neighbormodels.neighbors module¶

Primary method

count_neighbors Builds a data frame containing neighbor counts grouped over site-index pairs and separation distances.

Functions

`add_subspecie_labels_if_missing`	Makes a copy of `cell_structure` and then checks if `cell_structure` has the subspecie site property.
`append_site_i_neighbor_distance_data`	Helper function to append indices, species, and distances in the `neighbor_distances` dictionary.
`count_neighbors_within_distance_groups`	Count number of neighbors within each group of same-distance site-index pairs.
`define_bin_intervals`	Constructs bin intervals used to group over neighbor distances.
`define_bins_to_group_and_sort_by_distance`	Defines bin intervals to group and sort neighbor pairs by distance.
`extract_neighbor_distance_data`	Extracts the site indices, site species, and neighbor distances for each pair and stores it in a dictionary.
`find_unique_distances`	Finds the unique distances that define the neighbor groups.
`get_neighbor_distances_data_frame`	Get data frame of pairwise neighbor distances for each atom in the unit cell, out to a distance `r`.
`group_site_index_pairs_by_distance`	Iterate over all sites, grouping by site-index pairs, subspecies pairs, and bin intervals.

Classes