def _create_phono3py_phonon_fc2(phono3py, energy_to_eV, distance_to_A,
tsym_type, symmetrize_fc2, input_filename,
log_level):
if input_filename is None:
filename = 'disp_fc2.yaml'
else:
filename = 'disp_fc2.' + input_filename + '.yaml'
if log_level:
print("Displacement dataset is read from %s." % filename)
file_exists(filename, log_level)
disp_dataset = parse_disp_fc2_yaml(filename=filename)
num_atom = phono3py.get_phonon_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_FC2")
file_exists("FORCES_FC2", log_level)
forces_fc2 = parse_FORCES_FC2(disp_dataset)
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_phonon_fc2(phono3py, tsym_type, symmetrize_fc2,
input_filename, log_level):
if input_filename is None:
filename = 'disp_fc2.yaml'
else:
filename = 'disp_fc2.' + input_filename + '.yaml'
if log_level:
print("Displacement dataset is read from %s." % filename)
file_exists(filename, log_level)
disp_dataset = parse_disp_fc2_yaml(filename=filename)
if log_level:
print("Sets of supercell forces are read from %s." % "FORCES_FC2")
file_exists("FORCES_FC2", log_level)
forces_fc2 = parse_FORCES_FC2(disp_dataset)
phono3py.produce_fc2(forces_fc2,
displacement_dataset=disp_dataset,
translational_symmetry_type=tsym_type,
is_permutation_symmetry=symmetrize_fc2)
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_phonon_fc2(phono3py,
energy_to_eV,
distance_to_A,
tsym_type,
symmetrize_fc2,
input_filename,
log_level):
if input_filename is None:
filename = 'disp_fc2.yaml'
else:
filename = 'disp_fc2.' + input_filename + '.yaml'
if log_level:
print("Displacement dataset is read from %s." % filename)
file_exists(filename, log_level)
disp_dataset = parse_disp_fc2_yaml(filename=filename)
num_atom = phono3py.get_phonon_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_FC2")
file_exists("FORCES_FC2", log_level)
forces_fc2 = parse_FORCES_FC2(disp_dataset)
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_force_constants(phono3py,
phonon_supercell_matrix,
settings,
energy_to_eV=None,
distance_to_A=None,
input_filename=None,
output_filename=None,
log_level=1):
read_fc3 = settings.get_read_fc3()
read_fc2 = settings.get_read_fc2()
symmetrize_fc3_r = settings.get_is_symmetrize_fc3_r()
symmetrize_fc3_q = settings.get_is_symmetrize_fc3_q()
symmetrize_fc2 = settings.get_is_symmetrize_fc2()
if settings.get_is_translational_symmetry():
tsym_type = 1
elif settings.get_tsym_type() > 0:
tsym_type = settings.get_tsym_type()
else:
tsym_type = 0
if log_level:
show_phono3py_force_constants_settings(read_fc3, read_fc2, tsym_type,
symmetrize_fc3_r,
symmetrize_fc3_q,
symmetrize_fc2, settings)
# fc3
if (settings.get_is_joint_dos()
or (settings.get_is_isotope()
and not (settings.get_is_bterta() or settings.get_is_lbte()))
or settings.get_read_gamma() or settings.get_read_amplitude()
or settings.get_constant_averaged_pp_interaction() is not None):
pass
else:
if read_fc3: # Read fc3.hdf5
if input_filename is None:
filename = 'fc3.hdf5'
else:
filename = 'fc3.' + input_filename + '.hdf5'
file_exists(filename, log_level)
if log_level:
print("Reading fc3 from %s" % filename)
fc3 = read_fc3_from_hdf5(filename=filename)
num_atom = phono3py.get_supercell().get_number_of_atoms()
if fc3.shape[0] != num_atom:
print("Matrix shape of fc3 doesn't agree with supercell size.")
if log_level:
print_error()
sys.exit(1)
phono3py.set_fc3(fc3)
else: # fc3 from FORCES_FC3
if not _create_phono3py_fc3(
phono3py, energy_to_eV, distance_to_A, tsym_type,
symmetrize_fc3_r, symmetrize_fc2,
settings.get_cutoff_fc3_distance(), input_filename,
output_filename, log_level):
print("fc3 was not created properly.")
if log_level:
print_error()
sys.exit(1)
if log_level:
show_drift_fc3(phono3py.get_fc3())
# fc2
if read_fc2:
if input_filename is None:
filename = 'fc2.hdf5'
else:
filename = 'fc2.' + input_filename + '.hdf5'
file_exists(filename, log_level)
if log_level:
print("Reading fc2 from %s" % filename)
num_atom = phono3py.get_phonon_supercell().get_number_of_atoms()
phonon_fc2 = read_fc2_from_hdf5(filename=filename)
if phonon_fc2.shape[0] != num_atom:
print("Matrix shape of fc2 doesn't agree with supercell size.")
if log_level:
print_error()
sys.exit(1)
phono3py.set_fc2(phonon_fc2)
else:
if log_level:
print("Solving fc2")
if phonon_supercell_matrix is None:
if phono3py.get_fc2() is None:
if not _create_phono3py_fc2(
phono3py, energy_to_eV, distance_to_A, tsym_type,
symmetrize_fc2, input_filename, log_level):
print("fc2 was not created properly.")
if log_level:
print_error()
sys.exit(1)
else:
if not _create_phono3py_phonon_fc2(
phono3py, energy_to_eV, distance_to_A, tsym_type,
symmetrize_fc2, input_filename, log_level):
print("fc2 was not created properly.")
if log_level:
print_error()
sys.exit(1)
if output_filename is None:
filename = 'fc2.hdf5'
else:
filename = 'fc2.' + output_filename + '.hdf5'
if log_level:
print("Writing fc2 to %s" % filename)
write_fc2_to_hdf5(phono3py.get_fc2(), filename=filename)
if log_level:
show_drift_force_constants(phono3py.get_fc2(), name='fc2')
def create_phono3py_force_constants(phono3py, phonon_supercell_matrix,
settings, read_fc3, read_fc2, tsym_type,
symmetrize_fc3_r, symmetrize_fc3_q,
symmetrize_fc2, input_filename,
output_filename, log_level):
if log_level:
show_phono3py_force_constants_settings(read_fc3, read_fc2, tsym_type,
symmetrize_fc3_r,
symmetrize_fc3_q,
symmetrize_fc2, settings)
# fc3
if (settings.get_is_joint_dos()
or (settings.get_is_isotope()
and not (settings.get_is_bterta() or settings.get_is_lbte()))
or settings.get_read_gamma() or settings.get_read_amplitude()
or settings.get_constant_averaged_pp_interaction() is not None):
pass
else:
if read_fc3: # Read fc3.hdf5
if input_filename is None:
filename = 'fc3.hdf5'
else:
filename = 'fc3.' + input_filename + '.hdf5'
file_exists(filename, log_level)
if log_level:
print("Reading fc3 from %s" % filename)
fc3 = read_fc3_from_hdf5(filename=filename)
phono3py.set_fc3(fc3)
else: # fc3 from FORCES_THIRD and FORCES_SECOND
_create_phono3py_fc3(phono3py, tsym_type, symmetrize_fc3_r,
symmetrize_fc2,
settings.get_cutoff_fc3_distance(),
input_filename, output_filename, log_level)
if log_level:
show_drift_fc3(phono3py.get_fc3())
# fc2
if read_fc2:
if input_filename is None:
filename = 'fc2.hdf5'
else:
filename = 'fc2.' + input_filename + '.hdf5'
file_exists(filename, log_level)
if log_level:
print("Reading fc2 from %s" % filename)
phonon_supercell = phono3py.get_phonon_supercell()
phonon_fc2 = read_fc2_from_hdf5(filename=filename)
if phonon_fc2.shape[0] != phonon_supercell.get_number_of_atoms():
print("Matrix shape of fc2 doesn't agree with supercell.")
if log_level:
print_error()
sys.exit(1)
phono3py.set_fc2(phonon_fc2)
else:
if log_level:
print("Solving fc2")
if phonon_supercell_matrix is None:
if phono3py.get_fc2() is None:
_create_phono3py_fc2(phono3py, tsym_type, symmetrize_fc2,
input_filename, log_level)
else:
_create_phono3py_phonon_fc2(phono3py, tsym_type, symmetrize_fc2,
input_filename, log_level)
if output_filename is None:
filename = 'fc2.hdf5'
else:
filename = 'fc2.' + output_filename + '.hdf5'
if log_level:
print("Writing fc2 to %s" % filename)
write_fc2_to_hdf5(phono3py.get_fc2(), filename=filename)
if log_level:
show_drift_force_constants(phono3py.get_fc2(), name='fc2')
def create_phono3py_force_constants(phono3py,
phonon_supercell_matrix,
settings,
energy_to_eV=None,
distance_to_A=None,
input_filename=None,
output_filename=None,
log_level=1):
read_fc3 = settings.get_read_fc3()
read_fc2 = settings.get_read_fc2()
symmetrize_fc3_r = settings.get_is_symmetrize_fc3_r()
symmetrize_fc3_q = settings.get_is_symmetrize_fc3_q()
symmetrize_fc2 = settings.get_is_symmetrize_fc2()
if settings.get_is_translational_symmetry():
tsym_type = 1
elif settings.get_tsym_type() > 0:
tsym_type = settings.get_tsym_type()
else:
tsym_type = 0
if log_level:
show_phono3py_force_constants_settings(read_fc3,
read_fc2,
tsym_type,
symmetrize_fc3_r,
symmetrize_fc3_q,
symmetrize_fc2,
settings)
# fc3
if (settings.get_is_joint_dos() or
(settings.get_is_isotope() and
not (settings.get_is_bterta() or settings.get_is_lbte())) or
settings.get_read_gamma() or
settings.get_read_amplitude() or
settings.get_constant_averaged_pp_interaction() is not None):
pass
else:
if read_fc3: # Read fc3.hdf5
if input_filename is None:
filename = 'fc3.hdf5'
else:
filename = 'fc3.' + input_filename + '.hdf5'
file_exists(filename, log_level)
if log_level:
print("Reading fc3 from %s" % filename)
fc3 = read_fc3_from_hdf5(filename=filename)
num_atom = phono3py.get_supercell().get_number_of_atoms()
if fc3.shape[0] != num_atom:
print("Matrix shape of fc3 doesn't agree with supercell size.")
if log_level:
print_error()
sys.exit(1)
phono3py.set_fc3(fc3)
else: # fc3 from FORCES_FC3
if not _create_phono3py_fc3(phono3py,
energy_to_eV,
distance_to_A,
tsym_type,
symmetrize_fc3_r,
symmetrize_fc2,
settings.get_cutoff_fc3_distance(),
input_filename,
output_filename,
log_level):
print("fc3 was not created properly.")
if log_level:
print_error()
sys.exit(1)
if log_level:
show_drift_fc3(phono3py.get_fc3())
# fc2
if read_fc2:
if input_filename is None:
filename = 'fc2.hdf5'
else:
filename = 'fc2.' + input_filename + '.hdf5'
file_exists(filename, log_level)
if log_level:
print("Reading fc2 from %s" % filename)
num_atom = phono3py.get_phonon_supercell().get_number_of_atoms()
phonon_fc2 = read_fc2_from_hdf5(filename=filename)
if phonon_fc2.shape[0] != num_atom:
print("Matrix shape of fc2 doesn't agree with supercell size.")
if log_level:
print_error()
sys.exit(1)
phono3py.set_fc2(phonon_fc2)
else:
if log_level:
print("Solving fc2")
if phonon_supercell_matrix is None:
if phono3py.get_fc2() is None:
if not _create_phono3py_fc2(phono3py,
energy_to_eV,
distance_to_A,
tsym_type,
symmetrize_fc2,
input_filename,
log_level):
print("fc2 was not created properly.")
if log_level:
print_error()
sys.exit(1)
else:
if not _create_phono3py_phonon_fc2(phono3py,
energy_to_eV,
distance_to_A,
tsym_type,
symmetrize_fc2,
input_filename,
log_level):
print("fc2 was not created properly.")
if log_level:
print_error()
sys.exit(1)
if output_filename is None:
filename = 'fc2.hdf5'
else:
filename = 'fc2.' + output_filename + '.hdf5'
if log_level:
print("Writing fc2 to %s" % filename)
write_fc2_to_hdf5(phono3py.get_fc2(), filename=filename)
if log_level:
show_drift_force_constants(phono3py.get_fc2(), name='fc2')