<div><div dir="ltr"><div>Thanks a lot, Blaise. Yes. As you said, I have to define a  node set to find the edges we are interested in for Exodus II file.<br></div><div><br></div></div></div><div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Sep 22, 2024 at 9:26 AM Blaise Bourdin <<a href="mailto:bourdin@mcmaster.ca" target="_blank">bourdin@mcmaster.ca</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">



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<div>On Sep 21, 2024, at 9:54 AM, neil liu <<a href="mailto:liufield@gmail.com" target="_blank">liufield@gmail.com</a>> wrote:</div>
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<div><span style="font-weight:bold">Caution:<span> </span></span>External email.<span> </span></div>
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<div dir="ltr">Thanks a lot, David. That works.
<div>Then I tried another example from Cubit. The script is defined as follows,</div>
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<div><span style="color:rgb(221,221,221);font-family:Arial,sans-serif;font-size:15.008px;background-color:rgb(34,34,34)">reset</span><br style="color:rgb(221,221,221);font-family:Arial,sans-serif;font-size:15.008px;background-color:rgb(34,34,34)">
<span style="color:rgb(221,221,221);font-family:Arial,sans-serif;font-size:15.008px;background-color:rgb(34,34,34)">brick x 1</span><br style="color:rgb(221,221,221);font-family:Arial,sans-serif;font-size:15.008px;background-color:rgb(34,34,34)">
<span style="color:rgb(221,221,221);font-family:Arial,sans-serif;font-size:15.008px;background-color:rgb(34,34,34)">mesh vol 1</span><br style="color:rgb(221,221,221);font-family:Arial,sans-serif;font-size:15.008px;background-color:rgb(34,34,34)">
<span style="color:rgb(221,221,221);font-family:Arial,sans-serif;font-size:15.008px;background-color:rgb(34,34,34)">block 1 volume 1</span><br style="color:rgb(221,221,221);font-family:Arial,sans-serif;font-size:15.008px;background-color:rgb(34,34,34)">
<span style="color:rgb(221,221,221);font-family:Arial,sans-serif;font-size:15.008px;background-color:rgb(34,34,34)">sideset 1 surface 1</span><br style="color:rgb(221,221,221);font-family:Arial,sans-serif;font-size:15.008px;background-color:rgb(34,34,34)">
<span style="color:rgb(221,221,221);font-family:Arial,sans-serif;font-size:15.008px;background-color:rgb(34,34,34)">block 2 surface 1 </span><span style="color:rgb(221,221,221);font-family:Arial,sans-serif;font-size:15.008px;background-color:rgb(34,34,34)">#sides</span><span style="color:rgb(221,221,221);font-family:Arial,sans-serif;font-size:15.008px;background-color:rgb(34,34,34)"> of
 these elements can now be referenced in a sideset</span><br style="color:rgb(221,221,221);font-family:Arial,sans-serif;font-size:15.008px;background-color:rgb(34,34,34)">
<span style="color:rgb(221,221,221);font-family:Arial,sans-serif;font-size:15.008px;background-color:rgb(34,34,34)">block 2 element type quad</span><br style="color:rgb(221,221,221);font-family:Arial,sans-serif;font-size:15.008px;background-color:rgb(34,34,34)">
<span style="color:rgb(221,221,221);font-family:Arial,sans-serif;font-size:15.008px;background-color:rgb(34,34,34)">sideset 2 curve 1</span><br>
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<div>Then the mesh was exported as a exodus file (attached), and imported into Petsc. </div>
<div>Here, the code was stuck by the function, <span style="color:rgb(34,40,50);font-family:-apple-system,BlinkMacSystemFont,"Segoe UI","Helvetica Neue",Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol"">DMPlexCreate</span><span style="color:rgb(34,40,50);font-family:-apple-system,BlinkMacSystemFont,"Segoe UI","Helvetica Neue",Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol";box-sizing:border-box">Exodus().</span></div>
<div><span style="color:rgb(34,40,50);font-family:-apple-system,BlinkMacSystemFont,"Segoe UI","Helvetica Neue",Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol";box-sizing:border-box">I think maybe
 this is due to block 1 is 3D while block 2 is 2D. </span></div>
<div><span style="color:rgb(34,40,50);font-family:-apple-system,BlinkMacSystemFont,"Segoe UI","Helvetica Neue",Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol";box-sizing:border-box">But this
 seems necessary to define an edge using sideset. </span></div>
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<div><br>
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That is corrrect.</div>
<div>As far as I understand, one of the few assumptions in dmplex is that “cells” have the same topological dimension</div>
<div>Here sideset 1 and 2 have different dimensions.</div>
<div>As far as I remember, exodusII does not have “Edge sets”, so your best bet would be to define a node set for curve 1.</div>
<div><br>
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<div>Regards,</div>
<div>Blaise</div>
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<div><font face="-apple-system, BlinkMacSystemFont, Segoe UI, Helvetica Neue, Arial, sans-serif, Apple Color Emoji, Segoe UI Emoji, Segoe UI Symbol" color="#222832"><br>
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<div dir="ltr" class="gmail_attr">On Fri, Sep 20, 2024 at 3:15 PM David Andrs <<a href="mailto:andrsd@gmail.com" target="_blank">andrsd@gmail.com</a>> wrote:<br>
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<div>Before you export the mesh from Cubit, change the element type to something like QUAD4. PETSc does not automatically remap SHELL elements to QUADs.</div>
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<div>--</div>
<div>David</div>
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<div dir="ltr" class="gmail_attr">On Fri, Sep 20, 2024 at 8:05 AM neil liu <<a href="mailto:liufield@gmail.com" target="_blank">liufield@gmail.com</a>> wrote:<br>
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<div dir="ltr">Dear Petsc developers and users, 
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<div>I am trying to read an exodus II file from coreform cubit, but without success,</div>
<div>Then I used petsc's built-in exodus file, /share/petsc/datafiles/meshes/sevenside.exo.</div>
<div>This file can be read by petsc successfully. </div>
<div><br>
</div>
<div>And I did a test. This file, sevenside.exo, is imported into coreform Cubit, and then is saved as a new exodus file. This new exodus file can not be read by petsc successfully. </div>
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<div dir="ltr">[0]PETSC ERROR: Invalid argument<br>
[0]PETSC ERROR: Unrecognized element type SHELL<br>
[0]PETSC ERROR: See <a href="https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!fcN-KL0rs3WRHNRfT47zioS4djjyXM7OCr32LT2olmZHm3X1NIk-WMdU9-UR3rNotQSpINEm8NrcMtWTCFqKEg$" target="_blank">https://petsc.org/release/faq/</a> for trouble shooting.<br>
[0]PETSC ERROR: Petsc Release Version 3.21.1, Apr 26, 2024<br>
[0]PETSC ERROR: ./app on a arch-linux-c-opt named localhost.localdomain by xiaodongliu Fri Sep 20 09:36:16 2024<br>
[0]PETSC ERROR: Configure options -download-mumps -download-scalapack --with-cc=gcc --with-fc=gfortran --with-cxx=g++ --download-fblaslapack --download-mpich --with-scalar-type=complex --download-triangle --with-debugging=no --download-parmetis --download-metis
 -download-ptscotch --download-bison --download-hdf5 -download-mmg=/home/xiaodongliu/Documents/3rdPartyLib/d5c43d1bcefe598d51428f6a7fee10ec29478b79.tar.gz --download-ctetgen --download-pragmatic --download-eigen --download-netcdf=/home/xiaodongliu/Documents/3rdPartyLib/netcdf-c-4.9.2-p1.tar.gz
 --download-zlib --download-pnetcdf --download-exodusii<br>
[0]PETSC ERROR: #1 ExodusGetCellType_Internal() at /home/xiaodongliu/Documents/petsc-with-docs-3.21.1/petsc-3.21.1/src/dm/impls/plex/plexexodusii.c:1470<br>
[0]PETSC ERROR: #2 DMPlexCreateExodus() at /home/xiaodongliu/Documents/petsc-with-docs-3.21.1/petsc-3.21.1/src/dm/impls/plex/plexexodusii.c:1551<br>
[0]PETSC ERROR: #3 DMPlexCreateExodusFromFile() at /home/xiaodongliu/Documents/petsc-with-docs-3.21.1/petsc-3.21.1/src/dm/impls/plex/plexexodusii.c:1390</div>
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Thanks a lot.</div>
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<div>— <br>
Canada Research Chair in Mathematical and Computational Aspects of Solid Mechanics (Tier 1)</div>
<div>Professor, Department of Mathematics & Statistics<br>
Hamilton Hall room 409A, McMaster University<br>
1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada <br>
<a href="https://urldefense.us/v3/__https://www.math.mcmaster.ca/bourdin__;!!G_uCfscf7eWS!behGY_YKaZKejR7vV7vkVTAHTWR_Y1UTNxgJ-4rMSCrvsMTFm_QsFVjhbC6HhjoPQ4ThPerrFQAqNC3T_iAGGQ$" target="_blank">https://www.math.mcmaster.ca/bourdin</a> | +1 (905) 525 9140 ext. 27243</div>
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