[petsc-users] ex12 with Neumann BC

[Matthew Knepley]

On Thu, Oct 3, 2013 at 4:48 AM, Olivier Bonnefon <
olivier.bonnefon at avignon.inra.fr> wrote:

>  Hello,
>
> Thank you for your answer, I'm now able to run the ex12.c with Neumann BC
> (options -bc_type neumann   -interpolate 1).
>
> I have adapted the ex12.c for the 2D-system:
>
> -\Delta u +u =0
>
> It consists in adapting the fem->f0Funcs[0] function and adding the
> jacobian function fem->g0Funcs[0].
> My implementation works for Dirichlet BC.
> With Neumann BC(with options -bc_type neumann   -interpolate 1), the line
> search failed. I think my jacobian functions are corrects, because the
> option "-snes_mf_operator" leads to the same behavior.
>

Sorry this took me a long time. Do you mean that it converges with -snes_mf?


> Do you know what I have missed ?
> In Neumann case, Where is added the 1d-integral along \delta \Omega ?
>

You are correct that I am not doing the correct integral for the Jacobian.
I will put it in soon. That
is why it should work with the FD approximation since the residual is
correct.

  Thanks,

     Matt


> Thanks,
> Olivier Bonnefon
>
>
>
>
>
>
>
> On 09/26/2013 06:54 PM, Matthew Knepley wrote:
>
> On Thu, Sep 26, 2013 at 6:04 AM, Olivier Bonnefon <
> olivier.bonnefon at avignon.inra.fr> wrote:
>
>> Hello,
>>
>> I have implemented my own system from ex12.c. It works with Dirichlet BC,
>> but failed with Neumann one.
>>
>> So, I'm came back to the example /src/snes/example/tutorial/ex12.c, and I
>> tried with Neumann BC:
>>
>> ./ex12 -bc_type NEUMANN
>>
>
>  Here is the full list of tests I run (just checked that it passes in
> 'next'):
>
>
> https://bitbucket.org/petsc/petsc/src/f34a81fe8510aa025c9247a5b14f0fe30e3c0bed/config/builder.py?at=master#cl-175
>
>  Make sure you use an interpolated mesh with Neumann conditions since you
> need faces.
>
>     Matt
>
>
>> This leads to the following crach:
>>
>> [0]PETSC ERROR: --------------------- Error Message
>> ------------------------------------
>> [0]PETSC ERROR: No support for this operation for this object type!
>> [0]PETSC ERROR: Unsupported number of vertices 0 in cell 8 for element
>> geometry computation!
>> [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [0]PETSC ERROR: Petsc Release Version 3.4.2, Jul, 02, 2013
>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>> [0]PETSC ERROR: See docs/index.html for manual pages.
>> [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [0]PETSC ERROR: ./ex12 on a arch-linux2-c-debug named pcbiom38 by
>> olivierb Thu Sep 26 14:53:32 2013
>> [0]PETSC ERROR: Libraries linked from
>> /home/olivierb/SOFT/petsc-3.4.2/arch-linux2-c-debug/lib
>> [0]PETSC ERROR: Configure run at Thu Sep 26 14:44:42 2013
>> [0]PETSC ERROR: Configure options --with-debugging=1 --download-fiat
>> --download-scientificpython --download-generator --download-triangle
>> --download-ctetgen --download-chaco --download-netcdf --download-hdf5
>> [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [0]PETSC ERROR: DMPlexComputeCellGeometry() line 732 in
>> /home/olivierb/SOFT/petsc-3.4.2/src/dm/impls/plex/plexgeometry.c
>> [0]PETSC ERROR: DMPlexComputeResidualFEM() line 558 in
>> /home/olivierb/SOFT/petsc-3.4.2/src/dm/impls/plex/plexfem.c
>> [0]PETSC ERROR: SNESComputeFunction_DMLocal() line 75 in
>> /home/olivierb/SOFT/petsc-3.4.2/src/snes/utils/dmlocalsnes.c
>> [0]PETSC ERROR: SNESComputeFunction() line 1988 in
>> /home/olivierb/SOFT/petsc-3.4.2/src/snes/interface/snes.c
>> [0]PETSC ERROR: SNESSolve_NEWTONLS() line 162 in
>> /home/olivierb/SOFT/petsc-3.4.2/src/snes/impls/ls/ls.c
>> [0]PETSC ERROR: SNESSolve() line 3636 in
>> /home/olivierb/SOFT/petsc-3.4.2/src/snes/interface/snes.c
>> [0]PETSC ERROR: main() line 582 in
>> "unknowndirectory/"/home/olivierb/solvers/trunk/SandBox/PETSC/LANDSCAPE/REF/ex12.c
>> --------------------------------------------------------------------------
>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>> with errorcode 56.
>>
>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>> You may or may not see output from other processes, depending on
>> exactly when Open MPI kills them.
>> --------------------------------------------------------------------------
>>
>> With Gbd, I saw that DMPlexGetConeSize is 0 for the last point.
>>
>> Do I have forget a step to use Neumann BC ?
>>
>> Thanks
>> Olivier Bonnefon
>>
>> --
>> Olivier Bonnefon
>> INRA PACA-Avignon, Unité BioSP
>> Tel: +33 (0)4 32 72 21 58 <%2B33%20%280%294%2032%2072%2021%2058>
>>
>>
>
>
>  --
> 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
>
>
>
> --
> Olivier Bonnefon
> INRA PACA-Avignon, Unité BioSP
> Tel: +33 (0)4 32 72 21 58
>
>


-- 
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
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