Index

A

a_repulsive (topsearch.potentials.atomic.BinaryGupta attribute) active_bounds() (topsearch.data.coordinates.StandardCoordinates method) add_data() (topsearch.potentials.gaussian_process.GaussianProcess method) add_minimum() (topsearch.data.kinetic_transition_network.KineticTransitionNetwork method) add_network() (topsearch.data.kinetic_transition_network.KineticTransitionNetwork method) add_ts() (topsearch.data.kinetic_transition_network.KineticTransitionNetwork method) align() (topsearch.similarity.molecular_similarity.MolecularSimilarity method) all_bounds() (topsearch.data.coordinates.StandardCoordinates method) all_minima_connected() (in module topsearch.analysis.graph_properties) allow_inversion (topsearch.similarity.molecular_similarity.MolecularSimilarity attribute) analysis module

analytic_step_size() (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing method) append_data() (topsearch.data.model_data.ModelData method) are_nodes_connected() (in module topsearch.analysis.graph_properties) at_bounds() (topsearch.data.coordinates.StandardCoordinates method) atom_labels (topsearch.data.coordinates.AtomicCoordinates attribute) (topsearch.data.coordinates.MolecularCoordinates attribute) (topsearch.potentials.atomic.BinaryGupta attribute) (topsearch.potentials.dft.DensityFunctionalTheory attribute) (topsearch.potentials.ml_potentials.MachineLearningPotential attribute) AtomicCoordinates (class in topsearch.data.coordinates) AtomicPerturbation (class in topsearch.global_optimisation.perturbations)

B

band_bounds (topsearch.transition_states.nudged_elastic_band.NudgedElasticBand attribute) band_function_gradient() (topsearch.transition_states.nudged_elastic_band.NudgedElasticBand method) band_potential_function() (topsearch.transition_states.nudged_elastic_band.NudgedElasticBand method) barrier_batch_selector() (in module topsearch.analysis.batch_selection)

barrier_reweighting() (in module topsearch.plotting.network) BinaryGupta (class in topsearch.potentials.atomic) bounds (topsearch.data.coordinates.AtomicCoordinates attribute) (topsearch.data.coordinates.MolecularCoordinates attribute) (topsearch.data.coordinates.StandardCoordinates attribute)

C

calculator_type (topsearch.potentials.dft.DensityFunctionalTheory attribute) (topsearch.potentials.ml_potentials.MachineLearningPotential attribute) Camelback (class in topsearch.potentials.test_functions) centre() (topsearch.similarity.molecular_similarity.MolecularSimilarity method) (topsearch.similarity.similarity.StandardSimilarity method) change_bond_angles() (topsearch.data.coordinates.MolecularCoordinates method) change_bond_length() (topsearch.data.coordinates.MolecularCoordinates method) change_bond_lengths() (topsearch.data.coordinates.MolecularCoordinates method) change_dihedral_angles() (topsearch.data.coordinates.MolecularCoordinates method) check_atom_clashes() (topsearch.data.coordinates.AtomicCoordinates method) check_bounds() (topsearch.data.coordinates.StandardCoordinates method) check_eigenvector_direction() (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing method) check_valid_eigenvector() (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing method)

check_valid_minimum() (topsearch.potentials.potential.Potential method) check_valid_ts() (topsearch.potentials.potential.Potential method) closest_distance() (topsearch.similarity.molecular_similarity.MolecularSimilarity method) (topsearch.similarity.similarity.StandardSimilarity method) closest_enumeration() (in module topsearch.analysis.pair_selection) compute_function_grid() (in module topsearch.plotting.stationary_points) conf (topsearch.potentials.force_fields.MMFF94 attribute) connect_to_set() (in module topsearch.analysis.pair_selection) connect_unconnected() (in module topsearch.analysis.pair_selection) conv_crit (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing attribute) convex_hull() (topsearch.data.model_data.ModelData method) cut_line_collection() (in module topsearch.plotting.disconnectivity) cv_results (topsearch.potentials.dataset_fitting.DatasetRegression attribute)

D

data module DatasetInterpolation (class in topsearch.potentials.dataset_fitting) DatasetRegression (class in topsearch.potentials.dataset_fitting) DensityFunctionalTheory (class in topsearch.potentials.dft) dihedral_interpolation() (topsearch.transition_states.nudged_elastic_band.NudgedElasticBand method) disconnected_height() (in module topsearch.analysis.graph_properties)

distance() (topsearch.similarity.similarity.StandardSimilarity method) distance_criterion (topsearch.similarity.molecular_similarity.MolecularSimilarity attribute) (topsearch.similarity.similarity.StandardSimilarity attribute) do_pushoff() (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing method) dump_minima_csv() (topsearch.data.kinetic_transition_network.KineticTransitionNetwork method) dump_network() (topsearch.data.kinetic_transition_network.KineticTransitionNetwork method) dump_path (topsearch.data.kinetic_transition_network.KineticTransitionNetwork attribute) dump_suffix (topsearch.data.kinetic_transition_network.KineticTransitionNetwork attribute)

E

eig_bounds (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing attribute) energy_criterion (topsearch.similarity.molecular_similarity.MolecularSimilarity attribute) (topsearch.similarity.similarity.StandardSimilarity attribute)

epsilon (topsearch.potentials.atomic.LennardJones attribute) evaluate_batch() (in module topsearch.analysis.batch_selection) ExpectedImprovement (class in topsearch.potentials.bayesian_optimisation)

F

failure (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing attribute) feature_subset() (topsearch.data.model_data.ModelData method) fill_batch() (in module topsearch.analysis.batch_selection) find_parent() (in module topsearch.plotting.disconnectivity) find_pushoff() (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing method) find_tangent_differences() (topsearch.transition_states.nudged_elastic_band.NudgedElasticBand method) find_ts_candidates() (topsearch.transition_states.nudged_elastic_band.NudgedElasticBand method) force_constant (topsearch.transition_states.nudged_elastic_band.NudgedElasticBand attribute) force_constants (topsearch.transition_states.nudged_elastic_band.NudgedElasticBand attribute) force_field (topsearch.potentials.dft.DensityFunctionalTheory attribute) (topsearch.potentials.force_fields.MMFF94 attribute) function() (topsearch.potentials.atomic.BinaryGupta method) (topsearch.potentials.atomic.LennardJones method) (topsearch.potentials.bayesian_optimisation.ExpectedImprovement method) (topsearch.potentials.bayesian_optimisation.UpperConfidenceBound method) (topsearch.potentials.dataset_fitting.DatasetInterpolation method) (topsearch.potentials.dataset_fitting.DatasetRegression method) (topsearch.potentials.dft.DensityFunctionalTheory method) (topsearch.potentials.force_fields.MMFF94 method) (topsearch.potentials.gaussian_process.GaussianProcess method) (topsearch.potentials.ml_potentials.MachineLearningPotential method) (topsearch.potentials.potential.Potential method) (topsearch.potentials.test_functions.Camelback method) (topsearch.potentials.test_functions.Quadratic method) (topsearch.potentials.test_functions.Schwefel method)

function_and_std() (topsearch.potentials.gaussian_process.GaussianProcess method) function_call() (in module topsearch.plotting.stationary_points) function_gradient() (topsearch.potentials.atomic.LennardJones method) (topsearch.potentials.dft.DensityFunctionalTheory method) (topsearch.potentials.force_fields.MMFF94 method) (topsearch.potentials.ml_potentials.MachineLearningPotential method) (topsearch.potentials.potential.Potential method)

G

G (topsearch.data.kinetic_transition_network.KineticTransitionNetwork attribute) gaussian_process (topsearch.potentials.bayesian_optimisation.ExpectedImprovement attribute) (topsearch.potentials.bayesian_optimisation.UpperConfidenceBound attribute) GaussianProcess (class in topsearch.potentials.gaussian_process) generate_batch() (in module topsearch.analysis.batch_selection) generate_pairs() (topsearch.similarity.molecular_similarity.MolecularSimilarity method) generate_random_point() (topsearch.data.coordinates.StandardCoordinates method) generate_random_vector() (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing method) get_all_bounds_minima() (in module topsearch.analysis.minima_properties) get_atom() (topsearch.data.coordinates.AtomicCoordinates method) (topsearch.potentials.atomic.LennardJones method) get_batch_positions() (in module topsearch.analysis.batch_selection) get_bond_angle_info() (topsearch.data.coordinates.MolecularCoordinates method) get_bonds() (topsearch.data.coordinates.MolecularCoordinates method) get_bounds_minima() (in module topsearch.analysis.minima_properties) get_connected_atoms() (topsearch.data.coordinates.AtomicCoordinates method) (topsearch.data.coordinates.MolecularCoordinates method) get_connections() (in module topsearch.analysis.graph_properties) get_connectivity_graph() (in module topsearch.plotting.disconnectivity) get_distance_from_minimum() (in module topsearch.analysis.minima_properties) get_distance_matrix() (in module topsearch.analysis.minima_properties) get_excluded_minima() (in module topsearch.analysis.batch_selection) get_force_constants() (topsearch.transition_states.nudged_elastic_band.NudgedElasticBand method) get_furthest_from_centre() (topsearch.similarity.molecular_similarity.MolecularSimilarity method) get_furthest_perpendicular() (topsearch.similarity.molecular_similarity.MolecularSimilarity method) get_invalid_minima() (in module topsearch.analysis.minima_properties) get_line_collection() (in module topsearch.plotting.disconnectivity) get_local_bounds() (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing method)

get_minima_above_cutoff() (in module topsearch.analysis.minima_properties) get_minima_energies() (in module topsearch.analysis.minima_properties) get_minimum_coords() (topsearch.data.kinetic_transition_network.KineticTransitionNetwork method) get_minimum_energy() (topsearch.data.kinetic_transition_network.KineticTransitionNetwork method) get_model_error() (topsearch.potentials.dataset_fitting.DatasetRegression method) get_movable_atoms() (topsearch.data.coordinates.MolecularCoordinates method) get_ordered_minima() (in module topsearch.analysis.minima_properties) get_permutable_groups() (topsearch.similarity.molecular_similarity.MolecularSimilarity method) get_planar_rings() (topsearch.data.coordinates.MolecularCoordinates method) get_population() (in module topsearch.analysis.roughness) get_repeat_dihedrals() (topsearch.data.coordinates.MolecularCoordinates method) get_rotatable_dihedrals() (topsearch.data.coordinates.MolecularCoordinates method) get_rotation_matrix() (topsearch.data.coordinates.MolecularCoordinates method) get_score() (topsearch.potentials.gaussian_process.GaussianProcess method) get_similar_minima() (in module topsearch.analysis.minima_properties) get_smallest_eigenvector() (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing method) get_specific_bond_angle_info() (topsearch.data.coordinates.MolecularCoordinates method) get_ts_coords() (topsearch.data.kinetic_transition_network.KineticTransitionNetwork method) get_ts_energy() (topsearch.data.kinetic_transition_network.KineticTransitionNetwork method) global_optimisation module gpr (topsearch.potentials.gaussian_process.GaussianProcess attribute) gradient() (topsearch.potentials.atomic.LennardJones method) (topsearch.potentials.dft.DensityFunctionalTheory method) (topsearch.potentials.force_fields.MMFF94 method) (topsearch.potentials.ml_potentials.MachineLearningPotential method) (topsearch.potentials.potential.Potential method) (topsearch.potentials.test_functions.Camelback method)

H

hessian() (topsearch.potentials.dft.DensityFunctionalTheory method) (topsearch.potentials.potential.Potential method) (topsearch.potentials.test_functions.Camelback method)

hull (topsearch.data.model_data.ModelData attribute) HybridEigenvectorFollowing (class in topsearch.transition_states.hybrid_eigenvector_following)

I

image_density (topsearch.transition_states.nudged_elastic_band.NudgedElasticBand attribute) initial_interpolation() (topsearch.transition_states.nudged_elastic_band.NudgedElasticBand method) initialise_gaussian_process() (topsearch.potentials.gaussian_process.GaussianProcess method) initialise_kernel() (topsearch.potentials.gaussian_process.GaussianProcess method)

initialise_model() (topsearch.potentials.dataset_fitting.DatasetInterpolation method) (topsearch.potentials.dataset_fitting.DatasetRegression method) invert() (topsearch.similarity.molecular_similarity.MolecularSimilarity method) is_new_minimum() (topsearch.similarity.similarity.StandardSimilarity method) is_new_ts() (topsearch.similarity.similarity.StandardSimilarity method)

K

kernel_bounds (topsearch.potentials.gaussian_process.GaussianProcess attribute)

kernel_choice (topsearch.potentials.gaussian_process.GaussianProcess attribute) KineticTransitionNetwork (class in topsearch.data.kinetic_transition_network)

L

LennardJones (class in topsearch.potentials.atomic) limit_highest_data (topsearch.potentials.gaussian_process.GaussianProcess attribute) limit_response_maximum() (topsearch.data.model_data.ModelData method)

linear_interpolation() (topsearch.transition_states.nudged_elastic_band.NudgedElasticBand method) lowest_batch_selector() (in module topsearch.analysis.batch_selection) lowest_point() (topsearch.potentials.gaussian_process.GaussianProcess method)

M

MachineLearningPotential (class in topsearch.potentials.ml_potentials) make_xy_grid() (in module topsearch.plotting.stationary_points) matern_nu (topsearch.potentials.gaussian_process.GaussianProcess attribute) max_atoms (topsearch.global_optimisation.perturbations.AtomicPerturbation attribute) max_bonds (topsearch.global_optimisation.perturbations.MolecularPerturbation attribute) max_displacement (topsearch.global_optimisation.perturbations.AtomicPerturbation attribute) (topsearch.global_optimisation.perturbations.MolecularPerturbation attribute) (topsearch.global_optimisation.perturbations.StandardPerturbation attribute) max_images (topsearch.transition_states.nudged_elastic_band.NudgedElasticBand attribute) max_uphill_step_size (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing attribute) minimisation module minimise() (in module topsearch.minimisation.lbfgs) minimise_ase() (in module topsearch.minimisation.lbfgs) minimise_interpolation() (topsearch.transition_states.nudged_elastic_band.NudgedElasticBand method) minimiser (topsearch.transition_states.nudged_elastic_band.NudgedElasticBand attribute) MMFF94 (class in topsearch.potentials.force_fields) model (topsearch.potentials.dataset_fitting.DatasetInterpolation attribute) (topsearch.potentials.dataset_fitting.DatasetRegression attribute) model_data (topsearch.potentials.dataset_fitting.DatasetInterpolation attribute) (topsearch.potentials.dataset_fitting.DatasetRegression attribute) (topsearch.potentials.gaussian_process.GaussianProcess attribute) model_rand (topsearch.potentials.dataset_fitting.DatasetRegression attribute) ModelData (class in topsearch.data.model_data) module analysis data global_optimisation minimisation plotting potentials sampling similarity topsearch topsearch.analysis.batch_selection topsearch.analysis.graph_properties topsearch.analysis.minima_properties topsearch.analysis.pair_selection topsearch.analysis.roughness topsearch.data.coordinates topsearch.data.kinetic_transition_network topsearch.data.model_data topsearch.global_optimisation.perturbations topsearch.minimisation.lbfgs topsearch.plotting.disconnectivity topsearch.plotting.network topsearch.plotting.stationary_points topsearch.potentials.atomic topsearch.potentials.bayesian_optimisation topsearch.potentials.dataset_fitting topsearch.potentials.dft topsearch.potentials.force_fields topsearch.potentials.gaussian_process topsearch.potentials.ml_potentials topsearch.potentials.potential topsearch.potentials.test_functions topsearch.similarity.molecular_similarity topsearch.similarity.similarity topsearch.transition_states.hybrid_eigenvector_following topsearch.transition_states.nudged_elastic_band transition_states

MolecularCoordinates (class in topsearch.data.coordinates) MolecularPerturbation (class in topsearch.global_optimisation.perturbations) MolecularSimilarity (class in topsearch.similarity.molecular_similarity) molecule (topsearch.potentials.force_fields.MMFF94 attribute) monotonic_batch_selector() (in module topsearch.analysis.batch_selection) move_to_bounds() (topsearch.data.coordinates.StandardCoordinates method)

N

n_atoms (topsearch.potentials.force_fields.MMFF94 attribute) n_images (topsearch.transition_states.nudged_elastic_band.NudgedElasticBand attribute) n_minima (topsearch.data.kinetic_transition_network.KineticTransitionNetwork attribute) n_points (topsearch.data.model_data.ModelData attribute) n_ts (topsearch.data.kinetic_transition_network.KineticTransitionNetwork attribute)

ndim (topsearch.data.coordinates.AtomicCoordinates attribute) (topsearch.data.coordinates.MolecularCoordinates attribute) (topsearch.data.coordinates.StandardCoordinates attribute) normalise_response() (topsearch.data.model_data.ModelData method) normalise_training() (topsearch.data.model_data.ModelData method) NudgedElasticBand (class in topsearch.transition_states.nudged_elastic_band)

O

optimal_alignment() (topsearch.similarity.molecular_similarity.MolecularSimilarity method) (topsearch.similarity.similarity.StandardSimilarity method)

options (topsearch.potentials.dft.DensityFunctionalTheory attribute) original_image_density (topsearch.transition_states.nudged_elastic_band.NudgedElasticBand attribute)

P

p_range (topsearch.potentials.atomic.BinaryGupta attribute) pair_potential() (topsearch.potentials.atomic.LennardJones method) pairlist (topsearch.data.kinetic_transition_network.KineticTransitionNetwork attribute) parallel_component() (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing method) permutational_alignment() (topsearch.similarity.molecular_similarity.MolecularSimilarity method) perpendicular_component() (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing method) (topsearch.transition_states.nudged_elastic_band.NudgedElasticBand method) perturb() (topsearch.global_optimisation.perturbations.AtomicPerturbation method) (topsearch.global_optimisation.perturbations.MolecularPerturbation method) (topsearch.global_optimisation.perturbations.StandardPerturbation method) plot_contours() (in module topsearch.plotting.stationary_points) plot_disconnectivity_graph() (in module topsearch.plotting.disconnectivity) plot_network() (in module topsearch.plotting.network) plot_stationary_points() (in module topsearch.plotting.stationary_points) plotting module

point_in_hull() (topsearch.data.model_data.ModelData method) position (topsearch.data.coordinates.AtomicCoordinates attribute) (topsearch.data.coordinates.MolecularCoordinates attribute) (topsearch.data.coordinates.StandardCoordinates attribute) positive_eigenvalue_step (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing attribute) Potential (class in topsearch.potentials.potential) potential (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing attribute) (topsearch.transition_states.nudged_elastic_band.NudgedElasticBand attribute) potentials module prepare_training_data() (topsearch.potentials.gaussian_process.GaussianProcess method) project_onto_bounds() (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing method) proportional_distance (topsearch.global_optimisation.perturbations.StandardPerturbation attribute) (topsearch.similarity.similarity.StandardSimilarity attribute) pushoff (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing attribute)

Q

q_range (topsearch.potentials.atomic.BinaryGupta attribute)

Quadratic (class in topsearch.potentials.test_functions)

R

r_eq (topsearch.potentials.atomic.BinaryGupta attribute) random_rotation() (topsearch.similarity.molecular_similarity.MolecularSimilarity method) rayleigh_ritz_function_gradient() (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing method) read_data() (topsearch.data.model_data.ModelData method) read_network() (topsearch.data.kinetic_transition_network.KineticTransitionNetwork method) read_pairs() (in module topsearch.analysis.pair_selection) refit_model() (topsearch.potentials.dataset_fitting.DatasetInterpolation method) (topsearch.potentials.dataset_fitting.DatasetRegression method) (topsearch.potentials.gaussian_process.GaussianProcess method) remove_all_ts() (topsearch.data.kinetic_transition_network.KineticTransitionNetwork method) remove_all_tss() (topsearch.data.kinetic_transition_network.KineticTransitionNetwork method) remove_atom_clashes() (topsearch.data.coordinates.AtomicCoordinates method) (topsearch.data.coordinates.MolecularCoordinates method) remove_duplicates() (topsearch.data.model_data.ModelData method) remove_edges_threshold() (in module topsearch.analysis.graph_properties) remove_minima() (topsearch.data.kinetic_transition_network.KineticTransitionNetwork method) remove_minimum() (topsearch.data.kinetic_transition_network.KineticTransitionNetwork method)

remove_repeat_angles() (topsearch.data.coordinates.MolecularCoordinates method) remove_trans_rot (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing attribute) remove_ts() (topsearch.data.kinetic_transition_network.KineticTransitionNetwork method) remove_tss() (topsearch.data.kinetic_transition_network.KineticTransitionNetwork method) remove_zero_eigenvectors() (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing method) reset_network() (topsearch.data.kinetic_transition_network.KineticTransitionNetwork method) reset_options() (topsearch.potentials.dft.DensityFunctionalTheory method) resp_props (topsearch.data.model_data.ModelData attribute) response (topsearch.data.model_data.ModelData attribute) revert_image_density() (topsearch.transition_states.nudged_elastic_band.NudgedElasticBand method) rotate_angle() (topsearch.data.coordinates.MolecularCoordinates method) rotate_dihedral() (topsearch.data.coordinates.MolecularCoordinates method) rotational_alignment() (topsearch.similarity.molecular_similarity.MolecularSimilarity method) roughness_contributors() (in module topsearch.analysis.roughness) roughness_metric() (in module topsearch.analysis.roughness) run() (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing method) (topsearch.transition_states.nudged_elastic_band.NudgedElasticBand method)

S

same_bonds() (topsearch.data.coordinates.AtomicCoordinates method) (topsearch.data.coordinates.MolecularCoordinates method) sampling module Schwefel (class in topsearch.potentials.test_functions) select_batch() (in module topsearch.analysis.batch_selection) self_connected() (in module topsearch.plotting.stationary_points) set_step_sizes() (topsearch.global_optimisation.perturbations.StandardPerturbation method) set_xyz() (topsearch.potentials.force_fields.MMFF94 method) sigma (topsearch.potentials.atomic.LennardJones attribute) similarity module similarity (topsearch.data.kinetic_transition_network.KineticTransitionNetwork attribute)

smoothness (topsearch.potentials.dataset_fitting.DatasetInterpolation attribute) squared_distance() (topsearch.potentials.atomic.LennardJones method) StandardCoordinates (class in topsearch.data.coordinates) standardise_response (topsearch.potentials.gaussian_process.GaussianProcess attribute) standardise_response() (topsearch.data.model_data.ModelData method) standardise_training (topsearch.potentials.gaussian_process.GaussianProcess attribute) standardise_training() (topsearch.data.model_data.ModelData method) StandardPerturbation (class in topsearch.global_optimisation.perturbations) StandardSimilarity (class in topsearch.similarity.similarity) steepest_descent() (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing method) steepest_descent_paths() (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing method) subspace_function_gradient() (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing method) subspace_minimisation() (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing method) sufficient_barrier() (in module topsearch.analysis.batch_selection)

T

take_uphill_step() (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing method) test_convergence() (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing method) test_exact_same() (topsearch.similarity.molecular_similarity.MolecularSimilarity method) test_new_minimum() (topsearch.similarity.similarity.StandardSimilarity method) test_new_ts() (topsearch.similarity.similarity.StandardSimilarity method) test_same() (topsearch.similarity.molecular_similarity.MolecularSimilarity method) (topsearch.similarity.similarity.StandardSimilarity method) topographical_batch_selector() (in module topsearch.analysis.batch_selection) topsearch module topsearch.analysis.batch_selection module topsearch.analysis.graph_properties module topsearch.analysis.minima_properties module topsearch.analysis.pair_selection module topsearch.analysis.roughness module topsearch.data.coordinates module topsearch.data.kinetic_transition_network module topsearch.data.model_data module topsearch.global_optimisation.perturbations module topsearch.minimisation.lbfgs module topsearch.plotting.disconnectivity module topsearch.plotting.network module

topsearch.plotting.stationary_points module topsearch.potentials.atomic module topsearch.potentials.bayesian_optimisation module topsearch.potentials.dataset_fitting module topsearch.potentials.dft module topsearch.potentials.force_fields module topsearch.potentials.gaussian_process module topsearch.potentials.ml_potentials module topsearch.potentials.potential module topsearch.potentials.test_functions module topsearch.similarity.molecular_similarity module topsearch.similarity.similarity module topsearch.transition_states.hybrid_eigenvector_following module topsearch.transition_states.nudged_elastic_band module train_props (topsearch.data.model_data.ModelData attribute) training (topsearch.data.model_data.ModelData attribute) transition_states module ts_steps (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing attribute)

U

unconnected_component() (in module topsearch.analysis.graph_properties) unique_pairs() (in module topsearch.analysis.pair_selection) unnormalise_response() (topsearch.data.model_data.ModelData method) unnormalise_training() (topsearch.data.model_data.ModelData method) unstandardise_response() (topsearch.data.model_data.ModelData method)

unstandardise_training() (topsearch.data.model_data.ModelData method) update_bounds() (topsearch.potentials.gaussian_process.GaussianProcess method) update_eigenvector_bounds() (topsearch.transition_states.hybrid_eigenvector_following.HybridEigenvectorFollowing method) update_image_density() (topsearch.transition_states.nudged_elastic_band.NudgedElasticBand method) UpperConfidenceBound (class in topsearch.potentials.bayesian_optimisation)

W

weighted (topsearch.similarity.molecular_similarity.MolecularSimilarity attribute) write_data() (topsearch.data.model_data.ModelData method)

write_extended_xyz() (topsearch.data.coordinates.AtomicCoordinates method) write_fit() (topsearch.potentials.gaussian_process.GaussianProcess method) write_xyz() (topsearch.data.coordinates.AtomicCoordinates method)

X

xyz_file (topsearch.potentials.force_fields.MMFF94 attribute)

Z

zeta (topsearch.potentials.atomic.BinaryGupta attribute) (topsearch.potentials.bayesian_optimisation.ExpectedImprovement attribute) (topsearch.potentials.bayesian_optimisation.UpperConfidenceBound attribute)