merge_entropy_functions

[skfegan]

We want to merge the functions for calculating entropy from the two parts of the code (written by Argo and Jas). This is one step towards making the code more general and easier to maintain.

There will be three entropy functions - vibrational, orientation, and conformation.
The vibrational function will use the force or torque matrices to calculate the translational or rotational components of the entropy.
The orientation function will calculate the contribution to the entropy from the orientation of the unit relative to its neighbours.
The conformation function (in some places referred to as topographical) will calculate the contribution to the entropy from the flexibility of the dihedral angles.