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.

sPuReMD: update QMMM interface for specifying molecular charge constraints for charge model (EEM only currently).

sPuReMD: fix issue with atoms exactly on the upper boundary of the simulation box not being correctly binned into grid cells for the cell method. Refine conversion constants for kinetic energy and temperature calculations to obtain better agreement with the Fortran ReaxFF codebase.

sPuReMD: fix code to remove several compiler warnings. Remove unused code. Disable compilation of several debug routines. Other code clean-up.

sPuReMD: add support for user-defined molecular charge constraints with EEM (using MOLCHARGE keyword in BGF geometry files). Fix issue with far neighbor list not being initialized for certain edge cases.