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.

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.

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.

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

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: begin merging preconditioner code from sPuReMD. Make data structures between sPuReMD and PG-PuReMD consistent. Update control file parsing.

sPuReMD: make CoM logic consistent with PuReMD. Other build system updates for debugging and newer versions of MPICH.

sPuReMD: add checks on string and file handling. Rewrite PDB writing to be line-by-line. Other refactoring.

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.

All: fix issue with pi bonds being incorrectly computed in bond orders. Patch originally submitted to LAMMPS mailing list by Tomas Trnka, SCM (refer to Issue #837 on Github).

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

sPuReMD: refactor and clean up preconditioner application code (level scheduling, graph coloring, Jacobi iteration). Conditionally change charge matrix for setting up preconditioner for ICHOLT and ILU(T).