Parameter optimization for biphasic confined compression stress-relaxation

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  • takazam
    Junior Member
    • Mar 2011
    • 16

    #16
    Hi,

    Are these files still compatible with the latest FEBio version. I am getting the following error

    Failed importing FEBio.file
    Fatal ERROR: unrecoverable error (line 52)

    Thanks
    Michael

    Comment

    • ateshian
      Developer
      • Dec 2007
      • 1824

      #17
      Hi Michael,

      Only the model file (CCsrlxFit.feb) can be imported into PreView. The optimization file (CCsrlxOpt.feb), which is created manually, should be opened in a text editor.

      Best,

      Gerard

      Comment

      • takazam
        Junior Member
        • Mar 2011
        • 16

        #18
        Hi Gerard,

        Thanks for the speedy response. I have tried to run the optimization file from the command line, and I am getting an error message (Error message attached). The other file is running okay. Am I doing something wrong here ? OPT_Error.jpgAre there steps I am missing or something I am not doing correctly. My aim is to run your files first and then start working on my own model and experimental data

        Thanks

        Michael

        Comment

        • ateshian
          Developer
          • Dec 2007
          • 1824

          #19
          Hi Michael,

          To run an optimization file you need to use -s instead of -i.

          Best,

          Gerard

          Comment

          • takazam
            Junior Member
            • Mar 2011
            • 16

            #20
            Hi Gerard,

            I am getting the following error when I try to run the optimization file (FATAL ERROR: failed openning input file CCsrlxFit.feb). I have checked the file name and its correct and the CCsrlxFit model file run okay by its self. I was wondering if its a matter of running the wrong FEBio version. As stated on my previous discussion I have viscoelastic compressive experimental data that I want to see to simulate using the bi phasic method
            Untitled.jpg

            2nd question is: Do we have an FEBio biphasic model that I can use for transversely isotropic viscoelastic tissue properties. I have experimental data obtained when the load is applied with the muscle fibres oriented at the following angles 0, 15, 30, 45, 60, 75 and 90 degrees.

            Thanks

            Michael
            Last edited by takazam; 06-04-2013, 03:39 AM. Reason: Correcting the format

            Comment

            • hamed71200
              Junior Member
              • Apr 2013
              • 24

              #21
              Originally posted by ateshian View Post
              You can submit a feature request to add a "transversely isotropic" material in FEBio.
              How can I do that?

              Hamed

              Comment

              • ateshian
                Developer
                • Dec 2007
                • 1824

                #22
                Hi Michael,

                If you run the optimization file from a folder other than where it resides you must include the full path to the model filename in the optimization file.

                Best,

                Gerard

                Comment

                • ateshian
                  Developer
                  • Dec 2007
                  • 1824

                  #23
                  On the main MRL forum page click on "Send bug reports and request new features for FEBio."

                  Gerard

                  Comment

                  • takazam
                    Junior Member
                    • Mar 2011
                    • 16

                    #24
                    Dear Gerard

                    Thanks, optimization file is now running

                    Best Regards

                    Michael

                    Comment

                    • hamed71200
                      Junior Member
                      • Apr 2013
                      • 24

                      #25
                      Dr. Ateshian,

                      I am trying to run optimization for a tension test using a biphasic model. Neo-Hookean viscoelastic was chosen for the solid phase.
                      The first 10 points in the load curve are related to constant strain rate ramp and proceeding points are showing relaxation. While the optimization is running, in all iterations, when I compared the current column with required column, I saw that the load in the current column is increasing in the first 12 points. It seems that there is an inconsistency between the FEBio file and loadcurve in terms of time. I checked FEBio file and the time for prescribed displacement is the same as ramp time in the load curve data.

                      I would like to know if there is an explanation for it.
                      To help you understand the problem better, I have attached the FEBio file and Optimization file. Tension.febOp.feb

                      Regards,
                      Hamed

                      Comment

                      • ateshian
                        Developer
                        • Dec 2007
                        • 1824

                        #26
                        Hi Hamed,

                        You did not use must points in your Tension.feb file. This means that FEBio will not necessarily pass through the time point corresponding to the end of the ramp displacement (t=18 s according to your Op.feb file). That's why you are getting this problem.

                        Best,

                        Gerard

                        Comment

                        • ateshian
                          Developer
                          • Dec 2007
                          • 1824

                          #27
                          To run this example in FEBio2, use CCsrlxFit2.feb for the model file and CCsrlxOpt2.feb for the optimization file. Use the following command to run the optimization:
                          Code:
                          febio2 -i CCsrlxFit2.feb -s CCsrlxOpt2.feb
                          Gerard

                          Comment

                          • Sara
                            Junior Member
                            • Aug 2015
                            • 27

                            #28
                            Hi Gerard,

                            Thanks for example.

                            I am doing Optimisation on viscoelastic and hyperelastic material coefficients by simulating indentation test. By doing the optimisation, I got some coefficients, but the force-deformation graph using optimised values, have some positive loads which means tension. These positive values have effects on objective function and may change my final results.

                            I thought may be not a bad idea to change these positive values to zero, however I couldn't find any way to do it. Do you have any suggestion about this problem?

                            Opt-Sara-70%-all-param.febSara-70%.zip

                            Many thanks
                            Sara

                            Comment

                            • hipop1901
                              Junior Member
                              • Dec 2014
                              • 27

                              #29
                              Hi Gerard,

                              I found parameters in the "solid mixture" cannot be optimized. Is it possible to fix that? Correct me if I am wrong.

                              For example
                              <material id="1" name="Material1" type="solid mixture">
                              <solid type="fiber-pow-linear">
                              <E>20</E>
                              <beta>6</beta>
                              <lam0>1.05</lam0>
                              <fiber type="vector">0,0,1</fiber>
                              </solid>
                              <solid type="Mooney-Rivlin">
                              <density>1</density>
                              <c1>0.2</c1>
                              <c2>0.01</c2>
                              <k>6</k>
                              </solid>
                              </material>

                              Comment

                              • ateshian
                                Developer
                                • Dec 2007
                                • 1824

                                #30
                                Hi Bo,

                                When using solid mixtures, you need to assign a name to each mixture component, then use that name in the optimization file. For example, in the model file,
                                Code:
                                		<material id="1" name="Cartilage" type="biphasic">
                                			<phi0>0.2</phi0>
                                			<solid type="solid mixture">
                                				<solid name="fibers" type="spherical fiber distribution">
                                					<beta>2</beta>
                                					<ksi>3</ksi>
                                				</solid>
                                				<solid name="ground" type="neo-Hookean">
                                					<density>1</density>
                                					<E>0.92</E>
                                					<v>0</v>
                                				</solid>
                                			</solid>
                                			<permeability type="perm-const-iso">
                                				<perm>0.002</perm>
                                			</permeability>
                                		</material>
                                Then, in the optimization file,
                                Code:
                                  <Parameters>
                                    <param name="Cartilage.solid.ground.E">0.92, 0.2, 2.0,1</param>
                                    <param name="Cartilage.solid.fibers.ksi">2, 0.2, 10,1</param>
                                    <param name="Cartilage.permeability.perm">0.002, 0.0005, 0.01,0.005</param>
                                  </Parameters>
                                Best,

                                Gerard

                                Comment

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