def test_basis(self):
"""Tests that the output vectors behave correctly as a basis.
"""
sys1 = Atoms(symbols=["H", "H"], positions=[[1, 0, 0], [0, 1, 0]], cell=[2, 2, 2], pbc=True)
sys2 = Atoms(symbols=["O", "O"], positions=[[1, 0, 0], [0, 1, 0]], cell=[2, 2, 2], pbc=True)
sys3 = Atoms(symbols=["C", "C"], positions=[[1, 0, 0], [0, 1, 0]], cell=[2, 2, 2], pbc=True)
sys4 = Atoms(symbols=["H", "C"], positions=[[-1, 0, 0], [1, 0, 0]], cell=[2, 2, 2], pbc=True)
sys5 = Atoms(symbols=["H", "C"], positions=[[1, 0, 0], [0, 1, 0]], cell=[2, 2, 2], pbc=True)
sys6 = Atoms(symbols=["H", "O"], positions=[[1, 0, 0], [0, 1, 0]], cell=[2, 2, 2], pbc=True)
sys7 = Atoms(symbols=["C", "O"], positions=[[1, 0, 0], [0, 1, 0]], cell=[2, 2, 2], pbc=True)
desc = SOAP(
atomic_numbers=[1, 6, 8],
rcut=5,
nmax=3,
lmax=5,
periodic=False,
crossover=True,
sparse=False
)
# Create vectors for each system
vec1 = desc.create(sys1, positions=[[0, 0, 0]])[0, :]
vec2 = desc.create(sys2, positions=[[0, 0, 0]])[0, :]
vec3 = desc.create(sys3, positions=[[0, 0, 0]])[0, :]
vec4 = desc.create(sys4, positions=[[0, 0, 0]])[0, :]
vec5 = desc.create(sys5, positions=[[0, 0, 0]])[0, :]
vec6 = desc.create(sys6, positions=[[0, 0, 0]])[0, :]
vec7 = desc.create(sys7, positions=[[0, 0, 0]])[0, :]
# The dot-product should be zero when there are no overlapping elements
dot = np.dot(vec1, vec2)
self.assertEqual(dot, 0)
dot = np.dot(vec2, vec3)
self.assertEqual(dot, 0)
# The dot-product should be non-zero when there are overlapping elements
dot = np.dot(vec4, vec5)
self.assertNotEqual(dot, 0)
# Check that self-terms are in correct location
n_elem_feat = desc.get_number_of_element_features()
h_part1 = vec1[0:n_elem_feat]
h_part2 = vec2[0:n_elem_feat]
h_part4 = vec4[0:n_elem_feat]
self.assertNotEqual(np.sum(h_part1), 0)
self.assertEqual(np.sum(h_part2), 0)
self.assertNotEqual(np.sum(h_part4), 0)
# Check that cross terms are in correct location
hc_part1 = vec1[1*n_elem_feat:2*n_elem_feat]
hc_part4 = vec4[1*n_elem_feat:2*n_elem_feat]
co_part6 = vec6[4*n_elem_feat:5*n_elem_feat]
co_part7 = vec7[4*n_elem_feat:5*n_elem_feat]
self.assertEqual(np.sum(hc_part1), 0)
self.assertNotEqual(np.sum(hc_part4), 0)
self.assertEqual(np.sum(co_part6), 0)
self.assertNotEqual(np.sum(co_part7), 0)
def test_crossover(self):
"""Tests that disabling/enabling crossover works as expected.
"""
pos = [[0.1, 0.1, 0.1]]
# GTO
desc = SOAP(species=[1, 8],
rbf="gto",
crossover=True,
rcut=3,
nmax=5,
lmax=5,
periodic=False)
n_elem_feat = desc.get_number_of_element_features()
full_output = desc.create(H2O, positions=pos)
desc.crossover = False
partial_output = desc.create(H2O, positions=pos)
self.assertTrue(
np.array_equal(full_output[:, 0:n_elem_feat],
partial_output[:, 0:n_elem_feat]))
self.assertTrue(
np.array_equal(full_output[:, 2 * n_elem_feat:],
partial_output[:, n_elem_feat:]))
# Polynomial
desc = SOAP(species=[1, 8],
rbf="polynomial",
crossover=True,
rcut=3,
nmax=5,
lmax=5,
periodic=False)
n_elem_feat = desc.get_number_of_element_features()
full_output = desc.create(H2O, pos)
desc.crossover = False
partial_output = desc.create(H2O, pos)
self.assertTrue(
np.array_equal(full_output[:, 0:n_elem_feat],
partial_output[:, 0:n_elem_feat]))
self.assertTrue(
np.array_equal(full_output[:, 2 * n_elem_feat:],
partial_output[:, n_elem_feat:]))
