def test_neighbor_list_3D_empty_cells(self):
"""Test neighbor list on 3D example where cells are empty.
Stresses the failure mode where the neighboring cells are empty
so top_k will throw a failure.
"""
N_atoms = 4
start = 0
stop = 10
nbr_cutoff = 1
ndim = 3
M_nbrs = 1
# 1 and 2 are nbrs. 8 and 9 are nbrs
coords = np.array([[1.0, 0.0, 1.0], [2.0, 5.0, 2.0], [8.0, 8.0, 8.0],
[9.0, 9.0, 9.0]])
coords = np.reshape(coords, (N_atoms, ndim))
with self.test_session() as sess:
coords = tf.convert_to_tensor(coords, dtype=tf.float32)
nbr_list_layer = NeighborList(N_atoms, M_nbrs, ndim, nbr_cutoff,
start, stop)
nbr_list = nbr_list_layer.compute_nbr_list(coords)
nbr_list = np.squeeze(nbr_list.eval())
np.testing.assert_array_almost_equal(nbr_list,
np.array([-1, -1, 3, 2]))
def test_neighbor_list_2D(self):
"""Test neighbor list on 2D example."""
N_atoms = 4
start = 0
stop = 10
nbr_cutoff = 1
ndim = 2
M_nbrs = 1
# 1 and 2 are nbrs. 8 and 9 are nbrs
coords = np.array([[1.0, 1.0], [2.0, 2.0], [8.0, 8.0], [9.0, 9.0]])
coords = np.reshape(coords, (N_atoms, ndim))
with self.session() as sess:
coords = tf.convert_to_tensor(coords, dtype=tf.float32)
nbr_list_layer = NeighborList(N_atoms, M_nbrs, ndim, nbr_cutoff, start,
stop)
nbr_list = nbr_list_layer.compute_nbr_list(coords)
nbr_list = np.squeeze(nbr_list.eval())
np.testing.assert_array_almost_equal(nbr_list, np.array([1, 0, 3, 2]))
def test_neighbor_list_3D_empty_cells(self):
"""Test neighbor list on 3D example where cells are empty.
Stresses the failure mode where the neighboring cells are empty
so top_k will throw a failure.
"""
N_atoms = 4
start = 0
stop = 10
nbr_cutoff = 1
ndim = 3
M_nbrs = 1
# 1 and 2 are nbrs. 8 and 9 are nbrs
coords = np.array([[1.0, 0.0, 1.0], [2.0, 5.0, 2.0], [8.0, 8.0, 8.0],
[9.0, 9.0, 9.0]])
coords = np.reshape(coords, (N_atoms, ndim))
with self.session() as sess:
coords = tf.convert_to_tensor(coords, dtype=tf.float32)
nbr_list_layer = NeighborList(N_atoms, M_nbrs, ndim, nbr_cutoff, start,
stop)
nbr_list = nbr_list_layer.compute_nbr_list(coords)
nbr_list = np.squeeze(nbr_list.eval())
np.testing.assert_array_almost_equal(nbr_list, np.array([-1, -1, 3, 2]))