[Gmsh] Difficulty with generating a volume mesh from a stl file

[David Love]

Dear Geordie,

Thank you very much for your reply.

You are right, GMSH does not generate zero volume tetrahedra. I think the
issues with the finite element simulations are due to a combination of my
Matlab script and GMSH's volume meshing routine. When loading the volume
mesh into COMSOL a minimum quality factor of 6E-10 (average quality 0.66)
is obtained, which is rather poor. I think this is primarily due to
stretched tetrahedra, which due to rounding errors may have lead to the
interpretation of 'zero volume' elements. I also noticed that more recent
versions of GMSH have the tendency to fill a volume with 'super nodes' that
connect to many surface nodes. After optimisation with COMSOL the minimum
quality factor could be improved to 3E-2 (average quality 0.69) .

Aside: The mesh statistics use a quality metric that is worked out for each
tetrahedra in the mesh and is proportional to d_i/d_o, where d_i would be
the diameter of the largest sphere entirely enclosed in the tetrahedra, and
d_o is the diameter of the smallest sphere that can entirely enclose a
tetrahedra. This is normalised so that quality=1 for a equilateral shape.

For my simulations an ideal mesh has tetrahedrons with approximately the
same volumes, where each node is part of 4-10 tetrahedrons and where
tetrahedrons are not distorted. Do you know of any ways in GMSH to prevent
'super nodes' and encourage more consistent volumes when generating a
volume mesh?

Thank you again for your help.

Kind regards,
David



On Tue, May 26, 2015 at 1:47 AM, Geordie McBain <gdmcbain at freeshell.org>
wrote:

> 2015-05-26 2:06 GMT+10:00 David Love <dml42 at cam.ac.uk>:
> > Dear Sir/Madam,
> >
> > I have been experiencing difficulties generating a volume mesh (.geo and
> > .msh) from a surface mesh (.stl) generated in matlab. The main issue is
> that
> > I end up with zero volume tetrahedra (elements with four collinear
> points)
> > which causes difficulties in subsequent finite element simulations.
> >
> > I have attached an example of a surface mesh (.stl) that I start off
> with. I
> > then use the procedure outlined in the following link to create the
> volume
> > mesh (.geo and .msh):
> >
> http://fengl.org/2012/05/21/converting-stl-surface-mesh-to-volume-mesh-using-gmsh/
> >
> > My questions are:
> > - Is there a way to avoid zero volume tetrahedra or does the issue
> originate
> > from the matlab generated stl file? Do you have a suggestion to avoid
> this
> > issue?
>
> Hello.  I had a go at your STL surface and it seemed to work here.
>
> I meshed it with the attached, no frills, .geo file.
>
> To check that the mesh was O. K., I solved a Poisson problem on the
> volume with uniform forcing and zero Dirichlet conditions using P1
> elements in FreeFem++, using the attached .edp script.
>
> It computes the volume as 0.54956, the area as 15.7748, and the
> integral of the solution as 0.000286442.
>   I don't think that this would work if there were degenerate
> elements.  Is it possible that the error is in the solver rather than
> the mesh?
>
>
> > - Is there a possibility of generating a volume mesh in GMSH by defining
> the
> > surface boundary in an equation? For instance if I describe my shape in
> form
> > of a triple sinusoidal (as done in the matlab code) and then tell GMSH to
> > mesh the inner volume. If so could you point me towards some examples?
>
> I don't think that this can be done in a .geo file, but your first
> approach of generating the STL externally and merging it into Gmsh
> should work as you expected.
>
> I'm using gmsh 2.9.4 (compiled under 64-bit Debian from SVN sources),
> in case that matters.
>



-- 
David Love

PhD Candidate in Physics
Cavendish Laboratory
University of Cambridge

Office: +44 (0)1223 764169
Email: dml42 at cam.ac.uk
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