[petsc-users] Writing VTK output

Wed Jun 8 10:24:15 CDT 2022

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.
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
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 <mailto: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
>> www.samibenelhajsalah.com <http://www.samibenelhajsalah.com/> <https://samiben91.github.io/samibenelhajsalah/index.html <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>

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