[petsc-users] ex12 with Neumann BC
Olivier Bonnefon
olivier.bonnefon at avignon.inra.fr
Fri Oct 11 09:01:38 CDT 2013
Hello,
I now able to simulate a two fields non-linear system with fem, and I
get a good speed up with Dirichlet BC. Thanks for your help.
About Neumann BC, I need to add "-ksp_type fgmres", else the line search
failed (even with -snes_mf).
More over, the Neumann version works only in sequential. Indeed, in
parallel, the boundary conditions are applied inside the domain. I guess
it is because the label are automatically add after the mesh
partitioning. This problem doesn't appear in ex12 because there is a
test in the plugin function, but it is not possible to do the same thing
with a complex shape. I don't know what it must be done.
In Neumann case, the 1D-integral apears only in the residual part (ie
the right side hand of the system). Is it done in the
FEMIntegrateBdResidualBatch function ?
Thanks
Olivier B
On 10/10/2013 02:37 AM, Matthew Knepley wrote:
> On Thu, Oct 3, 2013 at 4:48 AM, Olivier Bonnefon
> <olivier.bonnefon at avignon.inra.fr
> <mailto: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
>> <mailto: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
>> <tel:%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 <tel:%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
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