Revert to Yb_2 on pre-PBE_54 input sets

pymatgen/analysis/tests/test_interface_reactions.py

@@ -145,13 +145,13 @@ def setUp(self):
             norm=True,
             use_hull_energy=False,
         )
-        with pytest.raises(Exception) as context1:
+        with pytest.raises(Exception) as exc_info:
             _ = InterfacialReactivity(Composition("Li2O2"), Composition("Li"), pd=self.gpd, norm=True)
-            assert (
-                str(context1.exception) == "Please use the GrandPotentialInterfacialReactivity "
-                "class for interfacial reactions with open elements!"
-            )
-        with pytest.raises(Exception) as context2:
+        assert (
+            str(exc_info.value) == "Please use the GrandPotentialInterfacialReactivity "
+            "class for interfacial reactions with open elements!"
+        )
+        with pytest.raises(Exception) as exc_info:
             _ = GrandPotentialInterfacialReactivity(
                 Composition("O2"),
                 Composition("Mn"),
@@ -160,7 +160,7 @@ def setUp(self):
                 norm=False,
                 include_no_mixing_energy=True,
             )
-            assert str(context2.exception) == "Please provide non-grand phase diagram to compute no_mixing_energy!"
+        assert str(exc_info.value) == "Please provide non-grand phase diagram to compute no_mixing_energy!"
 
         self.ir = [ir_0, ir_1, ir_2, ir_3, ir_4, ir_5, ir_6, ir_7, ir_8, ir_9, ir_10, ir_11, ir_12]
 

pymatgen/analysis/transition_state.py

@@ -8,8 +8,8 @@
 
 from __future__ import annotations
 
-import glob
 import os
+from glob import glob
 
 import numpy as np
 from monty.json import MSONable, jsanitize
@@ -254,14 +254,14 @@ def from_dir(cls, root_dir, relaxation_dirs=None, **kwargs):
         terminal_dirs.append([os.path.join(root_dir, d) for d in ["initial", "final"]])
 
         for i, d in neb_dirs:
-            outcar = glob.glob(os.path.join(d, "OUTCAR*"))
-            contcar = glob.glob(os.path.join(d, "CONTCAR*"))
-            poscar = glob.glob(os.path.join(d, "POSCAR*"))
+            outcar = glob(os.path.join(d, "OUTCAR*"))
+            contcar = glob(os.path.join(d, "CONTCAR*"))
+            poscar = glob(os.path.join(d, "POSCAR*"))
             terminal = i in [0, neb_dirs[-1][0]]
             if terminal:
                 for ds in terminal_dirs:
                     od = ds[0] if i == 0 else ds[1]
-                    outcar = glob.glob(os.path.join(od, "OUTCAR*"))
+                    outcar = glob(os.path.join(od, "OUTCAR*"))
                     if outcar:
                         outcar = sorted(outcar)
                         outcars.append(Outcar(outcar[-1]))

pymatgen/apps/borg/hive.py

@@ -5,11 +5,11 @@
 from __future__ import annotations
 
 import abc
-import glob
 import json
 import logging
 import os
 import warnings
+from glob import glob
 
 from monty.io import zopen
 from monty.json import MSONable
@@ -118,9 +118,9 @@ def assimilate(self, path):
         """
         files = os.listdir(path)
         if "relax1" in files and "relax2" in files:
-            filepath = glob.glob(os.path.join(path, "relax2", "vasprun.xml*"))[0]
+            filepath = glob(os.path.join(path, "relax2", "vasprun.xml*"))[0]
         else:
-            vasprun_files = glob.glob(os.path.join(path, "vasprun.xml*"))
+            vasprun_files = glob(os.path.join(path, "vasprun.xml*"))
             filepath = None
             if len(vasprun_files) == 1:
                 filepath = vasprun_files[0]
@@ -159,11 +159,8 @@ def get_valid_paths(self, path):
             (not parent.endswith("/relax1"))
             and (not parent.endswith("/relax2"))
             and (
-                len(glob.glob(os.path.join(parent, "vasprun.xml*"))) > 0
-                or (
-                    len(glob.glob(os.path.join(parent, "POSCAR*"))) > 0
-                    and len(glob.glob(os.path.join(parent, "OSZICAR*"))) > 0
-                )
+                len(glob(os.path.join(parent, "vasprun.xml*"))) > 0
+                or (len(glob(os.path.join(parent, "POSCAR*"))) > 0 and len(glob(os.path.join(parent, "OSZICAR*"))) > 0)
             )
         ):
             return [parent]
@@ -233,13 +230,13 @@ def assimilate(self, path):
             if "relax1" in files and "relax2" in files:
                 for filename in ("INCAR", "POTCAR", "POSCAR"):
                     search_str = os.path.join(path, "relax1", filename + "*")
-                    files_to_parse[filename] = glob.glob(search_str)[0]
+                    files_to_parse[filename] = glob(search_str)[0]
                 for filename in ("CONTCAR", "OSZICAR"):
                     search_str = os.path.join(path, "relax2", filename + "*")
-                    files_to_parse[filename] = glob.glob(search_str)[-1]
+                    files_to_parse[filename] = glob(search_str)[-1]
             else:
                 for filename in filenames:
-                    files = sorted(glob.glob(os.path.join(path, filename + "*")))
+                    files = sorted(glob(os.path.join(path, filename + "*")))
                     if len(files) == 1 or filename in ("INCAR", "POTCAR") or len(files) == 1 and filename == "DYNMAT":
                         files_to_parse[filename] = files[0]
                     elif len(files) > 1:
@@ -440,7 +437,7 @@ def _get_transformation_history(path):
     """
     Checks for a transformations.json* file and returns the history.
     """
-    trans_json = glob.glob(os.path.join(path, "transformations.json*"))
+    trans_json = glob(os.path.join(path, "transformations.json*"))
     if trans_json:
         try:
             with zopen(trans_json[0]) as f:

pymatgen/cli/pmg_config.py

@@ -6,11 +6,11 @@
 
 from __future__ import annotations
 
-import glob
 import os
 import shutil
 import subprocess
 from argparse import Namespace
+from glob import glob
 from typing import Literal
 from urllib.request import urlretrieve
 
@@ -31,17 +31,15 @@ def setup_cp2k_data(cp2k_data_dirs: list[str]) -> None:
             raise SystemExit(0)
     print("Generating pymatgen resource directory for CP2K...")
 
-    import glob
-
     from monty.json import jsanitize
     from ruamel import yaml
 
     from pymatgen.core import Element
     from pymatgen.io.cp2k.inputs import GaussianTypeOrbitalBasisSet, GthPotential
     from pymatgen.io.cp2k.utils import chunk
 
-    basis_files = glob.glob(os.path.join(data_dir, "*BASIS*"))
-    potential_files = glob.glob(os.path.join(data_dir, "*POTENTIAL*"))
+    basis_files = glob(os.path.join(data_dir, "*BASIS*"))
+    potential_files = glob(os.path.join(data_dir, "*POTENTIAL*"))
 
     settings: dict[str, dict] = {str(el): {"potentials": {}, "basis_sets": {}} for el in Element}
 
@@ -141,7 +139,7 @@ def setup_potcars(potcar_dirs: list[str]):
         basename = os.path.basename(parent)
         basename = name_mappings.get(basename, basename)
         for subdir in subdirs:
-            filenames = glob.glob(os.path.join(parent, subdir, "POTCAR*"))
+            filenames = glob(os.path.join(parent, subdir, "POTCAR*"))
             if len(filenames) > 0:
                 try:
                     base_dir = os.path.join(target_dir, basename)

pymatgen/command_line/bader_caller.py

@@ -14,11 +14,11 @@
 
 from __future__ import annotations
 
-import glob
 import os
 import shutil
 import subprocess
 import warnings
+from glob import glob
 from shutil import which
 
 import numpy as np
@@ -418,7 +418,7 @@ def from_path(cls, path, suffix=""):
 
         def _get_filepath(filename):
             name_pattern = filename + suffix + "*" if filename != "POTCAR" else filename + "*"
-            paths = glob.glob(os.path.join(path, name_pattern))
+            paths = glob(os.path.join(path, name_pattern))
             fpath = None
             if len(paths) >= 1:
                 # using reverse=True because, if multiple files are present,
@@ -478,7 +478,7 @@ def bader_analysis_from_path(path, suffix=""):
     """
 
     def _get_filepath(filename, warning, path=path, suffix=suffix):
-        paths = glob.glob(os.path.join(path, filename + suffix + "*"))
+        paths = glob(os.path.join(path, filename + suffix + "*"))
         if not paths:
             warnings.warn(warning)
             return None

pymatgen/command_line/chargemol_caller.py

@@ -42,11 +42,11 @@
 """
 from __future__ import annotations
 
-import glob
 import os
 import shutil
 import subprocess
 import warnings
+from glob import glob
 from shutil import which
 
 import numpy as np
@@ -155,7 +155,7 @@ def _get_filepath(path, filename, suffix=""):
             (str): Absolute path to the file.
         """
         name_pattern = f"{filename}{suffix}*" if filename != "POTCAR" else f"{filename}*"
-        paths = glob.glob(os.path.join(path, name_pattern))
+        paths = glob(os.path.join(path, name_pattern))
         fpath = None
         if len(paths) >= 1:
             # using reverse=True because, if multiple files are present,

pymatgen/command_line/critic2_caller.py

@@ -39,12 +39,12 @@
 
 from __future__ import annotations
 
-import glob
 import logging
 import os
 import subprocess
 import warnings
 from enum import Enum
+from glob import glob
 from shutil import which
 
 import numpy as np
@@ -322,7 +322,7 @@ def get_filepath(filename, warning, path, suffix):
         path: Path to search
         suffix: Suffixes to search.
     """
-    paths = glob.glob(os.path.join(path, filename + suffix + "*"))
+    paths = glob(os.path.join(path, filename + suffix + "*"))
     if not paths:
         warnings.warn(warning)
         return None

pymatgen/command_line/enumlib_caller.py

@@ -27,12 +27,12 @@
 from __future__ import annotations
 
 import fractions
-import glob
 import itertools
 import logging
 import math
 import re
 import subprocess
+from glob import glob
 from shutil import which
 from threading import Timer
 
@@ -364,7 +364,7 @@ def _get_structures(self, num_structs):
             ordered_structure = None  # to fix pylint E0601
             inv_org_latt = None
 
-        for file in glob.glob("vasp.*"):
+        for file in glob("vasp.*"):
             with open(file) as f:
                 data = f.read()
                 data = re.sub(r"scale factor", "1", data)

pymatgen/core/tests/test_lattice.py

@@ -185,7 +185,7 @@ def test_get_lll_reduced_lattice(self):
         lattice = Lattice([1.0, 1, 1, -1.0, 0, 2, 3.0, 5, 6])
         reduced_latt = lattice.get_lll_reduced_lattice()
 
-        expected_ans = Lattice(np.array([0.0, 1.0, 0.0, 1.0, 0.0, 1.0, -2.0, 0.0, 1.0]).reshape((3, 3)))
+        expected_ans = Lattice([0.0, 1.0, 0.0, 1.0, 0.0, 1.0, -2.0, 0.0, 1.0]).reshape((3, 3))
         assert round(abs(np.linalg.det(np.linalg.solve(expected_ans.matrix, reduced_latt.matrix)) - 1), 7) == 0
         self.assertArrayAlmostEqual(sorted(reduced_latt.abc), sorted(expected_ans.abc))
         assert round(abs(reduced_latt.volume - lattice.volume), 7) == 0
@@ -201,19 +201,17 @@ def test_get_lll_reduced_lattice(self):
             14.253000,
         ]
         expected_ans = Lattice(
-            np.array(
-                [
-                    -4.298850,
-                    2.481942,
-                    0.000000,
-                    2.865900,
-                    4.963884,
-                    0.000000,
-                    0.000000,
-                    0.000000,
-                    14.253000,
-                ]
-            )
+            [
+                -4.298850,
+                2.481942,
+                0.000000,
+                2.865900,
+                4.963884,
+                0.000000,
+                0.000000,
+                0.000000,
+                14.253000,
+            ]
         )
         reduced_latt = Lattice(latt).get_lll_reduced_lattice()
         assert round(abs(np.linalg.det(np.linalg.solve(expected_ans.matrix, reduced_latt.matrix)) - 1), 7) == 0
@@ -481,7 +479,7 @@ def test_get_distance_and_image_strict(self):
         for _ in range(10):
             lengths = [np.random.randint(1, 100) for i in range(3)]
             lattice = [np.random.rand(3) * lengths[i] for i in range(3)]
-            lattice = Lattice(np.array(lattice))
+            lattice = Lattice(lattice)
 
             f1 = np.random.rand(3)
             f2 = np.random.rand(3)

pymatgen/core/tests/test_sites.py

@@ -127,7 +127,7 @@ def test_distance_and_image(self):
         assert round(abs(distance - 19.461500456028563), 5) == 0
         # Test that old and new distance algo give the same ans for
         # "standard lattices"
-        lattice = Lattice(np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]))
+        lattice = Lattice([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
         site1 = PeriodicSite("Fe", np.array([0.01, 0.02, 0.03]), lattice)
         site2 = PeriodicSite("Fe", np.array([0.99, 0.98, 0.97]), lattice)
         assert round(abs(get_distance_and_image_old(site1, site2)[0] - site1.distance_and_image(site2)[0]), 7) == 0

pymatgen/io/cp2k/outputs.py

@@ -6,11 +6,11 @@
 
 from __future__ import annotations
 
-import glob
 import logging
 import os
 import re
 import warnings
+from glob import glob
 from itertools import chain
 
 import numpy as np
@@ -246,31 +246,31 @@ def parse_files(self):
         Identify files present in the directory with the cp2k output file. Looks for trajectories,
         dos, and cubes
         """
-        self.filenames["DOS"] = glob.glob(os.path.join(self.dir, "*.dos*"))
-        pdos = glob.glob(os.path.join(self.dir, "*pdos*"))
+        self.filenames["DOS"] = glob(os.path.join(self.dir, "*.dos*"))
+        pdos = glob(os.path.join(self.dir, "*pdos*"))
         self.filenames["PDOS"] = []
         self.filenames["LDOS"] = []
         for p in pdos:
             if "list" in p.split("/")[-1]:
                 self.filenames["LDOS"].append(p)
             else:
                 self.filenames["PDOS"].append(p)
-        self.filenames["band_structure"] = glob.glob(os.path.join(self.dir, "*BAND.bs*"))
-        self.filenames["trajectory"] = glob.glob(os.path.join(self.dir, "*pos*.xyz*"))
-        self.filenames["forces"] = glob.glob(os.path.join(self.dir, "*frc*.xyz*"))
-        self.filenames["stress"] = glob.glob(os.path.join(self.dir, "*stress*"))
-        self.filenames["cell"] = glob.glob(os.path.join(self.dir, "*.cell*"))
-        self.filenames["ener"] = glob.glob(os.path.join(self.dir, "*.ener*"))
-        self.filenames["electron_density"] = glob.glob(os.path.join(self.dir, "*ELECTRON_DENSITY*.cube*"))
-        self.filenames["spin_density"] = glob.glob(os.path.join(self.dir, "*SPIN_DENSITY*.cube*"))
-        self.filenames["v_hartree"] = glob.glob(os.path.join(self.dir, "*hartree*.cube*"))
-        self.filenames["hyperfine_tensor"] = glob.glob(os.path.join(self.dir, "*HYPERFINE*eprhyp*"))
-        self.filenames["g_tensor"] = glob.glob(os.path.join(self.dir, "*GTENSOR*data*"))
-        self.filenames["spinspin_tensor"] = glob.glob(os.path.join(self.dir, "*K*data*"))
-        self.filenames["chi_tensor"] = glob.glob(os.path.join(self.dir, "*CHI*data*"))
-        self.filenames["nmr_shift"] = glob.glob(os.path.join(self.dir, "*SHIFT*data*"))
-        self.filenames["raman"] = glob.glob(os.path.join(self.dir, "*raman*data*"))
-        restart = glob.glob(os.path.join(self.dir, "*restart*"))
+        self.filenames["band_structure"] = glob(os.path.join(self.dir, "*BAND.bs*"))
+        self.filenames["trajectory"] = glob(os.path.join(self.dir, "*pos*.xyz*"))
+        self.filenames["forces"] = glob(os.path.join(self.dir, "*frc*.xyz*"))
+        self.filenames["stress"] = glob(os.path.join(self.dir, "*stress*"))
+        self.filenames["cell"] = glob(os.path.join(self.dir, "*.cell*"))
+        self.filenames["ener"] = glob(os.path.join(self.dir, "*.ener*"))
+        self.filenames["electron_density"] = glob(os.path.join(self.dir, "*ELECTRON_DENSITY*.cube*"))
+        self.filenames["spin_density"] = glob(os.path.join(self.dir, "*SPIN_DENSITY*.cube*"))
+        self.filenames["v_hartree"] = glob(os.path.join(self.dir, "*hartree*.cube*"))
+        self.filenames["hyperfine_tensor"] = glob(os.path.join(self.dir, "*HYPERFINE*eprhyp*"))
+        self.filenames["g_tensor"] = glob(os.path.join(self.dir, "*GTENSOR*data*"))
+        self.filenames["spinspin_tensor"] = glob(os.path.join(self.dir, "*K*data*"))
+        self.filenames["chi_tensor"] = glob(os.path.join(self.dir, "*CHI*data*"))
+        self.filenames["nmr_shift"] = glob(os.path.join(self.dir, "*SHIFT*data*"))
+        self.filenames["raman"] = glob(os.path.join(self.dir, "*raman*data*"))
+        restart = glob(os.path.join(self.dir, "*restart*"))
         self.filenames["restart.bak"] = []
         self.filenames["restart"] = []
         for r in restart:
@@ -279,7 +279,7 @@ def parse_files(self):
             else:
                 self.filenames["restart"].append(r)
 
-        wfn = glob.glob(os.path.join(self.dir, "*.wfn*")) + glob.glob(os.path.join(self.dir, "*.kp*"))
+        wfn = glob(os.path.join(self.dir, "*.wfn*")) + glob(os.path.join(self.dir, "*.kp*"))
         self.filenames["wfn.bak"] = []
         for w in wfn:
             if "bak" in w.split("/")[-1]: