PG-PuReMD: merge memory management and step retry logic from MPI+GPU code into MPI-only code. Fix and backport numerous bugs (void pointer arithmetic and dereferences, etc.). Update code to match new data structures. Begin merging changes from OpenMP code (sPuReMD) for preconditioning work.

All: fix issue with pi bonds being incorrectly computed in bond orders. Patch originally submitted to LAMMPS mailing list by Tomas Trnka, SCM (refer to Issue #837 on Github).

PG-PuReMD: begin enhancements. Enable sim. step retries. Enable far neighbors list max per atom. Other general code clean-ups.

PG-PuReMD: fix include guards, resolve implicit function declarations, fix inline issues with GCC v5 (C99 std). Other general code clean-up.

Just removing now unnecessary printfs that clutter the code

The MPI-Not-GPU version is able to run through all benchmarks with decent agreement with the other versions now. The test harness has been modified to allow testing between the three functional versions.
Also added a README file in the test_harness directory about how to use the harness. Finally, I have saved one copy of the output from the previous test run to sim_output_082516.txt, for future comparison.