New alignment cv

[gervasiozaldivar]

I added a new CV defined by the cos^2 of the angle formed by the axis between two "rod-like" molecules (like a binding motif or a spacer). I also changed the name of the plate-rod aligment CV (used for gamma CD and binding motif aligment).

[franklhy]

I think mono_inertia and moment_inertia can be reused, so I remove the copy. I also correct the return function in each alignment Class.