def test_center_of_mass(ammonia):
"""See [1], Numerical Examples, p. 296, top left column."""
atoms, coords3d, masses = ammonia
com = center_of_mass(coords3d, masses)
com_ref = np.array((0.0281, -0.0487, 0.0199)) / BOHR2ANG
np.testing.assert_allclose(com, com_ref, atol=1e-4)
def test_arrangement(func, ref_arr, kwargs):
atoms, coords3d, masses = func()
coords3d -= center_of_mass(coords3d, masses)
pms, pas = diagonalized_inertia_tensor(coords3d, masses)
print("pms", pms)
arr = get_arrangement(pms, **kwargs)
assert arr == ref_arr
def test_proper_rotations(ammonia):
atoms, coords3d, masses = ammonia
coords3d = coords3d - center_of_mass(coords3d, masses)
cdm = pdist(coords3d)
dist_mat = squareform(cdm)
se_atoms = find_se_atoms(atoms, dist_mat)
h_se_atoms = se_atoms["h0"]
find_proper_rotations(coords3d, masses, h_se_atoms)
def test_inertia_tensor(ammonia):
"""See [1], Numerical Examples, p. 296, top left column."""
atoms, coords3d, masses = ammonia
coords3d = coords3d - center_of_mass(coords3d, masses)
I = inertia_tensor(coords3d, masses)
I_ref = np.array((
( 1.8871, -0.4175, 0.1704),
(-0.4175, 2.3692, -0.2952),
( 0.1704, -0.2952, 1.7666),
)) # in Ų/amu
I_ref = I_ref / BOHR2ANG**2 # to Bohr²/amu
np.testing.assert_allclose(I, I_ref, atol=1.21e-4)
def center_of_mass(self):
return center_of_mass(self.coords3d, self.masses)