Function soap_integration

tests/testutils.py:257–288

Used to numerically calculate the inner product coeffientes of SOAP with polynomial radial basis.

(system, centers, args, rbf_function)

def soap_integration(system, centers, args, rbf_function):
    """Used to numerically calculate the inner product coeffientes of SOAP
    with polynomial radial basis.
    """
    n_max = args["n_max"]
    l_max = args["l_max"]

    positions = system.get_positions()
    atomic_numbers = system.get_atomic_numbers()
    species_ordered = sorted(list(set(atomic_numbers)))
    n_elems = len(species_ordered)

    p_args = []
    p_index = []
    for i, ipos in enumerate(centers):
        for iZ, Z in enumerate(species_ordered):
            indices = np.argwhere(atomic_numbers == Z).flatten()
            elem_pos = positions[indices]
            # This centers the coordinate system at the soap center
            elem_pos -= ipos
            for n in range(n_max):
                for l in range(l_max + 1):
                    for im, m in enumerate(range(-l, l + 1)):
                        p_args.append((args, n, l, m, elem_pos, rbf_function))
                        p_index.append((i, iZ, n, l, im))

    results = Parallel(n_jobs=8, verbose=1)(delayed(integral)(*a) for a in p_args)

    coeffs = np.zeros((len(centers), n_elems, n_max, l_max + 1, 2 * l_max + 1))
    for index, value in zip(p_index, results):
        coeffs[index] = value
    return coeffs


def integral(args, n, l, m, elem_pos, rbf_function):