either a matplotlib figure or None to signal @@ -128,7 +128,7 @@

                                          -format_formula(formula)[source]
                                          +format_formula(formula)[source]

                                          Converts str of chemical formula into latex format for labelling purposes

                                          @@ -140,7 +140,7 @@
                                          -get_ax3d_fig_plt(ax=None, **kwargs)[source]
                                          +get_ax3d_fig_plt(ax=None, **kwargs)[source]

                                          Helper function used in plot functions supporting an optional Axes3D argument. If ax is None, we build the matplotlib figure and create the Axes3D else we return the current active figure.

                                          @@ -161,7 +161,7 @@
                                          -get_ax_fig_plt(ax=None, **kwargs)[source]
                                          +get_ax_fig_plt(ax=None, **kwargs)[source]

                                          Helper function used in plot functions supporting an optional Axes argument. If ax is None, we build the matplotlib figure and create the Axes else we return the current active figure.

                                          @@ -182,7 +182,7 @@
                                          -get_axarray_fig_plt(ax_array, nrows=1, ncols=1, sharex=False, sharey=False, squeeze=True, subplot_kw=None, gridspec_kw=None, **fig_kw)[source]
                                          +get_axarray_fig_plt(ax_array, nrows=1, ncols=1, sharex=False, sharey=False, squeeze=True, subplot_kw=None, gridspec_kw=None, **fig_kw)[source]

                                          Helper function used in plot functions that accept an optional array of Axes as argument. If ax_array is None, we build the matplotlib figure and create the array of Axes by calling plt.subplots else we return the @@ -201,7 +201,7 @@

                                          -periodic_table_heatmap(elemental_data, cbar_label='', cbar_label_size=14, show_plot=False, cmap='YlOrRd', cmap_range=None, blank_color='grey', edge_color='white', value_format=None, value_fontsize=10, symbol_fontsize=14, max_row=9, readable_fontcolor=False)[source]
                                          +periodic_table_heatmap(elemental_data, cbar_label='', cbar_label_size=14, show_plot=False, cmap='YlOrRd', cmap_range=None, blank_color='grey', edge_color='white', value_format=None, value_fontsize=10, symbol_fontsize=14, max_row=9, readable_fontcolor=False)[source]

                                          A static method that generates a heat map overlaid on a periodic table.

                                          Parameters
                                          @@ -240,7 +240,7 @@
                                          -pretty_plot(width=8, height=None, plt=None, dpi=None, color_cycle=('qualitative', 'Set1_9'))[source]
                                          +pretty_plot(width=8, height=None, plt=None, dpi=None, color_cycle=('qualitative', 'Set1_9'))[source]

                                          Provides a publication quality plot, with nice defaults for font sizes etc.

                                          Parameters
                                          @@ -263,7 +263,7 @@
                                          -pretty_plot_two_axis(x, y1, y2, xlabel=None, y1label=None, y2label=None, width=8, height=None, dpi=300, **plot_kwargs)[source]
                                          +pretty_plot_two_axis(x, y1, y2, xlabel=None, y1label=None, y2label=None, width=8, height=None, dpi=300, **plot_kwargs)[source]

                                          Variant of pretty_plot that does a dual axis plot. Adapted from matplotlib examples. Makes it easier to create plots with different axes.

                                          @@ -293,7 +293,7 @@
                                          -pretty_polyfit_plot(x, y, deg=1, xlabel=None, ylabel=None, **kwargs)[source]
                                          +pretty_polyfit_plot(x, y, deg=1, xlabel=None, ylabel=None, **kwargs)[source]

                                          Convenience method to plot data with trend lines based on polynomial fit.

                                          Parameters
                                          @@ -314,7 +314,7 @@
                                          -van_arkel_triangle(list_of_materials, annotate=True)[source]
                                          +van_arkel_triangle(list_of_materials, annotate=True)[source]
                                          A static method that generates a binary van Arkel-Ketelaar triangle to

                                          quantify the ionic, metallic and covalent character of a compound by plotting the electronegativity difference (y) vs average (x). diff --git a/docs/pymatgen.util.provenance.html b/docs/pymatgen.util.provenance.html index a6876abf98b..c0b841c297e 100644 --- a/docs/pymatgen.util.provenance.html +++ b/docs/pymatgen.util.provenance.html @@ -4,7 +4,7 @@ - pymatgen.util.provenance module — pymatgen 2022.5.18 documentation + pymatgen.util.provenance module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                          - 2022.5.18 + 2022.5.18.1
                                          @@ -118,31 +118,31 @@

                                          Classes and methods related to the Structure Notation Language (SNL)

                                          -class Author(name, email)[source]
                                          +class Author(name, email)[source]

                                          Bases: pymatgen.util.provenance.Author

                                          An Author contains two fields:

                                          -name[source]
                                          +name[source]

                                          Name of author (String)

                                          -email[source]
                                          +email[source]

                                          Email of author (String)

                                          Create new instance of Author(name, email)

                                          -as_dict()[source]
                                          +as_dict()[source]

                                          Returns: MSONable dict.

                                          -static from_dict(d)[source]
                                          +static from_dict(d)[source]
                                          Parameters

                                          d (dict) – Dict representation

                                          @@ -155,7 +155,7 @@
                                          -static parse_author(author)[source]
                                          +static parse_author(author)[source]

                                          Parses an Author object from either a String, dict, or tuple

                                          Parameters
                                          @@ -172,7 +172,7 @@
                                          -class HistoryNode(name, url, description)[source]
                                          +class HistoryNode(name, url, description)[source]

                                          Bases: pymatgen.util.provenance.HistoryNode

                                          A HistoryNode represents a step in the chain of events that lead to a Structure. HistoryNodes leave ‘breadcrumbs’ so that you can trace back how @@ -184,20 +184,20 @@

                                          A HistoryNode contains three fields:

                                          -name[source]
                                          +name[source]

                                          The name of a code or resource that this Structure encountered in its history (String)

                                          -url[source]
                                          +url[source]

                                          The URL of that code/resource (String)

                                          -description[source]
                                          +description[source]

                                          A free-form description of how the code/resource is related to the Structure (dict).

                                          @@ -205,13 +205,13 @@

                                          Create new instance of HistoryNode(name, url, description)

                                          -as_dict()[source]
                                          +as_dict()[source]

                                          Returns: Dict

                                          -static from_dict(h_node)[source]
                                          +static from_dict(h_node)[source]
                                          Parameters

                                          d (dict) – Dict representation

                                          @@ -224,7 +224,7 @@
                                          -static parse_history_node(h_node)[source]
                                          +static parse_history_node(h_node)[source]

                                          Parses a History Node object from either a dict or a tuple.

                                          Parameters
                                          @@ -241,7 +241,7 @@
                                          -class StructureNL(struct_or_mol, authors, projects=None, references='', remarks=None, data=None, history=None, created_at=None)[source]
                                          +class StructureNL(struct_or_mol, authors, projects=None, references='', remarks=None, data=None, history=None, created_at=None)[source]

                                          Bases: object

                                          The Structure Notation Language (SNL, pronounced ‘snail’) is container for a pymatgen Structure/Molecule object with some additional fields for @@ -283,13 +283,13 @@

                                          -as_dict()[source]
                                          +as_dict()[source]

                                          Returns: MSONable dict

                                          -classmethod from_dict(d)[source]
                                          +classmethod from_dict(d)[source]
                                          Parameters

                                          d (dict) – Dict representation

                                          @@ -302,7 +302,7 @@
                                          -classmethod from_structures(structures, authors, projects=None, references='', remarks=None, data=None, histories=None, created_at=None)[source]
                                          +classmethod from_structures(structures, authors, projects=None, references='', remarks=None, data=None, histories=None, created_at=None)[source]

                                          A convenience method for getting a list of StructureNL objects by specifying structures and metadata separately. Some of the metadata is applied to all of the structures for ease of use.

                                          @@ -335,7 +335,7 @@
                                          -is_valid_bibtex(reference)[source]
                                          +is_valid_bibtex(reference)[source]

                                          Use pybtex to validate that a reference is in proper BibTeX format

                                          Parameters
                                          diff --git a/docs/pymatgen.util.serialization.html b/docs/pymatgen.util.serialization.html index 623da105f89..9cd04362c8e 100644 --- a/docs/pymatgen.util.serialization.html +++ b/docs/pymatgen.util.serialization.html @@ -4,7 +4,7 @@ - pymatgen.util.serialization module — pymatgen 2022.5.18 documentation + pymatgen.util.serialization module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                          - 2022.5.18 + 2022.5.18.1
                                          @@ -119,13 +119,13 @@ monty.json and monty.serialization documentation.

                                          -class PmgPickler(file, protocol=None, fix_imports=True, buffer_callback=None)[source]
                                          +class PmgPickler(file, protocol=None, fix_imports=True, buffer_callback=None)[source]

                                          Bases: _pickle.Pickler

                                          Persistence of External Objects as described in section 12.1.5.1 of https://docs.python.org/3/library/pickle.html

                                          -persistent_id(obj)[source]
                                          +persistent_id(obj)[source]

                                          Instead of pickling as a regular class instance, we emit a persistent ID.

                                          @@ -134,13 +134,13 @@
                                          -class PmgUnpickler(file, *, fix_imports=True, encoding='ASCII', errors='strict', buffers=())[source]
                                          +class PmgUnpickler(file, *, fix_imports=True, encoding='ASCII', errors='strict', buffers=())[source]

                                          Bases: _pickle.Unpickler

                                          Persistence of External Objects as described in section 12.1.5.1 of https://docs.python.org/3/library/pickle.html

                                          -persistent_load(pid)[source]
                                          +persistent_load(pid)[source]

                                          This method is invoked whenever a persistent ID is encountered. Here, pid is the tuple returned by PmgPickler.

                                          @@ -149,7 +149,7 @@
                                          -class SlotPickleMixin[source]
                                          +class SlotPickleMixin[source]

                                          Bases: object

                                          This mixin makes it possible to pickle/unpickle objects with __slots__ defined.

                                          @@ -157,14 +157,14 @@
                                          -json_pretty_dump(obj, filename)[source]
                                          +json_pretty_dump(obj, filename)[source]

                                          Serialize obj as a JSON formatted stream to the given filename ( pretty printing version)

                                          -pmg_pickle_dump(obj, filobj, **kwargs)[source]
                                          +pmg_pickle_dump(obj, filobj, **kwargs)[source]

                                          Dump an object to a pickle file using PmgPickler.

                                          Parameters
                                          @@ -179,7 +179,7 @@
                                          -pmg_pickle_load(filobj, **kwargs)[source]
                                          +pmg_pickle_load(filobj, **kwargs)[source]

                                          Loads a pickle file and deserialize it with PmgUnpickler.

                                          Parameters
                                          @@ -196,7 +196,7 @@
                                          -pmg_serialize(method)[source]
                                          +pmg_serialize(method)[source]

                                          Decorator for methods that add MSON serializations keys to the dictionary. See documentation of MSON for more details

                                          diff --git a/docs/pymatgen.util.string.html b/docs/pymatgen.util.string.html index 1cedcb13f60..a201fb1f070 100644 --- a/docs/pymatgen.util.string.html +++ b/docs/pymatgen.util.string.html @@ -4,7 +4,7 @@ - pymatgen.util.string module — pymatgen 2022.5.18 documentation + pymatgen.util.string module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                          - 2022.5.18 + 2022.5.18.1
                                          @@ -118,24 +118,24 @@

                                          This module provides utility classes for string operations.

                                          -class Stringify[source]
                                          +class Stringify[source]

                                          Bases: object

                                          Mix-in class for string formatting, e.g. superscripting numbers and symbols or superscripting.

                                          -STRING_MODE = 'SUBSCRIPT'[source]
                                          +STRING_MODE = 'SUBSCRIPT'[source]
                                          -to_html_string() → str[source]
                                          +to_html_string() → str[source]

                                          Generates a HTML formatted string. This uses the output from to_latex_string to generate a HTML output. :return: HTML formatted string.

                                          -to_latex_string() → str[source]
                                          +to_latex_string() → str[source]

                                          Generates a LaTeX formatted string. The mode is set by the class variable STRING_MODE, which defaults to “SUBSCRIPT”. E.g., Fe2O3 is transformed to Fe$_{2}$O$_{3}$. Setting STRING_MODE to “SUPERSCRIPT” creates superscript, e.g., Fe2+ becomes Fe^{2+}. The initial string is obtained from the class’s __str__ method.

                                          @@ -148,7 +148,7 @@
                                          -to_pretty_string() → str[source]
                                          +to_pretty_string() → str[source]
                                          Returns

                                          A pretty string representation. By default, the __str__ output is used, but this method can be @@ -159,7 +159,7 @@

                                          -to_unicode_string()[source]
                                          +to_unicode_string()[source]
                                          Returns

                                          Unicode string with proper sub and superscripts. Note that this works only with systems where the sub @@ -172,7 +172,7 @@

                                          -charge_string(charge, brackets=True, explicit_one=True)[source]
                                          +charge_string(charge, brackets=True, explicit_one=True)[source]

                                          Returns a string representing the charge of an Ion. By default, the charge is placed in brackets with the sign preceding the magnitude, e.g., ‘[+2]’. For uncharged species, the string returned is ‘(aq)’

                                          @@ -189,7 +189,7 @@
                                          -disordered_formula(disordered_struct, symbols=('x', 'y', 'z'), fmt='plain')[source]
                                          +disordered_formula(disordered_struct, symbols=('x', 'y', 'z'), fmt='plain')[source]

                                          Returns a formula of a form like AxB1-x (x=0.5) for disordered structures. Will only return a formula for disordered structures with one @@ -212,7 +212,7 @@

                                          -formula_double_format(afloat, ignore_ones=True, tol=1e-08)[source]
                                          +formula_double_format(afloat, ignore_ones=True, tol=1e-08)[source]

                                          This function is used to make pretty formulas by formatting the amounts. Instead of Li1.0 Fe1.0 P1.0 O4.0, you get LiFePO4.

                                          @@ -231,7 +231,7 @@
                                          -htmlify(formula)[source]
                                          +htmlify(formula)[source]

                                          Generates a HTML formatted formula, e.g. Fe2O3 is transformed to Fe<sub>2</sub>O</sub>3</sub>

                                          Note that Composition now has a to_html_string() method that may @@ -248,7 +248,7 @@

                                          -latexify(formula)[source]
                                          +latexify(formula)[source]

                                          Generates a LaTeX formatted formula. E.g., Fe2O3 is transformed to Fe$_{2}$O$_{3}$.

                                          Note that Composition now has a to_latex_string() method that may @@ -265,7 +265,7 @@

                                          -latexify_spacegroup(spacegroup_symbol)[source]
                                          +latexify_spacegroup(spacegroup_symbol)[source]

                                          Generates a latex formatted spacegroup. E.g., P2_1/c is converted to P2$_{1}$/c and P-1 is converted to P$\overline{1}$.

                                          Note that SymmetryGroup now has a to_latex_string() method that may @@ -282,7 +282,7 @@

                                          -str_delimited(results, header=None, delimiter='\t')[source]
                                          +str_delimited(results, header=None, delimiter='\t')[source]

                                          Given a tuple of tuples, generate a delimited string form. >>> results = [[“a”,”b”,”c”],[“d”,”e”,”f”],[1,2,3]] >>> print(str_delimited(results,delimiter=”,”)) @@ -304,13 +304,13 @@

                                          -stream_has_colours(stream)[source]
                                          +stream_has_colours(stream)[source]

                                          True if stream supports colours. Python cookbook, #475186

                                          -transformation_to_string(matrix, translation_vec=(0, 0, 0), components=('x', 'y', 'z'), c='', delim=',')[source]
                                          +transformation_to_string(matrix, translation_vec=(0, 0, 0), components=('x', 'y', 'z'), c='', delim=',')[source]

                                          Convenience method. Given matrix returns string, e.g. x+2y+1/4 :param matrix :param translation_vec @@ -322,7 +322,7 @@

                                          -unicodeify(formula)[source]
                                          +unicodeify(formula)[source]

                                          Generates a formula with unicode subscripts, e.g. Fe2O3 is transformed to Fe₂O₃. Does not support formulae with decimal points.

                                          Note that Composition now has a to_unicode_string() method that may @@ -339,7 +339,7 @@

                                          -unicodeify_spacegroup(spacegroup_symbol)[source]
                                          +unicodeify_spacegroup(spacegroup_symbol)[source]

                                          Generates a unicode formatted spacegroup. E.g., P2$_{1}$/c is converted to P2₁/c and P$\overline{1}$ is converted to P̅1.

                                          Note that SymmetryGroup now has a to_unicode_string() method that @@ -356,7 +356,7 @@

                                          -unicodeify_species(specie_string)[source]
                                          +unicodeify_species(specie_string)[source]

                                          Generates a unicode formatted species string, with appropriate superscripts for oxidation states.

                                          Note that Species now has a to_unicode_string() method that diff --git a/docs/pymatgen.util.testing.html b/docs/pymatgen.util.testing.html index 0ef9de0024a..2aeb440796c 100644 --- a/docs/pymatgen.util.testing.html +++ b/docs/pymatgen.util.testing.html @@ -4,7 +4,7 @@ - pymatgen.util.testing module — pymatgen 2022.5.18 documentation + pymatgen.util.testing module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen

                                          - 2022.5.18 + 2022.5.18.1
                                          @@ -121,7 +121,7 @@ right away.

                                          -class PymatgenTest(methodName='runTest')[source]
                                          +class PymatgenTest(methodName='runTest')[source]

                                          Bases: unittest.case.TestCase

                                          Extends unittest.TestCase with functions (taken from numpy.testing.utils) that support the comparison of arrays.

                                          @@ -130,34 +130,34 @@ not have a method with the specified name.

                                          -MODULE_DIR = PosixPath('/Users/shyue/repos/pymatgen/docs_rst/../pymatgen/util')[source]
                                          +MODULE_DIR = PosixPath('/Users/shyue/repos/pymatgen/docs_rst/../pymatgen/util')[source]
                                          -STRUCTURES_DIR = PosixPath('/Users/shyue/repos/pymatgen/docs_rst/../pymatgen/util/structures')[source]
                                          +STRUCTURES_DIR = PosixPath('/Users/shyue/repos/pymatgen/docs_rst/../pymatgen/util/structures')[source]
                                          -TEST_FILES_DIR = PosixPath('/Users/shyue/repos/pymatgen/docs_rst/../pymatgen/util/../../test_files')[source]
                                          +TEST_FILES_DIR = PosixPath('/Users/shyue/repos/pymatgen/docs_rst/../pymatgen/util/../../test_files')[source]
                                          -TEST_STRUCTURES = {'BaNiO3': <pymatgen.alchemy.materials.TransformedStructure object>, 'CsCl': Structure Summary Lattice     abc : 4.209 4.209 4.209  angles : 90.0 90.0 90.0  volume : 74.56530132899998       A : 4.209 0.0 0.0       B : 0.0 4.209 0.0       C : 0.0 0.0 4.209 PeriodicSite: Cs (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Cl (2.1045, 2.1045, 2.1045) [0.5000, 0.5000, 0.5000], 'Graphite': Structure Summary Lattice     abc : 2.4700000000000006 2.47 6.8  angles : 90.0 90.0 120.00000000000001  volume : 35.928033824449685       A : -1.2350000000000005 -2.139082747347564 -3.024877593893963e-16       B : -1.2349999999999997 2.139082747347564 1.5124387969469814e-16       C : 0.0 0.0 -6.8 PeriodicSite: C0+ (-1.2350, -0.7132, -5.1000) [0.6667, 0.3333, 0.7500] PeriodicSite: C0+ (-1.2350, 0.7132, -1.7000) [0.3333, 0.6667, 0.2500] PeriodicSite: C0+ (0.0000, 0.0000, -5.1000) [0.0000, 0.0000, 0.7500] PeriodicSite: C0+ (0.0000, 0.0000, -1.7000) [0.0000, 0.0000, 0.2500], 'He_BCC': Structure Summary Lattice     abc : 2.737172073807164 2.7371720737557492 2.73717207  angles : 109.47122060669534 109.47122060631484 109.47122066304705  volume : 15.786447515629305       A : 2.58063058 0.0 -0.91239069       B : -1.29031529 2.23489164 -0.91239069       C : 0.0 0.0 2.73717207 PeriodicSite: He (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000], 'K2O2': Structure Summary Lattice     abc : 4.862375062662279 4.862375062662278 6.361  angles : 90.0 90.0 91.89149308502677  volume : 150.30921504900002       A : 3.3810000000000002 -3.4945000000000004 0.0       B : 3.381 3.4944999999999995 4.2795282396204257e-16       C : 0.0 0.0 -6.361 PeriodicSite: K+ (1.6905, -1.0861, -1.5902) [0.4054, 0.0946, 0.2500] PeriodicSite: K+ (1.6905, 1.0861, -4.7707) [0.0946, 0.4054, 0.7500] PeriodicSite: K+ (5.0715, 1.0861, -4.7707) [0.5946, 0.9054, 0.7500] PeriodicSite: K+ (5.0715, -1.0861, -1.5902) [0.9054, 0.5946, 0.2500] PeriodicSite: O- (3.3810, -0.6262, -3.6417) [0.5896, 0.4104, 0.5725] PeriodicSite: O- (3.3810, 0.6262, -2.7193) [0.4104, 0.5896, 0.4275] PeriodicSite: O- (3.3810, -2.8683, -0.4612) [0.9104, 0.0896, 0.0725] PeriodicSite: O- (3.3810, 2.8683, -5.8998) [0.0896, 0.9104, 0.9275], 'La2CoO4F': Structure Summary Lattice     abc : 6.847249 6.847249 5.748369  angles : 90.0 90.0 132.754623  volume : 197.89340779864318       A : 6.847249 0.0 4.192730785407457e-16       B : -4.648323410186749 5.027714027499061 4.192730785407457e-16       C : 0.0 0.0 5.748369 PeriodicSite: La3+ (-3.0614, 4.3336, 2.7708) [0.1380, 0.8620, 0.4820] PeriodicSite: La3+ (5.2603, 0.6941, 2.9775) [0.8620, 0.1380, 0.5180] PeriodicSite: La3+ (-0.4875, 3.2079, 5.6450) [0.3620, 0.6380, 0.9820] PeriodicSite: La3+ (2.6864, 1.8198, 0.1033) [0.6380, 0.3620, 0.0180] PeriodicSite: Co3+ (1.0995, 2.5139, 2.8742) [0.5000, 0.5000, 0.5000] PeriodicSite: Co3+ (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: O2- (-0.9933, 3.4292, 3.2966) [0.3180, 0.6821, 0.5735] PeriodicSite: O2- (3.1922, 1.5986, 2.4518) [0.6821, 0.3180, 0.4265] PeriodicSite: O2- (-2.5555, 4.1124, 0.4224) [0.1820, 0.8179, 0.0735] PeriodicSite: O2- (4.7545, 0.9153, 5.3260) [0.8179, 0.1820, 0.9265] PeriodicSite: O2- (1.4256, 3.8686, 1.4371) [0.7305, 0.7695, 0.2500] PeriodicSite: O2- (1.8728, 3.6730, 4.3113) [0.7695, 0.7305, 0.7500] PeriodicSite: O2- (0.3261, 1.3547, 1.4371) [0.2305, 0.2695, 0.2500] PeriodicSite: O2- (0.7734, 1.1591, 4.3113) [0.2695, 0.2305, 0.7500] PeriodicSite: F- (-2.3242, 2.5139, 4.3113) [0.0000, 0.5000, 0.7500] PeriodicSite: F2- (3.4236, 0.0000, 1.4371) [0.5000, 0.0000, 0.2500], 'Li10GeP2S12': Structure Summary Lattice     abc : 8.69407 8.69407 12.5994  angles : 90.0 90.0 90.0  volume : 952.3489977658411       A : -8.69407 0.0 -5.323582498531514e-16       B : 5.323582498531514e-16 -8.69407 -5.323582498531514e-16       C : 0.0 0.0 -12.5994 PeriodicSite: Li:0.691 (-6.4658, -6.3310, -10.2912) [0.7437, 0.7282, 0.8168] PeriodicSite: Li:0.691 (-2.2283, -2.3630, -10.2912) [0.2563, 0.2718, 0.8168] PeriodicSite: Li:0.691 (-6.7101, -2.1187, -3.9915) [0.7718, 0.2437, 0.3168] PeriodicSite: Li:0.691 (-1.9840, -6.5753, -3.9915) [0.2282, 0.7563, 0.3168] PeriodicSite: Li:0.691 (-6.5753, -1.9840, -8.6079) [0.7563, 0.2282, 0.6832] PeriodicSite: Li:0.691 (-2.1187, -6.7101, -8.6079) [0.2437, 0.7718, 0.6832] PeriodicSite: Li:0.691 (-6.3310, -6.4658, -2.3082) [0.7282, 0.7437, 0.1832] PeriodicSite: Li:0.691 (-2.3630, -2.2283, -2.3082) [0.2718, 0.2563, 0.1832] PeriodicSite: Li:0.691 (-6.5753, -6.7101, -8.6079) [0.7563, 0.7718, 0.6832] PeriodicSite: Li:0.691 (-2.1187, -1.9840, -8.6079) [0.2437, 0.2282, 0.6832] PeriodicSite: Li:0.691 (-6.3310, -2.2283, -2.3082) [0.7282, 0.2563, 0.1832] PeriodicSite: Li:0.691 (-2.3630, -6.4658, -2.3082) [0.2718, 0.7437, 0.1832] PeriodicSite: Li:0.691 (-6.4658, -2.3630, -10.2912) [0.7437, 0.2718, 0.8168] PeriodicSite: Li:0.691 (-2.2283, -6.3310, -10.2912) [0.2563, 0.7282, 0.8168] PeriodicSite: Li:0.691 (-6.7101, -6.5753, -3.9915) [0.7718, 0.7563, 0.3168] PeriodicSite: Li:0.691 (-1.9840, -2.1187, -3.9915) [0.2282, 0.2437, 0.3168] PeriodicSite: Li (0.0000, -4.3470, -0.6980) [0.0000, 0.5000, 0.0554] PeriodicSite: Li (0.0000, -4.3470, -6.9977) [0.0000, 0.5000, 0.5554] PeriodicSite: Li (-4.3470, 0.0000, -5.6017) [0.5000, 0.0000, 0.4446] PeriodicSite: Li (-4.3470, 0.0000, -11.9014) [0.5000, 0.0000, 0.9446] PeriodicSite: Li:0.643 (-6.5527, -6.5527, -0.0000) [0.7537, 0.7537, 0.0000] PeriodicSite: Li:0.643 (-2.1413, -2.1413, -0.0000) [0.2463, 0.2463, 0.0000] PeriodicSite: Li:0.643 (-6.4884, -2.2057, -6.2997) [0.7463, 0.2537, 0.5000] PeriodicSite: Li:0.643 (-2.2057, -6.4884, -6.2997) [0.2537, 0.7463, 0.5000] PeriodicSite: Li:0.643 (-6.4884, -6.4884, -6.2997) [0.7463, 0.7463, 0.5000] PeriodicSite: Li:0.643 (-2.2057, -2.2057, -6.2997) [0.2537, 0.2537, 0.5000] PeriodicSite: Li:0.643 (-6.5527, -2.1413, -0.0000) [0.7537, 0.2463, 0.0000] PeriodicSite: Li:0.643 (-2.1413, -6.5527, -0.0000) [0.2463, 0.7537, 0.0000] PeriodicSite: Ge:0.515, P:0.485 (0.0000, -4.3470, -3.8970) [0.0000, 0.5000, 0.3093] PeriodicSite: Ge:0.515, P:0.485 (0.0000, -4.3470, -10.1967) [0.0000, 0.5000, 0.8093] PeriodicSite: Ge:0.515, P:0.485 (-4.3470, 0.0000, -2.4027) [0.5000, 0.0000, 0.1907] PeriodicSite: Ge:0.515, P:0.485 (-4.3470, 0.0000, -8.7024) [0.5000, 0.0000, 0.6907] PeriodicSite: P (0.0000, 0.0000, -6.2997) [0.0000, 0.0000, 0.5000] PeriodicSite: P (-4.3470, -4.3470, -0.0000) [0.5000, 0.5000, 0.0000] PeriodicSite: S (-8.6941, -7.0918, -7.4299) [1.0000, 0.8157, 0.5897] PeriodicSite: S (0.0000, -1.6023, -7.4299) [0.0000, 0.1843, 0.5897] PeriodicSite: S (-5.9494, -4.3470, -1.1302) [0.6843, 0.5000, 0.0897] PeriodicSite: S (-2.7447, -4.3470, -1.1302) [0.3157, 0.5000, 0.0897] PeriodicSite: S (-4.3470, -2.7447, -11.4692) [0.5000, 0.3157, 0.9103] PeriodicSite: S (-4.3470, -5.9494, -11.4692) [0.5000, 0.6843, 0.9103] PeriodicSite: S (-7.0918, 0.0000, -5.1695) [0.8157, 0.0000, 0.4103] PeriodicSite: S (-1.6023, 0.0000, -5.1695) [0.1843, 0.0000, 0.4103] PeriodicSite: S (-8.6941, -6.0937, -11.4025) [1.0000, 0.7009, 0.9050] PeriodicSite: S (0.0000, -2.6004, -11.4025) [0.0000, 0.2991, 0.9050] PeriodicSite: S (-6.9474, -4.3470, -5.1028) [0.7991, 0.5000, 0.4050] PeriodicSite: S (-1.7466, -4.3470, -5.1028) [0.2009, 0.5000, 0.4050] PeriodicSite: S (-4.3470, -1.7466, -7.4966) [0.5000, 0.2009, 0.5950] PeriodicSite: S (-4.3470, -6.9474, -7.4966) [0.5000, 0.7991, 0.5950] PeriodicSite: S (-6.0937, 0.0000, -1.1969) [0.7009, 0.0000, 0.0950] PeriodicSite: S (-2.6004, 0.0000, -1.1969) [0.2991, 0.0000, 0.0950] PeriodicSite: S (0.0000, -2.6169, -2.6282) [0.0000, 0.3010, 0.2086] PeriodicSite: S (-8.6941, -6.0772, -2.6282) [1.0000, 0.6990, 0.2086] PeriodicSite: S (-1.7301, -4.3470, -8.9279) [0.1990, 0.5000, 0.7086] PeriodicSite: S (-6.9640, -4.3470, -8.9279) [0.8010, 0.5000, 0.7086] PeriodicSite: S (-4.3470, -6.9640, -3.6715) [0.5000, 0.8010, 0.2914] PeriodicSite: S (-4.3470, -1.7301, -3.6715) [0.5000, 0.1990, 0.2914] PeriodicSite: S (-2.6169, 0.0000, -9.9712) [0.3010, 0.0000, 0.7914] PeriodicSite: S (-6.0772, 0.0000, -9.9712) [0.6990, 0.0000, 0.7914], 'Li2O': Structure Summary Lattice     abc : 3.291071792359756 3.291071899625086 3.2910720568557887  angles : 60.12971043288485 60.12970952137675 60.12970313039097  volume : 25.279668381289053       A : 2.91738857 0.09789437 1.52000466       B : 0.96463406 2.75503561 1.52000466       C : 0.13320635 0.09789443 3.28691771 PeriodicSite: O2- (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Li+ (3.0121, 2.2136, 4.7463) [0.7502, 0.7502, 0.7502] PeriodicSite: Li+ (1.0031, 0.7372, 1.5806) [0.2498, 0.2498, 0.2498], 'Li2O2': Structure Summary Lattice     abc : 3.1830000000000007 3.1830000000000003 7.7258  angles : 90.0 90.0 120.00000000000001  volume : 67.7871492344378       A : -1.5915000000000006 -2.756558860245869 -3.898050761686025e-16       B : -1.5914999999999992 2.756558860245869 1.9490253808430124e-16       C : 0.0 0.0 -7.7258 PeriodicSite: Li+ (0.0000, 0.0000, -3.8629) [0.0000, 0.0000, 0.5000] PeriodicSite: Li+ (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Li+ (-1.5915, -0.9190, -5.7943) [0.6667, 0.3333, 0.7500] PeriodicSite: Li+ (-1.5915, 0.9190, -1.9314) [0.3333, 0.6667, 0.2500] PeriodicSite: O- (-1.5915, -0.9190, -1.1566) [0.6667, 0.3333, 0.1497] PeriodicSite: O- (-1.5915, 0.9190, -6.5692) [0.3333, 0.6667, 0.8503] PeriodicSite: O- (-1.5915, 0.9190, -5.0195) [0.3333, 0.6667, 0.6497] PeriodicSite: O- (-1.5915, -0.9190, -2.7063) [0.6667, 0.3333, 0.3503], 'Li3V2(PO4)3': Structure Summary Lattice     abc : 8.64068 8.67265 8.64068  angles : 61.21317 61.3442 61.21317  volume : 470.7978186322687       A : -2.470939478415996 -7.168424451387926 -4.143609518420984       B : -7.600861301025969 0.0 -4.17633397910965       C : 0.0 0.0 -8.64068 PeriodicSite: Li0+ (-9.8221, -7.1201, -8.1771) [0.9933, 0.9693, 0.0015] PeriodicSite: Li0+ (-5.2652, -3.5733, -8.6603) [0.4985, 0.5307, 0.5067] PeriodicSite: Li0+ (-6.0857, -1.1171, -6.7518) [0.1558, 0.7500, 0.3442] PeriodicSite: Li0+ (-3.9986, -6.0875, -10.1861) [0.8492, 0.2500, 0.6508] PeriodicSite: Li0+ (-4.4741, -5.3421, -5.9052) [0.7452, 0.3464, 0.1586] PeriodicSite: Li0+ (-2.0112, -2.4471, -8.5778) [0.3414, 0.1536, 0.7548] PeriodicSite: V0+ (-8.6165, -6.1274, -14.5645) [0.8548, 0.8558, 0.8621] PeriodicSite: V0+ (-6.4732, -4.5730, -10.9092) [0.6379, 0.6442, 0.6452] PeriodicSite: V0+ (-3.5744, -2.5407, -5.9951) [0.3544, 0.3550, 0.3522] PeriodicSite: V0+ (-1.4669, -1.0591, -2.4754) [0.1478, 0.1450, 0.1456] PeriodicSite: P0+ (-7.8497, -1.7789, -9.7592) [0.2482, 0.9521, 0.5503] PeriodicSite: P0+ (-6.5114, -6.8080, -8.3997) [0.9497, 0.5479, 0.2518] PeriodicSite: P0+ (-6.8308, -3.2786, -5.3958) [0.4574, 0.7500, 0.0426] PeriodicSite: P0+ (-3.2537, -3.9267, -11.5417) [0.5478, 0.2500, 0.9522] PeriodicSite: P0+ (-3.5598, -0.2774, -8.5391) [0.0387, 0.4558, 0.7494] PeriodicSite: P0+ (-2.1909, -5.3806, -7.2809) [0.7506, 0.0442, 0.4613] PeriodicSite: O0+ (-8.3983, -5.1136, -10.9141) [0.7133, 0.8730, 0.4991] PeriodicSite: O0+ (-6.5103, -3.5115, -12.5689) [0.4899, 0.6973, 0.8827] PeriodicSite: O0+ (-7.4256, -0.5548, -10.6251) [0.0774, 0.9518, 0.7325] PeriodicSite: O0+ (-7.9453, -1.4000, -8.2592) [0.1953, 0.9818, 0.3876] PeriodicSite: O0+ (-6.7928, -2.9117, -9.8164) [0.4062, 0.7617, 0.5732] PeriodicSite: O0+ (-5.7536, -6.2988, -11.6913) [0.8787, 0.4713, 0.7039] PeriodicSite: O0+ (-7.9023, -6.6440, -7.7347) [0.9268, 0.7384, 0.0938] PeriodicSite: O0+ (-6.0633, -5.5016, -9.1213) [0.7675, 0.5482, 0.4226] PeriodicSite: O0+ (-7.6267, -4.4251, -5.9980) [0.6173, 0.8027, 0.0101] PeriodicSite: O0+ (-7.5702, -1.8930, -5.4665) [0.2641, 0.9101, 0.0661] PeriodicSite: O0+ (-4.4855, -4.0749, -10.6051) [0.5685, 0.4053, 0.7588] PeriodicSite: O0+ (-4.7679, -0.0067, -9.4196) [0.0009, 0.6270, 0.7867] PeriodicSite: O0+ (-5.3896, -7.0627, -7.3776) [0.9852, 0.3888, 0.1934] PeriodicSite: O0+ (-5.5557, -3.1102, -6.2999) [0.4339, 0.5899, 0.2359] PeriodicSite: O0+ (-2.5509, -5.3129, -11.5157) [0.7412, 0.0947, 0.9316] PeriodicSite: O0+ (-2.3963, -2.7970, -10.9316) [0.3902, 0.1884, 0.9869] PeriodicSite: O0+ (-3.8311, -1.6586, -7.8407) [0.2314, 0.4288, 0.5892] PeriodicSite: O0+ (-2.2016, -0.4825, -9.2908) [0.0673, 0.2678, 0.9135] PeriodicSite: O0+ (-3.2143, -4.2040, -7.1387) [0.5865, 0.2322, 0.4327] PeriodicSite: O0+ (-4.2162, -0.8054, -5.2624) [0.1124, 0.5182, 0.3047] PeriodicSite: O0+ (-2.1852, -5.7069, -8.7871) [0.7961, 0.0287, 0.6213] PeriodicSite: O0+ (-2.7916, -6.5290, -6.3923) [0.9108, 0.0712, 0.2686] PeriodicSite: O0+ (-3.6360, -3.6778, -4.3760) [0.5131, 0.3116, 0.1098] PeriodicSite: O0+ (-1.6028, -2.1976, -6.1825) [0.3066, 0.1112, 0.5148], 'LiFePO4': Structure Summary Lattice     abc : 4.7448 6.0657700000000006 10.41037  angles : 90.50178999999999 90.00019 90.00362  volume : 299.60796771125047       A : 0.0 0.0 -4.7448       B : -0.053122654367700306 -6.065537365280947 0.00038324092231544317       C : 10.41036999994276 0.0 3.452209424235223e-05 PeriodicSite: Li (10.3571, -6.0655, 0.0004) [0.0000, 1.0000, 1.0000] PeriodicSite: Li (-0.0265, -3.0328, -4.7446) [1.0000, 0.5000, 0.0000] PeriodicSite: Li (5.1521, -6.0655, -2.3720) [0.5000, 1.0000, 0.5000] PeriodicSite: Li (5.1786, -3.0328, -2.3723) [0.5000, 0.5000, 0.5000] PeriodicSite: Fe (2.2647, -1.5372, -2.4912) [0.5251, 0.2534, 0.2188] PeriodicSite: Fe (2.8873, -4.5282, -0.1187) [0.0251, 0.7465, 0.2812] PeriodicSite: Fe (7.4699, -1.5374, -4.6259) [0.9750, 0.2535, 0.7188] PeriodicSite: Fe (8.0925, -4.5281, -2.2531) [0.4749, 0.7465, 0.7812] PeriodicSite: P (0.9432, -4.5594, -2.7614) [0.5821, 0.7517, 0.0944] PeriodicSite: P (4.2088, -1.5061, -0.3893) [0.0821, 0.2483, 0.4056] PeriodicSite: P (6.1483, -4.5597, -4.3551) [0.9179, 0.7517, 0.5944] PeriodicSite: P (9.4141, -1.5060, -1.9829) [0.4179, 0.2483, 0.9056] PeriodicSite: O (0.4361, -1.5232, -1.3833) [0.2916, 0.2511, 0.0432] PeriodicSite: O (0.9618, -4.5518, -1.2263) [0.2585, 0.7504, 0.0962] PeriodicSite: O (1.6753, -5.7983, -3.3849) [0.7135, 0.9559, 0.1658] PeriodicSite: O (1.6950, -3.3276, -3.3983) [0.7163, 0.5486, 0.1656] PeriodicSite: O (3.4570, -2.7380, -1.0261) [0.2163, 0.4514, 0.3344] PeriodicSite: O (3.4767, -0.2672, -1.0127) [0.2135, 0.0441, 0.3342] PeriodicSite: O (4.1902, -1.5137, -3.5989) [0.7585, 0.2495, 0.4038] PeriodicSite: O (4.7159, -4.5425, -3.7555) [0.7916, 0.7489, 0.4568] PeriodicSite: O (5.6412, -1.5231, -0.9889) [0.2084, 0.2511, 0.5432] PeriodicSite: O (6.1670, -4.5519, -1.1455) [0.2415, 0.7505, 0.5962] PeriodicSite: O (6.8801, -5.7988, -3.7318) [0.7866, 0.9560, 0.6658] PeriodicSite: O (6.9004, -3.3280, -3.7181) [0.7837, 0.5487, 0.6656] PeriodicSite: O (8.6620, -2.7376, -1.3457) [0.2837, 0.4513, 0.8344] PeriodicSite: O (8.6823, -0.2668, -1.3597) [0.2866, 0.0440, 0.8342] PeriodicSite: O (9.3954, -1.5138, -3.5181) [0.7415, 0.2496, 0.9038] PeriodicSite: O (9.9213, -4.5424, -3.3610) [0.7084, 0.7489, 0.9568], 'NaFePO4': Structure Summary Lattice     abc : 4.9955 6.28746 10.440590000000002  angles : 90.0 89.97269 90.0  volume : 327.9285211911844       A : 0.0 0.0 -4.9955       B : 3.849958881883509e-16 -6.28746 -3.849958881883509e-16       C : -10.440588813976833 0.0 -0.004976500966151329 PeriodicSite: Na (-10.4402, -6.2870, -5.0004) [1.0000, 0.9999, 1.0000] PeriodicSite: Na (-10.4402, -3.1442, -5.0004) [1.0000, 0.5001, 1.0000] PeriodicSite: Na (-5.2197, -6.2870, -2.5005) [0.5001, 0.9999, 0.4999] PeriodicSite: Na (-5.2197, -3.1442, -2.5005) [0.5001, 0.5001, 0.4999] PeriodicSite: Fe (-8.2056, -1.5719, -2.6193) [0.5235, 0.2500, 0.7859] PeriodicSite: Fe (-7.4584, -4.7156, -0.1238) [0.0241, 0.7500, 0.7144] PeriodicSite: Fe (-2.9844, -1.5719, -4.8792) [0.9764, 0.2500, 0.2859] PeriodicSite: Fe (-2.2367, -4.7156, -2.3805) [0.4763, 0.7500, 0.2142] PeriodicSite: P (-9.3366, -4.7156, -2.8377) [0.5672, 0.7500, 0.8943] PeriodicSite: P (-6.3250, -1.5719, -0.3370) [0.0669, 0.2500, 0.6058] PeriodicSite: P (-4.1164, -4.7156, -4.6625) [0.9329, 0.7500, 0.3943] PeriodicSite: P (-1.1040, -1.5719, -2.1641) [0.4331, 0.2500, 0.1057] PeriodicSite: O (-10.0753, -1.5719, -1.6636) [0.3321, 0.2500, 0.9650] PeriodicSite: O (-9.2800, -4.7156, -1.2986) [0.2591, 0.7500, 0.8888] PeriodicSite: O (-8.6132, -5.9528, -3.4881) [0.6974, 0.9468, 0.8250] PeriodicSite: O (-8.6132, -3.4783, -3.4881) [0.6974, 0.5532, 0.8250] PeriodicSite: O (-7.0467, -2.8104, -0.9879) [0.1971, 0.4470, 0.6749] PeriodicSite: O (-7.0467, -0.3333, -0.9879) [0.1971, 0.0530, 0.6749] PeriodicSite: O (-6.3830, -1.5719, -3.7937) [0.7588, 0.2500, 0.6114] PeriodicSite: O (-5.5841, -4.7156, -4.1557) [0.8314, 0.7500, 0.5348] PeriodicSite: O (-4.8549, -1.5719, -0.8420) [0.1681, 0.2500, 0.4650] PeriodicSite: O (-4.0586, -4.7156, -1.2059) [0.2410, 0.7500, 0.3887] PeriodicSite: O (-3.3933, -5.9537, -4.0111) [0.8026, 0.9469, 0.3250] PeriodicSite: O (-3.3933, -3.4775, -4.0111) [0.8026, 0.5531, 0.3250] PeriodicSite: O (-1.8263, -2.8099, -1.5129) [0.3027, 0.4469, 0.1749] PeriodicSite: O (-1.8263, -0.3338, -1.5129) [0.3027, 0.0531, 0.1749] PeriodicSite: O (-1.1622, -1.5719, -3.7030) [0.7412, 0.2500, 0.1113] PeriodicSite: O (-0.3650, -4.7156, -3.3387) [0.6683, 0.7500, 0.0350], 'Pb2TiZrO6': Structure Summary Lattice     abc : 4.505383 5.67298 5.67298  angles : 90.0 90.0 90.0  volume : 144.99539884709878       A : 0.0 0.0 4.505383       B : 5.67298 0.0 0.0       C : 0.0 5.67298 0.0 PeriodicSite: Zr (2.8365, 0.0000, 2.4376) [0.5410, 0.5000, -0.0000] PeriodicSite: Ti (0.0000, 2.8365, 2.4188) [0.5369, -0.0000, 0.5000] PeriodicSite: Pb (0.0000, 0.0000, 4.4114) [0.9791, -0.0000, -0.0000] PeriodicSite: Pb (2.8365, 2.8365, 4.4114) [0.9791, 0.5000, 0.5000] PeriodicSite: O (1.3704, 1.4661, 2.8748) [0.6381, 0.2416, 0.2584] PeriodicSite: O (1.3704, 4.2069, 2.8748) [0.6381, 0.2416, 0.7416] PeriodicSite: O (4.3026, 1.4661, 2.8748) [0.6381, 0.7584, 0.2584] PeriodicSite: O (4.3026, 4.2069, 2.8748) [0.6381, 0.7584, 0.7416] PeriodicSite: O (0.0000, 2.8365, 0.6698) [0.1487, -0.0000, 0.5000] PeriodicSite: O (2.8365, 0.0000, 0.4587) [0.1018, 0.5000, -0.0000], 'Si': Structure Summary Lattice     abc : 3.8401979337 3.840198994344244 3.8401979337177736  angles : 119.99999086398421 90.0 60.0000091373222  volume : 40.04479464425159       A : 3.8401979337 0.0 0.0       B : 1.9200989668 3.3257101909 0.0       C : 0.0 -2.2171384943 3.1355090603 PeriodicSite: Si (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Si (3.8402, 0.0000, 2.3516) [0.7500, 0.5000, 0.7500], 'SiO2': Structure Summary Lattice     abc : 5.0277818 5.0277817873408415 5.51891759  angles : 90.0 90.0 120.00000005747829  volume : 120.81959693044213       A : 5.0277818 6e-08 -0.0       B : -2.51389095 4.35418672 0.0       C : -0.0 0.0 5.51891759 PeriodicSite: Si (1.3140, 2.2760, 5.5189) [0.5227, 0.5227, 1.0000] PeriodicSite: Si (2.3997, -0.0000, 3.6792) [0.4773, -0.0000, 0.6667] PeriodicSite: Si (3.8279, 2.0782, 1.8396) [1.0000, 0.4773, 0.3333] PeriodicSite: O (0.8313, 3.6543, 4.8051) [0.5850, 0.8393, 0.8707] PeriodicSite: O (-1.0664, 3.2469, 2.9655) [0.1607, 0.7457, 0.5373] PeriodicSite: O (0.2352, 1.8071, 1.1259) [0.2543, 0.4150, 0.2040] PeriodicSite: O (2.7491, 2.5470, 0.7137) [0.8393, 0.5850, 0.1293] PeriodicSite: O (3.3452, 0.6999, 2.5533) [0.7457, 0.1607, 0.4626] PeriodicSite: O (1.4474, 1.1073, 4.3929) [0.4150, 0.2543, 0.7960], 'Si_SiO2_Interface': Structure Summary Lattice     abc : 10.160210588671637 10.160210588671637 29.156770002399192  angles : 90.0 90.0 59.99999999999999  volume : 2606.6064276838156       A : 10.160210588671637 0.0 6.221334688039882e-16       B : 5.080105294335819 8.799000477589283 6.221334688039882e-16       C : 0.0 0.0 29.156770002399192 PeriodicSite: Si (10.3416, 3.8758, 9.3499) [0.7976, 0.4405, 0.3207] PeriodicSite: Si (13.9703, 5.1328, 9.3499) [1.0833, 0.5833, 0.3207] PeriodicSite: Si (7.4387, 6.3898, 9.3499) [0.3690, 0.7262, 0.3207] PeriodicSite: Si (11.0674, 7.6468, 9.3499) [0.6548, 0.8690, 0.3207] PeriodicSite: Si (9.6159, 0.1048, 9.3499) [0.9405, 0.0119, 0.3207] PeriodicSite: Si (3.0843, 1.3618, 9.3499) [0.2262, 0.1548, 0.3207] PeriodicSite: Si (6.7130, 2.6188, 9.3499) [0.5119, 0.2976, 0.3207] PeriodicSite: Si (10.3416, 3.8758, 11.7016) [0.7976, 0.4405, 0.4013] PeriodicSite: Si (13.9703, 5.1328, 11.7016) [1.0833, 0.5833, 0.4013] PeriodicSite: Si (7.4387, 6.3898, 11.7016) [0.3690, 0.7262, 0.4013] PeriodicSite: Si (11.0674, 7.6468, 11.7016) [0.6548, 0.8690, 0.4013] PeriodicSite: Si (9.6159, 0.1048, 11.7016) [0.9405, 0.0119, 0.4013] PeriodicSite: Si (3.0843, 1.3618, 11.7016) [0.2262, 0.1548, 0.4013] PeriodicSite: Si (6.7130, 2.6188, 11.7016) [0.5119, 0.2976, 0.4013] PeriodicSite: Si (3.8678, 2.0998, 13.7016) [0.2614, 0.2386, 0.4699] PeriodicSite: Si (6.4078, 6.4993, 13.7016) [0.2614, 0.7386, 0.4699] PeriodicSite: Si (8.9479, 2.0998, 13.7016) [0.7614, 0.2386, 0.4699] PeriodicSite: Si (11.4879, 6.4993, 13.7016) [0.7614, 0.7386, 0.4699] PeriodicSite: Si (4.9647, 4.3995, 15.5412) [0.2386, 0.5000, 0.5330] PeriodicSite: Si (2.4247, 0.0000, 15.5412) [0.2386, 0.0000, 0.5330] PeriodicSite: Si (10.0448, 4.3995, 15.5412) [0.7386, 0.5000, 0.5330] PeriodicSite: Si (7.5048, 0.0000, 15.5412) [0.7386, 0.0000, 0.5330] PeriodicSite: Si (1.3277, 2.2997, 17.3808) [0.0000, 0.2614, 0.5961] PeriodicSite: Si (3.8678, 6.6992, 17.3808) [0.0000, 0.7614, 0.5961] PeriodicSite: Si (6.4078, 2.2997, 17.3808) [0.5000, 0.2614, 0.5961] PeriodicSite: Si (8.9479, 6.6992, 17.3808) [0.5000, 0.7614, 0.5961] PeriodicSite: O (3.3800, 0.7072, 14.4153) [0.2925, 0.0804, 0.4944] PeriodicSite: O (5.9200, 5.1067, 14.4153) [0.2925, 0.5804, 0.4944] PeriodicSite: O (8.4601, 0.7072, 14.4153) [0.7925, 0.0804, 0.4944] PeriodicSite: O (11.0001, 5.1067, 14.4153) [0.7925, 0.5804, 0.4944] PeriodicSite: O (1.4625, 1.1188, 16.2550) [0.0804, 0.1271, 0.5575] PeriodicSite: O (4.0026, 5.5183, 16.2550) [0.0804, 0.6271, 0.5575] PeriodicSite: O (6.5426, 1.1188, 16.2550) [0.5804, 0.1271, 0.5575] PeriodicSite: O (9.0827, 5.5183, 16.2550) [0.5804, 0.6271, 0.5575] PeriodicSite: O (2.7777, 2.5735, 18.0946) [0.1271, 0.2925, 0.6206] PeriodicSite: O (5.3177, 6.9730, 18.0946) [0.1271, 0.7925, 0.6206] PeriodicSite: O (7.8578, 2.5735, 18.0946) [0.6271, 0.2925, 0.6206] PeriodicSite: O (10.3978, 6.9730, 18.0946) [0.6271, 0.7925, 0.6206] PeriodicSite: O (5.3177, 1.8260, 18.5067) [0.4196, 0.2075, 0.6347] PeriodicSite: O (7.8578, 6.2255, 18.5067) [0.4196, 0.7075, 0.6347] PeriodicSite: O (10.3978, 1.8260, 18.5067) [0.9196, 0.2075, 0.6347] PeriodicSite: O (12.9379, 6.2255, 18.5067) [0.9196, 0.7075, 0.6347] PeriodicSite: O (5.9200, 3.6923, 16.6671) [0.3729, 0.4196, 0.5716] PeriodicSite: O (8.4601, 8.0918, 16.6671) [0.3729, 0.9196, 0.5716] PeriodicSite: O (11.0001, 3.6923, 16.6671) [0.8729, 0.4196, 0.5716] PeriodicSite: O (13.5402, 8.0918, 16.6671) [0.8729, 0.9196, 0.5716] PeriodicSite: O (4.0026, 3.2807, 14.8274) [0.2075, 0.3729, 0.5085] PeriodicSite: O (6.5426, 7.6802, 14.8274) [0.2075, 0.8729, 0.5085] PeriodicSite: O (9.0827, 3.2807, 14.8274) [0.7075, 0.3729, 0.5085] PeriodicSite: O (11.6227, 7.6802, 14.8274) [0.7075, 0.8729, 0.5085], 'Sn': Structure Summary Lattice     abc : 6.65061477 6.65061477 6.65061477  angles : 90.0 90.0 90.0  volume : 294.16119253915326       A : 6.65061477 0.0 0.0       B : 0.0 6.65061477 0.0       C : 0.0 0.0 6.65061477 PeriodicSite: Sn (2.4940, 5.8193, 2.4940) [0.3750, 0.8750, 0.3750] PeriodicSite: Sn (0.8313, 0.8313, 0.8313) [0.1250, 0.1250, 0.1250] PeriodicSite: Sn (2.4940, 2.4940, 5.8193) [0.3750, 0.3750, 0.8750] PeriodicSite: Sn (0.8313, 4.1566, 4.1566) [0.1250, 0.6250, 0.6250] PeriodicSite: Sn (5.8193, 5.8193, 5.8193) [0.8750, 0.8750, 0.8750] PeriodicSite: Sn (4.1566, 0.8313, 4.1566) [0.6250, 0.1250, 0.6250] PeriodicSite: Sn (5.8193, 2.4940, 2.4940) [0.8750, 0.3750, 0.3750] PeriodicSite: Sn (4.1566, 4.1566, 0.8313) [0.6250, 0.6250, 0.1250], 'SrTiO3': Structure Summary Lattice     abc : 3.905 3.905 3.905  angles : 90.0 90.0 90.0  volume : 59.54744262499999       A : 3.905 0.0 2.391122875335207e-16       B : -2.391122875335207e-16 3.905 2.391122875335207e-16       C : 0.0 0.0 3.905 PeriodicSite: Sr2+ (1.9525, 1.9525, 1.9525) [0.5000, 0.5000, 0.5000] PeriodicSite: Ti4+ (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: O2- (0.0000, 0.0000, 1.9525) [0.0000, 0.0000, 0.5000] PeriodicSite: O2- (-0.0000, 1.9525, 0.0000) [0.0000, 0.5000, 0.0000] PeriodicSite: O2- (1.9525, 0.0000, 0.0000) [0.5000, 0.0000, 0.0000], 'TiO2': <pymatgen.alchemy.materials.TransformedStructure object>, 'TlBiSe2': Structure Summary Lattice     abc : 4.372201544153475 61.149528191254596 59.08304095958131  angles : 3.6737691014605547 58.80413768014368 59.97014152897428  volume : 825.8885392060803       A : 3.74140218 -0.00027862 2.26231209       B : -1.13595131 3.78041753 61.02198666       C : 0.036913 0.04093202 59.08301525 PeriodicSite: Tl (2.5148, 3.6745, 63.4338) [0.9669, 0.9717, 0.0330] PeriodicSite: Tl (3.6037, 0.2035, 6.7146) [0.9793, 0.0537, 0.0207] PeriodicSite: Tl (3.5726, 0.5326, 10.9899) [0.9977, 0.1409, 0.0022] PeriodicSite: Tl (-0.2434, 0.8101, 13.0761) [0.0000, 0.2143, -0.0000] PeriodicSite: Tl (-0.2812, 1.1282, 76.5077) [0.0023, 0.2876, 0.9978] PeriodicSite: Tl (-0.3122, 1.4572, 80.7830) [0.0207, 0.3749, 0.9793] PeriodicSite: Tl (-0.3594, 1.7667, 85.0859) [0.0331, 0.4569, 0.9670] PeriodicSite: Bi (-0.4251, 2.0554, 89.4184) [0.0388, 0.5333, 0.9611] PeriodicSite: Bi (-0.5892, 2.2281, 93.9147) [0.0084, 0.5786, 0.9916] PeriodicSite: Bi (-0.6750, 2.4926, 98.2811) [0.0067, 0.6486, 0.9933] PeriodicSite: Bi (-0.8113, 2.7004, 43.5869) [0.0000, 0.7143, -0.0000] PeriodicSite: Bi (2.8309, 2.9491, 50.2379) [0.9934, 0.7801, 0.0066] PeriodicSite: Bi (2.7442, 3.2126, 54.6058) [0.9914, 0.8498, 0.0086] PeriodicSite: Bi (2.5805, 3.3856, 59.1013) [0.9611, 0.8952, 0.0389] PeriodicSite: Se (1.7377, 0.2085, 35.1484) [0.4743, 0.0495, 0.5256] PeriodicSite: Se (1.6987, 0.5271, 39.4370) [0.4897, 0.1339, 0.5104] PeriodicSite: Se (1.6462, 0.8311, 43.7478) [0.5002, 0.2145, 0.4998] PeriodicSite: Se (1.5935, 1.1347, 48.0594) [0.5106, 0.2949, 0.4893] PeriodicSite: Se (1.5531, 1.4514, 52.3505) [0.5255, 0.3788, 0.4747] PeriodicSite: Se (1.4871, 1.7413, 56.6824) [0.5312, 0.4556, 0.4685] PeriodicSite: Se (1.4204, 2.0277, 61.0185) [0.5364, 0.5314, 0.4634] PeriodicSite: Se (1.2436, 2.1850, 65.5372) [0.5013, 0.5726, 0.4986] PeriodicSite: Se (1.1826, 2.4786, 69.8633) [0.5087, 0.6503, 0.4913] PeriodicSite: Se (1.0777, 2.7207, 74.2599) [0.5000, 0.7143, 0.5000] PeriodicSite: Se (0.9728, 2.9625, 78.6564) [0.4913, 0.7782, 0.5088] PeriodicSite: Se (0.9121, 3.2562, 82.9823) [0.4987, 0.8560, 0.5014] PeriodicSite: Se (0.7353, 3.4138, 87.5010) [0.4636, 0.8973, 0.5365] PeriodicSite: Se (0.6680, 3.6996, 91.8379) [0.4687, 0.9729, 0.5316], 'VO2': <pymatgen.alchemy.materials.TransformedStructure object>}[source]
                                          +TEST_STRUCTURES = {'BaNiO3': <pymatgen.alchemy.materials.TransformedStructure object>, 'CsCl': Structure Summary Lattice     abc : 4.209 4.209 4.209  angles : 90.0 90.0 90.0  volume : 74.56530132899998       A : 4.209 0.0 0.0       B : 0.0 4.209 0.0       C : 0.0 0.0 4.209 PeriodicSite: Cs (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Cl (2.1045, 2.1045, 2.1045) [0.5000, 0.5000, 0.5000], 'Graphite': Structure Summary Lattice     abc : 2.4700000000000006 2.47 6.8  angles : 90.0 90.0 120.00000000000001  volume : 35.928033824449685       A : -1.2350000000000005 -2.139082747347564 -3.024877593893963e-16       B : -1.2349999999999997 2.139082747347564 1.5124387969469814e-16       C : 0.0 0.0 -6.8 PeriodicSite: C0+ (-1.2350, -0.7132, -5.1000) [0.6667, 0.3333, 0.7500] PeriodicSite: C0+ (-1.2350, 0.7132, -1.7000) [0.3333, 0.6667, 0.2500] PeriodicSite: C0+ (0.0000, 0.0000, -5.1000) [0.0000, 0.0000, 0.7500] PeriodicSite: C0+ (0.0000, 0.0000, -1.7000) [0.0000, 0.0000, 0.2500], 'He_BCC': Structure Summary Lattice     abc : 2.737172073807164 2.7371720737557492 2.73717207  angles : 109.47122060669534 109.47122060631484 109.47122066304705  volume : 15.786447515629305       A : 2.58063058 0.0 -0.91239069       B : -1.29031529 2.23489164 -0.91239069       C : 0.0 0.0 2.73717207 PeriodicSite: He (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000], 'K2O2': Structure Summary Lattice     abc : 4.862375062662279 4.862375062662278 6.361  angles : 90.0 90.0 91.89149308502677  volume : 150.30921504900002       A : 3.3810000000000002 -3.4945000000000004 0.0       B : 3.381 3.4944999999999995 4.2795282396204257e-16       C : 0.0 0.0 -6.361 PeriodicSite: K+ (1.6905, -1.0861, -1.5902) [0.4054, 0.0946, 0.2500] PeriodicSite: K+ (1.6905, 1.0861, -4.7707) [0.0946, 0.4054, 0.7500] PeriodicSite: K+ (5.0715, 1.0861, -4.7707) [0.5946, 0.9054, 0.7500] PeriodicSite: K+ (5.0715, -1.0861, -1.5902) [0.9054, 0.5946, 0.2500] PeriodicSite: O- (3.3810, -0.6262, -3.6417) [0.5896, 0.4104, 0.5725] PeriodicSite: O- (3.3810, 0.6262, -2.7193) [0.4104, 0.5896, 0.4275] PeriodicSite: O- (3.3810, -2.8683, -0.4612) [0.9104, 0.0896, 0.0725] PeriodicSite: O- (3.3810, 2.8683, -5.8998) [0.0896, 0.9104, 0.9275], 'La2CoO4F': Structure Summary Lattice     abc : 6.847249 6.847249 5.748369  angles : 90.0 90.0 132.754623  volume : 197.89340779864318       A : 6.847249 0.0 4.192730785407457e-16       B : -4.648323410186749 5.027714027499061 4.192730785407457e-16       C : 0.0 0.0 5.748369 PeriodicSite: La3+ (-3.0614, 4.3336, 2.7708) [0.1380, 0.8620, 0.4820] PeriodicSite: La3+ (5.2603, 0.6941, 2.9775) [0.8620, 0.1380, 0.5180] PeriodicSite: La3+ (-0.4875, 3.2079, 5.6450) [0.3620, 0.6380, 0.9820] PeriodicSite: La3+ (2.6864, 1.8198, 0.1033) [0.6380, 0.3620, 0.0180] PeriodicSite: Co3+ (1.0995, 2.5139, 2.8742) [0.5000, 0.5000, 0.5000] PeriodicSite: Co3+ (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: O2- (-0.9933, 3.4292, 3.2966) [0.3180, 0.6821, 0.5735] PeriodicSite: O2- (3.1922, 1.5986, 2.4518) [0.6821, 0.3180, 0.4265] PeriodicSite: O2- (-2.5555, 4.1124, 0.4224) [0.1820, 0.8179, 0.0735] PeriodicSite: O2- (4.7545, 0.9153, 5.3260) [0.8179, 0.1820, 0.9265] PeriodicSite: O2- (1.4256, 3.8686, 1.4371) [0.7305, 0.7695, 0.2500] PeriodicSite: O2- (1.8728, 3.6730, 4.3113) [0.7695, 0.7305, 0.7500] PeriodicSite: O2- (0.3261, 1.3547, 1.4371) [0.2305, 0.2695, 0.2500] PeriodicSite: O2- (0.7734, 1.1591, 4.3113) [0.2695, 0.2305, 0.7500] PeriodicSite: F- (-2.3242, 2.5139, 4.3113) [0.0000, 0.5000, 0.7500] PeriodicSite: F2- (3.4236, 0.0000, 1.4371) [0.5000, 0.0000, 0.2500], 'Li10GeP2S12': Structure Summary Lattice     abc : 8.69407 8.69407 12.5994  angles : 90.0 90.0 90.0  volume : 952.3489977658411       A : -8.69407 0.0 -5.323582498531514e-16       B : 5.323582498531514e-16 -8.69407 -5.323582498531514e-16       C : 0.0 0.0 -12.5994 PeriodicSite: Li:0.691 (-6.4658, -6.3310, -10.2912) [0.7437, 0.7282, 0.8168] PeriodicSite: Li:0.691 (-2.2283, -2.3630, -10.2912) [0.2563, 0.2718, 0.8168] PeriodicSite: Li:0.691 (-6.7101, -2.1187, -3.9915) [0.7718, 0.2437, 0.3168] PeriodicSite: Li:0.691 (-1.9840, -6.5753, -3.9915) [0.2282, 0.7563, 0.3168] PeriodicSite: Li:0.691 (-6.5753, -1.9840, -8.6079) [0.7563, 0.2282, 0.6832] PeriodicSite: Li:0.691 (-2.1187, -6.7101, -8.6079) [0.2437, 0.7718, 0.6832] PeriodicSite: Li:0.691 (-6.3310, -6.4658, -2.3082) [0.7282, 0.7437, 0.1832] PeriodicSite: Li:0.691 (-2.3630, -2.2283, -2.3082) [0.2718, 0.2563, 0.1832] PeriodicSite: Li:0.691 (-6.5753, -6.7101, -8.6079) [0.7563, 0.7718, 0.6832] PeriodicSite: Li:0.691 (-2.1187, -1.9840, -8.6079) [0.2437, 0.2282, 0.6832] PeriodicSite: Li:0.691 (-6.3310, -2.2283, -2.3082) [0.7282, 0.2563, 0.1832] PeriodicSite: Li:0.691 (-2.3630, -6.4658, -2.3082) [0.2718, 0.7437, 0.1832] PeriodicSite: Li:0.691 (-6.4658, -2.3630, -10.2912) [0.7437, 0.2718, 0.8168] PeriodicSite: Li:0.691 (-2.2283, -6.3310, -10.2912) [0.2563, 0.7282, 0.8168] PeriodicSite: Li:0.691 (-6.7101, -6.5753, -3.9915) [0.7718, 0.7563, 0.3168] PeriodicSite: Li:0.691 (-1.9840, -2.1187, -3.9915) [0.2282, 0.2437, 0.3168] PeriodicSite: Li (0.0000, -4.3470, -0.6980) [0.0000, 0.5000, 0.0554] PeriodicSite: Li (0.0000, -4.3470, -6.9977) [0.0000, 0.5000, 0.5554] PeriodicSite: Li (-4.3470, 0.0000, -5.6017) [0.5000, 0.0000, 0.4446] PeriodicSite: Li (-4.3470, 0.0000, -11.9014) [0.5000, 0.0000, 0.9446] PeriodicSite: Li:0.643 (-6.5527, -6.5527, -0.0000) [0.7537, 0.7537, 0.0000] PeriodicSite: Li:0.643 (-2.1413, -2.1413, -0.0000) [0.2463, 0.2463, 0.0000] PeriodicSite: Li:0.643 (-6.4884, -2.2057, -6.2997) [0.7463, 0.2537, 0.5000] PeriodicSite: Li:0.643 (-2.2057, -6.4884, -6.2997) [0.2537, 0.7463, 0.5000] PeriodicSite: Li:0.643 (-6.4884, -6.4884, -6.2997) [0.7463, 0.7463, 0.5000] PeriodicSite: Li:0.643 (-2.2057, -2.2057, -6.2997) [0.2537, 0.2537, 0.5000] PeriodicSite: Li:0.643 (-6.5527, -2.1413, -0.0000) [0.7537, 0.2463, 0.0000] PeriodicSite: Li:0.643 (-2.1413, -6.5527, -0.0000) [0.2463, 0.7537, 0.0000] PeriodicSite: Ge:0.515, P:0.485 (0.0000, -4.3470, -3.8970) [0.0000, 0.5000, 0.3093] PeriodicSite: Ge:0.515, P:0.485 (0.0000, -4.3470, -10.1967) [0.0000, 0.5000, 0.8093] PeriodicSite: Ge:0.515, P:0.485 (-4.3470, 0.0000, -2.4027) [0.5000, 0.0000, 0.1907] PeriodicSite: Ge:0.515, P:0.485 (-4.3470, 0.0000, -8.7024) [0.5000, 0.0000, 0.6907] PeriodicSite: P (0.0000, 0.0000, -6.2997) [0.0000, 0.0000, 0.5000] PeriodicSite: P (-4.3470, -4.3470, -0.0000) [0.5000, 0.5000, 0.0000] PeriodicSite: S (-8.6941, -7.0918, -7.4299) [1.0000, 0.8157, 0.5897] PeriodicSite: S (0.0000, -1.6023, -7.4299) [0.0000, 0.1843, 0.5897] PeriodicSite: S (-5.9494, -4.3470, -1.1302) [0.6843, 0.5000, 0.0897] PeriodicSite: S (-2.7447, -4.3470, -1.1302) [0.3157, 0.5000, 0.0897] PeriodicSite: S (-4.3470, -2.7447, -11.4692) [0.5000, 0.3157, 0.9103] PeriodicSite: S (-4.3470, -5.9494, -11.4692) [0.5000, 0.6843, 0.9103] PeriodicSite: S (-7.0918, 0.0000, -5.1695) [0.8157, 0.0000, 0.4103] PeriodicSite: S (-1.6023, 0.0000, -5.1695) [0.1843, 0.0000, 0.4103] PeriodicSite: S (-8.6941, -6.0937, -11.4025) [1.0000, 0.7009, 0.9050] PeriodicSite: S (0.0000, -2.6004, -11.4025) [0.0000, 0.2991, 0.9050] PeriodicSite: S (-6.9474, -4.3470, -5.1028) [0.7991, 0.5000, 0.4050] PeriodicSite: S (-1.7466, -4.3470, -5.1028) [0.2009, 0.5000, 0.4050] PeriodicSite: S (-4.3470, -1.7466, -7.4966) [0.5000, 0.2009, 0.5950] PeriodicSite: S (-4.3470, -6.9474, -7.4966) [0.5000, 0.7991, 0.5950] PeriodicSite: S (-6.0937, 0.0000, -1.1969) [0.7009, 0.0000, 0.0950] PeriodicSite: S (-2.6004, 0.0000, -1.1969) [0.2991, 0.0000, 0.0950] PeriodicSite: S (0.0000, -2.6169, -2.6282) [0.0000, 0.3010, 0.2086] PeriodicSite: S (-8.6941, -6.0772, -2.6282) [1.0000, 0.6990, 0.2086] PeriodicSite: S (-1.7301, -4.3470, -8.9279) [0.1990, 0.5000, 0.7086] PeriodicSite: S (-6.9640, -4.3470, -8.9279) [0.8010, 0.5000, 0.7086] PeriodicSite: S (-4.3470, -6.9640, -3.6715) [0.5000, 0.8010, 0.2914] PeriodicSite: S (-4.3470, -1.7301, -3.6715) [0.5000, 0.1990, 0.2914] PeriodicSite: S (-2.6169, 0.0000, -9.9712) [0.3010, 0.0000, 0.7914] PeriodicSite: S (-6.0772, 0.0000, -9.9712) [0.6990, 0.0000, 0.7914], 'Li2O': Structure Summary Lattice     abc : 3.291071792359756 3.291071899625086 3.2910720568557887  angles : 60.12971043288485 60.12970952137675 60.12970313039097  volume : 25.279668381289053       A : 2.91738857 0.09789437 1.52000466       B : 0.96463406 2.75503561 1.52000466       C : 0.13320635 0.09789443 3.28691771 PeriodicSite: O2- (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Li+ (3.0121, 2.2136, 4.7463) [0.7502, 0.7502, 0.7502] PeriodicSite: Li+ (1.0031, 0.7372, 1.5806) [0.2498, 0.2498, 0.2498], 'Li2O2': Structure Summary Lattice     abc : 3.1830000000000007 3.1830000000000003 7.7258  angles : 90.0 90.0 120.00000000000001  volume : 67.7871492344378       A : -1.5915000000000006 -2.756558860245869 -3.898050761686025e-16       B : -1.5914999999999992 2.756558860245869 1.9490253808430124e-16       C : 0.0 0.0 -7.7258 PeriodicSite: Li+ (0.0000, 0.0000, -3.8629) [0.0000, 0.0000, 0.5000] PeriodicSite: Li+ (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Li+ (-1.5915, -0.9190, -5.7943) [0.6667, 0.3333, 0.7500] PeriodicSite: Li+ (-1.5915, 0.9190, -1.9314) [0.3333, 0.6667, 0.2500] PeriodicSite: O- (-1.5915, -0.9190, -1.1566) [0.6667, 0.3333, 0.1497] PeriodicSite: O- (-1.5915, 0.9190, -6.5692) [0.3333, 0.6667, 0.8503] PeriodicSite: O- (-1.5915, 0.9190, -5.0195) [0.3333, 0.6667, 0.6497] PeriodicSite: O- (-1.5915, -0.9190, -2.7063) [0.6667, 0.3333, 0.3503], 'Li3V2(PO4)3': Structure Summary Lattice     abc : 8.64068 8.67265 8.64068  angles : 61.21317 61.3442 61.21317  volume : 470.7978186322687       A : -2.470939478415996 -7.168424451387926 -4.143609518420984       B : -7.600861301025969 0.0 -4.17633397910965       C : 0.0 0.0 -8.64068 PeriodicSite: Li0+ (-9.8221, -7.1201, -8.1771) [0.9933, 0.9693, 0.0015] PeriodicSite: Li0+ (-5.2652, -3.5733, -8.6603) [0.4985, 0.5307, 0.5067] PeriodicSite: Li0+ (-6.0857, -1.1171, -6.7518) [0.1558, 0.7500, 0.3442] PeriodicSite: Li0+ (-3.9986, -6.0875, -10.1861) [0.8492, 0.2500, 0.6508] PeriodicSite: Li0+ (-4.4741, -5.3421, -5.9052) [0.7452, 0.3464, 0.1586] PeriodicSite: Li0+ (-2.0112, -2.4471, -8.5778) [0.3414, 0.1536, 0.7548] PeriodicSite: V0+ (-8.6165, -6.1274, -14.5645) [0.8548, 0.8558, 0.8621] PeriodicSite: V0+ (-6.4732, -4.5730, -10.9092) [0.6379, 0.6442, 0.6452] PeriodicSite: V0+ (-3.5744, -2.5407, -5.9951) [0.3544, 0.3550, 0.3522] PeriodicSite: V0+ (-1.4669, -1.0591, -2.4754) [0.1478, 0.1450, 0.1456] PeriodicSite: P0+ (-7.8497, -1.7789, -9.7592) [0.2482, 0.9521, 0.5503] PeriodicSite: P0+ (-6.5114, -6.8080, -8.3997) [0.9497, 0.5479, 0.2518] PeriodicSite: P0+ (-6.8308, -3.2786, -5.3958) [0.4574, 0.7500, 0.0426] PeriodicSite: P0+ (-3.2537, -3.9267, -11.5417) [0.5478, 0.2500, 0.9522] PeriodicSite: P0+ (-3.5598, -0.2774, -8.5391) [0.0387, 0.4558, 0.7494] PeriodicSite: P0+ (-2.1909, -5.3806, -7.2809) [0.7506, 0.0442, 0.4613] PeriodicSite: O0+ (-8.3983, -5.1136, -10.9141) [0.7133, 0.8730, 0.4991] PeriodicSite: O0+ (-6.5103, -3.5115, -12.5689) [0.4899, 0.6973, 0.8827] PeriodicSite: O0+ (-7.4256, -0.5548, -10.6251) [0.0774, 0.9518, 0.7325] PeriodicSite: O0+ (-7.9453, -1.4000, -8.2592) [0.1953, 0.9818, 0.3876] PeriodicSite: O0+ (-6.7928, -2.9117, -9.8164) [0.4062, 0.7617, 0.5732] PeriodicSite: O0+ (-5.7536, -6.2988, -11.6913) [0.8787, 0.4713, 0.7039] PeriodicSite: O0+ (-7.9023, -6.6440, -7.7347) [0.9268, 0.7384, 0.0938] PeriodicSite: O0+ (-6.0633, -5.5016, -9.1213) [0.7675, 0.5482, 0.4226] PeriodicSite: O0+ (-7.6267, -4.4251, -5.9980) [0.6173, 0.8027, 0.0101] PeriodicSite: O0+ (-7.5702, -1.8930, -5.4665) [0.2641, 0.9101, 0.0661] PeriodicSite: O0+ (-4.4855, -4.0749, -10.6051) [0.5685, 0.4053, 0.7588] PeriodicSite: O0+ (-4.7679, -0.0067, -9.4196) [0.0009, 0.6270, 0.7867] PeriodicSite: O0+ (-5.3896, -7.0627, -7.3776) [0.9852, 0.3888, 0.1934] PeriodicSite: O0+ (-5.5557, -3.1102, -6.2999) [0.4339, 0.5899, 0.2359] PeriodicSite: O0+ (-2.5509, -5.3129, -11.5157) [0.7412, 0.0947, 0.9316] PeriodicSite: O0+ (-2.3963, -2.7970, -10.9316) [0.3902, 0.1884, 0.9869] PeriodicSite: O0+ (-3.8311, -1.6586, -7.8407) [0.2314, 0.4288, 0.5892] PeriodicSite: O0+ (-2.2016, -0.4825, -9.2908) [0.0673, 0.2678, 0.9135] PeriodicSite: O0+ (-3.2143, -4.2040, -7.1387) [0.5865, 0.2322, 0.4327] PeriodicSite: O0+ (-4.2162, -0.8054, -5.2624) [0.1124, 0.5182, 0.3047] PeriodicSite: O0+ (-2.1852, -5.7069, -8.7871) [0.7961, 0.0287, 0.6213] PeriodicSite: O0+ (-2.7916, -6.5290, -6.3923) [0.9108, 0.0712, 0.2686] PeriodicSite: O0+ (-3.6360, -3.6778, -4.3760) [0.5131, 0.3116, 0.1098] PeriodicSite: O0+ (-1.6028, -2.1976, -6.1825) [0.3066, 0.1112, 0.5148], 'LiFePO4': Structure Summary Lattice     abc : 4.7448 6.0657700000000006 10.41037  angles : 90.50178999999999 90.00019 90.00362  volume : 299.60796771125047       A : 0.0 0.0 -4.7448       B : -0.053122654367700306 -6.065537365280947 0.00038324092231544317       C : 10.41036999994276 0.0 3.452209424235223e-05 PeriodicSite: Li (10.3571, -6.0655, 0.0004) [0.0000, 1.0000, 1.0000] PeriodicSite: Li (-0.0265, -3.0328, -4.7446) [1.0000, 0.5000, 0.0000] PeriodicSite: Li (5.1521, -6.0655, -2.3720) [0.5000, 1.0000, 0.5000] PeriodicSite: Li (5.1786, -3.0328, -2.3723) [0.5000, 0.5000, 0.5000] PeriodicSite: Fe (2.2647, -1.5372, -2.4912) [0.5251, 0.2534, 0.2188] PeriodicSite: Fe (2.8873, -4.5282, -0.1187) [0.0251, 0.7465, 0.2812] PeriodicSite: Fe (7.4699, -1.5374, -4.6259) [0.9750, 0.2535, 0.7188] PeriodicSite: Fe (8.0925, -4.5281, -2.2531) [0.4749, 0.7465, 0.7812] PeriodicSite: P (0.9432, -4.5594, -2.7614) [0.5821, 0.7517, 0.0944] PeriodicSite: P (4.2088, -1.5061, -0.3893) [0.0821, 0.2483, 0.4056] PeriodicSite: P (6.1483, -4.5597, -4.3551) [0.9179, 0.7517, 0.5944] PeriodicSite: P (9.4141, -1.5060, -1.9829) [0.4179, 0.2483, 0.9056] PeriodicSite: O (0.4361, -1.5232, -1.3833) [0.2916, 0.2511, 0.0432] PeriodicSite: O (0.9618, -4.5518, -1.2263) [0.2585, 0.7504, 0.0962] PeriodicSite: O (1.6753, -5.7983, -3.3849) [0.7135, 0.9559, 0.1658] PeriodicSite: O (1.6950, -3.3276, -3.3983) [0.7163, 0.5486, 0.1656] PeriodicSite: O (3.4570, -2.7380, -1.0261) [0.2163, 0.4514, 0.3344] PeriodicSite: O (3.4767, -0.2672, -1.0127) [0.2135, 0.0441, 0.3342] PeriodicSite: O (4.1902, -1.5137, -3.5989) [0.7585, 0.2495, 0.4038] PeriodicSite: O (4.7159, -4.5425, -3.7555) [0.7916, 0.7489, 0.4568] PeriodicSite: O (5.6412, -1.5231, -0.9889) [0.2084, 0.2511, 0.5432] PeriodicSite: O (6.1670, -4.5519, -1.1455) [0.2415, 0.7505, 0.5962] PeriodicSite: O (6.8801, -5.7988, -3.7318) [0.7866, 0.9560, 0.6658] PeriodicSite: O (6.9004, -3.3280, -3.7181) [0.7837, 0.5487, 0.6656] PeriodicSite: O (8.6620, -2.7376, -1.3457) [0.2837, 0.4513, 0.8344] PeriodicSite: O (8.6823, -0.2668, -1.3597) [0.2866, 0.0440, 0.8342] PeriodicSite: O (9.3954, -1.5138, -3.5181) [0.7415, 0.2496, 0.9038] PeriodicSite: O (9.9213, -4.5424, -3.3610) [0.7084, 0.7489, 0.9568], 'NaFePO4': Structure Summary Lattice     abc : 4.9955 6.28746 10.440590000000002  angles : 90.0 89.97269 90.0  volume : 327.9285211911844       A : 0.0 0.0 -4.9955       B : 3.849958881883509e-16 -6.28746 -3.849958881883509e-16       C : -10.440588813976833 0.0 -0.004976500966151329 PeriodicSite: Na (-10.4402, -6.2870, -5.0004) [1.0000, 0.9999, 1.0000] PeriodicSite: Na (-10.4402, -3.1442, -5.0004) [1.0000, 0.5001, 1.0000] PeriodicSite: Na (-5.2197, -6.2870, -2.5005) [0.5001, 0.9999, 0.4999] PeriodicSite: Na (-5.2197, -3.1442, -2.5005) [0.5001, 0.5001, 0.4999] PeriodicSite: Fe (-8.2056, -1.5719, -2.6193) [0.5235, 0.2500, 0.7859] PeriodicSite: Fe (-7.4584, -4.7156, -0.1238) [0.0241, 0.7500, 0.7144] PeriodicSite: Fe (-2.9844, -1.5719, -4.8792) [0.9764, 0.2500, 0.2859] PeriodicSite: Fe (-2.2367, -4.7156, -2.3805) [0.4763, 0.7500, 0.2142] PeriodicSite: P (-9.3366, -4.7156, -2.8377) [0.5672, 0.7500, 0.8943] PeriodicSite: P (-6.3250, -1.5719, -0.3370) [0.0669, 0.2500, 0.6058] PeriodicSite: P (-4.1164, -4.7156, -4.6625) [0.9329, 0.7500, 0.3943] PeriodicSite: P (-1.1040, -1.5719, -2.1641) [0.4331, 0.2500, 0.1057] PeriodicSite: O (-10.0753, -1.5719, -1.6636) [0.3321, 0.2500, 0.9650] PeriodicSite: O (-9.2800, -4.7156, -1.2986) [0.2591, 0.7500, 0.8888] PeriodicSite: O (-8.6132, -5.9528, -3.4881) [0.6974, 0.9468, 0.8250] PeriodicSite: O (-8.6132, -3.4783, -3.4881) [0.6974, 0.5532, 0.8250] PeriodicSite: O (-7.0467, -2.8104, -0.9879) [0.1971, 0.4470, 0.6749] PeriodicSite: O (-7.0467, -0.3333, -0.9879) [0.1971, 0.0530, 0.6749] PeriodicSite: O (-6.3830, -1.5719, -3.7937) [0.7588, 0.2500, 0.6114] PeriodicSite: O (-5.5841, -4.7156, -4.1557) [0.8314, 0.7500, 0.5348] PeriodicSite: O (-4.8549, -1.5719, -0.8420) [0.1681, 0.2500, 0.4650] PeriodicSite: O (-4.0586, -4.7156, -1.2059) [0.2410, 0.7500, 0.3887] PeriodicSite: O (-3.3933, -5.9537, -4.0111) [0.8026, 0.9469, 0.3250] PeriodicSite: O (-3.3933, -3.4775, -4.0111) [0.8026, 0.5531, 0.3250] PeriodicSite: O (-1.8263, -2.8099, -1.5129) [0.3027, 0.4469, 0.1749] PeriodicSite: O (-1.8263, -0.3338, -1.5129) [0.3027, 0.0531, 0.1749] PeriodicSite: O (-1.1622, -1.5719, -3.7030) [0.7412, 0.2500, 0.1113] PeriodicSite: O (-0.3650, -4.7156, -3.3387) [0.6683, 0.7500, 0.0350], 'Pb2TiZrO6': Structure Summary Lattice     abc : 4.505383 5.67298 5.67298  angles : 90.0 90.0 90.0  volume : 144.99539884709878       A : 0.0 0.0 4.505383       B : 5.67298 0.0 0.0       C : 0.0 5.67298 0.0 PeriodicSite: Zr (2.8365, 0.0000, 2.4376) [0.5410, 0.5000, -0.0000] PeriodicSite: Ti (0.0000, 2.8365, 2.4188) [0.5369, -0.0000, 0.5000] PeriodicSite: Pb (0.0000, 0.0000, 4.4114) [0.9791, -0.0000, -0.0000] PeriodicSite: Pb (2.8365, 2.8365, 4.4114) [0.9791, 0.5000, 0.5000] PeriodicSite: O (1.3704, 1.4661, 2.8748) [0.6381, 0.2416, 0.2584] PeriodicSite: O (1.3704, 4.2069, 2.8748) [0.6381, 0.2416, 0.7416] PeriodicSite: O (4.3026, 1.4661, 2.8748) [0.6381, 0.7584, 0.2584] PeriodicSite: O (4.3026, 4.2069, 2.8748) [0.6381, 0.7584, 0.7416] PeriodicSite: O (0.0000, 2.8365, 0.6698) [0.1487, -0.0000, 0.5000] PeriodicSite: O (2.8365, 0.0000, 0.4587) [0.1018, 0.5000, -0.0000], 'Si': Structure Summary Lattice     abc : 3.8401979337 3.840198994344244 3.8401979337177736  angles : 119.99999086398421 90.0 60.0000091373222  volume : 40.04479464425159       A : 3.8401979337 0.0 0.0       B : 1.9200989668 3.3257101909 0.0       C : 0.0 -2.2171384943 3.1355090603 PeriodicSite: Si (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Si (3.8402, 0.0000, 2.3516) [0.7500, 0.5000, 0.7500], 'SiO2': Structure Summary Lattice     abc : 5.0277818 5.0277817873408415 5.51891759  angles : 90.0 90.0 120.00000005747829  volume : 120.81959693044213       A : 5.0277818 6e-08 -0.0       B : -2.51389095 4.35418672 0.0       C : -0.0 0.0 5.51891759 PeriodicSite: Si (1.3140, 2.2760, 5.5189) [0.5227, 0.5227, 1.0000] PeriodicSite: Si (2.3997, -0.0000, 3.6792) [0.4773, -0.0000, 0.6667] PeriodicSite: Si (3.8279, 2.0782, 1.8396) [1.0000, 0.4773, 0.3333] PeriodicSite: O (0.8313, 3.6543, 4.8051) [0.5850, 0.8393, 0.8707] PeriodicSite: O (-1.0664, 3.2469, 2.9655) [0.1607, 0.7457, 0.5373] PeriodicSite: O (0.2352, 1.8071, 1.1259) [0.2543, 0.4150, 0.2040] PeriodicSite: O (2.7491, 2.5470, 0.7137) [0.8393, 0.5850, 0.1293] PeriodicSite: O (3.3452, 0.6999, 2.5533) [0.7457, 0.1607, 0.4626] PeriodicSite: O (1.4474, 1.1073, 4.3929) [0.4150, 0.2543, 0.7960], 'Si_SiO2_Interface': Structure Summary Lattice     abc : 10.160210588671637 10.160210588671637 29.156770002399192  angles : 90.0 90.0 59.99999999999999  volume : 2606.6064276838156       A : 10.160210588671637 0.0 6.221334688039882e-16       B : 5.080105294335819 8.799000477589283 6.221334688039882e-16       C : 0.0 0.0 29.156770002399192 PeriodicSite: Si (10.3416, 3.8758, 9.3499) [0.7976, 0.4405, 0.3207] PeriodicSite: Si (13.9703, 5.1328, 9.3499) [1.0833, 0.5833, 0.3207] PeriodicSite: Si (7.4387, 6.3898, 9.3499) [0.3690, 0.7262, 0.3207] PeriodicSite: Si (11.0674, 7.6468, 9.3499) [0.6548, 0.8690, 0.3207] PeriodicSite: Si (9.6159, 0.1048, 9.3499) [0.9405, 0.0119, 0.3207] PeriodicSite: Si (3.0843, 1.3618, 9.3499) [0.2262, 0.1548, 0.3207] PeriodicSite: Si (6.7130, 2.6188, 9.3499) [0.5119, 0.2976, 0.3207] PeriodicSite: Si (10.3416, 3.8758, 11.7016) [0.7976, 0.4405, 0.4013] PeriodicSite: Si (13.9703, 5.1328, 11.7016) [1.0833, 0.5833, 0.4013] PeriodicSite: Si (7.4387, 6.3898, 11.7016) [0.3690, 0.7262, 0.4013] PeriodicSite: Si (11.0674, 7.6468, 11.7016) [0.6548, 0.8690, 0.4013] PeriodicSite: Si (9.6159, 0.1048, 11.7016) [0.9405, 0.0119, 0.4013] PeriodicSite: Si (3.0843, 1.3618, 11.7016) [0.2262, 0.1548, 0.4013] PeriodicSite: Si (6.7130, 2.6188, 11.7016) [0.5119, 0.2976, 0.4013] PeriodicSite: Si (3.8678, 2.0998, 13.7016) [0.2614, 0.2386, 0.4699] PeriodicSite: Si (6.4078, 6.4993, 13.7016) [0.2614, 0.7386, 0.4699] PeriodicSite: Si (8.9479, 2.0998, 13.7016) [0.7614, 0.2386, 0.4699] PeriodicSite: Si (11.4879, 6.4993, 13.7016) [0.7614, 0.7386, 0.4699] PeriodicSite: Si (4.9647, 4.3995, 15.5412) [0.2386, 0.5000, 0.5330] PeriodicSite: Si (2.4247, 0.0000, 15.5412) [0.2386, 0.0000, 0.5330] PeriodicSite: Si (10.0448, 4.3995, 15.5412) [0.7386, 0.5000, 0.5330] PeriodicSite: Si (7.5048, 0.0000, 15.5412) [0.7386, 0.0000, 0.5330] PeriodicSite: Si (1.3277, 2.2997, 17.3808) [0.0000, 0.2614, 0.5961] PeriodicSite: Si (3.8678, 6.6992, 17.3808) [0.0000, 0.7614, 0.5961] PeriodicSite: Si (6.4078, 2.2997, 17.3808) [0.5000, 0.2614, 0.5961] PeriodicSite: Si (8.9479, 6.6992, 17.3808) [0.5000, 0.7614, 0.5961] PeriodicSite: O (3.3800, 0.7072, 14.4153) [0.2925, 0.0804, 0.4944] PeriodicSite: O (5.9200, 5.1067, 14.4153) [0.2925, 0.5804, 0.4944] PeriodicSite: O (8.4601, 0.7072, 14.4153) [0.7925, 0.0804, 0.4944] PeriodicSite: O (11.0001, 5.1067, 14.4153) [0.7925, 0.5804, 0.4944] PeriodicSite: O (1.4625, 1.1188, 16.2550) [0.0804, 0.1271, 0.5575] PeriodicSite: O (4.0026, 5.5183, 16.2550) [0.0804, 0.6271, 0.5575] PeriodicSite: O (6.5426, 1.1188, 16.2550) [0.5804, 0.1271, 0.5575] PeriodicSite: O (9.0827, 5.5183, 16.2550) [0.5804, 0.6271, 0.5575] PeriodicSite: O (2.7777, 2.5735, 18.0946) [0.1271, 0.2925, 0.6206] PeriodicSite: O (5.3177, 6.9730, 18.0946) [0.1271, 0.7925, 0.6206] PeriodicSite: O (7.8578, 2.5735, 18.0946) [0.6271, 0.2925, 0.6206] PeriodicSite: O (10.3978, 6.9730, 18.0946) [0.6271, 0.7925, 0.6206] PeriodicSite: O (5.3177, 1.8260, 18.5067) [0.4196, 0.2075, 0.6347] PeriodicSite: O (7.8578, 6.2255, 18.5067) [0.4196, 0.7075, 0.6347] PeriodicSite: O (10.3978, 1.8260, 18.5067) [0.9196, 0.2075, 0.6347] PeriodicSite: O (12.9379, 6.2255, 18.5067) [0.9196, 0.7075, 0.6347] PeriodicSite: O (5.9200, 3.6923, 16.6671) [0.3729, 0.4196, 0.5716] PeriodicSite: O (8.4601, 8.0918, 16.6671) [0.3729, 0.9196, 0.5716] PeriodicSite: O (11.0001, 3.6923, 16.6671) [0.8729, 0.4196, 0.5716] PeriodicSite: O (13.5402, 8.0918, 16.6671) [0.8729, 0.9196, 0.5716] PeriodicSite: O (4.0026, 3.2807, 14.8274) [0.2075, 0.3729, 0.5085] PeriodicSite: O (6.5426, 7.6802, 14.8274) [0.2075, 0.8729, 0.5085] PeriodicSite: O (9.0827, 3.2807, 14.8274) [0.7075, 0.3729, 0.5085] PeriodicSite: O (11.6227, 7.6802, 14.8274) [0.7075, 0.8729, 0.5085], 'Sn': Structure Summary Lattice     abc : 6.65061477 6.65061477 6.65061477  angles : 90.0 90.0 90.0  volume : 294.16119253915326       A : 6.65061477 0.0 0.0       B : 0.0 6.65061477 0.0       C : 0.0 0.0 6.65061477 PeriodicSite: Sn (2.4940, 5.8193, 2.4940) [0.3750, 0.8750, 0.3750] PeriodicSite: Sn (0.8313, 0.8313, 0.8313) [0.1250, 0.1250, 0.1250] PeriodicSite: Sn (2.4940, 2.4940, 5.8193) [0.3750, 0.3750, 0.8750] PeriodicSite: Sn (0.8313, 4.1566, 4.1566) [0.1250, 0.6250, 0.6250] PeriodicSite: Sn (5.8193, 5.8193, 5.8193) [0.8750, 0.8750, 0.8750] PeriodicSite: Sn (4.1566, 0.8313, 4.1566) [0.6250, 0.1250, 0.6250] PeriodicSite: Sn (5.8193, 2.4940, 2.4940) [0.8750, 0.3750, 0.3750] PeriodicSite: Sn (4.1566, 4.1566, 0.8313) [0.6250, 0.6250, 0.1250], 'SrTiO3': Structure Summary Lattice     abc : 3.905 3.905 3.905  angles : 90.0 90.0 90.0  volume : 59.54744262499999       A : 3.905 0.0 2.391122875335207e-16       B : -2.391122875335207e-16 3.905 2.391122875335207e-16       C : 0.0 0.0 3.905 PeriodicSite: Sr2+ (1.9525, 1.9525, 1.9525) [0.5000, 0.5000, 0.5000] PeriodicSite: Ti4+ (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: O2- (0.0000, 0.0000, 1.9525) [0.0000, 0.0000, 0.5000] PeriodicSite: O2- (-0.0000, 1.9525, 0.0000) [0.0000, 0.5000, 0.0000] PeriodicSite: O2- (1.9525, 0.0000, 0.0000) [0.5000, 0.0000, 0.0000], 'TiO2': <pymatgen.alchemy.materials.TransformedStructure object>, 'TlBiSe2': Structure Summary Lattice     abc : 4.372201544153475 61.149528191254596 59.08304095958131  angles : 3.6737691014605547 58.80413768014368 59.97014152897428  volume : 825.8885392060803       A : 3.74140218 -0.00027862 2.26231209       B : -1.13595131 3.78041753 61.02198666       C : 0.036913 0.04093202 59.08301525 PeriodicSite: Tl (2.5148, 3.6745, 63.4338) [0.9669, 0.9717, 0.0330] PeriodicSite: Tl (3.6037, 0.2035, 6.7146) [0.9793, 0.0537, 0.0207] PeriodicSite: Tl (3.5726, 0.5326, 10.9899) [0.9977, 0.1409, 0.0022] PeriodicSite: Tl (-0.2434, 0.8101, 13.0761) [0.0000, 0.2143, -0.0000] PeriodicSite: Tl (-0.2812, 1.1282, 76.5077) [0.0023, 0.2876, 0.9978] PeriodicSite: Tl (-0.3122, 1.4572, 80.7830) [0.0207, 0.3749, 0.9793] PeriodicSite: Tl (-0.3594, 1.7667, 85.0859) [0.0331, 0.4569, 0.9670] PeriodicSite: Bi (-0.4251, 2.0554, 89.4184) [0.0388, 0.5333, 0.9611] PeriodicSite: Bi (-0.5892, 2.2281, 93.9147) [0.0084, 0.5786, 0.9916] PeriodicSite: Bi (-0.6750, 2.4926, 98.2811) [0.0067, 0.6486, 0.9933] PeriodicSite: Bi (-0.8113, 2.7004, 43.5869) [0.0000, 0.7143, -0.0000] PeriodicSite: Bi (2.8309, 2.9491, 50.2379) [0.9934, 0.7801, 0.0066] PeriodicSite: Bi (2.7442, 3.2126, 54.6058) [0.9914, 0.8498, 0.0086] PeriodicSite: Bi (2.5805, 3.3856, 59.1013) [0.9611, 0.8952, 0.0389] PeriodicSite: Se (1.7377, 0.2085, 35.1484) [0.4743, 0.0495, 0.5256] PeriodicSite: Se (1.6987, 0.5271, 39.4370) [0.4897, 0.1339, 0.5104] PeriodicSite: Se (1.6462, 0.8311, 43.7478) [0.5002, 0.2145, 0.4998] PeriodicSite: Se (1.5935, 1.1347, 48.0594) [0.5106, 0.2949, 0.4893] PeriodicSite: Se (1.5531, 1.4514, 52.3505) [0.5255, 0.3788, 0.4747] PeriodicSite: Se (1.4871, 1.7413, 56.6824) [0.5312, 0.4556, 0.4685] PeriodicSite: Se (1.4204, 2.0277, 61.0185) [0.5364, 0.5314, 0.4634] PeriodicSite: Se (1.2436, 2.1850, 65.5372) [0.5013, 0.5726, 0.4986] PeriodicSite: Se (1.1826, 2.4786, 69.8633) [0.5087, 0.6503, 0.4913] PeriodicSite: Se (1.0777, 2.7207, 74.2599) [0.5000, 0.7143, 0.5000] PeriodicSite: Se (0.9728, 2.9625, 78.6564) [0.4913, 0.7782, 0.5088] PeriodicSite: Se (0.9121, 3.2562, 82.9823) [0.4987, 0.8560, 0.5014] PeriodicSite: Se (0.7353, 3.4138, 87.5010) [0.4636, 0.8973, 0.5365] PeriodicSite: Se (0.6680, 3.6996, 91.8379) [0.4687, 0.9729, 0.5316], 'VO2': <pymatgen.alchemy.materials.TransformedStructure object>}[source]
                                          -static assertArrayAlmostEqual(actual, desired, decimal=7, err_msg='', verbose=True)[source]
                                          +static assertArrayAlmostEqual(actual, desired, decimal=7, err_msg='', verbose=True)[source]

                                          Tests if two arrays are almost equal to a tolerance. The CamelCase naming is so that it is consistent with standard unittest methods.

                                          -static assertArrayEqual(actual, desired, err_msg='', verbose=True)[source]
                                          +static assertArrayEqual(actual, desired, err_msg='', verbose=True)[source]
                                          Tests if two arrays are equal. The CamelCase naming is so that it is

                                          consistent with standard unittest methods.

                                          @@ -166,14 +166,14 @@
                                          -static assertDictsAlmostEqual(actual, desired, decimal=7, err_msg='', verbose=True)[source]
                                          +static assertDictsAlmostEqual(actual, desired, decimal=7, err_msg='', verbose=True)[source]

                                          Tests if two arrays are almost equal to a tolerance. The CamelCase naming is so that it is consistent with standard unittest methods.

                                          -assertMSONable(obj, test_if_subclass=True)[source]
                                          +assertMSONable(obj, test_if_subclass=True)[source]

                                          Tests if obj is MSONable and tries to verify whether the contract is fulfilled.

                                          By default, the method tests whether obj is an instance of MSONable. @@ -182,19 +182,19 @@

                                          -static assertStrContentEqual(actual, desired, err_msg='', verbose=True)[source]
                                          +static assertStrContentEqual(actual, desired, err_msg='', verbose=True)[source]

                                          Tests if two strings are equal, ignoring things like trailing spaces, etc.

                                          -fn = PosixPath('/Users/shyue/repos/pymatgen/docs_rst/../pymatgen/util/structures/SrTiO3.json')[source]
                                          +fn = PosixPath('/Users/shyue/repos/pymatgen/docs_rst/../pymatgen/util/structures/SrTiO3.json')[source]
                                          -classmethod get_mp_structure(mpid)[source]
                                          +classmethod get_mp_structure(mpid)[source]

                                          Get a structure from MP.

                                          Parameters
                                          @@ -208,7 +208,7 @@
                                          -classmethod get_structure(name)[source]
                                          +classmethod get_structure(name)[source]

                                          Get a structure from the template directories.

                                          Parameters
                                          @@ -222,7 +222,7 @@
                                          -serialize_with_pickle(objects, protocols=None, test_eq=True)[source]
                                          +serialize_with_pickle(objects, protocols=None, test_eq=True)[source]

                                          Test whether the object(s) can be serialized and deserialized with pickle. This method tries to serialize the objects with pickle and the protocols specified in input. Then it deserializes the pickle format @@ -245,7 +245,7 @@

                                          -warnings = <module 'warnings' from '/Users/shyue/miniconda3/envs/mavrl/lib/python3.9/warnings.py'>[source]
                                          +warnings = <module 'warnings' from '/Users/shyue/miniconda3/envs/mavrl/lib/python3.9/warnings.py'>[source]
                                          diff --git a/docs/pymatgen.util.typing.html b/docs/pymatgen.util.typing.html index 1b9e491f6ad..6239a5b274f 100644 --- a/docs/pymatgen.util.typing.html +++ b/docs/pymatgen.util.typing.html @@ -4,7 +4,7 @@ - pymatgen.util.typing module — pymatgen 2022.5.18 documentation + pymatgen.util.typing module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                          - 2022.5.18 + 2022.5.18.1
                                          diff --git a/docs/pymatgen.vis.html b/docs/pymatgen.vis.html index dea655f740e..32a54735f5f 100644 --- a/docs/pymatgen.vis.html +++ b/docs/pymatgen.vis.html @@ -4,7 +4,7 @@ - pymatgen.vis package — pymatgen 2022.5.18 documentation + pymatgen.vis package — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                          - 2022.5.18 + 2022.5.18.1
                                          diff --git a/docs/pymatgen.vis.plotters.html b/docs/pymatgen.vis.plotters.html index 828c6e4bebc..5a74a3036d2 100644 --- a/docs/pymatgen.vis.plotters.html +++ b/docs/pymatgen.vis.plotters.html @@ -4,7 +4,7 @@ - pymatgen.vis.plotters module — pymatgen 2022.5.18 documentation + pymatgen.vis.plotters module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                          - 2022.5.18 + 2022.5.18.1
                                          @@ -118,7 +118,7 @@

                                          This module defines generic plotters.

                                          -class SpectrumPlotter(xshift=0.0, yshift=0.0, stack=False, color_cycle=('qualitative', 'Set1_9'))[source]
                                          +class SpectrumPlotter(xshift=0.0, yshift=0.0, stack=False, color_cycle=('qualitative', 'Set1_9'))[source]

                                          Bases: object

                                          Class for plotting Spectrum objects and subclasses. Note that the interface is extremely flexible given that there are many different ways in which @@ -155,7 +155,7 @@

                                          -add_spectra(spectra_dict, key_sort_func=None)[source]
                                          +add_spectra(spectra_dict, key_sort_func=None)[source]

                                          Add a dictionary of doses, with an optional sorting function for the keys.

                                          @@ -170,7 +170,7 @@
                                          -add_spectrum(label, spectrum, color=None)[source]
                                          +add_spectrum(label, spectrum, color=None)[source]

                                          Adds a Spectrum for plotting.

                                          Parameters
                                          @@ -187,7 +187,7 @@
                                          -get_plot(xlim=None, ylim=None)[source]
                                          +get_plot(xlim=None, ylim=None)[source]

                                          Get a matplotlib plot showing the DOS.

                                          Parameters
                                          @@ -202,7 +202,7 @@
                                          -save_plot(filename, img_format='eps', **kwargs)[source]
                                          +save_plot(filename, img_format='eps', **kwargs)[source]

                                          Save matplotlib plot to a file.

                                          Parameters
                                          @@ -216,7 +216,7 @@
                                          -show(**kwargs)[source]
                                          +show(**kwargs)[source]

                                          Show the plot using matplotlib.

                                          diff --git a/docs/pymatgen.vis.structure_chemview.html b/docs/pymatgen.vis.structure_chemview.html index 748021c6fd1..d52ef019395 100644 --- a/docs/pymatgen.vis.structure_chemview.html +++ b/docs/pymatgen.vis.structure_chemview.html @@ -4,7 +4,7 @@ - pymatgen.vis.structure_chemview module — pymatgen 2022.5.18 documentation + pymatgen.vis.structure_chemview module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                          - 2022.5.18 + 2022.5.18.1
                                          @@ -118,7 +118,7 @@

                                          Visualization for structures using chemview.

                                          -quick_view(structure, bonds=True, conventional=False, transform=None, show_box=True, bond_tol=0.2, stick_radius=0.1)[source]
                                          +quick_view(structure, bonds=True, conventional=False, transform=None, show_box=True, bond_tol=0.2, stick_radius=0.1)[source]

                                          A function to visualize pymatgen Structure objects in jupyter notebook using chemview package.

                                          Parameters
                                          diff --git a/docs/pymatgen.vis.structure_vtk.html b/docs/pymatgen.vis.structure_vtk.html index bb54aa1dc2f..ea771fe2e19 100644 --- a/docs/pymatgen.vis.structure_vtk.html +++ b/docs/pymatgen.vis.structure_vtk.html @@ -4,7 +4,7 @@ - pymatgen.vis.structure_vtk module — pymatgen 2022.5.18 documentation + pymatgen.vis.structure_vtk module — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                          - 2022.5.18 + 2022.5.18.1
                                          @@ -118,7 +118,7 @@

                                          This module contains classes to wrap Python VTK to make nice molecular plots.

                                          -class MultiStructuresInteractorStyle(parent)[source]
                                          +class MultiStructuresInteractorStyle(parent)[source]

                                          Bases: pymatgen.vis.structure_vtk.StructureInteractorStyle

                                          Interactor for MultiStructureVis.

                                          @@ -128,7 +128,7 @@
                                          -keyPressEvent(obj, event)[source]
                                          +keyPressEvent(obj, event)[source]
                                          Parameters
                                            @@ -143,7 +143,7 @@
                                            -class MultiStructuresVis(element_color_mapping=None, show_unit_cell=True, show_bonds=False, show_polyhedron=False, poly_radii_tol_factor=0.5, excluded_bonding_elements=None, animated_movie_options={'looping_type': 'restart', 'number_of_loops': 1, 'time_between_frames': 0.1, 'time_between_loops': 1.0})[source]
                                            +class MultiStructuresVis(element_color_mapping=None, show_unit_cell=True, show_bonds=False, show_polyhedron=False, poly_radii_tol_factor=0.5, excluded_bonding_elements=None, animated_movie_options={'looping_type': 'restart', 'number_of_loops': 1, 'time_between_frames': 0.1, 'time_between_loops': 1.0})[source]

                                            Bases: pymatgen.vis.structure_vtk.StructureVis

                                            Visualization for multiple structures.

                                            @@ -173,24 +173,24 @@
                                            -DEFAULT_ANIMATED_MOVIE_OPTIONS = {'looping_type': 'restart', 'number_of_loops': 1, 'time_between_frames': 0.1, 'time_between_loops': 1.0}[source]
                                            +DEFAULT_ANIMATED_MOVIE_OPTIONS = {'looping_type': 'restart', 'number_of_loops': 1, 'time_between_frames': 0.1, 'time_between_loops': 1.0}[source]
                                            -apply_tags()[source]
                                            +apply_tags()[source]

                                            Apply tags.

                                            -display_help()[source]
                                            +display_help()[source]

                                            Display the help for various keyboard shortcuts.

                                            -display_info(info)[source]
                                            +display_info(info)[source]
                                            Parameters

                                            info (str) – Information.

                                            @@ -200,7 +200,7 @@
                                            -display_warning(warning)[source]
                                            +display_warning(warning)[source]
                                            Parameters

                                            warning (str) – Warning

                                            @@ -210,19 +210,19 @@
                                            -erase_info()[source]
                                            +erase_info()[source]

                                            Erase all info.

                                            -erase_warning()[source]
                                            +erase_warning()[source]

                                            Remove warnings.

                                            -set_animated_movie_options(animated_movie_options=None)[source]
                                            +set_animated_movie_options(animated_movie_options=None)[source]
                                            Parameters

                                            () (animated_movie_options) –

                                            @@ -232,7 +232,7 @@
                                            -set_structure(structure, reset_camera=True, to_unit_cell=False)[source]
                                            +set_structure(structure, reset_camera=True, to_unit_cell=False)[source]

                                            Add a structure to the visualizer.

                                            Parameters
                                            @@ -248,7 +248,7 @@
                                            -set_structures(structures, tags=None)[source]
                                            +set_structures(structures, tags=None)[source]

                                            Add list of structures to the visualizer.

                                            Parameters
                                            @@ -264,7 +264,7 @@
                                            -class StructureInteractorStyle(parent)[source]
                                            +class StructureInteractorStyle(parent)[source]

                                            Bases: object

                                            A custom interactor style for visualizing structures.

                                            @@ -274,7 +274,7 @@
                                            -keyPressEvent(obj, event)[source]
                                            +keyPressEvent(obj, event)[source]
                                            Parameters
                                              @@ -287,7 +287,7 @@
                                              -leftButtonPressEvent(obj, event)[source]
                                              +leftButtonPressEvent(obj, event)[source]
                                              Parameters
                                                @@ -300,7 +300,7 @@
                                                -leftButtonReleaseEvent(obj, event)[source]
                                                +leftButtonReleaseEvent(obj, event)[source]
                                                Parameters
                                                  @@ -313,7 +313,7 @@
                                                  -mouseMoveEvent(obj, event)[source]
                                                  +mouseMoveEvent(obj, event)[source]
                                                  Parameters
                                                    @@ -328,7 +328,7 @@
                                                    -class StructureVis(element_color_mapping=None, show_unit_cell=True, show_bonds=False, show_polyhedron=True, poly_radii_tol_factor=0.5, excluded_bonding_elements=None)[source]
                                                    +class StructureVis(element_color_mapping=None, show_unit_cell=True, show_bonds=False, show_polyhedron=True, poly_radii_tol_factor=0.5, excluded_bonding_elements=None)[source]

                                                    Bases: object

                                                    Provides Structure object visualization using VTK.

                                                    Constructs a Structure Visualization.

                                                    @@ -374,7 +374,7 @@
                                                    -add_bonds(neighbors, center, color=None, opacity=None, radius=0.1)[source]
                                                    +add_bonds(neighbors, center, color=None, opacity=None, radius=0.1)[source]

                                                    Adds bonds for a site.

                                                    Parameters
                                                    @@ -391,7 +391,7 @@
                                                    -add_edges(edges, type='line', linewidth=2, color=[0.0, 0.0, 0.0])[source]
                                                    +add_edges(edges, type='line', linewidth=2, color=[0.0, 0.0, 0.0])[source]
                                                    Parameters
                                                      @@ -406,7 +406,7 @@
                                                      -add_faces(faces, color, opacity=0.35)[source]
                                                      +add_faces(faces, color, opacity=0.35)[source]

                                                      Adding face of polygon.

                                                      Parameters
                                                      @@ -421,7 +421,7 @@
                                                      -add_line(start, end, color=(0.5, 0.5, 0.5), width=1)[source]
                                                      +add_line(start, end, color=(0.5, 0.5, 0.5), width=1)[source]

                                                      Adds a line.

                                                      Parameters
                                                      @@ -437,7 +437,7 @@
                                                      -add_partial_sphere(coords, radius, color, start=0, end=360, opacity=1.0)[source]
                                                      +add_partial_sphere(coords, radius, color, start=0, end=360, opacity=1.0)[source]

                                                      Adding a partial sphere (to display partial occupancies.

                                                      Parameters
                                                      @@ -455,19 +455,19 @@
                                                      -add_picker()[source]
                                                      +add_picker()[source]

                                                      Create a cell picker.

                                                      -add_picker_fixed()[source]
                                                      +add_picker_fixed()[source]

                                                      Create a cell picker.Returns:

                                                      -add_polyhedron(neighbors, center, color, opacity=1.0, draw_edges=False, edges_color=[0.0, 0.0, 0.0], edges_linewidth=2)[source]
                                                      +add_polyhedron(neighbors, center, color, opacity=1.0, draw_edges=False, edges_color=[0.0, 0.0, 0.0], edges_linewidth=2)[source]

                                                      Adds a polyhedron.

                                                      Parameters
                                                      @@ -486,7 +486,7 @@
                                                      -add_site(site)[source]
                                                      +add_site(site)[source]

                                                      Add a site to the render window. The site is displayed as a sphere, the color of which is determined based on the element. Partially occupied sites are displayed as a single element color, though the site info @@ -500,7 +500,7 @@

                                                      -add_text(coords, text, color=(0, 0, 0))[source]
                                                      +add_text(coords, text, color=(0, 0, 0))[source]

                                                      Add text at a coordinate.

                                                      Parameters
                                                      @@ -515,7 +515,7 @@
                                                      -add_triangle(neighbors, color, center=None, opacity=0.4, draw_edges=False, edges_color=[0.0, 0.0, 0.0], edges_linewidth=2)[source]
                                                      +add_triangle(neighbors, color, center=None, opacity=0.4, draw_edges=False, edges_color=[0.0, 0.0, 0.0], edges_linewidth=2)[source]

                                                      Adds a triangular surface between three atoms.

                                                      Parameters
                                                      @@ -534,19 +534,19 @@
                                                      -display_help()[source]
                                                      +display_help()[source]

                                                      Display the help for various keyboard shortcuts.

                                                      -orthongonalize_structure()[source]
                                                      +orthongonalize_structure()[source]

                                                      Orthogonalize the structure.

                                                      -redraw(reset_camera=False)[source]
                                                      +redraw(reset_camera=False)[source]

                                                      Redraw the render window.

                                                      Parameters
                                                      @@ -558,7 +558,7 @@
                                                      -rotate_view(axis_ind=0, angle=0)[source]
                                                      +rotate_view(axis_ind=0, angle=0)[source]

                                                      Rotate the camera view.

                                                      Parameters
                                                      @@ -572,7 +572,7 @@
                                                      -set_structure(structure, reset_camera=True, to_unit_cell=True)[source]
                                                      +set_structure(structure, reset_camera=True, to_unit_cell=True)[source]

                                                      Add a structure to the visualizer.

                                                      Parameters
                                                      @@ -588,13 +588,13 @@
                                                      -show()[source]
                                                      +show()[source]

                                                      Display the visualizer.

                                                      -write_image(filename='image.png', magnification=1, image_format='png')[source]
                                                      +write_image(filename='image.png', magnification=1, image_format='png')[source]

                                                      Save render window to an image.

                                                      Parameters
                                                      @@ -609,7 +609,7 @@
                                                      -zoom(factor)[source]
                                                      +zoom(factor)[source]

                                                      Zoom the camera view by a factor.

                                                      @@ -617,7 +617,7 @@
                                                      -make_movie(structures, output_filename='movie.mp4', zoom=1.0, fps=20, bitrate='10000k', quality=1, **kwargs)[source]
                                                      +make_movie(structures, output_filename='movie.mp4', zoom=1.0, fps=20, bitrate='10000k', quality=1, **kwargs)[source]

                                                      Generate a movie from a sequence of structures using vtk and ffmpeg.

                                                      Parameters
                                                      diff --git a/docs/references.html b/docs/references.html index 32fc9db1402..1a51544d9f5 100644 --- a/docs/references.html +++ b/docs/references.html @@ -4,7 +4,7 @@ - References — pymatgen 2022.5.18 documentation + References — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                      - 2022.5.18 + 2022.5.18.1
                                                      diff --git a/docs/search.html b/docs/search.html index 5666b3ad6d8..319c298a939 100644 --- a/docs/search.html +++ b/docs/search.html @@ -3,7 +3,7 @@ - Search — pymatgen 2022.5.18 documentation + Search — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                      - 2022.5.18 + 2022.5.18.1
                                                      diff --git a/docs/searchindex.js b/docs/searchindex.js index c5d57aaa8dc..35eec4ebfe6 100644 --- a/docs/searchindex.js +++ b/docs/searchindex.js @@ -1 +1 @@ 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skov":161,"new":[1,2,3,5,12,13,26,43,48,49,51,55,56,62,63,67,70,71,79,81,86,87,98,99,101,102,103,117,119,139,146,149,156,157,158,160,168,170,173,182,183,186,187,188,190,192,197,199,201,212,221,224,225,230,231,232,235,238,239,240,258,261,272,280,281,285,292],"null":79,"o\u00b2":283,"okuli\u010d":179,"p2\u2081":283,"pend\u00e1":139,"public":[3,4,6,44,56,92,157,240,280,290],"quir\u00f3":179,"ren\u00e8":291,"return":[1,3,4,6,11,12,13,15,16,17,20,21,22,23,25,26,28,29,30,32,34,35,36,37,38,39,40,41,43,44,45,46,48,49,51,52,53,54,55,56,58,59,60,61,62,63,66,67,68,70,71,74,78,79,81,82,83,84,85,86,87,88,89,90,91,92,93,94,96,97,98,100,101,102,103,105,106,109,110,112,113,116,117,118,119,120,122,123,127,130,137,138,139,141,142,143,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,164,165,167,168,169,170,171,172,173,175,176,177,179,180,182,183,186,187,188,189,190,191,192,193,194,195,196,197,199,200,201,202,203,204,206,208,209,210,211,212,213,215,217,219,221,222,223,224,225,226,227,228,230,231,233,234,237,238,239,240,241,242,243,245,247,248,251,252,254,255,256,257,258,260,261,262,263,265,266,267,269,270,271,272,273,275,276,277,278,279,280,281,282,283,284,287,288,289],"rodr\u00edguez":152,"se\u00e1n":291,"short":[44,51,79,145,230,240,248],"static":[1,12,13,25,44,45,53,70,71,79,82,83,84,85,87,91,93,94,97,101,105,108,109,141,143,145,146,149,150,152,153,158,165,168,172,177,182,186,190,191,192,193,194,195,196,199,200,201,203,206,208,209,210,211,212,213,221,224,228,230,231,238,239,240,241,243,245,247,248,261,263,265,269,272,280,281,284,292],"super":[20,55,71,77,78,113,118,119,155,157,199,201],"switch":[1,3,170,201,269],"throw":[58,89,239,272],"transient":182,"true":[1,2,11,12,13,15,16,20,22,25,26,28,29,30,34,37,39,40,43,44,45,48,49,51,52,54,56,58,62,66,67,68,70,71,74,76,79,81,83,84,85,87,88,89,91,93,96,98,101,102,103,105,108,109,110,116,117,118,119,120,122,138,139,141,143,146,147,148,149,150,152,153,154,156,157,158,159,164,165,167,168,169,170,172,174,175,177,182,186,187,188,189,190,192,195,196,197,199,200,201,208,210,211,212,215,219,221,222,223,226,231,233,238,239,240,242,243,254,256,257,258,260,262,263,269,271,272,273,275,276,277,278,279,280,282,283,284,288,289],"try":[1,2,5,12,37,47,58,67,71,81,82,139,165,169,182,190,238,239,269,289],"universit\u00e4t":291,"universit\u00e9":291,"var":188,"void":[1,248],"while":[0,2,3,5,11,25,29,34,45,66,70,76,79,84,85,105,116,137,156,157,170,182,200,201,215,217,238,239,272,292],A:[1,2,3,4,6,7,11,12,13,15,17,25,26,28,29,34,37,40,43,44,48,49,51,55,56,61,62,63,64,66,67,70,71,72,74,77,78,79,81,84,86,88,91,92,94,96,97,98,100,101,102,103,105,106,108,110,112,113,116,117,118,119,120,122,127,129,137,138,139,141,142,143,145,146,147,148,149,151,152,153,154,155,156,157,158,159,160,164,165,167,168,169,170,171,172,173,174,175,176,177,179,180,181,182,183,186,187,188,190,192,195,196,197,199,200,201,203,206,208,211,212,215,221,224,225,226,228,230,232,233,234,237,238,239,240,248,250,251,254,255,256,257,258,260,262,263,264,265,267,269,271,272,276,280,281,283,284,287,288,289,290,292],AND:[4,6,11,153,157,239,240],AS:[4,6],ASE:[1,5,62,193],AT:142,And:[79,239],As:[2,4,5,6,29,56,66,71,79,85,103,105,153,182,199,201,239,240,269,292],At:[3,4,6,56,85,97,105,153,201,218,240],BE:[4,6],BUT:[4,6],Be:[1,56,85,153,240],Being:66,But:[1,4,6,49,70,201,248,260,269,271,292],By:[5,11,12,13,37,49,53,55,66,70,71,74,88,91,94,122,139,147,156,157,165,169,170,190,200,201,230,238,239,260,269,283,284],FOR:[4,6,157],For:[1,2,3,4,5,6,11,12,17,20,25,26,29,34,40,41,43,44,49,53,54,55,56,58,66,70,71,78,79,84,88,94,97,98,100,105,106,109,117,118,119,122,137,138,139,141,145,146,147,148,149,152,153,156,157,160,161,165,168,169,170,171,172,173,175,176,180,182,183,186,187,188,190,195,199,200,201,202,204,212,215,216,221,223,224,225,228,232,233,238,239,240,248,252,260,262,269,271,272,281,283,286,287,289,290,292],IN:[4,6],IS:[4,6],If:[1,2,3,4,5,6,11,12,15,16,20,28,29,30,34,37,40,43,44,45,48,49,51,52,53,54,55,56,58,62,67,68,70,71,74,79,81,83,85,87,88,91,92,98,100,101,102,105,109,110,112,116,117,118,119,120,122,123,137,138,139,140,141,143,145,146,147,148,149,153,154,155,156,157,158,161,164,165,167,168,169,170,172,173,174,175,177,179,182,186,188,189,190,192,195,196,197,199,200,201,204,210,211,212,215,221,223,224,225,226,231,232,233,234,238,239,240,248,252,254,255,256,257,258,260,261,262,263,269,271,272,273,276,278,280,284,287,289,290,291,292],In:[1,3,4,5,6,28,29,34,40,56,71,74,84,85,87,88,92,97,103,110,139,146,149,152,153,156,157,158,169,170,172,177,182,188,196,199,201,204,225,230,232,238,239,240,243,247,263,264,292],Is:157,Ising:61,It:[0,1,3,4,5,6,13,16,17,45,49,55,56,63,66,70,71,77,79,82,84,88,102,105,113,117,122,123,146,147,149,156,157,158,159,160,161,164,165,167,169,170,172,174,177,180,183,187,188,199,201,212,215,219,220,236,238,239,240,250,251,254,260,262,263,269,271,272,276,281,292],Its:226,NO:[4,6],NOT:[4,6,41,43,49,71,88,188,201,215,232,239,240],Near:182,No:[1,11,25,26,35,37,55,56,61,63,98,116,153,156,179,215,216,238,272],Not:[5,20,25,88,156,183,186,196,215,269,270],OF:[4,6,92,232],ON:5,ONE:215,OR:[4,6,48,182],Of:196,On:[4,6,122,240],One:[4,6,34,56,117,156,170,186,201,231,238,239,248,258,260,269],Or:[98,152,281],Such:85,THE:[4,6,157],THe:169,TO:[4,6,157],That:[70,79,97,155],The:[1,2,3,4,5,6,11,12,13,15,17,20,25,26,28,29,30,34,36,37,40,42,45,46,47,48,49,51,52,53,54,55,56,58,61,62,63,66,67,68,70,71,72,74,78,79,84,85,87,88,89,91,92,93,94,96,97,98,100,101,102,105,106,108,109,110,112,113,117,118,119,120,121,122,123,137,139,145,146,147,148,149,151,152,153,154,155,156,157,159,160,161,162,164,165,167,168,169,170,172,173,177,179,180,181,182,183,186,188,189,190,191,192,193,195,196,197,199,200,201,202,204,208,209,210,211,212,215,216,217,218,219,222,223,224,225,226,228,230,232,233,234,238,239,240,241,248,250,251,254,255,256,257,258,259,260,261,262,263,264,268,269,271,272,274,278,279,280,281,283,284,286,287,289,290,291],Their:[84,145],Then:[1,2,3,5,49,82,199,202,260,284],There:[1,2,3,4,6,71,84,102,105,122,149,156,157,164,168,204,221,239,254,263,264,269,292],These:[1,4,6,26,29,56,58,63,71,78,88,109,180,182,196,199,201,212,223,226,239,240,291,292],To:[3,4,6,40,45,55,66,70,84,88,105,118,139,141,148,156,168,170,172,182,183,187,210,211,216,219,230,232,238,239,240,255,262,264,269,292],WILL:157,WITH:[4,6,157,164,254,256,272],Will:[1,63,71,81,83,157,197,199,200,201,208,221,223,239,256,258,269,272,283],With:[0,1,3,4,5,6,79,196,201,260,275],_:[1,13,55,182,190,215,240,283,290],__:201,__eq__:284,__getattr__:188,__getitem__:146,__hash__:1,__init__:[13,58,59,60,70,86,89,90,113,155,156,157,158,172,179,197,230,234,240],__main__:1,__module__:292,__name__:[1,292],__new__:[58,59,60,86,89,90,158,160],__repr__:1,__rmul__:1,__slots__:282,__str__:[146,197,208,212,225,230,238,283],_additional_condit:25,_angle_cutoff:25,_array_lik:[113,149,152,155,156,169,238],_b:170,_bp:239,_calculate_possible_shift:157,_cgraph:1,_comput:88,_continuous_symmetry_measure_cutoff:25,_decor:177,_del:210,_distance_cutoff:25,_ds1_:188,_ev:239,_extrema_df:49,_figur:[53,174],_filter_and_sort_entri:177,_get_nn_shell_info:79,_io:[187,190],_map:88,_materialsproject:[182,281],_matrix:63,_name_compat:174,_name_compatibilityuncertainti:174,_nested_sequ:[113,149,152,155,156,169,238],_nestedsequ:[113,149,152,155,156,169,238],_optimad:183,_parse_bool:238,_parse_float:238,_parse_int:238,_parse_list:238,_parse_str:238,_path:186,_pickl:282,_proj_height:157,_set:240,_site:156,_sl_vector:78,_sp:102,_supportsarrai:[113,149,152,155,156,169,238],_threshold:102,a1604:58,a1826:58,a1:[25,49,260],a1fdb1089d0727f415416ec8082246ba:240,a1fit:192,a2:[1,25,49,70,212,260,269],a2b2:1,a2c9485ea86b2a7cf175077e6e5c7b3:240,a32:70,a35:79,a38:70,a395eb3aaf2fcab12fac3030a1146f61:240,a3:[49,260],a40:70,a45:70,a604ea3c6a9cc23c739b762f625cf449:240,a67:240,a6fd9a46aec185f4ad2acd0cbe4ae2fa:240,a74:240,a9182d436a13194b744640ac940ab9b0:240,a_1:[149,156,239],a_1a:239,a_1c:239,a_1p:239,a_2:[149,156],a_3:[149,156,261,263],a_i:54,a_pw:239,a_tot:239,a_vib:93,a_xb_1:92,a_xi:279,a_xx:279,a_xz:279,a_yi:279,a_yz:279,a_zz:279,aa:[25,34,79,209,226],aa_i:34,aaa1000x:201,aachen:291,aaron:240,ab5424:1,ab:[66,91,146,165,169,170,239,276,279],ab_shift:[70,269],abandon:[1,183],abbrevi:[81,255,262],abc3:146,abc:[4,6,51,59,62,117,146,149,154,156,158,160,170,175,187,188,190,197,208,257,258,262,271,272,284],abcd:34,abcdefghijklmnopqrstuvwxyz0123456789:275,abcissa:212,abdulnour:63,aberr:53,abi:188,abi_arg:188,abi_kwarg:188,abi_object:188,abil:[1,48,199],abinit:[1,4,6,8,9,149,161,182,184,257,292],abinit_input:188,abinithead:189,abinitinput:188,abinitio:1,abinitixc_to_libxc:161,abinittim:187,abinittimerpars:187,abinittimerparsererror:187,abinittimersect:187,abiobject:[8,9,184,185],abipi:[188,256,257],abitim:[8,9,184,185],abivar:[149,156,186,188],abl:[2,5,48,66,70,84,153,261,269],abo3:[88,292],abo:187,aborpt:209,about:[1,2,20,25,28,29,34,41,70,79,94,105,139,152,156,157,161,164,165,173,177,182,183,199,204,222,223,225,239,247,281],abov:[3,4,5,6,15,16,20,25,49,58,68,74,83,88,91,93,120,139,147,157,172,174,175,186,201,232,240,272,291,292],abridg:204,abs_cap:279,abs_tol:169,abscissa:212,absenc:196,absent:58,absent_sym:58,absolut:[3,4,6,29,30,34,43,51,52,54,81,88,117,146,152,157,158,160,169,190,209,239,240,260,261,263,276,279],absorb:[96,112,157,182,208,209,210,269],absorbance_in_inverse_centimet:96,absorbing_atom:[208,209,210],absorbing_el:[112,182],absorbing_index:112,absorpt:[1,96,111,112,157,182,209,210,239,287],absorption_coeffici:96,abstractchemenvalgorithm:26,abstractchemenverror:33,abstractchemenvstrategi:25,abstractcompar:98,abstractdiffractionpatterncalcul:[51,52,53,54],abstractdron:[122,123],abstractelectrod:[117,118,119,120],abstractenvironmentnod:22,abstractfeffinputset:210,abstractgeometri:28,abstractinput:188,abstractmolatommapp:84,abstractratiofunct:36,abstractstructurefilt:[11,12],abstracttransform:[12,269,270,271,272,273],abstractvoltagepair:[117,118,119],abund:25,ac:[4,5,6,25,28,29,30,48,56,74,81,85,91,96,143,153,168,180,240],ac_:5,academ:2,acc_err:165,acc_factor:[61,63],acc_thr:165,acceler:[290,291],accept:[3,13,149,168,169,186,188,189,190,199,201,215,239,258,269,271,272,276,280],acceptor:44,access:[1,3,29,32,79,139,179,182,183,190,195,199,200,223,224,228,233,238,239,262,272,278],accident:1,accommod:[116,157],accomplish:292,accord:[1,15,26,53,56,58,59,60,78,79,84,86,88,89,90,91,105,112,145,146,153,156,158,164,165,170,177,186,187,188,189,190,199,202,215,226,239,254,260,261],accordingli:[40,55,85,140,157],account:[1,3,26,43,48,49,53,54,79,81,105,149,151,156,157,164,165,201,239,254,256,260,276,277],accur:[1,70,71,81,91,138,165,182,201,239,240,269,271],accuraci:[1,63,165,188,190,199,201,232,240,248,271,272],acel:[149,186],acet:68,acetonitril:232,achiev:[84,158,165,272],acid:[179,232],acknowledg:[1,4,6,85,239,290],aconvasp:[1,2,5],aconvasp_cal:5,acoust:[90,254,256],acoustic_debye_temp:256,acquir:173,across:[1,66,79,88,117,118,119,146,210,240],acrutt:1,act:[97,152,264],acta:[26,28,36,70,79,149],actinid:[146,148,153,280],actinoid:[146,153],action:[1,4,6],activ:[2,4,5,6,83,110,116,168,199,201,280],activate_fast_minim:201,activate_hybrid:201,activate_mot:201,activate_nonperiod:201,activate_robust_minim:201,activate_very_strict_minim:201,actual:[1,11,48,49,63,66,67,70,71,79,88,91,116,147,149,153,154,156,157,159,173,180,199,208,211,216,228,238,239,260,271,272,273,284,292],actual_kpoint:239,actual_kpoints_weight:239,ad:[1,2,4,5,6,12,15,23,25,29,43,47,49,55,59,68,71,79,103,109,117,138,146,156,157,170,182,188,195,199,201,212,215,226,232,239,240,258,262,269,271,283,288,289,292],adam:[1,113,149,291],adapt:[5,44,62,81,105,222,224,256,257,280],adapt_extremum_to_add_cond:222,adaptor:[1,193,195,213,292],add:[1,4,5,6,12,13,15,17,23,25,26,28,29,34,51,53,58,59,62,63,67,70,71,79,83,88,105,120,131,139,146,155,156,157,159,167,170,172,173,175,182,187,188,192,195,199,222,225,226,230,232,238,240,248,257,258,261,269,271,280,282,287,289,292],add_abiobject:188,add_adsorb:15,add_adsorbate_atom:157,add_b:170,add_bond:[23,289],add_charges_from_oxi_state_guess:146,add_cohp:170,add_cohp_dict:170,add_config_var:131,add_coord_geom:29,add_dens:169,add_do:[170,258],add_dos_dict:[170,258],add_edg:[71,289],add_electrod:120,add_eq:58,add_fac:289,add_fig_kwarg:[170,280],add_hydrogen:195,add_last:201,add_lin:289,add_m_list:63,add_neighbors_set:29,add_opposit:26,add_opt:192,add_oxidation_st:63,add_oxidation_state_by_el:156,add_oxidation_state_by_guess:156,add_oxidation_state_by_sit:156,add_oxidation_state_by_site_fract:17,add_partial_spher:289,add_pick:289,add_picker_fix:289,add_polyhedron:289,add_sit:[23,289],add_site_properti:[156,240],add_sourc:29,add_spectra:287,add_spectrum:287,add_spin_by_el:[156,240],add_spin_by_sit:156,add_strategy_visualization_to_subplot:25,add_subkei:192,add_tag:13,add_text:289,add_triangl:289,addadsorbatetransform:269,added_kpoint:240,addit:[1,4,5,6,12,13,25,26,28,29,30,35,43,49,53,62,67,70,71,77,79,87,94,109,141,142,146,147,148,152,155,156,157,160,173,174,182,183,189,193,196,197,199,206,212,215,216,222,224,226,234,240,248,254,256,269,281,283,291],addition:[16,240],additional_argu:[4,6],additional_condit:[25,28,29,30,32,222],additional_info:[25,26],additional_response_field:183,additionalcondit:[25,29,30,35],additionalconditionint:25,addnew_from:188,addon:[1,3,4,6,105],address:[1,182,240,290],address_basis_fil:[221,240],address_basis_file_max:221,address_basis_file_min:221,addsitepropertytransform:271,adengz:[1,291],adf:[1,8,9,184],adf_run:192,adfinput:192,adfinputerror:192,adfkei:192,adfoutput:192,adfoutputerror:192,adftask:192,adj_per_atom:173,adj_per_deg:173,adjac:[56,66,79,117,118,119],adjacent_onli:[117,118,119],adjstment:172,adjust:[40,66,79,96,105,165,172,173,177,182,199,210,239,260],admm:[201,202],adn:5,adopt:[2,3,4,6,225,239],adour:291,ads_coord:15,ads_entries_dict:105,ads_entry1:105,ads_entry2:105,adsorb:[15,105,147,157,269],adsorb_both_surfac:15,adsorbatesitefind:[1,15,269],adsorpt:[1,8,9,14,105,157],adsorption_sit:15,adsorptionsitefind:269,adv:[138,240],advanc:[4,5,6,139,168,172,182,183,269,290,291,292],advanced_transform:[5,8,9,268],advantag:[1,4,6],advic:5,advis:[5,44,269],aea79f322180fa6f0bfa74cb2a156dcf:240,aecar0:139,aecar2:139,aeccar0:[137,138,139],aeccar2:[137,139],aeccar:[49,137,138,139],affect:[1,3,156],affin:[152,156],affine_matrix:152,affine_transform:152,affine_transformation_matrix:152,afloat:283,aflow:[1,92,122,183],aflowprototypematch:92,afm:[81,82,186,188],afm_:82,afm_struct:82,afresh:79,after:[1,2,4,5,6,12,16,28,43,48,49,55,61,63,70,71,81,88,98,102,113,152,153,157,165,170,174,182,196,199,202,212,225,239,260,269,278],afterward:5,ag:[1,5,56,85,153,240],ag_sv_gw:240,again:[5,172,182,281],against:[1,44,55,92,105,145,172,182,238],agent:[1,182],aggreg:49,aggress:201,agka1:54,agka2:54,agka:54,agkb1:54,agr:110,agte3:91,ai:[1,180],aid:3,aiida:[1,183],aim:[67,83,195,269],aimd:55,ajjackson:1,aka:[67,149],al2o3:182,al3:269,al3sc:46,al:[1,5,36,44,47,48,49,55,56,72,79,81,85,91,93,97,137,153,161,165,169,170,172,173,182,183,239,240,261,290],al_gw:240,al_structur:186,alamo:291,alan:[1,290,291],alat:219,albalu:[1,291],alchemi:[1,8,9,271,272,273,284],alex:[1,113,291],alexand:[278,291],algebra:48,algo:[1,28,29,63,71,103,149,186,195,240,271,272],algo_:[271,272],algo_best_first:[63,271,272],algo_complet:[63,271,272],algo_enumer:[271,272],algo_fast:[63,271,272],algo_time_limit:63,algorithm:[1,3,11,15,17,20,26,28,29,40,47,48,49,52,54,56,58,66,68,70,71,75,77,78,79,82,84,87,88,97,98,101,102,116,137,140,147,149,156,157,169,186,188,195,199,201,224,226,232,238,239,240,248,250,251,252,260,269,271,272,276,290],algorithm_typ:26,alia:[71,79,81,86,142,160,183,187,188,189,199,238,258],alias:[1,161,183,199,201],aliases_or_resource_url:183,align:[15,28,34,44,84,86,149,170,204,208,238,248,283],aligned_lattic:149,aligned_matrix:149,alio_tol:269,alireza:1,alkali:[146,153,240],alkalin:[146,153,190],all:[1,2,3,4,5,6,7,11,12,13,15,16,17,25,26,28,29,30,34,35,36,37,38,43,44,45,48,49,51,52,53,54,55,56,58,62,63,66,67,68,70,71,74,77,78,79,81,84,87,88,91,94,96,98,102,103,105,109,110,112,113,115,116,117,118,119,120,122,130,131,139,142,145,146,149,153,154,155,156,157,158,159,160,164,165,167,168,169,170,171,172,173,174,175,176,177,179,181,182,183,186,187,188,189,190,192,195,196,197,199,200,201,210,211,212,215,216,221,222,223,224,226,228,230,231,232,233,237,238,239,240,246,247,252,254,255,257,258,260,261,262,263,264,266,267,269,271,272,275,276,277,278,281,284,287,289,292],all_cg:1,all_combin:70,all_combinations_for_el:190,all_comp:94,all_coord:[49,149,252],all_csm:28,all_dist:276,all_energi:239,all_entri:[88,91,94],all_entries_hulldata:88,all_famili:150,all_fil:190,all_geometri:26,all_geometries_latex:26,all_geometries_latex_imag:26,all_in_polar:66,all_input:[2,210],all_kind:150,all_molecul:247,all_nbs_sit:[29,222],all_nbs_sites_indic:29,all_nninfo:79,all_options_dict:25,all_oxi_st:146,all_simple_path:20,all_slab_entri:105,all_stable_entri:48,all_structur:272,all_unstable_entri:48,all_weight:71,allcoordinationgeometri:26,allen:110,allnc:190,allocations_kei:234,alloi:[140,269],allow:[1,2,3,4,5,6,12,13,15,25,26,29,30,37,40,43,46,52,53,54,58,66,70,74,78,79,84,87,88,91,94,98,109,116,117,118,119,145,146,147,154,156,157,159,160,165,167,170,172,175,177,181,182,199,201,212,215,220,221,224,230,232,236,238,239,240,269,271,272,273,276,277,290,292],allow_additional_charge_separ:16,allow_multi:190,allow_neg:[88,146],allow_patholog:79,allow_revers:71,allow_subset:98,allow_unst:[118,174],allowed_doping_speci:269,allowed_funct:36,allowed_hints_typ:26,allowed_valu:25,allpaw:190,allr:79,allsq:142,almost:[1,146,199,239,271,284,292],almost_equ:146,alon:199,along:[1,15,49,56,66,70,74,87,88,97,105,109,117,119,147,149,157,158,164,165,168,170,186,188,200,204,206,226,228,234,238,239,240,254,258,261,263,269,289],along_c:105,alpha:[15,25,36,38,70,101,102,105,110,149,156,157,170,196,199,200,211,212,239,263,269,272,292],alphabet:[71,88,146,148,208,238],alphabetical_formula:[146,148],alreadi:[3,4,5,6,12,13,23,26,28,29,34,45,49,56,63,84,88,94,102,105,117,143,146,147,157,160,177,188,197,200,260,269,292],also:[1,2,3,4,5,6,13,16,26,34,40,43,44,45,59,67,70,71,74,79,84,87,88,90,93,97,98,110,117,118,119,122,123,139,141,146,148,149,150,152,154,156,157,158,160,165,167,168,169,172,182,187,188,196,199,200,201,202,208,215,221,232,233,238,239,240,255,256,261,263,269,271,272,276,291,292],alt:71,alter:[12,13,71,215,240,261],alter_edg:71,altern:[1,2,5,12,13,26,63,67,87,153,167,170,174,177,187,188,201,216,224,239,258,262,269,287],alternate_direct:224,alternative_nam:26,although:[2,84,87],alwai:[2,3,4,6,34,49,71,83,84,91,97,98,105,117,153,156,157,165,168,172,177,182,199,200,215,224,238,239,260,261,275,292],am05:[161,238],am:[56,79,85,153,238,240],amanda:291,ambigu:[146,233,238],amend:71,american:[40,179],among:[16,56,191,232],amongst:25,amorph:[97,240],amount:[41,45,59,88,94,97,98,116,119,146,148,156,164,171,173,199,239,283,292],amount_tol:88,amount_toler:146,amp:74,amplitud:[156,269],amt:[59,94,98,146,171,173,176],amu:[153,160],an:[0,1,2,3,4,5,6,11,12,13,15,16,17,21,22,25,26,28,29,30,34,40,41,43,47,49,54,55,56,58,59,61,62,63,64,66,67,68,70,71,74,78,79,81,83,84,87,88,89,90,91,92,93,94,96,97,98,102,103,105,106,109,113,114,116,117,118,119,120,122,123,126,137,138,139,140,141,143,146,147,148,149,150,152,153,154,155,156,157,158,159,160,161,164,165,167,168,169,170,171,172,173,174,175,176,177,179,180,181,182,183,186,188,189,190,191,192,195,197,199,201,202,204,206,208,210,211,212,215,216,219,223,224,225,226,228,230,231,232,233,234,235,238,239,240,243,245,247,248,250,251,255,257,258,260,261,262,264,265,267,269,271,272,273,275,276,278,279,280,281,282,283,284,287,289,290,291,292],an_dw:165,an_up:165,anaconda:5,analogu:1,analys:[1,4,5,6,17,45,49,50,55,69,79,97,138,163,171,173,182,222,292],analysi:[0,1,2,3,4,5,6,7,8,9,11,116,118,119,121,129,130,137,138,139,145,149,156,157,159,165,169,173,175,176,177,182,192,199,200,222,224,232,238,239,240,248,253,266,269],analyt:[165,192,201,254,256],analyticalfreq:192,analyz:[1,4,6,7,8,9,11,14,17,18,19,24,28,49,55,56,57,65,66,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ict:[167,170],cohp_fil:167,cohpbetween:221,cohpcar:[167,169,222,223],cohpendenergi:221,cohpgener:221,cohplist:169,cohpplott:170,cohpstartenergi:221,cohpstep:221,cohsex_opt:211,coincid:[70,78,156,269],coka1:54,coka2:54,coka:54,cokb1:54,cole:291,collabor:[1,4,6,179],collect:[1,4,6,58,59,117,146,154,156,158,160,175,179,182,187,188,189,190,197,199,201,210,215,239,260,262],collection_angl:210,colleg:291,collinear:[34,81,82,138,156,168,186,239,269],collinearmagneticstructureanalyz:81,collis:153,colon:265,color:[29,40,62,71,88,105,110,170,280,287,289],color_area:110,color_cycl:[280,287],color_dict:105,color_palette_dict:105,color_schem:71,color_set:110,colorbar:280,colormap:[29,88,280],colour:283,column:[169,170,177,212,215,239,247,248],com:[1,3,5,15,49,84,96,108,113,139,140,156,180,182,189,227,257,269,281,291],comb:240,combatibilityerror:172,combin:[1,3,5,17,48,49,51,52,54,68,70,71,77,81,84,88,98,109,116,146,149,156,157,161,169,172,182,183,190,195,196,199,215,216,221,222,260,261,263,269,272,292],combine_neb_plot:109,combineddata:[1,215,216],come:[3,4,5,6,29,67,102,103,165,177,186,200,202,233,238,264],comm:88,comma:[182,192,232,281],command:[1,2,3,4,5,6,124,129,131,136,139,141,143,170,216,218,245,275,292],command_lin:[1,5,8,9,156],commandlin:141,commatsci:[4,6,92,93,240,260,261,263,290],commensur:56,comment:[1,66,186,188,196,199,201,204,208,210,215,227,238,239],commentari:[239,290],commerci:[4,6],commit:[1,3,4,6],common:[1,4,5,6,67,79,83,88,94,117,124,146,153,156,168,170,173,186,199,201,245,264,272,284],common_oxidation_st:[146,153],commonli:[1,54,139,160,238,240,265,274,287],commun:[2,3,5,47,49,139,153,165,173,290,291],comp1:[88,94],comp2:[88,94],comp:[1,4,6,17,41,49,88,94,118,140,146],comp_dict:91,comp_gz:174,comp_tol:88,compact:51,compar:[1,4,5,6,11,22,30,34,49,53,66,70,71,81,85,98,109,112,117,118,122,135,147,153,154,156,157,165,172,175,199,200,201,208,210,221,226,231,238,240,255,260,262,263,269,284,288,292],compare_structur:135,compare_sym_band:165,comparison:[1,11,25,29,70,84,85,88,98,147,156,157,170,175,258,260,262,284],compat:[1,4,5,6,8,9,29,43,45,48,62,81,82,88,91,139,153,156,157,171,173,175,177,182,201,220,223,224,226,236,238,239,263],compat_1:177,compat_2:177,compat_typ:172,compatibilityerror:[43,172,177],compatible_onli:182,compet:88,competit:105,comphi:93,compil:[1,3,4,5,6,113,137,138,139,140,143,239,240,264,278],complain:188,complet:[1,3,4,5,6,88,94,146,157,169,177,190,200,209,210,212,217,232,238,239,260,269,271,292],complete_do:[1,170,209,239],complete_ord:1,completecohp:[1,167,222],completedo:[113,165,169,170,200,209,223,255,287],completephonondo:[182,226,255,258],complex64:239,complex:[1,3,25,28,43,70,84,88,98,113,148,149,152,155,156,165,169,170,189,197,199,215,226,238,239,254,256,269],compli:263,complianc:[1,58],compliance_tensor:58,compliancetensor:58,compliant:[1,183],complic:269,compon:[20,30,40,55,56,60,72,84,86,88,91,96,105,146,165,168,170,186,201,239,240,257,261,263,283],compos:[34,170,173,200,233,239],composit:[1,2,4,6,8,9,17,40,41,43,46,74,88,91,94,98,101,102,105,117,118,144,147,148,151,153,154,156,159,169,171,172,173,175,176,177,179,182,272,276,283,292],composition_predict:101,compositionenergyadjust:173,compositionerror:[1,146],compositionlik:[66,154,156],compositon:[1,88],compound:[41,56,62,72,82,88,91,101,102,103,105,106,117,118,119,160,167,170,172,174,182,234,240,280,292],compoundpd:1,compoundphasediagram:88,comprehens:[4,6,138,182,188,292],compress:[1,123],comprhi:1,compris:[4,6,72,182,197],compromis:[2,195],comput:[1,4,5,6,20,23,25,26,28,29,30,33,34,39,43,44,46,47,48,49,51,52,53,54,55,56,63,66,70,79,82,84,86,88,91,92,93,94,97,98,105,110,117,137,138,139,141,143,147,149,156,157,164,165,169,170,172,173,174,177,179,182,186,187,188,190,192,199,201,209,211,212,222,224,230,238,239,240,248,250,251,260,261,263,269,271,272,276,280,290,291,292],computation:[201,239],compute_adj_neighbor:79,compute_average_oxidation_st:63,compute_coordination_environ:28,compute_correct:174,compute_defect_dens:46,compute_environ:39,compute_forc:63,compute_from_fil:174,compute_md5:190,compute_offset_vector:252,compute_partial_energi:63,compute_period:20,compute_periodicity_all_simple_paths_algorithm:20,compute_periodicity_cycle_basi:20,compute_structure_environ:28,compute_sub_structur:63,compute_trigonometric_term:79,computed_data:88,computed_entri:[8,9,40,105,117,118,119,171,172,177,292],computedentri:[1,40,88,91,94,117,118,119,122,171,172,173,174,175,177,182,239,292],computedreact:[94,292],computedslabentri:105,computedstructureentri:[1,91,105,119,122,172,173,175,177,182,239,292],computerentri:1,computi:186,computron:1,compyrhi:1,conc:[48,91],conc_dict:91,conc_term:91,concaten:[159,187,200,239],concentr:[43,46,48,91,140,165,169,170],concept:[117,210,240,292],conceptu:79,concern:[29,154,187],concis:53,concret:[36,190,210,235,240],concurr:[15,269],cond:165,cond_band:165,cond_dop:165,conda:[1,4,6],conden:[143,172],condens:[138,146],condit:[1,4,6,25,28,29,30,35,54,56,58,68,87,88,90,91,141,149,154,156,177,182,190,20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22,24,25,26,27,28,29,34,36,39,40,44,47,49,53,63,66,70,71,79,83,84,87,88,97,98,105,109,139,141,147,149,151,152,153,154,156,157,159,164,165,170,195,197,199,201,204,212,215,216,219,222,223,224,225,226,233,234,238,239,240,245,247,248,252,254,256,260,263,265,271,272,276,277,289,292],coordinate_fil:215,coordination_environ:[8,9,14,18,22,222],coordination_environments_atom_pres:29,coordination_environments_ion_pres:29,coordination_geometri:[9,14,18,24,28],coordination_geometries_fil:[9,14,18,24],coordination_geometry_find:[9,14,18,24],coordination_geometry_symmetry_measur:28,coordination_geometry_symmetry_measures_fallback_random:28,coordination_geometry_symmetry_measures_separation_plan:28,coordination_geometry_symmetry_measures_separation_plane_optim:28,coordination_geometry_symmetry_measures_sepplane_optim:28,coordination_geometry_symmetry_measures_standard:28,coordination_geometry_util:[9,14,18,31],coordination_no:269,coordination_numb:[26,28],coordination_sequ:20,coordinationgeometri:26,coords1:276,coords2:276,coords_a:149,coords_are_cartesian:[28,66,70,71,147,149,154,156,157,164,170,254,256,263,271],coords_are_displac:159,coords_b:149,coords_filenam:245,coords_set:15,coorind:215,copi:[1,3,4,6,12,34,43,49,70,71,94,146,147,149,155,156,157,159,188,190,211,239,240,267,271,272,276,278],copl:[167,219],copy_chgcar:240,copy_wavecar:240,cordero:79,core:[1,2,3,4,5,6,8,9,12,13,14,40,41,42,44,46,49,50,52,53,54,55,58,59,60,64,66,68,70,71,74,77,79,81,83,84,86,87,88,89,94,98,112,113,117,118,139,141,142,163,164,169,171,172,173,177,179,183,184,186,189,193,199,201,208,213,215,221,222,223,225,226,230,231,234,235,238,239,240,243,247,248,260,265,267,269,270,272,273,281,292],corehol:210,cormac:62,cornel:291,corner:[20,84,88],corr:165,corrao:40,correct:[1,4,5,6,8,9,14,26,42,43,45,48,52,54,55,70,74,81,88,105,118,146,157,165,170,172,173,174,177,179,186,196,199,200,201,211,212,221,224,239,240,254,261,263,269,292],correct_entri:[43,172],correct_peroxid:172,corrected_energi:172,correction_calcul:[8,9,171],correction_nam:[43,172],correction_per_atom:173,correction_uncertainti:[172,173],correction_uncertainty_per_atom:173,correctioncalcul:174,corrections_dict:174,corrections_std_error:174,correctionslist:172,correctli:[1,5,56,137,146,165,167,197,239,240],corrector:238,correl:[142,150,161,165,192,199,201,211,224,240,269],correlation_grid:211,correspond:[1,2,13,15,20,25,26,28,29,30,36,37,40,43,44,48,49,52,53,54,58,59,63,66,70,71,74,78,79,82,84,85,86,88,90,91,96,97,98,105,110,112,119,137,138,139,141,146,147,149,156,157,158,159,165,167,169,170,172,177,182,187,188,189,197,200,201,202,223,225,230,232,238,239,240,241,243,254,257,258,261,264,269,271,272,276],correspondisng:239,corrupt:1,cosin:79,cosinu:33,cosinus_step:38,cosmo:[1,224],cost:[1,8,9,14,63,186,199,232,238,250,251],cost_per_kg:41,costa:[1,239,291],costanalyz:41,costdb:41,costdbcsv:41,costentri:41,costli:201,coth:255,could:[4,6,26,29,53,146,165],coulomb:[186,201,202],coulomb_mod:186,council:291,count:[71,79,88,120,137,147,186,215,239,292],count_lay:147,counterbalanc:87,counterpart:[15,137,139],coupl:[1,3,44,71,82,86,108,165,190,224,239,240],coupling_const:86,cours:199,courtesi:1,coval:[79,85,145,151,156,215,280,288],covalent_radiu:85,covalentbond:[79,145,156],covalentbondnn:[1,79],covalentradiu:85,cover:[40,94,165,201,223,280],coverag:105,covl_k:239,cp2k:[1,8,9,184,292],cp2k_input:199,cp2k_version:200,cp2kinput:[199,201],cp2kinputset:201,cp2koutput:200,cp:[79,106],cpc:[46,139],cpcm:230,cpdname:106,cpep:139,cpfit:202,cpmd:204,cpp:5,cpreport:139,cpu:[142,175,182,187,239,269],cpu_fract:187,cpu_tim:187,cpuwall_histogram:187,cq:239,cr3:17,cr4:17,cr:[56,85,153,174,240,269],cr_pv:240,cr_sv_gw:240,cracknel:264,cramer:138,crash:[1,192],crc:153,creat:[1,3,4,6,12,13,15,20,25,29,30,34,40,43,48,49,51,55,58,59,60,62,63,66,70,71,74,78,79,81,82,86,88,89,90,91,94,105,108,118,119,146,147,148,149,150,152,154,156,157,158,159,161,164,165,167,168,169,170,173,174,177,181,182,183,186,187,190,195,196,197,199,200,201,202,203,204,208,209,210,211,212,215,216,219,221,223,224,226,228,230,231,238,239,240,242,243,247,248,258,264,269,271,280,281,283,284,289],create_directori:[12,13],create_saturated_interstitial_structur:43,create_slab_label:105,create_subsi:201,created_at:[182,281],createfatband:221,createmod:278,creation:[1,98,153,157,160,182,199,201,290],creator:157,credit:[1,62,291],crest:[1,244,245,246],crest_best:246,crest_in:245,crestinput:245,crestoutput:246,criteria:[1,11,15,44,58,70,77,79,85,108,117,156,157,177,182,199,201,269],criteria_str:182,criterion:[187,201,240,292],critic2:[1,5,79,139],critic2_cal:[1,5,8,9,136],critic2analysi:139,critic2cal:[1,5,79,139],critic2nn:79,critic:[1,2,4,5,6,53,82,88,110,119,139,143,153,182],critical_point:139,critical_temp:143,critical_temperatur:153,criticalpoint:139,criticalpointtyp:139,crka1:54,crka2:54,crka:54,crkb1:54,cross:[1,25,34,48,113,125,153,158,164,170,199,209,210],cross_sect:209,crosses_origin:34,crowd:71,crude:82,cryst:[26,28,36,70,79,97,179],crystal:[1,3,4,5,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,70,71,79,81,82,84,88,98,113,116,117,124,137,143,152,153,154,155,156,158,159,160,168,169,175,177,181,182,200,201,208,209,210,221,225,227,228,238,239,240,246,255,259,260,269,280,284,292],ethanol:232,ethyl:68,etsf:189,etsf_read:189,eu2:[1,240],eu3:[1,240],eu:[1,56,85,153,183,240],eu_2:240,euler:59,eulerian:261,ev:[1,40,43,44,49,62,63,64,71,74,88,91,93,96,105,112,113,151,153,160,165,167,169,170,172,173,174,177,182,186,188,200,209,211,212,219,223,224,239,240,254,256,258,292],ev_to_k:49,ev_to_kj_per_mol:74,eval:[4,6,239],evalu:[34,36,45,46,49,58,63,79,91,93,192,199,201,222,223,224,232,239,240,256],evaluate_wavefunc:239,evan:[143,291],even:[1,2,4,5,6,56,87,98,117,123,146,156,177,182,186,199,201,230,232,238,239,262,271,272,276,292],event:[4,6,280,281,289],eventu:[16,157],everi:[4,6,12,48,53,55,97,139,149,165,223,239,256,292],everyon:291,everyth:[3,164,200,201,292],everything_equ:22,evolut:[88,91],ewald:[1,3,8,9,14,44,49,61,269,271,272,292],ewaldelectrostaticmodel:61,ewaldminim:63,ewaldpap:63,ewaldsum:[61,221],ewaldsumm:[1,61,63],ex:[5,43,44,68,151,164,202,211,230,232,254],ex_mat:82,ex_param:[82,143],exact:[11,84,85,98,156,157,175,201,238,240,262],exactdens:192,exactli:[1,3,70,98,157,165,186,199,222,238,272],exaf:[112,155,208,209,210],examin:88,exampl:[1,2,3,5,11,12,13,17,20,26,28,37,41,43,48,55,56,63,66,71,79,84,88,94,97,98,100,105,106,109,116,117,118,119,122,145,146,148,149,152,153,155,156,157,160,161,165,169,170,172,173,175,182,186,187,188,190,199,200,202,204,210,212,216,220,224,225,228,232,233,236,238,239,240,243,260,262,265,269,271,272,276,280,281,286,287,289],exc_dft_opt:211,exc_typ:186,exce:[98,201,269],excel:[1,84,137,140,188,260,290],except:[1,3,33,37,49,59,62,71,79,87,88,94,98,102,140,141,146,148,152,153,156,160,165,169,172,182,187,188,192,196,199,204,208,224,228,233,238,239,240,260,275],exception:102,exception_on_bad_xml:239,excess:44,exchamiltonian:186,exchang:[1,71,81,82,143,150,152,161,183,186,192,199,201,210,224],exchange_const:71,excit:[1,8,9,14,53,184,209,211,212,224],excitationspectrum:[64,224],excitinginput:206,exclud:[11,28,44,49,88,90,156,157,172,174,177,188,190,218,240,280,289],exclude_dir:190,exclude_polyanion:174,exclude_self:156,excluded_atom:28,excluded_bonding_el:289,exclus:[2,161],execut:[1,5,11,133,137,138,139,140,141,143,179,199,219,225,278,284],exelf:210,exercis:239,exhf:239,exhibit:[137,138],exist:[1,2,3,4,5,6,11,26,28,29,44,45,48,49,53,55,58,62,71,81,85,87,88,91,98,102,138,145,156,157,167,168,170,173,177,190,192,197,199,200,202,210,216,219,238,240,260,275,280,292],existing_structur:11,exit:[87,239],exp:[36,49,54,55,58,174,182,226,239],exp_compound:174,exp_cos_aa:79,exp_entri:[8,9,171,174],exp_gz:174,expand:[1,3,4,5,6,70,269],expand_tim:[70,269],expans:[3,58,153,158,201],expect:[1,2,3,5,11,34,46,55,70,79,83,109,137,141,153,160,168,169,201,239,240,260,263,269],expected_charg:16,expens:[1,63,88,199,239,272],expentri:[176,182],experi:[5,91],experienc:216,experiment:[17,28,79,88,106,112,153,170,172,173,174,176,182,255,269,272],exphp:[1,291],explain:[1,139,165,170,172,173],explan:[1,70,146,170,172,173,182,292],explanaion:173,explicit:[25,26,28,186,195,196,238,239],explicit_indic:28,explicit_on:283,explicit_optimized_permut:26,explicit_path:186,explicit_permut:26,explicitli:[25,34,37,56,79,201,240],explicitpermutationsalgorithm:26,explor:[4,6,49,139,292],expnorm:49,expon:[25,79,142,165,201,269],exponenti:[49,275],export_msdt:55,expos:183,expr:58,express:[4,6,34,58,66,149,158,200,233,239],expt:173,ext:[0,1,2,3,4,6,8,9,187,190,264,292],extend:[1,12,13,15,41,49,58,60,74,86,87,88,146,152,155,156,159,169,176,188,189,199,210,232,255,269,284,292],extend_collect:13,extend_structure_molecul:79,extend_transform:[12,13],extens:[1,2,4,5,6,55,71,110,122,138,153,154,156,170,173,176,187,190,200,211,239,292],extern:[1,2,3,4,5,6,131,238,245,281,282],external_id:182,extra:[4,6,45,48,81,86,116,186,187,227,239,248,275,288],extra_nn_info:79,extract:[1,5,12,29,70,71,81,82,147,156,157,165,187,226,238,239,258,269,292],extract_clust:156,extracted_vasp_potcar:5,extrapol:[1,55,169,199,239],extrapolate_reciproc:275,extrapolate_simple_reciproc:275,extras_requir:[4,6],extrem:[1,4,6,47,63,103,156,170,182,201,239,240,258,262,271,272,287,292],extrema:[49,109,165],extrema_coord:49,extrema_df:49,extremum_icohpvalu:167,extrins:[116,117],ey:[149,186],f0:[168,169,170],f1:[4,6,34,168,170,264],f1d01e845dccc52d448679911f301a73:240,f2:[34,74,146,168,170,177,240,284],f3:[168,170],f4ff16a495dd361ff5824ee61b418bb0:240,f:[4,6,29,36,49,53,54,56,58,66,67,85,106,112,116,118,139,143,146,153,168,170,174,190,231,239,240,248,263,264,283,284,290,291,292],f_1:[168,170],f_2:[168,170],f_3:[168,170],f_:54,f_constant:212,f_d:169,f_gw:240,f_h:240,f_j:54,f_lower:34,f_upper:34,f_x:169,f_xyz:169,f_xz:169,f_y:169,f_yz:169,f_z:169,fac_aa:79,face:[15,26,77,79,97,248,289],face_dist:79,faces_color_overrid:39,facet:[28,34,51,54,74,77,79,88,97,105,110,149,276],facil:[173,291],facilit:[170,177,235,258,292],facmaxdl:49,fact:[4,6,79,84,164,254,292],factor:[1,17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singl:199,full_single_invers:[199,201],fulli:[40,67,117,146,157,201,238,240,292],fully_charged_entri:119,fully_discharged_entri:119,func:[62,155,182,280],func_group:[68,71,156],func_grp:[71,156],func_util:[9,14,18,31],function_comparison:34,functional_choic:238,functional_class:238,functional_dir:238,functional_group:[8,9,14],functional_tag:238,functionalgroupextractor:68,functool:160,fur:240,furnish:[4,6],further:[3,4,5,6,59,79,139,176,195,210,221,232,240,260,269,292],further_set:221,furthermor:[79,221],furthest:34,futur:[1,2,4,6,91,105,156,157,182,195,201],fuzzi:177,fuzzy_formula:146,fuzzy_match:177,fwhm:155,fyalcin:1,fysik:[5,161],g03:156,g09:156,g0:239,g1:49,g2:49,g3gn:224,g:[1,2,3,4,5,6,12,13,15,17,20,22,23,25,26,28,29,40,41,46,47,49,51,55,56,58,62,66,67,70,71,74,79,81,83,88,91,92,93,94,97,98,100,101,102,105,106,109,110,113,116,117,118,119,137,138,139,141,142,146,147,148,149,150,153,154,155,156,157,158,159,160,164,165,167,168,169,170,172,173,175,177,182,183,186,187,188,190,195,197,199,200,201,204,208,212,215,216,217,221,222,223,224,225,226,228,230,231,232,233,235,237,238,239,240,254,257,258,259,260,262,263,264,269,271,272,276,277,280,281,283,287,289,290,292],g_:[54,239],g_i:239,g_n:239,g_opt:93,g_r:58,g_reuss:58,g_v:58,g_vec:44,g_voigt:58,g_vrh:58,ga:[56,74,85,91,106,153,172,209,240],ga_d:240,ga_d_gw:240,gabaldon:138,gaff:195,gain:[3,137,138],gale:141,galor:[1,113],gam:239,gamma:[1,44,49,93,105,149,164,181,186,188,196,199,200,201,221,226,238,239,240,254,256,257,292],gamma_automat:238,gamma_cent:186,gamma_dict:105,gamma_onli:[186,239],gammacent:188,gammacenterd:188,ganos:[1,113,291],gap:[1,44,48,76,79,147,164,165,169,170,182,199,200,201,239,240],gap_dist:181,gapw:199,gascorrect:172,gase:[153,173],gaseou:[138,172],gass:1,gather:160,gau:292,gaultoi:72,gaunip:212,gauss:186,gaussian:[1,4,6,8,9,17,49,79,87,113,122,127,155,156,169,170,184,186,192,199,200,201,204,211,224,255,258,292],gaussian_analyz:[8,9,124],gaussian_smear:87,gaussianinput:[1,212,224,292],gaussianio:122,gaussianoutput:[1,122,212],gaussiansmearingwidth:221,gaussiantocomputedentrydron:122,gaussiantoentrydron:122,gaussion:1,gave:239,gb:[1,8,9,14,157,160,240,269,272],gb_from_paramet:70,gb_plane:[70,182],gbgener:1,gc:246,gcc:[4,5,6],gcheon:[56,291],gcut:49,gd3:240,gd:[56,85,153,240],gd_3:240,gdm:232,ge:[55,56,85,153,156,240,269,271,272,284],ge_d:240,ge_d_gw:240,gen3d:195,gen3d_conform:195,gen4438:291,gen:212,gen_basi:212,gen_potcar:133,gen_scfman:[1,232],gen_sl_transform_matrici:78,gener:[1,2,3,4,5,6,8,9,12,13,14,15,29,40,42,43,44,46,49,53,55,56,58,59,67,70,71,73,74,76,77,78,79,81,82,84,87,88,90,91,94,98,100,105,106,108,109,110,117,118,119,122,125,126,133,137,139,140,141,146,147,148,149,150,152,153,154,156,157,158,161,164,165,168,169,170,172,173,175,176,177,182,183,186,188,192,195,196,197,199,200,201,208,210,211,215,217,218,219,221,223,224,225,226,227,228,233,238,239,240,247,254,256,257,258,260,261,262,263,264,269,270,271,272,273,275,276,279,280,283,287,289,290,292],generate_adsorption_structur:15,generate_all_slab:157,generate_defect_structur:43,generate_displac:226,generate_entry_label:91,generate_full_symmop:260,generate_input:197,generate_point:53,generate_potcar:[133,240],generate_pseudo:58,generate_r_and_g_vec:49,generate_reciprocal_vectors_squar:49,generate_sl_transformation_set:78,generate_substitution_structur:15,generate_surface_vector:77,generic_groupbi:49,genet:84,geneticordermatch:84,genfmt:208,genom:[4,6,290],genrecip:49,geo:188,geo_opt:201,geo_subkei:192,geoffroi:[1,4,6,28,291],geograph:72,geom_opt_max_cycl:232,geometr:[25,79,84,87,116,290],geometri:[1,26,27,28,29,39,59,67,78,84,192,195,200,201,212,224,232,248,290],geometrically_equidist:25,geometry_info:25,geometry_opt:224,geometryoptim:192,geomstep:195,georg:[28,165,291],gerbrand:[4,6,87],germain:[1,170,291],get:[1,3,5,15,17,20,21,22,23,25,26,29,30,34,36,37,41,43,44,45,48,49,53,55,56,58,59,66,70,74,76,78,79,82,83,84,88,91,92,93,96,98,100,105,110,112,117,119,130,137,138,141,145,146,147,149,153,154,156,157,158,165,167,168,169,170,172,180,181,182,183,188,196,199,200,201,202,204,209,212,219,221,222,223,226,234,237,238,239,240,252,255,256,258,260,266,269,271,272,276,281,283,284,287,292],get_00t_magmom_with_xyz_saxi:168,get_13_bond:85,get_2d_orthonormal_vector:40,get_2d_transform:76,get_absorbing_atom_symbol_index:208,get_adjust:[172,177],get_adjusted_fermi_level:239,get_all_anonymous_map:98,get_all_chempot:88,get_all_dist:149,get_all_elementary_cycl:37,get_all_entri:119,get_all_functional_group:68,get_all_neighbor:[1,156],get_all_neighbors_old:156,get_all_neighbors_pi:156,get_all_nn:79,get_all_nn_info:79,get_all_possible_basis_combin:221,get_all_possible_basis_funct:221,get_all_simple_paths_edg:37,get_all_sit:79,get_all_substr:182,get_all_voronoi_polyhedra:79,get_allowed_speci:102,get_alpha:239,get_analysi:83,get_analysis_and_structur:83,get_angl:[156,276],get_anion_typ:222,get_arrhenius_plot:55,get_asum_fcm:90,get_atom:[193,213],get_atom_map:208,get_atomic_fract:[4,6,146],get_atomic_site_averag:204,get_atomic_site_tot:204,get_aux_basi:202,get_available_model:180,get_average_along_axi:[204,239],get_average_eff_mass:165,get_average_voltag:117,get_ax3d_fig_plt:280,get_ax_fig_plt:280,get_axarray_fig_plt:280,get_axis_grid:[204,239],get_band_cent:169,get_band_fil:169,get_band_gap:164,get_band_kurtosi:169,get_band_skew:169,get_band_structur:239,get_band_structure_from_vasp_multiple_branch:239,get_band_width:169,get_bandstructur:223,get_bandstructure_by_material_id:[182,292],get_basi:221,get_basic_functional_group:68,get_basis_and_potenti:202,get_bec_oper:90,get_best_electronegativity_anonymous_map:98,get_bibtex_str:196,get_bond_length:145,get_bond_ord:[138,145],get_bonded_structur:[1,56,79,100],get_box_shift:215,get_boxed_structur:156,get_branch:[164,254],get_brillouin_zon:149,get_capacity_grav:117,get_capacity_vol:117,get_carrier_concentr:165,get_cart_coord:212,get_cartesian_coord:149,get_cbm:164,get_cbm_vbm:169,get_celldm:228,get_center_of_arc:38,get_centered_molecul:156,get_central_sit:26,get_centroid_2d:40,get_charg:[137,138],get_charge_decorated_structur:137,get_charge_transf:[137,138],get_chempot_correct:74,get_chempot_range_map:[88,105],get_chempot_range_map_plot:88,get_chempot_range_stability_phas:88,get_chgint_plot:132,get_chunk:182,get_cn:79,get_cn_dict:79,get_cod_id:179,get_coeff:94,get_cohesive_energi:182,get_cohp:167,get_cohp_by_label:167,get_cohp_dict:170,get_complete_do:[113,165],get_complete_ph_do:226,get_complexity_factor:165,get_compliance_expans:58,get_composition_chempot:88,get_compound_pd:88,get_computed_entri:239,get_conduct:165,get_connect:97,get_connected_compon:23,get_connected_sit:71,get_consistent_set:168,get_consistent_set_and_saxi:168,get_continuous_path:261,get_contour_pd_plot:88,get_conventional_standard_structur:[1,260],get_conventional_to_primitive_transformation_matrix:260,get_conversion_factor:[55,160],get_coordinating_elements_cn:49,get_coordination_environ:29,get_coordination_numb:26,get_coordination_of_sit:71,get_coordination_symmetry_measur:28,get_coordination_symmetry_measures_optim:28,get_correct:[43,44,172],get_corrections_dict:172,get_cost_per_kg:41,get_cost_per_mol:41,get_covalent_bond:156,get_critical_composit:88,get_critical_original_kink_ratio:74,get_critical_point_for_sit:139,get_crystal_field_spin:153,get_crystal_system:260,get_csm:29,get_csm_and_map:29,get_cutoff_from_basi:202,get_d:157,get_data:[123,182,292],get_database_vers:182,get_datafram:[74,187],get_decomp_and_decomp_energi:88,get_decomp_and_e_above_hul:88,get_decomp_and_hull_energy_per_atom:88,get_decomp_and_phase_separation_energi:88,get_decomposit:88,get_decomposition_energi:91,get_decorated_structur:137,get_default_basis_set:192,get_default_geo:192,get_default_scf:192,get_default_unit:192,get_default_xc:192,get_defectsite_multipl:49,get_deformation_matrix:59,get_delta:37,get_delta_imag:23,get_dens:169,get_deriv:275,get_diff_coeff:58,get_dihedr:156,get_dimension:[1,2],get_dimensionality_cheon:56,get_dimensionality_gorai:56,get_dimensionality_larsen:56,get_dir_indir_gap:96,get_direct_band_gap:164,get_direct_band_gap_dict:164,get_disconnected_frag:71,get_displaced_structur:226,get_dist:156,get_distance_and_imag:149,get_doc:[182,223],get_dop:169,get_dopability_limit:48,get_dopants_from_shannon_radii:100,get_dopants_from_substitution_prob:100,get_dos_by_material_id:[182,292],get_dos_dict:[170,258],get_dos_plot:132,get_download_info:182,get_drift_corrected_structur:55,get_e_above_hul:[1,88],get_effective_csm:25,get_effective_ec:58,get_el_amount:94,get_el_amt_dict:146,get_el_sp:153,get_element_do:[169,255,258],get_element_fract:91,get_element_profil:88,get_element_spd_do:169,get_elements_between_band:239,get_elt_projected_plot:170,get_elt_projected_plots_color:170,get_energi:[61,127,130,141,146],get_energy_buckingham:141,get_energy_dens:117,get_energy_relax_structure_buckingham:141,get_energy_tersoff:141,get_entri:[1,41,182],get_entries_in_chemsi:[1,182,292],get_entry_by_material_id:182,get_environ:[8,9,124],get_environment_nod:22,get_environments_figur:29,get_equilibrium_reaction_energi:88,get_equiv_transform:78,get_equivalent_atom:260,get_equivalent_kpoint:164,get_equivalent_qpoint:254,get_exchang:82,get_exchange_group_info:81,get_excitation_spectrum:224,get_exp_entri:182,get_exp_thermo_data:182,get_explanation_dict:172,get_extended_surface_mesh:15,get_extrapolated_conduct:55,get_extrapolated_diffus:55,get_extrem:165,get_extrema:109,get_facet:88,get_factor:78,get_fcm_oper:90,get_fermi:169,get_fermi_interextrapol:[1,169],get_ferromagnetic_structur:81,get_filepath:139,get_first_point:53,get_form_energi:88,get_form_energy_per_atom:88,get_frac_coords_from_ll:149,get_fract:146,get_fractional_coord:149,get_framework_rms_plot:[1,55],get_free_sphere_param:248,get_from_hint:28,get_gap:169,get_gb_data:182,get_geometri:26,get_geometry_from_iucr_symbol:26,get_geometry_from_iupac_symbol:26,get_geometry_from_mp_symbol:26,get_geometry_from_nam:26,get_ggt:58,get_grouped_indic:158,get_gruneisen_paramet:58,get_gruneisen_ph_bs_symm_lin:226,get_gruneisenparamet:226,get_gs_ph_bs_symm_line_from_dict:226,get_hal:260,get_hall_carrier_concentr:165,get_hash:98,get_heat_capac:58,get_heisenberg_model:82,get_help:237,get_heteroatom:68,get_high_accuracy_voronoi_nod:248,get_hilbert_transform:169,get_hull_energi:[88,91],get_hull_energy_per_atom:88,get_icohp:167,get_icohp_by_label:167,get_icohp_dict_by_bondlength:167,get_icohp_dict_of_sit:167,get_ieee_rot:158,get_implemented_geometri:26,get_incar_tag:237,get_info_cohps_to_neighbor:222,get_info_icohps_between_neighbor:222,get_info_icohps_to_neighbor:222,get_input_set:[197,216,225,235,292],get_integer_formula_and_factor:146,get_integer_index:149,get_integrated_cohp_in_energy_rang:167,get_integrated_diff:239,get_interaction_graph:82,get_interfac:76,get_interface_react:182,get_interplanar_angl:53,get_interplanar_spac:53,get_interpolated_gap:169,get_interpolated_valu:[155,167,169,255],get_ir_mesh:1,get_ir_reciprocal_mesh:260,get_ir_spectra:257,get_ist_oper:90,get_keyword:199,get_kink:74,get_kpoint:[181,240,261,263],get_kpoint_degeneraci:164,get_kpoint_weight:260,get_label:[49,105],get_lattic:196,get_lattice_quanta:66,get_lattice_typ:260,get_light_structure_environ:222,get_lin:208,get_line_in_facet:110,get_linear_interpolated_valu:276,get_linearly_independent_vector:38,get_lll_frac_coord:149,get_lll_reduced_lattic:149,get_local_extrema:49,get_local_order_paramet:79,get_locpot_along_slab_plot:105,get_low_energy_ord:82,get_lower_and_upper_f:34,get_lowest_decomposit:41,get_magnet:130,get_magnitude_of_effect_from_speci:83,get_magnitude_of_effect_from_spin_config:83,get_magsymop:196,get_map:98,get_mass:160,get_materials_id:182,get_materials_id_from_task_id:182,get_materials_id_refer:[1,182],get_max_bond_dist:79,get_max_bond_length:97,get_max_capgrav:116,get_max_capvol:116,get_max_inst:119,get_max_muo2:119,get_mft_temperatur:82,get_mi_vec:15,get_miller_index_from_coord:149,get_miller_index_from_site_index:156,get_min_inst:119,get_min_muo2:119,get_mixing_state_data:177,get_molecul:193,get_molecule_hash:84,get_moment:168,get_moment_relative_to_crystal_ax:168,get_monolay:105,get_motif_typ:49,get_mp_structur:284,get_msd_plot:55,get_mu_bound:165,get_multipl:43,get_n_moment:169,get_nac_eigendisplacements_along_dir:254,get_nac_frequencies_along_dir:254,get_nam:26,get_nearest_sit:66,get_neighb_voronoi_indic:29,get_neighbor:[1,156],get_neighbor_list:156,get_neighbors_in_shel:156,get_neighbors_of_site_with_index:79,get_neighbors_old:156,get_next_index:63,get_niggli_reduced_lattic:149,get_nmr_quadrupole_mo:153,get_nn:79,get_nn_data:79,get_nn_imag:79,get_nn_info:[79,222],get_nn_shell_info:79,get_no_mixing_energi:74,get_nonmagnetic_structur:81,get_noppmodel:186,get_not_implemented_geometri:26,get_occup:239,get_okeeffe_distance_predict:79,get_okeeffe_param:79,get_op_valu:49,get_orbital_derivative_between_st:239,get_orbital_resolved_cohp:167,get_ord:156,get_order_paramet:79,get_orthogonal_c_slab:157,get_oxi_state_decorated_structur:17,get_oxidation_state_decorated_structur:137,get_paramet:79,get_parchg:239,get_partial_charg:[137,138],get_pattern:[51,52,53,54],get_pelecs_and_pion:66,get_percentag:231,get_percentage_bond_dist_chang:97,get_percentage_lattice_parameter_chang:97,get_percentage_volume_chang:97,get_perturbed_indic:59,get_ph_bs_symm_lin:226,get_ph_bs_symm_line_from_dict:226,get_ph_do:226,get_phase_separation_energi:88,get_phonon_band_structure_from_fc:226,get_phonon_band_structure_symm_line_from_fc:226,get_phonon_bandstructure_by_material_id:182,get_phonon_ddb_by_material_id:182,get_phonon_dos_by_material_id:182,get_phonon_dos_from_fc:226,get_phonon_frequ:239,get_phonopy_structur:226,get_piezo:90,get_plot:[1,40,51,88,109,110,120,170,258,287],get_plot_2d:53,get_plot_2d_concis:53,get_plot_coeff:53,get_plot_data:120,get_plot_g:258,get_plotli:110,get_plotly_figur:120,get_plott:257,get_pmesh:26,get_pmg_structur:226,get_point_group_oper:260,get_point_group_symbol:260,get_pointgroup:260,get_points_in_spher:149,get_points_in_sphere_old:149,get_points_in_sphere_pi:149,get_polarization_chang:66,get_polarization_change_norm:66,get_posit:53,get_potcar:239,get_potcar_file_hash:238,get_potcar_hash:238,get_potential_shift:44,get_pourbaix_domain:91,get_pourbaix_entri:182,get_pourbaix_plot:91,get_power_factor:165,get_predicted_structur:103,get_primitive_standard:1,get_primitive_standard_structur:[260,261,263],get_primitive_structur:[156,292],get_principal_axi:84,get_projected_plots_dot:170,get_projected_plots_dots_patom_pmorb:170,get_projection_on_el:[164,239],get_projections_on_elements_and_orbit:164,get_property_decorated_structur:138,get_prototyp:92,get_pseudos_for_structur:190,get_q2:79,get_q4:79,get_q6:79,get_rand_bec:90,get_rand_fcm:90,get_rand_ist:90,get_ratio:70,get_rdf_figur:30,get_react:182,get_real_summ:44,get_reasonable_repetit:254,get_recip_summ:44,get_reconstructed_band_structur:164,get_recp_symmetry_oper:149,get_reduced_composition_and_factor:146,get_reduced_formula_and_factor:[146,148],get_reduced_structur:156,get_reference_energy_per_atom:88,get_refined_structur:[196,260],get_relaxed_structur:141,get_removals_int_oxid:116,get_rms_anonym:98,get_rms_dist:98,get_rmsd:84,get_rot:15,get_rot_3d_for_2d:76,get_rotation_angle_from_sigma:[70,269],get_rotational_symmetry_numb:260,get_s2:53,get_s2_like_s1:98,get_sadf_figur:30,get_same_branch_polarization_data:66,get_scal:158,get_scan_plot:212,get_sect:[187,199],get_seebeck:165,get_seebeck_eff_mass:165,get_self_interact:44,get_set:[1,262],get_shannon_radiu:153,get_shared_symmetry_oper:266,get_shifts_based_on_adsorbate_sit:147,get_site_ce_fractions_and_neighbor:25,get_site_coordination_environ:25,get_site_coordination_environments_fract:25,get_site_do:[169,255],get_site_energi:63,get_site_info_for_specie_allc:29,get_site_info_for_specie_c:29,get_site_neighbor:25,get_site_orbital_do:169,get_site_spd_do:169,get_site_symmetri:266,get_site_t2g_eg_resolved_do:169,get_sitej:97,get_sites_in_spher:156,get_slab:157,get_slab_region:157,get_smeared_dens:[169,255],get_snl:183,get_snls_with_filt:183,get_sorted_structur:[1,70,147,156,157],get_space_group_info:156,get_space_group_numb:260,get_space_group_oper:260,get_space_group_symbol:[4,6,260],get_spd:[170,287],get_spd_do:[169,170],get_special_carbon:68,get_specific_energi:117,get_spectre_plot:212,get_spectrum:257,get_stability_criteria:58,get_stabl:[1,182],get_stable_entri:[91,119],get_stable_entry_at_u:105,get_stable_fcm:90,get_statist:29,get_str:[159,197,199,208,215,219,230,238,239],get_strain_from_stress:58,get_strain_state_dict:58,get_structur:[1,28,159,182,183,193,196,213,234,284,292],get_structure_by_formula:179,get_structure_by_id:179,get_structure_by_material_id:[1,182,292],get_structure_compon:56,get_structure_connect:21,get_structure_from_dict:226,get_structure_from_mp:1,get_structure_from_prev_run:240,get_structure_property_dict:58,get_structure_with_charg:223,get_structure_with_nod:49,get_structure_with_only_magnetic_atom:81,get_structure_with_site_potenti:223,get_structure_with_spin:81,get_structure_with_total_grosspop:223,get_structures_with_filt:183,get_sub_electrod:[117,118,119],get_subgraphs_as_molecul:71,get_subset_in_chemsi:175,get_substr:182,get_suggested_saxi:168,get_summary_dict:[55,93,117,118,119],get_summed_cohp_by_label_and_orbital_list:167,get_summed_cohp_by_label_list:167,get_summed_icohp_by_label_list:167,get_supercell_matrix:98,get_surface_data:182,get_surface_equilibrium:105,get_surface_sit:157,get_sym_eq_kpoint:164,get_symbol_cn_map:26,get_symbol_dict:158,get_symbol_list:58,get_symbol_name_map:26,get_symm_band:165,get_symmetric_neighbor_list:156,get_symmetric_sit:157,get_symmetric_wallace_tensor:58,get_symmetrically_distinct_miller_indic:157,get_symmetrically_equivalent_miller_indic:157,get_symmetrized_fcm:90,get_symmetrized_structur:[260,267],get_symmetry_dataset:260,get_symmetry_oper:[1,260],get_symop:196,get_task_data:182,get_tasker2_slab:157,get_tgt:58,get_thermal_conduct:165,get_tick:[170,258],get_ticks_old:170,get_total_ionic_dipol:66,get_trajectori:239,get_trans_mat:70,get_transform:98,get_transition_chempot:88,get_tri_area:110,get_truncated_coulomb_cutoff:202,get_typ:79,get_unique_famili:51,get_unique_site_indic:202,get_unit_primitive_area:105,get_unreconstructed_slab:157,get_unstable_entri:119,get_unstable_fcm:90,get_upper_band_edg:169,get_uvec:158,get_v:87,get_val:17,get_valid_magmom_struct:240,get_valid_path:122,get_valu:[187,191],get_vasp_input:[1,12,240],get_vasprun_outcar:240,get_vbm:164,get_vector_along_lattice_direct:[1,149],get_void_volume_surfarea:248,get_voigt_dict:158,get_volume_and_charge_for_sit:139,get_volumetricdata_dens:223,get_volumetricdata_imaginari:223,get_volumetricdata_r:223,get_voronoi_nod:248,get_voronoi_polyhedra:79,get_wallace_tensor:58,get_weight:275,get_weights_of_nn_sit:79,get_wigner_seitz_cel:149,get_wt_fract:146,get_wulff_shap:182,get_xas_data:182,get_xc_funct:202,get_xrd_plot:[1,132],get_xyz_magmom_with_001_saxi:168,get_yield_stress:58,get_z_ordered_elmap:17,get_zmatrix:212,get_zt:165,getmu_vertices_stability_phas:88,gf_sisso:173,gfactor:234,gflop:187,gfortran:[5,131],gfortranbinari:5,gga:[1,17,28,44,48,87,150,161,172,177,182,201,238,239,240,272,290],gga_c_am05:[150,161],gga_c_apb:150,gga_c_bgcp:150,gga_c_fract:201,gga_c_ft97:150,gga_c_gam:150,gga_c_hcth_a:150,gga_c_lm:150,gga_c_lyp:[150,161],gga_c_n12:150,gga_c_n12_sx:150,gga_c_op_b88:150,gga_c_op_g96:150,gga_c_op_pb:150,gga_c_op_pw91:150,gga_c_op_xalpha:150,gga_c_optc:150,gga_c_p86:150,gga_c_pb:[150,161],gga_c_pbe_jrgx:150,gga_c_pbe_sol:[150,161],gga_c_pbef:150,gga_c_pbeint:150,gga_c_pbeloc:150,gga_c_pw91:[150,161],gga_c_q2d:150,gga_c_regtpss:150,gga_c_revtca:150,gga_c_rge2:150,gga_c_sogga11:150,gga_c_sogga11_x:150,gga_c_spb:150,gga_c_tca:150,gga_c_wi0:150,gga_c_wi:150,gga_c_wl:150,gga_c_xpb:150,gga_c_zpbeint:150,gga_c_zpbesol:150,gga_def:182,gga_k_absp1:150,gga_k_absp2:150,gga_k_apb:150,gga_k_apbeint:150,gga_k_baltin:150,gga_k_dk:150,gga_k_ernzerhof:150,gga_k_fr_b88:150,gga_k_fr_pw86:150,gga_k_ge2:150,gga_k_golden:150,gga_k_gp85:150,gga_k_gr:150,gga_k_lc94:150,gga_k_lieb:150,gga_k_llp:150,gga_k_ludena:150,gga_k_mey:150,gga_k_ol1:150,gga_k_ol2:150,gga_k_pearson:150,gga_k_perdew:150,gga_k_revapb:150,gga_k_revapbeint:150,gga_k_tfvw:150,gga_k_thakkar:150,gga_k_tw1:150,gga_k_tw2:150,gga_k_tw3:150,gga_k_tw4:150,gga_k_vjk:150,gga_k_vsk:150,gga_k_vw:150,gga_k_yt65:150,gga_lin:182,gga_opt:182,gga_relax:28,gga_stat:182,gga_static_diel:182,gga_uniform:182,gga_x_2d_b86:150,gga_x_2d_b86_mgc:150,gga_x_2d_b88:150,gga_x_2d_pb:150,gga_x_airi:150,gga_x_ak13:150,gga_x_am05:[150,161],gga_x_apb:150,gga_x_b86:150,gga_x_b86_mgc:150,gga_x_b86_r:150,gga_x_b88:[150,161],gga_x_bayesian:150,gga_x_bgcp:150,gga_x_bpccac:150,gga_x_c09x:150,gga_x_cap:150,gga_x_dk87_r1:150,gga_x_dk87_r2:150,gga_x_ev93:150,gga_x_fract:201,gga_x_ft97_a:150,gga_x_ft97_b:150,gga_x_g96:150,gga_x_gam:150,gga_x_hcth_a:150,gga_x_herman:150,gga_x_hjs_b88:150,gga_x_hjs_b88_v2:150,gga_x_hjs_b97x:150,gga_x_hjs_pb:150,gga_x_hjs_pbe_sol:150,gga_x_htb:150,gga_x_ityh:150,gga_x_kt1:150,gga_x_lag:150,gga_x_lambda_ch_n:150,gga_x_lambda_lo_n:150,gga_x_lambda_oc2_n:150,gga_x_lb:150,gga_x_lbm:150,gga_x_lg93:150,gga_x_lv_rpw86:150,gga_x_mb88:150,gga_x_mpb:150,gga_x_mpw91:150,gga_x_n12:150,gga_x_ol2:150,gga_x_optb88_vdw:150,gga_x_optpbe_vdw:150,gga_x_optx:150,gga_x_pb:[150,161],gga_x_pbe_jsjr:150,gga_x_pbe_mol:150,gga_x_pbe_r:[150,161],gga_x_pbe_sol:[150,161],gga_x_pbe_tca:150,gga_x_pbea:150,gga_x_pbef:150,gga_x_pbeint:150,gga_x_pbek1_vdw:150,gga_x_pw86:150,gga_x_pw91:[150,161],gga_x_q2d:150,gga_x_rge2:150,gga_x_rpb:[150,161],gga_x_rpw86:150,gga_x_sfat:150,gga_x_sogga11:150,gga_x_sogga:150,gga_x_ssb:150,gga_x_ssb_d:150,gga_x_ssb_sw:150,gga_x_vmt84_g:150,gga_x_vmt84_pb:150,gga_x_vmt_g:150,gga_x_vmt_pb:150,gga_x_wc:150,gga_x_wpbeh:150,gga_x_xpb:150,gga_xc_b97_d:150,gga_xc_b97_gga1:150,gga_xc_edf1:150,gga_xc_hcth_120:150,gga_xc_hcth_147:150,gga_xc_hcth_407:150,gga_xc_hcth_407p:150,gga_xc_hcth_93:150,gga_xc_hcth_p14:150,gga_xc_hcth_p76:150,gga_xc_kt2:150,gga_xc_mohlyp2:150,gga_xc_mohlyp:150,gga_xc_mpwlyp1w:150,gga_xc_oblyp_d:150,gga_xc_opbe_d:150,gga_xc_opwlyp_d:150,gga_xc_pbe1w:150,gga_xc_pbelyp1w:150,gga_xc_th1:150,gga_xc_th2:150,gga_xc_th3:150,gga_xc_th4:150,gga_xc_th_fc:150,gga_xc_th_fcfo:150,gga_xc_th_fco:150,gga_xc_th_fl:150,gga_xc_vv10:150,gga_xc_xlyp:150,ggau_def:182,ggau_lin:182,ggau_opt:182,ggau_stat:182,ggau_static_diel:182,ggau_uniform:182,ggt:58,ghemic:195,ghost:199,ghost_sit:157,gian:28,giantomassi:[1,257,291],gibb:[1,88,91,93,105,165,170,172,173,212,291],gibbs_binding_energi:105,gibbs_model:173,gibbscomputedstructureentri:[1,173],gigaflop:187,gin:141,git:[1,3,5],github:[1,2,3,4,6,84,96,110,113,139,140,180,182,226,254,257,291],give:[1,4,6,29,34,40,41,43,48,63,66,70,71,78,79,81,83,87,88,92,98,103,105,116,139,141,146,152,165,168,169,170,182,201,204,212,219,222,223,239,260,269,276,277,292],give_only_index:260,given:[1,3,4,5,6,11,15,16,17,20,21,22,23,25,26,28,29,30,34,36,38,40,41,43,44,45,48,49,52,54,55,56,58,61,63,66,67,70,71,74,76,77,78,79,81,83,84,87,88,91,92,93,94,96,97,98,100,101,102,103,105,109,110,116,117,119,137,139,145,146,149,152,153,154,156,157,158,159,164,165,167,168,169,170,172,174,175,180,182,183,186,187,188,190,192,199,200,201,202,208,212,216,221,222,230,231,232,234,238,239,240,241,248,250,251,254,256,258,260,261,263,265,269,271,272,276,279,282,283,287,290,292],gjf:[4,6,156,292],gkantoniu:291,gl:161,glaum:28,glob:200,global:[1,4,6,168,188,195,199,200,201,269],global_mo:168,gmail:[182,281],gmatteo:[1,62],gmolecul:192,gnu:5,gnuplot:[46,275],go:[1,2,3,5,71,88,102,156,157,182,196,248,260,264,271,278,292],goal:157,godbi:186,goe:[54,201,208,210,278,291],goebel:28,gold:199,golden:[62,280],gonz:[28,165],gonze1997:257,good:[5,55,67,71,87,98,102,152,157,183,187,199,201,238,240,292],good_sect:187,goodal:291,googlecod:189,gorai:56,gostin:1,gout:141,gov:[151,153,215],govern:154,gowoon:56,gpa:[62,93],gpa_to_ev_a3:58,gpaw:161,gpetretto:1,gpoint:239,gpretto:1,gpw:[199,201],grab:[1,200],grad:139,gradep:139,gradient:[59,60,86,87,139,186,192,195,199,201,224,232,239,240,272],gradual:92,graef:[52,54,262],grain:[1,8,9,14,69,182,240,269,292],grain_label:70,grainboundari:70,grainboundarygener:70,grainboundarytransform:[1,269],grammar:154,grammat:153,gramschmidt:79,grand:[1,74,88,105,290],grand_pd:74,grandpotentialinterfacialreact:74,grandpotentialphasediagram:[1,74,88],grandpotpdentri:88,grant:[4,6],granular:55,graph:[1,5,8,9,14,20,22,23,37,55,56,67,68,79,82,100,139,143,170,174,180,258,261],graph_data:71,graph_dict:71,graph_obj:[53,110,174],graph_residual_error:174,graph_residual_error_per_speci:174,graph_util:[9,14,18,31],graphic:[4,6,88,170],graphit:284,graphviz:[5,71],grav:116,gravimetr:117,graviometr:120,grazuli:179,great:110,greater:[1,4,6,11,45,79,123,146,156,174,182,201,240,255],greatest:[38,146],greatli:[4,6,175],greedi:169,green:[58,59,71,170,186],green_kristoffel:58,green_lagrange_strain:59,grei:[264,280,289],grep:[1,200,228,233,239,240],grid:[1,25,29,44,49,51,62,87,96,139,165,169,170,186,187,188,190,199,201,204,211,221,223,226,228,234,238,239,240,241,256,257,258,260],grid_off:110,gridspec_kw:280,grip:[4,6],gross:149,grosspop:[1,223],grosspopul:223,ground:[1,74,77,82,143,153,172,175,177,182,188],ground_level:153,ground_stat:175,ground_state_energi:77,ground_state_term_symbol:153,group:[1,4,5,6,8,9,13,26,28,34,43,49,55,56,66,68,71,81,84,92,98,109,139,146,148,149,153,156,157,158,174,175,177,182,187,189,196,199,200,208,215,219,233,238,239,240,259,260,261,263,264,265,266,272,290,291,292],group_array_indic:158,group_by_typ:156,group_entries_by_composit:175,group_entries_by_structur:175,group_molecul:84,group_structur:[1,98],grow:[4,6],growth:[77,104],grueneisen:[226,256],gruenisen:256,gruneisen:[8,9,58,93,226,253,258],gruneisen_dict:226,gruneisen_paramet:93,gruneisen_path:226,gruneisenparamet:[226,256,258],gruneisenphononbandstructur:[226,256],gruneisenphononbandstructuresummlin:256,gruneisenphononbandstructuresymmlin:[226,256,258],gruneisenphononbsplott:258,gruneisenplott:258,gs:188,gs_input:188,gt:182,gth:202,gth_basi:199,gth_potenti:199,gu:[1,5,140,271],guarante:[0,1,3,4,6,71,81,84,113,155,157,172,199,260,271,272,292],guard:182,guassian:201,guess:[1,55,66,67,81,103,146,156,199,201,215,240,272,275,292],guess_el:215,guesstim:83,guesstimate_spin:83,gui:291,guid:[1,5,66,292],guidanc:182,guidelin:[1,4,5,6],guido:[1,256,257,291],gulp:[1,5,61,63,141,243,248],gulp_cal:[1,5,8,9,136],gulp_cmd:141,gulpcal:141,gulpconvergenceerror:141,gulperror:141,gulpio:141,gunter:[4,6,290],gupta:291,gvallver:170,gvallverdu:1,gw:[1,186,211,238,240],gw_fiesta:211,gw_option:211,gw_qprang:186,gwcalctyp:186,gweight:25,gwpara:186,gz:[4,5,6,123,137,139,174],gzip:[1,123,137,138,139,196],h1:105,h2:[74,105,146,172,177],h2o2:[146,148],h2o:[91,148,172],h2o_adjust:172,h2o_energi:172,h4o4:148,h:[1,4,5,6,29,40,51,55,56,62,68,70,74,85,86,87,91,105,106,110,116,137,146,148,149,153,157,160,165,170,174,186,187,199,215,224,238,240,248,257,258,262,265,289,290,292],h_gw:240,h_node:281,ha:[1,2,3,4,5,6,12,23,28,29,30,36,45,48,55,58,62,63,66,67,70,79,81,84,88,90,91,94,105,113,117,122,137,138,139,149,152,153,156,157,158,160,161,165,168,170,177,182,186,188,190,192,197,199,201,202,204,208,212,215,216,222,223,224,225,227,231,238,239,240,241,251,254,258,260,264,269,272,282,283,291,292],had:[1,2,43,63,165],haeberlen:86,haeberlen_valu:86,haeberlennot:86,hafner:46,half:[1,98,157,202,212],halfspac:48,halfspaceinterect:48,halfspaceintersect:[40,91],halit:157,halite_111_octopolar_2x2:157,hall:[165,170,179,260],hall_dop:165,hallten:165,halogen:[146,153,232],halogen_list:85,hamilton:[1,167,170],hamiltonian:[81,82,186,199],hammer:[161,169],hand:[1,2,5,122],handbook:153,handl:[1,4,6,56,105,129,131,135,137,148,167,168,177,194,199,216,221,230,239,240,257,260],hanmei:[1,291],hanmeitang:1,hansen:161,hanson:92,happen:[43,49,79,84,182],happi:3,haranczyk:[47,49,248,290],hard:[1,83,153,215,271,272],harmon:93,harri:86,hart:[1,5,92,140,271],hartman:291,hartre:[186,190,199,201,204,224,239],harvard:291,has_antibnd_states_below_efermi:167,has_dojo_report:190,has_eigendisplac:254,has_error:196,has_good_quality_check_occupied_band:223,has_good_quality_maxdevi:223,has_hint:190,has_imaginary_freq:254,has_intersect:25,has_magmom:[261,263],has_materials_project_access:32,has_nac:[226,254],has_onsite_density_matric:239,has_opt:192,has_same_structur:188,has_subkei:192,hash:[1,5,84,98,153,158,172,190,238,239,240],hashabl:[84,98,146,154,156,161],hasn:238,hautier:[1,4,6,28,88,101,102,165,240,290,291],have:[1,2,3,4,5,6,11,15,16,17,20,23,26,28,29,30,37,40,43,45,48,55,56,59,61,63,66,67,68,70,71,78,79,81,82,83,84,85,87,88,97,98,100,105,109,110,116,117,118,119,122,123,136,137,141,142,146,147,151,153,154,156,157,158,159,160,164,165,168,169,170,172,173,177,182,183,187,188,189,190,192,195,199,200,201,202,204,215,221,226,234,238,239,240,241,248,252,256,258,260,261,269,271,272,273,276,278,283,284,290,291,292],have_consistent_saxi:168,haven:[1,63],haydock:186,hayn:153,hbar:[49,58],hcp:[79,110,140,272],hdf5:[1,239],he:[1,56,85,153,238,240,254,256,284,292],he_bcc:284,he_gw:240,head:218,headach:240,header:[1,5,181,187,189,196,200,204,208,209,210,219,227,231,233,239,243,283],header_pattern:[200,233,239],header_str:208,header_string_from_fil:208,heat:[58,255,258,280],heatmap:[1,280],heavi:[1,5,88,182,292],heavier:173,heavili:[276,292],hedin:238,height:[15,62,79,120,170,269,280],heisenberg:[1,8,9,14,71,80],heisenbergmapp:82,heisenbergmodel:[82,143],heisenbergscreen:82,helmholtz:[93,255],helmholtz_free_energi:255,helmoltz:258,help:[1,3,4,6,8,9,15,40,45,66,70,71,81,87,88,105,149,157,169,170,182,184,199,221,236,240,257,289],helper:[1,13,15,23,34,49,58,71,79,96,97,105,108,110,123,142,146,157,158,182,199,208,228,237,238,257,280],hematit:106,henc:[91,177,238,272,278],henchforth:1,heng:1,henkelman:[109,137,239,290],henkelmann:[1,5,137,290],henriqu:291,henriquemiranda:[1,254],herath:291,herbst:291,here:[0,4,5,6,37,56,79,81,84,98,105,157,161,173,190,200,201,226,232,234,239,278,282,292],herebi:[4,6],herfindahl:72,hermann:262,hessian:[1,139,170,212,224],heteroatom:68,heterostructur:[56,78],heurist:[81,83],hex:[1,70,263],hex_angle_tol:149,hex_bipyr:79,hex_length_tol:149,hex_pyr:79,hexagon:[1,70,79,110,149,157,186,188,238,240,260,262,264,265,269],hf:[56,85,153,200,201,212,239,240],hf_fraction:201,hf_pv:240,hf_sv_gw:240,hfscreen:240,hfx:[200,201],hg:[56,85,153,240],hg_sv_gw:240,hhi:[1,8,9,14],hi:262,hick:92,hide:71,hide_image_edg:71,hide_neg:120,hide_unconnected_nod:71,hierarchi:[197,292],high:[1,3,4,6,13,40,49,81,82,83,101,105,108,140,153,165,170,177,180,188,190,195,199,201,224,226,238,240,248,260,261,263,289,290,291],highcharg:46,highchart:46,higher:[29,48,49,58,61,79,88,102,105,165,170,201,239,240,272],highest:[15,49,56,58,88,97,117,151,165,169,187,199,271,292],highest_protocol:284,highli:[1,3,4,6,91,169,186,201,238,239,271,292],highlight:292,highsymmkpath:[170,206,238,261],hilber:186,hilbert:[169,186],hilberttransform:186,hill:[58,146,183],hill_formula:146,hillari:[1,291],hint:[1,25,26,28,29,81,190,285],hint_for_accuraci:190,hints_info:26,hints_typ:26,hinuma:[261,263],hiphiv:269,hirerachi:292,hirschman:72,hirshfeld:[138,200,240],histo:165,histogram:[165,187],histor:[5,153,199],histori:[12,13,182,271,272,273,281],history_restart:199,historynod:281,hit:275,hitachi:291,hive:[8,9,114,121,123,292],hkil:[110,157],hkill:110,hkl:[1,51,53,54,56,110,149,157],hkl_list:110,hkl_transform:157,hkl_tuple_to_str:110,hl:[161,238],hm:143,hmlli:291,hmodel:82,ho3:240,ho:[56,85,146,148,153,174,240],ho_3:240,hold:[70,157,248],holder:[4,6,173],hole:[44,45,48,165,169],hollow:15,holm:291,home:[4,6,225],homepag:183,homo:[151,199,200,201],homogen:[58,186],homogeneous_poisson:58,hongyi:[1,291],hook:[1,3],hop:79,hope:201,hopkin:1,hopp:79,horizont:[48,91],horton:[1,28,47,49,172,291],host:[45,49,117,120,175],hot:5,hou:291,hous:1,hove:[0,4,6],how:[0,1,15,25,28,29,30,45,51,61,63,66,68,71,72,98,146,149,156,157,165,167,170,173,177,182,197,199,200,201,202,222,239,240,269,275,281,292],howev:[1,2,4,5,6,12,13,49,66,67,71,79,88,94,105,118,122,156,157,170,177,188,210,232,238,239,240,264,272,292],hpoint:230,href:180,hs:[56,153],hse06:201,hse:[1,201,239,240],hsuan:291,ht:292,html:[1,4,5,6,63,110,161,181,189,207,211,215,237,242,248,282,283],htmlifi:283,http:[1,4,5,6,40,49,63,66,74,84,91,92,93,96,105,108,110,113,137,138,139,140,141,142,143,151,152,153,161,165,168,170,172,173,180,181,182,183,189,204,207,211,215,225,226,227,234,239,240,242,248,254,257,260,263,264,276,282,290,292],htz1992213:1,hu:238,huang:[87,290],hubbard:[172,182,200,239,240,292],hubbard_u:240,huck:[239,291],huebsch:291,huge:[55,88,199,201],hui:1,hull:[1,41,74,88,91,110,117,118,119,174,175,177,182],hull_energy_1:177,hull_energy_2:177,human:[173,183,292],humbert:291,humboldt:291,hund:153,hundr:195,hung:291,hungarian:84,hungarianordermatch:84,hv:84,hvec:58,hyb:161,hyb_gga_x_n12_sx:150,hyb_gga_x_sogga11_x:150,hyb_gga_xc_b1lyp:150,hyb_gga_xc_b1pw91:150,hyb_gga_xc_b1wc:150,hyb_gga_xc_b3lyp5:150,hyb_gga_xc_b3lyp:150,hyb_gga_xc_b3p86:150,hyb_gga_xc_b3pw91:150,hyb_gga_xc_b97:150,hyb_gga_xc_b97_1:150,hyb_gga_xc_b97_1p:150,hyb_gga_xc_b97_2:150,hyb_gga_xc_b97_3:150,hyb_gga_xc_b97_k:150,hyb_gga_xc_bhandh:150,hyb_gga_xc_bhandhlyp:150,hyb_gga_xc_cam_b3lyp:150,hyb_gga_xc_camy_b3lyp:150,hyb_gga_xc_camy_blyp:150,hyb_gga_xc_cap0:150,hyb_gga_xc_edf2:150,hyb_gga_xc_hjs_b88:150,hyb_gga_xc_hjs_b97x:150,hyb_gga_xc_hjs_pb:150,hyb_gga_xc_hjs_pbe_sol:150,hyb_gga_xc_hpbeint:150,hyb_gga_xc_hse03:150,hyb_gga_xc_hse06:150,hyb_gga_xc_lc_vv10:150,hyb_gga_xc_lcy_blyp:150,hyb_gga_xc_lcy_pb:150,hyb_gga_xc_lrc_wpb:150,hyb_gga_xc_lrc_wpbeh:150,hyb_gga_xc_mb3lyp_rc04:150,hyb_gga_xc_mpw1k:150,hyb_gga_xc_mpw1pw:150,hyb_gga_xc_mpw3lyp:150,hyb_gga_xc_mpw3pw:150,hyb_gga_xc_mpwlyp1m:150,hyb_gga_xc_o3lyp:150,hyb_gga_xc_pbe0_13:150,hyb_gga_xc_pbeh:150,hyb_gga_xc_revb3lyp:150,hyb_gga_xc_sb98_1a:150,hyb_gga_xc_sb98_1b:150,hyb_gga_xc_sb98_1c:150,hyb_gga_xc_sb98_2a:150,hyb_gga_xc_sb98_2b:150,hyb_gga_xc_sb98_2c:150,hyb_gga_xc_tuned_cam_b3lyp:150,hyb_gga_xc_wb97:150,hyb_gga_xc_wb97x:150,hyb_gga_xc_wb97x_d:150,hyb_gga_xc_wb97x_v:150,hyb_gga_xc_x3lyp:150,hyb_mgga_x_dldf:150,hyb_mgga_x_mn12_sx:150,hyb_mgga_x_mn15:150,hyb_mgga_x_ms2h:150,hyb_mgga_x_mvsh:150,hyb_mgga_x_scan0:150,hyb_mgga_xc_b86b95:150,hyb_mgga_xc_b88b95:150,hyb_mgga_xc_bb1k:150,hyb_mgga_xc_m05:150,hyb_mgga_xc_m05_2x:150,hyb_mgga_xc_m06:150,hyb_mgga_xc_m06_2x:150,hyb_mgga_xc_m06_hf:150,hyb_mgga_xc_m08_hx:150,hyb_mgga_xc_m08_so:150,hyb_mgga_xc_m11:150,hyb_mgga_xc_mpw1b95:150,hyb_mgga_xc_mpwb1k:150,hyb_mgga_xc_pw6b95:150,hyb_mgga_xc_pw86b95:150,hyb_mgga_xc_pwb6k:150,hyb_mgga_xc_revtpssh:150,hyb_mgga_xc_tpssh:150,hyb_mgga_xc_wb97m_v:150,hyb_mgga_xc_x1b95:150,hyb_mgga_xc_xb1k:150,hybersten:186,hybrid:[1,44,48,150,151,201,202,215,231,239],hybrid_cbm:[44,45],hybrid_funct:201,hybrid_vbm:[44,45],hybridcelloptset:201,hybridrelaxset:201,hybridstaticset:201,hydrat:[148,172],hydrogen:[1,68,91,139,146,148,153,195],hydroxid:97,hyperdimension:40,hyperfin:239,hyperplan:[40,48,91],hyperplane_entri:40,i:[1,2,3,4,5,6,15,26,29,34,36,40,48,49,51,53,54,56,58,59,62,63,66,68,70,71,74,78,79,82,85,88,89,91,93,97,98,102,105,113,116,117,118,119,120,122,137,138,143,145,146,148,149,153,154,155,156,157,158,159,160,164,165,167,168,169,170,172,174,175,177,180,182,186,187,188,190,199,200,201,202,208,209,212,215,216,225,226,228,230,233,234,235,238,239,240,250,251,256,257,258,260,263,264,267,268,269,276,277,278,283,289,292],i_:54,i_central_sit:22,i_gw:240,ia:98,ialgo:1,ian496:1,iatom:212,ib:98,ibrion:[239,240],ibz:[186,238],ibzkpt:239,ic102031h:[101,102],icam:165,icharg:240,iclud:1,icobi:[167,223],icohp:[167,170,222,223],icohpcollect:[1,167,223],icohplist:[1,167,222,223],icohpvalu:167,icoop:[167,223],icooplist:[167,222,223],icor:238,icsd:[1,17,32,102,103,146,153,281],icsd_id:182,icsd_oxidation_st:[146,153],icsd_vol:103,id:[1,2,3,4,6,43,102,143,173,179,180,182,183,208,210,215,222,239,264,282,284,292],id_gener:275,idea:[84,197,210,292],ideal:[26,49,79,110,142,153,167,202,223,269],ident:[34,58,59,60,79,98,119,156,165,177,201,231,233,239,265,272],identif:[26,28,36,56,79,139,165,209],identifi:[1,3,22,25,26,28,29,43,56,58,67,68,70,77,79,82,84,101,104,105,110,143,150,165,173,182,199,200,208,210,222,232,238,254,257,260,262,290],identify_potcar:238,ido:239,idx1:195,idx2:195,idx:[59,228],ie:[34,105,157],ieee:[1,77,158],iek:1,ifftn:239,ignor:[1,56,58,71,79,81,84,98,130,153,154,155,173,177,187,188,217,219,238,239,256,283,284],ignore_error:58,ignore_ionic_bond:85,ignore_on:283,ignore_warn:84,ignored_speci:98,igpar:239,igraph:[1,82],igw:79,igw_ep:79,igw_spp:79,igw_ta:79,ii:[1,34,79,98,149,153,154,156,157,269],iii:[45,79,149,154,156,157],iiipi:153,ij:269,ijkl:58,ik:241,ill:169,illustr:[4,6],im:257,imag:[1,20,23,29,49,55,56,66,71,79,87,88,97,109,120,149,154,156,170,212,215,227,240,252,258,269,287,289],imag_partxi:239,imag_partxx:239,imag_partxz:239,imag_partyi:239,imag_partyz:239,imag_partzz:239,image_format:[88,120,289],image_index:97,image_label:71,imagej:97,imagenam:29,imaginari:[96,186,223,239,254,257],imcn:291,img_format:[170,212,258,287],immedi:[200,233,239],immut:[1,146,153,156,292],imolecul:[1,2,156,195,292],impact:[4,6,48,98],imperi:291,implaus:81,implement:[1,12,13,17,21,25,26,28,30,36,40,42,44,45,47,50,51,52,53,54,56,61,62,69,70,75,78,82,84,87,93,98,105,117,122,123,128,130,131,132,133,134,135,137,138,139,140,143,145,146,151,152,155,157,158,160,161,168,170,171,172,173,175,177,180,182,185,186,188,190,197,199,201,210,211,212,215,216,217,219,220,222,223,224,228,229,232,234,235,236,238,239,240,244,247,248,250,251,256,257,258,259,263,267,269,270,272,274,286,289,290,292],implemented_geometri:26,impli:[1,4,6,13,97,98,149,154,156,175,201],implic:105,implicit:[1,232],impos:71,imposs:[98,208],improp:[1,56,66,158,215,240],improv:[1,3,4,5,6,123,138,146,151,175,239,240],imtd:246,in_array_list:262,in_coord_list:276,in_coord_list_pbc:[15,276],in_d:240,in_d_gw:240,in_lay:76,in_plac:[1,154],in_plane_offset:147,in_simplex:276,in_unit_plan:[157,269],inaccur:[109,153,271],inaccuraci:226,inact:257,inb_set:28,inc:[199,291],inc_molecule_graph:56,inc_orient:56,inc_site_id:56,inc_structur:[122,182,239],inc_vertic:56,incar:[1,44,122,168,181,197,221,236,237,238,239,240],incar_input:221,incar_output:221,incar_paramet:1,inch:[62,170,280],inchi:84,inchimolatommapp:84,incid:210,includ:[0,1,3,4,5,6,12,13,15,20,25,26,28,29,41,43,44,45,49,54,55,56,58,59,63,66,67,70,71,74,77,79,88,91,102,105,115,119,122,138,146,147,148,149,152,154,155,156,157,158,159,160,165,167,169,171,172,173,174,175,176,177,181,182,186,187,188,192,196,197,199,201,204,206,210,215,216,221,223,226,231,232,238,239,240,246,256,260,263,264,269,283,292],include_base_prop:58,include_bv_charg:47,include_central_site_in_centroid:28,include_cif:[13,240],include_critical_point:139,include_deactiv:26,include_dist:98,include_gamma:181,include_ignored_speci:98,include_imag:156,include_improp:158,include_index:156,include_mscd_t:55,include_msd_t:55,include_myself:119,include_no_mixing_energi:74,include_reconstruct:157,include_sourc:20,include_unprocessed_entri:91,include_user_ag:182,include_work_of_separ:182,inclus:[146,173,264],inclusionari:269,inclvkb:186,incompat:[1,4,5,6,48,172,196],incomplet:[28,217],inconsist:[55,158,168,177],incorpor:[3,71,151,172,182,239],incorrect:[1,263],incorrectli:1,incr:105,increas:[1,2,29,34,49,63,70,97,103,146,156,182,199,232,238,240,269,279,289],incred:157,increment:[105,165,239],ind1:156,ind2:156,ind:[84,149,204,239],ind_zero_freq:255,inde:188,indent:199,independ:[1,58,59,78,88,105,164,186,192,212,224,239],index1:[97,252],index2:[97,252],index:[1,4,6,15,22,23,25,28,29,30,34,37,44,45,46,49,56,58,59,63,66,67,70,71,72,74,76,77,79,84,85,90,97,105,110,112,137,138,139,143,149,153,154,156,157,158,159,164,165,168,170,182,183,186,187,188,189,191,192,195,199,202,204,208,209,210,211,212,215,218,222,228,232,239,240,241,245,254,255,256,257,263,264,266,269,271,276,277,279,289,292],index_from:138,index_non:70,index_of_sit:157,index_to:138,indexerror:[12,13],indic:[1,3,12,13,15,26,28,29,30,34,37,44,49,51,53,56,58,59,63,68,70,71,77,78,79,84,87,88,91,97,98,105,110,112,137,139,145,146,147,149,152,154,156,157,158,164,165,167,168,169,170,175,186,196,202,208,212,215,221,222,238,239,240,254,260,262,263,264,269,271,273,276,277,279,281,287],indices_from_symbol:156,indices_left:63,indices_neigh:79,indices_separ:34,indices_species_map:271,indices_to_mov:271,indices_to_remov:271,indirect:96,individidu:190,individu:[1,4,6,55,91,105,109,167,170,239,261,292],induc:71,inequival:[81,226],inertia:[84,260],inf:[29,169,186,269],infer:[200,215],infin:[1,25,105],infinit:[30,36,79,84,149,165,292],infit:[47,49],influenc:[63,165,174],info:[1,4,6,25,26,28,29,53,79,84,93,130,182,187,199,200,202,204,209,211,215,222,223,239,240,289],info_dict:[29,150],inform:[1,4,5,6,16,20,25,28,29,34,40,43,45,49,55,56,70,71,74,79,81,88,94,97,98,113,118,119,130,139,141,143,147,148,151,156,157,158,159,160,161,164,165,167,168,171,173,177,182,183,195,196,197,199,200,204,208,216,221,222,223,225,230,239,240,243,247,248,254,256,258,264,269,271,272,273,289,290,292],informat:240,infos_on_basis_set:211,infos_on_system:211,infrastructur:[240,290],inher:[157,269],inherit:[53,58,66,171,197,201,240,271,272,292],iniit:188,init:[1,49,70,79,83,141,146,150,157,177,180,225,237,239,240],init_3point:34,init_cel:70,init_mesh:226,init_neighbors_set:29,init_slab:157,init_u_ramping_each_scf:199,initi:[1,3,5,12,13,16,17,25,26,28,29,30,34,43,44,45,47,49,52,54,55,58,61,62,63,67,70,77,78,79,81,84,85,86,88,91,97,103,105,109,112,116,118,137,138,141,145,146,152,153,156,157,158,160,167,168,169,170,171,172,173,174,182,186,187,188,192,195,199,200,201,204,211,221,228,238,240,241,242,258,260,261,262,263,264,265,272,276,283,287,292],initial_angle_tol:92,initial_comp:118,initial_comp_formula:118,initial_defect_structur:[44,45],initial_disp:55,initial_entri:16,initial_fit:158,initial_ltol:92,initial_molecul:16,initial_norm:29,initial_r:29,initial_stol:92,initial_structur:[55,70,97,157],initial_structure_environ:28,initialis:[79,199],initialization_opt:25,initio:[165,170],inner:[29,149,156,201,204],innov:290,inorgan:[101,102,146,148,153,173,240,280],inp:[156,188,199,208,209,210,225,292],inp_struct:202,inpfil:192,inplac:240,input:[1,3,4,5,6,8,9,11,12,13,15,21,26,43,49,51,52,53,54,55,56,58,62,63,66,68,70,71,79,81,82,83,84,86,88,91,92,96,97,98,101,102,103,110,119,122,139,141,142,143,146,147,149,151,153,156,157,158,159,164,165,167,170,171,172,173,175,176,182,184,185,186,190,191,192,194,195,196,197,198,200,201,202,203,205,207,209,210,211,212,214,215,217,218,219,220,222,224,225,227,228,229,231,232,233,234,235,236,239,240,241,243,244,247,248,260,261,263,267,269,271,272,273,275,276,279,283,284],input_arrai:[58,89,158,160],input_dir:[210,238],input_fil:232,input_filenam:[4,6,199,218],input_gen:292,input_grid:221,input_matrix:[58,89,90],input_mil:110,input_paramet:212,input_script:139,input_set:172,input_str:[156,242],input_vasp_arrai:89,inputfil:[197,225,230,292],inputgener:[197,225,235,292],inputset:[172,197,216,225,240,292],inputvari:191,inria:291,inscrib:269,insensit:[188,199],insert:[1,49,70,71,116,117,118,119,156,182,199,201,221,269,271,292],insert_nod:71,inserterd:49,insertion_batteri:[8,9,114,115],insertionelectrod:[1,2,115,119],insertionvoltagepair:119,insertsitestransform:271,insid:[15,29,137,165,170,196,199,211,239,269],inspect:269,inspir:[53,84,161,172],instabl:[88,119,201],instal:[1,2,3,4,6,8,9,79,131,141,156,184,195,215,225,269,271,292],install_softwar:131,instanc:[1,2,4,6,11,12,20,26,41,63,68,71,79,81,86,88,91,102,103,139,142,149,153,154,156,160,161,165,170,172,177,182,183,186,188,189,190,195,197,199,215,216,230,232,238,240,257,258,260,269,272,281,282,284,292],instanti:[44,68,156,170,171,177,182,186,189,190,193,197,199,225,234,240,292],instead:[1,4,5,6,11,52,55,56,62,67,74,79,81,88,91,98,102,105,109,122,130,139,145,146,148,152,154,156,157,160,164,165,172,177,190,201,212,222,228,239,240,242,254,258,260,267,279,282,283,292],institut:[4,6,291],instruct:[1,3,4,5,6,137,139,140,143,157,197,225,230,232,248],insuffici:[43,67,177],insul:[169,170,224,239,240],int_:[169,277],int_numb:[260,262],int_symbol:[260,262],intact:157,integ:[1,25,34,38,43,49,59,66,70,78,79,81,88,98,109,116,122,146,149,151,152,153,156,157,160,161,167,170,182,188,190,201,208,215,222,228,231,234,238,239,241,269,272,280,283],integr:[1,2,4,5,6,44,45,58,93,132,137,139,158,165,167,169,170,192,199,201,204,222,223,224,239,255],intellig:[1,4,6,239],intend:[1,3,71,79,82,88,91,92,158,171,172,177,183,199,201,238,240],intens:[1,49,51,52,53,54,64,112,113,155,182,212,239],inter:[98,156],inter_elem:49,interact:[1,5,40,44,61,63,70,82,138,142,143,150,151,156,160,170,201,222,240,261,269,278,291],interactor:289,interatom:[79,199,269],intercal:[1,56,98,116,119],intercept:[34,105],interdepend:172,interest:[3,5,56,68,87,105,116,122,156,167,200,201,233,239,292],interfac:[1,4,6,8,9,14,40,63,74,120,124,137,138,139,140,141,143,144,150,153,157,161,170,172,179,180,181,182,183,188,190,195,197,225,226,240,258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:[1,221,234,240],reciprocal_lattic:[149,170],reciprocal_lattice_crystallograph:149,reciprocal_space_energi:63,reciprocal_space_energy_matrix:63,recogn:[49,79,148,177],recognit:3,recommend:[1,2,3,5,11,56,66,87,97,146,148,153,182,186,199,201,215,232,238,239,240,292],recompil:239,recomput:28,reconstitut:[43,48,88,146,156],reconstruct:[1,20,23,25,26,29,30,105,156,157,158,159,164,239],reconstruction_bas:157,reconstruction_nam:157,reconstructiongener:157,reconstructions_arch:157,record:[4,6,187,225],recov:[66,192],recp_oper:110,recreat:239,rect:105,rectangl:[25,34],rectangle_crosses_area:25,rectangle_surface_intersect:34,rectangular:[79,225,250,251],recurs:[63,156,199,260],red:[71,110,170,258],redefin:[1,248],redo:[12,13],redo_last_transform:1,redo_next_chang:[12,13],redox:116,redraw:289,reduc:[1,4,6,15,26,28,40,41,55,70,78,82,88,91,98,105,117,146,148,149,152,156,157,165,170,175,182,186,192,199,208,212,239,240,263,269,272,280],reduce_formula:146,reduce_mat:70,reduce_structur:240,reduce_vector:78,reduced_cell_composit:146,reduced_cell_formula:146,reduced_composit:146,reduced_formula:[146,148,171,173,177,182,292],reduct:[1,15,59,98,116,149,156,157,269],reduction_algo:[156,269],redund:70,ree:[1,291],reed:56,ref:[58,63,79,97,106,141,165,170],ref_delu:105,ref_el:105,ref_entri:105,ref_idx:187,ref_permut:26,ref_separation_perm:26,ref_structur:103,refactor:[1,62,150],refer:[0,1,3,4,6,26,28,29,36,40,41,44,46,52,62,66,70,71,74,88,96,98,102,103,105,106,109,117,137,139,149,151,153,157,161,164,165,168,169,170,172,173,180,181,182,187,196,200,201,228,232,239,240,245,254,256,264,265,280,281,282,292],referenc:[40,43,74,88,105,157,172,173,177,240],reference_fnm:245,refin:[28,52,53,54,70,158,199,201,260,269],refine_rot:158,refine_struct:196,refine_structur:269,reflect:[71,152,153,215],reform:67,reformat:3,refract:232,refractic:153,refractive_index:153,refresh:183,refresh_alias:183,reg_tri:79,regard:[79,271,272],regardless:[56,98,117,157,174,182,240],regen_libxcfunc:150,regener:150,regent:[4,6],regex:[200,228,233,239,278],region:[29,44,45,48,49,91,105,139,157,165],regist:[4,6,161,173,182,292],regoutz:113,regrep:[200,228,239],regress:[3,55],regular:[79,200,233,239,240,241,256,282],regulargridinterpol:239,regularli:[4,6],reim:257,reimplement:109,reject:[3,156],rel:[3,4,6,15,29,30,48,58,63,70,78,79,81,87,88,145,146,156,157,158,160,168,169,174,182,187,199,202,209,222,223,243],rel_angl:78,rel_cutoff:[199,201,202],rel_strain:78,rel_tol:108,relat:[3,4,5,6,55,58,75,79,90,105,115,117,119,120,138,141,146,149,152,156,159,163,164,165,169,171,182,200,215,216,225,267,281],relationship:[58,71],relative_cutoff:97,relative_e_fermi:167,relative_energi:209,relative_mu:182,relativist:[53,192],relax1:[122,137,139],relax2:122,relax:[17,28,43,44,45,70,81,82,87,97,109,141,143,165,170,177,182,186,188,201,212,239,240,243,260,269,272,292],relax_sit:87,relaxation_dir:109,relaxation_tim:[165,170],relaxationanalyz:[1,97],relaxationmethod:186,relaxed_structur:272,relaxset:201,releas:[0,1,2,4,5,6,105,157,182,240],relev:[1,16,21,23,53,60,71,74,79,88,91,105,118,123,146,153,156,157,167,177,182,232,239,292],reli:[2,4,5,6,102,103,190,197,264],reliabl:[0,3,4,6,55,87,157,172,201,238],reload:[4,6,292],rem:[230,232],rem_templ:230,remain:[1,98,157,158,173,182,200,240],remaind:158,remap:[71,146],remark:[182,281],rememb:[3,240],remind:1,remot:3,remov:[1,2,4,5,6,11,12,15,43,49,51,58,62,63,67,70,71,81,88,98,102,105,116,146,150,156,157,159,165,170,172,175,177,187,188,192,195,196,199,200,233,238,239,240,243,257,258,269,271,272,281,289,292],remove_bond:195,remove_charg:146,remove_collis:49,remove_dupl:102,remove_duplicate_structur:269,remove_empty_lin:278,remove_exist:102,remove_nod:71,remove_non_ground_st:175,remove_opt:192,remove_oxidation_st:156,remove_sit:[71,156],remove_site_properti:[1,156],remove_speci:156,remove_spin:156,remove_subkei:192,remove_symmetri:181,remove_var:188,removed_indic:63,removeduplicatesfilt:11,removeexistingfilt:11,removesitestransform:271,removespeciestransform:[272,292],removespecietransform:292,renam:[1,2,81,156,278],render:[200,228,233,239,289],renew:291,renpj:291,reorder:156,reorgan:[1,2],reorient:[15,157,269],reorient_lattic:157,reorient_z:15,rep:143,repair:157,repair_broken_bond:157,repars:113,repeat:[15,102,157,199,201,269],repeatedli:71,repetit:[88,157,254],replac:[1,2,4,6,12,71,81,119,146,156,169,173,186,201,226,233,235,269,271,292],replace_al:81,replace_all_if_undefin:81,replace_group:71,replace_speci:156,replacesitespeciestransform:271,replic:71,replicate_input:188,repo:[1,3,4,5,6,211,216,221,284],repons:1,report:[1,66,146,161,168,170,172,200,239],repositori:[3,4,5,6,182],repres:[1,15,20,25,26,29,41,43,44,46,49,56,58,59,60,63,68,70,71,74,79,84,86,88,89,90,94,97,101,105,112,113,117,118,119,144,146,148,149,151,152,153,154,155,156,157,158,160,164,165,167,169,170,175,182,189,197,199,200,206,210,212,215,217,224,225,226,230,232,238,239,240,241,245,247,248,254,255,260,262,267,281,283,289,292],represent:[1,4,6,11,12,20,25,26,29,30,36,43,48,49,51,55,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ergon:62,underli:[49,71,79,153,197],underscor:[182,202,262,281],understand:[3,43,74,139,239],undirect:71,undisturb:271,undo:[1,12,13,292],undo_last_chang:[12,13],undon:[12,13],unequ:1,unequival:29,unevenli:83,unexpect:[177,280],unfamiliar:5,unfeas:84,unfold:239,unform:84,unicamp:225,unicod:[1,167,283],unicodeifi:283,unicodeify_spacegroup:283,unicodeify_speci:283,uniform:[1,84,156,182,226,239,240,272],uniform_label:84,union:[71,113,142,145,146,149,152,155,156,169,172,197,216,225,235,238,264,265,272],uniqu:[1,25,29,43,49,51,58,67,70,71,78,82,86,88,97,105,143,146,147,156,157,158,164,170,173,177,186,199,202,208,219,222,238,258,260,264,269,287],unique_site_id:[82,143],uniquelin:88,uniquely_determines_coordination_environ:[25,29,222],unit:[1,2,8,9,15,25,29,44,49,53,55,58,62,63,66,70,71,76,78,86,87,88,96,97,105,110,116,117,120,139,141,143,144,147,149,152,153,154,156,157,158,164,165,168,169,170,173,174,182,186,188,190,191,192,196,199,201,204,206,209,218,223,224,234,238,239,240,248,255,258,260,264,269,270,271,272,276,288,289],unit_cell_composit:146,unit_cell_formula:182,unit_def:160,unit_typ:160,unitcel:46,uniterror:160,uniti:81,unitless:93,units_in_jperm2:110,unittest:[1,3,4,5,6,284],univ:170,univeristi:291,univers:[0,4,6,52,58,93,117,180,239,291],universal_anisotropi:58,univi:[4,6,168],unk:[1,239,241],unknown:[29,81,83,103],unknownpotcarwarn:238,unkxxxxx:241,unless:[149,152,153,156,197,224,238,240],unlik:[146,156,169,182,188,192,199,239,240,292],unnatur:199,unnecessari:[2,52,156,182],unoccupi:[151,199],unord:17,unpair:[156,212,224,239],unphys:[58,103,105],unpickl:282,unpolar:[186,188],unpredict:5,unprocess:91,unprocessed_entri:[91,292],unrecogn:79,unreconstruct:157,unreduc:146,unrel:[4,6],unrelax:272,unrelaxed_structur:272,unrestrict:[192,199,212],unscal:105,unset:[1,105,199,240],unset_encut:240,unsort:49,unspecif:79,unspecifi:40,unstabl:[48,88,90,91,118,119,174],unstable_entri:[88,91,119],unsupport:215,unsym_cs_tensor:239,unsymmeter:90,unsymmetr:[81,239],unsymmetrized_fcm:90,until:[1,92,156,157,158,165,199,200,233,239,269,285],unto:260,untouch:238,unus:63,uo2:88,uo:88,up:[1,2,3,4,5,6,12,20,23,25,28,29,30,36,55,67,70,88,91,97,98,105,118,123,137,143,145,146,149,151,157,164,165,167,168,169,170,182,187,195,200,201,222,223,239,240,269,270,271,277,289,292],updat:[0,1,2,5,28,29,45,56,63,71,97,131,138,182,183,199,201,234,240,260],update_charge_from_potcar:239,update_coordination_environ:29,update_nb_set_environ:28,update_potcar_spec:239,update_site_info:29,upf:228,upgrad:[1,2,4,6,201],upload:181,upon:[1,2,74,239,263],upper:[25,34,36,48,59,88,93,169,192,279],upper_csm:36,upper_point:34,upstream:3,uptak:88,upward:240,urgent:1,url:[1,63,182,183,281],us:[0,1,2,3,11,12,13,15,17,20,21,22,25,26,28,29,30,32,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,51,52,53,54,55,56,58,59,60,61,62,63,66,67,68,70,71,72,74,77,78,79,81,83,84,86,87,88,89,90,91,92,93,96,97,98,100,101,102,103,105,106,109,110,112,113,116,117,118,119,120,122,123,130,135,136,137,138,139,140,141,143,145,146,147,148,149,150,151,152,153,154,156,157,158,159,160,161,164,165,167,168,169,170,171,172,173,174,175,176,177,179,180,182,183,186,187,188,189,190,192,194,195,196,197,199,200,201,202,204,208,210,212,215,216,219,221,222,224,225,226,228,230,231,232,233,234,235,237,238,239,240,242,243,247,248,252,254,255,256,257,258,260,261,262,263,264,265,269,271,272,274,275,276,277,278,279,280,281,282,283,284,287,288,289,290,291,292],usabl:[5,186,238,292],usag:[1,2,3,5,55,62,109,139,156,160,165,168,169,170,182,183,186,238,258,269,287],use_averag:165,use_bandedgeshift:45,use_bandfil:45,use_bv:103,use_cg:186,use_cor:243,use_direct_diago:186,use_entry_label:105,use_external_qhul:1,use_fictive_radiu:79,use_haydock:186,use_hilbert:186,use_hull_energi:[74,182],use_metal_edge_extend:67,use_mie_gruneisen:93,use_multiprocess:[271,273],use_overall_norm:117,use_ppmodel:186,use_site_prop:156,use_structure_charg:[43,240],use_symmetri:186,use_time_revers:186,use_weight:[71,79,222],usedecimalplac:221,usel:105,useoriginaltetrahedronmethod:221,user:[0,1,2,3,4,5,6,15,16,25,37,43,49,56,70,74,88,137,139,156,157,167,182,183,192,199,201,208,210,211,212,216,221,224,230,235,238,239,240,261,263,269,284,292],user_:240,user_api_kei:292,user_eels_set:210,user_incar_set:[1,240],user_input_set:[139,143],user_kpoints_set:[1,240],user_potcar_funct:240,user_potcar_set:240,user_supplied_basi:240,user_tag_set:210,userecommendedbasisfunct:221,usernam:5,userwarn:[238,240],usnistgov:96,usr:5,usual:[1,4,5,6,26,43,49,55,63,71,79,118,139,147,154,156,157,161,165,167,170,173,188,200,201,238,239,240,258,260,269,272,287],utexa:[5,137],utf:[1,187,190],uthpala:291,uthpalah:1,util:[1,4,5,6,8,9,12,14,18,25,29,30,42,91,99,109,146,148,153,173,184,198,214,229,240,249,262],utopianf:291,uu:34,uv:212,v0:[62,284],v1:[84,183,260,276],v2019:2,v2022:[0,3],v2:[4,6,84,182,260,276],v3:260,v3p8o29:117,v4:[4,6],v9:201,v:[56,70,71,84,85,86,87,91,93,98,101,102,117,138,139,141,146,153,165,174,179,199,211,226,232,240,260,269],v_e:153,v_hartree_cub:199,v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,226,228,233,238,239,240,243,254,255,256,257,258,260,261,263,264,269,271,272,273,275,276,277,278,280,283,287,289,290,292],which_charg:222,white:280,whitespac:278,who:[4,6,40,70,157,215,240,291,292],whole:[53,149,165,210,223,240],whom:[4,6],whose:[28,34,49,53,79,87,90,105,182,187,199,230],why:[66,98,199,208,238],wi:238,wiberg:212,wide:[138,179,201,204,272],wider:1,widom:239,width:[15,44,49,62,79,81,87,120,156,169,170,200,212,224,269,280,289],widthsampl:44,wigner:[1,44,45,97,139,149,170,238],wiki:[1,5,84,152,153,161,168,237,240,276],wikipedia:[84,152,153,276],wild:[1,182,292],wildcard:[182,190,217],wilei:[86,110,140],willem:[248,290],william:[1,4,6,78],wimperi:86,win:1,window:[1,2,4,6,15,88,289],winner:291,winston:[105,110,157,182,290,291],wip:3,wire:56,wisconsin:291,wise:[112,239],wisesa:[181,240],wish:[44,63,113,271,290,292],with_dojo_report:190,with_edg:71,with_empty_graph:71,with_head:187,with_label:51,with_lf:186,with_local_env_strategi:71,with_pseudo:188,with_structur:188,within:[1,2,3,11,15,25,34,40,43,45,48,49,51,52,53,54,68,70,78,79,81,87,88,98,105,117,118,119,146,149,154,156,157,158,172,187,199,201,225,239,248,252,254,260,263,275,276,292],without:[1,2,4,6,28,29,37,43,49,53,67,74,81,84,85,88,98,108,146,153,156,157,158,165,169,182,183,186,192,199,200,201,210,215,233,238,239,240,260,263,278,291,292],wmdrichard:291,wn:[142,269],wo4:174,wo:239,won:[91,110,123,165],wood:[1,157,291],woods_not:157,woodward:46,word:[71,215],work:[1,2,3,4,5,6,11,17,43,49,56,62,70,74,87,88,91,92,96,102,103,105,113,116,117,118,119,120,122,138,139,146,152,153,154,155,156,157,160,164,168,169,174,176,177,179,180,182,197,199,201,203,211,215,223,224,225,231,238,239,240,241,243,245,260,262,269,272,276,283,284,290,291,292],work_funct:105,worker:153,workflow:[1,4,6,16],workfunctionanalyz:105,working_dir:245,working_ion:[49,116,117],working_ion_entri:[117,118,119],working_ion_symbol:118,workshop:[4,6],world:[3,4,6,179],worst:[84,187],would:[3,4,5,6,11,12,34,45,49,55,98,102,117,118,142,146,149,153,156,157,168,170,172,188,192,199,201,208,210,238,239,240,269,291,292],wq:239,wq_:239,wr:[142,269],wrap:[1,189,289],wrapper:[5,46,58,61,62,71,136,152,158,167,169,189,195,196,218,255],write:[0,1,2,4,6,12,13,49,55,88,139,146,156,159,165,168,170,175,187,188,192,194,196,197,199,200,201,203,206,208,210,211,212,215,216,218,219,221,225,227,228,230,232,234,235,238,239,240,241,243,245,247,254,258,278,287],write_cif:240,write_cml:139,write_cub:[199,201],write_def:165,write_endpoint_input:240,write_energi:165,write_etre:206,write_fil:[192,195,196,197,199,203,206,208,211,212,215,216,219,223,224,228,238,239,241,243,247,292],write_imag:[88,289],write_incar:221,write_input:[165,197,210,216,238,240,292],write_input_fil:245,write_intran:165,write_json:[139,257],write_kpoint:221,write_lammps_input:216,write_lobsterin:221,write_magmom:196,write_mol:1,write_multi_job_fil:230,write_path_cif:240,write_phononwebsit:254,write_poscar_with_standard_primit:221,write_proj:165,write_str:206,write_struct:165,write_structur:1,write_topolog:49,write_unk:239,write_vasp_input:[12,13],write_xdatcar:159,writeabl:278,writebasisfunct:221,writematricestofil:221,writer:[192,238],written:[1,3,4,6,16,55,88,141,146,148,156,189,197,204,208,215,216,221,225,234,235,238,239,247,248,256,276,290,292],wrong:[1,70,172,192,240],wrongli:153,wrt:[62,88,93,105,158],wrt_cder_between_states_format:239,ws:139,wswq:[1,239],wsyxbcl:[1,291],wu:291,wulff:[1,8,9,14,105,182],wulff_area:110,wulff_cv_simp:110,wulff_from_chempot:105,wulff_gform_and_r:105,wulff_pt_list:110,wulfffacet:110,wulffshap:[1,105,110,182],wuxiaohua1011:1,www:[1,4,5,6,49,63,108,142,151,153,165,182,183,208,221,223,239,240,242,248,264,292],wyckoff:[1,43,82,196,260,267],wyckoff_id:82,wyckoff_lett:267,x0:40,x1:[34,40,48,109],x2:[34,109,153,211],x2y2:146,x3:153,x86_64:[4,5,6],x:[1,2,4,6,13,28,34,36,44,48,49,51,52,53,55,64,71,74,85,88,105,111,112,113,120,140,142,143,146,149,152,153,154,155,156,158,161,164,165,168,169,170,173,182,201,204,208,211,215,222,238,239,247,248,250,251,255,258,269,271,275,276,280,283,287],x_0:155,x_c:92,x_charg:117,x_cross:48,x_diff_weight:79,x_discharg:117,x_form:120,x_min:74,x_name:161,x_ray_factor:53,x_valu:[275,276],x_y0:34,xa:[1,8,9,14,155,182,212,287],xaf:112,xane:[112,155,182,208,209,210],xanes_k:112,xangst:186,xarg:[1,2,4,6],xas_list:112,xavier:[28,211],xaxi:120,xc:[150,161,192,199,202,224],xc_:[150,161],xc_correl:150,xc_famili:150,xc_family_lda:150,xc_function:[161,199],xcart:186,xcenc:239,xcfunc:[8,9,144,150,189],xcode:5,xcrysden:[1,8,9,184],xdatacar:1,xdatcar:[1,159,239],xdatcar_from_struct:159,xe2o:182,xe:[56,85,153,210,240],xe_gw:240,xhi:[91,225],xhqu1981:291,xiangguo:[1,291],xiao:[1,74,291],xiaohui:[1,86],xin:[1,169,224,291],xlabel:[51,64,112,113,155,169,280],xlim:[48,88,105,170,222,257,258,287],xlo:[91,225],xmcd:210,xml:[1,4,6,55,96,122,130,156,159,161,169,206,221,223,239,240,292],xmu:[125,209],xmu_dat_fil:209,xp:[1,8,9,14],xr:[8,9,184],xrang:105,xrd:[1,8,9,14,50,51,52,53,132,155],xrdcalcul:[1,52,54],xrdpat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Add-ons","Change log","Compatibility","Contributing","Introduction","Installation","Introduction","Change log","pymatgen","pymatgen namespace","pymatgen.alchemy package","pymatgen.alchemy.filters module","pymatgen.alchemy.materials module","pymatgen.alchemy.transmuters module","pymatgen.analysis namespace","pymatgen.analysis.adsorption module","pymatgen.analysis.bond_dissociation module","pymatgen.analysis.bond_valence module","pymatgen.analysis.chemenv package","pymatgen.analysis.chemenv.connectivity package","pymatgen.analysis.chemenv.connectivity.connected_components module","pymatgen.analysis.chemenv.connectivity.connectivity_finder module","pymatgen.analysis.chemenv.connectivity.environment_nodes module","pymatgen.analysis.chemenv.connectivity.structure_connectivity module","pymatgen.analysis.chemenv.coordination_environments package","pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies module","pymatgen.analysis.chemenv.coordination_environments.coordination_geometries module","pymatgen.analysis.chemenv.coordination_environments.coordination_geometries_files package","pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder module","pymatgen.analysis.chemenv.coordination_environments.structure_environments module","pymatgen.analysis.chemenv.coordination_environments.voronoi module","pymatgen.analysis.chemenv.utils package","pymatgen.analysis.chemenv.utils.chemenv_config module","pymatgen.analysis.chemenv.utils.chemenv_errors module","pymatgen.analysis.chemenv.utils.coordination_geometry_utils module","pymatgen.analysis.chemenv.utils.defs_utils module","pymatgen.analysis.chemenv.utils.func_utils module","pymatgen.analysis.chemenv.utils.graph_utils module","pymatgen.analysis.chemenv.utils.math_utils module","pymatgen.analysis.chemenv.utils.scripts_utils module","pymatgen.analysis.chempot_diagram module","pymatgen.analysis.cost module","pymatgen.analysis.defects package","pymatgen.analysis.defects.core module","pymatgen.analysis.defects.corrections module","pymatgen.analysis.defects.defect_compatibility module","pymatgen.analysis.defects.dilute_solution_model module","pymatgen.analysis.defects.generators module","pymatgen.analysis.defects.thermodynamics module","pymatgen.analysis.defects.utils module","pymatgen.analysis.diffraction package","pymatgen.analysis.diffraction.core module","pymatgen.analysis.diffraction.neutron module","pymatgen.analysis.diffraction.tem module","pymatgen.analysis.diffraction.xrd module","pymatgen.analysis.diffusion_analyzer module","pymatgen.analysis.dimensionality module","pymatgen.analysis.elasticity package","pymatgen.analysis.elasticity.elastic module","pymatgen.analysis.elasticity.strain module","pymatgen.analysis.elasticity.stress module","pymatgen.analysis.energy_models module","pymatgen.analysis.eos module","pymatgen.analysis.ewald module","pymatgen.analysis.excitation module","pymatgen.analysis.ferroelectricity package","pymatgen.analysis.ferroelectricity.polarization module","pymatgen.analysis.fragmenter module","pymatgen.analysis.functional_groups module","pymatgen.analysis.gb package","pymatgen.analysis.gb.grain module","pymatgen.analysis.graphs module","pymatgen.analysis.hhi module","pymatgen.analysis.interface module","pymatgen.analysis.interface_reactions module","pymatgen.analysis.interfaces package","pymatgen.analysis.interfaces.coherent_interfaces module","pymatgen.analysis.interfaces.substrate_analyzer module","pymatgen.analysis.interfaces.zsl module","pymatgen.analysis.local_env module","pymatgen.analysis.magnetism package","pymatgen.analysis.magnetism.analyzer module","pymatgen.analysis.magnetism.heisenberg module","pymatgen.analysis.magnetism.jahnteller module","pymatgen.analysis.molecule_matcher module","pymatgen.analysis.molecule_structure_comparator module","pymatgen.analysis.nmr module","pymatgen.analysis.path_finder module","pymatgen.analysis.phase_diagram module","pymatgen.analysis.piezo module","pymatgen.analysis.piezo_sensitivity module","pymatgen.analysis.pourbaix_diagram module","pymatgen.analysis.prototypes module","pymatgen.analysis.quasiharmonic module","pymatgen.analysis.reaction_calculator module","pymatgen.analysis.solar package","pymatgen.analysis.solar.slme module","pymatgen.analysis.structure_analyzer module","pymatgen.analysis.structure_matcher module","pymatgen.analysis.structure_prediction package","pymatgen.analysis.structure_prediction.dopant_predictor module","pymatgen.analysis.structure_prediction.substitution_probability module","pymatgen.analysis.structure_prediction.substitutor module","pymatgen.analysis.structure_prediction.volume_predictor module","pymatgen.analysis.substrate_analyzer module","pymatgen.analysis.surface_analysis module","pymatgen.analysis.thermochemistry module","pymatgen.analysis.topological package","pymatgen.analysis.topological.spillage 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package","pymatgen.command_line.bader_caller module","pymatgen.command_line.chargemol_caller module","pymatgen.command_line.critic2_caller module","pymatgen.command_line.enumlib_caller module","pymatgen.command_line.gulp_caller module","pymatgen.command_line.mcsqs_caller module","pymatgen.command_line.vampire_caller module","pymatgen.core package","pymatgen.core.bonds module","pymatgen.core.composition module","pymatgen.core.interface module","pymatgen.core.ion module","pymatgen.core.lattice module","pymatgen.core.libxcfunc module","pymatgen.core.molecular_orbitals module","pymatgen.core.operations module","pymatgen.core.periodic_table module","pymatgen.core.sites module","pymatgen.core.spectrum module","pymatgen.core.structure module","pymatgen.core.surface module","pymatgen.core.tensors module","pymatgen.core.trajectory module","pymatgen.core.units module","pymatgen.core.xcfunc module","pymatgen.dao module","pymatgen.electronic_structure package","pymatgen.electronic_structure.bandstructure module","pymatgen.electronic_structure.boltztrap module","pymatgen.electronic_structure.boltztrap2 module","pymatgen.electronic_structure.cohp module","pymatgen.electronic_structure.core module","pymatgen.electronic_structure.dos module","pymatgen.electronic_structure.plotter module","pymatgen.entries package","pymatgen.entries.compatibility module","pymatgen.entries.computed_entries module","pymatgen.entries.correction_calculator module","pymatgen.entries.entry_tools module","pymatgen.entries.exp_entries module","pymatgen.entries.mixing_scheme module","pymatgen.ext namespace","pymatgen.ext.cod module","pymatgen.ext.crystalsai module","pymatgen.ext.jhu module","pymatgen.ext.matproj module","pymatgen.ext.optimade module","pymatgen.io namespace","pymatgen.io.abinit package","pymatgen.io.abinit.abiobjects module","pymatgen.io.abinit.abitimer module","pymatgen.io.abinit.inputs module","pymatgen.io.abinit.netcdf module","pymatgen.io.abinit.pseudos module","pymatgen.io.abinit.variable module","pymatgen.io.adf module","pymatgen.io.ase module","pymatgen.io.atat module","pymatgen.io.babel module","pymatgen.io.cif module","pymatgen.io.core module","pymatgen.io.cp2k package","pymatgen.io.cp2k.inputs module","pymatgen.io.cp2k.outputs module","pymatgen.io.cp2k.sets module","pymatgen.io.cp2k.utils module","pymatgen.io.cssr module","pymatgen.io.cube module","pymatgen.io.exciting package","pymatgen.io.exciting.inputs module","pymatgen.io.feff package","pymatgen.io.feff.inputs module","pymatgen.io.feff.outputs module","pymatgen.io.feff.sets module","pymatgen.io.fiesta module","pymatgen.io.gaussian module","pymatgen.io.jarvis module","pymatgen.io.lammps package","pymatgen.io.lammps.data module","pymatgen.io.lammps.inputs module","pymatgen.io.lammps.outputs module","pymatgen.io.lammps.utils module","pymatgen.io.lmto module","pymatgen.io.lobster package","pymatgen.io.lobster.inputs module","pymatgen.io.lobster.lobsterenv module","pymatgen.io.lobster.outputs module","pymatgen.io.nwchem module","pymatgen.io.packmol module","pymatgen.io.phonopy module","pymatgen.io.prismatic module","pymatgen.io.pwscf module","pymatgen.io.qchem package","pymatgen.io.qchem.inputs module","pymatgen.io.qchem.outputs module","pymatgen.io.qchem.sets module","pymatgen.io.qchem.utils module","pymatgen.io.shengbte module","pymatgen.io.template module","pymatgen.io.vasp package","pymatgen.io.vasp.help module","pymatgen.io.vasp.inputs module","pymatgen.io.vasp.outputs module","pymatgen.io.vasp.sets module","pymatgen.io.wannier90 module","pymatgen.io.xcrysden module","pymatgen.io.xr module","pymatgen.io.xtb package","pymatgen.io.xtb.inputs module","pymatgen.io.xtb.outputs module","pymatgen.io.xyz module","pymatgen.io.zeopp module","pymatgen.optimization package","pymatgen.optimization.linear_assignment module","pymatgen.optimization.linear_assignment_numpy module","pymatgen.optimization.neighbors module","pymatgen.phonon package","pymatgen.phonon.bandstructure module","pymatgen.phonon.dos module","pymatgen.phonon.gruneisen module","pymatgen.phonon.ir_spectra module","pymatgen.phonon.plotter module","pymatgen.symmetry package","pymatgen.symmetry.analyzer module","pymatgen.symmetry.bandstructure module","pymatgen.symmetry.groups module","pymatgen.symmetry.kpath module","pymatgen.symmetry.maggroups module","pymatgen.symmetry.settings module","pymatgen.symmetry.site_symmetries module","pymatgen.symmetry.structure module","pymatgen.transformations package","pymatgen.transformations.advanced_transformations module","pymatgen.transformations.defect_transformations module","pymatgen.transformations.site_transformations module","pymatgen.transformations.standard_transformations module","pymatgen.transformations.transformation_abc module","pymatgen.util package","pymatgen.util.convergence module","pymatgen.util.coord module","pymatgen.util.coord_cython module","pymatgen.util.io_utils module","pymatgen.util.num module","pymatgen.util.plotting module","pymatgen.util.provenance module","pymatgen.util.serialization module","pymatgen.util.string module","pymatgen.util.testing module","pymatgen.util.typing module","pymatgen.vis package","pymatgen.vis.plotters module","pymatgen.vis.structure_chemview module","pymatgen.vis.structure_vtk module","References","Development 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\ No newline at end of file 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00f3nsson":290,"long":[1,3,44,51,85,153,188,199,200,233,239,260,292],"lua\u00f1a":139,"mart\u00edn":139,"n\u00f8rskov":161,"new":[1,2,3,5,12,13,26,43,48,49,51,55,56,62,63,67,70,71,79,81,86,87,98,99,101,102,103,117,119,139,146,149,156,157,158,160,168,170,173,182,183,186,187,188,190,192,197,199,201,212,221,224,225,230,231,232,235,238,239,240,258,261,272,280,281,285,292],"null":79,"o\u00b2":283,"okuli\u010d":179,"p2\u2081":283,"pend\u00e1":139,"public":[3,4,6,44,56,92,157,240,280,290],"quir\u00f3":179,"ren\u00e8":291,"return":[1,3,4,6,11,12,13,15,16,17,20,21,22,23,25,26,28,29,30,32,34,35,36,37,38,39,40,41,43,44,45,46,48,49,51,52,53,54,55,56,58,59,60,61,62,63,66,67,68,70,71,74,78,79,81,82,83,84,85,86,87,88,89,90,91,92,93,94,96,97,98,100,101,102,103,105,106,109,110,112,113,116,117,118,119,120,122,123,127,130,137,138,139,141,142,143,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,164,165,167,168,169,170,171,172,173,175,176,177,179,180,182,183,186,187,188,189,190,191,192,193,194,195,196,197,199,200,201,202,203,204,206,208,209,210,211,212,213,215,217,219,221,222,223,224,225,226,227,228,230,231,233,234,237,238,239,240,241,242,243,245,247,248,251,252,254,255,256,257,258,260,261,262,263,265,266,267,269,270,271,272,273,275,276,277,278,279,280,281,282,283,284,287,288,289],"rodr\u00edguez":152,"se\u00e1n":291,"short":[44,51,79,145,230,240,248],"static":[1,12,13,25,44,45,53,70,71,79,82,83,84,85,87,91,93,94,97,101,105,108,109,141,143,145,146,149,150,152,153,158,165,168,172,177,182,186,190,191,192,193,194,195,196,199,200,201,203,206,208,209,210,211,212,213,221,224,228,230,231,238,239,240,241,243,245,247,248,261,263,265,269,272,280,281,284,292],"super":[20,55,71,77,78,113,118,119,155,157,199,201],"switch":[1,3,170,201,269],"throw":[58,89,239,272],"transient":182,"true":[1,2,11,12,13,15,16,20,22,25,26,28,29,30,34,37,39,40,43,44,45,48,49,51,52,54,56,58,62,66,67,68,70,71,74,76,79,81,83,84,85,87,88,89,91,93,96,98,101,102,103,105,108,109,110,116,117,118,119,120,122,138,139,141,143,146,147,148,149,150,152,153,154,156,157,158,159,164,165,167,168,169,170,172,174,175,177,182,186,187,188,189,190,192,195,196,197,199,200,201,208,210,211,212,215,219,221,222,223,226,231,233,238,239,240,242,243,254,256,257,258,260,262,263,269,271,272,273,275,276,277,278,279,280,282,283,284,288,289],"try":[1,2,5,12,37,47,58,67,71,81,82,139,165,169,182,190,238,239,269,289],"universit\u00e4t":291,"universit\u00e9":291,"var":188,"void":[1,248],"while":[0,2,3,5,11,25,29,34,45,66,70,76,79,84,85,105,116,137,156,157,170,182,200,201,215,217,238,239,272,292],A:[1,2,3,4,6,11,12,13,15,17,25,26,28,29,34,37,40,43,44,48,49,51,55,56,61,62,63,64,66,67,70,71,72,74,77,78,79,81,84,86,88,91,92,94,96,97,98,100,101,102,103,105,106,108,110,112,113,116,117,118,119,120,122,127,129,137,138,139,141,142,143,145,146,147,148,149,151,152,153,154,155,156,157,158,159,160,164,165,167,168,169,170,171,172,173,174,175,176,177,179,180,181,182,183,186,187,188,190,192,195,196,197,199,200,201,203,206,208,211,212,215,221,224,225,226,228,230,232,233,234,237,238,239,240,248,250,251,254,255,256,257,258,260,262,263,264,265,267,269,271,272,276,280,281,283,284,287,288,289,290,292],AND:[4,6,11,153,157,239,240],AS:[4,6],ASE:[1,5,62,193],AT:142,And:[79,239],As:[2,4,5,6,29,56,66,71,79,85,103,105,153,182,199,201,239,240,269,292],At:[3,4,6,56,85,97,105,153,201,218,240],BE:[4,6],BUT:[4,6],Be:[1,56,85,153,240],Being:66,But:[1,4,6,49,70,201,248,260,269,271,292],By:[5,11,12,13,37,49,53,55,66,70,71,74,88,91,94,122,139,147,156,157,165,169,170,190,200,201,230,238,239,260,269,283,284],FOR:[4,6,157],For:[1,2,3,4,5,6,11,12,17,20,25,26,29,34,40,41,43,44,49,53,54,55,56,58,66,70,71,78,79,84,88,94,97,98,100,105,106,109,117,118,119,122,137,138,139,141,145,146,147,148,149,152,153,156,157,160,161,165,168,169,170,171,172,173,175,176,180,182,183,186,187,188,190,195,199,200,201,202,204,212,215,216,221,223,224,225,228,232,233,238,239,240,248,252,260,262,269,271,272,281,283,286,287,289,290,292],IN:[4,6],IS:[4,6],If:[1,2,3,4,5,6,11,12,15,16,20,28,29,30,34,37,40,43,44,45,48,49,51,52,53,54,55,56,58,62,67,68,70,71,74,79,81,83,85,87,88,91,92,98,100,101,102,105,109,110,112,116,117,118,119,120,122,123,137,138,139,140,141,143,145,146,147,148,149,153,154,155,156,157,158,161,164,165,167,168,169,170,172,173,174,175,177,179,182,186,188,189,190,192,195,196,197,199,200,201,204,210,211,212,215,221,223,224,225,226,231,232,233,234,238,239,240,248,252,254,255,256,257,258,260,261,262,263,269,271,272,273,276,278,280,284,287,289,290,291,292],In:[1,3,4,5,6,28,29,34,40,56,71,74,84,85,87,88,92,97,103,110,139,146,149,152,153,156,157,158,169,170,172,177,182,188,196,199,201,204,225,230,232,238,239,240,243,247,263,264,292],Is:157,Ising:61,It:[0,1,3,4,5,6,13,16,17,45,49,55,56,63,66,70,71,77,79,82,84,88,102,105,113,117,122,123,146,147,149,156,157,158,159,160,161,164,165,167,169,170,172,174,177,180,183,187,188,199,201,212,215,219,220,236,238,239,240,250,251,254,260,262,263,269,271,272,276,281,292],Its:226,NO:[4,6],NOT:[4,6,41,43,49,71,88,188,201,215,232,239,240],Near:182,No:[1,11,25,26,35,37,55,56,61,63,98,116,153,156,179,215,216,238,272],Not:[5,20,25,88,156,183,186,196,215,269,270],OF:[4,6,92,232],ON:5,ONE:215,OR:[4,6,48,182],Of:196,On:[4,6,122,240],One:[4,6,34,56,117,156,170,186,201,231,238,239,248,258,260,269],Or:[98,152,281],Such:85,THE:[4,6,157],THe:169,TO:[4,6,157],That:[70,79,97,155],The:[1,2,3,4,5,6,11,12,13,15,17,20,25,26,28,29,30,34,36,37,40,42,45,46,47,48,49,51,52,53,54,55,56,58,61,62,63,66,67,68,70,71,72,74,78,79,84,85,87,88,89,91,92,93,94,96,97,98,100,101,102,105,106,108,109,110,112,113,117,118,119,120,121,122,123,137,139,145,146,147,148,149,151,152,153,154,155,156,157,159,160,161,162,164,165,167,168,169,170,172,173,177,179,180,181,182,183,186,188,189,190,191,192,193,195,196,197,199,200,201,202,204,208,209,210,211,212,215,216,217,218,219,222,223,224,225,226,228,230,232,233,234,238,239,240,241,248,250,251,254,255,256,257,258,259,260,261,262,263,264,268,269,271,272,274,278,279,280,281,283,284,286,287,289,290,291],Their:[84,145],Then:[1,2,3,5,49,82,199,202,260,284],There:[1,2,3,4,6,71,84,102,105,122,149,156,157,164,168,204,221,239,254,263,264,269,292],These:[1,4,6,26,29,56,58,63,71,78,88,109,180,182,196,199,201,212,223,226,239,240,291,292],To:[3,4,6,40,45,55,66,70,84,88,105,118,139,141,148,156,168,170,172,182,183,187,210,211,216,219,230,232,238,239,240,255,262,264,269,292],WILL:157,WITH:[4,6,157,164,254,256,272],Will:[1,63,71,81,83,157,197,199,200,201,208,221,223,239,256,258,269,272,283],With:[0,1,3,4,5,6,79,196,201,260,275],_:[1,13,55,182,190,215,240,283,290],__:201,__eq__:284,__getattr__:188,__getitem__:146,__hash__:1,__init__:[13,58,59,60,70,86,89,90,113,155,156,157,158,172,179,197,230,234,240],__main__:1,__module__:292,__name__:[1,292],__new__:[58,59,60,86,89,90,158,160],__repr__:1,__rmul__:1,__slots__:282,__str__:[146,197,208,212,225,230,238,283],_additional_condit:25,_angle_cutoff:25,_array_lik:[113,149,152,155,156,169,238],_b:170,_bp:239,_calculate_possible_shift:157,_cgraph:1,_comput:88,_continuous_symmetry_measure_cutoff:25,_decor:177,_del:210,_distance_cutoff:25,_ds1_:188,_ev:239,_extrema_df:49,_figur:[53,174],_filter_and_sort_entri:177,_get_nn_shell_info:79,_io:[187,190],_map:88,_materialsproject:[182,281],_matrix:63,_name_compat:174,_name_compatibilityuncertainti:174,_nested_sequ:[113,149,152,155,156,169,238],_nestedsequ:[113,149,152,155,156,169,238],_optimad:183,_parse_bool:238,_parse_float:238,_parse_int:238,_parse_list:238,_parse_str:238,_path:186,_pickl:282,_proj_height:157,_set:240,_site:156,_sl_vector:78,_sp:102,_supportsarrai:[113,149,152,155,156,169,238],_threshold:102,a1604:58,a1826:58,a1:[25,49,260],a1fdb1089d0727f415416ec8082246ba:240,a1fit:192,a2:[1,25,49,70,212,260,269],a2b2:1,a2c9485ea86b2a7cf175077e6e5c7b3:240,a32:70,a35:79,a38:70,a395eb3aaf2fcab12fac3030a1146f61:240,a3:[49,260],a40:70,a45:70,a604ea3c6a9cc23c739b762f625cf449:240,a67:240,a6fd9a46aec185f4ad2acd0cbe4ae2fa:240,a74:240,a9182d436a13194b744640ac940ab9b0:240,a_1:[149,156,239],a_1a:239,a_1c:239,a_1p:239,a_2:[149,156],a_3:[149,156,261,263],a_i:54,a_pw:239,a_tot:239,a_vib:93,a_xb_1:92,a_xi:279,a_xx:279,a_xz:279,a_yi:279,a_yz:279,a_zz:279,aa:[25,34,79,209,226],aa_i:34,aaa1000x:201,aachen:291,aaron:240,ab5424:1,ab:[66,91,146,165,169,170,239,276,279],ab_shift:[70,269],abandon:[1,183],abbrevi:[81,255,262],abc3:146,abc:[4,6,51,59,62,117,146,149,154,156,158,160,170,175,187,188,190,197,208,257,258,262,271,272,284],abcd:34,abcdefghijklmnopqrstuvwxyz0123456789:275,abcissa:212,abdulnour:63,aberr:53,abi:188,abi_arg:188,abi_kwarg:188,abi_object:188,abil:[1,48,199],abinit:[1,4,6,8,9,149,161,182,184,257,292],abinit_input:188,abinithead:189,abinitinput:188,abinitio:1,abinitixc_to_libxc:161,abinittim:187,abinittimerpars:187,abinittimerparsererror:187,abinittimersect:187,abiobject:[8,9,184,185],abipi:[188,256,257],abitim:[8,9,184,185],abivar:[149,156,186,188],abl:[2,5,48,66,70,84,153,261,269],abo3:[88,292],abo:187,aborpt:209,about:[1,2,20,25,28,29,34,41,70,79,94,105,139,152,156,157,161,164,165,173,177,182,183,199,204,222,223,225,239,247,281],abov:[3,4,5,6,15,16,20,25,49,58,68,74,83,88,91,93,120,139,147,157,172,174,175,186,201,232,240,272,291,292],abridg:204,abs_cap:279,abs_tol:169,abscissa:212,absenc:196,absent:58,absent_sym:58,absolut:[3,4,6,29,30,34,43,51,52,54,81,88,117,146,152,157,158,160,169,190,209,239,240,260,261,263,276,279],absorb:[96,112,157,182,208,209,210,269],absorbance_in_inverse_centimet:96,absorbing_atom:[208,209,210],absorbing_el:[112,182],absorbing_index:112,absorpt:[1,96,111,112,157,182,209,210,239,287],absorption_coeffici:96,abstractchemenvalgorithm:26,abstractchemenverror:33,abstractchemenvstrategi:25,abstractcompar:98,abstractdiffractionpatterncalcul:[51,52,53,54],abstractdron:[122,123],abstractelectrod:[117,118,119,120],abstractenvironmentnod:22,abstractfeffinputset:210,abstractgeometri:28,abstractinput:188,abstractmolatommapp:84,abstractratiofunct:36,abstractstructurefilt:[11,12],abstracttransform:[12,269,270,271,272,273],abstractvoltagepair:[117,118,119],abund:25,ac:[4,5,6,25,28,29,30,48,56,74,81,85,91,96,143,153,168,180,240],ac_:5,academ:2,acc_err:165,acc_factor:[61,63],acc_thr:165,acceler:[290,291],accept:[3,13,149,168,169,186,188,189,190,199,201,215,239,258,269,271,272,276,280],acceptor:44,access:[1,3,29,32,79,139,179,182,183,190,195,199,200,223,224,228,233,238,239,262,272,278],accident:1,accommod:[116,157],accomplish:292,accord:[1,15,26,53,56,58,59,60,78,79,84,86,88,89,90,91,105,112,145,146,153,156,158,164,165,170,177,186,187,188,189,190,199,202,215,226,239,254,260,261],accordingli:[40,55,85,140,157],account:[1,3,26,43,48,49,53,54,79,81,105,149,151,156,157,164,165,201,239,254,256,260,276,277],accur:[1,70,71,81,91,138,165,182,201,239,240,269,271],accuraci:[1,63,165,188,190,199,201,232,240,248,271,272],acel:[149,186],acet:68,acetonitril:232,achiev:[84,158,165,272],acid:[179,232],acknowledg:[1,4,6,85,239,290],aconvasp:[1,2,5],aconvasp_cal:5,acoust:[90,254,256],acoustic_debye_temp:256,acquir:173,across:[1,66,79,88,117,118,119,146,210,240],acrutt:1,act:[97,152,264],acta:[26,28,36,70,79,149],actinid:[146,148,153,280],actinoid:[146,153],action:[1,4,6],activ:[2,4,5,6,83,110,116,168,199,201,280],activate_fast_minim:201,activate_hybrid:201,activate_mot:201,activate_nonperiod:201,activate_robust_minim:201,activate_very_strict_minim:201,actual:[1,11,48,49,63,66,67,70,71,79,88,91,116,147,149,153,154,156,157,159,173,180,199,208,211,216,228,238,239,260,271,272,273,284,292],actual_kpoint:239,actual_kpoints_weight:239,ad:[1,2,4,5,6,12,15,23,25,29,43,47,49,55,59,68,71,79,103,109,117,138,146,156,157,170,182,188,195,199,201,212,215,226,232,239,240,258,262,269,271,283,288,289,292],adam:[1,113,149,291],adapt:[5,44,62,81,105,222,224,256,257,280],adapt_extremum_to_add_cond:222,adaptor:[1,193,195,213,292],add:[1,4,5,6,12,13,15,17,23,25,26,28,29,34,51,53,58,59,62,63,67,70,71,79,83,88,105,120,131,139,146,155,156,157,159,167,170,172,173,175,182,187,188,192,195,199,222,225,226,230,232,238,240,248,257,258,261,269,271,280,282,287,289,292],add_abiobject:188,add_adsorb:15,add_adsorbate_atom:157,add_b:170,add_bond:[23,289],add_charges_from_oxi_state_guess:146,add_cohp:170,add_cohp_dict:170,add_config_var:131,add_coord_geom:29,add_dens:169,add_do:[170,258],add_dos_dict:[170,258],add_edg:[71,289],add_electrod:120,add_eq:58,add_fac:289,add_fig_kwarg:[170,280],add_hydrogen:195,add_last:201,add_lin:289,add_m_list:63,add_neighbors_set:29,add_opposit:26,add_opt:192,add_oxidation_st:63,add_oxidation_state_by_el:156,add_oxidation_state_by_guess:156,add_oxidation_state_by_sit:156,add_oxidation_state_by_site_fract:17,add_partial_spher:289,add_pick:289,add_picker_fix:289,add_polyhedron:289,add_sit:[23,289],add_site_properti:[156,240],add_sourc:29,add_spectra:287,add_spectrum:287,add_spin_by_el:[156,240],add_spin_by_sit:156,add_strategy_visualization_to_subplot:25,add_subkei:192,add_tag:13,add_text:289,add_triangl:289,addadsorbatetransform:269,added_kpoint:240,addit:[1,4,5,6,12,13,25,26,28,29,30,35,43,49,53,62,67,70,71,77,79,87,94,109,141,142,146,147,148,152,155,156,157,160,173,174,182,183,189,193,196,197,199,206,212,215,216,222,224,226,234,240,248,254,256,269,281,283,291],addition:[16,240],additional_argu:[4,6],additional_condit:[25,28,29,30,32,222],additional_info:[25,26],additional_response_field:183,additionalcondit:[25,29,30,35],additionalconditionint:25,addnew_from:188,addon:[1,3,4,6,105],address:[1,182,240,290],address_basis_fil:[221,240],address_basis_file_max:221,address_basis_file_min:221,addsitepropertytransform:271,adengz:[1,291],adf:[1,8,9,184],adf_run:192,adfinput:192,adfinputerror:192,adfkei:192,adfoutput:192,adfoutputerror:192,adftask:192,adj_per_atom:173,adj_per_deg:173,adjac:[56,66,79,117,118,119],adjacent_onli:[117,118,119],adjstment:172,adjust:[40,66,79,96,105,165,172,173,177,182,199,210,239,260],admm:[201,202],adn:5,adopt:[2,3,4,6,225,239],adour:291,ads_coord:15,ads_entries_dict:105,ads_entry1:105,ads_entry2:105,adsorb:[15,105,147,157,269],adsorb_both_surfac:15,adsorbatesitefind:[1,15,269],adsorpt:[1,8,9,14,105,157],adsorption_sit:15,adsorptionsitefind:269,adv:[138,240],advanc:[4,5,6,139,168,172,182,183,269,290,291,292],advanced_transform:[5,8,9,268],advantag:[1,4,6],advic:5,advis:[5,44,269],aea79f322180fa6f0bfa74cb2a156dcf:240,aecar0:139,aecar2:139,aeccar0:[137,138,139],aeccar2:[137,139],aeccar:[49,137,138,139],affect:[1,3,156],affin:[152,156],affine_matrix:152,affine_transform:152,affine_transformation_matrix:152,afloat:283,aflow:[1,92,122,183],aflowprototypematch:92,afm:[81,82,186,188],afm_:82,afm_struct:82,afresh:79,after:[1,2,4,5,6,12,16,28,43,48,49,55,61,63,70,71,81,88,98,102,113,152,153,157,165,170,174,182,196,199,202,212,225,239,260,269,278],afterward:5,ag:[1,5,56,85,153,240],ag_sv_gw:240,again:[5,172,182,281],against:[1,44,55,92,105,145,172,182,238],agent:[1,182],aggreg:49,aggress:201,agka1:54,agka2:54,agka:54,agkb1:54,agr:110,agte3:91,ai:[1,180],aid:3,aiida:[1,183],aim:[67,83,195,269],aimd:55,ajjackson:1,aka:[67,149],al2o3:182,al3:269,al3sc:46,al:[1,5,36,44,47,48,49,55,56,72,79,81,85,91,93,97,137,153,161,165,169,170,172,173,182,183,239,240,261,290],al_gw:240,al_structur:186,alamo:291,alan:[1,290,291],alat:219,albalu:[1,291],alchemi:[1,8,9,271,272,273,284],alex:[1,113,291],alexand:[278,291],algebra:48,algo:[1,28,29,63,71,103,149,186,195,240,271,272],algo_:[271,272],algo_best_first:[63,271,272],algo_complet:[63,271,272],algo_enumer:[271,272],algo_fast:[63,271,272],algo_time_limit:63,algorithm:[1,3,11,15,17,20,26,28,29,40,47,48,49,52,54,56,58,66,68,70,71,75,77,78,79,82,84,87,88,97,98,101,102,116,137,140,147,149,156,157,169,186,188,195,199,201,224,226,232,238,239,240,248,250,251,252,260,269,271,272,276,290],algorithm_typ:26,alia:[71,79,81,86,142,160,183,187,188,189,199,238,258],alias:[1,161,183,199,201],aliases_or_resource_url:183,align:[15,28,34,44,84,86,149,170,204,208,238,248,283],aligned_lattic:149,aligned_matrix:149,alio_tol:269,alireza:1,alkali:[146,153,240],alkalin:[146,153,190],all:[1,2,3,4,5,6,11,12,13,15,16,17,25,26,28,29,30,34,35,36,37,38,43,44,45,48,49,51,52,53,54,55,56,58,62,63,66,67,68,70,71,74,77,78,79,81,84,87,88,91,94,96,98,102,103,105,109,110,112,113,115,116,117,118,119,120,122,130,131,139,142,145,146,149,153,154,155,156,157,158,159,160,164,165,167,168,169,170,171,172,173,174,175,176,177,179,181,182,183,186,187,188,189,190,192,195,196,197,199,200,201,210,211,212,215,216,221,222,223,224,226,228,230,231,232,233,237,238,239,240,246,247,252,254,255,257,258,260,261,262,263,264,266,267,269,271,272,275,276,277,278,281,284,287,289,292],all_cg:1,all_combin:70,all_combinations_for_el:190,all_comp:94,all_coord:[49,149,252],all_csm:28,all_dist:276,all_energi:239,all_entri:[88,91,94],all_entries_hulldata:88,all_famili:150,all_fil:190,all_geometri:26,all_geometries_latex:26,all_geometries_latex_imag:26,all_in_polar:66,all_input:[2,210],all_kind:150,all_molecul:247,all_nbs_sit:[29,222],all_nbs_sites_indic:29,all_nninfo:79,all_options_dict:25,all_oxi_st:146,all_simple_path:20,all_slab_entri:105,all_stable_entri:48,all_structur:272,all_unstable_entri:48,all_weight:71,allcoordinationgeometri:26,allen:110,allnc:190,allocations_kei:234,alloi:[140,269],allow:[1,2,3,4,5,6,12,13,15,25,26,29,30,37,40,43,46,52,53,54,58,66,70,74,78,79,84,87,88,91,94,98,109,116,117,118,119,145,146,147,154,156,157,159,160,165,167,170,172,175,177,181,182,199,201,212,215,220,221,224,230,232,236,238,239,240,269,271,272,273,276,277,290,292],allow_additional_charge_separ:16,allow_multi:190,allow_neg:[88,146],allow_patholog:79,allow_revers:71,allow_subset:98,allow_unst:[118,174],allowed_doping_speci:269,allowed_funct:36,allowed_hints_typ:26,allowed_valu:25,allpaw:190,allr:79,allsq:142,almost:[1,146,199,239,271,284,292],almost_equ:146,alon:199,along:[1,15,49,56,66,70,74,87,88,97,105,109,117,119,147,149,157,158,164,165,168,170,186,188,200,204,206,226,228,234,238,239,240,254,258,261,263,269,289],along_c:105,alpha:[15,25,36,38,70,101,102,105,110,149,156,157,170,196,199,200,211,212,239,263,269,272,292],alphabet:[71,88,146,148,208,238],alphabetical_formula:[146,148],alreadi:[3,4,5,6,12,13,23,26,28,29,34,45,49,56,63,84,88,94,102,105,117,143,146,147,157,160,177,188,197,200,260,269,292],also:[1,2,3,4,5,6,13,16,26,34,40,43,44,45,59,67,70,71,74,79,84,87,88,90,93,97,98,110,117,118,119,122,123,139,141,146,148,149,150,152,154,156,157,158,160,165,167,168,169,172,182,187,188,196,199,200,201,202,208,215,221,232,233,238,239,240,255,256,261,263,269,271,272,276,291,292],alt:71,alter:[12,13,71,215,240,261],alter_edg:71,altern:[1,2,5,12,13,26,63,67,87,153,167,170,174,177,187,188,201,216,224,239,258,262,269,287],alternate_direct:224,alternative_nam:26,although:[2,84,87],alwai:[2,3,4,6,34,49,71,83,84,91,97,98,105,117,153,156,157,165,168,172,177,182,199,200,215,224,238,239,260,261,275,292],am05:[161,238],am:[56,79,85,153,238,240],amanda:291,ambigu:[146,233,238],amend:71,american:[40,179],among:[16,56,191,232],amongst:25,amorph:[97,240],amount:[41,45,59,88,94,97,98,116,119,146,148,156,164,171,173,199,239,283,292],amount_tol:88,amount_toler:146,amp:74,amplitud:[156,269],amt:[59,94,98,146,171,173,176],amu:[153,160],an:[0,1,2,3,4,5,6,11,12,13,15,16,17,21,22,25,26,28,29,30,34,40,41,43,47,49,54,55,56,58,59,61,62,63,64,66,67,68,70,71,74,78,79,81,83,84,87,88,89,90,91,92,93,94,96,97,98,102,103,105,106,109,113,114,116,117,118,119,120,122,123,126,137,138,139,140,141,143,146,147,148,149,150,152,153,154,155,156,157,158,159,160,161,164,165,167,168,169,170,171,172,173,174,175,176,177,179,180,181,182,183,186,188,189,190,191,192,195,197,199,201,202,204,206,208,210,211,212,215,216,219,223,224,225,226,228,230,231,232,233,234,235,238,239,240,243,245,247,248,250,251,255,257,258,260,261,262,264,265,267,269,271,272,273,275,276,278,279,280,281,282,283,284,287,289,290,291,292],an_dw:165,an_up:165,anaconda:5,analogu:1,analys:[1,4,5,6,17,45,49,50,55,69,79,97,138,163,171,173,182,222,292],analysi:[0,1,2,3,4,5,6,8,9,11,116,118,119,121,129,130,137,138,139,145,149,156,157,159,165,169,173,175,176,177,182,192,199,200,222,224,232,238,239,240,248,253,266,269],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condens:[138,146],condit:[1,4,6,25,28,29,30,35,54,56,58,68,87,88,90,91,141,149,154,156,177,182,190,200,222,263,276,277,292],condition_descript:35,conditional_probability_list:102,condten:165,conduct:[4,6,55,93,153,157,165,170,211,224,234,239,256],conductor:[49,55,183,240],conf_cutoff:195,confab:195,confab_conform:195,confid:117,config:[1,3,4,5,6,131,153,172,210,238,240],config_dict:[210,240],config_fil:172,configur:[1,5,15,26,32,81,82,84,105,131,140,153,186,201,208,224,238,240,269],configure_pmg:131,confin:72,confirm:[43,66,177],conflict:[2,3],conform:[1,68,195,230,248],confus:269,congruenc:[199,201],conjug:[186,195,199,201],conjunct:[103,169],connect:[1,4,6,8,9,14,18,25,56,68,71,85,87,97,109,139,152,156,182,201,218,230,231,232,238,261,269],connected_compon:[9,14,18,19],connected_matrix:56,connectedcompon:20,connectedsit:71,connectivity_arrai:97,connectivity_find:[9,14,18,19],connectivity_graph:23,connectivityfind:21,conp:141,conrad:291,consecut:[159,209,218],consequ:[79,91],conserv:[2,188,190,201],consid:[1,4,6,16,20,23,28,30,34,40,43,45,47,48,49,55,56,62,74,77,78,79,83,87,88,91,93,97,98,102,105,110,116,122,141,145,149,152,156,157,164,167,169,170,177,182,183,195,201,212,216,222,239,252,256,260,269,272,279,289,290],consider:[29,45,55,72,116,123,240,277],consist:[1,28,48,58,70,74,88,152,157,158,164,168,170,172,186,199,201,204,210,215,238,239,240,243,245,272,284,292],consitu:151,consolid:[1,182],constant:[1,17,36,44,49,52,55,58,79,86,87,90,93,96,98,105,157,160,165,170,172,173,200,212,224,226,232,234,238,239,240,255,258],constant_lattic:159,constantenergyadjust:173,constantli:[1,2,292],constitu:151,constitut:[26,46,55,58,153,201,280],constrain:[40,88,168,186,240,245],constrain_latt:156,constrain_total_magmom:240,constrained_c_frac:49,constrains_templ:245,constraint:[1,49,90,91,186,199,201,230,232,240,245,269],construct:[1,5,15,29,30,34,36,37,40,48,49,56,58,59,66,71,75,76,79,82,88,91,118,137,139,146,148,156,158,160,172,173,182,186,188,189,192,197,199,216,222,223,225,230,238,239,240,256,265,269,289,292],constructor:[1,13,16,20,21,22,23,25,26,28,29,30,36,55,58,59,60,67,71,79,84,86,88,89,90,93,109,118,137,146,149,152,156,157,158,159,165,173,174,186,193,199,201,215,216,217,222,226,234,238,239],consult:[3,4,5,6,71,139,182,195,199,291,292],consum:[28,271],consumpt:1,contact:[239,240],contain:[1,2,4,6,11,12,13,23,25,26,28,29,30,32,33,34,35,36,37,38,39,40,43,44,49,56,63,66,68,70,71,74,79,84,88,91,92,96,97,98,102,105,106,110,113,115,117,118,119,121,122,123,124,136,137,139,141,143,144,146,148,149,151,153,156,157,160,163,164,165,167,169,170,171,172,173,174,175,176,177,182,186,187,188,189,190,192,195,197,199,200,201,205,206,208,209,211,212,215,216,217,219,222,225,226,231,235,238,239,240,241,245,248,251,254,255,257,260,261,263,264,271,272,276,277,280,281,289,290,292],contains_element_typ:146,contains_only_one_anion:29,contains_only_one_anion_atom:29,contains_peroxid:97,containsspeciefilt:11,contcar:[109,122,156,238,292],content:[8,9,14,84,158,165,184,190,194,197,200,212,225,247,248],context:[1,168,182],continu:[1,2,3,4,6,25,26,28,29,36,48,98,169,170,222,261],continuous_symmetry_measure_cutoff:[25,32],continuum:[4,6,230],contirbut:239,contour:88,contract:[4,6,186,224,273,284],contrast:169,contribut:[0,1,2,44,48,51,58,66,79,91,93,105,167,170,201,223,224,239,254,255,256,258,287,290,291],contributor:[1,4,6,157],control:[3,34,51,62,98,123,130,132,154,170,181,186,187,199,201,208,210,224,228,234,245,257,258,292],control_dict:234,control_param:225,conv:[1,275],conv_fact:63,conveni:[1,2,4,6,13,15,43,49,55,62,66,70,81,83,94,118,123,127,129,137,138,139,146,149,156,157,158,159,161,167,168,175,182,183,186,199,212,238,239,240,272,280,281,283,285,292],convent:[1,3,37,56,58,66,70,77,109,110,117,137,138,141,146,152,157,161,164,182,183,186,189,196,200,201,202,204,206,219,238,240,254,256,260,261,263,264,270,272,288],conventional_unit_cel:182,conventionalcelltransform:272,converg:[1,8,9,44,49,55,61,63,87,88,90,105,141,157,158,165,169,199,200,201,210,232,234,239,240,274,290],converged_electron:239,converged_ion:239,convergence_angl:210,convers:[1,53,55,58,87,88,117,118,124,149,158,160,193,203,213,258,292],conversion_batteri:[8,9,114,115],conversion_electrod:118,conversionelectrod:[2,115,118],conversionvoltagepair:118,convert:[1,4,6,15,49,55,56,58,59,63,66,67,71,76,78,79,88,94,96,98,105,122,135,137,146,149,153,156,158,159,160,161,168,170,172,182,186,187,188,189,190,192,196,200,208,215,219,224,226,228,231,233,238,239,260,261,268,276,280,283,292],convert_fmt:135,convert_gpa_to_ev:58,convert_strain_to_deform:59,convert_to_iee:158,convert_to_muc_per_cm2:66,convex:[40,41,74,88,110,117,118,119,182],convexhul:[1,110],coo19128:208,coo:[202,208],cookbook:283,cool:292,coop:[167,170,221,223],coopcar:[167,223],coord:[1,4,6,8,9,28,29,34,49,66,70,71,79,84,88,97,110,139,147,149,154,156,157,164,170,199,208,212,225,226,233,239,254,256,260,265,271,274,277,289,292],coord_cython:[8,9,274],coord_geom:29,coord_left:53,coord_list:276,coord_list_map:276,coord_list_mapping_pbc:[276,277],coord_precis:247,coord_right:53,coord_typ:238,coord_util:1,coordin:[1,4,6,15,20,21,22,24,25,26,27,28,29,34,36,39,40,44,47,49,53,63,66,70,71,79,83,84,87,88,97,98,105,109,139,141,147,149,151,152,153,154,156,157,159,164,165,170,195,197,199,201,204,212,215,216,219,222,223,224,225,226,233,234,238,239,240,245,247,248,252,254,256,260,263,265,271,272,276,277,289,292],coordinate_fil:215,coordination_environ:[8,9,14,18,22,222],coordination_environments_atom_pres:29,coordination_environments_ion_pres:29,coordination_geometri:[9,14,18,24,28],coordination_geometries_fil:[9,14,18,24],coordination_geometry_find:[9,14,18,24],coordination_geometry_symmetry_measur:28,coordination_geometry_symmetry_measures_fallback_random:28,coordination_geometry_symmetry_measures_separation_plan:28,coordination_geometry_symmetry_measures_separation_plane_optim:28,coordination_geometry_symmetry_measures_sepplane_optim:28,coordination_geometry_symmetry_measures_standard:28,coordination_geometry_util:[9,14,18,31],coordination_no:269,coordination_numb:[26,28],coordination_sequ:20,coordinationgeometri:26,coords1:276,coords2:276,coords_a:149,coords_are_cartesian:[28,66,70,71,147,149,154,156,157,164,170,254,256,263,271],coords_are_displac:159,coords_b:149,coords_filenam:245,coords_set:15,coorind:215,copi:[1,3,4,6,12,34,43,49,70,71,94,146,147,149,155,156,157,159,188,190,211,239,240,267,271,272,276,278],copl:[167,219],copy_chgcar:240,copy_wavecar:240,cordero:79,core:[1,2,3,4,5,6,8,9,12,13,14,40,41,42,44,46,49,50,52,53,54,55,58,59,60,64,66,68,70,71,74,77,79,81,83,84,86,87,88,89,94,98,112,113,117,118,139,141,142,163,164,169,171,172,173,177,179,183,184,186,189,193,199,201,208,213,215,221,222,223,225,226,230,231,234,235,238,239,240,243,247,248,260,265,267,269,270,272,273,281,292],corehol:210,cormac:62,cornel:291,corner:[20,84,88],corr:165,corrao:40,correct:[1,4,5,6,8,9,14,26,42,43,45,48,52,54,55,70,74,81,88,105,118,146,157,165,170,172,173,174,177,179,186,196,199,200,201,211,212,221,224,239,240,254,261,263,269,292],correct_entri:[43,172],correct_peroxid:172,corrected_energi:172,correction_calcul:[8,9,171],correction_nam:[43,172],correction_per_atom:173,correction_uncertainti:[172,173],correction_uncertainty_per_atom:173,correctioncalcul:174,corrections_dict:174,corrections_std_error:174,correctionslist:172,correctli:[1,5,56,137,146,165,167,197,239,240],corrector:238,correl:[142,150,161,165,192,199,201,211,224,240,269],correlation_grid:211,correspond:[1,2,13,15,20,25,26,28,29,30,36,37,40,43,44,48,49,52,53,54,58,59,63,66,70,71,74,78,79,82,84,85,86,88,90,91,96,97,98,105,110,112,119,137,138,139,141,146,147,149,156,157,158,159,165,167,169,170,172,177,182,187,188,189,197,200,201,202,223,225,230,232,238,239,240,241,243,254,257,258,261,264,269,271,272,276],correspondisng:239,corrupt:1,cosin:79,cosinu:33,cosinus_step:38,cosmo:[1,224],cost:[1,8,9,14,63,186,199,232,238,250,251],cost_per_kg:41,costa:[1,239,291],costanalyz:41,costdb:41,costdbcsv:41,costentri:41,costli:201,coth:255,could:[4,6,26,29,53,146,165],coulomb:[186,201,202],coulomb_mod:186,council:291,count:[71,79,88,120,137,147,186,215,239,292],count_lay:147,counterbalanc:87,counterpart:[15,137,139],coupl:[1,3,44,71,82,86,108,165,190,224,239,240],coupling_const:86,cours:199,courtesi:1,coval:[79,85,145,151,156,215,280,288],covalent_radiu:85,covalentbond:[79,145,156],covalentbondnn:[1,79],covalentradiu:85,cover:[40,94,165,201,223,280],coverag:105,covl_k:239,cp2k:[1,8,9,184,292],cp2k_input:199,cp2k_version:200,cp2kinput:[199,201],cp2kinputset:201,cp2koutput:200,cp:[79,106],cpc:[46,139],cpcm:230,cpdname:106,cpep:139,cpfit:202,cpmd:204,cpp:5,cpreport:139,cpu:[142,175,182,187,239,269],cpu_fract:187,cpu_tim:187,cpuwall_histogram:187,cq:239,cr3:17,cr4:17,cr:[56,85,153,174,240,269],cr_pv:240,cr_sv_gw:240,cracknel:264,cramer:138,crash:[1,192],crc:153,creat:[1,3,4,6,12,13,15,20,25,29,30,34,40,43,48,49,51,55,58,59,60,62,63,66,70,71,74,78,79,81,82,86,88,89,90,91,94,105,108,118,119,146,147,148,149,150,152,154,156,157,158,159,161,164,165,167,168,169,170,173,174,177,181,182,183,186,187,190,195,196,197,199,200,201,202,203,204,208,209,210,211,212,215,216,219,221,223,224,226,228,230,231,238,239,240,242,243,247,248,258,264,269,271,280,281,283,284,289],create_directori:[12,13],create_saturated_interstitial_structur:43,create_slab_label:105,create_subsi:201,created_at:[182,281],createfatband:221,createmod:278,creation:[1,98,153,157,160,182,199,201,290],creator:157,credit:[1,62,291],crest:[1,244,245,246],crest_best:246,crest_in:245,crestinput:245,crestoutput:246,criteria:[1,11,15,44,58,70,77,79,85,108,117,156,157,177,182,199,201,269],criteria_str:182,criterion:[187,201,240,292],critic2:[1,5,79,139],critic2_cal:[1,5,8,9,136],critic2analysi:139,critic2cal:[1,5,79,139],critic2nn:79,critic:[1,2,4,5,6,53,82,88,110,119,139,143,153,182],critical_point:139,critical_temp:143,critical_temperatur:153,criticalpoint:139,criticalpointtyp:139,crka1:54,crka2:54,crka:54,crkb1:54,cross:[1,25,34,48,113,125,153,158,164,170,199,209,21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61,165,169,170,172,173,183,206,239,261,290],eta:[61,63,86,165,239],eta_from_seebeck:165,etc:[0,1,3,4,5,6,43,48,55,58,68,70,71,79,81,82,84,88,98,113,116,117,124,137,143,152,153,154,155,156,158,159,160,168,169,175,177,181,182,200,201,208,209,210,221,225,227,228,238,239,240,246,255,259,260,269,280,284,292],ethanol:232,ethyl:68,etsf:189,etsf_read:189,eu2:[1,240],eu3:[1,240],eu:[1,56,85,153,183,240],eu_2:240,euler:59,eulerian:261,ev:[1,40,43,44,49,62,63,64,71,74,88,91,93,96,105,112,113,151,153,160,165,167,169,170,172,173,174,177,182,186,188,200,209,211,212,219,223,224,239,240,254,256,258,292],ev_to_k:49,ev_to_kj_per_mol:74,eval:[4,6,239],evalu:[34,36,45,46,49,58,63,79,91,93,192,199,201,222,223,224,232,239,240,256],evaluate_wavefunc:239,evan:[143,291],even:[1,2,4,5,6,56,87,98,117,123,146,156,177,182,186,199,201,230,232,238,239,262,271,272,276,292],event:[4,6,280,281,289],eventu:[16,157],everi:[4,6,12,48,53,55,97,139,149,165,223,239,256,292],everyon:291,everyth:[3,164,200,201,292],everything_equ:22,evolut:[88,91],ewald:[1,3,8,9,14,44,49,61,269,271,272,292],ewaldelectrostaticmodel:61,ewaldminim:63,ewaldpap:63,ewaldsum:[61,221],ewaldsumm:[1,61,63],ex:[5,43,44,68,151,164,202,211,230,232,254],ex_mat:82,ex_param:[82,143],exact:[11,84,85,98,156,157,175,201,238,240,262],exactdens:192,exactli:[1,3,70,98,157,165,186,199,222,238,272],exaf:[112,155,208,209,210],examin:88,exampl:[1,2,3,5,11,12,13,17,20,26,28,37,41,43,48,55,56,63,66,71,79,84,88,94,97,98,100,105,106,109,116,117,118,119,122,145,146,148,149,152,153,155,156,157,160,161,165,169,170,172,173,175,182,186,187,188,190,199,200,202,204,210,212,216,220,224,225,228,232,233,236,238,239,240,243,260,262,265,269,271,272,276,280,281,286,287,289],exc_dft_opt:211,exc_typ:186,exce:[98,201,269],excel:[1,84,137,140,188,260,290],except:[1,3,33,37,49,59,62,71,79,87,88,94,98,102,140,141,146,148,152,153,156,160,165,169,172,182,187,188,192,196,199,204,208,224,228,233,238,239,240,260,275],exception:102,exception_on_bad_xml:239,excess:44,exchamiltonian:186,exchang:[1,71,81,82,143,150,152,161,183,186,192,199,201,210,224],exchange_const:71,excit:[1,8,9,14,53,184,209,211,212,224],excitationspectrum:[64,224],excitinginput:206,exclud:[11,28,44,49,88,90,156,157,172,174,177,188,190,218,240,280,289],exclude_dir:190,exclude_polyanion:174,exclude_self:156,excluded_atom:28,excluded_bonding_el:289,exclus:[2,161],execut:[1,5,11,133,137,138,139,140,141,143,179,199,219,225,278,284],exelf:210,exercis:239,exhf:239,exhibit:[137,138],exist:[1,2,3,4,5,6,11,26,28,29,44,45,48,49,53,55,58,62,71,81,85,87,88,91,98,102,138,145,156,157,167,168,170,173,177,190,192,197,199,200,202,210,216,219,238,240,260,275,280,292],existing_structur:11,exit:[87,239],exp:[36,49,54,55,58,174,182,226,239],exp_compound:174,exp_cos_aa:79,exp_entri:[8,9,171,174],exp_gz:174,expand:[1,3,4,5,6,70,269],expand_tim:[70,269],expans:[3,58,153,158,201],expect:[1,2,3,5,11,34,46,55,70,79,83,109,137,141,153,160,168,169,201,239,240,260,263,269],expected_charg:16,expens:[1,63,88,199,239,272],expentri:[176,182],experi:[5,91],experienc:216,experiment:[17,28,79,88,106,112,153,170,172,173,174,176,182,255,269,272],exphp:[1,291],explain:[1,139,165,170,172,173],explan:[1,70,146,170,172,173,182,292],explanaion:173,explicit:[25,26,28,186,195,196,238,239],explicit_indic:28,explicit_on:283,explicit_optimized_permut:26,explicit_path:186,explicit_permut:26,explicitli:[25,34,37,56,79,201,240],explicitpermutationsalgorithm:26,explor:[4,6,49,139,292],expnorm:49,expon:[25,79,142,165,201,269],exponenti:[49,275],export_msdt:55,expos:183,expr:58,express:[4,6,34,58,66,149,158,200,233,239],expt:173,ext:[0,1,2,3,4,6,8,9,187,190,264,292],extend:[1,12,13,15,41,49,58,60,74,86,87,88,146,152,155,156,159,169,176,188,189,199,210,232,255,269,284,292],extend_collect:13,extend_structure_molecul:79,extend_transform:[12,13],extens:[1,2,4,5,6,55,71,110,122,138,153,154,156,170,173,176,187,190,200,211,239,292],extern:[1,2,3,4,5,6,131,238,245,281,282],external_id:182,extra:[4,6,45,48,81,86,116,186,187,227,239,248,275,288],extra_nn_info:79,extract:[1,5,12,29,70,71,81,82,147,156,157,165,187,226,238,239,258,269,292],extract_clust:156,extracted_vasp_potcar:5,extrapol:[1,55,169,199,239],extrapolate_reciproc:275,extrapolate_simple_reciproc:275,extras_requir:[4,6],extrem:[1,4,6,47,63,103,156,170,182,201,239,240,258,262,271,272,287,292],extrema:[49,109,165],extrema_coord:49,extrema_df:49,extremum_icohpvalu:167,extrins:[116,117],ey:[149,186],f0:[168,169,170],f1:[4,6,34,168,170,264],f1d01e845dccc52d448679911f301a73:240,f2:[34,74,146,168,170,177,240,284],f3:[168,170],f4ff16a495dd361ff5824ee61b418bb0:240,f:[4,6,29,36,49,53,54,56,58,66,67,85,106,112,116,118,139,143,146,153,168,170,174,190,231,239,240,248,263,264,283,284,290,291,292],f_1:[168,170],f_2:[168,170],f_3:[168,170],f_:54,f_constant:212,f_d:169,f_gw:240,f_h:240,f_j:54,f_lower:34,f_upper:34,f_x:169,f_xyz:169,f_xz:169,f_y:169,f_yz:169,f_z:169,fac_aa:79,face:[15,26,77,79,97,248,289],face_dist:79,faces_color_overrid:39,facet:[28,34,51,54,74,77,79,88,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211,full_ce_info:25,full_electronic_structur:153,full_grid:199,full_kinet:[199,201],full_s_invers:199,full_singl:199,full_single_invers:[199,201],fulli:[40,67,117,146,157,201,238,240,292],fully_charged_entri:119,fully_discharged_entri:119,func:[62,155,182,280],func_group:[68,71,156],func_grp:[71,156],func_util:[9,14,18,31],function_comparison:34,functional_choic:238,functional_class:238,functional_dir:238,functional_group:[8,9,14],functional_tag:238,functionalgroupextractor:68,functool:160,fur:240,furnish:[4,6],further:[3,4,5,6,59,79,139,176,195,210,221,232,240,260,269,292],further_set:221,furthermor:[79,221],furthest:34,futur:[1,2,4,6,91,105,156,157,182,195,201],fuzzi:177,fuzzy_formula:146,fuzzy_match:177,fwhm:155,fyalcin:1,fysik:[5,161],g03:156,g09:156,g0:239,g1:49,g2:49,g3gn:224,g:[1,2,3,4,5,6,12,13,15,17,20,22,23,25,26,28,29,40,41,46,47,49,51,55,56,58,62,66,67,70,71,74,79,81,83,88,91,92,93,94,97,98,100,101,102,105,106,109,110,113,116,117,118,119,137,138,139,141,142,146,147,148,149,150,153,154,155,156,157,158,159,160,164,165,167,168,169,170,172,173,175,177,182,183,186,187,188,190,195,197,199,200,201,204,208,212,215,216,217,221,222,223,224,225,226,228,230,231,232,233,235,237,238,239,240,254,257,258,259,260,262,263,264,269,271,272,276,277,280,281,283,287,289,290,292],g_:[54,239],g_i:239,g_n:239,g_opt:93,g_r:58,g_reuss:58,g_v:58,g_vec:44,g_voigt:58,g_vrh:58,ga:[56,74,85,91,106,153,172,209,240],ga_d:240,ga_d_gw:240,gabaldon:138,gaff:195,gain:[3,137,138],gale:141,galor:[1,113],gam:239,gamma:[1,44,49,93,105,149,164,181,186,188,196,199,200,201,221,226,238,239,240,254,256,257,292],gamma_automat:238,gamma_cent:186,gamma_dict:105,gamma_onli:[186,239],gammacent:188,gammacenterd:188,ganos:[1,113,291],gap:[1,44,48,76,79,147,164,165,169,170,182,199,200,201,239,240],gap_dist:181,gapw:199,gascorrect:172,gase:[153,173],gaseou:[138,172],gass:1,gather:160,gau:292,gaultoi:72,gaunip:212,gauss:186,gaussian:[1,4,6,8,9,17,49,79,87,113,122,127,155,156,169,170,184,186,192,199,200,201,204,211,224,255,258,292],gaussian_analyz:[8,9,124],gaussian_smear:87,gaussianinput:[1,212,224,292],gaussianio:122,gaussianoutput:[1,122,212],gaussiansmearingwidth:221,gaussiantocomputedentrydron:122,gaussiantoentrydron:122,gaussion:1,gave:239,gb:[1,8,9,14,157,160,240,269,272],gb_from_paramet:70,gb_plane:[70,182],gbgener:1,gc:246,gcc:[4,5,6],gcheon:[56,291],gcut:49,gd3:240,gd:[56,85,153,240],gd_3:240,gdm:232,ge:[55,56,85,153,156,240,269,271,272,284],ge_d:240,ge_d_gw:240,gen3d:195,gen3d_conform:195,gen4438:291,gen:212,gen_basi:212,gen_potcar:133,gen_scfman:[1,232],gen_sl_transform_matrici:78,gener:[1,2,3,4,5,6,8,9,12,13,14,15,29,40,42,43,44,46,49,53,55,56,58,59,67,70,71,73,74,76,77,78,79,81,82,84,87,88,90,91,94,98,100,105,106,108,109,110,117,118,119,122,125,126,133,137,139,140,141,146,147,148,149,150,152,153,154,156,157,158,161,164,165,168,169,170,172,173,175,176,177,182,183,186,188,192,195,196,197,199,200,201,208,210,211,215,217,218,219,221,223,224,225,226,227,228,233,238,239,240,247,254,256,257,258,260,261,262,263,264,269,270,271,272,273,275,276,279,280,283,287,289,290,292],generate_adsorption_structur:15,generate_all_slab:157,generate_defect_structur:43,generate_displac:226,generate_entry_label:91,generate_full_symmop:260,generate_input:197,generate_point:53,generate_potcar:[133,240],generate_pseudo:58,generate_r_and_g_vec:49,generate_reciprocal_vectors_squar:49,generate_sl_transformation_set:78,generate_substitution_structur:15,generate_surface_vector:77,generic_groupbi:49,genet:84,geneticordermatch:84,genfmt:208,genom:[4,6,290],genrecip:49,geo:188,geo_opt:201,geo_subkei:192,geoffroi:[1,4,6,28,291],geograph:72,geom_opt_max_cycl:232,geometr:[25,79,84,87,116,290],geometri:[1,26,27,28,29,39,59,67,78,84,192,195,200,201,212,224,232,248,290],geometrically_equidist:25,geometry_info:25,geometry_opt:224,geometryoptim:192,geomstep:195,georg:[28,165,291],gerbrand:[4,6,87],germain:[1,170,291],get:[1,3,5,15,17,20,21,22,23,25,26,29,30,34,36,37,41,43,44,45,48,49,53,55,56,58,59,66,70,74,76,78,79,82,83,84,88,91,92,93,96,98,100,105,110,112,117,119,130,137,138,141,145,146,147,149,153,154,156,157,158,165,167,168,169,170,172,180,181,182,183,188,196,199,200,201,202,204,209,212,219,221,222,223,226,234,237,238,239,240,252,255,256,258,260,266,269,271,272,276,281,283,284,287,292],get_00t_magmom_with_xyz_saxi:168,get_13_bond:85,get_2d_orthonormal_vector:40,get_2d_transform:76,get_absorbing_atom_symbol_index:208,get_adjust:[172,177],get_adjusted_fermi_level:239,get_all_anonymous_map:98,get_all_chempot:88,get_all_dist:149,get_all_elementary_cycl:37,get_all_entri:119,get_all_functional_group:68,get_all_neighbor:[1,156],get_all_neighbors_old:156,get_all_neighbors_pi:156,get_all_nn:79,get_all_nn_info:79,get_all_possible_basis_combin:221,get_all_possible_basis_funct:221,get_all_simple_paths_edg:37,get_all_sit:79,get_all_substr:182,get_all_voronoi_polyhedra:79,get_allowed_speci:102,get_alpha:239,get_analysi:83,get_analysis_and_structur:83,get_angl:[156,276],get_anion_typ:222,get_arrhenius_plot:55,get_asum_fcm:90,get_atom:[193,213],get_atom_map:208,get_atomic_fract:[4,6,146],get_atomic_site_averag:204,get_atomic_site_tot:204,get_aux_basi:202,get_available_model:180,get_average_along_axi:[204,239],get_average_eff_mass:165,get_average_voltag:117,get_ax3d_fig_plt:280,get_ax_fig_plt:280,get_axarray_fig_plt:280,get_axis_grid:[204,239],get_band_cent:169,get_band_fil:169,get_band_gap:164,get_band_kurtosi:169,get_band_skew:169,get_band_structur:239,get_band_structure_from_vasp_multiple_branch:239,get_band_width:169,get_bandstructur:223,get_bandstructure_by_material_id:[182,292],get_basi:221,get_basic_functional_group:68,get_basis_and_potenti:202,get_bec_oper:90,get_best_electronegativity_anonymous_map:98,get_bibtex_str:196,get_bond_length:145,get_bond_ord:[138,145],get_bonded_structur:[1,56,79,100],get_box_shift:215,get_boxed_structur:156,get_branch:[164,254],get_brillouin_zon:149,get_capacity_grav:117,get_capacity_vol:117,get_carrier_concentr:165,get_cart_coord:212,get_cartesian_coord:149,get_cbm:164,get_cbm_vbm:169,get_celldm:228,get_center_of_arc:38,get_centered_molecul:156,get_central_sit:26,get_centroid_2d:40,get_charg:[137,138],get_charge_decorated_structur:137,get_charge_transf:[137,138],get_chempot_correct:74,get_chempot_range_map:[88,105],get_chempot_range_map_plot:88,get_chempot_range_stability_phas:88,get_chgint_plot:132,get_chunk:182,get_cn:79,get_cn_dict:79,get_cod_id:179,get_coeff:94,get_cohesive_energi:182,get_cohp:167,get_cohp_by_label:167,get_cohp_dict:170,get_complete_do:[113,165],get_complete_ph_do:226,get_complexity_factor:165,get_compliance_expans:58,get_composition_chempot:88,get_compound_pd:88,get_computed_entri:239,get_conduct:165,get_connect:97,get_connected_compon:23,get_connected_sit:71,get_consistent_set:168,get_consistent_set_and_saxi:168,get_continuous_path:261,get_contour_pd_plot:88,get_conventional_standard_structur:[1,260],get_conventional_to_primitive_transformation_matrix:260,get_conversion_factor:[55,160],get_coordinating_elements_cn:49,get_coordination_environ:29,get_coordination_numb:26,get_coordination_of_sit:71,get_coordination_symmetry_measur:28,get_coordination_symmetry_measures_optim:28,get_correct:[43,44,172],get_corrections_dict:172,get_cost_per_kg:41,get_cost_per_mol:41,get_covalent_bond:156,get_critical_composit:88,get_critical_original_kink_ratio:74,get_critical_point_for_sit:139,get_crystal_field_spin:153,get_crystal_system:260,get_csm:29,get_csm_and_map:29,get_cutoff_from_basi:202,get_d:157,get_data:[123,182,292],get_database_vers:182,get_datafram:[74,187],get_decomp_and_decomp_energi:88,get_decomp_and_e_above_hul:88,get_decomp_and_hull_energy_per_atom:88,get_decomp_and_phase_separation_energi:88,get_decomposit:88,get_decomposition_energi:91,get_decorated_structur:137,get_default_basis_set:192,get_default_geo:192,get_default_scf:192,get_default_unit:192,get_default_xc:192,get_defectsite_multipl:49,get_deformation_matrix:59,get_delta:37,get_delta_imag:23,get_dens:169,get_deriv:275,get_diff_coeff:58,get_dihedr:156,get_dimension:[1,2],get_dimensionality_cheon:56,get_dimensionality_gorai:56,get_dimensionality_larsen:56,get_dir_indir_gap:96,get_direct_band_gap:164,get_direct_band_gap_dict:164,get_disconnected_frag:71,get_displaced_structur:226,get_dist:156,get_distance_and_imag:149,get_doc:[182,223],get_dop:169,get_dopability_limit:48,get_dopants_from_shannon_radii:100,get_dopants_from_substitution_prob:100,get_dos_by_material_id:[182,292],get_dos_dict:[170,258],get_dos_plot:132,get_download_info:182,get_drift_corrected_structur:55,get_e_above_hul:[1,88],get_effective_csm:25,get_effective_ec:58,get_el_amount:94,get_el_amt_dict:146,get_el_sp:153,get_element_do:[169,255,258],get_element_fract:91,get_element_profil:88,get_element_spd_do:169,get_elements_between_band:239,get_elt_projected_plot:170,get_elt_projected_plots_color:170,get_energi:[61,127,130,141,146],get_energy_buckingham:141,get_energy_dens:117,get_energy_relax_structure_buckingham:141,get_energy_tersoff:141,get_entri:[1,41,182],get_entries_in_chemsi:[1,182,292],get_entry_by_material_id:182,get_environ:[8,9,124],get_environment_nod:22,get_environments_figur:29,get_equilibrium_reaction_energi:88,get_equiv_transform:78,get_equivalent_atom:260,get_equivalent_kpoint:164,get_equivalent_qpoint:254,get_exchang:82,get_exchange_group_info:81,get_excitation_spectrum:224,get_exp_entri:182,get_exp_thermo_data:182,get_explanation_dict:172,get_extended_surface_mesh:15,get_extrapolated_conduct:55,get_extrapolated_diffus:55,get_extrem:165,get_extrema:109,get_facet:88,get_factor:78,get_fcm_oper:90,get_fermi:169,get_fermi_interextrapol:[1,169],get_ferromagnetic_structur:81,get_filepath:139,get_first_point:53,get_form_energi:88,get_form_energy_per_atom:88,get_frac_coords_from_ll:149,get_fract:146,get_fractional_coord:149,get_framework_rms_plot:[1,55],get_free_sphere_param:248,get_from_hint:28,get_gap:169,get_gb_data:182,get_geometri:26,get_geometry_from_iucr_symbol:26,get_geometry_from_iupac_symbol:26,get_geometry_from_mp_symbol:26,get_geometry_from_nam:26,get_ggt:58,get_grouped_indic:158,get_gruneisen_paramet:58,get_gruneisen_ph_bs_symm_lin:226,get_gruneisenparamet:226,get_gs_ph_bs_symm_line_from_dict:226,get_hal:260,get_hall_carrier_concentr:165,get_hash:98,get_heat_capac:58,get_heisenberg_model:82,get_help:237,get_heteroatom:68,get_high_accuracy_voronoi_nod:248,get_hilbert_transform:169,get_hull_energi:[88,91],get_hull_energy_per_atom:88,get_icohp:167,get_icohp_by_label:167,get_icohp_dict_by_bondlength:167,get_icohp_dict_of_sit:167,get_ieee_rot:158,get_implemented_geometri:26,get_incar_tag:237,get_info_cohps_to_neighbor:222,get_info_icohps_between_neighbor:222,get_info_icohps_to_neighbor:222,get_input_set:[197,216,225,235,292],get_integer_formula_and_factor:146,get_integer_index:149,get_integrated_cohp_in_energy_rang:167,get_integrated_diff:239,get_interaction_graph:82,get_interfac:76,get_interface_react:182,get_interplanar_angl:53,get_interplanar_spac:53,get_interpolated_gap:169,get_interpolated_valu:[155,167,169,255],get_ir_mesh:1,get_ir_reciprocal_mesh:260,get_ir_spectra:257,get_ist_oper:90,get_keyword:199,get_kink:74,get_kpoint:[181,240,261,263],get_kpoint_degeneraci:164,get_kpoint_weight:260,get_label:[49,105],get_lattic:196,get_lattice_quanta:66,get_lattice_typ:260,get_light_structure_environ:222,get_lin:208,get_line_in_facet:110,get_linear_interpolated_valu:276,get_linearly_independent_vector:38,get_lll_frac_coord:149,get_lll_reduced_lattic:149,get_local_extrema:49,get_local_order_paramet:79,get_locpot_along_slab_plot:105,get_low_energy_ord:82,get_lower_and_upper_f:34,get_lowest_decomposit:41,get_magnet:130,get_magnitude_of_effect_from_speci:83,get_magnitude_of_effect_from_spin_config:83,get_magsymop:196,get_map:98,get_mass:160,get_materials_id:182,get_materials_id_from_task_id:182,get_materials_id_refer:[1,182],get_max_bond_dist:79,get_max_bond_length:97,get_max_capgrav:116,get_max_capvol:116,get_max_inst:119,get_max_muo2:119,get_mft_temperatur:82,get_mi_vec:15,get_miller_index_from_coord:149,get_miller_index_from_site_index:156,get_min_inst:119,get_min_muo2:119,get_mixing_state_data:177,get_molecul:193,get_molecule_hash:84,get_moment:168,get_moment_relative_to_crystal_ax:168,get_monolay:105,get_motif_typ:49,get_mp_structur:284,get_msd_plot:55,get_mu_bound:165,get_multipl:43,get_n_moment:169,get_nac_eigendisplacements_along_dir:254,get_nac_frequencies_along_dir:254,get_nam:26,get_nearest_sit:66,get_neighb_voronoi_indic:29,get_neighbor:[1,156],get_neighbor_list:156,get_neighbors_in_shel:156,get_neighbors_of_site_with_index:79,get_neighbors_old:156,get_next_index:63,get_niggli_reduced_lattic:149,get_nmr_quadrupole_mo:153,get_nn:79,get_nn_data:79,get_nn_imag:79,get_nn_info:[79,222],get_nn_shell_info:79,get_no_mixing_energi:74,get_nonmagnetic_structur:81,get_noppmodel:186,get_not_implemented_geometri:26,get_occup:239,get_okeeffe_distance_predict:79,get_okeeffe_param:79,get_op_valu:49,get_orbital_derivative_between_st:239,get_orbital_resolved_cohp:167,get_ord:156,get_order_paramet:79,get_orthogonal_c_slab:157,get_oxi_state_decorated_structur:17,get_oxidation_state_decorated_structur:137,get_paramet:79,get_parchg:239,get_partial_charg:[137,138],get_pattern:[51,52,53,54],get_pelecs_and_pion:66,get_percentag:231,get_percentage_bond_dist_chang:97,get_percentage_lattice_parameter_chang:97,get_percentage_volume_chang:97,get_perturbed_indic:59,get_ph_bs_symm_lin:226,get_ph_bs_symm_line_from_dict:226,get_ph_do:226,get_phase_separation_energi:88,get_phonon_band_structure_from_fc:226,get_phonon_band_structure_symm_line_from_fc:226,get_phonon_bandstructure_by_material_id:182,get_phonon_ddb_by_material_id:182,get_phonon_dos_by_material_id:182,get_phonon_dos_from_fc:226,get_phonon_frequ:239,get_phonopy_structur:226,get_piezo:90,get_plot:[1,40,51,88,109,110,120,170,258,287],get_plot_2d:53,get_plot_2d_concis:53,get_plot_coeff:53,get_plot_data:120,get_plot_g:258,get_plotli:110,get_plotly_figur:120,get_plott:257,get_pmesh:26,get_pmg_structur:226,get_point_group_oper:260,get_point_group_symbol:260,get_pointgroup:260,get_points_in_spher:149,get_points_in_sphere_old:149,get_points_in_sphere_pi:149,get_polarization_chang:66,get_polarization_change_norm:66,get_posit:53,get_potcar:239,get_potcar_file_hash:238,get_potcar_hash:238,get_potential_shift:44,get_pourbaix_domain:91,get_pourbaix_entri:182,get_pourbaix_plot:91,get_power_factor:165,get_predicted_structur:103,get_primitive_standard:1,get_primitive_standard_structur:[260,261,263],get_primitive_structur:[156,292],get_principal_axi:84,get_projected_plots_dot:170,get_projected_plots_dots_patom_pmorb:170,get_projection_on_el:[164,239],get_projections_on_elements_and_orbit:164,get_property_decorated_structur:138,get_prototyp:92,get_pseudos_for_structur:190,get_q2:79,get_q4:79,get_q6:79,get_rand_bec:90,get_rand_fcm:90,get_rand_ist:90,get_ratio:70,get_rdf_figur:30,get_react:182,get_real_summ:44,get_reasonable_repetit:254,get_recip_summ:44,get_reconstructed_band_structur:164,get_recp_symmetry_oper:149,get_reduced_composition_and_factor:146,get_reduced_formula_and_factor:[146,148],get_reduced_structur:156,get_reference_energy_per_atom:88,get_refined_structur:[196,260],get_relaxed_structur:141,get_removals_int_oxid:116,get_rms_anonym:98,get_rms_dist:98,get_rmsd:84,get_rot:15,get_rot_3d_for_2d:76,get_rotation_angle_from_sigma:[70,269],get_rotational_symmetry_numb:260,get_s2:53,get_s2_like_s1:98,get_sadf_figur:30,get_same_branch_polarization_data:66,get_scal:158,get_scan_plot:212,get_sect:[187,199],get_seebeck:165,get_seebeck_eff_mass:165,get_self_interact:44,get_set:[1,262],get_shannon_radiu:153,get_shared_symmetry_oper:266,get_shifts_based_on_adsorbate_sit:147,get_site_ce_fractions_and_neighbor:25,get_site_coordination_environ:25,get_site_coordination_environments_fract:25,get_site_do:[169,255],get_site_energi:63,get_site_info_for_specie_allc:29,get_site_info_for_specie_c:29,get_site_neighbor:25,get_site_orbital_do:169,get_site_spd_do:169,get_site_symmetri:266,get_site_t2g_eg_resolved_do:169,get_sitej:97,get_sites_in_spher:156,get_slab:157,get_slab_region:157,get_smeared_dens:[169,255],get_snl:183,get_snls_with_filt:183,get_sorted_structur:[1,70,147,156,157],get_space_group_info:156,get_space_group_numb:260,get_space_group_oper:260,get_space_group_symbol:[4,6,260],get_spd:[170,287],get_spd_do:[169,170],get_special_carbon:68,get_specific_energi:117,get_spectre_plot:212,get_spectrum:257,get_stability_criteria:58,get_stabl:[1,182],get_stable_entri:[91,119],get_stable_entry_at_u:105,get_stable_fcm:90,get_statist:29,get_str:[159,197,199,208,215,219,230,238,239],get_strain_from_stress:58,get_strain_state_dict:58,get_structur:[1,28,159,182,183,193,196,213,234,284,292],get_structure_by_formula:179,get_structure_by_id:179,get_structure_by_material_id:[1,182,292],get_structure_compon:56,get_structure_connect:21,get_structure_from_dict:226,get_structure_from_mp:1,get_structure_from_prev_run:240,get_structure_property_dict:58,get_structure_with_charg:223,get_structure_with_nod:49,get_structure_with_only_magnetic_atom:81,get_structure_with_site_potenti:223,get_structure_with_spin:81,get_structure_with_total_grosspop:223,get_structures_with_filt:183,get_sub_electrod:[117,118,119],get_subgraphs_as_molecul:71,get_subset_in_chemsi:175,get_substr:182,get_suggested_saxi:168,get_summary_dict:[55,93,117,118,119],get_summed_cohp_by_label_and_orbital_list:167,get_summed_cohp_by_label_list:167,get_summed_icohp_by_label_list:167,get_supercell_matrix:98,get_surface_data:182,get_surface_equilibrium:105,get_surface_sit:157,get_sym_eq_kpoint:164,get_symbol_cn_map:26,get_symbol_dict:158,get_symbol_list:58,get_symbol_name_map:26,get_symm_band:165,get_symmetric_neighbor_list:156,get_symmetric_sit:157,get_symmetric_wallace_tensor:58,get_symmetrically_distinct_miller_indic:157,get_symmetrically_equivalent_miller_indic:157,get_symmetrized_fcm:90,get_symmetrized_structur:[260,267],get_symmetry_dataset:260,get_symmetry_oper:[1,260],get_symop:196,get_task_data:182,get_tasker2_slab:157,get_tgt:58,get_thermal_conduct:165,get_tick:[170,258],get_ticks_old:170,get_total_ionic_dipol:66,get_trajectori:239,get_trans_mat:70,get_transform:98,get_transition_chempot:88,get_tri_area:110,get_truncated_coulomb_cutoff:202,get_typ:79,get_unique_famili:51,get_unique_site_indic:202,get_unit_primitive_area:105,get_unreconstructed_slab:157,get_unstable_entri:119,get_unstable_fcm:90,get_upper_band_edg:169,get_uvec:158,get_v:87,get_val:17,get_valid_magmom_struct:240,get_valid_path:122,get_valu:[187,191],get_vasp_input:[1,12,240],get_vasprun_outcar:240,get_vbm:164,get_vector_along_lattice_direct:[1,149],get_void_volume_surfarea:248,get_voigt_dict:158,get_volume_and_charge_for_sit:139,get_volumetricdata_dens:223,get_volumetricdata_imaginari:223,get_volumetricdata_r:223,get_voronoi_nod:248,get_voronoi_polyhedra:79,get_wallace_tensor:58,get_weight:275,get_weights_of_nn_sit:79,get_wigner_seitz_cel:149,get_wt_fract:146,get_wulff_shap:182,get_xas_data:182,get_xc_funct:202,get_xrd_plot:[1,132],get_xyz_magmom_with_001_saxi:168,get_yield_stress:58,get_z_ordered_elmap:17,get_zmatrix:212,get_zt:165,getmu_vertices_stability_phas:88,gf_sisso:173,gfactor:234,gflop:187,gfortran:[5,131],gfortranbinari:5,gga:[1,17,28,44,48,87,150,161,172,177,182,201,238,239,240,272,290],gga_c_am05:[150,161],gga_c_apb:150,gga_c_bgcp:150,gga_c_fract:201,gga_c_ft97:150,gga_c_gam:150,gga_c_hcth_a:150,gga_c_lm:150,gga_c_lyp:[150,161],gga_c_n12:150,gga_c_n12_sx:150,gga_c_op_b88:150,gga_c_op_g96:150,gga_c_op_pb:150,gga_c_op_pw91:150,gga_c_op_xalpha:150,gga_c_optc:150,gga_c_p86:150,gga_c_pb:[150,161],gga_c_pbe_jrgx:150,gga_c_pbe_sol:[150,161],gga_c_pbef:150,gga_c_pbeint:150,gga_c_pbeloc:150,gga_c_pw91:[150,161],gga_c_q2d:150,gga_c_regtpss:150,gga_c_revtca:150,gga_c_rge2:150,gga_c_sogga11:150,gga_c_sogga11_x:150,gga_c_spb:150,gga_c_tca:150,gga_c_wi0:150,gga_c_wi:150,gga_c_wl:150,gga_c_xpb:150,gga_c_zpbeint:150,gga_c_zpbesol:150,gga_def:182,gga_k_absp1:150,gga_k_absp2:150,gga_k_apb:150,gga_k_apbeint:150,gga_k_baltin:150,gga_k_dk:150,gga_k_ernzerhof:150,gga_k_fr_b88:150,gga_k_fr_pw86:150,gga_k_ge2:150,gga_k_golden:150,gga_k_gp85:150,gga_k_gr:150,gga_k_lc94:150,gga_k_lieb:150,gga_k_llp:150,gga_k_ludena:150,gga_k_mey:150,gga_k_ol1:150,gga_k_ol2:150,gga_k_pearson:150,gga_k_perdew:150,gga_k_revapb:150,gga_k_revapbeint:150,gga_k_tfvw:150,gga_k_thakkar:150,gga_k_tw1:150,gga_k_tw2:150,gga_k_tw3:150,gga_k_tw4:150,gga_k_vjk:150,gga_k_vsk:150,gga_k_vw:150,gga_k_yt65:150,gga_lin:182,gga_opt:182,gga_relax:28,gga_stat:182,gga_static_diel:182,gga_uniform:182,gga_x_2d_b86:150,gga_x_2d_b86_mgc:150,gga_x_2d_b88:150,gga_x_2d_pb:150,gga_x_airi:150,gga_x_ak13:150,gga_x_am05:[150,161],gga_x_apb:150,gga_x_b86:150,gga_x_b86_mgc:150,gga_x_b86_r:150,gga_x_b88:[150,161],gga_x_bayesian:150,gga_x_bgcp:150,gga_x_bpccac:150,gga_x_c09x:150,gga_x_cap:150,gga_x_dk87_r1:150,gga_x_dk87_r2:150,gga_x_ev93:150,gga_x_fract:201,gga_x_ft97_a:150,gga_x_ft97_b:150,gga_x_g96:150,gga_x_gam:150,gga_x_hcth_a:150,gga_x_herman:150,gga_x_hjs_b88:150,gga_x_hjs_b88_v2:150,gga_x_hjs_b97x:150,gga_x_hjs_pb:150,gga_x_hjs_pbe_sol:150,gga_x_htb:150,gga_x_ityh:150,gga_x_kt1:150,gga_x_lag:150,gga_x_lambda_ch_n:150,gga_x_lambda_lo_n:150,gga_x_lambda_oc2_n:150,gga_x_lb:150,gga_x_lbm:150,gga_x_lg93:150,gga_x_lv_rpw86:150,gga_x_mb88:150,gga_x_mpb:150,gga_x_mpw91:150,gga_x_n12:150,gga_x_ol2:150,gga_x_optb88_vdw:150,gga_x_optpbe_vdw:150,gga_x_optx:150,gga_x_pb:[150,161],gga_x_pbe_jsjr:150,gga_x_pbe_mol:150,gga_x_pbe_r:[150,161],gga_x_pbe_sol:[150,161],gga_x_pbe_tca:150,gga_x_pbea:150,gga_x_pbef:150,gga_x_pbeint:150,gga_x_pbek1_vdw:150,gga_x_pw86:150,gga_x_pw91:[150,161],gga_x_q2d:150,gga_x_rge2:150,gga_x_rpb:[150,161],gga_x_rpw86:150,gga_x_sfat:150,gga_x_sogga11:150,gga_x_sogga:150,gga_x_ssb:150,gga_x_ssb_d:150,gga_x_ssb_sw:150,gga_x_vmt84_g:150,gga_x_vmt84_pb:150,gga_x_vmt_g:150,gga_x_vmt_pb:150,gga_x_wc:150,gga_x_wpbeh:150,gga_x_xpb:150,gga_xc_b97_d:150,gga_xc_b97_gga1:150,gga_xc_edf1:150,gga_xc_hcth_120:150,gga_xc_hcth_147:150,gga_xc_hcth_407:150,gga_xc_hcth_407p:150,gga_xc_hcth_93:150,gga_xc_hcth_p14:150,gga_xc_hcth_p76:150,gga_xc_kt2:150,gga_xc_mohlyp2:150,gga_xc_mohlyp:150,gga_xc_mpwlyp1w:150,gga_xc_oblyp_d:150,gga_xc_opbe_d:150,gga_xc_opwlyp_d:150,gga_xc_pbe1w:150,gga_xc_pbelyp1w:150,gga_xc_th1:150,gga_xc_th2:150,gga_xc_th3:150,gga_xc_th4:150,gga_xc_th_fc:150,gga_xc_th_fcfo:150,gga_xc_th_fco:150,gga_xc_th_fl:150,gga_xc_vv10:150,gga_xc_xlyp:150,ggau_def:182,ggau_lin:182,ggau_opt:182,ggau_stat:182,ggau_static_diel:182,ggau_uniform:182,ggt:58,ghemic:195,ghost:199,ghost_sit:157,gian:28,giantomassi:[1,257,291],gibb:[1,88,91,93,105,165,170,172,173,212,291],gibbs_binding_energi:105,gibbs_model:173,gibbscomputedstructureentri:[1,173],gigaflop:187,gin:141,git:[1,3,5],github:[1,2,3,4,6,84,96,110,113,139,140,180,182,226,254,257,291],give:[1,4,6,29,34,40,41,43,48,63,66,70,71,78,79,81,83,87,88,92,98,103,105,116,139,141,146,152,165,168,169,170,182,201,204,212,219,222,223,239,260,269,276,277,292],give_only_index:260,given:[1,3,4,5,6,11,15,16,17,20,21,22,23,25,26,28,29,30,34,36,38,40,41,43,44,45,48,49,52,54,55,56,58,61,63,66,67,70,71,74,76,77,78,79,81,83,84,87,88,91,92,93,94,96,97,98,100,101,102,103,105,109,110,116,117,119,137,139,145,146,149,152,153,154,156,157,158,159,164,165,167,168,169,170,172,174,175,180,182,183,186,187,188,190,192,199,200,201,202,208,212,216,221,222,230,231,232,234,238,239,240,241,248,250,251,254,256,258,260,261,263,265,269,271,272,276,279,282,283,287,290,292],gjf:[4,6,156,292],gkantoniu:291,gl:161,glaum:28,glob:200,global:[1,4,6,168,188,195,199,200,201,269],global_mo:168,gmail:[182,281],gmatteo:[1,62],gmolecul:192,gnu:5,gnuplot:[46,275],go:[1,2,3,5,71,88,102,156,157,182,196,248,260,264,271,278,292],goal:157,godbi:186,goe:[54,201,208,210,278,291],goebel:28,gold:199,golden:[62,280],gonz:[28,165],gonze1997:257,good:[5,55,67,71,87,98,102,152,157,183,187,199,201,238,240,292],good_sect:187,goodal:291,googlecod:189,gorai:56,gostin:1,gout:141,gov:[151,153,215],govern:154,gowoon:56,gpa:[62,93],gpa_to_ev_a3:58,gpaw:161,gpetretto:1,gpoint:239,gpretto:1,gpw:[199,201],grab:[1,200],grad:139,gradep:139,gradient:[59,60,86,87,139,186,192,195,199,201,224,232,239,240,272],gradual:92,graef:[52,54,262],grain:[1,8,9,14,69,182,240,269,292],grain_label:70,grainboundari:70,grainboundarygener:70,grainboundarytransform:[1,269],grammar:154,grammat:153,gramschmidt:79,grand:[1,74,88,105,290],grand_pd:74,grandpotentialinterfacialreact:74,grandpotentialphasediagram:[1,74,88],grandpotpdentri:88,grant:[4,6],granular:55,graph:[1,5,8,9,14,20,22,23,37,55,56,67,68,79,82,100,139,143,170,174,180,258,261],graph_data:71,graph_dict:71,graph_obj:[53,110,174],graph_residual_error:174,graph_residual_error_per_speci:174,graph_util:[9,14,18,31],graphic:[4,6,88,170],graphit:284,graphviz:[5,71],grav:116,gravimetr:117,graviometr:120,grazuli:179,great:110,greater:[1,4,6,11,45,79,123,146,156,174,182,201,240,255],greatest:[38,146],greatli:[4,6,175],greedi:169,green:[58,59,71,170,186],green_kristoffel:58,green_lagrange_strain:59,grei:[264,280,289],grep:[1,200,228,233,239,240],grid:[1,25,29,44,49,51,62,87,96,139,165,169,170,186,187,188,190,199,201,204,211,221,223,226,228,234,238,239,240,241,256,257,258,260],grid_off:110,gridspec_kw:280,grip:[4,6],gross:149,grosspop:[1,223],grosspopul:223,ground:[1,74,77,82,143,153,172,175,177,182,188],ground_level:153,ground_stat:175,ground_state_energi:77,ground_state_term_symbol:153,group:[1,4,5,6,8,9,13,26,28,34,43,49,55,56,66,68,71,81,84,92,98,109,139,146,148,149,153,156,157,158,174,175,177,182,187,189,196,199,200,208,215,219,233,238,239,240,259,260,261,263,264,265,266,272,290,291,292],group_array_indic:158,group_by_typ:156,group_entries_by_composit:175,group_entries_by_structur:175,group_molecul:84,group_structur:[1,98],grow:[4,6],growth:[77,104],grueneisen:[226,256],gruenisen:256,gruneisen:[8,9,58,93,226,253,258],gruneisen_dict:226,gruneisen_paramet:93,gruneisen_path:226,gruneisenparamet:[226,256,258],gruneisenphononbandstructur:[226,256],gruneisenphononbandstructuresummlin:256,gruneisenphononbandstructuresymmlin:[226,256,258],gruneisenphononbsplott:258,gruneisenplott:258,gs:188,gs_input:188,gt:182,gth:202,gth_basi:199,gth_potenti:199,gu:[1,5,140,271],guarante:[0,1,3,4,6,71,81,84,113,155,157,172,199,260,271,272,292],guard:182,guassian:201,guess:[1,55,66,67,81,103,146,156,199,201,215,240,272,275,292],guess_el:215,guesstim:83,guesstimate_spin:83,gui:291,guid:[1,5,66,292],guidanc:182,guidelin:[1,4,5,6],guido:[1,256,257,291],gulp:[1,5,61,63,141,243,248],gulp_cal:[1,5,8,9,136],gulp_cmd:141,gulpcal:141,gulpconvergenceerror:141,gulperror:141,gulpio:141,gunter:[4,6,290],gupta:291,gvallver:170,gvallverdu:1,gw:[1,186,211,238,240],gw_fiesta:211,gw_option:211,gw_qprang:186,gwcalctyp:186,gweight:25,gwpara:186,gz:[4,5,6,123,137,139,174],gzip:[1,123,137,138,139,196],h1:105,h2:[74,105,146,172,177],h2o2:[146,148],h2o:[91,148,172],h2o_adjust:172,h2o_energi:172,h4o4:148,h:[1,4,5,6,29,40,51,55,56,62,68,70,74,85,86,87,91,105,106,110,116,137,146,148,149,153,157,160,165,170,174,186,187,199,215,224,238,240,248,257,258,262,265,289,290,292],h_gw:240,h_node:281,ha:[1,2,3,4,5,6,12,23,28,29,30,36,45,48,55,58,62,63,66,67,70,79,81,84,88,90,91,94,105,113,117,122,137,138,139,149,152,153,156,157,158,160,161,165,168,170,177,182,186,188,190,192,197,199,201,202,204,208,212,215,216,222,223,224,225,227,231,238,239,240,241,251,254,258,260,264,269,272,282,283,291,292],had:[1,2,43,63,165],haeberlen:86,haeberlen_valu:86,haeberlennot:86,hafner:46,half:[1,98,157,202,212],halfspac:48,halfspaceinterect:48,halfspaceintersect:[40,91],halit:157,halite_111_octopolar_2x2:157,hall:[165,170,179,260],hall_dop:165,hallten:165,halogen:[146,153,232],halogen_list:85,hamilton:[1,167,170],hamiltonian:[81,82,186,199],hammer:[161,169],hand:[1,2,5,122],handbook:153,handl:[1,4,6,56,105,129,131,135,137,148,167,168,177,194,199,216,221,230,239,240,257,260],hanmei:[1,291],hanmeitang:1,hansen:161,hanson:92,happen:[43,49,79,84,182],happi:3,haranczyk:[47,49,248,290],hard:[1,83,153,215,271,272],harmon:93,harri:86,hart:[1,5,92,140,271],hartman:291,hartre:[186,190,199,201,204,224,239],harvard:291,has_antibnd_states_below_efermi:167,has_dojo_report:190,has_eigendisplac:254,has_error:196,has_good_quality_check_occupied_band:223,has_good_quality_maxdevi:223,has_hint:190,has_imaginary_freq:254,has_intersect:25,has_magmom:[261,263],has_materials_project_access:32,has_nac:[226,254],has_onsite_density_matric:239,has_opt:192,has_same_structur:188,has_subkei:192,hash:[1,5,84,98,153,158,172,190,238,239,240],hashabl:[84,98,146,154,156,161],hasn:238,hautier:[1,4,6,28,88,101,102,165,240,290,291],have:[1,2,3,4,5,6,11,15,16,17,20,23,26,28,29,30,37,40,43,45,48,55,56,59,61,63,66,67,68,70,71,78,79,81,82,83,84,85,87,88,97,98,100,105,109,110,116,117,118,119,122,123,136,137,141,142,146,147,151,153,154,156,157,158,159,160,164,165,168,169,170,172,173,177,182,183,187,188,189,190,192,195,199,200,201,202,204,215,221,226,234,238,239,240,241,248,252,256,258,260,261,269,271,272,273,276,278,283,284,290,291,292],have_consistent_saxi:168,haven:[1,63],haydock:186,hayn:153,hbar:[49,58],hcp:[79,110,140,272],hdf5:[1,239],he:[1,56,85,153,238,240,254,256,284,292],he_bcc:284,he_gw:240,head:218,headach:240,header:[1,5,181,187,189,196,200,204,208,209,210,219,227,231,233,239,243,283],header_pattern:[200,233,239],header_str:208,header_string_from_fil:208,heat:[58,255,258,280],heatmap:[1,280],heavi:[1,5,88,182,292],heavier:173,heavili:[276,292],hedin:238,height:[15,62,79,120,170,269,280],heisenberg:[1,8,9,14,71,80],heisenbergmapp:82,heisenbergmodel:[82,143],heisenbergscreen:82,helmholtz:[93,255],helmholtz_free_energi:255,helmoltz:258,help:[1,3,4,6,8,9,15,40,45,66,70,71,81,87,88,105,149,157,169,170,182,184,199,221,236,240,257,289],helper:[1,13,15,23,34,49,58,71,79,96,97,105,108,110,123,142,146,157,158,182,199,208,228,237,238,257,280],hematit:106,henc:[91,177,238,272,278],henchforth:1,heng:1,henkelman:[109,137,239,290],henkelmann:[1,5,137,290],henriqu:291,henriquemiranda:[1,254],herath:291,herbst:291,here:[0,4,5,6,37,56,79,81,84,98,105,157,161,173,190,200,201,226,232,234,239,278,282,292],herebi:[4,6],herfindahl:72,hermann:262,hessian:[1,139,170,212,224],heteroatom:68,heterostructur:[56,78],heurist:[81,83],hex:[1,70,263],hex_angle_tol:149,hex_bipyr:79,hex_length_tol:149,hex_pyr:79,hexagon:[1,70,79,110,149,157,186,188,238,240,260,262,264,265,269],hf:[56,85,153,200,201,212,239,240],hf_fraction:201,hf_pv:240,hf_sv_gw:240,hfscreen:240,hfx:[200,201],hg:[56,85,153,240],hg_sv_gw:240,hhi:[1,8,9,14],hi:262,hick:92,hide:71,hide_image_edg:71,hide_neg:120,hide_unconnected_nod:71,hierarchi:[197,292],high:[1,3,4,6,13,40,49,81,82,83,101,105,108,140,153,165,170,177,180,188,190,195,199,201,224,226,238,240,248,260,261,263,289,290,291],highcharg:46,highchart:46,higher:[29,48,49,58,61,79,88,102,105,165,170,201,239,240,272],highest:[15,49,56,58,88,97,117,151,165,169,187,199,271,292],highest_protocol:284,highli:[1,3,4,6,91,169,186,201,238,239,271,292],highlight:292,highsymmkpath:[170,206,238,261],hilber:186,hilbert:[169,186],hilberttransform:186,hill:[58,146,183],hill_formula:146,hillari:[1,291],hint:[1,25,26,28,29,81,190,285],hint_for_accuraci:190,hints_info:26,hints_typ:26,hinuma:[261,263],hiphiv:269,hirerachi:292,hirschman:72,hirshfeld:[138,200,240],histo:165,histogram:[165,187],histor:[5,153,199],histori:[12,13,182,271,272,273,281],history_restart:199,historynod:281,hit:275,hitachi:291,hive:[8,9,114,121,123,292],hkil:[110,157],hkill:110,hkl:[1,51,53,54,56,110,149,157],hkl_list:110,hkl_transform:157,hkl_tuple_to_str:110,hl:[161,238],hm:143,hmlli:291,hmodel:82,ho3:240,ho:[56,85,146,148,153,174,240],ho_3:240,hold:[70,157,248],holder:[4,6,173],hole:[44,45,48,165,169],hollow:15,holm:291,home:[4,6,225],homepag:183,homo:[151,199,200,201],homogen:[58,186],homogeneous_poisson:58,hongyi:[1,291],hook:[1,3],hop:79,hope:201,hopkin:1,hopp:79,horizont:[48,91],horton:[1,28,47,49,172,291],host:[45,49,117,120,175],hot:5,hou:291,hous:1,hove:[0,4,6],how:[0,1,15,25,28,29,30,45,51,61,63,66,68,71,72,98,146,149,156,157,165,167,170,173,177,182,197,199,200,201,202,222,239,240,269,275,281,292],howev:[1,2,4,5,6,12,13,49,66,67,71,79,88,94,105,118,122,156,157,170,177,188,210,232,238,239,240,264,272,292],hpoint:230,href:180,hs:[56,153],hse06:201,hse:[1,201,239,240],hsuan:291,ht:292,html:[1,4,5,6,63,110,161,181,189,207,211,215,237,242,248,282,283],htmlifi:283,http:[1,4,5,6,40,49,63,66,74,84,91,92,93,96,105,108,110,113,137,138,139,140,141,142,143,151,152,153,161,165,168,170,172,173,180,181,182,183,189,204,207,211,215,225,226,227,234,239,240,242,248,254,257,260,263,264,276,282,290,292],htz1992213:1,hu:238,huang:[87,290],hubbard:[172,182,200,239,240,292],hubbard_u:240,huck:[239,291],huebsch:291,huge:[55,88,199,201],hui:1,hull:[1,41,74,88,91,110,117,118,119,174,175,177,182],hull_energy_1:177,hull_energy_2:177,human:[173,183,292],humbert:291,humboldt:291,hund:153,hundr:195,hung:291,hungarian:84,hungarianordermatch:84,hv:84,hvec:58,hyb:161,hyb_gga_x_n12_sx:150,hyb_gga_x_sogga11_x:150,hyb_gga_xc_b1lyp:150,hyb_gga_xc_b1pw91:150,hyb_gga_xc_b1wc:150,hyb_gga_xc_b3lyp5:150,hyb_gga_xc_b3lyp:150,hyb_gga_xc_b3p86:150,hyb_gga_xc_b3pw91:150,hyb_gga_xc_b97:150,hyb_gga_xc_b97_1:150,hyb_gga_xc_b97_1p:150,hyb_gga_xc_b97_2:150,hyb_gga_xc_b97_3:150,hyb_gga_xc_b97_k:150,hyb_gga_xc_bhandh:150,hyb_gga_xc_bhandhlyp:150,hyb_gga_xc_cam_b3lyp:150,hyb_gga_xc_camy_b3lyp:150,hyb_gga_xc_camy_blyp:150,hyb_gga_xc_cap0:150,hyb_gga_xc_edf2:150,hyb_gga_xc_hjs_b88:150,hyb_gga_xc_hjs_b97x:150,hyb_gga_xc_hjs_pb:150,hyb_gga_xc_hjs_pbe_sol:150,hyb_gga_xc_hpbeint:150,hyb_gga_xc_hse03:150,hyb_gga_xc_hse06:150,hyb_gga_xc_lc_vv10:150,hyb_gga_xc_lcy_blyp:150,hyb_gga_xc_lcy_pb:150,hyb_gga_xc_lrc_wpb:150,hyb_gga_xc_lrc_wpbeh:150,hyb_gga_xc_mb3lyp_rc04:150,hyb_gga_xc_mpw1k:150,hyb_gga_xc_mpw1pw:150,hyb_gga_xc_mpw3lyp:150,hyb_gga_xc_mpw3pw:150,hyb_gga_xc_mpwlyp1m:150,hyb_gga_xc_o3lyp:150,hyb_gga_xc_pbe0_13:150,hyb_gga_xc_pbeh:150,hyb_gga_xc_revb3lyp:150,hyb_gga_xc_sb98_1a:150,hyb_gga_xc_sb98_1b:150,hyb_gga_xc_sb98_1c:150,hyb_gga_xc_sb98_2a:150,hyb_gga_xc_sb98_2b:150,hyb_gga_xc_sb98_2c:150,hyb_gga_xc_tuned_cam_b3lyp:150,hyb_gga_xc_wb97:150,hyb_gga_xc_wb97x:150,hyb_gga_xc_wb97x_d:150,hyb_gga_xc_wb97x_v:150,hyb_gga_xc_x3lyp:150,hyb_mgga_x_dldf:150,hyb_mgga_x_mn12_sx:150,hyb_mgga_x_mn15:150,hyb_mgga_x_ms2h:150,hyb_mgga_x_mvsh:150,hyb_mgga_x_scan0:150,hyb_mgga_xc_b86b95:150,hyb_mgga_xc_b88b95:150,hyb_mgga_xc_bb1k:150,hyb_mgga_xc_m05:150,hyb_mgga_xc_m05_2x:150,hyb_mgga_xc_m06:150,hyb_mgga_xc_m06_2x:150,hyb_mgga_xc_m06_hf:150,hyb_mgga_xc_m08_hx:150,hyb_mgga_xc_m08_so:150,hyb_mgga_xc_m11:150,hyb_mgga_xc_mpw1b95:150,hyb_mgga_xc_mpwb1k:150,hyb_mgga_xc_pw6b95:150,hyb_mgga_xc_pw86b95:150,hyb_mgga_xc_pwb6k:150,hyb_mgga_xc_revtpssh:150,hyb_mgga_xc_tpssh:150,hyb_mgga_xc_wb97m_v:150,hyb_mgga_xc_x1b95:150,hyb_mgga_xc_xb1k:150,hybersten:186,hybrid:[1,44,48,150,151,201,202,215,231,239],hybrid_cbm:[44,45],hybrid_funct:201,hybrid_vbm:[44,45],hybridcelloptset:201,hybridrelaxset:201,hybridstaticset:201,hydrat:[148,172],hydrogen:[1,68,91,139,146,148,153,195],hydroxid:97,hyperdimension:40,hyperfin:239,hyperplan:[40,48,91],hyperplane_entri:40,i:[1,2,3,4,5,6,15,26,29,34,36,40,48,49,51,53,54,56,58,59,62,63,66,68,70,71,74,78,79,82,85,88,89,91,93,97,98,102,105,113,116,117,118,119,120,122,137,138,143,145,146,148,149,153,154,155,156,157,158,159,160,164,165,167,168,169,170,172,174,175,177,180,182,186,187,188,190,199,200,201,202,208,209,212,215,216,225,226,228,230,233,234,235,238,239,240,250,251,256,257,258,260,263,264,267,268,269,276,277,278,283,289,292],i_:54,i_central_sit:22,i_gw:240,ia:98,ialgo:1,ian496:1,iatom:212,ib:98,ibrion:[239,240],ibz:[186,238],ibzkpt:239,ic102031h:[101,102],icam:165,icharg:240,iclud:1,icobi:[167,223],icohp:[167,170,222,223],icohpcollect:[1,167,223],icohplist:[1,167,222,223],icohpvalu:167,icoop:[167,223],icooplist:[167,222,223],icor:238,icsd:[1,17,32,102,103,146,153,281],icsd_id:182,icsd_oxidation_st:[146,153],icsd_vol:103,id:[1,2,3,4,6,43,102,143,173,179,180,182,183,208,210,215,222,239,264,282,284,292],id_gener:275,idea:[84,197,210,292],ideal:[26,49,79,110,142,153,167,202,223,269],ident:[34,58,59,60,79,98,119,156,165,177,201,231,233,239,265,272],identif:[26,28,36,56,79,139,165,209],identifi:[1,3,22,25,26,28,29,43,56,58,67,68,70,77,79,82,84,101,104,105,110,143,150,165,173,182,199,200,208,210,222,232,238,254,257,260,262,290],identify_potcar:238,ido:239,idx1:195,idx2:195,idx:[59,228],ie:[34,105,157],ieee:[1,77,158],iek:1,ifftn:239,ignor:[1,56,58,71,79,81,84,98,130,153,154,155,173,177,187,188,217,219,238,239,256,283,284],ignore_error:58,ignore_ionic_bond:85,ignore_on:283,ignore_warn:84,ignored_speci:98,igpar:239,igraph:[1,82],igw:79,igw_ep:79,igw_spp:79,igw_ta:79,ii:[1,34,79,98,149,153,154,156,157,269],iii:[45,79,149,154,156,157],iiipi:153,ij:269,ijkl:58,ik:241,ill:169,illustr:[4,6],im:257,imag:[1,20,23,29,49,55,56,66,71,79,87,88,97,109,120,149,154,156,170,212,215,227,240,252,258,269,287,289],imag_partxi:239,imag_partxx:239,imag_partxz:239,imag_partyi:239,imag_partyz:239,imag_partzz:239,image_format:[88,120,289],image_index:97,image_label:71,imagej:97,imagenam:29,imaginari:[96,186,223,239,254,257],imcn:291,img_format:[170,212,258,287],immedi:[200,233,239],immut:[1,146,153,156,292],imolecul:[1,2,156,195,292],impact:[4,6,48,98],imperi:291,implaus:81,implement:[1,12,13,17,21,25,26,28,30,36,40,42,44,45,47,50,51,52,53,54,56,61,62,69,70,75,78,82,84,87,93,98,105,117,122,123,128,130,131,132,133,134,135,137,138,139,140,143,145,146,151,152,155,157,158,160,161,168,170,171,172,173,175,177,180,182,185,186,188,190,197,199,201,210,211,212,215,216,217,219,220,222,223,224,228,229,232,234,235,236,238,239,240,244,247,248,250,251,256,257,258,259,263,267,269,270,272,274,286,289,290,292],implemented_geometri:26,impli:[1,4,6,13,97,98,149,154,156,175,201],implic:105,implicit:[1,232],impos:71,imposs:[98,208],improp:[1,56,66,158,215,240],improv:[1,3,4,5,6,123,138,146,151,175,239,240],imtd:246,in_array_list:262,in_coord_list:276,in_coord_list_pbc:[15,276],in_d:240,in_d_gw:240,in_lay:76,in_plac:[1,154],in_plane_offset:147,in_simplex:276,in_unit_plan:[157,269],inaccur:[109,153,271],inaccuraci:226,inact:257,inb_set:28,inc:[199,291],inc_molecule_graph:56,inc_orient:56,inc_site_id:56,inc_structur:[122,182,239],inc_vertic:56,incar:[1,44,122,168,181,197,221,236,237,238,239,240],incar_input:221,incar_output:221,incar_paramet:1,inch:[62,170,280],inchi:84,inchimolatommapp:84,incid:210,includ:[0,1,3,4,5,6,12,13,15,20,25,26,28,29,41,43,44,45,49,54,55,56,58,59,63,66,67,70,71,74,77,79,88,91,102,105,115,119,122,138,146,147,148,149,152,154,155,156,157,158,159,160,165,167,169,171,172,173,174,175,176,177,181,182,186,187,188,192,196,197,199,201,204,206,210,215,216,221,223,226,231,232,238,239,240,246,256,260,263,264,269,283,292],include_base_prop:58,include_bv_charg:47,include_central_site_in_centroid:28,include_cif:[13,240],include_critical_point:139,include_deactiv:26,include_dist:98,include_gamma:181,include_ignored_speci:98,include_imag:156,include_improp:158,include_index:156,include_mscd_t:55,include_msd_t:55,include_myself:119,include_no_mixing_energi:74,include_reconstruct:157,include_sourc:20,include_unprocessed_entri:91,include_user_ag:182,include_work_of_separ:182,inclus:[146,173,264],inclusionari:269,inclvkb:186,incompat:[1,4,5,6,48,172,196],incomplet:[28,217],inconsist:[55,158,168,177],incorpor:[3,71,151,172,182,239],incorrect:[1,263],incorrectli:1,incr:105,increas:[1,2,29,34,49,63,70,97,103,146,156,182,199,232,238,240,269,279,289],incred:157,increment:[105,165,239],ind1:156,ind2:156,ind:[84,149,204,239],ind_zero_freq:255,inde:188,indent:199,independ:[1,58,59,78,88,105,164,186,192,212,224,239],index1:[97,252],index2:[97,252],index:[1,4,6,15,22,23,25,28,29,30,34,37,44,45,46,49,56,58,59,63,66,67,70,71,72,74,76,77,79,84,85,90,97,105,110,112,137,138,139,143,149,153,154,156,157,158,159,164,165,168,170,182,183,186,187,188,189,191,192,195,199,202,204,208,209,210,211,212,215,218,222,228,232,239,240,241,245,254,255,256,257,263,264,266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:263,order:[1,5,12,17,25,26,28,34,37,38,40,44,45,49,53,55,58,62,63,66,67,71,79,81,82,83,84,85,88,91,94,96,97,98,109,110,116,119,130,138,143,145,146,148,153,154,156,157,158,164,165,167,168,169,170,174,177,182,186,187,190,196,199,201,209,212,216,224,226,231,232,234,238,239,240,254,260,261,262,263,264,269,271,272,292],order_assimil:123,order_paramet:269,order_phase_diagram:88,order_sect:187,orderdisordercompar:1,orderdisorderedstructur:269,orderdisorderedstructuretransform:272,orderdisorderedtransform:269,orderdisorderelementcompar:98,ordered_plan:26,ordered_point_group:26,ordered_structur:[82,143],orderparamet:1,ordin:[1,71],ordinarili:105,ordkei:187,orfc1:263,orfc2:263,orfc3:263,org:[1,4,5,6,40,66,74,84,91,92,93,96,105,113,139,141,152,153,172,173,180,182,183,207,208,234,239,240,242,248,263,264,276,282,290,292],organ:[139,210,291],orient:[43,51,56,70,77,79,98,156,157,182,204,212,234,239,240,292],oriented_unit_cel:[70,157],orig:[173,199],orig_str:196,origin:[3,15,29,34,40,44,55,62,63,71,74,79,84,87,88,98,100,103,109,113,147,149,152,156,157,158,170,172,177,196,199,200,204,208,215,222,239,240,257,258,260,262,264,265,267,269,271,272,276,278],origin_shift:265,origin_sit:260,original_speci:100,original_structur:158,orion:291,orioncohen:1,orth:108,orthogon:[1,34,58,70,79,156,157,158,201,215,269,272,289],orthogonorm:239,orthongonalize_structur:289,orthonorm:[34,40,108],orthonormal_vector:34,orthonormal_vectors_old:2,orthorhomb:[70,149,156,260,269],os:[1,56,85,122,153,240],os_pv:240,os_sv_gw:240,osc_strength:224,oscil:257,oscillatator_strength:257,oscillator_strength:257,oscillatori:212,oskar:291,ostler:143,oszicar:[1,122,130,239],ot:[91,199,201],otero:139,other:[1,2,3,4,5,6,11,15,22,25,26,28,29,30,34,49,51,53,55,58,62,68,70,71,79,81,84,87,88,90,91,97,98,102,103,105,110,112,113,117,118,119,122,132,139,146,149,153,154,155,156,157,165,167,168,169,170,171,172,173,176,177,182,186,187,192,193,194,195,197,199,200,201,202,208,212,215,216,221,222,224,231,232,234,238,239,240,246,255,258,260,269,271,272,273,275,276,277,280,292],other_argu:[269,271,272,273],other_arrai:158,other_dielectr:239,other_direct:192,other_lattic:149,other_nb_set:25,other_origin:29,other_paramet:[12,13],other_plan:53,other_plane_point:26,other_plott:[170,258],other_set:216,other_symmetry_measur:29,others_do:[170,287],otherwis:[1,4,5,6,22,25,29,34,49,52,53,54,55,62,71,79,81,87,97,98,105,112,117,146,149,153,154,156,157,164,165,167,169,170,172,182,186,188,189,192,199,200,211,212,215,221,222,234,238,239,240,243,254,261,269,271,273,276,277,280],ouput:1,our:[1,2,3,4,5,6,66,291],out:[1,3,4,5,6,41,53,63,70,71,79,82,88,97,117,139,148,156,157,182,192,194,195,196,199,200,201,203,211,212,224,225,238,240,243,260,262,269,291,292],outcar:[1,44,66,105,109,130,200,228,239,240],outcar_filenam:105,outer:[201,204],outer_max_scf:201,outermost:157,outfil:87,outlier:84,outlin:[1,3,40,48,79,260,263,290,292],output:[1,2,3,4,5,6,8,9,12,13,15,63,71,79,87,88,97,102,105,122,127,137,138,139,141,143,146,156,159,160,165,167,170,177,182,184,185,187,188,189,192,194,195,196,197,198,199,201,203,204,207,208,210,211,212,214,215,216,220,221,222,224,225,226,228,229,234,236,238,240,241,243,244,247,261,263,269,283,289],output_dir:[12,13,165,199,210,216,238,240],output_fil:[165,238],output_file_def:165,output_file_proj:165,output_filenam:[4,6,246,289],output_list:63,outputfil:225,outputtran:165,outsid:[44,45,97,105,157],outtran:165,outweigh:201,over:[1,4,6,17,28,40,44,53,55,76,98,123,147,153,156,157,158,164,165,169,170,200,201,221,239,264,272,277,292],overal:[43,55,66,156,165,199,201,240,292],overarch:114,overestim:63,overflow:[4,6],overhaul:2,overhead:192,overlaid:280,overlap:[43,49,98,167,170,200,222,223,239],overlap_so_spinpol:108,overlin:[262,283],overload:[13,197,271,272],overrid:[1,26,29,62,63,70,79,146,154,156,157,160,199,201,210,238,240],overridden:[62,146,271,273,283,287],override_default_param:201,override_default_set:201,override_from_prev_calc:240,overriden:5,overstabil:91,overview:[4,6,199,292],overwrit:[79,81,197,200,221,232,238],overwrite_input:232,overwrite_magmom_mod:81,overwritedict:221,overwritemagmommod:81,overwritten:[1,156],own:[0,2,3,4,6,70,74,88,105,110,188,230,232,240,261,292],oxana:[1,291],oxford:264,oxi_overrid:116,oxi_prob:146,oxi_st:[17,153,199,202],oxi_state_guess:[146,156],oxi_states_overrid:146,oxid:[1,11,17,28,40,47,55,63,66,79,83,88,91,97,98,100,102,103,105,116,137,141,146,153,156,157,165,172,174,182,196,199,240,269,271,272,283,292],oxidation_st:[17,153,156,269,272],oxidationstatedecorationtransform:272,oxidationstateremovaltransform:272,oxide_typ:[97,182],oxidetersoffpotentialenti:141,oxidetyp:97,oxiran:68,oxy_overrid:116,oxygen:[25,35,68,88,91,119,148,170,172,222],ozonid:[97,172],p0:284,p0_exponenti:275,p0_reciproc:275,p0_simple_2reciproc:275,p0_simple_4reciproc:275,p0_simple_5reciproc:275,p0_simple_reciproc:275,p0_single_reciproc:275,p1:[34,38,53,146,208,239,283],p2:[34,38,53,239,240,262,283],p2_1:283,p2o5:88,p2o7:174,p3:[34,53],p4:[146,148],p6_3:262,p:[1,5,17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ntum:[3,16,66,168,169,170,192,199,204,223],quantumespresso:1,quantumexpresso:1,quarter:34,quarter_ellipsis_funct:34,quartil:256,quasi:[56,93,201],quasiharmon:[8,9,14,62],quasiharmonicdebyeapprox:[1,93],quasirandom:269,quation:106,qudropol:239,queen:[8,9,114,121,292],quench:48,quench_temperatur:48,queri:[1,117,134,179,182,183],query_snl:182,question:[4,6,49,278],queue:1,quick:[1,4,6,48,130,195,199,201,239,292],quick_gen:[70,269],quick_start:1,quick_view:288,quicker:98,quickli:[4,6,70,156,183,195,224,269,271],quickstep:[199,201],quirki:122,quiro:179,quit:[83,88,201],quot:68,quotat:212,qz:97,r2scan:[177,240],r3:265,r:[3,34,40,44,47,49,53,54,58,61,66,70,79,86,87,92,105,109,110,139,141,143,149,156,157,165,170,172,173,179,182,200,228,233,239,250,251,252,260,262,265,271,289,290,291,292],r_a:152,r_angl:70,r_axi:70,r_b:152,r_fraction:269,r_i:66,r_mass:212,r_matrix:70,r_unit:105,r_vec:44,ra:[26,56,85,153,240,291],ra_sv:240,rachel:291,rad_dict:248,radhakrishnan:[105,110,157,182,290],radial:[30,105,271],radialsitedistortiontransform:[1,271],radian:[53,79,152,156,272,276],radiat:[1,52,54],radii:[1,49,56,79,97,100,103,153,156,230,232,239,248,269,288,289],radii_diff:100,radii_typ:103,radiu:[1,15,17,38,44,45,49,51,52,54,56,61,63,66,79,85,97,103,105,110,145,149,153,156,201,204,208,210,230,232,239,248,252,272,288,289],radius_typ:153,rae:183,rai:[52,53,64,111,112,113,153,182],rais:[12,13,17,28,29,30,34,37,43,58,71,79,84,141,146,153,154,156,160,165,172,174,177,182,187,188,189,190,192,197,199,208,225,231,233,238,260,265,272,284],raise_error_if_unphys:58,raise_on_fail:37,rajeshsharma98:291,rajput:1,ram:[201,239],rambalachandran:239,ramp:199,ran:[172,200],ran_successfulli:200,rand_piezo:90,random:[28,34,90,156,199,218,225,269,272],random_rot:[28,156],random_scal:28,random_transl:28,randomli:[105,269],randomrotorsearch:195,rang:[1,2,44,48,49,51,52,54,79,87,88,91,105,106,119,138,142,153,157,165,169,170,183,188,226,230,234,240,257,258,260,269,279,280],range1:105,range2:105,range_tol:[15,269],rangeo:105,rank:[17,58,61,146,152,158,187,239,269,271,273],ranked_compositions_from_indeterminate_formula:146,rapid:180,rappres:170,rare:[1,2,56,153,157,240,260],rare_earth_met:146,rate:60,rather:[1,5,13,58,59,60,66,86,88,89,90,97,98,118,137,148,152,156,158,168,195,230,232,238,240,251,272,283,287,292],ratio:[1,25,26,36,58,62,70,74,78,85,87,93,153,170,182,269,280],ratio_alpha:70,ratiofunct:36,ration:[1,36,70],raton:153,rattl:269,rattle_std:269,raug:238,raw:[137,149,182,209,238,239,264],rb2o2:146,rb:[56,85,153,240],rb_pv:240,rb_sv:240,rb_sv_gw:240,rbo:146,rc:26,rcloc:238,rcond:90,rcondi:90,rcore:238,rct:292,rcubed_mo:138,rcut2:238,rcut:238,rdep:238,rdept:238,rdf:[0,4,6,30],rdvxcpsi:211,rdylbu_r:91,re:[1,56,67,84,85,88,153,182,192,240,254,256,257,289],re_pv:240,re_sv_gw:240,reach:[105,141,199,239,254,260],reachabl:20,reactant1:[74,182],reactant2:[74,182],reactant:[1,74,94,182],reactant_entri:94,reactants_coeff:94,reaction:[1,4,6,40,74,88,91,94,109,118,172,176,182],reaction_calcul:[8,9,14,74,118,182,292],reaction_energi:74,reaction_equ:74,reactiondiagram:[1,88],reactionerror:94,read:[0,1,4,5,6,41,58,79,105,109,127,138,139,141,149,152,156,157,158,159,165,187,188,189,192,194,195,196,197,199,200,203,204,206,208,210,211,212,215,216,219,221,223,224,225,228,230,232,233,234,238,239,240,241,242,243,248],read_abinit_hdr:189,read_abinit_xcfunc:189,read_avg_core_pot:239,read_avg_core_poten:239,read_chemical_shield:239,read_core_state_eigen:239,read_core_state_eign:239,read_correct:239,read_cs_core_contribut:239,read_cs_g0_contribut:239,read_cs_raw_symmetrized_tensor:239,read_cube_fil:[165,170],read_data:[215,216],read_dimvalu:189,read_elastic_tensor:239,read_electrostatic_potenti:239,read_excitation_energi:212,read_fermi_contact_shift:239,read_freq_dielectr:239,read_igpar:239,read_internal_strain_tensor:239,read_kei:189,read_lcalcpol:239,read_lepsilon:239,read_lepsilon_ion:239,read_mol:1,read_molecul:230,read_nbo:230,read_neb:239,read_nmr_efg:239,read_nmr_efg_tensor:239,read_onsite_density_matric:239,read_opt:230,read_pattern:[200,228,233,239],read_pcm:230,read_piezo_tensor:239,read_plot:230,read_pseudo_zv:239,read_rem:230,read_route_lin:212,read_scan:[212,230],read_sect:230,read_smx:230,read_solv:230,read_structur:[1,189],read_table_pattern:[200,233,239],read_valu:189,read_vari:189,read_varnam:189,read_vdw:230,read_veloc:238,readabl:[1,173,183,190,199,280,292],readable_fontcolor:280,reader:[189,199,211,238,239],readi:[3,183],readjust:79,readm:140,real:[3,25,29,44,49,55,61,63,79,87,96,97,165,181,186,199,201,223,234,238,239,257,261,263],real_partxi:239,real_partxx:239,real_partxz:239,real_partyi:239,real_partyz:239,real_partzz:239,real_space_cut:[61,63],real_space_energi:63,real_space_energy_matrix:63,real_vector:44,realli:[49,271],realspacehamiltonian:221,realspaceoverlap:221,reanalyz:[127,130],reason:[1,2,11,66,79,87,97,98,139,160,168,177,188,199,201,208,238,240,271],rec_lattic:263,recalcul:[88,199],receiv:[45,148,186,188,271],recent:[1,4,6,79],recip:[49,197,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,142,146,149,152,153,154,156,157,158,160,164,165,167,168,169,170,171,172,173,174,175,177,182,183,190,195,196,197,199,200,201,202,204,208,210,211,212,215,219,221,222,223,224,225,226,228,233,238,239,240,243,254,255,256,257,258,260,261,263,264,269,271,272,273,275,276,277,278,280,283,287,289,290,292],which_charg:222,white:280,whitespac:278,who:[4,6,40,70,157,215,240,291,292],whole:[53,149,165,210,223,240],whom:[4,6],whose:[28,34,49,53,79,87,90,105,182,187,199,230],why:[66,98,199,208,238],wi:238,wiberg:212,wide:[138,179,201,204,272],wider:1,widom:239,width:[15,44,49,62,79,81,87,120,156,169,170,200,212,224,269,280,289],widthsampl:44,wigner:[1,44,45,97,139,149,170,238],wiki:[1,5,84,152,153,161,168,237,240,276],wikipedia:[84,152,153,276],wild:[1,182,292],wildcard:[182,190,217],wilei:[86,110,140],willem:[248,290],william:[1,4,6,78],wimperi:86,win:1,window:[1,2,4,6,15,88,289],winner:291,winston:[105,110,157,182,290,291],wip:3,wire:56,wisconsin:291,wise:[112,239],wisesa:[181,240],wish:[44,63,113,271,290,292],with_dojo_report:190,with_edg:71,with_empty_graph:71,with_head:187,with_label:51,with_lf:186,with_local_env_strategi:71,with_pseudo:188,with_structur:188,within:[1,2,3,11,15,25,34,40,43,45,48,49,51,52,53,54,68,70,78,79,81,87,88,98,105,117,118,119,146,149,154,156,157,158,172,187,199,201,225,239,248,252,254,260,263,275,276,292],without:[1,2,4,6,28,29,37,43,49,53,67,74,81,84,85,88,98,108,146,153,156,157,158,165,169,182,183,186,192,199,200,201,210,215,233,238,239,240,260,263,278,291,292],wmdrichard:291,wn:[142,269],wo4:174,wo:239,won:[91,110,123,165],wood:[1,157,291],woods_not:157,woodward:46,word:[71,215],work:[1,2,3,4,5,6,11,17,43,49,56,62,70,74,87,88,91,92,96,102,103,105,113,116,117,118,119,120,122,138,139,146,152,153,154,155,156,157,160,164,168,169,174,176,177,179,180,182,197,199,201,203,211,215,223,224,225,231,238,239,240,241,243,245,260,262,269,272,276,283,284,290,291,292],work_funct:105,worker:153,workflow:[1,4,6,16],workfunctionanalyz:105,working_dir:245,working_ion:[49,116,117],working_ion_entri:[117,118,119],working_ion_symbol:118,workshop:[4,6],world:[3,4,6,179],worst:[84,187],would:[3,4,5,6,11,12,34,45,49,55,98,102,117,118,142,146,149,153,156,157,168,170,172,188,192,199,201,208,210,238,239,240,269,291,292],wq:239,wq_:239,wr:[142,269],wrap:[1,189,289],wrapper:[5,46,58,61,62,71,136,152,158,167,169,189,195,196,218,255],write:[0,1,2,4,6,12,13,49,55,88,139,146,156,159,165,168,170,175,187,188,192,194,196,197,199,200,201,203,206,208,210,211,212,215,216,218,219,221,225,227,228,230,232,234,235,238,239,240,241,243,245,247,254,258,278,287],write_cif:240,write_cml:139,write_cub:[199,201],write_def:165,write_endpoint_input:240,write_energi:165,write_etre:206,write_fil:[192,195,196,197,199,203,206,208,211,212,215,216,219,223,224,228,238,239,241,243,247,292],write_imag:[88,289],write_incar:221,write_input:[165,197,210,216,238,240,292],write_input_fil:245,write_intran:165,write_json:[139,257],write_kpoint:221,write_lammps_input:216,write_lobsterin:221,write_magmom:196,write_mol:1,write_multi_job_fil:230,write_path_cif:240,write_phononwebsit:254,write_poscar_with_standard_primit:221,write_proj:165,write_str:206,write_struct:165,write_structur:1,write_topolog:49,write_unk:239,write_vasp_input:[12,13],write_xdatcar:159,writeabl:278,writebasisfunct:221,writematricestofil:221,writer:[192,238],written:[1,3,4,6,16,55,88,141,146,148,156,189,197,204,208,215,216,221,225,234,235,238,239,247,248,256,276,290,292],wrong:[1,70,172,192,240],wrongli:153,wrt:[62,88,93,105,158],wrt_cder_between_states_format:239,ws:139,wswq:[1,239],wsyxbcl:[1,291],wu:291,wulff:[1,8,9,14,105,182],wulff_area:110,wulff_cv_simp:110,wulff_from_chempot:105,wulff_gform_and_r:105,wulff_pt_list:110,wulfffacet:110,wulffshap:[1,105,110,182],wuxiaohua1011:1,www:[1,4,5,6,49,63,108,142,151,153,165,182,183,208,221,223,239,240,242,248,264,292],wyckoff:[1,43,82,196,260,267],wyckoff_id:82,wyckoff_lett:267,x0:40,x1:[34,40,48,109],x2:[34,109,153,211],x2y2:146,x3:153,x86_64:[4,5,6],x:[1,2,4,6,13,28,34,36,44,48,49,51,52,53,55,64,71,74,85,88,105,111,112,113,120,140,142,143,146,149,152,153,154,155,156,158,161,164,165,168,169,170,173,182,201,204,208,211,215,222,238,239,247,248,250,251,255,258,269,271,275,276,280,283,287],x_0:155,x_c:92,x_charg:117,x_cross:48,x_diff_weight:79,x_discharg:117,x_form:120,x_min:74,x_name:161,x_ray_factor:53,x_valu:[275,276],x_y0:34,xa:[1,8,9,14,155,182,212,287],xaf:112,xane:[112,155,182,208,209,210],xanes_k:112,xangst:186,xarg:[1,2,4,6],xas_list:112,xavier:[28,211],xaxi:120,xc:[150,161,192,199,202,224],xc_:[150,161],xc_correl:150,xc_famili:150,xc_family_lda:150,xc_function:[161,199],xcart:186,xcenc:239,xcfunc:[8,9,144,150,189],xcode:5,xcrysden:[1,8,9,184],xdatacar:1,xdatcar:[1,159,239],xdatcar_from_struct:159,xe2o:182,xe:[56,85,153,210,240],xe_gw:240,xhi:[91,225],xhqu1981:291,xiangguo:[1,291],xiao:[1,74,291],xiaohui:[1,86],xin:[1,169,224,291],xlabel:[51,64,112,113,155,169,280],xlim:[48,88,105,170,222,257,258,287],xlo:[91,225],xmcd:210,xml:[1,4,6,7,55,96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Add-ons","Change log","Compatibility","Contributing","Introduction","Installation","Introduction","Change log","pymatgen","pymatgen namespace","pymatgen.alchemy package","pymatgen.alchemy.filters module","pymatgen.alchemy.materials module","pymatgen.alchemy.transmuters module","pymatgen.analysis namespace","pymatgen.analysis.adsorption module","pymatgen.analysis.bond_dissociation module","pymatgen.analysis.bond_valence module","pymatgen.analysis.chemenv package","pymatgen.analysis.chemenv.connectivity package","pymatgen.analysis.chemenv.connectivity.connected_components module","pymatgen.analysis.chemenv.connectivity.connectivity_finder module","pymatgen.analysis.chemenv.connectivity.environment_nodes module","pymatgen.analysis.chemenv.connectivity.structure_connectivity module","pymatgen.analysis.chemenv.coordination_environments package","pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies module","pymatgen.analysis.chemenv.coordination_environments.coordination_geometries module","pymatgen.analysis.chemenv.coordination_environments.coordination_geometries_files package","pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder module","pymatgen.analysis.chemenv.coordination_environments.structure_environments module","pymatgen.analysis.chemenv.coordination_environments.voronoi module","pymatgen.analysis.chemenv.utils package","pymatgen.analysis.chemenv.utils.chemenv_config module","pymatgen.analysis.chemenv.utils.chemenv_errors module","pymatgen.analysis.chemenv.utils.coordination_geometry_utils module","pymatgen.analysis.chemenv.utils.defs_utils module","pymatgen.analysis.chemenv.utils.func_utils module","pymatgen.analysis.chemenv.utils.graph_utils module","pymatgen.analysis.chemenv.utils.math_utils module","pymatgen.analysis.chemenv.utils.scripts_utils module","pymatgen.analysis.chempot_diagram module","pymatgen.analysis.cost module","pymatgen.analysis.defects package","pymatgen.analysis.defects.core module","pymatgen.analysis.defects.corrections module","pymatgen.analysis.defects.defect_compatibility module","pymatgen.analysis.defects.dilute_solution_model module","pymatgen.analysis.defects.generators module","pymatgen.analysis.defects.thermodynamics module","pymatgen.analysis.defects.utils module","pymatgen.analysis.diffraction package","pymatgen.analysis.diffraction.core module","pymatgen.analysis.diffraction.neutron module","pymatgen.analysis.diffraction.tem module","pymatgen.analysis.diffraction.xrd module","pymatgen.analysis.diffusion_analyzer module","pymatgen.analysis.dimensionality module","pymatgen.analysis.elasticity package","pymatgen.analysis.elasticity.elastic module","pymatgen.analysis.elasticity.strain module","pymatgen.analysis.elasticity.stress module","pymatgen.analysis.energy_models module","pymatgen.analysis.eos module","pymatgen.analysis.ewald module","pymatgen.analysis.excitation module","pymatgen.analysis.ferroelectricity package","pymatgen.analysis.ferroelectricity.polarization module","pymatgen.analysis.fragmenter module","pymatgen.analysis.functional_groups module","pymatgen.analysis.gb package","pymatgen.analysis.gb.grain module","pymatgen.analysis.graphs module","pymatgen.analysis.hhi module","pymatgen.analysis.interface module","pymatgen.analysis.interface_reactions module","pymatgen.analysis.interfaces package","pymatgen.analysis.interfaces.coherent_interfaces module","pymatgen.analysis.interfaces.substrate_analyzer module","pymatgen.analysis.interfaces.zsl module","pymatgen.analysis.local_env module","pymatgen.analysis.magnetism package","pymatgen.analysis.magnetism.analyzer module","pymatgen.analysis.magnetism.heisenberg module","pymatgen.analysis.magnetism.jahnteller module","pymatgen.analysis.molecule_matcher module","pymatgen.analysis.molecule_structure_comparator module","pymatgen.analysis.nmr module","pymatgen.analysis.path_finder 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\ No newline at end of file diff --git a/docs/team.html b/docs/team.html index 4d7223a8046..d03ebb37cf3 100644 --- a/docs/team.html +++ b/docs/team.html @@ -4,7 +4,7 @@ - Development Team — pymatgen 2022.5.18 documentation + Development Team — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                      - 2022.5.18 + 2022.5.18.1
                                                      diff --git a/docs/usage.html b/docs/usage.html index efa30b9dd46..29cd08cae38 100644 --- a/docs/usage.html +++ b/docs/usage.html @@ -4,7 +4,7 @@ - Usage — pymatgen 2022.5.18 documentation + Usage — pymatgen 2022.5.18.1 documentation @@ -39,7 +39,7 @@ pymatgen
                                                      - 2022.5.18 + 2022.5.18.1
                                                      diff --git a/docs_rst/change_log.rst b/docs_rst/change_log.rst index 58bafce2acf..78c8342f331 100644 --- a/docs_rst/change_log.rst +++ b/docs_rst/change_log.rst @@ -1,6 +1,10 @@ Change log ========== +v2022.5.18.1 +------------ +* Initial support for parsing ML MD runs from vasprun.xml (@shyuep). + v2022.5.18 ---------- * Bug fix for sulfide_type. Sometimes symmetry analysis fails because of tolerance issues. A fallback to analyze all sites. diff --git a/docs_rst/latest_changes.rst b/docs_rst/latest_changes.rst index 57b56cd2519..d95d643725d 100644 --- a/docs_rst/latest_changes.rst +++ b/docs_rst/latest_changes.rst @@ -1,6 +1,6 @@ Change log ========== -v2022.5.18 ----------- -* Bug fix for sulfide_type. Sometimes symmetry analysis fails because of tolerance issues. A fallback to analyze all sites. +v2022.5.18.1 +------------ +* Initial support for parsing ML MD runs from vasprun.xml (@shyuep). diff --git a/pymatgen/core/__init__.py b/pymatgen/core/__init__.py index ef28fecb258..a1b9c6dc123 100644 --- a/pymatgen/core/__init__.py +++ b/pymatgen/core/__init__.py @@ -23,7 +23,7 @@ __email__ = "pymatgen@googlegroups.com" __maintainer__ = "Shyue Ping Ong" __maintainer_email__ = "shyuep@gmail.com" -__version__ = "2022.5.18" +__version__ = "2022.5.18.1" SETTINGS_FILE = os.path.join(os.path.expanduser("~"), ".pmgrc.yaml") diff --git a/setup.py b/setup.py index 396aabef960..499e2976012 100644 --- a/setup.py +++ b/setup.py @@ -76,7 +76,7 @@ include=["pymatgen.*", "pymatgen.analysis.*", "pymatgen.io.*", "pymatgen.ext.*"], exclude=["pymatgen.*.tests", "pymatgen.*.*.tests", "pymatgen.*.*.*.tests"], ), - version="2022.5.18", + version="2022.5.18.1", python_requires=">=3.8", setup_requires=[ "Cython>=0.29.23",