PG-PuReMD: fixes to NVT with Berendsen thermostat. Use updated constants from sPuReMD. Add BGF geometry file parser. Other code clean-up.

PG-PuReMD: begin enhancements. Enable sim. step retries. Enable far neighbors list max per atom. Other general code clean-ups.

sPuReMD: complete preconditioner application using level scheduling with permutations based on graph coloring.

sPuReMD: expand domain-based QEq matrix cut-off and add control file parameter. Update control file.

Add minor checks to PG-PuReMD and PuReMD. Major refactoring of sPuReMD: backport much of PuReMD code and add CUSTOM geo format.

sPuReMD: fix SuperLU build and code. Fix ILU_PAR (compute factors separately). Move diagonal preconditioner computation. Refactor precondition computations. General code clean-up.