def create_FORCE_SETS_from_FORCES_FCx_then_exit(phonon_smat,
input_filename: Optional[str],
cell_filename: Optional[str],
log_level):
"""Convert FORCES_FC3 or FORCES_FC2 to FORCE_SETS."""
if cell_filename is not None:
disp_filename = cell_filename
elif input_filename is None:
disp_filename = "phono3py_disp.yaml"
else:
disp_filename = f"phono3py_disp.{input_filename}.yaml"
if phonon_smat is not None:
forces_filename = "FORCES_FC2"
else:
forces_filename = "FORCES_FC3"
if log_level:
print(f'Displacement dataset is read from "{disp_filename}".')
print(f'Forces are read from "{forces_filename}"')
with open(forces_filename, "r") as f:
len_first_line = get_length_of_first_line(f)
if len_first_line == 3:
file_exists(disp_filename, log_level)
file_exists(forces_filename, log_level)
ph3yml = Phono3pyYaml()
ph3yml.read(disp_filename)
if phonon_smat is None:
dataset = copy.deepcopy(ph3yml.dataset)
smat = ph3yml.supercell_matrix
else:
dataset = copy.deepcopy(ph3yml.phonon_dataset)
smat = ph3yml.phonon_supercell_matrix
if smat is None or (phonon_smat is not None and
(phonon_smat != smat).any()):
if log_level:
print("")
print("Supercell matrix is inconsistent.")
print(f'Supercell matrix read from "{disp_filename}":')
print(smat)
print("Supercell matrix given by --dim-fc2:")
print(phonon_smat)
print_error()
sys.exit(1)
parse_FORCES_FC2(dataset, filename=forces_filename)
write_FORCE_SETS(dataset)
if log_level:
print("FORCE_SETS has been created.")
print_end()
else:
if log_level:
print("The file format of %s is already readable by phonopy." %
forces_filename)
print_end()
sys.exit(0)
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_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_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_FORCE_SETS_from_FORCES_FCx_then_exit(phonon_smat, input_filename,
log_level):
if phonon_smat is not None:
if input_filename is None:
disp_filename = 'disp_fc2.yaml'
else:
disp_filename = 'disp_fc2.' + input_filename + '.yaml'
forces_filename = "FORCES_FC2"
else:
if input_filename is None:
disp_filename = 'disp_fc3.yaml'
else:
disp_filename = 'disp_fc3.' + input_filename + '.yaml'
forces_filename = "FORCES_FC3"
with open(forces_filename, 'r') as f:
len_first_line = get_length_of_first_line(f)
if len_first_line == 3:
file_exists(disp_filename, log_level)
disp_dataset = parse_disp_fc2_yaml(filename=disp_filename)
file_exists(forces_filename, log_level)
parse_FORCES_FC2(disp_dataset, filename=forces_filename)
if log_level:
print("Displacement dataset was read from \"%s\"." % disp_filename)
write_FORCE_SETS(disp_dataset)
if log_level:
print("FORCE_SETS has been created.")
print_end()
else:
if log_level:
print("The file format of %s is already readable by phonopy." %
forces_filename)
print_end()
sys.exit(0)
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 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