Merge branch 'master' into fix-position-check-in-get-slabs

pymatgen/alchemy/materials.py

@@ -8,7 +8,7 @@
 import datetime
 import json
 import re
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING
 from warnings import warn
 
 from monty.json import MSONable, jsanitize
@@ -22,6 +22,7 @@
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
+    from typing import Any
 
     from typing_extensions import Self
 

pymatgen/alchemy/transmuters.py

@@ -12,13 +12,14 @@
 import os
 import re
 from multiprocessing import Pool
-from typing import TYPE_CHECKING, Callable
+from typing import TYPE_CHECKING
 
 from pymatgen.alchemy.materials import TransformedStructure
 from pymatgen.io.vasp.sets import MPRelaxSet, VaspInputSet
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
+    from typing import Callable
 
     from typing_extensions import Self
 

pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py

@@ -13,13 +13,15 @@
 import itertools
 import json
 import os
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING
 
 import numpy as np
 from monty.json import MontyDecoder, MSONable
 from scipy.special import factorial
 
 if TYPE_CHECKING:
+    from typing import Any
+
     from typing_extensions import Self
 
 __author__ = "David Waroquiers"

pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py

@@ -218,7 +218,7 @@ def points_wcs_csc(self, permutation=None):
         """
         if permutation is None:
             return self._points_wcs_csc
-        return np.concatenate((self._points_wcs_csc[0:1], self._points_wocs_csc.take(permutation, axis=0)))
+        return np.concatenate((self._points_wcs_csc[:1], self._points_wocs_csc.take(permutation, axis=0)))
 
     def points_wocs_csc(self, permutation=None):
         """
@@ -238,7 +238,7 @@ def points_wcs_ctwcc(self, permutation=None):
             return self._points_wcs_ctwcc
         return np.concatenate(
             (
-                self._points_wcs_ctwcc[0:1],
+                self._points_wcs_ctwcc[:1],
                 self._points_wocs_ctwcc.take(permutation, axis=0),
             )
         )
@@ -261,7 +261,7 @@ def points_wcs_ctwocc(self, permutation=None):
             return self._points_wcs_ctwocc
         return np.concatenate(
             (
-                self._points_wcs_ctwocc[0:1],
+                self._points_wcs_ctwocc[:1],
                 self._points_wocs_ctwocc.take(permutation, axis=0),
             )
         )

pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py

@@ -3,7 +3,7 @@
 from __future__ import annotations
 
 import math
-from typing import TYPE_CHECKING, Callable
+from typing import TYPE_CHECKING
 
 import numpy as np
 from numpy.linalg import norm
@@ -14,6 +14,8 @@
 from pymatgen.analysis.chemenv.utils.chemenv_errors import SolidAngleError
 
 if TYPE_CHECKING:
+    from typing import Callable
+
     from numpy.typing import ArrayLike
     from typing_extensions import Self
 
@@ -901,7 +903,7 @@ def project_and_to2dim(self, pps, plane_center):
         xypps = []
         for pp in proj:
             xyzpp = np.dot(pp, PP)
-            xypps.append(xyzpp[0:2])
+            xypps.append(xyzpp[:2])
         if str(plane_center) == "mean":
             mean = np.zeros(2, float)
             for pp in xypps:
@@ -910,7 +912,7 @@ def project_and_to2dim(self, pps, plane_center):
             xypps = [pp - mean for pp in xypps]
         elif plane_center is not None:
             projected_plane_center = self.projectionpoints([plane_center])[0]
-            xy_projected_plane_center = np.dot(projected_plane_center, PP)[0:2]
+            xy_projected_plane_center = np.dot(projected_plane_center, PP)[:2]
             xypps = [pp - xy_projected_plane_center for pp in xypps]
         return xypps
 
@@ -960,7 +962,7 @@ def coefficients(self):
     @property
     def abcd(self):
         """A tuple with the plane coefficients."""
-        return tuple(self._coefficients[0:4])
+        return tuple(self._coefficients[:4])
 
     @property
     def a(self):

pymatgen/analysis/elasticity/elastic.py

@@ -9,7 +9,7 @@
 import itertools
 import math
 import warnings
-from typing import TYPE_CHECKING, Literal
+from typing import TYPE_CHECKING
 
 import numpy as np
 import sympy as sp
@@ -25,6 +25,7 @@
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
+    from typing import Literal
 
     from numpy.typing import ArrayLike
     from typing_extensions import Self

pymatgen/analysis/elasticity/strain.py

@@ -8,7 +8,7 @@
 
 import collections
 import itertools
-from typing import TYPE_CHECKING, Literal
+from typing import TYPE_CHECKING
 
 import numpy as np
 import scipy
@@ -18,6 +18,7 @@
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
+    from typing import Literal
 
     from numpy.typing import ArrayLike
     from typing_extensions import Self

pymatgen/analysis/ewald.py

@@ -3,10 +3,10 @@
 from __future__ import annotations
 
 import bisect
+import math
 from copy import copy, deepcopy
 from datetime import datetime
-from math import log, pi, sqrt
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING
 from warnings import warn
 
 import numpy as np
@@ -18,6 +18,8 @@
 from pymatgen.util.due import Doi, due
 
 if TYPE_CHECKING:
+    from typing import Any
+
     from typing_extensions import Self
 
 __author__ = "Shyue Ping Ong, William Davidson Richard"
@@ -55,7 +57,7 @@ class EwaldSummation(MSONable):
     """
 
     # Converts unit of q*q/r into eV
-    CONV_FACT = 1e10 * constants.e / (4 * pi * constants.epsilon_0)
+    CONV_FACT = 1e10 * constants.e / (4 * math.pi * constants.epsilon_0)
 
     def __init__(
         self,
@@ -102,12 +104,12 @@ def __init__(
 
         self._acc_factor = acc_factor
         # set screening length
-        self._eta = eta or (len(structure) * w / (self._vol**2)) ** (1 / 3) * pi
-        self._sqrt_eta = sqrt(self._eta)
+        self._eta = eta or (len(structure) * w / (self._vol**2)) ** (1 / 3) * math.pi
+        self._sqrt_eta = math.sqrt(self._eta)
 
         # acc factor used to automatically determine the optimal real and
         # reciprocal space cutoff radii
-        self._accf = sqrt(log(10**acc_factor))
+        self._accf = math.sqrt(math.log(10**acc_factor))
 
         self._rmax = real_space_cut or self._accf / self._sqrt_eta
         self._gmax = recip_space_cut or 2 * self._sqrt_eta * self._accf
@@ -307,7 +309,7 @@ def _calc_recip(self):
         This method is heavily vectorized to utilize numpy's C backend for speed.
         """
         n_sites = len(self._struct)
-        prefactor = 2 * pi / self._vol
+        prefactor = 2 * math.pi / self._vol
         e_recip = np.zeros((n_sites, n_sites), dtype=np.float64)
         forces = np.zeros((n_sites, 3), dtype=np.float64)
         coords = self._coords
@@ -332,7 +334,7 @@ def _calc_recip(self):
 
         for g, g2, gr, exp_val, s_real, s_imag in zip(gs, g2s, grs, exp_vals, s_reals, s_imags):
             # Uses the identity sin(x)+cos(x) = 2**0.5 sin(x + pi/4)
-            m = np.sin((gr[None, :] + pi / 4) - gr[:, None])
+            m = np.sin((gr[None, :] + math.pi / 4) - gr[:, None])
             m *= exp_val / g2
 
             e_recip += m
@@ -350,7 +352,7 @@ def _calc_recip(self):
     def _calc_real_and_point(self):
         """Determine the self energy -(eta/pi)**(1/2) * sum_{i=1}^{N} q_i**2."""
         frac_coords = self._struct.frac_coords
-        force_pf = 2 * self._sqrt_eta / sqrt(pi)
+        force_pf = 2 * self._sqrt_eta / math.sqrt(math.pi)
         coords = self._coords
         n_sites = len(self._struct)
         e_real = np.empty((n_sites, n_sites), dtype=np.float64)
@@ -359,7 +361,7 @@ def _calc_real_and_point(self):
 
         qs = np.array(self._oxi_states)
 
-        e_point = -(qs**2) * sqrt(self._eta / pi)
+        e_point = -(qs**2) * math.sqrt(self._eta / math.pi)
 
         for idx in range(n_sites):
             nf_coords, rij, js, _ = self._struct.lattice.get_points_in_sphere(

pymatgen/analysis/ferroelectricity/polarization.py

@@ -130,7 +130,7 @@ def get_nearest_site(struct: Structure, coords: Sequence[float], site: PeriodicS
     # Sort by distance to coords
     ns.sort(key=lambda x: x[1])
     # Return PeriodicSite and distance of closest image
-    return ns[0][0:2]
+    return ns[0][:2]
 
 
 class Polarization:

pymatgen/analysis/interface_reactions.py

@@ -8,7 +8,7 @@
 import json
 import os
 import warnings
-from typing import Literal
+from typing import TYPE_CHECKING
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -23,6 +23,9 @@
 from pymatgen.util.plotting import pretty_plot
 from pymatgen.util.string import htmlify, latexify
 
+if TYPE_CHECKING:
+    from typing import Literal
+
 __author__ = "Yihan Xiao, Matthew McDermott"
 __maintainer__ = "Matthew McDermott"
 __email__ = "mcdermott@lbl.gov"

pymatgen/analysis/magnetism/analyzer.py

@@ -1011,7 +1011,7 @@ def _add_structures(ordered_structures, ordered_structures_origins, structures_t
 
             # ...and decide which ones to keep
             if len(max_symmetries) > self.truncate_by_symmetry:
-                max_symmetries = max_symmetries[0:5]
+                max_symmetries = max_symmetries[:5]
             structs_to_keep = [(idx, num) for idx, num in enumerate(num_sym_ops) if num in max_symmetries]
 
             # sort so that highest symmetry structs are first

pymatgen/analysis/magnetism/jahnteller.py

@@ -4,7 +4,7 @@
 
 import os
 import warnings
-from typing import TYPE_CHECKING, Any, Literal, cast
+from typing import TYPE_CHECKING, Literal, cast
 
 import numpy as np
 
@@ -14,6 +14,8 @@
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 
 if TYPE_CHECKING:
+    from typing import Any
+
     from pymatgen.core import Structure
 
 MODULE_DIR = os.path.dirname(os.path.abspath(__file__))

pymatgen/analysis/phase_diagram.py

@@ -11,7 +11,7 @@
 import warnings
 from collections import defaultdict
 from functools import lru_cache
-from typing import TYPE_CHECKING, Any, Literal, no_type_check
+from typing import TYPE_CHECKING, no_type_check
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -38,6 +38,7 @@
 if TYPE_CHECKING:
     from collections.abc import Collection, Iterator, Sequence
     from io import StringIO
+    from typing import Any, Literal
 
     from numpy.typing import ArrayLike
     from typing_extensions import Self

pymatgen/analysis/pourbaix_diagram.py

@@ -12,7 +12,7 @@
 from copy import deepcopy
 from functools import cmp_to_key, partial
 from multiprocessing import Pool
-from typing import TYPE_CHECKING, Any, no_type_check
+from typing import TYPE_CHECKING, no_type_check
 
 import numpy as np
 from monty.json import MontyDecoder, MSONable
@@ -31,6 +31,8 @@
 from pymatgen.util.string import Stringify
 
 if TYPE_CHECKING:
+    from typing import Any
+
     import matplotlib.pyplot as plt
     from typing_extensions import Self
 

pymatgen/analysis/structure_matcher.py

@@ -4,7 +4,7 @@
 
 import abc
 import itertools
-from typing import TYPE_CHECKING, Literal
+from typing import TYPE_CHECKING
 
 import numpy as np
 from monty.json import MSONable
@@ -16,6 +16,7 @@
 
 if TYPE_CHECKING:
     from collections.abc import Mapping, Sequence
+    from typing import Literal
 
     from typing_extensions import Self
 

pymatgen/cli/pmg_config.py

@@ -8,7 +8,7 @@
 import shutil
 import subprocess
 from glob import glob
-from typing import TYPE_CHECKING, Literal
+from typing import TYPE_CHECKING
 from urllib.request import urlretrieve
 
 from monty.json import jsanitize
@@ -21,6 +21,7 @@
 
 if TYPE_CHECKING:
     from argparse import Namespace
+    from typing import Literal
 
 
 def setup_cp2k_data(cp2k_data_dirs: list[str]) -> None:

pymatgen/command_line/bader_caller.py

@@ -22,7 +22,7 @@
 from pathlib import Path
 from shutil import which
 from tempfile import TemporaryDirectory
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING
 
 import numpy as np
 from monty.dev import deprecated
@@ -34,6 +34,8 @@
 from pymatgen.io.vasp.outputs import Chgcar
 
 if TYPE_CHECKING:
+    from typing import Any
+
     from typing_extensions import Self
 
     from pymatgen.core import Structure

pymatgen/command_line/gulp_caller.py

@@ -585,7 +585,7 @@ def get_relaxed_structure(gout: str):
                 # read the site coordinates in the following lines
                 idx += 6
                 line = output_lines[idx]
-                while line[0:2] != "--":
+                while line[:2] != "--":
                     structure_lines.append(line)
                     idx += 1
                     line = output_lines[idx]

pymatgen/command_line/mcsqs_caller.py

@@ -261,7 +261,7 @@ def _parse_clusters(filename):
         for point in range(cluster_dict["num_points_in_cluster"]):
             line = cluster[3 + point].split(" ")
             point_dict = {}
-            point_dict["coordinates"] = [float(line) for line in line[0:3]]
+            point_dict["coordinates"] = [float(line) for line in line[:3]]
             point_dict["num_possible_species"] = int(line[3]) + 2  # see ATAT manual for why +2
             point_dict["cluster_function"] = float(line[4])  # see ATAT manual for what "function" is
             points.append(point_dict)