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.

sPuReMD: complete preconditioner application using level scheduling with permutations based on graph coloring.

sPuReMD: fix Jacobi iteration synchronization issues and change inner SpMV thread scheduling policy to guided for load balancing.

sPuReMD: expand domain-based QEq matrix cut-off and add control file parameter. Update control file.

sPuReMD: fix incorrect thread parallelism inside bonded force routines. Update default value of CFLAGS in autotools.

sPuReMD: refactor tri solve level sched memory management. Change OpenMP thread scheduling policy to static. Modify logging output format.

sPuReMD: fix diagonal preconditioner computation and level scheduling application. Modify preconditioner logic to compute and cache sparsity-based info. Update run script.