Calculate the non-elasticity terms in the TDGL and diffusion equations

Lines 680-807.

Belongs in takeTimeStep().

It isn't very obvious how to break this up. As a first pass, I think maybe just put this all in one function. It isn't clear how many variables come out of this section vs intermediate variables. It might only be a half dozen. Whoever ports this will have to carefully figure out the inputs and outputs to this section of code.

Not much of this looks like it is straightforwardly testable.