Index

A

adjust_random_displacements() (in module auto_kappa.alamode.displacements) adjust_vacuum_size() (in module auto_kappa.structure.two) AkLog (class in auto_kappa.alamode.log_parser) AlamodeDisplace (class in auto_kappa.alamode.tools.GenDisplacement) AlamodeInput (class in auto_kappa.io.alm) 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_obj() (in module auto_kappa.alamode.tools.analyze_phonons) AnphonInput (class in auto_kappa.io.alm) 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.displacements module auto_kappa.alamode.errors 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.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.calculators module auto_kappa.calculators.compat module auto_kappa.calculators.kmesh_int module auto_kappa.compat module auto_kappa.cui module auto_kappa.cui.ak_log module auto_kappa.cui.ak_parser module auto_kappa.cui.compat module auto_kappa.io.alm module auto_kappa.io.band module auto_kappa.io.files module auto_kappa.math module auto_kappa.math.statistics module auto_kappa.parameters 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.config module auto_kappa.utils.isotopes module auto_kappa.utils.system module auto_kappa.utils.version module auto_kappa.vasp module auto_kappa.vasp.params module auto_kappa.version module

B

Band (class in auto_kappa.io.band)

C

calc_g2_factor() (in module auto_kappa.io.alm) cells_equal() (in module auto_kappa.structure.comparison) center (auto_kappa.almlog.interaction.PairAtoms attribute) change_structure_format() (in module auto_kappa.structure.utils) check_2d_structure() (in module auto_kappa.structure.two) check_ak_options() (in module auto_kappa.cui.compat) check_parameters() (auto_kappa.io.alm.AlmInput method) (auto_kappa.io.alm.AnphonInput method)

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) convert_numpy() (in module auto_kappa.io.files) copy() (auto_kappa.io.alm.AlamodeInput method) (auto_kappa.io.alm.AlmInput method) (auto_kappa.io.alm.AnphonInput method)

D

deep_update() (in module auto_kappa.utils.config) dim (auto_kappa.io.alm.AlamodeInput property) (auto_kappa.io.alm.AlmInput property) (auto_kappa.io.alm.AnphonInput property)

directory (auto_kappa.alamode.log_parser.AkLog property) distance (auto_kappa.almlog.interaction.NeighborAtoms attribute) duration (auto_kappa.almlog.core.ALMLOG property)

E

element (auto_kappa.almlog.interaction.Atom attribute) end_autokappa() (in module auto_kappa.cui.ak_log) 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

found_rank_deficient() (in module auto_kappa.alamode.errors) frequencies (auto_kappa.almlog.core.ALMLOG 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

general_keys (auto_kappa.io.alm.AlmInput attribute) (auto_kappa.io.alm.AnphonInput attribute) generate() (auto_kappa.alamode.tools.GenDisplacement.AlamodeDisplace method) generate_displaced_structures() (in module auto_kappa.alamode.displacements) 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_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_band_section_indices_labels() (in module auto_kappa.io.band) get_bose() (in module auto_kappa.math.statistics) get_both_axis() (in module auto_kappa.plot.initialize) get_commensurate_points() (in module auto_kappa.structure.crystal) get_cpu_info() (in module auto_kappa.utils.system) get_cpu_model() (in module auto_kappa.utils.system) get_customized_cmap() (in module auto_kappa.plot.initialize) get_diagonal_length() (in module auto_kappa.structure.two) get_diffrential_statistics() (in module auto_kappa.math.statistics) get_diffrential_statistics2() (in module auto_kappa.math.statistics) get_displacements() (auto_kappa.alamode.tools.VASP.VaspParser method) get_eigen() (in module auto_kappa.io.band) get_eigenvalues_from_logfile() (in module auto_kappa.alamode.log_parser) get_fd() (in module auto_kappa.math.statistics) get_formula() (in module auto_kappa.structure.crystal) get_isofact_info() (in module auto_kappa.io.alm) get_kmesh_interpolate() (in module auto_kappa.calculators.kmesh_int) get_kpath() (in module auto_kappa.alamode.log_parser) get_kpoint_path() (in module auto_kappa.io.alm) get_mass_info() (in module auto_kappa.io.alm) get_minimum_frequency_from_logfile() (in module auto_kappa.alamode.log_parser) 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_os_info() (in module auto_kappa.utils.system) 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_potcar_setups() (in module auto_kappa.utils.config) get_previous_parameters() (in module auto_kappa.vasp.params) get_previously_used_structure() (in module auto_kappa.compat) get_primitive() (auto_kappa.io.alm.AlmInput method) (auto_kappa.io.alm.AnphonInput method) get_primitive_info() (auto_kappa.almlog.core.ALMLOG method) get_primitive_structure_spglib() (in module auto_kappa.structure.crystal) get_scph_bands() (in module auto_kappa.io.band) 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_statistical() (in module auto_kappa.math.statistics) get_status() (in module auto_kappa.alamode.io) get_structure_matcher() (in module auto_kappa.structure.comparison) get_supercell() (in module auto_kappa.structure.crystal) get_symmetry_dataset() (in module auto_kappa.structure.crystal) 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_thickness() (in module auto_kappa.structure.two) get_times() (auto_kappa.alamode.log_parser.AkLog method) get_transformation_matrix() (in module auto_kappa.structure.utils) get_transformation_matrix_prim2scell() (in module auto_kappa.structure.crystal) get_used_memory() (in module auto_kappa.alamode.memory) get_vasp_parameters() (in module auto_kappa.utils.config) get_vasp_parameters_by_mode() (in module auto_kappa.utils.config) get_version() (in module auto_kappa.alamode.log_parser) (in module auto_kappa.utils.version) get_xc() (in module auto_kappa.utils.config)

I

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) items() (auto_kappa.io.alm.AlamodeInput method) (auto_kappa.io.alm.AlmInput method) (auto_kappa.io.alm.AnphonInput method)

K

kappa_keys_2 (auto_kappa.io.alm.AnphonInput attribute) keys() (auto_kappa.io.alm.AlamodeInput method) (auto_kappa.io.alm.AlmInput method) (auto_kappa.io.alm.AnphonInput method)

kmax (auto_kappa.io.band.Band property) (auto_kappa.io.band.SCPHBand property) kpoints (auto_kappa.almlog.core.ALMLOG property)

L

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

load_default_config() (in module auto_kappa.utils.config) load_initial_structure() (auto_kappa.alamode.tools.VASP.VaspParser method) load_user_config() (in module auto_kappa.utils.config)

M

main() (in module auto_kappa.alamode.log_parser) make_figure() (in module auto_kappa.plot.initialize) match_structures() (in module auto_kappa.structure.comparison) module auto_kappa auto_kappa.alamode auto_kappa.alamode.displacements auto_kappa.alamode.errors auto_kappa.alamode.io auto_kappa.alamode.log_parser auto_kappa.alamode.memory auto_kappa.alamode.parameters 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.calculators auto_kappa.calculators.compat auto_kappa.calculators.kmesh_int auto_kappa.compat auto_kappa.cui auto_kappa.cui.ak_log auto_kappa.cui.ak_parser auto_kappa.cui.compat auto_kappa.io.alm auto_kappa.io.band auto_kappa.io.files auto_kappa.math auto_kappa.math.statistics auto_kappa.parameters 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.config auto_kappa.utils.isotopes auto_kappa.utils.system auto_kappa.utils.version auto_kappa.vasp auto_kappa.vasp.params auto_kappa.version

N

nat (auto_kappa.alamode.tools.VASP.VaspParser property) nbands (auto_kappa.io.band.Band property) (auto_kappa.io.band.SCPHBand 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)

nk (auto_kappa.io.band.Band property) (auto_kappa.io.band.SCPHBand property) norm_idx() (auto_kappa.io.alm.AnphonInput method) ntemps (auto_kappa.io.band.SCPHBand property) num_neighbors (auto_kappa.almlog.interaction.NeighborAtoms attribute)

O

optimize_keys (auto_kappa.io.alm.AlmInput attribute)

out (auto_kappa.alamode.log_parser.AkLog property)

P

PairAtoms (class in auto_kappa.almlog.interaction) parse() (auto_kappa.alamode.tools.VASP.VaspParser method) parse_data_line() (in module auto_kappa.almlog.utils) plot() (auto_kappa.io.band.Band method) (auto_kappa.io.band.SCPHBand method) plot_all_kappa() (in module auto_kappa.plot.pltalm) 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_result() (in module auto_kappa.plot.fitting) plot_cumulative_kappa() (in module auto_kappa.plot.pltalm) plot_cvsets() (in module auto_kappa.plot.pltalm) 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) prepare_bandos_axes() (in module auto_kappa.plot.initialize) prepare_two_axes() (in module auto_kappa.plot.initialize) primitive (auto_kappa.almlog.core.ALMLOG property) (auto_kappa.io.alm.AlmInput property) (auto_kappa.io.alm.AnphonInput property) print_2d_system_notation() (in module auto_kappa.structure.two) print_conditions() (in module auto_kappa.cui.ak_log) print_cpu_info() (in module auto_kappa.cui.ak_log) print_hostname() (in module auto_kappa.cui.ak_log) print_length_info() (in module auto_kappa.structure.two) print_options() (in module auto_kappa.cui.ak_log) print_os_info() (in module auto_kappa.cui.ak_log) print_space_group() (in module auto_kappa.cui.ak_log) print_system_info() (in module auto_kappa.cui.ak_log) print_times() (in module auto_kappa.cui.ak_log) proc_val() (in module auto_kappa.io.alm)

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_bfile_scph() (auto_kappa.io.band.SCPHBand method) read_dmatrix() (in module auto_kappa.almlog.dmatrix) read_fcs() (in module auto_kappa.almlog.fcs) read_frequencies() (in module auto_kappa.almlog.frequencies) read_interaction() (in module auto_kappa.almlog.interaction) read_kpoints() (in module auto_kappa.almlog.kpoint) 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_section() (in module auto_kappa.almlog.utils) 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) 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) 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) run() (in module auto_kappa.utils.system) run_alamode() (in module auto_kappa.alamode.runjob)

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) sci2text() (in module auto_kappa.plot.initialize) 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_axis() (in module auto_kappa.plot.initialize) set_axis_lim() (in module auto_kappa.plot.initialize) set_center() (in module auto_kappa.structure.two) set_eigen_values() (auto_kappa.io.band.Band method) (auto_kappa.io.band.SCPHBand method) set_eigen_values_scph() (auto_kappa.io.band.SCPHBand method) set_initial_structure() (auto_kappa.alamode.tools.VASP.VaspParser method) set_kpoint() (auto_kappa.io.alm.AnphonInput method) set_legend() (in module auto_kappa.plot.initialize)

set_logging() (in module auto_kappa.cui.ak_log) set_matplot() (in module auto_kappa.plot.initialize) set_parameters_evec() (in module auto_kappa.alamode.parameters) set_parameters_kappa() (in module auto_kappa.alamode.parameters) set_primitive() (auto_kappa.io.alm.AnphonInput method) set_second_axis() (in module auto_kappa.plot.initialize) set_spaces() (in module auto_kappa.plot.initialize) set_symmetry_points() (auto_kappa.io.band.Band method) (auto_kappa.io.band.SCPHBand 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) start_autokappa() (in module auto_kappa.cui.ak_log) start_larger_supercell() (in module auto_kappa.cui.ak_log) structure (auto_kappa.io.alm.AlmInput property) suggest_fc2_cutoff() (in module auto_kappa.structure.two) switch_abc_axis() (in module auto_kappa.structure.two) symmetry_error() (in module auto_kappa.cui.ak_log)

T

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)

transform_prim2unit() (in module auto_kappa.structure.crystal) transform_unit2prim() (in module auto_kappa.structure.crystal)

U

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)

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)

W

wasfinished_alamode() (in module auto_kappa.alamode.io) write_displacement_info() (in module auto_kappa.alamode.io)

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)