def _create_phono3py_fc2(phono3py, energy_to_eV, distance_to_A, tsym_type,
symmetrize_fc2, input_filename, log_level):
if input_filename is None:
filename = 'disp_fc3.yaml'
else:
filename = 'disp_fc3.' + input_filename + '.yaml'
if log_level:
print("Displacement dataset is read from %s." % filename)
file_exists(filename, log_level)
disp_dataset = parse_disp_fc3_yaml(filename=filename)
num_atom = phono3py.get_supercell().get_number_of_atoms()
if disp_dataset['natom'] != num_atom:
print("Number of atoms in supercell is not consistent with %s" %
filename)
if log_level:
print_error()
sys.exit(1)
_convert_displacement_unit(disp_dataset, distance_to_A, is_fc2=True)
if log_level:
print("Sets of supercell forces are read from %s." % "FORCES_FC3")
file_exists("FORCES_FC3", log_level)
forces_fc2 = parse_FORCES_FC2(disp_dataset, filename="FORCES_FC3")
if not forces_fc2:
return False
_convert_force_unit(forces_fc2, energy_to_eV, distance_to_A)
phono3py.produce_fc2(forces_fc2,
displacement_dataset=disp_dataset,
translational_symmetry_type=tsym_type,
is_permutation_symmetry=symmetrize_fc2)
return True
def _create_phono3py_fc3(phono3py, tsym_type, symmetrize_fc3_r, symmetrize_fc2,
cutoff_distance, input_filename, output_filename,
log_level):
if input_filename is None:
filename = 'disp_fc3.yaml'
else:
filename = 'disp_fc3.' + input_filename + '.yaml'
file_exists(filename, log_level)
if log_level:
print("Displacement dataset is read from %s." % filename)
disp_dataset = parse_disp_fc3_yaml(filename=filename)
file_exists("FORCES_FC3", log_level)
if log_level:
print("Sets of supercell forces are read from %s." % "FORCES_FC3")
forces_fc3 = parse_FORCES_FC3(disp_dataset)
phono3py.produce_fc3(forces_fc3,
displacement_dataset=disp_dataset,
cutoff_distance=cutoff_distance,
translational_symmetry_type=tsym_type,
is_permutation_symmetry=symmetrize_fc3_r,
is_permutation_symmetry_fc2=symmetrize_fc2)
if output_filename is None:
filename = 'fc3.hdf5'
else:
filename = 'fc3.' + output_filename + '.hdf5'
if log_level:
print("Writing fc3 to %s" % filename)
write_fc3_to_hdf5(phono3py.get_fc3(), filename=filename)
def _create_phono3py_fc3(phono3py,
energy_to_eV,
distance_to_A,
tsym_type,
symmetrize_fc3_r,
symmetrize_fc2,
cutoff_distance,
input_filename,
output_filename,
log_level):
if input_filename is None:
filename = 'disp_fc3.yaml'
else:
filename = 'disp_fc3.' + input_filename + '.yaml'
file_exists(filename, log_level)
if log_level:
print("Displacement dataset is read from %s." % filename)
disp_dataset = parse_disp_fc3_yaml(filename=filename)
num_atom = phono3py.get_supercell().get_number_of_atoms()
if disp_dataset['natom'] != num_atom:
print("Number of atoms in supercell is not consistent with %s" %
filename)
if log_level:
print_error()
sys.exit(1)
_convert_displacement_unit(disp_dataset, distance_to_A)
file_exists("FORCES_FC3", log_level)
if log_level:
print("Sets of supercell forces are read from %s." % "FORCES_FC3")
forces_fc3 = parse_FORCES_FC3(disp_dataset)
if not forces_fc3:
return False
_convert_force_unit(forces_fc3, energy_to_eV, distance_to_A)
phono3py.produce_fc3(
forces_fc3,
displacement_dataset=disp_dataset,
cutoff_distance=cutoff_distance,
translational_symmetry_type=tsym_type,
is_permutation_symmetry=symmetrize_fc3_r,
is_permutation_symmetry_fc2=symmetrize_fc2)
if output_filename is None:
filename = 'fc3.hdf5'
else:
filename = 'fc3.' + output_filename + '.hdf5'
if log_level:
print("Writing fc3 to %s" % filename)
write_fc3_to_hdf5(phono3py.get_fc3(), filename=filename)
return True
def _create_phono3py_fc2(phono3py, tsym_type, symmetrize_fc2, input_filename,
log_level):
if input_filename is None:
filename = 'disp_fc3.yaml'
else:
filename = 'disp_fc3.' + input_filename + '.yaml'
if log_level:
print("Displacement dataset is read from %s." % filename)
file_exists(filename, log_level)
disp_dataset = parse_disp_fc3_yaml(filename=filename)
if log_level:
print("Sets of supercell forces are read from %s." % "FORCES_FC3")
file_exists("FORCES_FC3", log_level)
forces_fc3 = parse_FORCES_FC3(disp_dataset)
phono3py.produce_fc2(forces_fc3,
displacement_dataset=disp_dataset,
translational_symmetry_type=tsym_type,
is_permutation_symmetry=symmetrize_fc2)
parse_FORCES_FC3,
read_fc3_from_hdf5,
read_fc2_from_hdf5)
cell = read_vasp("POSCAR-unitcell")
mesh = [11, 11, 11]
phono3py = Phono3py(cell,
np.diag([2, 2, 2]),
primitive_matrix=[[0, 0.5, 0.5],
[0.5, 0, 0.5],
[0.5, 0.5, 0]],
mesh=mesh,
log_level=1) # log_level=0 make phono3py quiet
# Create fc3 and fc2 from disp_fc3.yaml and FORCES_FC3
disp_dataset = parse_disp_fc3_yaml(filename="disp_fc3.yaml")
forces_fc3 = parse_FORCES_FC3(disp_dataset, filename="FORCES_FC3")
phono3py.produce_fc3(
forces_fc3,
displacement_dataset=disp_dataset,
is_translational_symmetry=True,
is_permutation_symmetry=True,
is_permutation_symmetry_fc2=True)
fc3 = phono3py.get_fc3()
fc2 = phono3py.get_fc2()
# # Create fc2 from disp_fc2.yaml and FORCES_FC2
# disp_dataset2 = parse_disp_fc2_yaml(filename="disp_fc2.yaml")
# forces_fc2 = parse_FORCES_FC2(disp_dataset2, filename="FORCES_FC2")
# phono3py.produce_fc2(
# forces_fc2,
from anharmonic.phonon3 import Phono3py
from anharmonic.file_IO import (parse_disp_fc3_yaml, parse_disp_fc2_yaml,
parse_FORCES_FC2, parse_FORCES_FC3,
read_fc3_from_hdf5, read_fc2_from_hdf5)
cell = read_vasp("POSCAR-unitcell")
mesh = [11, 11, 11]
phono3py = Phono3py(cell,
np.diag([2, 2, 2]),
primitive_matrix=[[0, 0.5, 0.5], [0.5, 0, 0.5],
[0.5, 0.5, 0]],
mesh=mesh,
log_level=1) # log_level=0 make phono3py quiet
# Create fc3 and fc2 from disp_fc3.yaml and FORCES_FC3
disp_dataset = parse_disp_fc3_yaml(filename="disp_fc3.yaml")
forces_fc3 = parse_FORCES_FC3(disp_dataset, filename="FORCES_FC3")
phono3py.produce_fc3(forces_fc3,
displacement_dataset=disp_dataset,
is_translational_symmetry=True,
is_permutation_symmetry=True,
is_permutation_symmetry_fc2=True)
fc3 = phono3py.get_fc3()
fc2 = phono3py.get_fc2()
# # Create fc2 from disp_fc2.yaml and FORCES_FC2
# disp_dataset2 = parse_disp_fc2_yaml(filename="disp_fc2.yaml")
# forces_fc2 = parse_FORCES_FC2(disp_dataset2, filename="FORCES_FC2")
# phono3py.produce_fc2(
# forces_fc2,
# displacement_dataset=disp_dataset2,
