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.

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.

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: remove debug prints. Default to no good initial guess for out of range values for spline extrapolation.

sPuReMD: move NaN checks on system energy to after logging. This allows better diagnostics for, e.g., the potential logging.

sPuReMD: separate total energy computation and fix Python driver bug with structure definition for ctypes. Allow disabling file logging during simulation.

sPuReMD: further OpenMP work on force computations and interaction lists. Minor data structure scope changes. Fix numereous non-critical memory leaks. Add tear-down code. Other general refactoring.

Add minor checks to PG-PuReMD and PuReMD. Major refactoring of sPuReMD: backport much of PuReMD code and add CUSTOM geo format.