sPuReMD: refactor preconditioning using control file parameters. Add ILUT_PAR precondioner method. Fix control file parsing bugs.

sPuReMD: begin refactoring data structures from array of structs to struct or arrays (sparse_matrix).

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

Test harness has been rewritten to get rid of unnecessary compiles. Also small issue resulting from two active jobs writing into same file has been resolved.

Integrating the test bed I have been working on. Also integrates the bug fix in cuda_valence_angles. Also one little issue in cuda_forces has been resolved.

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