def test_make_defect_entries(tmpdir, supercell_info):
tmpdir.chdir()
supercell_info.to_json_file()
defect_set = DefectSet({SimpleDefect(None, "He1", [-1, 0])})
defect_set.to_yaml()
args = Namespace()
make_defect_entries(args)
names = {str(name) for name in Path(".").glob("*")}
assert names == {
'Va_He1_-1', 'defect_in.yaml', 'perfect', 'Va_He1_0',
'supercell_info.json'
}
perfect_structure = Structure.from_file(str(Path("perfect") / "POSCAR"))
assert perfect_structure == supercell_info.structure
file_names = {
str(file_name.name)
for file_name in Path("Va_He1_-1").glob("*")
}
assert file_names == {"POSCAR", "defect_entry.json", "prior_info.yaml"}
expected = """charge: -1
"""
assert Path("Va_He1_-1/prior_info.yaml").read_text() == expected
def test_defect_entries_maker(cubic_supercell_info, cubic_supercell, mocker):
mock = mocker.patch("pydefect.input_maker.defect_entries_maker.defaults")
mock.displace_distance = 0.0
defect_set = DefectSet(defects={
SimpleDefect(None, "H1", [1]),
SimpleDefect("Ne", "He1", [0])
})
maker = DefectEntriesMaker(cubic_supercell_info, defect_set)
va_h1_str = cubic_supercell.copy()
va_h1_str.pop(0)
va_h1_str = to_istructure(va_h1_str)
ne_he1_str = cubic_supercell.copy()
coords = ne_he1_str.pop(32).frac_coords
ne_he1_str.append("Ne", coords)
ne_he1_str = to_istructure(ne_he1_str)
defect_entries = {
DefectEntry("Ne_He1", 0, ne_he1_str, ne_he1_str.copy(), "m-3m",
(0.25, 0.0, 0.0)),
DefectEntry("Va_H1", 1, va_h1_str, va_h1_str.copy(), "m-3m",
(0.0, 0.0, 0.0)),
}
assert maker.defect_entries == defect_entries
def make_defect_entries(args):
supercell_info: SupercellInfo = loadfn("supercell_info.json")
perfect = Path("perfect")
try:
perfect.mkdir()
logger.info("Making perfect dir...")
supercell_info.structure.to(filename=perfect / "POSCAR")
except FileExistsError:
logger.info(f"perfect dir exists, so skipped...")
defect_set = DefectSet.from_yaml()
maker = DefectEntriesMaker(supercell_info, defect_set)
for defect_entry in maker.defect_entries:
dir_path = Path(defect_entry.full_name)
try:
dir_path.mkdir()
logger.info(f"Making {dir_path} dir...")
if defect_entry.perturbed_structure:
defect_entry.perturbed_structure.to(filename=dir_path /
"POSCAR")
else:
defect_entry.structure.to(filename=dir_path / "POSCAR")
defect_entry.to_json_file(filename=dir_path / "defect_entry.json")
defect_entry.to_prior_info(filename=dir_path / "prior_info.yaml")
except FileExistsError:
logger.info(f"{dir_path} dir exists, so skipped...")
def test_defect_entries_interstitials(cubic_supercell_info, mocker):
mock = mocker.patch("pydefect.input_maker.defect_entries_maker.defaults")
mock.displace_distance = 0.0
defect_set = DefectSet(defects={SimpleDefect("H", "i1", [0])})
maker = DefectEntriesMaker(cubic_supercell_info, defect_set)
defect_entry = maker.defect_entries.pop()
actual = defect_entry.structure[0].frac_coords
np.testing.assert_array_equal(actual, [0.25, 0.25, 0.25])
def test_make_defect_set(oxi_states, he_vacancy_charge, tmpdir, supercell_info):
tmpdir.chdir()
supercell_info.to_json_file()
args = Namespace(oxi_states=oxi_states, dopants=["Li"], kwargs=["Li_H1", "Va_He1", "Va_H1_-1"])
make_defect_set(args)
simple_defects = {SimpleDefect(None, "He1", he_vacancy_charge),
SimpleDefect(None, "H1", [-1]),
SimpleDefect("Li", "H1", [0])}
DefectSet(defects=simple_defects).to_yaml("expected.yaml")
assert Path("defect_in.yaml").read_text() == Path("expected.yaml").read_text()
def test_defect_entries_maker_insert_host_atoms(cubic_supercell_info, mocker):
mock = mocker.patch("pydefect.input_maker.defect_entries_maker.defaults")
mock.displace_distance = 0.0
defect_set = DefectSet(defects={SimpleDefect("He", "H1", [0]),
SimpleDefect("H", "He1", [0])})
maker = DefectEntriesMaker(cubic_supercell_info, defect_set)
for defect_entry in maker.defect_entries:
if defect_entry.name == "H_He1":
actual = defect_entry.structure[0].frac_coords
np.testing.assert_array_equal(actual, [0.25, 0.0, 0.0])
if defect_entry.name == "He_H1":
actual = defect_entry.structure[31].frac_coords
np.testing.assert_array_equal(actual, [0.0, 0.0, 0.0])
def _create_defect_set(self):
result = self._create_vacancy_set()
result.update(self._create_substitutional_set())
result.update(self._create_interstitial_set())
return DefectSet(result)