[petsc-users] Periodic boundary conditions in DMPlex

[Pierre Seize]

I read everything again, I think I did not understand you at first. The 
first solution is to modify the DAG, so that the rightmost cell is 
linked to the leftmost face, right ? To do that, do I have to manually 
edit the DAG (the mesh is read from a file) ? If so, the mesh 
connectivity is like the one of a torus, then how does it work with the 
cells/faces coordinates ?

Now I think the second method may be more straightforward. What's the 
idea ? Get the mapping with DMGetLocalToGlobalMapping, then create the 
mapping corresponding to the periodicity with 
ISLocalToGlobalMappingCreate, and finally 
ISLocalToGlobalMappingConcatenate ? I'm not sure this is the way, and I 
did not find something like DMSetLocalToGlobalMapping to restore the 
modified mapping.


Pierre


On 15/10/21 15:33, Pierre Seize wrote:
>
> When I first tried to handle the periodicity, I found the 
> DMPlexCreateBoxMesh function (I cannot find the cylinder one).
>
> From reading the sources, I understand that we do some work either in 
> DMPlexCreateCubeMesh_Internal or with DMSetPeriodicity.
>
> I tried to use DMSetPeriodicity before, for example with a 2x2 box on 
> length 10. I did something like:
>
> const PetscReal maxCell[] = {2, 2};
> const PetscReal L[] = {10, 10};
> const DMBoundaryType bd[] = {DM_BOUNDARY_PERIODIC, DM_BOUNDARY_PERIODIC};
> DMSetPeriodicity(dm, PETSC_TRUE, maxCell, L, bd);
> // or:
> DMSetPeriodicity(dm, PETSC_TRUE, NULL, L, bd);
>
> but it did not work:
>
> VecSet(X, 1);
> DMGetLocalVector(dm, &locX);
> VecZeroEntries(locX);
> DMGlobalToLocalBegin(dm, X, INSERT_VALUES, locX);
> DMGlobalToLocalEnd(dm, X, INSERT_VALUES, locX);
> VecView(locX, PETSC_VIEWER_STDOUT_WORLD);
>
> but the ghost cells values are all 0, only the real cells are 1. So I 
> guess DMSetPeriodicity alone is not sufficient to handle the 
> periodicity. Is there a way to do what I want ? That is set up my 
> DMPlex in a way that DMGlobalToLocalBegin/DMGlobalToLocalEnd do 
> exchange values between procs AND exchange the periodic values?
>
>
> Thanks for the help
>
>
> Pierre
>
>
> On 15/10/21 14:03, Matthew Knepley wrote:
>> On Fri, Oct 15, 2021 at 7:31 AM Pierre Seize <pierre.seize at onera.fr 
>> <mailto:pierre.seize at onera.fr>> wrote:
>>
>>     It makes sense, thank you. In fact, both ways seems better than
>>     my way. The first one looks the most straightforward.
>>     Unfortunately I do not know how to implement either of them.
>>     Could you please direct me to the corresponding PETSc functions ?
>>
>> The first way is implemented for example in DMPlexCreateBoxMesh() and 
>> DMPlexCreateCylinderMesh(). The second is not implemented since
>> there did not seem to be a general way to do it. I would help if you 
>> wanted to try coding it up.
>>
>>   Thanks,
>>
>>     Matt
>>
>>     Pierre
>>
>>
>>     On 15/10/21 13:25, Matthew Knepley wrote:
>>>     On Fri, Oct 15, 2021 at 7:08 AM Pierre Seize
>>>     <pierre.seize at onera.fr <mailto:pierre.seize at onera.fr>> wrote:
>>>
>>>         Hi,
>>>
>>>         I'm writing a code using PETSc to solve NS equations with FV
>>>         on an
>>>         unstructured mesh. Therefore I use DMPlex.
>>>
>>>         Regarding periodicity, I manage to implement it this way:
>>>
>>>            - for each couple of boundaries that is linked with
>>>         periodicity, I
>>>         create a buffer vector with an ISLocalToGlobalMapping
>>>
>>>            - then, when I need to fill the ghost cells corresponding
>>>         to the
>>>         periodicity, the i "true" cell of the local vector fills the
>>>         buffer
>>>         vector on location i with VecSetValuesBlockedLocal, then
>>>         VecAssemblyBegin/VecAssemblyEnd ensure each value is send to
>>>         the correct
>>>         location thanks to the mapping, then the i "ghost" cell of
>>>         the local
>>>         vector reads the vector on location i to get it's value.
>>>
>>>
>>>         It works, but it seems to me there is a better way, with
>>>         maybe PetscSF,
>>>         VecScatter, or something I don't know yet. Does anyone have
>>>         any advice ?
>>>
>>>
>>>     There are at least two other ways to handle this. First, the
>>>     method that is advocated in
>>>     Plex is to actually make a periodic geometry, meaning connect
>>>     the cells that are meant
>>>     to be connected. Then, if you partition with overlap = 1,
>>>     PetscGlobalToLocal() will fill in
>>>     these cell values automatically.
>>>
>>>     Second, you could use a non-periodic geometry, but alter the
>>>     LocalToGlobal map such
>>>     that the cells gets filled in anyway. Many codes use this scheme
>>>     and it is straightforward
>>>     with Plex just by augmenting the map it makes automatically.
>>>
>>>     Does this make sense?
>>>
>>>       Thanks,
>>>
>>>          Matt
>>>
>>>         Pierre Seize
>>>
>>>     -- 
>>>     What most experimenters take for granted before they begin their
>>>     experiments is infinitely more interesting than any results to
>>>     which their experiments lead.
>>>     -- Norbert Wiener
>>>
>>>     https://www.cse.buffalo.edu/~knepley/
>>>     <http://www.cse.buffalo.edu/%7Eknepley/>
>>
>>
>>
>> -- 
>> What most experimenters take for granted before they begin their 
>> experiments is infinitely more interesting than any results to which 
>> their experiments lead.
>> -- Norbert Wiener
>>
>> https://www.cse.buffalo.edu/~knepley/ 
>> <http://www.cse.buffalo.edu/%7Eknepley/>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20211015/0997ef6a/attachment-0001.html>