Jane,
 

> For more info, the VectorTools flux conditions are in my setup_dofs code, 
> within costraints.clear()... constraints.close(). After assembling the 
> system, I don't use the distribute local to global function but I instead 
> distribute the constraints onto the solution after I have solved the 
> system. Is there something wrong with the order?? I am getting a similar 
> issue with equations like step-22 but I will post separately as it is 
> different. 
>

That sounds a bit strange to me. If you are using a ConstraintMatrix object 
(or an AffineConstraints object), you should normally take the constraints 
into account while assembling, i.e. use

constraints.distrbiute_local_to_glocal(cell_matrix, cell_rhs, dof_indices, 
system_matrix, system_rhs);

and again after solving using

constraints.distribute(solution);

Best,
Daniel

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