DEMO_febio_0020_vessel_balloon_inflate

Below is a demonstration for:

Building geometry for a cylindrical vessel with hexahedral elements
Defining the boundary conditions
Coding the febio structure
Running the model
Importing and visualizing the displacement results

Keywords
Plot settings
Control parameters
Creating model boundary polygons
Creating model boundary surfaces
Joining node sets
Defining the boundary conditions
Define contact
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
vessel, cylinder, balloon
prescribed displacement
contact, sliding
hexahedral elements, hex8
tube, cylindrical
static, solid, multistep
hyperelastic, Ogden
displacement logfile
stress logfile
Nodal displacement mapping
Shell thickness specification

clear; close all; clc;

Plot settings

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

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_strain=[febioFebFileNamePart,'_strain_out.txt']; %Log file name for exporting strain

%Specifying geometry parameters vessel (mm)
pointSpacing=1;
radiusOuter1=6.5/2;
radiusInner1=5.4/2;
radiusOuter2=5.8/2;
radiusInner2=4.7/2;
vesselLength=40;
contactInitialOffset=0.1;

radiusBalloon=min([radiusInner1 radiusInner2])-contactInitialOffset;
pointSpacingBalloon=pointSpacing/2;
balloonExtraLength=pointSpacing/2;

%Define applied bc's
radialDisplacement=1; %radial displacement after touch
radialDisplacementTotal=radialDisplacement+contactInitialOffset; %Total radial displacement

%Material parameter set
c1=1e-3; %Shear-modulus-like parameter
m1=2; %Material parameter setting degree of non-linearity
k_factor=100; %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=10; %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;

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

%Contact parameters
contactPenalty=0.5;
laugon=0;
minaug=1;
maxaug=10;
fric_coeff=0;

%Visualization parameters
colorLimits_volumeRatio=[0.99 1.01];

Creating model boundary polygons

nRad=round((2*pi*max([radiusOuter1 radiusOuter2]))/pointSpacing); %Number of radial steps

t=linspace(0,2*pi,nRad)'; %Angles
t=t(1:end-1); %take away last which equals start
v1_Outer=[-(vesselLength/2)*ones(size(t)) radiusOuter1*sin(t) radiusOuter1*cos(t)]; %Circular coordinates

t=linspace(0,2*pi,nRad)'; %Angles
t=t(1:end-1); %take away last which equals start
v2_Outer=[(vesselLength/2)*ones(size(t)) radiusOuter2*sin(t) radiusOuter2*cos(t)]; %Circular coordinates

t=linspace(0,2*pi,nRad)'; %Angles
t=t(1:end-1); %take away last which equals start
v1_Inner=[-(vesselLength/2)*ones(size(t)) radiusInner1*sin(t) radiusInner1*cos(t)]; %Circular coordinates

t=linspace(0,2*pi,nRad)'; %Angles
t=t(1:end-1); %take away last which equals start
v2_Inner=[(vesselLength/2)*ones(size(t)) radiusInner2*sin(t) radiusInner2*cos(t)]; %Circular coordinates

t=linspace(0,2*pi,nRad)'; %Angles
t=t(1:end-1); %take away last which equals start
v1_balloon=[-((vesselLength/2)+balloonExtraLength)*ones(size(t)) radiusBalloon*sin(t) radiusBalloon*cos(t)]; %Circular coordinates
v2_balloon=[ ((vesselLength/2)+balloonExtraLength)*ones(size(t)) radiusBalloon*sin(t) radiusBalloon*cos(t)]; %Circular coordinates

Plotting model boundary polygons

cFigure;
hold on;
title('Model boundary polygons','FontSize',fontSize);
plotV(v1_Outer,'r.-')
plotV(v1_Inner,'g.-')
plotV(v2_Outer,'b.-')
plotV(v2_Inner,'y.-')
plotV(v1_balloon,'c.-')
plotV(v2_balloon,'k.-')
axisGeom(gca,fontSize);

drawnow;

Creating model boundary surfaces

controlStructLoft.numSteps=ceil(vesselLength./pointSpacing);
controlStructLoft.closeLoopOpt=1;
controlStructLoft.patchType='quad';

%Meshing outer surface
[F1,V1,indStart1]=polyLoftLinear(v1_Outer,v2_Outer,controlStructLoft);

%Meshing inner surface
[F2,V2,indStart2]=polyLoftLinear(v1_Inner,v2_Inner,controlStructLoft);

%Compose hexahedral elements
indStart2=indStart2+size(V1,1);
F2=F2+size(V1,1);
E=[F1 F2];
V=[V1;V2];
[FE]=element2patch(E,[],'hex8');
indBoundary=tesBoundary(FE);
Fb=FE(indBoundary,:);

%Meshing balloon surface
[Fs,Vs]=polyLoftLinear(v1_balloon,v2_balloon,controlStructLoft);
Fs=fliplr(Fs); %Invert orientation
[Fs,Vs]=subQuad(Fs,Vs,1);

Plotting model boundary surfaces

cFigure;
hold on;
title('Model boundary surfaces','FontSize',fontSize);

gpatch(FE,V,'rw','k',0.5);
patchNormPlot(FE,V);

gpatch(F1,V,'bw');
patchNormPlot(F1,V);

gpatch(F2,V,'gw');
patchNormPlot(F2,V);

gpatch(Fs,Vs,'kw');
patchNormPlot(Fs,Vs);

colormap(gca,gjet(4));
icolorbar;

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

Joining node sets

Fs=Fs+size(V,1);
V=[V;Vs];

Defining the boundary conditions

The visualization of the model boundary shows colors for each side of the cube. These labels can be used to define boundary conditions.

%Define X supported node set
bcSupportList_X=unique([indStart1(:);indStart2(:)]); %Node set part of selected face

% %Define Y supported node set
% bcSupportList_Y=unique(Fb(Cb==4,:)); %Node set part of selected face

%Radial expansion prescribed displacement
bcPrescribeList=(size(V,1)-size(Vs,1)+1):size(V,1);

%Define presribed displacements
[t,r,z]  = cart2pol(V(bcPrescribeList,2),V(bcPrescribeList,3),V(bcPrescribeList,1));
[y2,z2,x2] = pol2cart(t,r+radialDisplacementTotal,z);
Ux=x2-V(bcPrescribeList,1);
Uy=y2-V(bcPrescribeList,2);
Uz=z2-V(bcPrescribeList,3);

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

cFigure;
title('Boundary conditions','FontSize',fontSize);
xlabel('X','FontSize',fontSize); ylabel('Y','FontSize',fontSize); zlabel('Z','FontSize',fontSize);
hold on;

gpatch(FE,V,'kw','k',0.5);
gpatch(Fs,V,'kw','k',0.5);

hl(1)=plotV(V(bcSupportList_X,:),'k.','MarkerSize',markerSize);
hl(2)=gpatch(Fs,V,'rw','r',0.5);

legend(hl,{'BC X support','BC prescribe'});

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

Define contact

F_contact_primary=Fs;
F_contact_secondary=F2;

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

hf=cFigure;
title('Boundary conditions','FontSize',fontSize);
xlabel('X','FontSize',fontSize); ylabel('Y','FontSize',fontSize); zlabel('Z','FontSize',fontSize);
hold on;

gpatch(FE,V,'kw','none',0.5);

h1(1)=gpatch(F_contact_primary,V,'gw','g',0.5);
patchNormPlot(F_contact_primary,V);
h1(2)=gpatch(F_contact_secondary,V,'rw','r',0.5);
patchNormPlot(F_contact_secondary,V);

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

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='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;

materialName2='Material2';
febio_spec.Material.material{2}.ATTR.name=materialName2;
febio_spec.Material.material{2}.ATTR.type='Ogden';
febio_spec.Material.material{2}.ATTR.id=2;
febio_spec.Material.material{2}.c1=c1;
febio_spec.Material.material{2}.m1=m1;
febio_spec.Material.material{2}.c2=c1;
febio_spec.Material.material{2}.m2=-m1;
febio_spec.Material.material{2}.k=k;

%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,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='quad4'; %Element type
febio_spec.Mesh.Elements{2}.elem.ATTR.id=size(E,1)+(1:1:size(Fs,1))'; %Element id's
febio_spec.Mesh.Elements{2}.elem.VAL=Fs; %The element matrix

% -> Surfaces
surfaceName1='contactSurface1';
febio_spec.Mesh.Surface{1}.ATTR.name=surfaceName1;
febio_spec.Mesh.Surface{1}.quad4.ATTR.id=(1:1:size(F_contact_primary,1))';
febio_spec.Mesh.Surface{1}.quad4.VAL=F_contact_primary;

surfaceName2='contactSurface2';
febio_spec.Mesh.Surface{2}.ATTR.name=surfaceName2;
febio_spec.Mesh.Surface{2}.quad4.ATTR.id=(1:1:size(F_contact_secondary,1))';
febio_spec.Mesh.Surface{2}.quad4.VAL=F_contact_secondary;

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

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

nodeSetName2='bcPrescribeList';
febio_spec.Mesh.NodeSet{2}.ATTR.name=nodeSetName2;
febio_spec.Mesh.NodeSet{2}.VAL=mrow(bcPrescribeList);

%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;
febio_spec.MeshDomains.ShellDomain.shell_thickness=0.01;

%-> Node data
meshDataName_Ux='DisplacementData_X';
febio_spec.MeshData.NodeData{1}.ATTR.name=meshDataName_Ux;
febio_spec.MeshData.NodeData{1}.ATTR.node_set=nodeSetName2;
febio_spec.MeshData.NodeData{1}.ATTR.data_type='scalar';
febio_spec.MeshData.NodeData{1}.node.ATTR.lid=(1:numel(bcPrescribeList))';
febio_spec.MeshData.NodeData{1}.node.VAL=Ux(:);

meshDataName_Uy='DisplacementData_Y';
febio_spec.MeshData.NodeData{2}.ATTR.name=meshDataName_Uy;
febio_spec.MeshData.NodeData{2}.ATTR.node_set=nodeSetName2;
febio_spec.MeshData.NodeData{2}.ATTR.data_type='scalar';
febio_spec.MeshData.NodeData{2}.node.ATTR.lid=(1:numel(bcPrescribeList))';
febio_spec.MeshData.NodeData{2}.node.VAL=Uy(:);

meshDataName_Uz='DisplacementData_Z';
febio_spec.MeshData.NodeData{3}.ATTR.name=meshDataName_Uz;
febio_spec.MeshData.NodeData{3}.ATTR.node_set=nodeSetName2;
febio_spec.MeshData.NodeData{3}.ATTR.data_type='scalar';
febio_spec.MeshData.NodeData{3}.node.ATTR.lid=(1:numel(bcPrescribeList))';
febio_spec.MeshData.NodeData{3}.node.VAL=Uz(:);

%Boundary condition section
% -> Fix boundary conditions
febio_spec.Boundary.bc{1}.ATTR.name='zero_displacement_x';
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=0;
febio_spec.Boundary.bc{1}.z_dof=0;

% -> Prescribe boundary conditions
febio_spec.Boundary.bc{2}.ATTR.name='prescibed_displacement_x';
febio_spec.Boundary.bc{2}.ATTR.type='prescribed displacement';
febio_spec.Boundary.bc{2}.ATTR.node_set=nodeSetName2;
febio_spec.Boundary.bc{2}.dof='x';
febio_spec.Boundary.bc{2}.value.ATTR.lc=1;
febio_spec.Boundary.bc{2}.value.ATTR.type='map';
febio_spec.Boundary.bc{2}.value.VAL=meshDataName_Ux;
febio_spec.Boundary.bc{2}.relative=0;

febio_spec.Boundary.bc{3}.ATTR.name='prescibed_displacement_y';
febio_spec.Boundary.bc{3}.ATTR.type='prescribed displacement';
febio_spec.Boundary.bc{3}.ATTR.node_set=nodeSetName2;
febio_spec.Boundary.bc{3}.dof='y';
febio_spec.Boundary.bc{3}.value.ATTR.lc=1;
febio_spec.Boundary.bc{3}.value.ATTR.type='map';
febio_spec.Boundary.bc{3}.value.VAL=meshDataName_Uy;
febio_spec.Boundary.bc{3}.relative=0;

febio_spec.Boundary.bc{4}.ATTR.name='prescibed_displacement_z';
febio_spec.Boundary.bc{4}.ATTR.type='prescribed displacement';
febio_spec.Boundary.bc{4}.ATTR.node_set=nodeSetName2;
febio_spec.Boundary.bc{4}.dof='z';
febio_spec.Boundary.bc{4}.value.ATTR.lc=1;
febio_spec.Boundary.bc{4}.value.ATTR.type='map';
febio_spec.Boundary.bc{4}.value.VAL=meshDataName_Uz;
febio_spec.Boundary.bc{4}.relative=0;

%Contact section
febio_spec.Contact.contact{1}.ATTR.type='sliding-elastic';
febio_spec.Contact.contact{1}.ATTR.surface_pair=febio_spec.Mesh.SurfacePair{1}.ATTR.name;
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_strain;
febio_spec.Output.logfile.element_data{1}.ATTR.data='E1';
febio_spec.Output.logfile.element_data{1}.ATTR.delim=',';

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 febView(febio_spec)

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;%'internal';

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

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-------->    RUNNING/MONITORING FEBIO JOB    <-------- 24-Jul-2023 10:42:55
FEBio path: /home/kevin/FEBioStudio/bin/febio4
# Attempt removal of existing log files                24-Jul-2023 10:42:55
 * Removal succesful                                   24-Jul-2023 10:42:55
# Attempt removal of existing .xplt files              24-Jul-2023 10:42:55
 * Removal succesful                                   24-Jul-2023 10:42:55
# Starting FEBio...                                    24-Jul-2023 10:42:55
  Max. total analysis time is: Inf s
 * Waiting for log file creation                       24-Jul-2023 10:42:55
   Max. wait time: 30 s
 * Log file found.                                     24-Jul-2023 10:42:55
# Parsing log file...                                  24-Jul-2023 10:42:55
    number of iterations   : 4                         24-Jul-2023 10:42:56
    number of reformations : 4                         24-Jul-2023 10:42:56
------- converged at time : 0.1                        24-Jul-2023 10:42:56
    number of iterations   : 7                         24-Jul-2023 10:42:57
    number of reformations : 7                         24-Jul-2023 10:42:57
------- converged at time : 0.2                        24-Jul-2023 10:42:57
    number of iterations   : 6                         24-Jul-2023 10:42:59
    number of reformations : 6                         24-Jul-2023 10:42:59
------- converged at time : 0.3                        24-Jul-2023 10:42:59
    number of iterations   : 6                         24-Jul-2023 10:43:00
    number of reformations : 6                         24-Jul-2023 10:43:00
------- converged at time : 0.4                        24-Jul-2023 10:43:00
    number of iterations   : 4                         24-Jul-2023 10:43:02
    number of reformations : 4                         24-Jul-2023 10:43:02
------- converged at time : 0.5                        24-Jul-2023 10:43:02
    number of iterations   : 4                         24-Jul-2023 10:43:03
    number of reformations : 4                         24-Jul-2023 10:43:03
------- converged at time : 0.6                        24-Jul-2023 10:43:03
    number of iterations   : 4                         24-Jul-2023 10:43:05
    number of reformations : 4                         24-Jul-2023 10:43:05
------- converged at time : 0.7                        24-Jul-2023 10:43:05
    number of iterations   : 5                         24-Jul-2023 10:43:06
    number of reformations : 5                         24-Jul-2023 10:43:06
------- converged at time : 0.8                        24-Jul-2023 10:43:06
    number of iterations   : 5                         24-Jul-2023 10:43:06
    number of reformations : 5                         24-Jul-2023 10:43:06
------- converged at time :                            24-Jul-2023 10:43:06
    number of iterations   : 5                         24-Jul-2023 10:43:07
    number of reformations : 5                         24-Jul-2023 10:43:07
------- converged at time : 1                          24-Jul-2023 10:43:07
 Elapsed time : 0:00:12                                24-Jul-2023 10:43:07
 N O R M A L   T E R M I N A T I O N
# Done                                                 24-Jul-2023 10:43:07
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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.FaceColor='interp';
    hp2=gpatch(Fs,V,'w','k',1); %A static graphics object

    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 hp2]; %Handles of objects to animate
        animStruct.Props{qt}={'Vertices','CData','Vertices'}; %Properties of objects to animate
        animStruct.Set{qt}={V_DEF(:,:,qt),DN_magnitude,V_DEF(:,:,qt)}; %Property values for to set in order to animate
    end
    anim8(hf,animStruct); %Initiate animation feature
    drawnow;

Importing element stress from a log file

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

    %Access data
    E_strain_mat=dataStruct.data;
    E_strain_mat(isnan(E_strain_mat))=0;

Plotting the simulated results using anim8 to visualize and animate deformations

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

    % Create basic view and store graphics handle to initiate animation
    hf=cFigure; %Open figure
    gtitle([febioFebFileNamePart,': Press play to animate']);
    title('$\varepsilon_{1}$ [.]','Interpreter','Latex')
    hp=gpatch(Fb,V_DEF(:,:,end),CV,'k',1); %Add graphics object to animate
    hp.FaceColor='interp';
    hp2=gpatch(Fs,V,'w','k',1); %A static graphics object

    axisGeom(gca,fontSize);
    colormap(gjet(250)); colorbar;
    caxis([min(E_strain_mat(:)) max(E_strain_mat(:))]);
    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_strain_mat(:,:,qt));

        %Set entries in animation structure
        animStruct.Handles{qt}=[hp hp 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]

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.

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/.