Dear Jennifer,

have you solved the problem yet?

This looks like you are applying the constraints several times:

>  std::set<unsigned char> no_normal_flux_boundaries;
>  no_normal_flux_boundaries.insert (0);
>  VectorTools::compute_no_normal_flux_constraints
>    (dof_handler, 0,
>     no_normal_flux_boundaries,
>     constraints);
>  no_normal_flux_boundaries.insert (1);
>  VectorTools::compute_no_normal_flux_constraints
>    (dof_handler, 0,
>     no_normal_flux_boundaries,
>     constraints);
> ...

Just insert all boundaries into the set and call
compute_no_normal_flux_constraints() once.

If that is not the problem, try to reduce the number of cells and
boundary conditions further. I don't think you would need that many
conditions to trigger the problem. Then you can try to print the
constraint matrix out to see what is going on.

Hope that helps.

-- 
Timo Heister
http://www.math.tamu.edu/~heister/
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