clinamen2 package

Subpackages

• clinamen2.cmaes package
  • Submodules
  • clinamen2.cmaes.cmaes_criteria module
    • ConditionCovCriterion
      • ConditionCovCriterion.init()
      • ConditionCovCriterion.met()
      • ConditionCovCriterion.update()
    • ConditionCovState
      • ConditionCovState.cond
    • EqualFunValuesCriterion
      • EqualFunValuesCriterion.init()
      • EqualFunValuesCriterion.met()
      • EqualFunValuesCriterion.update()
    • EqualFunValuesState
      • EqualFunValuesState.fun_values
    • TolXUpCriterion
      • TolXUpCriterion.init()
      • TolXUpCriterion.met()
      • TolXUpCriterion.update()
    • TolXUpState
      • TolXUpState.compare_to
      • TolXUpState.latest_diff
  • clinamen2.cmaes.params_and_state module
    • AlgorithmParameters
      • AlgorithmParameters.c_1
      • AlgorithmParameters.c_c
      • AlgorithmParameters.c_m
      • AlgorithmParameters.c_mu
      • AlgorithmParameters.c_sigma
      • AlgorithmParameters.d_sigma
      • AlgorithmParameters.dimension
      • AlgorithmParameters.initial_step_size
      • AlgorithmParameters.mu
      • AlgorithmParameters.pop_size
      • AlgorithmParameters.random_seed
      • AlgorithmParameters.weights
    • AlgorithmState
      • AlgorithmState.cholesky_factor
      • AlgorithmState.generation
      • AlgorithmState.mean
      • AlgorithmState.p_c
      • AlgorithmState.p_sigma
      • AlgorithmState.random_state
      • AlgorithmState.step_size
    • calculate_new_mean()
    • create_init_algorithm_state()
    • create_resample_and_evaluate()
    • create_sample_and_evaluate()
    • create_sample_and_run()
    • create_sample_and_sequential_evaluate()
    • create_sample_from_state()
    • create_update_algorithm_state()
    • init_default_algorithm_parameters()
    • rank_one_update()
  • clinamen2.cmaes.termination_criterion module
    • CriteriaAnd
      • CriteriaAnd.met()
    • CriteriaAndState
    • CriteriaCombination
      • CriteriaCombination.init()
      • CriteriaCombination.met()
      • CriteriaCombination.update()
    • CriteriaCombinationState
      • CriteriaCombinationState.criteria_states
    • CriteriaOr
      • CriteriaOr.met()
    • CriteriaOrState
    • Criterion
      • Criterion.init()
      • Criterion.met()
      • Criterion.update()
    • StaleLossCriterion
      • StaleLossCriterion.init()
      • StaleLossCriterion.met()
      • StaleLossCriterion.update()
    • StaleLossState
      • StaleLossState.compare_to
      • StaleLossState.counter
    • StaleStdCriterion
      • StaleStdCriterion.init()
      • StaleStdCriterion.met()
      • StaleStdCriterion.update()
    • StaleStdState
    • StaleStepCriterion
      • StaleStepCriterion.init()
      • StaleStepCriterion.met()
      • StaleStepCriterion.update()
    • StaleStepState
  • Module contents
• clinamen2.runner package
  • Submodules
  • clinamen2.runner.basic_runner module
    • FunctionRunner
      • FunctionRunner.pop()
      • FunctionRunner.submit()
    • Runner
      • Runner.pop()
      • Runner.submit()
      • Runner.submit_batch()
    • ScriptRunner
      • ScriptRunner.peek_script()
      • ScriptRunner.pop()
      • ScriptRunner.script_driver()
      • ScriptRunner.submit()
      • ScriptRunner.submit_batch()
    • WorkerResult
      • WorkerResult.information
      • WorkerResult.loss
  • Module contents
• clinamen2.utils package
  • Submodules
  • clinamen2.utils.bipop_restart module
    • BIPOP
      • BIPOP.default_pop_size
      • BIPOP.default_step_size
      • BIPOP.eval_counter
      • BIPOP.large_restart_counter
      • BIPOP.latest_large_pop_size
      • BIPOP.random_state
    • bipop_init()
    • bipop_next_restart()
    • bipop_update()
  • clinamen2.utils.file_handling module
    • CMAFileHandler
      • CMAFileHandler.get_evolution_filename()
      • CMAFileHandler.get_generation_filename()
      • CMAFileHandler.load_evolution()
      • CMAFileHandler.load_generation()
      • CMAFileHandler.save_evolution()
      • CMAFileHandler.save_generation()
      • CMAFileHandler.update_evolution()
    • JSONDecoder
      • JSONDecoder.object_hook()
    • JSONEncoder
      • JSONEncoder.default()
  • clinamen2.utils.jax_data module
    • JSONEncoderwithJNP
      • JSONEncoderwithJNP.default()
  • clinamen2.utils.lennard_jones module
    • PositionException
    • create_evaluate_lj_potential()
    • create_position_filter()
    • get_max_span_from_lj_cluster()
    • lj_argparse()
  • clinamen2.utils.neuralil_evaluation module
  • clinamen2.utils.plot_functions module
    • CMAPlotHelper
      • CMAPlotHelper.classify_additional_information()
      • CMAPlotHelper.get_data_from_generations()
      • CMAPlotHelper.plot_additional_information_per_generation()
      • CMAPlotHelper.plot_additional_per_individual()
      • CMAPlotHelper.plot_loss_boxplots()
      • CMAPlotHelper.plot_loss_per_generation()
      • CMAPlotHelper.plot_loss_with_errorbars()
      • CMAPlotHelper.plot_mean_loss_per_generation()
      • CMAPlotHelper.plot_stepsize_ax2()
  • clinamen2.utils.script_functions module
    • cma_parser()
    • cma_setup()
    • generate_result_figures()
  • clinamen2.utils.structure_setup module
    • AnchorToImmutable
    • DofPipeline
      • DofPipeline.anchor_to_immutable
      • DofPipeline.apply_weights
      • DofPipeline.dof_to_atoms
    • DofToAtoms
    • FilterEvalWorkflow
      • FilterEvalWorkflow.evaluate_loss
      • FilterEvalWorkflow.filter
    • bias_covariance_matrix_gauss()
    • bias_covariance_matrix_r()
    • create_apply_weights()
    • create_filter_eval_workflow()
    • create_split_atom()
    • create_transform_dof()
    • dir_context()
    • get_distances_from_position()
    • get_distances_from_scaled_position()
    • place_atoms_packmol()
    • place_atoms_random_cube()
    • place_atoms_random_sphere()
    • prepare_dof_and_pipeline()
  • Module contents

Submodules

clinamen2.test_functions module

This module contains auxiliary test functions as defined in table 1 of

[1] O. Krause, D. R. Arbonès, C. Igel, “CMA-ES with Optimal Covariance

Update and Storage Complexity”, part of [2], 2016.

[2] D. Lee, M. Sugiyama, U. Luxburg, I. Guyon, R. Garnett, “Advances

in Neural Information Processing Systems 29, 2016.

clinamen2.test_functions.create_ackley_function()

Create Ackley test function.

Args:

Return type:

Callable

Returns:

The Ackley test function.

clinamen2.test_functions.create_cigar_function()

Create cigar test function.

Args:

Return type:

Callable

Returns:

The Cigar test function.

clinamen2.test_functions.create_diffpowers_function()

Different Powers test function.

Args:

Return type:

Callable

Returns:

The Diffpowers test function.

clinamen2.test_functions.create_discus_function()

Create discus test function.

Args:

Return type:

Callable

Returns:

The Discus test function.

clinamen2.test_functions.create_ellipsoid_function()

Create ellipsoid test function.

Args:

Return type:

Callable

Returns:

The Ellipsoid test function.

clinamen2.test_functions.create_rosenbrock_function()

Create Rosenbrock test function.

Args:

Return type:

Callable

Returns:

The Rosenbrock test function.

clinamen2.test_functions.create_sphere_function()

Create sphere test function.

Args:

Return type:

Callable

Returns:

The Sphere test function.

Module contents

Copyright 2023-2025 The Clinamen2 contributors

Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.