Mpi index fixes

DeWitt, Stephenrequested to merge
71d/mmmm:mpi_index_fixes into master

Some index mistakes in a few places were causing the MPI issues, those are now fixed.

Nominally, master now has all of the fixes from my "integration_testing_updated" branch, which works on CPU and GPU for both 1 and 4 MPI tasks, and gets the same result as the Fortran code to something like 13 digits.

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