Merge pull request #2684 from RosettaCommons/aleaverfay/fix_spades_performance2
Spades performance bugfix part two
Actually comment out the code that I meant to comment out the first time. What happened was, I commented it out, and then while trying to understand the nature of the trajectory changes, commented it back in and promptly forgot I had done so.
Also fixing a 3 year old bug that declared some functions that should not have been virtual functions as virtual. This slowed down atom-pair-energy evaluation a bit. (By having non-virtual functions, the functions can be inlined, and called at 0 overhead -- these functions are needed by the functions that live in atom_pair_energy_inline.hh).