def test_from_defect_structure_complex(self):
perfect_structure = self.get_structure_by_name(name="MgO64atoms")
expected = self.MgO_complex.as_dict()
actual = DefectEntry.from_defect_structure(
defect_structure=self.initial_structure_complex,
perfect_structure=perfect_structure,
defect_name="complex_2").as_dict()
for d in expected:
self.assertEqual(expected[d], actual[d])
def defect_entry(args):
if args.print:
print(DefectEntry.load_json(args.json))
elif args.make_defect_entry:
defect_structure = Structure.from_file(args.defect_poscar)
perfect_structure = Structure.from_file(args.perfect_poscar)
defect_entry_from_yaml = DefectEntry.from_defect_structure(
defect_structure=defect_structure,
perfect_structure=perfect_structure,
displacement_distance=args.displacement_distance,
defect_name=args.defect_name)
defect_entry_from_yaml.to_json_file(args.json)
else:
logger.critical("Set make_defect_entry or print option.")