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.

PG-PuReMD: complete memory changes. Remove max register per CUDA function option in build. Other misc. changes.

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

PG-PuReMD: only perform device-side reductions on energy at requested update energy frequency. Fix trajectory file output. Add num. retries of main simulation loop to log file. Other refactoring.

PG-PuReMD: fix nvcc build issue where incorrect C++ compiler was utilized. Fix race condition with three body list computation. Remove debug code. Other misc. refactoring.