<div dir="ltr"><div dir="ltr">On Wed, Jun 8, 2022 at 11:24 AM Sami BEN ELHAJ SALAH <<a href="mailto:sami.ben-elhaj-salah@ensma.fr">sami.ben-elhaj-salah@ensma.fr</a>> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;">Yes, the file "sami.vtu" is loaded correctly in paraview and I have the good output like you.<div><br></div><div>In my code, I tried with the same command given in your last answer and I still have the wrong .vtu file.</div></div></blockquote><div><br></div><div>Hi Sami,</div><div><br></div><div>What do you mean by wrong?</div><div><br></div><div>Can you just use the simple procedure:</div><div><br></div><div> PetscCall(DMCreate(comm, dm));<br> PetscCall(DMSetType(*dm, DMPLEX));<br> PetscCall(DMSetFromOptions(*dm));<br> PetscCall(DMViewFromOptions(*dm, NULL, "-dm_view"));<br></div><div><br></div><div>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.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;"><div>I use this:<br><div>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</div><div><br></div><div><br></div><div>Thanks,</div><div>Sami,</div><div><br><div>
<div dir="auto" style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><div dir="auto" style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><div dir="auto" style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><div dir="auto" style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">--</div><div dir="auto" style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">Dr. Sami BEN ELHAJ SALAH<br>Ingénieur de Recherche (CNRS)<br>Institut Pprime - ISAE - ENSMA<br>Mobile: 06.62.51.26.74<br><a href="mailto:sami.ben-elhaj-salah@ensma.fr" target="_blank">Email: sami.ben-elhaj-salah@ensma.fr</a></div><div dir="auto" style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><a href="https://samiben91.github.io/samibenelhajsalah/index.html" target="_blank">www.samibenelhajsalah.com</a><br><br><br></div></div></div></div>
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<div><br><blockquote type="cite"><div>Le 8 juin 2022 à 16:25, Jed Brown <<a href="mailto:jed@jedbrown.org" target="_blank">jed@jedbrown.org</a>> a écrit :</div><br><div><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">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.</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span id="gmail-m_2080728392201155584cid:9141E41F-766F-4335-99D2-04F631D6CB6F"><sami.vtu></span><span id="gmail-m_2080728392201155584cid:0CECECD3-7616-4FB0-A886-99D8B7F7FC11"><sami.png></span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Sami BEN ELHAJ SALAH <</span><a href="mailto:sami.ben-elhaj-salah@ensma.fr" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">sami.ben-elhaj-salah@ensma.fr</a><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">> writes:</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><blockquote type="cite" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">Hi Jed,<br><br>Thank you for your answer.<br><br>When I use a ‘’solution.vtu'', I obtain a wrong file.<span> </span><br><br><?xml version="1.0"?><br><VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian"><br><UnstructuredGrid><br><Piece NumberOfPoints="12" NumberOfCells="2"><br><Points><br><DataArray type="Float64" Name="Position" NumberOfComponents="3" format="appended" offset="0" /><br></Points><br><Cells><br><DataArray type="Int32" Name="connectivity" NumberOfComponents="1" format="appended" offset="292" /><br><DataArray type="Int32" Name="offsets" NumberOfComponents="1" format="appended" offset="360" /><br><DataArray type="UInt8" Name="types" NumberOfComponents="1" format="appended" offset="372" /><br></Cells><br><CellData><br><DataArray type="Int32" Name="Rank" NumberOfComponents="1" format="appended" offset="378" /><br></CellData><br><PointData><br><DataArray type="Float64" Name="dU_x(null)" NumberOfComponents="3" format="appended" offset="390" /><br></PointData><br></Piece><br></UnstructuredGrid><br><AppendedData encoding="raw"><br>_ $@$@$@$@$@$@$@$@$@$@$@$@4@$@$@4@$@4@4@$@@ <span style="white-space:pre-wrap"> </span><br> �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��_#�����?<span style="white-space:pre-wrap"> </span>�333�?��333��b#�����?(�333�?'�333�?a#�����?�333��>�333�?<br></AppendedData><br></VTKFile><br><br><br>If I understand your answer, to solve my problem, should just upgrade all my software ?<br><br>Thanks,<br>Sami,<br><br><br>--<br>Dr. Sami BEN ELHAJ SALAH<br>Ingénieur de Recherche (CNRS)<br>Institut Pprime - ISAE - ENSMA<br>Mobile: 06.62.51.26.74<br><a href="mailto:sami.ben-elhaj-salah@ensma.fr" target="_blank">Email: sami.ben-elhaj-salah@ensma.fr</a><br><a href="http://www.samibenelhajsalah.com/" target="_blank">www.samibenelhajsalah.com</a><span> </span><<a href="https://samiben91.github.io/samibenelhajsalah/index.html" target="_blank">https://samiben91.github.io/samibenelhajsalah/index.html</a>><br><br><br><br><blockquote type="cite">Le 8 juin 2022 à 15:37, Jed Brown <<a href="mailto:jed@jedbrown.org" target="_blank">jed@jedbrown.org</a>> a écrit :<br><br>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?<br><br>Sami BEN ELHAJ SALAH <<a href="mailto:sami.ben-elhaj-salah@ensma.fr" target="_blank">sami.ben-elhaj-salah@ensma.fr</a>> writes:<br><br><blockquote type="cite">Dear Petsc Developer team,<br><br>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.<br><br>1) Algorithm 1<span> </span><br>err = SNESSolve(_snes, bc_vec_test, solution);<br>CHKERRABORT(FOX::Parallel::COMM_WORLD,err);<br>PetscViewer vtk;<span> </span><br>PetscViewerVTKOpen(FOX::Parallel::COMM_WORLD,"solution.vtk",FILE_MODE_WRITE,&vtk);<span> </span><br>VecView(solution,vtk);<br>PetscViewerDestroy(&vtk);<br><br><br>2) Algorithm 2<br>err = SNESSolve(_snes, bc_vec_test, solution);<br>CHKERRABORT(FOX::Parallel::COMM_WORLD,err);<br>PetscViewer vtk;<span> </span><br>PetscViewerCreate(FOX::Parallel::COMM_WORLD, &vtk);<span> </span><br>PetscViewerSetType(vtk, PETSCVIEWERVTK);<span> </span><br>PetscViewerFileSetName(vtk, "sol.vtk");<span> </span><br>VecView(solution, vtk);<span> </span><br>PetscViewerDestroy(&vtk);<br><br>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?<br><br>Other information used:<br>- gmsh format 2.2<span> </span><br>- Vtk version: 7.1.1<br>- Petsc version: 3.13/opt<span> </span><br><br>Below my two files gmsh and vtk:<br><br>Gmsh file:<br>$MeshFormat<br>2.2 0 8<br>$EndMeshFormat<br>$Nodes<br>12<br>1 0.0 10.0 10.0<br>2 0.0 0.0 10.0<br>3 0.0 0.0 0.0<br>4 0.0 10.0 0.0<br>5 10.0 10.0 10.0<br>6 10.0 0.0 10.0<br>7 10.0 0.0 0.0<br>8 10.0 10.0 0.0<br>9 20.0 10.0 10.0<br>10 20.0 0.0 10.0<br>11 20.0 0.0 0.0<br>12 20.0 10.0 0.0<br>$EndNodes<br>$Elements<br>2<br>1 5 2 68 60 1 2 3 4 5 6 7 8<br>2 5 2 68 60 5 6 7 8 9 10 11 12<br>$EndElements<br><br>Vtk file :<br># vtk DataFile Version 2.0<br>Simplicial Mesh Example<br>ASCII<br>DATASET UNSTRUCTURED_GRID<br>POINTS 12 double<br>0.000000e+00 1.000000e+01 1.000000e+01<br>0.000000e+00 0.000000e+00 1.000000e+01<br>0.000000e+00 0.000000e+00 0.000000e+00<br>0.000000e+00 1.000000e+01 0.000000e+00<br>1.000000e+01 1.000000e+01 1.000000e+01<br>1.000000e+01 0.000000e+00 1.000000e+01<br>1.000000e+01 0.000000e+00 0.000000e+00<br>1.000000e+01 1.000000e+01 0.000000e+00<br>2.000000e+01 1.000000e+01 1.000000e+01<br>2.000000e+01 0.000000e+00 1.000000e+01<br>2.000000e+01 0.000000e+00 0.000000e+00<br>2.000000e+01 1.000000e+01 0.000000e+00<br>CELLS 2 18<br>8 0 3 2 1 4 5 6 7<br>8 4 7 6 5 8 9 10 11<br>CELL_TYPES 2<br>12<br>12<br>POINT_DATA 12<br>VECTORS dU_x double<br>2.754808e-10 -8.653846e-11 -8.653846e-11<br>2.754808e-10 8.653846e-11 -8.653846e-11<br>2.754808e-10 8.653846e-11 8.653846e-11<br>2.754808e-10 -8.653846e-11 8.653846e-11<br>4.678571e-01 -9.107143e-02 -9.107143e-02<br>4.678571e-01 9.107143e-02 -9.107143e-02<br>4.678571e-01 9.107143e-02 9.107143e-02<br>4.678571e-01 -9.107143e-02 9.107143e-02<br>1.000000e+00 -7.500000e-02 -7.500000e-02<br>1.000000e+00 7.500000e-02 -7.500000e-02<br>1.000000e+00 7.500000e-02 7.500000e-02<br>1.000000e+00 -7.500000e-02 7.500000e-02<br><br>Thank you in advance and have a good day !<br><br>Sami,<br><br>--<br>Dr. Sami BEN ELHAJ SALAH<br>Ingénieur de Recherche (CNRS)<br>Institut Pprime - ISAE - ENSMA<br>Mobile: 06.62.51.26.74<br>Email: <a href="mailto:sami.ben-elhaj-salah@ensma.fr" target="_blank">sami.ben-elhaj-salah@ensma.fr</a><br><a href="http://www.samibenelhajsalah.com" target="_blank">www.samibenelhajsalah.com</a> <<a href="https://samiben91.github.io/samibenelhajsalah/index.html" target="_blank">https://samiben91.github.io/samibenelhajsalah/index.html</a>></blockquote></blockquote></blockquote></div></blockquote></div><br></div></div></div></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>