Index

A

additional_directory (auto_kappa.alamode.almcalc.AlamodeCalc property) adjust_cutoff3() (auto_kappa.alamode.almcalc.AlamodeCalc method) adjust_keys_of_suggested_structures() (in module auto_kappa.alamode.compat) adjust_vacuum_size() (in module auto_kappa.structure.two) AkLog (class in auto_kappa.alamode.log_parser) AlamodeCalc (class in auto_kappa.alamode.almcalc) AlamodeDisplace (class in auto_kappa.alamode.tools.GenDisplacement) AlamodeForceCalculator (class in auto_kappa.alamode.helpers) AlamodeInput (class in auto_kappa.io.alm) AlamodeInputWriter (class in auto_kappa.alamode.helpers) AlamodePlotter (class in auto_kappa.alamode.plotter) all_keys (auto_kappa.io.alm.AnphonInput attribute) AlmInput (class in auto_kappa.io.alm) ALMLOG (class in auto_kappa.almlog.core) analysis_keys (auto_kappa.io.alm.AnphonInput attribute) analysis_keys_2 (auto_kappa.io.alm.AnphonInput attribute) analyze_harmonic_properties() (in module auto_kappa.calculators.alamode) analyze_harmonic_property() (auto_kappa.alamode.almcalc.AlamodeCalc method) analyze_harmonic_with_larger_supercells() (in module auto_kappa.calculators.alamode) analyze_obj() (in module auto_kappa.alamode.tools.analyze_phonons) analyze_phonon_properties() (in module auto_kappa.calculators.alamode) analyze_phonon_properties_with_larger_supercells() (in module auto_kappa.calculators.alamode) AnphonInput (class in auto_kappa.io.alm) ApdbVasp (class in auto_kappa.apdb) are_forces_available() (in module auto_kappa.alamode.helpers) as_dict() (auto_kappa.io.alm.AlamodeInput method) (auto_kappa.io.alm.AlmInput method) (auto_kappa.io.alm.AnphonInput method) Atom (class in auto_kappa.almlog.interaction) atomic_kinds (auto_kappa.alamode.tools.VASP.VaspParser property) atoms_equal() (in module auto_kappa.structure.comparison) atoms_no_mass (auto_kappa.io.alm.AnphonInput attribute) auto_kappa module auto_kappa.alamode module auto_kappa.alamode.almcalc module auto_kappa.alamode.compat module auto_kappa.alamode.errors module auto_kappa.alamode.gruneisen module auto_kappa.alamode.helpers module auto_kappa.alamode.io module auto_kappa.alamode.log_parser module auto_kappa.alamode.memory module auto_kappa.alamode.parameters module auto_kappa.alamode.pes module auto_kappa.alamode.plotter module auto_kappa.alamode.runjob module auto_kappa.alamode.tools module auto_kappa.alamode.tools.analyze_phonons module auto_kappa.alamode.tools.GenDisplacement module auto_kappa.alamode.tools.VASP module auto_kappa.almlog module auto_kappa.almlog.core module auto_kappa.almlog.dmatrix module auto_kappa.almlog.fcs module auto_kappa.almlog.frequencies module auto_kappa.almlog.interaction module auto_kappa.almlog.kpoint module auto_kappa.almlog.structure module auto_kappa.almlog.symmetry module auto_kappa.almlog.system module auto_kappa.almlog.utils module auto_kappa.almlog.variables module auto_kappa.apdb module auto_kappa.calculators module auto_kappa.calculators.alamode module

auto_kappa.calculators.compat module auto_kappa.calculators.scph module auto_kappa.calculators.vasp module auto_kappa.compat module auto_kappa.cui module auto_kappa.cui.ak_log module auto_kappa.cui.ak_parser module auto_kappa.cui.ak_scripts module auto_kappa.cui.compat module auto_kappa.cui.initialization module auto_kappa.cui.suggest module auto_kappa.io module auto_kappa.io.alm module auto_kappa.io.analyzer module auto_kappa.io.band module auto_kappa.io.born module auto_kappa.io.dos module auto_kappa.io.fcs module auto_kappa.io.files module auto_kappa.io.gruneisen module auto_kappa.io.isotope module auto_kappa.io.kl module auto_kappa.io.participation module auto_kappa.io.phonondb module auto_kappa.io.result module auto_kappa.io.scattering module auto_kappa.io.suggest module auto_kappa.io.thermo module auto_kappa.io.times module auto_kappa.io.vasp module auto_kappa.plot module auto_kappa.plot.bandos module auto_kappa.plot.fitting module auto_kappa.plot.initialize module auto_kappa.plot.pltalm module auto_kappa.structure module auto_kappa.structure.comparison module auto_kappa.structure.crystal module auto_kappa.structure.supercell module auto_kappa.structure.two module auto_kappa.structure.utils module auto_kappa.units module auto_kappa.utils module auto_kappa.utils.isotopes module auto_kappa.utils.version module auto_kappa.vasp module auto_kappa.vasp.params module auto_kappa.vasp.relax module auto_kappa.version module averaged_velocities (auto_kappa.io.scattering.Scattering property)

B

backup_previous_results() (in module auto_kappa.alamode.compat) backup_vasp() (in module auto_kappa.calculators.vasp) Band (class in auto_kappa.io.band)

BandPR (class in auto_kappa.io.participation) base_directory (auto_kappa.alamode.almcalc.AlamodeCalc property) (auto_kappa.apdb.ApdbVasp property) BORNINFO (class in auto_kappa.io.born)

C

calc_forces() (auto_kappa.alamode.almcalc.AlamodeCalc method) calc_g2_factor() (in module auto_kappa.io.alm) calculate_cubic_force_constants() (in module auto_kappa.calculators.alamode) calculate_evec() (in module auto_kappa.alamode.pes) calculate_forces (auto_kappa.alamode.almcalc.AlamodeCalc property) calculate_gruneisen_parameters() (auto_kappa.alamode.almcalc.AlamodeCalc method) (auto_kappa.alamode.gruneisen.GruneisenCalculator method) calculate_high_order_force_constants() (in module auto_kappa.calculators.scph) calculate_pes() (auto_kappa.alamode.almcalc.AlamodeCalc method) (in module auto_kappa.alamode.pes) calculate_thermal_conductivities() (in module auto_kappa.calculators.alamode) cell (auto_kappa.io.fcs.FCSxml property) cells_equal() (in module auto_kappa.structure.comparison) center (auto_kappa.almlog.interaction.PairAtoms attribute) change_grain_size() (auto_kappa.io.scattering.Scattering method) change_structure_format() (in module auto_kappa.structure.utils) change_temperature() (auto_kappa.io.scattering.Scattering method) CHARGE (class in auto_kappa.io.born) check_2d_structure() (in module auto_kappa.structure.two) check_ak_options() (in module auto_kappa.cui.compat) check_directory_name_for_pristine() (in module auto_kappa.alamode.compat) check_parameters() (auto_kappa.io.alm.AlmInput method) (auto_kappa.io.alm.AnphonInput method)

check_previous_borninfo() (in module auto_kappa.alamode.compat) check_previous_structures() (in module auto_kappa.alamode.compat) check_unexpected_errors() (in module auto_kappa.alamode.errors) clear() (auto_kappa.io.alm.AlamodeInput method) (auto_kappa.io.alm.AlmInput method) (auto_kappa.io.alm.AnphonInput method) cmap (auto_kappa.io.thermo.Thermo attribute) command (auto_kappa.apdb.ApdbVasp property) commands (auto_kappa.alamode.almcalc.AlamodeCalc property) conduct_scph_calculation() (in module auto_kappa.calculators.scph) contents (auto_kappa.io.suggest.SuggestLogParser property) convert_gamma2scatrate() (in module auto_kappa.io.scattering) convert_gamma2tau() (in module auto_kappa.io.analyzer) convert_numpy() (in module auto_kappa.io.files) convert_scatrate2lifetime() (in module auto_kappa.io.scattering) copy() (auto_kappa.io.alm.AlamodeInput method) (auto_kappa.io.alm.AlmInput method) (auto_kappa.io.alm.AnphonInput method) cube_dfset (auto_kappa.alamode.almcalc.AlamodeCalc property) cutoff2 (auto_kappa.alamode.almcalc.AlamodeCalc property) cutoff3 (auto_kappa.alamode.almcalc.AlamodeCalc property) cutoffs (auto_kappa.alamode.almcalc.AlamodeCalc property)

D

dim (auto_kappa.alamode.almcalc.AlamodeCalc property) (auto_kappa.io.alm.AlamodeInput property) (auto_kappa.io.alm.AlmInput property) (auto_kappa.io.alm.AnphonInput property) (auto_kappa.vasp.relax.StrictRelaxation property)

directory (auto_kappa.alamode.log_parser.AkLog property) distance (auto_kappa.almlog.interaction.NeighborAtoms attribute) distances (auto_kappa.io.fcs.FCSxml property) Dos (class in auto_kappa.io.dos)

E

elem_natoms (auto_kappa.io.dos.Dos property) element (auto_kappa.almlog.interaction.Atom attribute) end_autokappa() (in module auto_kappa.cui.ak_log) energies (auto_kappa.vasp.relax.StrictRelaxation property) estimate_supercell_matrix() (in module auto_kappa.structure.supercell)

estimate_supercell_matrix_2d() (in module auto_kappa.structure.two) exceed_memory() (in module auto_kappa.alamode.log_parser) extract_afterward_lines() (in module auto_kappa.almlog.utils) extract_data_from_file() (in module auto_kappa.io.files) extract_lines_with_index() (in module auto_kappa.almlog.utils)

F

fc2 (auto_kappa.io.fcs.FCSxml property) fc2xml (auto_kappa.alamode.almcalc.AlamodeCalc property) fc3 (auto_kappa.io.fcs.FCSxml property) fc3_type (auto_kappa.alamode.almcalc.AlamodeCalc property) fc3xml (auto_kappa.alamode.almcalc.AlamodeCalc property) fc4 (auto_kappa.io.fcs.FCSxml property) fcsxml (auto_kappa.alamode.almcalc.AlamodeCalc property) FCSxml (class in auto_kappa.io.fcs) file_bands (auto_kappa.io.participation.BandPR property) file_pr (auto_kappa.io.participation.BandPR property) file_xml (auto_kappa.io.fcs.FCSxml property) filename (auto_kappa.io.dos.Dos property) (auto_kappa.io.gruneisen.GruAll property) (auto_kappa.io.suggest.Pattern property) (auto_kappa.io.suggest.SuggestLogParser property) filenames (auto_kappa.io.phonondb.Phonondb property) filenames_as_dict (auto_kappa.io.phonondb.Phonondb property) found_rank_deficient() (in module auto_kappa.alamode.errors)

frequencies (auto_kappa.almlog.core.ALMLOG property) (auto_kappa.io.gruneisen.GruAll property) (auto_kappa.io.gruneisen.Gruneisen property) (auto_kappa.io.result.Result attribute) (auto_kappa.io.scattering.Scattering property) frequency_range (auto_kappa.alamode.almcalc.AlamodeCalc property) from_dict() (auto_kappa.io.alm.AlamodeInput class method) (auto_kappa.io.alm.AlmInput class method) (auto_kappa.io.alm.AnphonInput class method) from_file() (auto_kappa.io.alm.AlamodeInput class method) (auto_kappa.io.alm.AlmInput class method) (auto_kappa.io.alm.AnphonInput class method) from_structure() (auto_kappa.io.alm.AlmInput class method) (auto_kappa.io.alm.AnphonInput class method) from_structure_file() (auto_kappa.io.alm.AlmInput class method) (auto_kappa.io.alm.AnphonInput class method) fromkeys() (auto_kappa.io.alm.AlamodeInput class method) (auto_kappa.io.alm.AlmInput class method) (auto_kappa.io.alm.AnphonInput class method)

G

gammas (auto_kappa.io.result.Result attribute) general (auto_kappa.io.result.Result attribute) general_keys (auto_kappa.io.alm.AlmInput attribute) (auto_kappa.io.alm.AnphonInput attribute) generate() (auto_kappa.alamode.tools.GenDisplacement.AlamodeDisplace method) generate_mapping_s2p() (in module auto_kappa.structure.comparison) generate_structures() (auto_kappa.alamode.tools.VASP.VaspParser method) get() (auto_kappa.io.alm.AlamodeInput method) (auto_kappa.io.alm.AlmInput method) (auto_kappa.io.alm.AnphonInput method) get_ak_logs() (in module auto_kappa.alamode.log_parser) get_alamode_variables_from_structure() (in module auto_kappa.io.alm) get_all_directories() (in module auto_kappa.io.times) get_amin_parameter() (in module auto_kappa.vasp.params) get_atomic_distance_list() (in module auto_kappa.structure.crystal) get_automatic_kmesh() (in module auto_kappa.structure.crystal) get_availabilities() (in module auto_kappa.calculators.scph) get_average_at_degenerate_point() (in module auto_kappa.io.analyzer) get_band_section_indices_labels() (in module auto_kappa.io.band) get_base_directory_name() (in module auto_kappa.cui.initialization) get_born_charges_from_vasprun() (in module auto_kappa.io.born) get_both_axis() (in module auto_kappa.plot.initialize) get_calculated_volumes_and_energies() (auto_kappa.vasp.relax.StrictRelaxation method) get_calculator() (auto_kappa.apdb.ApdbVasp method) get_cell() (auto_kappa.io.fcs.FCSxml method) get_center_of_primitive_cells() (auto_kappa.io.fcs.FCSxml method) get_commensurate_points() (in module auto_kappa.structure.crystal) get_cumulative_kappa() (auto_kappa.io.scattering.Scattering method) get_customized_cmap() (in module auto_kappa.plot.initialize) get_cutoffs_automatically() (in module auto_kappa.alamode.helpers) get_dfset() (in module auto_kappa.io.vasp) get_diagonal_length() (in module auto_kappa.structure.two) get_displacements() (auto_kappa.alamode.tools.VASP.VaspParser method) (auto_kappa.io.suggest.Pattern method) get_distances() (auto_kappa.io.fcs.FCSxml method) (auto_kappa.io.suggest.Pattern method) get_dos() (in module auto_kappa.io.dos) get_eigen() (in module auto_kappa.io.band) get_eigenvalues_from_logfile() (in module auto_kappa.alamode.log_parser) get_elements() (in module auto_kappa.io.dos) get_enmax() (in module auto_kappa.calculators.vasp) get_entropy() (auto_kappa.io.thermo.Thermo method) get_fc2() (auto_kappa.io.fcs.FCSxml method) get_fc3() (auto_kappa.io.fcs.FCSxml method) get_fc3_distances() (auto_kappa.io.fcs.FCSxml method) get_fc4() (auto_kappa.io.fcs.FCSxml method) get_fitting_error() (auto_kappa.vasp.relax.StrictRelaxation method) get_fmin_scph() (auto_kappa.alamode.almcalc.AlamodeCalc method) (in module auto_kappa.calculators.scph) get_formula() (in module auto_kappa.structure.crystal) get_free_energy() (auto_kappa.io.result.Result method) (auto_kappa.io.thermo.Thermo method) get_heat_capacity() (in module auto_kappa.io.analyzer) get_internal_energy() (auto_kappa.io.thermo.Thermo method) get_isofact_info() (in module auto_kappa.io.alm) get_kappa() (auto_kappa.io.kl.KappaShare method) (auto_kappa.io.kl.Kboth method) (auto_kappa.io.kl.KL method) get_kappa_directories() (auto_kappa.alamode.almcalc.AlamodeCalc method) (auto_kappa.alamode.plotter.AlamodePlotter method) get_kmin_cahill() (auto_kappa.io.scattering.Scattering method) get_kmode() (in module auto_kappa.io.analyzer) get_kpath() (in module auto_kappa.alamode.log_parser) get_kpoint_path() (in module auto_kappa.io.alm) get_kpoints() (auto_kappa.io.phonondb.Phonondb method) get_map_p2s() (auto_kappa.io.fcs.FCSxml method) get_mass_info() (in module auto_kappa.io.alm) get_minimum_frequency() (auto_kappa.alamode.almcalc.AlamodeCalc method) get_minimum_frequency_from_logfile() (in module auto_kappa.alamode.log_parser) get_neighboring_distances() (auto_kappa.io.suggest.SuggestLogParser method)

get_neighboring_info() (auto_kappa.io.suggest.SuggestLogParser method) get_nfreq() (in module auto_kappa.io.dos) get_nk_nbands() (in module auto_kappa.io.band) get_normal_bands() (in module auto_kappa.io.band) get_normal_index() (in module auto_kappa.structure.two) get_number_of_errors() (in module auto_kappa.vasp.params) get_number_of_same_structures() (in module auto_kappa.alamode.compat) get_optimal_nac() (auto_kappa.alamode.almcalc.AlamodeCalc method) get_optimal_structure() (auto_kappa.vasp.relax.StrictRelaxation method) get_optimal_volume() (in module auto_kappa.vasp.relax) get_output() (in module auto_kappa.utils.version) get_parser() (in module auto_kappa.alamode.log_parser) (in module auto_kappa.cui.ak_parser) get_position_list() (in module auto_kappa.almlog.utils) get_positions_symbols() (auto_kappa.io.fcs.FCSxml method) get_previous_nac() (in module auto_kappa.cui.initialization) get_previous_parameters() (in module auto_kappa.vasp.params) get_previously_calculated_structure() (in module auto_kappa.alamode.compat) get_previously_used_structure() (in module auto_kappa.compat) get_primitive() (auto_kappa.io.alm.AlmInput method) (auto_kappa.io.alm.AnphonInput method) (auto_kappa.io.phonondb.Phonondb method) get_primitive_info() (auto_kappa.almlog.core.ALMLOG method) get_primitive_structure_spglib() (in module auto_kappa.structure.crystal) get_relative_path() (auto_kappa.alamode.almcalc.AlamodeCalc method) get_representative_kpoint() (in module auto_kappa.alamode.pes) get_representative_kpoint_with_negative_freq() (in module auto_kappa.alamode.pes) get_required_parameters() (in module auto_kappa.cui.initialization) get_scattering_info() (auto_kappa.alamode.almcalc.AlamodeCalc method) (auto_kappa.alamode.plotter.AlamodePlotter method) get_scph_bands() (in module auto_kappa.io.band) get_specific_heat() (auto_kappa.io.thermo.Thermo method) get_spg_number() (in module auto_kappa.structure.crystal) get_standardized_structure() (in module auto_kappa.structure.crystal) get_standardized_structure_spglib() (in module auto_kappa.structure.crystal) get_status() (in module auto_kappa.alamode.io) get_strained_structure() (in module auto_kappa.vasp.relax) get_structure_matcher() (in module auto_kappa.structure.comparison) get_structures() (auto_kappa.apdb.ApdbVasp method) get_suggested_l1alpha() (auto_kappa.alamode.almcalc.AlamodeCalc method) get_suggested_structures() (auto_kappa.alamode.almcalc.AlamodeCalc method) (auto_kappa.io.suggest.Pattern method) get_supercell() (auto_kappa.io.fcs.FCSxml method) (auto_kappa.io.phonondb.Phonondb method) (in module auto_kappa.structure.crystal) get_symmetry_dataset() (in module auto_kappa.structure.crystal) get_symmetry_points_for_kpoint() (in module auto_kappa.alamode.pes) get_symmetry_points_from_file() (in module auto_kappa.io.band) get_symmetry_points_from_string() (in module auto_kappa.io.band) get_symprec() (in module auto_kappa.vasp.params) get_temperature() (auto_kappa.io.thermo.Thermo method) get_thickness() (in module auto_kappa.structure.two) get_times() (auto_kappa.alamode.log_parser.AkLog method) (in module auto_kappa.io.times) get_transformation() (auto_kappa.io.born.BORNINFO method) get_transformation_matrix() (in module auto_kappa.structure.utils) get_unitcell() (auto_kappa.io.phonondb.Phonondb method) get_unitcell_and_primitive_matrix() (in module auto_kappa.cui.suggest) get_used_memory() (in module auto_kappa.alamode.memory) get_vasp_calculator() (in module auto_kappa.calculators.vasp) get_version() (in module auto_kappa.alamode.log_parser) (in module auto_kappa.utils.version) get_volume() (in module auto_kappa.vasp.relax) get_working_directory() (auto_kappa.alamode.almcalc.AlamodeCalc method) (auto_kappa.alamode.helpers.AlamodeInputWriter method) gru_params (auto_kappa.io.gruneisen.GruAll property) (auto_kappa.io.gruneisen.Gruneisen property) GruAll (class in auto_kappa.io.gruneisen) Gruneisen (class in auto_kappa.io.gruneisen) GruneisenCalculator (class in auto_kappa.alamode.gruneisen)

H

harm_dfset (auto_kappa.alamode.almcalc.AlamodeCalc property) has_gap() (auto_kappa.io.scattering.Scattering method)

higher_dfset (auto_kappa.alamode.almcalc.AlamodeCalc property) higher_fcsxml (auto_kappa.alamode.almcalc.AlamodeCalc property)

I

include_isotope_effect() (auto_kappa.io.kl.KL method) index (auto_kappa.almlog.interaction.Atom attribute) interaction_keys (auto_kappa.io.alm.AlmInput attribute) inverse_lattice_vector (auto_kappa.alamode.tools.VASP.VaspParser property) inverse_transformation() (in module auto_kappa.structure.crystal) is_fc_given() (in module auto_kappa.alamode.errors)

is_node_busy() (in module auto_kappa.alamode.memory) is_perpendicular() (in module auto_kappa.structure.two) Isotope (class in auto_kappa.io.isotope) items() (auto_kappa.io.alm.AlamodeInput method) (auto_kappa.io.alm.AlmInput method) (auto_kappa.io.alm.AnphonInput method)

K

kappa (auto_kappa.io.scattering.Scattering property) kappa_keys_2 (auto_kappa.io.alm.AnphonInput attribute) KappaShare (class in auto_kappa.io.kl) Kboth (class in auto_kappa.io.kl) keys() (auto_kappa.io.alm.AlamodeInput method) (auto_kappa.io.alm.AlmInput method) (auto_kappa.io.alm.AnphonInput method) KL (class in auto_kappa.io.kl) klength2mesh() (in module auto_kappa.cui.suggest)

kmax (auto_kappa.io.band.Band property) (auto_kappa.io.band.SCPHBand property) kmode (auto_kappa.io.result.Result attribute) (auto_kappa.io.scattering.Scattering property) kpoints (auto_kappa.almlog.core.ALMLOG property) (auto_kappa.io.gruneisen.GruAll property) (auto_kappa.io.gruneisen.Gruneisen property) (auto_kappa.io.participation.BandPR property) (auto_kappa.io.scattering.Scattering property)

L

lattice_vector (auto_kappa.alamode.tools.VASP.VaspParser property) lifetime (auto_kappa.io.scattering.Scattering property) lmode (auto_kappa.io.result.Result attribute)

load() (auto_kappa.io.alm.AlamodeInput class method) (auto_kappa.io.alm.AlmInput class method) (auto_kappa.io.alm.AnphonInput class method) load_initial_structure() (auto_kappa.alamode.tools.VASP.VaspParser method)

M

magnitude (auto_kappa.alamode.almcalc.AlamodeCalc property) magnitude2 (auto_kappa.alamode.almcalc.AlamodeCalc property) main() (in module auto_kappa.alamode.log_parser) (in module auto_kappa.cui.ak_scripts) make_figure() (in module auto_kappa.plot.initialize) make_figure_bec() (in module auto_kappa.io.born) map_p2s (auto_kappa.io.fcs.FCSxml property) match_structures() (in module auto_kappa.structure.comparison) mater_dim (auto_kappa.apdb.ApdbVasp property) mfp (auto_kappa.io.scattering.Scattering property) minimum_frequency (auto_kappa.alamode.almcalc.AlamodeCalc property) modify_parameters_for_4ph() (auto_kappa.alamode.almcalc.AlamodeCalc method) module auto_kappa auto_kappa.alamode auto_kappa.alamode.almcalc auto_kappa.alamode.compat auto_kappa.alamode.errors auto_kappa.alamode.gruneisen auto_kappa.alamode.helpers auto_kappa.alamode.io auto_kappa.alamode.log_parser auto_kappa.alamode.memory auto_kappa.alamode.parameters auto_kappa.alamode.pes auto_kappa.alamode.plotter auto_kappa.alamode.runjob auto_kappa.alamode.tools auto_kappa.alamode.tools.analyze_phonons auto_kappa.alamode.tools.GenDisplacement auto_kappa.alamode.tools.VASP auto_kappa.almlog auto_kappa.almlog.core auto_kappa.almlog.dmatrix auto_kappa.almlog.fcs auto_kappa.almlog.frequencies auto_kappa.almlog.interaction auto_kappa.almlog.kpoint auto_kappa.almlog.structure auto_kappa.almlog.symmetry auto_kappa.almlog.system auto_kappa.almlog.utils auto_kappa.almlog.variables auto_kappa.apdb auto_kappa.calculators auto_kappa.calculators.alamode auto_kappa.calculators.compat auto_kappa.calculators.scph auto_kappa.calculators.vasp auto_kappa.compat auto_kappa.cui auto_kappa.cui.ak_log auto_kappa.cui.ak_parser auto_kappa.cui.ak_scripts auto_kappa.cui.compat auto_kappa.cui.initialization auto_kappa.cui.suggest auto_kappa.io auto_kappa.io.alm auto_kappa.io.analyzer auto_kappa.io.band auto_kappa.io.born auto_kappa.io.dos auto_kappa.io.fcs auto_kappa.io.files auto_kappa.io.gruneisen auto_kappa.io.isotope auto_kappa.io.kl auto_kappa.io.participation auto_kappa.io.phonondb auto_kappa.io.result auto_kappa.io.scattering auto_kappa.io.suggest auto_kappa.io.thermo auto_kappa.io.times auto_kappa.io.vasp auto_kappa.plot auto_kappa.plot.bandos auto_kappa.plot.fitting auto_kappa.plot.initialize auto_kappa.plot.pltalm auto_kappa.structure auto_kappa.structure.comparison auto_kappa.structure.crystal auto_kappa.structure.supercell auto_kappa.structure.two auto_kappa.structure.utils auto_kappa.units auto_kappa.utils auto_kappa.utils.isotopes auto_kappa.utils.version auto_kappa.vasp auto_kappa.vasp.params auto_kappa.vasp.relax auto_kappa.version

multiplicity (auto_kappa.io.result.Result attribute)

N

nac (auto_kappa.io.phonondb.Phonondb property) NameHandler (class in auto_kappa.alamode.helpers) nat (auto_kappa.alamode.tools.VASP.VaspParser property) natom_prim (auto_kappa.io.fcs.FCSxml property) natom_super (auto_kappa.io.fcs.FCSxml property) natoms (auto_kappa.io.dos.Dos property) nbands (auto_kappa.io.band.Band property) (auto_kappa.io.band.SCPHBand property) (auto_kappa.io.participation.BandPR property) nbody (auto_kappa.alamode.almcalc.AlamodeCalc property) negative_frequency() (in module auto_kappa.cui.ak_log) NeighborAtoms (class in auto_kappa.almlog.interaction) neighbors (auto_kappa.almlog.interaction.NeighborAtoms attribute) (auto_kappa.almlog.interaction.PairAtoms attribute)

nelems (auto_kappa.io.dos.Dos property) nfreq (auto_kappa.io.dos.Dos property) nk (auto_kappa.io.band.Band property) (auto_kappa.io.band.SCPHBand property) nmax_suggest (auto_kappa.alamode.almcalc.AlamodeCalc property) norm_idx() (auto_kappa.io.alm.AnphonInput method) norm_idx_abc (auto_kappa.alamode.almcalc.AlamodeCalc property) norm_idx_xyz (auto_kappa.alamode.almcalc.AlamodeCalc property) ntemps (auto_kappa.io.band.SCPHBand property) ntrans (auto_kappa.io.fcs.FCSxml property) num_elems (auto_kappa.alamode.almcalc.AlamodeCalc property) num_neighbors (auto_kappa.almlog.interaction.NeighborAtoms attribute)

O

optimal_volume (auto_kappa.vasp.relax.StrictRelaxation property) optimize_keys (auto_kappa.io.alm.AlmInput attribute)

out (auto_kappa.alamode.log_parser.AkLog property) output_structures() (auto_kappa.apdb.ApdbVasp method) (auto_kappa.vasp.relax.StrictRelaxation method)

P

PairAtoms (class in auto_kappa.almlog.interaction) params_mod (auto_kappa.apdb.ApdbVasp property) parse() (auto_kappa.alamode.tools.VASP.VaspParser method) parse_data_line() (in module auto_kappa.almlog.utils) parse_file_pr() (in module auto_kappa.io.participation) parse_gru_all() (in module auto_kappa.io.gruneisen) parse_neighbor_data() (in module auto_kappa.io.suggest) parse_suggest_log() (in module auto_kappa.io.suggest) parse_vasp_params() (in module auto_kappa.cui.compat) parse_xml() (auto_kappa.io.fcs.FCSxml method) Pattern (class in auto_kappa.io.suggest) patterns (auto_kappa.io.suggest.Pattern property) phonon (auto_kappa.io.phonondb.Phonondb property) Phonondb (class in auto_kappa.io.phonondb) plot() (auto_kappa.io.band.Band method) (auto_kappa.io.band.SCPHBand method) (auto_kappa.io.dos.Dos method) (auto_kappa.io.gruneisen.GruAll method) (auto_kappa.io.gruneisen.Gruneisen method) (auto_kappa.io.kl.Kboth method) (auto_kappa.io.kl.KL method) (auto_kappa.io.participation.BandPR method) (auto_kappa.io.thermo.Thermo method) plot_all_kappa() (auto_kappa.alamode.almcalc.AlamodeCalc method) (auto_kappa.alamode.plotter.AlamodePlotter method) (in module auto_kappa.plot.pltalm) plot_bandos() (auto_kappa.alamode.almcalc.AlamodeCalc method) (auto_kappa.alamode.plotter.AlamodePlotter method) plot_bandos_for_different_sizes() (in module auto_kappa.plot.bandos) plot_bands() (auto_kappa.io.band.Band method) (auto_kappa.io.band.SCPHBand method) plot_bm() (auto_kappa.vasp.relax.StrictRelaxation method) plot_bm_result() (in module auto_kappa.plot.fitting) plot_cumulative_kappa() (auto_kappa.alamode.almcalc.AlamodeCalc method) (auto_kappa.alamode.plotter.AlamodePlotter method) (in module auto_kappa.plot.pltalm) plot_cvsets() (in module auto_kappa.plot.pltalm) plot_entropy() (auto_kappa.io.thermo.Thermo method) plot_fc2() (auto_kappa.io.fcs.FCSxml method) plot_fc3() (auto_kappa.io.fcs.FCSxml method) plot_fc4() (auto_kappa.io.fcs.FCSxml method) plot_force_constants() (auto_kappa.alamode.almcalc.AlamodeCalc method) (auto_kappa.alamode.plotter.AlamodePlotter method) plot_free_energy() (auto_kappa.io.thermo.Thermo method) plot_internal_energy() (auto_kappa.io.thermo.Thermo method) plot_kappa() (auto_kappa.alamode.almcalc.AlamodeCalc method) (auto_kappa.alamode.plotter.AlamodePlotter method) plot_kappa_vs_grain_size() (in module auto_kappa.alamode.plotter) plot_lifetime() (auto_kappa.alamode.almcalc.AlamodeCalc method) (auto_kappa.alamode.plotter.AlamodePlotter method) (auto_kappa.io.scattering.Scattering method) plot_pdos() (auto_kappa.io.dos.Dos method)

plot_physical_properties() (auto_kappa.vasp.relax.StrictRelaxation method) plot_scattering_rates() (auto_kappa.alamode.almcalc.AlamodeCalc method) (auto_kappa.alamode.plotter.AlamodePlotter method) (auto_kappa.io.scattering.Scattering method) plot_scph_force_constants() (in module auto_kappa.calculators.scph) plot_specific_heat() (auto_kappa.io.thermo.Thermo method) plot_tensor_ellipsoid() (in module auto_kappa.io.born) plot_thermodynamic_properties() (auto_kappa.alamode.almcalc.AlamodeCalc method) (auto_kappa.alamode.plotter.AlamodePlotter method) plot_times() (auto_kappa.alamode.log_parser.AkLog method) plot_times_with_pie() (in module auto_kappa.plot.pltalm) plot_with_weighted_colors() (auto_kappa.io.band.Band method) (auto_kappa.io.band.SCPHBand method) pop() (auto_kappa.io.alm.AlamodeInput method) (auto_kappa.io.alm.AlmInput method) (auto_kappa.io.alm.AnphonInput method) popitem() (auto_kappa.io.alm.AlamodeInput method) (auto_kappa.io.alm.AlmInput method) (auto_kappa.io.alm.AnphonInput method) prefix (auto_kappa.alamode.almcalc.AlamodeCalc property) prepare_bandos_axes() (in module auto_kappa.plot.initialize) prepare_two_axes() (in module auto_kappa.plot.initialize) prim_fcs (auto_kappa.io.born.BORNINFO property) prim_vasp (auto_kappa.io.born.BORNINFO property) primitive (auto_kappa.alamode.almcalc.AlamodeCalc property) (auto_kappa.almlog.core.ALMLOG property) (auto_kappa.apdb.ApdbVasp property) (auto_kappa.io.alm.AlmInput property) (auto_kappa.io.alm.AnphonInput property) (auto_kappa.io.phonondb.Phonondb property) primitive_matrix (auto_kappa.alamode.almcalc.AlamodeCalc property) (auto_kappa.apdb.ApdbVasp property) (auto_kappa.io.phonondb.Phonondb property) primitive_positions (auto_kappa.io.fcs.FCSxml property) primitive_symbols (auto_kappa.io.fcs.FCSxml property) print_2d_system_notation() (in module auto_kappa.structure.two) print_conditions() (in module auto_kappa.cui.ak_log) print_fc2_phonopy() (auto_kappa.io.fcs.FCSxml method) print_fc3_phonopy() (auto_kappa.io.fcs.FCSxml method) print_fc4_phonopy() (auto_kappa.io.fcs.FCSxml method) print_fc_error() (auto_kappa.alamode.almcalc.AlamodeCalc method) print_length_info() (in module auto_kappa.structure.two) print_machine_info() (in module auto_kappa.cui.ak_log) print_neighboring_info() (auto_kappa.io.suggest.SuggestLogParser method) print_options() (in module auto_kappa.cui.ak_log) print_patterns() (auto_kappa.io.suggest.Pattern method) print_results() (auto_kappa.vasp.relax.StrictRelaxation method) print_space_group() (in module auto_kappa.cui.ak_log) print_times() (in module auto_kappa.cui.ak_log) print_vasp_params() (in module auto_kappa.io.vasp) proc_val() (in module auto_kappa.io.alm) propts_mode_type (auto_kappa.alamode.almcalc.AlamodeCalc attribute) prs (auto_kappa.io.participation.BandPR property)

Q

qha_keys (auto_kappa.io.alm.AnphonInput attribute)

R

read_alamode_input() (in module auto_kappa.io.alm) read_alamode_log() (in module auto_kappa.almlog.core) read_bfile() (auto_kappa.io.band.Band method) (auto_kappa.io.band.SCPHBand method) read_born_info() (in module auto_kappa.io.born) read_classical() (in module auto_kappa.io.result) read_dfset() (in module auto_kappa.io.vasp) read_dmatrix() (in module auto_kappa.almlog.dmatrix) read_fcs() (in module auto_kappa.almlog.fcs) read_fcsxml() (in module auto_kappa.io.result) read_file() (auto_kappa.io.dos.Dos method) read_forcesets() (in module auto_kappa.io.phonondb) read_frequencies() (in module auto_kappa.almlog.frequencies) read_frequency() (in module auto_kappa.io.result) read_frequency_range() (in module auto_kappa.alamode.helpers) read_incar() (in module auto_kappa.io.vasp) read_interaction() (in module auto_kappa.almlog.interaction) read_isotope() (in module auto_kappa.io.isotope) read_kappa() (in module auto_kappa.alamode.helpers) read_kl_file() (in module auto_kappa.io.kl) read_kpoint() (in module auto_kappa.io.result) read_kpoints() (in module auto_kappa.almlog.kpoint) (in module auto_kappa.io.vasp) read_log_eigen() (in module auto_kappa.alamode.log_parser) read_log_fc() (in module auto_kappa.alamode.log_parser) read_log_fc2() (in module auto_kappa.alamode.log_parser) read_log_forces() (in module auto_kappa.alamode.log_parser) read_log_kappa() (in module auto_kappa.alamode.log_parser) read_log_kappa_each() (in module auto_kappa.alamode.log_parser) read_log_lasso() (in module auto_kappa.alamode.log_parser) read_log_nac() (in module auto_kappa.alamode.log_parser) read_log_relax() (in module auto_kappa.alamode.log_parser) read_log_suggest() (in module auto_kappa.alamode.log_parser)

read_outcar() (in module auto_kappa.io.vasp) read_parameters_from_phonondb() (in module auto_kappa.cui.initialization) read_phonondb() (in module auto_kappa.cui.initialization) read_phonopy_conf() (in module auto_kappa.io.phonondb) read_relaxation_time() (in module auto_kappa.io.result) read_result_file() (in module auto_kappa.io.result) read_section() (in module auto_kappa.almlog.utils) read_smearing() (in module auto_kappa.io.result) read_structure() (in module auto_kappa.almlog.structure) read_structure_from_file() (in module auto_kappa.io.alm) read_symmetry() (in module auto_kappa.almlog.symmetry) read_system() (in module auto_kappa.almlog.system) (in module auto_kappa.io.result) read_temperature() (in module auto_kappa.io.result) read_thermo_file() (in module auto_kappa.io.thermo) read_variables() (in module auto_kappa.almlog.variables) REDIRECT (auto_kappa.io.alm.AlamodeInput attribute) (auto_kappa.io.alm.AlmInput attribute) (auto_kappa.io.alm.AnphonInput attribute) reflect_previous_jobs() (in module auto_kappa.vasp.params) relax_keys (auto_kappa.io.alm.AnphonInput attribute) relaxation_with_different_volumes() (in module auto_kappa.vasp.relax) remove_old_kappa_data() (in module auto_kappa.calculators.compat) replace_symbols_to_blank() (in module auto_kappa.almlog.utils) required_params (auto_kappa.io.alm.AlmInput attribute) (auto_kappa.io.alm.AnphonInput attribute) rerun_with_omp() (in module auto_kappa.cui.ak_log) Result (class in auto_kappa.io.result) run_alamode() (auto_kappa.alamode.almcalc.AlamodeCalc method) (in module auto_kappa.alamode.runjob) run_relaxation() (auto_kappa.apdb.ApdbVasp method) run_vasp() (auto_kappa.apdb.ApdbVasp method) (in module auto_kappa.calculators.vasp) run_vasp_with_custodian() (in module auto_kappa.calculators.vasp)

S

save() (auto_kappa.io.alm.AlamodeInput method) (auto_kappa.io.alm.AlmInput method) (auto_kappa.io.alm.AnphonInput method) savefigure() (in module auto_kappa.plot.pltalm) Scattering (class in auto_kappa.io.scattering) scattering_rates (auto_kappa.io.scattering.Scattering attribute) scell_matrix (auto_kappa.alamode.almcalc.AlamodeCalc property) (auto_kappa.apdb.ApdbVasp property) (auto_kappa.io.phonondb.Phonondb property) scph_keys (auto_kappa.io.alm.AnphonInput attribute) SCPHBand (class in auto_kappa.io.band) sections (auto_kappa.almlog.core.ALMLOG property) serial (auto_kappa.almlog.interaction.NeighborAtoms attribute) set4bandos() (in module auto_kappa.plot.initialize) set_averaged_velocities() (auto_kappa.io.scattering.Scattering method) set_axis() (in module auto_kappa.plot.initialize) set_axis_lim() (in module auto_kappa.plot.initialize) set_basedir_name() (auto_kappa.alamode.almcalc.AlamodeCalc method) set_born_info() (auto_kappa.io.born.BORNINFO method) set_center() (in module auto_kappa.structure.two) set_cutoffs() (auto_kappa.alamode.almcalc.AlamodeCalc method) set_eigen_values() (auto_kappa.io.band.Band method) (auto_kappa.io.band.SCPHBand method) set_initial_structure() (auto_kappa.alamode.tools.VASP.VaspParser method) set_kmode() (auto_kappa.io.scattering.Scattering method) set_kpoint() (auto_kappa.io.alm.AnphonInput method) set_legend() (in module auto_kappa.plot.initialize) set_lifetime() (auto_kappa.io.scattering.Scattering method) set_logging() (in module auto_kappa.cui.ak_log) set_matplot() (in module auto_kappa.plot.initialize) set_mfp() (auto_kappa.io.scattering.Scattering method) set_modified_params() (auto_kappa.apdb.ApdbVasp method) set_nbody_automatically() (auto_kappa.alamode.almcalc.AlamodeCalc method) set_neighboring_info() (auto_kappa.io.suggest.SuggestLogParser method) set_parameters_evec() (in module auto_kappa.alamode.parameters) set_parameters_kappa() (in module auto_kappa.alamode.parameters) set_parameters_scph() (in module auto_kappa.calculators.scph) set_pattern_info() (auto_kappa.io.suggest.Pattern method)

set_prim_fcs() (auto_kappa.io.born.BORNINFO method) set_primitive() (auto_kappa.io.alm.AnphonInput method) set_result() (auto_kappa.io.result.Result method) set_scattering_rate_boundary() (auto_kappa.io.scattering.Scattering method) set_scattering_rate_isotope() (auto_kappa.io.scattering.Scattering method) set_scattering_rate_phph() (auto_kappa.io.scattering.Scattering method) set_second_axis() (in module auto_kappa.plot.initialize) set_spaces() (in module auto_kappa.plot.initialize) set_structure() (auto_kappa.io.suggest.Pattern method) set_symmetry_points() (auto_kappa.io.band.Band method) (auto_kappa.io.band.SCPHBand method) set_thermo_data() (auto_kappa.io.thermo.Thermo method) set_total_scattering_rate() (auto_kappa.io.scattering.Scattering method) set_vacuum_to_2d_structure() (in module auto_kappa.structure.two) set_xticks_labels() (in module auto_kappa.plot.bandos) setdefault() (auto_kappa.io.alm.AlamodeInput method) (auto_kappa.io.alm.AlmInput method) (auto_kappa.io.alm.AnphonInput method) should_rerun_alamode() (in module auto_kappa.alamode.helpers) should_rerun_band() (in module auto_kappa.alamode.helpers) size (auto_kappa.io.scattering.Scattering property) space_group (auto_kappa.io.suggest.SuggestLogParser property) start_autokappa() (in module auto_kappa.cui.ak_log) start_larger_supercell() (in module auto_kappa.cui.ak_log) StrictRelaxation (class in auto_kappa.vasp.relax) structure (auto_kappa.io.alm.AlmInput property) (auto_kappa.io.suggest.Pattern property) (auto_kappa.io.suggest.SuggestLogParser property) structures (auto_kappa.apdb.ApdbVasp property) suggest_fc2_cutoff() (in module auto_kappa.structure.two) suggest_structures_and_kmeshes() (in module auto_kappa.cui.suggest) SuggestLogParser (class in auto_kappa.io.suggest) supercell (auto_kappa.alamode.almcalc.AlamodeCalc property) (auto_kappa.apdb.ApdbVasp property) (auto_kappa.io.fcs.FCSxml property) (auto_kappa.io.phonondb.Phonondb property) switch_abc_axis() (in module auto_kappa.structure.two) symmetry_error() (in module auto_kappa.cui.ak_log)

T

temperature (auto_kappa.io.scattering.Scattering property) temperatures (auto_kappa.io.kl.KappaShare property) (auto_kappa.io.kl.Kboth property) (auto_kappa.io.kl.KL property) (auto_kappa.io.scattering.Scattering property) Thermo (class in auto_kappa.io.thermo) thickness (auto_kappa.alamode.almcalc.AlamodeCalc property) to_file() (auto_kappa.io.alm.AlmInput method) (auto_kappa.io.alm.AnphonInput method)

to_json() (auto_kappa.io.alm.AlamodeInput method) (auto_kappa.io.alm.AlmInput method) (auto_kappa.io.alm.AnphonInput method) too_many_errors() (in module auto_kappa.apdb) total_scattering_rate (auto_kappa.io.scattering.Scattering property) trajectory (auto_kappa.apdb.ApdbVasp property) transform_prim2unit() (in module auto_kappa.structure.crystal) transform_unit2prim() (in module auto_kappa.structure.crystal)

U

unitcell (auto_kappa.alamode.almcalc.AlamodeCalc property) (auto_kappa.apdb.ApdbVasp property) (auto_kappa.io.phonondb.Phonondb property) unsafe_hash() (auto_kappa.io.alm.AlamodeInput method) (auto_kappa.io.alm.AlmInput method) (auto_kappa.io.alm.AnphonInput method)

update() (auto_kappa.io.alm.AlamodeInput method) (auto_kappa.io.alm.AlmInput method) (auto_kappa.io.alm.AnphonInput method) update_command() (auto_kappa.apdb.ApdbVasp method) update_commands() (auto_kappa.alamode.almcalc.AlamodeCalc method) update_structures() (auto_kappa.apdb.ApdbVasp method) use_omp_for_anphon() (in module auto_kappa.cui.initialization)

V

validate_monty_v1() (auto_kappa.io.alm.AlamodeInput class method) (auto_kappa.io.alm.AlmInput class method) (auto_kappa.io.alm.AnphonInput class method) validate_monty_v2() (auto_kappa.io.alm.AlamodeInput class method) (auto_kappa.io.alm.AlmInput class method) (auto_kappa.io.alm.AnphonInput class method) values() (auto_kappa.io.alm.AlamodeInput method) (auto_kappa.io.alm.AlmInput method) (auto_kappa.io.alm.AnphonInput method)

variables (auto_kappa.almlog.core.ALMLOG property) VaspParser (class in auto_kappa.alamode.tools.VASP) velocities (auto_kappa.io.result.Result attribute) verbose (auto_kappa.alamode.almcalc.AlamodeCalc property) volumes (auto_kappa.vasp.relax.StrictRelaxation property)

W

was_primitive_changed() (in module auto_kappa.alamode.compat) was_tolerance_changed() (in module auto_kappa.alamode.compat) wasfinished() (in module auto_kappa.io.vasp) wasfinished_alamode() (in module auto_kappa.alamode.io) with_different_volumes() (auto_kappa.vasp.relax.StrictRelaxation method) write() (auto_kappa.io.born.BORNINFO method) write_alamode_input() (auto_kappa.alamode.almcalc.AlamodeCalc method) write_born_info() (in module auto_kappa.io.born)

write_displacement_info() (in module auto_kappa.alamode.io) write_kappa_vs_grain_size() (auto_kappa.alamode.almcalc.AlamodeCalc method) (auto_kappa.alamode.plotter.AlamodePlotter method) write_lifetime_at_given_temperature() (auto_kappa.alamode.almcalc.AlamodeCalc method) (auto_kappa.alamode.plotter.AlamodePlotter method) write_output_yaml() (in module auto_kappa.io.files) write_parameters() (in module auto_kappa.cui.ak_log) write_yaml() (auto_kappa.alamode.log_parser.AkLog method)

X

x_fractional (auto_kappa.alamode.tools.VASP.VaspParser property)

Y

yamlfile_for_outdir (auto_kappa.alamode.almcalc.AlamodeCalc property)