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
Am Di., 8. Dez. 2020 um 20:14 Uhr schrieb Aaditya Lakshmanan <
aaditya8...@gmail.com>:
> 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
>
> On Tuesday, December 8, 2020 at 7:20:56 PM UTC-5 Aaditya Lakshmanan wrote:
>
>> 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
>>
>> On Tuesday, December 8, 2020 at 7:01:07 PM UTC-5 mafe...@gmail.com wrote:
>>
>>> 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
>>>
>>> On Saturday, December 5, 2020 at 10:12:00 PM UTC-7 aadit...@gmail.com
>>> wrote:
>>>
>>>> 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
>>>>
>>> --
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