npl package

Subpackages

• npl.calculators package
  • Submodules
  • npl.calculators.base_calculator module
  • npl.calculators.energy_calculator module
    • BayesianRRCalculator
      • BayesianRRCalculator.compute_energy()
      • BayesianRRCalculator.fit()
      • BayesianRRCalculator.get_coefficients()
      • BayesianRRCalculator.set_coefficients()
      • BayesianRRCalculator.set_feature_key()
      • BayesianRRCalculator.validate()
    • DipoleMomentCalculator
      • DipoleMomentCalculator.compute_dipole_moment()
      • DipoleMomentCalculator.get_dipole_moments()
      • DipoleMomentCalculator.get_environments()
      • DipoleMomentCalculator.get_total_dipole_moment()
    • EMTCalculator
      • EMTCalculator.compute_energy()
    • EnergyCalculator
      • EnergyCalculator.compute_energy()
      • EnergyCalculator.get_energy_key()
      • EnergyCalculator.load()
      • EnergyCalculator.save()
      • EnergyCalculator.set_energy_key()
    • GPRCalculator
      • GPRCalculator.compute_energy()
      • GPRCalculator.fit()
    • LateralInteractionCalculator
      • LateralInteractionCalculator.bind_grid()
      • LateralInteractionCalculator.compute_energy()
      • LateralInteractionCalculator.construct_interatomic_potential_matrix()
    • MixingEnergyCalculator
      • MixingEnergyCalculator.compute_energy()
      • MixingEnergyCalculator.compute_mixing_parameters()
    • compute_coefficients_for_linear_topological_model()
    • compute_coefficients_for_shape_optimization()
  • npl.calculators.top_calculator module
    • TOPCalculator
      • TOPCalculator.calculate()
      • TOPCalculator.compute_energy()
      • TOPCalculator.get_coefficients()
      • TOPCalculator.get_data_by_stoichiometry()
      • TOPCalculator.get_energy_key()
      • TOPCalculator.get_feature_classifier()
      • TOPCalculator.get_feature_key()
      • TOPCalculator.load_coefficients()
      • TOPCalculator.load_model()
      • TOPCalculator.set_coefficients()
  • Module contents
    • BayesianRRCalculator
      • BayesianRRCalculator.compute_energy()
      • BayesianRRCalculator.fit()
      • BayesianRRCalculator.get_coefficients()
      • BayesianRRCalculator.set_coefficients()
      • BayesianRRCalculator.set_feature_key()
      • BayesianRRCalculator.validate()
    • EMTCalculator
      • EMTCalculator.compute_energy()
    • EnergyCalculator
      • EnergyCalculator.compute_energy()
      • EnergyCalculator.get_energy_key()
      • EnergyCalculator.load()
      • EnergyCalculator.save()
      • EnergyCalculator.set_energy_key()
    • TOPCalculator
      • TOPCalculator.calculate()
      • TOPCalculator.compute_energy()
      • TOPCalculator.get_coefficients()
      • TOPCalculator.get_data_by_stoichiometry()
      • TOPCalculator.get_energy_key()
      • TOPCalculator.get_feature_classifier()
      • TOPCalculator.get_feature_key()
      • TOPCalculator.load_coefficients()
      • TOPCalculator.load_model()
      • TOPCalculator.set_coefficients()
    • compute_coefficients_for_linear_topological_model()
• npl.core package
  • Submodules
  • npl.core.adsorption module
    • AdsorptionSiteList
      • AdsorptionSiteList.build_site_list()
      • AdsorptionSiteList.construct()
      • AdsorptionSiteList.get_number_of_adsorbates()
      • AdsorptionSiteList.get_occupation_status_by_indices()
      • AdsorptionSiteList.get_occupation_vector()
      • AdsorptionSiteList.get_site_atom_indices()
      • AdsorptionSiteList.get_site_size()
      • AdsorptionSiteList.get_total_number_of_sites()
      • AdsorptionSiteList.occupation_vector()
      • AdsorptionSiteList.random_occupation()
      • AdsorptionSiteList.swap_status()
    • FindAdsorptionSites
      • FindAdsorptionSites.find_atom_plane_vec()
      • FindAdsorptionSites.find_direction_for_edges()
      • FindAdsorptionSites.find_plane_for_bridge_atoms()
      • FindAdsorptionSites.get_bridge_sites()
      • FindAdsorptionSites.get_hollow_sites()
      • FindAdsorptionSites.get_ontop_sites()
    • PlaceAddAtoms
      • PlaceAddAtoms.bind_particle()
      • PlaceAddAtoms.get_bridge_sties()
      • PlaceAddAtoms.get_hollow_sties()
      • PlaceAddAtoms.get_ontop_sites()
      • PlaceAddAtoms.get_total_adsorption_sites()
      • PlaceAddAtoms.get_xyz_site_from_atom_indices()
      • PlaceAddAtoms.place_add_atom()
  • npl.core.atom_wrapper module
    • AtomWrapper
      • AtomWrapper.add_atoms()
      • AtomWrapper.get_all_symbols()
      • AtomWrapper.get_ase_atoms()
      • AtomWrapper.get_atoms()
      • AtomWrapper.get_indices()
      • AtomWrapper.get_indices_by_symbol()
      • AtomWrapper.get_n_atoms()
      • AtomWrapper.get_n_atoms_of_symbol()
      • AtomWrapper.get_position()
      • AtomWrapper.get_positions()
      • AtomWrapper.get_stoichiometry()
      • AtomWrapper.get_symbol()
      • AtomWrapper.get_symbols()
      • AtomWrapper.random_ordering()
      • AtomWrapper.remove_atoms()
      • AtomWrapper.swap_symbols()
      • AtomWrapper.transform_atoms()
      • AtomWrapper.translate_atoms_positions()
  • npl.core.base_nanoparticle module
    • BaseNanoparticle
      • BaseNanoparticle.add_atoms()
      • BaseNanoparticle.build_from_dictionary()
      • BaseNanoparticle.construct_adsorption_list()
      • BaseNanoparticle.construct_neighbor_list()
      • BaseNanoparticle.get_adsorption_as_list()
      • BaseNanoparticle.get_adsorption_list()
      • BaseNanoparticle.get_all_symbols()
      • BaseNanoparticle.get_as_dictionary()
      • BaseNanoparticle.get_ase_atoms()
      • BaseNanoparticle.get_atom_feature()
      • BaseNanoparticle.get_atom_features()
      • BaseNanoparticle.get_atom_indices_from_coordination_number()
      • BaseNanoparticle.get_atoms()
      • BaseNanoparticle.get_atoms_in_the_surface_plane()
      • BaseNanoparticle.get_coordination_atoms()
      • BaseNanoparticle.get_coordination_number()
      • BaseNanoparticle.get_energy()
      • BaseNanoparticle.get_feature_vector()
      • BaseNanoparticle.get_generalized_coordination_number()
      • BaseNanoparticle.get_generalized_coordination_numbers()
      • BaseNanoparticle.get_geometrical_data()
      • BaseNanoparticle.get_indices()
      • BaseNanoparticle.get_indices_by_symbol()
      • BaseNanoparticle.get_indices_of_adsorbates()
      • BaseNanoparticle.get_local_environment()
      • BaseNanoparticle.get_local_environments()
      • BaseNanoparticle.get_n_atoms()
      • BaseNanoparticle.get_n_atoms_of_symbol()
      • BaseNanoparticle.get_n_bonds()
      • BaseNanoparticle.get_neighbor_list()
      • BaseNanoparticle.get_number_of_adsorbates()
      • BaseNanoparticle.get_occupation_status_by_indices()
      • BaseNanoparticle.get_occupation_vector()
      • BaseNanoparticle.get_position()
      • BaseNanoparticle.get_site_atom_indices()
      • BaseNanoparticle.get_stoichiometry()
      • BaseNanoparticle.get_symbol()
      • BaseNanoparticle.get_symbols()
      • BaseNanoparticle.get_total_number_of_sites()
      • BaseNanoparticle.has_energy()
      • BaseNanoparticle.is_pure()
      • BaseNanoparticle.load_npl_format()
      • BaseNanoparticle.random_occupation()
      • BaseNanoparticle.random_ordering()
      • BaseNanoparticle.read()
      • BaseNanoparticle.remove_atoms()
      • BaseNanoparticle.save_npl_format()
      • BaseNanoparticle.set_atom_feature()
      • BaseNanoparticle.set_atom_features()
      • BaseNanoparticle.set_energy()
      • BaseNanoparticle.set_feature_vector()
      • BaseNanoparticle.set_local_environment()
      • BaseNanoparticle.set_local_environments()
      • BaseNanoparticle.swap_status()
      • BaseNanoparticle.swap_symbols()
      • BaseNanoparticle.transform_atoms()
      • BaseNanoparticle.translate_atoms_positions()
      • BaseNanoparticle.write()
  • npl.core.database_class module
  • npl.core.nanoparticle module
    • Nanoparticle
      • Nanoparticle.adjust_stoichiometry()
      • Nanoparticle.truncated_octahedron()
  • npl.core.neighbor_list module
    • NeighborList
      • NeighborList.construct()
      • NeighborList.get_atom_indices_from_coordination_number()
      • NeighborList.get_atoms_in_the_surface_plane()
      • NeighborList.get_coordination_atoms()
      • NeighborList.get_coordination_number()
      • NeighborList.get_generalized_coordination_number()
      • NeighborList.get_max_coordination_number()
      • NeighborList.get_n_bonds()
  • npl.core.profiler module
    • profile()
  • Module contents
    • BaseNanoparticle
      • BaseNanoparticle.add_atoms()
      • BaseNanoparticle.build_from_dictionary()
      • BaseNanoparticle.construct_adsorption_list()
      • BaseNanoparticle.construct_neighbor_list()
      • BaseNanoparticle.get_adsorption_as_list()
      • BaseNanoparticle.get_adsorption_list()
      • BaseNanoparticle.get_all_symbols()
      • BaseNanoparticle.get_as_dictionary()
      • BaseNanoparticle.get_ase_atoms()
      • BaseNanoparticle.get_atom_feature()
      • BaseNanoparticle.get_atom_features()
      • BaseNanoparticle.get_atom_indices_from_coordination_number()
      • BaseNanoparticle.get_atoms()
      • BaseNanoparticle.get_atoms_in_the_surface_plane()
      • BaseNanoparticle.get_coordination_atoms()
      • BaseNanoparticle.get_coordination_number()
      • BaseNanoparticle.get_energy()
      • BaseNanoparticle.get_feature_vector()
      • BaseNanoparticle.get_generalized_coordination_number()
      • BaseNanoparticle.get_generalized_coordination_numbers()
      • BaseNanoparticle.get_geometrical_data()
      • BaseNanoparticle.get_indices()
      • BaseNanoparticle.get_indices_by_symbol()
      • BaseNanoparticle.get_indices_of_adsorbates()
      • BaseNanoparticle.get_local_environment()
      • BaseNanoparticle.get_local_environments()
      • BaseNanoparticle.get_n_atoms()
      • BaseNanoparticle.get_n_atoms_of_symbol()
      • BaseNanoparticle.get_n_bonds()
      • BaseNanoparticle.get_neighbor_list()
      • BaseNanoparticle.get_number_of_adsorbates()
      • BaseNanoparticle.get_occupation_status_by_indices()
      • BaseNanoparticle.get_occupation_vector()
      • BaseNanoparticle.get_position()
      • BaseNanoparticle.get_site_atom_indices()
      • BaseNanoparticle.get_stoichiometry()
      • BaseNanoparticle.get_symbol()
      • BaseNanoparticle.get_symbols()
      • BaseNanoparticle.get_total_number_of_sites()
      • BaseNanoparticle.has_energy()
      • BaseNanoparticle.is_pure()
      • BaseNanoparticle.load_npl_format()
      • BaseNanoparticle.random_occupation()
      • BaseNanoparticle.random_ordering()
      • BaseNanoparticle.read()
      • BaseNanoparticle.remove_atoms()
      • BaseNanoparticle.save_npl_format()
      • BaseNanoparticle.set_atom_feature()
      • BaseNanoparticle.set_atom_features()
      • BaseNanoparticle.set_energy()
      • BaseNanoparticle.set_feature_vector()
      • BaseNanoparticle.set_local_environment()
      • BaseNanoparticle.set_local_environments()
      • BaseNanoparticle.swap_status()
      • BaseNanoparticle.swap_symbols()
      • BaseNanoparticle.transform_atoms()
      • BaseNanoparticle.translate_atoms_positions()
      • BaseNanoparticle.write()
    • FindAdsorptionSites
      • FindAdsorptionSites.find_atom_plane_vec()
      • FindAdsorptionSites.find_direction_for_edges()
      • FindAdsorptionSites.find_plane_for_bridge_atoms()
      • FindAdsorptionSites.get_bridge_sites()
      • FindAdsorptionSites.get_hollow_sites()
      • FindAdsorptionSites.get_ontop_sites()
    • Nanoparticle
      • Nanoparticle.adjust_stoichiometry()
      • Nanoparticle.truncated_octahedron()
    • NeighborList
      • NeighborList.construct()
      • NeighborList.get_atom_indices_from_coordination_number()
      • NeighborList.get_atoms_in_the_surface_plane()
      • NeighborList.get_coordination_atoms()
      • NeighborList.get_coordination_number()
      • NeighborList.get_generalized_coordination_number()
      • NeighborList.get_max_coordination_number()
      • NeighborList.get_n_bonds()
• npl.descriptors package
  • Submodules
  • npl.descriptors.global_feature_classifier module
    • AdsorptionFeatureVector
      • AdsorptionFeatureVector.compute_feature_vector()
      • AdsorptionFeatureVector.get_features()
    • AtomicCoordinationTypes
      • AtomicCoordinationTypes.compute_atom_feature()
      • AtomicCoordinationTypes.compute_feature_vector()
      • AtomicCoordinationTypes.compute_n_features()
    • CoordinationFeatureClassifier
      • CoordinationFeatureClassifier.compute_feature_vector()
    • DipoleMomentCalculator
      • DipoleMomentCalculator.compute_feature_vector()
    • ExtendedTopologicalFeaturesClassifier
      • ExtendedTopologicalFeaturesClassifier.compute_atom_feature()
      • ExtendedTopologicalFeaturesClassifier.compute_atom_features()
      • ExtendedTopologicalFeaturesClassifier.compute_feature_vector()
      • ExtendedTopologicalFeaturesClassifier.downgrade_feature_vector()
      • ExtendedTopologicalFeaturesClassifier.get_bond_types()
      • ExtendedTopologicalFeaturesClassifier.get_coordination_index()
      • ExtendedTopologicalFeaturesClassifier.get_feature_labels()
      • ExtendedTopologicalFeaturesClassifier.get_layer_types()
      • ExtendedTopologicalFeaturesClassifier.get_number_of_feature()
      • ExtendedTopologicalFeaturesClassifier.get_sublayer_indices()
      • ExtendedTopologicalFeaturesClassifier.update_atom_feature()
      • ExtendedTopologicalFeaturesClassifier.update_feature_vector()
    • GeneralizedCoordinationNumber
      • GeneralizedCoordinationNumber.compute_feature_vector()
    • GlobalFeatureClassifier
      • GlobalFeatureClassifier.compute_feature_vector()
      • GlobalFeatureClassifier.get_feature_key()
      • GlobalFeatureClassifier.set_feature_key()
    • LayererTopologicalDescriptors
      • LayererTopologicalDescriptors.compute_feature_vector()
      • LayererTopologicalDescriptors.compute_layers()
      • LayererTopologicalDescriptors.get_layer_indices()
      • LayererTopologicalDescriptors.get_layers_occupacy()
    • SimpleFeatureClassifier
      • SimpleFeatureClassifier.compute_feature_vector()
      • SimpleFeatureClassifier.compute_respective_bond_counts()
    • TopologicalFeatureClassifier
      • TopologicalFeatureClassifier.compute_feature_vector()
      • TopologicalFeatureClassifier.get_feature_labels()
    • testTopologicalFeatureClassifier
      • testTopologicalFeatureClassifier.compute_feature_vector()
      • testTopologicalFeatureClassifier.get_feature_labels()
  • npl.descriptors.local_environment_calculator module
    • LocalEnvironmentCalculator
      • LocalEnvironmentCalculator.compute_local_environment()
      • LocalEnvironmentCalculator.compute_local_environments()
      • LocalEnvironmentCalculator.predict_local_environment()
    • NeighborCountingEnvironmentCalculator
      • NeighborCountingEnvironmentCalculator.predict_local_environment()
    • SOAPCalculator
      • SOAPCalculator.predict_local_environment()
  • npl.descriptors.local_environment_feature_classifier module
    • CoordinationNumberClassifier
      • CoordinationNumberClassifier.compute_n_features()
      • CoordinationNumberClassifier.predict_atom_feature()
    • KMeansClassifier
      • KMeansClassifier.compute_n_features()
      • KMeansClassifier.kmeans_clustering()
      • KMeansClassifier.predict_atom_feature()
    • LocalEnvironmentFeatureClassifier
      • LocalEnvironmentFeatureClassifier.compute_atom_feature()
      • LocalEnvironmentFeatureClassifier.compute_atom_features()
      • LocalEnvironmentFeatureClassifier.compute_feature_vector()
      • LocalEnvironmentFeatureClassifier.compute_n_features()
      • LocalEnvironmentFeatureClassifier.get_feature_key()
      • LocalEnvironmentFeatureClassifier.predict_atom_feature()
      • LocalEnvironmentFeatureClassifier.set_feature_key()
    • TopologicalEnvironmentClassifier
      • TopologicalEnvironmentClassifier.compute_n_features()
      • TopologicalEnvironmentClassifier.predict_atom_feature()
  • Module contents
    • LocalEnvironmentCalculator
      • LocalEnvironmentCalculator.compute_local_environment()
      • LocalEnvironmentCalculator.compute_local_environments()
      • LocalEnvironmentCalculator.predict_local_environment()
• npl.monte_carlo package
  • Subpackages
    • npl.monte_carlo.ensembles package
      • Submodules
      • npl.monte_carlo.ensembles.base_ensemble module
      • npl.monte_carlo.ensembles.canonical_ensemble module
      • Module contents
  • Submodules
  • npl.monte_carlo.monte_carlo module
    • mc_run()
    • run_monte_carlo_for_adsorbates()
    • run_monte_carlo_ordering_adsorbates()
    • setup_monte_carlo()
    • update_atomic_features()
  • npl.monte_carlo.monte_carlo_etop module
    • features_to_update()
    • run_monte_carlo()
    • setup_monte_carlo()
  • npl.monte_carlo.monte_carlo_global_features module
    • run_monte_carlo()
    • setup_monte_carlo()
  • npl.monte_carlo.random_exchange_operator module
    • RandomExchangeOperator
      • RandomExchangeOperator.bind_adsorbates()
      • RandomExchangeOperator.bind_particle()
      • RandomExchangeOperator.coupled_random_exchange()
      • RandomExchangeOperator.random_adsorbate_migration()
      • RandomExchangeOperator.random_exchange()
  • npl.monte_carlo.random_exchange_operator_etop module
    • RandomExchangeOperatorExtended
      • RandomExchangeOperatorExtended.bind_particle()
      • RandomExchangeOperatorExtended.get_swap_porbability()
      • RandomExchangeOperatorExtended.random_exchange()
  • Module contents
    • BaseEnsemble
      • BaseEnsemble.atoms
      • BaseEnsemble.initialize_outfile()
      • BaseEnsemble.step
      • BaseEnsemble.write_outfile()
      • BaseEnsemble.write_traj_file()
    • CanonicalEnsemble
      • CanonicalEnsemble.do_mutation()
      • CanonicalEnsemble.relax()
      • CanonicalEnsemble.run()
      • CanonicalEnsemble.trial_step()
    • mc_run()
    • run_monte_carlo()
• npl.optimization package
  • Subpackages
    • npl.optimization.basin_hopping package
      • Submodules
      • npl.optimization.basin_hopping.basin_hopping module
      • Module contents
    • npl.optimization.genetic_algoritm package
      • Submodules
      • 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
      • Module contents
    • npl.optimization.local_optimization package
      • Submodules
      • npl.optimization.local_optimization.garbage_exchange_operator module
      • npl.optimization.local_optimization.guided_exchange_operator module
      • npl.optimization.local_optimization.local_optimization module
      • Module contents
  • Submodules
  • npl.optimization.go_search module
    • GASearch
      • GASearch.build_args_list_for_gm_search()
      • GASearch.build_kwargs_list_for_gm_search()
      • GASearch.fit_energy_expression()
    • GOSearch
      • GOSearch.build_args_list_for_gm_search()
      • GOSearch.build_kwargs_list_for_gm_search()
      • GOSearch.fit_energy_expression()
      • GOSearch.run_multiple_simulations()
    • GuidedSearch
      • GuidedSearch.build_args_list_for_gm_search()
      • GuidedSearch.build_kwargs_list_for_gm_search()
      • GuidedSearch.fit_energy_expression()
    • MCSearch
      • MCSearch.build_args_list_for_gm_search()
      • MCSearch.build_kwargs_list_for_gm_search()
      • MCSearch.fit_energy_expression()
      • MCSearch.set_beta()
      • MCSearch.set_n_steps()
  • Module contents
    • GASearch
      • GASearch.build_args_list_for_gm_search()
      • GASearch.build_kwargs_list_for_gm_search()
      • GASearch.fit_energy_expression()
    • GOSearch
      • GOSearch.build_args_list_for_gm_search()
      • GOSearch.build_kwargs_list_for_gm_search()
      • GOSearch.fit_energy_expression()
      • GOSearch.run_multiple_simulations()
    • GuidedSearch
      • GuidedSearch.build_args_list_for_gm_search()
      • GuidedSearch.build_kwargs_list_for_gm_search()
      • GuidedSearch.fit_energy_expression()
    • MCSearch
      • MCSearch.build_args_list_for_gm_search()
      • MCSearch.build_kwargs_list_for_gm_search()
      • MCSearch.fit_energy_expression()
      • MCSearch.set_beta()
      • MCSearch.set_n_steps()
• npl.utils package
  • Submodules
  • npl.utils.cutting_plane_utilities module
    • CuttingPlane
      • CuttingPlane.split_atom_indices()
    • SphericalCuttingPlaneGenerator
      • SphericalCuttingPlaneGenerator.generate_new_cutting_plane()
      • SphericalCuttingPlaneGenerator.set_center()
      • SphericalCuttingPlaneGenerator.set_max_radius()
  • npl.utils.math_modules module
    • find_middle_point()
    • get_atom_position()
    • get_bridge_perpendicular_line()
    • get_dot_product()
    • get_normal_vector()
    • get_perpendicular_edge_vector()
    • get_perpendicular_vector()
    • get_plane()
    • get_unit_vector()
  • npl.utils.utils module
    • get_crystalline_structure()
  • Module contents

Module contents

NPlib - A library for numerical processing.

This package provides various numerical processing utilities.