PuReMD: split Init_Forces into 3 functions: Init_Distance, Init_CM and Init_Bond, and add timings for those functions

PuReMD-old: fix timing issues. Remove fine-grained timing of Init_Forces due to high overhead. Disable SAI preconditioner optimization of changing far nbr list and matrix formats based on preconditioner refactoring step (not working). Tweak to not product numeric overflow when setting up SAI preconditioner (pivot sampling).

PuReMD-old: more clean-up of linear algebra code. Remove or conditionally enable debugging code (DEBUG preprocessor). Fix memory leak in SAI setup. Better memory allocation checks.

PuReMD-old: remove non-source junk files. Clean-up to remove debugging code for neutral territory. Conditionally toggle SpMV implementation (Sparse_MatVec) debugging on if neutral territory is selected.

Merge branch 'full-far-nbrs-list-charge-matrix' into full-far-nbrs-list-charge-matrix-half-full-refactor.

Merge branch 'full-far-nbrs-list-charge-matrix-half-full-refactor' into full-far-nbrs-list-charge-matrix-half-full-refactor2.

Fix issue with bonds list ordering leading to different torsion and conjugation energies due to changing the far neighbors list to a full list.

Merge branch 'full-far-nbrs-list-charge-matrix' of https://gitlab.msu.edu/SParTA/PuReMD into full-far-nbrs-list-charge-matrix.

PuReMD: refactor to allow selection of far range interaction Verlet list format at runtime (half or full). Similar change for symmetric charge matrix format (half or full). For SAI, toggle between half and full depending on whether it is a refactoring step.

Merge branch 'full-far-nbrs-list-charge-matrix' of https://gitlab.msu.edu/SParTA/PuReMD into full-far-nbrs-list-charge-matrix.