<div dir="ltr">On Thu, Oct 3, 2013 at 4:48 AM, Olivier Bonnefon <span dir="ltr"><<a href="mailto:olivier.bonnefon@avignon.inra.fr" target="_blank">olivier.bonnefon@avignon.inra.fr</a>></span> wrote:<br><div class="gmail_extra">
<div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div>Hello,<br>
<br>
Thank you for your answer, I'm now able to run the ex12.c with
Neumann BC (options -bc_type neumann -interpolate 1).<br>
<br>
I have adapted the ex12.c for the 2D-system:<br>
<br>
-\Delta u +u =0<br>
<br>
It consists in adapting the fem->f0Funcs[0] function and adding
the jacobian function fem->g0Funcs[0].<br>
My implementation works for Dirichlet BC.<br>
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.<br></div></div></blockquote><div><br></div><div>Sorry this took me a long time. Do you mean that it converges with -snes_mf?</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Do you know what I have missed ?<br>
In Neumann case, Where is added the 1d-integral along \delta
\Omega ?<br></div></div></blockquote><div><br></div><div>You are correct that I am not doing the correct integral for the Jacobian. I will put it in soon. That</div><div>is why it should work with the FD approximation since the residual is correct.</div>
<div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div bgcolor="#FFFFFF" text="#000000">
<div>
Thanks,<br>
Olivier Bonnefon<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
On 09/26/2013 06:54 PM, Matthew Knepley wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">On Thu, Sep 26, 2013 at 6:04 AM, Olivier Bonnefon <span dir="ltr"><<a href="mailto:olivier.bonnefon@avignon.inra.fr" target="_blank">olivier.bonnefon@avignon.inra.fr</a>></span>
wrote:<br>
<div class="gmail_extra">
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">Hello,<br>
<br>
I have implemented my own system from ex12.c. It works
with Dirichlet BC, but failed with Neumann one.<br>
<br>
So, I'm came back to the example
/src/snes/example/tutorial/ex12.c, and I tried with
Neumann BC:<br>
<br>
./ex12 -bc_type NEUMANN<br>
</blockquote>
<div><br>
</div>
<div>Here is the full list of tests I run (just checked that
it passes in 'next'):</div>
<div><br>
</div>
<div> <a href="https://bitbucket.org/petsc/petsc/src/f34a81fe8510aa025c9247a5b14f0fe30e3c0bed/config/builder.py?at=master#cl-175" target="_blank">https://bitbucket.org/petsc/petsc/src/f34a81fe8510aa025c9247a5b14f0fe30e3c0bed/config/builder.py?at=master#cl-175</a></div>
<div><br>
</div>
<div>Make sure you use an interpolated mesh with Neumann
conditions since you need faces.</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">This
leads to the following crach:<br>
<br>
[0]PETSC ERROR: --------------------- Error Message
------------------------------------<br>
[0]PETSC ERROR: No support for this operation for this
object type!<br>
[0]PETSC ERROR: Unsupported number of vertices 0 in cell 8
for element geometry computation!<br>
[0]PETSC ERROR: ------------------------------------------------------------------------<br>
[0]PETSC ERROR: Petsc Release Version 3.4.2, Jul, 02, 2013<br>
[0]PETSC ERROR: See docs/changes/index.html for recent
updates.<br>
[0]PETSC ERROR: See docs/faq.html for hints about trouble
shooting.<br>
[0]PETSC ERROR: See docs/index.html for manual pages.<br>
[0]PETSC ERROR: ------------------------------------------------------------------------<br>
[0]PETSC ERROR: ./ex12 on a arch-linux2-c-debug named
pcbiom38 by olivierb Thu Sep 26 14:53:32 2013<br>
[0]PETSC ERROR: Libraries linked from
/home/olivierb/SOFT/petsc-3.4.2/arch-linux2-c-debug/lib<br>
[0]PETSC ERROR: Configure run at Thu Sep 26 14:44:42 2013<br>
[0]PETSC ERROR: Configure options --with-debugging=1
--download-fiat --download-scientificpython
--download-generator --download-triangle
--download-ctetgen --download-chaco --download-netcdf
--download-hdf5<br>
[0]PETSC ERROR: ------------------------------------------------------------------------<br>
[0]PETSC ERROR: DMPlexComputeCellGeometry() line 732 in
/home/olivierb/SOFT/petsc-3.4.2/src/dm/impls/plex/plexgeometry.c<br>
[0]PETSC ERROR: DMPlexComputeResidualFEM() line 558 in
/home/olivierb/SOFT/petsc-3.4.2/src/dm/impls/plex/plexfem.c<br>
[0]PETSC ERROR: SNESComputeFunction_DMLocal() line 75 in
/home/olivierb/SOFT/petsc-3.4.2/src/snes/utils/dmlocalsnes.c<br>
[0]PETSC ERROR: SNESComputeFunction() line 1988 in
/home/olivierb/SOFT/petsc-3.4.2/src/snes/interface/snes.c<br>
[0]PETSC ERROR: SNESSolve_NEWTONLS() line 162 in
/home/olivierb/SOFT/petsc-3.4.2/src/snes/impls/ls/ls.c<br>
[0]PETSC ERROR: SNESSolve() line 3636 in
/home/olivierb/SOFT/petsc-3.4.2/src/snes/interface/snes.c<br>
[0]PETSC ERROR: main() line 582 in
"unknowndirectory/"/home/olivierb/solvers/trunk/SandBox/PETSC/LANDSCAPE/REF/ex12.c<br>
--------------------------------------------------------------------------<br>
MPI_ABORT was invoked on rank 0 in communicator
MPI_COMM_WORLD<br>
with errorcode 56.<br>
<br>
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI
processes.<br>
You may or may not see output from other processes,
depending on<br>
exactly when Open MPI kills them.<br>
--------------------------------------------------------------------------<br>
<br>
With Gbd, I saw that DMPlexGetConeSize is 0 for the last
point.<br>
<br>
Do I have forget a step to use Neumann BC ?<br>
<br>
Thanks<span><font color="#888888"><br>
Olivier Bonnefon<br>
<br>
-- <br>
Olivier Bonnefon<br>
INRA PACA-Avignon, Unité BioSP<br>
Tel: <a href="tel:%2B33%20%280%294%2032%2072%2021%2058" value="+33432722158" target="_blank">+33 (0)4 32 72
21 58</a><br>
<br>
</font></span></blockquote>
</div>
<br>
<br clear="all"><span class="HOEnZb"><font color="#888888">
<div><br>
</div>
-- <br>
What most experimenters take for granted before they begin
their experiments is infinitely more interesting than any
results to which their experiments lead.<br>
-- Norbert Wiener
</font></span></div><span class="HOEnZb"><font color="#888888">
</font></span></div><span class="HOEnZb"><font color="#888888">
</font></span></blockquote><span class="HOEnZb"><font color="#888888">
<br>
<br>
<pre cols="72">--
Olivier Bonnefon
INRA PACA-Avignon, Unité BioSP
Tel: <a href="tel:%2B33%20%280%294%2032%2072%2021%2058" value="+33432722158" target="_blank">+33 (0)4 32 72 21 58</a></pre>
</font></span></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener
</div></div>