Index

A

align() (StructureAligner method) aligned_structure (ReferenceBasedSites attribute) alignment_metrics (ReferenceBasedSites attribute) analyse_structure() (DynamicVoronoiSiteCollection method) (PolyhedralSiteCollection method) (SiteCollection method) (SphericalSiteCollection method) (Trajectory method) (VoronoiSiteCollection method) append_timestep() (Trajectory method) apply_legacy_pbc_correction() (in module site_analysis.pbc_utils) as_dict() (Atom method) (DynamicVoronoiSite method) (PolyhedralSite method) (Site method) (SphericalSite method) (VoronoiSite method)

assign_coords() (Atom method) assign_site_occupations() (DynamicVoronoiSiteCollection method) (PolyhedralSiteCollection method) (SiteCollection method) (SphericalSiteCollection method) (Trajectory method) (VoronoiSiteCollection method) assign_vertex_coords() (PolyhedralSite method) at (Trajectory property) Atom (class in site_analysis.atom) atom_by_index() (Trajectory method) atom_sites (Trajectory property) atoms_from_indices() (in module site_analysis.atom) atoms_from_species_string() (in module site_analysis.atom) atoms_from_structure() (in module site_analysis.atom) atoms_trajectory (Trajectory property) average_occupation (Site property)

B

build() (TrajectoryBuilder method)

C

calculate_centre() (DynamicVoronoiSite method) calculate_species_distances() (in module site_analysis.tools) centre (DynamicVoronoiSite property) (PolyhedralSite property) (Site property) (SphericalSite property) (VoronoiSite property) centre_coords (DynamicVoronoiSite attribute) cn (DynamicVoronoiSite property) (PolyhedralSite property) construct_neighbouring_sites() (in module site_analysis.polyhedral_site_collection) contains_atom() (PolyhedralSite method) (Site method) (SphericalSite method) contains_atoms (Site attribute) contains_point() (DynamicVoronoiSite method) (FaceTopologyCache method) (PolyhedralSite method) (Site method) (SphericalSite method) (VoronoiSite method)

coordination_number (DynamicVoronoiSite property) (PolyhedralSite property) (Site property) CoordinationEnvironmentFinder (class in site_analysis.reference_workflow.coord_finder) correct_pbc() (in module site_analysis.pbc_utils) create_dynamic_voronoi_sites() (ReferenceBasedSites method) (SiteFactory method) create_polyhedral_sites() (ReferenceBasedSites method) (SiteFactory method) create_trajectory_with_dynamic_voronoi_sites() (in module site_analysis.builders) create_trajectory_with_polyhedral_sites() (in module site_analysis.builders) create_trajectory_with_spherical_sites() (in module site_analysis.builders) create_trajectory_with_voronoi_sites() (in module site_analysis.builders)

D

delaunay (PolyhedralSite property)

DynamicVoronoiSite (class in site_analysis.dynamic_voronoi_site) DynamicVoronoiSiteCollection (class in site_analysis.dynamic_voronoi_site_collection)

F

face_simplices (FaceTopologyCache attribute) FaceTopologyCache (class in site_analysis.polyhedral_site) filter() (TransitionTable method) find_environments() (CoordinationEnvironmentFinder method) frac_coords (Atom property) (SphericalSite attribute) (VoronoiSite attribute)

from_dict() (Atom class method) (DynamicVoronoiSite class method) (PolyhedralSite class method) (Site class method) (SphericalSite class method) (VoronoiSite class method) from_file() (Atom class method) from_str() (Atom class method)

G

get() (TransitionTable method) get_coordination_indices() (in module site_analysis.tools)

get_nearest_neighbour_indices() (in module site_analysis.tools) get_vertex_indices() (in module site_analysis.tools) get_vertex_species() (PolyhedralSite method)

I

in_site (Atom attribute) index (Atom attribute) (Site attribute)

IndexMapper (class in site_analysis.reference_workflow.index_mapper) indices_for_species() (in module site_analysis.tools)

K

keys (TransitionTable property)

M

map_coordinating_atoms() (IndexMapper method) matrix (TransitionTable property) module site_analysis.atom site_analysis.builders site_analysis.dynamic_voronoi_site site_analysis.dynamic_voronoi_site_collection site_analysis.pbc_utils site_analysis.polyhedral_site site_analysis.polyhedral_site_collection site_analysis.reference_workflow site_analysis.reference_workflow.coord_finder site_analysis.reference_workflow.index_mapper site_analysis.reference_workflow.reference_based_sites site_analysis.reference_workflow.site_factory site_analysis.reference_workflow.structure_aligner site_analysis.site site_analysis.site_collection site_analysis.spherical_site site_analysis.spherical_site_collection site_analysis.tools site_analysis.trajectory site_analysis.transition_table site_analysis.voronoi_site site_analysis.voronoi_site_collection

most_frequent_transitions() (Site method) most_recent_site (Atom property)

N

neighbouring_sites() (PolyhedralSiteCollection method) (SiteCollection method)

notify_structure_changed() (PolyhedralSite method)

P

points (Site attribute) PolyhedralSite (class in site_analysis.polyhedral_site)

PolyhedralSiteCollection (class in site_analysis.polyhedral_site_collection) PriorityAssignmentMixin (class in site_analysis.site_collection)

R

rcut (SphericalSite attribute) reference_center (PolyhedralSite attribute) reference_indices (DynamicVoronoiSite attribute) reference_structure (ReferenceBasedSites attribute) ReferenceBasedSites (class in site_analysis.reference_workflow.reference_based_sites) reorder() (TransitionTable method) reset() (Atom method) (DynamicVoronoiSite method) (DynamicVoronoiSiteCollection method) (PolyhedralSite method) (Site method) (SiteCollection method) (Trajectory method) (TrajectoryBuilder method)

reset_index() (Site class method) reset_site_occupations() (SiteCollection method) residence_times() (Site method)

S

Site (class in site_analysis.site) site_analysis.atom module site_analysis.builders module site_analysis.dynamic_voronoi_site module site_analysis.dynamic_voronoi_site_collection module site_analysis.pbc_utils module site_analysis.polyhedral_site module site_analysis.polyhedral_site_collection module site_analysis.reference_workflow module site_analysis.reference_workflow.coord_finder module site_analysis.reference_workflow.index_mapper module site_analysis.reference_workflow.reference_based_sites module site_analysis.reference_workflow.site_factory module site_analysis.reference_workflow.structure_aligner module site_analysis.site module site_analysis.site_collection module site_analysis.spherical_site module site_analysis.spherical_site_collection module

site_analysis.tools module site_analysis.trajectory module site_analysis.transition_table module site_analysis.voronoi_site module site_analysis.voronoi_site_collection module site_by_index() (SiteCollection method) (Trajectory method) site_coordination_numbers() (Trajectory method) site_index_mapping() (in module site_analysis.tools) site_labels() (Trajectory method) site_occupations (Trajectory property) site_summaries() (Trajectory method) SiteCollection (class in site_analysis.site_collection) SiteFactory (class in site_analysis.reference_workflow.site_factory) sites (DynamicVoronoiSiteCollection attribute) (PolyhedralSiteCollection attribute) (SiteCollection attribute) sites_contain_points() (PolyhedralSiteCollection method) (SiteCollection method) sites_from_reference_indices() (DynamicVoronoiSite class method) sites_from_vertex_indices() (PolyhedralSite class method) sites_trajectory (Trajectory property) species_string_from_site() (in module site_analysis.tools) SphericalSite (class in site_analysis.spherical_site) SphericalSiteCollection (class in site_analysis.spherical_site_collection) st (Trajectory property) structure (SiteFactory attribute) StructureAligner (class in site_analysis.reference_workflow.structure_aligner) summaries() (SiteCollection method) summary() (Site method)

T

target_structure (ReferenceBasedSites attribute) to() (Atom method) to_dict() (TransitionTable method) trajectory (Atom attribute) Trajectory (class in site_analysis.trajectory) trajectory (Site attribute) trajectory_from_structures() (Trajectory method)

TrajectoryBuilder (class in site_analysis.builders) transition_counts_by_label() (Trajectory method) transition_counts_by_site() (Trajectory method) transition_probabilities_by_label() (Trajectory method) transition_probabilities_by_site() (Trajectory method) transitions (Site attribute) TransitionTable (class in site_analysis.transition_table) translation_vector (ReferenceBasedSites attribute)

U

unwrap_vertices_to_reference_center() (in module site_analysis.pbc_utils) update() (FaceTopologyCache method) update_occupation() (in module site_analysis.trajectory) (SiteCollection method)

update_pbc_shifts() (in module site_analysis.pbc_utils) update_recent_site() (Atom method)

V

vertex_coords (PolyhedralSite attribute) vertex_indices (PolyhedralSite attribute)

VoronoiSite (class in site_analysis.voronoi_site) VoronoiSiteCollection (class in site_analysis.voronoi_site_collection)

W

with_dynamic_voronoi_sites() (TrajectoryBuilder method) with_existing_atoms() (TrajectoryBuilder method) with_existing_sites() (TrajectoryBuilder method) with_min_atom_distance() (TrajectoryBuilder method) with_mobile_species() (TrajectoryBuilder method) with_polyhedral_sites() (TrajectoryBuilder method)

with_reference_structure() (TrajectoryBuilder method) with_site_mapping() (TrajectoryBuilder method) with_spherical_sites() (TrajectoryBuilder method) with_structure() (TrajectoryBuilder method) with_structure_alignment() (TrajectoryBuilder method) with_voronoi_sites() (TrajectoryBuilder method) write_site_summaries() (Trajectory method)

X

x_pbc() (in module site_analysis.tools)