PG-PuReMD: fix issue with charge solver preconditioner refactoring rate causes issues with reneighboring actions (preconditionering rate was previously coupled with reneighoring rate for SAI but this causes issues for Jacobi, etc.). Be more greedy with memory allocation sizes to decrease reallocation frequency (MPI buffers, etc.). More GPU code clean-up.

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: fix issue with divergent MPI_Reduce calls by multiple MPI processes (timing logging code). Add run-time MPI routine error checking. Fix issue with upper limit of hydrogen atoms allowed being hard-coded in GPU code (use dynamic memory allocation instead). Other code clean-up.

PG-PuReMD: improve memory management around temporary storage space on both the host and device (i.e., scratch space).

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

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

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