[petsc-users] Writing VTK output

Wed Jun 8 09:25:51 CDT 2022

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.

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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@           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
> Ing?nieur 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 ? 15:37, Jed Brown <jed at jedbrown.org> a ?crit :
>> 
>> 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
>>> Ing?nieur 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>