[CIG-SEISMO] Negative Jacobian in specfem2d

[Dimitri Komatitsch]

Hi Jami,

Thanks! Probably mesh quality that is not good enough, two elements that 
are almost flat. Try to see the quality histogram in Gmsh to see if 
these two elements are poor (in which case even if you manage to run 
that mesh in SPECFEM2D it will likely blow up). There is also a tool for 
that in SPECFEM2D:

src/auxiliaries/check_quality_external_mesh.f90

If it turns out to be a bug in the code (unlikely, but worth checking) 
please let us know.

Thanks,
Best wishes,

Dimitri.

On 03/08/2016 10:01, Jami Johnson wrote:
> Hello,
> I have created a very dense mesh with Gmsh, and when I check for the
> values of the Jacobian in Gmsh they are all positive.  However, when I
> run it in specfem2d, an error is thrown due to a negative Jacobian.  It
> seems to be a very small percentage of my elements causing a problem.  I
> believe all of my line loops are oriented correctly.  Are there any
> other potential causes of a negative Jacobian?
>
> Error in specfem2d:
> --------------------------
>  2  elements have a negative Jacobian, out of      1313871
>
> geo file:
> -----------
> lc=0.00003;
> xmax=0.015;
> xmin=0.0;
> ymin=-0.015;
> ymax=0.0;
> Point(1) = {xmax,ymax , 0, lc};
> Point(2) = {xmax, ymin, 0, lc};
> Point(3) = {xmin, ymin, 0, lc};
> Point(4) = {xmin, ymax, 0, lc};
> Line(1) = {1, 4};
> Line(2) = {4, 3};
> Line(3) = {3, 2};
> Line(4) = {2, 1};
> R=0.00025;
> Centx=0.0075;
> Centy=-0.005;
> Point(5) = {Centx, R+Centy, 0, lc};
> Point(6) = {R+Centx, Centy, 0, lc};
> Point(7) = {-R+Centx, Centy, 0, lc};
> Point(8) = {Centx, -R+Centy, 0, lc};
> Point(9) = {Centx, Centy, 0, lc};
> Circle(5) = {5, 9, 7};
> Circle(6) = {7, 9, 8};
> Circle(7) = {8, 9, 6};
> Circle(8) = {6, 9, 5};
> Line Loop(9) = {5, 6, 7, 8};
> Line Loop(10) = {1, 2, 3, 4};
>
> Plane Surface(10) = {10, 9};
> Plane Surface(11) = {9};
>
> Recombine Surface{10,11};
> Mesh.SubdivisionAlgorithm=1;
> Physical Line("Top") = {1};
> Physical Line("Left") = {2};
> Physical Line("Bottom") = {3};
> Physical Line("Right") = {4};
> Physical Surface("M1") = {10};
> Physical Surface("M2") = {11};
>
>
>
>
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-- 
Dimitri Komatitsch
CNRS Research Director (DR CNRS), Laboratory of Mechanics and Acoustics,
UPR 7051, Marseille, France    http://komatitsch.free.fr