[Gmsh] gmsh generates corrupt 3D mesh (Re: gmsh mesh gives "Degenerate 3D element" error in Elmer)

Mon Mar 4 13:30:11 CET 2013

Hi again,

here is the geo file for the case described below.

Thanks,

Matthias

_____________________________________________
Von: Zenker, Dr. Matthias
Gesendet: Montag, 4. März 2013 13:28
An: 'gmsh at geuz.org'
Cc: 'Christophe Geuzaine [cgeuzaine at ulg.ac.be] (cgeuzaine at ulg.ac.be)'
Betreff: gmsh generates corrupt 3D mesh (Re: gmsh mesh gives "Degenerate 3D element" error in Elmer)

     Hi,

     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.
     To reproduce just mesh the geo file in the attachment, with everything set to default.
     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):
     ERROR:: ElementMetric: Degenerate 3D element: 176234
     DetG:-0.557E-18
     ElementMetric: Dir: 1 Coord: -1.40      2.15      3.50
     ElementMetric: Dir: 2 Coord: -1.40      2.15      4.00
     ElementMetric: Dir: 3 Coord: -1.40      1.66      3.75
     ERROR:: ElementMetric: Degenerate 3D element: 176887
     ElementMetric: DetG:-0.274E-18
     ElementMetric: Dir: 1 Coord: -1.40      1.67      7.75
     ElementMetric: Dir: 2 Coord: -1.40      2.15      7.50
     ElementMetric: Dir: 3 Coord: -1.40      1.80      7.25
     ERROR:: ElementMetric: Degenerate 3D element: 177378
     ElementMetric: DetG:-0.963E-19
     ElementMetric: Dir: 1 Coord: -1.40      2.15      9.50
     ElementMetric: Dir: 2 Coord: -1.40      2.15      10.0
     ElementMetric: Dir: 3 Coord: -1.40      1.67      9.75
     ERROR:: ElementMetric: Degenerate 3D element: 179163
     ElementMetric: DetG:-0.194E-17
     ElementMetric: Dir: 1 Coord:-0.900      1.80      4.25
     ElementMetric: Dir: 2 Coord:-0.900      2.15      4.00
     ElementMetric: Dir: 3 Coord:-0.900      1.67      3.75
     ERROR:: ElementMetric: Degenerate 3D element: 179367
     ElementMetric: DetG:-0.654E-19
     ElementMetric: Dir: 1 Coord:-0.900      2.15      10.0
     ElementMetric: Dir: 2 Coord:-0.900      1.67      9.75
     ElementMetric: Dir: 3 Coord:-0.900      1.80      10.3

     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 4th 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.
     I doesn't help if I set the Min Element Size to the smallest characteristic length in Tools-Options-Mesh-General.

     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.

     I consider this, if not a bug, then at least a problematic feature in gmsh.
     At the moment I cannot do a certain simulation due to this problem.

     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.
     BTW I have used gmsh 2.6.2-svn, downloaded 31.01.2013, under Windows XP.

     Thank you,

     Matthias

           _____________________________________________
           Von: Zenker, Dr. Matthias
           Gesendet: Dienstag, 26. Februar 2013 16:26
           An: gmsh at geuz.org<mailto:gmsh at geuz.org>
           Cc: Christophe Geuzaine [cgeuzaine at ulg.ac.be] (cgeuzaine at ulg.ac.be<mailto:cgeuzaine at ulg.ac.be>)
           Betreff: gmsh mesh gives "Degenerate 3D element" error in Elmer

           Hi,

           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).
           My questions are:

1.      How can I find out if there are degenerate elements? Is there a way to check the mesh quality in gmsh?
2.      What can I do to avoid degenerate elements?

           Thank you for helpful hints,

           Matthias

            < Datei: test.geo >>

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