DEMO_febio_0054_lattice_hydrostatic_01

Below is a demonstration for:

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

Keywords
Plot settings
Control parameters
Create lattice
DEFINE BC's
Smoothing lattice
Defining the FEBio input structure
Quick viewing of the FEBio input file structure
Exporting the FEBio input file
Running the FEBio analysis
Import FEBio results

Keywords

febio_spec version 3.0
febio, FEBio
uniaxial loading
compression, tension, compressive, tensile
displacement control, displacement boundary condition
hexahedral elements, hex8
cube, box, rectangular
static, solid
hyperelastic, Ogden
displacement logfile
stress logfile

clear; close all; clc;

Plot settings

fontSize=15;
faceAlpha1=0.8;
faceAlpha2=1;
edgeColor=0.25*ones(1,3);
edgeWidth=1.5;
markerSize=25;
cMap=gjet(4);

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_force=[febioFebFileNamePart,'_force_out.txt']; %Log file name for exporting force
febioLogFileName_stress=[febioFebFileNamePart,'_stress_out.txt']; %Log file name for exporting stress
febioLogFileName_stiffness=[febioFebFileNamePart,'_stiffness_out.txt']; %Log file name for exporting stiffness

%Specifying dimensions and number of elements
sampleSize=10;
latticeType=1;

%Define applied displacement
J_final=0.7; %Final Jacobian or volume ration
lambdaFinal=J_final^(1/3); %Stretch values in all directions
displacementMagnitude=((lambdaFinal*sampleSize)-sampleSize)/2; %The displacement magnitude

%Material parameter set
c1=1; %Shear-modulus-like parameter
m1=2;
k=50*c1;

% FEA control settings
numTimeSteps=50; %Number of time steps desired
max_refs=50; %Max reforms
max_ups=0; %Set to zero to use full-Newton iterations
opt_iter=25; %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
min_residual=1e-20;
symmetric_stiffness=0;
runMode='external';

%Specifying dimensions and number of elements
r=0.5; %Radii, results in a width of 1
n=4;
nCopies=n*ones(1,3); %Number of offset copies
d=2*r; %Diameter
w=(n-1)*d; %sampleSize

Create lattice

switch latticeType
    case 1 %Octet truss
        [Er,Vr,Cr,Fr,CFr]=rhombicDodecahedronMesh(r,nCopies);
        Vr=Vr./(n-1);
        Vr=Vr*sampleSize;

        [indBoundary]=tesBoundary(Fr,Vr);
        cPar.shrinkFactor=0.15; %Strut sides are formed by shrinking the input mesh faces by this factor
        cPar.meshType='hex'; %desired output mesh type
        cPar.indBoundary=indBoundary; %indices of the boundary faces
        cPar.hexSplit=2;
        cPar.latticeSide=2; %1=side 1 the edge lattice, 2=side 2 the dual lattice to the edge lattice
        [E,V,C]=element2lattice(Er,Vr,cPar); %Get lattice structure

        logicKeep1=~(V(:,1)<=-1e-3);
        logicKeep2=~(V(:,2)<=-1e-3);
        logicKeep3=~(V(:,3)<=-1e-3);
        logicKeep4=~(V(:,1)>=sampleSize+1e-3);
        logicKeep5=~(V(:,2)>=sampleSize+1e-3);
        logicKeep6=~(V(:,3)>=sampleSize+1e-3);

        logicKeepEs=sum(logicKeep1(E),2)>=4 &...
            sum(logicKeep2(E),2)>=4 &...
            sum(logicKeep3(E),2)>=4 &...
            sum(logicKeep4(E),2)>=4 &...
            sum(logicKeep5(E),2)>=4 &...
            sum(logicKeep6(E),2)>=4;

        E=E(logicKeepEs,:);
        C=C(logicKeepEs,:);
        [E,V,indFix]=patchCleanUnused(E,V);

        % [Es,Vs,~,~]=subHex(Es,Vs,1,1);
        % Cs=repmat(Cs,8,1);

        % Create patch Data for visualization
        [Fs,CsF]=element2patch(E,C); %Patch data for plotting

        %Get new boundary set
        indB=tesBoundary(Fs,V);
        Fb=Fs(indB,:);
    case 2 %Rhombic dodecahedron mesh ("dual" of octet truss lattice)
        [Er,Vr,Cr,Fr,CFr]=rhombicDodecahedronMesh(r,nCopies);
        Vr=Vr./(n-1);
        Vr=Vr*sampleSize;

        [indBoundary]=tesBoundary(Fr,Vr);
        cPar.shrinkFactor=0.15; %Strut sides are formed by shrinking the input mesh faces by this factor
        cPar.meshType='hex'; %desired output mesh type
        cPar.indBoundary=indBoundary; %indices of the boundary faces
        cPar.hexSplit=2;
        cPar.latticeSide=1; %1=side 1 the edge lattice, 2=side 2 the dual lattice to the edge lattice
        [E,V,C]=element2lattice(Er,Vr,cPar); %Get lattice structure

        logicKeep1=~(V(:,1)<=-1e-3);
        logicKeep2=~(V(:,2)<=-1e-3);
        logicKeep3=~(V(:,3)<=-1e-3);
        logicKeep4=~(V(:,1)>=sampleSize+1e-3);
        logicKeep5=~(V(:,2)>=sampleSize+1e-3);
        logicKeep6=~(V(:,3)>=sampleSize+1e-3);

        logicKeepEs=sum(logicKeep1(E),2)>=4 &...
            sum(logicKeep2(E),2)>=4 &...
            sum(logicKeep3(E),2)>=4 &...
            sum(logicKeep4(E),2)>=4 &...
            sum(logicKeep5(E),2)>=4 &...
            sum(logicKeep6(E),2)>=4;

        E=E(logicKeepEs,:);
        C=C(logicKeepEs,:);
        [E,V,indFix]=patchCleanUnused(E,V);

        % [Es,Vs,~,~]=subHex(Es,Vs,1,1);
        % Cs=repmat(Cs,8,1);

        % Create patch Data for visualization
        [Fs,CsF]=element2patch(E,C); %Patch data for plotting

        %Get new boundary set
        indB=tesBoundary(Fs,V);
        Fb=Fs(indB,:);
    case 3
        boxDim=sampleSize*[1 1 1];
        boxEl=[2 2 2];
        [meshStruct]=hexMeshBox(boxDim,boxEl);
        Er=meshStruct.E;
        Vr=meshStruct.V;
        minV=min(Vr,[],1); %Get lower left front corner
        Vr=Vr-minV(ones(size(Vr,1),1),:); %Set corner as origin
        [Er,Vr,~]=hex2tet(Er,Vr,[],1); %Convert to tetrahedral elements
        [Fr,Cr]=element2patch(Er,[]); %Patch data for plotting
        [indBoundary]=tesBoundary(Fr,Vr);

        % Create lattice structure
        controlParameter.latticeSide=1;
        controlParameter.numDigitKeep=5; %used for merging nodes
        controlParameter.indBoundary=indBoundary; %indices of the boundary faces
        controlParameter.shrinkFactor=0.15;
        controlParameter.meshType='hex';
        controlParameter.hexSplit=2;

        [E,V,C]=element2lattice(Er,Vr,controlParameter); %Get lattice structure

        % Create patch Data for visualization
        [Fs,CsF]=element2patch(E,C); %Patch data for plotting

        indB=tesBoundary(Fs,V);
        Fb=Fs(indB,:);
end

Visualizing input mesh and lattic structures

cFigure;
hs=subplot(1,2,1);
title('The input mesh','fontSize',fontSize)
hold on;
gpatch(Fr,Vr,0.5*ones(1,3),'k',0.5);
axisGeom(gca,fontSize);
camlight headlight; lighting flat;

subplot(1,2,2);
title('Lattice side 1','fontSize',fontSize)
hold on;
gpatch(Fb,V,'bw','k',1);
% patchNormPlot(Fs,Vs);
axisGeom(gca,fontSize);
camlight headlight; lighting flat;

drawnow;

DEFINE BC's

% Define node set logics
indAll=(1:1:size(V,1))';
logicBoundary=ismember(indAll,Fb);

Z=V(:,3);
logicTop=Z>=(sampleSize-eps(sampleSize))& logicBoundary;
logicBottom=Z<=eps(sampleSize) & logicBoundary;

X=V(:,1);
logicSide1=X>=(sampleSize-eps(sampleSize))& logicBoundary;
logicSide2=X<=eps(sampleSize)& logicBoundary;

Y=V(:,2);
logicSide3=Y>=(sampleSize-eps(sampleSize))& logicBoundary;
logicSide4=Y<=eps(sampleSize)& logicBoundary;

%Prescribed force nodes
bcPrescribeListCell{1}=find(logicSide1)';
bcPrescribeListCell{2}=find(logicSide2)';
bcPrescribeListCell{3}=find(logicSide3)';
bcPrescribeListCell{4}=find(logicSide4)';
bcPrescribeListCell{5}=find(logicTop)';
bcPrescribeListCell{6}=find(logicBottom)';

Smoothing lattice

% indKeep=unique([bcPrescribeListCell{:}]);
% [Fb_clean,Vb_clean,indFix]=patchCleanUnused(Fb,Vs);
%
% cPar.Method='HC';
% cPar.n=6;
%
% cPar.RigidConstraints=indFix(indKeep);
% % cPar.RigidConstraints=cPar.RigidConstraints(cPar.RigidConstraints>0);
%
% [Vb_clean]=tesSmooth(Fb_clean,Vb_clean,[],cPar);
% ind=Fb(:);
% ind=unique(ind(:));
% Vs(ind,:)=Vb_clean;

% cFigure; hold on;
% gpatch(Fb,Vs,'bw','k',1);
% % patchNormPlot(Fs,Vs);
% % plotV(Vs(indKeep,:),'k.','MarkerSize',25)
% axisGeom(gca,fontSize);
% camlight headlight; lighting flat;
% drawnow;

Visualizing input mesh and lattic structures

cFigure;
hs=subplot(1,2,1);
title('The input mesh','fontSize',fontSize)
hold on;
gpatch(Fr,Vr,0.5*ones(1,3),'k',0.5);
axisGeom(gca,fontSize);
camlight headlight; lighting flat;

subplot(1,2,2);
title('Lattice side 1','fontSize',fontSize)
hold on;
gpatch(Fb,V,'bw');
% patchNormPlot(Fs,Vs);
axisGeom(gca,fontSize);
camlight headlight; lighting flat;

drawnow;

Visualize BC's

cFigure; hold on;
title('Boundary conditions','FontSize',fontSize);
gpatch(Fb,V,'kw','none',0.4);
hl=gobjects(1,6);
plotColors=gjet(6);
for q=1:1:numel(bcPrescribeListCell)
    hl(q)=plotV(V(bcPrescribeListCell{q},:),'k.','MarkerSize',markerSize);
    hl(q).Color=plotColors(q,:);
end

legend(hl,{'BC 1','BC 2','BC 3','BC 4','BC 5','BC 6'});
axisGeom;
camlight headlight;
set(gca,'FontSize',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';

%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.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;


% Mesh section
% -> Nodes
febio_spec.Mesh.Nodes{1}.ATTR.name='Object1_lattice'; %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_lattice';
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

% -> NodeSets
for q=1:1:numel(bcPrescribeListCell)
    febio_spec.Mesh.NodeSet{q}.ATTR.name=['bcPrescribeList_',num2str(q)];
    febio_spec.Mesh.NodeSet{q}.node.ATTR.id=bcPrescribeListCell{q}';
end

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

%Boundary condition section

% -> Prescribe boundary conditions
directionStringSet={'x','x','y','y','z','z'};
displacementMagnitudeDir=[1 -1 1 -1 1 -1];
for q=1:1:numel(bcPrescribeListCell)
    nodeSetName=febio_spec.Mesh.NodeSet{q}.ATTR.name;
    febio_spec.Boundary.bc{q}.ATTR.type='prescribe';
    febio_spec.Boundary.bc{q}.ATTR.node_set=nodeSetName;
    febio_spec.Boundary.bc{q}.dof=directionStringSet{q};
    febio_spec.Boundary.bc{q}.scale.ATTR.lc=1;
    febio_spec.Boundary.bc{q}.scale.VAL=displacementMagnitudeDir(q).*displacementMagnitude;
    febio_spec.Boundary.bc{q}.relative=0;
end

%LoadData section
% -> load_controller
febio_spec.LoadData.load_controller{1}.ATTR.id=1;
febio_spec.LoadData.load_controller{1}.ATTR.type='loadcurve';
febio_spec.LoadData.load_controller{1}.interpolate='LINEAR';
febio_spec.LoadData.load_controller{1}.points.point.VAL=[0 0; 1 1];

%Output section
% -> log file
febio_spec.Output.logfile.ATTR.file=febioLogFileName;

febio_spec.Output.logfile.node_data{1}.ATTR.file=febioLogFileName_disp;
febio_spec.Output.logfile.node_data{1}.ATTR.data='ux;uy;uz';
febio_spec.Output.logfile.node_data{1}.ATTR.delim=',';

febio_spec.Output.logfile.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_stress;
febio_spec.Output.logfile.element_data{1}.ATTR.data='sz';
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
%system(['gedit ',febioFebFileName,' &']);

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;
febioAnalysis.maxLogCheckTime=10; %Max log file checking time

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

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-------->    RUNNING/MONITORING FEBIO JOB    <-------- 09-Sep-2021 17:05:28
FEBio path: /home/kevin/FEBioStudio/bin/febio3
# Attempt removal of existing log files                09-Sep-2021 17:05:28
 * Removal succesful                                   09-Sep-2021 17:05:28
# Attempt removal of existing .xplt files              09-Sep-2021 17:05:28
 * Removal succesful                                   09-Sep-2021 17:05:28
# Starting FEBio...                                    09-Sep-2021 17:05:28
  Max. total analysis time is: Inf s
 * Waiting for log file creation                       09-Sep-2021 17:05:28
   Max. wait time: 10 s
 * Log file found.                                     09-Sep-2021 17:05:29
# Parsing log file...                                  09-Sep-2021 17:05:29
    number of iterations   : 2                         09-Sep-2021 17:05:30
    number of reformations : 2                         09-Sep-2021 17:05:30
------- converged at time : 0.02                       09-Sep-2021 17:05:30
    number of iterations   : 2                         09-Sep-2021 17:05:31
    number of reformations : 2                         09-Sep-2021 17:05:31
------- converged at time : 0.04                       09-Sep-2021 17:05:31
    number of iterations   : 2                         09-Sep-2021 17:05:33
    number of reformations : 2                         09-Sep-2021 17:05:33
------- converged at time : 0.06                       09-Sep-2021 17:05:33
    number of iterations   : 31                        09-Sep-2021 17:05:48
    number of reformations : 31                        09-Sep-2021 17:05:48
------- converged at time : 0.08                       09-Sep-2021 17:05:48
    number of iterations   : 12                        09-Sep-2021 17:05:57
    number of reformations : 12                        09-Sep-2021 17:05:57
------- converged at time : 0.0949841                  09-Sep-2021 17:05:57
    number of iterations   : 12                        09-Sep-2021 17:06:04
    number of reformations : 12                        09-Sep-2021 17:06:04
------- converged at time : 0.110971                   09-Sep-2021 17:06:04
    number of iterations   : 16                        09-Sep-2021 17:06:12
    number of reformations : 16                        09-Sep-2021 17:06:12
------- converged at time : 0.127761                   09-Sep-2021 17:06:12
    number of iterations   : 5                         09-Sep-2021 17:06:15
    number of reformations : 5                         09-Sep-2021 17:06:15
------- converged at time : 0.145193                   09-Sep-2021 17:06:15
    number of iterations   : 4                         09-Sep-2021 17:06:17
    number of reformations : 4                         09-Sep-2021 17:06:17
------- converged at time : 0.163139                   09-Sep-2021 17:06:17
    number of iterations   : 4                         09-Sep-2021 17:06:19
    number of reformations : 4                         09-Sep-2021 17:06:19
------- converged at time : 0.181495                   09-Sep-2021 17:06:19
    number of iterations   : 4                         09-Sep-2021 17:06:21
    number of reformations : 4                         09-Sep-2021 17:06:21
------- converged at time : 0.20018                    09-Sep-2021 17:06:21
    number of iterations   : 4                         09-Sep-2021 17:06:24
    number of reformations : 4                         09-Sep-2021 17:06:24
------- converged at time : 0.219128                   09-Sep-2021 17:06:24
    number of iterations   : 7                         09-Sep-2021 17:06:28
    number of reformations : 7                         09-Sep-2021 17:06:28
------- converged at time : 0.238287                   09-Sep-2021 17:06:28
    number of iterations   : 5                         09-Sep-2021 17:06:31
    number of reformations : 5                         09-Sep-2021 17:06:31
------- converged at time : 0.257613                   09-Sep-2021 17:06:31
    number of iterations   : 4                         09-Sep-2021 17:06:33
    number of reformations : 4                         09-Sep-2021 17:06:33
------- converged at time : 0.277075                   09-Sep-2021 17:06:33
    number of iterations   : 6                         09-Sep-2021 17:06:36
    number of reformations : 6                         09-Sep-2021 17:06:36
------- converged at time : 0.296644                   09-Sep-2021 17:06:36
    number of iterations   : 9                         09-Sep-2021 17:06:41
    number of reformations : 9                         09-Sep-2021 17:06:41
------- converged at time : 0.316299                   09-Sep-2021 17:06:41
    number of iterations   : 5                         09-Sep-2021 17:06:44
    number of reformations : 5                         09-Sep-2021 17:06:44
------- converged at time : 0.336024                   09-Sep-2021 17:06:44
    number of iterations   : 4                         09-Sep-2021 17:06:46
    number of reformations : 4                         09-Sep-2021 17:06:46
------- converged at time : 0.355803                   09-Sep-2021 17:06:46
    number of iterations   : 4                         09-Sep-2021 17:06:50
    number of reformations : 4                         09-Sep-2021 17:06:50
------- converged at time : 0.375626                   09-Sep-2021 17:06:50
    number of iterations   : 4                         09-Sep-2021 17:06:52
    number of reformations : 4                         09-Sep-2021 17:06:52
------- converged at time : 0.395485                   09-Sep-2021 17:06:52
    number of iterations   : 4                         09-Sep-2021 17:06:55
    number of reformations : 4                         09-Sep-2021 17:06:55
------- converged at time : 0.415372                   09-Sep-2021 17:06:55
    number of iterations   : 4                         09-Sep-2021 17:06:57
    number of reformations : 4                         09-Sep-2021 17:06:57
------- converged at time : 0.435282                   09-Sep-2021 17:06:57
    number of iterations   : 4                         09-Sep-2021 17:07:00
    number of reformations : 4                         09-Sep-2021 17:07:00
------- converged at time : 0.45521                    09-Sep-2021 17:07:00
    number of iterations   : 4                         09-Sep-2021 17:07:02
    number of reformations : 4                         09-Sep-2021 17:07:02
------- converged at time : 0.475152                   09-Sep-2021 17:07:02
    number of iterations   : 4                         09-Sep-2021 17:07:05
    number of reformations : 4                         09-Sep-2021 17:07:05
------- converged at time : 0.495106                   09-Sep-2021 17:07:05
    number of iterations   : 4                         09-Sep-2021 17:07:07
    number of reformations : 4                         09-Sep-2021 17:07:07
------- converged at time : 0.515069                   09-Sep-2021 17:07:07
    number of iterations   : 3                         09-Sep-2021 17:07:09
    number of reformations : 3                         09-Sep-2021 17:07:09
------- converged at time : 0.535039                   09-Sep-2021 17:07:09
    number of iterations   : 3                         09-Sep-2021 17:07:11
    number of reformations : 3                         09-Sep-2021 17:07:11
------- converged at time : 0.555015                   09-Sep-2021 17:07:11
    number of iterations   : 3                         09-Sep-2021 17:07:13
    number of reformations : 3                         09-Sep-2021 17:07:13
------- converged at time : 0.574996                   09-Sep-2021 17:07:13
    number of iterations   : 3                         09-Sep-2021 17:07:14
    number of reformations : 3                         09-Sep-2021 17:07:14
------- converged at time : 0.594981                   09-Sep-2021 17:07:14
    number of iterations   : 3                         09-Sep-2021 17:07:16
    number of reformations : 3                         09-Sep-2021 17:07:16
------- converged at time : 0.614969                   09-Sep-2021 17:07:16
    number of iterations   : 3                         09-Sep-2021 17:07:18
    number of reformations : 3                         09-Sep-2021 17:07:18
------- converged at time : 0.634959                   09-Sep-2021 17:07:18
    number of iterations   : 3                         09-Sep-2021 17:07:20
    number of reformations : 3                         09-Sep-2021 17:07:20
------- converged at time : 0.654952                   09-Sep-2021 17:07:20
    number of iterations   : 3                         09-Sep-2021 17:07:22
    number of reformations : 3                         09-Sep-2021 17:07:22
------- converged at time : 0.674945                   09-Sep-2021 17:07:22
    number of iterations   : 3                         09-Sep-2021 17:07:24
    number of reformations : 3                         09-Sep-2021 17:07:24
------- converged at time : 0.69494                    09-Sep-2021 17:07:24
    number of iterations   : 3                         09-Sep-2021 17:07:26
    number of reformations : 3                         09-Sep-2021 17:07:26
------- converged at time : 0.714936                   09-Sep-2021 17:07:26
    number of iterations   : 3                         09-Sep-2021 17:07:28
    number of reformations : 3                         09-Sep-2021 17:07:28
------- converged at time : 0.734933                   09-Sep-2021 17:07:28
    number of iterations   : 3                         09-Sep-2021 17:07:30
    number of reformations : 3                         09-Sep-2021 17:07:30
------- converged at time : 0.754931                   09-Sep-2021 17:07:30
    number of iterations   : 3                         09-Sep-2021 17:07:32
    number of reformations : 3                         09-Sep-2021 17:07:32
------- converged at time : 0.774929                   09-Sep-2021 17:07:32
    number of iterations   : 3                         09-Sep-2021 17:07:34
    number of reformations : 3                         09-Sep-2021 17:07:34
------- converged at time : 0.794927                   09-Sep-2021 17:07:34
    number of iterations   : 3                         09-Sep-2021 17:07:36
    number of reformations : 3                         09-Sep-2021 17:07:36
------- converged at time : 0.814926                   09-Sep-2021 17:07:36
    number of iterations   : 3                         09-Sep-2021 17:07:38
    number of reformations : 3                         09-Sep-2021 17:07:38
------- converged at time : 0.834925                   09-Sep-2021 17:07:38
    number of iterations   : 3                         09-Sep-2021 17:07:40
    number of reformations : 3                         09-Sep-2021 17:07:40
------- converged at time : 0.854924                   09-Sep-2021 17:07:40
    number of iterations   : 3                         09-Sep-2021 17:07:42
    number of reformations : 3                         09-Sep-2021 17:07:42
------- converged at time : 0.874923                   09-Sep-2021 17:07:42
    number of iterations   : 3                         09-Sep-2021 17:07:44
    number of reformations : 3                         09-Sep-2021 17:07:44
------- converged at time : 0.894923                   09-Sep-2021 17:07:44
    number of iterations   : 3                         09-Sep-2021 17:07:46
    number of reformations : 3                         09-Sep-2021 17:07:46
------- converged at time : 0.914922                   09-Sep-2021 17:07:46
    number of iterations   : 3                         09-Sep-2021 17:07:48
    number of reformations : 3                         09-Sep-2021 17:07:48
------- converged at time : 0.934922                   09-Sep-2021 17:07:48
    number of iterations   : 3                         09-Sep-2021 17:07:50
    number of reformations : 3                         09-Sep-2021 17:07:50
------- converged at time : 0.954922                   09-Sep-2021 17:07:50
    number of iterations   : 3                         09-Sep-2021 17:07:51
    number of reformations : 3                         09-Sep-2021 17:07:51
------- converged at time : 0.974921                   09-Sep-2021 17:07:51
    number of iterations   : 3                         09-Sep-2021 17:07:54
    number of reformations : 3                         09-Sep-2021 17:07:54
------- converged at time : 0.994921                   09-Sep-2021 17:07:54
    number of iterations   : 2                         09-Sep-2021 17:07:56
    number of reformations : 2                         09-Sep-2021 17:07:56
------- converged at time : 1                          09-Sep-2021 17:07:56
 Elapsed time : 0:02:26                                09-Sep-2021 17:07:56
 N O R M A L   T E R M I N A T I O N
# Done                                                 09-Sep-2021 17:07:56
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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),1,1);

    %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 nodal forces
    dataStruct=importFEBio_logfile(fullfile(savePath,febioLogFileName_force),1,1);
    N_force_mat=dataStruct.data;

    indicesSide=bcPrescribeListCell{1};
    areaSide=sampleSize.^2;

    stressVal=mean(squeeze(N_force_mat(indicesSide,1,:))./areaSide,1);
    J_Val=1-((1-J_final).*timeVec(:));

    cFigure; hold on;
    xlabel('$J$','Interpreter','Latex'); ylabel('$\sigma^*$','Interpreter','Latex');
    plot(J_Val(:),stressVal(:),'r.-','LineWidth',3,'MarkerSize',15);
    axis square; axis tight; grid on; box on;
    set(gca,'FontSize',fontSize);
    drawnow;

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']);
    hp=gpatch(Fb,V_DEF(:,:,end),DN_magnitude,'k',1); %Add graphics object to animate
    %     gpatch(Fb,Vs,'kw','none',0.25); %A static graphics object
    hp.FaceColor='interp';

    axisGeom(gca,fontSize);
    colormap(gjet(250)); colorbar;
    caxis([0 max(DN_magnitude)]);
    axis(axisLim(V_DEF)); %Set axis limits statically
    %     view(130,25); %Set view direction
    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=N_disp_mat(:,:,qt); %Current displacement
        DN_magnitude=sqrt(sum(DN.^2,2)); %Current displacement magnitude

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