def run(self):
"""
For disordered systems with relaxed atomic positions,
it might be better to use initial atomic positions to use the
symmetry of the structure (POSCAR_initial).
"""
poscar = Poscar('POSCAR')
number_of_atoms = poscar.get_atoms().get_number_of_atoms()
dummy_symbols = self.create_dummy_symbols(number_of_atoms)
poscar.get_atoms().set_chemical_symbols(dummy_symbols)
poscar.write_poscar('POSCAR_ideal')
def __init__(self,
spg_number,
mesh=None,
tmax=None,
is_sqs=False,
is_average_mass=False,
dim_sqs=None,
prior_primitive_axis=None,
band_points=None,
poscar_name="POSCAR",
magmom_line=None,
mode_mean_masses="a",
is_primitive=False,
is_fct=False,
is_bcm=False,
variables=None,
nac=None):
if variables is None:
self._dos_input = {
"f_min": -10.0, # THz
"f_max": 15.0, # THz
"d_freq": 0.01, # THz
"sigma": 0.1, # THz
}
else:
self._dos_input = variables
if mesh is None:
mesh = [1, 1, 1]
if dim_sqs is None:
dim_sqs = [1, 1, 1]
self._dictionary = {}
self._poscar = Poscar(poscar_name)
self._mesh = mesh
self._tmax = tmax
self._band_points = band_points
self._spg_number = spg_number
self._is_sqs = is_sqs
self._is_average_mass = is_average_mass
self._dim_sqs = dim_sqs
self._is_primitive = is_primitive
self._is_fct = is_fct
self._is_bcm = is_bcm
self._prior_primitive_axis = prior_primitive_axis
self._mode_mean_masses = mode_mean_masses
self._magmom_line = magmom_line
self._nac = nac
self._dim = get_dim('writefc.conf')
def create_randomized_configurations(mapfile,
infile,
random_seed,
numconf,
is_sorted):
"""
Parameters
----------
mapfile : String
Input file including mapping information.
infile : String
POSCAR filename.
"""
import json
from vasp.poscar import Poscar
from collections import OrderedDict
atoms = Poscar(infile).get_atoms()
with open(mapfile, "r") as f:
map_s2s = json.load(f, object_pairs_hook=OrderedDict)
order = create_order_of_symbols(map_s2s)
configuration_randomizer = ConfigurationRandomizer(
atoms=atoms,
map_s2s=map_s2s,
random_seed=random_seed,
)
for i in range(numconf):
atoms = configuration_randomizer.create_randomized_configuration()
filename = "RPOSCAR-{}".format(i + 1)
poscar = Poscar().set_atoms(atoms)
if is_sorted:
poscar.sort_by_symbols(order=order)
poscar.write(filename)
def create_spg_number(self):
"""
spg_number is used to determine the primitive axis and band paths.
"""
if self._poscar_average_filename is not None:
poscar_filename = self._poscar_average_filename
else:
poscar_filename = self._poscar_filename
print('SPG number is searched from {}'.format(poscar_filename))
spg_number = Poscar(poscar_filename).get_symmetry_dataset()["number"]
print("spg_number:", spg_number)
return spg_number
def write_cell_enlarged_ideal(self, filename):
poscar = Poscar()
poscar.set_atoms(self._enlarged_cell_average)
poscar.write(filename)
def write_cell_enlarged(self, filename):
poscar = Poscar()
poscar.set_atoms(self._enlarged_cell)
poscar.write(filename)
def __init__(self,
poscar_filename="POSCAR",
fc_filename="FORCE_CONSTANTS"):
self._poscar = Poscar(poscar_filename)
self._force_constants = parse_FORCE_CONSTANTS(fc_filename)
self._fc_reduced = None
