[petsc-users] Periodic BC in petsc DMPlex / firedrake

[Stefano Zampini]

Matt,

you can reproduce it via

$ valgrind ./ex12 -quiet -run_type test -interpolate 1 -bc_type dirichlet
-petscspace_degree 1 -vec_view vtk:test.vtu:vtk_vtu -f
${PETSC_DIR}/share/petsc/datafiles/meshes/square_periodic.msh
-dm_plex_gmsh_periodic

Long time ago I added support for viewing meshes with periodic vertices in
the VTK_VTU viewer, but I did not fix the part that writes fields


Il giorno mer 24 ott 2018 alle ore 21:04 Matthew Knepley <knepley at gmail.com>
ha scritto:

> On Wed, Oct 24, 2018 at 11:36 AM Maximilian Hartig <
> imilian.hartig at gmail.com> wrote:
>
>>
>>
>> On 24. Oct 2018, at 12:49, Matthew Knepley <knepley at gmail.com> wrote:
>>
>> On Wed, Oct 24, 2018 at 6:29 AM Lawrence Mitchell <wence at gmx.li> wrote:
>>
>>> Hi Max,
>>>
>>> (I'm cc'ing in the petsc-users mailing list which may have more advice,
>>> if you are using PETSc you should definitely subscribe!
>>>
>>> > On 24 Oct 2018, at 09:27, Maximilian Hartig <imilian.hartig at gmail.com>
>>> wrote:
>>> >
>>> > Hello Lawrence,
>>> >
>>> > sorry to message you out of the blue. My name is Max and I found your
>>> post on GitHub (
>>> https://github.com/firedrakeproject/firedrake/issues/1246 ) on DMPlex
>>> being able to read periodic gmsh files. I am currently trying to do just
>>> that (creating a periodic DMPlex mesh with gmsh) in the context of my PhD
>>> work. So far I haven’ t found any documentation on the periodic BC’s with
>>> DMPlex and gmsh in the official petsc documentation.
>>> > I was wondering whether you’d be so kind as to point me in a general
>>> direction concerning how to achieve this. You seem experienced in using
>>> petsc and I would greatly appreciate your help.
>>>
>>>
>>> I think the answer is "it depends". If you're just using DMPlex directly
>>> and all the of the functionality with PetscDS, then I /think/ that reading
>>> periodic meshes via gmsh (assuming you're using the appropriate gmsh mesh
>>> format [v2]) "just works".
>>>
>>
>> There are two phases here: topological and geometric. DMPlex represents
>> the periodic topological entity directly. For example,  a circle is just a
>> segment with one end hooked to the other. Vertices are not duplicated, or
>> mapped to each other. This makes topology simple and easy to implement.
>> However, then geometry is more complicated. What Plex does is allow
>> coordinates to be represented by a discontinuous field taking values on
>> cells, in addition to vertices. In our circle example, each cells near the
>> cut will have 2 coordinates, one for each vertex, but they will not agree
>> across the cut. If you define a periodic domain, then Plex can construct
>> this coordinate field automatically using DMPlexLocalize(). These DG
>> coordinates are then used by the integration routines.
>>
>>
>> Ok, I think I understand the concept. DMPlex reads information about both
>> topology and coordinates from the .msh file. Creating a periodic mesh in
>> gmsh then should allow DMPlex to identify the periodic boundaries as the
>> “cut” and build the mesh topology accordingly. Coordinate information is
>> handled separately.
>> That means, as Lawrence suggested, building periodic meshes in gmsh and
>> reading them in to petsc’s DMPlex should indeed “just work”.  (From the
>> user perspective). The only extra step is to call DMLocalizeCoordinates()
>> after DMPlexReadFromFile(). Sorry to reiterate, I am just trying to make
>> sense of this.
>>
>>
>>
>>> From my side, the issue is to do with mapping that coordinate field into
>>> one that I understand (within Firedrake). You may not have this problem.
>>>
>>
>> Firedrake uses its own coordinate mapping and integration routines, so
>> they must manage the second part independently. I hope to get change this
>> slightly soon by making the Firedrake representation a DMField, so that it
>> looks the same to Plex.
>>
>>   Thanks,
>>
>>     Matt
>>
>>
>>> Thanks,
>>>
>>> Lawrence
>>
>>
>>
>> --
>> 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/
>>
>>
>> To read periodic meshes from GMSH, you need to use the option
>> -dm_plex_gmsh_periodic and DMPlexCreateFromFile
>>
>>
>> Ahh, thanks. I was missing the option " -dm_plex_gmsh_periodic “. But
>> using this option I now generate a segmentation fault error when calling
>> VecView() on the solution vector with vtk and hdf5 viewers. Any suggestions?
>>
>
>  Small example? VTK is deprecated. HDF5 should work, although it will
> require you to have proper coordinates I think. We have to
> think about what you mean. If its for a checkpoint, there is no problem,
> but for viz, those programs do not understand periodicity. Thus I embed it
> in a higher dimensional space.
>
>    Matt
>
>> See  src/dm/impls/plex/examples/tests/ex1.c. An example runs
>>
>> $ ./ex1 -filename
>> ${PETSC_DIR}/share/petsc/datafiles/meshes/cube_periodic_bin.msh
>> -dm_plex_gmsh_periodic -dm_view ::ascii_info_detail -interpolate -test_shape
>>
>> generating periodic meshes in gmsh may be tricky, Lisandro for sure may
>> advice.
>>
>>
>> Thanks,
>> Max
>>
>>
>
> --
> 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/>
>


-- 
Stefano
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