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

Tools: fix MPI command. Change control file generation to be in running directory (for temporary directories and files) => necessary for running with MPI (shared filesystem needed across nodes).

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

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

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.