DEMO_febio_0055_clot_tube_slide_pressure.m

Below is a demonstration for:

Building geometry for a spherical blob with tetrahedral elements which is being aspirated into a tube. This demo consists off:
Defining the boundary conditions
Coding the febio structure
Running the model
Importing and visualizing the displacement results

Keywords
Plot settings
Control parameters
Creating model geometry and mesh
Creating tube model
Join model node sets
Get contact surfaces
Get pressure surface
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 3.0
febio, FEBio
blood clot
contact, sliding, friction
rigid body constraints
hexahedral elements, hex8
quadrilaterl elements, quad4
shell elements
sphere
hyperelastic, Ogden
displacement logfile
stress logfile

clear; close all; clc;

Plot settings

fontSize=15;
faceAlpha1=0.8;
faceAlpha2=0.3;
markerSize=40;
lineWidth=3;
cMap=[1 0.5 0.4; 0.9 0.3 0.27; 0.8 0.2 0.18; 0.7 0.1 0.09; 0.6 0 0; 0.5 0 0; 0.4 0 0;];
[cMap]=resampleColormap(cMap,250);

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=fullfile(savePath,[febioFebFileNamePart,'.txt']); %FEBio log file name
febioLogFileName_disp=[febioFebFileNamePart,'_disp_out.txt']; %Log file name for exporting displacement
febioLogFileName_strainEnergy=[febioFebFileNamePart,'_energy_out.txt']; %Log file name for exporting strain energy density

% Sphere parameters
sphereRadius=3;%
numElementsMantel=6;

% Ground plate parameters
tubeRadius=sphereRadius.*[1 0.1];
tubeAngle=3*(pi/180);
tubeLength=abs(diff(tubeRadius))/tan(tubeAngle);

% Material parameter set
c1=1e-4; %Shear-modulus-like parameter MPa
m1=2; %Material parameter setting degree of non-linearity
k_factor=10; %Bulk modulus factor
k=c1*k_factor; %Bulk modulus
d=1e-9; %Density

% FEA control settings
max_refs=25; %Max reforms
max_ups=0; %Set to zero to use full-Newton iterations
opt_iter=15; %Optimum number of iterations
max_retries=25; %Maximum number of retires
symmetric_stiffness=0;
min_residual=1e-20;

timeTotal=1; %Analysis time
numTimeSteps=100; %Number of time steps desired
step_size=timeTotal/numTimeSteps;
dtmin=(timeTotal/numTimeSteps)/100; %Minimum time step size
dtmax=(timeTotal/numTimeSteps)*10; %Maximum time step size
analysisType='DYNAMIC';

%Contact parameters
contactPenalty=10;
laugon=0;
minaug=1;
maxaug=10;
fric_coeff=0.1;

%Specifying load
pressureValue=7.5e-5;

Creating model geometry and mesh

%Control settings
cPar.sphereRadius=sphereRadius;
cPar.coreRadius=cPar.sphereRadius/2;
cPar.numElementsMantel=numElementsMantel;
cPar.numElementsCore=round(numElementsMantel*1.5);
cPar.outputStructType=2;
cPar.makeHollow=0;
cPar.cParSmooth.n=25;

%Creating sphere
[meshOutput]=hexMeshSphere(cPar);

% Access model element and patch data
Fb_blob=meshOutput.facesBoundary;
Cb_blob=meshOutput.boundaryMarker;
V_blob=meshOutput.nodes;
E_blob=meshOutput.elements;

Visualize blob mesh

hFig=cFigure;
subplot(1,2,1); hold on;
gpatch(Fb_blob,V_blob,Cb_blob,'k',0.8);
patchNormPlot(Fb_blob,V_blob);
axisGeom(gca,fontSize);
colormap(gjet); icolorbar;
camlight headlight;

hs=subplot(1,2,2); hold on;
title('Cut view of solid mesh','FontSize',fontSize);
optionStruct.hFig=[hFig hs];
gpatch(Fb_blob,V_blob,'kw','none',0.25);
meshView(meshOutput,optionStruct);
axisGeom(gca,fontSize);
drawnow;

Creating tube model

pointSpacingBlob=mean(patchEdgeLengths(Fb_blob,V_blob));
pointSpacingTube=pointSpacingBlob;

rEnd=sphereRadius+(sphereRadius.*((sphereRadius-tubeRadius(2))/tubeLength));
V_curve_tube=[sphereRadius rEnd 0; -tubeLength tubeRadius(2) 0;];

nResample=ceil(max(pathLength(V_curve_tube))./pointSpacingTube);
V_curve_tube=evenlySampleCurve(V_curve_tube,nResample,'pchip',0);

cPar.closeLoopOpt=1;
cPar.numSteps=[]; %If empty the number of steps is derived from point spacing of input curve
cPar.w=[1 0 0];
[F_tube,V_tube]=polyRevolve(V_curve_tube,cPar);
[F_tube,V_tube]=mergeVertices(F_tube,V_tube);
center_of_mass_tube=mean(V_tube,1);

Join model node sets

V=[V_blob; V_tube; ];
F_tube=F_tube+size(V_blob,1);

Visualizing model

cFigure; hold on;
gtitle('Model components',fontSize);
hl(1)=gpatch(Fb_blob,V,'rw','k',0.8);
hl(2)=gpatch(F_tube,V,'kw','k',0.5);
legend(hl,{'Blob','Tube'}); clear hl;
axisGeom(gca,fontSize);
camlight headlight;
drawnow;

Get contact surfaces

F_contact_blob=Fb_blob;

Visualize contact surfaces

cFigure; hold on;
title('Tube blob contact pair','fontsize',fontSize);
hl(1)=gpatch(F_tube,V,'rw','k',0.8);
patchNormPlot(F_tube,V);
hl(2)=gpatch(F_contact_blob,V,'kw','k',0.5);
patchNormPlot(F_contact_blob,V);
legend(hl,{'Master','Slave'}); clear hl;
axisGeom(gca,fontSize);
camlight headlight;
drawnow;

Get pressure surface

N=patchNormal(F_contact_blob,V);
x=[1 0 0];
D=dot(N,x(ones(size(N,1),1),:),2);

logicFace=D>-1e-6; %Logic for current face set
F_pressure=F_contact_blob(logicFace,:); %The current face set

Visualizing boundary conditions. Markers plotted on the semi-transparent model denote the nodes in the various boundary condition lists.

cFigure; hold on;
title('Pressure surface','fontsize',fontSize);

gpatch(F_pressure,V,'kw','k',0.5);
patchNormPlot(F_pressure,V);

% legend(hl,{'Master','Slave'}); clear hl;
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='3.0';

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

%Control section
febio_spec.Control.analysis=analysisType;
febio_spec.Control.time_steps=numTimeSteps;
febio_spec.Control.step_size=timeTotal/numTimeSteps;
febio_spec.Control.solver.max_refs=max_refs;
febio_spec.Control.solver.max_ups=max_ups;
febio_spec.Control.solver.symmetric_stiffness=symmetric_stiffness;
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='Ogden unconstrained';
febio_spec.Material.material{1}.ATTR.id=1;
febio_spec.Material.material{1}.c1=c1;
febio_spec.Material.material{1}.m1=m1;
febio_spec.Material.material{1}.c2=c1;
febio_spec.Material.material{1}.m2=-m1;
febio_spec.Material.material{1}.cp=k;
febio_spec.Material.material{1}.density=d;

materialName2='Material2';
febio_spec.Material.material{2}.ATTR.name=materialName2;
febio_spec.Material.material{2}.ATTR.type='rigid body';
febio_spec.Material.material{2}.ATTR.id=2;
febio_spec.Material.material{2}.density=1;
febio_spec.Material.material{2}.center_of_mass=center_of_mass_tube;

%Mesh section
% -> Nodes
febio_spec.Mesh.Nodes{1}.ATTR.name='nodeSet_all'; %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_blob,1))'; %Element id's
febio_spec.Mesh.Elements{1}.elem.VAL=E_blob; %The element matrix

partName2='Part2';
febio_spec.Mesh.Elements{2}.ATTR.name=partName2; %Name of this part
febio_spec.Mesh.Elements{2}.ATTR.type='quad4'; %Element type
febio_spec.Mesh.Elements{2}.elem.ATTR.id=size(E_blob,1)+(1:1:size(F_tube,1))'; %Element id's
febio_spec.Mesh.Elements{2}.elem.VAL=F_tube; %The element matrix

% -> Surfaces
surfaceName1='Surface1_contact';
febio_spec.Mesh.Surface{1}.ATTR.name=surfaceName1;
febio_spec.Mesh.Surface{1}.quad4.ATTR.id=(1:1:size(F_tube,1))';
febio_spec.Mesh.Surface{1}.quad4.VAL=F_tube;

surfaceName2='Surface2_contact';
febio_spec.Mesh.Surface{2}.ATTR.name=surfaceName2;
febio_spec.Mesh.Surface{2}.quad4.ATTR.id=(1:1:size(F_contact_blob,1))';
febio_spec.Mesh.Surface{2}.quad4.VAL=F_contact_blob;

surfaceName3='Surface3_pressure';
febio_spec.Mesh.Surface{3}.ATTR.name=surfaceName3;
febio_spec.Mesh.Surface{3}.quad4.ATTR.id=(1:1:size(F_pressure,1))';
febio_spec.Mesh.Surface{3}.quad4.VAL=F_pressure;

% -> Surface pairs
contactPairName='Contact1';
febio_spec.Mesh.SurfacePair{1}.ATTR.name=contactPairName;
febio_spec.Mesh.SurfacePair{1}.primary=surfaceName2;
febio_spec.Mesh.SurfacePair{1}.secondary=surfaceName1;

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

febio_spec.MeshDomains.ShellDomain.ATTR.name=partName2;
febio_spec.MeshDomains.ShellDomain.ATTR.mat=materialName2;

%Loads
febio_spec.Loads.surface_load{1}.ATTR.type='pressure';
febio_spec.Loads.surface_load{1}.ATTR.surface=surfaceName3;
febio_spec.Loads.surface_load{1}.pressure.ATTR.lc=1;
febio_spec.Loads.surface_load{1}.pressure.VAL=pressureValue;
febio_spec.Loads.surface_load{1}.symmetric_stiffness=1;


%Rigid section
% -> Prescribed rigid body boundary conditions
febio_spec.Rigid.rigid_constraint{1}.ATTR.name='RigidFix_1';
febio_spec.Rigid.rigid_constraint{1}.ATTR.type='fix';
febio_spec.Rigid.rigid_constraint{1}.rb=2;
febio_spec.Rigid.rigid_constraint{1}.dofs='Rx,Ry,Rz,Ru,Rv,Rw';

%Contact section
febio_spec.Contact.contact{1}.ATTR.type='sliding-elastic';
febio_spec.Contact.contact{1}.ATTR.surface_pair=contactPairName;
febio_spec.Contact.contact{1}.two_pass=0;
febio_spec.Contact.contact{1}.laugon=laugon;
febio_spec.Contact.contact{1}.tolerance=0.2;
febio_spec.Contact.contact{1}.gaptol=0;
febio_spec.Contact.contact{1}.minaug=minaug;
febio_spec.Contact.contact{1}.maxaug=maxaug;
febio_spec.Contact.contact{1}.search_tol=0.01;
febio_spec.Contact.contact{1}.search_radius=0.01*sqrt(sum((max(V,[],1)-min(V,[],1)).^2,2));
febio_spec.Contact.contact{1}.symmetric_stiffness=0;
febio_spec.Contact.contact{1}.auto_penalty=1;
febio_spec.Contact.contact{1}.penalty=contactPenalty;
febio_spec.Contact.contact{1}.fric_coeff=fric_coeff;

%LoadData section
% -> load_controller
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}.points.point.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=',';

febio_spec.Output.logfile.element_data{1}.ATTR.file=febioLogFileName_strainEnergy;
febio_spec.Output.logfile.element_data{1}.ATTR.data='sed';
febio_spec.Output.logfile.element_data{1}.ATTR.delim=',';
febio_spec.Output.logfile.element_data{1}.VAL=1:size(E_blob,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.runMode='external';%'internal';

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

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-------->    RUNNING/MONITORING FEBIO JOB    <-------- 10-Sep-2021 10:59:28
FEBio path: /home/kevin/FEBioStudio/bin/febio3
# Attempt removal of existing log files                10-Sep-2021 10:59:28
 * Removal succesful                                   10-Sep-2021 10:59:28
# Attempt removal of existing .xplt files              10-Sep-2021 10:59:29
 * Removal succesful                                   10-Sep-2021 10:59:29
# Starting FEBio...                                    10-Sep-2021 10:59:29
  Max. total analysis time is: Inf s
 * Waiting for log file creation                       10-Sep-2021 10:59:29
   Max. wait time: 30 s
 * Log file found.                                     10-Sep-2021 10:59:29
# Parsing log file...                                  10-Sep-2021 10:59:29
    number of iterations   : 4                         10-Sep-2021 10:59:31
    number of reformations : 4                         10-Sep-2021 10:59:31
------- converged at time : 0.01                       10-Sep-2021 10:59:31
    number of iterations   : 5                         10-Sep-2021 10:59:33
    number of reformations : 5                         10-Sep-2021 10:59:33
------- converged at time : 0.038                      10-Sep-2021 10:59:33
    number of iterations   : 6                         10-Sep-2021 10:59:36
    number of reformations : 6                         10-Sep-2021 10:59:36
------- converged at time : 0.0804                     10-Sep-2021 10:59:36
    number of iterations   : 7                         10-Sep-2021 10:59:39
    number of reformations : 7                         10-Sep-2021 10:59:39
------- converged at time : 0.13432                    10-Sep-2021 10:59:39
    number of iterations   : 7                         10-Sep-2021 10:59:43
    number of reformations : 7                         10-Sep-2021 10:59:43
------- converged at time : 0.197456                   10-Sep-2021 10:59:43
    number of iterations   : 4                         10-Sep-2021 10:59:44
    number of reformations : 4                         10-Sep-2021 10:59:44
------- converged at time : 0.267965                   10-Sep-2021 10:59:44
    number of iterations   : 7                         10-Sep-2021 10:59:48
    number of reformations : 7                         10-Sep-2021 10:59:48
------- converged at time : 0.344372                   10-Sep-2021 10:59:48
    number of iterations   : 19                        10-Sep-2021 10:59:56
    number of reformations : 19                        10-Sep-2021 10:59:56
------- converged at time : 0.425497                   10-Sep-2021 10:59:56
    number of iterations   : 10                        10-Sep-2021 11:00:01
    number of reformations : 10                        10-Sep-2021 11:00:01
------- converged at time : 0.497591                   10-Sep-2021 11:00:01
    number of iterations   : 8                         10-Sep-2021 11:00:04
    number of reformations : 8                         10-Sep-2021 11:00:04
------- converged at time : 0.575265                   10-Sep-2021 11:00:04
    number of iterations   : 11                        10-Sep-2021 11:00:09
    number of reformations : 11                        10-Sep-2021 11:00:09
------- converged at time : 0.657405                   10-Sep-2021 11:00:09
    number of iterations   : 6                         10-Sep-2021 11:00:12
    number of reformations : 6                         10-Sep-2021 11:00:12
------- converged at time : 0.74254                    10-Sep-2021 11:00:12
    number of iterations   : 12                        10-Sep-2021 11:00:18
    number of reformations : 12                        10-Sep-2021 11:00:18
------- converged at time : 0.830649                   10-Sep-2021 11:00:18
    number of iterations   : 7                         10-Sep-2021 11:00:21
    number of reformations : 7                         10-Sep-2021 11:00:21
------- converged at time : 0.920161                   10-Sep-2021 11:00:21
    number of iterations   : 13                        10-Sep-2021 11:00:27
    number of reformations : 13                        10-Sep-2021 11:00:27
------- converged at time : 1                          10-Sep-2021 11:00:27
 Elapsed time : 0:00:58                                10-Sep-2021 11:00:27
 N O R M A L   T E R M I N A T I O N
# Done                                                 10-Sep-2021 11:00:27
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Import FEBio results

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

    % Importing nodal displacements from a log file
    [time_mat, N_disp_mat,~]=importFEBio_logfile(fullfile(savePath,febioLogFileName_disp)); %Nodal displacements
    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.^2,2));
    V_def=V+DN;
    V_DEF=N_disp_mat+repmat(V,[1 1 size(N_disp_mat,3)]);
    X_DEF=V_DEF(:,1,:);
    Y_DEF=V_DEF(:,2,:);
    Z_DEF=V_DEF(:,3,:);
    %     [CF]=vertexToFaceMeasure(Fb_all,DN_magnitude);

Importing element strain energies from a log file

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

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

    %Add initial state i.e. zero displacement
    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;

    indBlob=unique(Fb_blob(:));
    t=linspace(0,2*pi,250)';

    V_def_blob=V(indBlob,:)+N_disp_mat(indBlob,:,end);

    [~,indMin]=min(V_def_blob(:,1));
    [~,indMax]=max(V_def_blob(:,1));

    xEnd=V_def_blob(indMin,1);
    xStart=V_def_blob(indMax,1);
    rEnd=sphereRadius+(xEnd.*((sphereRadius-tubeRadius(2))/tubeLength));
    rStart=sphereRadius+(xStart.*((sphereRadius-tubeRadius(2))/tubeLength));

    xMid=mean([xStart xEnd]);%sum([rStart rEnd].*[xStart xEnd])./sum([rStart rEnd]);
    rMid=sphereRadius+(xMid.*((sphereRadius-tubeRadius(2))/tubeLength));

    V_plot_xEnd=[xEnd*ones(size(t)) rEnd*cos(t) rEnd*sin(t)];
    V_plot_xMid=[xMid*ones(size(t)) rMid*cos(t) rMid*sin(t)];
    V_plot_xStart=[xStart*ones(size(t)) rStart*cos(t) rStart*sin(t)];

Plotting the simulated results using anim8 to visualize and animate deformations

    % Create basic view and store graphics handle to initiate animation
    hf=cFigure; hold on;
    ht=gtitle(['Radial stretch: ',num2str(rMid/sphereRadius)]);
    hp1=gpatch(Fb_blob,V_def,DN_magnitude,'none',1); %Add graphics object to animate

    hp2=plotV(V_plot_xEnd  ,'r-','LineWidth',3);
    hp3=plotV(V_plot_xMid  ,'r-','LineWidth',3);
    hp4=plotV(V_plot_xStart,'r-','LineWidth',3);

    gpatch(F_tube,V_def,'kw','none',0.25); %Add graphics object to animate
    axisGeom(gca,fontSize);
    colormap(cMap); colorbar;
    caxis([0 max(DN_magnitude(:))]); caxis manual;
    axis([min(X_DEF(:)) max(X_DEF(:)) min(Y_DEF(:)) max(Y_DEF(:)) min(Z_DEF(:)) max(Z_DEF(:))]);
    camlight headlight; lighting gouraud;
    view(0,0);
%     view(-30,30); zoom(1.5);
    axis off;
    drawnow;

    LMid=1;

    % 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 displacement
        DN_magnitude=sqrt(sum(DN.^2,2));
        V_def=V+DN; %Current nodal coordinates

        V_def_blob=V_def(indBlob,:);
        [~,indMin]=min(V_def_blob(:,1));
        [~,indMax]=max(V_def_blob(:,1));

        xEnd=V_def_blob(indMin,1);
        xStart=V_def_blob(indMax,1);
        rEnd=sphereRadius+(xEnd.*((sphereRadius-tubeRadius(2))/tubeLength));
        rStart=sphereRadius+(xStart.*((sphereRadius-tubeRadius(2))/tubeLength));

        xMid=mean([xStart xEnd]);%sum([rStart rEnd].*[xStart xEnd])./sum([rStart rEnd]);
        rMid=sphereRadius+(xMid.*((sphereRadius-tubeRadius(2))/tubeLength));

        LMid=min(LMid,rMid/sphereRadius);

        V_plot_xEnd=[xEnd*ones(size(t)) rEnd*cos(t) rEnd*sin(t)];
        V_plot_xMid=[xMid*ones(size(t)) rMid*cos(t) rMid*sin(t)];
        V_plot_xStart=[xStart*ones(size(t)) rStart*cos(t) rStart*sin(t)];

        %Set entries in animation structure
        animStruct.Handles{qt}=[hp1 hp1 hp2 hp2 hp2 hp3 hp3 hp3 hp4 hp4 hp4 ht]; %Handles of objects to animate
        animStruct.Props{qt}={'Vertices','CData','XData','YData','ZData','XData','YData','ZData','XData','YData','ZData','String'}; %Properties of objects to animate
        animStruct.Set{qt}={V_def,DN_magnitude,...
            V_plot_xEnd(:,1),V_plot_xEnd(:,2),V_plot_xEnd(:,3),...
            V_plot_xMid(:,1),V_plot_xMid(:,2),V_plot_xMid(:,3),...
            V_plot_xStart(:,1),V_plot_xStart(:,2),V_plot_xStart(:,3),...
            ['Radial stretch: ',num2str(rMid/sphereRadius)]}; %Property values for to set in order to animate
    end
    anim8(hf,animStruct); %Initiate animation feature

    drawnow;

end

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.

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/.