<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><br class=""><div><blockquote type="cite" class=""><div dir="ltr" class=""><div class="">When I execute this I get a Petsc error, object in wrong state missing diagonal entry.</div></div></blockquote><div><br class=""></div> When do you get this error? During a TSSolve? While KSP is building a preconditioner.</div><div><br class=""></div><div> Some parts of PETSc require that you put entries (even if they are zero) on all diagonal entries in the Jacobian. So likely you need to just make sure that your populate jac routine puts/adds 0 to all diagonal entries.</div><div><br class=""></div><div> Barry</div><div><br class=""></div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Jun 11, 2021, at 10:16 AM, Kaushik Vijaykumar <<a href="mailto:kaushikv318@gmail.com" class="">kaushikv318@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Thanks Barry for your comments. Based on your suggestion I tried the following<div class=""><br class=""></div><div class="">Main()</div><div class="">{</div><div class="">ierr = SNESSetFunction(snes,r1,FormFunction,&this_ctx);CHKERRQ(ierr);</div><div class="">ierr = SNESSetJacobian(snes,jac,NULL,FormJacobian,&this_ctx);CHKERRQ(ierr);<br class=""> ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);<br class=""> ierr = SNESSolve(snes, NULL, u);CHKERRQ(ierr);<br class=""></div><div class="">}</div><div class=""><br class=""></div><div class="">In formfunction I populate the jacobian "<b class="">jac</b>"</div><div class=""><br class=""></div><div class="">Formfunction(snes,Vec x,Vec F,void* ctx)</div><div class="">{</div><div class="">ierr = SNESGetJacobian(snes,&jac,Null,NULL,NULL);CHKERRQ(ierr);<br class=""></div><div class=""><br class=""></div><div class="">// "<b class="">Populate jac</b>"</div><div class="">ierr = MatAssemblyBegin(jac,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);<br class=""> ierr = MatAssemblyEnd(jac,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); <br class=""></div><div class=""><br class=""></div><div class="">}</div><div class=""><div class="">FormJacobian(SNES snes,Vec x,Mat jac,Mat B,void *ctx)</div><div class="">{</div><div class="">ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);<br class=""> ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);<br class=""><br class=""> ierr = MatAssemblyBegin(jac,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);<br class=""> ierr = MatAssemblyEnd(jac,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);<br class=""></div><div class="">}</div></div><div class=""><br class=""></div><div class="">When I execute this I get a Petsc error, object in wrong state missing diagonal entry.</div><div class=""><br class=""></div><div class="">I am not sure what I am missing here? </div><div class=""><br class=""></div><div class="">Thanks</div><div class="">Kaushik</div><div class=""><br class=""></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Jun 10, 2021 at 6:37 PM Barry Smith <<a href="mailto:bsmith@petsc.dev" class="">bsmith@petsc.dev</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><br class="">
<br class="">
> On Jun 10, 2021, at 3:29 PM, Kaushik Vijaykumar <<a href="mailto:kaushikv318@gmail.com" target="_blank" class="">kaushikv318@gmail.com</a>> wrote:<br class="">
> <br class="">
> Hi everyone,<br class="">
> <br class="">
> I am trying to copy the stiffness matrix that I generated in form function to the jacobian matrix jac in form jacobian. The piece of code for that:<br class="">
> <br class="">
> <br class="">
If you have created jac and B in your main program and passed them with SNESSetJacobian() then you should be able to just use<br class="">
<br class="">
> ierr = MatCopy(ptr->K,jac,SAME_NONZERO_PATTERN);CHKERRQ(ierr);<br class="">
<br class="">
Generally jac and B are the same matrix so you don't need the second copy. <br class="">
> ierr = MatCopy(ptr->K,B,SAME_NONZERO_PATTERN);CHKERRQ(ierr); <br class="">
<br class="">
If they are sometimes the same and sometime not you can do<br class="">
<br class="">
if (jac != B) {ierr = MatCopy(ptr->K,B,SAME_NONZERO_PATTERN);CHKERRQ(ierr); }<br class="">
<br class="">
<br class="">
The following won't work because you are creating new local matrices in your form jacobian that don't exist outside of that routine.<br class="">
<br class="">
> <br class="">
> ierr = MatDuplicate(ptr->K,MAT_COPY_VALUES,&jac);CHKERRQ(ierr);<br class="">
> ierr = MatDuplicate(ptr->K,MAT_COPY_VALUES,&B);CHKERRQ(ierr);<br class="">
> <br class="">
> ierr = MatCopy(ptr->K,jac,SAME_NONZERO_PATTERN);CHKERRQ(ierr);<br class="">
> ierr = MatCopy(ptr->K,B,SAME_NONZERO_PATTERN);CHKERRQ(ierr); <br class="">
> <br class="">
> <br class="">
If the matrix you are creating in form function is the Jacobian then you don't need to use the memory and time to make copies. You can just form the matrix directly into the Jacobian you will use for SNES. You can obtain this with a call <br class="">
<br class="">
SNESGetJacobian(snes,&jac,NULL,NULL,NULL); <br class="">
<br class="">
in your form function and just put the matrix values directly into jac. Then your form Jacobian does not need to do anything but return since the jac already contains the Jacobian.<br class="">
<br class="">
On the off-change you are using the iteration A(x^n) x^{n+1} = b(x^n} and not using Newtons' method (which is why you compute A in form function, then you might be better off using SNESSetPicard() instead of SNESSetFunction(), SNESSetJacobian().<br class="">
<br class="">
> <br class="">
> Thanks<br class="">
> Kaushik<br class="">
<br class="">
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