def phonopyAtoms_to_aseAtoms(PhonopyAtoms, pbc=[True, True, True]):
aseAtoms = ase.Atoms(symbols=PhonopyAtoms.get_chemical_symbols(),
positions=PhonopyAtoms.get_positions(),
cell=PhonopyAtoms.get_cell())
aseAtoms.set_pbc(pbc)
aseAtoms.set_masses(PhonopyAtoms.get_masses())
Atomic_numbers = PhonopyAtoms.get_atomic_numbers()
Atomic_type_tags = np.zeros(np.shape(Atomic_numbers))
atomic_type_unique = np.unique(Atomic_numbers)
for i, iZ in enumerate(atomic_type_unique):
Atomic_type_tags[Atomic_numbers == iZ] = i
aseAtoms.set_tags(Atomic_type_tags)
aseAtoms.set_initial_charges()
return aseAtoms
def get_cell_from_phonopy_structure(ph_structure: PhonopyAtoms,
use_atomic_number: bool = False) -> tuple:
"""
Get cell from phonopy structure
Args:
ph_structure: PhonopyAtoms object
use_atomic_number: if True, use atomic number intead of atomic symbol
Returns:
tuple: (lattice, scaled_positions, symbols).
"""
lattice = ph_structure.get_cell()
scaled_positions = ph_structure.get_scaled_positions()
if use_atomic_number:
elements = list(ph_structure.get_atomic_numbers())
else:
elements = ph_structure.get_chemical_symbols()
return (lattice, scaled_positions, elements)
def assert_same_phonopy_atoms(actual: PhonopyAtoms, expected: PhonopyAtoms):
assert (actual.get_cell() == expected.get_cell()).all()
assert (actual.get_scaled_positions() == expected.get_scaled_positions()
).all()
assert actual.symbols == expected.symbols
