Potential unit inconsistencies

[jchodera]

I find it's much more foolproof to store work in units of kT whenever we need to store them as a unitless array. We appear to use kJ/mol in the code at various places, such as here, which has the potential to cause some confusion at best and errors at worst (if we accidentally feed them to, say, EXP or BAR before converting to kT).

If we do store energies or work with specific units, we should make sure to actually store unit-bearing quantities. Code like this has the potential to cause confusion by returning unitless quantities that must be interpreted in kJ/mol.

The best policy is

• If the quantity is supposed to be unit-bearing, make sure it is a simtk.unit.Quantity with the appropriate units
• If you want it to be dimensionless, convert it to units of kT; it's then safe to be unitless