sPuReMD: fix bug in GMRES where vector inputs and outputs to apply_preconditioner were being overwritten. Refactor OpenMP code in GMRES.

sPuReMD: split into library and driver for, e.g., optimization integration. Fix bug with interaction lists being allocated for hydrogen bonds when no hydorgen atoms present. Fix minimum allocation size of 3-body lists (uncovered with small lithium geometries). Refactor naming of conflicting data structures. Update .gitignore.

PG-PuReMD: fix error due to function prototype change. PuReMD: fix issues with GCC new inline behavior, fix reax_list bugs. sPuReMD: change exit code to zero.

sPuReMD: remove unnecessary explicit OpenMP barriers. Conditionally enable OpenMP linear algebra code. Other general refactoring.

sPuReMD: change inline functions to be generated for each translational unit. Begin adding vectorization support via OpenMP SIMD.

sPuReMD: fix complaints by Valgrind for indexing before head of array pointer (i.e., passed as function parameters).

sPuReMD: add safe memory allocation functions. Fix issue with certain parameters for shielded van der Waals interactions not being correctly initialized. Other general refactoring.

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.

sPuReMD: begin merging code from LAMMPS USER-REAXC-OMP/USER-OMP. Fix ACKS2 charge matrix coefficients.

sPuReMD: fix linear solver to work with no preconditioner. Fix issue when precondition recomputation frequency is zero. Other misc. changes.

PG-PuReMD: fix include guards, resolve implicit function declarations, fix inline issues with GCC v5 (C99 std). Other general code clean-up.

sPuReMD: enable debug builds. Fix compilation issues when optimizations disabled (-O0). Fix graph coloring data structure management.