PG-PuReMD: fix compilation error (remove variable). Fix issue with dual CG solver for QEq (local arithmetic in SpMV was incorrect). Revert CG solver convergence criterion to use norm of the preconditioned residual vector.

PG-PuReMD: fix issue with some interaction lists not being initialized on first step of simulations from restarted runs. Fix typos in C++ code for utilizing C code (__cplusplus). Clean up C code for utilizing C++ code (unconditional extern's for unmangled member naming). Ensure that CUDA thread and block sizes are correctly set. Tweaks to memory transfers and allocation logic in integration code (GPU). Fix logic error with charge matrix allocation in GPU code. Other code clean-up.

PG-PuReMD: add BiCGStab solver for GPU code. Corrections to CUDA block and thread sizes for some kernels. Fix some variables being used with uninitialized values.

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 host-device transfers for charge solver code (SpMV data transfer sizes). Remove unused code. Other general 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: 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: refactoring to unify CUDA code naming conventions and to simply code in cuda_system_props.cu.

PG-PuReMD: fix issue with portions of interaction lists not being initialized for Cuda_Init_Forces. Utilize more targeted debugging prints (DEBUG -> DEBUG_FOCUS). Other general code cleanup.

PG-PuReMD: fix charge matrix allocation issue. Update CUDA code to reflect data structure changes. Begin removing global variables. Seperate struct declarations and definitions to avoid circular data dependencies when refactoring data structures. Small I/O updates.

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: 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.

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.