Analytical gradients not being applied to atomic indices about kappa

[ajkerr0]

There's a good chance I never actually got the analytical gradients from the numpy vectorized operations, just the slow for loop method. It would explain why I didn't remember the broadcasting problem where you need to do something like parameterList[:,None] to do the operations element-wise

I might want to use np.where(bondList==index) (for example) to assign the forces to the right atoms; I used that command when I had the energy and gradient in the same factory function (because I thought that would be more effective seeing the code in one single place). I had a keyword argument that defaulted to False that signified if the gradient was being calculated or not. If so, only the energy associated with bonds, angles, etc that involved the atom in question were calculated.

[ajkerr0]

Closing this issue. The fix involves applying the respective forces to the right atomic indices in the gradient. For now this is done via for loops as first attempts at vectorized application did not work.