[petsc-users] Writing VTK output

Wed Jun 8 10:57:47 CDT 2022

On Wed, Jun 8, 2022 at 11:24 AM Sami BEN ELHAJ SALAH <
sami.ben-elhaj-salah at ensma.fr> wrote:

> Yes, the file "sami.vtu" is loaded correctly in paraview and I have the
> good output like you.
>
> In my code, I tried with the same command given in your last answer and I
> still have the wrong .vtu file.
>

Hi Sami,

What do you mean by wrong?

Can you just use the simple procedure:

  PetscCall(DMCreate(comm, dm));
  PetscCall(DMSetType(*dm, DMPLEX));
  PetscCall(DMSetFromOptions(*dm));
  PetscCall(DMViewFromOptions(*dm, NULL, "-dm_view"));

This is the one that works for us. Then we can change it in your code one
step at a time until you get what you need.

  Thanks,

    Matt

> I use this:
> mpirun -np 1 /home/benelhasa/fox_petsc/build_test/bin/Debug/FoXtroT
> -snes_test_jacobian_view -snes_converged_reason -snes_monitor -ksp_monitor
> -ksp_xmonitor -dm_plex_filename cub_2C3D8_msh.msh -dm_view
> vtk:cub_2C3D8_msh.vtu cub_8C3D8.fxt
>
>
> Thanks,
> Sami,
>
> --
> Dr. Sami BEN ELHAJ SALAH
> Ingénieur de Recherche (CNRS)
> Institut Pprime - ISAE - ENSMA
> Mobile: 06.62.51.26.74
> Email: sami.ben-elhaj-salah at ensma.fr <sami.ben-elhaj-salah at ensma.fr>
> www.samibenelhajsalah.com
> <https://samiben91.github.io/samibenelhajsalah/index.html>
>
>
>
> Le 8 juin 2022 à 16:25, Jed Brown <jed at jedbrown.org> a écrit :
>
> Does the file load in paraview? When I load your *.msh in a tutorial with
> -dm_plex_filename sami.msh -dm_view vtk:sami.vtu, I get this good output.
>
> <sami.vtu><sami.png>
> Sami BEN ELHAJ SALAH <sami.ben-elhaj-salah at ensma.fr> writes:
>
> Hi Jed,
>
> Thank you for your answer.
>
> When I use a ‘’solution.vtu'', I obtain a wrong file.
>
> <?xml version="1.0"?>
> <VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian">
> <UnstructuredGrid>
> <Piece NumberOfPoints="12" NumberOfCells="2">
> <Points>
> <DataArray type="Float64" Name="Position" NumberOfComponents="3"
> format="appended" offset="0" />
> </Points>
> <Cells>
> <DataArray type="Int32" Name="connectivity" NumberOfComponents="1"
> format="appended" offset="292" />
> <DataArray type="Int32" Name="offsets" NumberOfComponents="1"
> format="appended" offset="360" />
> <DataArray type="UInt8" Name="types" NumberOfComponents="1"
> format="appended" offset="372" />
> </Cells>
> <CellData>
> <DataArray type="Int32" Name="Rank" NumberOfComponents="1"
> format="appended" offset="378" />
> </CellData>
> <PointData>
> <DataArray type="Float64" Name="dU_x(null)" NumberOfComponents="3"
> format="appended" offset="390" />
> </PointData>
> </Piece>
> </UnstructuredGrid>
> <AppendedData encoding="raw">
> _ $@$@$@$@$@$@$@$@$@$@$@$@4@$@$@4@$@4 at 4@$@@
> �p�O��=��sT��׽��sT��׽�p�O��=��sT���=��sT��׽�p�O��=��sT���=��sT���=�p�O��=��sT��׽��sT���=o
> _��?�� uP���� uP��o _��?�� uP�?�� uP��o _��?�� uP�?�� uP�?o _��?�� uP����
> uP�?b#�����?�333����333��_#�����?
> �333�?��333��b#�����?(�333�?'�333�?a#�����?�333��>�333�?
> </AppendedData>
> </VTKFile>
>
>
> If I understand your answer, to solve my problem, should just upgrade all
> my software ?
>
> Thanks,
> Sami,
>
>
> --
> Dr. Sami BEN ELHAJ SALAH
> Ingénieur de Recherche (CNRS)
> Institut Pprime - ISAE - ENSMA
> Mobile: 06.62.51.26.74
> Email: sami.ben-elhaj-salah at ensma.fr <sami.ben-elhaj-salah at ensma.fr>
> www.samibenelhajsalah.com <
> https://samiben91.github.io/samibenelhajsalah/index.html>
>
>
>
> Le 8 juin 2022 à 15:37, Jed Brown <jed at jedbrown.org> a écrit :
>
> You're using pretty old versions of all software; I'd recommend upgrading.
> I recommend choosing the file name "solution.vtu" to use the modern
> (non-legacy) format. Does that work for you?
>
> Sami BEN ELHAJ SALAH <sami.ben-elhaj-salah at ensma.fr> writes:
>
> Dear Petsc Developer team,
>
> I solved a linear elastic problem in 3D using a DMPLEX. My system is
> converging, then I would like to write out my solution vector to a vtk file
> where I use unstructured mesh. Currently, I tried two algorithms and I have
> the same result.
>
> 1) Algorithm 1
> err = SNESSolve(_snes, bc_vec_test, solution);
> CHKERRABORT(FOX::Parallel::COMM_WORLD,err);
> PetscViewer vtk;
>
> PetscViewerVTKOpen(FOX::Parallel::COMM_WORLD,"solution.vtk",FILE_MODE_WRITE,&vtk);
>
> VecView(solution,vtk);
> PetscViewerDestroy(&vtk);
>
>
> 2) Algorithm 2
> err = SNESSolve(_snes, bc_vec_test, solution);
> CHKERRABORT(FOX::Parallel::COMM_WORLD,err);
> PetscViewer vtk;
> PetscViewerCreate(FOX::Parallel::COMM_WORLD, &vtk);
> PetscViewerSetType(vtk, PETSCVIEWERVTK);
> PetscViewerFileSetName(vtk, "sol.vtk");
> VecView(solution, vtk);
> PetscViewerDestroy(&vtk);
>
> The result seems correct except for the rotation order of the nodes (see
> the red lines on gmsh and vtk file respectively). Then, I visualized my vtk
> file with paraview, and I remarked that my geometry is not correct and not
> conserved when comparing it with my gmsh file. So, I didn’t understand why
> the rotation order of nodes is not conserved when saving my result to a vtk
> file?
>
> Other information used:
> - gmsh format 2.2
> - Vtk version: 7.1.1
> - Petsc version: 3.13/opt
>
> Below my two files gmsh and vtk:
>
> Gmsh file:
> $MeshFormat
> 2.2 0 8
> $EndMeshFormat
> $Nodes
> 12
> 1 0.0 10.0 10.0
> 2 0.0 0.0 10.0
> 3 0.0 0.0 0.0
> 4 0.0 10.0 0.0
> 5 10.0 10.0 10.0
> 6 10.0 0.0 10.0
> 7 10.0 0.0 0.0
> 8 10.0 10.0 0.0
> 9 20.0 10.0 10.0
> 10 20.0 0.0 10.0
> 11 20.0 0.0 0.0
> 12 20.0 10.0 0.0
> $EndNodes
> $Elements
> 2
> 1 5 2 68 60 1 2 3 4 5 6 7 8
> 2 5 2 68 60 5 6 7 8 9 10 11 12
> $EndElements
>
> Vtk file :
> # vtk DataFile Version 2.0
> Simplicial Mesh Example
> ASCII
> DATASET UNSTRUCTURED_GRID
> POINTS 12 double
> 0.000000e+00 1.000000e+01 1.000000e+01
> 0.000000e+00 0.000000e+00 1.000000e+01
> 0.000000e+00 0.000000e+00 0.000000e+00
> 0.000000e+00 1.000000e+01 0.000000e+00
> 1.000000e+01 1.000000e+01 1.000000e+01
> 1.000000e+01 0.000000e+00 1.000000e+01
> 1.000000e+01 0.000000e+00 0.000000e+00
> 1.000000e+01 1.000000e+01 0.000000e+00
> 2.000000e+01 1.000000e+01 1.000000e+01
> 2.000000e+01 0.000000e+00 1.000000e+01
> 2.000000e+01 0.000000e+00 0.000000e+00
> 2.000000e+01 1.000000e+01 0.000000e+00
> CELLS 2 18
> 8 0 3 2 1 4 5 6 7
> 8 4 7 6 5 8 9 10 11
> CELL_TYPES 2
> 12
> 12
> POINT_DATA 12
> VECTORS dU_x double
> 2.754808e-10 -8.653846e-11 -8.653846e-11
> 2.754808e-10 8.653846e-11 -8.653846e-11
> 2.754808e-10 8.653846e-11 8.653846e-11
> 2.754808e-10 -8.653846e-11 8.653846e-11
> 4.678571e-01 -9.107143e-02 -9.107143e-02
> 4.678571e-01 9.107143e-02 -9.107143e-02
> 4.678571e-01 9.107143e-02 9.107143e-02
> 4.678571e-01 -9.107143e-02 9.107143e-02
> 1.000000e+00 -7.500000e-02 -7.500000e-02
> 1.000000e+00 7.500000e-02 -7.500000e-02
> 1.000000e+00 7.500000e-02 7.500000e-02
> 1.000000e+00 -7.500000e-02 7.500000e-02
>
> Thank you in advance and have a good day !
>
> Sami,
>
> --
> Dr. Sami BEN ELHAJ SALAH
> Ingénieur de Recherche (CNRS)
> Institut Pprime - ISAE - ENSMA
> Mobile: 06.62.51.26.74
> Email: sami.ben-elhaj-salah at ensma.fr
> www.samibenelhajsalah.com <
> https://samiben91.github.io/samibenelhajsalah/index.html>
>
>
>

-- 
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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