[petsc-users] Writing VTK output
Sami BEN ELHAJ SALAH
sami.ben-elhaj-salah at ensma.fr
Wed Jun 8 09:14:13 CDT 2022
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
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 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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