neighbormodels.neighbors moduleΒΆ

Primary method

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


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.