PG-PuReMD: merge changes from sPuReMD and PuReMD for validation work for simulation accuracy. Small correction to lone pair energy calculation. PuReMD: code formatting changes to better align with sPuReMD. sPuReMD: fix issue with valence angle calculations not setting list indices under certain sitations (taking previous continue statement missed index assignment).

PG-PuReMD: fix initial list offsets for creating lists. Fix far neighbor and hydrogen bond reallocation checks. Begin refactoring function defitions and declarations to allow compiler to enforce intentions of pointer usage.

PG-PuReMD: fix charge matrix allocation issue. Update CUDA code to reflect data structure changes. Begin removing global variables. Seperate struct declarations and definitions to avoid circular data dependencies when refactoring data structures. Small I/O updates.

PG-PuReMD: merge memory management and step retry logic from MPI+GPU code into MPI-only code. Fix and backport numerous bugs (void pointer arithmetic and dereferences, etc.). Update code to match new data structures. Begin merging changes from OpenMP code (sPuReMD) for preconditioning work.