Index

A

AbortOnCollision (class in wfl.generate.md.abort) AbortSimBase (class in wfl.generate.md.abort_base) ace_fit_jl_path() (in module wfl.fit.utils) Aims (class in wfl.calculators.aims) all_written() (wfl.configset.OutputSpec method) antisite() (in module wfl.generate.supercells) at_copy_save_results() (in module wfl.utils.at_copy_save_results) atomization_energy() (in module wfl.utils.configs)

atoms_ok() (wfl.generate.md.abort.AbortOnCollision method) (wfl.generate.md.abort_base.AbortSimBase method) atoms_to_list() (in module wfl.utils.misc) AutoparaInfo (class in wfl.autoparallelize) (class in wfl.autoparallelize.autoparainfo) autoparallelize() (in module wfl.autoparallelize) (in module wfl.autoparallelize.base) autoparallelize_docstring() (in module wfl.autoparallelize) (in module wfl.autoparallelize.base)

B

BasinHoppingORCA (class in wfl.calculators.orca.basinhopping) biased_select_conf() (in module wfl.select.flat_histogram)

buildcell() (in module wfl.generate.buildcell) by_bool_func() (in module wfl.select.simple) by_index() (in module wfl.select.simple)

C

calc_list() (in module wfl.utils.ndim_neighbor_list) calc_list_cells() (in module wfl.utils.ndim_neighbor_list) calculate() (in module wfl.calculators.generic) (in module wfl.descriptors.quippy) (wfl.calculators.aims.Aims method) (wfl.calculators.castep.Castep method) (wfl.calculators.espresso.Espresso method) (wfl.calculators.mopac.MOPAC method) (wfl.calculators.orca.basinhopping.BasinHoppingORCA method) (wfl.calculators.orca.ORCA method) (wfl.calculators.vasp.Vasp method) calculate_committee() (in module wfl.calculators.committee) calculate_descriptor() (in module wfl.cli.commands.descriptor) Castep (class in wfl.calculators.castep) chunks() (in module wfl.utils.misc) clean_dir() (in module wfl.utils.file_utils) clean_rundir() (in module wfl.calculators.utils) (wfl.calculators.wfl_fileio_calculator.WFLFileIOCalculator method)

cleanup() (wfl.calculators.orca.ORCA method) (wfl.calculators.wfl_fileio_calculator.WFLFileIOCalculator method) close() (wfl.configset.OutputSpec method) compare_manual_minima() (in module wfl.select.selection_space) composition_space_coord() (in module wfl.utils.vol_composition_space) composition_space_Zs() (in module wfl.utils.vol_composition_space) config_type_append() (in module wfl.generate.utils) ConfigSet (class in wfl.configset) construct_calculator_picklesafe() (in module wfl.utils.parallel) construct_glue_2b() (in module wfl.fit.gap.glue_2b) conv_buildcell_out() (in module wfl.generate.buildcell) copy_properties() (in module wfl.fit.utils) create_input() (in module wfl.generate.buildcell) CUR() (in module wfl.select.by_descriptor) CUR_conf_global() (in module wfl.select.by_descriptor) cur_iter (wfl.utils.params.Params property) cur_loc (wfl.configset.ConfigSet property)

D

default_parameters (wfl.calculators.orca.ORCA attribute) (wfl.calculators.vasp.Vasp attribute) derive_normal_mode_info() (wfl.generate.normal_modes.NormalModes method) descriptor_2brn_uniform_file() (in module wfl.descriptor_heuristics) descriptors_from_length_scales() (in module wfl.descriptor_heuristics) dft_code (wfl.utils.params.Params property)

dft_params (wfl.utils.params.Params property) dict_to_gap_fit_string() (in module wfl.fit.gap.simple) dict_to_quip_str() (in module wfl.utils.quip_cli_strings) dict_tuple_keys_to_str() (in module wfl.utils.misc) do_in_pool() (in module wfl.autoparallelize.pool) do_remotely() (in module wfl.autoparallelize.remote) do_svd() (in module wfl.select.by_descriptor)

E

Espresso (class in wfl.calculators.espresso) evals_to_freqs() (wfl.generate.normal_modes.NormalModes static method) evaluate_basin_hopping() (in module wfl.calculators.orca.basinhopping)

evecs_to_modes() (wfl.generate.normal_modes.NormalModes static method) extra_info() (in module wfl.cli.cli_options) extract_e0() (in module wfl.utils.gap_xml_tools)

F

find_hull() (in module wfl.utils.convex_hull) find_isolated_atoms() (in module wfl.utils.configs) find_voids() (in module wfl.utils.find_voids) fit() (in module wfl.fit.ace) (in module wfl.fit.gap.multistage) (in module wfl.fit.mace)

fix_stress_virial() (in module wfl.fit.utils) freqs_to_evals() (wfl.generate.normal_modes.NormalModes static method) from_any_to_Descriptor() (in module wfl.descriptors.quippy)

G

gap_relocate() (in module wfl.fit.gap.relocate) GAP_xml_modify_label() (in module wfl.fit.gap.multistage) generate_normal_modes_parallel_atoms() (in module wfl.generate.normal_modes) generate_normal_modes_parallel_hessian() (in module wfl.generate.normal_modes) get() (wfl.utils.params.Params method) get_default_multiplicity() (wfl.calculators.orca.ORCA static method)

get_homo() (wfl.calculators.orca.basinhopping.BasinHoppingORCA method) get_multiplicity() (wfl.calculators.orca.basinhopping.BasinHoppingORCA method) get_remote_info() (in module wfl.autoparallelize.utils) get_wfl_version() (in module wfl.utils.version) greedy_fps_conf_global() (in module wfl.select.by_descriptor) grouper() (in module wfl.autoparallelize.utils) groups() (wfl.configset.ConfigSet method)

I

implemented_calculators (wfl.utils.params.Params attribute) implemented_properties (wfl.calculators.aims.Aims attribute) (wfl.calculators.castep.Castep attribute) (wfl.calculators.espresso.Espresso attribute) (wfl.calculators.orca.basinhopping.BasinHoppingORCA attribute) (wfl.calculators.orca.ORCA attribute)

increment_active_iter() (in module wfl.utils.logging) init() (in module wfl.autoparallelize.mpipool_support) inputs() (in module wfl.cli.cli_options) interstitial() (in module wfl.generate.supercells) is_converged() (wfl.calculators.orca.ORCA method) isolated_atom_from_e0() (in module wfl.generate.atoms_and_dimers) items_inputs_generator() (in module wfl.autoparallelize.utils)

J

julia_exec_path() (in module wfl.utils.julia)

L

largest_bulk() (in module wfl.generate.supercells)

len_scale_pair() (in module wfl.descriptor_heuristics) list_to_sigma_dict() (in module wfl.fit.modify_database.simple_factor_nonperiodic)

M

map() (in module wfl.map) max_cutoff() (in module wfl.fit.gap.multistage) md() (in module wfl.generate.md) minima_among_neighbors() (in module wfl.select.selection_space) minimahopping() (in module wfl.generate.minimahopping) modes_to_evecs() (wfl.generate.normal_modes.NormalModes static method) modify() (in module wfl.fit.modify_database.gap_rss_set_config_sigmas_from_convex_hull) (in module wfl.fit.modify_database.scale_orig) (in module wfl.fit.modify_database.simple_factor_nonperiodic) modify_cell() (in module wfl.fit.modify_database.simple_factor_nonperiodic) modify_with_factor() (in module wfl.fit.modify_database.simple_factor_nonperiodic) module wfl wfl.autoparallelize wfl.autoparallelize.autoparainfo wfl.autoparallelize.base wfl.autoparallelize.mpipool_support wfl.autoparallelize.pool wfl.autoparallelize.remote wfl.autoparallelize.remoteinfo wfl.autoparallelize.utils wfl.calculators wfl.calculators.aims wfl.calculators.castep wfl.calculators.committee wfl.calculators.espresso wfl.calculators.generic wfl.calculators.kpts wfl.calculators.mopac wfl.calculators.orca wfl.calculators.orca.basinhopping wfl.calculators.utils wfl.calculators.vasp wfl.calculators.wfl_fileio_calculator wfl.cli wfl.cli.cli_options wfl.cli.commands wfl.cli.commands.descriptor wfl.cli.commands.eval wfl.cli.commands.generate wfl.cli.commands.select wfl.configset wfl.descriptor_heuristics wfl.descriptors wfl.descriptors.quippy wfl.fit wfl.fit.ace wfl.fit.gap wfl.fit.gap.glue_2b wfl.fit.gap.multistage wfl.fit.gap.relocate wfl.fit.gap.simple wfl.fit.mace wfl.fit.modify_database wfl.fit.modify_database.gap_rss_set_config_sigmas_from_convex_hull wfl.fit.modify_database.scale_orig wfl.fit.modify_database.simple_factor_nonperiodic wfl.fit.utils wfl.generate wfl.generate.atoms_and_dimers wfl.generate.buildcell wfl.generate.md wfl.generate.md.abort wfl.generate.md.abort_base wfl.generate.minimahopping wfl.generate.neb wfl.generate.normal_modes wfl.generate.optimize wfl.generate.phonopy wfl.generate.smiles wfl.generate.supercells wfl.generate.utils wfl.map wfl.select wfl.select.by_descriptor wfl.select.convex_hull wfl.select.flat_histogram wfl.select.selection_space wfl.select.simple wfl.utils wfl.utils.at_copy_save_results wfl.utils.configs wfl.utils.convex_hull wfl.utils.file_utils wfl.utils.find_voids wfl.utils.gap_xml_tools wfl.utils.julia wfl.utils.logging wfl.utils.misc wfl.utils.ndim_neighbor_list wfl.utils.parallel wfl.utils.params wfl.utils.pressure wfl.utils.quip_cli_strings wfl.utils.replace_eval_in_strs wfl.utils.round_sig_figs wfl.utils.version wfl.utils.vol_composition_space

MOPAC (class in wfl.calculators.mopac)

N

natural_population_analysis() (in module wfl.calculators.orca) NEB() (in module wfl.generate.neb)

NormalModes (class in wfl.generate.normal_modes) num_hess_delta (wfl.generate.normal_modes.NormalModes attribute) num_inputs_per_python_subprocess() (in module wfl.cli.cli_options)

O

one_file() (wfl.configset.ConfigSet method) optimize() (in module wfl.generate.optimize)

ORCA (class in wfl.calculators.orca) outputs() (in module wfl.cli.cli_options) OutputSpec (class in wfl.configset)

P

param_dict_of_key() (wfl.calculators.vasp.Vasp method) param_fname() (in module wfl.cli.cli_options) Params (class in wfl.utils.params) parse_genericfileio_profile_argv() (in module wfl.calculators.utils) parse_npa_output() (in module wfl.calculators.orca) per_config_restore() (wfl.calculators.vasp.Vasp method) per_config_setup() (wfl.calculators.vasp.Vasp method) phonopy() (in module wfl.generate.phonopy) pick_task() (wfl.calculators.orca.ORCA method) piecewise_linear() (in module wfl.fit.modify_database.gap_rss_set_config_sigmas_from_convex_hull)

prep_descs_and_exclude() (in module wfl.select.by_descriptor) prep_params() (in module wfl.fit.gap.multistage) prepare() (in module wfl.generate.atoms_and_dimers) prepare_configs() (in module wfl.fit.ace) prepare_params() (in module wfl.fit.ace) PressureRecursionError print_log() (in module wfl.utils.logging) process_active_iter() (in module wfl.utils.logging) process_results() (wfl.calculators.orca.basinhopping.BasinHoppingORCA method) prop_prefix() (in module wfl.cli.cli_options) pyjulip_ace() (in module wfl.cli.commands.eval)

R

read_dipole() (wfl.calculators.orca.ORCA method) read_frequencies() (wfl.calculators.orca.ORCA method) read_opt_atoms() (wfl.calculators.orca.ORCA method) read_results() (wfl.calculators.orca.ORCA method) read_trajectory() (wfl.calculators.orca.ORCA method)

RemoteInfo (class in wfl.autoparallelize) (class in wfl.autoparallelize.remoteinfo) replace_eval_in_strs() (in module wfl.utils.replace_eval_in_strs) round_sig_figs() (in module wfl.utils.round_sig_figs) run_ace_fit() (in module wfl.fit.ace) run_gap_fit() (in module wfl.fit.gap.simple)

S

sample_normal_modes() (in module wfl.generate.normal_modes) (wfl.generate.normal_modes.NormalModes method) sample_pressure() (in module wfl.utils.pressure) save_results() (in module wfl.calculators.utils) select() (in module wfl.select.convex_hull) set_autopara_per_item_info() (in module wfl.autoparallelize.utils) setup_calc_params() (wfl.calculators.castep.Castep method) (wfl.calculators.espresso.Espresso method) setup_rundir() (wfl.calculators.wfl_fileio_calculator.WFLFileIOCalculator method)

shutdown_and_barrier() (in module wfl.autoparallelize.mpipool_support) smi_to_atoms() (in module wfl.generate.smiles) smiles() (in module wfl.generate.smiles) stop() (wfl.generate.md.abort_base.AbortSimBase method) store() (wfl.configset.OutputSpec method) subselect_from_traj() (in module wfl.generate.neb) (in module wfl.generate.optimize) summary() (wfl.generate.normal_modes.NormalModes method) surface() (in module wfl.generate.supercells)

T

to_ConfigSet() (wfl.configset.OutputSpec method)

U

universal_kspacing_k_mesh() (in module wfl.calculators.kpts) universal_kspacing_n_k() (in module wfl.calculators.kpts)

update_defaults() (wfl.autoparallelize.AutoparaInfo method) (wfl.autoparallelize.autoparainfo.AutoparaInfo method)

V

vacancy() (in module wfl.generate.supercells) val_relative_to_nearby_composition_volume_min() (in module wfl.select.selection_space)

Vasp (class in wfl.calculators.vasp) vertical_dist_from_hull() (in module wfl.utils.convex_hull) view() (wfl.generate.normal_modes.NormalModes method)

W

wfl module wfl.autoparallelize module wfl.autoparallelize.autoparainfo module wfl.autoparallelize.base module wfl.autoparallelize.mpipool_support module wfl.autoparallelize.pool module wfl.autoparallelize.remote module wfl.autoparallelize.remoteinfo module wfl.autoparallelize.utils module wfl.calculators module wfl.calculators.aims module wfl.calculators.castep module wfl.calculators.committee module wfl.calculators.espresso module wfl.calculators.generic module wfl.calculators.kpts module wfl.calculators.mopac module wfl.calculators.orca module wfl.calculators.orca.basinhopping module wfl.calculators.utils module wfl.calculators.vasp module wfl.calculators.wfl_fileio_calculator module wfl.cli module wfl.cli.cli_options module wfl.cli.commands module wfl.cli.commands.descriptor module wfl.cli.commands.eval module wfl.cli.commands.generate module wfl.cli.commands.select module wfl.configset module wfl.descriptor_heuristics module wfl.descriptors module wfl.descriptors.quippy module wfl.fit module wfl.fit.ace module wfl.fit.gap module wfl.fit.gap.glue_2b module wfl.fit.gap.multistage module wfl.fit.gap.relocate module wfl.fit.gap.simple module wfl.fit.mace module wfl.fit.modify_database module wfl.fit.modify_database.gap_rss_set_config_sigmas_from_convex_hull module wfl.fit.modify_database.scale_orig module wfl.fit.modify_database.simple_factor_nonperiodic module wfl.fit.utils module

wfl.generate module wfl.generate.atoms_and_dimers module wfl.generate.buildcell module wfl.generate.md module wfl.generate.md.abort module wfl.generate.md.abort_base module wfl.generate.minimahopping module wfl.generate.neb module wfl.generate.normal_modes module wfl.generate.optimize module wfl.generate.phonopy module wfl.generate.smiles module wfl.generate.supercells module wfl.generate.utils module wfl.map module wfl.select module wfl.select.by_descriptor module wfl.select.convex_hull module wfl.select.flat_histogram module wfl.select.selection_space module wfl.select.simple module wfl.utils module wfl.utils.at_copy_save_results module wfl.utils.configs module wfl.utils.convex_hull module wfl.utils.file_utils module wfl.utils.find_voids module wfl.utils.gap_xml_tools module wfl.utils.julia module wfl.utils.logging module wfl.utils.misc module wfl.utils.ndim_neighbor_list module wfl.utils.parallel module wfl.utils.params module wfl.utils.pressure module wfl.utils.quip_cli_strings module wfl.utils.replace_eval_in_strs module wfl.utils.round_sig_figs module wfl.utils.version module wfl.utils.vol_composition_space module wfl_generic_default_autopara_info (wfl.calculators.aims.Aims attribute) (wfl.calculators.castep.Castep attribute) (wfl.calculators.espresso.Espresso attribute) (wfl.calculators.mopac.MOPAC attribute) (wfl.calculators.orca.ORCA attribute) wfl_generic_num_inputs_per_python_subprocess (wfl.calculators.vasp.Vasp attribute) WFLFileIOCalculator (class in wfl.calculators.wfl_fileio_calculator) write() (wfl.configset.OutputSpec method) write_input() (wfl.calculators.orca.ORCA method) write_selected_and_clean() (in module wfl.select.by_descriptor)