DEMO_febio_0047_cylinder_embedded_probe_01
Below is a demonstration for:
- Building geometry for a tissue segment with an embedded probe
- Defining the boundary conditions
- Coding the febio structure
- Running the model
- Importing and visualizing the displacement results
Contents
Keywords
- febio_spec version 3.0
- febio, FEBio
- probe
- rigid body constraints
- tetrahedral elements, tet4
- triangular elements, tri3
- slab, block, rectangular
- sphere
- static, solid
- hyperelastic, Ogden
- displacement logfile
- stress logfile
clear; close all; clc;
Plot settings
fontSize=15;
faceAlpha=1;
lineWidth1=1.5;
lineWidth2=3;
markerSize1=15;
markerSize2=30;
edgeWidth=2;
edgeColor='k';
faceAlpha1=1;
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_force=[febioFebFileNamePart,'_force_out.txt']; %Log file name for exporting force febioLogFileName_strainEnergy=[febioFebFileNamePart,'_energy_out.txt']; %Log file name for exporting strain energy density febioLogFileName_strain=[febioFebFileNamePart,'_strain_out.txt']; %Log file name for exporting strain probeHeight=75; probeRadius=2; % The radius of the hemi-spher portion nRefine=0; % Number of |subtri| refinements for icosahedron pointSpacing=3; dAdd=7; tissueRadius=probeRadius+dAdd; tissueHeight=probeHeight+dAdd; volumeFactor=5; displacementMagnitude=-1; %Material parameter set c1=1e-3; %Shear-modulus-like parameter m1=2; %Material parameter setting degree of non-linearity k_factor=1e2; %Bulk modulus factor k=c1*k_factor; %Bulk modulus % 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
Build probe
probeMeshInputStruct.sphereRadius=probeRadius;% => The radius of the hemi-spher portion probeMeshInputStruct.nRefine=nRefine;% => Number of |subtri| refinements for icosahedron probeMeshInputStruct.cylinderHeight=probeHeight-probeRadius;% => height of the cylinder part probeMeshInputStruct.cylinderStepSize=[];% => Aproximate node spacing for cylinder portion probeMeshInputStruct.patchType='tri'; [Fp,Vp,Cp]=hemiSphereCylMesh(probeMeshInputStruct); Fp=fliplr(Fp); %Invert face orientation Vp(:,3)=Vp(:,3)-max(Vp(:,3)); %Get top curve Eb=patchBoundary(Fp); indProbeTop=edgeListToCurve(Eb); indProbeTop=indProbeTop(1:end-1); Vst=Vp(indProbeTop,:);
cFigure; hold on; gpatch(Fp,Vp,'gw','k'); plotV(Vst,'b.-','lineWidth',lineWidth1,'MarkerSize',markerSize1); patchNormPlot(Fp,Vp); axisGeom(gca,fontSize); drawnow;

Build tissue
%Sketching profile ns=150; t=linspace(0,2*pi,ns); t=t(1:end-1); x=tissueRadius*cos(t); y=tissueRadius*sin(t); z=zeros(size(x)); Vc=[x(:) y(:) z(:)]; np=ceil(max(pathLength(Vc))./pointSpacing); [Vc]=evenlySampleCurve(Vc,np,'pchip',1); % Extruding model cPar.numSteps=round(tissueHeight/pointSpacing); cPar.depth=tissueHeight; cPar.patchType='tri'; cPar.dir=-1; cPar.closeLoopOpt=1; [Fg,Vg]=polyExtrude(Vc,cPar); Fg=fliplr(Fg); Vgb=Vg(cPar.numSteps:cPar.numSteps:end,:); Vgt=Vg(1:cPar.numSteps:end,:);
Cap ends
regionCell={Vgt(:,[1 2]),Vst(:,[1 2])};
[Ft,Vt]=regionTriMesh2D(regionCell,pointSpacing,0,0);
Vt(:,3)=mean(Vgt(:,3));
regionCell={Vgb(:,[1 2])};
[Fb,Vb]=regionTriMesh2D(regionCell,pointSpacing,0,0);
Fb=fliplr(Fb); %flip face orientation
Vb(:,3)=mean(Vgb(:,3));
Visualize
cFigure; hold on; gpatch(Fp,Vp,'rw','k',0.5); gpatch(Fg,Vg,'gw','k',0.5); gpatch(Fb,Vb,'bw','k',0.5); gpatch(Ft,Vt,'bw','k',0.5); plotV(Vgb,'b.-','lineWidth',lineWidth1,'MarkerSize',markerSize1); plotV(Vgt,'b.-','lineWidth',lineWidth1,'MarkerSize',markerSize1); plotV(Vst,'b.-','lineWidth',lineWidth1,'MarkerSize',markerSize1); axisGeom(gca,fontSize); drawnow;

Merge model components
[F,V,C]=joinElementSets({Fg,Ft,Fb,Fp},{Vg,Vt,Vb,Vp}); [F,V]=mergeVertices(F,V);
cFigure; subplot(1,2,1); hold on; gpatch(F,V,C,'none',0.5); axisGeom(gca,fontSize); colormap gjet; icolorbar; subplot(1,2,2); hold on; gpatch(F,V,C); patchNormPlot(F,V,2); plotV(Vst,'b.-','lineWidth',lineWidth1,'MarkerSize',markerSize1); axisGeom(gca,fontSize); colormap gjet; icolorbar; drawnow;

Mesh solid using tetgen
Create tetgen meshing input structure
[regionA]=tetVolMeanEst(F,V); %Volume for a regular tet based on edge lengths V_inner=getInnerPoint(F,V); %Interior point for region inputStruct.stringOpt='-pq1.2AaY'; inputStruct.Faces=F; inputStruct.Nodes=V; inputStruct.holePoints=[]; inputStruct.faceBoundaryMarker=C; %Face boundary markers inputStruct.regionPoints=V_inner; %region points inputStruct.regionA=regionA*volumeFactor; %Desired volume for tets inputStruct.minRegionMarker=2; %Minimum region marker
Mesh model using tetrahedral elements using tetGen
[meshOutput]=runTetGen(inputStruct); %Run tetGen
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% --- TETGEN Tetrahedral meshing --- 25-Feb-2022 15:44:52 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% --- Writing SMESH file --- 25-Feb-2022 15:44:52 ----> Adding node field ----> Adding facet field ----> Adding holes specification ----> Adding region specification --- Done --- 25-Feb-2022 15:44:52 --- Running TetGen to mesh input boundary--- 25-Feb-2022 15:44:52 Opening /mnt/data/MATLAB/GIBBON/data/temp/temp.smesh. Delaunizing vertices... Delaunay seconds: 0.067594 Creating surface mesh ... Surface mesh seconds: 0.002337 Recovering boundaries... Boundary recovery seconds: 0.005187 Removing exterior tetrahedra ... Spreading region attributes. Exterior tets removal seconds: 0.001597 Recovering Delaunayness... Delaunay recovery seconds: 0.002223 Refining mesh... Refinement seconds: 0.034687 Smoothing vertices... Mesh smoothing seconds: 0.068068 Improving mesh... Mesh improvement seconds: 0.002167 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: 0.033442 Total running seconds: 0.217468 Statistics: Input points: 1164 Input facets: 2324 Input segments: 3486 Input holes: 0 Input regions: 1 Mesh points: 2181 Mesh tetrahedra: 9862 Mesh faces: 20886 Mesh faces on exterior boundary: 2324 Mesh faces on input facets: 2324 Mesh edges on input segments: 3486 Steiner points inside domain: 1017 --- Done --- 25-Feb-2022 15:44:52 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% --- Importing TetGen files --- 25-Feb-2022 15:44:52 --- Done --- 25-Feb-2022 15:44:53
Visualize mesh
meshView(meshOutput);

Access model element and patch data
F=meshOutput.faces; V=meshOutput.nodes; C=meshOutput.faceMaterialID; E=meshOutput.elements; elementMaterialID=meshOutput.elementMaterialID; Fb=meshOutput.facesBoundary; Cb=meshOutput.boundaryMarker;
Define boundary condition node sets
logicRigid= Cb==1 | Cb==3; bcSupportList=Fb(logicRigid,:); bcSupportList=unique(bcSupportList(:)); logicIndentor= Cb==4; bcPrescribeList=Fb(logicIndentor,:); bcPrescribeList=unique(bcPrescribeList(:));
Visualize boundary conditions
cFigure; hold on; gpatch(Fb,V,'bw','none',0.5); hp(1)=plotV(V(bcSupportList,:),'k.','lineWidth',lineWidth1,'MarkerSize',markerSize1); hp(2)=plotV(V(bcPrescribeList,:),'r.','lineWidth',lineWidth1,'MarkerSize',markerSize1); legend(hp,{'BC Full support','BC Prescribed displacement'}); axisGeom(gca,fontSize); 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'; %Create control structure for use by all steps stepStruct.Control.time_steps=numTimeSteps; stepStruct.Control.step_size=1/numTimeSteps; stepStruct.Control.solver.max_refs=max_refs; stepStruct.Control.solver.max_ups=max_ups; stepStruct.Control.time_stepper.dtmin=dtmin; stepStruct.Control.time_stepper.dtmax=dtmax; stepStruct.Control.time_stepper.max_retries=max_retries; stepStruct.Control.time_stepper.opt_iter=opt_iter; %Add template based default settings to proposed control section [stepStruct.Control]=structComplete(stepStruct.Control,febio_spec.Control,1); %Complement provided with default if missing %Remove control field (part of template) since step specific control sections are used febio_spec=rmfield(febio_spec,'Control'); febio_spec.Step.step{1}.Control=stepStruct.Control; febio_spec.Step.step{1}.ATTR.id=1; febio_spec.Step.step{2}.Control=stepStruct.Control; febio_spec.Step.step{2}.ATTR.id=2; %Material section materialName1='Material1'; febio_spec.Material.material{1}.ATTR.name=materialName1; febio_spec.Material.material{1}.ATTR.type='Ogden'; 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}.k=k; % 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='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 % -> NodeSets nodeSetName1='bcSupportList'; nodeSetName2='bcPrescribeList'; febio_spec.Mesh.NodeSet{1}.ATTR.name=nodeSetName1; febio_spec.Mesh.NodeSet{1}.node.ATTR.id=bcSupportList(:); febio_spec.Mesh.NodeSet{2}.ATTR.name=nodeSetName2; febio_spec.Mesh.NodeSet{2}.node.ATTR.id=bcPrescribeList(:); %MeshDomains section febio_spec.MeshDomains.SolidDomain.ATTR.name=partName1; febio_spec.MeshDomains.SolidDomain.ATTR.mat=materialName1; %Boundary condition section %-> Fix boundary conditions febio_spec.Boundary.bc{1}.ATTR.type='fix'; febio_spec.Boundary.bc{1}.ATTR.node_set=nodeSetName1; febio_spec.Boundary.bc{1}.dofs='x,y,z'; % -> Prescribe boundary conditions %STEP 1 Up/down febio_spec.Step.step{1}.Boundary.bc{1}.ATTR.type='prescribe'; febio_spec.Step.step{1}.Boundary.bc{1}.ATTR.node_set=nodeSetName2; febio_spec.Step.step{1}.Boundary.bc{1}.dof='z'; febio_spec.Step.step{1}.Boundary.bc{1}.scale.ATTR.lc=1; febio_spec.Step.step{1}.Boundary.bc{1}.scale.VAL=displacementMagnitude; febio_spec.Step.step{1}.Boundary.bc{1}.relative=1; febio_spec.Step.step{1}.Boundary.bc{2}.ATTR.type='fix'; febio_spec.Step.step{1}.Boundary.bc{2}.ATTR.node_set=nodeSetName2; febio_spec.Step.step{1}.Boundary.bc{2}.dofs='x,y'; %STEP 2 Sideways febio_spec.Step.step{2}.Boundary.bc{1}.ATTR.type='prescribe'; febio_spec.Step.step{2}.Boundary.bc{1}.ATTR.node_set=nodeSetName2; febio_spec.Step.step{2}.Boundary.bc{1}.dof='x'; febio_spec.Step.step{2}.Boundary.bc{1}.scale.ATTR.lc=2; febio_spec.Step.step{2}.Boundary.bc{1}.scale.VAL=displacementMagnitude; febio_spec.Step.step{2}.Boundary.bc{1}.relative=1; febio_spec.Step.step{2}.Boundary.bc{2}.ATTR.type='fix'; febio_spec.Step.step{2}.Boundary.bc{2}.ATTR.node_set=nodeSetName2; febio_spec.Step.step{2}.Boundary.bc{2}.dofs='y,z'; %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; 0.25 1; 0.5 0; 0.75 -1; 1 0]; febio_spec.LoadData.load_controller{2}.ATTR.id=2; febio_spec.LoadData.load_controller{2}.ATTR.type='loadcurve'; febio_spec.LoadData.load_controller{2}.interpolate='LINEAR'; febio_spec.LoadData.load_controller{2}.points.point.VAL=[1 0; 1.25 1; 1.5 0; 1.75 -1; 2 0]; %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{2}.ATTR.file=febioLogFileName_force; febio_spec.Output.logfile.node_data{2}.ATTR.data='Rx;Ry;Rz'; febio_spec.Output.logfile.node_data{2}.ATTR.delim=','; febio_spec.Output.logfile.element_data{1}.ATTR.file=febioLogFileName_strain; febio_spec.Output.logfile.element_data{1}.ATTR.data='E1;E2;E3'; febio_spec.Output.logfile.element_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='external';%'internal' or 'external'; [runFlag]=runMonitorFEBio(febioAnalysis);%START FEBio NOW!!!!!!!!
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% --------> RUNNING/MONITORING FEBIO JOB <-------- 25-Feb-2022 15:44:58 FEBio path: /home/kevin/FEBioStudio/bin/febio3 # Attempt removal of existing log files 25-Feb-2022 15:44:58 * Removal succesful 25-Feb-2022 15:44:58 # Attempt removal of existing .xplt files 25-Feb-2022 15:44:58 * Removal succesful 25-Feb-2022 15:44:58 # Starting FEBio... 25-Feb-2022 15:44:58 Max. total analysis time is: Inf s * Waiting for log file creation 25-Feb-2022 15:44:58 Max. wait time: 30 s * Log file found. 25-Feb-2022 15:44:58 # Parsing log file... 25-Feb-2022 15:44:58 number of iterations : 3 25-Feb-2022 15:44:58 number of reformations : 3 25-Feb-2022 15:44:58 ------- converged at time : 0.1 25-Feb-2022 15:44:58 number of iterations : 3 25-Feb-2022 15:44:59 number of reformations : 3 25-Feb-2022 15:44:59 ------- converged at time : 0.2 25-Feb-2022 15:44:59 number of iterations : 1 25-Feb-2022 15:44:59 number of reformations : 1 25-Feb-2022 15:44:59 ------- converged at time : 0.3 25-Feb-2022 15:44:59 number of iterations : 3 25-Feb-2022 15:44:59 number of reformations : 3 25-Feb-2022 15:44:59 ------- converged at time : 0.4 25-Feb-2022 15:44:59 number of iterations : 3 25-Feb-2022 15:44:59 number of reformations : 3 25-Feb-2022 15:44:59 ------- converged at time : 0.5 25-Feb-2022 15:44:59 number of iterations : 3 25-Feb-2022 15:45:00 number of reformations : 3 25-Feb-2022 15:45:00 ------- converged at time : 0.6 25-Feb-2022 15:45:00 number of iterations : 3 25-Feb-2022 15:45:00 number of reformations : 3 25-Feb-2022 15:45:00 ------- converged at time : 0.7 25-Feb-2022 15:45:00 number of iterations : 1 25-Feb-2022 15:45:00 number of reformations : 1 25-Feb-2022 15:45:00 ------- converged at time : 0.8 25-Feb-2022 15:45:00 number of iterations : 3 25-Feb-2022 15:45:00 number of reformations : 3 25-Feb-2022 15:45:00 ------- converged at time : 0.9 25-Feb-2022 15:45:00 number of iterations : 3 25-Feb-2022 15:45:01 number of reformations : 3 25-Feb-2022 15:45:01 ------- converged at time : 1 25-Feb-2022 15:45:01 number of iterations : 3 25-Feb-2022 15:45:01 number of reformations : 3 25-Feb-2022 15:45:01 ------- converged at time : 1.1 25-Feb-2022 15:45:01 number of iterations : 3 25-Feb-2022 15:45:01 number of reformations : 3 25-Feb-2022 15:45:01 ------- converged at time : 1.2 25-Feb-2022 15:45:01 number of iterations : 1 25-Feb-2022 15:45:01 number of reformations : 1 25-Feb-2022 15:45:01 ------- converged at time : 1.3 25-Feb-2022 15:45:01 number of iterations : 3 25-Feb-2022 15:45:02 number of reformations : 3 25-Feb-2022 15:45:02 ------- converged at time : 1.4 25-Feb-2022 15:45:02 number of iterations : 3 25-Feb-2022 15:45:02 number of reformations : 3 25-Feb-2022 15:45:02 ------- converged at time : 1.5 25-Feb-2022 15:45:02 number of iterations : 3 25-Feb-2022 15:45:02 number of reformations : 3 25-Feb-2022 15:45:02 ------- converged at time : 1.6 25-Feb-2022 15:45:02 number of iterations : 3 25-Feb-2022 15:45:03 number of reformations : 3 25-Feb-2022 15:45:03 ------- converged at time : 1.7 25-Feb-2022 15:45:03 number of iterations : 1 25-Feb-2022 15:45:03 number of reformations : 1 25-Feb-2022 15:45:03 ------- converged at time : 1.8 25-Feb-2022 15:45:03 number of iterations : 3 25-Feb-2022 15:45:03 number of reformations : 3 25-Feb-2022 15:45:03 ------- converged at time : 1.9 25-Feb-2022 15:45:03 number of iterations : 3 25-Feb-2022 15:45:04 number of reformations : 3 25-Feb-2022 15:45:04 ------- converged at time : 2 25-Feb-2022 15:45:04 Elapsed time : 0:00:06 25-Feb-2022 15:45:04 N O R M A L T E R M I N A T I O N # Done 25-Feb-2022 15:45:04 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Import FEBio results
if 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_MAG=sqrt(sum(N_disp_mat.^2,2)); DN=N_disp_mat(:,:,end); DN_magnitude=sqrt(sum(DN(:,3).^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_def]=vertexToFaceMeasure(Fb,DN_magnitude);
Importing element data from a log file
[~,E_data,~]=importFEBio_logfile(fullfile(savePath,febioLogFileName_strain)); %Element data %Remove nodal index column E_data=E_data(:,2:end,:); E_data=sqrt(0.5*( (E_data(:,1,:)-E_data(:,2,:)).^2 + (E_data(:,2,:)-E_data(:,3,:)).^2 + (E_data(:,3,:)-E_data(:,1,:)).^2 )); %Add initial state i.e. zero sizImport=size(E_data); sizImport(3)=sizImport(3)+1; E_data_mat_n=zeros(sizImport); E_data_mat_n(:,:,2:end)=E_data; E_data=E_data_mat_n; VE=patchCentre(E,V); logicCutElements=VE(:,2)>=0; [F_cut,CF_cut_data]=element2patch(E(logicCutElements,:),E_data(logicCutElements,:,1)); [indBoundary]=tesBoundary(F_cut); CV=faceToVertexMeasure(F_cut(indBoundary,:),V,CF_cut_data(indBoundary,:));
Plotting the simulated results using anim8 to visualize and animate deformations
% Create basic view and store graphics handle to initiate animation hf=cFigure; %Open figure gtitle([febioFebFileNamePart,': Press play to animate']); % subplot(1,2,1); hp1=gpatch(Fb,V_def,'kw','none',0.25); %Add graphics object to animate hp2=gpatch(F_cut(indBoundary,:),V_def,CV,'k',1); %Add graphics object to animate hp2.FaceColor='interp'; % gpatch(Fb,V,0.5*ones(1,3),'k',0.25); %A static graphics object colormap(gjet(250)); colorbar; caxis([0 max(E_data(:))/3]); axisGeom(gca,fontSize); axis([min(X_DEF(:)) max(X_DEF(:)) min(Y_DEF(:)) max(Y_DEF(:)) min(Z_DEF(:)) max(Z_DEF(:))]); axis manual; camlight headlight; drawnow; % 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)); %Current displacement magnitude V_def=V+DN; %Current nodal coordinates % [CF_def]=vertexToFaceMeasure(Fb,DN_magnitude); %Current color data to use [~,CF_cut_data]=element2patch(E(logicCutElements,:),E_data(logicCutElements,:,qt)); CV=faceToVertexMeasure(F_cut(indBoundary,:),V,CF_cut_data(indBoundary,:)); %Set entries in animation structure animStruct.Handles{qt}=[hp1 hp2 hp2]; %Handles of objects to animate animStruct.Props{qt}={'Vertices','Vertices','CData'}; %Properties of objects to animate animStruct.Set{qt}={V_def,V_def,CV}; %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.
Copyright (C) 2006-2022 Kevin Mattheus Moerman and the GIBBON contributors
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.
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