reaction-diffusion module repository

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  • pludo
    Junior Member
    • Jul 2023
    • 12

    reaction-diffusion module repository

    Hello,

    I am using FEBio for modelling of two solutes reacting and diffusing, till now i was using a multiphasic study where i
    1. In the multiphasic material, i set "osm-coef-const" value to 0.
    2. Fix the x,y,z-displacement components of the entire multiphasic domain to zero.
    3. Similarly, fix the fluid pressure to zero.
    However now i am trying to shift onto the reaction diffusion module of FEBio, To understand this module, i tries to run repositories files and i am not able to run any repository file, i am thrown with this error(shown below), is there a problem with the repository file or is it any other issue? i have also attached one of the repository file for your reference.
    ch01.feb ch02.feb

    Thanks in advance.

    Best regards,
    Nisarg


    Error: "
    ************************************************** ***********************

    * ERROR *

    * The property "species" failed to initialize or was not defined. *

    ************************************************** ***********************




    ************************************************** ***********************

    * ERROR *

    * Failed initializing material 1 (name="Material1") *

    ************************************************** ***********************




    ************************************************** ***********************

    * ERROR *

    * Model initialization failed *

    ************************************************** ***********************
    Attached Files
  • maas
    Lead Code Developer
    • Nov 2007
    • 3369

    #2
    Hi Nisarg,

    Thanks for bringing this to my attention. It looks like these files are not being read in correctly in FEBio Studio so I will look into that and see if I can resolve that. These files do run correctly in FEBio. To test this, when you open the file, select "Edit XML", instead of "Import as Model". Then run the file FEBio and it should give you a normal termination.
    In any case, I'll let you know when a fix is available.

    Best,

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

    Comment

    • pludo
      Junior Member
      • Jul 2023
      • 12

      #3
      Thanks Steve,

      Also to add to it, when you make your own reaction-diffusion model, it also shows the same error, and because the model is saved as a .fs2 file, there is no option of "edit as XML" to run it. Therefore currently i am not able to use reaction diffusion module at all. Let me know if you comeup with a fix whenever you do.

      Thanks in Advance

      Regards,
      Nisarg

      Comment

      • maas
        Lead Code Developer
        • Nov 2007
        • 3369

        #4
        Hi Nisarg,

        I think I fixed the problem, and it turns out that it was actually the export of these models that had a bug in it. Since it was the export, I don't think your fs2 models are affected and should work now as well. So please do a dev update and then give it another try. Let me know what you find.

        Best,

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

        Comment

        • pludo
          Junior Member
          • Jul 2023
          • 12

          #5
          Steve,

          Yes i believe that issue is solved however there are still some files where the initial condition is used on a part and not a surface(ch24.feb), it wont load the selection in the model and when selected a part for initial condition of a species, the file throws an error : "* Can't find map "IC" for parameter "value" *"

          Also is there a way to define the species name when defining a material under the material section, or is it only possible by editing the feb file?

          Thanks,
          Nisarg

          Comment

          • maas
            Lead Code Developer
            • Nov 2007
            • 3369

            #6
            Hi Nisarg,

            Yep, that was another bug, but I think I got that fixed as well now. Please do another dev update and let me know what you find.

            Thanks,

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

            Comment

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