DEMO_febio_0050_foot_insole_01

Below is a demonstration for:

Contents

Keywords

clear; close all; clc;

Plot settings

fontSize=10;
faceAlpha1=1;
faceAlpha2=0.3;
markerSize1=15;
markerSize2=10;
lineWidth=2;

Control parameters

% Path names
defaultFolder = fileparts(fileparts(mfilename('fullpath')));
savePath=fullfile(defaultFolder,'data','temp');
loadPathSurfaces=fullfile(defaultFolder,'data','STL','leg','post');

% 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_strainEnergy=[febioFebFileNamePart,'_energy_out.txt']; %Log file name for exporting strain energy density
% Surface model file names
fileNameBones=fullfile(loadPathSurfaces,'Foot_bulk.stl');
fileNameSkin=fullfile(loadPathSurfaces,'Skin_coarse.stl');

%Geometric parameters
soleOffsetOutward=3; %How much the insole protrudes outward from the foot
numSmoothIterations_sole_Z=10; %Number of smoothing iterations for the sole Z value
soleMinThickness=6; %Sole thickness
volumeFactor=2; %Volume factor used in tetgen, larger means larger internal elements

%Material parameter set
c1_1=1e-3; %Shear-modulus-like parameter
m1_1=2; %Material parameter setting degree of non-linearity
k_1=c1_1*100; %Bulk modulus

c1_2=c1_1*10; %Shear-modulus-like parameter
m1_2=2; %Material parameter setting degree of non-linearity
k_2=c1_2*10; %Bulk modulus

% FEA control settings
numTimeSteps=10; %Number of time steps desired
max_refs=25; %Max reforms
max_ups=0; %Set to zero to use full-Newton iterations
opt_iter=10; %Optimum number of iterations
max_retries=5; %Maximum number of retires
dtmin=(1/numTimeSteps)/100; %Minimum time step size
dtmax=1/numTimeSteps; %Maximum time step size
symmetric_stiffness=0;
min_residual=1e-20;

%Boundary condition parameters
displacementMagnitude=-3; %Displacement applied to the bones

%Contact parameters
contactPenalty=20;
laugon=0;
minaug=1;
maxaug=10;
fric_coeff=0.25;

Import surface models

%Import STL file for the bones
[stlStruct] = import_STL(fileNameBones);
F1=stlStruct.solidFaces{1}; %Faces
V1=stlStruct.solidVertices{1}; %Vertices
[F1,V1]=mergeVertices(F1,V1); %Merge nodes

%Import STL file for the skin
[stlStruct] = import_STL(fileNameSkin);
F2=stlStruct.solidFaces{1}; %Faces
V2=stlStruct.solidVertices{1}; %Vertices
[F2,V2]=mergeVertices(F2,V2); %Merge nodes
V2=V2*100; %Scale

Visualize imported surfaces

cFigure; hold on;
gpatch(F1,V1,'bw','none',1);
gpatch(F2,V2,'rw','none',0.5);
camlight('headlight');
axisGeom(gca,fontSize);
drawnow;

Compute mesh derived parameters

Compute point spacings for the surfaces meshes. These are useful to relate other mesh sizes to.

pointSpacing1=mean(patchEdgeLengths(F1,V1));
pointSpacing2=mean(patchEdgeLengths(F2,V2));
pointSpacing=mean([pointSpacing1 pointSpacing2]);

Reorient surfaces

Reorient so that the leg points up in a forward view with the toes pointing towards the viewer.

R=euler2DCM([-0.5*pi 0 -0.5*pi]);
V1=V1*R;
V2=V2*R;

Visualize reoriented surfaces

cFigure; hold on;
gpatch(F1,V1,'bw','none',1);
gpatch(F2,V2,'rw','none',0.5);
camlight('headlight');
axisGeom(gca,fontSize);
drawnow;

Cut skin surface

The skin surface is cut such that it stops where the bones of the ankle end in the z direction.

%Create a logic for cutting away faces
max_Z1=max(V1(:,3))+2*pointSpacing; %Max Z-level used for cutting
logicVertices=V2(:,3)<max_Z1; %Logic for the points below this level
logicFaces=all(logicVertices(F2),2); %Logic for the faces
logicFaces=triSurfLogicSharpFix(F2,logicFaces,3); %Altered logic so it is smoother

Visualize

cFigure; hold on;
gpatch(F1,V1,'bw','none',1);
gpatch(F2,V2,logicFaces,'none',0.5);
camlight('headlight');
axisGeom(gca,fontSize);
drawnow;

Cut away faces using logic

F2=F2(logicFaces,:); %The faces to keep
[F2,V2]=patchCleanUnused(F2,V2); %Remove unused points

%Attempt to self triangulate potentially jagged edge
Eb=patchBoundary(F2,V2); %Get boundary edges
indBoundary=edgeListToCurve(Eb); %Convert boundary edges to a curve list
indBoundary=indBoundary(1:end-1); %Trim off last point since it is equal to first on a closed loop
angleThreshold=pi*(120/180); %threshold for self triangulation
[F2,V2,indBoundaryTop]=triSurfSelfTriangulateBoundary(F2,V2,indBoundary,angleThreshold,1);

%Force boundary to have the max Z level chosen
V2(indBoundaryTop,3)=max_Z1;

Visualize

cFigure; hold on;
gpatch(F1,V1,'bw','none',1);
gpatch(F2,V2,'rw','k',0.5);
plotV(V2(indBoundaryTop,:),'r-','LineWidth',lineWidth);
camlight('headlight');
axisGeom(gca,fontSize);
drawnow;

Close over top of skin

The top boundary curve of the cut surface is filled with triangles. This is a 2D method. The z-coordinate is added after.

[F2t,V2t]=regionTriMesh2D({V2(indBoundaryTop,[1 2])},pointSpacing2,0,0);
V2t(:,3)=max_Z1; %Add/set z-level

Visualize

cFigure; hold on;
gpatch(F1,V1,'bw','none',1);
gpatch(F2,V2,'rw','k',0.5);
gpatch(F2t,V2t,'gw','k',1);
plotV(V2(indBoundaryTop,:),'r-','LineWidth',lineWidth);
camlight('headlight');
axisGeom(gca,fontSize);
drawnow;

Joining surface features

Add all surface sets together in joint list of faces, vertices

[FT,VT,CT]=joinElementSets({F1,F2,F2t},{V1,V2,V2t});

Merge shared nodes

The join operation only adds the sets together. Nodes with the same coordinates are not seen as the same yet and need to be merged.

[FT,VT]=mergeVertices(FT,VT); %Merge nodes

Visualize

cFigure; hold on;
gpatch(FT,VT,CT,'k',0.5);
patchNormPlot(FT,VT);
camlight('headlight');
axisGeom(gca,fontSize);
colormap gjet; icolorbar;
drawnow;

Mesh foot with tetrahedral elements

Tet meshing is based on tetgen. TetGen requires a interior points for regions to be meshed, as well as intertior points for holes.

Define region points

[V_region]=getInnerPoint({FT(CT==2 | CT==3,:),FT(CT==1,:)},{VT,VT});
[V_hole]=getInnerPoint(FT(CT==1,:),VT);

Visualize interior points

cFigure; hold on;
gpatch(FT,VT,'kw','none',0.2);
hp1=plotV(V_region,'r.','markerSize',markerSize1);
hp2=plotV(V_hole,'b.','markerSize',markerSize1);
legend([hp1 hp2],{'Region point','Hole point'});
camlight('headlight');
axisGeom(gca,fontSize);
drawnow;

Mesh using tetgen

inputStruct.stringOpt='-pq1.2AaY'; %TetGen option string
inputStruct.Faces=FT; %The faces
inputStruct.Nodes=VT; %The vertices
inputStruct.holePoints=V_hole; %The hole interior points
inputStruct.faceBoundaryMarker=CT; %Face boundary markers
inputStruct.regionPoints=V_region; %The region interior points
inputStruct.regionA=tetVolMeanEst(FT,VT)*volumeFactor; %Volume for regular tets

Mesh model using tetrahedral elements using tetGen

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

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- TETGEN Tetrahedral meshing --- 26-Aug-2019 22:02:05
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Writing SMESH file --- 26-Aug-2019 22:02:05
----> Adding node field
----> Adding facet field
----> Adding holes specification
----> Adding region specification
--- Done --- 26-Aug-2019 22:02:05
--- Running TetGen to mesh input boundary--- 26-Aug-2019 22:02:05
Opening /mnt/data/MATLAB/GIBBON/data/temp/temp.smesh.
Delaunizing vertices...
Delaunay seconds:  0.039281
Creating surface mesh ...
Surface mesh seconds:  0.011722
Recovering boundaries...
Boundary recovery seconds:  0.025185
Removing exterior tetrahedra ...
Spreading region attributes.
Exterior tets removal seconds:  0.014681
Recovering Delaunayness...
Delaunay recovery seconds:  0.012726
Refining mesh...
Refinement seconds:  0.25109
Optimizing mesh...
Optimization seconds:  0.013221

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:  0.172519
Total running seconds:  0.540901

Statistics:

  Input points: 6509
  Input facets: 13010
  Input segments: 19515
  Input holes: 1
  Input regions: 1

  Mesh points: 14265
  Mesh tetrahedra: 70418
  Mesh faces: 147341
  Mesh faces on exterior boundary: 13010
  Mesh faces on input facets: 13010
  Mesh edges on input segments: 19515
  Steiner points inside domain: 7756

--- Done --- 26-Aug-2019 22:02:06
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Importing TetGen files --- 26-Aug-2019 22:02:06
--- Done --- 26-Aug-2019 22:02:07

Access model element and patch data

Fb_foot=meshOutput.facesBoundary; %Boundary faces of the foot
Cb_foot=meshOutput.boundaryMarker; %Boundary marker/color data for the foot
V_foot=meshOutput.nodes; %The vertices/nodes
E_foot=meshOutput.elements; %The tet4 elements

Visualizing mesh using meshView, see also anim8

meshView(meshOutput);

Build insole

The insole is created by taking the 2D convex hull of the foot (ignoring the z-direction). Next this convex hull is resampled and filled with triangular elements. The z-coordinates are then based on the nearest foot nodes. The z-coordinate data is next smoothed to create a smooth surface. This surface is next thickened to form hexahedral elements.

Create sole boundary curve in 2D

% Offset surface outward to thicken so sole is enlarged outward
[~,~,Nv]=patchNormal(FT,VT);
VT_sole=VT+soleOffsetOutward.*Nv;

P=VT_sole(:,[1 2]); %Point set flattened to 2D
DT=delaunayTriangulation(P); %Delaunay triangulation of 2D set
VD=DT.Points; %Delaunay point set
VD(:,3)=min(VT(:,3)); %Set z-coord to minimum for now
indChull=DT.convexHull; %Ordered point list for conhex hull
indChull=indChull(1:end-1); %Trim away last (=start) point to avoid double
V_chull=VD(indChull,:); %Vertices for convex hull
D=max(pathLength(V_chull)); %Get length of sole curve for resampling
numResample=ceil(D./pointSpacing);
V_sole_curve=evenlySampleCurve(V_chull,numResample,'pchip',1);

Visualize

cFigure; hold on;
gpatch(FT,VT,'kw','none',0.25);
plotV(P,'k.','MarkerSize',markerSize2);
plotV(V_chull,'r.','MarkerSize',markerSize1*2);
plotV(V_sole_curve,'b.-','MarkerSize',markerSize1,'LineWidth',lineWidth);
camlight('headlight');
axisGeom(gca,fontSize);
colormap gjet; icolorbar;
drawnow;

Build sole top surface

[F_sole_top,V_sole_top]=regionTriMesh2D({V_sole_curve(:,[1 2])},pointSpacing*2,0,0);
V_sole_top(:,3)=mean(V_sole_curve(:,3));

tri2quad_optionStruct.maxAngleDeviation=60*(pi/180);
tri2quad_optionStruct.selectionMethod='best';
tri2quad_optionStruct.triangleConvert=1;
tri2quad_optionStruct.fourConnectConvert=1;
[F_sole_top,V_sole_top]=tri2quadGroupSplit(F_sole_top,V_sole_top,tri2quad_optionStruct);
Eb=patchBoundary(F_sole_top,V_sole_top);
indB=unique(Eb(:));

%Free smoothing of boundary
clear cParSmooth;
cParSmooth.n=25;
cParSmooth.Method='HC';
[p]=patchSmooth(Eb,V_sole_top,[],cParSmooth);
V_sole_top(indB,:)=p(indB,:);

%Constrained smoothing
clear cParSmooth;
cParSmooth.n=25;
cParSmooth.Method='HC';
cParSmooth.RigidConstraints=indB;
[V_sole_top]=patchSmooth(F_sole_top,V_sole_top,[],cParSmooth);

%Get z-coordinate
[~,indMin]=minDist(V_sole_top,VT);
V_sole_top(:,3)=VT(indMin,3);

clear cParSmooth;
cParSmooth.n=numSmoothIterations_sole_Z;
cParSmooth.Method='LAP';
[V_sole_top(:,3)]=patchSmooth(F_sole_top,V_sole_top(:,3),[],cParSmooth);

%Free smoothing of boundary
clear cParSmooth;
cParSmooth.n=numSmoothIterations_sole_Z;
cParSmooth.Method='LAP';
[p]=patchSmooth(Eb,V_sole_top,[],cParSmooth);
V_sole_top(indB,3)=p(indB,3);

V_sole_top(:,3)=V_sole_top(:,3)-pointSpacing/3;

pointSpacingSole=mean(patchEdgeLengths(F_sole_top,V_sole_top));

Visualize

cFigure; hold on;
gpatch(FT,VT,'kw','none',0.25);
gpatch(F_sole_top,V_sole_top,'gw','k',1);
patchNormPlot(F_sole_top,V_sole_top);
camlight('headlight');
axisGeom(gca,fontSize);
colormap gjet; icolorbar;
drawnow;

Create bottom surface of sole

F_sole_bottom=F_sole_top;
V_sole_bottom=V_sole_top;
V_sole_bottom(:,3)=(V_sole_top(:,3))-soleMinThickness;

cFigure; hold on;
gpatch(FT,VT,'kw','none',0.25);
gpatch(F_sole_top,V_sole_top,'gw','k',1);
gpatch(F_sole_bottom,V_sole_bottom,'bw','k',1);
patchNormPlot(F_sole_top,V_sole_top);
camlight('headlight');
axisGeom(gca,fontSize);
colormap gjet; icolorbar;
drawnow;

Create hexahedral elements

V_sole=[V_sole_bottom;V_sole_top];
E_sole=[F_sole_bottom F_sole_top+size(V_sole_bottom,1)];
F_sole_top=F_sole_top+size(V_sole_bottom,1); %Fix indices

%Use element2patch to get patch data
F_E_sole=element2patch(E_sole);
indBoundaryFaces=tesBoundary(F_E_sole,V_sole);
Fb_sole=F_E_sole(indBoundaryFaces,:);

Visualize

cFigure; hold on;
title('Hexahedral mesh');
gpatch(FT,VT,'kw','none',0.25);
gpatch(Fb_sole,V_sole,'bw','k',1);
patchNormPlot(Fb_sole,V_sole);
axisGeom;
camlight headlight;
drawnow;

Joining node sets

V=[V_foot;V_sole;]; %Combined node sets
E_sole=E_sole+size(V_foot,1); %Fixed element indices
F_sole_top=F_sole_top+size(V_foot,1); %Fixed element indices
F_sole_bottom=F_sole_bottom+size(V_foot,1); %Fixed indices
F_E_sole=F_E_sole+size(V_foot,1); %Fixed element indices
Fb_sole=Fb_sole+size(V_foot,1); %Fixed element indices

Visualize

cFigure; hold on;
title('Hexahedral mesh');
gpatch(Fb_foot,V,Cb_foot,'k',1);
gpatch(Fb_sole,V,'kw','k',1);
% patchNormPlot(FEs,V);
colormap gjet; icolorbar;
axisGeom;
camlight headlight;
drawnow;

Define contact surfaces

% The rigid master surface of the sphere
F_contact_master=F_sole_top;

% The deformable slave surface of the slab
F_contact_slave=fliplr(Fb_foot(Cb_foot==2,:));

Visualize contact surfaces

cFigure; hold on;
title('Contact sets and normal directions','FontSize',fontSize);

gpatch(Fb_foot,V,'kw','none',faceAlpha2);
gpatch(Fb_sole,V,'kw','none',faceAlpha2);

hl(1)=gpatch(F_contact_master,V,'gw','k',1);
patchNormPlot(F_contact_master,V);
hl(2)=gpatch(F_contact_slave,V,'bw','k',1);
patchNormPlot(F_contact_slave,V);

legend(hl,{'Master','Slave'});

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

Define boundary conditions

%Supported nodes
bcSupportList=unique(F_sole_bottom);

%Prescribed displacement nodes
bcPrescribeList=unique(Fb_foot(Cb_foot==1,:));

Visualize BC's

hf=cFigure; hold on;
title('Boundary conditions model','FontSize',fontSize);
gpatch(Fb_foot,V,'kw','none',faceAlpha2);
gpatch(Fb_sole,V,'kw','none',faceAlpha2);
hl2(1)=plotV(V(bcPrescribeList,:),'r.','MarkerSize',markerSize2);
hl2(2)=plotV(V(bcSupportList,:),'k.','MarkerSize',markerSize2);
legend(hl2,{'BC prescribe','BC support'});
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';

%Control section
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;
febio_spec.Control.symmetric_stiffness=symmetric_stiffness;
febio_spec.Control.min_residual=min_residual;

%Material section
febio_spec.Material.material{1}.ATTR.type='Ogden';
febio_spec.Material.material{1}.ATTR.id=1;
febio_spec.Material.material{1}.c1=c1_1;
febio_spec.Material.material{1}.m1=m1_1;
febio_spec.Material.material{1}.c2=c1_1;
febio_spec.Material.material{1}.m2=-m1_1;
febio_spec.Material.material{1}.k=k_1;

febio_spec.Material.material{2}.ATTR.type='Ogden unconstrained';
febio_spec.Material.material{2}.ATTR.id=2;
febio_spec.Material.material{2}.c1=c1_2;
febio_spec.Material.material{2}.m1=m1_2;
febio_spec.Material.material{2}.c2=c1_2;
febio_spec.Material.material{2}.m2=-m1_2;
febio_spec.Material.material{2}.cp=k_2;

%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='tet4'; %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='Foot'; %Name of the element set
febio_spec.Geometry.Elements{1}.elem.ATTR.id=(1:1:size(E_foot,1))'; %Element id's
febio_spec.Geometry.Elements{1}.elem.VAL=E_foot;

febio_spec.Geometry.Elements{2}.ATTR.type='hex8'; %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='Sole'; %Name of the element set
febio_spec.Geometry.Elements{2}.elem.ATTR.id=size(E_foot,1)+(1:1:size(E_sole,1))'; %Element id's
febio_spec.Geometry.Elements{2}.elem.VAL=E_sole;

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

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}.tri3.ATTR.lid=(1:1:size(F_contact_slave,1))';
febio_spec.Geometry.Surface{2}.tri3.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;

%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;

febio_spec.Boundary.fix{4}.ATTR.bc='x';
febio_spec.Boundary.fix{4}.ATTR.node_set=febio_spec.Geometry.NodeSet{2}.ATTR.name;
febio_spec.Boundary.fix{5}.ATTR.bc='y';
febio_spec.Boundary.fix{5}.ATTR.node_set=febio_spec.Geometry.NodeSet{2}.ATTR.name;

% -> Prescribed boundary conditions
febio_spec.Boundary.prescribe{1}.ATTR.bc='z';
febio_spec.Boundary.prescribe{1}.ATTR.node_set=febio_spec.Geometry.NodeSet{2}.ATTR.name;
febio_spec.Boundary.prescribe{1}.scale.ATTR.lc=1;
febio_spec.Boundary.prescribe{1}.scale.VAL=1;
febio_spec.Boundary.prescribe{1}.relative=1;
febio_spec.Boundary.prescribe{1}.value=displacementMagnitude;

%Contact section
%Contact section
febio_spec.Contact.contact{1}.ATTR.surface_pair=febio_spec.Geometry.SurfacePair{1}.ATTR.name;
febio_spec.Contact.contact{1}.ATTR.type='sliding-elastic';
febio_spec.Contact.contact{1}.two_pass=1;
febio_spec.Contact.contact{1}.laugon=laugon;
febio_spec.Contact.contact{1}.tolerance=0.2;
febio_spec.Contact.contact{1}.gaptol=0;
febio_spec.Contact.contact{1}.minaug=minaug;
febio_spec.Contact.contact{1}.maxaug=maxaug;
febio_spec.Contact.contact{1}.search_tol=0.01;
febio_spec.Contact.contact{1}.search_radius=0.1;
febio_spec.Contact.contact{1}.symmetric_stiffness=0;
febio_spec.Contact.contact{1}.auto_penalty=1;
febio_spec.Contact.contact{1}.penalty=contactPenalty;
febio_spec.Contact.contact{1}.fric_coeff=fric_coeff;

%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.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.node_data{2}.VAL=1:size(V,1);

febio_spec.Output.logfile.element_data{1}.ATTR.file=febioLogFileName_strainEnergy;
febio_spec.Output.logfile.element_data{1}.ATTR.data='sed';
febio_spec.Output.logfile.element_data{1}.ATTR.delim=',';
febio_spec.Output.logfile.element_data{1}.VAL=1:size(E_foot,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='external';%'internal';
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!!!!!!!!

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- STARTING FEBIO JOB --- 26-Aug-2019 22:02:16
Waiting for log file...
Proceeding to check log file...26-Aug-2019 22:02:17
------- converged at time : 0.1
------- converged at time : 0.2
------- converged at time : 0.3
------- converged at time : 0.4
------- converged at time : 0.5
------- converged at time : 0.6
------- converged at time : 0.695393
------- converged at time : 0.782561
------- converged at time : 0.862222
------- converged at time : 0.932212
------- converged at time : 0.996191
------- converged at time : 1
--- Done --- 26-Aug-2019 22:04:30

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);

    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,:);

    C=sqrt(sum(DN(:,3).^2,2));
    [CF]=vertexToFaceMeasure(Fb_foot,C);

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_foot,C_energy_foot]=element2patch(E_foot,E_energy(:,:,end));
%     [FE_foot,C_energy_foot]=element2patch(E_foot,E_energy(1:size(E_foot,1),:,1));
    indBoundaryFacesFoot=tesBoundary(FE_foot,V);

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,': Press play to animate']);
    hp1=gpatch(Fb_foot,V_def,[1 0.95 0.8],'none',0.25); %Add graphics object to animate
    hp2=gpatch(F_sole_top,V_def,C,'none',1); %Add graphics object to animate
    hp2.FaceColor='Interp';
%     gpatch(Fb_sole,V_def,'kw','none',0.2); %Add graphics object to animate

    axisGeom(gca,fontSize);
    colormap(flipud(kvw(250))); colorbar;
    caxis([0 max(C)/6]);
    axis([min(X_DEF(:)) max(X_DEF(:)) min(Y_DEF(:)) max(Y_DEF(:)) min(Z_DEF(:)) max(Z_DEF(:))]);
    view([-30 -30]);
    camlight headlight;
    lighting gouraud;

    % 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

        C=sqrt(sum(DN(:,3).^2,2)); %New color

        %Set entries in animation structure
        animStruct.Handles{qt}=[hp2 hp2 hp1]; %Handles of objects to animate
        animStruct.Props{qt}={'Vertices','CData','Vertices'}; %Properties of objects to animate
        animStruct.Set{qt}={V_def,C,V_def}; %Property values for to set in order to animate
    end
    anim8(hf,animStruct); %Initiate animation feature
    drawnow;

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,': Press play to animate']);
    [CV]=faceToVertexMeasure(FE_foot(indBoundaryFacesFoot,:),V,C_energy_foot(indBoundaryFacesFoot,:));
    hp1=gpatch(FE_foot(indBoundaryFacesFoot,:),V_def,CV,'w',1); %Add graphics object to animate
    hp1.FaceColor='Interp';
    hp2=gpatch(Fb_sole,V_def,'gw','none',0.5); %Add graphics object to animate

    axisGeom(gca,fontSize);
    colormap(gjet(250)); colorbar;
    caxis([0 max(C_energy_foot)/100]);
    axis([min(X_DEF(:)) max(X_DEF(:)) min(Y_DEF(:)) max(Y_DEF(:)) min(Z_DEF(:)) max(Z_DEF(:))]);
    view([-30 -30]);
    camlight headlight;
    lighting gouraud;

    % 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_foot,C_energy_foot]=element2patch(E_foot,E_energy(:,:,qt));
        [CV]=faceToVertexMeasure(FE_foot(indBoundaryFacesFoot,:),V,C_energy_foot(indBoundaryFacesFoot,:));
        %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 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) 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/.

Published with MATLAB® R2019b