def _read_disp_fc_yaml(disp_filename, fc_type):
if fc_type == "phonon_fc2":
dataset = parse_disp_fc2_yaml(filename=disp_filename)
else:
dataset = parse_disp_fc3_yaml(filename=disp_filename)
return dataset
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_phonon_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_FC2", log_level)
natom = phono3py.phonon_supercell.get_number_of_atoms()
disp_dataset = _get_type2_dataset(natom, filename="FORCES_FC2")
if disp_dataset:
if log_level:
print("%d snapshots were found in %s." %
(len(disp_dataset['displacements']), "FORCES_FC2"))
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_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 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_FC2")
# forces are stored in disp_dataset.
parse_FORCES_FC2(disp_dataset, 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_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_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_FORCES_FC3_and_FORCES_FC2_then_exit(settings, input_filename,
output_filename, log_level):
interface_mode = settings.calculator
#####################
# Create FORCES_FC3 #
#####################
if settings.create_forces_fc3 or settings.create_forces_fc3_file:
if input_filename is None:
disp_fc3_filename = 'disp_fc3.yaml'
else:
disp_fc3_filename = 'disp_fc3.' + input_filename + '.yaml'
ph3py_yaml = None
disp_filenames = files_exist(['phono3py_disp.yaml', disp_fc3_filename],
log_level,
is_any=True)
if disp_filenames[0] == 'phono3py_disp.yaml':
try:
ph3py_yaml = Phono3pyYaml()
ph3py_yaml.read('phono3py_disp.yaml')
if ph3py_yaml.calculator is not None:
interface_mode = ph3py_yaml.calculator # overwrite
disp_filename = 'phono3py_disp.yaml'
except KeyError:
file_exists('disp_fc3.yaml', log_level)
if log_level > 0:
print("\"phono3py_disp.yaml\" was found but wasn't used.")
disp_filename = disp_fc3_filename
else:
disp_filename = disp_filenames[0]
if ph3py_yaml is None:
file_exists(disp_filename, log_level)
disp_dataset = parse_disp_fc3_yaml(filename=disp_filename)
else:
disp_dataset = ph3py_yaml.dataset
if log_level:
print('')
print("Displacement dataset was read from \"%s\"." % disp_filename)
num_atoms = disp_dataset['natom']
num_disps = len(disp_dataset['first_atoms'])
for d1 in disp_dataset['first_atoms']:
for d2 in d1['second_atoms']:
if 'included' not in d2 or d2['included']:
num_disps += 1
if settings.create_forces_fc3_file:
file_exists(settings.create_forces_fc3_file, log_level)
force_filenames = [
x.strip() for x in open(settings.create_forces_fc3_file)
]
else:
force_filenames = settings.create_forces_fc3
for filename in force_filenames:
file_exists(filename, log_level)
if log_level > 0:
print("Number of displacements: %d" % num_disps)
print("Number of supercell files: %d" % len(force_filenames))
if not check_number_of_force_files(num_disps, force_filenames,
disp_filename):
force_sets = []
else:
force_sets = get_force_sets(interface_mode,
num_atoms,
num_disps,
force_filenames,
disp_filename=disp_filename,
verbose=(log_level > 0))
if settings.subtract_forces:
force_filename = settings.subtract_forces
file_exists(force_filename, log_level)
force_set_zero = get_force_sets(interface_mode,
num_atoms,
1, [
force_filename,
],
verbose=(log_level > 0))[0]
for fs in force_sets:
fs -= force_set_zero
if log_level > 0:
print(
"Forces in \'%s\' were subtracted from supercell forces." %
force_filename)
if force_sets:
write_FORCES_FC3(disp_dataset, force_sets, filename="FORCES_FC3")
if log_level:
print("")
print("%s has been created." % "FORCES_FC3")
print_end()
sys.exit(0)
else:
if log_level:
print("")
print("%s could not be created." % "FORCES_FC3")
print_error()
sys.exit(1)
#####################
# Create FORCES_FC2 #
#####################
if settings.create_forces_fc2:
if input_filename is None:
disp_filename = 'disp_fc2.yaml'
else:
disp_filename = 'disp_fc2.' + input_filename + '.yaml'
file_exists(disp_filename, log_level)
disp_dataset = parse_disp_fc2_yaml(filename=disp_filename)
if log_level:
print("Displacement dataset was read from \"%s\"." % disp_filename)
num_atoms = disp_dataset['natom']
num_disps = len(disp_dataset['first_atoms'])
force_filenames = settings.create_forces_fc2
for filename in force_filenames:
file_exists(filename, log_level)
if log_level > 0:
print("Number of displacements: %d" % num_disps)
print("Number of supercell files: %d" % len(force_filenames))
force_sets = get_force_sets(interface_mode,
num_atoms,
num_disps,
force_filenames,
disp_filename,
verbose=(log_level > 0))
if settings.subtract_forces:
force_filename = settings.subtract_forces
file_exists(force_filename, log_level)
force_set_zero = get_force_sets(interface_mode,
num_atoms,
1, [
force_filename,
],
verbose=(log_level > 0))[0]
for fs in force_sets:
fs -= force_set_zero
if log_level > 0:
print(
"Forces in \'%s\' were subtracted from supercell forces." %
force_filename)
if force_sets:
write_FORCES_FC2(disp_dataset,
forces_fc2=force_sets,
filename="FORCES_FC2")
if log_level:
print("")
print("%s has been created." % "FORCES_FC2")
print_end()
sys.exit(0)
else:
if log_level:
print("")
print("%s could not be created." % "FORCES_FC2")
print_error()
sys.exit(1)
def create_FORCES_FC3_and_FORCES_FC2_then_exit(settings, input_filename,
log_level):
"""Create FORCES_FC3 and FORCES_FC2 from files."""
interface_mode = settings.calculator
ph3py_yaml = None
#####################
# Create FORCES_FC3 #
#####################
if settings.create_forces_fc3 or settings.create_forces_fc3_file:
if input_filename is None:
disp_fc3_filename = "disp_fc3.yaml"
else:
disp_fc3_filename = "disp_fc3." + input_filename + ".yaml"
disp_filenames = files_exist(["phono3py_disp.yaml", disp_fc3_filename],
log_level,
is_any=True)
disp_filename = disp_filenames[0]
if "phono3py_disp.yaml" in disp_filename:
ph3py_yaml = Phono3pyYaml()
ph3py_yaml.read(disp_filename)
if ph3py_yaml.calculator is not None:
interface_mode = ph3py_yaml.calculator # overwrite
disp_dataset = ph3py_yaml.dataset
else:
file_exists(disp_filename, log_level)
disp_dataset = parse_disp_fc3_yaml(filename=disp_filename)
if log_level:
print("")
print('Displacement dataset was read from "%s".' % disp_filename)
num_atoms = disp_dataset["natom"]
num_disps = len(disp_dataset["first_atoms"])
for d1 in disp_dataset["first_atoms"]:
for d2 in d1["second_atoms"]:
if "included" not in d2 or d2["included"]:
num_disps += 1
if settings.create_forces_fc3_file:
file_exists(settings.create_forces_fc3_file, log_level)
force_filenames = [
x.strip() for x in open(settings.create_forces_fc3_file)
]
else:
force_filenames = settings.create_forces_fc3
for filename in force_filenames:
file_exists(filename, log_level)
if log_level > 0:
print("Number of displacements: %d" % num_disps)
print("Number of supercell files: %d" % len(force_filenames))
if not check_number_of_force_files(num_disps, force_filenames,
disp_filename):
force_sets = []
else:
force_sets = get_force_sets(
interface_mode,
num_atoms,
force_filenames,
verbose=(log_level > 0),
)
if settings.subtract_forces:
force_filename = settings.subtract_forces
file_exists(force_filename, log_level)
force_set_zero = get_force_sets(
interface_mode,
num_atoms,
[
force_filename,
],
verbose=(log_level > 0),
)[0]
for fs in force_sets:
fs -= force_set_zero
if log_level > 0:
print("Forces in '%s' were subtracted from supercell forces." %
force_filename)
if force_sets:
write_FORCES_FC3(disp_dataset,
forces_fc3=force_sets,
filename="FORCES_FC3")
if log_level:
print("")
print("%s has been created." % "FORCES_FC3")
print_end()
sys.exit(0)
else:
if log_level:
print("")
print("%s could not be created." % "FORCES_FC3")
print_error()
sys.exit(1)
#####################
# Create FORCES_FC2 #
#####################
if settings.create_forces_fc2:
if input_filename is None:
disp_fc2_filename = "disp_fc2.yaml"
else:
disp_fc2_filename = "disp_fc2." + input_filename + ".yaml"
disp_filenames = files_exist(["phono3py_disp.yaml", disp_fc2_filename],
log_level,
is_any=True)
if "phono3py_disp.yaml" in disp_filenames[0]:
# ph3py_yaml is not None, phono3py_disp.yaml is already read.
if ph3py_yaml is None:
disp_filename = disp_filenames[0]
ph3py_yaml = Phono3pyYaml()
ph3py_yaml.read(disp_filename)
if ph3py_yaml.calculator is not None:
interface_mode = ph3py_yaml.calculator # overwrite
disp_dataset = ph3py_yaml.phonon_dataset
else:
disp_filename = disp_filenames[0]
file_exists(disp_filename, log_level)
disp_dataset = parse_disp_fc2_yaml(filename=disp_filename)
if log_level:
print('Displacement dataset was read from "%s".' % disp_filename)
num_atoms = disp_dataset["natom"]
num_disps = len(disp_dataset["first_atoms"])
force_filenames = settings.create_forces_fc2
for filename in force_filenames:
file_exists(filename, log_level)
if log_level > 0:
print("Number of displacements: %d" % num_disps)
print("Number of supercell files: %d" % len(force_filenames))
force_sets = get_force_sets(
interface_mode,
num_atoms,
force_filenames,
verbose=(log_level > 0),
)
if settings.subtract_forces:
force_filename = settings.subtract_forces
file_exists(force_filename, log_level)
force_set_zero = get_force_sets(
interface_mode,
num_atoms,
[
force_filename,
],
verbose=(log_level > 0),
)[0]
for fs in force_sets:
fs -= force_set_zero
if log_level > 0:
print("Forces in '%s' were subtracted from supercell forces." %
force_filename)
if force_sets:
write_FORCES_FC2(disp_dataset,
forces_fc2=force_sets,
filename="FORCES_FC2")
if log_level:
print("")
print("%s has been created." % "FORCES_FC2")
print_end()
sys.exit(0)
else:
if log_level:
print("")
print("%s could not be created." % "FORCES_FC2")
print_error()
sys.exit(1)
