Periodic boundary conditions : Error using GridTools::collect_periodic_facepairs

[Aaditya Lakshmanan]

Hi,

   I am trying to simulate a reaction-diffusion system containing two species on a square domain(structured mesh) with periodic boundary conditions enforced on the concentration fields on opposite edges. After testing my implementation on a single processor I obtain the following error message : 

---------------------------------------------------------                                                                                                           TimerOutput objects finalize timed values printed to the                                                                                                            screen by communicating over MPI in their destructors.                                                                                                              Since an exception is currently uncaught, this                                                                                                                      synchronization (and subsequent output) will be skipped                                                                                                             to avoid a possible deadlock.                                                                                                                                       ---------------------------------------------------------                                                                                                                                                                                                                                                                                                                                                                                                                                                   ----------------------------------------------------                                                                                                                Exception on processing:                                                                                                                                                                                                                                                                                                                --------------------------------------------------------                                                                                                            An error occurred in line <2107> of file </home/aadi/dealii-9.2.0/source/grid/grid_tools_dof_handlers.cc> in function                                                   void dealii::GridTools::match_periodic_face_pairs(std::set<std::pair<CellIterator, unsigned int> >&, std::set<std::pair<typename dealii::identity<RangeType>::type, unsigned int> >&, int, std::vector<dealii::GridTools::PeriodicFacePair<CellIterator> >&, const dealii::Tensor<1, typename FaceIterator::AccessorType:: space_dimension>&, const dealii::FullMatrix<double>&) [with CellIterator = dealii::TriaIterator<dealii::CellAccessor<2, 2> >; typename dealii::identity<RangeType>::type = dealii::TriaIterator<dealii::CellAccessor<2, 2> >; typename FaceIterator::AccessorType = dealii::CellAccessor<2, 2>]                                                  The violated condition was:                                                                                                                                             n_matches == pairs1.size() && pairs2.size() == 0                                                                                                                Additional information:                                                                                                                                                 Unmatched faces on periodic boundaries                                                                                                                          --------------------------------------------------------                                                                                                                                                                                                                                                                                Aborting!  

Additional Details : The error message is associated with the create_mesh() method of the problem class whose implementation I have included below. The part highlighted in red is the cause of the error message :

template <int dim>

  void Schnakenberg<dim>::create_mesh()   

  {

      TimerOutput::Scope t(computing_timer, "setup");

      GridGenerator::hyper_cube(triangulation, min_coord, max_coord, true);

      std::vector<GridTools::PeriodicFacePair<

typename parallel::distributed::Triangulation<dim>::cell_iterator>>

periodicity_vector;

  

      GridTools::collect_periodic_faces(triangulation,

0,

1,

0,

periodicity_vector);

      GridTools::collect_periodic_faces(triangulation,

2,

3,

0,

periodicity_vector);

     triangulation.add_periodicity(periodicity_vector);

   

      triangulation.refine_global(refine_factor); 

 

  }   

Also, I am curious as to what the 'direction' argument in the GridTools::collect_periodic_faces function should be for a scalar solution field. I would appreciate some insight on this. Thank you.

Best,

Aaditya

[Marc Fehling]

Hi Aaditya,

on first look your implementation looks good to me. Does the same error occur when you are using a standard `Triangulation` object instead of a `parallel::distributed::Triangulation`?

As far as I know, the direction parameter does not matter for scalar fields (see also step-45).

Would you mind sharing your source code?

Best,

Marc

[Aaditya Lakshmanan]

Hi Mark,

    Thank you for responding. I haven't tried using a standard 'Triangulation' object instead of its parallel counterpart. I will try another implementation with the appropriate substitutions. 

 Based on some trials I ran since I posted the question, my code runs without issues(even on multiple processors) when I make the following changes(enforcing periodicity on the triangulation and constraints) : 

GridTools::collect_periodic_faces(triangulation,

                                                            0,

                                                            1,

                                                            0,

                                                           periodicity_vector);

GridTools::collect_periodic_faces(triangulation,

                                                             2,

                                                             3,

                                                             1,                                // The earlier 0 changed to 1 does not yield errors and results are periodic 

                                                             periodicity_vector); 

   Although, as you mention, based on the documentation the direction argument shouldn't play a role in the problem I am trying to simulate. I have attached my code here. I am running my simulations with deal.II version 9.2.0 compiled with Trilinos.

Best,

Aaditya

[Aaditya Lakshmanan]

Hi Mark,

   Quick update. I tried running a simulation with an implementation using the 'Triangulation' object instead and I face the same issue as earlier. It returns the same error message as in the parallel case. Also, making the change in the direction argument from 0 to 1 for the constraints between faces with boundary indicators 2 and 3 resulted in the code running just fine and yielding periodic variation of the fields.

Best,

Aaditya 

[Daniel Arndt]

Aaditya,

 the documentation says

"[...] More precisely, faces with coordinates only differing in the direction component are identified."

Hence, it is crucial to choose this correctly. For a cube with standard coloring faces 2 and 3 share the x-coordinates so direction must be 1.

Best,

Daniel

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[Aaditya Lakshmanan]

Hi Daniel,

      The serial implementation of the code was exiting with error in the function call to GridTools::collect_periodic_faces() so I was looking in documentation for details on specifically that function. I see now that the role of the 'direction' argument is mentioned explicitly in the documentation for GridTools::make_periodicity_constraints(). Thank you for pointing that out. I understand the significance now.

Best,

Aaditya