Update CCW - CW explanations in functions

[nawtrey]

The convention chosen for calculating pi differences and thermodynamic forces is CCW - CW, but the way they are explained in the documentation is not quite clear about why this is. This needs to be updated so it is clear what is going on and why.

[nawtrey]

Looking at this now --

It looks like there are a couple things to mention:

1. The equations need to be put into the documentation somewhere. Some of our functions are actually named after components of the equations, so it would be useful to know the context.
2. We need to clarify (somewhere, at least in calc_net_cycle_flux()) that cycles must be chosen in a consistent manner. Probably just take some text right out of the KDA manuscript

Here is a list of functions that need to be gone through (from kda.calculations):

• calc_sigma
• calc_sigma_K
• calc_pi_difference
• calc_net_cycle_flux
• calc_net_cycle_flux_from_diags
• calc_thermo_force

It might be good to handle #65 at the same time.

[nawtrey]

Addressed in GH-92. Closing.