variables + cleaning shake bonds code

git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@4833 90e2fc84-bd37-0410-82f1-ae2f889bfac2
vars

git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@4834 90e2fc84-bd37-0410-82f1-ae2f889bfac2