def test_orientation2positions_invert_xy(mol):
position = np.array([[0, 0, 0]], dtype=np.float32)
orientation = np.array([[0, 0, 0, 1]], dtype=np.float32)
xy_inv_pos = np.copy(mol.positions)
xy_inv_pos[:, :2] = -xy_inv_pos[:, :2]
rotated_pos = orientation2positions(mol, position, orientation)
assert np.allclose(rotated_pos, xy_inv_pos, atol=1e5)
def test_orientation2positions_moved_rot(mol):
position = np.array([[4, 2, 0]], dtype=np.float32)
orientation = np.array([[0, 0, 0, 1]], dtype=np.float32)
rotated_pos = orientation2positions(mol, position, orientation)
xy_inv_pos = np.copy(mol.positions)
xy_inv_pos[:, :2] = -xy_inv_pos[:, :2]
moved_pos = xy_inv_pos + np.tile(position, (mol.num_particles, 1))
assert np.allclose(rotated_pos, moved_pos)
def test_orientation2positions_moved_rot_multiple(mol):
position = np.array([[4, 2, 0], [0, 0, 0]], dtype=np.float32)
orientation = np.array([[0, 0, 0, 1], [0, 0, 0, 1]], dtype=np.float32)
rotated_pos = orientation2positions(mol, position, orientation)
xy_inv_pos = np.copy(mol.positions)
xy_inv_pos[:, :2] = -xy_inv_pos[:, :2]
moved_pos = np.repeat(xy_inv_pos, position.shape[0], axis=0) + np.tile(
position, (mol.num_particles, 1)
)
assert np.allclose(rotated_pos, moved_pos)
def test_orientation2positions_moved(mol):
position = np.array([[1, 1, 0]], dtype=np.float32)
orientation = np.array([[1, 0, 0, 0]], dtype=np.float32)
rotated_pos = orientation2positions(mol, position, orientation)
moved_pos = mol.positions + np.repeat(position, mol.num_particles, axis=0)
assert np.allclose(rotated_pos, moved_pos)