[petsc-users] Periodic boundary conditions in DMPlex

[Pierre Seize]

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/>

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