PG-PuReMD: add several warp optimized kernels (Verlet list generation, storage estimation routines for initialization, etc.). Rework nonbonded kernels to decease the number of arithmetic instructions. Optimize three dimensional vector functions. Other code clean-up.

PG-PuReMD: fix issue with hydrogen bond interactions being evaluated for structures with no hydrogen atoms.

PG-PuReMD (MPI): optimize valence and torsion interactions by pruning based on existence of parameters in the force field parameter file.

PG-PuReMD: properly initialize MPI for threading (MPI_THREAD_FUNNELED). Optimize SAI preconditioner computation to avoid MPI communications when neighbor MPI process is yourself in the presence of periodic boundary conditions.

PG-PuReMD: add OpenMP support for SAI preconditioner computation (--enable-openmp=yes flag in configure script). Other code clean-up.

Tools: enable setting of the number of CUDA streams (gpu_streams control file keyword). sPuReMD: update control file parser for this new keyword (valid but ignored).

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: simplify preconditioner selection logic. Fix issue with SpMV's applying SAI preconditioning (full row not applied during multiplication). Change solver iterations counts in MPI+CUDA code to match MPI-only code. 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: standardize and clean-up CUB usage. Add wrapper for non-CUB reductions (rvec, rvec2). Other code clean-up.

PG-PuReMD: add support for using cuBLAS routines for dense linear algebra (mainly level-1 routines in sparse linear solver). Clean-up solver code for using streams.

PG-PuReMD: split van der Waals and Coulomb force and energy computation kernels and execute in seperate streams. Change stream of Coulomb-related kernels (init, charge solver, Coulomb). Use math function for cubic root calculations. Other code clean-up.

PG-PuReMD: default to using bundled CUB library witn recent CUDA SDK version (>= v11.x), while retaining older CUB submodule for older CUDA capabilities (use NVCCFLAGS to manually include CUB in this case). Refactor timing code to more accurately measure kernel timing. Refactor stream logic to expose more parallelism (valence+torsion branch) and to perform fewer synchronizations. Other code clean-up and refactoring.

sPuReMD: refactor contiguous and custom charge constraint code. Make applicable API functions available to all interfaces.

sPuReMD: fix issue with API functions (setup2 / reset2 -> cleanup) regarding new contiguous and custom charge constraint implementation (identified and suggested fix by Cagri Kaymak).

sPuReMD: do not compute hydrogen bond interactions when there are no valid force field parameters available for the given triplet of atom types. Allow arbitrary numbers of H-bond interactions per atom.

sPuReMD: fix issue with sparse charge matrix (for preconditioning) not being reallocated upon out-of-memory condition. Fix issues where charge matrix and bond/H-bond list entries were reading from and potentially writing to invalid memory locations. Remove unused code for grid. Other code clean-up.

sPuReMD: fix uninitialized variable issue with API functions (charge constraints => setup2, reset2).

sPuReMD: add error checks around I/O routines to silence warnings regarding disregarded return values.

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.

Fix memory allocation issue with API usage

Closes #9

See merge request !5

Fix memory allocation issues related to API usage (setup => cleanup but no simulate) as detailed in Issue #9.

sPuReMD: rework memory management logic to better match PG-PuReMD code. Adapt new memory management logic for multiple simulation logic (as motivated by memory issues observed with QM/MM code for AMBER integration work). Other code clean-up.

PG-PuReMD: fix bugs in the SAI preconditioner for the charge solver (memory leak, incorrect row numbers).

PG-PuReMD: port SAI preconditioner from MPI codebase. Rework charge solver preconditioner code. Other code clean-up.

sPuReMD: change dummy atom behavior to participate only in Coulomb interactions (exclude from van der Waal interactions in this changeset).