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.

PG-PuReMD: update build system for LAPACKE. Conditionally include LAPACKE header based on results of compilation.

Merge branch 'full-far-nbrs-list-charge-matrix' of https://gitlab.msu.edu/SParTA/PuReMD into full-far-nbrs-list-charge-matrix.

PG-PuReMD: fix initial list offsets for creating lists. Fix far neighbor and hydrogen bond reallocation checks. Begin refactoring function defitions and declarations to allow compiler to enforce intentions of pointer usage.

PG-PuReMD: fix charge extrapolation. Improve memory management of local portion of charge matrix and reset linear system size for each time step.

PG-PuReMD: add deallocation routines at simulation termination for aiding with validating memory management.

PG-PuReMD: fix CUDA compilation error. Revert library building via libtool due to issues with recognizing custom suffix rules for building CUDA source files and revisit at a later date.

Change MPI build target to use newer MPI-only code by default, and add option to build older MPI code (to be removed in the future).

PG-PuReMD: fix issue with MPI outgoinging buffer size. Refactor MPI communication code for better encapsulation. Continue cleaning up linear solver code.

PG-PuReMD: fix charge matrix allocation issue. Update CUDA code to reflect data structure changes. Begin removing global variables. Seperate struct declarations and definitions to avoid circular data dependencies when refactoring data structures. Small I/O updates.