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.

PG-PuReMD: fix issue with hydrogen bond cutoff with systems without hydrogen atoms. Remove debugging info for MPI-only version of PG-PuReMD.

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.