def test_mol2particles_zero():
position = np.zeros((1, 3))
orientation = util.zero_quaternion(1)
mol_vector = np.ones((1, 3))
result = dynamics._util.molecule2particles(position, orientation,
mol_vector)
assert np.allclose(result, np.ones((1, 3)))
def test_large_rotation():
orientation = util.zero_quaternion(10)
dyn = dynamics.Dynamics(0, np.ones(3), np.zeros((10, 3)), orientation)
for i in range(10):
dyn.add(
np.zeros((10, 3)),
rowan.from_euler(
np.ones(10) * np.pi / 4 * i, np.zeros(10), np.zeros(10)),
)
assert np.allclose(np.linalg.norm(dyn.delta_rotation, axis=1),
np.pi / 4 * 9)
def test_struct(translation, rotation):
translation = np.append(translation, np.zeros((1, 1)), axis=1)
init_pos = np.zeros((1, 3))
init_orient = util.zero_quaternion(1)
dyn = dynamics.Dynamics(0,
np.ones(3) * 10,
init_pos,
init_orient,
wave_number=2.9,
molecule=Trimer())
orientation = rowan.from_euler(rotation[:, 0], rotation[:, 1], rotation[:,
2])
dyn.add(translation, orientation)
assert np.allclose(dyn.delta_rotation, rotation, atol=2e-7)
assert np.allclose(dyn.delta_translation, translation, atol=8e-7)
def test_struct_rotation():
init_pos = np.array([[0.0, 0, 0]])
init_orient = util.zero_quaternion(1)
dyn = dynamics.Dynamics(0,
np.ones(3) * 10,
init_pos,
init_orient,
wave_number=3.14,
molecule=Trimer())
pos1 = np.array([[0.1, 0.1, 0]])
dyn.add(pos1)
assert dyn.compute_struct_relax() == 1
pos2 = np.array([[0.4, 0.0, 0]])
dyn.add(pos2)
assert dyn.compute_struct_relax() == 1
pos2 = np.array([[0.6, 0.0, 0]])
dyn.add(pos2)
assert dyn.compute_struct_relax() == 0