DEMO_febio_0021_bone_three_point_bending
Below is a demonstration for:
- Building geometry for a bone
- Defining the boundary conditions
- Coding the febio structure
- Running the model
- Importing and visualizing the displacement results
Contents
- Keywords
- Plot settings
- Control parameters
- Get bone geometry
- Remesh using geomgram
- Create and position cylinder geometry
- Mesh using tetgen
- Visualize interior point
- Define material regions in bone
- Visualizing solid mesh
- Joining node sets
- Define boundary conditions
- Define bone contact surfaces
- 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
- indentation
- contact, sliding, sticky, friction
- rigid body constraints
- tetrahedral elements, tet4
- triangular elements, tri3
- three point bending
- static, solid
- hyperelastic, Ogden
- displacement logfile
- stress logfile
clear; close all; clc;
Plot settings
fontSize=15; faceAlpha1=0.8; faceAlpha2=0.3; markerSize=40; lineWidth=3;
Control parameters
% Path names defaultFolder = fileparts(fileparts(mfilename('fullpath'))); savePath=fullfile(defaultFolder,'data','temp'); pathNameSTL=fullfile(defaultFolder,'data','STL'); % Defining file names febioFebFileNamePart='tempModel'; febioFebFileName=fullfile(savePath,[febioFebFileNamePart,'.feb']); %FEB file name febioLogFileName=[febioFebFileNamePart,'.txt']; %FEBio log file name febioLogFileName_disp=[febioFebFileNamePart,'_disp_out.txt']; %Log file name for exporting displacement febioLogFileName_force=[febioFebFileNamePart,'_force_out.txt']; %Log file name for exporting force febioLogFileName_stress=[febioFebFileNamePart,'_stress_out.txt']; %Log file name for exporting stress %Geometric parameters corticalThickness=3; %Thickness used for cortical material definition volumeFactor=10; %Factor to scale desired volume for interior elements w.r.t. boundary elements pointSpacing=5; %Material parameter set D_density=1e-9; %Density for all materials E_youngs1=17000; %Youngs modulus nu1=0.25; %Poissons ratio % Cancellous bone E_youngs2=1500; %Youngs modulus nu2=0.25; %Poissons ratio % FEA control settings analysisType='STATIC'; numTimeSteps=20; %Number of time steps desired max_refs=25; %Max reforms max_ups=0; %Set to zero to use full-Newton iterations opt_iter=15; %Optimum number of iterations max_retries=6; %Maximum number of retires dtmin=(1/numTimeSteps)/100; %Minimum time step size dtmax=1/numTimeSteps; %Maximum time step size min_residual=1e-10; symmetric_stiffness=1; runMode='external'; %Contact parameters contactInitialOffset=0.1; contactPenalty=1000; laugon=0; minaug=1; maxaug=10; %Boundary conditions specification bcFix=0; %Loading parameters zDisp=-20-2*contactInitialOffset;
Get bone geometry
%Load basic model [F_bone,V_bone]=graphicsModels(5); V_bone=V_bone*1000; %Scale to mm %Reorient V_mean=mean(V_bone,1); V_bone=V_bone-V_mean(ones(size(V_bone,1),1),:); %Center around origin [R]=pointSetPrincipalDir(V_bone); %Get rotation matrix V_bone=V_bone*R; %Rotate
Remesh using geomgram
optionStruct.pointSpacing=pointSpacing; optionStruct.disp_on=0; [F_bone,V_bone]=ggremesh(F_bone,V_bone,optionStruct);
Create and position cylinder geometry
pointSpacingBeams=pointSpacing/2; inputStruct.cylRadius=10; inputStruct.numRadial=round((2*pi*inputStruct.cylRadius)./pointSpacingBeams); inputStruct.cylHeight=max(V_bone(:,2))-min(V_bone(:,2)); nh=round(inputStruct.cylHeight./pointSpacingBeams); nh=nh+double(iseven(nh)); inputStruct.numHeight=nh; inputStruct.meshType='quad'; inputStruct.closeOpt=0; % Derive patch data for a cylinder [Fc,Vc,Cc]=patchcylinder(inputStruct); R=euler2DCM([0.5*pi 0 0]); Vc=Vc*R; Vc1=Vc; Vc2=Vc; Vc2(:,1)=Vc2(:,1)-60; Vc3=Vc; Vc3(:,1)=Vc3(:,1)+60; logicSelect=min(Vc1(:,1))<V_bone(:,1) & max(Vc1(:,1))>V_bone(:,1); zOffset=max(V_bone(logicSelect,3)); Vc1(:,3)=Vc1(:,3)-min(Vc1(:,3))+zOffset+contactInitialOffset; logicSelect=min(Vc2(:,1))<V_bone(:,1) & max(Vc2(:,1))>V_bone(:,1); zOffset=min(V_bone(logicSelect,3)); Vc2(:,3)=Vc2(:,3)-max(Vc2(:,3))+zOffset-contactInitialOffset; logicSelect=min(Vc3(:,1))<V_bone(:,1) & max(Vc3(:,1))>V_bone(:,1); zOffset=min(V_bone(logicSelect,3)); Vc3(:,3)=Vc3(:,3)-max(Vc3(:,3))+zOffset-contactInitialOffset;
Plotting surface geometry
cFigure; hold on; gpatch(F_bone,V_bone,'kw','k',1); gpatch(Fc,Vc1,'gw','g',1); gpatch(Fc,Vc2,'rw','r',1); gpatch(Fc,Vc3,'bw','b',1); axisGeom; camlight headlight; drawnow

Mesh using tetgen
%Find interior point
V_inner_bone=getInnerPoint(F_bone,V_bone);
Visualize interior point
cFigure; hold on; gpatch(F_bone,V_bone,'w','none',0.5); plotV(V_inner_bone,'r.','MarkerSize',25) axisGeom; camlight headlight; drawnow;

Regional mesh volume parameter
tetVolume=tetVolMeanEst(F_bone,V_bone); %Volume for regular tets tetGenStruct.stringOpt='-pq1.2AaY'; tetGenStruct.Faces=F_bone; tetGenStruct.Nodes=V_bone; tetGenStruct.holePoints=[]; tetGenStruct.faceBoundaryMarker=ones(size(F_bone,1),1); %Face boundary markers tetGenStruct.regionPoints=V_inner_bone; %region points tetGenStruct.regionA=tetVolume*volumeFactor; [meshOutput]=runTetGen(tetGenStruct); %Run tetGen % Access elements, nodes, and boundary faces E=meshOutput.elements; V=meshOutput.nodes; Fb=meshOutput.facesBoundary; Cb=meshOutput.boundaryMarker; CE=meshOutput.elementMaterialID;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% --- TETGEN Tetrahedral meshing --- 11-Dec-2020 12:23:50 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% --- Writing SMESH file --- 11-Dec-2020 12:23:50 ----> Adding node field ----> Adding facet field ----> Adding holes specification ----> Adding region specification --- Done --- 11-Dec-2020 12:23:50 --- Running TetGen to mesh input boundary--- 11-Dec-2020 12:23:50 Opening /mnt/data/MATLAB/GIBBON/data/temp/temp.smesh. Delaunizing vertices... Delaunay seconds: 0.021244 Creating surface mesh ... Surface mesh seconds: 0.005698 Recovering boundaries... Boundary recovery seconds: 0.009494 Removing exterior tetrahedra ... Spreading region attributes. Exterior tets removal seconds: 0.005688 Recovering Delaunayness... Delaunay recovery seconds: 0.005711 Refining mesh... Refinement seconds: 0.060124 Optimizing mesh... Optimization seconds: 0.003415 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: 0.057795 Total running seconds: 0.169426 Statistics: Input points: 3386 Input facets: 6768 Input segments: 10152 Input holes: 0 Input regions: 1 Mesh points: 4749 Mesh tetrahedra: 18254 Mesh faces: 39892 Mesh faces on exterior boundary: 6768 Mesh faces on input facets: 6768 Mesh edges on input segments: 10152 Steiner points inside domain: 1363 --- Done --- 11-Dec-2020 12:23:51 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% --- Importing TetGen files --- 11-Dec-2020 12:23:51 --- Done --- 11-Dec-2020 12:23:51
Define material regions in bone
indBoundary=unique(Fb(Cb==1,:)); DE=minDist(V,V(indBoundary,:)); logicCorticalNodes=DE<=corticalThickness; logicCorticalElements=any(logicCorticalNodes(E),2); logicCancellousElements=~logicCorticalElements; E1=E(logicCorticalElements,:); E2=E(logicCancellousElements,:); E=[E1;E2]; elementMaterialID=[ones(size(E1,1),1);2*ones(size(E2,1),1);]; meshOutput.elements=E; meshOutput.elementMaterialID=elementMaterialID;
Visualizing solid mesh
hFig=cFigure; hold on;
optionStruct.hFig=hFig;
meshView(meshOutput,optionStruct);
axisGeom;
drawnow;

Joining node sets
Fc1=Fc+size(V,1); Fc2=Fc+size(V,1)+size(Vc1,1); Fc3=Fc+size(V,1)+size(Vc1,1)+size(Vc2,1); V=[V;Vc1;Vc2;Vc3];
Define boundary conditions
if bcFix==1
%Supported nodes
indb=unique(Fb(:));
logicLeft=V(indb,1)<-200;
bcSupportList=indb(logicLeft);
Visualize BC's
hf=cFigure; title('Boundary conditions model','FontSize',fontSize); xlabel('X','FontSize',fontSize); ylabel('Y','FontSize',fontSize); zlabel('Z','FontSize',fontSize); hold on; gpatch(Fb,V,'kw','none',faceAlpha2); hp1(1)=plotV(V(bcSupportList,:),'k.','MarkerSize',markerSize); legend(hp1,{'BC support'}); axisGeom(gca,fontSize); camlight headlight; drawnow;
end
Define bone contact surfaces
N=patchNormal(fliplr(Fb),V); nz=[0 0 -1]; d=dot(N,nz(ones(size(N,1),1),:),2); contactAdd=pointSpacing; VF=patchCentre(Fb,V); logicSecondary1=VF(:,1)>(min(Vc1(:,1))-contactAdd) & VF(:,1)<(max(Vc1(:,1))+contactAdd) & d<0; logicSecondary2=VF(:,1)>(min(Vc2(:,1))-contactAdd) & VF(:,1)<(max(Vc2(:,1))+contactAdd) & d>0; logicSecondary3=VF(:,1)>(min(Vc3(:,1))-contactAdd) & VF(:,1)<(max(Vc3(:,1))+contactAdd) & d>0; F_sec1=fliplr(Fb(logicSecondary1,:)); F_sec2=fliplr(Fb(logicSecondary2,:)); F_sec3=fliplr(Fb(logicSecondary3,:));
Visualize
cFigure; hold on; gpatch(Fb,V,'w','none',0.5); hp2(1)=gpatch(F_sec1,V,'r','k',1); patchNormPlot(F_sec1,V); hp2(2)=gpatch(F_sec2,V,'g','k',1); patchNormPlot(F_sec2,V); hp2(3)=gpatch(F_sec3,V,'b','k',1); patchNormPlot(F_sec3,V); hp2(4)=gpatch(Fc1,V,'c','k',1); patchNormPlot(Fc1,V); hp2(5)=gpatch(Fc2,V,'y','k',1); patchNormPlot(Fc2,V); hp2(6)=gpatch(Fc3,V,'m','k',1); patchNormPlot(Fc3,V); legend(hp2,{'secondary 1','secondary 2','secondary 3','primary 1','primary 2','primary 3'}); 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='3.0'; %Module section febio_spec.Module.ATTR.type='solid'; %Control section febio_spec.Control.analysis=analysisType; 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; febio_spec.Control.solver.min_residual=min_residual; %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; febio_spec.Material.material{1}.density=D_density; 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; febio_spec.Material.material{2}.density=D_density; 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=D_density; febio_spec.Material.material{3}.center_of_mass=mean(Vc1,1); materialName4='Material4'; febio_spec.Material.material{4}.ATTR.name=materialName4; febio_spec.Material.material{4}.ATTR.type='rigid body'; febio_spec.Material.material{4}.ATTR.id=4; febio_spec.Material.material{4}.density=D_density; febio_spec.Material.material{4}.center_of_mass=mean(Vc2,1); materialName5='Material5'; febio_spec.Material.material{5}.ATTR.name=materialName5; febio_spec.Material.material{5}.ATTR.type='rigid body'; febio_spec.Material.material{5}.ATTR.id=5; febio_spec.Material.material{5}.density=D_density; febio_spec.Material.material{5}.center_of_mass=mean(Vc3,1); %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='CorticalBone'; febio_spec.Mesh.Elements{1}.ATTR.name=partName1; %Name of this part febio_spec.Mesh.Elements{1}.ATTR.type='tet4'; %Element type of this set febio_spec.Mesh.Elements{1}.ATTR.mat=1; %material index for this set febio_spec.Mesh.Elements{1}.elem.ATTR.id=(1:1:size(E1,1))'; %Element id's febio_spec.Mesh.Elements{1}.elem.VAL=E1; partName2='CancellousBone'; febio_spec.Mesh.Elements{2}.ATTR.name=partName2; %Name of this part febio_spec.Mesh.Elements{2}.ATTR.type='tet4'; %Element type of this set febio_spec.Mesh.Elements{2}.ATTR.mat=2; %material index for this set febio_spec.Mesh.Elements{2}.elem.ATTR.id=size(E1,1)+(1:1:size(E2,1))'; %Element id's febio_spec.Mesh.Elements{2}.elem.VAL=E2; partName3='Part3'; febio_spec.Mesh.Elements{3}.ATTR.name=partName3; %Name of this part febio_spec.Mesh.Elements{3}.ATTR.type='quad4'; %Element type of this set febio_spec.Mesh.Elements{3}.ATTR.mat=3; %material index for this set febio_spec.Mesh.Elements{3}.elem.ATTR.id=size(E1,1)+size(E2,1)+(1:1:size(Fc1,1))'; %Element id's febio_spec.Mesh.Elements{3}.elem.VAL=Fc1; partName4='Part4'; febio_spec.Mesh.Elements{4}.ATTR.name=partName4; %Name of this part febio_spec.Mesh.Elements{4}.ATTR.type='quad4'; %Element type of this set febio_spec.Mesh.Elements{4}.ATTR.mat=4; %material index for this set febio_spec.Mesh.Elements{4}.elem.ATTR.id=size(E1,1)+size(E2,1)+size(Fc1,1)+(1:1:size(Fc2,1))'; %Element id's febio_spec.Mesh.Elements{4}.elem.VAL=Fc2; partName5='Part5'; febio_spec.Mesh.Elements{5}.ATTR.name=partName5; %Name of this part febio_spec.Mesh.Elements{5}.ATTR.type='quad4'; %Element type of this set febio_spec.Mesh.Elements{5}.ATTR.mat=5; %material index for this set febio_spec.Mesh.Elements{5}.elem.ATTR.id=size(E1,1)+size(E2,1)+size(Fc1,1)+size(Fc2,1)+(1:1:size(Fc3,1))'; %Element id's febio_spec.Mesh.Elements{5}.elem.VAL=Fc3; %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; febio_spec.MeshDomains.ShellDomain{2}.ATTR.name=partName4; febio_spec.MeshDomains.ShellDomain{2}.ATTR.mat=materialName4; febio_spec.MeshDomains.ShellDomain{3}.ATTR.name=partName5; febio_spec.MeshDomains.ShellDomain{3}.ATTR.mat=materialName5; % -> NodeSets if bcFix==1 nodeSetName1='bcSupportList'; febio_spec.Mesh.NodeSet{1}.ATTR.name=nodeSetName1; febio_spec.Mesh.NodeSet{1}.node.ATTR.id=bcSupportList(:); end % -> Surfaces surfaceNamePrim1='contact_primary1'; febio_spec.Mesh.Surface{1}.ATTR.name=surfaceNamePrim1; febio_spec.Mesh.Surface{1}.quad4.ATTR.id=(1:1:size(Fc1,1))'; febio_spec.Mesh.Surface{1}.quad4.VAL=Fc1; surfaceNamePrim2='contact_primary2'; febio_spec.Mesh.Surface{2}.ATTR.name=surfaceNamePrim2; febio_spec.Mesh.Surface{2}.quad4.ATTR.id=(1:1:size(Fc2,1))'; febio_spec.Mesh.Surface{2}.quad4.VAL=Fc2; surfaceNamePrim3='contact_primary3'; febio_spec.Mesh.Surface{3}.ATTR.name=surfaceNamePrim3; febio_spec.Mesh.Surface{3}.quad4.ATTR.id=(1:1:size(Fc3,1))'; febio_spec.Mesh.Surface{3}.quad4.VAL=Fc3; surfaceNameSec1='contact_secondary1'; febio_spec.Mesh.Surface{4}.ATTR.name=surfaceNameSec1; febio_spec.Mesh.Surface{4}.tri3.ATTR.id=(1:1:size(F_sec1,1))'; febio_spec.Mesh.Surface{4}.tri3.VAL=F_sec1; surfaceNameSec2='contact_secondary2'; febio_spec.Mesh.Surface{5}.ATTR.name=surfaceNameSec2; febio_spec.Mesh.Surface{5}.tri3.ATTR.id=(1:1:size(F_sec2,1))'; febio_spec.Mesh.Surface{5}.tri3.VAL=F_sec2; surfaceNameSec3='contact_secondary3'; febio_spec.Mesh.Surface{6}.ATTR.name=surfaceNameSec3; febio_spec.Mesh.Surface{6}.tri3.ATTR.id=(1:1:size(F_sec3,1))'; febio_spec.Mesh.Surface{6}.tri3.VAL=F_sec3; % -> Surface pairs febio_spec.Mesh.SurfacePair{1}.ATTR.name='Contact1'; febio_spec.Mesh.SurfacePair{1}.primary=surfaceNamePrim1; febio_spec.Mesh.SurfacePair{1}.secondary=surfaceNameSec1; febio_spec.Mesh.SurfacePair{2}.ATTR.name='Contact2'; febio_spec.Mesh.SurfacePair{2}.primary=surfaceNamePrim2; febio_spec.Mesh.SurfacePair{2}.secondary=surfaceNameSec2; febio_spec.Mesh.SurfacePair{3}.ATTR.name='Contact3'; febio_spec.Mesh.SurfacePair{3}.primary=surfaceNamePrim3; febio_spec.Mesh.SurfacePair{3}.secondary=surfaceNameSec3; %Boundary condition section % -> Fix boundary conditions if bcFix==1 febio_spec.Boundary.bc{1}.ATTR.type='fix'; febio_spec.Boundary.bc{1}.ATTR.node_set=nodeSetName1; febio_spec.Boundary.bc{1}.dofs='x,y,z'; end %Rigid section % -> Prescribed rigid body boundary conditions febio_spec.Rigid.rigid_constraint{1}.ATTR.name='RigidFix_1'; febio_spec.Rigid.rigid_constraint{1}.ATTR.type='fix'; febio_spec.Rigid.rigid_constraint{1}.rb=3; febio_spec.Rigid.rigid_constraint{1}.dofs='Rx,Ry,Ru,Rv,Rw'; febio_spec.Rigid.rigid_constraint{2}.ATTR.name='RigidFix_2'; febio_spec.Rigid.rigid_constraint{2}.ATTR.type='fix'; febio_spec.Rigid.rigid_constraint{2}.rb=4; febio_spec.Rigid.rigid_constraint{2}.dofs='Rx,Ry,Rz,Ru,Rv,Rw'; febio_spec.Rigid.rigid_constraint{3}.ATTR.name='RigidFix_3'; febio_spec.Rigid.rigid_constraint{3}.ATTR.type='fix'; febio_spec.Rigid.rigid_constraint{3}.rb=5; febio_spec.Rigid.rigid_constraint{3}.dofs='Rx,Ry,Rz,Ru,Rv,Rw'; febio_spec.Rigid.rigid_constraint{4}.ATTR.name='RigidPrescribe'; febio_spec.Rigid.rigid_constraint{4}.ATTR.type='prescribe'; febio_spec.Rigid.rigid_constraint{4}.rb=3; febio_spec.Rigid.rigid_constraint{4}.dof='Rz'; febio_spec.Rigid.rigid_constraint{4}.value.ATTR.lc=1; febio_spec.Rigid.rigid_constraint{4}.value.VAL=zDisp; febio_spec.Rigid.rigid_constraint{4}.relative=0; %Contact section for qc=1:1:3 febio_spec.Contact.contact{qc}.ATTR.surface_pair=febio_spec.Mesh.SurfacePair{qc}.ATTR.name; febio_spec.Contact.contact{qc}.ATTR.type='sticky'; febio_spec.Contact.contact{qc}.penalty=contactPenalty; febio_spec.Contact.contact{qc}.laugon=laugon; febio_spec.Contact.contact{qc}.tolerance=0.2; febio_spec.Contact.contact{qc}.minaug=minaug; febio_spec.Contact.contact{qc}.maxaug=maxaug; febio_spec.Contact.contact{qc}.snap_tol=0.01; febio_spec.Contact.contact{qc}.max_traction=0; febio_spec.Contact.contact{qc}.search_tolerance=0.01; 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{1}.VAL=1:size(V,1); 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; febio_spec.Output.logfile.element_data{1}.ATTR.file=febioLogFileName_stress; febio_spec.Output.logfile.element_data{1}.ATTR.data='s1'; febio_spec.Output.logfile.element_data{1}.ATTR.delim=','; febio_spec.Output.logfile.element_data{1}.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
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; febioAnalysis.t_check=0.25; %Time for checking log file (dont set too small) febioAnalysis.maxtpi=1e99; %Max analysis time febioAnalysis.maxLogCheckTime=10; %Max log file checking time [runFlag]=runMonitorFEBio(febioAnalysis);%START FEBio NOW!!!!!!!!
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% --------> RUNNING/MONITORING FEBIO JOB <-------- 11-Dec-2020 12:23:56 FEBio path: /home/kevin/FEBioStudio/bin/febio3 # Attempt removal of existing log files 11-Dec-2020 12:23:56 * Removal succesful 11-Dec-2020 12:23:56 # Attempt removal of existing .xplt files 11-Dec-2020 12:23:56 * Removal succesful 11-Dec-2020 12:23:56 # Starting FEBio... 11-Dec-2020 12:23:56 Max. total analysis time is: 1e+99 s * Waiting for log file creation 11-Dec-2020 12:23:56 Max. wait time: 10 s * Log file found. 11-Dec-2020 12:23:56 # Parsing log file... 11-Dec-2020 12:23:56 number of iterations : 13 11-Dec-2020 12:23:59 number of reformations : 13 11-Dec-2020 12:23:59 ------- converged at time : 0.05 11-Dec-2020 12:23:59 number of iterations : 3 11-Dec-2020 12:24:00 number of reformations : 3 11-Dec-2020 12:24:00 ------- converged at time : 0.1 11-Dec-2020 12:24:00 number of iterations : 4 11-Dec-2020 12:24:01 number of reformations : 4 11-Dec-2020 12:24:01 ------- converged at time : 0.15 11-Dec-2020 12:24:01 number of iterations : 4 11-Dec-2020 12:24:01 number of reformations : 4 11-Dec-2020 12:24:01 ------- converged at time : 0.2 11-Dec-2020 12:24:01 number of iterations : 3 11-Dec-2020 12:24:02 number of reformations : 3 11-Dec-2020 12:24:02 ------- converged at time : 0.25 11-Dec-2020 12:24:02 number of iterations : 3 11-Dec-2020 12:24:03 number of reformations : 3 11-Dec-2020 12:24:03 ------- converged at time : 0.3 11-Dec-2020 12:24:03 number of iterations : 4 11-Dec-2020 12:24:04 number of reformations : 4 11-Dec-2020 12:24:04 ------- converged at time : 0.35 11-Dec-2020 12:24:04 number of iterations : 3 11-Dec-2020 12:24:05 number of reformations : 3 11-Dec-2020 12:24:05 ------- converged at time : 0.4 11-Dec-2020 12:24:05 number of iterations : 4 11-Dec-2020 12:24:05 number of reformations : 4 11-Dec-2020 12:24:05 ------- converged at time : 0.45 11-Dec-2020 12:24:05 number of iterations : 4 11-Dec-2020 12:24:06 number of reformations : 4 11-Dec-2020 12:24:06 ------- converged at time : 0.5 11-Dec-2020 12:24:06 number of iterations : 4 11-Dec-2020 12:24:07 number of reformations : 4 11-Dec-2020 12:24:07 ------- converged at time : 0.55 11-Dec-2020 12:24:07 number of iterations : 4 11-Dec-2020 12:24:08 number of reformations : 4 11-Dec-2020 12:24:08 ------- converged at time : 0.6 11-Dec-2020 12:24:08 number of iterations : 3 11-Dec-2020 12:24:09 number of reformations : 3 11-Dec-2020 12:24:09 ------- converged at time : 0.65 11-Dec-2020 12:24:09 number of iterations : 4 11-Dec-2020 12:24:09 number of reformations : 4 11-Dec-2020 12:24:09 ------- converged at time : 0.7 11-Dec-2020 12:24:09 number of iterations : 4 11-Dec-2020 12:24:10 number of reformations : 4 11-Dec-2020 12:24:10 ------- converged at time : 0.75 11-Dec-2020 12:24:10 number of iterations : 4 11-Dec-2020 12:24:11 number of reformations : 4 11-Dec-2020 12:24:11 ------- converged at time : 0.8 11-Dec-2020 12:24:11 number of iterations : 4 11-Dec-2020 12:24:12 number of reformations : 4 11-Dec-2020 12:24:12 ------- converged at time : 0.85 11-Dec-2020 12:24:12 number of iterations : 4 11-Dec-2020 12:24:13 number of reformations : 4 11-Dec-2020 12:24:13 ------- converged at time : 0.9 11-Dec-2020 12:24:13 number of iterations : 4 11-Dec-2020 12:24:14 number of reformations : 4 11-Dec-2020 12:24:14 ------- converged at time : 0.95 11-Dec-2020 12:24:14 number of iterations : 4 11-Dec-2020 12:24:15 number of reformations : 4 11-Dec-2020 12:24:15 ------- converged at time : 1 11-Dec-2020 12:24:15 Elapsed time : 0:00:19 11-Dec-2020 12:24:15 N O R M A L T E R M I N A T I O N # Done 11-Dec-2020 12:24:15 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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 element stress from a log file
dataStruct=importFEBio_logfile(fullfile(savePath,febioLogFileName_stress),1,1);
%Access data
E_stress_mat=dataStruct.data;
E_stress_mat(isnan(E_stress_mat))=0;
Plotting the simulated results using anim8 to visualize and animate deformations
[CV]=faceToVertexMeasure(E,V,E_stress_mat(:,:,end)); % Create basic view and store graphics handle to initiate animation hf=cFigure; %Open figure gtitle([febioFebFileNamePart,': Press play to animate']); title('$\sigma_{1}$ [MPa]','Interpreter','Latex') hp=gpatch(Fb,V_DEF(:,:,end),CV,'k',1); %Add graphics object to animate hp.FaceColor='interp'; hp2=gpatch([Fc1;Fc2;Fc3],V,'w','k',0.5); axisGeom(gca,fontSize); colormap(gjet(250)); colorbar; caxis([min(E_stress_mat(:)) max(E_stress_mat(:))]/20); 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_stress_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;

Importing rigidbody force data from a log file
dataStruct=importFEBio_logfile(fullfile(savePath,febioLogFileName_force),1,1);
%Access data
Force_mat=dataStruct.data;
Fz=squeeze(Force_mat(:,3,:));
Visualize stress-stretch curve
cFigure; hold on; title('Force-displacement curve','FontSize',fontSize); xlabel('Displacement [mm]','FontSize',fontSize,'Interpreter','Latex'); ylabel('$F_z$ [N]','FontSize',fontSize,'Interpreter','Latex'); plot(timeVec(:).*zDisp,Fz(:),'r-','lineWidth',lineWidth); view(2); axis tight; grid on; axis square; box on; set(gca,'FontSize',fontSize); drawnow;

end
GIBBON www.gibboncode.org
Kevin Mattheus Moerman, [email protected]
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License: https://github.com/gibbonCode/GIBBON/blob/primary/LICENSE
GIBBON: The Geometry and Image-based Bioengineering add-On. A toolbox for image segmentation, image-based modeling, meshing, and finite element analysis.
Copyright (C) 2006-2020 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/.