def __init__(self, geometry=None, **kwargs) -> None:
if geometry == None:
atoms = Atoms(**kwargs)
elif type(geometry) == ase.atoms.Atoms:
atoms = geometry.copy()
elif Path(geometry).is_file():
if str(Path(geometry).parts[-1]) == "geometry.in.next_step":
atoms = ase.io.read(geometry, format="aims")
else:
try:
atoms = ase.io.read(geometry)
except Exception as excpt:
logger.error(str(excpt))
raise Exception(
"ASE was not able to recognize the file format, e.g., a non-standard cif-format."
)
elif Path(geometry).is_dir():
raise Exception(
"You specified a directory as input. The geometry must be a file."
)
else:
atoms = None
assert type(atoms) == ase.atoms.Atoms, "Atoms not read correctly."
# Get data from another Atoms object:
numbers = atoms.get_atomic_numbers()
positions = atoms.get_positions()
cell = atoms.get_cell()
celldisp = atoms.get_celldisp()
pbc = atoms.get_pbc()
constraint = [c.copy() for c in atoms.constraints]
masses = atoms.get_masses()
magmoms = None
charges = None
momenta = None
if atoms.has("initial_magmoms"):
magmoms = atoms.get_initial_magnetic_moments()
if atoms.has("initial_charges"):
charges = atoms.get_initial_charges()
if atoms.has("momenta"):
momenta = atoms.get_momenta()
self.arrays = {}
super().__init__(
numbers=numbers,
positions=positions,
cell=cell,
celldisp=celldisp,
pbc=pbc,
constraint=constraint,
masses=masses,
magmoms=magmoms,
charges=charges,
momenta=momenta,
)
self._is_1d = None
self._is_2d = None
self._is_3d = None
self._periodic_axes = None
self._check_lattice_vectors()
try:
self.sg = ase.spacegroup.get_spacegroup(self, symprec=1e-2)
except:
self.sg = ase.spacegroup.Spacegroup(1)
self.lattice = self.cell.get_bravais_lattice().crystal_family
