vectorize remaining uncertainty computations

[mrshirts]

Performing multiple loops can be pretty inefficient for computing uncertainties. In most cases, they can be rewritten into matrix/array operations.

computeExpectations and computeEntropyAndEnthalpy are the remaining that need to be vectorized. See free energy routines for ways this is done.

[mrshirts]

This was done in the nk branch merge. The actual speed difference was not tested, though, and should be checked.