[CIG-SEISMO] gmsh and specfem2D

[Dimitri Komatitsch]

Hi Giuseppe,

My colleague Paul Cristini, who is a Gmsh expert, may have ideas about 
how to fix this; thus I cc him.

Best regards,
Dimitri.

On 09/06/2012 04:41 PM, giuseppe.digiulio at ingv.it wrote:
> I am a new user of specfem2D and I am trying to generate an external
> simple 2D mesh using gmsh; this seems one nice external fe grid
> generator as indicated by specfem2d user manual (version 7, page 10).
>
> My question is about Jacobian as returned by the script
> xcheck_quality_external_mesh.
>
> I built using gmsh a simple geometry file composed of three uniform
> layers (see the attached *geo file).
>
> I performed a 2D mesh using allquads following the example shown in
> specfem2D manual (fixing a minimum element size of 20 because dimension
> of my model is relatively big).
>
> gmsh 3UFscale_allquad.geo -2 -clmin 20 -order 2
>
> I set the absorbing conditions with the python script
> python ../LibGmsh2Specfem.py 3UFscale_allquad -t A -b A -r A -l A
>
> obtaining the Mesh* Material* Nodes* Surf_abs_* and Surf_free* files.
>
> Now my problem is in the quality of my mesh as returned by
> xcheck_quality_external_mesh because it returns negative jacobian.
>
> xcheck_quality_external_mesh
> :::::::
> start reading the external node file: Nodes_3UFscale_allquad
> start reading the external mesh file: Mesh_3UFscale_allquad
> NPOIN = 12663
> NSPEC = 12462
> done reading the external files
>
> start checking if any element with a negative Jacobian is found
> element 6251 has a negative Jacobian
> STOP negative Jacobian found
> ::::::
>
> I do not know how can I improve my mesh to pass this check; I try to
> delete the element 6251 with negative Jacobian but this is not the only
> one. I tried different options in the 2D meshing, but still obtaining
> negative jacobian.
>
> And it is also strange that the Jmin seems 0.497 when I use Tool/plugins
> og gmsh to analyseCurveMesh (see picture in attach). If I understood
> well from gmsh manual (pa. 66) Jmin should be the minimum Jacobian and
> this seems not negative.
>
> I also attached the output files output_mesher.txt and output_solver.txt
> obtained by xmeshfem2D and xspecfem2D, respectively.
> Of course xspecfem2D crashs, and all elements with negative Jacobian are
> reported into output_solver.txt.
>
> So my question is: how can I improve my external 2D mesh built by gmsh
> for having positive jacobian everywhere ?
>
> If someone of developpers has any suggestions to improve my mesh
> deleting elements with negative jacobian in my mesh, these are welcome!!!
>
> The file *tar.gz contains my trial of mesh
>
> Best regards and thank you in advance!
>
> Giuseppe Di Giulio
> ----------------------------------------------------------------
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-- 
Dimitri Komatitsch - komatitsch aT lma.cnrs-mrs.fr
CNRS Research Director (DR CNRS), Laboratory of Mechanics and Acoustics,
UPR 7051, Marseille, France    http://komatitsch.free.fr