Merge pull request #6 from funkayMan/funkay_dev

Funkay dev
Added a declaration for a loop variable. A couple Minor formatting changes.
Merged changes from funkay_dev
Merge remote-tracking branch 'funkayMan/funkay_dev' into black_dev
Changed the subscripts to match x first and used the transpose of the derivative matrix.
Merge pull request #13 from KellyBlack/black_dev

Black dev