_pdist

mbgdml._gdml.desc._pdist(r, lat_and_inv=None)

Compute pairwise Euclidean distance matrix between all atoms.

Parameters:

• r (numpy.ndarray) – Array of size \(3N\) containing the Cartesian coordinates of each atom.

• lat_and_inv (tuple of numpy.ndarray, optional) – Tuple of \(3 \times 3\) matrix containing lattice vectors as columns and its inverse.

Returns:

Array of size \(N(N-1)/2\) containing the upper triangle of the pairwise distance matrix between atoms.

Return type:

numpy.ndarray