One piece of information that would be useful is what ordering PETSc uses for the Jacobian in the snes_test_display. Is it a natural ordering, or the PETSc ordering? For debugging the Jacobian manually, the natural ordering is much easier to work with. For -n 1, are the orderings the same?
If I use a MatStencil r to represent a field with 3 degrees of freedom, and the dimensions of my 3D DMDA are MxNxP, which row of the Jacobian corresponds to r.i=x, r.j=y, r.k=z, r.c=f?
