Clean up test files: VASP inputs

pymatgen/util/testing/__init__.py

@@ -26,6 +26,7 @@
 MODULE_DIR = Path(__file__).absolute().parent
 STRUCTURES_DIR = MODULE_DIR / ".." / "structures"
 TEST_FILES_DIR = Path(SETTINGS.get("PMG_TEST_FILES_DIR", f"{ROOT}/tests/files"))
+VASP_IN_DIR = f"{TEST_FILES_DIR}/vasp/inputs"
 VASP_OUT_DIR = f"{TEST_FILES_DIR}/vasp/outputs"
 # fake POTCARs have original header information, meaning properties like number of electrons,
 # nuclear charge, core radii, etc. are unchanged (important for testing) while values of the and

tests/alchemy/test_transmuters.py

@@ -8,7 +8,7 @@
     RemoveSpeciesTransformation,
     SubstitutionTransformation,
 )
-from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, PymatgenTest
 
 
 class TestCifTransmuter(PymatgenTest):
@@ -25,15 +25,15 @@ def test_init(self):
 class TestPoscarTransmuter(PymatgenTest):
     def test_init(self):
         trafos = [SubstitutionTransformation({"Fe": "Mn"})]
-        tsc = PoscarTransmuter.from_filenames([f"{TEST_FILES_DIR}/POSCAR", f"{TEST_FILES_DIR}/POSCAR"], trafos)
+        tsc = PoscarTransmuter.from_filenames([f"{VASP_IN_DIR}/POSCAR", f"{VASP_IN_DIR}/POSCAR"], trafos)
         assert len(tsc) == 2
         expected = {"Mn", "O", "P"}
         for substitution in tsc:
             els = {el.symbol for el in substitution.final_structure.elements}
             assert expected == els
 
     def test_transmuter(self):
-        tsc = PoscarTransmuter.from_filenames([f"{TEST_FILES_DIR}/POSCAR"])
+        tsc = PoscarTransmuter.from_filenames([f"{VASP_IN_DIR}/POSCAR"])
         tsc.append_transformation(RemoveSpeciesTransformation("O"))
         assert len(tsc[0].final_structure) == 8
 

tests/analysis/test_ewald.py

@@ -8,12 +8,12 @@
 
 from pymatgen.analysis.ewald import EwaldMinimizer, EwaldSummation
 from pymatgen.core.structure import Structure
-from pymatgen.util.testing import TEST_FILES_DIR
+from pymatgen.util.testing import VASP_IN_DIR
 
 
 class TestEwaldSummation(unittest.TestCase):
     def setUp(self):
-        filepath = f"{TEST_FILES_DIR}/POSCAR"
+        filepath = f"{VASP_IN_DIR}/POSCAR"
         self.original_struct = Structure.from_file(filepath)
         self.struct = self.original_struct.copy()
         self.struct.add_oxidation_state_by_element({"Li": 1, "Fe": 2, "P": 5, "O": -2})
@@ -107,7 +107,7 @@ def test_init(self):
 
     def test_site(self):
         """Test that uses an uncharged structure."""
-        filepath = f"{TEST_FILES_DIR}/POSCAR"
+        filepath = f"{VASP_IN_DIR}/POSCAR"
         struct = Structure.from_file(filepath)
         s = struct.copy()
         s.add_oxidation_state_by_element({"Li": 1, "Fe": 3, "P": 5, "O": -2})

tests/analysis/test_structure_analyzer.py

@@ -18,7 +18,7 @@
 )
 from pymatgen.core import Element, Lattice, Structure
 from pymatgen.io.vasp.outputs import Xdatcar
-from pymatgen.util.testing import TEST_FILES_DIR, VASP_OUT_DIR, PymatgenTest
+from pymatgen.util.testing import VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest
 
 
 class TestVoronoiAnalyzer(PymatgenTest):
@@ -39,8 +39,8 @@ def test_analyze(self):
 
 class TestRelaxationAnalyzer(unittest.TestCase):
     def setUp(self):
-        s1 = Structure.from_file(f"{TEST_FILES_DIR}/POSCAR.Li2O")
-        s2 = Structure.from_file(f"{VASP_OUT_DIR}/CONTCAR.Li2O")
+        s1 = Structure.from_file(f"{VASP_IN_DIR}/POSCAR_Li2O")
+        s2 = Structure.from_file(f"{VASP_OUT_DIR}/CONTCAR_Li2O")
         self.analyzer = RelaxationAnalyzer(s1, s2)
 
     def test_vol_and_para_changes(self):

tests/analysis/test_structure_matcher.py

@@ -17,7 +17,7 @@
 )
 from pymatgen.core import Element, Lattice, Structure, SymmOp
 from pymatgen.util.coord import find_in_coord_list_pbc
-from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, PymatgenTest
 
 
 class TestStructureMatcher(PymatgenTest):
@@ -27,12 +27,12 @@ def setUp(self):
         self.struct_list = [ent.structure for ent in entries]
         self.oxi_structs = [
             self.get_structure("Li2O"),
-            Structure.from_file(f"{TEST_FILES_DIR}/POSCAR.Li2O"),
+            Structure.from_file(f"{VASP_IN_DIR}/POSCAR_Li2O"),
         ]
 
     def test_ignore_species(self):
         s1 = Structure.from_file(f"{TEST_FILES_DIR}/LiFePO4.cif")
-        s2 = Structure.from_file(f"{TEST_FILES_DIR}/POSCAR")
+        s2 = Structure.from_file(f"{VASP_IN_DIR}/POSCAR")
         matcher = StructureMatcher(ignored_species=["Li"], primitive_cell=False, attempt_supercell=True)
         assert matcher.fit(s1, s2)
         assert matcher.fit_anonymous(s1, s2)
@@ -283,8 +283,8 @@ def test_fit(self):
         # test symmetric
         sm_coarse = sm = StructureMatcher(comparator=ElementComparator(), ltol=0.6, stol=0.6, angle_tol=6)
 
-        struct1 = Structure.from_file(f"{TEST_FILES_DIR}/fit_symm_s1.vasp")
-        struct2 = Structure.from_file(f"{TEST_FILES_DIR}/fit_symm_s2.vasp")
+        struct1 = Structure.from_file(f"{VASP_IN_DIR}/POSCAR_fit_symm_s1")
+        struct2 = Structure.from_file(f"{VASP_IN_DIR}/POSCAR_fit_symm_s2")
         assert sm_coarse.fit(struct1, struct2)
         assert sm_coarse.fit(struct2, struct1) is False
         assert sm_coarse.fit(struct1, struct2, symmetric=True) is False
@@ -317,12 +317,12 @@ def test_class(self):
 
     def test_mix(self):
         structures = list(map(self.get_structure, ["Li2O", "Li2O2", "LiFePO4"]))
-        structures += [Structure.from_file(f"{TEST_FILES_DIR}/{fname}") for fname in ["POSCAR.Li2O", "POSCAR.LiFePO4"]]
+        structures += [Structure.from_file(f"{VASP_IN_DIR}/{fname}") for fname in ["POSCAR_Li2O", "POSCAR_LiFePO4"]]
         sm = StructureMatcher(comparator=ElementComparator())
         groups = sm.group_structures(structures)
         for group in groups:
             formula = group[0].reduced_formula
-            assert len(group) == (2 if formula in ["Li2O", "LiFePO4"] else 1)
+            assert len(group) == (2 if formula in {"Li2O", "LiFePO4"} else 1)
 
     def test_left_handed_lattice(self):
         """Ensure Left handed lattices are accepted."""

tests/command_line/test_bader_caller.py

@@ -12,7 +12,7 @@
 from pytest import approx
 
 from pymatgen.command_line.bader_caller import BaderAnalysis, bader_analysis_from_path
-from pymatgen.util.testing import TEST_FILES_DIR, VASP_OUT_DIR, PymatgenTest
+from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest
 
 
 @unittest.skipIf(not which("bader"), "bader executable not present")
@@ -24,7 +24,7 @@ def test_init(self):
         # test with reference file
         analysis = BaderAnalysis(
             chgcar_filename=f"{VASP_OUT_DIR}/CHGCAR.Fe3O4.gz",
-            potcar_filename=f"{TEST_FILES_DIR}/POTCAR.Fe3O4",
+            potcar_filename=f"{VASP_IN_DIR}/POTCAR_Fe3O4",
             chgref_filename=f"{VASP_OUT_DIR}/CHGCAR.Fe3O4_ref.gz",
         )
         assert len(analysis.data) == 14
@@ -119,7 +119,7 @@ def test_atom_parsing(self):
         # test with reference file
         analysis = BaderAnalysis(
             chgcar_filename=f"{VASP_OUT_DIR}/CHGCAR.Fe3O4.gz",
-            potcar_filename=f"{TEST_FILES_DIR}/POTCAR.Fe3O4",
+            potcar_filename=f"{VASP_IN_DIR}/POTCAR_Fe3O4",
             chgref_filename=f"{VASP_OUT_DIR}/CHGCAR.Fe3O4_ref.gz",
             parse_atomic_densities=True,
         )

tests/command_line/test_gulp_caller.py

@@ -25,7 +25,7 @@
     get_energy_tersoff,
 )
 from pymatgen.core.structure import Structure
-from pymatgen.util.testing import TEST_FILES_DIR
+from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR
 
 gulp_present = which("gulp") and os.getenv("GULP_LIB") and ("win" not in sys.platform)
 # disable gulp tests for now. Right now, it is compiled against libgfortran3, which is no longer supported in the new
@@ -99,7 +99,7 @@ def test_decimal(self):
 @unittest.skipIf(not gulp_present, "gulp not present.")
 class TestGulpIO(unittest.TestCase):
     def setUp(self):
-        self.structure = Structure.from_file(f"{TEST_FILES_DIR}/POSCAR.Al12O18")
+        self.structure = Structure.from_file(f"{VASP_IN_DIR}/POSCAR_Al12O18")
         self.gio = GulpIO()
 
     def test_keyword_line_with_correct_keywords(self):
@@ -280,7 +280,7 @@ def setUp(self):
         self.val_dict = dict(zip(el, val))
 
     def test_get_energy_tersoff(self):
-        structure = Structure.from_file(f"{TEST_FILES_DIR}/POSCAR.Al12O18")
+        structure = Structure.from_file(f"{VASP_IN_DIR}/POSCAR_Al12O18")
         energy = get_energy_tersoff(structure)
         assert isinstance(energy, float)
 

tests/core/test_structure.py

@@ -29,7 +29,7 @@
 from pymatgen.io.ase import AseAtomsAdaptor
 from pymatgen.io.cif import CifParser
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
-from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, PymatgenTest
 
 try:
     from ase.atoms import Atoms
@@ -1807,7 +1807,7 @@ def test_to_ase_atoms(self):
         assert AseAtomsAdaptor.get_structure(atoms) == self.struct
 
     def test_struct_with_isotope(self):
-        struct = Structure.from_file(f"{TEST_FILES_DIR}/POSCAR.LiFePO4")
+        struct = Structure.from_file(f"{VASP_IN_DIR}/POSCAR_LiFePO4")
         struct = struct.replace_species({"Li": "H"})
 
         struct_deuter = struct.copy()

tests/core/test_trajectory.py

@@ -10,7 +10,7 @@
 from pymatgen.core.trajectory import Trajectory
 from pymatgen.io.qchem.outputs import QCOutput
 from pymatgen.io.vasp.outputs import Xdatcar
-from pymatgen.util.testing import TEST_FILES_DIR, VASP_OUT_DIR, PymatgenTest
+from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest
 
 
 class TestTrajectory(PymatgenTest):
@@ -418,7 +418,7 @@ def test_length(self):
         assert len(self.traj_mols) == len(self.molecules)
 
     def test_displacements(self):
-        structures = [Structure.from_file(f"{TEST_FILES_DIR}/POSCAR")]
+        structures = [Structure.from_file(f"{VASP_IN_DIR}/POSCAR")]
         displacements = np.zeros((11, *np.shape(structures[-1].frac_coords)))
 
         for i in range(10):

tests/electronic_structure/test_bandstructure.py

@@ -20,7 +20,7 @@
 from pymatgen.electronic_structure.core import Orbital, Spin
 from pymatgen.electronic_structure.plotter import BSPlotterProjected
 from pymatgen.io.vasp import BSVasprun
-from pymatgen.util.testing import TEST_FILES_DIR, VASP_OUT_DIR, PymatgenTest
+from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest
 
 
 class TestKpoint(unittest.TestCase):
@@ -268,7 +268,7 @@ def test_vasprun_bs(self):
             parse_projected_eigen=True,
             parse_potcar_file=True,
         )
-        bs = bsv.get_band_structure(kpoints_filename=f"{TEST_FILES_DIR}/KPOINTS.band", line_mode=True)
+        bs = bsv.get_band_structure(kpoints_filename=f"{VASP_IN_DIR}/KPOINTS_band", line_mode=True)
         bs.get_projection_on_elements()
 
 

tests/electronic_structure/test_plotter.py

@@ -30,7 +30,7 @@
     plot_ellipsoid,
 )
 from pymatgen.io.vasp import Vasprun
-from pymatgen.util.testing import TEST_FILES_DIR, VASP_OUT_DIR, PymatgenTest
+from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest
 
 rc("text", usetex=False)  # Disabling latex is needed for this test to work.
 
@@ -214,7 +214,7 @@ class TestBSDOSPlotter(unittest.TestCase):
     def test_methods(self):
         vasp_run = Vasprun(f"{VASP_OUT_DIR}/vasprun_Si_bands.xml.gz")
         plotter = BSDOSPlotter()
-        band_struct = vasp_run.get_band_structure(kpoints_filename=f"{TEST_FILES_DIR}/KPOINTS_Si_bands")
+        band_struct = vasp_run.get_band_structure(kpoints_filename=f"{VASP_IN_DIR}/KPOINTS_Si_bands")
         ax = plotter.get_plot(band_struct)
         assert isinstance(ax, plt.Axes)
         plt.close()

tests/files/vasp/inputs/INCAR_C2

@@ -0,0 +1,20 @@
+ALGO = Normal
+EDIFF = 1e-06
+ENCUT = 520
+IBRION = -1
+ICHARG = 0
+ISIF = 3
+ISMEAR = -5
+ISPIN = 2
+ISYM = 0
+LASPH = True
+LORBIT = 11
+LREAL = Auto
+LWAVE = True
+MAGMOM = 2*0.0
+NBANDS = 8
+NELM = 100
+NPAR = 12
+NSW = 0
+PREC = Accurate
+SIGMA = 0.05

tests/files/vasp/inputs/POSCAR_C2

@@ -0,0 +1,10 @@
+C2
+1.0
+0.000000 1.786855 1.786855
+1.786855 0.000000 1.786855
+1.786855 1.786855 0.000000
+C
+2
+direct
+0.250000 0.250000 0.250000 C
+0.000000 0.000000 0.000000 C

tests/files/POSCAR.LiFePO4 → tests/files/vasp/inputs/POSCAR_LiFePO4

@@ -33,4 +33,5 @@ direct
 0.094714 0.250071 0.418190 P
 0.405225 0.750080 0.918200 P
 0.594775 0.249920 0.081800 P
-0.905286 0.749929 0.581810 P
+0.905286 0.749929 0.581810 P
+