DEMO_febio_0062_femur_load_01

Below is a demonstration for:

Contents

Keywords

clear; close all; clc;

Plot settings

fontSize=20;
faceAlpha1=0.8;
markerSize=40;
markerSize2=20;
lineWidth=3;

Control parameters

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

% Defining file names
febioFebFileNamePart='tempModel';
febioFebFileName=fullfile(savePath,[febioFebFileNamePart,'.feb']); %FEB file name
febioLogFileName=fullfile(savePath,[febioFebFileNamePart,'.txt']); %FEBio log file name
febioLogFileName_disp=[febioFebFileNamePart,'_disp_out.txt']; %Log file name for exporting displacement
febioLogFileName_force=[febioFebFileNamePart,'_force_out.txt']; %Log file name for exporting force
febioLogFileName_stress=[febioFebFileNamePart,'_stress_out.txt']; %Log file name for exporting stresses
febioLogFileName_strainEnergy=[febioFebFileNamePart,'_energy_out.txt']; %Log file name for exporting strain energy density

%Geometric parameters
distanceCut=250; %Distance from femur to cut bone at
corticalThickness=3; %Thickness used for cortical material definition
volumeFactor=2; %Factor to scale desired volume for interior elements w.r.t. boundary elements

%Define applied force
forceTotal=[-405 -246 -1717.5]; %x,y,z force in Newton

%Material parameters (MPa if spatial units are mm)
% Cortical bone
E_youngs1=17000; %Youngs modulus
nu1=0.25; %Poissons ratio

% Cancellous bone
E_youngs2=1500; %Youngs modulus
nu2=0.25; %Poissons ratio

% 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'; %'external' or 'internal'

Import bone surface model

[stlStruct] = import_STL(fullfile(pathNameSTL,'femur_iso.stl'));
F_bone=stlStruct.solidFaces{1}; %Faces
V_bone=stlStruct.solidVertices{1}; %Vertices

Scale and reorient

V_bone=V_bone.*1000; %Scale to mm

[F_bone,V_bone]=mergeVertices(F_bone,V_bone); % Merging nodes
Q1=euler2DCM([0 0 0.065*pi]);
V_bone=V_bone*Q1;
Q2=euler2DCM([-0.5*pi 0 0]);
V_bone=V_bone*Q2;
Q3=euler2DCM([0 0 0.36*pi]);
V_bone=V_bone*Q3;

Visualize bone surface

cFigure; hold on;
gpatch(F_bone,V_bone,'w','k',1);
% patchNormPlot(F_bone,V_bone)
axisGeom; camlight headlight;
drawnow;

Cut bone surface

%Slicing surface

[F_bone,V_bone,~,logicSide,~]=triSurfSlice(F_bone,V_bone,[],[0 0 -distanceCut],[0 0 1]);

F_bone=F_bone(logicSide==0,:);
[F_bone,V_bone]=patchCleanUnused(F_bone,V_bone);

Eb=patchBoundary(F_bone,V_bone);
indCurve=edgeListToCurve(Eb);
indCurve=indCurve(1:end-1);

cparSmooth.n=5;
cparSmooth.Method='HC';
[V_Eb_smooth]=patchSmooth(Eb,V_bone(:,[1 2]),[],cparSmooth);
V_bone(indCurve,[1 2])=V_Eb_smooth(indCurve,:);

cparSmooth.n=5;
cparSmooth.Method='HC';
cparSmooth.RigidConstraints=indCurve;
[V_bone]=patchSmooth(F_bone,V_bone,[],cparSmooth);

pointSpacing=mean(patchEdgeLengths(F_bone,V_bone));

[F_bone2,V_bone2]=regionTriMesh3D({V_bone(indCurve,:)},pointSpacing,0,'linear');
if dot(mean(patchNormal(F_bone2,V_bone2)),[0 0 1])>0
    F_bone2=fliplr(F_bone2);
end

[F_bone,V_bone,C_bone]=joinElementSets({F_bone,F_bone2},{V_bone,V_bone2});
[F_bone,V_bone]=mergeVertices(F_bone,V_bone);

Visualize bone surface

cFigure; hold on;
gpatch(F_bone,V_bone,C_bone,'k',1);
patchNormPlot(F_bone,V_bone);
axisGeom; camlight headlight;
drawnow;

Mesh using tetgen

%Find interior point
V_inner_bone=getInnerPoint(F_bone,V_bone);

Visualize interior point

cFigure; hold on;
gpatch(F_bone,V_bone,'w','none',0.5);
plotV(V_inner_bone,'r.','MarkerSize',25)
axisGeom; camlight headlight;
drawnow;

Regional mesh volume parameter

tetVolume=tetVolMeanEst(F_bone,V_bone); %Volume for regular tets

tetGenStruct.stringOpt='-pq1.2AaY';
tetGenStruct.Faces=F_bone;
tetGenStruct.Nodes=V_bone;
tetGenStruct.holePoints=[];
tetGenStruct.faceBoundaryMarker=C_bone; %Face boundary markers
tetGenStruct.regionPoints=V_inner_bone; %region points
tetGenStruct.regionA=tetVolume*volumeFactor;

[meshOutput]=runTetGen(tetGenStruct); %Run tetGen

% Access elements, nodes, and boundary faces
E=meshOutput.elements;
V=meshOutput.nodes;
Fb=meshOutput.facesBoundary;
Cb=meshOutput.boundaryMarker;
CE=meshOutput.elementMaterialID;
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- TETGEN Tetrahedral meshing --- 07-Jul-2020 21:58:13
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Writing SMESH file --- 07-Jul-2020 21:58:13
----> Adding node field
----> Adding facet field
----> Adding holes specification
----> Adding region specification
--- Done --- 07-Jul-2020 21:58:13
--- Running TetGen to mesh input boundary--- 07-Jul-2020 21:58:13
Opening /mnt/data/MATLAB/GIBBON/data/temp/temp.smesh.
Delaunizing vertices...
Delaunay seconds:  0.02198
Creating surface mesh ...
Surface mesh seconds:  0.004832
Recovering boundaries...
Boundary recovery seconds:  0.007776
Removing exterior tetrahedra ...
Spreading region attributes.
Exterior tets removal seconds:  0.0048
Recovering Delaunayness...
Delaunay recovery seconds:  0.004102
Refining mesh...
Refinement seconds:  0.106503
Optimizing mesh...
Optimization seconds:  0.007717

Writing /mnt/data/MATLAB/GIBBON/data/temp/temp.1.node.
Writing /mnt/data/MATLAB/GIBBON/data/temp/temp.1.ele.
Writing /mnt/data/MATLAB/GIBBON/data/temp/temp.1.face.
Writing /mnt/data/MATLAB/GIBBON/data/temp/temp.1.edge.

Output seconds:  0.104961
Total running seconds:  0.262971

Statistics:

  Input points: 2957
  Input facets: 5910
  Input segments: 8865
  Input holes: 0
  Input regions: 1

  Mesh points: 8145
  Mesh tetrahedra: 41862
  Mesh faces: 86679
  Mesh faces on exterior boundary: 5910
  Mesh faces on input facets: 5910
  Mesh edges on input segments: 8865
  Steiner points inside domain: 5188

--- Done --- 07-Jul-2020 21:58:13
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Importing TetGen files --- 07-Jul-2020 21:58:13
--- Done --- 07-Jul-2020 21:58:13

Define material regions in bone

indBoundary=unique(Fb(Cb==1,:));
DE=minDist(V,V(indBoundary,:));
logicCorticalNodes=DE<=corticalThickness;
logicCorticalElements=any(logicCorticalNodes(E),2);
logicCancellousElements=~logicCorticalElements;

E1=E(logicCorticalElements,:);
E2=E(logicCancellousElements,:);
E=[E1;E2];
elementMaterialID=[ones(size(E1,1),1);2*ones(size(E2,1),1);];
meshOutput.elements=E;
meshOutput.elementMaterialID=elementMaterialID;

Visualizing solid mesh

hFig=cFigure; hold on;
optionStruct.hFig=hFig;
meshView(meshOutput,optionStruct);
axisGeom;
drawnow;

Find femoral head

w=100;
f=[1 2 3 4];
v=w*[-1 -1 0; -1 1 0; 1 1 0; 1 -1 0];

p=[0 0 0];
Q=euler2DCM([0 (150/180)*pi 0]);
v=v*Q;
v=v+p;

Vr=V*Q';
Vr=Vr+p;
logicHeadNodes=Vr(:,3)<0;
logicHeadFaces=all(logicHeadNodes(Fb),2);
bcPrescribeList=unique(Fb(logicHeadFaces,:));

Visualize femoral head nodes for prescribed force boundary conditions

cFigure;
hold on;
gpatch(Fb,V,'w','k',1);
gpatch(f,v,'r','k',0.5);
plotV(V(bcPrescribeList,:),'r.','markerSize',15)
axisGeom; camlight headlight;
drawnow;

Work out force distribution on femoral head surface nodes

This is based on surface normal directions. Forces are assumed to only be able to act in a compressive sense on the bone.

[~,~,N]=patchNormal(fliplr(Fb),V); %Nodal normal directions

FX=[forceTotal(1) 0 0]; %X force vector
FY=[0 forceTotal(2) 0]; %Y force vector
FZ=[0 0 forceTotal(3)]; %Z force vector

wx=dot(N(bcPrescribeList,:),FX(ones(numel(bcPrescribeList),1),:),2);
wy=dot(N(bcPrescribeList,:),FY(ones(numel(bcPrescribeList),1),:),2);
wz=dot(N(bcPrescribeList,:),FZ(ones(numel(bcPrescribeList),1),:),2);

%Force zero
wx(wx>0)=0; wy(wy>0)=0; wz(wz>0)=0;

force_X=forceTotal(1).*ones(numel(bcPrescribeList),1).*wx;
force_Y=forceTotal(2).*ones(numel(bcPrescribeList),1).*wy;
force_Z=forceTotal(3).*ones(numel(bcPrescribeList),1).*wz;

force_X=force_X./sum(force_X(:)); %sum now equal to 1
force_X=force_X.*forceTotal(1); %sum now equal to desired

force_Y=force_Y./sum(force_Y(:)); %sum now equal to 1
force_Y=force_Y.*forceTotal(2); %sum now equal to desired

force_Z=force_Z./sum(force_Z(:)); %sum now equal to 1
force_Z=force_Z.*forceTotal(3); %sum now equal to desired
cFigure;
subplot(1,3,1);hold on;
title('F_x');
gpatch(Fb,V,'w','none',0.5);
quiverVec([0 0 0],FX,100,'k');
% scatterV(V(indicesHeadNodes,:),15)
quiverVec(V(bcPrescribeList,:),N(bcPrescribeList,:),10,force_X);
axisGeom; camlight headlight;
colormap(gca,gjet(250)); colorbar;

subplot(1,3,2);hold on;
title('F_y');
gpatch(Fb,V,'w','none',0.5);
quiverVec([0 0 0],FY,100,'k');
% scatterV(V(indicesHeadNodes,:),15)
quiverVec(V(bcPrescribeList,:),N(bcPrescribeList,:),10,force_Y);
axisGeom; camlight headlight;
colormap(gca,gjet(250)); colorbar;

subplot(1,3,3);hold on;
title('F_z');
gpatch(Fb,V,'w','none',0.5);
quiverVec([0 0 0],FZ,100,'k');
% scatterV(V(indicesHeadNodes,:),15)
quiverVec(V(bcPrescribeList,:),N(bcPrescribeList,:),10,force_Z);
axisGeom; camlight headlight;
colormap(gca,gjet(250)); colorbar;

drawnow;

Visualizing boundary conditions

F_bottomSupport=Fb(Cb==2,:);
bcSupportList=unique(F_bottomSupport(:));

hFig=cFigure; hold on;
gpatch(Fb,V,'kw','none',0.25);
hl(1)=plotV(V(bcSupportList,:),'k.','MarkerSize',25);
hl(2)=plotV(V(bcPrescribeList,:),'r.','MarkerSize',25);
legend(hl,{'BC support','BC force prescribe'});
axisGeom;
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='2.5';

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

%Control section
febio_spec.Control.analysis.ATTR.type='static';
febio_spec.Control.time_steps=numTimeSteps;
febio_spec.Control.step_size=1/numTimeSteps;
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;
febio_spec.Control.max_refs=max_refs;
febio_spec.Control.max_ups=max_ups;

%Material section
febio_spec.Material.material{1}.ATTR.type='neo-Hookean';
febio_spec.Material.material{1}.ATTR.id=1;
febio_spec.Material.material{1}.E=E_youngs1;
febio_spec.Material.material{1}.v=nu1;

febio_spec.Material.material{2}.ATTR.type='neo-Hookean';
febio_spec.Material.material{2}.ATTR.id=2;
febio_spec.Material.material{2}.E=E_youngs2;
febio_spec.Material.material{2}.v=nu2;

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

% -> Elements
febio_spec.Geometry.Elements{1}.ATTR.type='tet4'; %Element type of this set
febio_spec.Geometry.Elements{1}.ATTR.mat=1; %material index for this set
febio_spec.Geometry.Elements{1}.ATTR.name='CorticalBone'; %Name of the element set
febio_spec.Geometry.Elements{1}.elem.ATTR.id=(1:1:size(E1,1))'; %Element id's
febio_spec.Geometry.Elements{1}.elem.VAL=E1;

febio_spec.Geometry.Elements{2}.ATTR.type='tet4'; %Element type of this set
febio_spec.Geometry.Elements{2}.ATTR.mat=2; %material index for this set
febio_spec.Geometry.Elements{2}.ATTR.name='CancellousBone'; %Name of the element set
febio_spec.Geometry.Elements{2}.elem.ATTR.id=size(E1,1)+(1:1:size(E2,1))'; %Element id's
febio_spec.Geometry.Elements{2}.elem.VAL=E2;

% -> NodeSets
febio_spec.Geometry.NodeSet{1}.ATTR.name='bcSupportList';
febio_spec.Geometry.NodeSet{1}.node.ATTR.id=bcSupportList(:);

febio_spec.Geometry.NodeSet{2}.ATTR.name='indicesHeadSurfaceNodes';
febio_spec.Geometry.NodeSet{2}.node.ATTR.id=bcPrescribeList(:);

%Boundary condition section
% -> Fix boundary conditions
febio_spec.Boundary.fix{1}.ATTR.bc='x';
febio_spec.Boundary.fix{1}.ATTR.node_set=febio_spec.Geometry.NodeSet{1}.ATTR.name;
febio_spec.Boundary.fix{2}.ATTR.bc='y';
febio_spec.Boundary.fix{2}.ATTR.node_set=febio_spec.Geometry.NodeSet{1}.ATTR.name;
febio_spec.Boundary.fix{3}.ATTR.bc='z';
febio_spec.Boundary.fix{3}.ATTR.node_set=febio_spec.Geometry.NodeSet{1}.ATTR.name;

febio_spec.MeshData.NodeData{1}.ATTR.name='force_X';
febio_spec.MeshData.NodeData{1}.ATTR.node_set=febio_spec.Geometry.NodeSet{2}.ATTR.name;
febio_spec.MeshData.NodeData{1}.node.VAL=force_X;
febio_spec.MeshData.NodeData{1}.node.ATTR.lid=(1:1:numel(bcPrescribeList))';

febio_spec.MeshData.NodeData{2}.ATTR.name='force_Y';
febio_spec.MeshData.NodeData{2}.ATTR.node_set=febio_spec.Geometry.NodeSet{2}.ATTR.name;
febio_spec.MeshData.NodeData{2}.node.VAL=force_Y;
febio_spec.MeshData.NodeData{2}.node.ATTR.lid=(1:1:numel(bcPrescribeList))';

febio_spec.MeshData.NodeData{3}.ATTR.name='force_Z';
febio_spec.MeshData.NodeData{3}.ATTR.node_set=febio_spec.Geometry.NodeSet{2}.ATTR.name;
febio_spec.MeshData.NodeData{3}.node.VAL=force_Z;
febio_spec.MeshData.NodeData{3}.node.ATTR.lid=(1:1:numel(bcPrescribeList))';

%Loads section
% -> Prescribed nodal forces
febio_spec.Loads.nodal_load{1}.ATTR.bc='x';
febio_spec.Loads.nodal_load{1}.ATTR.node_set=febio_spec.Geometry.NodeSet{2}.ATTR.name;
febio_spec.Loads.nodal_load{1}.scale.ATTR.lc=1;
febio_spec.Loads.nodal_load{1}.scale.VAL=1;
febio_spec.Loads.nodal_load{1}.value.ATTR.node_data=febio_spec.MeshData.NodeData{1}.ATTR.name;

febio_spec.Loads.nodal_load{2}.ATTR.bc='y';
febio_spec.Loads.nodal_load{2}.ATTR.node_set=febio_spec.Geometry.NodeSet{2}.ATTR.name;
febio_spec.Loads.nodal_load{2}.scale.ATTR.lc=1;
febio_spec.Loads.nodal_load{2}.scale.VAL=1;
febio_spec.Loads.nodal_load{2}.value.ATTR.node_data=febio_spec.MeshData.NodeData{2}.ATTR.name;

febio_spec.Loads.nodal_load{3}.ATTR.bc='z';
febio_spec.Loads.nodal_load{3}.ATTR.node_set=febio_spec.Geometry.NodeSet{2}.ATTR.name;
febio_spec.Loads.nodal_load{3}.scale.ATTR.lc=1;
febio_spec.Loads.nodal_load{3}.scale.VAL=1;
febio_spec.Loads.nodal_load{3}.value.ATTR.node_data=febio_spec.MeshData.NodeData{3}.ATTR.name;

%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=',';
febio_spec.Output.logfile.node_data{1}.VAL=1:size(V,1);

febio_spec.Output.logfile.element_data{1}.ATTR.file=febioLogFileName_stress;
febio_spec.Output.logfile.element_data{1}.ATTR.data='s1;s2;s3';
febio_spec.Output.logfile.element_data{1}.ATTR.delim=',';
febio_spec.Output.logfile.element_data{1}.VAL=1:1:size(E,1); %Rigid body material id

febio_spec.Output.logfile.element_data{2}.ATTR.file=febioLogFileName_strainEnergy;
febio_spec.Output.logfile.element_data{2}.ATTR.data='sed';
febio_spec.Output.logfile.element_data{2}.ATTR.delim=',';
febio_spec.Output.logfile.element_data{2}.VAL=1:1:size(E,1);

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.disp_log_on=1; %Display convergence information in the command window
febioAnalysis.runMode=runMode;%'internal';
febioAnalysis.t_check=0.25; %Time for checking log file (dont set too small)
febioAnalysis.maxtpi=1e99; %Max analysis time
febioAnalysis.maxLogCheckTime=10; %Max log file checking time

[runFlag]=runMonitorFEBio(febioAnalysis);%START FEBio NOW!!!!!!!!
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- STARTING FEBIO JOB --- 07-Jul-2020 21:58:20
Waiting for log file...
Proceeding to check log file...07-Jul-2020 21:58:21
------- converged at time : 0.1
------- converged at time : 0.2
------- converged at time : 0.3
------- converged at time : 0.4
------- converged at time : 0.5
------- converged at time : 0.6
------- converged at time : 0.7
------- converged at time : 0.8
------- converged at time : 0.9
------- converged at time : 1
--- Done --- 07-Jul-2020 21:58:37

Import FEBio results

if runFlag==1 %i.e. a succesful run
    % Importing nodal displacancellousBones from a log file
    [time_mat, N_disp_mat,~]=importFEBio_logfile(fullfile(savePath,febioLogFileName_disp)); %Nodal displacancellousBones
    time_mat=[0; time_mat(:)]; %Time

    N_disp_mat=N_disp_mat(:,2:end,:);
    sizImport=size(N_disp_mat);
    sizImport(3)=sizImport(3)+1;
    N_disp_mat_n=zeros(sizImport);
    N_disp_mat_n(:,:,2:end)=N_disp_mat;
    N_disp_mat=N_disp_mat_n;
    DN=N_disp_mat(:,:,end);
    DN_magnitude=sqrt(sum(DN(:,3).^2,2));
    V_DEF=N_disp_mat+repmat(V,[1 1 size(N_disp_mat,3)]);

Importing element strain energies from a log file

    [~,E_energy,~]=importFEBio_logfile(fullfile(savePath,febioLogFileName_strainEnergy)); %Element strain energy

    %Remove nodal index column
    E_energy=E_energy(:,2:end,:);

    %Add initial state i.e. zero energy
    sizImport=size(E_energy);
    sizImport(3)=sizImport(3)+1;
    E_energy_mat_n=zeros(sizImport);
    E_energy_mat_n(:,:,2:end)=E_energy;
    E_energy=E_energy_mat_n;
    [FE_face,C_energy_face]=element2patch(E,E_energy(:,:,end),'tet4');
    [CV]=faceToVertexMeasure(FE_face,V,C_energy_face);
    [indBoundary]=tesBoundary(FE_face,V);
    Fb=FE_face(indBoundary,:);

Plotting the simulated results using anim8 to visualize and animate deformations

    axLim=[min(min(V_DEF,[],3),[],1); max(max(V_DEF,[],3),[],1)];

    % Create basic view and store graphics handle to initiate animation
    hf=cFigure; %Open figure
    title('Strain energy density')
    gtitle([febioFebFileNamePart,': Press play to animate']);
    hp1=gpatch(Fb,V_DEF(:,:,end),CV,'k',1); %Add graphics object to animate
    hp1.FaceColor='Interp';

    axisGeom(gca,fontSize);
    colormap(gjet(250)); colorbar;
    caxis([0 max(E_energy(:))/25]);
    axis(axLim(:)'); %Set axis limits statically
    camlight headlight;

    % Set up animation features
    animStruct.Time=time_mat; %The time vector
    for qt=1:1:size(N_disp_mat,3) %Loop over time increments
        DN=N_disp_mat(:,:,qt); %Current displacancellousBone

        [FE_face,C_energy_face]=element2patch(E,E_energy(:,:,qt),'tet4');
        [CV]=faceToVertexMeasure(FE_face,V,C_energy_face);

        %Set entries in animation structure
        animStruct.Handles{qt}=[hp1 hp1]; %Handles of objects to animate
        animStruct.Props{qt}={'Vertices','CData'}; %Properties of objects to animate
        animStruct.Set{qt}={V_DEF(:,:,qt),CV}; %Property values for to set in order to animate
    end
    anim8(hf,animStruct); %Initiate animation feature
    drawnow;
end

GIBBON footer text

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.

Copyright (C) 2006-2020 Kevin Mattheus Moerman

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.