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  • Jun 12 16:38
    Kevin-Mattheus-Moerman closed #99
  • Jun 12 16:38
    Kevin-Mattheus-Moerman commented #99
  • Jun 12 13:47
    jszyszko commented #99
  • Jun 11 15:07
    muntahi398 commented #97
  • Jun 10 18:41
    Kevin-Mattheus-Moerman labeled #97
  • Jun 10 18:41
    Kevin-Mattheus-Moerman commented #97
  • Jun 10 15:51
    DebjitHore opened #100
  • Jun 10 10:28
    Kevin-Mattheus-Moerman commented #99
  • Jun 10 10:25
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  • Jun 10 10:25
    Kevin-Mattheus-Moerman commented #98
  • Jun 10 09:57

    Kevin-Mattheus-Moerman on master

    Add spatially varying thickness… (compare)

  • Jun 10 09:53

    Kevin-Mattheus-Moerman on master

    Add hear mesh warping demo Simplified hip demo and avoid e… (compare)

  • Jun 10 08:53

    Kevin-Mattheus-Moerman on master

    Update hexMeshCylinder.m I tri… Update hexMeshCylinder.m Merge pull request #92 from Fir… (compare)

  • Jun 10 08:53
    Kevin-Mattheus-Moerman closed #92
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    Kevin-Mattheus-Moerman commented #92
  • Jun 10 08:47
    Kevin-Mattheus-Moerman synchronize #92
  • Jun 08 17:15

    Kevin-Mattheus-Moerman on master

    Fixed minor issue in demo (compare)

  • Jun 08 13:15
    jszyszko opened #99
  • Jun 08 12:09

    Kevin-Mattheus-Moerman on master

    Speed up to imx contour growing… (compare)

  • Jun 08 11:06
    mbarzegary opened #98
danielcpnkimo
@danielcpnkimo
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Is there a way for Gibbon code to have feature like I can assign the direction and material properties of of each fiber in Gibbon? I have a matrix of all the fiber direction in the order of their element number.
alexsafar
@alexsafar

Hey guys, there seems to be various problems with the installer and/or code base centred around 1. 'Undefined function 'contains' for input arguments of type 'cell' and 2. Error using builddocsearchdb (line 29)
There is no installed product with this help location.
Documentation that is not associated with a product will not be displayed in the help browser.

Error in addHelpSearch (line 8)
builddocsearchdb(gibbonHelpPath);

Error in createHelpDemoDocumentation (line 75)
addHelpSearch;

Error in installGibbon (line 198)
createHelpDemoDocumentation;

Kevin Mattheus Moerman
@Kevin-Mattheus-Moerman
Thanks I'll check this out
Contains is a new function in MATLAB 2018
alexsafar
@alexsafar
Ah I see, trying to run in 2016a at the moment so I'll see if I can update versions. Thanks for your quick reply!
alexsafar
@alexsafar
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I have found your lattice generating code very helpful with the work I am trying to achieve, but I have found that where the struts are intersecting, gaps are being created (element2lattice). I have shown here a slice plot in the z planee PostView results
alexsafar
@alexsafar
Thank you for making this extensive code collection available for us. Im currently trying to fix this myself but after a week I have not been able to make significant progress. I have even tried reprogramming this from scratch and although I can generate the structure and apply boundary conditions, I find that my main obstacle is FEBio outputting errors containing "Did you use the right node numbering?"
Kevin Mattheus Moerman
@Kevin-Mattheus-Moerman
I can help. Can you send me the setting that you use for element2lattice? Perhaps also send me more pictures of the problem. kevin.moerman@gmail.com
Marco Marra
@Marra_gitlab
Hi @Kevin-Mattheus-Moerman , Marco Marra from University of Twente here! Is there already a function in GIBBON to extract the (external) surface mesh from a FE solid mesh (eight-node brick element, C3D8)? Thank you
Kevin Mattheus Moerman
@Kevin-Mattheus-Moerman
Hi @Marra_gitlab thanks for your question.
F=element2patch(E);
indBoundaryFaces=tesBoundary(F,V);
Fb=F(indBoundaryFaces,:); %Boundary faces
In the above I use the tesBoundary function to get the boundary faces of the mesh defined by the hexahedral elements E and the nodes V
Use this longer form if you want to "book keep" some sort of element data e.g. element labels/colors defined by C
[F,CF]=element2patch(E,C,'hex8');
indBoundaryFaces=tesBoundary(F,V);
Fb=F(indBoundaryFaces,:); %Boundary faces
Cb=CF(indBoundaryFaces); %Boundary colors
Does that help?
Marco Marra
@Marra_gitlab
Hi @Kevin-Mattheus-Moerman, thank you for your reply. I guess we just have to try it out 😀 , but I think that does exactly what we are looking for. I will pass it through and let you know
Kevin Mattheus Moerman
@Kevin-Mattheus-Moerman
@Marra_gitlab how did you get on? Let me know if you need help
Marco Marra
@Marra_gitlab
Hi @Kevin-Mattheus-Moerman, what you proposed worked for us indeed. Since we need a triangular mesh in the end, we figured we should first convert the hex to tet mesh and then extract the boundary (or alternatively obtain a quad boundary mesh and then convert it to triangles). I've handed this over to @oguldeniz_gitlab who is currently working on this.
Kevin Mattheus Moerman
@Kevin-Mattheus-Moerman
@Marra_gitlab great. Yeah converting the quad mesh to triangles is best. The quad2tri function can help with that.
@Marra_gitlab @oguldeniz_gitlab let me know if you develop any interesting functionality which you think could be added to GIBBON
I'm always looking for contributors and people to join the team. To join the team I can render you on the website. After a number of contributions you can optionally join as coauthor on the next GIBBON paper too.
Marco Marra
@Marra_gitlab
That's good to hear, thank you. We'll keep that in mind
sroyiitd
@sroyiitd
Hi @Kevin-Mattheus-Moerman I am trying to run one of the demo problems in GIBBON to run FEBio simulation, but facing a an error like the appended one. I tried to change the savepath but it is not working.

rror using fprintf
Invalid file identifier. Use fopen to generate a valid file identifier.

Error in cell2txtfile (line 63)
fprintf(fid,'%s\r\n', T{:});

Error in febioStruct2xml>textModeElementAttributeParse (line 351)
cell2txtfile(fileName,totalTextCell,0,0); %Export to text file

Error in febioStruct2xml>febioStruct2xmlStep (line 208)
[domNode,rootNode]=textModeElementAttributeParse(domNode,rootNode,currentFieldName,attributeStruct,arrayDataSet,numArray,fieldNameSetSub,fileName,arrayParseMethod);

@Kevin-Mattheus-Moerman Could you please help on this?
sroyiitd
@sroyiitd
I was trying to reinstall my GIBBON files, by running installGibbon ...now I am getting an error lke bellow

Error using builddocsearchdb (line 38)
Could not write search database.

Error in addHelpSearch (line 8)
builddocsearchdb(gibbonHelpPath);

Error in createHelpDemoDocumentation (line 75)
addHelpSearch;

Error in installGibbon (line 195)
createHelpDemoDocumentation;

Kevin Mattheus Moerman
@Kevin-Mattheus-Moerman
@sroyiitd I think both of the above are file writing permission issues. I've commented on your issue posted on GitHub, lets proceed there with the discussions on this. gibbonCode/GIBBON#89
Tim Gadzella
@JustTwigIt_twitter
Hi everyone, I'm building a multi-body simulation in GIBBON for some future IFEA. I've built the mesh from stl files and the MATLAB pde mesher. For some reason my contacts seem to be inverting and causing negative Jacobians in the first substep of my analysis. I've tried fliplr to invert the normals but no luck - has anyone run into this before? Thanks in advance!
Kevin Mattheus Moerman
@Kevin-Mattheus-Moerman
Hi @JustTwigIt_twitter welcome. What type of elements do you have? 4-noded tetrahedra? If your elements are E, try E=E(:,[4 3 2 1]); or other permutations. Perhaps the PDE mesher convention differs from FEBio (are you using FEBio?)
For contact the faces need to "point at each other", so perhaps you can plot the normal directions for the contact surfaces and check if they are indeed doing that. Let me know if you are still stuck, if so perhaps create an issue on the github repo and add some more details and info on your model/code.
Tim Gadzella
@JustTwigIt_twitter
@Kevin-Mattheus-Moerman Thanks Dr. Moerman, I am using 4-noded tets but I'm defining tri3 elements in the surface pairs. I've tried flipping the element orders to no avail and when I take a look at the mesh in PreView I think my elements look ok (no obvious inversions). I'm really only using the pdeMesher to do surface recognition on import of my model STLs. I'll post the details on the github repo!
omcgee
@omcgee
Hi everyone, I have just recently started using the Gibbon Toolbox so I hope this question isn't too basic.
I'm trying to go from an STL and create a volume mesh exported as an Abaqus .inp.
I'm able to get the volume mesh and view but I'm having trouble exporting it as an INP file (or STL).
Currently, I'm using Help Export INP and I'm trying to create elementstruct and nodestruct from the mesh output structure that's created using runtetgen but I'm unsure as to where to find the element and nodal indices fields.
Can anyone give me some advice as to where I'm going wrong or a better way to do this? Thanks!
Kevin Mattheus Moerman
@Kevin-Mattheus-Moerman
@omcgee thanks could you post an issue relating to this on the GitHub repo? Also can you give more details. If I understand it correctly you imported and STL and want to mesh it using TetGen and then export it to an INP file for ABAQUS.
Kevin Mattheus Moerman
@Kevin-Mattheus-Moerman
FYI the export_INP function only exports the geometry, the Abaqus demos, e.g. DEMO_abaqus_0001_cube_uniaxial show how to code full models (and run them) from MATLAB
For export_INP the indices can just be coded (tetgen doesn't use them) e.g. you create them like E_ind=(1:1:size(E,1))'; and similarly for the nodes.
Does this help? If you need more help let me know
omcgee
@omcgee
Hi Kevin, sorry I was looking to export the indices from tetgen but coding them myself makes sense. Just looking to export the geometry as an .inp for now. Thanks so much for the quick response, if I have any other issues down the line I'll create an issue on the GitHub repo. Thanks again.
DebjitHore
@DebjitHore

HI @Kevin-Mattheus-Moerman I have recently started out working with FEBio and I have been trying to do some post-processing on a simulation I set up and successfully ran via FEBio Studio, and for this purpose, I am using the Gibbon package on MATLAB.
In order to get the displacement and stress data, I am using the importFEBio_logfile function in Gibbon which makes use of the log file. Now, the second part, that would allow me to successfully attempt what I am trying to achieve is to retrieve the mesh data in the form of a struct in MATLAB. According to my understanding, I can do this from either the .feb file or the .xplt file (am I correct?).

  1. If I can do it from the .xplt file, and access it in MATLAB, how can I do that?
  2. Currently I had been trying to do it through the .FEB file using import_FEB function like so:
    [febXML,nodeStruct,elementCell]=import_FEB(febFileName);
    But the error I keep hitting is as follows:

Dot indexing is not supported for variables of this type.
Error in import_FEB>get_FEB_nodes (line 67)
NODES_FEB_XML = GEO_FEB_XML.item(0).getElementsByTagName('Nodes');

If someone takes time out to look at these issues and help me figure this out it will be a big help, thanks.

PS: There's a DEMO_importFEB_exportINP file included with the Gibbon package and I was trying to replicate how they have read the data in that particular demo. (I can attach the files I was working it if somebody wants to replicate or try this one out)

DebjitHore
@DebjitHore
Should i raise an issue on the github page instead?
Kevin Mattheus Moerman
@Kevin-Mattheus-Moerman
@DebjitHore apologies for the delay. Thanks for your question.
I've just fixed the import_FEB function in the latest version. It was not ready yet for the new febio_spec (3.0)
Can you test it again? Also it would be easiest to code the whole model in GIBBON so you always have the entire structure.
Let me know if you have more questions.
DebjitHore
@DebjitHore
@Kevin-Mattheus-Moerman thanks for the fix. I am yet to try it out, but i will let you know if it resolves my issue.
DebjitHore
@DebjitHore
The eventual plan is to code the whole model in gibbon, but for the time being i am just trying to get used to gibbon and tinkering around in the meanwhile. Also, while we're at this discussion, i would like to ask something. Is there any provision in gibbon to take into account contact interaction of surfaces, that are not rigid but instead elastomeric, like in soft actuators. I think i saw two contact based demos one of a rolling self contact and the blob shear contact demo file, but in the pneunet actuator demo i didn't see any block of code that looked to me as handling contact interaction? Once again, i am a beginner and my understanding may not be complete, so pardon me if I'm asking something obvious. Thank you for your time.
DebjitHore
@DebjitHore
The fix works, i can access the meshStruct via the .FEB file. Thanks a lot.