sPuReMD, PG-PuReMD: add control file keyword (include_polarization_energy) to toggle polarization energy calcuation in ReaxFF.

PG-PuReMD: fixes to NVT with Berendsen thermostat. Use updated constants from sPuReMD. Add BGF geometry file parser. Other code clean-up.

PG-PuReMD: fix performance logging code around GPU code. Rearrange header files to allow some preprocessor definitions to be defined via options in configure script. Rework Autoconf and Automake code to allow passing flags directly to nvcc compiler wrapper (for CUDA code). Enable C11 and C++11 standard targets during compilation.

PG-PuReMD: fix MPI buffer allocations sizes. Ensure that nonblocking MPI messages have completed for each dimension before continuing. Rework reallocation checks in integration routines. Temporarily disable CUDA-aware MPI code paths (need to perform packing/unpacking first on device before handing off pointers). Other code clean-up.

PG-PuReMD: merge changes from sPuReMD and PuReMD for validation work for simulation accuracy. Small correction to lone pair energy calculation. PuReMD: code formatting changes to better align with sPuReMD. sPuReMD: fix issue with valence angle calculations not setting list indices under certain sitations (taking previous continue statement missed index assignment).

PG-PuReMD: backport fixes from sPuReMD to control file parsing. Tools: formatting tweaks for MPI-GPU code.

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

PG-PuReMD: begin merging preconditioner code from sPuReMD. Make data structures between sPuReMD and PG-PuReMD consistent. Update control file parsing.

PG-PuReMD: merge memory management and step retry logic from MPI+GPU code into MPI-only code. Fix and backport numerous bugs (void pointer arithmetic and dereferences, etc.). Update code to match new data structures. Begin merging changes from OpenMP code (sPuReMD) for preconditioning work.

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

PG-PuReMD: begin enhancements. Enable sim. step retries. Enable far neighbors list max per atom. Other general code clean-ups.