Index

A

AnalizeRun (class in clinamen.cmaes.population_evolver) as_dict() (clinamen.cmaes.evolution.CMAES method) (clinamen.cmaes.evolution.GpCMAES method) (clinamen.cmaes.evolution.StrategyParameters method) (clinamen.cmaes.evolution.TerminationCriteria method)

atoms_within_cutoff() (clinamen.cmaes.population_evolver.SSPopulationEvolver property)

B

BadPopulationMember BaseExactGPMetaModel (class in clinamen.metamodel.metamodel)

BasePCAExactGPMetaModel (class in clinamen.metamodel.metamodel) basis_coefficients() (clinamen.cmaes.population_evolver.SSPopulationEvolver property)

C

C() (clinamen.cmaes.evolution.CMAES property) calculate_B_coefficient_gaussians() (in module clinamen.clustering.stats_tools) calculate_B_distance_gaussians() (in module clinamen.clustering.stats_tools) calculate_comparison_distances() (clinamen.evpd.core.individual.Individual method) calculate_H_distance_gaussians() (in module clinamen.clustering.stats_tools) calculate_k_distances() (in module clinamen.clustering.misc) calculate_KL_divergence_gaussians() (in module clinamen.clustering.stats_tools) calculation_required() (clinamen.evpd.core.individual.Individual method) chromosome() (clinamen.evpd.core.individual.Individual property) clinamen module clinamen.clustering.misc module clinamen.clustering.stats_tools module clinamen.cmaes.evolution module clinamen.cmaes.fitness_calculators module

clinamen.cmaes.population_evolver module clinamen.descriptors.utils module clinamen.evpd.core.individual module clinamen.evpd.core.population module clinamen.metamodel.metamodel module clone() (clinamen.evpd.core.individual.Individual method) CMAES (class in clinamen.cmaes.evolution) cmaes_obj (clinamen.cmaes.population_evolver.GpPopulationEvolver attribute) (clinamen.cmaes.population_evolver.PopulationEvolver attribute) (clinamen.cmaes.population_evolver.RSPopulationEvolverGrad attribute) cmaes_parameters() (clinamen.cmaes.population_evolver.PopulationEvolver property) cost() (clinamen.evpd.core.individual.Individual property)

D

defect_position() (clinamen.evpd.core.individual.Individual property) distances_from_defect() (clinamen.evpd.core.individual.Individual property)

dmax() (clinamen.evpd.core.individual.Individual property) dmin() (clinamen.evpd.core.individual.Individual property) drel() (clinamen.evpd.core.individual.Individual property)

E

etol() (clinamen.evpd.core.individual.Individual property) evolve() (clinamen.cmaes.evolution.CMAES method) (clinamen.cmaes.population_evolver.AnalizeRun method)

evolve_population() (clinamen.cmaes.population_evolver.PopulationEvolver method) ExactGPMetaModel (class in clinamen.metamodel.metamodel)

F

find_centroids() (in module clinamen.clustering.misc) fit() (clinamen.metamodel.metamodel.GPMetaModel method) fitness() (clinamen.evpd.core.individual.Individual property) fitness_calc_obj (clinamen.cmaes.population_evolver.GpPopulationEvolver attribute) (clinamen.cmaes.population_evolver.PopulationEvolver attribute) (clinamen.cmaes.population_evolver.RSPopulationEvolver attribute) (clinamen.cmaes.population_evolver.RSPopulationEvolverGrad attribute) (clinamen.cmaes.population_evolver.RSPopulationEvolverMetamodel attribute)

FitnessCalculator (class in clinamen.cmaes.fitness_calculators) FitnessGradientCalculator (class in clinamen.cmaes.fitness_calculators)

G

g() (clinamen.cmaes.evolution.CMAES property) get_forces() (clinamen.evpd.core.individual.Individual method) get_gradients() (clinamen.cmaes.fitness_calculators.FitnessGradientCalculator method) (clinamen.cmaes.fitness_calculators.RSFitnessGradientCalculator method) get_object_parameters() (clinamen.cmaes.population_evolver.PopulationEvolver method) (clinamen.cmaes.population_evolver.RSPopulationEvolver method)

get_structure_group_index() (in module clinamen.clustering.misc) GpCMAES (class in clinamen.cmaes.evolution) GPMetaModel (class in clinamen.metamodel.metamodel) GpPopulationEvolver (class in clinamen.cmaes.population_evolver) gradient_coefficient() (clinamen.cmaes.evolution.GpCMAES property) group_structures_in_clusters() (in module clinamen.clustering.misc)

H

has_proper_structure() (clinamen.evpd.core.individual.Individual method)

I

Individual (class in clinamen.evpd.core.individual) individuals_fitness() (clinamen.evpd.core.population.Population property) initialize() (clinamen.cmaes.population_evolver.AnalizeRun method)

initialize_model() (clinamen.metamodel.metamodel.ExactGPMetaModel method) (clinamen.metamodel.metamodel.GPMetaModel method) insert() (clinamen.evpd.core.population.Population method) integral_multivariate_standard_normal_rectangular_region() (in module clinamen.clustering.stats_tools)

L

load_dataframe() (clinamen.cmaes.population_evolver.AnalizeRun method) load_status() (clinamen.cmaes.evolution.CMAES class method) (clinamen.cmaes.evolution.GpCMAES class method)

loaded_state() (clinamen.metamodel.metamodel.GPMetaModel property)

M

m() (clinamen.cmaes.evolution.CMAES property) make_individual_from_ase_atoms() (clinamen.evpd.core.individual.Individual static method) make_reachability_plot() (in module clinamen.clustering.misc) MetaRSFitnessCalculator (class in clinamen.cmaes.fitness_calculators) metric_tensor() (clinamen.evpd.core.individual.Individual property) module clinamen clinamen.clustering.misc clinamen.clustering.stats_tools clinamen.cmaes.evolution clinamen.cmaes.fitness_calculators clinamen.cmaes.population_evolver clinamen.descriptors.utils clinamen.evpd.core.individual clinamen.evpd.core.population clinamen.metamodel.metamodel

mutated_offspring() (clinamen.cmaes.evolution.CMAES property) my_name() (clinamen.evpd.core.individual.Individual property)

N

nn_cutoff() (clinamen.cmaes.population_evolver.SSPopulationEvolver property)

number_of_nn() (clinamen.cmaes.population_evolver.SSPopulationEvolver property)

O

offspring() (clinamen.cmaes.evolution.CMAES property)

optimize_structure() (clinamen.evpd.core.individual.Individual method)

P

plot_cluster_plot() (in module clinamen.clustering.misc) plot_data_vs_generation() (clinamen.cmaes.population_evolver.AnalizeRun static method) plot_energy_vs_generation() (clinamen.cmaes.population_evolver.AnalizeRun method) pop_size() (clinamen.cmaes.evolution.CMAES property)

Population (class in clinamen.evpd.core.population) population() (clinamen.cmaes.population_evolver.PopulationEvolver property) PopulationEvolver (class in clinamen.cmaes.population_evolver) predict() (clinamen.metamodel.metamodel.GPMetaModel method)

R

random_seed() (clinamen.cmaes.evolution.CMAES property) read_cmaes_status() (in module clinamen.clustering.stats_tools) read_descriptors() (clinamen.metamodel.metamodel.GPMetaModel method) read_descriptors_by_id() (in module clinamen.descriptors.utils) RSFitnessCalculator (class in clinamen.cmaes.fitness_calculators)

RSFitnessGradientCalculator (class in clinamen.cmaes.fitness_calculators) RSPopulationEvolver (class in clinamen.cmaes.population_evolver) RSPopulationEvolverGrad (class in clinamen.cmaes.population_evolver) RSPopulationEvolverMetamodel (class in clinamen.cmaes.population_evolver) run() (clinamen.cmaes.population_evolver.AnalizeRun method)

S

save_model() (clinamen.metamodel.metamodel.GPMetaModel method) save_population() (clinamen.cmaes.population_evolver.PopulationEvolver method) save_status() (clinamen.cmaes.evolution.CMAES method) selected_subspace_basis() (clinamen.cmaes.population_evolver.SSPopulationEvolver property) set_calculator_factory() (clinamen.evpd.core.individual.Individual method) set_cmaes() (clinamen.cmaes.population_evolver.PopulationEvolver method) set_fitness_calculator() (clinamen.cmaes.evolution.CMAES method) set_gradient_coefficient() (clinamen.cmaes.evolution.GpCMAES method) set_mutated_offspring() (clinamen.cmaes.evolution.CMAES method)

set_object_parameters() (clinamen.cmaes.fitness_calculators.FitnessCalculator method) (clinamen.cmaes.fitness_calculators.RSFitnessCalculator method) set_params() (clinamen.cmaes.evolution.TerminationCriteria method) set_strategy_parameters() (clinamen.cmaes.population_evolver.PopulationEvolver method) set_termination_criteria() (clinamen.cmaes.population_evolver.PopulationEvolver method) SSPopulationEvolver (class in clinamen.cmaes.population_evolver) step_size() (clinamen.cmaes.evolution.CMAES property) StrategyParameters (class in clinamen.cmaes.evolution) StrategyParameters() (clinamen.cmaes.evolution.CMAES property)

T

TerminationConditionMet TerminationCriteria (class in clinamen.cmaes.evolution)

Terminator() (clinamen.cmaes.evolution.CMAES property) total_energy_calculations() (clinamen.evpd.core.individual.Individual property)

U

update_fitness() (clinamen.evpd.core.individual.Individual method)

use_reduced_population_size() (clinamen.cmaes.population_evolver.RSPopulationEvolver property)

W

write_clustered_structures() (in module clinamen.clustering.misc) write_descriptors() (clinamen.metamodel.metamodel.GPMetaModel method) (in module clinamen.descriptors.utils)

write_poscar() (clinamen.evpd.core.individual.Individual method) write_train_hdf5() (in module clinamen.cmaes.fitness_calculators)