amep.pbc.distances

amep.pbc.distances(coords, other_coords=None)

Returns a 1D array of all pairwise distances.

Notes

If other=None, only the upper half of the distance matrix with the diagonal excluded is returned as a flattened 1D array.

This method does not consider periodic boundary conditions.

Parameters:

• coords (np.ndarray) – Coordinate array of shape (N,3).

• other_coords (np.ndarray, optional) – Coordinate array of shape (N,3). The default is None.

Returns:

d – 1D array of pairwise distances.

Return type:

np.ndarray