def parse_forces(natom,
force_to_eVperA,
distance_to_A,
cutoff_pair_distance=None,
force_filename="FORCES_FC3",
disp_filename=None,
is_fc2=False,
log_level=0):
disp_dataset = _get_type2_dataset(natom, filename=force_filename)
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 log_level:
print("Displacement dataset for %s is read from \"%s\"." %
("fc2" if is_fc2 else "fc3", disp_filename))
if is_fc2:
disp_dataset = parse_disp_fc2_yaml(filename=disp_filename)
else:
disp_dataset = parse_disp_fc3_yaml(filename=disp_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)
if disp_dataset['natom'] != natom:
msg = ("Number of atoms in supercell is not consistent with "
"\"%s\"." % disp_filename)
raise RuntimeError(msg)
_convert_displacement_unit(disp_dataset, distance_to_A, is_fc2=is_fc2)
if log_level:
print("Sets of supercell forces are read from \"%s\"." %
force_filename)
sys.stdout.flush()
# forces are stored in disp_dataset.
if is_fc2:
parse_FORCES_FC2(disp_dataset,
filename=force_filename,
unit_conversion_factor=force_to_eVperA)
else:
parse_FORCES_FC3(disp_dataset,
filename=force_filename,
unit_conversion_factor=force_to_eVperA)
return disp_dataset
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_supercells_with_displacements(phono3py):
phono3py.generate_displacements(distance=0.03)
scells_with_disps = phono3py.get_supercells_with_displacements()
# from phonopy.interface.vasp import write_vasp
# for i, scell in enumerate(scells_with_disps):
# write_vasp("POSCAR-%05d" % (i + 1), scell)
# # print(scell)
# A dataset of displacements. The dictionary format is shown at
# phono3py.phonon3.displacement_fc3.get_third_order_displacements.
print("Displacement sets")
disp_dataset = phono3py.get_displacement_dataset()
count = 0
for i, disp1 in enumerate(disp_dataset['first_atoms']):
print("%4d: %4d %s" % (
count + 1,
disp1['number'] + 1,
np.around(disp1['displacement'], decimals=3)))
count += 1
distances = []
for i, disp1 in enumerate(disp_dataset['first_atoms']):
for j, disp2 in enumerate(disp1['second_atoms']):
print("%4d: %4d-%4d (%6.3f) %s %s" % (
count + 1,
disp1['number'] + 1,
disp2['number'] + 1,
disp2['pair_distance'],
np.around(disp1['displacement'], decimals=3),
np.around(disp2['displacement'], decimals=3)))
distances.append(disp2['pair_distance'])
count += 1
# Find unique pair distances
distances = np.array(distances)
distances_int = (distances * 1e5).astype(int)
unique_distances = np.unique(distances_int) * 1e-5 # up to 5 decimals
print("Unique pair distances")
print(unique_distances)
# FORCES_FC3 is created as follows:
from phono3py.file_IO import write_FORCES_FC3
# force_sets is a simple force array:
# [len(scells_with_disps), num_supercell_atoms, 3].
force_sets = parse_FORCES_FC3(disp_dataset, filename="FORCES_FC3")
write_FORCES_FC3(disp_dataset, force_sets, filename="FORCES_FC3_new")
def run_thermal_conductivity(phono3py):
# 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,
# is_translational_symmetry=True,
# is_permutation_symmetry=True)
# # Read fc3 and fc2 from c3.hdf5 and fc2.hdf5
# fc3 = read_fc3_from_hdf5(filename="fc3.hdf5")
# fc2 = read_fc2_from_hdf5(filename="fc2.hdf5")
# phono3py.set_fc3(fc3)
# phono3py.set_fc2(fc2)
show_drift_fc3(fc3)
show_drift_force_constants(fc2, name='fc2')
# # For special cases like NAC
# primitive = phono3py.get_phonon_primitive()
# nac_params = parse_BORN(primitive, filename="BORN")
# nac_params['factor'] = Hartree * Bohr
# 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)
# Conductivity_RTA object (https://git.io/vVRUW)
cond_rta = phono3py.get_thermal_conductivity()
def create_supercells_with_displacements(phono3py):
phono3py.generate_displacements(distance=0.03)
scells_with_disps = phono3py.get_supercells_with_displacements()
print(len(scells_with_disps))
# from phonopy.interface.vasp import write_vasp
# for i, scell in enumerate(scells_with_disps):
# write_vasp("POSCAR-%05d" % (i + 1), scell)
# # print(scell)
# A dataset of displacements. The dictionary format is shown at
# phono3py.phonon3.displacement_fc3.get_third_order_displacements.
disp_dataset = phono3py.get_displacement_dataset()
# FORCES_FC3 is created as follows:
from phono3py.file_IO import write_FORCES_FC3
# force_sets is a simple force array:
# [len(scells_with_disps), num_supercell_atoms, 3].
force_sets = parse_FORCES_FC3(disp_dataset, filename="FORCES_FC3")
write_FORCES_FC3(disp_dataset, force_sets, filename="FORCES_FC3_new")
def parse_forces(
phono3py,
ph3py_yaml=None,
cutoff_pair_distance=None,
force_filename="FORCES_FC3",
disp_filename=None,
fc_type=None,
log_level=0,
):
"""Read displacements and forces."""
filename_read_from = None
if fc_type == "phonon_fc2":
natom = len(phono3py.phonon_supercell)
else:
natom = len(phono3py.supercell)
# Get dataset from ph3py_yaml. dataset can be None.
dataset = _extract_datast_from_ph3py_yaml(ph3py_yaml, fc_type)
if dataset:
filename_read_from = ph3py_yaml.yaml_filename
# Try to read FORCES_FC* if type-2 and return dataset.
# None is returned unless type-2.
# can emit FileNotFoundError.
if dataset is None or dataset is not None and not forces_in_dataset(
dataset):
_dataset = _get_type2_dataset(natom,
phono3py.calculator,
filename=force_filename,
log_level=log_level)
# Do not overwrite dataset when _dataset is None.
if _dataset:
filename_read_from = force_filename
dataset = _dataset
if dataset is None:
# Displacement dataset is obtained from disp_filename.
# can emit FileNotFoundError.
dataset = _read_disp_fc_yaml(disp_filename, fc_type)
filename_read_from = disp_filename
if "natom" in dataset and dataset["natom"] != natom:
msg = ("Number of atoms in supercell is not consistent with "
'"%s".' % filename_read_from)
raise RuntimeError(msg)
if log_level and filename_read_from is not None:
print('Displacement dataset for %s was read from "%s".' %
(fc_type, filename_read_from))
# Overwrite dataset['cutoff_distance'] when necessary.
if cutoff_pair_distance:
if "cutoff_distance" not in dataset or (
"cutoff_distance" in dataset
and cutoff_pair_distance < dataset["cutoff_distance"]):
dataset["cutoff_distance"] = cutoff_pair_distance
if log_level:
print("Cutoff-pair-distance: %f" % cutoff_pair_distance)
# Type-1 FORCES_FC*.
# dataset comes either from disp_fc*.yaml or phono3py*.yaml.
if not forces_in_dataset(dataset):
if fc_type == "phonon_fc2":
parse_FORCES_FC2(dataset, filename=force_filename)
else:
parse_FORCES_FC3(dataset, filename=force_filename)
if log_level:
print('Sets of supercell forces were read from "%s".' %
force_filename)
sys.stdout.flush()
_convert_unit_in_dataset(dataset, phono3py.calculator)
return dataset
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