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Test: fix Python wrapper for QM/MM (interfaces out-of-date).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.

sPuReMD: standardize QM/MM interface. Add test codes for QM/MM interface for AVE dataset in Python and Fortran.

sPuReMD: merge changes from branch 'new_setup'. Rework interface for geometry initialization without file I/O. Other code clean-up.

sPuReMD: fix BGF parser to correctly remap atom coordinates to internal simulation box boundaries. Fix reax_list to handle case when total interactions is zero instead of terminating program.

sPuReMD: rework Fortran F90 interfaces for Amber specifics and declare this interface for such usage.

sPuReMD: fix Coulomb energy calculations for QM/MM mode. Indicate QEq model not supported with QM/MM mode. Add Fortran interface for QM/MM mode.

sPuReMD: add QMMM library interface for external codes (e.g., Amber). Rework file I/O parsing to jive with multiple consecutive simulation code changes. Improve file parser error checking (numeric types). Other code clean-up.

sPuReMD: fixes for multiple consecutive simulation codepath. Reorganization to this codepath (some data structure now carry a flag to designation their allocation state). Fix bug in force field parser (atom type not truncated correctly). Charge sparse_matrix structs to be non-pointers to jive with new allocation state flag. Other code clean-up.

sPuReMD: finalize sPuReMD multiple consecutive simulation code (for integration with other codebases).

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.

sPuReMD: fix memory leak with ICHOLT preconditioner (droptol for OpenMP only) for charge solver. Default to Jacobi preconditioner. Resolve several compiler warnings around C strings (snprintf, etc.). Other code clean-up.

sPuReMD: add functionality to run multiple MD simulations (for usage via integration with external codebases).

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

sPuReMD: resolve OpenMP build errors with GCC v10 (behavior changes for function arguments). Suppress possibly unitialized variable warnings for BiCGStab.

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.