structuretoolkit.analyse.spatial

Functions

cluster_by_steinhardt(positions, neigh, ...)	Clusters candidate positions via Steinhardt parameters and the variance in distances to host atoms.
create_gridpoints(structure[, ...])	Create grid points within the structure.
get_cluster_positions(structure[, ...])	Cluster positions according to the distances.
get_delaunay_neighbors(structure[, width_buffer])	Get indices of atoms sharing the same Delaunay tetrahedrons (commonly known as Delaunay triangles), i.e. indices of neighboring atoms, which form a tetrahedron, in which no other atom exists.
get_interstitials(structure, num_neighbors)	Function to search for interstitial sites
get_layers(structure[, distance_threshold, ...])	Get an array of layer numbers.
get_mean_positions(positions, cell, pbc, labels)	This function calculates the average position(-s) across periodic boundary conditions according to the labels
get_voronoi_neighbors(structure[, width_buffer])	Get pairs of atom indices sharing the same Voronoi vertices/areas.
get_voronoi_vertices(structure[, epsilon, ...])	Get voronoi vertices of the box.
remove_too_close(positions, structure[, ...])	Remove positions that are too close to the neighboring atoms.
set_to_high_symmetry_points(positions, ...)	Adjusts the positions to the nearest high symmetry points in the structure.

Classes

Interstitials(structure, num_neighbors[, ...])

Class to search for interstitial sites