def test_screen_defect():
defect = SimpleDefect(None, "O1", [1, 2])
assert screen_simple_defect(defect, ["Va_O1"]) == \
SimpleDefect(None, "O1", [1, 2])
assert screen_simple_defect(defect, ["Va_O1_1"]) == \
SimpleDefect(None, "O1", [1])
assert screen_simple_defect(defect, ["Va_N1"]) is None
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 test_defect_set_maker(supercell_info):
defect_maker = DefectSetMaker(supercell_info)
expected = {SimpleDefect(None, "H1", [-1, 0, 1]),
SimpleDefect(None, "He1", [0]),
SimpleDefect("H", "i1", [-1, 0, 1]),
SimpleDefect("He", "i1", [0])}
assert defect_maker.defect_set == expected
def test_defect_set_maker_oxi_state(supercell_info):
defect_maker = DefectSetMaker(supercell_info, {"H": 2})
assert defect_maker.defect_set.defects == {
SimpleDefect(None, "H1", [-2, -1, 0]),
SimpleDefect(None, "He1", [0]),
SimpleDefect("H", "i1", [0, 1, 2]),
SimpleDefect("He", "i1", [0])
}
def test_defect_set_maker_electroneg_diff(supercell_info):
defect_maker = DefectSetMaker(supercell_info, dopants=["Li"],
ele_neg_diff=2.2 - 0.98 - 1e-5)
assert set(defect_maker.defect_set) == {
SimpleDefect(None, "H1", [-1, 0, 1]),
SimpleDefect(None, "He1", [0]),
SimpleDefect("H", "i1", [-1, 0, 1]),
SimpleDefect("He", "i1", [0]),
SimpleDefect("Li", "i1", [-1, 0, 1]),
}
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 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 from_yaml(cls, filename: str = "defect_in.yaml") -> "DefectSet":
d = loadfn(filename)
names = set()
for name, charges in d.items():
in_name, out_name = name.split("_")
names.add(SimpleDefect(in_name, out_name, tuple(charges)))
return cls(names)
def _create_vacancy_set(self):
result = set()
for out_name, site in self.supercell_info.sites.items():
minus_oxi_stat = -self._oxidation_state(site.element)
result.add(SimpleDefect(None, out_name,
charge_set(minus_oxi_stat)))
return result
def _create_interstitial_set(self):
result = set()
for in_name in self._subs:
oxi_stat = self._oxidation_state(in_name)
for i in range(len(self.supercell_info.interstitials)):
result.add(
SimpleDefect(in_name, f"i{i + 1}", charge_set(oxi_stat)))
return result
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_defect_set_maker_dopants(supercell_info):
defect_maker = DefectSetMaker(supercell_info, dopants=["Li"])
assert set(defect_maker.defect_set) == {
SimpleDefect(None, "H1", [-1, 0, 1]),
SimpleDefect(None, "He1", [0]),
SimpleDefect("Li", "H1", [0]),
SimpleDefect("H", "i1", [-1, 0, 1]),
SimpleDefect("He", "i1", [0]),
SimpleDefect("Li", "i1", [-1, 0, 1]),
}
def _create_substitutional_set(self):
result = set()
for in_name, (out_name, site) \
in product(self._subs, self.supercell_info.sites.items()):
host_element = site.element
sub_en = electronegativity(in_name)
host_en = electronegativity(host_element)
are_same_elem = in_name == host_element
if None in (sub_en, host_en) or are_same_elem or \
abs(sub_en - host_en) > self._ele_neg_diff:
continue
sub_oxi = self._oxidation_state(in_name)
host_oxi = self._oxidation_state(host_element)
oxi_diff = sub_oxi - host_oxi
result.add(SimpleDefect(in_name, out_name, charge_set(oxi_diff)))
return result
def test_simple_defect_msonable():
defect = SimpleDefect("Va", "O1", [1, 2])
assert_msonable(defect)
def test_defect_set_maker_screening(supercell_info):
defect_maker = DefectSetMaker(supercell_info, keywords=["Va_H1"])
expected = {SimpleDefect(None, "H1", [-1, 0, 1])}
assert defect_maker.defect_set == expected
def test_simple_defect_hashable():
defect = SimpleDefect(None, "O1", (1, 2))
d = {defect: 1}
def test_simple_defect():
defect = SimpleDefect(None, "O1", [1, 2])
expected = Defect("Va_O1", (1, 2))
assert defect.name == expected.name
assert defect.charge_list == expected.charge_list
assert defect.in_atom is None
