sPuReMD: default to vlist_buffer of 2.5 angstroms. Fixes to cutoffs used in far neighbor list generation.

sPuReMD: re-enable SMALL_BOX_SUPPORT. Fix issue with far nbrs list being incorrectly generated for small boxes (missing nbr ID). Fix issue with ACKS2 matrix being incorrect for small boxes due to multiple non-zeros being added for each perioidic image of an atom (accumulate instead). Add missing ACKS2-specific energy and forces term. Clean-up far nbr list estimation and generation code for small boxes. Do not add far list struct entries unless the atom is below the specified cutoff.

Build systems updates for sPuReMD, PuReMD-GPU, and PG-PuReMD (use safer optimization level defaults).

Tools: add functionality to run different code version (serial, OpenMP, MPI, MPI+GPU). Update sPuReMD control file parser to ignore non-shared memory parameters.

Tools: update run_sim.py to work with absolute paths (by refereing supplied executable path). Begin updating testing scripts.

sPuReMD: refactoring to align code with PuReMD. Disable SMALL_BOX_SUPPORT. Refactor to remove union-based polymorphic behavior for reax_list. Other general code clean-ups.

sPuReMD: fix ILUTP bug with order of permutation matrix application. Refactor dense vector permutation code (GC, ILUTP).

sPuReMD: backport efforts for SMALL_BOX_SUPPORT from OGOLEM version of code and conditionally compile. Remove unused code. Other code clean-up.

sPuReMD: backport changes for reax_list, struct declaration/definition separation, interaction_function.

PG-PuReMD: fix function pointers for bonded forces. Declare constants appropriately in bonded force computations. Fix sym_index computation for bond list. Other code clean-up.