>> 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
Building the small example I realised that hdf5 wasn’t working altogether. I’m
trying to fix this and see if I can run VecView with the periodic DMPlex then.
I planned using this for visualisation.
> On 25. Oct 2018, at 15:36, Stefano Zampini <stefano.zamp...@gmail.com> wrote:
>
> Maybe this is a fix
>
> diff --git a/src/dm/impls/plex/plexvtu.c b/src/dm/impls/plex/plexvtu.c
> index acdea12c2f..1a8bbada6a 100644
> --- a/src/dm/impls/plex/plexvtu.c
> +++ b/src/dm/impls/plex/plexvtu.c
> @@ -465,10 +465,11 @@ PetscErrorCode DMPlexVTKWriteAll_VTU(DM dm,PetscViewer
> viewer)
> if ((closure[v] >= vStart) && (closure[v] < vEnd)) {
> PetscScalar *xpoint;
>
> - ierr = DMPlexPointLocalRead(dm,v,x,&xpoint);CHKERRQ(ierr);
> + ierr =
> DMPlexPointLocalRead(dm,closure[v],x,&xpoint);CHKERRQ(ierr);
> y[cnt + off++] = xpoint[i];
> }
> }
> + cnt += off;
> ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE,
> &closureSize, &closure);CHKERRQ(ierr);
> }
> }
>
> Max, does this fix your problem? If you confirm, I'll fix this in the maint
> branch
It did indeed fix the issue! Thank you. I’ve had problems with hdf5 before and
switched to vtk. It’s good news I can continue to use it.
>
> If I run the below command line with the patch and with snes tutorials ex12 I
> get the nice picture attached
> $ ./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 -x_periodicity periodic -y_periodicity periodic
> -dm_refine 4
>
> Il giorno gio 25 ott 2018 alle ore 15:11 Stefano Zampini
> <stefano.zamp...@gmail.com <mailto:stefano.zamp...@gmail.com>> ha scritto:
> 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 <knep...@gmail.com
> <mailto:knep...@gmail.com>> ha scritto:
> On Wed, Oct 24, 2018 at 11:36 AM Maximilian Hartig <imilian.har...@gmail.com
> <mailto:imilian.har...@gmail.com>> wrote:
>
>
>> On 24. Oct 2018, at 12:49, Matthew Knepley <knep...@gmail.com
>> <mailto:knep...@gmail.com>> wrote:
>>
>> On Wed, Oct 24, 2018 at 6:29 AM Lawrence Mitchell <we...@gmx.li
>> <mailto:we...@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.har...@gmail.com
>> > <mailto:imilian.har...@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
>> > <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/ <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
>
>
> --
> Stefano
> <periodic.png>
