Merge branch 'master' into aims_kpoint_density_fix

.gitignore

@@ -1,9 +1,6 @@
 __pycache__/
 .DS_Store
 pymatgen.egg-info
-dependencies/PyCifRW-3.3/PyCifRW.egg-info
-dependencies/spglib*/pyspglib.egg-info
-dependencies/spglib*/build
 *.o
 *.so
 *.pyc
@@ -26,7 +23,6 @@ setuptools*
 .cache
 .tox
 .eggs/
-gulptmp_4_1
 .coverage
 .*_cache
 # VS Code

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.0
+    rev: v0.5.4
     hooks:
       - id: ruff
         args: [ --fix, --unsafe-fixes ]
@@ -22,7 +22,7 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.10.1
+    rev: v1.11.0
     hooks:
       - id: mypy
 
@@ -65,6 +65,6 @@ repos:
         args: [ --drop-empty-cells, --keep-output ]
 
   - repo: https://github.com/RobertCraigie/pyright-python
-    rev: v1.1.369
+    rev: v1.1.373
     hooks:
       - id: pyright

src/pymatgen/analysis/graphs.py

@@ -808,8 +808,7 @@ def get_coordination_of_site(self, n: int) -> int:
         Returns:
             int: number of neighbors of site n.
         """
-        n_self_loops = sum(1 for n, v in self.graph.edges(n) if n == v)
-        return self.graph.degree(n) - n_self_loops
+        return self.graph.degree(n)
 
     def draw_graph_to_file(
         self,
@@ -2478,8 +2477,7 @@ def get_coordination_of_site(self, n) -> int:
         Returns:
             int: the number of neighbors of site n.
         """
-        n_self_loops = sum(1 for n, v in self.graph.edges(n) if n == v)
-        return self.graph.degree(n) - n_self_loops
+        return self.graph.degree(n)
 
     def draw_graph_to_file(
         self,

src/pymatgen/analysis/local_env.py

@@ -3048,7 +3048,7 @@ def get_order_parameters(
                                 norms[idx][j][kc] += 1
 
                         for m in range(n_neighbors):
-                            if (m != j) and (m != k) and (not flag_xaxis):
+                            if m not in {j, k} and (not flag_xaxis):
                                 tmp = max(-1.0, min(np.inner(zaxis, rij_norm[m]), 1.0))
                                 thetam = math.acos(tmp)
                                 x_two_axis_tmp = gramschmidt(rij_norm[m], zaxis)

src/pymatgen/analysis/magnetism/jahnteller.py

@@ -345,7 +345,7 @@ def _get_number_of_d_electrons(species: Species) -> float:
 
         # taken from get_crystal_field_spin
         elec = species.element.full_electronic_structure
-        if len(elec) < 4 or elec[-1][1] != "s" or elec[-2][1] != "d":
+        if len(elec) < 4 or elec[-2][1] != "s" or elec[-1][1] != "d":
             raise AttributeError(f"Invalid element {species.symbol} for crystal field calculation.")
         n_electrons = int(elec[-1][2] + elec[-2][2] - species.oxi_state)  # type: ignore[operator]
         if n_electrons < 0 or n_electrons > 10:

src/pymatgen/core/__init__.py

@@ -37,9 +37,12 @@
 def _load_pmg_settings() -> dict[str, Any]:
     settings: dict[str, Any] = {}
 
+    # PMG_CONFIG_FILE takes precedence over default settings location
+    settings_file = os.getenv("PMG_CONFIG_FILE") or SETTINGS_FILE
+
     # Load .pmgrc.yaml file
     yaml = YAML()
-    for file_path in (SETTINGS_FILE, OLD_SETTINGS_FILE):
+    for file_path in (settings_file, OLD_SETTINGS_FILE):
         try:
             with open(file_path, encoding="utf-8") as yml_file:
                 settings = yaml.load(yml_file) or {}

src/pymatgen/core/composition.py

@@ -487,7 +487,7 @@ def chemical_system(self) -> str:
         sorted alphabetically and joined by dashes, by convention for use
         in database keys.
         """
-        return "-".join(sorted(el.symbol for el in self.elements))
+        return "-".join(sorted(self.chemical_system_set))
 
     @property
     def num_atoms(self) -> float:

src/pymatgen/core/periodic_table.py

@@ -33,6 +33,28 @@
 
 _pt_row_sizes = (2, 8, 8, 18, 18, 32, 32)
 
+_madelung = [
+    (1, "s"),
+    (2, "s"),
+    (2, "p"),
+    (3, "s"),
+    (3, "p"),
+    (4, "s"),
+    (3, "d"),
+    (4, "p"),
+    (5, "s"),
+    (4, "d"),
+    (5, "p"),
+    (6, "s"),
+    (4, "f"),
+    (5, "d"),
+    (6, "p"),
+    (7, "s"),
+    (5, "f"),
+    (6, "d"),
+    (7, "p"),
+]
+
 
 @functools.total_ordering
 @unique
@@ -422,11 +444,12 @@ def icsd_oxidation_states(self) -> tuple[int, ...]:
     @property
     def full_electronic_structure(self) -> list[tuple[int, str, int]]:
         """Full electronic structure as list of tuples, in order of increasing
-        principal (n) and angular momentum (l)  quantum numbers.
+        energy level (according to the Madelung rule). Therefore, the final
+        element in the list gives the electronic structure of the valence shell.
 
         For example, the electronic structure for Fe is represented as:
         [(1, "s", 2), (2, "s", 2), (2, "p", 6), (3, "s", 2), (3, "p", 6),
-        (3, "d", 6), (4, "s", 2)].
+        (4, "s", 2), (3, "d", 6)].
 
         References:
             Kramida, A., Ralchenko, Yu., Reader, J., and NIST ASD Team (2023). NIST
@@ -445,7 +468,13 @@ def parse_orbital(orb_str):
         if data[0][0] == "[":
             sym = data[0].replace("[", "").replace("]", "")
             data = list(Element(sym).full_electronic_structure) + data[1:]
-        return data
+        # sort the final electronic structure by increasing energy level
+        return sorted(data, key=lambda x: _madelung.index((x[0], x[1])))
+
+    @property
+    def n_electrons(self) -> int:
+        """Total number of electrons in the Element."""
+        return sum([t[-1] for t in self.full_electronic_structure])
 
     @property
     def valence(self) -> tuple[int | np.nan, int]:
@@ -1117,7 +1146,8 @@ def electronic_structure(self) -> str:
     @property
     def full_electronic_structure(self) -> list[tuple[int, str, int]]:
         """Full electronic structure as list of tuples, in order of increasing
-        principal (n) and angular momentum (l)  quantum numbers.
+        energy level (according to the Madelung rule). Therefore, the final
+        element in the list gives the electronic structure of the valence shell.
 
         For example, the electronic structure for Fe+2 is represented as:
         [(1, "s", 2), (2, "s", 2), (2, "p", 6), (3, "s", 2), (3, "p", 6),
@@ -1140,7 +1170,15 @@ def parse_orbital(orb_str):
         if data[0][0] == "[":
             sym = data[0].replace("[", "").replace("]", "")
             data = list(Element(sym).full_electronic_structure) + data[1:]
-        return data
+        # sort the final electronic structure by increasing energy level
+        return sorted(data, key=lambda x: _madelung.index((x[0], x[1])))
+
+    # NOTE - copied exactly from Element. Refactoring / inheritance may improve
+    # robustness
+    @property
+    def n_electrons(self) -> int:
+        """Total number of electrons in the Species."""
+        return sum([t[-1] for t in self.full_electronic_structure])
 
     # NOTE - copied exactly from Element. Refactoring / inheritance may improve
     # robustness
@@ -1319,7 +1357,7 @@ def get_crystal_field_spin(
             raise ValueError("Invalid coordination or spin config")
 
         elec = self.element.full_electronic_structure
-        if len(elec) < 4 or elec[-1][1] != "s" or elec[-2][1] != "d":
+        if len(elec) < 4 or elec[-2][1] != "s" or elec[-1][1] != "d":
             raise AttributeError(f"Invalid element {self.symbol} for crystal field calculation")
 
         assert self.oxi_state is not None

src/pymatgen/electronic_structure/boltztrap.py

@@ -1,16 +1,13 @@
-"""This module provides classes to run and analyze boltztrap on pymatgen band
-structure objects. Boltztrap is a software interpolating band structures and
-computing materials properties from this band structure using Boltzmann
-semi-classical transport theory.
+"""This module provides classes to run and analyze BoltzTraP on pymatgen band
+structure objects. BoltzTraP is a software developed by Georg Madsen to
+interpolate band structures and compute materials properties from this
+band structure using Boltzmann semi-classical transport theory.
 
-Boltztrap has been developed by Georg Madsen.
-
-http://www.icams.de/content/research/software-development/boltztrap/
+https://www.tuwien.at/en/tch/tc/theoretical-materials-chemistry/boltztrap
 
 You need version 1.2.3 or higher
 
-References are:
-
+References:
     Madsen, G. K. H., and Singh, D. J. (2006).
     BoltzTraP. A code for calculating band-structure dependent quantities.
     Computer Physics Communications, 175, 67-71
@@ -60,13 +57,13 @@
 
 
 class BoltztrapRunner(MSONable):
-    """This class is used to run Boltztrap on a band structure object."""
+    """This class is used to run BoltzTraP on a band structure object."""
 
     @requires(
         which("x_trans"),
         "BoltztrapRunner requires the executables 'x_trans' to be in PATH. Please download "
-        "Boltztrap at http://www.icams.de/content/research/software-development/boltztrap/ "
-        "and follow the instructions in the README to compile Bolztrap accordingly. "
+        "BoltzTraP at https://www.tuwien.at/en/tch/tc/theoretical-materials-chemistry/boltztrap "
+        "and follow the instructions in the README to compile BoltzTraP accordingly. "
         "Then add x_trans to your path",
     )
     def __init__(
@@ -144,7 +141,7 @@ def __init__(
                 electron occupations. If the band structure comes from a soc
                 computation, you should set soc to True (default False)
             doping:
-                the fixed doping levels you want to compute. Boltztrap provides
+                the fixed doping levels you want to compute. BoltzTraP provides
                 both transport values depending on electron chemical potential
                 (fermi energy) and for a series of fixed carrier
                 concentrations. By default, this is set to 1e16 to 1e22 in
@@ -734,7 +731,7 @@ def __init__(
         bz_kpoints=None,
         fermi_surface_data=None,
     ) -> None:
-        """Constructor taking directly all the data generated by Boltztrap. You
+        """Constructor taking directly all the data generated by BoltzTraP. You
         won't probably use it directly but instead use the from_files and
         from_dict methods.
 
@@ -760,7 +757,7 @@ def __init__(
                 each Fermi level in mu_steps]}
                 The units are m^3/C
             doping: The different doping levels that have been given to
-                Boltztrap. The format is {'p':[],'n':[]} with an array of
+                BoltzTraP. The format is {'p':[],'n':[]} with an array of
                 doping levels. The units are cm^-3
             mu_doping: Gives the electron chemical potential (or Fermi level)
                 for a given set of doping.
@@ -802,7 +799,7 @@ def __init__(
             intrans: a dictionary of inputs e.g. {"scissor": 0.0}
             carrier_conc: The concentration of carriers in electron (or hole)
                 per unit cell
-            dos: The dos computed by Boltztrap given as a pymatgen Dos object
+            dos: The dos computed by BoltzTraP given as a pymatgen Dos object
             dos_partial: Data for the partial DOS projected on sites and
                 orbitals
             vol: Volume of the unit cell in angstrom cube (A^3)
@@ -837,13 +834,13 @@ def __init__(
         self.fermi_surface_data = fermi_surface_data
 
     def get_symm_bands(self, structure: Structure, efermi, kpt_line=None, labels_dict=None):
-        """Useful to read bands from Boltztrap output and get a BandStructureSymmLine object
+        """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 and labels_dict is the standard path of high symmetry
         k-point for the specified structure. They could be extracted from the
         BandStructureSymmLine object that you want to compare with. efermi variable must
         be specified to create the BandStructureSymmLine object (usually it comes from DFT
-        or Boltztrap calc).
+        or BoltzTraP calc).
         """
         try:
             if kpt_line is None:
@@ -1640,7 +1637,7 @@ def get_carrier_concentration(self):
 
     def get_hall_carrier_concentration(self):
         """Get the Hall carrier concentration (in cm^-3). This is the trace of
-        the Hall tensor (see Boltztrap source code) Hall carrier concentration
+        the Hall tensor (see BoltzTraP source code) Hall carrier concentration
         are not always exactly the same than carrier concentration.
 
         Returns:
@@ -1770,7 +1767,7 @@ def parse_intrans(path_dir):
             path_dir: (str) dir containing the boltztrap.intrans file
 
         Returns:
-            dict: various inputs that had been used in the Boltztrap run.
+            dict: various inputs that had been used in the BoltzTraP run.
         """
         intrans = {}
         with open(f"{path_dir}/boltztrap.intrans") as file:

src/pymatgen/ext/matproj.py

@@ -178,7 +178,7 @@ def get_summary_by_material_id(self, material_id: str, fields: list | None = Non
             Dict
         """
         get = "_all_fields=True" if fields is None else "_fields=" + ",".join(fields)
-        return self.request(f"materials/summary/{material_id}/?{get}")[0]
+        return self.request(f"materials/summary/?{get}", payload={"material_ids": material_id})[0]
 
     get_doc = get_summary_by_material_id
 
@@ -349,6 +349,32 @@ def get_entries_in_chemsys(self, elements, *args, **kwargs):
 
         return self.get_entries(criteria, *args, **kwargs)
 
+    def get_phonon_bandstructure_by_material_id(self, material_id: str):
+        """Get phonon bandstructure by material_id.
+
+        Args:
+            material_id (str): Materials Project material_id
+
+        Returns:
+            PhononBandStructureSymmLine: A phonon band structure.
+        """
+        prop = "ph_bs"
+        response = self.request(f"materials/phonon/?material_ids={material_id}&_fields={prop}")
+        return response[0][prop]
+
+    def get_phonon_dos_by_material_id(self, material_id: str):
+        """Get phonon density of states by material_id.
+
+        Args:
+            material_id (str): Materials Project material_id
+
+        Returns:
+            CompletePhononDos: A phonon DOS object.
+        """
+        prop = "ph_dos"
+        response = self.request(f"materials/phonon/?material_ids={material_id}&_fields={prop}")
+        return response[0][prop]
+
 
 class MPRester:
     """A class to conveniently interface with the new and legacy Materials Project REST interface.

src/pymatgen/io/abinit/netcdf.py

@@ -15,6 +15,7 @@
 from pymatgen.core.structure import Structure
 from pymatgen.core.units import ArrayWithUnit
 from pymatgen.core.xcfunc import XcFunc
+from pymatgen.electronic_structure.core import Magmom
 
 if TYPE_CHECKING:
     from typing_extensions import Self
@@ -315,6 +316,23 @@ def structure_from_ncdata(ncdata, site_properties=None, cls=Structure):
     # type_atom[:natom] --> index Between 1 and number of atom species
     type_atom = ncdata.read_value("atom_species")
 
+    try:
+        intgden = ncdata.read_value("intgden")
+        nspden = intgden.shape[1]
+    except NetcdfReaderError:
+        intgden = None
+        nspden = None
+
+    if intgden is not None:
+        if nspden == 2:
+            magmoms = Magmom(intgden[:, 1] - intgden[:, 0])
+        elif nspden == 4:
+            magmoms = [Magmom([intg_at[1], intg_at[2], intg_at[3]]) for intg_at in intgden]
+        else:
+            magmoms = None
+    else:
+        magmoms = None
+
     # Fortran to C index and float --> int conversion.
     species = n_atom * [None]
     for atom in range(n_atom):
@@ -326,6 +344,9 @@ def structure_from_ncdata(ncdata, site_properties=None, cls=Structure):
         for prop in site_properties:
             dct[prop] = ncdata.read_value(prop)
 
+    if magmoms is not None and "magmom" not in dct:
+        dct["magmom"] = magmoms
+
     structure = cls(lattice, species, red_coords, site_properties=dct)
 
     # Quick and dirty hack.