Index

A

add_atoms() (npl.core.atom_wrapper.AtomWrapper method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) add_offspring() (npl.optimization.genetic_algoritm.NichedPopulation.NichedPopulation method) (npl.optimization.genetic_algoritm.NichedPopulation.Population method) adjust_stoichiometry() (npl.core.Nanoparticle method) (npl.core.nanoparticle.Nanoparticle method)

AdsorptionFeatureVector (class in npl.descriptors.global_feature_classifier) AdsorptionSiteList (class in npl.core.adsorption) AtomicCoordinationTypes (class in npl.descriptors.global_feature_classifier) atoms (npl.monte_carlo.BaseEnsemble property) (npl.monte_carlo.ensembles.base_ensemble.BaseEnsemble property) AtomWrapper (class in npl.core.atom_wrapper)

B

BaseEnsemble (class in npl.monte_carlo) (class in npl.monte_carlo.ensembles.base_ensemble) BaseNanoparticle (class in npl.core) (class in npl.core.base_nanoparticle) basin_hop_step() (npl.optimization.local_optimization.garbage_exchange_operator.GuidedExchangeOperator method) (npl.optimization.local_optimization.guided_exchange_operator.GuidedExchangeOperator method) BayesianRRCalculator (class in npl.calculators) (class in npl.calculators.energy_calculator) bind_adsorbates() (npl.monte_carlo.random_exchange_operator.RandomExchangeOperator method) bind_grid() (npl.calculators.energy_calculator.LateralInteractionCalculator method) bind_particle() (npl.core.adsorption.PlaceAddAtoms method) (npl.monte_carlo.random_exchange_operator.RandomExchangeOperator method) (npl.monte_carlo.random_exchange_operator_etop.RandomExchangeOperatorExtended method) (npl.optimization.local_optimization.garbage_exchange_operator.GuidedExchangeOperator method) (npl.optimization.local_optimization.guided_exchange_operator.GuidedExchangeOperator method) build_args_list_for_gm_search() (npl.optimization.GASearch method) (npl.optimization.go_search.GASearch method) (npl.optimization.go_search.GOSearch method) (npl.optimization.go_search.GuidedSearch method) (npl.optimization.go_search.MCSearch method) (npl.optimization.GOSearch method) (npl.optimization.GuidedSearch method) (npl.optimization.MCSearch method)

build_from_dictionary() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) build_kwargs_list_for_gm_search() (npl.optimization.GASearch method) (npl.optimization.go_search.GASearch method) (npl.optimization.go_search.GOSearch method) (npl.optimization.go_search.GuidedSearch method) (npl.optimization.go_search.MCSearch method) (npl.optimization.GOSearch method) (npl.optimization.GuidedSearch method) (npl.optimization.MCSearch method) build_site_list() (npl.core.adsorption.AdsorptionSiteList method)

C

calculate() (npl.calculators.top_calculator.TOPCalculator method) (npl.calculators.TOPCalculator method) CanonicalEnsemble (class in npl.monte_carlo) (class in npl.monte_carlo.ensembles.canonical_ensemble) compute_atom_feature() (npl.descriptors.global_feature_classifier.AtomicCoordinationTypes method) (npl.descriptors.global_feature_classifier.ExtendedTopologicalFeaturesClassifier method) (npl.descriptors.local_environment_feature_classifier.LocalEnvironmentFeatureClassifier method) compute_atom_features() (npl.descriptors.global_feature_classifier.ExtendedTopologicalFeaturesClassifier method) (npl.descriptors.local_environment_feature_classifier.LocalEnvironmentFeatureClassifier method) compute_coefficients_for_linear_topological_model() (in module npl.calculators) (in module npl.calculators.energy_calculator) compute_coefficients_for_shape_optimization() (in module npl.calculators.energy_calculator) compute_dipole_moment() (npl.calculators.energy_calculator.DipoleMomentCalculator method) compute_energy() (npl.calculators.BayesianRRCalculator method) (npl.calculators.EMTCalculator method) (npl.calculators.energy_calculator.BayesianRRCalculator method) (npl.calculators.energy_calculator.EMTCalculator method) (npl.calculators.energy_calculator.EnergyCalculator method) (npl.calculators.energy_calculator.GPRCalculator method) (npl.calculators.energy_calculator.LateralInteractionCalculator method) (npl.calculators.energy_calculator.MixingEnergyCalculator method) (npl.calculators.EnergyCalculator method) (npl.calculators.top_calculator.TOPCalculator method) (npl.calculators.TOPCalculator method) compute_feature_vector() (npl.descriptors.global_feature_classifier.AdsorptionFeatureVector method) (npl.descriptors.global_feature_classifier.AtomicCoordinationTypes method) (npl.descriptors.global_feature_classifier.CoordinationFeatureClassifier method) (npl.descriptors.global_feature_classifier.DipoleMomentCalculator method) (npl.descriptors.global_feature_classifier.ExtendedTopologicalFeaturesClassifier method) (npl.descriptors.global_feature_classifier.GeneralizedCoordinationNumber method) (npl.descriptors.global_feature_classifier.GlobalFeatureClassifier method) (npl.descriptors.global_feature_classifier.LayererTopologicalDescriptors method) (npl.descriptors.global_feature_classifier.SimpleFeatureClassifier method) (npl.descriptors.global_feature_classifier.testTopologicalFeatureClassifier method) (npl.descriptors.global_feature_classifier.TopologicalFeatureClassifier method) (npl.descriptors.local_environment_feature_classifier.LocalEnvironmentFeatureClassifier method)

compute_fitness() (in module npl.optimization.genetic_algoritm.SingleParticleGA) (npl.optimization.genetic_algoritm.NichedPopulation.NichedPopulation method) (npl.optimization.genetic_algoritm.NichedPopulation.Population method) compute_layers() (npl.descriptors.global_feature_classifier.LayererTopologicalDescriptors method) compute_local_environment() (npl.descriptors.local_environment_calculator.LocalEnvironmentCalculator method) (npl.descriptors.LocalEnvironmentCalculator method) compute_local_environments() (npl.descriptors.local_environment_calculator.LocalEnvironmentCalculator method) (npl.descriptors.LocalEnvironmentCalculator method) compute_mixing_parameters() (npl.calculators.energy_calculator.MixingEnergyCalculator method) compute_n_features() (npl.descriptors.global_feature_classifier.AtomicCoordinationTypes method) (npl.descriptors.local_environment_feature_classifier.CoordinationNumberClassifier method) (npl.descriptors.local_environment_feature_classifier.KMeansClassifier method) (npl.descriptors.local_environment_feature_classifier.LocalEnvironmentFeatureClassifier method) (npl.descriptors.local_environment_feature_classifier.TopologicalEnvironmentClassifier method) compute_respective_bond_counts() (npl.descriptors.global_feature_classifier.SimpleFeatureClassifier method) construct() (npl.core.adsorption.AdsorptionSiteList method) (npl.core.neighbor_list.NeighborList method) (npl.core.NeighborList method) construct_adsorption_list() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) construct_interatomic_potential_matrix() (npl.calculators.energy_calculator.LateralInteractionCalculator method) construct_neighbor_list() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) CoordinationFeatureClassifier (class in npl.descriptors.global_feature_classifier) CoordinationNumberClassifier (class in npl.descriptors.local_environment_feature_classifier) coupled_random_exchange() (npl.monte_carlo.random_exchange_operator.RandomExchangeOperator method) cut_and_splice() (npl.optimization.genetic_algoritm.CutAndSpliceOperator.CutAndSpliceOperator method) CutAndSpliceOperator (class in npl.optimization.genetic_algoritm.CutAndSpliceOperator) CuttingPlane (class in npl.utils.cutting_plane_utilities)

D

DipoleMomentCalculator (class in npl.calculators.energy_calculator) (class in npl.descriptors.global_feature_classifier) do_mutation() (npl.monte_carlo.CanonicalEnsemble method) (npl.monte_carlo.ensembles.canonical_ensemble.CanonicalEnsemble method)

downgrade_feature_vector() (npl.descriptors.global_feature_classifier.ExtendedTopologicalFeaturesClassifier method) draw_from_geometric_distribution() (npl.optimization.genetic_algoritm.MutationOperator.MutationOperator method)

E

EMTCalculator (class in npl.calculators) (class in npl.calculators.energy_calculator) EnergyCalculator (class in npl.calculators) (class in npl.calculators.energy_calculator)

env_from_feature() (npl.optimization.local_optimization.garbage_exchange_operator.GuidedExchangeOperator method) (npl.optimization.local_optimization.guided_exchange_operator.GuidedExchangeOperator method) ExchangeOperator (class in npl.optimization.genetic_algoritm.ExchangeOperator) ExtendedTopologicalFeaturesClassifier (class in npl.descriptors.global_feature_classifier)

F

features_to_update() (in module npl.monte_carlo.monte_carlo_etop) find_atom_plane_vec() (npl.core.adsorption.FindAdsorptionSites method) (npl.core.FindAdsorptionSites method) find_direction_for_edges() (npl.core.adsorption.FindAdsorptionSites method) (npl.core.FindAdsorptionSites method) find_middle_point() (in module npl.utils.math_modules) find_plane_for_bridge_atoms() (npl.core.adsorption.FindAdsorptionSites method) (npl.core.FindAdsorptionSites method) FindAdsorptionSites (class in npl.core) (class in npl.core.adsorption)

fit() (npl.calculators.BayesianRRCalculator method) (npl.calculators.energy_calculator.BayesianRRCalculator method) (npl.calculators.energy_calculator.GPRCalculator method) fit_energy_expression() (npl.optimization.GASearch method) (npl.optimization.go_search.GASearch method) (npl.optimization.go_search.GOSearch method) (npl.optimization.go_search.GuidedSearch method) (npl.optimization.go_search.MCSearch method) (npl.optimization.GOSearch method) (npl.optimization.GuidedSearch method) (npl.optimization.MCSearch method)

G

GASearch (class in npl.optimization) (class in npl.optimization.go_search) gaussian_tournament() (npl.optimization.genetic_algoritm.NichedPopulation.NichedPopulation method) (npl.optimization.genetic_algoritm.NichedPopulation.Population method) GeneralizedCoordinationNumber (class in npl.descriptors.global_feature_classifier) generate_new_cutting_plane() (npl.utils.cutting_plane_utilities.SphericalCuttingPlaneGenerator method) get_adsorption_as_list() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_adsorption_list() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_all_symbols() (npl.core.atom_wrapper.AtomWrapper method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_as_dictionary() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_as_list() (npl.optimization.genetic_algoritm.NichedPopulation.NichedPopulation method) get_ase_atoms() (npl.core.atom_wrapper.AtomWrapper method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_atom_feature() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_atom_features() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_atom_indices_from_coordination_number() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) (npl.core.neighbor_list.NeighborList method) (npl.core.NeighborList method) get_atom_position() (in module npl.utils.math_modules) get_atoms() (npl.core.atom_wrapper.AtomWrapper method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_atoms_in_the_surface_plane() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) (npl.core.neighbor_list.NeighborList method) (npl.core.NeighborList method) get_bond_types() (npl.descriptors.global_feature_classifier.ExtendedTopologicalFeaturesClassifier method) get_bridge_perpendicular_line() (in module npl.utils.math_modules) get_bridge_sites() (npl.core.adsorption.FindAdsorptionSites method) (npl.core.FindAdsorptionSites method) get_bridge_sties() (npl.core.adsorption.PlaceAddAtoms method) get_coefficients() (npl.calculators.BayesianRRCalculator method) (npl.calculators.energy_calculator.BayesianRRCalculator method) (npl.calculators.top_calculator.TOPCalculator method) (npl.calculators.TOPCalculator method) get_convex_hull() (npl.optimization.genetic_algoritm.NichedPopulation.NichedPopulation method) get_coordination_atoms() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) (npl.core.neighbor_list.NeighborList method) (npl.core.NeighborList method) get_coordination_index() (npl.descriptors.global_feature_classifier.ExtendedTopologicalFeaturesClassifier method) get_coordination_number() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) (npl.core.neighbor_list.NeighborList method) (npl.core.NeighborList method) get_crystalline_structure() (in module npl.utils.utils) get_data_by_stoichiometry() (npl.calculators.top_calculator.TOPCalculator method) (npl.calculators.TOPCalculator method) get_dipole_moments() (npl.calculators.energy_calculator.DipoleMomentCalculator method) get_dot_product() (in module npl.utils.math_modules) get_energy() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_energy_key() (npl.calculators.energy_calculator.EnergyCalculator method) (npl.calculators.EnergyCalculator method) (npl.calculators.top_calculator.TOPCalculator method) (npl.calculators.TOPCalculator method) get_environments() (npl.calculators.energy_calculator.DipoleMomentCalculator method) get_feature_classifier() (npl.calculators.top_calculator.TOPCalculator method) (npl.calculators.TOPCalculator method) get_feature_key() (npl.calculators.top_calculator.TOPCalculator method) (npl.calculators.TOPCalculator method) (npl.descriptors.global_feature_classifier.GlobalFeatureClassifier method) (npl.descriptors.local_environment_feature_classifier.LocalEnvironmentFeatureClassifier method) get_feature_labels() (npl.descriptors.global_feature_classifier.ExtendedTopologicalFeaturesClassifier method) (npl.descriptors.global_feature_classifier.testTopologicalFeatureClassifier method) (npl.descriptors.global_feature_classifier.TopologicalFeatureClassifier method) get_feature_vector() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_features() (npl.descriptors.global_feature_classifier.AdsorptionFeatureVector method) get_generalized_coordination_number() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) (npl.core.neighbor_list.NeighborList method) (npl.core.NeighborList method) get_generalized_coordination_numbers() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_geometrical_data() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method)

get_hollow_sites() (npl.core.adsorption.FindAdsorptionSites method) (npl.core.FindAdsorptionSites method) get_hollow_sties() (npl.core.adsorption.PlaceAddAtoms method) get_indices() (npl.core.atom_wrapper.AtomWrapper method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_indices_by_symbol() (npl.core.atom_wrapper.AtomWrapper method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_indices_of_adsorbates() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_layer_indices() (npl.descriptors.global_feature_classifier.LayererTopologicalDescriptors method) get_layer_types() (npl.descriptors.global_feature_classifier.ExtendedTopologicalFeaturesClassifier method) get_layers_occupacy() (npl.descriptors.global_feature_classifier.LayererTopologicalDescriptors method) get_local_environment() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_local_environments() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_max_coordination_number() (npl.core.neighbor_list.NeighborList method) (npl.core.NeighborList method) get_n_atoms() (npl.core.atom_wrapper.AtomWrapper method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_n_atoms_of_symbol() (npl.core.atom_wrapper.AtomWrapper method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_n_bonds() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) (npl.core.neighbor_list.NeighborList method) (npl.core.NeighborList method) get_neighbor_list() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_niche() (npl.optimization.genetic_algoritm.NichedPopulation.NichedPopulation method) get_normal_vector() (in module npl.utils.math_modules) get_number_of_adsorbates() (npl.core.adsorption.AdsorptionSiteList method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_number_of_feature() (npl.descriptors.global_feature_classifier.ExtendedTopologicalFeaturesClassifier method) get_occupation_status_by_indices() (npl.core.adsorption.AdsorptionSiteList method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_occupation_vector() (npl.core.adsorption.AdsorptionSiteList method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_ontop_sites() (npl.core.adsorption.FindAdsorptionSites method) (npl.core.adsorption.PlaceAddAtoms method) (npl.core.FindAdsorptionSites method) get_perpendicular_edge_vector() (in module npl.utils.math_modules) get_perpendicular_vector() (in module npl.utils.math_modules) get_plane() (in module npl.utils.math_modules) get_position() (npl.core.atom_wrapper.AtomWrapper method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_positions() (npl.core.atom_wrapper.AtomWrapper method) get_site_atom_indices() (npl.core.adsorption.AdsorptionSiteList method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_site_size() (npl.core.adsorption.AdsorptionSiteList method) get_stoichiometry() (npl.core.atom_wrapper.AtomWrapper method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_sublayer_indices() (npl.descriptors.global_feature_classifier.ExtendedTopologicalFeaturesClassifier method) get_swap_porbability() (npl.monte_carlo.random_exchange_operator_etop.RandomExchangeOperatorExtended method) get_symbol() (npl.core.atom_wrapper.AtomWrapper method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_symbols() (npl.core.atom_wrapper.AtomWrapper method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_total_adsorption_sites() (npl.core.adsorption.PlaceAddAtoms method) get_total_dipole_moment() (npl.calculators.energy_calculator.DipoleMomentCalculator method) get_total_number_of_sites() (npl.core.adsorption.AdsorptionSiteList method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) get_unit_vector() (in module npl.utils.math_modules) get_xyz_site_from_atom_indices() (npl.core.adsorption.PlaceAddAtoms method) GlobalFeatureClassifier (class in npl.descriptors.global_feature_classifier) GOSearch (class in npl.optimization) (class in npl.optimization.go_search) GPRCalculator (class in npl.calculators.energy_calculator) guided_exchange() (npl.optimization.local_optimization.garbage_exchange_operator.GuidedExchangeOperator method) (npl.optimization.local_optimization.guided_exchange_operator.GuidedExchangeOperator method) GuidedExchangeOperator (class in npl.optimization.local_optimization.garbage_exchange_operator) (class in npl.optimization.local_optimization.guided_exchange_operator) GuidedSearch (class in npl.optimization) (class in npl.optimization.go_search)

H

has_energy() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method)

I

initialize_outfile() (npl.monte_carlo.BaseEnsemble method) (npl.monte_carlo.ensembles.base_ensemble.BaseEnsemble method)

is_pure() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method)

K

kmeans_clustering() (npl.descriptors.local_environment_feature_classifier.KMeansClassifier method)

KMeansClassifier (class in npl.descriptors.local_environment_feature_classifier)

L

LateralInteractionCalculator (class in npl.calculators.energy_calculator) LayererTopologicalDescriptors (class in npl.descriptors.global_feature_classifier) load() (npl.calculators.energy_calculator.EnergyCalculator static method) (npl.calculators.EnergyCalculator static method) load_coefficients() (npl.calculators.top_calculator.TOPCalculator method) (npl.calculators.TOPCalculator method) load_model() (npl.calculators.top_calculator.TOPCalculator method) (npl.calculators.TOPCalculator method)

load_npl_format() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) local_optimization() (in module npl.optimization.local_optimization.local_optimization) (npl.optimization.genetic_algoritm.LocalOptimizationOperator.LocalOptimizationOperator method) LocalEnvironmentCalculator (class in npl.descriptors) (class in npl.descriptors.local_environment_calculator) LocalEnvironmentFeatureClassifier (class in npl.descriptors.local_environment_feature_classifier) LocalOptimizationOperator (class in npl.optimization.genetic_algoritm.LocalOptimizationOperator) locate_convex_hull() (in module npl.optimization.genetic_algoritm.ConvexHull)

M

mc_run() (in module npl.monte_carlo) (in module npl.monte_carlo.monte_carlo) MCSearch (class in npl.optimization) (class in npl.optimization.go_search) MixingEnergyCalculator (class in npl.calculators.energy_calculator) module npl npl.calculators npl.calculators.base_calculator npl.calculators.energy_calculator npl.calculators.top_calculator npl.core npl.core.adsorption npl.core.atom_wrapper npl.core.base_nanoparticle npl.core.nanoparticle npl.core.neighbor_list npl.core.profiler npl.descriptors npl.descriptors.global_feature_classifier npl.descriptors.local_environment_calculator npl.descriptors.local_environment_feature_classifier npl.monte_carlo npl.monte_carlo.ensembles npl.monte_carlo.ensembles.base_ensemble npl.monte_carlo.ensembles.canonical_ensemble npl.monte_carlo.monte_carlo npl.monte_carlo.monte_carlo_etop npl.monte_carlo.monte_carlo_global_features npl.monte_carlo.random_exchange_operator npl.monte_carlo.random_exchange_operator_etop npl.optimization npl.optimization.basin_hopping npl.optimization.basin_hopping.basin_hopping npl.optimization.genetic_algoritm npl.optimization.genetic_algoritm.ConvexHull npl.optimization.genetic_algoritm.CutAndSpliceOperator npl.optimization.genetic_algoritm.ExchangeOperator npl.optimization.genetic_algoritm.LocalOptimizationOperator npl.optimization.genetic_algoritm.MutationOperator npl.optimization.genetic_algoritm.NichedPopulation npl.optimization.genetic_algoritm.SingleParticleGA npl.optimization.go_search npl.optimization.local_optimization npl.optimization.local_optimization.garbage_exchange_operator npl.optimization.local_optimization.guided_exchange_operator npl.optimization.local_optimization.local_optimization npl.utils npl.utils.cutting_plane_utilities npl.utils.math_modules npl.utils.utils

MutationOperator (class in npl.optimization.genetic_algoritm.MutationOperator)

N

Nanoparticle (class in npl.core) (class in npl.core.nanoparticle) NeighborCountingEnvironmentCalculator (class in npl.descriptors.local_environment_calculator) NeighborList (class in npl.core) (class in npl.core.neighbor_list) NichedPopulation (class in npl.optimization.genetic_algoritm.NichedPopulation) npl module npl.calculators module npl.calculators.base_calculator module npl.calculators.energy_calculator module npl.calculators.top_calculator module npl.core module npl.core.adsorption module npl.core.atom_wrapper module npl.core.base_nanoparticle module npl.core.nanoparticle module npl.core.neighbor_list module npl.core.profiler module npl.descriptors module npl.descriptors.global_feature_classifier module npl.descriptors.local_environment_calculator module npl.descriptors.local_environment_feature_classifier module npl.monte_carlo module npl.monte_carlo.ensembles module npl.monte_carlo.ensembles.base_ensemble module npl.monte_carlo.ensembles.canonical_ensemble module npl.monte_carlo.monte_carlo module

npl.monte_carlo.monte_carlo_etop module npl.monte_carlo.monte_carlo_global_features module npl.monte_carlo.random_exchange_operator module npl.monte_carlo.random_exchange_operator_etop module npl.optimization module npl.optimization.basin_hopping module npl.optimization.basin_hopping.basin_hopping module npl.optimization.genetic_algoritm module npl.optimization.genetic_algoritm.ConvexHull module npl.optimization.genetic_algoritm.CutAndSpliceOperator module npl.optimization.genetic_algoritm.ExchangeOperator module npl.optimization.genetic_algoritm.LocalOptimizationOperator module npl.optimization.genetic_algoritm.MutationOperator module npl.optimization.genetic_algoritm.NichedPopulation module npl.optimization.genetic_algoritm.SingleParticleGA module npl.optimization.go_search module npl.optimization.local_optimization module npl.optimization.local_optimization.garbage_exchange_operator module npl.optimization.local_optimization.guided_exchange_operator module npl.optimization.local_optimization.local_optimization module npl.utils module npl.utils.cutting_plane_utilities module npl.utils.math_modules module npl.utils.utils module

O

occupation_vector() (npl.core.adsorption.AdsorptionSiteList method)

P

place_add_atom() (npl.core.adsorption.PlaceAddAtoms method) PlaceAddAtoms (class in npl.core.adsorption) Population (class in npl.optimization.genetic_algoritm.NichedPopulation) predict_atom_feature() (npl.descriptors.local_environment_feature_classifier.CoordinationNumberClassifier method) (npl.descriptors.local_environment_feature_classifier.KMeansClassifier method) (npl.descriptors.local_environment_feature_classifier.LocalEnvironmentFeatureClassifier method) (npl.descriptors.local_environment_feature_classifier.TopologicalEnvironmentClassifier method)

predict_local_environment() (npl.descriptors.local_environment_calculator.LocalEnvironmentCalculator method) (npl.descriptors.local_environment_calculator.NeighborCountingEnvironmentCalculator method) (npl.descriptors.local_environment_calculator.SOAPCalculator method) (npl.descriptors.LocalEnvironmentCalculator method) profile() (in module npl.core.profiler)

R

random_adsorbate_migration() (npl.monte_carlo.random_exchange_operator.RandomExchangeOperator method) random_exchange() (npl.monte_carlo.random_exchange_operator.RandomExchangeOperator method) (npl.monte_carlo.random_exchange_operator_etop.RandomExchangeOperatorExtended method) (npl.optimization.genetic_algoritm.ExchangeOperator.ExchangeOperator method) random_mutation() (npl.optimization.genetic_algoritm.MutationOperator.MutationOperator method) random_occupation() (npl.core.adsorption.AdsorptionSiteList method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) random_ordering() (npl.core.atom_wrapper.AtomWrapper method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) random_selection() (npl.optimization.genetic_algoritm.NichedPopulation.NichedPopulation method) (npl.optimization.genetic_algoritm.NichedPopulation.Population method) RandomExchangeOperator (class in npl.monte_carlo.random_exchange_operator) RandomExchangeOperatorExtended (class in npl.monte_carlo.random_exchange_operator_etop) read() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method)

relax() (npl.monte_carlo.CanonicalEnsemble method) (npl.monte_carlo.ensembles.canonical_ensemble.CanonicalEnsemble method) remove_atoms() (npl.core.atom_wrapper.AtomWrapper method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) run() (npl.monte_carlo.CanonicalEnsemble method) (npl.monte_carlo.ensembles.canonical_ensemble.CanonicalEnsemble method) run_basin_hopping() (in module npl.optimization.basin_hopping.basin_hopping) run_monte_carlo() (in module npl.monte_carlo) (in module npl.monte_carlo.monte_carlo_etop) (in module npl.monte_carlo.monte_carlo_global_features) run_monte_carlo_for_adsorbates() (in module npl.monte_carlo.monte_carlo) run_monte_carlo_ordering_adsorbates() (in module npl.monte_carlo.monte_carlo) run_multiple_simulations() (npl.optimization.go_search.GOSearch method) (npl.optimization.GOSearch method) run_single_particle_ga() (in module npl.optimization.genetic_algoritm.SingleParticleGA)

S

save() (npl.calculators.energy_calculator.EnergyCalculator method) (npl.calculators.EnergyCalculator method) save_npl_format() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) set_atom_feature() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) set_atom_features() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) set_beta() (npl.optimization.go_search.MCSearch method) (npl.optimization.MCSearch method) set_center() (npl.utils.cutting_plane_utilities.SphericalCuttingPlaneGenerator method) set_coefficients() (npl.calculators.BayesianRRCalculator method) (npl.calculators.energy_calculator.BayesianRRCalculator method) (npl.calculators.top_calculator.TOPCalculator method) (npl.calculators.TOPCalculator method) set_energy() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) set_energy_key() (npl.calculators.energy_calculator.EnergyCalculator method) (npl.calculators.EnergyCalculator method) set_feature_key() (npl.calculators.BayesianRRCalculator method) (npl.calculators.energy_calculator.BayesianRRCalculator method) (npl.descriptors.global_feature_classifier.GlobalFeatureClassifier method) (npl.descriptors.local_environment_feature_classifier.LocalEnvironmentFeatureClassifier method) set_feature_vector() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method)

set_local_environment() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) set_local_environments() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) set_max_radius() (npl.utils.cutting_plane_utilities.SphericalCuttingPlaneGenerator method) set_n_steps() (npl.optimization.go_search.MCSearch method) (npl.optimization.MCSearch method) setup_local_optimization() (in module npl.optimization.local_optimization.local_optimization) setup_monte_carlo() (in module npl.monte_carlo.monte_carlo) (in module npl.monte_carlo.monte_carlo_etop) (in module npl.monte_carlo.monte_carlo_global_features) SimpleFeatureClassifier (class in npl.descriptors.global_feature_classifier) SOAPCalculator (class in npl.descriptors.local_environment_calculator) SphericalCuttingPlaneGenerator (class in npl.utils.cutting_plane_utilities) split_atom_indices() (npl.utils.cutting_plane_utilities.CuttingPlane method) step (npl.monte_carlo.BaseEnsemble property) (npl.monte_carlo.ensembles.base_ensemble.BaseEnsemble property) swap_status() (npl.core.adsorption.AdsorptionSiteList method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) swap_symbols() (npl.core.atom_wrapper.AtomWrapper method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method)

T

testTopologicalFeatureClassifier (class in npl.descriptors.global_feature_classifier) TOPCalculator (class in npl.calculators) (class in npl.calculators.top_calculator) TopologicalEnvironmentClassifier (class in npl.descriptors.local_environment_feature_classifier) TopologicalFeatureClassifier (class in npl.descriptors.global_feature_classifier) tournament_selection() (npl.optimization.genetic_algoritm.NichedPopulation.NichedPopulation method) (npl.optimization.genetic_algoritm.NichedPopulation.Population method) transform_atoms() (npl.core.atom_wrapper.AtomWrapper method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method)

translate_atoms_positions() (npl.core.atom_wrapper.AtomWrapper method) (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) trial_step() (npl.monte_carlo.CanonicalEnsemble method) (npl.monte_carlo.ensembles.canonical_ensemble.CanonicalEnsemble method) truncated_octahedron() (npl.core.Nanoparticle method) (npl.core.nanoparticle.Nanoparticle method)

U

update() (npl.optimization.local_optimization.garbage_exchange_operator.GuidedExchangeOperator method) (npl.optimization.local_optimization.guided_exchange_operator.GuidedExchangeOperator method) update_atom_feature() (npl.descriptors.global_feature_classifier.ExtendedTopologicalFeaturesClassifier method)

update_atomic_features() (in module npl.monte_carlo.monte_carlo) (in module npl.optimization.local_optimization.local_optimization) update_feature_vector() (npl.descriptors.global_feature_classifier.ExtendedTopologicalFeaturesClassifier method)

V

validate() (npl.calculators.BayesianRRCalculator method) (npl.calculators.energy_calculator.BayesianRRCalculator method)

W

write() (npl.core.base_nanoparticle.BaseNanoparticle method) (npl.core.BaseNanoparticle method) write_outfile() (npl.monte_carlo.BaseEnsemble method) (npl.monte_carlo.ensembles.base_ensemble.BaseEnsemble method)

write_traj_file() (npl.monte_carlo.BaseEnsemble method) (npl.monte_carlo.ensembles.base_ensemble.BaseEnsemble method)