uf3.representation.distances.get_distance_matrix

get_distance_matrix(geom: ase.atoms.Atoms, supercell: Optional[ase.atoms.Atoms] = None) → numpy.ndarray

Get distance matrix from geometry and, optionally, supercell including atoms from adjacent images.

Parameters

• geom (ase.Atoms) – unit cell of interest.

• supercell (ase.Atoms) – ase.Atoms output of get_supercell used to account for atoms in periodic images.

Returns

square (n x n) if supercell

is not provided, rectangular (n x m) otherwise, where n and m are the number of atoms in the geometry and its supercell, respectively.

Return type

distance_matrix (np.ndarray)