def _get_delta_fc3(dataset_first_atom, fc3, supercell, reduced_site_sym,
translational_symmetry_type, is_permutation_symmetry,
symprec, verbose):
disp_fc3 = _get_constrained_fc3(supercell, dataset_first_atom,
reduced_site_sym,
translational_symmetry_type,
is_permutation_symmetry, symprec, verbose)
if verbose:
show_drift_fc3(disp_fc3, name="delta fc3")
return disp_fc3 - fc3
def _get_delta_fc3(dataset_first_atom,
fc3,
supercell,
reduced_site_sym,
is_translational_symmetry,
is_permutation_symmetry,
symprec,
verbose):
disp_fc3 = _get_constrained_fc3(supercell,
dataset_first_atom,
reduced_site_sym,
is_translational_symmetry,
is_permutation_symmetry,
symprec,
verbose)
if verbose:
show_drift_fc3(disp_fc3, name="fc3 with disp.")
return disp_fc3 - fc3
def create_phono3py_force_constants(phono3py,
phonon_supercell_matrix,
settings,
energy_to_eV=None,
distance_to_A=None,
input_filename=None,
output_filename=None,
log_level=1):
read_fc3 = settings.get_read_fc3()
read_fc2 = settings.get_read_fc2()
symmetrize_fc3_r = settings.get_is_symmetrize_fc3_r()
symmetrize_fc3_q = settings.get_is_symmetrize_fc3_q()
symmetrize_fc2 = settings.get_is_symmetrize_fc2()
if settings.get_is_translational_symmetry():
tsym_type = 1
elif settings.get_tsym_type() > 0:
tsym_type = settings.get_tsym_type()
else:
tsym_type = 0
if log_level:
show_phono3py_force_constants_settings(read_fc3, read_fc2, tsym_type,
symmetrize_fc3_r,
symmetrize_fc3_q,
symmetrize_fc2, settings)
# fc3
if (settings.get_is_joint_dos()
or (settings.get_is_isotope()
and not (settings.get_is_bterta() or settings.get_is_lbte()))
or settings.get_read_gamma() or settings.get_read_amplitude()
or settings.get_constant_averaged_pp_interaction() is not None):
pass
else:
if read_fc3: # Read fc3.hdf5
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)
fc3 = read_fc3_from_hdf5(filename=filename)
num_atom = phono3py.get_supercell().get_number_of_atoms()
if fc3.shape[0] != num_atom:
print("Matrix shape of fc3 doesn't agree with supercell size.")
if log_level:
print_error()
sys.exit(1)
phono3py.set_fc3(fc3)
else: # fc3 from FORCES_FC3
if not _create_phono3py_fc3(
phono3py, energy_to_eV, distance_to_A, tsym_type,
symmetrize_fc3_r, symmetrize_fc2,
settings.get_cutoff_fc3_distance(), input_filename,
output_filename, log_level):
print("fc3 was not created properly.")
if log_level:
print_error()
sys.exit(1)
if log_level:
show_drift_fc3(phono3py.get_fc3())
# fc2
if read_fc2:
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.get_phonon_supercell().get_number_of_atoms()
phonon_fc2 = read_fc2_from_hdf5(filename=filename)
if phonon_fc2.shape[0] != num_atom:
print("Matrix shape of fc2 doesn't agree with supercell size.")
if log_level:
print_error()
sys.exit(1)
phono3py.set_fc2(phonon_fc2)
else:
if log_level:
print("Solving fc2")
if phonon_supercell_matrix is None:
if phono3py.get_fc2() is None:
if not _create_phono3py_fc2(
phono3py, energy_to_eV, distance_to_A, tsym_type,
symmetrize_fc2, input_filename, log_level):
print("fc2 was not created properly.")
if log_level:
print_error()
sys.exit(1)
else:
if not _create_phono3py_phonon_fc2(
phono3py, energy_to_eV, distance_to_A, tsym_type,
symmetrize_fc2, input_filename, log_level):
print("fc2 was not created properly.")
if log_level:
print_error()
sys.exit(1)
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.get_fc2(), filename=filename)
if log_level:
show_drift_force_constants(phono3py.get_fc2(), name='fc2')
def create_phono3py_force_constants(phono3py, phonon_supercell_matrix,
settings, read_fc3, read_fc2, tsym_type,
symmetrize_fc3_r, symmetrize_fc3_q,
symmetrize_fc2, input_filename,
output_filename, log_level):
if log_level:
show_phono3py_force_constants_settings(read_fc3, read_fc2, tsym_type,
symmetrize_fc3_r,
symmetrize_fc3_q,
symmetrize_fc2, settings)
# fc3
if (settings.get_is_joint_dos()
or (settings.get_is_isotope()
and not (settings.get_is_bterta() or settings.get_is_lbte()))
or settings.get_read_gamma() or settings.get_read_amplitude()
or settings.get_constant_averaged_pp_interaction() is not None):
pass
else:
if read_fc3: # Read fc3.hdf5
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)
fc3 = read_fc3_from_hdf5(filename=filename)
phono3py.set_fc3(fc3)
else: # fc3 from FORCES_THIRD and FORCES_SECOND
_create_phono3py_fc3(phono3py, tsym_type, symmetrize_fc3_r,
symmetrize_fc2,
settings.get_cutoff_fc3_distance(),
input_filename, output_filename, log_level)
if log_level:
show_drift_fc3(phono3py.get_fc3())
# fc2
if read_fc2:
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)
phonon_supercell = phono3py.get_phonon_supercell()
phonon_fc2 = read_fc2_from_hdf5(filename=filename)
if phonon_fc2.shape[0] != phonon_supercell.get_number_of_atoms():
print("Matrix shape of fc2 doesn't agree with supercell.")
if log_level:
print_error()
sys.exit(1)
phono3py.set_fc2(phonon_fc2)
else:
if log_level:
print("Solving fc2")
if phonon_supercell_matrix is None:
if phono3py.get_fc2() is None:
_create_phono3py_fc2(phono3py, tsym_type, symmetrize_fc2,
input_filename, log_level)
else:
_create_phono3py_phonon_fc2(phono3py, tsym_type, symmetrize_fc2,
input_filename, 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.get_fc2(), filename=filename)
if log_level:
show_drift_force_constants(phono3py.get_fc2(), name='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),
write_kappa=True)
# Conductivity_RTA object (https://git.io/vVRUW)
cond_rta = phono3py.get_thermal_conductivity()
# # 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),
write_kappa=True)
# Conductivity_RTA object (https://git.io/vVRUW)
cond_rta = phono3py.get_thermal_conductivity()
def create_phono3py_force_constants(phono3py,
phonon_supercell_matrix,
settings,
energy_to_eV=None,
distance_to_A=None,
input_filename=None,
output_filename=None,
log_level=1):
read_fc3 = settings.get_read_fc3()
read_fc2 = settings.get_read_fc2()
symmetrize_fc3_r = settings.get_is_symmetrize_fc3_r()
symmetrize_fc3_q = settings.get_is_symmetrize_fc3_q()
symmetrize_fc2 = settings.get_is_symmetrize_fc2()
if settings.get_is_translational_symmetry():
tsym_type = 1
elif settings.get_tsym_type() > 0:
tsym_type = settings.get_tsym_type()
else:
tsym_type = 0
if log_level:
show_phono3py_force_constants_settings(read_fc3,
read_fc2,
tsym_type,
symmetrize_fc3_r,
symmetrize_fc3_q,
symmetrize_fc2,
settings)
# fc3
if (settings.get_is_joint_dos() or
(settings.get_is_isotope() and
not (settings.get_is_bterta() or settings.get_is_lbte())) or
settings.get_read_gamma() or
settings.get_read_amplitude() or
settings.get_constant_averaged_pp_interaction() is not None):
pass
else:
if read_fc3: # Read fc3.hdf5
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)
fc3 = read_fc3_from_hdf5(filename=filename)
num_atom = phono3py.get_supercell().get_number_of_atoms()
if fc3.shape[0] != num_atom:
print("Matrix shape of fc3 doesn't agree with supercell size.")
if log_level:
print_error()
sys.exit(1)
phono3py.set_fc3(fc3)
else: # fc3 from FORCES_FC3
if not _create_phono3py_fc3(phono3py,
energy_to_eV,
distance_to_A,
tsym_type,
symmetrize_fc3_r,
symmetrize_fc2,
settings.get_cutoff_fc3_distance(),
input_filename,
output_filename,
log_level):
print("fc3 was not created properly.")
if log_level:
print_error()
sys.exit(1)
if log_level:
show_drift_fc3(phono3py.get_fc3())
# fc2
if read_fc2:
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.get_phonon_supercell().get_number_of_atoms()
phonon_fc2 = read_fc2_from_hdf5(filename=filename)
if phonon_fc2.shape[0] != num_atom:
print("Matrix shape of fc2 doesn't agree with supercell size.")
if log_level:
print_error()
sys.exit(1)
phono3py.set_fc2(phonon_fc2)
else:
if log_level:
print("Solving fc2")
if phonon_supercell_matrix is None:
if phono3py.get_fc2() is None:
if not _create_phono3py_fc2(phono3py,
energy_to_eV,
distance_to_A,
tsym_type,
symmetrize_fc2,
input_filename,
log_level):
print("fc2 was not created properly.")
if log_level:
print_error()
sys.exit(1)
else:
if not _create_phono3py_phonon_fc2(phono3py,
energy_to_eV,
distance_to_A,
tsym_type,
symmetrize_fc2,
input_filename,
log_level):
print("fc2 was not created properly.")
if log_level:
print_error()
sys.exit(1)
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.get_fc2(), filename=filename)
if log_level:
show_drift_force_constants(phono3py.get_fc2(), name='fc2')