up_sample

Author: jmmshn

pymatgen/analysis/defects/corrections/freysoldt.py

@@ -412,8 +412,8 @@ def plot_plnr_avg(plot_data, title=None, saved=False, ax=None):
     )
 
     ax.set_xlim(round(x[0]), round(x[-1]))
-    ymin = min(min(v_R), min(dft_diff), min(short_range))
-    ymax = max(max(v_R), max(dft_diff), max(short_range))
+    ymin = min(v_R + dft_diff + short_range)
+    ymax = max(v_R + dft_diff + short_range)
     ax.set_ylim(-0.2 + ymin, 0.2 + ymax)
     ax.set_xlabel(r"distance along axis ($\AA$)", fontsize=15)
     ax.set_ylabel("Potential (V)", fontsize=15)

pymatgen/analysis/defects/generators.py

@@ -21,6 +21,8 @@
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 
 if TYPE_CHECKING:
+    from typing import Sequence
+
     from pymatgen.analysis.defects.core import Defect
     from pymatgen.io.vasp import VolumetricData
 
@@ -86,7 +88,10 @@ def __init__(
         self.angle_tolerance = angle_tolerance
 
     def generate(
-        self, structure: Structure, rm_species: list[str | Species] = None, **kwargs
+        self,
+        structure: Structure,
+        rm_species: list[str | Species] | None = None,
+        **kwargs,
     ) -> Generator[Vacancy, None, None]:
         """Generate a vacancy defects.
 
@@ -254,9 +259,10 @@ def __init__(self, min_dist: float = 0.5) -> None:
     def generate(
         self,
         structure: Structure,
-        insertions: dict[str, list[list[float]]],
-        multiplicities: dict[str, list[int]] | None = None,
-        equivalent_positions: dict[str, list[list[list[float]]]] | None = None,
+        insertions: dict[str, Sequence[Sequence[float]]],
+        multiplicities: dict[str, Sequence[int]] | None = None,
+        equivalent_positions: dict[str, Sequence[Sequence[Sequence[float]]]]
+        | None = None,
         **kwargs,
     ) -> Generator[Interstitial, None, None]:
         """Generate interstitials.
@@ -306,8 +312,8 @@ def generate(
                 )
 
     def _filter_colliding(
-        self, fcoords: list[list[float]], structure: Structure
-    ) -> Generator[tuple[int, list[float]], None, None]:
+        self, fcoords: Sequence[Sequence[float]], structure: Structure
+    ) -> Generator[tuple[int, Sequence[float]], None, None]:
         """Check the sites for collisions.
 
         Args:

pymatgen/analysis/defects/plotting/optics.py

@@ -27,9 +27,9 @@ def plot_optical_transitions(
     kpt_index: int = 0,
     band_window: int = 5,
     user_defect_band: tuple = tuple(),
-    other_defect_bands: list[int] = None,
-    ijdirs: list[tuple] = None,
-    shift_eig: dict[tuple, float] = None,
+    other_defect_bands: list[int] | None = None,
+    ijdirs: list[tuple] | None = None,
+    shift_eig: dict[tuple, float] | None = None,
     x0: float = 0,
     x_width: float = 2,
     ax=None,
@@ -118,9 +118,9 @@ def get_bs_eigenvalues(
     defect: HarmonicDefect,
     kpt_index: int = 0,
     band_window: int = 5,
-    user_defect_band: tuple = None,
-    other_defect_bands: list[int] = None,
-    shift_eig: dict[tuple, float] = None,
+    user_defect_band: tuple | None = None,
+    other_defect_bands: list[int] | None = None,
+    shift_eig: dict[tuple, float] | None = None,
 ) -> dict[tuple, float]:
     """Read the eigenvalues from `HarmonicDefect.relaxed_bandstructure`.
 

pymatgen/analysis/defects/thermo.py

@@ -879,7 +879,7 @@ def ensure_stable_bulk(
     stable_entry = ComputedEntry(
         entry.composition, pd.get_hull_energy(entry.composition) - threshold
     )
-    pd = PhaseDiagram(pd.all_entries + [stable_entry])
+    pd = PhaseDiagram([*pd.all_entries, stable_entry])
     return pd
 
 
@@ -1200,8 +1200,8 @@ def plot_formation_energy_diagrams(
             )
         )
         trans_y = trans[:, 1]
-        ymin = min(ymin, min(trans_y))
-        ymax = max(ymax, max(trans_y))
+        ymin = min(ymin, *trans_y)
+        ymax = max(ymax, *trans_y)
 
         dfct: Defect = single_fed.defect_entries[0].defect
         latexname = dfct.latex_name