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<p>Thank you very much!</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> knepley@gmail.com <knepley@gmail.com><br>
<b>Sent:</b> Sunday, July 24, 2022 5:32:34 PM<br>
<b>To:</b> Duan Junming<br>
<b>Cc:</b> PETSc<br>
<b>Subject:</b> Re: [petsc-users] Adding more dofs to the coordinate DM crashes with either PetscSectionSetDof or PetscSectionFieldDof</font>
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<div dir="ltr">On Sun, Jul 24, 2022 at 8:46 AM Duan Junming via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a>> wrote:<br>
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<p>Dear all,</p>
<p><br>
</p>
<p>I want to add more dofs to the coordinate DM to represent a curved mesh.</p>
<p>I first create a simple box mesh with one cell:</p>
<p><br>
</p>
<p></p>
<div> PetscCall(DMCreate(comm, &dm));</div>
<div> PetscCall(DMSetType(dm, DMPLEX));</div>
<div> dim = 2;</div>
<div> PetscInt n_faces[2] = {1, 1};</div>
<div> DMBoundaryType periodicity[2] = {DM_BOUNDARY_GHOSTED, DM_BOUNDARY_GHOSTED};</div>
<div> DMPlexCreateBoxMesh(comm, dim, PETSC_FALSE, n_faces, NULL, NULL, periodicity, PETSC_TRUE, &dm);</div>
<div><br>
</div>
<div>Then I add more dofs to cdm using section:</div>
<div><br>
</div>
<div>
<div> PetscCall(DMGetCoordinateDM(dm, &cdm));</div>
<div> PetscCall(DMGetLocalSection(cdm, &cs));</div>
<div> PetscCall(DMPlexGetChart(dm, &pStart, &pEnd));</div>
<div> PetscCall(PetscSectionSetChart(cs, pStart, pEnd));</div>
<div> degree = 3;</div>
<div> for(depth = 0; depth <= dim; ++ depth) {</div>
<div> PetscCall(DMPlexGetDepthStratum(cdm, depth, &pStart, &pEnd));</div>
<div> for(p = pStart; p < pEnd; ++p) {</div>
<div> <b>PetscCall(PetscSectionSetDof(cs, p, dim*PetscPowInt(degree-1, depth)));</b></div>
<div><b> PetscCall(PetscSectionSetFieldDof(cs, p, 0, dim*PetscPowInt(degree-1, depth)));</b></div>
<div> }</div>
<div> }</div>
<div> PetscCall(PetscSectionSetUp(cs));</div>
<div> PetscCall(DMSetUp(cdm));</div>
<div><br>
</div>
<div>Finally, I wish to get the vec to set the coordinates:</div>
<div><br>
</div>
<div>
<div> PetscCall(DMCreateLocalVector(cdm, &coordinates));</div>
<div> PetscScalar *pCoords = NULL;</div>
<div> PetscCall(DMPlexVecGetClosure(cdm, NULL, coordinates, 0, &pSize, &pCoords));</div>
<div> printf("pSize: %d\n", pSize);</div>
<div><br>
</div>
</div>
However, if I only use <b style="font-family:"Times New Roman",Times,serif,Times,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px">PetscSectionSetDof</b>, the code reports "<span>Section
size 32 does not match Vec closure size 0</span>".</div>
<div>Instead, if I only use <b style="font-family:"Times New Roman",Times,serif,Times,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px">
PetscSectionSetFieldDof</b>, the code crashes with "<span>Checking the memory for corruption."</span></div>
<div><span>It runs without error when I use both <b style="font-family:"Times New Roman",Times,serif,Times,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px">
PetscSectionSetDof </b>and <b style="font-family:"Times New Roman",Times,serif,Times,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px">
PetscSectionSetFieldDof</b>.</span></div>
<div><span><span style="font-family:"Times New Roman",Times,serif,Times,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px"><br>
</span></span></div>
<div><span><span style="font-family:"Times New Roman",Times,serif,Times,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px">Maybe I have missed something, but c</span></span>ould you help
to explain why I should both functions <b>PetscSectionSetDof</b> and <b>PetscSectionSetFieldDof?</b></div>
<div><span><span style="font-family:"Times New Roman",Times,serif,Times,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px"><span style="font-family:"Times New Roman",Times,serif,Times,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px"><span style="font-family:"Times New Roman",Times,serif,Times,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px">It
is not straightforward that I should again set the dofs of the section after each field of the section has been set.</span></span></span></span></div>
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<div>This is the intended behavior, and how we use it internally. The use of fields is optional in order to allow Section to be as lightweight</div>
<div>as possible. We do not enforce consistency between the field and overall sizes.</div>
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<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
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<div>I can also see that <b style="font-family:"Times New Roman",Times,serif,Times,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px">PetscSectionSetFieldDof </b>call
<span style="font-family:"Times New Roman",Times,serif,Times,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px">
<b>PetscSectionSetDof </b>on the specific field of the section,</span></div>
<div><span>and cs->field[0] doesn't share the same address as cs itself.</span></div>
<div><span><br>
</span></div>
<div><span>Thanks in advance!</span></div>
<div>Junming</div>
<div><span><br>
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