def __init__(self, filename=None, args=None):
self._settings = Phono3pySettings()
if filename is not None:
ConfParser.__init__(self, filename=filename)
self.parse_conf() # self.parameters[key] = val
self._parse_conf()
self._set_settings()
if args is not None:
ConfParser.__init__(self, args=args)
self.read_options() # store data in self._confs
self._read_options()
self.parse_conf() # self.parameters[key] = val
self._parse_conf()
self._set_settings()
def _set_settings(self):
ConfParser.set_settings(self)
params = self._parameters
# Supercell size for fc2
if params.has_key('dim_extra'):
self._settings.set_supercell_matrix_extra(params['dim_extra'])
# Sets of band indices that are summed
if params.has_key('band_indices'):
self._settings.set_band_indices(params['band_indices'])
if params.has_key('mesh_shift'):
self._settings.set_mesh_shift(params['mesh_shift'])
# Grid points
if params.has_key('grid_points'):
self._settings.set_grid_points(params['grid_points'])
# Calculate thermal conductivity in BTE-RTA
if params.has_key('is_bterta'):
self._settings.set_is_bterta(params['is_bterta'])
# Calculate linewidths
if params.has_key('is_linewidth'):
self._settings.set_is_linewidth(params['is_linewidth'])
# Tell Normal and Umklapp process apart
if params.has_key("read_fc2"):
self._settings.set_read_fc2(params['read_fc2'])
if params.has_key("read_fc2_extra"):
self._settings.set_read_fc2_extra(params['read_fc2_extra'])
# Read gammas from hdf5
if params.has_key('read_gamma'):
self._settings.set_read_gamma(params['read_gamma'])
# Sum partial kappa at q-stars
if params.has_key('no_kappa_stars'):
self._settings.set_no_kappa_stars(params['no_kappa_stars'])
# Temperatures
if params.has_key('temperature'):
self._settings.set_temperature(params['temperature'])
# Write gamma to hdf5
if params.has_key('write_gamma'):
self._settings.set_write_gamma(params['write_gamma'])
def _set_settings(self):
ConfParser.set_settings(self)
params = self._parameters
# Supercell size for fc2
if params.has_key('dim_extra'):
self._settings.set_supercell_matrix_extra(params['dim_extra'])
# Sets of band indices that are summed
if params.has_key('band_indices'):
self._settings.set_band_indices(params['band_indices'])
if params.has_key('mesh_shift'):
self._settings.set_mesh_shift(params['mesh_shift'])
# Grid points
if params.has_key('grid_points'):
self._settings.set_grid_points(params['grid_points'])
# Calculate thermal conductivity in BTE-RTA
if params.has_key('is_bterta'):
self._settings.set_is_bterta(params['is_bterta'])
# Calculate linewidths
if params.has_key('is_linewidth'):
self._settings.set_is_linewidth(params['is_linewidth'])
# Tell Normal and Umklapp process apart
if params.has_key("read_fc2"):
self._settings.set_read_fc2(params['read_fc2'])
if params.has_key("read_fc2_extra"):
self._settings.set_read_fc2_extra(params['read_fc2_extra'])
# Read gammas from hdf5
if params.has_key('read_gamma'):
self._settings.set_read_gamma(params['read_gamma'])
# Sum partial kappa at q-stars
if params.has_key('no_kappa_stars'):
self._settings.set_no_kappa_stars(params['no_kappa_stars'])
# Temperatures
if params.has_key('temperature'):
self._settings.set_temperature(params['temperature'])
# Write gamma to hdf5
if params.has_key('write_gamma'):
self._settings.set_write_gamma(params['write_gamma'])
def __init__(self, filename=None, args=None, default_settings=None):
self._settings = Phono3pySettings(default=default_settings)
confs = {}
if filename is not None:
ConfParser.__init__(self, filename=filename)
self.read_file() # store .conf file setting in self._confs
self._parse_conf()
self._set_settings()
confs.update(self._confs)
if args is not None:
ConfParser.__init__(self, args=args)
self._read_options()
self._parse_conf()
self._set_settings()
confs.update(self._confs)
self._confs = confs
def _set_settings(self):
ConfParser.set_settings(self)
params = self._parameters
# Supercell dimension for fc2
if params.has_key('dim_fc2'):
self._settings.set_phonon_supercell_matrix(params['dim_fc2'])
# Boundary mean free path for thermal conductivity calculation
if params.has_key('boundary_mfp'):
self._settings.set_boundary_mfp(params['boundary_mfp'])
# Peierls type approximation for squared ph-ph interaction strength
if params.has_key('constant_averaged_pp_interaction'):
self._settings.set_constant_averaged_pp_interaction(
params['constant_averaged_pp_interaction'])
# Cutoff distance of third-order force constants. Elements where any
# pair of atoms has larger distance than cut-off distance are set zero.
if params.has_key('cutoff_fc3_distance'):
self._settings.set_cutoff_fc3_distance(
params['cutoff_fc3_distance'])
# Cutoff distance between pairs of displaced atoms used for supercell
# creation with displacements and making third-order force constants
if params.has_key('cutoff_pair_distance'):
self._settings.set_cutoff_pair_distance(
params['cutoff_pair_distance'])
# Grid addresses (sets of three integer values)
if params.has_key('grid_addresses'):
self._settings.set_grid_addresses(params['grid_addresses'])
# Grid points
if params.has_key('grid_points'):
self._settings.set_grid_points(params['grid_points'])
# Atoms are clamped under applied strain in Gruneisen parameter calculation
if params.has_key('ion_clamped'):
self._settings.set_ion_clamped(params['ion_clamped'])
# Calculate thermal conductivity in BTE-RTA
if params.has_key('is_bterta'):
self._settings.set_is_bterta(params['is_bterta'])
# Calculate imaginary part of self energy
if params.has_key('is_imag_self_energy'):
self._settings.set_is_imag_self_energy(
params['is_imag_self_energy'])
# Calculate lifetime due to isotope scattering
if params.has_key('is_isotope'):
self._settings.set_is_isotope(params['is_isotope'])
# Calculate thermal conductivity in LBTE with Chaput's method
if params.has_key('is_lbte'):
self._settings.set_is_lbte(params['is_lbte'])
# Calculate linewidths
if params.has_key('is_linewidth'):
self._settings.set_is_linewidth(params['is_linewidth'])
# Calculate frequency_shifts
if params.has_key('is_frequency_shift'):
self._settings.set_is_frequency_shift(params['is_frequency_shift'])
# Mass variance parameters
if params.has_key('mass_variances'):
self._settings.set_mass_variances(params['mass_variances'])
# Maximum mean free path
if params.has_key('max_freepath'):
self._settings.set_max_freepath(params['max_freepath'])
# Divisors for mesh numbers
if params.has_key('mesh_divisors'):
self._settings.set_mesh_divisors(params['mesh_divisors'][:3])
if len(params['mesh_divisors']) > 3:
self._settings.set_coarse_mesh_shifts(
params['mesh_divisors'][3:])
# Cutoff frequency for pseudo inversion of collision matrix
if params.has_key('pinv_cutoff'):
self._settings.set_pinv_cutoff(params['pinv_cutoff'])
# Read phonon-phonon interaction amplitudes from hdf5
if params.has_key('read_amplitude'):
self._settings.set_read_amplitude(params['read_amplitude'])
# Read collision matrix and gammas from hdf5
if params.has_key('read_collision'):
self._settings.set_read_collision(params['read_collision'])
# Read gammas from hdf5
if params.has_key('read_gamma'):
self._settings.set_read_gamma(params['read_gamma'])
# Calculate imag-part self energy with integration weights from gaussian
# smearing function
if params.has_key('run_with_g'):
self._settings.set_run_with_g(params['run_with_g'])
# Sum partial kappa at q-stars
if params.has_key('no_kappa_stars'):
self._settings.set_no_kappa_stars(params['no_kappa_stars'])
# Scattering event class 1 or 2
if params.has_key('scattering_event_class'):
self._settings.set_scattering_event_class(
params['scattering_event_class'])
# Temperatures
if params.has_key('temperatures'):
self._settings.set_temperatures(params['temperatures'])
# Use averaged ph-ph interaction
if params.has_key('average_pp_interaction'):
self._settings.set_average_pp_interaction(
params['average_pp_interaction'])
# Write phonon-phonon interaction amplitudes to hdf5
if params.has_key('write_amplitude'):
self._settings.set_write_amplitude(params['write_amplitude'])
# Write detailed imag-part of self energy to hdf5
if params.has_key('write_detailed_gamma'):
self._settings.set_write_detailed_gamma(
params['write_detailed_gamma'])
# Write imag-part of self energy to hdf5
if params.has_key('write_gamma'):
self._settings.set_write_gamma(params['write_gamma'])
# Write collision matrix and gammas to hdf5
if params.has_key('write_collision'):
self._settings.set_write_collision(params['write_collision'])
def __init__(self, filename=None, options=None, option_list=None):
ConfParser.__init__(self, filename, options, option_list)
self._read_options()
self._parse_conf()
self._settings = Phono3pySettings()
self._set_settings()
def _set_settings(self):
ConfParser.set_settings(self)
params = self._parameters
# Is getting least displacements?
if 'create_displacements' in params:
if params['create_displacements']:
self._settings.set_create_displacements('displacements')
# Supercell dimension for fc2
if 'dim_fc2' in params:
self._settings.set_phonon_supercell_matrix(params['dim_fc2'])
# Boundary mean free path for thermal conductivity calculation
if 'boundary_mfp' in params:
self._settings.set_boundary_mfp(params['boundary_mfp'])
# Peierls type approximation for squared ph-ph interaction strength
if 'constant_averaged_pp_interaction' in params:
self._settings.set_constant_averaged_pp_interaction(
params['constant_averaged_pp_interaction'])
# Cutoff distance of third-order force constants. Elements where any
# pair of atoms has larger distance than cut-off distance are set zero.
if 'cutoff_fc3_distance' in params:
self._settings.set_cutoff_fc3_distance(
params['cutoff_fc3_distance'])
# Cutoff distance between pairs of displaced atoms used for supercell
# creation with displacements and making third-order force constants
if 'cutoff_pair_distance' in params:
self._settings.set_cutoff_pair_distance(
params['cutoff_pair_distance'])
# This scale factor is multiplied to frequencies only, i.e., changes
# frequencies but assumed not to change the physical unit
if 'frequency_scale_factor' in params:
self._settings.set_frequency_scale_factor(
params['frequency_scale_factor'])
# Gamma unit conversion factor
if 'gamma_conversion_factor' in params:
self._settings.set_gamma_conversion_factor(
params['gamma_conversion_factor'])
# Grid addresses (sets of three integer values)
if 'grid_addresses' in params:
self._settings.set_grid_addresses(params['grid_addresses'])
# Grid points
if 'grid_points' in params:
self._settings.set_grid_points(params['grid_points'])
# Atoms are clamped under applied strain in Gruneisen parameter calculation
if 'ion_clamped' in params:
self._settings.set_ion_clamped(params['ion_clamped'])
# Calculate thermal conductivity in BTE-RTA
if 'is_bterta' in params:
self._settings.set_is_bterta(params['is_bterta'])
# Calculate frequency_shifts
if 'is_frequency_shift' in params:
self._settings.set_is_frequency_shift(params['is_frequency_shift'])
# Calculate full ph-ph interaction strength for RTA conductivity
if 'is_full_pp' in params:
self._settings.set_is_full_pp(params['is_full_pp'])
# Calculate phonon-Gruneisen parameters
if 'is_gruneisen' in params:
self._settings.set_is_gruneisen(params['is_gruneisen'])
# Calculate imaginary part of self energy
if 'is_imag_self_energy' in params:
self._settings.set_is_imag_self_energy(
params['is_imag_self_energy'])
# Calculate lifetime due to isotope scattering
if 'is_isotope' in params:
self._settings.set_is_isotope(params['is_isotope'])
# Calculate joint-DOS
if 'is_joint_dos' in params:
self._settings.set_is_joint_dos(params['is_joint_dos'])
# Calculate thermal conductivity in LBTE with Chaput's method
if 'is_lbte' in params:
self._settings.set_is_lbte(params['is_lbte'])
# Calculate linewidths
if 'is_linewidth' in params:
self._settings.set_is_linewidth(params['is_linewidth'])
# Solve reducible collision matrix but not reduced matrix
if 'is_reducible_collision_matrix' in params:
self._settings.set_is_reducible_collision_matrix(
params['is_reducible_collision_matrix'])
# Symmetrize fc2 by index exchange
if 'is_symmetrize_fc2' in params:
self._settings.set_is_symmetrize_fc2(params['is_symmetrize_fc2'])
# Symmetrize phonon fc3 by index exchange
if 'is_symmetrize_fc3_q' in params:
self._settings.set_is_symmetrize_fc3_q(
params['is_symmetrize_fc3_q'])
# Symmetrize fc3 by index exchange
if 'is_symmetrize_fc3_r' in params:
self._settings.set_is_symmetrize_fc3_r(
params['is_symmetrize_fc3_r'])
# Mass variance parameters
if 'mass_variances' in params:
self._settings.set_mass_variances(params['mass_variances'])
# Maximum mean free path
if 'max_freepath' in params:
self._settings.set_max_freepath(params['max_freepath'])
# Divisors for mesh numbers
if 'mesh_divisors' in params:
self._settings.set_mesh_divisors(params['mesh_divisors'][:3])
if len(params['mesh_divisors']) > 3:
self._settings.set_coarse_mesh_shifts(
params['mesh_divisors'][3:])
# Cutoff frequency for pseudo inversion of collision matrix
if 'pinv_cutoff' in params:
self._settings.set_pinv_cutoff(params['pinv_cutoff'])
# Ph-ph interaction unit conversion factor
if 'pp_conversion_factor' in params:
self._settings.set_pp_conversion_factor(
params['pp_conversion_factor'])
# Read phonon-phonon interaction amplitudes from hdf5
if 'read_amplitude' in params:
self._settings.set_read_amplitude(params['read_amplitude'])
# Read collision matrix and gammas from hdf5
if 'read_collision' in params:
self._settings.set_read_collision(params['read_collision'])
# Read fc2 from hdf5
if 'read_fc2' in params:
self._settings.set_read_fc2(params['read_fc2'])
# Read fc3 from hdf5
if 'read_fc3' in params:
self._settings.set_read_fc3(params['read_fc3'])
# Read gammas from hdf5
if 'read_gamma' in params:
self._settings.set_read_gamma(params['read_gamma'])
# Read phonons from hdf5
if 'read_phonon' in params:
self._settings.set_read_phonon(params['read_phonon'])
# Calculate imag-part self energy with integration weights from gaussian
# smearing function
if 'run_with_g' in params:
self._settings.set_run_with_g(params['run_with_g'])
# Sum partial kappa at q-stars
if 'is_kappa_star' in params:
self._settings.set_is_kappa_star(params['is_kappa_star'])
# Scattering event class 1 or 2
if 'scattering_event_class' in params:
self._settings.set_scattering_event_class(
params['scattering_event_class'])
# Temperatures
if 'temperatures' in params:
self._settings.set_temperatures(params['temperatures'])
# Use averaged ph-ph interaction
if 'use_ave_pp' in params:
self._settings.set_use_ave_pp(params['use_ave_pp'])
# Write phonon-phonon interaction amplitudes to hdf5
if 'write_amplitude' in params:
self._settings.set_write_amplitude(params['write_amplitude'])
# Write detailed imag-part of self energy to hdf5
if 'write_detailed_gamma' in params:
self._settings.set_write_detailed_gamma(
params['write_detailed_gamma'])
# Write imag-part of self energy to hdf5
if 'write_gamma' in params:
self._settings.set_write_gamma(params['write_gamma'])
# Write collision matrix and gammas to hdf5
if 'write_collision' in params:
self._settings.set_write_collision(params['write_collision'])
# Write all phonons on grid points to hdf5
if 'write_phonon' in params:
self._settings.set_write_phonon(params['write_phonon'])
def __init__(self, filename=None, options=None, option_list=None):
ConfParser.__init__(self, filename, options, option_list)
self._read_options()
self._parse_conf()
self._settings = PhonompySettings()
self._set_settings()
def _set_settings(self):
ConfParser.set_settings(self)
params = self._parameters
# Supercell size for fc2
if params.has_key('dim_extra'):
self._settings.set_supercell_matrix_extra(params['dim_extra'])
# Sets of band indices that are summed
if params.has_key('band_indices'):
self._settings.set_band_indices(params['band_indices'])
# Cutoff distance between pairs of displaced atoms used for supercell
# creation with displacements and making third-order force constants
if params.has_key('cutoff_pair'):
self._settings.set_cutoff_pair(
params['cutoff_pair'])
# Cutoff distance of third-order force constants. Elements where any
# pair of atoms has larger distance than cut-off distance are set zero.
if params.has_key('cutoff_triplet'):
self._settings.set_cutoff_triplet(params['cutoff_triplet'])
# Cutoff distance of reciprocal third-order force constants.
if params.has_key('cutoff_radius'):
self._settings.set_cutoff_radius(params['cutoff_radius'])
#Cutoff sigmas for gaussian smearing.
if params.has_key("cutoff_delta"):
self._settings.set_cutoff_delta(params["cutoff_delta"])
# Phonon modes larger than this frequency are ignored.
if params.has_key('cutoff_hfrequency'):
self._settings.set_cutoff_hfrequency(params['cutoff_hfrequency'])
# Phonon modes smaller than this frequency are ignored.
if params.has_key('cutoff_frequency'):
self._settings.set_cutoff_frequency(params['cutoff_frequency'])
# Cutoff lifetime used for thermal conductivity calculation
if params.has_key('cutoff_lifetime'):
self._settings.set_cutoff_lifetime(params['cutoff_lifetime'])
# different lifetime (relative) used for iterative method
if params.has_key('diff_kappa'):
self._settings.set_diff_kappa(params['diff_kappa'])
# Grid points
if params.has_key('grid_points'):
self._settings.set_grid_points(params['grid_points'])
# Atoms are clamped under applied strain in Gruneisen parameter calculation
if params.has_key('ion_clamped'):
self._settings.set_ion_clamped(params['ion_clamped'])
#Solve the Boltzmann Transport Equation Iteratively
if params.has_key("is_ite"):
self._settings.set_is_ite(params['is_ite'])
#Solve the Boltzmann Transport Equation Iteratively using the conjugate gradient method
if params.has_key("is_ite_cg"):
self._settings.set_is_ite_cg(params['is_ite_cg'])
#Get the image self energy for a specific grid point and band index
if params.has_key("is_ise"):
self._settings.set_is_ise(params['is_ise'])
#The maximum iteration steps for the iterative method
if params.has_key("max_ite"):
self._settings.set_max_ite(params['max_ite'])
#The sample length considering phonon boundary scattering
if params.has_key("length"):
self._settings.set_length(params['length'])
# Calculate thermal conductivity in BTE-RTA
if params.has_key('is_bterta'):
self._settings.set_is_bterta(params['is_bterta'])
# Calculate linewidths
if params.has_key('is_linewidth'):
self._settings.set_is_linewidth(params['is_linewidth'])
# Tell Normal and Umklapp process apart
if params.has_key('nu'):
self._settings.set_nu(params['nu'])
if params.has_key("read_fc2"):
self._settings.set_read_fc2(params['read_fc2'])
if params.has_key("read_fc2_extra"):
self._settings.set_read_fc2_extra(params['read_fc2_extra'])
if params.has_key("read_fc3"):
self._settings.set_read_fc3(params['read_fc3'])
# Calculate frequency_shifts
if params.has_key('is_frequency_shift'):
self._settings.set_is_frequency_shift(params['is_frequency_shift'])
# Mass variance parameters
if params.has_key('mass_variances'):
self._settings.set_mass_variances(params['mass_variances'])
# Maximum mean free path
if params.has_key('max_freepath'):
self._settings.set_max_freepath(params['max_freepath'])
# Divisors for mesh numbers
if params.has_key('mesh_divisors'):
self._settings.set_mesh_divisors(params['mesh_divisors'][:3])
if len(params['mesh_divisors']) > 3:
self._settings.set_coarse_mesh_shifts(
params['mesh_divisors'][3:])
# Multiple sigmas
if params.has_key('multiple_sigmas'):
self._settings.set_multiple_sigmas(params['multiple_sigmas'])
#Adaptive smearing factor
if params.has_key('adaptive_sigma_step'):
if params['adaptive_sigma_step'] <= 0:
print "Error! Step cannot be negative or 0"
sys.exit(1)
self._settings.set_adaptive_sigma_step(params['adaptive_sigma_step'])
if params.has_key('kappa_write_step'):
self._settings.set_kappa_write_step(params['kappa_write_step'])
# Read phonon-phonon interaction amplitudes from hdf5
if params.has_key('read_amplitude'):
self._settings.set_read_amplitude(params['read_amplitude'])
# Read gammas from hdf5
if params.has_key('read_gamma'):
self._settings.set_read_gamma(params['read_gamma'])
# Sum partial kappa at q-stars
if params.has_key('no_kappa_stars'):
self._settings.set_no_kappa_stars(params['no_kappa_stars'])
# Temperatures
if params.has_key('temperatures'):
self._settings.set_temperatures(params['temperatures'])
# Write phonon-phonon interaction amplitudes to hdf5
if params.has_key('write_amplitude'):
self._settings.set_write_amplitude(params['write_amplitude'])
# Write gamma to hdf5
if params.has_key('write_gamma'):
self._settings.set_write_gamma(params['write_gamma'])
#write triplets to a file
if params.has_key("write_triplet"):
self._settings.set_write_triplet(params['write_triplet'])
def _set_settings(self):
ConfParser.set_settings(self)
params = self._parameters
# Is getting least displacements?
if 'create_displacements' in params:
if params['create_displacements']:
self._settings.set_create_displacements('displacements')
# Supercell dimension for fc2
if 'dim_fc2' in params:
self._settings.set_phonon_supercell_matrix(params['dim_fc2'])
# Boundary mean free path for thermal conductivity calculation
if 'boundary_mfp' in params:
self._settings.set_boundary_mfp(params['boundary_mfp'])
# Peierls type approximation for squared ph-ph interaction strength
if 'constant_averaged_pp_interaction' in params:
self._settings.set_constant_averaged_pp_interaction(
params['constant_averaged_pp_interaction'])
# Cutoff distance of third-order force constants. Elements where any
# pair of atoms has larger distance than cut-off distance are set zero.
if 'cutoff_fc3_distance' in params:
self._settings.set_cutoff_fc3_distance(params['cutoff_fc3_distance'])
# Cutoff distance between pairs of displaced atoms used for supercell
# creation with displacements and making third-order force constants
if 'cutoff_pair_distance' in params:
self._settings.set_cutoff_pair_distance(
params['cutoff_pair_distance'])
# This scale factor is multiplied to frequencies only, i.e., changes
# frequencies but assumed not to change the physical unit
if 'frequency_scale_factor' in params:
self._settings.set_frequency_scale_factor(
params['frequency_scale_factor'])
# Gamma unit conversion factor
if 'gamma_conversion_factor' in params:
self._settings.set_gamma_conversion_factor(
params['gamma_conversion_factor'])
# Grid addresses (sets of three integer values)
if 'grid_addresses' in params:
self._settings.set_grid_addresses(params['grid_addresses'])
# Grid points
if 'grid_points' in params:
self._settings.set_grid_points(params['grid_points'])
# Atoms are clamped under applied strain in Gruneisen parameter calculation
if 'ion_clamped' in params:
self._settings.set_ion_clamped(params['ion_clamped'])
# Calculate thermal conductivity in BTE-RTA
if 'is_bterta' in params:
self._settings.set_is_bterta(params['is_bterta'])
# Calculate frequency_shifts
if 'is_frequency_shift' in params:
self._settings.set_is_frequency_shift(params['is_frequency_shift'])
# Calculate full ph-ph interaction strength for RTA conductivity
if 'is_full_pp' in params:
self._settings.set_is_full_pp(params['is_full_pp'])
# Calculate phonon-Gruneisen parameters
if 'is_gruneisen' in params:
self._settings.set_is_gruneisen(params['is_gruneisen'])
# Calculate imaginary part of self energy
if 'is_imag_self_energy' in params:
self._settings.set_is_imag_self_energy(params['is_imag_self_energy'])
# Calculate lifetime due to isotope scattering
if 'is_isotope' in params:
self._settings.set_is_isotope(params['is_isotope'])
# Calculate joint-DOS
if 'is_joint_dos' in params:
self._settings.set_is_joint_dos(params['is_joint_dos'])
# Calculate thermal conductivity in LBTE with Chaput's method
if 'is_lbte' in params:
self._settings.set_is_lbte(params['is_lbte'])
# Calculate linewidths
if 'is_linewidth' in params:
self._settings.set_is_linewidth(params['is_linewidth'])
# Solve reducible collision matrix but not reduced matrix
if 'is_reducible_collision_matrix' in params:
self._settings.set_is_reducible_collision_matrix(
params['is_reducible_collision_matrix'])
# Symmetrize fc2 by index exchange
if 'is_symmetrize_fc2' in params:
self._settings.set_is_symmetrize_fc2(params['is_symmetrize_fc2'])
# Symmetrize phonon fc3 by index exchange
if 'is_symmetrize_fc3_q' in params:
self._settings.set_is_symmetrize_fc3_q(params['is_symmetrize_fc3_q'])
# Symmetrize fc3 by index exchange
if 'is_symmetrize_fc3_r' in params:
self._settings.set_is_symmetrize_fc3_r(params['is_symmetrize_fc3_r'])
# Mass variance parameters
if 'mass_variances' in params:
self._settings.set_mass_variances(params['mass_variances'])
# Maximum mean free path
if 'max_freepath' in params:
self._settings.set_max_freepath(params['max_freepath'])
# Divisors for mesh numbers
if 'mesh_divisors' in params:
self._settings.set_mesh_divisors(params['mesh_divisors'][:3])
if len(params['mesh_divisors']) > 3:
self._settings.set_coarse_mesh_shifts(
params['mesh_divisors'][3:])
# Cutoff frequency for pseudo inversion of collision matrix
if 'pinv_cutoff' in params:
self._settings.set_pinv_cutoff(params['pinv_cutoff'])
# Ph-ph interaction unit conversion factor
if 'pp_conversion_factor' in params:
self._settings.set_pp_conversion_factor(params['pp_conversion_factor'])
# Read phonon-phonon interaction amplitudes from hdf5
if 'read_amplitude' in params:
self._settings.set_read_amplitude(params['read_amplitude'])
# Read collision matrix and gammas from hdf5
if 'read_collision' in params:
self._settings.set_read_collision(params['read_collision'])
# Read fc2 from hdf5
if 'read_fc2' in params:
self._settings.set_read_fc2(params['read_fc2'])
# Read fc3 from hdf5
if 'read_fc3' in params:
self._settings.set_read_fc3(params['read_fc3'])
# Read gammas from hdf5
if 'read_gamma' in params:
self._settings.set_read_gamma(params['read_gamma'])
# Read phonons from hdf5
if 'read_phonon' in params:
self._settings.set_read_phonon(params['read_phonon'])
# Calculate imag-part self energy with integration weights from gaussian
# smearing function
if 'run_with_g' in params:
self._settings.set_run_with_g(params['run_with_g'])
# Sum partial kappa at q-stars
if 'is_kappa_star' in params:
self._settings.set_is_kappa_star(params['is_kappa_star'])
# Scattering event class 1 or 2
if 'scattering_event_class' in params:
self._settings.set_scattering_event_class(
params['scattering_event_class'])
# Temperatures
if 'temperatures' in params:
self._settings.set_temperatures(params['temperatures'])
# Use averaged ph-ph interaction
if 'use_ave_pp' in params:
self._settings.set_use_ave_pp(params['use_ave_pp'])
# Write phonon-phonon interaction amplitudes to hdf5
if 'write_amplitude' in params:
self._settings.set_write_amplitude(params['write_amplitude'])
# Write detailed imag-part of self energy to hdf5
if 'write_detailed_gamma' in params:
self._settings.set_write_detailed_gamma(
params['write_detailed_gamma'])
# Write imag-part of self energy to hdf5
if 'write_gamma' in params:
self._settings.set_write_gamma(params['write_gamma'])
# Write collision matrix and gammas to hdf5
if 'write_collision' in params:
self._settings.set_write_collision(params['write_collision'])
# Write all phonons on grid points to hdf5
if 'write_phonon' in params:
self._settings.set_write_phonon(params['write_phonon'])
def _set_settings(self):
ConfParser.set_settings(self)
params = self._parameters
# Supercell dimension for fc2
if params.has_key('dim_fc2'):
self._settings.set_phonon_supercell_matrix(params['dim_fc2'])
# Boundary mean free path for thermal conductivity calculation
if params.has_key('boundary_mfp'):
self._settings.set_boundary_mfp(params['boundary_mfp'])
# Peierls type approximation for squared ph-ph interaction strength
if params.has_key('constant_averaged_pp_interaction'):
self._settings.set_constant_averaged_pp_interaction(
params['constant_averaged_pp_interaction'])
# Cutoff distance of third-order force constants. Elements where any
# pair of atoms has larger distance than cut-off distance are set zero.
if params.has_key('cutoff_fc3_distance'):
self._settings.set_cutoff_fc3_distance(params['cutoff_fc3_distance'])
# Cutoff distance between pairs of displaced atoms used for supercell
# creation with displacements and making third-order force constants
if params.has_key('cutoff_pair_distance'):
self._settings.set_cutoff_pair_distance(
params['cutoff_pair_distance'])
# Grid addresses (sets of three integer values)
if params.has_key('grid_addresses'):
self._settings.set_grid_addresses(params['grid_addresses'])
# Grid points
if params.has_key('grid_points'):
self._settings.set_grid_points(params['grid_points'])
# Atoms are clamped under applied strain in Gruneisen parameter calculation
if params.has_key('ion_clamped'):
self._settings.set_ion_clamped(params['ion_clamped'])
# Calculate thermal conductivity in BTE-RTA
if params.has_key('is_bterta'):
self._settings.set_is_bterta(params['is_bterta'])
# Calculate lifetime due to isotope scattering
if params.has_key('is_isotope'):
self._settings.set_is_isotope(params['is_isotope'])
# Calculate thermal conductivity in LBTE with Chaput's method
if params.has_key('is_lbte'):
self._settings.set_is_lbte(params['is_lbte'])
# Calculate linewidths
if params.has_key('is_linewidth'):
self._settings.set_is_linewidth(params['is_linewidth'])
# Calculate frequency_shifts
if params.has_key('is_frequency_shift'):
self._settings.set_is_frequency_shift(params['is_frequency_shift'])
# Mass variance parameters
if params.has_key('mass_variances'):
self._settings.set_mass_variances(params['mass_variances'])
# Maximum mean free path
if params.has_key('max_freepath'):
self._settings.set_max_freepath(params['max_freepath'])
# Divisors for mesh numbers
if params.has_key('mesh_divisors'):
self._settings.set_mesh_divisors(params['mesh_divisors'][:3])
if len(params['mesh_divisors']) > 3:
self._settings.set_coarse_mesh_shifts(
params['mesh_divisors'][3:])
# Cutoff frequency for pseudo inversion of collision matrix
if params.has_key('pinv_cutoff'):
self._settings.set_pinv_cutoff(params['pinv_cutoff'])
# Read phonon-phonon interaction amplitudes from hdf5
if params.has_key('read_amplitude'):
self._settings.set_read_amplitude(params['read_amplitude'])
# Read gammas from hdf5
if params.has_key('read_gamma'):
self._settings.set_read_gamma(params['read_gamma'])
# Read collision matrix and gammas from hdf5
if params.has_key('read_collision'):
self._settings.set_read_collision(params['read_collision'])
# Sum partial kappa at q-stars
if params.has_key('no_kappa_stars'):
self._settings.set_no_kappa_stars(params['no_kappa_stars'])
# Scattering event class 1 or 2
if params.has_key('scattering_event_class'):
self._settings.set_scattering_event_class(
params['scattering_event_class'])
# Temperatures
if params.has_key('temperatures'):
self._settings.set_temperatures(params['temperatures'])
# Use averaged ph-ph interaction
if params.has_key('average_pp_interaction'):
self._settings.set_average_pp_interaction(
params['average_pp_interaction'])
# Write phonon-phonon interaction amplitudes to hdf5
if params.has_key('write_amplitude'):
self._settings.set_write_amplitude(params['write_amplitude'])
# Write gammas to hdf5
if params.has_key('write_gamma'):
self._settings.set_write_gamma(params['write_gamma'])
# Write collision matrix and gammas to hdf5
if params.has_key('write_collision'):
self._settings.set_write_collision(params['write_collision'])
def _set_settings(self):
ConfParser.set_settings(self)
params = self._parameters
# Supercell size for fc2
if params.has_key('dim_extra'):
self._settings.set_supercell_matrix_extra(params['dim_extra'])
# Sets of band indices that are summed
if params.has_key('band_indices'):
self._settings.set_band_indices(params['band_indices'])
# Cutoff distance between pairs of displaced atoms used for supercell
# creation with displacements and making third-order force constants
if params.has_key('cutoff_pair'):
self._settings.set_cutoff_pair(params['cutoff_pair'])
# Cutoff distance of third-order force constants. Elements where any
# pair of atoms has larger distance than cut-off distance are set zero.
if params.has_key('cutoff_triplet'):
self._settings.set_cutoff_triplet(params['cutoff_triplet'])
# Cutoff distance of reciprocal third-order force constants.
if params.has_key('cutoff_radius'):
self._settings.set_cutoff_radius(params['cutoff_radius'])
#Cutoff sigmas for gaussian smearing.
if params.has_key("cutoff_delta"):
self._settings.set_cutoff_delta(params["cutoff_delta"])
# Phonon modes larger than this frequency are ignored.
if params.has_key('cutoff_hfrequency'):
self._settings.set_cutoff_hfrequency(params['cutoff_hfrequency'])
# Phonon modes smaller than this frequency are ignored.
if params.has_key('cutoff_frequency'):
self._settings.set_cutoff_frequency(params['cutoff_frequency'])
# Cutoff lifetime used for thermal conductivity calculation
if params.has_key('cutoff_lifetime'):
self._settings.set_cutoff_lifetime(params['cutoff_lifetime'])
# different lifetime (relative) used for iterative method
if params.has_key('diff_kappa'):
self._settings.set_diff_kappa(params['diff_kappa'])
# Grid points
if params.has_key('grid_points'):
self._settings.set_grid_points(params['grid_points'])
# Atoms are clamped under applied strain in Gruneisen parameter calculation
if params.has_key('ion_clamped'):
self._settings.set_ion_clamped(params['ion_clamped'])
#Solve the Boltzmann Transport Equation Iteratively
if params.has_key("is_ite"):
self._settings.set_is_ite(params['is_ite'])
#Solve the Boltzmann Transport Equation Iteratively using the conjugate gradient method
if params.has_key("is_ite_cg"):
self._settings.set_is_ite_cg(params['is_ite_cg'])
#Get the image self energy for a specific grid point and band index
if params.has_key("is_ise"):
self._settings.set_is_ise(params['is_ise'])
#The maximum iteration steps for the iterative method
if params.has_key("max_ite"):
self._settings.set_max_ite(params['max_ite'])
#The sample length considering phonon boundary scattering
if params.has_key("length"):
self._settings.set_length(params['length'])
# Calculate thermal conductivity in BTE-RTA
if params.has_key('is_bterta'):
self._settings.set_is_bterta(params['is_bterta'])
# Calculate linewidths
if params.has_key('is_linewidth'):
self._settings.set_is_linewidth(params['is_linewidth'])
# Tell Normal and Umklapp process apart
if params.has_key('nu'):
self._settings.set_nu(params['nu'])
if params.has_key("read_fc2"):
self._settings.set_read_fc2(params['read_fc2'])
if params.has_key("read_fc2_extra"):
self._settings.set_read_fc2_extra(params['read_fc2_extra'])
if params.has_key("read_fc3"):
self._settings.set_read_fc3(params['read_fc3'])
# Calculate frequency_shifts
if params.has_key('is_frequency_shift'):
self._settings.set_is_frequency_shift(params['is_frequency_shift'])
# Mass variance parameters
if params.has_key('mass_variances'):
self._settings.set_mass_variances(params['mass_variances'])
# Maximum mean free path
if params.has_key('max_freepath'):
self._settings.set_max_freepath(params['max_freepath'])
# Divisors for mesh numbers
if params.has_key('mesh_divisors'):
self._settings.set_mesh_divisors(params['mesh_divisors'][:3])
if len(params['mesh_divisors']) > 3:
self._settings.set_coarse_mesh_shifts(
params['mesh_divisors'][3:])
# Multiple sigmas
if params.has_key('multiple_sigmas'):
self._settings.set_multiple_sigmas(params['multiple_sigmas'])
#Adaptive smearing factor
if params.has_key('adaptive_sigma_step'):
if params['adaptive_sigma_step'] <= 0:
print "Error! Step cannot be negative or 0"
sys.exit(1)
self._settings.set_adaptive_sigma_step(
params['adaptive_sigma_step'])
if params.has_key('kappa_write_step'):
self._settings.set_kappa_write_step(params['kappa_write_step'])
# Read phonon-phonon interaction amplitudes from hdf5
if params.has_key('read_amplitude'):
self._settings.set_read_amplitude(params['read_amplitude'])
# Read gammas from hdf5
if params.has_key('read_gamma'):
self._settings.set_read_gamma(params['read_gamma'])
# Sum partial kappa at q-stars
if params.has_key('no_kappa_stars'):
self._settings.set_no_kappa_stars(params['no_kappa_stars'])
# Temperatures
if params.has_key('temperatures'):
self._settings.set_temperatures(params['temperatures'])
# Write phonon-phonon interaction amplitudes to hdf5
if params.has_key('write_amplitude'):
self._settings.set_write_amplitude(params['write_amplitude'])
# Write gamma to hdf5
if params.has_key('write_gamma'):
self._settings.set_write_gamma(params['write_gamma'])
#write triplets to a file
if params.has_key("write_triplet"):
self._settings.set_write_triplet(params['write_triplet'])
def _parse_conf(self):
ConfParser.parse_conf(self)
confs = self._confs
for conf_key in confs.keys():
# Boolean
if conf_key in ('read_fc2', 'read_fc3', 'read_gamma',
'read_phonon', 'read_pp', 'use_ave_pp',
'collective_phonon', 'write_gamma_detail',
'write_gamma', 'write_collision', 'write_phonon',
'write_pp', 'write_LBTE_solution', 'full_pp',
'ion_clamped', 'bterta', 'compact_fc',
'real_self_energy', 'gruneisen',
'imag_self_energy', 'isotope', 'joint_dos', 'lbte',
'N_U', 'spectral_function',
'reducible_collision_matrix', 'symmetrize_fc2',
'symmetrize_fc3_q', 'symmetrize_fc3_r',
'kappa_star'):
if confs[conf_key].lower() == '.true.':
self.set_parameter(conf_key, True)
elif confs[conf_key].lower() == '.false.':
self.set_parameter(conf_key, False)
# float
if conf_key in ('boundary_mfp', 'cutoff_fc3_distance',
'cutoff_pair_distance', 'gamma_conversion_factor',
'max_freepath', 'pinv_cutoff',
'pp_conversion_factor', 'sigma_cutoff_width'):
self.set_parameter(conf_key, float(confs[conf_key]))
# int
if conf_key in ('pinv_solver', 'num_points_in_batch'):
self.set_parameter(conf_key, int(confs[conf_key]))
# specials
if conf_key in ('create_forces_fc2', 'create_forces_fc3'):
if type(confs[conf_key]) is str:
fnames = confs[conf_key].split()
else:
fnames = confs[conf_key]
self.set_parameter(conf_key, fnames)
if conf_key == 'dim_fc2':
matrix = [int(x) for x in confs['dim_fc2'].split()]
if len(matrix) == 9:
matrix = np.array(matrix).reshape(3, 3)
elif len(matrix) == 3:
matrix = np.diag(matrix)
else:
self.setting_error(
"Number of elements of dim2 has to be 3 or 9.")
if matrix.shape == (3, 3):
if np.linalg.det(matrix) < 1:
self.setting_error(
"Determinant of supercell matrix has " +
"to be positive.")
else:
self.set_parameter('dim_fc2', matrix)
if conf_key in ('constant_averaged_pp_interaction' 'const_ave_pp'):
self.set_parameter('const_ave_pp',
float(confs['const_ave_pp']))
if conf_key == 'grid_addresses':
vals = [
int(x)
for x in confs['grid_addresses'].replace(',', ' ').split()
]
if len(vals) % 3 == 0 and len(vals) > 0:
self.set_parameter('grid_addresses',
np.reshape(vals, (-1, 3)))
else:
self.setting_error("Grid addresses are incorrectly set.")
if conf_key == 'grid_points':
vals = [
int(x)
for x in confs['grid_points'].replace(',', ' ').split()
]
self.set_parameter('grid_points', vals)
if conf_key == 'lapack_zheev_uplo':
self.set_parameter('lapack_zheev_uplo',
confs['lapack_zheev_uplo'].upper())
if conf_key == 'mass_variances':
vals = [fracval(x) for x in confs['mass_variances'].split()]
if len(vals) < 1:
self.setting_error(
"Mass variance parameters are incorrectly set.")
else:
self.set_parameter('mass_variances', vals)
if conf_key == 'mesh_divisors':
vals = [x for x in confs['mesh_divisors'].split()]
if len(vals) == 3:
self.set_parameter('mesh_divisors', [int(x) for x in vals])
elif len(vals) == 6:
divs = [int(x) for x in vals[:3]]
is_shift = [x.lower() == 't' for x in vals[3:]]
for i in range(3):
if is_shift[i] and (divs[i] % 2 != 0):
is_shift[i] = False
self.setting_error(
"Coarse grid shift along the " +
["first", "second", "third"][i] +
" axis is not allowed.")
self.set_parameter('mesh_divisors', divs + is_shift)
else:
self.setting_error("Mesh divisors are incorrectly set.")
if conf_key == 'read_collision':
if confs['read_collision'] == 'all':
self.set_parameter('read_collision', 'all')
else:
vals = [int(x) for x in confs['read_collision'].split()]
self.set_parameter('read_collision', vals)
if conf_key == 'scattering_event_class':
self.set_parameter('scattering_event_class',
int(confs['scattering_event_class']))
def _read_options(self):
ConfParser.read_options(self) # store data in self._confs
if 'phonon_supercell_dimension' in self._args:
dim_fc2 = self._args.phonon_supercell_dimension
if dim_fc2 is not None:
self._confs['dim_fc2'] = " ".join(dim_fc2)
if 'boundary_mfp' in self._args:
if self._args.boundary_mfp is not None:
self._confs['boundary_mfp'] = self._args.boundary_mfp
if 'const_ave_pp' in self._args:
const_ave_pp = self._args.const_ave_pp
if const_ave_pp is not None:
self._confs['const_ave_pp'] = const_ave_pp
if 'create_forces_fc2' in self._args:
if self._args.create_forces_fc2:
self._confs['create_forces_fc2'] = self._args.create_forces_fc2
if 'create_forces_fc3' in self._args:
if self._args.create_forces_fc3:
self._confs['create_forces_fc3'] = self._args.create_forces_fc3
if 'create_forces_fc3_file' in self._args:
if self._args.create_forces_fc3_file:
cfc3_file = self._args.create_forces_fc3_file
self._confs['create_forces_fc3_file'] = cfc3_file
if 'cutoff_fc3_distance' in self._args:
cutoff_fc3 = self._args.cutoff_fc3_distance
if cutoff_fc3 is not None:
self._confs['cutoff_fc3_distance'] = cutoff_fc3
if 'cutoff_pair_distance' in self._args:
cutoff_pair = self._args.cutoff_pair_distance
if cutoff_pair is not None:
self._confs['cutoff_pair_distance'] = cutoff_pair
if 'gamma_conversion_factor' in self._args:
g_conv_factor = self._args.gamma_conversion_factor
if g_conv_factor is not None:
self._confs['gamma_conversion_factor'] = g_conv_factor
if 'grid_addresses' in self._args:
grid_adrs = self._args.grid_addresses
if grid_adrs is not None:
self._confs['grid_addresses'] = " ".join(grid_adrs)
if 'grid_points' in self._args:
if self._args.grid_points is not None:
self._confs['grid_points'] = " ".join(self._args.grid_points)
if 'ion_clamped' in self._args:
if self._args.ion_clamped:
self._confs['ion_clamped'] = '.true.'
if 'is_bterta' in self._args:
if self._args.is_bterta:
self._confs['bterta'] = '.true.'
if 'is_compact_fc' in self._args:
if self._args.is_compact_fc:
self._confs['compact_fc'] = '.true.'
if 'is_gruneisen' in self._args:
if self._args.is_gruneisen:
self._confs['gruneisen'] = '.true.'
if 'is_full_pp' in self._args:
if self._args.is_full_pp:
self._confs['full_pp'] = '.true.'
if 'is_imag_self_energy' in self._args:
if self._args.is_imag_self_energy:
self._confs['imag_self_energy'] = '.true.'
if 'is_isotope' in self._args:
if self._args.is_isotope:
self._confs['isotope'] = '.true.'
if 'is_joint_dos' in self._args:
if self._args.is_joint_dos:
self._confs['joint_dos'] = '.true.'
if 'no_kappa_stars' in self._args:
if self._args.no_kappa_stars:
self._confs['kappa_star'] = '.false.'
if 'is_lbte' in self._args:
if self._args.is_lbte:
self._confs['lbte'] = '.true.'
if 'is_N_U' in self._args:
if self._args.is_N_U:
self._confs['N_U'] = '.true.'
if 'is_real_self_energy' in self._args:
if self._args.is_real_self_energy:
self._confs['real_self_energy'] = '.true.'
if 'is_reducible_collision_matrix' in self._args:
if self._args.is_reducible_collision_matrix:
self._confs['reducible_collision_matrix'] = '.true.'
if 'is_spectral_function' in self._args:
if self._args.is_spectral_function:
self._confs['spectral_function'] = '.true.'
if 'is_symmetrize_fc2' in self._args:
if self._args.is_symmetrize_fc2:
self._confs['symmetrize_fc2'] = '.true.'
if 'is_symmetrize_fc3_q' in self._args:
if self._args.is_symmetrize_fc3_q:
self._confs['symmetrize_fc3_q'] = '.true.'
if 'is_symmetrize_fc3_r' in self._args:
if self._args.is_symmetrize_fc3_r:
self._confs['symmetrize_fc3_r'] = '.true.'
if 'lapack_zheev_uplo' in self._args:
if self._args.lapack_zheev_uplo is not None:
self._confs['lapack_zheev_uplo'] = self._args.lapack_zheev_uplo
if 'mass_variances' in self._args:
mass_variances = self._args.mass_variances
if mass_variances is not None:
self._confs['mass_variances'] = " ".join(mass_variances)
if 'max_freepath' in self._args:
if self._args.max_freepath is not None:
self._confs['max_freepath'] = self._args.max_freepath
if 'mesh_divisors' in self._args:
mesh_divisors = self._args.mesh_divisors
if mesh_divisors is not None:
self._confs['mesh_divisors'] = " ".join(mesh_divisors)
if 'num_points_in_batch' in self._args:
num_points_in_batch = self._args.num_points_in_batch
if num_points_in_batch is not None:
self._confs['num_points_in_batch'] = num_points_in_batch
if 'pinv_cutoff' in self._args:
if self._args.pinv_cutoff is not None:
self._confs['pinv_cutoff'] = self._args.pinv_cutoff
if 'pinv_solver' in self._args:
if self._args.pinv_solver is not None:
self._confs['pinv_solver'] = self._args.pinv_solver
if 'pp_conversion_factor' in self._args:
pp_conv_factor = self._args.pp_conversion_factor
if pp_conv_factor is not None:
self._confs['pp_conversion_factor'] = pp_conv_factor
if 'read_fc2' in self._args:
if self._args.read_fc2:
self._confs['read_fc2'] = '.true.'
if 'read_fc3' in self._args:
if self._args.read_fc3:
self._confs['read_fc3'] = '.true.'
if 'read_gamma' in self._args:
if self._args.read_gamma:
self._confs['read_gamma'] = '.true.'
if 'read_phonon' in self._args:
if self._args.read_phonon:
self._confs['read_phonon'] = '.true.'
if 'read_pp' in self._args:
if self._args.read_pp:
self._confs['read_pp'] = '.true.'
if 'read_collision' in self._args:
if self._args.read_collision is not None:
self._confs['read_collision'] = self._args.read_collision
if 'scattering_event_class' in self._args:
scatt_class = self._args.scattering_event_class
if scatt_class is not None:
self._confs['scattering_event_class'] = scatt_class
if 'sigma_cutoff_width' in self._args:
sigma_cutoff = self._args.sigma_cutoff_width
if sigma_cutoff is not None:
self._confs['sigma_cutoff_width'] = sigma_cutoff
if 'solve_collective_phonon' in self._args:
if self._args.solve_collective_phonon:
self._confs['collective_phonon'] = '.true.'
if 'subtract_forces' in self._args:
if self._args.subtract_forces:
self._confs['subtract_forces'] = self._args.subtract_forces
if 'use_ave_pp' in self._args:
if self._args.use_ave_pp:
self._confs['use_ave_pp'] = '.true.'
if 'write_gamma_detail' in self._args:
if self._args.write_gamma_detail:
self._confs['write_gamma_detail'] = '.true.'
if 'write_gamma' in self._args:
if self._args.write_gamma:
self._confs['write_gamma'] = '.true.'
if 'write_collision' in self._args:
if self._args.write_collision:
self._confs['write_collision'] = '.true.'
if 'write_phonon' in self._args:
if self._args.write_phonon:
self._confs['write_phonon'] = '.true.'
if 'write_pp' in self._args:
if self._args.write_pp:
self._confs['write_pp'] = '.true.'
if 'write_LBTE_solution' in self._args:
if self._args.write_LBTE_solution:
self._confs['write_LBTE_solution'] = '.true.'
def _set_settings(self):
ConfParser.set_settings(self)
params = self._parameters
# Supercell size for fc2
if params.has_key('dim_extra'):
self._settings.set_phonon_supercell_matrix(params['dim_extra'])
# Cutoff distance of third-order force constants. Elements where any
# pair of atoms has larger distance than cut-off distance are set zero.
if params.has_key('cutoff_fc3_distance'):
self._settings.set_cutoff_fc3_distance(params['cutoff_fc3_distance'])
# Cutoff distance between pairs of displaced atoms used for supercell
# creation with displacements and making third-order force constants
if params.has_key('cutoff_pair_distance'):
self._settings.set_cutoff_pair_distance(
params['cutoff_pair_distance'])
# Phonon modes below this frequency are ignored.
if params.has_key('cutoff_frequency'):
self._settings.set_cutoff_frequency(params['cutoff_frequency'])
# Cutoff lifetime used for thermal conductivity calculation
if params.has_key('cutoff_lifetime'):
self._settings.set_cutoff_lifetime(params['cutoff_lifetime'])
# Grid points
if params.has_key('grid_points'):
self._settings.set_grid_points(params['grid_points'])
# Atoms are clamped under applied strain in Gruneisen parameter calculation
if params.has_key('ion_clamped'):
self._settings.set_ion_clamped(params['ion_clamped'])
# Calculate thermal conductivity in BTE-RTA
if params.has_key('is_bterta'):
self._settings.set_is_bterta(params['is_bterta'])
# Calculate thermal conductivity in LBTE with Chaput's method
if params.has_key('is_lbte'):
self._settings.set_is_lbte(params['is_lbte'])
# Calculate linewidths
if params.has_key('is_linewidth'):
self._settings.set_is_linewidth(params['is_linewidth'])
# Calculate frequency_shifts
if params.has_key('is_frequency_shift'):
self._settings.set_is_frequency_shift(params['is_frequency_shift'])
# Mass variance parameters
if params.has_key('mass_variances'):
self._settings.set_mass_variances(params['mass_variances'])
# Maximum mean free path
if params.has_key('max_freepath'):
self._settings.set_max_freepath(params['max_freepath'])
# Divisors for mesh numbers
if params.has_key('mesh_divisors'):
self._settings.set_mesh_divisors(params['mesh_divisors'][:3])
if len(params['mesh_divisors']) > 3:
self._settings.set_coarse_mesh_shifts(
params['mesh_divisors'][3:])
# Read phonon-phonon interaction amplitudes from hdf5
if params.has_key('read_amplitude'):
self._settings.set_read_amplitude(params['read_amplitude'])
# Read gammas from hdf5
if params.has_key('read_gamma'):
self._settings.set_read_gamma(params['read_gamma'])
# Read collision matrix and gammas from hdf5
if params.has_key('read_collision'):
self._settings.set_read_collision(params['read_collision'])
# Sum partial kappa at q-stars
if params.has_key('no_kappa_stars'):
self._settings.set_no_kappa_stars(params['no_kappa_stars'])
# Temperatures
if params.has_key('temperatures'):
self._settings.set_temperatures(params['temperatures'])
# Write phonon-phonon interaction amplitudes to hdf5
if params.has_key('write_amplitude'):
self._settings.set_write_amplitude(params['write_amplitude'])
# Write gammas to hdf5
if params.has_key('write_gamma'):
self._settings.set_write_gamma(params['write_gamma'])
# Write collision matrix and gammas to hdf5
if params.has_key('write_collision'):
self._settings.set_write_collision(params['write_collision'])
