DEMO_febio_0040_propeller_contact

Below is a demonstration for:

Building geometry for a slab with hexahedral elements, and a triangulated sphere.
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 triangulated bar mesh
Mesh using tetrahedral elements
Visualizing mesh using meshView, see also anim8
Joining node sets
Define contact surfaces
Define central cylinder body
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
indentation
contact, sliding, sticky, friction
rigid body constraints
hexahedral elements, hex8
triangular elements, tri3
slab, block, rectangular
sphere
static, solid
hyperelastic, Ogden
displacement logfile
stress logfile

clear; close all; clc;

Plot settings

fontSize=15;
faceAlpha1=0.8;
faceAlpha2=0.3;
markerSize=40;
lineWidth=3;
markerSize2=25;

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
febioLogFileName_strainEnergy=[febioFebFileNamePart,'_energy_out.txt']; %Log file name for exporting strain energy density

% Propeller
pointSpacing=8;

% Bar
barRadius=20;

% Define prescribed rotation
prescribedRotation=pi/3;

%Material parameters (MPa if spatial units are mm)
E_youngs1=17000; %Youngs modulus
nu1=0.25; %Poissons ratio
materialDensity=1e-9; %Density (not required for static analysis)

% 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=12; %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
symmetric_stiffness=0;
min_residual=1e-20;

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

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

Creating model geometry and mesh

% Import STL surface model
fileName=fullfile(defaultFolder,'data','STL','propeller.stl');
[stlStruct] = import_STL(fileName);

% Access the data from the STL struct
F=stlStruct.solidFaces{1}; %Faces
V=stlStruct.solidVertices{1}; %Vertices

% Merging nodes
[F,V]=mergeVertices(F,V);

% Shift around mean
V=V-mean(V,1);

% % Remeshing and labelling
optionStructRemesh.pointSpacing=pointSpacing; %Set desired point spacing
optionStructRemesh.disp_on=0;
[Fp,Vp]=ggremesh(F,V,optionStructRemesh);

D=sqrt(sum(Vp(:,[1 2]).^2,2));
N=patchNormal(Fp,Vp);

Cp=all(D(Fp)<=10,2) & abs(N(:,3))<=0.5;

w=max(abs(max(Vp,[],1)-min(Vp,[],1))); %Width measure

pointSpacing=mean(patchEdgeLengths(Fp,Vp));

Creating triangulated bar mesh

h=w/2;
nh=round(h/(pointSpacing/2));
nh=iseven(nh)+nh;
nr=round((2*pi*barRadius)/(pointSpacing/2));

optionStruct.cylRadius=barRadius;
optionStruct.numRadial=nr;
optionStruct.cylHeight=h;
optionStruct.numHeight=nh;
optionStruct.meshType='tri';
optionStruct.closeOpt=0;
[Fc,Vc]=patchcylinder(optionStruct);

%Shift bar
Vc(:,1)=Vc(:,1)-w/3;
Vc(:,2)=Vc(:,2)-w/3;

center_of_mass=mean(Vc,1);

Plotting model boundary surfaces and a cut view

hFig=cFigure;
title('Model boundary surfaces and labels','FontSize',fontSize);
gpatch(Fp,Vp,Cp,'k',faceAlpha1);
gpatch(Fc,Vc,'kw','k',faceAlpha1);

colormap(gjet(250)); colorbar;
axisGeom(gca,fontSize);
camlight headlight;

drawnow;

Mesh using tetrahedral elements

stringOpt='-pq1.2AaY';

inputStruct.stringOpt=stringOpt;
inputStruct.Faces=Fp;
inputStruct.Nodes=Vp;
inputStruct.holePoints=[];
inputStruct.faceBoundaryMarker=Cp; %Face boundary markers
inputStruct.regionPoints=getInnerPoint(Fp,Vp); %region points
inputStruct.regionA=tetVolMeanEst(Fp,Vp)*5; %Volume for regular tets
inputStruct.minRegionMarker=2; %Minimum region marker

% Mesh model using tetrahedral elements using tetGen
[meshOutput]=runTetGen(inputStruct); %Run tetGen

% Access model element and patch data
Fb=meshOutput.facesBoundary;
Cb=meshOutput.boundaryMarker;
V=meshOutput.nodes;
CE=meshOutput.elementMaterialID;
E=meshOutput.elements;

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- TETGEN Tetrahedral meshing --- 20-Apr-2023 18:05:53
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Writing SMESH file --- 20-Apr-2023 18:05:53
----> Adding node field
----> Adding facet field
----> Adding holes specification
----> Adding region specification
--- Done --- 20-Apr-2023 18:05:53
--- Running TetGen to mesh input boundary--- 20-Apr-2023 18:05:53
Opening /mnt/data/MATLAB/GIBBON/data/temp/temp.smesh.
Delaunizing vertices...
Delaunay seconds:  0.005485
Creating surface mesh ...
Surface mesh seconds:  0.001866
Recovering boundaries...
Boundary recovery seconds:  0.002999
Removing exterior tetrahedra ...
Spreading region attributes.
Exterior tets removal seconds:  0.001977
Recovering Delaunayness...
Delaunay recovery seconds:  0.001714
Refining mesh...
Refinement seconds:  0.004088
Smoothing vertices...
Mesh smoothing seconds:  0.003553
Improving mesh...
Mesh improvement seconds:  0.001235

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:  0.020581
Total running seconds:  0.04364

Statistics:

  Input points: 1139
  Input facets: 2278
  Input segments: 3417
  Input holes: 0
  Input regions: 1

  Mesh points: 1210
  Mesh tetrahedra: 3689
  Mesh faces: 8517
  Mesh faces on exterior boundary: 2278
  Mesh faces on input facets: 2278
  Mesh edges on input segments: 3417
  Steiner points inside domain: 71

--- Done --- 20-Apr-2023 18:05:53
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Importing TetGen files --- 20-Apr-2023 18:05:53
--- Done --- 20-Apr-2023 18:05:53

Visualizing mesh using `meshView`, see also `anim8`

meshView(meshOutput);

Joining node sets

Fc=Fc+size(V,1); %Fixed element indices
V=[V;Vc;]; %Combined node sets

Plotting joined geometry

cFigure;
title('Joined node sets','FontSize',fontSize);
hold on;
gpatch(Fb,V,Cp,'k',faceAlpha1);
gpatch(Fc,V,'kw','k',faceAlpha1);
colormap(gjet(6)); icolorbar;
axisGeom(gca,fontSize);
camlight headlight;
drawnow;

Define contact surfaces

Vbc=patchCentre(Fb,V);
Db=sqrt(sum(Vbc(:,[1 2]).^2,2));

Vcc=patchCentre(Fc,V);
Dc=sqrt(sum(Vcc(:,[1 2]).^2,2));

% The rigid Primary surface of the sphere
F_contact_primary=Fc;

% The deformable Secondary surface of the slab
F_contact_secondary=fliplr(Fb(Cb==0 & Db>=(min(Dc(:))-pointSpacing),:));

Visualize contact surfaces

cFigure; hold on;
title('Contact sets and normal directions','FontSize',fontSize);

gpatch(Fb,V,'kw','none',faceAlpha2);
hl(1)=gpatch(F_contact_primary,V,'gw','k',1);
patchNormPlot(F_contact_primary,V);
hl(2)=gpatch(F_contact_secondary,V,'bw','k',1);
patchNormPlot(F_contact_secondary,V);

legend(hl,{'Primary','Secondary'});

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

clear hl;

Define central cylinder body

F_shaft=Fb(Cb==1,:);

Visualize BC's

hf=cFigure;
title('Boundary conditions model','FontSize',fontSize);
hold on;

gpatch(Fb,V,'w','none',faceAlpha2);
gpatch(Fc,V,'w','none',faceAlpha2);

hl(1)=gpatch(F_shaft,V,'rw','k',1);

legend(hl,{'Central shaft rigid body'});

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.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='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{1}.density=materialDensity;

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=materialDensity;
febio_spec.Material.material{2}.center_of_mass=mean(V(unique(Fc),:),1);

materialName3='Material3';
febio_spec.Material.material{3}.ATTR.name=materialName3;
febio_spec.Material.material{3}.ATTR.type='rigid body';
febio_spec.Material.material{3}.ATTR.id=3;
febio_spec.Material.material{3}.density=materialDensity;
febio_spec.Material.material{3}.center_of_mass=mean(V(unique(F_shaft),:),1);

%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's3
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='tet4'; %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

partName2='Part2';
febio_spec.Mesh.Elements{2}.ATTR.name=partName2; %Name of this part
febio_spec.Mesh.Elements{2}.ATTR.type='tri3'; %Element type
febio_spec.Mesh.Elements{2}.elem.ATTR.id=size(E,1)+(1:1:size(Fc,1))'; %Element id's
febio_spec.Mesh.Elements{2}.elem.VAL=Fc; %The element matrix

partName3='Part3';
febio_spec.Mesh.Elements{3}.ATTR.name=partName3; %Name of this part
febio_spec.Mesh.Elements{3}.ATTR.type='tri3'; %Element type
febio_spec.Mesh.Elements{3}.elem.ATTR.id=size(E,1)+size(Fc,1)+(1:1:size(F_shaft,1))'; %Element id's
febio_spec.Mesh.Elements{3}.elem.VAL=F_shaft; %The element matrix

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

febio_spec.MeshDomains.ShellDomain{1}.ATTR.name=partName2;
febio_spec.MeshDomains.ShellDomain{1}.ATTR.mat=materialName2;

febio_spec.MeshDomains.ShellDomain{2}.ATTR.name=partName3;
febio_spec.MeshDomains.ShellDomain{2}.ATTR.mat=materialName3;

% -> Surfaces
surfaceName1='contactSurface1';
febio_spec.Mesh.Surface{1}.ATTR.name=surfaceName1;
febio_spec.Mesh.Surface{1}.tri3.ATTR.id=(1:1:size(F_contact_primary,1))';
febio_spec.Mesh.Surface{1}.tri3.VAL=F_contact_primary;

surfaceName2='contactSurface2';
febio_spec.Mesh.Surface{2}.ATTR.name=surfaceName2;
febio_spec.Mesh.Surface{2}.tri3.ATTR.id=(1:1:size(F_contact_secondary,1))';
febio_spec.Mesh.Surface{2}.tri3.VAL=F_contact_secondary;

% -> Surface pairs
contactPairName1='ContactPair1';
febio_spec.Mesh.SurfacePair{1}.ATTR.name=contactPairName1;
febio_spec.Mesh.SurfacePair{1}.primary=surfaceName1;
febio_spec.Mesh.SurfacePair{1}.secondary=surfaceName2;

%Rigid section
% ->Rigid body fix boundary conditions
febio_spec.Rigid.rigid_bc{1}.ATTR.name='RigidFix_RB2';
febio_spec.Rigid.rigid_bc{1}.ATTR.type='rigid_fixed';
febio_spec.Rigid.rigid_bc{1}.rb=2;
febio_spec.Rigid.rigid_bc{1}.Rx_dof=1;
febio_spec.Rigid.rigid_bc{1}.Ry_dof=1;
febio_spec.Rigid.rigid_bc{1}.Rz_dof=1;
febio_spec.Rigid.rigid_bc{1}.Ru_dof=1;
febio_spec.Rigid.rigid_bc{1}.Rv_dof=1;
febio_spec.Rigid.rigid_bc{1}.Rw_dof=1;

febio_spec.Rigid.rigid_bc{2}.ATTR.name='RigidFix_RB3';
febio_spec.Rigid.rigid_bc{2}.ATTR.type='rigid_fixed';
febio_spec.Rigid.rigid_bc{2}.rb=3;
febio_spec.Rigid.rigid_bc{2}.Rx_dof=1;
febio_spec.Rigid.rigid_bc{2}.Ry_dof=1;
febio_spec.Rigid.rigid_bc{2}.Rz_dof=1;
febio_spec.Rigid.rigid_bc{2}.Ru_dof=1;
febio_spec.Rigid.rigid_bc{2}.Rv_dof=1;

% ->Rigid body prescribe boundary conditions
febio_spec.Rigid.rigid_bc{3}.ATTR.name='RigidPrescribed_rot_RB3';
febio_spec.Rigid.rigid_bc{3}.ATTR.type='rigid_rotation';
febio_spec.Rigid.rigid_bc{3}.rb=3;
febio_spec.Rigid.rigid_bc{3}.dof='Rw';
febio_spec.Rigid.rigid_bc{3}.value.ATTR.lc=1;
febio_spec.Rigid.rigid_bc{3}.value.VAL=prescribedRotation;
febio_spec.Rigid.rigid_bc{3}.relative=0;

%Contact section
febio_spec.Contact.contact{1}.ATTR.type='sliding-elastic';
febio_spec.Contact.contact{1}.ATTR.surface_pair=contactPairName1;
febio_spec.Contact.contact{1}.two_pass=1;
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=0.1*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.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=',';

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}.ATTR.elem_set=partName1;

% Plotfile section
febio_spec.Output.plotfile.compression=0;

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 18:06:01
FEBio path: /home/kevin/FEBioStudio2/bin/febio4
# Attempt removal of existing log files                20-Apr-2023 18:06:01
 * Removal succesful                                   20-Apr-2023 18:06:01
# Attempt removal of existing .xplt files              20-Apr-2023 18:06:01
 * Removal succesful                                   20-Apr-2023 18:06:01
# Starting FEBio...                                    20-Apr-2023 18:06:01
  Max. total analysis time is: Inf s
 * Waiting for log file creation                       20-Apr-2023 18:06:01
   Max. wait time: 30 s
 * Log file found.                                     20-Apr-2023 18:06:01
# Parsing log file...                                  20-Apr-2023 18:06:01
    number of iterations   : 4                         20-Apr-2023 18:06:02
    number of reformations : 4                         20-Apr-2023 18:06:02
------- converged at time : 0.1                        20-Apr-2023 18:06:02
    number of iterations   : 4                         20-Apr-2023 18:06:02
    number of reformations : 4                         20-Apr-2023 18:06:02
------- converged at time : 0.2                        20-Apr-2023 18:06:02
    number of iterations   : 7                         20-Apr-2023 18:06:02
    number of reformations : 7                         20-Apr-2023 18:06:02
------- converged at time : 0.3                        20-Apr-2023 18:06:02
    number of iterations   : 6                         20-Apr-2023 18:06:03
    number of reformations : 6                         20-Apr-2023 18:06:03
------- converged at time : 0.4                        20-Apr-2023 18:06:03
    number of iterations   : 6                         20-Apr-2023 18:06:03
    number of reformations : 6                         20-Apr-2023 18:06:03
------- converged at time : 0.5                        20-Apr-2023 18:06:03
    number of iterations   : 7                         20-Apr-2023 18:06:03
    number of reformations : 7                         20-Apr-2023 18:06:03
------- converged at time : 0.6                        20-Apr-2023 18:06:03
    number of iterations   : 7                         20-Apr-2023 18:06:04
    number of reformations : 7                         20-Apr-2023 18:06:04
------- converged at time : 0.7                        20-Apr-2023 18:06:04
    number of iterations   : 7                         20-Apr-2023 18:06:04
    number of reformations : 7                         20-Apr-2023 18:06:04
------- converged at time : 0.8                        20-Apr-2023 18:06:04
    number of iterations   : 9                         20-Apr-2023 18:06:05
    number of reformations : 9                         20-Apr-2023 18:06:05
------- converged at time : 0.9                        20-Apr-2023 18:06:05
    number of iterations   : 7                         20-Apr-2023 18:06:07
    number of reformations : 7                         20-Apr-2023 18:06:07
------- converged at time : 0.983333                   20-Apr-2023 18:06:07
    number of iterations   : 10                        20-Apr-2023 18:06:08
    number of reformations : 10                        20-Apr-2023 18:06:08
------- converged at time : 1                          20-Apr-2023 18:06:08
 Elapsed time : 0:00:06                                20-Apr-2023 18:06:08
 N O R M A L   T E R M I N A T I O N
# Done                                                 20-Apr-2023 18:06:08
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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)]);

Importing element stress from a log file

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

    %Access data
    E_energy=dataStruct.data;

Plotting the simulated results using anim8 to visualize and animate deformations

    [CV]=faceToVertexMeasure(E,V,E_energy(:,:,end));

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

    hp2=gpatch(Fc,V_DEF(:,:,end),'kw','none',0.5); %Add graphics object to animate

    axisGeom(gca,fontSize);
    colormap(gjet(250)); colorbar;
    caxis([0 max(E_energy(:))/20]);
    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

        [CV]=faceToVertexMeasure(E,V,E_energy(:,:,qt));

        %Set entries in animation structure
        animStruct.Handles{qt}=[hp1 hp1 hp2]; %Handles of objects to animate
        animStruct.Props{qt}={'Vertices','CData','Vertices'}; %Properties of objects to animate
        animStruct.Set{qt}={V_DEF(:,:,qt),CV,V_DEF(:,:,qt)}; %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/.