<div><br><br>---------------- Forwarded Message ----------------<br>From:
Matthew Knepley <knepley@gmail.com><br>Date: Wed, Jul 21, 2010 09:50
PM<br>Subject: Re: [petsc-users] TSDefaultComputeJacobian<br>To: PETSc users
list <petsc-users@mcs.anl.gov><br><br><span><span><p>Yes, you have setup
the Jacobian function, but you never setup the residual function, which</p>
<div>is what the error is complaining
about.<br><br>-----------------------------------------<br><br><br>Could you
please give me some suggestions about how to setup residual function? Is there
some example?<br><br><br><br><br></div>
<div><br></div>
<div> Matt<br><br><div class="gmail_quote">On Thu, Jul 22, 2010 at
11:43 AM, Xuan YU <span dir=""><<a href="#">xxy113@psu.edu</a>></span>
wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex;
border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div
style="word-wrap: break-word;">
<br><div>
<br><div>Begin forwarded message:</div>
<br><blockquote type="">
<div>
<div style="margin: 0px;">
<font style="font: 12px Helvetica; color: rgb(0, 0, 0);" size="3"
color="#000000" face="Helvetica"><b>From: </b></font><font style="font: 12px
Helvetica;" size="3" face="Helvetica">Jed Brown <<a href="#"
target="">jed@59A2.org</a>></font>
</div>
<div style="margin: 0px;">
<font style="font: 12px Helvetica; color: rgb(0, 0, 0);" size="3"
color="#000000" face="Helvetica"><b>Date: </b></font><font style="font: 12px
Helvetica;" size="3" face="Helvetica">July 21, 2010 8:04:17 PM EDT</font>
</div>
<div style="margin: 0px;">
<font style="font: 12px Helvetica; color: rgb(0, 0, 0);" size="3"
color="#000000" face="Helvetica"><b>To: </b></font><font style="font: 12px
Helvetica;" size="3" face="Helvetica">Xuan YU <<a href="#"
target="">xxy113@psu.edu</a>>, PETSc users list <<a href="#"
target="">petsc-users@mcs.anl.gov</a>></font>
</div>
<div style="margin: 0px;">
<font style="font: 12px Helvetica; color: rgb(0, 0, 0);" size="3"
color="#000000" face="Helvetica"><b>Subject: </b></font><font style="font: 12px
Helvetica;" size="3" face="Helvetica"><b>Re: [petsc-users]
TSDefaultComputeJacobian</b></font>
</div>
<div style="margin: 0px; min-height: 14px;"><br></div> </div>
<div>On Wed, 21 Jul 2010 19:52:23 -0400, Xuan YU <<a href="#"
target="">xxy113@psu.edu</a>> wrote:<br><blockquote type="">Hi,<br>
</blockquote>
<blockquote type=""><br></blockquote>
<blockquote type="">In SNES, Petsc can compute Jacobian by:<br>
</blockquote>
<blockquote type=""><br></blockquote>
<blockquote type="">
ierr = <br>
</blockquote>
<blockquote type="">SNESSetJacobian <br>
</blockquote>
<blockquote
type="">(snes,J,J,SNESDefaultComputeJacobian,PETSC_NULL);CHKERRQ(ierr);<br>
</blockquote>
<blockquote type=""><br></blockquote>
<blockquote type="">How about TS? I don't want to provide Jacobian function by
myself, but <br>
</blockquote>
<blockquote type="">I didn't find something like TSDefaultComputeJacobian.<br>
</blockquote>
<br>You can use -snes_fd (or -snes_mf or -snes_mf_operator) with TS.<br>
Programmatically,<br><br> TSGetSNES(ts,&snes);<br>
</div>
</blockquote>
<blockquote
type=""><div> SNESSetJacobian(snes,A,B,SNESDefaultComputeJacobian,ts);<br><br>
</div></blockquote>
<div><br></div>
<div>I have already tried this function.</div>
<div><br></div>
<div>I want to use <span style="font-size: 15px;">Finite Difference Jacobian Approximations</span>
</div>
<div><br></div>
<div>So, before I call the function: MatGetColoring(J,MATCOLORINGSL,&iscoloring);CHKERRQ(ierr); I should assemble J. I tried to use SNESComputeJacobian(snes,x,&J,&J,&flag) to assemble J.</div>
<div><br></div>
<div>Here is the code</div>
<div><br></div>
<div><br></div>
<div><br></div>
<div>
<div> ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,N,N,10,PETSC_NULL,&J);CHKERRQ(ierr);</div>
<div> ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);</div>
<div> ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);</div>
<div> ierr = TSMonitorSet(ts,Monitor,&appctx,PETSC_NULL);CHKERRQ(ierr);</div>
<div> ierr = TSSetSolution(ts,CV_Y);CHKERRQ(ierr);</div>
<div> ierr = TSSetRHSFunction(ts,f,&appctx);CHKERRQ(ierr);</div>
<div> ierr = TSSetType(ts,TSBEULER);CHKERRQ(ierr);</div>
<div> ierr = TSGetSNES(ts,&ts_snes);</div>
<div> ierr= SNESSetJacobian(ts_snes,J,J,SNESDefaultComputeJacobian,PETSC_NULL);CHKERRQ(ierr);</div>
<div> MatStructure flag;</div>
<div> ierr = SNESComputeJacobian(ts_snes,CV_Y,&J,&J,&flag);CHKERRQ(ierr);</div>
<div> ierr = MatGetColoring(J,MATCOLORINGSL,&iscoloring);CHKERRQ(ierr);</div>
<div> ierr = MatFDColoringCreate(J,iscoloring,&matfdcoloring);CHKERRQ(ierr);</div>
<div> ISColoringDestroy(iscoloring);</div>
<div><br></div>
<div> ierr = MatFDColoringSetFunction(matfdcoloring,(PetscErrorCode (*)(void))f,(void*)&appctx);CHKERRQ(ierr);</div>
<div> ierr = MatFDColoringSetFromOptions(matfdcoloring);CHKERRQ(ierr);</div>
<div> ierr = TSSetRHSJacobian(ts,J,J,TSDefaultComputeJacobianColor,matfdcoloring);</div>
<div><br></div>
</div>But I got the error:</div>
<div>
<div>[0]PETSC ERROR: --------------------- Error Message ------------------------------------</div>
<div>[0]PETSC ERROR: Object is in wrong state!</div>
<div>[0]PETSC ERROR: Must call SNESSetFunction() before SNESComputeFunction(), likely called from SNESSolve().!</div>
<div>[0]PETSC ERROR: ------------------------------------------------------------------------</div>
<div>[0]PETSC ERROR: Petsc Development HG revision: fdc7be12de37b8a400b6e561de9850bcc7e79f4f HG Date: Fri Jul 02 21:17:36 2010 -0500</div>
<div>[0]PETSC ERROR: See docs/changes/index.html for recent updates.</div>
<div>[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.</div>
<div>[0]PETSC ERROR: See docs/index.html for manual pages.</div>
<div>
[0]PETSC ERROR: ------------------------------------------------------------------------</div>
<div>[0]PETSC ERROR: ./pihm on a arch-linu named <a href="http://kernighan.aset.psu.edu" target="" onclick="window.open('http://kernighan.aset.psu.edu');return false;">kernighan.aset.psu.edu</a> by xxy113 Wed Jul 21 21:35:01 2010</div>
<div>[0]PETSC ERROR: Libraries linked from /gpfs/home/xxy113/soft/petsc-dev/arch-linux-gnu-c-debug/lib</div>
<div>[0]PETSC ERROR: Configure run at Sun Jul 4 14:09:16 2010</div>
<div>[0]PETSC ERROR: Configure options --download-f-blas-lapack=1 --download-mpich=1</div>
<div>[0]PETSC ERROR: ------------------------------------------------------------------------</div>
<div>[0]PETSC ERROR: SNESComputeFunction() line 1180 in src/snes/interface/snes.c</div>
<div>[0]PETSC ERROR: SNESDefaultComputeJacobian() line 77 in src/snes/interface/snesj.c</div>
<div>[0]PETSC ERROR: SNESComputeJacobian() line 1264 in src/snes/interface/snes.c</div>
<div>[0]PETSC ERROR: VecRestoreArrayPrivate3() line 234 in /work/petsc/pihm.c</div>
<div><br></div>
<div><br></div>
<div><br></div>
<blockquote type="">
<div>Jed<br><br>
</div>
</blockquote>
</div>
<br>
</div></blockquote>
</div>
<br><br clear="all"><br>-- <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<br>
</div></span></span><br><br><br></div>