Magda, [...] > DoFTools::make_periodicity_constraints(dof_handler, 2, 3, 1, constraints); > DoFTools::make_periodicity_constraints(dof_handler, 4, 1, 0, constraints); > > These two lines imply that you want to impose periodic boundary conditions for all the components. Assuming the dof_handler variable is of type FESystem and describes both velocity and pressure (as is the case in the code-gallery example), this in particular holds true for the pressure. Is that what you are intending? If so, you probably need another constraint to make the pressure unique. Otherwise, you might want to have a look at step-45 <https://www.dealii.org/9.0.0/doxygen/deal.II/step_45.html> where a Stokes problem is solved with periodic boundary conditions on part of the boundary. There only periodicity constraints for the velocity are stored in the ConstraintMatrix object.
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