def test_make_defect_entry(defect_entry):
relaxed_coords = \
[[0.25, 0.0, 0.0], [0.5, 0.5, 0.0], [0.5, 0.0, 0.5], [0.0, 0.5, 0.5],
[0.0, 0.0, 0.51], [0.0, 0.51, 0.0], [0.5, 0.0, 0.0], [0.5, 0.5, 0.5]]
relaxed_defect = IStructure(
Lattice.cubic(10.0), ["Li"] + ["H"] * 3 + ["He"] * 4, relaxed_coords)
unrelaxed_coords = \
[[0.25, 0.0, 0.0], [0.5, 0.5, 0.0], [0.5, 0.0, 0.5], [0.0, 0.5, 0.5],
[0.0, 0.0, 0.5], [0.0, 0.5, 0.0], [0.5, 0.0, 0.0], [0.5, 0.5, 0.5]]
unrelaxed_defect = IStructure(
Lattice.cubic(10.0), ["Li"] + ["H"] * 3 + ["He"] * 4, unrelaxed_coords)
actual = make_defect_entry(name="Va_O1",
charge=1,
perfect_structure=perfect,
defect_structure=relaxed_defect)
expected = DefectEntry(name="Va_O1",
charge=1,
structure=unrelaxed_defect,
perturbed_structure=None,
site_symmetry="4mm",
defect_center=(0.125, 0.0, 0.0))
assert actual == expected
def make_defect_entry_main(args):
charge_state = calc_charge_state(args)
structure = Structure.from_file(args.dir / "POSCAR")
defect_entry = make_defect_entry(name=args.name,
charge=charge_state,
perfect_structure=args.perfect,
defect_structure=structure)
defect_entry.to_json_file()
def make_defect_entry_from_poscars(dirname, perf_poscar, defect_poscar):
names = dirname.split("_")
try:
name = "_".join(names[:-1])
charge = int(names[-1])
except ValueError:
logger.warning(f"Directory name {dirname} is invalid.")
raise
perfect = IStructure.from_file(perf_poscar)
defect = IStructure.from_file(defect_poscar)
defect_entry = make_defect_entry(name=name,
charge=charge,
perfect_structure=perfect,
defect_structure=defect)
defect_entry.to_json_file()