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Thread: Negative Jacobian and Node Numbering

  1. #11

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    Hi Steve,

    I tried removing the surface definition from the file like you said. I just opened my .msh file in notepad and deleted the 2's from the second column in the element section. However, now PreView crashes on me when I try to upload the file. Thanks again for the help.

    Christina

  2. #12
    Join Date
    Nov 2007
    Location
    Salt Lake City, UTAH
    Posts
    1,664

    Default

    Christina,

    Try the latest version of PreView on the web. There was a bug in some of the file readers that was fixed recently. I wonder if that's the problem. Let me know if the problem persists in the latest version.

    Cheers,

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

  3. #13

    Default

    Steve,

    I tried loading the newest version of PreView but it still crashed on me. Any other ideas? Thank you!

    Christina

  4. #14
    Join Date
    Nov 2007
    Location
    Salt Lake City, UTAH
    Posts
    1,664

    Default

    I'll have to take a look at the file. Could you please send it to me? If it's not too big, just attach it to this thread, otherwise you can email it to me at steve dot maas at utah dot edu.

    Thanks,

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

  5. #15
    Join Date
    Nov 2013
    Posts
    8

    Default

    Based on the previous posts regarding surface elements, I found a workaround for this issue. After importing your mesh to preview, select the object and then go to tools --> mesh inspector. On the upper right menu, click on your tri elements. At the bottom, enter min and max values that include the values for all of your tri elements, then hit select. Now, close the mesh inspector and go to the mesh tab on the left-hand menu. Make sure the element box is selected. Then, click detach. Select "detach to object" and hit apply. Finally, click on the model tab on the left-hand menu and find the new object. Right click on the newly detached object and select delete. Now you should be good to go! The surface elements that were imported have been successfully deleted!

    Hope it helps some of you.

    Best,

    Steve

  6. #16
    Join Date
    Apr 2015
    Posts
    8

    Default

    Hello Steve,

    I am experiencing a node-numbering issue as well while trying to solve a problem based on an imported mesh (in .hmascii). The run in FEBio2 is aborted with the message "Found ### initially inverted elements." I have tried to follow your above instructions to rectify the issue (just in case my mesh was imported with both surface and volume elements). However, when I attempt to "detach" the selected elements, PreView tells me that "Selection cannot be detached." Does this mean I don't have surface elements after all?

    Any help working through this problem would be greatly appreciated!

    Best,
    Zac

  7. #17
    Join Date
    Nov 2007
    Location
    Salt Lake City, UTAH
    Posts
    1,664

    Default

    Hi Zac,

    Could you please upload the .hmascii file? If I can recreate the issue on my end, I will be able to assist you much better.

    Cheers,

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

  8. #18
    Join Date
    Apr 2015
    Posts
    8

    Default .hmascii mesh file

    Steve,

    I could not get my .hmascii file to attach here, so I will email it to you shortly.

    I now actually suspect that my imported mesh may only be a surface mesh, but the TetGen feature crashes PreView on me. I've been attempting to figure out how to create a volume mesh in Gmsh, but so far without success. I'd be truly grateful for your help!

    Many thanks,
    Zac

  9. #19
    Join Date
    Apr 2015
    Posts
    8

    Default

    Hi Steve (and User Community),

    I was finally able to generate a "clean" surface mesh in my surface generation program (the report created in that program says my triangles are of good quality, with no intersections or anything), but PreView still crashes when I use the "TetGen" function to create a volume mesh.

    I can't figure out why this is happening, and I'm especially confused as to why this feature sometimes does work with more complicated surface meshes that contain many more triangles and have much poorer quality. I am using PreView 1.16.3 and my surface geometry was imported in .hmascii format. Are there steps I am missing in the process of generating a Tet mesh? Any advice would be most welcome!

    Best,
    Zac

  10. #20
    Join Date
    Aug 2015
    Location
    Brazil
    Posts
    13

    Default

    Dear Steve/all,

    I'm starting my trail on the Febio's software family and facing the same problem with the Jacobian while setting the .feb, as mentioned in this thread.
    Too many elements are problematic.

    My geometry is that one of a trabecular bone, however not perfectly flat over the bounding box.
    I attach a Preview's figure showing the normals of this structure, although it can seem a bit messy for visual analysis.
    My point in showing it is also to clear up some doubts. So,

    i) I'd like to know if someone of you could give me a trick on how to solve this problem;

    ii) I can't interpret which direction the normal vectors point to only looking at the color. I suppose that {R,G,B} represent {x,y,z} axis, in this order, and that an inclined normal, for instance, results from an interpolated color. Sorry for this question, but is it right?? Further, how do I know when the normal points outward/inward? Is there an option to show/hide the {x,y,z} axis labels?

    iii) I've heard about other softwares like Meshlab to correct/repair a surface mesh. Would it be the case of working more in depth in the mesh in order to "smooth" such a bad elements? Suggestions?

    Thank you.

    2015-08-18-04.55.52-pm.png
    Last edited by opcg; 08-18-2015 at 02:01 PM. Reason: Attachment forgotten.

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