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Fix bad refactoring.
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Shyue Ping Ong committed Aug 3, 2023
1 parent cecf3a2 commit 0eacafa
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Showing 2 changed files with 65 additions and 64 deletions.
127 changes: 64 additions & 63 deletions tests/io/vasp/test_inputs.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -26,11 +26,12 @@
UnknownPotcarWarning,
VaspInput,
)
from pymatgen.util.testing import PymatgenTest


class TestPoscar:
def test_init(self, TEST_FILES_DIR):
filepath = f"{TEST_FILES_DIR}/POSCAR"
def test_init(self):
filepath = f"{PymatgenTest.TEST_FILES_DIR}/POSCAR"
poscar = Poscar.from_file(filepath, check_for_POTCAR=False)
comp = poscar.structure.composition
assert comp == Composition("Fe4P4O16")
Expand Down Expand Up @@ -84,8 +85,8 @@ def test_init(self, TEST_FILES_DIR):
assert selective_dynamics == [[True, True, True], [False, False, False]]
self.selective_poscar = poscar

def test_from_file(self, TEST_FILES_DIR):
filepath = f"{TEST_FILES_DIR}/POSCAR.symbols_natoms_multilines"
def test_from_file(self):
filepath = f"{PymatgenTest.TEST_FILES_DIR}/POSCAR.symbols_natoms_multilines"
poscar = Poscar.from_file(filepath, check_for_POTCAR=False, read_velocities=False)
ordered_expected_elements = [
"Fe",
Expand Down Expand Up @@ -262,17 +263,17 @@ def test_str(self):
poscar = Poscar.from_str(poscar_string)
assert str(poscar) == expected

def test_from_md_run(self, TEST_FILES_DIR):
def test_from_md_run(self):
# Parsing from an MD type run with velocities and predictor corrector data
p = Poscar.from_file(f"{TEST_FILES_DIR}/CONTCAR.MD", check_for_POTCAR=False)
p = Poscar.from_file(f"{PymatgenTest.TEST_FILES_DIR}/CONTCAR.MD", check_for_POTCAR=False)
assert np.sum(np.array(p.velocities)) == approx(0.0065417961324)
assert p.predictor_corrector[0][0][0] == 0.33387820e00
assert p.predictor_corrector[0][1][1] == -0.10583589e-02

def test_write_md_poscar(self, TEST_FILES_DIR):
def test_write_md_poscar(self):
# Parsing from an MD type run with velocities and predictor corrector data
# And writing a new POSCAR from the new structure
p = Poscar.from_file(f"{TEST_FILES_DIR}/CONTCAR.MD", check_for_POTCAR=False)
p = Poscar.from_file(f"{PymatgenTest.TEST_FILES_DIR}/CONTCAR.MD", check_for_POTCAR=False)

path = Path("POSCAR.testing.md")
p.write_file(path)
Expand All @@ -284,8 +285,8 @@ def test_write_md_poscar(self, TEST_FILES_DIR):
assert p.predictor_corrector_preamble == p3.predictor_corrector_preamble
path.unlink()

def test_setattr(self, TEST_FILES_DIR):
filepath = f"{TEST_FILES_DIR}/POSCAR"
def test_setattr(self):
filepath = f"{PymatgenTest.TEST_FILES_DIR}/POSCAR"
poscar = Poscar.from_file(filepath, check_for_POTCAR=False)
with pytest.raises(ValueError, match="velocities array must be same length as the structure"):
poscar.velocities = [[0, 0, 0]]
Expand Down Expand Up @@ -358,17 +359,17 @@ def test_velocities(self):
temperature = struct[0].specie.atomic_mass.to("kg") * np.sum(v**2) / (3 * const.k) * 1e10
assert temperature == approx(700, abs=1e-4), "Temperature instantiated incorrectly"

def test_write(self, TEST_FILES_DIR):
filepath = f"{TEST_FILES_DIR}/POSCAR"
def test_write(self):
filepath = f"{PymatgenTest.TEST_FILES_DIR}/POSCAR"
poscar = Poscar.from_file(filepath)
tempfname = Path("POSCAR.testing")
poscar.write_file(tempfname)
p = Poscar.from_file(tempfname)
assert np.allclose(poscar.structure.lattice.abc, p.structure.lattice.abc, 5)
tempfname.unlink()

def test_selective_dynamics(self, TEST_FILES_DIR):
filepath = f"{TEST_FILES_DIR}/POSCAR.Fe3O4"
def test_selective_dynamics(self):
filepath = f"{PymatgenTest.TEST_FILES_DIR}/POSCAR.Fe3O4"
poscar = Poscar.from_file(filepath)
structure = poscar.structure

Expand Down Expand Up @@ -397,8 +398,8 @@ def test_selective_dynamics(self, TEST_FILES_DIR):


class TestIncar:
def setUp(self, TEST_FILES_DIR):
file_name = f"{TEST_FILES_DIR}/INCAR"
def setup(self):
file_name = f"{PymatgenTest.TEST_FILES_DIR}/INCAR"
self.incar = Incar.from_file(file_name)

def test_init(self):
Expand All @@ -408,10 +409,10 @@ def test_init(self):
assert float(incar["EDIFF"]) == 1e-4, "Wrong EDIFF"
assert isinstance(incar["LORBIT"], int)

def test_diff(self, TEST_FILES_DIR):
filepath1 = f"{TEST_FILES_DIR}/INCAR"
def test_diff(self):
filepath1 = f"{PymatgenTest.TEST_FILES_DIR}/INCAR"
incar1 = Incar.from_file(filepath1)
filepath2 = f"{TEST_FILES_DIR}/INCAR.2"
filepath2 = f"{PymatgenTest.TEST_FILES_DIR}/INCAR.2"
incar2 = Incar.from_file(filepath2)
incar3 = Incar.from_file(filepath2)
assert incar1.diff(incar2) == {
Expand Down Expand Up @@ -732,28 +733,28 @@ def test_check_params(self):


class TestKpoints:
def test_init(self, TEST_FILES_DIR):
filepath = f"{TEST_FILES_DIR}/KPOINTS.auto"
def test_init(self):
filepath = f"{PymatgenTest.TEST_FILES_DIR}/KPOINTS.auto"
kpoints = Kpoints.from_file(filepath)
assert kpoints.kpts == [[10]], "Wrong kpoint lattice read"
filepath = f"{TEST_FILES_DIR}/KPOINTS.cartesian"
filepath = f"{PymatgenTest.TEST_FILES_DIR}/KPOINTS.cartesian"
kpoints = Kpoints.from_file(filepath)
assert kpoints.kpts == [[0.25, 0, 0], [0, 0.25, 0], [0, 0, 0.25]], "Wrong kpoint lattice read"
assert kpoints.kpts_shift == [0.5, 0.5, 0.5], "Wrong kpoint shift read"

filepath = f"{TEST_FILES_DIR}/KPOINTS"
filepath = f"{PymatgenTest.TEST_FILES_DIR}/KPOINTS"
kpoints = Kpoints.from_file(filepath)
self.kpoints = kpoints
assert kpoints.kpts == [[2, 4, 6]]

filepath = f"{TEST_FILES_DIR}/KPOINTS.band"
filepath = f"{PymatgenTest.TEST_FILES_DIR}/KPOINTS.band"
kpoints = Kpoints.from_file(filepath)
assert kpoints.labels is not None
assert kpoints.style == Kpoints.supported_modes.Line_mode
kpoints_str = str(kpoints)
assert kpoints_str.split("\n")[3] == "Reciprocal"

filepath = f"{TEST_FILES_DIR}/KPOINTS.explicit"
filepath = f"{PymatgenTest.TEST_FILES_DIR}/KPOINTS.explicit"
kpoints = Kpoints.from_file(filepath)
assert kpoints.kpts_weights is not None
assert (
Expand All @@ -767,18 +768,18 @@ def test_init(self, TEST_FILES_DIR):
0.5 0.5 0.5 4 None"""
)

filepath = f"{TEST_FILES_DIR}/KPOINTS.explicit_tet"
filepath = f"{PymatgenTest.TEST_FILES_DIR}/KPOINTS.explicit_tet"
kpoints = Kpoints.from_file(filepath)
assert kpoints.tet_connections == [(6, [1, 2, 3, 4])]

def test_style_setter(self, TEST_FILES_DIR):
filepath = f"{TEST_FILES_DIR}/KPOINTS"
def test_style_setter(self):
filepath = f"{PymatgenTest.TEST_FILES_DIR}/KPOINTS"
kpoints = Kpoints.from_file(filepath)
assert kpoints.style == Kpoints.supported_modes.Monkhorst
kpoints.style = "G"
assert kpoints.style == Kpoints.supported_modes.Gamma

def test_static_constructors(self, TEST_FILES_DIR):
def test_static_constructors(self):
kpoints = Kpoints.gamma_automatic([3, 3, 3], [0, 0, 0])
assert kpoints.style == Kpoints.supported_modes.Gamma
assert kpoints.kpts == [[3, 3, 3]]
Expand All @@ -788,7 +789,7 @@ def test_static_constructors(self, TEST_FILES_DIR):
kpoints = Kpoints.automatic(100)
assert kpoints.style == Kpoints.supported_modes.Automatic
assert kpoints.kpts == [[100]]
filepath = f"{TEST_FILES_DIR}/POSCAR"
filepath = f"{PymatgenTest.TEST_FILES_DIR}/POSCAR"
poscar = Poscar.from_file(filepath)
kpoints = Kpoints.automatic_density(poscar.structure, 500)
assert kpoints.kpts == [[1, 3, 3]]
Expand Down Expand Up @@ -825,8 +826,8 @@ def test_as_dict_from_dict(self):
assert k.style == k2.style
assert k.kpts_shift == k2.kpts_shift

def test_kpt_bands_as_dict_from_dict(self, TEST_FILES_DIR):
file_name = f"{TEST_FILES_DIR}/KPOINTS.band"
def test_kpt_bands_as_dict_from_dict(self):
file_name = f"{PymatgenTest.TEST_FILES_DIR}/KPOINTS.band"
k = Kpoints.from_file(file_name)
d = k.as_dict()
import json
Expand Down Expand Up @@ -863,8 +864,8 @@ def test_automatic_kpoint(self):
class TestPotcarSingle:
_multiprocess_shared_ = True

def setUp(self, TEST_FILES_DIR):
self.psingle = PotcarSingle.from_file(f"{TEST_FILES_DIR}/POT_GGA_PAW_PBE/POTCAR.Mn_pv.gz")
def setup(self):
self.psingle = PotcarSingle.from_file(f"{PymatgenTest.TEST_FILES_DIR}/POT_GGA_PAW_PBE/POTCAR.Mn_pv.gz")

def test_keywords(self):
data = {
Expand Down Expand Up @@ -896,8 +897,8 @@ def test_keywords(self):
}
assert self.psingle.keywords == data

def test_psctr(self, TEST_FILES_DIR):
filename = f"{TEST_FILES_DIR}/POT_GGA_PAW_PBE_54/POTCAR.Fe.gz"
def test_psctr(self):
filename = f"{PymatgenTest.TEST_FILES_DIR}/POT_GGA_PAW_PBE_54/POTCAR.Fe.gz"

psingle = PotcarSingle.from_file(filename)

Expand Down Expand Up @@ -966,14 +967,14 @@ def test_bad_value(self):
def test_hash(self):
assert self.psingle.get_potcar_hash() == "fa52f891f234d49bb4cb5ea96aae8f98"

def test_functional_types(self, TEST_FILES_DIR):
def test_functional_types(self):
assert self.psingle.functional == "PBE"

assert self.psingle.functional_class == "GGA"

assert self.psingle.potential_type == "PAW"

psingle = PotcarSingle.from_file(f"{TEST_FILES_DIR}/POT_LDA_PAW/POTCAR.Fe.gz")
psingle = PotcarSingle.from_file(f"{PymatgenTest.TEST_FILES_DIR}/POT_LDA_PAW/POTCAR.Fe.gz")

assert psingle.functional == "Perdew-Zunger81"

Expand All @@ -983,30 +984,30 @@ def test_functional_types(self, TEST_FILES_DIR):

assert self.psingle.symbol == "Mn_pv"

def test_identify_potcar(self, TEST_FILES_DIR):
filename = f"{TEST_FILES_DIR}/POT_GGA_PAW_PBE_54/POTCAR.Fe.gz"
def test_identify_potcar(self):
filename = f"{PymatgenTest.TEST_FILES_DIR}/POT_GGA_PAW_PBE_54/POTCAR.Fe.gz"

psingle = PotcarSingle.from_file(filename)
assert "PBE_54" in psingle.identify_potcar()[0]
assert "Fe" in psingle.identify_potcar()[1]

def test_potcar_hash_warning(self, TEST_FILES_DIR):
filename = f"{TEST_FILES_DIR}/modified_potcars_data/POT_GGA_PAW_PBE/POTCAR.Fe_pv"
def test_potcar_hash_warning(self):
filename = f"{PymatgenTest.TEST_FILES_DIR}/modified_potcars_data/POT_GGA_PAW_PBE/POTCAR.Fe_pv"
with pytest.warns(UnknownPotcarWarning, match="POTCAR is known to match the following functionals:"):
PotcarSingle.from_file(filename)

def test_potcar_file_hash_warning(self, TEST_FILES_DIR):
filename = f"{TEST_FILES_DIR}/modified_potcars_header/POT_GGA_PAW_PBE/POTCAR.Fe_pv"
def test_potcar_file_hash_warning(self):
filename = f"{PymatgenTest.TEST_FILES_DIR}/modified_potcars_header/POT_GGA_PAW_PBE/POTCAR.Fe_pv"
with pytest.warns(UnknownPotcarWarning, match="POTCAR is corrupted"):
PotcarSingle.from_file(filename)

def test_verify_faulty_potcar_with_hash(self, TEST_FILES_DIR):
filename = f"{TEST_FILES_DIR}/modified_potcars_data/POT_GGA_PAW_PBE_54/POTCAR.Fe_pv_with_hash"
def test_verify_faulty_potcar_with_hash(self):
filename = f"{PymatgenTest.TEST_FILES_DIR}/modified_potcars_data/POT_GGA_PAW_PBE_54/POTCAR.Fe_pv_with_hash"
with pytest.warns(UnknownPotcarWarning, match="POTCAR with symbol Fe_pv has metadata that "):
PotcarSingle.from_file(filename)

def test_verify_correct_potcar_with_hash(self, TEST_FILES_DIR):
filename = f"{TEST_FILES_DIR}/POT_GGA_PAW_PBE_54/POTCAR.Fe_pv_with_hash.gz"
def test_verify_correct_potcar_with_hash(self):
filename = f"{PymatgenTest.TEST_FILES_DIR}/POT_GGA_PAW_PBE_54/POTCAR.Fe_pv_with_hash.gz"
vaspdir = os.path.abspath(os.path.dirname(pymatgen.io.vasp.__file__))
file_hash_db = loadfn(os.path.join(vaspdir, "vasp_potcar_file_hashes.json"))
metadata_hash_db = loadfn(os.path.join(vaspdir, "vasp_potcar_pymatgen_hashes.json"))
Expand All @@ -1016,8 +1017,8 @@ def test_verify_correct_potcar_with_hash(self, TEST_FILES_DIR):
assert psingle.file_hash in file_hash_db
assert psingle.hash_sha256_computed == psingle.hash_sha256_from_file

def test_multi_potcar_with_and_without_hash(self, TEST_FILES_DIR):
filename = f"{TEST_FILES_DIR}/POT_GGA_PAW_PBE_54/POTCAR.Fe_O.gz"
def test_multi_potcar_with_and_without_hash(self):
filename = f"{PymatgenTest.TEST_FILES_DIR}/POT_GGA_PAW_PBE_54/POTCAR.Fe_O.gz"
vaspdir = os.path.abspath(os.path.dirname(pymatgen.io.vasp.__file__))
loadfn(os.path.join(vaspdir, "vasp_potcar_file_hashes.json"))
Potcar.from_file(filename)
Expand All @@ -1039,10 +1040,10 @@ def test_multi_potcar_with_and_without_hash(self, TEST_FILES_DIR):


class TestPotcar:
def setUp(self, TEST_FILES_DIR):
def setup(self):
if "PMG_VASP_PSP_DIR" not in SETTINGS:
SETTINGS["PMG_VASP_PSP_DIR"] = str(TEST_FILES_DIR)
self.filepath = f"{TEST_FILES_DIR}/POTCAR"
SETTINGS["PMG_VASP_PSP_DIR"] = str(PymatgenTest.TEST_FILES_DIR)
self.filepath = f"{PymatgenTest.TEST_FILES_DIR}/POTCAR"
self.potcar = Potcar.from_file(self.filepath)

def test_init(self):
Expand All @@ -1053,8 +1054,8 @@ def test_init(self):
def test_from_file(self):
assert {d.header for d in self.potcar} == {"PAW_PBE O 08Apr2002", "PAW_PBE P 17Jan2003", "PAW_PBE Fe 06Sep2000"}

def test_potcar_map(self, TEST_FILES_DIR):
fe_potcar = zopen(f"{TEST_FILES_DIR}/POT_GGA_PAW_PBE/POTCAR.Fe_pv.gz").read().decode("utf-8")
def test_potcar_map(self):
fe_potcar = zopen(f"{PymatgenTest.TEST_FILES_DIR}/POT_GGA_PAW_PBE/POTCAR.Fe_pv.gz").read().decode("utf-8")
# specify V instead of Fe - this makes sure the test won't pass if the
# code just grabs the POTCAR from the config file (the config file would
# grab the V POTCAR)
Expand Down Expand Up @@ -1110,16 +1111,16 @@ def test_pickle(self):


class TestVaspInput:
def setUp(self, TEST_FILES_DIR):
filepath = f"{TEST_FILES_DIR}/INCAR"
def setup(self):
filepath = f"{PymatgenTest.TEST_FILES_DIR}/INCAR"
incar = Incar.from_file(filepath)
filepath = f"{TEST_FILES_DIR}/POSCAR"
filepath = f"{PymatgenTest.TEST_FILES_DIR}/POSCAR"
poscar = Poscar.from_file(filepath, check_for_POTCAR=False)
if "PMG_VASP_PSP_DIR" not in os.environ:
os.environ["PMG_VASP_PSP_DIR"] = str(TEST_FILES_DIR)
filepath = f"{TEST_FILES_DIR}/POTCAR"
os.environ["PMG_VASP_PSP_DIR"] = str(PymatgenTest.TEST_FILES_DIR)
filepath = f"{PymatgenTest.TEST_FILES_DIR}/POTCAR"
potcar = Potcar.from_file(filepath)
filepath = f"{TEST_FILES_DIR}/KPOINTS.auto"
filepath = f"{PymatgenTest.TEST_FILES_DIR}/KPOINTS.auto"
kpoints = Kpoints.from_file(filepath)
self.vasp_input = VaspInput(incar, kpoints, poscar, potcar)

Expand Down Expand Up @@ -1148,8 +1149,8 @@ def test_run_vasp(self):
output = f.read()
assert output.split("\n")[0] == "ALGO = Damped"

def test_from_directory(self, TEST_FILES_DIR):
vi = VaspInput.from_directory(TEST_FILES_DIR, optional_files={"CONTCAR.Li2O": Poscar})
def test_from_directory(self):
vi = VaspInput.from_directory(PymatgenTest.TEST_FILES_DIR, optional_files={"CONTCAR.Li2O": Poscar})
assert vi["INCAR"]["ALGO"] == "Damped"
assert "CONTCAR.Li2O" in vi
d = vi.as_dict()
Expand Down
2 changes: 1 addition & 1 deletion tests/util/test_coord.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -243,7 +243,7 @@ def test_get_angle(self):


class TestSimplex:
def setUp(self):
def setup(self):
coords = []
coords.append([0, 0, 0])
coords.append([0, 1, 0])
Expand Down

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