<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div><br><blockquote type="cite"><div>On Sep 22, 2024, at 07:26, Blaise Bourdin <bourdin@mcmaster.ca> wrote:</div><br class="Apple-interchange-newline"><div><meta charset="UTF-8"><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><br class="Apple-interchange-newline"><br><blockquote type="cite"><div>On Sep 21, 2024, at 9:54 AM, neil liu <<a href="mailto:liufield@gmail.com">liufield@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div><table border="0" cellspacing="0" cellpadding="0" align="left" width="100%" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; letter-spacing: normal; text-transform: none; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><tbody><tr><td style="background: rgb(122, 0, 60); padding: 5pt 2pt;"></td><td width="100%" cellpadding="7px 6px 7px 15px" style="padding: 5pt 4pt 5pt 12pt; overflow-wrap: break-word;"><div><span style="font-weight: bold;">Caution:<span class="Apple-converted-space"> </span></span>External email.<span class="Apple-converted-space"> </span></div></td></tr></tbody></table><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div dir="ltr"><div dir="ltr"><div dir="ltr">Thanks a lot, David. That works.<div>Then I tried another example from Cubit. The script is defined as follows,</div><div><br></div><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 class="gmail-hashtag" 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></div><div><br></div><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 class="gmail-highlighted" 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 class="gmail-highlighted" 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 class="gmail-highlighted" 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></div></div></div></div></div></blockquote><div><br></div><div><br></div>That is corrrect.</div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">As far as I understand, one of the few assumptions in dmplex is that “cells” have the same topological dimension</div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">Here sideset 1 and 2 have different dimensions.</div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">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></blockquote><div><br></div><div>I have not seen the concept of edge sets discussed in the official exodusII doc [1]. However, they have an enum called ex_entity_type which does have a EX_EDGE_SET [2] value :thinking: </div><div>IDK, how much developed that is. I have not used this myself. Most codes I have seen just use SIDE/NODE sets… </div><div>Just sharing something I recently spotted…</div><div><br></div><div>[1] <a href="https://urldefense.us/v3/__https://sandialabs.github.io/seacas-docs/exodusII-new.pdf__;!!G_uCfscf7eWS!ZXJZphkaSn_4MhiE6JwD78s0zYdnwitEqgRtuh997d8-EpF-ebRBxfAqlqjCsPAyPs6UAv6MOex2ksU4efI$">https://sandialabs.github.io/seacas-docs/exodusII-new.pdf</a></div><div>[2] <a href="https://urldefense.us/v3/__https://sandialabs.github.io/seacas-docs/html/exodusII_8h.html*a1f649ed288d305ab55773ffd1d220490__;Iw!!G_uCfscf7eWS!ZXJZphkaSn_4MhiE6JwD78s0zYdnwitEqgRtuh997d8-EpF-ebRBxfAqlqjCsPAyPs6UAv6MOex2PdimBKk$">https://sandialabs.github.io/seacas-docs/html/exodusII_8h.html#a1f649ed288d305ab55773ffd1d220490</a></div><div><br></div><div>—</div><div>David</div><br><blockquote type="cite"><div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><br></div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">Regards,</div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">Blaise</div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><br></div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><blockquote type="cite"><div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><span class="gmail-highlighted" 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;"><br></span></div><div><font color="#222832" face="-apple-system, BlinkMacSystemFont, Segoe UI, Helvetica Neue, Arial, sans-serif, Apple Color Emoji, Segoe UI Emoji, Segoe UI Symbol">Thanks,</font></div><div><font color="#222832" face="-apple-system, BlinkMacSystemFont, Segoe UI, Helvetica Neue, Arial, sans-serif, Apple Color Emoji, Segoe UI Emoji, Segoe UI Symbol"><br></font></div><div><font color="#222832" face="-apple-system, BlinkMacSystemFont, Segoe UI, Helvetica Neue, Arial, sans-serif, Apple Color Emoji, Segoe UI Emoji, Segoe UI Symbol">Xiaodong </font></div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Sep 20, 2024 at 3:15 PM David Andrs <<a href="mailto:andrsd@gmail.com">andrsd@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;"><div dir="ltr"><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><div><br></div><div>--</div><div>David</div><br><div class="gmail_quote"><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></div><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;"><div dir="ltr"><div dir="ltr"><div dir="ltr">Dear Petsc developers and users, <div><br></div><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><div><br></div><div><div style="min-height: 100%;"><div style="width: 1540px;"><div><div><div><div><div><div><div><div id="m_9133974286637224946m_4954793584285953066gmail-:3" style="height: 625px;"><div id="m_9133974286637224946m_4954793584285953066gmail-:1" style="min-height: 434.521px;"><div><div role="main"><div><div><div><div><div role="list"><div role="listitem" aria-expanded="true"><div style="border-top-color: rgb(239, 239, 239); width: 1196.2px;"><div style="border-top-width: 1px; border-top-style: solid; border-top-color: rgba(100, 121, 143, 0.12);"><div id="m_9133974286637224946m_4954793584285953066gmail-:2rd"><div><div><div><div id="m_9133974286637224946m_4954793584285953066gmail-:2rg"><div id="m_9133974286637224946m_4954793584285953066gmail-:2rf"><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><div><div id="m_9133974286637224946m_4954793584285953066gmail-:2ru" role="button" aria-label="Show trimmed content" aria-expanded="false"><br></div><div id="m_9133974286637224946m_4954793584285953066gmail-:2ru" role="button" aria-label="Show trimmed content" aria-expanded="false">Thanks a lot.</div><div id="m_9133974286637224946m_4954793584285953066gmail-:2ru" role="button" aria-label="Show trimmed content" aria-expanded="false"><br></div><div id="m_9133974286637224946m_4954793584285953066gmail-:2ru" role="button" aria-label="Show trimmed content" aria-expanded="false">Xiaodong </div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div><div><div style="height: 672.516px;"><div style="height: 672.513px;"><div role="complementary" aria-label="Side panel" style="height: 672.513px;"><div><div role="tablist"><div id="m_9133974286637224946m_4954793584285953066gmail-gsc-gab-6" role="tab" aria-label="Calendar" aria-disabled="false" aria-selected="false"><div></div><div></div><div style="background-image: url("https://www.gstatic.com/companion/icon_assets/calendar_2020q4_2x.png");"></div></div><div id="m_9133974286637224946m_4954793584285953066gmail-gsc-gab-2" role="tab" aria-label="Keep" aria-disabled="false" aria-selected="false"><div></div><div></div><div style="background-image: 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0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div dir="auto" style="caret-color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="caret-color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="caret-color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="caret-color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="caret-color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; 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overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="caret-color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="caret-color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="caret-color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="caret-color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><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!ZXJZphkaSn_4MhiE6JwD78s0zYdnwitEqgRtuh997d8-EpF-ebRBxfAqlqjCsPAyPs6UAv6MOex2EiOeyPQ$">https://www.math.mcmaster.ca/bourdin</a><span class="Apple-converted-space"> </span>| +1 (905) 525 9140 ext. 27243</div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></blockquote></div><br></body></html>