Merge branch 'master' of github.com:materialsproject/pymatgen

Author: Shyue Ping Ong

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.5
+    rev: v0.1.7
     hooks:
       - id: ruff
         args: [--fix]
@@ -22,7 +22,7 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.6.1
+    rev: v1.7.1
     hooks:
       - id: mypy
 
@@ -35,7 +35,7 @@ repos:
         additional_dependencies: [tomli] # needed to read pyproject.toml below py3.11
 
   - repo: https://github.com/MarcoGorelli/cython-lint
-    rev: v0.15.0
+    rev: v0.16.0
     hooks:
       - id: cython-lint
         args: [--no-pycodestyle]

pymatgen/analysis/adsorption.py

@@ -576,12 +576,12 @@ def substitute(site, i):
         # surface atoms, i.e. search for sites above (below) the bottom (top) surface
         sorted_sites = sorted(sym_slab, key=lambda site: site.frac_coords[2])
         if sorted_sites[0].surface_properties == "surface":
-            d = sorted_sites[0].frac_coords[2] + dist_from_surf
+            dist = sorted_sites[0].frac_coords[2] + dist_from_surf
         else:
-            d = sorted_sites[-1].frac_coords[2] - dist_from_surf
+            dist = sorted_sites[-1].frac_coords[2] - dist_from_surf
 
         for idx, site in enumerate(sym_slab):
-            if d - range_tol < site.frac_coords[2] < d + range_tol and (
+            if dist - range_tol < site.frac_coords[2] < dist + range_tol and (
                 target_species and site.species_string in target_species or not target_species
             ):
                 substituted_slabs.append(substitute(site, idx))

pymatgen/analysis/chemenv/connectivity/connected_components.py

@@ -155,14 +155,7 @@ def make_supergraph(graph, multiplicity, periodicity_vectors):
                 connecting_edges.append((n1, n2, key, new_data))
             else:
                 if not np.all(np.array(data["delta"]) == 0):
-                    print(
-                        "delta not equal to periodicity nor 0 ... : ",
-                        n1,
-                        n2,
-                        key,
-                        data["delta"],
-                        data,
-                    )
+                    print("delta not equal to periodicity nor 0 ... : ", n1, n2, key, data["delta"], data)
                     input("Are we ok with this ?")
                 other_edges.append((n1, n2, key, data))
 

pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py

@@ -1129,22 +1129,22 @@ def _get_map(self, isite):
         target_cns = [cg.coordination_number for cg in target_cgs]
         for ii in range(min([len(maps_and_surfaces), self.max_nabundant])):
             my_map_and_surface = maps_and_surfaces[order[ii]]
-            mymap = my_map_and_surface["map"]
-            cn = mymap[0]
+            my_map = my_map_and_surface["map"]
+            cn = my_map[0]
             if cn not in target_cns or cn > 12 or cn == 0:
                 continue
             all_conditions = [params[2] for params in my_map_and_surface["parameters_indices"]]
             if self._additional_condition not in all_conditions:
                 continue
-            cg, cgdict = self.structure_environments.ce_list[self.structure_environments.sites_map[isite]][mymap[0]][
-                mymap[1]
+            cg, cgdict = self.structure_environments.ce_list[self.structure_environments.sites_map[isite]][my_map[0]][
+                my_map[1]
             ].minimum_geometry(symmetry_measure_type=self._symmetry_measure_type)
             if (
                 cg in self.target_environments
                 and cgdict["symmetry_measure"] <= self.max_csm
                 and cgdict["symmetry_measure"] < current_target_env_csm
             ):
-                current_map = mymap
+                current_map = my_map
                 current_target_env_csm = cgdict["symmetry_measure"]
         if current_map is not None:
             return current_map

pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py

@@ -882,19 +882,19 @@ def __init__(self, permutations_safe_override=False, only_symbols=None):
         dict.__init__(self)
         self.cg_list = []
         if only_symbols is None:
-            with open(f"{module_dir}/coordination_geometries_files/allcg.txt") as f:
-                data = f.readlines()
+            with open(f"{module_dir}/coordination_geometries_files/allcg.txt") as file:
+                data = file.readlines()
             for line in data:
                 cg_file = f"{module_dir}/{line.strip()}"
-                with open(cg_file) as f:
-                    dd = json.load(f)
+                with open(cg_file) as file:
+                    dd = json.load(file)
                 self.cg_list.append(CoordinationGeometry.from_dict(dd))
         else:
             for symbol in only_symbols:
                 fsymbol = symbol.replace(":", "#")
                 cg_file = f"{module_dir}/coordination_geometries_files/{fsymbol}.json"
-                with open(cg_file) as f:
-                    dd = json.load(f)
+                with open(cg_file) as file:
+                    dd = json.load(file)
                 self.cg_list.append(CoordinationGeometry.from_dict(dd))
 
         self.cg_list.append(CoordinationGeometry(UNKNOWN_ENVIRONMENT_SYMBOL, "Unknown environment", deactivate=True))

pymatgen/analysis/elasticity/elastic.py

@@ -599,7 +599,6 @@ def get_tgt(self, temperature: float | None = None, structure: Structure = None,
         """
         if temperature and not structure:
             raise ValueError("If using temperature input, you must also include structure")
-        assert structure  # for mypy
 
         quad = quad or DEFAULT_QUAD
         points = quad["points"]
@@ -611,7 +610,7 @@ def get_tgt(self, temperature: float | None = None, structure: Structure = None,
             us = [u / np.linalg.norm(u) for u in np.transpose(us)]
             for u in us:
                 # TODO: this should be benchmarked
-                if temperature:
+                if temperature and structure:
                     c = self.get_heat_capacity(temperature, structure, p, u)
                 num += c * self.get_ggt(p, u) * w
                 denom += c * w

pymatgen/analysis/phase_diagram.py

@@ -2276,7 +2276,11 @@ def show(self, *args, **kwargs) -> None:
             *args: Passed to get_plot.
             **kwargs: Passed to get_plot.
         """
-        self.get_plot(*args, **kwargs).show()
+        plot = self.get_plot(*args, **kwargs)
+        if self.backend == "matplotlib":
+            plot.get_figure().show()
+        else:
+            plot.show()
 
     def write_image(self, stream: str | StringIO, image_format: str = "svg", **kwargs) -> None:
         """

pymatgen/analysis/pourbaix_diagram.py

@@ -473,15 +473,15 @@ def __init__(
             for entry in ion_entries:
                 ion_elts = list(set(entry.elements) - ELEMENTS_HO)
                 # TODO: the logic here for ion concentration setting is in two
-                #       places, in PourbaixEntry and here, should be consolidated
+                # places, in PourbaixEntry and here, should be consolidated
                 if len(ion_elts) == 1:
                     entry.concentration = conc_dict[ion_elts[0].symbol] * entry.normalization_factor
                 elif len(ion_elts) > 1 and not entry.concentration:
                     raise ValueError("Elemental concentration not compatible with multi-element ions")
 
             self._unprocessed_entries = solid_entries + ion_entries
 
-            if not len(solid_entries + ion_entries) == len(entries):
+            if len(solid_entries + ion_entries) != len(entries):
                 raise ValueError('All supplied entries must have a phase type of either "Solid" or "Ion"')
 
             if self.filter_solids:

pymatgen/core/composition.py

@@ -363,7 +363,7 @@ def get_reduced_formula_and_factor(self, iupac_ordering: bool = False) -> tuple[
         if not all_int:
             return self.formula.replace(" ", ""), 1
         d = {k: int(round(v)) for k, v in self.get_el_amt_dict().items()}
-        (formula, factor) = reduce_formula(d, iupac_ordering=iupac_ordering)
+        formula, factor = reduce_formula(d, iupac_ordering=iupac_ordering)
 
         if formula in Composition.special_formulas:
             formula = Composition.special_formulas[formula]

pymatgen/core/structure.py

@@ -357,6 +357,11 @@ def formula(self) -> str:
         """Returns the formula as a string."""
         return self.composition.formula
 
+    @property
+    def alphabetical_formula(self) -> str:
+        """Returns the formula as a string."""
+        return self.composition.alphabetical_formula
+
     @property
     def elements(self) -> list[Element | Species | DummySpecies]:
         """Returns the elements in the structure as a list of Element objects."""
@@ -1172,11 +1177,9 @@ def from_magnetic_spacegroup(
                 f"{msg.sg_symbol}!"
             )
 
-        if len(species) != len(coords):
-            raise ValueError(f"Supplied species and coords lengths ({len(species)} vs {len(coords)}) are different!")
-
-        if len(species) != len(magmoms):
-            raise ValueError(f"Supplied species and magmom lengths ({len(species)} vs {len(magmoms)}) are different!")
+        for name, var in (("coords", coords), ("magmoms", magmoms)):
+            if len(var) != len(species):
+                raise ValueError(f"Length mismatch: len({name})={len(var)} != {len(species)=}")
 
         frac_coords = coords if not coords_are_cartesian else latt.get_fractional_coords(coords)
 
@@ -2138,13 +2141,16 @@ def interpolate(
         interpolate_lattices: bool = False,
         pbc: bool = True,
         autosort_tol: float = 0,
+        end_amplitude: float = 1,
     ) -> list[IStructure | Structure]:
         """Interpolate between this structure and end_structure. Useful for
-        construction of NEB inputs.
+        construction of NEB inputs. To obtain useful results, the cell setting
+        and order of sites must consistent across the start and end structures.
 
         Args:
             end_structure (Structure): structure to interpolate between this
-                structure and end.
+                structure and end. Must be in the same setting and have the
+                same site ordering to yield useful results.
             nimages (int,list): No. of interpolation images or a list of
                 interpolation images. Defaults to 10 images.
             interpolate_lattices (bool): Whether to interpolate the lattices.
@@ -2157,6 +2163,13 @@ def interpolate(
                 closest points in this particular structure. This is usually
                 what you want in a NEB calculation. 0 implies no sorting.
                 Otherwise, a 0.5 value usually works pretty well.
+            end_amplitude (float): The fractional amplitude of the endpoint
+                of the interpolation, or a cofactor of the distortion vector
+                connecting structure to end_structure. Thus, 0 implies no
+                distortion, 1 implies full distortion to end_structure
+                (default), 0.5 implies distortion to a point halfway
+                between structure and end_structure, and -1 implies full
+                distortion in the opposite direction to end_structure.
 
         Returns:
             List of interpolated structures. The starting and ending
@@ -2212,7 +2225,7 @@ def interpolate(
 
             end_coords = sorted_end_coords
 
-        vec = end_coords - start_coords
+        vec = end_amplitude * (end_coords - start_coords)
         if pbc:
             vec[:, self.pbc] -= np.round(vec[:, self.pbc])
         sp = self.species_and_occu
@@ -2222,7 +2235,7 @@ def interpolate(
             # interpolate lattice matrices using polar decomposition
             # u is a unitary rotation, p is stretch
             u, p = polar(np.dot(end_structure.lattice.matrix.T, np.linalg.inv(self.lattice.matrix.T)))
-            lvec = p - np.identity(3)
+            lvec = end_amplitude * (p - np.identity(3))
             lstart = self.lattice.matrix.T
 
         for x in images: