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

Author: Shyue Ping Ong

.github/workflows/test.yml

@@ -78,6 +78,13 @@ jobs:
           for pkg in cmd_line/*;
             do echo "$(pwd)/cmd_line/$pkg/Linux_64bit" >> "$GITHUB_PATH";
           done
+      - name: Install Bader
+        if: runner.os == 'Linux'
+        run: |
+          wget http://theory.cm.utexas.edu/henkelman/code/bader/download/bader_lnx_64.tar.gz
+          tar xvzf bader_lnx_64.tar.gz
+          sudo mv bader /usr/local/bin/
+        continue-on-error: true
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip wheel
@@ -130,7 +137,9 @@ jobs:
         name: Install Python
         with:
           python-version: "3.10"
-      - run: python -m pip install build
+      - run: |
+          python -m pip install build
+          pip install -e .
       - name: Build sdist
         run: python -m build --sdist
       - uses: actions/upload-artifact@v3

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.279
+    rev: v0.0.281
     hooks:
       - id: ruff
         args: [--fix]

pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py

@@ -2024,7 +2024,6 @@ def __init__(
             self.area_weight = self.w_area_has_intersection
         elif weight_type == "has_intersection_smoothstep":
             raise NotImplementedError
-            # self.area_weight = self.w_area_has_intersection_smoothstep
         else:
             raise ValueError(f'Weight type is {weight_type!r} while it should be "has_intersection"')
         self.surface_definition = surface_definition
@@ -2064,28 +2063,6 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
             additional_info=additional_info,
         )
 
-    def w_area_has_intersection_smoothstep(self, nb_set, structure_environments, cn_map, additional_info):
-        """Get intersection of the neighbors set area with the surface.
-
-        :param nb_set: Neighbors set.
-        :param structure_environments: Structure environments.
-        :param cn_map: Mapping index of the neighbors set.
-        :param additional_info: Additional information.
-        :return: Area intersection between neighbors set and surface.
-        """
-        w_area = self.w_area_intersection_specific(
-            nb_set=nb_set,
-            structure_environments=structure_environments,
-            cn_map=cn_map,
-            additional_info=additional_info,
-        )
-        if w_area > 0:
-            if self.smoothstep_distance is not None:
-                w_area = w_area
-            if self.smoothstep_angle is not None:
-                w_area = w_area
-        return w_area
-
     def w_area_has_intersection(self, nb_set, structure_environments, cn_map, additional_info):
         """Get intersection of the neighbors set area with the surface.
 

pymatgen/analysis/gb/grain.py

@@ -21,6 +21,7 @@
 if TYPE_CHECKING:
     from numpy.typing import ArrayLike
 
+    from pymatgen.core.trajectory import Vector3D
     from pymatgen.util.typing import CompositionLike
 
 # This module implements representations of grain boundaries, as well as
@@ -55,10 +56,10 @@ def __init__(
         lattice: np.ndarray | Lattice,
         species: Sequence[CompositionLike],
         coords: Sequence[ArrayLike],
-        rotation_axis: tuple[float, float, float],
+        rotation_axis: Vector3D,
         rotation_angle: float,
-        gb_plane: tuple[float, float, float],
-        join_plane: tuple[float, float, float],
+        gb_plane: Vector3D,
+        join_plane: Vector3D,
         init_cell: Structure,
         vacuum_thickness: float,
         ab_shift: tuple[float, float],

pymatgen/analysis/local_env.py

@@ -3649,12 +3649,13 @@ def get_nn_info(self, structure: Structure, n: int):
         site = structure[n]
         neighbors = structure.get_neighbors(site, self.cutoff)
 
-        if self.cation_anion and hasattr(site.specie, "oxi_state"):
+        oxi_state = getattr(site.specie, "oxi_state", None)
+        if self.cation_anion and oxi_state is not None:
             # filter out neighbor of like charge (except for neutral sites)
-            if site.specie.oxi_state >= 0:
+            if oxi_state >= 0:
                 neighbors = [n for n in neighbors if n.oxi_state <= 0]
-            elif site.specie.oxi_state <= 0:
-                neighbors = [n for n in neighbors if n.oxi_state >= 0]
+            elif oxi_state < 0:
+                neighbors = [nghbr for nghbr in neighbors if nghbr.oxi_state >= 0]
 
         if self.use_fictive_radius:
             # calculate fictive ionic radii
@@ -3882,7 +3883,8 @@ def get_nn_data(self, structure: Structure, n: int, length=None):
             target = []
             m_oxi = structure[n].specie.oxi_state
             for site in structure:
-                if site.specie.oxi_state * m_oxi <= 0:  # opposite charge
+                oxi_state = getattr(site.specie, "oxi_state", None)
+                if oxi_state is not None and oxi_state * m_oxi <= 0:  # opposite charge
                     target.append(site.specie)
             if not target:
                 raise ValueError("No valid targets for site within cation_anion constraint!")

pymatgen/analysis/wulff.py

@@ -462,7 +462,6 @@ def get_plot(
         ax.set_zlim([-r_range * 1.1, r_range * 1.1])  # pylint: disable=E1101
         # add legend
         if legend_on:
-            color_proxy = color_proxy
             if show_area:
                 ax.legend(
                     color_proxy,

pymatgen/apps/battery/conversion_battery.py

@@ -72,7 +72,6 @@ def from_composition_and_pd(cls, comp, pd, working_ion_symbol="Li", allow_unstab
         profile.reverse()
         if len(profile) < 2:
             return None
-        working_ion_entry = working_ion_entry
         working_ion = working_ion_entry.composition.elements[0].symbol
         normalization_els = {}
         for el, amt in comp.items():
@@ -83,7 +82,7 @@ def from_composition_and_pd(cls, comp, pd, working_ion_symbol="Li", allow_unstab
             framework.pop(working_ion)
         framework = Composition(framework)
 
-        vpairs = [
+        v_pairs = [
             ConversionVoltagePair.from_steps(
                 profile[i],
                 profile[i + 1],
@@ -94,7 +93,7 @@ def from_composition_and_pd(cls, comp, pd, working_ion_symbol="Li", allow_unstab
         ]
 
         return ConversionElectrode(  # pylint: disable=E1123
-            voltage_pairs=vpairs,
+            voltage_pairs=v_pairs,
             working_ion_entry=working_ion_entry,
             initial_comp_formula=comp.reduced_formula,
             framework_formula=framework.reduced_formula,
@@ -338,26 +337,24 @@ def from_steps(cls, step1, step2, normalization_els, framework_formula):
             sum(curr_rxn.all_comp[i].weight * abs(curr_rxn.coeffs[i]) for i in range(len(curr_rxn.all_comp))) / 2
         )
         mass_charge = prev_mass_dischg
-        mass_discharge = mass_discharge
         vol_discharge = sum(
             abs(curr_rxn.get_coeff(e.composition)) * e.structure.volume
             for e in step2["entries"]
             if e.composition.reduced_formula != working_ion
         )
 
-        totalcomp = Composition({})
+        total_comp = Composition({})
         for comp in prev_rxn.products:
             if comp.reduced_formula != working_ion:
-                totalcomp += comp * abs(prev_rxn.get_coeff(comp))
-        frac_charge = totalcomp.get_atomic_fraction(Element(working_ion))
+                total_comp += comp * abs(prev_rxn.get_coeff(comp))
+        frac_charge = total_comp.get_atomic_fraction(Element(working_ion))
 
-        totalcomp = Composition({})
+        total_comp = Composition({})
         for comp in curr_rxn.products:
             if comp.reduced_formula != working_ion:
-                totalcomp += comp * abs(curr_rxn.get_coeff(comp))
-        frac_discharge = totalcomp.get_atomic_fraction(Element(working_ion))
+                total_comp += comp * abs(curr_rxn.get_coeff(comp))
+        frac_discharge = total_comp.get_atomic_fraction(Element(working_ion))
 
-        rxn = rxn
         entries_charge = step1["entries"]
         entries_discharge = step2["entries"]