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 _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 _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 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 _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'])
