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 store_force_constants(phono3py, settings, ph3py_yaml, physical_units,
input_filename, output_filename, load_phono3py_yaml,
log_level):
if load_phono3py_yaml:
if log_level:
print("-" * 29 + " Force constants " + "-" * 30)
(fc_calculator,
fc_calculator_options) = get_fc_calculator_params(settings)
read_fc = set_dataset_and_force_constants(
phono3py,
ph3py_yaml=ph3py_yaml,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options,
symmetrize_fc=settings.fc_symmetry,
is_compact_fc=settings.is_compact_fc,
log_level=log_level)
if log_level:
if phono3py.fc3 is None:
print("fc3 could not be obtained.")
if phono3py.fc2 is None:
print("fc2 could not be obtained.")
if phono3py.fc3 is None or phono3py.fc2 is None:
print_error()
sys.exit(1)
if not read_fc['fc3']:
write_fc3_to_hdf5(phono3py.fc3,
p2s_map=phono3py.primitive.p2s_map,
compression=settings.hdf5_compression)
if log_level:
print("fc3 was written into \"fc3.hdf5\".")
if not read_fc['fc2']:
write_fc2_to_hdf5(phono3py.fc2,
p2s_map=phono3py.primitive.p2s_map,
physical_unit='eV/angstrom^2',
compression=settings.hdf5_compression)
if log_level:
print("fc2 was written into \"fc2.hdf5\".")
else:
create_phono3py_force_constants(phono3py,
settings,
ph3py_yaml=ph3py_yaml,
input_filename=input_filename,
output_filename=output_filename,
log_level=log_level)
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_force_constants(
phono3py,
settings,
ph3py_yaml=None,
input_filename=None,
output_filename=None,
log_level=1,
):
"""Read or calculate force constants."""
if settings.fc_calculator is None:
symmetrize_fc3r = settings.is_symmetrize_fc3_r or settings.fc_symmetry
symmetrize_fc2 = settings.is_symmetrize_fc2 or settings.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.is_joint_dos or
(settings.is_isotope and not (settings.is_bterta or settings.is_lbte))
or settings.read_gamma or settings.read_pp
or (not settings.is_bterta and settings.write_phonon)
or settings.constant_averaged_pp_interaction is not None):
pass
else:
if settings.read_fc3:
_read_phono3py_fc3(phono3py, symmetrize_fc3r, input_filename,
log_level)
else: # fc3 from FORCES_FC3 or ph3py_yaml
_create_phono3py_fc3(
phono3py,
ph3py_yaml,
symmetrize_fc3r,
input_filename,
settings.is_compact_fc,
settings.cutoff_pair_distance,
settings.fc_calculator,
settings.fc_calculator_options,
log_level,
)
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=settings.hdf5_compression,
)
cutoff_distance = settings.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.fc3, primitive=phono3py.primitive)
#######
# fc2 #
#######
phonon_primitive = phono3py.phonon_primitive
p2s_map = phonon_primitive.p2s_map
if settings.read_fc2:
_read_phono3py_fc2(phono3py, symmetrize_fc2, input_filename, log_level)
else:
if phono3py.phonon_supercell_matrix is None:
if settings.fc_calculator == "alm" and phono3py.fc2 is not None:
if log_level:
print("fc2 that was fit simultaneously with fc3 "
"by ALM is used.")
else:
_create_phono3py_fc2(
phono3py,
ph3py_yaml,
symmetrize_fc2,
input_filename,
settings.is_compact_fc,
settings.fc_calculator,
settings.fc_calculator_options,
log_level,
)
else:
_create_phono3py_phonon_fc2(
phono3py,
ph3py_yaml,
symmetrize_fc2,
input_filename,
settings.is_compact_fc,
settings.fc_calculator,
settings.fc_calculator_options,
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.fc2,
filename=filename,
p2s_map=p2s_map,
physical_unit="eV/angstrom^2",
compression=settings.hdf5_compression,
)
if log_level:
show_drift_force_constants(phono3py.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 write_fc3_to_hdf5_file(force_constants, filename):
from phono3py.file_IO import write_fc3_to_hdf5
write_fc3_to_hdf5(force_constants.get_data(), filename)
log_level=1)
phono3py.produce_fc3(force_sets.get_forces3(),
displacement_dataset=force_sets.get_data_sets3(),
is_translational_symmetry=True,
is_permutation_symmetry=True,
is_permutation_symmetry_fc2=True)
fc3 = phono3py.get_fc3()
fc2 = phono3py.get_fc2()
if True:
from phono3py.file_IO import write_fc2_to_hdf5, write_fc3_to_hdf5
print ('Writing FC2 and FC3 into HDF5 files')
write_fc2_to_hdf5(fc3, filename='fc2.hdf5')
write_fc3_to_hdf5(fc3, filename='fc3.hdf5')
show_drift_fc3(fc3)
show_drift_force_constants(fc2, name='fc2')
# Use NAC if available
use_nac = False
if 'nac_data' in wc.get_outputs():
primitive = phono3py.get_phonon_primitive()
nac_params = wc.out.nac_data.get_born_parameters_phonopy(primitive_cell=primitive.get_cell())
phono3py.set_phph_interaction(nac_params=nac_params)
phono3py.run_thermal_conductivity(temperatures=range(0, 1001, 10),
boundary_mfp=1e6, # This is to avoid divergence of phonon life time.
write_kappa=True)
def store_force_constants(
phono3py,
settings,
ph3py_yaml,
input_filename,
output_filename,
load_phono3py_yaml,
log_level,
):
"""Calculate, read, and write force constants."""
if load_phono3py_yaml:
if log_level:
print("-" * 29 + " Force constants " + "-" * 30)
(fc_calculator,
fc_calculator_options) = get_fc_calculator_params(settings)
read_fc = set_dataset_and_force_constants(
phono3py,
ph3py_yaml=ph3py_yaml,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options,
symmetrize_fc=settings.fc_symmetry,
is_compact_fc=settings.is_compact_fc,
cutoff_pair_distance=settings.cutoff_pair_distance,
log_level=log_level,
)
if log_level:
if phono3py.fc3 is None:
print("fc3 could not be obtained.")
if phono3py.fc2 is None:
print("fc2 could not be obtained.")
if phono3py.fc3 is None or phono3py.fc2 is None:
print_error()
sys.exit(1)
if not read_fc["fc3"]:
write_fc3_to_hdf5(
phono3py.fc3,
p2s_map=phono3py.primitive.p2s_map,
compression=settings.hdf5_compression,
)
if log_level:
print('fc3 was written into "fc3.hdf5".')
if not read_fc["fc2"]:
write_fc2_to_hdf5(
phono3py.fc2,
p2s_map=phono3py.primitive.p2s_map,
physical_unit="eV/angstrom^2",
compression=settings.hdf5_compression,
)
if log_level:
print('fc2 was written into "fc2.hdf5".')
else:
create_phono3py_force_constants(
phono3py,
settings,
ph3py_yaml=ph3py_yaml,
input_filename=input_filename,
output_filename=output_filename,
log_level=log_level,
)