Index

A

AlgorithmParameters (class in clinamen2.cmaes.params_and_state) AlgorithmState (class in clinamen2.cmaes.params_and_state)

anchor_to_immutable (clinamen2.utils.structure_setup.DofPipeline attribute) AnchorToImmutable (class in clinamen2.utils.structure_setup) apply_weights (clinamen2.utils.structure_setup.DofPipeline attribute)

B

bias_covariance_matrix_gauss() (in module clinamen2.utils.structure_setup) bias_covariance_matrix_r() (in module clinamen2.utils.structure_setup) BIPOP (class in clinamen2.utils.bipop_restart)

bipop_init() (in module clinamen2.utils.bipop_restart) bipop_next_restart() (in module clinamen2.utils.bipop_restart) bipop_update() (in module clinamen2.utils.bipop_restart)

C

c_1 (clinamen2.cmaes.params_and_state.AlgorithmParameters attribute) c_c (clinamen2.cmaes.params_and_state.AlgorithmParameters attribute) c_m (clinamen2.cmaes.params_and_state.AlgorithmParameters attribute) c_mu (clinamen2.cmaes.params_and_state.AlgorithmParameters attribute) c_sigma (clinamen2.cmaes.params_and_state.AlgorithmParameters attribute) calculate_new_mean() (in module clinamen2.cmaes.params_and_state) cholesky_factor (clinamen2.cmaes.params_and_state.AlgorithmState attribute) classify_additional_information() (clinamen2.utils.plot_functions.CMAPlotHelper method) clinamen2 module clinamen2.cmaes module clinamen2.cmaes.cmaes_criteria module clinamen2.cmaes.params_and_state module clinamen2.cmaes.termination_criterion module clinamen2.runner module clinamen2.runner.basic_runner module clinamen2.test_functions module clinamen2.utils module clinamen2.utils.bipop_restart module clinamen2.utils.file_handling module clinamen2.utils.jax_data module clinamen2.utils.lennard_jones module clinamen2.utils.plot_functions module clinamen2.utils.script_functions module clinamen2.utils.structure_setup module

cma_parser() (in module clinamen2.utils.script_functions) cma_setup() (in module clinamen2.utils.script_functions) CMAFileHandler (class in clinamen2.utils.file_handling) CMAPlotHelper (class in clinamen2.utils.plot_functions) compare_to (clinamen2.cmaes.cmaes_criteria.TolXUpState attribute) (clinamen2.cmaes.termination_criterion.StaleLossState attribute) cond (clinamen2.cmaes.cmaes_criteria.ConditionCovState attribute) ConditionCovCriterion (class in clinamen2.cmaes.cmaes_criteria) ConditionCovState (class in clinamen2.cmaes.cmaes_criteria) counter (clinamen2.cmaes.termination_criterion.StaleLossState attribute) create_ackley_function() (in module clinamen2.test_functions) create_apply_weights() (in module clinamen2.utils.structure_setup) create_cigar_function() (in module clinamen2.test_functions) create_diffpowers_function() (in module clinamen2.test_functions) create_discus_function() (in module clinamen2.test_functions) create_ellipsoid_function() (in module clinamen2.test_functions) create_evaluate_lj_potential() (in module clinamen2.utils.lennard_jones) create_filter_eval_workflow() (in module clinamen2.utils.structure_setup) create_init_algorithm_state() (in module clinamen2.cmaes.params_and_state) create_position_filter() (in module clinamen2.utils.lennard_jones) create_resample_and_evaluate() (in module clinamen2.cmaes.params_and_state) create_rosenbrock_function() (in module clinamen2.test_functions) create_sample_and_evaluate() (in module clinamen2.cmaes.params_and_state) create_sample_and_run() (in module clinamen2.cmaes.params_and_state) create_sample_and_sequential_evaluate() (in module clinamen2.cmaes.params_and_state) create_sample_from_state() (in module clinamen2.cmaes.params_and_state) create_sphere_function() (in module clinamen2.test_functions) create_split_atom() (in module clinamen2.utils.structure_setup) create_transform_dof() (in module clinamen2.utils.structure_setup) create_update_algorithm_state() (in module clinamen2.cmaes.params_and_state) criteria_states (clinamen2.cmaes.termination_criterion.CriteriaCombinationState attribute) CriteriaAnd (class in clinamen2.cmaes.termination_criterion) CriteriaAndState (in module clinamen2.cmaes.termination_criterion) CriteriaCombination (class in clinamen2.cmaes.termination_criterion) CriteriaCombinationState (class in clinamen2.cmaes.termination_criterion) CriteriaOr (class in clinamen2.cmaes.termination_criterion) CriteriaOrState (in module clinamen2.cmaes.termination_criterion) Criterion (class in clinamen2.cmaes.termination_criterion)

D

d_sigma (clinamen2.cmaes.params_and_state.AlgorithmParameters attribute) default() (clinamen2.utils.file_handling.JSONEncoder method) (clinamen2.utils.jax_data.JSONEncoderwithJNP method) default_pop_size (clinamen2.utils.bipop_restart.BIPOP attribute) default_step_size (clinamen2.utils.bipop_restart.BIPOP attribute)

dimension (clinamen2.cmaes.params_and_state.AlgorithmParameters attribute) dir_context() (in module clinamen2.utils.structure_setup) dof_to_atoms (clinamen2.utils.structure_setup.DofPipeline attribute) DofPipeline (class in clinamen2.utils.structure_setup) DofToAtoms (class in clinamen2.utils.structure_setup)

E

EqualFunValuesCriterion (class in clinamen2.cmaes.cmaes_criteria) EqualFunValuesState (class in clinamen2.cmaes.cmaes_criteria)

eval_counter (clinamen2.utils.bipop_restart.BIPOP attribute) evaluate_loss (clinamen2.utils.structure_setup.FilterEvalWorkflow attribute)

F

filter (clinamen2.utils.structure_setup.FilterEvalWorkflow attribute) FilterEvalWorkflow (class in clinamen2.utils.structure_setup)

fun_values (clinamen2.cmaes.cmaes_criteria.EqualFunValuesState attribute) FunctionRunner (class in clinamen2.runner.basic_runner)

G

generate_result_figures() (in module clinamen2.utils.script_functions) generation (clinamen2.cmaes.params_and_state.AlgorithmState attribute) get_data_from_generations() (clinamen2.utils.plot_functions.CMAPlotHelper method) get_distances_from_position() (in module clinamen2.utils.structure_setup)

get_distances_from_scaled_position() (in module clinamen2.utils.structure_setup) get_evolution_filename() (clinamen2.utils.file_handling.CMAFileHandler method) get_generation_filename() (clinamen2.utils.file_handling.CMAFileHandler method) get_max_span_from_lj_cluster() (in module clinamen2.utils.lennard_jones)

I

information (clinamen2.runner.basic_runner.WorkerResult attribute) init() (clinamen2.cmaes.cmaes_criteria.ConditionCovCriterion method) (clinamen2.cmaes.cmaes_criteria.EqualFunValuesCriterion method) (clinamen2.cmaes.cmaes_criteria.TolXUpCriterion method) (clinamen2.cmaes.termination_criterion.CriteriaCombination method) (clinamen2.cmaes.termination_criterion.Criterion method) (clinamen2.cmaes.termination_criterion.StaleLossCriterion method) (clinamen2.cmaes.termination_criterion.StaleStdCriterion method) (clinamen2.cmaes.termination_criterion.StaleStepCriterion method)

init_default_algorithm_parameters() (in module clinamen2.cmaes.params_and_state) initial_step_size (clinamen2.cmaes.params_and_state.AlgorithmParameters attribute)

J

JSONDecoder (class in clinamen2.utils.file_handling)

JSONEncoder (class in clinamen2.utils.file_handling) JSONEncoderwithJNP (class in clinamen2.utils.jax_data)

L

large_restart_counter (clinamen2.utils.bipop_restart.BIPOP attribute) latest_diff (clinamen2.cmaes.cmaes_criteria.TolXUpState attribute) latest_large_pop_size (clinamen2.utils.bipop_restart.BIPOP attribute)

lj_argparse() (in module clinamen2.utils.lennard_jones) load_evolution() (clinamen2.utils.file_handling.CMAFileHandler method) load_generation() (clinamen2.utils.file_handling.CMAFileHandler method) loss (clinamen2.runner.basic_runner.WorkerResult attribute)

M

mean (clinamen2.cmaes.params_and_state.AlgorithmState attribute) met() (clinamen2.cmaes.cmaes_criteria.ConditionCovCriterion method) (clinamen2.cmaes.cmaes_criteria.EqualFunValuesCriterion method) (clinamen2.cmaes.cmaes_criteria.TolXUpCriterion method) (clinamen2.cmaes.termination_criterion.CriteriaAnd method) (clinamen2.cmaes.termination_criterion.CriteriaCombination method) (clinamen2.cmaes.termination_criterion.CriteriaOr method) (clinamen2.cmaes.termination_criterion.Criterion method) (clinamen2.cmaes.termination_criterion.StaleLossCriterion method) (clinamen2.cmaes.termination_criterion.StaleStdCriterion method) (clinamen2.cmaes.termination_criterion.StaleStepCriterion method) module clinamen2 clinamen2.cmaes clinamen2.cmaes.cmaes_criteria clinamen2.cmaes.params_and_state clinamen2.cmaes.termination_criterion clinamen2.runner clinamen2.runner.basic_runner clinamen2.test_functions clinamen2.utils clinamen2.utils.bipop_restart clinamen2.utils.file_handling clinamen2.utils.jax_data clinamen2.utils.lennard_jones clinamen2.utils.plot_functions clinamen2.utils.script_functions clinamen2.utils.structure_setup

mu (clinamen2.cmaes.params_and_state.AlgorithmParameters attribute)

O

object_hook() (clinamen2.utils.file_handling.JSONDecoder method)

P

p_c (clinamen2.cmaes.params_and_state.AlgorithmState attribute) p_sigma (clinamen2.cmaes.params_and_state.AlgorithmState attribute) peek_script() (clinamen2.runner.basic_runner.ScriptRunner method) place_atoms_packmol() (in module clinamen2.utils.structure_setup) place_atoms_random_cube() (in module clinamen2.utils.structure_setup) place_atoms_random_sphere() (in module clinamen2.utils.structure_setup) plot_additional_information_per_generation() (clinamen2.utils.plot_functions.CMAPlotHelper method) plot_additional_per_individual() (clinamen2.utils.plot_functions.CMAPlotHelper method) plot_loss_boxplots() (clinamen2.utils.plot_functions.CMAPlotHelper method)

plot_loss_per_generation() (clinamen2.utils.plot_functions.CMAPlotHelper method) plot_loss_with_errorbars() (clinamen2.utils.plot_functions.CMAPlotHelper method) plot_mean_loss_per_generation() (clinamen2.utils.plot_functions.CMAPlotHelper method) plot_stepsize_ax2() (clinamen2.utils.plot_functions.CMAPlotHelper method) pop() (clinamen2.runner.basic_runner.FunctionRunner method) (clinamen2.runner.basic_runner.Runner method) (clinamen2.runner.basic_runner.ScriptRunner method) pop_size (clinamen2.cmaes.params_and_state.AlgorithmParameters attribute) PositionException prepare_dof_and_pipeline() (in module clinamen2.utils.structure_setup)

R

random_seed (clinamen2.cmaes.params_and_state.AlgorithmParameters attribute) random_state (clinamen2.cmaes.params_and_state.AlgorithmState attribute) (clinamen2.utils.bipop_restart.BIPOP attribute)

rank_one_update() (in module clinamen2.cmaes.params_and_state) Runner (class in clinamen2.runner.basic_runner)

S

save_evolution() (clinamen2.utils.file_handling.CMAFileHandler method) save_generation() (clinamen2.utils.file_handling.CMAFileHandler method) script_driver() (clinamen2.runner.basic_runner.ScriptRunner static method) ScriptRunner (class in clinamen2.runner.basic_runner) StaleLossCriterion (class in clinamen2.cmaes.termination_criterion) StaleLossState (class in clinamen2.cmaes.termination_criterion) StaleStdCriterion (class in clinamen2.cmaes.termination_criterion) StaleStdState (in module clinamen2.cmaes.termination_criterion)

StaleStepCriterion (class in clinamen2.cmaes.termination_criterion) StaleStepState (in module clinamen2.cmaes.termination_criterion) step_size (clinamen2.cmaes.params_and_state.AlgorithmState attribute) submit() (clinamen2.runner.basic_runner.FunctionRunner method) (clinamen2.runner.basic_runner.Runner method) (clinamen2.runner.basic_runner.ScriptRunner method) submit_batch() (clinamen2.runner.basic_runner.Runner method) (clinamen2.runner.basic_runner.ScriptRunner method)

T

TolXUpCriterion (class in clinamen2.cmaes.cmaes_criteria)

TolXUpState (class in clinamen2.cmaes.cmaes_criteria)

U

update() (clinamen2.cmaes.cmaes_criteria.ConditionCovCriterion method) (clinamen2.cmaes.cmaes_criteria.EqualFunValuesCriterion method) (clinamen2.cmaes.cmaes_criteria.TolXUpCriterion method) (clinamen2.cmaes.termination_criterion.CriteriaCombination method) (clinamen2.cmaes.termination_criterion.Criterion method) (clinamen2.cmaes.termination_criterion.StaleLossCriterion method) (clinamen2.cmaes.termination_criterion.StaleStdCriterion method) (clinamen2.cmaes.termination_criterion.StaleStepCriterion method)

update_evolution() (clinamen2.utils.file_handling.CMAFileHandler method)

W

weights (clinamen2.cmaes.params_and_state.AlgorithmParameters attribute)

WorkerResult (class in clinamen2.runner.basic_runner)