[Gmsh] gmsh generates corrupt 3D mesh (Re: gmsh mesh gives "Degenerate 3D element" error in Elmer)
Zenker, Dr. Matthias
Matthias.Zenker at erbe-med.com
Mon Mar 4 14:13:32 CET 2013
Hi Christophe,
thank you for the prompt reply.
"Optimize 3D" didn't help. I will try "Optimize (Netgen)" and report back tomorrow.
Thank you,
Matthias
> -----Ursprüngliche Nachricht-----
> Von: Christophe Geuzaine [mailto:cgeuzaine at ulg.ac.be]
> Gesendet: Montag, 4. März 2013 13:43
> An: Zenker, Dr. Matthias
> Cc: 'gmsh at geuz.org'
> Betreff: Re: gmsh generates corrupt 3D mesh (Re: gmsh mesh gives
> "Degenerate 3D element" error in Elmer)
>
>
> Hi Matthias,
>
> Did you optimize the 3D mesh (-optimize and/or -optimize_netgen on the
> command line, or "Optimize 3D" in the GUI) ?
>
> Christophe
>
> On 04 Mar 2013, at 13:27, "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-
> med.com> wrote:
>
> > 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
> > Cc: Christophe Geuzaine [cgeuzaine at ulg.ac.be] (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:
> >
> > * How can I find out if there are degenerate elements? Is there a way
> to check the mesh quality in gmsh?
> > * What can I do to avoid degenerate elements?
> >
> > Thank you for helpful hints,
> >
> > Matthias
> >
> > < Datei: test.geo >>
> >
> >
> >
> >
> __________________________________________________________
> ___________
> > ERBE Elektromedizin GmbH
> > Firmensitz: 72072 Tuebingen
> > Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede
> > Registergericht: Stuttgart HRB 380137
>
> --
> Prof. Christophe Geuzaine
> University of Liege, Electrical Engineering and Computer Science
> http://www.montefiore.ulg.ac.be/~geuzaine
>
>
_____________________________________________________________________
ERBE Elektromedizin GmbH
Firmensitz: 72072 Tuebingen
Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede
Registergericht: Stuttgart HRB 380137