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()
def test_make_recommended_supercell(simple_cubic, simple_cubic_2x2x2, tmpdir):
args = Namespace(unitcell=simple_cubic, matrix=None, min_num_atoms=8, max_num_atoms=8)
tmpdir.chdir()
make_supercell(args)
info = loadfn("supercell_info.json")
assert IStructure.from_file("SPOSCAR") == simple_cubic_2x2x2
assert info.structure == simple_cubic_2x2x2
assert info.transformation_matrix == [[2, 0, 0], [0, 2, 0], [0, 0, 2]]
def test_make_supercell_from_matrix(simple_cubic, simple_cubic_2x1x1, tmpdir):
matrix = [2, 1, 1]
args = Namespace(unitcell=simple_cubic, matrix=matrix, min_num_atoms=None, max_num_atoms=None)
tmpdir.chdir()
make_supercell(args)
info = loadfn("supercell_info.json")
assert IStructure.from_file("SPOSCAR") == simple_cubic_2x1x1
assert info.structure == simple_cubic_2x1x1
assert info.transformation_matrix == [[2, 0, 0], [0, 1, 0], [0, 0, 1]]
