PG-PuReMD: implement MPI+CUDA versions of SDM, PIPECG, PIPECR for charge solver methods (along with missing dual QEq versions).

PG-PuReMD: use a warp of threads for addtional bonded interaction computations (bond orders, bonds, lone pair/over/under).

PG-PuReMD: use a warp of threads for apply bond derivatives to forces and simplify these code paths.

PG-PuReMD: fix incorrect summations in kinetic energy and temperature calculation functions. Replace several hand-coded device-wide reduction kernels with CUB libary reduction.

PG-PuReMD: split bond and hbond initialization kernels for future optimizations. Cleanup CUDA code related to far neighbor list being in full format (remove unnecessary conditionals and arithmetic).

sPuReMD: make zlib dependency optional (trajectory file compression). PG-PuReMD: remove erroneous zlib header file inclusion.

PG-PuReMD: handle a few missed reductions in nonbonded interactions more efficiently. Clean-up bonded interactions functions and do not export kernels via header files. Increase C++ standard to c++14 for CUB (Thrust dependency). Continue with bundled CUB version and transition to version included with CUDA SDK in the future.

PG-PuReMD: use atomics for both partial energy and force accumulation (small reworks to reduce number of atomic operations). Remove several unneccesary cudaMemset calls. Other code clean-up.

Test: fix Python wrapper for QM/MM (interfaces out-of-date). Fix Fortran tester bugs. Add test artifacts.

PG-PuReMD: fix BGF parser for >1 process (correct atom counts within local simulation box boundaries).

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

PG-PuReMD: in-progress implementation of CUDA-aware MPI for charge solver communications using OpenMPI (default off).

PG-PuReMD: fix van der Waals and Coulomb force computations for 1 warp per atom implementation, and enable this implementation by default.

PG-PuReMD: use registers for local arithmetic in CUDA nonbonded calculations and fix shared memory usage in 1 warp per atom implementation.

PG-PuReMD: switch timers to use CUDA events and add additional timers for kernels to match MPI code. Other code cleanup.

This reverts commit 6a1385e9.

PG-PuReMD: align CSR sparse matrix data structure to 128-bit/256-bit segments for memory coalescing (for 1 warp per row SpMV implementation). Change default interaction list and sparse matrix allocations to be multiples of 32 for aforementioned memory coalescing.

PG-PuReMD: switch from using strtok_r to strtok to avoid reliance on GNU extensions with building for the C11/C++11 standard.

PG-PuReMD: only copy host generated grid to device on reneighboring steps (after rebinning atoms and regenerating the grid). Fix small NVE integration bug (reallocation checks before copying new atom info to device).

PG-PuReMD: change CUDA kernel error checking to only make calls to cudaDeviceSynchronize when in debugging mode (non-debug builds thus have better performance with kernel asynchronous launch behavior in single default stream). Change file I/O to only flush when in debugging mode (non-debug builds allow the I/O operations to be grouped for better performance).

PG-PuReMD: add support for symmetric, half stored format (SYM_HALF_MATRIX) of the sparse matrix for the charge model (add initialization routines and fix-up solver).

PG-PuReMD: rework custom reduction functions to use less shared memory and to have the correct thread and block counts. Fix bug in charge matrix initialization (under-allocated space previously). Split charge matrix and bonds/hydrogen bonds memory management routines to mirror the similar splitting of the initialization routines. Code clean-up related to half vs. full list and sparse matrix formats.