sPuReMD: fix issue with hbonds list indices not being reset correctly. Small algebraic rearrangements of valence angle calculations to match Fortran ReaxFF code (no numeric changes). Fix issue with rvec_isZero being incorrect. Fix issue with debugging arrays for TEST_FORCES not having indicies initialized. Other clean-up work.

sPuReMD: revert force tabulation changes. Temporarily work around out-of-bound memory accesses in cubic spline interpolation routes (for force tabulation) by expanding array sizes. Revisit at a later date.

sPuReMD: fix several more warning from Valgrind (out-of-bounds accesses in force tabulation lookup tables, sparse matrices with EE/ACKS2 with tabulation). Remove unused variables. Fixes to string handling. Other code clean-up.

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.