<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Tue, Mar 8, 2016 at 7:10 AM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br><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"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><span class="">On Mon, Mar 7, 2016 at 1:28 PM, Morten Nobel-Jørgensen <span dir="ltr"><<a href="mailto:mono@mek.dtu.dk" target="_blank">mono@mek.dtu.dk</a>></span> wrote:<br><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">
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<div style="direction:ltr;font-family:Tahoma;color:rgb(0,0,0);font-size:10pt">I have some problems using DMPlex on unstructured grids in 3D.
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<div>After I have created the DMPlex and assigned dofs (3 dofs on each node), I run into some problems when assembling the global stiffness matrix. I have created a small example in the attached cc file. My problems are:</div>
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<li>It seems like the matrix (created using DMCreateMatrix) contains no non-zero elements. I was under the impression that the sparsity pattern of the matrix would be created automatically when the dofs has been assigned to the default section.</li><li>(Probably as a consequence of this) when assigning values to the matrix I get an: "Argument of of range. <span style="font-size:10pt">New nonzero at (0,0) caused a malloc. </span><span style="font-size:10pt">Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR,
PETSC_FALSE) to turn off this check"</span></li><li><span style="font-size:10pt">Finally, I'm reading the nodes of each element using the get-transitive-clojure (where I test if each point is inside the node range), but I have a hard time understanding if the returned values are sorted. And if not, how
to sort the values (e.g. using orientation which the get-transitive-clojure function also returns).</span></li></ul>
<div>I hope someone can guide me in the right direction :)</div></div></div></div></blockquote><div><br></div></span><div>I will take a look today or tomorrow. The first thing to do is to look at the nonzero pattern of the Jacobian. I use -mat_view draw -draw_pause -1</div></div></div></div></blockquote><div><br></div><div>I admit that this problem is counter-intuitive, and I will think about a good error check. The problem is that I allow "inconsistent"</div><div>sections, meaning that the dof for each field do not add up to the total dof. In your code, when you call</div><div><br></div><div> ierr = PetscSectionSetDof(s, v, 3);CHKERRQ(ierr);</div><div><br></div><div>you should also call</div><div><br></div><div> ierr = PetscSectionSetFieldDof(s, v, 0, 3);CHKERRQ(ierr);</div><div><br></div><div>Then everything works. I am attaching my slight rewrite of your code.</div><div><br></div><div> Thanks,</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"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div> Thanks,</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"><div><div style="direction:ltr;font-family:Tahoma;color:rgb(0,0,0);font-size:10pt"><div>
<div>Kind regards,</div>
<div>Morten </div><span class=""><font color="#888888">
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</font></span></blockquote></div><span class=""><font color="#888888"><br><br clear="all"><div><br></div>-- <br><div>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>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature">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>
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