[petsc-users] DMPlex box mesh periodicity bug (?)

[Thibault Bridel-Bertomeu]

Hi Matt,

Thank you for taking the time to take a look  !

1) Yea ... I know most visualization softwares and most storage formats do
not like periodicity (a.k.a. infinity) ... but fo CFD-research it's a great
tool so we keep trying ... x) The thing that surprised me is that my mwe
works perfectly well in 2D, and not in 3D : that's why I ventured to call
it a bug !

2) Hmm I tried adding a "DMLocalizeCoordinates" after the
"DMPlexConstructGhostCells" but it does not change anything, the result is
still exactly the same as I showed above.

As for your code, it compiles fine and I can execute it as well, thanks !
However ...
1) when I run it in 2D and ask for the HDF5 output, and then run the
petsc_gen_xdmf.py script, I get the attached result (sol_2D.png) : it seems
either Paraview cannot handle what's in the HDF file or the HDF file does
not contain something consistent,
2) when I run it in 3D and ask for the HDF5 output + run petsc_gen_xdmf.py
I can see ... nothing : paraview does not show anything when I try to open
the XDMF file, although it seems syntaxically correct (the HDF file as well)
3) when I run it in 3D and ask for VTU output, I get exactly the same thing
as what I got with my F90 program (see sol_3D.png attached) - my command
line is ./thibault -dm_plex_dim 3 -dm_plex_simplex 0 -dm_plex_box_faces
16,16,16 -dm_plex_box_lower -5,-5,-5 -dm_plex_box_upper 5,5,5
-dm_plex_box_bd periodic,periodic,periodic -dm_plex_create_fv_ghost_cells
-dm_plex_periodic_cut -vec_view vtk:sol.vtu

Does your piece of code yields different results on your end ?

(P.S. I am using the main branch, commit id ae6adb75dd).

Thank you very much for your support !!

Thibault



Le lun. 2 août 2021 à 15:48, Matthew Knepley <knepley at gmail.com> a écrit :

> On Sat, Jul 31, 2021 at 6:01 AM Thibault Bridel-Bertomeu <
> thibault.bridelbertomeu at gmail.com> wrote:
>
>> Dear all,
>>
>> I have noticed what I think is a bug with a 3D DMPlex box mesh with
>> periodic boundaries.
>> When I project a function onto it, it behaves as if the last row of cells
>> in X and in Y direction do not have the right coordinates.
>>
>> I attach to this email a minimal example that reproduces the bug (files
>> mwe_periodic_3d.F90, wrapper_petsc.c, wrapper_petsc.h90, makefile), as well
>> as the output of this code (initmesh.vtu for an output of the DM,
>> solution.vtu for an output of the data projected onto the mesh). There is
>> also a screenshot of what's going on.
>> If one considers the function I project onto the mesh, what should
>> normally happen is that there is a "hole" is the density field around the
>> x=0, y=0 region, the rest being equal to one.
>>
>> I hope it is just a mishandling from my end !!
>>
>
> Hi Thibault,
>
> 1) The main thing happening here is that visualization has some problems
> for completely periodic things. It is on my list to fix, but below other
> things.
>
> 2) Second, it looks like you need to localize coordinates again after
> creating ghost cells. Everything is in the right order if you use the
> command line to create
>     the mesh. I have attached a C example where I do this. In your code, I
> think just adding Localize again will work.
>
> In my example, you can see 2D as well as 3D, and change from non-periodic
> to periodic to see what is happening.
>
>   Thanks,
>
>      Matt
>
>
>> Thank you in advance for your help,
>>
>> Cheers,
>>
>> Thibault
>>
>>
>
> --
> 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/~knepley/>
>
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