DEMO_febio_0051_hip_implant_01

Below is a demonstration for:

Building geometry for a a hip implant and bone

Keywords
Plot settings
Control parameters
Visualizing solid mesh
Visualizing boundary conditions
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
parameterised hip creation
Tetrahedral meshing, tet4
force control boundary condition
static, solid
displacement logfile
stress logfile

clear; close all; clc;

Plot settings

fontSize=20;
faceAlpha1=0.8;
markerSize=40;
markerSize2=20;
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_force=[febioFebFileNamePart,'_force_out.txt']; %Log file name for exporting force
febioLogFileName_stress=[febioFebFileNamePart,'_stress_out.txt']; %Log file name for exporting stresses
febioLogFileName_strainEnergy=[febioFebFileNamePart,'_energy_out.txt']; %Log file name for exporting strain energy density

%Define applied force
forceBody=-(120*9.81)/2;

%Material parameters (MPa if spatial units are mm)
% Cortical bone
E_youngs1=17000; %Youngs modulus
nu1=0.25; %Poissons ratio

% Cement
E_youngs2=1500; %Youngs modulus
nu2=0.25; %Poissons ratio

% 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=1;
runMode='external'; %'external' or 'internal'

n1=[1 0 0];
n2=vecnormalize([1 1 0]);
boneExtension=40;
cementThickness=3;
boneBaseThickness=6;
boneScaleFactors=[1.1 1.1];
volumeFactor=10;

hipParStruct.ballRadius=20;
hipParStruct.stickRadius=7;
hipParStruct.stickLength=21;
hipParStruct.stickLengthStraight=hipParStruct.stickLength-6;
hipParStruct.neckRadius=15;
hipParStruct.neckEllipseScale=2;
hipParStruct.collarThickness=3;
hipParStruct.loftOffset=20;
hipParStruct.loftLenght=40;
hipParStruct.stemRadius=8;
hipParStruct.stemLength=50;
hipParStruct.stemAngle=0.25*pi;
hipParStruct.pointSpacing=2;

[F_implant,V_implant,C_implant,curveSet]=parHipImplant(hipParStruct);
Qz=euler2DCM([0 0 0.25*pi]);
Qy=euler2DCM([0 -0.5*pi 0 ]);
Qzz=euler2DCM([0 0 0.5*pi]);

pointSpacing=mean(patchEdgeLengths(F_implant,V_implant));
[~,~,N_implant]=patchNormal(F_implant,V_implant);

indTop=curveSet{2};
indBottom=curveSet{4};

cFigure; hold on;
gpatch(F_implant,V_implant,C_implant,'k',1);
% gpatch(F_bone,V_bone,boneColor,'k',1);
for q=1:1:numel(curveSet)
   plotV(V_implant(curveSet{q},:),'r.-','MarkerSize',25,'LineWidth',3);
end
axisGeom;
camlight headlight;
colormap gjet; icolorbar;
drawnow;

logicSelect=ismember(C_implant,[4 5]);
F_cement=F_implant(logicSelect,:);
C_cement=C_implant(logicSelect);

V_cement=V_implant;
[F_cement,V_cement,indFix]=patchCleanUnused(F_cement,V_cement);
indTopCement=indFix(indTop);
indBottomCement=indFix(indBottom);
[~,~,N_cement]=patchNormal(F_cement,V_cement);
Eb_cement=patchBoundary(F_cement,V_cement);
indBoundaryCement=unique(Eb_cement);
N_cement(indTopCement,1)=0;
N_cement(indTopCement,:)=vecnormalize(N_cement(indTopCement,:));
V_cement=V_cement+cementThickness.*N_cement;

F_cement=F_cement(C_cement~=6,:);
[F_cement,V_cement]=patchCleanUnused(F_cement,V_cement);

Warning: Second input (vertices) no longer required. Update code to avoid
future error.

numStepsExtrude=ceil(boneExtension./pointSpacing);
numStepsExtrude=numStepsExtrude+double(iseven(numStepsExtrude));

clear cParExtrude;
cParExtrude.depth=boneExtension;
cParExtrude.patchType='tri';
cParExtrude.dir=1;
cParExtrude.n=n2;
cParExtrude.closeLoopOpt=1;
cParExtrude.numSteps=numStepsExtrude;
[F_cement_extInner,V_cement_extInner]=polyExtrude(V_implant(indBottom,:),cParExtrude);
indEndCementInner=numStepsExtrude:numStepsExtrude:size(V_cement_extInner,1);
[F_cement_extOuter,V_cement_extOuter]=polyExtrude(V_cement(indBottomCement,:),cParExtrude);
indEndCementOuter=numStepsExtrude:numStepsExtrude:size(V_cement_extOuter,1);

pointSpacingNow=mean(sqrt(sum(diff(V_cement_extOuter(indEndCementOuter,:),1,1).^2,2)));
[F_cement_bottom,V_cement_bottom]=regionTriMesh3D({V_cement_extOuter(indEndCementOuter,:),...
                                                   V_cement_extInner(indEndCementInner,:)},pointSpacingNow,0,'linear');
N_cement_bottom=mean(patchNormal(F_cement_bottom,V_cement_bottom),1);
if dot(N_cement_bottom,n2)<1
    F_cement_bottom=fliplr(F_cement_bottom);
end

pointSpacingNow=mean(sqrt(sum(diff(V_implant(indTop,:),1,1).^2,2)));
[F_cement_top,V_cement_top]=regionTriMesh3D({V_implant(indTop,:),...
                                                   V_cement(indTopCement,:)},pointSpacingNow,0,'linear');
N_cement_top=mean(patchNormal(F_cement_top,V_cement_top),1);
if dot(N_cement_top,[1 0 0])>0
    F_cement_top=fliplr(F_cement_top);
end

[Fc,Vc,Cc]=joinElementSets({F_cement,F_cement_top,F_cement_bottom,F_cement_extInner,F_cement_extOuter},...
                           {V_cement,V_cement_top,V_cement_bottom,V_cement_extInner,V_cement_extOuter});
[Fc,Vc]=mergeVertices(Fc,Vc);

cFigure; hold on;
title('Cement');
gpatch(F_implant,V_implant,'w','none',0.5);
gpatch(Fc,Vc,Cc,'k',0.5);
colormap gjet; icolorbar;
axisGeom; camlight headlight;
drawnow;

N_implant(indTop,1)=0;
N_implant(indTop,:)=vecnormalize(N_implant(indTop,:));

V_loft1=V_implant(indTop,:)+(boneBaseThickness+cementThickness).*N_implant(indTop,:);
logicLow=V_loft1(:,2)<0;
V_loft1(logicLow,2)=V_loft1(logicLow,2)*boneScaleFactors(1);
V_loft1(~logicLow,2)=V_loft1(~logicLow,2)*boneScaleFactors(2);

[~,indMax]=max(V_loft1(:,3));
if indMax>1
    V_loft1=V_loft1([indMax:size(V_loft1,1) 1:indMax-1],:);
end
V_loft2=V_implant(indBottom,:)+(boneBaseThickness+cementThickness).*N_implant(indBottom,:);
V_loft2=V_loft2+boneExtension*n2(ones(size(V_loft2,1),1),:);

[~,indMax]=max(V_loft2(:,3));
if indMax>1
    V_loft2=V_loft2([indMax:size(V_loft2,1) 1:indMax-1],:);
end
V_loft2=flipud(V_loft2);

p1=mean(V_loft1,1);
p2=mean(V_loft2,1);
d=sqrt(sum((p1-p2).^2));
numStepsCurve=ceil(d/pointSpacing);
numStepsCurve=numStepsCurve+double(iseven(numStepsCurve));
f=d/3;
p=[p1;p1+f*n1; p2-f*n2;p2];

Vg=bezierCurve(p,numStepsCurve);

[F_loft,V_loft,C_loft]=sweepLoft(V_loft1,V_loft2,n1,n2,Vg);
E=F_loft(iseven(C_loft),[1 2]);
VE=patchCentre(E,V_loft);
V_loft(E(:,1),:)=VE;
indTopBone=1:numStepsCurve:size(V_loft,1);
indBottomBone=numStepsCurve:numStepsCurve:size(V_loft,1);
[F_loft,V_loft,C_loft]=quad2tri(F_loft,V_loft,'a',C_loft);

pointSpacingNow=mean(sqrt(sum(diff(V_loft(indTopBone,:),1,1).^2,2)));
[F_bone_top,V_bone_top]=regionTriMesh3D({V_loft(indTopBone,:),...
                                         V_cement(indTopCement,:)},pointSpacingNow,0,'linear');

N_bone_top=mean(patchNormal(F_bone_top,V_bone_top),1);
if dot(N_bone_top,[1 0 0])>0
    F_bone_top=fliplr(F_bone_top);
end

pointSpacingNow=mean(sqrt(sum(diff(V_loft(indBottomBone,:),1,1).^2,2)));
[F_bone_bottom,V_bone_bottom]=regionTriMesh3D({V_loft(indBottomBone,:),...
                                         V_cement_extOuter(indEndCementOuter,:)},pointSpacingNow,0,'linear');

N_bone_bottom=mean(patchNormal(F_bone_bottom,V_bone_bottom),1);
if dot(N_bone_bottom,[1 0 0])>0
    F_bone_bottom=fliplr(F_bone_bottom);
end

[F_bone,V_bone,C_bone]=joinElementSets({F_loft,F_bone_top,F_bone_bottom},...
                           {V_loft,V_bone_top,V_bone_bottom});
[F_bone,V_bone]=mergeVertices(F_bone,V_bone);

cFigure; hold on;
gpatch(F_implant,V_implant,'w','none',0.5);
gpatch(Fc,Vc,'bw','none',0.5);
gpatch(F_bone,V_bone,C_bone,'none',0.5);
axisGeom; camlight headlight;
drawnow;

C_bone=C_bone+max(C_implant)+max(Cc);
Cc=Cc+max(C_implant);
[FT,VT,CT]=joinElementSets({F_implant,Fc,F_bone},{V_implant,Vc,V_bone},{C_implant,Cc,C_bone});
[FT,VT]=mergeVertices(FT,VT);
VT=VT*Qz*Qy*Qzz;

cFigure; hold on;
gpatch(FT,VT,CT,'none',0.5);
axisGeom; camlight headlight;
colormap gjet; icolorbar;
drawnow;

logicBone=ismember(CT,[7 11 12 13 14]);

V_inner_bone=getInnerPoint(FT(logicBone,:),VT);

cFigure; hold on;
gpatch(FT(logicBone,:),VT,'w','none',0.5);
plotV(V_inner_bone,'k.','MarkerSize',25)
axisGeom; camlight headlight;
drawnow;

logicCement=ismember(CT,[4 5 7 8 9 10 11]);

V_inner_cement=getInnerPoint(FT(logicCement,:),VT);

cFigure; hold on;
gpatch(FT(logicCement,:),VT,'w','none',0.5);
plotV(V_inner_cement,'k.','MarkerSize',25)
axisGeom; camlight headlight;
drawnow;

F_solid=FT(logicCement | logicBone,:);
C_solid=CT(logicCement | logicBone);
[F_solid,V_solid]=patchCleanUnused(F_solid,VT);

logicImplant=ismember(CT,1:6);
F_implant=FT(logicImplant,:);
C_implant=CT(logicImplant);
[F_implant,V_implant]=patchCleanUnused(F_implant,VT);

Regional mesh volume parameter

tetVolumes(1)=tetVolMeanEst(FT(logicBone,:),VT); %Volume for regular tets
tetVolumes(2)=tetVolMeanEst(FT(logicCement,:),VT); %Volume for regular tets

tetGenStruct.stringOpt='-pq1.2AaY';
tetGenStruct.Faces=F_solid;
tetGenStruct.Nodes=V_solid;
tetGenStruct.holePoints=[];
tetGenStruct.faceBoundaryMarker=C_solid; %Face boundary markers
tetGenStruct.regionPoints=[V_inner_bone;V_inner_cement]; %region points
tetGenStruct.regionA=tetVolumes*volumeFactor;

[meshOutput]=runTetGen(tetGenStruct); %Run tetGen

% Access elements, nodes, and boundary faces
E_solid=meshOutput.elements;
V_solid=meshOutput.nodes;
Fb_solid=meshOutput.facesBoundary;
Cb_solid=meshOutput.boundaryMarker;
CE_solid=meshOutput.elementMaterialID;

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- TETGEN Tetrahedral meshing --- 21-Apr-2023 10:53:38
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Writing SMESH file --- 21-Apr-2023 10:53:38
----> Adding node field
----> Adding facet field
----> Adding holes specification
----> Adding region specification
--- Done --- 21-Apr-2023 10:53:38
--- Running TetGen to mesh input boundary--- 21-Apr-2023 10:53:38
Opening /mnt/data/MATLAB/GIBBON/data/temp/temp.smesh.
Delaunizing vertices...
Delaunay seconds:  0.319242
Creating surface mesh ...
Surface mesh seconds:  0.025246
Recovering boundaries...
Boundary recovery seconds:  0.077812
Removing exterior tetrahedra ...
Spreading region attributes.
Exterior tets removal seconds:  0.024774
Recovering Delaunayness...
Delaunay recovery seconds:  0.04799
Refining mesh...
Refinement seconds:  0.295274
Smoothing vertices...
Mesh smoothing seconds:  0.514086
Improving mesh...
Mesh improvement seconds:  0.021089

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:  0.214143
Total running seconds:  1.54053

Statistics:

  Input points: 11942
  Input facets: 23964
  Input segments: 35906
  Input holes: 0
  Input regions: 2

  Mesh points: 18060
  Mesh tetrahedra: 87221
  Mesh faces: 182424
  Mesh faces on exterior boundary: 15964
  Mesh faces on input facets: 23964
  Mesh edges on input segments: 35906
  Steiner points inside domain: 6118

--- Done --- 21-Apr-2023 10:53:40
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Importing TetGen files --- 21-Apr-2023 10:53:40
--- Done --- 21-Apr-2023 10:53:40

V=[V_solid;V_implant];
F_implant=F_implant+size(V_solid,1);

numDigitsMerge=6-numOrder(mean(patchEdgeLengths(F_implant,V)));

[~,indKeep,indFix]=unique(pround(V,numDigitsMerge),'rows');
V=V(indKeep,:);
F_implant=indFix(F_implant);
E_solid=indFix(E_solid);
Fb_solid=indFix(Fb_solid);
E_cement=E_solid(CE_solid==-3,:);
E_bone=E_solid(CE_solid==-2,:);
E_solid=[E_bone;E_cement];

Visualizing solid mesh

hFig=cFigure; hold on;
gpatch(F_implant,V,'w','none',0.5);
optionStruct.hFig=hFig;
meshView(meshOutput,optionStruct);
axisGeom;
drawnow;

Visualizing boundary conditions

F_bottomSupport=Fb_solid(ismember(Cb_solid,[9 14]),:);
bcSupportList=unique(F_bottomSupport(:));

hFig=cFigure; hold on;
gpatch(Fb_solid,V,'kw','none',0.25);
hl(1)=plotV(V(bcSupportList,:),'k.','MarkerSize',25);
hl(2)=gpatch(F_implant,V,'rw','r',1);
legend(hl,{'BC support','BC prescribe'});
axisGeom;
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.time_stepper.dtmin=dtmin;
febio_spec.Control.time_stepper.dtmax=dtmax;
febio_spec.Control.time_stepper.max_retries=max_retries;
febio_spec.Control.time_stepper.opt_iter=opt_iter;

%Material section
materialName1='Material1';
febio_spec.Material.material{1}.ATTR.name=materialName1;
febio_spec.Material.material{1}.ATTR.type='neo-Hookean';
febio_spec.Material.material{1}.ATTR.id=1;
febio_spec.Material.material{1}.E=E_youngs1;
febio_spec.Material.material{1}.v=nu1;

materialName2='Material2';
febio_spec.Material.material{2}.ATTR.name=materialName2;
febio_spec.Material.material{2}.ATTR.type='neo-Hookean';
febio_spec.Material.material{2}.ATTR.id=2;
febio_spec.Material.material{2}.E=E_youngs2;
febio_spec.Material.material{2}.v=nu2;

materialName3='Material3';
febio_spec.Material.material{3}.ATTR.name=materialName3;
febio_spec.Material.material{3}.ATTR.type='rigid body';
febio_spec.Material.material{3}.ATTR.id=3;
febio_spec.Material.material{3}.density=1;
febio_spec.Material.material{3}.center_of_mass=[0 0 0];

%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='tet4'; %Element type
febio_spec.Mesh.Elements{1}.elem.ATTR.id=(1:1:size(E_bone,1))'; %Element id's
febio_spec.Mesh.Elements{1}.elem.VAL=E_bone; %The element matrix

partName2='Part2';
febio_spec.Mesh.Elements{2}.ATTR.name=partName2; %Name of this part
febio_spec.Mesh.Elements{2}.ATTR.type='tet4'; %Element type
febio_spec.Mesh.Elements{2}.elem.ATTR.id=size(E_bone,1)+(1:1:size(E_cement,1))'; %Element id's
febio_spec.Mesh.Elements{2}.elem.VAL=E_cement; %The element matrix

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

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

%MeshDomains section
febio_spec.MeshDomains.SolidDomain{1}.ATTR.name=partName1;
febio_spec.MeshDomains.SolidDomain{1}.ATTR.mat=materialName1;

febio_spec.MeshDomains.SolidDomain{2}.ATTR.name=partName2;
febio_spec.MeshDomains.SolidDomain{2}.ATTR.mat=materialName2;

febio_spec.MeshDomains.ShellDomain{1}.ATTR.name=partName3;
febio_spec.MeshDomains.ShellDomain{1}.ATTR.mat=materialName3;

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

%Rigid section
% ->Rigid body fix boundary conditions
% febio_spec.Rigid.rigid_bc{1}.ATTR.name='RigidFix';
% febio_spec.Rigid.rigid_bc{1}.ATTR.type='rigid_fixed';
% febio_spec.Rigid.rigid_bc{1}.rb=3;
% febio_spec.Rigid.rigid_bc{1}.Rx_dof=1;
% febio_spec.Rigid.rigid_bc{1}.Ry_dof=1;
% febio_spec.Rigid.rigid_bc{1}.Ru_dof=1;
% febio_spec.Rigid.rigid_bc{1}.Rv_dof=1;
% febio_spec.Rigid.rigid_bc{1}.Rw_dof=1;

% ->Rigid body prescribe boundary conditions
febio_spec.Rigid.rigid_load{1}.ATTR.name='RigidPrescribedForce';
febio_spec.Rigid.rigid_load{1}.ATTR.type='rigid_force';
febio_spec.Rigid.rigid_load{1}.rb=3;
febio_spec.Rigid.rigid_load{1}.dof='Rz';
febio_spec.Rigid.rigid_load{1}.value.ATTR.lc=1;
febio_spec.Rigid.rigid_load{1}.value.VAL=forceBody;
febio_spec.Rigid.rigid_load{1}.load_type=0;

%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.rigid_body_data{1}.ATTR.file=febioLogFileName_force;
febio_spec.Output.logfile.rigid_body_data{1}.ATTR.data='Fx;Fy;Fz';
febio_spec.Output.logfile.rigid_body_data{1}.ATTR.delim=',';
febio_spec.Output.logfile.rigid_body_data{1}.VAL=3; %Rigid body material id

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{2}.VAL=1:1:size(E_solid,1);

febio_spec.Output.logfile.element_data{2}.ATTR.file=febioLogFileName_strainEnergy;
febio_spec.Output.logfile.element_data{2}.ATTR.data='sed';
febio_spec.Output.logfile.element_data{2}.ATTR.delim=',';
febio_spec.Output.logfile.element_data{2}.VAL=1:1:size(E_solid,1);

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

Quick viewing of the FEBio input file structure

The febView function can be used to view the xml structure in a MATLAB figure window.

febView(febio_spec); %Viewing the febio file

Exporting the FEBio input file

Exporting the febio_spec structure to an FEBio input file is done using the febioStruct2xml function.

febioStruct2xml(febio_spec,febioFebFileName); %Exporting to file and domNode

Running the FEBio analysis

To run the analysis defined by the created FEBio input file the runMonitorFEBio function is used. The input for this function is a structure defining job settings e.g. the FEBio input file name. The optional output runFlag informs the user if the analysis was run succesfully.

febioAnalysis.run_filename=febioFebFileName; %The input file name
febioAnalysis.run_logname=febioLogFileName; %The name for the log file
febioAnalysis.disp_on=1; %Display information on the command window
febioAnalysis.runMode=runMode;

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

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-------->    RUNNING/MONITORING FEBIO JOB    <-------- 21-Apr-2023 10:53:47
FEBio path: /home/kevin/FEBioStudio2/bin/febio4
# Attempt removal of existing log files                21-Apr-2023 10:53:47
 * Removal succesful                                   21-Apr-2023 10:53:47
# Attempt removal of existing .xplt files              21-Apr-2023 10:53:47
 * Removal succesful                                   21-Apr-2023 10:53:47
# Starting FEBio...                                    21-Apr-2023 10:53:47
  Max. total analysis time is: Inf s
 * Waiting for log file creation                       21-Apr-2023 10:53:47
   Max. wait time: 30 s
 * Log file found.                                     21-Apr-2023 10:53:48
# Parsing log file...                                  21-Apr-2023 10:53:48
    number of iterations   : 2                         21-Apr-2023 10:53:52
    number of reformations : 2                         21-Apr-2023 10:53:52
------- converged at time : 0.1                        21-Apr-2023 10:53:52
    number of iterations   : 2                         21-Apr-2023 10:53:56
    number of reformations : 2                         21-Apr-2023 10:53:56
------- converged at time : 0.2                        21-Apr-2023 10:53:56
    number of iterations   : 2                         21-Apr-2023 10:54:01
    number of reformations : 2                         21-Apr-2023 10:54:01
------- converged at time : 0.3                        21-Apr-2023 10:54:01
    number of iterations   : 3                         21-Apr-2023 10:54:05
    number of reformations : 3                         21-Apr-2023 10:54:05
------- converged at time : 0.4                        21-Apr-2023 10:54:05
    number of iterations   : 3                         21-Apr-2023 10:54:10
    number of reformations : 3                         21-Apr-2023 10:54:10
------- converged at time : 0.5                        21-Apr-2023 10:54:10
    number of iterations   : 3                         21-Apr-2023 10:54:15
    number of reformations : 3                         21-Apr-2023 10:54:15
------- converged at time : 0.6                        21-Apr-2023 10:54:15
    number of iterations   : 3                         21-Apr-2023 10:54:20
    number of reformations : 3                         21-Apr-2023 10:54:20
------- converged at time : 0.7                        21-Apr-2023 10:54:20
    number of iterations   : 3                         21-Apr-2023 10:54:25
    number of reformations : 3                         21-Apr-2023 10:54:25
------- converged at time : 0.8                        21-Apr-2023 10:54:25
    number of iterations   : 3                         21-Apr-2023 10:54:30
    number of reformations : 3                         21-Apr-2023 10:54:30
------- converged at time : 0.9                        21-Apr-2023 10:54:30
    number of iterations   : 3                         21-Apr-2023 10:54:35
    number of reformations : 3                         21-Apr-2023 10:54:35
------- converged at time : 1                          21-Apr-2023 10:54:35
 Elapsed time : 0:00:47                                21-Apr-2023 10:54:36
 N O R M A L   T E R M I N A T I O N
# Done                                                 21-Apr-2023 10:54:36
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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=N_disp_mat(:,:,end);
    DN_magnitude=sqrt(sum(DN(:,3).^2,2));
    V_def=V+DN;

Importing element strain energies from a log file

    [~,E_energy,~]=importFEBio_logfile(fullfile(savePath,febioLogFileName_strainEnergy)); %Element strain energy

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

    %Add initial state i.e. zero energy
    sizImport=size(E_energy);
    sizImport(3)=sizImport(3)+1;
    E_energy_mat_n=zeros(sizImport);
    E_energy_mat_n(:,:,2:end)=E_energy;
    E_energy=E_energy_mat_n;

    [FE_face,C_energy_face]=element2patch(E_solid,E_energy(:,:,end),'tet4');
    [CV]=faceToVertexMeasure(FE_face,V,C_energy_face);
    [indBoundary]=tesBoundary(FE_face,V);
    Fb_solid=FE_face(indBoundary,:);

Warning: Second input (vertices) no longer required. Update code to avoid
future error.

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
    title('Strain energy density')
    gtitle([febioFebFileNamePart,': Press play to animate']);
    hp1=gpatch(Fb_solid,V_def,CV,'k',1); %Add graphics object to animate
    hp1.FaceColor='Interp';

    hp2=gpatch(F_implant,V,0.5*ones(1,3),'none',0.25); %A static graphics object

    axisGeom(gca,fontSize);
    colormap(gjet(250)); colorbar;
    caxis([0 max(E_energy(:))/25]);
    axis([min(V_def(:,1)) max(V_def(:,1)) min(V_def(:,2)) max(V_def(:,2)) min(V_def(:,3)) max(V_def(:,3))]); %Set axis limits statically
    camlight headlight;

    % 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


        V_def=V+DN; %Current nodal coordinates

        [FE_face,C_energy_face]=element2patch(E_solid,E_energy(:,:,qt),'tet4');
        [CV]=faceToVertexMeasure(FE_face,V,C_energy_face);

        %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,CV,V_def}; %Property values for to set in order to animate
    end
    anim8(hf,animStruct); %Initiate animation feature
    drawnow;

end

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/.