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<div>Hi again,</div>
<div> </div>
<div>here is the geo file for the case described below.</div>
<div> </div>
<div>Thanks,</div>
<div> </div>
<div>Matthias</div>
<div> </div>
<div><font face="Tahoma" size="2"><span style="font-size:10pt;"> </span></font></div>
<div><font face="Tahoma" size="2"><span style="font-size:10pt;">_____________________________________________<br>
<b>Von:</b> Zenker, Dr. Matthias <br>
<b>Gesendet:</b> Montag, 4. März 2013 13:28<br>
<b>An:</b> 'gmsh@geuz.org'<br>
<b>Cc:</b> 'Christophe Geuzaine [cgeuzaine@ulg.ac.be] (cgeuzaine@ulg.ac.be)'<br>
<b>Betreff:</b> gmsh generates corrupt 3D mesh (Re: gmsh mesh gives "Degenerate 3D element" error in Elmer)</span></font></div>
<div style="padding-left:35.4pt;"> </div>
<div style="padding-left:35.4pt;"> </div>
<div style="padding-left:35.4pt;">Hi,</div>
<div style="padding-left:35.4pt;"> </div>
<div style="padding-left:35.4pt;">I have examined the problem described below more closely and found that unfortunately it seems tob e gmsh’s fault: There are tetrahedra with all 3 nodes having the same x coordinate, which seems obviously erroneous. </div>
<div style="padding-left:35.4pt;">To reproduce just mesh the geo file in the attachment, with everything set to default.</div>
<div style="padding-left:35.4pt;">I cannot tell exactly which elements are degenerate since Elmer renumbers everything. However, problematic coordinates seem to be (extract from Elmer’s error messages which give the coordinates of 3 nodes of problematic tetrahedra):</div>
<div style="padding-left:35.4pt;">ERROR:: ElementMetric: Degenerate 3D element: 176234</div>
<div style="padding-left:35.4pt;">DetG:-0.557E-18</div>
<div style="padding-left:35.4pt;">ElementMetric: Dir: 1 Coord: -1.40 2.15 3.50</div>
<div style="padding-left:35.4pt;">ElementMetric: Dir: 2 Coord: -1.40 2.15 4.00</div>
<div style="padding-left:35.4pt;">ElementMetric: Dir: 3 Coord: -1.40 1.66 3.75</div>
<div style="padding-left:35.4pt;">ERROR:: ElementMetric: Degenerate 3D element: 176887</div>
<div style="padding-left:35.4pt;">ElementMetric: DetG:-0.274E-18</div>
<div style="padding-left:35.4pt;">ElementMetric: Dir: 1 Coord: -1.40 1.67 7.75</div>
<div style="padding-left:35.4pt;">ElementMetric: Dir: 2 Coord: -1.40 2.15 7.50</div>
<div style="padding-left:35.4pt;">ElementMetric: Dir: 3 Coord: -1.40 1.80 7.25</div>
<div style="padding-left:35.4pt;">ERROR:: ElementMetric: Degenerate 3D element: 177378</div>
<div style="padding-left:35.4pt;">ElementMetric: DetG:-0.963E-19</div>
<div style="padding-left:35.4pt;">ElementMetric: Dir: 1 Coord: -1.40 2.15 9.50</div>
<div style="padding-left:35.4pt;">ElementMetric: Dir: 2 Coord: -1.40 2.15 10.0</div>
<div style="padding-left:35.4pt;">ElementMetric: Dir: 3 Coord: -1.40 1.67 9.75</div>
<div style="padding-left:35.4pt;">ERROR:: ElementMetric: Degenerate 3D element: 179163</div>
<div style="padding-left:35.4pt;">ElementMetric: DetG:-0.194E-17</div>
<div style="padding-left:35.4pt;">ElementMetric: Dir: 1 Coord:-0.900 1.80 4.25</div>
<div style="padding-left:35.4pt;">ElementMetric: Dir: 2 Coord:-0.900 2.15 4.00</div>
<div style="padding-left:35.4pt;">ElementMetric: Dir: 3 Coord:-0.900 1.67 3.75</div>
<div style="padding-left:35.4pt;">ERROR:: ElementMetric: Degenerate 3D element: 179367</div>
<div style="padding-left:35.4pt;">ElementMetric: DetG:-0.654E-19</div>
<div style="padding-left:35.4pt;">ElementMetric: Dir: 1 Coord:-0.900 2.15 10.0</div>
<div style="padding-left:35.4pt;">ElementMetric: Dir: 2 Coord:-0.900 1.67 9.75</div>
<div style="padding-left:35.4pt;">ElementMetric: Dir: 3 Coord:-0.900 1.80 10.3</div>
<div style="padding-left:35.4pt;"> </div>
<div style="padding-left:35.4pt;">I have tried to track down the first element (number 176234 above) in the msh file generated by gmsh, compared to the one written out by Elmergrid (which for debugging and mesh inspection purposes can write gmsh format since
some time). I find all 4 nodes of the tetrahedron with x coordinate equal to -1.4 in the file written by Elmergrid. In the original msh file generated by gmsh, 3 nodes have x coordinate -1.4 and the 4<font size="1"><span style="font-size:7.3pt;"><sup>th</sup></span></font>
one has -1.399999999999556. I would consider this a VERY flat tetrahedron, and the height in x direction is by far smaller than the characteristic lengths I have set in the geo file. I suspect that Elmer will interpret the x coordinate as being equal due to
rounding.</div>
<div style="padding-left:35.4pt;">I doesn’t help if I set the Min Element Size to the smallest characteristic length in Tools-Options-Mesh-General. </div>
<div style="padding-left:35.4pt;"> </div>
<div style="padding-left:35.4pt;">It is not the first time that I have this problem. In the past, it mysteriously went away sometimes after remeshing, sometimes after coarsening the characteristic lengths a bit. But this time, it won’t.</div>
<div style="padding-left:35.4pt;"> </div>
<div style="padding-left:35.4pt;">I consider this, if not a bug, then at least a problematic feature in gmsh.</div>
<div style="padding-left:35.4pt;">At the moment I cannot do a certain simulation due to this problem.</div>
<div style="padding-left:35.4pt;"> </div>
<div style="padding-left:35.4pt;">I would very much appreciate if someone knowledgeable could have a look on this case and fix it or state how to avoid this kind of problems. </div>
<div style="padding-left:35.4pt;">BTW I have used gmsh 2.6.2-svn, downloaded 31.01.2013, under Windows XP.</div>
<div style="padding-left:35.4pt;"> </div>
<div style="padding-left:35.4pt;">Thank you,</div>
<div style="padding-left:35.4pt;"> </div>
<div style="padding-left:35.4pt;">Matthias</div>
<div style="padding-left:35.4pt;"> </div>
<div style="padding-left:35.4pt;"> </div>
<div style="padding-left:35.4pt;"> </div>
<div style="padding-left:70.8pt;"><font face="Tahoma" size="2"><span style="font-size:10pt;">_____________________________________________<br>
<b>Von:</b> Zenker, Dr. Matthias <br>
<b>Gesendet:</b> Dienstag, 26. Februar 2013 16:26<br>
<b>An:</b> <a href="mailto:gmsh@geuz.org"><font color="blue"><u>gmsh@geuz.org</u></font></a><br>
<b>Cc:</b> Christophe Geuzaine [cgeuzaine@ulg.ac.be] (<a href="mailto:cgeuzaine@ulg.ac.be"><font color="blue"><u>cgeuzaine@ulg.ac.be</u></font></a>)<br>
<b>Betreff:</b> gmsh mesh gives "Degenerate 3D element" error in Elmer</span></font></div>
<div style="padding-left:70.8pt;"> </div>
<div style="padding-left:70.8pt;"> </div>
<div style="padding-left:70.8pt;">Hi,</div>
<div style="padding-left:70.8pt;"> </div>
<div style="padding-left:70.8pt;">I have a problem with a 3D mesh generated by gmsh: I get a Degenerate 3D element" error when I use this mesh with the Elmer FEM software. The mesh is produced when I mesh the attached geo file , just using the default settings
in gmsh (2.6.2-svn, Windows XP). </div>
<div style="padding-left:70.8pt;">My questions are:</div>
<div style="padding-left:70.8pt;"> </div>
<ol style="margin:0;padding-left:106.8pt;">
<li>How can I find out if there are degenerate elements? Is there a way to check the mesh quality in gmsh?</li><li>What can I do to avoid degenerate elements?</li></ol>
<div style="padding-left:70.8pt;"> </div>
<div style="padding-left:70.8pt;">Thank you for helpful hints,</div>
<div style="padding-left:70.8pt;"> </div>
<div style="padding-left:70.8pt;">Matthias</div>
<div style="padding-left:70.8pt;"> </div>
<div style="padding-left:70.8pt;"> < Datei: test.geo >> </div>
<div style="padding-left:70.8pt;"> </div>
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