[petsc-users] View 3D DMPlex

[Matthew Knepley]

On Tue, Sep 10, 2019 at 12:20 PM Amir <mhbaghaei at mail.sjtu.edu.cn> 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
> [image: Sent from Mailspring]
>
> ---------- Forwarded Message ---------
>
> From: Matthew Knepley <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>
> Cc: PETSc <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> 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> 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/ <http://www.cse.buffalo.edu/~knepley/>
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