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.")