[petsc-users] View 3D DMPlex

[Amir]

I tried DMPlexCreateBoxMesh(). It shows points and nodes on the boundary surface. Plus, I do see easily and correctly the interior edge/node inside by clipping the volume mesh. Do you think my dm setup is wrong that I cant see the same using my DAG settings in Paraview.
Thanks
Amir

On Sep 11 2019, at 2:27 am, Matthew Knepley <knepley at gmail.com> wrote:
> On Tue, Sep 10, 2019 at 12:20 PM Amir <mhbaghaei at mail.sjtu.edu.cn (https://link.getmailspring.com/link/D5CB7218-13F0-46E6-9D32-1BEE866C43CA@getmailspring.com/0?redirect=mailto%3Amhbaghaei%40mail.sjtu.edu.cn&recipient=cGV0c2MtdXNlcnNAbWNzLmFubC5nb3Y%3D)> wrote:
>
> >
> >
> > The mesh contains a cube. I tried to change the ordering in cone of dm. In some ordering, in Paraview, I also noticed too many interior edges and saw the interior nodes. I have not yet been able to see the interior edge correctly placed. Do you suggest to output in other format? I do not really know where this misplacing of edges comes from.
>
> How about first using DMPlexCreateBoxMesh(), and seeing if you can visualize it. Then if that works, we can talk about
> inputting your mesh from scratch.
>
> Thanks,
>
> Matt
>
> > PetscInt numPoints[2] = {27, 8};
> > PetscInt coneSize[35] = {8,8,8,8,8,8,8,8, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0};
> > PetscInt cones[64] = { 8, 9, 16, 15, 17, 24, 25, 18,
> > 9, 10,11, 16, 18, 25, 20, 19,
> > 16,11, 12,13, 25, 22, 21, 20,
> > 15,16, 13,14, 24, 23, 22, 25, /////////// Not see the interior node and edge
> > 17,18,25, 24, 26, 33, 34, 27,
> > 18,19,20, 25, 27, 34, 29, 28,
> > 25,20,21, 22, 34, 31, 30, 29,
> > 24,25,22, 23, 33, 32, 31, 34} ;
> > PetscInt cones2[64] = { 8, 15, 16, 9, 17, 18, 25, 24,
> > 9, 16,11, 10, 18, 19, 20, 25, /////////// See the interior node and edge
> > 16,13, 12,11, 25, 20, 21, 22,
> > 15,14, 13,16, 24, 25, 22, 23,
> > 17,18,25, 24, 26, 27, 34, 33,
> > 18,19,20, 25, 27, 28, 29, 34,
> > 25,20,21, 22, 34, 29, 30, 31,
> > 24,25,22, 23, 33, 34, 31, 32} ;
> > PetscInt coneOrientations[64] = {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0};
> > PetscScalar vertexCoords[81] = {0.0,0.0,0.0, 1.0,0.0, 0.0, 2.0,0.0,0.0, 2.0,1.0,0.0, 2.0,2.0, 0.0, 1.0,2.0,0.0,
> > 0.0,2.0,0.0, 0.0,1.0, 0.0, 1.0,1.0,0.0,
> > 0.0,0.0,1.0, 1.0,0.0, 1.0, 2.0,0.0,1.0, 2.0,1.0,1.0, 2.0,2.0, 1.0, 1.0,2.0,1.0,
> > 0.0,2.0,1.0, 0.0,1.0, 1.0, 1.0,1.0,1.0,
> > 0.0,0.0,2.0, 1.0,0.0, 2.0, 2.0,0.0,2.0, 2.0,1.0,2.0, 2.0,2.0, 2.0, 1.0,2.0,2.0,
> > 0.0,2.0,2.0, 0.0,1.0, 2.0, 1.0,1.0,2.0};
> > Thanks
> > Amir
> >
> > ---------- Forwarded Message ---------
> > From: Matthew Knepley <knepley at gmail.com (mailto:knepley at gmail.com)>
> > Subject: Re: [petsc-users] View 3D DMPlex
> > Date: Sep 10 2019, at 9:08 pm
> > To: Amir <mhbaghaei at mail.sjtu.edu.cn (mailto:mhbaghaei at mail.sjtu.edu.cn)>
> > Cc: PETSc <petsc-users at mcs.anl.gov (mailto:petsc-users at mcs.anl.gov)>
> >
> > On Tue, Sep 10, 2019 at 9:00 AM Amir via petsc-users <petsc-users at mcs.anl.gov (mailto:petsc-users at mcs.anl.gov)> wrote:
> > > Hi
> > > I am trying to view a cubic mesh constructed by DMPlex. I noticed that the interior point is not seen in the output VTU file.
> > > It means that I do not see an edge inside the cube. I tried to check some detail of DM using --in_dm_view. The detail does not show any problem. Do you think there is a problem in my vtk output or dm setup.
> >
> >
> > By default, Paraview does not show interior edges. You have to use a filter, like "Extract Edges".
> >
> > Thanks,
> >
> > Matt
> >
> > > Thanks
> > > Amir
> > > DM_0x84000000_0 in 3 dimensions:
> > > 0-cells: 27
> > > 1-cells: 54
> > > 2-cells: 36
> > > 3-cells: 8
> > > Labels:
> > > depth: 4 strata with value/size (0 (27), 1 (54), 2 (36), 3 (8))
> > >
> >
> >
> > --
> > 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/)
> > On Sep 10 2019, at 9:08 pm, Matthew Knepley <knepley at gmail.com (mailto:knepley at gmail.com)> wrote:
> > > On Tue, Sep 10, 2019 at 9:00 AM Amir via petsc-users <petsc-users at mcs.anl.gov (https://link.getmailspring.com/link/CE107FD7-8BE8-492B-98A7-90F4EEAA18F2@getmailspring.com/0?redirect=mailto%3Apetsc-users%40mcs.anl.gov&recipient=a25lcGxleUBnbWFpbC5jb20%3D)> wrote:
> > >
> > > > Hi
> > > > I am trying to view a cubic mesh constructed by DMPlex. I noticed that the interior point is not seen in the output VTU file.
> > > > It means that I do not see an edge inside the cube. I tried to check some detail of DM using --in_dm_view. The detail does not show any problem. Do you think there is a problem in my vtk output or dm setup.
> > >
> > >
> > > By default, Paraview does not show interior edges. You have to use a filter, like "Extract Edges".
> > >
> > > Thanks,
> > >
> > > Matt
> > >
> > > > Thanks
> > > > Amir
> > > > DM_0x84000000_0 in 3 dimensions:
> > > > 0-cells: 27
> > > > 1-cells: 54
> > > > 2-cells: 36
> > > > 3-cells: 8
> > > > Labels:
> > > > depth: 4 strata with value/size (0 (27), 1 (54), 2 (36), 3 (8))
> > > >
> > >
> > >
> > > --
> > > 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/ (https://link.getmailspring.com/link/CE107FD7-8BE8-492B-98A7-90F4EEAA18F2@getmailspring.com/1?redirect=http%3A%2F%2Fwww.cse.buffalo.edu%2F~knepley%2F&recipient=a25lcGxleUBnbWFpbC5jb20%3D)
>
> --
> 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/ (https://link.getmailspring.com/link/D5CB7218-13F0-46E6-9D32-1BEE866C43CA@getmailspring.com/1?redirect=http%3A%2F%2Fwww.cse.buffalo.edu%2F~knepley%2F&recipient=cGV0c2MtdXNlcnNAbWNzLmFubC5nb3Y%3D)
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