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.

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).

sPuReMD: fix issue with graph coloring causing sporadic failures in solver convergence for EE and ACKS2. Conditionally change the charge matrix for ICHOLT and ILU(T) preconditioning. Refactor graph coloring code.

sPuReMD: remove force tabulation for charge matrices. Revise list references to mirror MPI code. Revert GMRES iteration counter.

sPuReMD: fix GMRES bug introduced from previous refactoring. Explicitly link OpenMP for library. Refactoring to remove global variables. Remove unnecessary OpenMP barriers after single regions.

sPuReMD: fixes to remove compilatoin warnings. Replace standard library functions with safer versions to avoid buffer overruns. Safer use of placeholders in format strings for printing.