DEMO_febio_0024_active_contraction_tongue

Importing geometry for a basic tongue model
Assigning fiber directions
Defining the boundary conditions
Coding the febio structure
Running the model
Importing and visualizing results

Keywords
Control parameters
Set up geometry for the tongue model
Defining fiber directions and boundary conditions
Defining the FEBio input structure
Quick viewing of the FEBio input file structure
Exporting the FEBio input file
Running the FEBio analysis
Import FEBio results

Keywords

febio_spec version 4.0
febio, FEBio
pressure loading
hexahedral elements, hex8
tongue
static, solid
Active contraction
hyperelastic, Ogden
displacement logfile

clear; close all; clc;

Plot settings

fontSize=15;
markerSize=25;
markerSize2=20;
plotColor='rw';
vectorPlotSize=10;

Control parameters

% Path names
defaultFolder = fileparts(fileparts(mfilename('fullpath')));
savePath=fullfile(defaultFolder,'data','temp');

% Defining file names
febioFebFileNamePart='tempModel';
febioFebFileName=fullfile(savePath,[febioFebFileNamePart,'.feb']); %FEB file name
febioLogFileName=[febioFebFileNamePart,'.txt']; %FEBio log file name
febioLogFileName_disp=[febioFebFileNamePart,'_disp_out.txt']; %Log file name for exporting displacement

%Material parameter set
c1=1e-3; %Shear-modulus-like parameter
m1=2; %Material parameter setting degree of non-linearity
ksi=c1*100; %Fiber "modulus"
alphaPar=1e-20;
beta=3;
k_factor=1e2; %Bulk modulus factor
k=0.5.*(c1+ksi)*k_factor; %Bulk modulus
T0=10e-3; %Active stress

% FEA control settings
numTimeSteps=10; %Number of time steps desired
max_refs=25; %Max reforms
max_ups=0; %Set to zero to use full-Newton iterations
opt_iter=6; %Optimum number of iterations
max_retries=5; %Maximum number of retires
dtmin=(1/numTimeSteps)/100; %Minimum time step size
dtmax=1/numTimeSteps; %Maximum time step size

runMode='external';% 'internal' or 'external'

Set up geometry for the tongue model

% Import model geometry. This geometry was obtained with permission from the Artisynth project (https://www.artisynth.org/Demo/BiomechanicalTongueModel)
loadNameOff=fullfile(defaultFolder,'data','OFF','tongue_mesh.off'); %File name for off file
[E,V] = import_off(loadNameOff); %Import mesh data

[F,~]=element2patch(E,[]); %Get mesh faces for visualization

Visualize imported mesh

% Plotting model
cFigure; hold on;
gtitle('Tongue model geometry',fontSize);
gpatch(F,V,plotColor,'k',0.5); %Visualize mesh faces
% patchNormPlot(F,V); %Visualize normal directions
axisGeom(gca,fontSize);
camlight headlight;
drawnow;

Defining fiber directions and boundary conditions

Fiber directions are here defined as running from the bottom of elements to the top of elements, this is not physiological.

%Get boundary faces
[indBoundary]=tesBoundary(F,V); %Get boundary face indices
Fb=F(indBoundary,:); %Boundary faces

%Get top and bottom faces for boundary conditions
F_element_bottoms=E(:,[1 4 8 5]); %Get element bottom faces
F_element_tops=E(:,[2 3 7 6]); %Get element top faces

X=V(:,1); Y=V(:,2); Z=V(:,3); % Nodal coordinate components

%Compute element centre coordinates (used as fiber origins in visualization)
[VE]=patchCentre(E,V);

%Define fibers as going from one face center to the other
e1_dir_bottom=patchCentre(F_element_bottoms,V); %Middle of bottom faces
e1_dir_top=patchCentre(F_element_tops,V); %Middle of top faces
e1_dir=vecnormalize(e1_dir_top-e1_dir_bottom); %Normalized fiber vectors

[e2_dir,e3_dir]=vectorOrthogonalPair(e1_dir); %Get orthogonal vector pair

%Get boundary directions faces to set-up support
F_bottom=F_element_bottoms(all(ismember(F_element_bottoms,Fb),2),:); %The faces at the bottom
bcSupportList=unique(F_bottom(:)); %The node list for the bottom nodes

Warning: Second input (vertices) no longer required. Update code to avoid
future error.

Visualize boundary conditions

cFigure; hold on;
gtitle('Boundary conditions and fiber directions',fontSize);

gpatch(Fb,V,plotColor,'none',0.25);
hf(1)=quiverVec(VE,e1_dir,10,'r');
hf(2)=quiverVec(VE,e2_dir,5,'g');
hf(3)=quiverVec(VE,e3_dir,5,'b');
hf(4)=plotV(V(bcSupportList,:),'k.','MarkerSize',markerSize);

legend(hf,{'e1-direction (fiber)','e2-direction','e3-direction','Bc fix nodes'});

axisGeom(gca,fontSize);
camlight headlight;
drawnow;

Defining the FEBio input structure

See also febioStructTemplate and febioStruct2xml and the FEBio user manual.

%Get a template with default settings
[febio_spec]=febioStructTemplate;

%febio_spec version
febio_spec.ATTR.version='4.0';

%Module section
febio_spec.Module.ATTR.type='solid';

%Control section
febio_spec.Control.analysis='STATIC';
febio_spec.Control.time_steps=numTimeSteps;
febio_spec.Control.step_size=1/numTimeSteps;
febio_spec.Control.solver.max_refs=max_refs;
febio_spec.Control.solver.qn_method.max_ups=max_ups;
febio_spec.Control.time_stepper.dtmin=dtmin;
febio_spec.Control.time_stepper.dtmax=dtmax;
febio_spec.Control.time_stepper.max_retries=max_retries;
febio_spec.Control.time_stepper.opt_iter=opt_iter;

%Material section
materialName1='Material1';
febio_spec.Material.material{1}.ATTR.name=materialName1;
febio_spec.Material.material{1}.ATTR.type='solid mixture';
febio_spec.Material.material{1}.ATTR.id=1;

%Solid component
febio_spec.Material.material{1}.solid{1}.ATTR.type='Ogden unconstrained';
febio_spec.Material.material{1}.solid{1}.c1=c1;
febio_spec.Material.material{1}.solid{1}.m1=m1;
febio_spec.Material.material{1}.solid{1}.c2=c1;
febio_spec.Material.material{1}.solid{1}.m2=-m1;
febio_spec.Material.material{1}.solid{1}.cp=k;

%The passive fiber component
febio_spec.Material.material{1}.solid{2}.ATTR.type='fiber-exp-pow';
febio_spec.Material.material{1}.solid{2}.ksi=ksi;
febio_spec.Material.material{1}.solid{2}.alpha=alphaPar;
febio_spec.Material.material{1}.solid{2}.beta=beta;
febio_spec.Material.material{1}.solid{2}.fiber.ATTR.type='vector';
febio_spec.Material.material{1}.solid{2}.fiber.VAL=[1 0 0];

%The active fiber component
febio_spec.Material.material{1}.solid{3}.ATTR.type='prescribed uniaxial active contraction';
febio_spec.Material.material{1}.solid{3}.T0.VAL=T0;
febio_spec.Material.material{1}.solid{3}.T0.ATTR.lc=1;

% Mesh section
% -> Nodes
febio_spec.Mesh.Nodes{1}.ATTR.name='Object1'; %The node set name
febio_spec.Mesh.Nodes{1}.node.ATTR.id=(1:size(V,1))'; %The node id's
febio_spec.Mesh.Nodes{1}.node.VAL=V; %The nodel coordinates

% -> Elements
partName1='Part1';
febio_spec.Mesh.Elements{1}.ATTR.name=partName1; %Name of this part
febio_spec.Mesh.Elements{1}.ATTR.type='hex8'; %Element type
febio_spec.Mesh.Elements{1}.elem.ATTR.id=(1:1:size(E,1))'; %Element id's
febio_spec.Mesh.Elements{1}.elem.VAL=E; %The element matrix

% -> NodeSets
nodeSetName1='bcSupportList';
febio_spec.Mesh.NodeSet{1}.ATTR.name=nodeSetName1;
febio_spec.Mesh.NodeSet{1}.VAL=mrow(bcSupportList);

%MeshDomains section
febio_spec.MeshDomains.SolidDomain.ATTR.name=partName1;
febio_spec.MeshDomains.SolidDomain.ATTR.mat=materialName1;

%MeshData section
% -> ElementData
febio_spec.MeshData.ElementData{1}.ATTR.elem_set=partName1;
febio_spec.MeshData.ElementData{1}.ATTR.type='mat_axis';

for q=1:1:size(E,1)
    febio_spec.MeshData.ElementData{1}.elem{q}.ATTR.lid=q;
    febio_spec.MeshData.ElementData{1}.elem{q}.a=e1_dir(q,:);
    febio_spec.MeshData.ElementData{1}.elem{q}.d=e2_dir(q,:);
end

%Boundary condition section
% -> Fix boundary conditions
febio_spec.Boundary.bc{1}.ATTR.name='zero_displacement_xyz';
febio_spec.Boundary.bc{1}.ATTR.type='zero displacement';
febio_spec.Boundary.bc{1}.ATTR.node_set=nodeSetName1;
febio_spec.Boundary.bc{1}.x_dof=1;
febio_spec.Boundary.bc{1}.y_dof=1;
febio_spec.Boundary.bc{1}.z_dof=1;

%LoadData section
% -> load_controller
febio_spec.LoadData.load_controller{1}.ATTR.name='LC_1';
febio_spec.LoadData.load_controller{1}.ATTR.id=1;
febio_spec.LoadData.load_controller{1}.ATTR.type='loadcurve';
febio_spec.LoadData.load_controller{1}.interpolate='LINEAR';
%febio_spec.LoadData.load_controller{1}.extend='CONSTANT';
febio_spec.LoadData.load_controller{1}.points.pt.VAL=[0 0; 1 1];

%Output section
% -> log file
febio_spec.Output.logfile.ATTR.file=febioLogFileName;
febio_spec.Output.logfile.node_data{1}.ATTR.file=febioLogFileName_disp;
febio_spec.Output.logfile.node_data{1}.ATTR.data='ux;uy;uz';
febio_spec.Output.logfile.node_data{1}.ATTR.delim=',';

Quick viewing of the FEBio input file structure

The febView function can be used to view the xml structure in a MATLAB figure window.

febView(febio_spec); %Viewing the febio file

Exporting the FEBio input file

Exporting the febio_spec structure to an FEBio input file is done using the febioStruct2xml function.

febioStruct2xml(febio_spec,febioFebFileName); %Exporting to file and domNode

Running the FEBio analysis

To run the analysis defined by the created FEBio input file the runMonitorFEBio function is used. The input for this function is a structure defining job settings e.g. the FEBio input file name. The optional output runFlag informs the user if the analysis was run succesfully.

febioAnalysis.run_filename=febioFebFileName; %The input file name
febioAnalysis.run_logname=febioLogFileName; %The name for the log file
febioAnalysis.disp_on=1; %Display information on the command window
febioAnalysis.runMode=runMode;

[runFlag]=runMonitorFEBio(febioAnalysis);%START FEBio NOW!!!!!!!!

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-------->    RUNNING/MONITORING FEBIO JOB    <-------- 20-Apr-2023 11:12:39
FEBio path: /home/kevin/FEBioStudio2/bin/febio4
# Attempt removal of existing log files                20-Apr-2023 11:12:39
 * Removal succesful                                   20-Apr-2023 11:12:39
# Attempt removal of existing .xplt files              20-Apr-2023 11:12:39
 * Removal succesful                                   20-Apr-2023 11:12:39
# Starting FEBio...                                    20-Apr-2023 11:12:39
  Max. total analysis time is: Inf s
 * Waiting for log file creation                       20-Apr-2023 11:12:39
   Max. wait time: 30 s
 * Log file found.                                     20-Apr-2023 11:12:40
# Parsing log file...                                  20-Apr-2023 11:12:40
    number of iterations   : 7                         20-Apr-2023 11:12:41
    number of reformations : 7                         20-Apr-2023 11:12:41
------- converged at time : 0.0333333                  20-Apr-2023 11:12:41
    number of iterations   : 5                         20-Apr-2023 11:12:41
    number of reformations : 5                         20-Apr-2023 11:12:41
------- converged at time : 0.0642682                  20-Apr-2023 11:12:41
    number of iterations   : 5                         20-Apr-2023 11:12:41
    number of reformations : 5                         20-Apr-2023 11:12:41
------- converged at time : 0.101795                   20-Apr-2023 11:12:41
    number of iterations   : 4                         20-Apr-2023 11:12:41
    number of reformations : 4                         20-Apr-2023 11:12:41
------- converged at time : 0.145285                   20-Apr-2023 11:12:41
    number of iterations   : 6                         20-Apr-2023 11:12:41
    number of reformations : 6                         20-Apr-2023 11:12:41
------- converged at time : 0.200076                   20-Apr-2023 11:12:41
    number of iterations   : 4                         20-Apr-2023 11:12:41
    number of reformations : 4                         20-Apr-2023 11:12:41
------- converged at time : 0.254868                   20-Apr-2023 11:12:41
    number of iterations   : 4                         20-Apr-2023 11:12:41
    number of reformations : 4                         20-Apr-2023 11:12:41
------- converged at time : 0.318701                   20-Apr-2023 11:12:41
    number of iterations   : 4                         20-Apr-2023 11:12:41
    number of reformations : 4                         20-Apr-2023 11:12:41
------- converged at time : 0.389768                   20-Apr-2023 11:12:41
    number of iterations   : 6                         20-Apr-2023 11:12:41
    number of reformations : 6                         20-Apr-2023 11:12:41
------- converged at time : 0.466621                   20-Apr-2023 11:12:41
    number of iterations   : 5                         20-Apr-2023 11:12:41
    number of reformations : 5                         20-Apr-2023 11:12:41
------- converged at time : 0.543474                   20-Apr-2023 11:12:41
    number of iterations   : 6                         20-Apr-2023 11:12:41
    number of reformations : 6                         20-Apr-2023 11:12:41
------- converged at time : 0.622537                   20-Apr-2023 11:12:41
    number of iterations   : 4                         20-Apr-2023 11:12:41
    number of reformations : 4                         20-Apr-2023 11:12:41
------- converged at time : 0.701599                   20-Apr-2023 11:12:41
    number of iterations   : 4                         20-Apr-2023 11:12:41
    number of reformations : 4                         20-Apr-2023 11:12:41
------- converged at time : 0.78485                    20-Apr-2023 11:12:41
    number of iterations   : 4                         20-Apr-2023 11:12:41
    number of reformations : 4                         20-Apr-2023 11:12:41
------- converged at time : 0.87145                    20-Apr-2023 11:12:41
    number of iterations   : 4                         20-Apr-2023 11:12:42
    number of reformations : 4                         20-Apr-2023 11:12:42
------- converged at time : 0.96073                    20-Apr-2023 11:12:42
    number of iterations   : 3                         20-Apr-2023 11:12:42
    number of reformations : 3                         20-Apr-2023 11:12:42
------- converged at time : 1                          20-Apr-2023 11:12:42
 Elapsed time : 0:00:02                                20-Apr-2023 11:12:42
 N O R M A L   T E R M I N A T I O N
# Done                                                 20-Apr-2023 11:12:42
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Import FEBio results

if runFlag==1 %i.e. a succesful run

Importing nodal displacements from a log file

    dataStruct=importFEBio_logfile(fullfile(savePath,febioLogFileName_disp),0,1);

    %Access data
    N_disp_mat=dataStruct.data; %Displacement
    timeVec=dataStruct.time; %Time

    %Create deformed coordinate set
    V_DEF=N_disp_mat+repmat(V,[1 1 size(N_disp_mat,3)]);

Plotting the simulated results using anim8 to visualize and animate deformations

    DN_magnitude=sqrt(sum(N_disp_mat(:,:,end).^2,2)); %Current displacement magnitude

    % Create basic view and store graphics handle to initiate animation
    hf=cFigure; %Open figure
    gtitle([febioFebFileNamePart,': Press play to animate']);
    title('Displacement magnitude [mm]','Interpreter','Latex')
    hp=gpatch(Fb,V_DEF(:,:,end),DN_magnitude,'k',1); %Add graphics object to animate
    hp.Marker='.';
    hp.MarkerSize=markerSize2;
    hp.FaceColor='interp';

    axisGeom(gca,fontSize);
    colormap(gjet(250)); colorbar;
    caxis([0 max(DN_magnitude)]);
    axis(axisLim(V_DEF)); %Set axis limits statically
    camlight headlight;

    % Set up animation features
    animStruct.Time=timeVec; %The time vector
    for qt=1:1:size(N_disp_mat,3) %Loop over time increments
        DN_magnitude=sqrt(sum(N_disp_mat(:,:,qt).^2,2)); %Current displacement magnitude

        %Set entries in animation structure
        animStruct.Handles{qt}=[hp hp]; %Handles of objects to animate
        animStruct.Props{qt}={'Vertices','CData'}; %Properties of objects to animate
        animStruct.Set{qt}={V_DEF(:,:,qt),DN_magnitude}; %Property values for to set in order to animate
    end
    anim8(hf,animStruct); %Initiate animation feature
    drawnow;

end

Publishing GIF animation in html folder to render documentation with gif

% Uncomment to re-create gif
% [docsPath,docName,~]=fileparts(mfilename('fullpath'));
% inputStruct.defaultPath=fullfile(defaultFolder,'docs','html');
% inputStruct.imName=[docName,'_anim8'];
% exportGifAnim8(hf,inputStruct,0);

GIBBON www.gibboncode.org

Kevin Mattheus Moerman, [email protected]

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License: https://github.com/gibbonCode/GIBBON/blob/master/LICENSE

GIBBON: The Geometry and Image-based Bioengineering add-On. A toolbox for image segmentation, image-based modeling, meshing, and finite element analysis.

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