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.primitive.p2s_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.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.fc3 = fc3
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.fc2 = phonon_fc2
def read_phono3py_settings(args, argparse_control, log_level):
"""Read phono3py settings"""
load_phono3py_yaml = argparse_control.get('load_phono3py_yaml', False)
if len(args.filename) > 0:
file_exists(args.filename[0], log_level)
if load_phono3py_yaml:
phono3py_conf_parser = Phono3pyConfParser(
args=args, default_settings=argparse_control)
cell_filename = args.filename[0]
else:
if is_file_phonopy_yaml(args.filename[0], keyword='phono3py'):
phono3py_conf_parser = Phono3pyConfParser(args=args)
cell_filename = args.filename[0]
else:
phono3py_conf_parser = Phono3pyConfParser(
filename=args.filename[0], args=args)
cell_filename = phono3py_conf_parser.settings.cell_filename
else:
phono3py_conf_parser = Phono3pyConfParser(args=args)
cell_filename = phono3py_conf_parser.settings.cell_filename
confs = phono3py_conf_parser.confs.copy()
settings = phono3py_conf_parser.settings
return settings, confs, cell_filename
def _create_phono3py_phonon_fc2(phono3py, ph3py_yaml, 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'
_ph3py_yaml = _get_ph3py_yaml(disp_filename, ph3py_yaml)
try:
dataset = parse_forces(phono3py,
ph3py_yaml=_ph3py_yaml,
force_filename="FORCES_FC2",
disp_filename=disp_filename,
fc_type='phonon_fc2',
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.phonon_dataset = dataset
phono3py.produce_fc2(symmetrize_fc2=symmetrize_fc2,
is_compact_fc=is_compact_fc,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options)
def _create_phono3py_fc3(
phono3py,
ph3py_yaml,
symmetrize_fc3r,
input_filename,
is_compact_fc,
cutoff_pair_distance,
fc_calculator,
fc_calculator_options,
log_level,
):
"""Read or calculate fc3.
Note
----
cutoff_pair_distance is the parameter to determine each displaced
supercell is included to the computation of fc3. It is assumed that
cutoff_pair_distance is stored in the step to create sets of
displacements and the value is stored n the displacement dataset and
also as the parameter 'included': True or False for each displacement.
The parameter cutoff_pair_distance here can be used in the step to
create fc3 by overwriting original cutoff_pair_distance value only
when the former value is smaller than the later.
"""
if input_filename is None:
disp_filename = "disp_fc3.yaml"
else:
disp_filename = "disp_fc3." + input_filename + ".yaml"
_ph3py_yaml = _get_ph3py_yaml(disp_filename, ph3py_yaml)
try:
dataset = parse_forces(
phono3py,
ph3py_yaml=_ph3py_yaml,
cutoff_pair_distance=cutoff_pair_distance,
force_filename="FORCES_FC3",
disp_filename=disp_filename,
fc_type="fc3",
log_level=log_level,
)
except RuntimeError as e:
# from _parse_forces_type1
if log_level:
print(str(e))
print_error()
sys.exit(1)
except FileNotFoundError as e:
# from _get_type2_dataset
file_exists(e.filename, log_level)
phono3py.dataset = dataset
phono3py.produce_fc3(
symmetrize_fc3r=symmetrize_fc3r,
is_compact_fc=is_compact_fc,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options,
)
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 create_FORCES_FC2_from_FORCE_SETS_then_exit(log_level):
filename = 'FORCE_SETS'
file_exists(filename, log_level)
disp_dataset = parse_FORCE_SETS(filename=filename)
write_FORCES_FC2(disp_dataset)
write_disp_fc2_yaml(disp_dataset, None)
if log_level:
print("FORCES_FC2 and disp_fc2.yaml have been created from "
"FORCE_SETS.")
print_end()
sys.exit(0)
def read_phono3py_settings(args, argparse_control, log_level):
"""Read phono3py settings.
From:
* Traditional configuration file.
* phono3py.yaml type file
* Command line options
"""
load_phono3py_yaml = argparse_control.get("load_phono3py_yaml", False)
if len(args.filename) > 0:
file_exists(args.filename[0], log_level)
if load_phono3py_yaml:
phono3py_conf_parser = Phono3pyConfParser(
filename=args.conf_filename,
args=args,
default_settings=argparse_control,
)
cell_filename = args.filename[0]
else:
if is_file_phonopy_yaml(args.filename[0], keyword="phono3py"):
phono3py_conf_parser = Phono3pyConfParser(
args=args, default_settings=argparse_control)
cell_filename = args.filename[0]
else:
phono3py_conf_parser = Phono3pyConfParser(
filename=args.filename[0],
args=args,
default_settings=argparse_control,
)
cell_filename = phono3py_conf_parser.settings.cell_filename
else:
if load_phono3py_yaml:
phono3py_conf_parser = Phono3pyConfParser(
args=args,
filename=args.conf_filename,
default_settings=argparse_control,
)
else:
phono3py_conf_parser = Phono3pyConfParser(
args=args, default_settings=argparse_control)
cell_filename = phono3py_conf_parser.settings.cell_filename
confs_dict = phono3py_conf_parser.confs.copy()
settings = phono3py_conf_parser.settings
return settings, confs_dict, cell_filename
def create_FORCES_FC2_from_FORCE_SETS_then_exit(log_level):
"""Convert FORCE_SETS to FORCES_FC2."""
filename = "FORCE_SETS"
file_exists(filename, log_level)
disp_dataset = parse_FORCE_SETS(filename=filename)
write_FORCES_FC2(disp_dataset)
if log_level:
print("")
print("FORCES_FC2 has been created from FORCE_SETS.")
print("The following yaml lines should replace respective part of")
print("phono3py_disp.yaml made with --dim-fc2=dim_of_FORCE_SETS.")
print("")
print("\n".join(displacements_yaml_lines_type1(disp_dataset)))
if log_level:
print_end()
sys.exit(0)
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)
