[petsc-users] How to output VTK file with Vec associating with DMPLEX

[Tsung-Hsing Chen]

Vertex-based is what I want.
Here I don't think I have created any PetscSection yet.
Do I need to create the PetscSection, if I already have a mesh file from
gmsh?
or just I simply use DMPlexGetConeSection() to get vertex-based vector?

Thanks,
Barry


Matthew Knepley <knepley at gmail.com> 於 2018年12月10日 週一 上午7:27寫道：

> On Sun, Dec 9, 2018 at 5:47 PM Tsung-Hsing Chen via petsc-users <
> petsc-users at mcs.anl.gov> wrote:
>
>> Hi,
>> I want to output a VTK file containing Vec which associate with DMPLEX,
>> but I keep getting some errors.
>>
>
> The really easy way is to put
>
>   ierr = VecViewFromOptions(x, NULL, "-myvec_view");CHKERRQ(ierr);
>
> in your code and then give
>
>   -myvec_view vtk:sol.vtk
>
> on the command line.
>
>
>> I use PetscViewerVTKOpen() to create the vtk file.
>> Then I saw many examples just use DMCreateGlobalVector() to create the
>> Vec associate with DM.
>> However, almost all of them aren't DMPLEX but are DMDA.
>> I don't know whether it will cause some problems.
>> These is what I write:
>>
>
> 1) ALWAYS check return values. Your VecSetValue is failing.
>
> 2) VTK can only display two kinds of information, vertex-based and
> cell-based. DMDA only allows vertex based
>     information in Vecs. Since DMPLEX allows any kind of distribution,
> when we output VTK we need to determine
>     what kind of vector we have, vertex-based or cell-based. Here I cannot
> determine it, probably because your
>     PetscSection is not setup correctly. How is data supposed to be laid
> out on the Plex?
>
>   Thanks,
>
>      Matt
>
>
>>   PetscViewerCreate(PETSC_COMM_WORLD, &viewer);
>>   PetscViewerVTKOpen(PETSC_COMM_WORLD, "vtk_output_test.vtk",
>> FILE_MODE_WRITE, &viewer);
>>   DMCreateGlobalVector(dm, &x);
>>   VecSetValue();   //Set value for x
>>   VecView(x, viewer);
>>
>> Here is the error output:
>> [0]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [0]PETSC ERROR: Argument out of range
>> [0]PETSC ERROR: Out of range index value 1 maximum 0
>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [0]PETSC ERROR: Petsc Release Version 3.10.2, unknown
>> [0]PETSC ERROR: ./test3 on a arch-linux2-c-debug named barry-PhysioMech
>> by barry Mon Dec 10 05:52:19 2018
>> [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
>> --with-fc=gfortran --download-mpich --download-fblaslapack --download-mumps
>> --download-scalapack --download-ctetgen
>> [0]PETSC ERROR: #3 VecSetValues_Seq() line 726 in
>> /home/barry/petsc/src/vec/vec/impls/seq/bvec2.c
>> [0]PETSC ERROR: #4 VecSetValues() line 856 in
>> /home/barry/petsc/src/vec/vec/interface/rvector.c
>>
>> [0]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [0]PETSC ERROR: Invalid argument
>> [0]PETSC ERROR: Could not classify input Vec for VTK
>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [0]PETSC ERROR: Petsc Release Version 3.10.2, unknown
>> [0]PETSC ERROR: ./test3 on a arch-linux2-c-debug named barry-PhysioMech
>> by barry Mon Dec 10 05:52:19 2018
>> [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
>> --with-fc=gfortran --download-mpich --download-fblaslapack --download-mumps
>> --download-scalapack --download-ctetgen
>> [0]PETSC ERROR: #17 DMPlexGetFieldType_Internal() line 134 in
>> /home/barry/petsc/src/dm/impls/plex/plex.c
>> [0]PETSC ERROR: #18 VecView_Plex_Local_VTK() line 294 in
>> /home/barry/petsc/src/dm/impls/plex/plex.c
>> [0]PETSC ERROR: #19 VecView_Plex_Local() line 335 in
>> /home/barry/petsc/src/dm/impls/plex/plex.c
>> [0]PETSC ERROR: #20 VecView_Plex() line 382 in
>> /home/barry/petsc/src/dm/impls/plex/plex.c
>> [0]PETSC ERROR: #21 VecView() line 590 in
>> /home/barry/petsc/src/vec/vec/interface/vector.c
>>
>> I think the first part of the error comes from VecSetValue(), but I don't
>> know how to fix it.
>> And I totally don't know what its mean in the second part of the error.
>>
>> Thank you,
>> Barry
>>
>
>
> --
> 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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