Function test_padding

tests/test_soap.py:786–844

Tests that the padding used in constructing extended systems is sufficient.

()

def test_padding():
    """Tests that the padding used in constructing extended systems is
    sufficient.
    """
    # Fix random seed for tests
    np.random.seed(7)

    # Loop over different cell sizes
    for ncells in range(1, 6):
        ncells = int(ncells)

        # Loop over different radial cutoffs
        for r_cut in np.linspace(2, 10, 11):
            # Loop over different sigmas
            for sigma in np.linspace(0.5, 2, 4):
                # Create descriptor generators
                soap_generator = SOAP(
                    r_cut=r_cut,
                    n_max=4,
                    l_max=4,
                    sigma=sigma,
                    species=["Ni", "Ti"],
                    periodic=True,
                )

                # Define unit cell
                a = 2.993
                niti = Atoms(
                    "NiTi",
                    positions=[[0.0, 0.0, 0.0], [a / 2, a / 2, a / 2]],
                    cell=[a, a, a],
                    pbc=[1, 1, 1],
                )

                # Replicate system
                niti = niti * ncells
                a *= ncells

                # Add some noise to positions
                positions = niti.get_positions()
                noise = np.random.normal(scale=0.5, size=positions.shape)
                niti.set_positions(positions + noise)
                niti.wrap()

                # Evaluate descriptors for orthogonal unit cell
                orthogonal_soaps = soap_generator.create(niti)

                # Redefine the cubic unit cell as monoclinic with a 45-degree
                # angle, this should not affect the descriptors
                niti.set_cell([[a, 0, 0], [0, a, 0], [a, 0, a]])
                niti.wrap()

                # Evaluate descriptors for new, monoclinic unit cell
                non_orthogonal_soaps = soap_generator.create(niti)

                # Check that the relative or absolute error is small enough
                assert np.allclose(
                    orthogonal_soaps, non_orthogonal_soaps, atol=1e-8, rtol=1e-6