Neighbor API

This is a bare bones neighbor lists support so that for basic utilization there is no external library needed. This module was taken from the KLIFF package and modified to support ASE Atoms object, instead of KLIFF Configuration object. This makes ASE a hard dependency.

NeighborList can be imported from the libdescriptor module as

from libdescriptor.neighbor import NeighborList

Classes

class NeigborList

This class accepts an ASE atoms configuration and cutoff.

get_neigh(index)

Get neighbors for index

get_numneigh_and_neighlist_1D()

Return list number of neighbors and linear neighbor list for the configuration

get_coords()

Get the complete padded coordinates.

get_species()

get_species_code(mapping)

get_image()

Get padded images

get_padding_coords()

get_padding_species()

get_padding_species_code(mapping)

get_padding_image()