def test_mass_align():
cartesians = cc.xyz_functions.read_molden(
get_complete_path('total_movement.molden'), start_index=1)
m1, m2 = cartesians[0], cartesians[-1]
m2 = dot(get_rotation_matrix([1, 1, 1], 0.334), m2) + 5
m1, m2_aligned = m1.align(m2, mass_weight=True)
assert cc.xyz_functions.allclose(
m1.align(m2_aligned, mass_weight=True)[1], m2_aligned)
def test_align():
cartesians = cc.xyz_functions.read_molden(
get_complete_path('total_movement.molden'), start_index=1)
m1, m2 = cartesians[0], cartesians[-1]
m2 = dot(get_rotation_matrix([1, 1, 1], 0.334), m2) + 5
m1, m2_aligned = m1.align(m2)
dev = abs((m2_aligned - m1).loc[:, ['x', 'y', 'z']]).sum() / len(m1)
assert np.allclose(dev, [0.73398451, 1.61863496, 0.13181807])
def test_get_inertia():
A = molecule.get_inertia()
eig, t_mol = A['eigenvectors'], A['transformed_Cartesian']
assert cc.xyz_functions.allclose(
(molecule - molecule.get_barycenter()).__rmatmul__(eig), t_mol)
assert cc.xyz_functions.allclose(
dot(eig, (molecule - molecule.get_barycenter())), t_mol)
molecule2 = dot(get_rotation_matrix([1, 1, 1], 72), molecule)
B = molecule2.get_inertia()
assert cc.xyz_functions.allclose(B['transformed_Cartesian'], t_mol)
def test_align_and_reindex_similar():
cartesians = cc.xyz_functions.read_molden(
get_complete_path('total_movement.molden'), start_index=1)
m2 = cartesians[-1]
m2_shuffled = dot(get_rotation_matrix([1, 1, 1], .2), m2) + 8
np.random.seed(77)
m2_shuffled.index = np.random.permutation(m2.index)
m2, m2_shuffled = m2.align(m2_shuffled,
indices=[[42, 41, 153, 152], [87, 115, 24,
208]])
m2_backindexed = m2.reindex_similar(m2_shuffled)
assert cc.xyz_functions.allclose(m2, m2_backindexed)
def test_align_and_reindex_similar():
cartesians = cc.xyz_functions.read_molden(
get_complete_path('total_movement.molden'), start_index=1)
m2 = cartesians[-1]
m2_shuffled = dot(get_rotation_matrix([1, 1, 1], .2), m2) + 8
np.random.seed(77)
m2_shuffled.index = np.random.permutation(m2.index)
m2 = (m2 - m2.get_centroid()).sort_index()
m2_shuffled = (m2_shuffled - m2_shuffled.get_centroid()).sort_index()
R = m2.loc[[42, 41, 153, 152], :].reset_index().get_align_transf(
m2_shuffled.loc[[87, 115, 24, 208], :].reset_index())
m2_shuffled = R @ m2_shuffled
m2_backindexed = m2.reindex_similar(m2_shuffled)
assert cc.xyz_functions.allclose(m2, m2_backindexed)