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).

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.

sPuReMD, PG-PuReMD: add control file keyword (include_polarization_energy) to toggle polarization energy calcuation in ReaxFF.

sPuReMD: rework charge solver for QMMM to not require explicit masking (MM atom fixed charges are not respected). Other code clean-up.

sPuReMD: ensure reallocation for multi-simulation runs happens correctly for the charge solver codepath.

sPuReMD: ensure matrix reallocation correctly occurs in multiple simulation cases where the linear system size increases.

sPuReMD: add dummy atom support for other geometry file formats (PDB, custom). Rework interal logging during debugging for memory management. Other code clean-up.