_r_to_d_desc#

mbgdml._gdml.desc._r_to_d_desc(r, pdist, lat_and_inv=None)[source]#

Generate descriptor Jacobian for a set of atom positions in Cartesian coordinates.

This method can apply the minimum-image convention as periodic boundary condition for distances between atoms, given the edge length of the (square) unit cell.

Parameters:

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

  • pdist (numpy.ndarray) – Array of size \(N \times N\) containing the Euclidean distance (L2-norm) for each pair of atoms.

  • 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 \(N(N-1)/2 \times 3N\) containing all partial derivatives of the descriptor.

Return type:

numpy.ndarray