When should we rotate our structures?

[pc494]

Describe the bug
simulate_rotated_structure(), in theory, "rotates" a diffpy lattice. In practice ... it's not that simple.

To Reproduce

Make a boring orthorhombic lattice.
Make a second "rotated" lattice - the rotation here is a cut down version of what we do in simulate_rotated_structure()

canonical = diffpy.structure.lattice.Lattice(4,2,1, 90, 90, 90)
R = np.asarray([[1/np.sqrt(2),1/np.sqrt(2),0],[-1/np.sqrt(2),1/np.sqrt(2),0],[0,0,1]])
halfhalf  = diffpy.structure.lattice.Lattice(base=(R@canonical.base))

The problem is that the halfhalf lattice has two cell parameters of 3.162... ~ this makes life hard work.

Solution
Cut all the rotation code that involved diffpy, spit cartesians out of get_points_sphere() then
manually rotate the cartesians with a rotation matrix. I actually think this might be quite simple.
get_kinematical_intensities might also need a revisit

[pc494]

Taking from @EirikOpheim's example - the implementation goes

from transforms3d.euler import euler2mat

### Case 1
cartesian_coordinates = np.asarray([[1,0,0],[0,1,1]])
rotation = (60,60,0)
ai,aj,ak = np.deg2rad(rotation[0]),np.deg2rad(rotation[1]),np.deg2rad(rotation[2])
R = euler2mat(ai,aj,ak,axes='rzxz')
cartesian_coordinates = np.matmul(R,cartesian_coordinates.T).T

#### Case 2
cartesian_coordinates = np.asarray([[1,0,0],[0,1,1]])
rotation = (30,60,0)
ai,aj,ak = np.deg2rad(rotation[0]),np.deg2rad(rotation[1]),np.deg2rad(rotation[2])
R = euler2mat(ai,aj,ak,axes='rzxz')
cartesian_coordinates = np.matmul(R,cartesian_coordinates.T).T

[pc494]

This was resolved by #60