PG-PuReMD: disable grid optimization which requires the Verlet list be in half format (all MPI+CUDA code and SAI code uses full format). Fix H-bond list initialization issue in MPI-only code. Re-write SAI MPI code to avoid extraneous data movement. Other code clean-up.

PG-PuReMD: fixes to SAI preconditioner computation (message size mismatch). Rework MPI communications to not exchange data over MPI when messages are exchanged with oneself (i.e., neighboring processor is oneself via periodic boundary conditions). Backport hydrogen bond fix from sPuReMD (omit interactions when no valid parameters in force field file). Other code clean-up.

PG-PuReMD: fix potential MPI message collision issue in SAI preconditioner (same tags to same source rank => use different tags). Reorder communications to allow message size detection and buffer reallocation if needed.

PG-PuReMD: fix cross-stream race conditions on intermediary force calculation variables (CdDelta, Cdbo, etc.). Rework valency and torsion calculations to minmize the number of atomic operations performed. Split lone pair and over-/under-coordination kernels. Fix small size mismatch in allocation routines (over-allocation). Other code clean-up.

PG-PuReMD: fix warnings (and errors) from several uninitialized memory regions due to multiple stream change. Fix race condition with valence angle computation due to mistake with dynamic shared memory. Add control file parameter for setting the number of CUDA streams. 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 issue with certain data structures not being reallocated when the local number of atoms owned by a processor increases after exchanging messages with neighbor processors. Fix an issue where the MPI send message buffer may be overwritten by a received message (Coll). Small fix to not overwrite the program status return value with local function return values. Other code clean-up.

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: 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: 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 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: fix issue with MPI outgoinging buffer size. Refactor MPI communication code for better encapsulation. Continue cleaning up linear solver code.

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.