def make_defect_set(self,
keywords: Union[str, list, None] = None,
specified_defects: Optional[list] = None) -> None:
"""Return defect name list based on DefectInitialSetting object. """
defects = {}
# vacancies
defects.update(
self._substituted_set(removed_sites=self.irreducible_sites,
inserted_element=None))
# substituted + antisite
configs = self.antisite_configs + self.dopant_configs
for in_elem, out_elem in configs:
removed_sites = [
i for i in self.irreducible_sites if out_elem == i.element
]
substituted = self._substituted_set(removed_sites=removed_sites,
inserted_element=in_elem)
defects.update(substituted)
# interstitials
inserted_elements = self.structure.symbol_set + tuple(self.dopants)
defects.update(
self._interstitial_set(inserted_elements=inserted_elements))
# complex defects
defects.update(self._complex_set())
defects = select_defects(defect_set=defects,
keywords=keywords,
included=self.included,
excluded=self.excluded,
specified_defects=specified_defects)
self.defect_entries = []
for name, defect in defects.items():
center = defect.pop("center")
for charge in defect.pop("charges"):
inserted_indices = \
[i["index"] for i in defect["inserted_atoms"]]
# By default, neighboring atoms are perturbed.
# If one wants to avoid it, set displacement_distance = 0
perturbed_structure, neighboring_sites = \
perturb_neighboring_atoms(
structure=defect["initial_structure"],
center=center,
cutoff=defect["cutoff"],
distance=self.displacement_distance,
inserted_atom_indices=inserted_indices)
defect["initial_structure"].set_charge(charge)
perturbed_structure.set_charge(charge)
self.defect_entries.append(
DefectEntry(
name=name,
perturbed_initial_structure=perturbed_structure,
charge=charge,
neighboring_sites=neighboring_sites,
**defect))
def setUp(self):
""" """
# DefectEntry class object for a single vacancy
name = "Va_O1"
defect_type = DefectType.from_string("vacancy")
self.initial_structure_vacancy = \
self.get_structure_by_name(name="MgO64atoms-Va_O_0-unrelaxed")
perturbed_initial_structure = self.initial_structure_vacancy.copy()
removed_atoms = [{"element": "O", "index": 32, "coords": [0.25, 0, 0]}]
inserted_atoms = []
changes_of_num_elements = {"O": -1}
charge = 2
initial_site_symmetry = "m-3m"
multiplicity = 32
neighboring_sites = [0, 4, 16, 17, 24, 26]
cutoff = round(8.419456 / 4 * CUTOFF_FACTOR, 2)
self.MgO_Va_O1_2 = \
DefectEntry(name=name,
defect_type=defect_type,
initial_structure=self.initial_structure_vacancy,
perturbed_initial_structure=perturbed_initial_structure,
removed_atoms=removed_atoms,
inserted_atoms=inserted_atoms,
changes_of_num_elements=changes_of_num_elements,
charge=charge,
initial_site_symmetry=initial_site_symmetry,
cutoff=cutoff,
neighboring_sites=neighboring_sites,
multiplicity=multiplicity)
name = "complex"
defect_type = DefectType.from_string("complex")
self.initial_structure_complex = \
self.get_structure_by_name(name="MgO64atoms-Va_Mg+Va_O+Ca_i")
perturbed_initial_structure = self.initial_structure_complex.copy()
removed_atoms = [{
"element": "Mg",
"index": 0,
"coords": [0, 0, 0]
}, {
"element": "O",
"index": 32,
"coords": [0.25, 0, 0]
}]
inserted_atoms = [{
"element": "Ca",
"index": 0,
"coords": [0.125, 0, 0]
}]
changes_of_num_elements = {"Mg": -1, "Ca": 1, "O": -1}
charge = 2
initial_site_symmetry = "4mm"
multiplicity = 192
neighboring_sites = [16, 17, 24, 26, 47, 48, 55, 57]
cutoff = round(8.419456 / 4 * CUTOFF_FACTOR, 2)
self.MgO_complex = \
DefectEntry(name=name,
defect_type=defect_type,
initial_structure=self.initial_structure_complex,
perturbed_initial_structure=perturbed_initial_structure,
removed_atoms=removed_atoms,
inserted_atoms=inserted_atoms,
changes_of_num_elements=changes_of_num_elements,
charge=charge,
initial_site_symmetry=initial_site_symmetry,
cutoff=cutoff,
neighboring_sites=neighboring_sites,
multiplicity=multiplicity)