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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Hello,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Thank you for the response. I shall try it out.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Regards,<br>Sharan<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>From:</span></b><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> Matthew Knepley [mailto:knepley@gmail.com] <br><b>Sent:</b> Wednesday, 8 November 2023 23:09<br><b>To:</b> Blaise Bourdin <bourdin@mcmaster.ca><br><b>Cc:</b> Sharan Roongta <s.roongta@mpie.de>; petsc-users@mcs.anl.gov<br><b>Subject:</b> [BULK] Re: [petsc-users] DMPlex and Gmsh<br><b>Importance:</b> Low<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On Wed, Nov 8, 2023 at 4:50 PM Blaise Bourdin <<a href="mailto:bourdin@mcmaster.ca">bourdin@mcmaster.ca</a>> wrote:<o:p></o:p></p></div><div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm'><div><p class=MsoNormal>Hi, <o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>I think that you need to use the magical keyword “<span style='font-size:8.5pt;font-family:"Fira Code",serif'>-dm_plex_gmsh_mark_vertices” for that</span><o:p></o:p></p></div></div></blockquote><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>I try to describe the options here:<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal> <a href="https://petsc.org/main/manualpages/DMPlex/DMPlexCreateGmsh/">https://petsc.org/main/manualpages/DMPlex/DMPlexCreateGmsh/</a><o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal> Thanks,<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal> Matt<o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm'><div><div><p class=MsoNormal><span style='font-size:8.5pt;font-family:"Fira Code",serif'>Blaise</span><o:p></o:p></p><div><p class=MsoNormal><br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal>On Nov 8, 2023, at 1:13 PM, Sharan Roongta <<a href="mailto:s.roongta@mpie.de" target="_blank">s.roongta@mpie.de</a>> wrote:<o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p><div><table class=MsoNormalTable border=0 cellspacing=0 cellpadding=0 align=left width="100%" style='width:100.0%;word-spacing:0px'><tr><td style='background:#7A003C;padding:5.0pt 2.0pt 5.0pt 2.0pt'></td><td width="100%" style='width:100.0%;padding:5.0pt 4.0pt 5.0pt 12.0pt'><div><p class=MsoNormal style='mso-element:frame;mso-element-frame-hspace:2.25pt;mso-element-wrap:around;mso-element-anchor-vertical:paragraph;mso-element-anchor-horizontal:column;mso-height-rule:exactly'><b><span style='font-family:"Helvetica",sans-serif'>Caution: </span></b><span style='font-family:"Helvetica",sans-serif'>External email. <o:p></o:p></span></p></div></td></tr></table><p class=MsoNormal><o:p> </o:p></p><div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Dear Petsc team,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>I want to load a .msh file generated using Gmsh software into the DMPlex object. There are several things I would want to clarify, but I would like to start with “Physical tags”.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>If I have defined “Physical Points”, “Physical Surface”, and “Physical Volume” in my .geo file, I get the physical tags in the “.msh” file.<br>When I load this mesh in DMPlex, and view the DM:<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>call DMView(globalMesh, PETSC_VIEWER_STDOUT_WORLD,err_PETSc)<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> CHKERRQ(err_PETSc)<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>This is the output I get:<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>DM Object: n/a 1 MPI process<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> type: plex<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>n/a in 3 dimensions:<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> Number of 0-cells per rank: 14<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> Number of 1-cells per rank: 49<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> Number of 2-cells per rank: 60<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> Number of 3-cells per rank: 24<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Labels:<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> celltype: 4 strata with value/size (0 (14), 6 (24), 3 (60), 1 (49))<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> depth: 4 strata with value/size (0 (14), 1 (49), 2 (60), 3 (24))<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> Cell Sets: 1 strata with value/size (8 (24))<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> Face Sets: 6 strata with value/size (2 (4), 3 (4), 4 (4), 5 (4), 6 (4), 7 (4))<br><br>I was expecting to get the “Node Sets” or “Vertex Sets” also. Is my assumption wrong?<br><br>If yes, then how can one figure out the boundary nodes and their tags where I want to apply certain boundary conditions?<br>Currently we apply boundary conditions on faces, therefore “Face Sets” was enough. But now we want to apply displacements on certain boundary nodes.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>I have also attached the .geo and .msh file (hope you can open it)<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>The Petsc version I am using is 3.18.6.<br><br><br>Thanks and Regards,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Sharan Roongta<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New"'>-----------------------------------------------<br>Max-Planck-Institut für Eisenforschung GmbH <br>Max-Planck-Straße 1 <br>D-40237 Düsseldorf <br><br>Handelsregister B 2533 <br>Amtsgericht Düsseldorf <br> <br>Geschäftsführung <br>Prof. Dr. Gerhard Dehm <br>Prof. Dr. Jörg Neugebauer <br>Prof. Dr. Dierk Raabe <br>Dr. Kai de Weldige <br><br>Ust.-Id.-Nr.: DE 11 93 58 514 <br>Steuernummer: 105 5891 1000 <br>------------------------------------------------- <br>Please consider that invitations and e-mails of our institute are <br>only valid if they end with …@<a href="http://mpie.de" target="_blank">mpie.de</a>. <br>If you are not sure of the validity please contact <a href="mailto:rco@mpie.de" target="_blank">rco@mpie.de</a><br><br>Bitte beachten Sie, dass Einladungen zu Veranstaltungen und E-Mails <br>aus unserem Haus nur mit der Endung …@<a href="http://mpie.de" target="_blank">mpie.de</a> gültig sind. <br>In Zweifelsfällen wenden Sie sich bitte an <a href="mailto:rco@mpie.de" target="_blank">rco@mpie.de</a></span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> <o:p></o:p></span></p></div></div><p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif'><o:p> </o:p></span></p><div class=MsoNormal align=center style='text-align:center'><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif'><hr size=2 width="100%" align=center></span></div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>-------------------------------------------------<br>Stay up to date and follow us on LinkedIn, Twitter and YouTube.<br><br>Max-Planck-Institut für Eisenforschung GmbH<br>Max-Planck-Straße 1<br>D-40237 Düsseldorf<br> <br>Handelsregister B 2533 <br>Amtsgericht Düsseldorf<br> <br>Geschäftsführung<br>Prof. Dr. Gerhard Dehm<br>Prof. Dr. Jörg Neugebauer<br>Prof. Dr. Dierk Raabe<br>Dr. Kai de Weldige<br> <br>Ust.-Id.-Nr.: DE 11 93 58 514 <br>Steuernummer: 105 5891 1000<br><br><br>Please consider that invitations and e-mails of our institute are <br>only valid if they end with …@<a href="http://mpie.de" target="_blank">mpie.de</a>. <br>If you are not sure of the validity please contact <a href="mailto:rco@mpie.de" target="_blank"><span style='color:#954F72'>rco@mpie.de</span></a><br><br>Bitte beachten Sie, dass Einladungen zu Veranstaltungen und E-Mails<br>aus unserem Haus nur mit der Endung …@<a href="http://mpie.de" target="_blank">mpie.de</a> gültig sind. <br>In Zweifelsfällen wenden Sie sich bitte an <a href="mailto:rco@mpie.de" target="_blank"><span style='color:#954F72'>rco@mpie.de</span></a><br>-------------------------------------------------<o:p></o:p></span></p></div><p class=MsoNormal><cube_check.msh><cube_check.geo><o:p></o:p></p></div></blockquote></div><p class=MsoNormal><o:p> </o:p></p><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><p class=MsoNormal><span style='color:black'>— <br>Canada Research Chair in Mathematical and Computational Aspects of Solid Mechanics (Tier 1)<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'>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://www.math.mcmaster.ca/bourdin" target="_blank">https://www.math.mcmaster.ca/bourdin</a> | +1 (905) 525 9140 ext. 27243<o:p></o:p></span></p></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div><p class=MsoNormal><o:p> </o:p></p></div></div></blockquote></div><p class=MsoNormal><br clear=all><o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal><span class=gmailsignatureprefix>-- </span><o:p></o:p></p><div><div><div><div><div><div><div><p class=MsoNormal>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<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><o:p></o:p></p></div></div></div></div></div></div></div></div></div><BR />
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Stay up to date and follow us on LinkedIn, Twitter and YouTube.<BR />
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Max-Planck-Institut für Eisenforschung GmbH<BR />
Max-Planck-Straße 1<BR />
D-40237 Düsseldorf<BR />
<BR />
Handelsregister B 2533 <BR />
Amtsgericht Düsseldorf<BR />
<BR />
Geschäftsführung<BR />
Prof. Dr. Gerhard Dehm<BR />
Prof. Dr. Jörg Neugebauer<BR />
Prof. Dr. Dierk Raabe<BR />
Dr. Kai de Weldige<BR />
<BR />
Ust.-Id.-Nr.: DE 11 93 58 514 <BR />
Steuernummer: 105 5891 1000<BR />
<BR />
<BR />
Please consider that invitations and e-mails of our institute are <BR />
only valid if they end with …@mpie.de. <BR />
If you are not sure of the validity please contact rco@mpie.de<BR />
<BR />
Bitte beachten Sie, dass Einladungen zu Veranstaltungen und E-Mails<BR />
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