def axes(self):
"""
Return principal, secondary and perpendicular axes of the Mol
Returns
-------
axes_out : 3 x 3 np array
Principal, followed by secondary and perpendicular axes of the molecule
"""
if np.count_nonzero(self.geom.plane_coeffs) == 0:
self.calc_plane_coeffs()
# get the quadrangle which best describes the coordinates (possibly a
# triangle with the far point repeated twice)
vertices = ao.quadrangle_from_coord(self.geom.coord_array)
# if the mol is linear, we need to reorder the quadrangle
if self.geom.linear:
vertices = np.array([vertices[1],vertices[2],vertices[3],vertices[0]])
# if the mole is rectangular, we want an embedded quadrangle
else:
# get the embedded quadrangle vertices
vertices = ao.embedded_vert(vertices)
# get vectors from projected diagonals
axes_out_raw = ao.project_quad_to_vectors(vertices,self.geom.plane_coeffs)
# we want the first raw to be the secondary and vice versa and the principal
# to be *(-1) in order to maintain a convention
axes_out_unnormal = np.array([-axes_out_raw[1], axes_out_raw[0]])
# orthonogalise them
# if the mol is linear, just move the secondary axis
if self.geom.linear:
axes_out_prin_sec = ao.orthogonalise_asym(axes_out_unnormal)
# if the mol is not linear, move principal and secondary axes equally
else:
axes_out_prin_sec = ao.orthogonalise_sym(axes_out_unnormal)
# get the perpendicular vector
perp = np.cross(axes_out_prin_sec[0], axes_out_prin_sec[1])
# ensure normalisation
perp = perp/np.linalg.norm(perp)
lis_axes_out = list(axes_out_prin_sec)
lis_axes_out.append(perp)
axes_out = np.array(lis_axes_out)
return axes_out
def test_tri_project_quad_to_vectors(triangle_corners_4, z_plane_coeffs):
emb_vert = ao.embedded_vert(triangle_corners_4)
projected_vecs = ao.project_quad_to_vectors(emb_vert, z_plane_coeffs)
expected = np.array([[0., -1., 0.], [-0.995037, 0.099504, 0.]])
assert_allclose(projected_vecs, expected, rtol=1e-4)
return
def test_tri_embedded_vert(triangle_corners_4):
new_pairs = ao.embedded_vert(triangle_corners_4)
expected = np.array([[3.5, 3., 0.], [6., 2., 0.], [3.5, 1.5, 0.],
[1., 2.5, 0.]])
assert_allclose(new_pairs, expected)
def test_embedded_vert(rectangle_array):
new_vert = ao.embedded_vert(rectangle_array)
expected = np.array([[0., 1., 0.], [2., 2., 0.], [4., 1., 0.],
[2., 0., 0.]])
assert_allclose(new_vert, expected)
def test_arb_project_quad_to_vectors(arbitrary_flat_vertices, z_plane_coeffs):
emb_vert = ao.embedded_vert(arbitrary_flat_vertices)
projected_vecs = ao.project_quad_to_vectors(emb_vert, z_plane_coeffs)
expected = np.array([[0.03173, -0.999496, 0.], [-0.999966, 0.008196, 0.]])
assert_allclose(projected_vecs, expected, rtol=1e-4)
return
def test_arb_embedded_vert(arbitrary_flat_vertices):
new_pairs = ao.embedded_vert(arbitrary_flat_vertices)
expected = np.array([[3., 3.05, 0.], [6.1, 1.45, 0.], [3.1, -0.1, 0.],
[0., 1.5, 0.]])
assert_allclose(new_pairs, expected)