diff --git a/docs/apidoc/conf.py b/docs/apidoc/conf.py
index fe33a4e80b8..997b86a1608 100644
--- a/docs/apidoc/conf.py
+++ b/docs/apidoc/conf.py
@@ -362,4 +362,4 @@ def find_source():
# no need to be relative to core here as module includes full path.
filename = info["module"].replace(".", "/") + ".py"
- return f"https://github.com/materialsproject/pymatgen/blob/v{__version__}/{filename}"
+ return f"https://github.com/materialsproject/pymatgen/blob/v{__version__}/src/{filename}"
diff --git a/docs/pymatgen.alchemy.html b/docs/pymatgen.alchemy.html
index a036e5f2ecc..70a81f96363 100644
--- a/docs/pymatgen.alchemy.html
+++ b/docs/pymatgen.alchemy.html
@@ -175,13 +175,13 @@
Submodules[source]
Bases: MSONable
, ABC
Structures that return True when passed to the test() method are retained during
transmutation. Those that return False are removed.
-
-abstract test(structure: Structure)[source]
+abstract test(structure: Structure)[source]
Structures that return true are kept in the Transmuter object during filtering.
- Parameters:
@@ -200,7 +200,7 @@ Submodules[source]
Bases: AbstractStructureFilter
This filter removes structures that are not charge balanced from the
transmuter. This only works if the structure is oxidation state
@@ -209,7 +209,7 @@
Submodules[source]
True if structure is neutral.
@@ -217,7 +217,7 @@ Submodules[source]
Bases: AbstractStructureFilter
Filter for structures containing certain elements or species.
By default compares by atomic number.
@@ -235,13 +235,13 @@ Submodules[source]
Get MSONable dict.
-
-classmethod from_dict(dct: dict) → Self[source]
+classmethod from_dict(dct: dict) → Self[source]
- Parameters:
dct (dict) – Dict representation.
@@ -254,7 +254,7 @@ Submodules[source]
True if structure does not contain specified species.
@@ -262,7 +262,7 @@ Submodules[source]
Bases: AbstractStructureFilter
This filter removes exact duplicate structures from the transmuter.
Remove duplicate structures based on the structure matcher
@@ -280,7 +280,7 @@
Submodules[source]
- Parameters:
structure (Structure) – Input structure to test.
@@ -298,7 +298,7 @@ Submodules[source]
Bases: AbstractStructureFilter
This filter removes structures existing in a given list from the transmuter.
Remove existing structures based on the structure matcher
@@ -317,13 +317,13 @@
Submodules[source]
Get MSONable dict.
-
-test(structure: Structure)[source]
+test(structure: Structure)[source]
True if structure is not in existing list.
@@ -331,7 +331,7 @@ Submodules[source]
Bases: AbstractStructureFilter
This filter removes structures that have certain species that are too close together.
@@ -346,13 +346,13 @@ Submodules[source]
Get MSONable dict.
-
-classmethod from_dict(dct: dict) → Self[source]
+classmethod from_dict(dct: dict) → Self[source]
- Parameters:
dct (dict) – Dict representation.
@@ -365,7 +365,7 @@ Submodules[source]
True if structure does not contain species within specified distances.
@@ -373,7 +373,7 @@ Submodules[source]
Bases: 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
@@ -393,7 +393,7 @@
Submodules[source]
True if structure contains the two species but their distance is greater than max_dist.
@@ -407,7 +407,7 @@ Submodules[source]
Bases: MSONable
Container for new structures that include history of transformations.
Each transformed structure is made up of a sequence of structures with
@@ -425,7 +425,7 @@
Submodules[source]
Add a filter.
- Parameters:
@@ -437,7 +437,7 @@ Submodules[source]
Append a transformation to the TransformedStructure.
- Parameters:
@@ -459,13 +459,13 @@ Submodules[source]
Dict representation of the TransformedStructure.
-
-extend_transformations(transformations: list[AbstractTransformation], return_alternatives: bool = False) → None[source]
+extend_transformations(transformations: list[AbstractTransformation], return_alternatives: bool = False) → None[source]
Extend a sequence of transformations to the TransformedStructure.
- Parameters:
@@ -482,7 +482,7 @@ Submodules[source]
Generate TransformedStructure from a CIF string.
- Parameters:
@@ -510,13 +510,13 @@ Submodules[source]
Create a TransformedStructure from a dict.
-
-classmethod from_poscar_str(poscar_string: str, transformations: list[AbstractTransformation] | None = None) → Self[source]
+classmethod from_poscar_str(poscar_string: str, transformations: list[AbstractTransformation] | None = None) → Self[source]
Generate TransformedStructure from a poscar string.
- Parameters:
@@ -531,7 +531,7 @@ Submodules[source]
Create TransformedStructure from SNL.
- Parameters:
@@ -545,7 +545,7 @@ Submodules[source]
Get VASP input as a dict of VASP objects.
- Parameters:
@@ -560,7 +560,7 @@ Submodules[source]
Redo the last undone change in the TransformedStructure.
- Raises:
@@ -571,7 +571,7 @@ Submodules[source]
Set a parameter.
- Parameters:
@@ -588,14 +588,14 @@ Submodules[source]
Copy of all structures in the TransformedStructure. A
structure is stored after every single transformation.
-
-to_snl(authors: list[str], **kwargs) → StructureNL[source]
+to_snl(authors: list[str], **kwargs) → StructureNL[source]
Generate a StructureNL from TransformedStructure.
- Parameters:
@@ -615,7 +615,7 @@ Submodules[source]
Undo the last change in the TransformedStructure.
- Raises:
@@ -626,7 +626,7 @@ Submodules[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
@@ -635,7 +635,7 @@
Submodules[source]
Write VASP input to an output_dir.
- Parameters:
@@ -664,7 +664,7 @@ Submodules[source]
Bases: StandardTransmuter
Generate a Transmuter from a CIF string, possibly containing multiple structures.
Generate a Transmuter from a CIF string, possibly
@@ -685,7 +685,7 @@
Submodules[source]
Generate a TransformedStructureCollection from a cif, possibly
containing multiple structures.
@@ -705,7 +705,7 @@ Submodules[source]
Bases: StandardTransmuter
Generate a transmuter from a sequence of POSCARs.
@@ -721,7 +721,7 @@ Submodules[source]
Convenient constructor to generates a POSCAR transmuter from a list of
POSCAR filenames.
@@ -740,13 +740,13 @@ Submodules[source]
Bases: object
An example of a Transmuter object, which performs a sequence of
transformations on many structures to generate TransformedStructures.
-
-transformed_structures[source]
+transformed_structures[source]
List of all transformed structures.
- Type:
@@ -776,7 +776,7 @@ Submodules[source]
Add tags for the structures generated by the transmuter.
- Parameters:
@@ -788,7 +788,7 @@ Submodules[source]
Append a transformation to all TransformedStructures.
- Parameters:
@@ -818,7 +818,7 @@ Submodules[source]
Overloaded to accept either a list of transformed structures
or transmuter, it which case it appends the second transmuter’s structures.
@@ -830,7 +830,7 @@ Submodules[source]
Apply a structure_filter to the list of TransformedStructures
in the transmuter.
@@ -842,7 +842,7 @@ Submodules[source]
Extend a sequence of transformations to the TransformedStructure.
- Parameters:
@@ -853,7 +853,7 @@ Submodules[source]
Alternative constructor from structures rather than
TransformedStructures.
@@ -876,7 +876,7 @@ Submodules[source]
Redo the last undone transformation in the TransformedStructure.
- Raises:
@@ -887,7 +887,7 @@ Submodules[source]
Add parameters to the transmuter. Additional parameters are stored in
the as_dict() output.
@@ -902,7 +902,7 @@ Submodules[source]
Undo the last transformation in the TransformedStructure.
- Raises:
@@ -913,7 +913,7 @@ Submodules[source]
Batch write vasp input for a sequence of transformed structures to
output_dir, following the format output_dir/{formula}_{number}.
@@ -927,7 +927,7 @@ Submodules[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.chemenv.connectivity.html b/docs/pymatgen.analysis.chemenv.connectivity.html
index 325d6cc2b0e..32c1b704951 100644
--- a/docs/pymatgen.analysis.chemenv.connectivity.html
+++ b/docs/pymatgen.analysis.chemenv.connectivity.html
@@ -175,7 +175,7 @@ Submodules[source]
Bases: MSONable
Describe the connected components in a structure in terms of coordination environments.
Constructor for the ConnectedComponent object.
@@ -198,7 +198,7 @@ Submodules[source]
Bson-serializable dict representation of the ConnectedComponent object.
- Returns:
@@ -212,7 +212,7 @@ Submodules[source]
- Parameters:
algorithm (str) – Algorithm to use to compute the periodicity vectors. Can be
@@ -223,19 +223,19 @@
Submodules[source]
Get the periodicity vectors of the connected component.
-
-compute_periodicity_cycle_basis() → None[source]
+compute_periodicity_cycle_basis() → None[source]
Compute periodicity vectors of the connected component.
-
-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:
@@ -285,7 +285,7 @@ Submodules[source]
- Parameters:
full (bool) – Whether to return a short or full description.
@@ -301,7 +301,7 @@ Submodules[source]
- Parameters:
start_node (Node, optional) – Node to start the elastic centering from.
@@ -318,7 +318,7 @@
Submodules[source]
Reconstructs the ConnectedComponent object from a dict representation of the
ConnectedComponent object created using the as_dict method.
@@ -336,7 +336,7 @@ Submodules[source]
Constructor for the ConnectedComponent object from a graph of the connected component.
- Parameters:
@@ -353,44 +353,44 @@ Submodules[source]
The Networkx MultiGraph object of this connected component with environment as nodes and links
between these nodes as edges with information about the image cell difference if any.
-
-property is_0d: bool[source]
+property is_0d: bool[source]
Whether this connected component is 0-dimensional.
-
-property is_1d: bool[source]
+property is_1d: bool[source]
Whether this connected component is 1-dimensional.
-
-property is_2d: bool[source]
+property is_2d: bool[source]
Whether this connected component is 2-dimensional.
-
-property is_3d: bool[source]
+property is_3d: bool[source]
Whether this connected component is 3-dimensional.
-
-property is_periodic: bool[source]
+property is_periodic: bool[source]
Whether this connected component is periodic.
-
-make_supergraph(multiplicity)[source]
+make_supergraph(multiplicity)[source]
- Parameters:
multiplicity (int) – Multiplicity of the super graph.
@@ -406,19 +406,19 @@ Submodules[source]
Periodicity of this connected component.
-
-property periodicity_vectors[source]
+property periodicity_vectors[source]
Periodicity vectors of this connected component.
-
-show_graph(graph: MultiGraph | None = None, save_file: str | None = None, drawing_type: str = 'internal') → None[source]
+show_graph(graph: MultiGraph | None = None, save_file: str | None = None, drawing_type: str = 'internal') → None[source]
Displays the graph using the specified drawing type.
- Parameters:
@@ -436,7 +436,7 @@ Submodules[source]
Draw network of environments in a matplotlib figure axes.
- Parameters:
@@ -453,7 +453,7 @@ Submodules[source]
Make super graph from a graph of environments.
- Parameters:
@@ -478,7 +478,7 @@ Submodules[source]
Bases: object
Main class used to find the structure connectivity of a structure.
Constructor for the ConnectivityFinder.
@@ -493,7 +493,7 @@ Submodules[source]
Get the structure connectivity from the coordination environments provided
as an input.
@@ -512,7 +512,7 @@ Submodules[source]
Setup of the parameters for the connectivity finder.
@@ -524,7 +524,7 @@ Submodules[source]
Bases: MSONable
Abstract class used to define an environment as a node in a graph.
Constructor for the AbstractEnvironmentNode object.
@@ -539,104 +539,104 @@
-
-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]
Check 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.
@@ -644,7 +644,7 @@ Submodules[source]
Bases: AbstractEnvironmentNode
Define an environment as a node in a graph.
Constructor for the EnvironmentNode object.
@@ -660,13 +660,13 @@ Submodules[source]
Coordination environment of this node.
-
-everything_equal(other)[source]
+everything_equal(other)[source]
Compare with another environment node.
- Returns:
@@ -682,7 +682,7 @@ Submodules[source]
Get the EnvironmentNode class or subclass for the given site and symbol.
- Parameters:
@@ -704,7 +704,7 @@ Submodules[source]
Bases: MSONable
Main class containing the connectivity of a structure.
Constructor for the StructureConnectivity object.
@@ -725,7 +725,7 @@ Submodules[source]
Add the bonds for a given site index to the structure connectivity graph.
- Parameters:
@@ -739,19 +739,19 @@ Submodules[source]
Add the sites in the structure connectivity graph.
-
-as_dict()[source]
+as_dict()[source]
Convert to MSONable dict.
-
-environment_subgraph(environments_symbols=None, only_atoms=None)[source]
+environment_subgraph(environments_symbols=None, only_atoms=None)[source]
- Parameters:
@@ -770,7 +770,7 @@ Submodules[source]
- Parameters:
dct (dict)
@@ -783,33 +783,33 @@
-
-print_links() → None[source]
+print_links() → None[source]
Print all links in the graph.
-
-setup_atom_environment_subgraph(atom_environment)[source]
+setup_atom_environment_subgraph(atom_environment)[source]
-
-setup_atom_environments_subgraph(atoms_environments)[source]
+setup_atom_environments_subgraph(atoms_environments)[source]
-
-setup_connectivity_description()[source]
+setup_connectivity_description()[source]
-
-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:
@@ -823,14 +823,14 @@
-
-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.html b/docs/pymatgen.analysis.chemenv.coordination_environments.html
index 9794c27e85f..295f97887a8 100644
--- a/docs/pymatgen.analysis.chemenv.coordination_environments.html
+++ b/docs/pymatgen.analysis.chemenv.coordination_environments.html
@@ -557,7 +557,7 @@ Submodules[source]
Bases: MSONable
, ABC
Base class to define a Chemenv strategy for the neighbors and coordination environment
to be applied to a StructureEnvironments object.
@@ -570,32 +570,32 @@
-
-DEFAULT_SYMMETRY_MEASURE_TYPE = 'csm_wcs_ctwcc'[source]
+DEFAULT_SYMMETRY_MEASURE_TYPE = 'csm_wcs_ctwcc'[source]
-
-STRATEGY_DESCRIPTION: str | None = None[source]
+STRATEGY_DESCRIPTION: str | None = None[source]
-
-STRATEGY_INFO_FIELDS: ClassVar[list] = [][source]
+STRATEGY_INFO_FIELDS: ClassVar[list] = [][source]
-
-STRATEGY_OPTIONS: ClassVar[dict[str, dict]] = {}[source]
+STRATEGY_OPTIONS: ClassVar[dict[str, dict]] = {}[source]
-
-abstract as_dict()[source]
+abstract as_dict()[source]
Bson-serializable dict representation of the SimplestChemenvStrategy object.
- Returns:
@@ -606,7 +606,7 @@ Submodules[source]
Get the equivalent site and corresponding symmetry+translation transformations.
- Parameters:
@@ -620,7 +620,7 @@ Submodules[source]
Reconstructs the SimpleAbundanceChemenvStrategy object from a dict representation of the
SimpleAbundanceChemenvStrategy object created using the as_dict method.
@@ -635,7 +635,7 @@ Submodules[source]
Applies the strategy to the structure_environments object in order to get coordination environments, their
fraction, csm, geometry_info, and neighbors.
@@ -651,7 +651,7 @@ Submodules[source]
Applies the strategy to the structure_environments object in order to define the coordination environment of
a given site.
@@ -667,7 +667,7 @@ Submodules[source]
Applies the strategy to the structure_environments object in order to define the coordination environment of
a given site.
@@ -683,7 +683,7 @@ Submodules[source]
Applies the strategy to the structure_environments object in order to define the coordination environment of
a given site.
@@ -699,7 +699,7 @@ Submodules[source]
Applies the strategy to the structure_environments object in order to get the neighbors of a given site.
- Parameters:
@@ -718,13 +718,13 @@ Submodules[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:
@@ -738,7 +738,7 @@ Submodules[source]
Set the structure environments to this strategy.
- Parameters:
@@ -749,7 +749,7 @@ Submodules[source]
Set up options for this strategy based on a dict.
- Parameters:
@@ -760,13 +760,13 @@ Submodules[source]
Type of symmetry measure.
-
-property uniquely_determines_coordination_environments[source]
+property uniquely_determines_coordination_environments[source]
True if the strategy leads to a unique coordination environment.
@@ -774,29 +774,29 @@ Submodules[source]
Bases: int
, StrategyOption
Integer representing an additional condition in a strategy.
Special int representing additional conditions.
-
-allowed_values: str | None = "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: str | None = "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(dct: dict) → Self[source]
+classmethod from_dict(dct: dict) → Self[source]
Initialize additional condition from dict.
- Parameters:
@@ -807,14 +807,14 @@
-
-class AngleCutoffFloat(cutoff)[source]
+class AngleCutoffFloat(cutoff)[source]
Bases: float
, StrategyOption
Angle cutoff in a strategy.
Special float that should be between 0 and 1.
@@ -825,18 +825,18 @@
-
-as_dict()[source]
+as_dict()[source]
MSONable dict.
-
-classmethod from_dict(dct: dict) → Self[source]
+classmethod from_dict(dct: dict) → Self[source]
Initialize angle cutoff from dict.
- Parameters:
@@ -849,7 +849,7 @@ Submodules[source]
Bases: NbSetWeight
Weight of neighbors set based on the angle.
Initialize AngleNbSetWeight estimator.
@@ -860,12 +860,12 @@
-
-static angle_sum(nb_set)[source]
+static angle_sum(nb_set)[source]
Sum of all angles in a neighbors set.
- Parameters:
@@ -879,7 +879,7 @@ Submodules[source]
Sum of all angles to a given power in a neighbors set.
- Parameters:
@@ -893,19 +893,19 @@ Submodules[source]
MSONable dict.
-
-classmethod from_dict(dct: dict) → Self[source]
+classmethod from_dict(dct: dict) → Self[source]
Construct AngleNbSetWeight from dict representation.
-
-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:
@@ -929,7 +929,7 @@ Submodules[source]
Bases: NbSetWeight
Weight of neighbors set based on the angle.
Initialize AnglePlateauNbSetWeight.
@@ -943,18 +943,18 @@
-
-as_dict()[source]
+as_dict()[source]
MSONable dict.
-
-classmethod from_dict(dct: dict) → Self[source]
+classmethod from_dict(dct: dict) → Self[source]
Initialize from dict.
- Parameters:
@@ -968,7 +968,7 @@ Submodules[source]
Get the weight of a given neighbors set.
- Parameters:
@@ -992,7 +992,7 @@ Submodules[source]
Bases: NbSetWeight
Weight of neighbors set based on specific biases towards specific coordination numbers.
Initialize CNBiasNbSetWeight.
@@ -1006,18 +1006,18 @@
-
-as_dict()[source]
+as_dict()[source]
MSONable dict.
-
-classmethod explicit(cn_weights)[source]
+classmethod explicit(cn_weights)[source]
Initialize weights explicitly for each coordination.
- Parameters:
@@ -1031,7 +1031,7 @@ Submodules[source]
Initialize weights from description.
- Parameters:
@@ -1045,7 +1045,7 @@ Submodules[source]
Initialize from dict.
- Parameters:
@@ -1059,7 +1059,7 @@ Submodules[source]
Initialize geometrically equidistant weights for each coordination.
- Arge:
weight_cn1: Weight of coordination 1.
@@ -1075,7 +1075,7 @@
Submodules[source]
Initialize linearly equidistant weights for each coordination.
- Parameters:
@@ -1092,7 +1092,7 @@ Submodules[source]
Get the weight of a given neighbors set.
- Parameters:
@@ -1116,7 +1116,7 @@ Submodules[source]
Bases: float
, StrategyOption
Real number representing a Continuous Symmetry Measure.
Special float that should be between 0 and 100.
@@ -1127,18 +1127,18 @@
-
-as_dict()[source]
+as_dict()[source]
MSONable dict.
-
-classmethod from_dict(dct: dict) → Self[source]
+classmethod from_dict(dct: dict) → Self[source]
Initialize CSM from dict.
- Parameters:
@@ -1151,7 +1151,7 @@ Submodules[source]
Bases: NbSetWeight
Weight of neighbors set based on the differences of CSM.
Initialize DeltaCSMNbSetWeight.
@@ -1167,33 +1167,33 @@
-
-DEFAULT_SYMMETRY_MEASURE_TYPE = 'csm_wcs_ctwcc'[source]
+DEFAULT_SYMMETRY_MEASURE_TYPE = 'csm_wcs_ctwcc'[source]
-
-DEFAULT_WEIGHT_ESTIMATOR: ClassVar = {'function': 'smootherstep', 'options': {'delta_csm_max': 3.0, 'delta_csm_min': 0.5}}[source]
+DEFAULT_WEIGHT_ESTIMATOR: ClassVar = {'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.
-
-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]
Initialize DeltaCSMNbSetWeight from specific coordination number differences.
- Parameters:
@@ -1213,7 +1213,7 @@ Submodules[source]
Initialize from dict.
- Parameters:
@@ -1227,7 +1227,7 @@ Submodules[source]
Get the weight of a given neighbors set.
- Parameters:
@@ -1251,7 +1251,7 @@ Submodules[source]
Bases: NbSetWeight
Weight of neighbors set based on the difference of distances.
Initialize DeltaDistanceNbSetWeight.
@@ -1265,18 +1265,18 @@
-
-as_dict()[source]
+as_dict()[source]
MSONable dict.
-
-classmethod from_dict(dct: dict) → Self[source]
+classmethod from_dict(dct: dict) → Self[source]
Initialize from dict.
- Parameters:
@@ -1290,7 +1290,7 @@ Submodules[source]
Get the weight of a given neighbors set.
- Parameters:
@@ -1314,7 +1314,7 @@ Submodules[source]
Bases: NbSetWeight
Weight of neighbors set based on the area in the distance-angle space.
Initialize CNBiasNbSetWeight.
@@ -1333,28 +1333,28 @@
-
-DEFAULT_SURFACE_DEFINITION: ClassVar = {'angle_bounds': {'lower': 0.1, 'upper': 0.8}, 'distance_bounds': {'lower': 1.2, 'upper': 1.8}, 'type': 'standard_elliptic'}[source]
+DEFAULT_SURFACE_DEFINITION: ClassVar = {'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(dct: dict) → Self[source]
+classmethod from_dict(dct: dict) → Self[source]
Initialize from dict.
- Parameters:
@@ -1368,7 +1368,7 @@ Submodules[source]
Whether a given rectangle crosses the area defined by the upper and lower curves.
- Parameters:
@@ -1384,7 +1384,7 @@ Submodules[source]
Get intersection of the neighbors set area with the surface.
- Parameters:
@@ -1403,7 +1403,7 @@ Submodules[source]
Get intersection of the neighbors set area with the surface.
- Parameters:
@@ -1422,7 +1422,7 @@ Submodules[source]
Get the weight of a given neighbors set.
- Parameters:
@@ -1446,7 +1446,7 @@ Submodules[source]
Bases: float
, StrategyOption
Distance cutoff in a strategy.
Special float that should be between 1 and infinity.
@@ -1457,18 +1457,18 @@
-
-as_dict()[source]
+as_dict()[source]
MSONable dict.
-
-classmethod from_dict(dct: dict) → Self[source]
+classmethod from_dict(dct: dict) → Self[source]
Initialize distance cutoff from dict.
- Parameters:
@@ -1481,7 +1481,7 @@ Submodules[source]
Bases: NbSetWeight
Weight of neighbors set based on the distance.
Initialize DistanceNbSetWeight.
@@ -1495,18 +1495,18 @@
-
-as_dict()[source]
+as_dict()[source]
MSOnable dict.
-
-classmethod from_dict(dct: dict) → Self[source]
+classmethod from_dict(dct: dict) → Self[source]
Initialize from dict.
- Parameters:
@@ -1520,7 +1520,7 @@ Submodules[source]
Get the weight of a given neighbors set.
- Parameters:
@@ -1544,7 +1544,7 @@ Submodules[source]
Bases: NbSetWeight
Weight of neighbors set based on the distance.
Initialize DistancePlateauNbSetWeight.
@@ -1558,18 +1558,18 @@
-
-as_dict()[source]
+as_dict()[source]
MSONable dict.
-
-classmethod from_dict(dct: dict) → Self[source]
+classmethod from_dict(dct: dict) → Self[source]
Initialize from dict.
- Parameters:
@@ -1583,7 +1583,7 @@ Submodules[source]
Get the weight of a given neighbors set.
- Parameters:
@@ -1607,7 +1607,7 @@ Submodules[source]
Bases: WeightedNbSetChemenvStrategy
MultiWeightsChemenvStrategy.
Constructor for the MultiWeightsChemenvStrategy.
@@ -1619,17 +1619,17 @@
-
-STRATEGY_DESCRIPTION: str | None = 'Multi Weights ChemenvStrategy'[source]
+STRATEGY_DESCRIPTION: str | None = 'Multi Weights ChemenvStrategy'[source]
-
-as_dict()[source]
+as_dict()[source]
- Returns:
Bson-serializable dict representation of the MultiWeightsChemenvStrategy object.
@@ -1639,7 +1639,7 @@ Submodules[source]
Reconstructs the MultiWeightsChemenvStrategy object from a dict representation of the
MultipleAbundanceChemenvStrategy object created using the as_dict method.
@@ -1654,13 +1654,13 @@ Submodules