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Thread: Negative Jacobian and Node Numbering

  1. #1
    Join Date
    Jul 2011
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    21

    Default Negative Jacobian and Node Numbering

    Hi,

    I'm having a problem running files I import from Gmsh into preview. The file imports fine and everything but when I try running it in febio i get an error saying "negative jacobian detected at integration point 'x' of element 'y'. Did you use the right node numbering?" The file isn't complicated, just a simple block in compression I was testing.

    Thanks,

    Hugh

  2. #2
    Join Date
    Nov 2007
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    Salt Lake City, UTAH
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    Default

    Hi Hugh,

    It seems that you have quad elements lying on top of a hex mesh. The node numberings of these quad elements appears backwards to what FEBio expects and hence the negative jacobians. If you don't need the quads, just remove them and the problem is fixed. If you do need them, you can invert their node numbering in PreView (from the Mesh Panel, Select Elements, Invert) but you must do this before you create any boundary conditions. Hope this helps.

    Cheers,

    Steve.
    Department of Bioengineering, University of Utah
    Scientific Computing and Imaging institute, University of Utah

  3. #3
    Join Date
    Jul 2011
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    Default

    Hi Steve,
    I tried inverting the elements but I still get the same error? I've attached the file with the inverted quad elements. Also someone was asking me if meshes created in cubit can be supported in preview and febio and if they can then which file type should be used?

    Thanks,

    Hugh

  4. #4
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    Nov 2007
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    Default

    Hi Hugh,

    Did you invert just the quad elements? When I remove the quad elements and then inspect the jacobians, I still see a whole bunch of negative volume elements using the Mesh Inspector.

    What formats does cubit export? If there is format you prefer, and if it is a text based format, I can look into adding it to PreView.

    Cheers,

    Steve.
    Department of Bioengineering, University of Utah
    Scientific Computing and Imaging institute, University of Utah

  5. #5
    Join Date
    Jul 2011
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    Default

    Hi Steve,
    I got the mesh working now thanks. And we found that cubit can export abaqus files which can be imported into preview.

    Thanks,

    Hugh

  6. #6
    Join Date
    Jul 2012
    Posts
    2

    Default Similar problem with the meshes : From Gmsh to Preview conversion- -ve Jacobians

    Dear steve

    I am facing the same problem with all of my meshes. I tried all that you have said. But it doesnt seem to work have attached the .feb files

    Midhun
    Attached Files Attached Files

  7. #7
    Join Date
    Nov 2007
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    Salt Lake City, UTAH
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    Default

    Hi Midhun,

    You are defining both tets and shell elements. Is that your intention? In your input file, the shell elements have zero thickness which will cause zero jacobians. The strange thing is that I can't see the elements in PreView which makes me suspect that the local element node numbering is off. I will take a closer look but in the mean time try creating your mesh without the shells.

    Cheers,

    Steve.
    Department of Bioengineering, University of Utah
    Scientific Computing and Imaging institute, University of Utah

  8. #8
    Join Date
    Jul 2012
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    2

    Default

    Hi Steve,

    THere are triangles and tets . I am using Gmsh for this and was just doing the initial trial run . Can you give me a fool proof method starting from a cube-step file through gmsh to preview which will definitely work(with any type of elements). Or could you suggest any other opensource mesh generation software(CAD to Mesh) which is compatible with Febio and preview.

    Regards
    Midhun

  9. #9

    Default

    Hugh,

    What did you end up doing to get the mesh working? I'm having the same error as you once were getting. Thank you.

    Christina

  10. #10
    Join Date
    Nov 2007
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    Salt Lake City, UTAH
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    Default

    Hi Midhun (and Christina)

    So, this seem to be a common problem, so I will figure out an elegant way to get around this. To reiterated, the problem is that GMsh outputs the surface mesh as well as the volume mesh. For a volume mesh, PreView doesn't like the surface definition in the file since it creates its own surface mesh directly from the volume mesh. To circumvent this problem, only export the volume mesh to your gmsh file. If you are working with existing files, remove the surface definition from the file (in the element section, all lines that have a "2" in the second column). Hope this workaround works for now. Let me know if you have any more questions.

    Cheers,

    Steve
    Department of Bioengineering, University of Utah
    Scientific Computing and Imaging institute, University of Utah

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