def test_unitcell_1():
# try round-tripping some random lengths and angles through
# lengths_and_angles_to_box_vectors and box_vectors_to_lengths_and_angles,
# and make sure we get back to where we started
for _ in range(10):
arg = np.hstack((random.rand(3), random.uniform(70, 110, size=3)))
vectors = lengths_and_angles_to_box_vectors(*arg)
out = box_vectors_to_lengths_and_angles(*vectors)
np.testing.assert_array_almost_equal(arg, out)
def test_unitcell_1():
# try round-tripping some random lengths and angles through
# lengths_and_angles_to_box_vectors and box_vectors_to_lengths_and_angles,
# and make sure we get back to where we started
for _ in range(10):
arg = np.hstack((random.rand(3), random.uniform(70, 110, size=3)))
vectors = lengths_and_angles_to_box_vectors(*arg)
out = box_vectors_to_lengths_and_angles(*vectors)
np.testing.assert_array_almost_equal(arg, out)
def test_box_vector_calculation(len_a, len_b, len_c, alpha, beta, gamma):
box = struc.vectors_from_unitcell(len_a, len_b, len_c, np.deg2rad(alpha),
np.deg2rad(beta), np.deg2rad(gamma))
from mdtraj.utils import lengths_and_angles_to_box_vectors
ref_box = np.stack(
lengths_and_angles_to_box_vectors(len_a, len_b, len_c, alpha, beta,
gamma))
assert np.allclose(box, ref_box)
assert struc.unitcell_from_vectors(box) == pytest.approx(
(len_a, len_b, len_c, alpha * 2 * np.pi / 360, beta * 2 * np.pi / 360,
gamma * 2 * np.pi / 360))
def test_unitcell_0():
result = lengths_and_angles_to_box_vectors(1, 1, 1, 90.0, 90.0, 90.0)
expected = (np.array([1, 0, 0]), np.array([0., 1.,
0.]), np.array([0., 0., 1.]))
for (a, b) in zip(result, expected):
np.testing.assert_array_almost_equal(a, b)
def test_unitcell_0():
result = lengths_and_angles_to_box_vectors(1, 1, 1, 90.0, 90.0, 90.0)
expected = (np.array([1, 0, 0]), np.array([ 0., 1., 0.]), np.array([ 0., 0., 1.]))
for (a, b) in zip(result, expected):
np.testing.assert_array_almost_equal(a, b)
