def read_pwscf(filename):
pwscf_in = PwscfIn(open(filename).readlines())
tags = pwscf_in.get_tags()
lattice = tags['cell_parameters']
positions = [pos[1] for pos in tags['atomic_positions']]
species = [pos[0] for pos in tags['atomic_positions']]
mass_map = {}
pp_map = {}
for vals in tags['atomic_species']:
mass_map[vals[0]] = vals[1]
pp_map[vals[0]] = vals[2]
masses = [mass_map[x] for x in species]
pp_all_filenames = [pp_map[x] for x in species]
unique_species = []
for x in species:
if x not in unique_species:
unique_species.append(x)
numbers = []
is_unusual = False
for x in species:
if x in symbol_map:
numbers.append(symbol_map[x])
else:
numbers.append(-unique_species.index(x))
is_unusual = True
if is_unusual:
positive_numbers = []
for n in numbers:
if n > 0:
if n not in positive_numbers:
positive_numbers.append(n)
available_numbers = range(1, 119)
for pn in positive_numbers:
available_numbers.remove(pn)
for i, n in enumerate(numbers):
if n < 1:
numbers[i] = available_numbers[-n]
cell = Atoms(numbers=numbers,
masses=masses,
cell=lattice,
scaled_positions=positions)
else:
cell = Atoms(numbers=numbers,
cell=lattice,
scaled_positions=positions)
unique_symbols = []
pp_filenames = {}
for i, symbol in enumerate(cell.get_chemical_symbols()):
if symbol not in unique_symbols:
unique_symbols.append(symbol)
pp_filenames[symbol] = pp_all_filenames[i]
return cell, pp_filenames
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)
