sPuReMD: fix several issues with strings not being null-terminated. Fix use of uninitialized values reported by Valgrind (heap memory). Other general clean-ups.

sPuReMD: fix issue with list for debugging forces not having indices initialized (dDelta, dBO). Fix interaction counting in OpenMP code (greater than 1 thread). Other general clean-up.

sPuReMD: fix small differences in valence angle energy term with Fortran ReaxFF code. Other minor code updates.

sPuReMD: change log file column headers to be contigious strings of non-whitespace characters to facilitate post-processing.

Fix build issue where config.h.in is only generated once (for sPuReMD) => common file across all versions.

sPuReMD: fix issue with incorrect cutoff being applied for periodic neighbors in small simulation boxes (nonb_cut -> vlist_cut). Other clean-up and debug I/O updates.

Build toos: refactor to remove recurisve Makefiles. Fix issue with OpenMP flags being overridden when user supplied value for CFLAGS variable.

PuReMD-old: fix issue where nonbonded time was incorrect when energy_update_freq > 1. Update tools/run_sim.py to include both total simulation time and mean time per step.

PuReMD-old: increase precision in log file to 4 decimal places for select fields. Merge MPI log parsing logic.

PuReMD-old: fix communications to only use full shell pattern for non-charge methods (bug only present using neutral territory communication method). TODO: revisit code structure at a later date.

PuReMD-old: fix convergence checks for PIPECG and PIPECR. Update CG to used preconditioned residual in it's check.

PuReMD-old: protect against buffer overflows for traj_title. NOTE: strcpy IS NOT SAFE, DO NOT USE EVER. USE strncpy INSTEAD.

PuReMD-old: back-port run_sim.py from master branch. Update control file parsing to ignore sPuReMD/PG-PuReMD options.

sPuReMD: add ACKS2 geometry-dependent forces to tabulated computation of van der Waals and Coulomb terms. Replace double precision equality check with difference comparison.

sPuReMD: add missing header files when distributing (make dist). Fix OpenMP bug with ACKS2 geometry-dependent force contribution. Fix small OpenMP compilation issue. Update tools/run_sim.py to respect geo_format parameter and infer if not present for md_run_custom.

PuReMD-old: optimizations in Init_Bond_Full for fusing hbond and bond list computation and removing unnecessary sorting and sym_index updating.

PuReMD-old: clean-up and comment initialization optimizations. WIP: remove redundant computation of bonds list (not working for full far nbrs list). Improve hbond list computation for full far nbr list case.