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

[Matthew Knepley]

On Sun, Dec 9, 2018 at 7:31 PM Tsung-Hsing Chen <barrydog505 at gmail.com>
wrote:

> Vertex-based is what I want.
> Here I don't think I have created any PetscSection yet.
> Do I need to create the PetscSection,
>

Yes. There is a manual chapter with this in it.


> if I already have a mesh file from gmsh?
>

That is just topology and geometry. It says nothing about data layout.


> or just I simply use DMPlexGetConeSection() to get vertex-based vector?
>

That is a Section which describes the layout of topology data.

  Thanks,

     Matt


> 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/>
>>
>

-- 
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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