Ensure potential energy terms are defined consistently

[maxentile]

• Coulomb missing from energy.py (present in energy_ii.py)
• Spring constant k parameter unused in angle and bond terms in energy_ii.py
• Periodic torsion terms in energy.py should be updated (following Allow periodicity > 1 in torsion term? #1)
• Add reference for higher-order coupling terms, and compare to that reference
• Exceptions and exclusions are always tricky and should be double-checked
• Add test for energy and force consistency with OpenMM

Depending on refactoring cost:

• Switch from k, eq naming for interactions that don't have spring constants or equilibrium lengths

[yuanqing-wang]

Ideally we would just have a module where we list all the choices, and have arguments in a separate script allowing users to pick.

[maxentile]

Ideally we would just have a module where we list all the choices, and have arguments in a separate script allowing users to pick.

Mostly agreed, hard part is defining the collection of choices, and how we index into that collection. (For "class-ii" coupling terms, do we have a master switch that says "add all coupling terms we've thought of so far", or one that says "add torsion-torsion coupling terms for all pairs of torsions," or ones that depends on further parameters, "add coupling terms for all adjacent pairs of torsions that meet such-and-such condition.")

Terms that will be exported to an MD engine (such as harmonic bond and angle terms) should be interpreted here in the same ways an MD engine would interpret them.