uf3.representation.distances.mask_matrix_by_pair_interaction

mask_matrix_by_pair_interaction(pair: Union[List, Tuple], geo_composition: numpy.ndarray, sup_composition: Optional[numpy.ndarray] = None) → numpy.ndarray

Generates boolean mask for the distance matrix based on composition

vectors i.e. from ase.Atoms.get_atomic_numbers()

e.g. identifying A-B interactions:

supercell

geometry A | - X - - X X

B | X - X X - -

Parameters

• pair (tuple) – pair interaction of interest e.g. (A-B)

• geo_composition (list, np.ndarray) – list of elements for each atom in geometry.

• sup_composition (list, np.ndarray) – optional list of elements for each atom in supercell.

Returns

Boolean mask of dimension (n x m)

corresponding to pair interactions of the specified type, where n and m are the number of atoms in the geometry and its supercell, respectively.

Return type

comp_mask (np.ndarray)