def _create_phono3py_phonon_fc2(phono3py, force_to_eVperA, distance_to_A,
symmetrize_fc2, input_filename, is_compact_fc,
fc_calculator, fc_calculator_options,
log_level):
if input_filename is None:
disp_filename = 'disp_fc2.yaml'
else:
disp_filename = 'disp_fc2.' + input_filename + '.yaml'
natom = phono3py.phonon_supercell.get_number_of_atoms()
try:
disp_dataset = parse_forces(natom,
force_to_eVperA,
distance_to_A,
force_filename="FORCES_FC2",
disp_filename=disp_filename,
is_fc2=True,
log_level=log_level)
except RuntimeError as e:
if log_level:
print(str(e))
print_error()
sys.exit(1)
except FileNotFoundError as e:
file_exists(e.filename, log_level)
phono3py.produce_fc2(displacement_dataset=disp_dataset,
symmetrize_fc2=symmetrize_fc2,
is_compact_fc=is_compact_fc,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options)
return True
def _read_phono3py_fc2(phono3py, symmetrize_fc2, input_filename, log_level):
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.phonon_supercell.get_number_of_atoms()
p2s_map = phono3py.phonon_primitive.p2s_map
try:
phonon_fc2 = read_fc2_from_hdf5(filename=filename, p2s_map=p2s_map)
except RuntimeError:
import traceback
traceback.print_exc()
if log_level:
print_error()
sys.exit(1)
if phonon_fc2.shape[1] != num_atom:
print("Matrix shape of fc2 doesn't agree with supercell size.")
if log_level:
print_error()
sys.exit(1)
if symmetrize_fc2:
if phonon_fc2.shape[0] == phonon_fc2.shape[1]:
symmetrize_force_constants(phonon_fc2)
else:
symmetrize_compact_force_constants(phonon_fc2,
phono3py.phonon_primitive)
phono3py.set_fc2(phonon_fc2)
def _read_phono3py_fc3(phono3py, symmetrize_fc3r, input_filename, log_level):
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)
p2s_map = phono3py.get_primitive().get_primitive_to_supercell_map()
try:
fc3 = read_fc3_from_hdf5(filename=filename, p2s_map=p2s_map)
except RuntimeError:
import traceback
traceback.print_exc()
if log_level:
print_error()
sys.exit(1)
num_atom = phono3py.get_supercell().get_number_of_atoms()
if fc3.shape[1] != num_atom:
print("Matrix shape of fc3 doesn't agree with supercell size.")
if log_level:
print_error()
sys.exit(1)
if symmetrize_fc3r:
set_translational_invariance_fc3(fc3)
set_permutation_symmetry_fc3(fc3)
phono3py.set_fc3(fc3)
def _create_phono3py_fc2(phono3py, energy_to_eV, distance_to_A, tsym_type,
symmetrize_fc2, input_filename, use_alm, 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,
is_permutation_symmetry=symmetrize_fc2,
translational_symmetry_type=tsym_type,
use_alm=use_alm)
return True
def _create_phono3py_fc3(phono3py, force_to_eVperA, distance_to_A,
symmetrize_fc3r, symmetrize_fc2, input_filename,
output_filename, is_compact_fc, cutoff_pair_distance,
use_alm, alm_options, compression, 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 for fc3 is read from %s." % filename)
disp_dataset = parse_disp_fc3_yaml(filename=filename)
if cutoff_pair_distance:
if ('cutoff_distance' not in disp_dataset
or 'cutoff_distance' in disp_dataset
and cutoff_pair_distance < disp_dataset['cutoff_distance']):
disp_dataset['cutoff_distance'] = cutoff_pair_distance
if log_level:
print("Cutoff-pair-distance: %f" % cutoff_pair_distance)
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")
sys.stdout.flush()
forces_fc3 = parse_FORCES_FC3(disp_dataset)
_convert_force_unit(forces_fc3, force_to_eVperA)
phono3py.produce_fc3(forces_fc3,
displacement_dataset=disp_dataset,
symmetrize_fc3r=symmetrize_fc3r,
is_compact_fc=is_compact_fc,
use_alm=use_alm,
alm_options=alm_options)
if output_filename is None:
filename = 'fc3.hdf5'
else:
filename = 'fc3.' + output_filename + '.hdf5'
if log_level:
print("Writing fc3 to %s" % filename)
p2s_map = phono3py.get_primitive().get_primitive_to_supercell_map()
write_fc3_to_hdf5(phono3py.get_fc3(),
filename=filename,
p2s_map=p2s_map,
compression=compression)
return True
def _create_phono3py_fc3(phono3py,
force_to_eVperA,
distance_to_A,
tsym_type,
symmetrize_fc3_r,
symmetrize_fc2,
cutoff_distance,
input_filename,
output_filename,
use_alm,
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, force_to_eVperA)
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,
use_alm=use_alm)
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, force_to_eVperA, distance_to_A,
symmetrize_fc2, input_filename, is_compact_fc,
fc_calculator, fc_calculator_options, log_level):
file_exists("FORCES_FC3", log_level)
natom = phono3py.supercell.get_number_of_atoms()
disp_dataset = _get_type2_dataset(natom, filename="FORCES_FC3")
if disp_dataset:
if log_level:
print("%d snapshots were found in %s." %
(len(disp_dataset['displacements']), "FORCES_FC3"))
if force_to_eVperA is not None:
disp_dataset['forces'] *= force_to_eVperA
if distance_to_A is not None:
disp_dataset['displacements'] *= distance_to_A
else:
if input_filename is None:
filename = 'disp_fc3.yaml'
else:
filename = 'disp_fc3.' + input_filename + '.yaml'
if log_level:
print("Displacement dataset for fc2 is read from %s." % filename)
file_exists(filename, log_level)
disp_dataset = parse_disp_fc3_yaml(filename=filename)
if disp_dataset['natom'] != natom:
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")
# forces are stored in disp_dataset.
parse_FORCES_FC2(disp_dataset,
filename="FORCES_FC3",
unit_conversion_factor=force_to_eVperA)
phono3py.produce_fc2(displacement_dataset=disp_dataset,
symmetrize_fc2=symmetrize_fc2,
is_compact_fc=is_compact_fc,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options)
return True
def _create_phono3py_fc3(phono3py, force_to_eVperA, distance_to_A,
symmetrize_fc3r, symmetrize_fc2, input_filename,
output_filename, is_compact_fc, cutoff_pair_distance,
fc_calculator, fc_calculator_options, compression,
log_level):
if input_filename is None:
disp_filename = 'disp_fc3.yaml'
else:
disp_filename = 'disp_fc3.' + input_filename + '.yaml'
natom = phono3py.supercell.get_number_of_atoms()
try:
disp_dataset = parse_forces(natom,
force_to_eVperA,
distance_to_A,
cutoff_pair_distance=cutoff_pair_distance,
force_filename="FORCES_FC3",
disp_filename=disp_filename,
log_level=log_level)
except RuntimeError as e:
if log_level:
print(str(e))
print_error()
sys.exit(1)
except FileNotFoundError as e:
file_exists(e.filename, log_level)
phono3py.produce_fc3(displacement_dataset=disp_dataset,
symmetrize_fc3r=symmetrize_fc3r,
is_compact_fc=is_compact_fc,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options)
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.fc3,
filename=filename,
p2s_map=phono3py.primitive.p2s_map,
compression=compression)
return True
def _create_phono3py_phonon_fc2(phono3py,
force_to_eVperA,
distance_to_A,
symmetrize_fc2,
input_filename,
is_compact_fc,
use_alm,
alm_options,
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, force_to_eVperA)
phono3py.produce_fc2(
forces_fc2,
displacement_dataset=disp_dataset,
symmetrize_fc2=symmetrize_fc2,
is_compact_fc=is_compact_fc,
use_alm=use_alm,
alm_options=alm_options)
return True
def create_phono3py_force_constants(phono3py,
phonon_supercell_matrix,
settings,
force_to_eVperA=None,
distance_to_A=None,
compression=None,
input_filename=None,
output_filename=None,
log_level=1):
if settings.get_fc_calculator() is None:
symmetrize_fc3r = (settings.get_is_symmetrize_fc3_r()
or settings.get_fc_symmetry())
symmetrize_fc2 = (settings.get_is_symmetrize_fc2()
or settings.get_fc_symmetry())
else: # Rely on fc calculator the symmetrization of fc.
symmetrize_fc2 = False
symmetrize_fc3r = False
if log_level:
show_phono3py_force_constants_settings(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_pp()
or settings.get_write_phonon()
or settings.get_constant_averaged_pp_interaction() is not None):
pass
else:
if settings.get_read_fc3(): # Read fc3.hdf5
_read_phono3py_fc3(phono3py, symmetrize_fc3r, input_filename,
log_level)
else: # fc3 from FORCES_FC3
if not _create_phono3py_fc3(
phono3py, force_to_eVperA, distance_to_A, symmetrize_fc3r,
symmetrize_fc2, input_filename, output_filename,
settings.get_is_compact_fc(),
settings.get_cutoff_pair_distance(),
settings.get_fc_calculator(),
settings.get_fc_calculator_options(), compression,
log_level):
print("fc3 was not created properly.")
if log_level:
print_error()
sys.exit(1)
cutoff_distance = settings.get_cutoff_fc3_distance()
if cutoff_distance is not None and cutoff_distance > 0:
if log_level:
print("Cutting-off fc3 by zero (cut-off distance: %f)" %
cutoff_distance)
phono3py.cutoff_fc3_by_zero(cutoff_distance)
if log_level:
show_drift_fc3(phono3py.get_fc3(),
primitive=phono3py.get_primitive())
#######
# fc2 #
#######
phonon_primitive = phono3py.get_phonon_primitive()
p2s_map = phonon_primitive.p2s_map
if settings.get_read_fc2():
_read_phono3py_fc2(phono3py, symmetrize_fc2, input_filename, log_level)
else:
if phonon_supercell_matrix is None:
if settings.get_fc_calculator() is not None:
pass
elif not _create_phono3py_fc2(
phono3py, force_to_eVperA, distance_to_A, symmetrize_fc2,
input_filename, settings.get_is_compact_fc(),
settings.get_fc_calculator(),
settings.get_fc_calculator_options(), log_level):
print("fc2 was not created properly.")
if log_level:
print_error()
sys.exit(1)
else:
if not _create_phono3py_phonon_fc2(
phono3py, force_to_eVperA, distance_to_A, symmetrize_fc2,
input_filename, settings.get_is_compact_fc(),
settings.get_fc_calculator(),
settings.get_fc_calculator_options(), 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,
p2s_map=p2s_map,
physical_unit='eV/Angstrom^2',
compression=compression)
if log_level:
show_drift_force_constants(phono3py.get_fc2(),
primitive=phonon_primitive,
name='fc2')
def _create_phono3py_fc3(phono3py, force_to_eVperA, distance_to_A,
symmetrize_fc3r, symmetrize_fc2, input_filename,
output_filename, is_compact_fc, cutoff_pair_distance,
fc_calculator, fc_calculator_options, compression,
log_level):
file_exists("FORCES_FC3", log_level)
natom = phono3py.supercell.get_number_of_atoms()
disp_dataset = _get_type2_dataset(natom, filename="FORCES_FC3")
if disp_dataset: # type2
if log_level:
print("%d snapshots were found in %s." %
(len(disp_dataset['displacements']), "FORCES_FC3"))
if force_to_eVperA is not None:
disp_dataset['forces'] *= force_to_eVperA
if distance_to_A is not None:
disp_dataset['displacements'] *= distance_to_A
else: # type1
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 for fc3 is read from %s." % filename)
disp_dataset = parse_disp_fc3_yaml(filename=filename)
if cutoff_pair_distance:
if ('cutoff_distance' not in disp_dataset
or 'cutoff_distance' in disp_dataset and
cutoff_pair_distance < disp_dataset['cutoff_distance']):
disp_dataset['cutoff_distance'] = cutoff_pair_distance
if log_level:
print("Cutoff-pair-distance: %f" % cutoff_pair_distance)
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)
if log_level:
print("Sets of supercell forces are read from %s." % "FORCES_FC3")
sys.stdout.flush()
# forces are stored in disp_dataset.
parse_FORCES_FC3(disp_dataset, unit_conversion_factor=force_to_eVperA)
phono3py.produce_fc3(displacement_dataset=disp_dataset,
symmetrize_fc3r=symmetrize_fc3r,
is_compact_fc=is_compact_fc,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options)
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,
p2s_map=phono3py.primitive.p2s_map,
compression=compression)
return True
def create_phono3py_force_constants(phono3py,
phonon_supercell_matrix,
settings,
force_to_eVperA=None,
distance_to_A=None,
compression=None,
input_filename=None,
output_filename=None,
log_level=1):
read_fc3 = settings.get_read_fc3()
read_fc2 = settings.get_read_fc2()
symmetrize_fc3r = (settings.get_is_symmetrize_fc3_r() or
settings.get_fc_symmetry())
symmetrize_fc3q = settings.get_is_symmetrize_fc3_q()
symmetrize_fc2 = (settings.get_is_symmetrize_fc2() or
settings.get_fc_symmetry())
if settings.get_use_alm_fc2():
symmetrize_fc2 = False
if settings.get_use_alm_fc3():
symmetrize_fc3r = False
alm_options = None
if settings.get_use_alm_fc3() or settings.get_use_alm_fc2():
if settings.get_alm_options() is not None:
alm_option_types = {'solver': str,
'cutoff_distance': float}
alm_options = {}
for option_str in settings.get_alm_options().split(","):
key, val = [x.strip() for x in option_str.split('=')[:2]]
if key.lower() in alm_option_types:
option_value = alm_option_types[key.lower()](val)
alm_options[key.lower()] = option_value
if log_level:
show_phono3py_force_constants_settings(read_fc3,
read_fc2,
symmetrize_fc3r,
symmetrize_fc3q,
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_pp() or
settings.get_write_phonon() 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)
p2s_map = phono3py.get_primitive().get_primitive_to_supercell_map()
try:
fc3 = read_fc3_from_hdf5(filename=filename, p2s_map=p2s_map)
except RuntimeError:
import traceback
traceback.print_exc()
if log_level:
print_error()
sys.exit(1)
num_atom = phono3py.get_supercell().get_number_of_atoms()
if fc3.shape[1] != num_atom:
print("Matrix shape of fc3 doesn't agree with supercell size.")
if log_level:
print_error()
sys.exit(1)
if symmetrize_fc3r:
set_translational_invariance_fc3(fc3)
set_permutation_symmetry_fc3(fc3)
phono3py.set_fc3(fc3)
else: # fc3 from FORCES_FC3
if not _create_phono3py_fc3(phono3py,
force_to_eVperA,
distance_to_A,
symmetrize_fc3r,
symmetrize_fc2,
input_filename,
output_filename,
settings.get_is_compact_fc(),
settings.get_use_alm_fc3(),
alm_options,
compression,
log_level):
print("fc3 was not created properly.")
if log_level:
print_error()
sys.exit(1)
cutoff_distance = settings.get_cutoff_fc3_distance()
if cutoff_distance is not None and cutoff_distance > 0:
if log_level:
print("Cutting-off fc3 by zero (cut-off distance: %f)" %
cutoff_distance)
phono3py.cutoff_fc3_by_zero(cutoff_distance)
if log_level:
show_drift_fc3(phono3py.get_fc3(),
primitive=phono3py.get_primitive())
# fc2
phonon_primitive = phono3py.get_phonon_primitive()
phonon_supercell = phono3py.get_phonon_supercell()
p2s_map = phonon_primitive.get_primitive_to_supercell_map()
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 = phonon_supercell.get_number_of_atoms()
try:
phonon_fc2 = read_fc2_from_hdf5(filename=filename, p2s_map=p2s_map)
except RuntimeError:
import traceback
traceback.print_exc()
if log_level:
print_error()
sys.exit(1)
if phonon_fc2.shape[1] != num_atom:
print("Matrix shape of fc2 doesn't agree with supercell size.")
if log_level:
print_error()
sys.exit(1)
if symmetrize_fc2:
if phonon_fc2.shape[0] == phonon_fc2.shape[1]:
symmetrize_force_constants(phonon_fc2)
else:
symmetrize_compact_force_constants(phonon_fc2,
phonon_primitive)
phono3py.set_fc2(phonon_fc2)
else:
if phonon_supercell_matrix is None:
if not _create_phono3py_fc2(phono3py,
force_to_eVperA,
distance_to_A,
symmetrize_fc2,
input_filename,
settings.get_is_compact_fc(),
settings.get_use_alm_fc2(),
alm_options,
log_level):
print("fc2 was not created properly.")
if log_level:
print_error()
sys.exit(1)
else:
if not _create_phono3py_phonon_fc2(phono3py,
force_to_eVperA,
distance_to_A,
symmetrize_fc2,
input_filename,
settings.get_is_compact_fc(),
settings.get_use_alm_fc2(),
alm_options,
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,
p2s_map=p2s_map,
compression=compression)
if log_level:
show_drift_force_constants(phono3py.get_fc2(),
primitive=phonon_primitive,
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, settings.get_use_alm(), 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,
settings.get_use_alm(), 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,
settings.get_use_alm(), 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')
