Index

_

__call__() (kmos3.run.Model_Parameters method) (kmos3.run.Model_Rate_Constants method) __product() (kmos3.run.ModelRunner method) __run_sublist() (kmos3.run.ModelRunner method) __split_seq() (kmos3.run.ModelRunner method) __touch() (kmos3.run.ModelRunner method) _adjust_database() (kmos3.run.KMC_Model method) _benchmark() (in module kmos3.cli) _build() (in module kmos3.cli) _casetree_dict() (in module kmos3.io) _chop_line() (in module kmos3.io) _db_print() (kmos3.io.ProcListWriter method) _export() (in module kmos3.cli) _flatten() (in module kmos3.io) _get_configuration() (kmos3.run.KMC_Model method) _get_etree_xml() (kmos3.types.Project method) _get_genstring() (kmos3.types.Coord method) _get_ini_string() (kmos3.types.Project method) _get_lat_int_groups() (kmos3.io.ProcListWriter method) _get_max_d() (kmos3.types.Process method)

_get_site_params() (kmos3.io.ProcListWriter method) _get_xml_string() (kmos3.types.Project method) _gpl_message() (kmos3.io.ProcListWriter method) _import() (in module kmos3.cli) _most_common() (in module kmos3.io) _otf_get_auxilirary_params() (kmos3.io.ProcListWriter method) _parse_otf_rate() (kmos3.io.ProcListWriter method) _parse_otf_rate_line() (kmos3.io.ProcListWriter method) _parser() (in module kmos3.cli) _print_dict() (in module kmos3.io) _put() (kmos3.run.KMC_Model method) _rebuild() (in module kmos3.cli) _set_configuration() (kmos3.run.KMC_Model method) _settings_export() (in module kmos3.cli) _shell() (in module kmos3.cli) _shorthand() (kmos3.types.Bystander method) (kmos3.types.ConditionAction method) _view() (in module kmos3.cli) _write_optimal_iftree() (kmos3.io.ProcListWriter method) _write_optimal_iftree_otf() (kmos3.io.ProcListWriter method) _xml() (in module kmos3.cli)

A

Action (in module kmos3.types) add() (kmos3.types.Meta method) add_action() (kmos3.types.Process method) add_bystander() (kmos3.types.Process method) add_condition() (kmos3.types.Process method) add_layer() (kmos3.types.Project method) add_parameter() (kmos3.types.Project method) add_process() (kmos3.types.Project method) add_site() (kmos3.types.Layer method) (kmos3.types.Project method) add_species() (kmos3.types.Project method) attributes (kmos3.types.Bystander attribute) (kmos3.types.ConditionAction attribute) (kmos3.types.Coord attribute) (kmos3.types.FixedObject attribute) (kmos3.types.LatIntProcess attribute) (kmos3.types.Layer attribute) (kmos3.types.LayerList attribute) (kmos3.types.OutputItem attribute) (kmos3.types.OutputList attribute) (kmos3.types.Parameter attribute) (kmos3.types.ParameterList attribute) (kmos3.types.Process attribute) (kmos3.types.ProcessFormSite attribute) (kmos3.types.ProcessList attribute) (kmos3.types.SingleLatIntProcess attribute) (kmos3.types.Site attribute) (kmos3.types.Species attribute) (kmos3.types.SpeciesList attribute)

AutoScrollbar (class in kmos3.view)

B

build() (in module kmos3.utils)

by_name() (kmos3.run.Model_Rate_Constants method) Bystander (class in kmos3.types)

C

clear_model() (in module kmos3.io) (kmos3.types.Project method) cmp_coords() (in module kmos3.types) col_str2tuple() (in module kmos3.utils) col_tuple2str() (in module kmos3.utils) compile_model() (kmos3.types.Project method)

Condition (in module kmos3.types) ConditionAction (class in kmos3.types) Coord (class in kmos3.types) CorrectlyNamed (class in kmos3.utils) create_configuration_plot() (kmos3.run.KMC_Model method) create_kmc_model() (in module kmos3.types)

D

deallocate() (kmos3.run.KMC_Model method) do_acc_steps() (kmos3.run.KMC_Model method) do_steps() (kmos3.run.KMC_Model method)

do_steps_time() (kmos3.run.KMC_Model method) double() (kmos3.run.KMC_Model method) dump_config() (kmos3.run.KMC_Model method)

E

eq_mod_offset() (kmos3.types.Coord method) evaluate_kind_values() (in module kmos3.utils) evaluate_rate_expression() (kmos3.types.Process method) evaluate_template() (in module kmos3.utils) executing_coord() (kmos3.types.Process method)

exit() (kmos3.view.KMC_Viewer method) export_movie() (kmos3.run.KMC_Model method) export_picture() (kmos3.run.KMC_Model method) export_source() (in module kmos3.io) export_xml() (in module kmos3.io) export_xml_file() (kmos3.types.Project method)

F

ff() (kmos3.types.Coord method)

FixedObject (class in kmos3.types)

G

generate_coord() (kmos3.types.LayerList method) generate_coord_set() (kmos3.types.LayerList method) get_ase_constructor() (in module kmos3.utils) get_atoms() (kmos3.run.KMC_Model method) get_avail() (kmos3.run.KMC_Model method) get_backend() (kmos3.run.KMC_Model method) get_buffer_parameter() (kmos3.run.KMC_Model method) get_executed_rates() (kmos3.run.KMC_Model method) get_executed_rates_limit() (kmos3.run.KMC_Model method) get_execution_steps() (kmos3.run.KMC_Model method) get_extra() (kmos3.types.Meta method) get_global_configuration() (kmos3.run.KMC_Model method) get_grid() (kmos3.run.LinearParameter method) (kmos3.run.LogParameter method) (kmos3.run.ModelParameter method) (kmos3.run.PressureParameter method) (kmos3.run.TemperatureParameter method) get_info() (kmos3.types.Layer method) (kmos3.types.Parameter method) (kmos3.types.Process method)

get_local_configurations() (kmos3.run.KMC_Model method) get_next_kmc_step() (kmos3.run.KMC_Model method) get_occupation_header() (kmos3.run.KMC_Model method) get_options() (in module kmos3.cli) get_param_header() (kmos3.run.KMC_Model method) get_param_value() (kmos3.run.KMC_Model method) get_parameters() (kmos3.types.Project method) get_processes() (kmos3.types.Project method) get_sampling_steps() (kmos3.run.KMC_Model method) get_save_limit() (kmos3.run.KMC_Model method) get_saved_executions() (kmos3.run.KMC_Model method) get_scaling_stats() (kmos3.run.KMC_Model method) get_site() (kmos3.types.Layer method) get_species_coordinates() (kmos3.run.KMC_Model method) get_speciess() (kmos3.types.Project method) get_std_header() (kmos3.run.KMC_Model method) get_std_sampled_data() (kmos3.run.KMC_Model method) get_threshold_parameter() (kmos3.run.KMC_Model method) get_tof_header() (kmos3.run.KMC_Model method)

H

halve() (kmos3.run.KMC_Model method)

I

import_file() (kmos3.types.Project method) import_ini_file() (kmos3.types.Project method) import_xml() (in module kmos3.io)

import_xml_file() (in module kmos3.io) (kmos3.types.Project method) inverse() (kmos3.run.KMC_Model method) (kmos3.run.Model_Rate_Constants method)

J

jmolcolor_in_hex() (in module kmos3.utils)

K

KMC_Model (class in kmos3.run) KMC_PlotBox (class in kmos3.view) KMC_Viewer (class in kmos3.view) kmos3 module kmos3.cli module kmos3.io module

kmos3.run module kmos3.types module kmos3.utils module kmos3.view module

L

LatIntProcess (class in kmos3.types) Layer (class in kmos3.types) LayerList (class in kmos3.types)

LinearParameter (class in kmos3.run) linlog_scale_format() (kmos3.view.ParamSlider method) load_config() (kmos3.run.KMC_Model method) LogParameter (class in kmos3.run)

M

main() (in module kmos3.cli) (in module kmos3.view) Meta (class in kmos3.types) Model_Parameters (class in kmos3.run) Model_Rate_Constants (class in kmos3.run) ModelParameter (class in kmos3.run) ModelRunner (class in kmos3.run)

module kmos3 kmos3.cli kmos3.io kmos3.run kmos3.types kmos3.utils kmos3.view

N

name (kmos3.types.Meta attribute) names() (kmos3.run.Model_Parameters method) (kmos3.run.Model_Rate_Constants method)

nr2site() (kmos3.run.KMC_Model method)

O

on_adjustable__do_toggled() (kmos3.types.Parameter method) on_name__content_changed() (kmos3.types.Parameter method) on_name__validate() (kmos3.utils.CorrectlyNamed method)

on_resize() (kmos3.view.KMC_PlotBox method) OutputItem (class in kmos3.types) OutputList (class in kmos3.types)

P

p_grid() (in module kmos3.utils) Parameter (class in kmos3.types) parameter_callback() (kmos3.view.KMC_Viewer method) ParameterList (class in kmos3.types) parameters (kmos3.run.ModelRunner attribute) ParamSlider (class in kmos3.view) parse_and_add_process() (kmos3.types.Project method) parse_chemical_expression() (in module kmos3.types) parse_process() (in module kmos3.types) (kmos3.types.Project method) peek() (kmos3.run.KMC_Model method) pickle_export_atoms() (kmos3.run.KMC_Model method) play_ascii_movie() (kmos3.run.KMC_Model method) plot() (kmos3.run.ModelRunner method) plot_configuration() (kmos3.run.KMC_Model method) pos (kmos3.types.Coord attribute) post_mortem() (kmos3.run.KMC_Model method) PressureParameter (class in kmos3.run) prettify_xml() (in module kmos3.types)

print_accum_rate_summation() (kmos3.run.KMC_Model method) print_adjustable_parameters() (kmos3.run.KMC_Model method) print_coverages() (kmos3.run.KMC_Model method) print_kmc_state() (kmos3.run.KMC_Model method) print_proc_pair_eq() (kmos3.run.KMC_Model method) print_procstat() (kmos3.run.KMC_Model method) print_scaling_factors() (kmos3.run.KMC_Model method) print_scaling_stats() (kmos3.run.KMC_Model method) print_state_summary() (kmos3.run.KMC_Model method) print_statistics() (kmos3.types.Project method) Process (class in kmos3.types) ProcessFormSite (class in kmos3.types) ProcessList (class in kmos3.types) ProcListWriter (class in kmos3.io) procstat_normalized() (kmos3.run.KMC_Model method) procstat_pprint() (kmos3.run.KMC_Model method) product() (in module kmos3.utils) Project (class in kmos3.types) put() (kmos3.run.KMC_Model method)

R

radd_ff() (kmos3.types.Coord method) rate_ratios() (kmos3.run.KMC_Model method) reset() (kmos3.run.KMC_Model method) rsub_ff() (kmos3.types.Coord method)

run() (kmos3.run.KMC_Model method) (kmos3.run.ModelRunner method) run_proc_nr() (kmos3.run.KMC_Model method) runner_name (kmos3.run.ModelRunner attribute)

S

save() (kmos3.types.Project method) save_model() (kmos3.types.Project method) set() (kmos3.run.Model_Rate_Constants method) (kmos3.view.AutoScrollbar method) set_buffer_parameter() (kmos3.run.KMC_Model method) set_debug_level() (kmos3.run.KMC_Model method) set_executed_rates_limit() (kmos3.run.KMC_Model method) set_execution_steps() (kmos3.run.KMC_Model method) set_meta() (kmos3.types.Project method) set_representation() (kmos3.types.LayerList method) set_sampling_steps() (kmos3.run.KMC_Model method) set_save_limit() (kmos3.run.KMC_Model method) set_threshold_parameter() (kmos3.run.KMC_Model method)

setattribute() (kmos3.types.Meta method) shell() (in module kmos3.cli) shorten_names() (kmos3.types.Project method) show() (kmos3.run.KMC_Model method) show_ascii_picture() (kmos3.run.KMC_Model method) SingleLatIntProcess (class in kmos3.types) Site (class in kmos3.types) site_offset_unpacked() (kmos3.types.Coord method) sort_key() (kmos3.types.Coord method) Species (class in kmos3.types) SpeciesList (class in kmos3.types) split_sequence() (in module kmos3.utils) switch_surface_processes_off() (kmos3.run.KMC_Model method) switch_surface_processes_on() (kmos3.run.KMC_Model method)

T

T_grid() (in module kmos3.utils)

TemperatureParameter (class in kmos3.run) timeit() (in module kmos3.utils)

U

update_plots() (kmos3.view.KMC_PlotBox method)

V

validate_model() (kmos3.types.Project method)

value_changed() (kmos3.view.ParamSlider method) view() (kmos3.run.KMC_Model method)

W

write_proclist() (kmos3.io.ProcListWriter method) write_proclist_acf() (kmos3.io.ProcListWriter method) write_proclist_acf_end() (kmos3.io.ProcListWriter method) write_proclist_constants() (kmos3.io.ProcListWriter method) write_proclist_end() (kmos3.io.ProcListWriter method) write_proclist_generic_part() (kmos3.io.ProcListWriter method) write_proclist_generic_subroutines() (kmos3.io.ProcListWriter method) write_proclist_generic_subroutines_acf() (kmos3.io.ProcListWriter method) write_proclist_get_diff_sites_acf_otf() (kmos3.io.ProcListWriter method) write_proclist_get_diff_sites_acf_smart() (kmos3.io.ProcListWriter method) write_proclist_get_diff_sites_displacement_otf() (kmos3.io.ProcListWriter method) write_proclist_get_diff_sites_displacement_smart() (kmos3.io.ProcListWriter method) write_proclist_lat_int() (kmos3.io.ProcListWriter method) write_proclist_lat_int_nli_caselist() (kmos3.io.ProcListWriter method) write_proclist_lat_int_nli_casetree() (kmos3.io.ProcListWriter method)

write_proclist_lat_int_run_proc() (kmos3.io.ProcListWriter method) write_proclist_lat_int_run_proc_nr() (kmos3.io.ProcListWriter method) write_proclist_lat_int_touchup() (kmos3.io.ProcListWriter method) write_proclist_multilattice() (kmos3.io.ProcListWriter method) write_proclist_otf() (kmos3.io.ProcListWriter method) write_proclist_pars_otf() (kmos3.io.ProcListWriter method) write_proclist_put_take() (kmos3.io.ProcListWriter method) write_proclist_run_proc_name_otf() (kmos3.io.ProcListWriter method) write_proclist_run_proc_nr_otf() (kmos3.io.ProcListWriter method) write_proclist_run_proc_nr_smart() (kmos3.io.ProcListWriter method) write_proclist_touchup() (kmos3.io.ProcListWriter method) write_proclist_touchup_otf() (kmos3.io.ProcListWriter method) write_py() (in module kmos3.utils) write_settings() (kmos3.io.ProcListWriter method) write_template() (kmos3.io.ProcListWriter method)

X

xml() (kmos3.run.KMC_Model method)