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Thread: Set coordinate system and fiber orientation for irregular geometry

  1. #1
    Join Date
    Apr 2016
    Posts
    14

    Default Set coordinate system and fiber orientation for irregular geometry

    Hi all,

    I have an irregular geometry (with different curvature at different parts) meshed with tet4 and imported in preview. I want to apply fiber orientation in circumferential direction of the geometry. I used the following code in my .feb file:

    <fiber type="cylindrical">
    <center>0,0,0</center>
    <axis>0,0,1</axis>
    <vector>0,1,0</vector>
    </fiber>

    when I checked the field vector in post view, it is like some parts of the geometry have circumferential fibers, some parts have fibers perpendicular to the surface either inward or outward with different angles (Attached fig 1, 2). So, I tried to play with the axis and vector numbers to fix it. This time the fiber orientation changed, but again some parts had circumferential fibers and some parts perpendicular fibers.

    So, I decided to first define material axis in preview (to define redial, circumferential and longitudinal axes for my geometry accurately) and then define fiber orientation based on the new coordinate system. I did the following steps in preview:

    editable mesh>select elements>selected all elements in the geometry>set axes>node numbering>defined the node numbers>apply

    But still the result is not what It should be for my geometry. However, for a simple, symmetric geometry this method works perfectly (Fig 3)

    Well, I have these questions now:

    1- Is this the right approach for applying fiber orientation to the irregular geometry? (first defining new coordinates, then applying fiber direction based on this coordinate)
    2- If the answer is yes, Are my steps correct?
    3- If the answer to all questions are no, Can you show me how to set fibers?

    P.S.) My material model is uncoupled solid mixture of Fung and uniaxial active contraction in fiber direction. So, without defining the fiber orientation correctly, I won't be able to run the model with active contraction.


    Thank you very much.

    SanazCapture7.PNGCapture8.PNGCapture9.PNG
    Last edited by Sanaz; 06-29-2017 at 05:20 PM.

  2. #2
    Join Date
    Nov 2007
    Location
    Salt Lake City, UTAH
    Posts
    1,683

    Default

    Hi Sanaz,

    It would be helpful if you can send us the .feb file so we can take a closer look at your material definition. I have a hard time discerning from the images if the fiber definition you provided is correct or not.

    I'm also not sure what you mean by "first define material axis in preview [...] and then define fiber orientation based on the new coordinate system". How are you doing that?

    I do not recommend using "node number" as the fiber generator for tet4 meshes, since usually there is no structure in nodal connectivity for a tet4 mesh. (The "node number" approach is useful for highly regular hexahedral meshes.)

    How did you export the fiber vector to PostView? I may need to double-check, but you can only export the parent's material fiber vectors. I don't think there is a way for exporting the fiber vector of a nested material. But again, if you can send us your .feb file, I'll have a better idea.

    Cheers,

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

  3. #3
    Join Date
    Apr 2016
    Posts
    14

    Default

    Hi Steve,

    What I meant was to define a cylindrical coordinate system for my geometry. Then change the fiber direction with respect to the circumferential direction of that coordinate. However, I am not sure if this is the correct approach.

    I added <var type="fiber vector"/> to .feb file and run it. Then in Postview, I was able to visualize the field vector.

    I sent the .feb file to your emai

    Thank you.

    Sanaz

  4. #4
    Join Date
    Apr 2016
    Posts
    14

    Default

    Hi

    I finally was able to find the fiber direction for all the elements of my geometry, i.e., I have 634273 elements and 634273 corresponding fiber directions.
    I tried to input the fiber directions into .feb file <ElementData> field element-by-element like this.

    <elem id="634273"> 16313,100563, 88652, 8018</elem>
    <fiber type="vector">-0.071377895,0.899416633,0.431224901</fiber>

    This method was suggested in one post in the forum by Dr. Ateshian

    "There are two methods for specifying material fibers/axes in FEBio: Either in the material definition or on an element-by-element basis, see the User's Manual. You can check for the presence of an <ElementData> field in the input file to see if element-by-element data is provided in that file. The issues you are encountering arise because PreView is not treating both methods consistently for fibers and material axes. This needs to be fixed."


    But Febio is not able to run the code. The window get closed immediately after I run the code.

    How can I fix it? Is this the right method to specify element-by-element fiber direction? Has anybody tried element-by-element fiber assignment before?

    Any help is greatly appreciated!

    Thank you

    Sanaz

  5. #5
    Join Date
    Dec 2007
    Posts
    652

    Default

    Hi Sanaz,

    Are you using the 2.0 format or 2.5? The element data specification is different for these two formats.

    Best,

    Gerard

  6. #6
    Join Date
    Apr 2016
    Posts
    14

    Default

    Hi Dr. Ateshian,

    I am using <febio_spec version="2.5">.
    I defined the elements and fibers like this:

    <Elements type="tet4" mat="1" name="Part1">
    <elem id="1"> 14642,75361,14644,14645</elem>
    <fiber type="vector">-0.41597638,0.419080947,0.807053165</fiber>
    <elem id="2"> 76415,114102,76561,56342</elem>
    <fiber type="vector">-0.193078189,-0.980325608,-0.041018482</fiber>
    :
    :
    :
    <elem id="634273"> 16313,100563, 88652, 8018</elem>
    <fiber type="vector">-0.071377895,0.899416633,0.431224901</fiber>

    I tried the exact same code without fibers and Febio converged. But after adding fiber directions using element-by-element approach, Febio window get closed before running.

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