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

[Matthew Knepley]

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/>
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