Add harmonic bond, harmonic angle, periodic torsion, rb torsion to potential templates

[ahy3nz]

No description provided.

[rmatsum836]

These look good to merge.

[rsdefever]

These all look good.

A couple of questions:

(1) Why does PotentialTemplate inherit from Potential and then all other potentials inherit from PotentialTemplate? (i.e., vs. just inheriting from Potential?)
(2) The functional forms are pretty self-explanatory, but how is the documentation going to tie into all of this. Just thinking we should be careful with respect to details like the definition of phi (is phi=0 or phi=180 the cis conformation), and factors of 0.5 on the force constants.

[ahy3nz]

These all look good.

A couple of questions:

(1) Why does PotentialTemplate inherit from Potential and then all other potentials inherit from PotentialTemplate? (i.e., vs. just inheriting from Potential?)

See the original PR
A PotentialTemplate is a Potential that doesn't have parameters associated with it. To avoid copy+pasting redundant code to make a new PotentialTemplate class, we slightly modified the Potential class.

A LennardJonesPotential is really just an object that contains information about the canonical LJ expression, its name, and independent variables - no explicit parameters are needed. The goal of PotentialTemplates was for properly writing out topologies to simulation engines. Yes it's great that you can have a string/sympy expression for a mathematical function, but at some point you need to match it a gromacs function type integer, an openmm function object, hoomd function object, etc., and the goal of the PotentialTemplates was to be the reference comparison to ensure that YOUR Potential with an LJ expression matches a simulation engine's LJ potential, or throw an error if your custom Potential would not fit within a particular engine

(2) The functional forms are pretty self-explanatory, but how is the documentation going to tie into all of this. Just thinking we should be careful with respect to details like the definition of phi (is phi=0 or phi=180 the cis conformation), and factors of 0.5 on the force constants.

Good point, we have a running issue here to try to log all the various nuances and how this package reconciles them.

Lastly, tagging @umesh-timalsina if he has a better idea to match our topology Potential objects to respective functions supported in other engines