[CIG-SEISMO] Negative Jacobian in specfem2d

[cristini]

Hi Jami,

I did a quick test and did not find any problem. This is probably a Gmsh 
issue that you should fix easily by upgrading to a more recent version.

I took you .geo file and got a very good mesh without any negative jacobian.

Thanks,

Best wishes

Paul

PS: the histogram I got

histogram of skewness (0. good - 1. bad):

   0.0000000E+00  -   5.0000001E-02      984857     95.14644      %
   5.0000001E-02  -   0.1000000           40000     3.864376      %
   0.1000000      -   0.1500000            2983    0.2881858      %
   0.1500000      -   0.2000000            2547    0.2460641      %
   0.2000000      -   0.2500000            1288    0.1244329      %
   0.2500000      -   0.3000000            1358    0.1311956      %
   0.3000000      -   0.3500000             597    5.7675809E-02  %
   0.3500000      -   0.4000000             595    5.7482593E-02  %
   0.4000000      -   0.4500000             619    5.9801217E-02  %
   0.4500000      -   0.5000000             189    1.8259175E-02  %
   0.5000000      -   0.5500000              61    5.8931732E-03  %
   0.5500000      -   0.6000000               1    9.6609394E-05  %
   0.6000000      -   0.6500000               0    0.0000000E+00  %
   0.6500000      -   0.7000000               1    9.6609394E-05  %
   0.7000000      -   0.7500000               0    0.0000000E+00  %
   0.7500000      -   0.8000000               0    0.0000000E+00  %
   0.8000000      -   0.8500000               0    0.0000000E+00  %
   0.8500000      -   0.9000000               0    0.0000000E+00  %
   0.9000000      -   0.9500000               0    0.0000000E+00  %
   0.9500000      -    1.000000               0    0.0000000E+00  %

  total number of elements =      1035096




On 03/08/2016 15:43, Dimitri Komatitsch wrote:
>
> 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};
>>
>>
>>
>>
>> _______________________________________________
>> CIG-SEISMO mailing list
>> CIG-SEISMO at geodynamics.org
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo
>>
>

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