DEMO_febio_0020_vessel_balloon_inflate

Below is a demonstration for:

Contents

Keywords

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=fullfile(savePath,[febioFebFileNamePart,'.txt']); %FEBio log file name
febioLogFileName_disp=[febioFebFileNamePart,'_disp_out.txt']; %Log file name for exporting displacement
febioLogFileName_stress=[febioFebFileNamePart,'_stress_out.txt']; %Log file name for exporting stress
febioLogFileName_strain=[febioFebFileNamePart,'_strain_out.txt']; %Log file name for exporting strain
febioLogFileName_volumeRatio=[febioFebFileNamePart,'_volumeRatio_out.txt']; %Log file name for exporting volume ratio

%Contact parameters
%***
contactInitialOffset=0.1;
contactAlg=2;
switch contactAlg
    case 1
        contactType='sticky';
    case 2
        contactType='facet-to-facet sliding';
    case 3
        contactType='sliding_with_gaps';
        fric_coeff=0;
        fric_penalty=1;
    case 4
        contactType='sliding2';
end

%Specifying geometry parameters vessel (mm)***
pointSpacing=1;
radiusOuter1=6.5/2;
radiusInner1=5.4/2;
radiusOuter2=5.8/2;
radiusInner2=4.7/2;
vesselLength=85;

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

%Define applied bc's
radialDisplacement=2; %radial displacement after touch
radialDisplacementTotal=radialDisplacement+contactInitialOffset; %Total radial displacement
numSteps=1; %Number of steps

%Material parameter set
c1=1e-3; %Shear-modulus-like parameter
m1=2; %Material parameter setting degree of non-linearity
k_factor=500; %Bulk modulus factor
k=c1*k_factor; %Bulk modulus
fomulationType=1; %1=uncoupled, 2=coupled

% 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=0; %Maximum number of retires
dtmin=(1/numTimeSteps)/100; %Minimum time step size
dtmax=1/numTimeSteps; %Maximum time step size
runMode='external';

%Contact parameters
contactPenalty=1;

%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');

%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);
radialDisplacementStep=radialDisplacementTotal/numSteps; %The radial displacement increment for each step
[th,r,z] = cart2pol(V(bcPrescribeList,2),V(bcPrescribeList,3),V(bcPrescribeList,1));
r2=r+radialDisplacementStep;
V2=V;
[V2(bcPrescribeList,2),V2(bcPrescribeList,3),V2(bcPrescribeList,1)] = pol2cart(th,r2,z);

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

hl(1)=plotV(V(bcSupportList_X,:),'k.','MarkerSize',markerSize);
hl(2)=gpatch(Fs,V2,'rw','r',0.5);

legend(hl,{'BC X support','BC prescribe 1 step'});

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

Define contact

F_contact_master=Fs;
F_contact_slave=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_master,V,'gw','g',0.5);
patchNormPlot(F_contact_master,V);
h1(2)=gpatch(F_contact_slave,V,'rw','r',0.5);
patchNormPlot(F_contact_slave,V);

legend(hl,{'Master surface','Slave 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='2.5';

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

%Create control structure for use by all steps
stepStruct.Control.analysis.ATTR.type='static';
stepStruct.Control.time_steps=numTimeSteps;
stepStruct.Control.step_size=1/numTimeSteps;
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;
stepStruct.Control.max_refs=max_refs;
stepStruct.Control.max_ups=max_ups;

%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');

%Material section
if fomulationType==1
    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;

    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;
elseif fomulationType==2
    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{2}.ATTR.type='Ogden unconstrained';
    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}.cp=k;
end

%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='hex8'; %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='Vessel'; %Name of the element set
febio_spec.Geometry.Elements{1}.elem.ATTR.id=(1:1:size(E,1))'; %Element id's
febio_spec.Geometry.Elements{1}.elem.VAL=E;

febio_spec.Geometry.Elements{2}.ATTR.type='quad4'; %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='Balloon'; %Name of the element set
febio_spec.Geometry.Elements{2}.elem.ATTR.id=size(E,1)+(1:1:size(Fs,1))'; %Element id's
febio_spec.Geometry.Elements{2}.elem.VAL=Fs;

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

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

% -> Surfaces
febio_spec.Geometry.Surface{1}.ATTR.name='contact_master';
febio_spec.Geometry.Surface{1}.quad4.ATTR.lid=(1:1:size(F_contact_master,1))';
febio_spec.Geometry.Surface{1}.quad4.VAL=F_contact_master;

febio_spec.Geometry.Surface{2}.ATTR.name='contact_slave';
febio_spec.Geometry.Surface{2}.quad4.ATTR.lid=(1:1:size(F_contact_slave,1))';
febio_spec.Geometry.Surface{2}.quad4.VAL=F_contact_slave;

% -> Surface pairs
febio_spec.Geometry.SurfacePair{1}.ATTR.name='Contact1';
febio_spec.Geometry.SurfacePair{1}.master.ATTR.surface=febio_spec.Geometry.Surface{1}.ATTR.name;
febio_spec.Geometry.SurfacePair{1}.slave.ATTR.surface=febio_spec.Geometry.Surface{2}.ATTR.name;

%MeshData section
febio_spec.MeshData.ElementData{1}.ATTR.var='shell thickness';
febio_spec.MeshData.ElementData{1}.ATTR.elem_set=febio_spec.Geometry.Elements{2}.ATTR.name;
febio_spec.MeshData.ElementData{1}.elem.ATTR.lid=(1:size(Fs,1))';
febio_spec.MeshData.ElementData{1}.elem.VAL=0.1*ones(size(Fs));

%Create steps
[th,r2,z] = cart2pol(V(bcPrescribeList,2),V(bcPrescribeList,3),V(bcPrescribeList,1));
nodeSetName=febio_spec.Geometry.NodeSet{2}.ATTR.name;
febio_spec.MeshData.NodeData=[];%Initialize so we can use end+1 indexing
bcNames={'x','y','z'};

if numSteps==1

    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;

    %Define prescribed displacements
    bcPrescribeMagnitudesStep=V2(bcPrescribeList,:)-V(bcPrescribeList,:);

    %Define mesh data and prescribed displacements
    for q_dir=1:1:3 %Loop over coordinates dimensions

        %Define mesh data for displacement increments
        c=numel(febio_spec.MeshData.NodeData)+1; %Current step index
        febio_spec.MeshData.NodeData{c}.ATTR.name=['displacement_',bcNames{q_dir},'_1'];
        febio_spec.MeshData.NodeData{c}.ATTR.node_set=nodeSetName;
        febio_spec.MeshData.NodeData{c}.node.ATTR.lid=(1:1:numel(bcPrescribeList))';
        febio_spec.MeshData.NodeData{c}.node.VAL=bcPrescribeMagnitudesStep(:,q_dir);

        %Define prescribed displacements
        febio_spec.Boundary.prescribe{q_dir}.ATTR.bc=bcNames{q_dir};
        febio_spec.Boundary.prescribe{q_dir}.ATTR.relative=1;
        febio_spec.Boundary.prescribe{q_dir}.ATTR.node_set=nodeSetName;
        febio_spec.Boundary.prescribe{q_dir}.scale.ATTR.lc=1;
        febio_spec.Boundary.prescribe{q_dir}.scale.VAL=1;
        febio_spec.Boundary.prescribe{q_dir}.relative=1;
        febio_spec.Boundary.prescribe{q_dir}.value.ATTR.node_data=febio_spec.MeshData.NodeData{c}.ATTR.name;
    end
else
    V2n=V;
    V2=V;
    for q=1:1:numSteps
        %Step specific control section
        febio_spec.Step{q}.ATTR.id=q;
        febio_spec.Step{q}.Control=stepStruct.Control;

        %Offset coordinates
        r2=r2+radialDisplacementStep;
        V2n=V2;
        [V2n(bcPrescribeList,2),V2n(bcPrescribeList,3),V2n(bcPrescribeList,1)] = pol2cart(th,r2,z); %The current set

        %Define prescribed displacements
        bcPrescribeMagnitudesStep=V2n(bcPrescribeList,:)-V2(bcPrescribeList,:);
        V2=V2n;

        %Define mesh data and prescribed displacements
        for q_dir=1:1:3 %Loop over coordinates dimensions

            %Define mesh data for displacement increments
            c=numel(febio_spec.MeshData.NodeData)+1; %Current step index
            febio_spec.MeshData.NodeData{c}.ATTR.name=['displacement_',bcNames{q_dir},'_step_',num2str(q)];
            febio_spec.MeshData.NodeData{c}.ATTR.node_set=nodeSetName;
            febio_spec.MeshData.NodeData{c}.node.ATTR.lid=(1:1:numel(bcPrescribeList))';
            febio_spec.MeshData.NodeData{c}.node.VAL=bcPrescribeMagnitudesStep(:,q_dir);

            %Define prescribed displacements
            febio_spec.Step{q}.Boundary.prescribe{q_dir}.ATTR.bc=bcNames{q_dir};
            febio_spec.Step{q}.Boundary.prescribe{q_dir}.ATTR.relative=1;
            febio_spec.Step{q}.Boundary.prescribe{q_dir}.ATTR.node_set=nodeSetName;
            febio_spec.Step{q}.Boundary.prescribe{q_dir}.scale.ATTR.lc=1;
            febio_spec.Step{q}.Boundary.prescribe{q_dir}.scale.VAL=1;
            febio_spec.Step{q}.Boundary.prescribe{q_dir}.relative=1;
            febio_spec.Step{q}.Boundary.prescribe{q_dir}.value.ATTR.node_data=febio_spec.MeshData.NodeData{c}.ATTR.name;
        end

    end

end
%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;

%Contact section
switch contactType
    case 'sticky'
        febio_spec.Contact.contact{1}.ATTR.surface_pair=febio_spec.Geometry.SurfacePair{1}.ATTR.name;
        febio_spec.Contact.contact{1}.ATTR.type='sticky';
        febio_spec.Contact.contact{1}.penalty=contactPenalty;
        febio_spec.Contact.contact{1}.laugon=0;
        febio_spec.Contact.contact{1}.tolerance=0.1;
        febio_spec.Contact.contact{1}.minaug=0;
        febio_spec.Contact.contact{1}.maxaug=10;
        febio_spec.Contact.contact{1}.snap_tol=0;
        febio_spec.Contact.contact{1}.max_traction=0;
        febio_spec.Contact.contact{1}.search_tolerance=0.1;
    case 'facet-to-facet sliding'
        febio_spec.Contact.contact{1}.ATTR.surface_pair=febio_spec.Geometry.SurfacePair{1}.ATTR.name;
        febio_spec.Contact.contact{1}.ATTR.type='facet-to-facet sliding';
        febio_spec.Contact.contact{1}.penalty=contactPenalty;
        febio_spec.Contact.contact{1}.auto_penalty=1;
        febio_spec.Contact.contact{1}.two_pass=0;
        febio_spec.Contact.contact{1}.laugon=0;
        febio_spec.Contact.contact{1}.tolerance=0.1;
        febio_spec.Contact.contact{1}.gaptol=0;
        febio_spec.Contact.contact{1}.minaug=0;
        febio_spec.Contact.contact{1}.maxaug=10;
        febio_spec.Contact.contact{1}.search_tol=0.01;
        febio_spec.Contact.contact{1}.search_radius=pointSpacing/10;
    case 'sliding_with_gaps'
        febio_spec.Contact.contact{1}.ATTR.surface_pair=febio_spec.Geometry.SurfacePair{1}.ATTR.name;
        febio_spec.Contact.contact{1}.ATTR.type='sliding_with_gaps';
        febio_spec.Contact.contact{1}.penalty=contactPenalty;
        febio_spec.Contact.contact{1}.auto_penalty=1;
        febio_spec.Contact.contact{1}.two_pass=0;
        febio_spec.Contact.contact{1}.laugon=0;
        febio_spec.Contact.contact{1}.tolerance=0.1;
        febio_spec.Contact.contact{1}.gaptol=0;
        febio_spec.Contact.contact{1}.minaug=0;
        febio_spec.Contact.contact{1}.maxaug=10;
        febio_spec.Contact.contact{1}.fric_coeff=fric_coeff;
        febio_spec.Contact.contact{1}.fric_penalty=fric_penalty;
        febio_spec.Contact.contact{1}.ktmult=1;
        febio_spec.Contact.contact{1}.seg_up=0;
        febio_spec.Contact.contact{1}.search_tol=0.01;
    case 'sliding2'
        febio_spec.Contact.contact{1}.ATTR.surface_pair=febio_spec.Geometry.SurfacePair{1}.ATTR.name;
        febio_spec.Contact.contact{1}.ATTR.type='sliding2';
        febio_spec.Contact.contact{1}.penalty=contactPenalty;
        febio_spec.Contact.contact{1}.auto_penalty=1;
        febio_spec.Contact.contact{1}.two_pass=0;
        febio_spec.Contact.contact{1}.laugon=0;
        febio_spec.Contact.contact{1}.tolerance=0.1;
        febio_spec.Contact.contact{1}.gaptol=0;
        febio_spec.Contact.contact{1}.symmetric_stiffness=0;
        febio_spec.Contact.contact{1}.search_tol=0.01;
        febio_spec.Contact.contact{1}.search_radius=pointSpacing/2;
end

% LoadData section
febio_spec.LoadData.loadcurve{1}.ATTR.id=1;
febio_spec.LoadData.loadcurve{1}.ATTR.type='linear';
febio_spec.LoadData.loadcurve{1}.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.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:size(E,1);

febio_spec.Output.logfile.element_data{2}.ATTR.file=febioLogFileName_strain;
febio_spec.Output.logfile.element_data{2}.ATTR.data='E1;E2;E3';
febio_spec.Output.logfile.element_data{2}.ATTR.delim=',';
febio_spec.Output.logfile.element_data{2}.VAL=1:size(E,1);

febio_spec.Output.logfile.element_data{3}.ATTR.file=febioLogFileName_volumeRatio;
febio_spec.Output.logfile.element_data{3}.ATTR.data='J';
febio_spec.Output.logfile.element_data{3}.ATTR.delim=',';
febio_spec.Output.logfile.element_data{3}.VAL=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 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.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=30; %Max log file checking time

[runFlag]=runMonitorFEBio(febioAnalysis);%START FEBio NOW!!!!!!!!
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- STARTING FEBIO JOB --- 04-Jun-2019 12:50:05
Waiting for log file...
Proceeding to check log file...04-Jun-2019 12:50:06
------- converged at time : 0.1
------- converged at time : 0.2
------- converged at time : 0.274116
------- converged at time : 0.348233
------- converged at time : 0.427526
------- converged at time : 0.51096
------- converged at time : 0.597708
------- converged at time : 0.687106
------- converged at time : 0.778624
------- converged at time : 0.871839
------- converged at time : 0.966411
------- converged at time : 1
--- Done --- 04-Jun-2019 12:50:43

Import FEBio results

if runFlag==1 | runFlag==0 %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]=vertexToFaceMeasure(Fb,DN_magnitude);

    for q=1:1:numel(febio_spec.Output.logfile.element_data)

        elementDataFileName=febio_spec.Output.logfile.element_data{q}.ATTR.file;

        % Importing element data from log file
        [~,E_data,~]=importFEBio_logfile(fullfile(savePath,elementDataFileName)); %Element data

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

        %Add initial state
        sizImport=size(E_data);
        sizImport(3)=sizImport(3)+1;
        if strcmp('J',febio_spec.Output.logfile.element_data{q}.ATTR.data)
            E_data_mat_n=ones(sizImport);
        else
            E_data_mat_n=zeros(sizImport);
        end
        E_data_mat_n(:,:,2:end)=E_data;
        E_data=E_data_mat_n;

        for qd=1:1:size(E_data,2)
            E_data_now=E_data(:,qd,:);

            [F,CF]=element2patch(E,E_data_now(:,:,1));

            % 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,', data: ',febio_spec.Output.logfile.element_data{q}.ATTR.data,', index: ',num2str(qd)]);

            hold on;
            hp1=gpatch(F,V_def,CF,'k',1); %Add graphics object to animate
            hp2=gpatch(Fs,V_def,'kw','k',1); %Add graphics object to animate
            %     gpatch(FE,V,0.5*ones(1,3),'k',0.25); %A static graphics object

            colormap(gca,gjet(250)); hc=colorbar;

            caxis([min(E_data_now(:)) max(E_data_now(:))]);
            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]=element2patch(E,E_data_now(:,:,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,CF,V_def}; %Property values for to set in order to animate
            end
            anim8(hf,animStruct); %Initiate animation feature
            drawnow;

        end
    end

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.

Copyright (C) 2018 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/.

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) 2019 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/.