chemlab.utils

chemlab.utils.distances_within(coords_a, coords_b, cutoff, periodic=False, method='simple')

Calculate distances between the array of coordinates coord_a and coord_b within a certain cutoff.

This function is a wrapper around different routines and data structures for distance searches. It return a np.ndarray containing the distances.

Parameters

coords_a: np.ndarray((N, 3), dtype=float)

First coordinate array

coords_b: np.ndarray((N, 3), dtype=float)

Second coordinate array

cutoff: float

Maximum distance to search for

periodic: False or np.ndarray((3,), dtype=float)

If False, don’t consider periodic images. Otherwise periodic is an array containing the periodicity in the 3 dimensions.

method: “simple” | “cell-lists”

The method to use. simple is a brute-force distance search, kdtree uses scipy ckdtree module (periodic not available) and cell-lists uses the cell linked list method.