refactor data file paths

pymatgen/analysis/hhi.py

@@ -25,7 +25,8 @@
 __date__ = "Oct 27, 2014"
 
 
-csv_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), "hhi_data.csv")
+module_dir = os.path.dirname(os.path.abspath(__file__))
+csv_path = f"{module_dir}/hhi_data.csv"
 
 
 @singleton

pymatgen/analysis/local_env.py

@@ -46,16 +46,16 @@
 __status__ = "Production"
 __date__ = "August 17, 2017"
 
-_directory = os.path.join(os.path.dirname(__file__))
+module_dir = os.path.dirname(os.path.abspath(__file__))
 yaml = YAML()
 
-with open(f"{_directory}/op_params.yaml") as f:
+with open(f"{module_dir}/op_params.yaml") as f:
     default_op_params = yaml.load(f)
 
-with open(f"{_directory}/cn_opt_params.yaml") as f:
+with open(f"{module_dir}/cn_opt_params.yaml") as f:
     cn_opt_params = yaml.load(f)
 
-with open(f"{_directory}/ionic_radii.json") as fp:
+with open(f"{module_dir}/ionic_radii.json") as fp:
     _ion_radii = json.load(fp)
 
 
@@ -1210,7 +1210,7 @@ def __init__(
         self.min_bond_distance = min_bond_distance
 
         # Load elemental radii table
-        bonds_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), "bonds_jmol_ob.yaml")
+        bonds_file = f"{module_dir}/bonds_jmol_ob.yaml"
         with open(bonds_file) as f:
             yaml = YAML()
             self.el_radius = yaml.load(f)
@@ -4210,7 +4210,7 @@ def from_preset(cls, preset) -> CutOffDictNN:
             A CutOffDictNN using the preset cut-off dictionary.
         """
         if preset == "vesta_2019":
-            cut_offs = loadfn(f"{_directory}/vesta_cutoffs.yaml")
+            cut_offs = loadfn(f"{module_dir}/vesta_cutoffs.yaml")
             return cls(cut_off_dict=cut_offs)
 
         raise ValueError(f"Unknown {preset=}")

pymatgen/analysis/prototypes.py

@@ -25,7 +25,7 @@
     from pymatgen.core import Structure
 
 module_dir = os.path.dirname(os.path.abspath(__file__))
-AFLOW_PROTOTYPE_LIBRARY = loadfn(os.path.join(os.path.dirname(os.path.abspath(__file__)), "aflow_prototypes.json"))
+AFLOW_PROTOTYPE_LIBRARY = loadfn(f"{module_dir}/aflow_prototypes.json")
 
 
 @due.dcite(
@@ -66,8 +66,8 @@ def __init__(self, initial_ltol=0.2, initial_stol=0.3, initial_angle_tol=5):
     def _match_prototype(structure_matcher, structure):
         tags = []
         for d in AFLOW_PROTOTYPE_LIBRARY:
-            p = d["snl"].structure
-            match = structure_matcher.fit_anonymous(p, structure)
+            struct = d["snl"].structure
+            match = structure_matcher.fit_anonymous(struct, structure)
             if match:
                 tags.append(d)
         return tags

pymatgen/io/lammps/generators.py

@@ -27,7 +27,8 @@
 __version__ = "0.2"
 
 logger = logging.getLogger(__name__)
-template_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "templates")
+module_dir = os.path.dirname(os.path.abspath(__file__))
+template_dir = f"{module_dir}/templates"
 
 
 @dataclass

pymatgen/io/lammps/inputs.py

@@ -37,6 +37,9 @@
 __email__ = "[email protected], [email protected]"
 __date__ = "Nov 2022"
 
+module_dir = os.path.dirname(os.path.abspath(__file__))
+template_dir = f"{module_dir}/templates"
+
 
 class LammpsInputFile(InputFile):
     """
@@ -868,8 +871,6 @@ class LammpsRun(MSONable):
     templates.
     """
 
-    template_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "templates")
-
     def __init__(self, script_template: str, settings: dict, data: LammpsData | str, script_filename: str) -> None:
         """
         Base constructor.
@@ -931,7 +932,7 @@ def md(
             other_settings (dict): other settings to be filled into
                 placeholders.
         """
-        template_path = os.path.join(cls.template_dir, "md.template")
+        template_path = os.path.join(template_dir, "md.template")
         with open(template_path) as f:
             script_template = f.read()
         settings = other_settings.copy() if other_settings else {}

pymatgen/io/lammps/sets.py

@@ -25,7 +25,8 @@
 __version__ = "0.2"
 
 logger = logging.getLogger(__name__)
-template_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "templates")
+module_dir = os.path.dirname(os.path.abspath(__file__))
+template_dir = f"{module_dir}/templates"
 
 
 class LammpsInputSet(InputSet):

tests/io/vasp/test_outputs.py

@@ -1466,49 +1466,49 @@ def test_interpolation(self):
 class TestProcar(PymatgenTest):
     def test_init(self):
         filepath = f"{TEST_FILES_DIR}/PROCAR.simple"
-        p = Procar(filepath)
-        assert p.get_occupation(0, "d")[Spin.up] == approx(0)
-        assert p.get_occupation(0, "s")[Spin.up] == approx(0.35381249999999997)
-        assert p.get_occupation(0, "p")[Spin.up] == approx(1.19540625)
+        procar = Procar(filepath)
+        assert procar.get_occupation(0, "d")[Spin.up] == approx(0)
+        assert procar.get_occupation(0, "s")[Spin.up] == approx(0.35381249999999997)
+        assert procar.get_occupation(0, "p")[Spin.up] == approx(1.19540625)
         with pytest.raises(ValueError, match="'m' is not in list"):
-            p.get_occupation(1, "m")
-        assert p.nbands == 10
-        assert p.nkpoints == 10
-        assert p.nions == 3
+            procar.get_occupation(1, "m")
+        assert procar.nbands == 10
+        assert procar.nkpoints == 10
+        assert procar.nions == 3
         filepath = f"{TEST_FILES_DIR}/PROCAR"
-        p = Procar(filepath)
-        assert p.get_occupation(0, "dxy")[Spin.up] == approx(0.96214813853000025)
-        assert p.get_occupation(0, "dxy")[Spin.down] == approx(0.85796295426000124)
+        procar = Procar(filepath)
+        assert procar.get_occupation(0, "dxy")[Spin.up] == approx(0.96214813853000025)
+        assert procar.get_occupation(0, "dxy")[Spin.down] == approx(0.85796295426000124)
 
     def test_phase_factors(self):
         filepath = f"{TEST_FILES_DIR}/PROCAR.phase"
-        p = Procar(filepath)
-        assert p.phase_factors[Spin.up][0, 0, 0, 0] == approx(-0.746 + 0.099j)
-        assert p.phase_factors[Spin.down][0, 0, 0, 0] == approx(0.372 - 0.654j)
+        procar = Procar(filepath)
+        assert procar.phase_factors[Spin.up][0, 0, 0, 0] == approx(-0.746 + 0.099j)
+        assert procar.phase_factors[Spin.down][0, 0, 0, 0] == approx(0.372 - 0.654j)
 
         # Two Li should have same phase factor.
-        assert p.phase_factors[Spin.up][0, 0, 0, 0] == approx(p.phase_factors[Spin.up][0, 0, 1, 0])
-        assert p.phase_factors[Spin.up][0, 0, 2, 0] == approx(-0.053 + 0.007j)
-        assert p.phase_factors[Spin.down][0, 0, 2, 0] == approx(0.027 - 0.047j)
+        assert procar.phase_factors[Spin.up][0, 0, 0, 0] == approx(procar.phase_factors[Spin.up][0, 0, 1, 0])
+        assert procar.phase_factors[Spin.up][0, 0, 2, 0] == approx(-0.053 + 0.007j)
+        assert procar.phase_factors[Spin.down][0, 0, 2, 0] == approx(0.027 - 0.047j)
 
         # new style phase factors (VASP 5.4.4+)
         filepath = f"{TEST_FILES_DIR}/PROCAR.new_format_5.4.4"
-        p = Procar(filepath)
-        assert p.phase_factors[Spin.up][0, 0, 0, 0] == approx(-0.13 + 0.199j)
+        procar = Procar(filepath)
+        assert procar.phase_factors[Spin.up][0, 0, 0, 0] == approx(-0.13 + 0.199j)
 
     def test_get_projection_on_elements(self):
         filepath = f"{TEST_FILES_DIR}/PROCAR.simple"
-        p = Procar(filepath)
+        procar = Procar(filepath)
         struct = Structure(
             Lattice.cubic(3.0),
             ["Li", "Na", "K"],
             [[0.0, 0.0, 0.0], [0.25, 0.25, 0.25], [0.75, 0.75, 0.75]],
         )
-        d = p.get_projection_on_elements(struct)
-        assert d[Spin.up][2][2] == approx({"Na": 0.042, "K": 0.646, "Li": 0.042})
+        dct = procar.get_projection_on_elements(struct)
+        assert dct[Spin.up][2][2] == approx({"Na": 0.042, "K": 0.646, "Li": 0.042})
         # https://github.com/materialsproject/pymatgen/pull/3261
         struct.replace_species({"K": "Na"})
-        d2 = p.get_projection_on_elements(struct)
+        d2 = procar.get_projection_on_elements(struct)
         assert d2[Spin.up][2][2] == approx({"Na": 0.688, "Li": 0.042})
 
 
@@ -1556,47 +1556,42 @@ def test_init(self):
 
 class TestWavecar(PymatgenTest):
     def setUp(self):
-        a = np.array([[10.0, 0.0, 0.0], [0.0, 10.0, 0.0], [0.0, 0.0, 10.0]])
-        self.vol = np.dot(a[0, :], np.cross(a[1, :], a[2, :]))
-        b = np.array(
-            [
-                np.cross(a[1, :], a[2, :]),
-                np.cross(a[2, :], a[0, :]),
-                np.cross(a[0, :], a[1, :]),
-            ]
-        )
+        a = np.array([[10, 0, 0], [0, 10, 0], [0, 0, 10]], dtype=float)  # lattice vectors
+        self.vol = np.dot(a[0, :], np.cross(a[1, :], a[2, :]))  # unit cell volume
+        # reciprocal lattice vectors
+        b = np.array([np.cross(a[1, :], a[2, :]), np.cross(a[2, :], a[0, :]), np.cross(a[0, :], a[1, :])])
         self.b = 2 * np.pi * b / self.vol
         self.a = a
-        self.w = Wavecar(f"{TEST_FILES_DIR}/WAVECAR.N2")
+        self.wavecar = Wavecar(f"{TEST_FILES_DIR}/WAVECAR.N2")
         self.wH2 = Wavecar(f"{TEST_FILES_DIR}/WAVECAR.H2_low_symm")
         self.wH2_gamma = Wavecar(f"{TEST_FILES_DIR}/WAVECAR.H2_low_symm.gamma")
         self.w_ncl = Wavecar(f"{TEST_FILES_DIR}/WAVECAR.H2.ncl")
         self.w_frac_encut = Wavecar(f"{TEST_FILES_DIR}/WAVECAR.frac_encut")
 
     def test_standard(self):
-        w = self.w
+        wavecar = self.wavecar
         a = np.array([[10.0, 0.0, 0.0], [0.0, 10.0, 0.0], [0.0, 0.0, 10.0]])
         vol = np.dot(a[0, :], np.cross(a[1, :], a[2, :]))
         b = np.array([np.cross(a[1, :], a[2, :]), np.cross(a[2, :], a[0, :]), np.cross(a[0, :], a[1, :])])
         b = 2 * np.pi * b / vol
 
-        assert w.filename == f"{TEST_FILES_DIR}/WAVECAR.N2"
-        assert w.efermi == approx(-5.7232, abs=1e-4)
-        assert w.encut == 25.0
-        assert w.nb == 9
-        assert w.nk == 1
-        assert_allclose(w.a, a)
-        assert_allclose(w.b, b)
-        assert w.vol == approx(vol)
-        assert len(w.kpoints) == w.nk
-        assert len(w.coeffs) == w.nk
-        assert len(w.coeffs[0]) == w.nb
-        assert len(w.band_energy) == w.nk
-        assert w.band_energy[0].shape == (w.nb, 3)
-        assert len(w.Gpoints[0]) <= 257
-        for k in range(w.nk):
-            for b in range(w.nb):
-                assert len(w.coeffs[k][b]) == len(w.Gpoints[k])
+        assert wavecar.filename == f"{TEST_FILES_DIR}/WAVECAR.N2"
+        assert wavecar.efermi == approx(-5.7232, abs=1e-4)
+        assert wavecar.encut == 25.0
+        assert wavecar.nb == 9
+        assert wavecar.nk == 1
+        assert_allclose(wavecar.a, a)
+        assert_allclose(wavecar.b, b)
+        assert wavecar.vol == approx(vol)
+        assert len(wavecar.kpoints) == wavecar.nk
+        assert len(wavecar.coeffs) == wavecar.nk
+        assert len(wavecar.coeffs[0]) == wavecar.nb
+        assert len(wavecar.band_energy) == wavecar.nk
+        assert wavecar.band_energy[0].shape == (wavecar.nb, 3)
+        assert len(wavecar.Gpoints[0]) <= 257
+        for k in range(wavecar.nk):
+            for b in range(wavecar.nb):
+                assert len(wavecar.coeffs[k][b]) == len(wavecar.Gpoints[k])
 
         # Test WAVECAR with fractional encut
         assert self.w_frac_encut.encut == 100.5
@@ -1624,21 +1619,21 @@ def test_standard(self):
             sys.stdout = saved_stdout
 
     def test_n2_45210(self):
-        w = Wavecar(f"{TEST_FILES_DIR}/WAVECAR.N2.45210")
-        assert w.filename == f"{TEST_FILES_DIR}/WAVECAR.N2.45210"
-        assert w.efermi == approx(-5.7232, abs=1e-4)
-        assert w.encut == 25.0
-        assert w.nb == 9
-        assert w.nk == 1
-        assert_allclose(w.a, self.a)
-        assert_allclose(w.b, self.b)
-        assert w.vol == approx(self.vol)
-        assert len(w.kpoints) == w.nk
-        assert len(w.coeffs) == w.nk
-        assert len(w.coeffs[0]) == w.nb
-        assert len(w.band_energy) == w.nk
-        assert w.band_energy[0].shape == (w.nb, 3)
-        assert len(w.Gpoints[0]) <= 257
+        wavecar = Wavecar(f"{TEST_FILES_DIR}/WAVECAR.N2.45210")
+        assert wavecar.filename == f"{TEST_FILES_DIR}/WAVECAR.N2.45210"
+        assert wavecar.efermi == approx(-5.7232, abs=1e-4)
+        assert wavecar.encut == 25.0
+        assert wavecar.nb == 9
+        assert wavecar.nk == 1
+        assert_allclose(wavecar.a, self.a)
+        assert_allclose(wavecar.b, self.b)
+        assert wavecar.vol == approx(self.vol)
+        assert len(wavecar.kpoints) == wavecar.nk
+        assert len(wavecar.coeffs) == wavecar.nk
+        assert len(wavecar.coeffs[0]) == wavecar.nb
+        assert len(wavecar.band_energy) == wavecar.nk
+        assert wavecar.band_energy[0].shape == (wavecar.nb, 3)
+        assert len(wavecar.Gpoints[0]) <= 257
 
     def test_n2_spin(self):
         w = Wavecar(f"{TEST_FILES_DIR}/WAVECAR.N2.spin")
@@ -1658,21 +1653,21 @@ def test_n2_spin(self):
             Wavecar._generate_G_points = temp_ggp
 
     def test_generate_nbmax(self):
-        self.w._generate_nbmax()
-        assert self.w._nbmax.tolist() == [5, 5, 5]
+        self.wavecar._generate_nbmax()
+        assert self.wavecar._nbmax.tolist() == [5, 5, 5]
 
     def test_generate_g_points(self):
-        for k in range(self.w.nk):
-            kp = self.w.kpoints[k]
-            assert len(self.w._generate_G_points(kp)) <= 257
+        for k in range(self.wavecar.nk):
+            kp = self.wavecar.kpoints[k]
+            assert len(self.wavecar._generate_G_points(kp)) <= 257
 
     def test_evaluate_wavefunc(self):
-        self.w.Gpoints.append(np.array([0, 0, 0]))
-        self.w.kpoints.append(np.array([0, 0, 0]))
-        self.w.coeffs.append([[1 + 1j]])
-        assert self.w.evaluate_wavefunc(-1, -1, [0, 0, 0]) == approx((1 + 1j) / np.sqrt(self.vol), abs=1e-4)
-        assert self.w.evaluate_wavefunc(0, 0, [0, 0, 0]) == approx(
-            np.sum(self.w.coeffs[0][0]) / np.sqrt(self.vol), abs=1e-4
+        self.wavecar.Gpoints.append(np.array([0, 0, 0]))
+        self.wavecar.kpoints.append(np.array([0, 0, 0]))
+        self.wavecar.coeffs.append([[1 + 1j]])
+        assert self.wavecar.evaluate_wavefunc(-1, -1, [0, 0, 0]) == approx((1 + 1j) / np.sqrt(self.vol), abs=1e-4)
+        assert self.wavecar.evaluate_wavefunc(0, 0, [0, 0, 0]) == approx(
+            np.sum(self.wavecar.coeffs[0][0]) / np.sqrt(self.vol), abs=1e-4
         )
         w = Wavecar(f"{TEST_FILES_DIR}/WAVECAR.N2.spin")
         w.Gpoints.append(np.array([0, 0, 0]))
@@ -1681,11 +1676,11 @@ def test_evaluate_wavefunc(self):
         assert w.evaluate_wavefunc(-1, -1, [0, 0, 0]) == approx((1 + 1j) / np.sqrt(self.vol), abs=1e-4)
 
     def test_fft_mesh_basic(self):
-        mesh = self.w.fft_mesh(0, 5)
+        mesh = self.wavecar.fft_mesh(0, 5)
         ind = np.argmax(np.abs(mesh))
         assert np.unravel_index(ind, mesh.shape) == (14, 1, 1)
-        assert mesh[tuple((self.w.ng / 2).astype(int))] == 0j
-        mesh = self.w.fft_mesh(0, 5, shift=False)
+        assert mesh[tuple((self.wavecar.ng / 2).astype(int))] == 0j
+        mesh = self.wavecar.fft_mesh(0, 5, shift=False)
         ind = np.argmax(np.abs(mesh))
         assert np.unravel_index(ind, mesh.shape) == (6, 8, 8)
         assert mesh[0, 0, 0] == 0j
@@ -1744,7 +1739,7 @@ def test_fft_mesh_advanced(self):
     def test_get_parchg(self):
         poscar = Poscar.from_file(f"{TEST_FILES_DIR}/POSCAR")
 
-        w = self.w
+        w = self.wavecar
         c = w.get_parchg(poscar, 0, 0, spin=0, phase=False)
         assert "total" in c.data
         assert "diff" not in c.data
@@ -1803,17 +1798,17 @@ def test_write_unks(self):
         unk_ncl = Unk.from_file(f"{TEST_FILES_DIR}/UNK.H2.ncl")
 
         with pytest.raises(ValueError, match="invalid directory"):
-            self.w.write_unks(f"{TEST_FILES_DIR}/UNK.N2.std")
+            self.wavecar.write_unks(f"{TEST_FILES_DIR}/UNK.N2.std")
 
         # different grids
-        self.w.write_unks("./unk_dir")
+        self.wavecar.write_unks("./unk_dir")
         assert len(list(Path("./unk_dir").glob("UNK*"))) == 1
         unk = Unk.from_file("./unk_dir/UNK00001.1")
         assert unk != unk_std
 
         # correct grid
-        self.w.ng = np.array([12, 12, 12])
-        self.w.write_unks(".")
+        self.wavecar.ng = np.array([12, 12, 12])
+        self.wavecar.write_unks(".")
         unk = Unk.from_file("UNK00001.1")
         assert unk == unk_std