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

Author: Shyue Ping Ong

pymatgen/core/structure.py

@@ -1271,7 +1271,7 @@ def __eq__(self, other: object) -> bool:
             # return NotImplemented as in https://docs.python.org/3/library/functools.html#functools.total_ordering
             return NotImplemented
 
-        other = cast(Structure, other)  # to make mypy happy
+        other = cast(Structure, other)  # make mypy happy
 
         if other is self:
             return True

pymatgen/electronic_structure/plotter.py

@@ -233,7 +233,7 @@ def get_plot(
         # Remove duplicate labels with a dictionary
         handles, labels = ax.get_legend_handles_labels()
         label_dict = dict(zip(labels, handles))
-        ax.legend(label_dict.values(), label_dict.keys())
+        ax.legend(label_dict.values(), label_dict)
         legend_text = ax.get_legend().get_texts()  # all the text.Text instance in the legend
         plt.setp(legend_text, fontsize=30)
         plt.tight_layout()

pymatgen/io/lammps/inputs.py

@@ -669,7 +669,7 @@ def _initialize_stage(self, stage_name: str | None = None, stage_index: int | No
 
     @staticmethod
     def _check_stage_format(stage: dict):
-        if list(stage.keys()) != ["stage_name", "commands"]:
+        if list(stage) != ["stage_name", "commands"]:
             raise KeyError(
                 "The provided stage does not have the correct keys. It should be 'stage_name' and 'commands'."
             )

pymatgen/io/vasp/sets.py

@@ -932,28 +932,30 @@ class MPScanRelaxSet(DictSet):
     CONFIG = _load_yaml_config("MPSCANRelaxSet")
     _valid_potcars = ("PBE_52", "PBE_54")
 
-    def __init__(self, structure: Structure, bandgap=0, **kwargs):
+    def __init__(self, structure: Structure, bandgap: float = 0, bandgap_tol: float = 1e-4, **kwargs) -> None:
         """
         Args:
             structure (Structure): Input structure.
-            bandgap (int): Bandgap of the structure in eV. The bandgap is used to
-                    compute the appropriate k-point density and determine the
-                    smearing settings.
-
-                    Metallic systems (default, bandgap = 0) use a KSPACING value of 0.22
-                    and Methfessel-Paxton order 2 smearing (ISMEAR=2, SIGMA=0.2).
-
-                    Non-metallic systems (bandgap > 0) use the tetrahedron smearing
-                    method (ISMEAR=-5, SIGMA=0.05). The KSPACING value is
-                    calculated from the bandgap via Eqs. 25 and 29 of Wisesa, McGill,
-                    and Mueller [1] (see References). Note that if 'user_incar_settings'
-                    or 'user_kpoints_settings' override KSPACING, the calculation from
-                    bandgap is not performed.
-
+            bandgap (float): Bandgap of the structure in eV. The bandgap is used to
+                compute the appropriate k-point density and determine the
+                smearing settings.
+
+                Metallic systems (default, bandgap = 0) use a KSPACING value of 0.22
+                and Methfessel-Paxton order 2 smearing (ISMEAR=2, SIGMA=0.2).
+
+                Non-metallic systems (bandgap > 0) use the tetrahedron smearing
+                method (ISMEAR=-5, SIGMA=0.05). The KSPACING value is
+                calculated from the bandgap via Eqs. 25 and 29 of Wisesa, McGill,
+                and Mueller [1] (see References). Note that if 'user_incar_settings'
+                or 'user_kpoints_settings' override KSPACING, the calculation from
+                bandgap is not performed.
+            bandgap_tol (float): Tolerance for determining if a system is metallic.
+                If the bandgap is less than this value, the system is considered
+                metallic. Defaults to 1e-4 (eV).
             vdw (str): set "rVV10" to enable SCAN+rVV10, which is a versatile
-                    van der Waals density functional by combing the SCAN functional
-                    with the rVV10 non-local correlation functional. rvv10 is the only
-                    dispersion correction available for SCAN at this time.
+                van der Waals density functional by combing the SCAN functional
+                with the rVV10 non-local correlation functional. rvv10 is the only
+                dispersion correction available for SCAN at this time.
             **kwargs: Same as those supported by DictSet.
 
         References:
@@ -966,33 +968,21 @@ def __init__(self, structure: Structure, bandgap=0, **kwargs):
         super().__init__(structure, MPScanRelaxSet.CONFIG, **kwargs)
         self.bandgap = bandgap
         self.kwargs = kwargs
+        self.bandgap_tol = bandgap_tol
 
-        updates = {}
+        updates: dict[str, float] = {}
         # select the KSPACING and smearing parameters based on the bandgap
         if self.bandgap < 1e-4:
-            updates["KSPACING"] = 0.22
-            updates["SIGMA"] = 0.2
-            updates["ISMEAR"] = 2
+            updates.update(KSPACING=0.22, SIGMA=0.2, ISMEAR=2)
         else:
             rmin = 25.22 - 2.87 * bandgap  # Eq. 25
             kspacing = 2 * np.pi * 1.0265 / (rmin - 1.0183)  # Eq. 29
             # cap the KSPACING at a max of 0.44, per internal benchmarking
-            if 0.22 < kspacing < 0.44:
-                updates["KSPACING"] = kspacing
-            else:
-                updates["KSPACING"] = 0.44
-            updates["ISMEAR"] = -5
-            updates["SIGMA"] = 0.05
+            updates.update(KSPACING=kspacing if 0.22 < kspacing < 0.44 else 0.44, SIGMA=0.05, ISMEAR=-5)
 
         # Don't overwrite things the user has supplied
-        if self.user_incar_settings.get("KSPACING"):
-            del updates["KSPACING"]
-
-        if self.user_incar_settings.get("ISMEAR"):
-            del updates["ISMEAR"]
-
-        if self.user_incar_settings.get("SIGMA"):
-            del updates["SIGMA"]
+        for key in self.user_incar_settings:
+            updates.pop(key, None)
 
         if self.vdw and self.vdw != "rvv10":
             warnings.warn("Use of van der waals functionals other than rVV10 with SCAN is not supported at this time. ")

tests/electronic_structure/test_plotter.py

@@ -8,6 +8,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import scipy
+from matplotlib import rc
 from numpy.testing import assert_allclose
 from pytest import approx
 
@@ -54,8 +55,6 @@ def test_get_dos_dict(self):
     # it can actually execute.
     def test_get_plot(self):
         # Disabling latex is needed for this test to work.
-        from matplotlib import rc
-
         rc("text", usetex=False)
         self.plotter.add_dos_dict(self.dos.get_element_dos(), key_sort_func=lambda x: x.X)
         ax = self.plotter.get_plot()

tests/io/qchem/test_outputs.py

@@ -468,7 +468,7 @@ def test_cmirs_water(self):
 
     def test_NBO_hyperbonds(self):
         data = QCOutput(f"{TEST_FILES_DIR}/molecules/new_qchem_files/hyper.qout").data
-        assert len(data["nbo_data"]["hyperbonds"][0]["hyperbond index"].keys()) == 2
+        assert len(data["nbo_data"]["hyperbonds"][0]["hyperbond index"]) == 2
         assert data["nbo_data"]["hyperbonds"][0]["BD(A-B)"][1] == 106
         assert data["nbo_data"]["hyperbonds"][0]["bond atom 2 symbol"][0] == "C"
         assert data["nbo_data"]["hyperbonds"][0]["occ"][1] == 3.0802

tests/io/vasp/test_sets.py

@@ -1483,25 +1483,24 @@ def test_scan_substitute(self):
         incar = mp_scan_sub.incar
         assert incar["METAGGA"] == "Scan"
 
-    def test_nonmetal(self):
-        # Test that KSPACING and ISMEAR change with a nonmetal structure
-        file_path = f"{TEST_FILES_DIR}/POSCAR.O2"
-        struct = Poscar.from_file(file_path, check_for_POTCAR=False).structure
-        scan_nonmetal_set = MPScanRelaxSet(struct, bandgap=1.1)
-        incar = scan_nonmetal_set.incar
-        assert incar["KSPACING"] == approx(0.3064757, abs=1e-5)
-        assert incar["ISMEAR"] == -5
-        assert incar["SIGMA"] == 0.05
-
-    def test_kspacing_cap(self):
+    def test_bandgap_tol(self):
+        # Test that the bandgap tolerance is applied correctly
+        bandgap = 0.01
+        for bandgap_tol, expected_kspacing in ((0.001, 0.2668137888), (0.02, 0.26681378884)):
+            incar = MPScanRelaxSet(self.struct, bandgap=0.01, bandgap_tol=bandgap_tol).incar
+            assert incar["KSPACING"] == approx(expected_kspacing, abs=1e-5), f"{bandgap_tol=}, {bandgap=}"
+            assert incar["ISMEAR"] == -5
+            assert incar["SIGMA"] == 0.05
+
+    def test_kspacing(self):
         # Test that KSPACING is capped at 0.44 for insulators
         file_path = f"{TEST_FILES_DIR}/POSCAR.O2"
         struct = Poscar.from_file(file_path, check_for_POTCAR=False).structure
-        scan_nonmetal_set = MPScanRelaxSet(struct, bandgap=10)
-        incar = scan_nonmetal_set.incar
-        assert incar["KSPACING"] == approx(0.44, abs=1e-5)
-        assert incar["ISMEAR"] == -5
-        assert incar["SIGMA"] == 0.05
+        for bandgap, expected in ((10, 0.44), (3, 0.4136617), (1.1, 0.3064757)):
+            incar = MPScanRelaxSet(struct, bandgap=bandgap).incar
+            assert incar["KSPACING"] == approx(expected, abs=1e-5)
+            assert incar["ISMEAR"] == -5
+            assert incar["SIGMA"] == 0.05
 
     def test_incar_overrides(self):
         # use 'user_incar_settings' to override the KSPACING, ISMEAR, and SIGMA