[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
Tue Mar 5 10:11:49 CET 2013
Hi Christophe and Jean-Francois,
thank you for your replies.
After meshing and optimizing again the error went away, even though I did not (yet) use netgen optimization. This seems to be due to the random factor contained in the mesh. I hope the error will not come back... ;)
Thank you again!
Matthias
> -----Ursprüngliche Nachricht-----
> Von: Zenker, Dr. Matthias
> Gesendet: Montag, 4. März 2013 14:14
> An: 'Christophe Geuzaine'
> Cc: 'gmsh at geuz.org'
> Betreff: AW: gmsh generates corrupt 3D mesh (Re: gmsh mesh gives
> "Degenerate 3D element" error in Elmer)
>
> 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