DEMO_febio_0059_face_mask_loading

Below is a demonstration for:

Building triangulated surface geometry for a face
Meshing the face using pentahedral elements
Building model of a tube
Defining the boundary conditions
Coding the febio structure
Running the model
Importing and visualizing results

Keywords
Control parameters
Load face geometry
Remeshing surface
Centre on nose and rotate to face face looking down Z-axis
Construct mask rim curve
Join and merge rim surfaces
Join and merge mask body components
Join node sets
Define contact surfaces
Define 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 3.0
febio, FEBio
face
contact, sliding, friction
pentahedral elements, penta6
static, solid
hyperelastic, Ogden
displacement logfile

clear; close all; clc;

Plot settings

fontSize=15;
faceAlpha1=1;
faceAlpha2=0.3;
markerSize1=15;
markerSize2=10;
lineWidth=2;
cMap=spectral(250);

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_strainEnergy=[febioFebFileNamePart,'_energy_out.txt']; %Log file name for exporting strain energy density

% Geometry parameters
pointSpacingTissue=6;
faceTissueThickness=6;
pointSpacingMask=pointSpacingTissue/2;
maskRimWidth=5;
maskRimFilletRadius=6;
maskDiscRadius1=25;
maskDiscRadius2=maskDiscRadius1+4;
maskDiscOffset=25;
bezierTangency=0.1;

distInclude=40; %Distance from mask to include face in FEA

%Ray tracing parameters
optionStructRayTrace.tolEps        = 1e-6;
optionStructRayTrace.triSide       = 0;
optionStructRayTrace.rayType       = 'ray';
optionStructRayTrace.exclusionType = 'inclusive';
optionStructRayTrace.paired        = 0;

%Material parameters
c1_tissue=1e-3; %Shear-modulus-like parameter
m1_tissue=2; %Material parameter setting degree of non-linearity
k_tissue=c1_tissue*100; %Bulk modulus

c1_rim=c1_tissue*5; %Shear-modulus-like parameter
m1_rim=2; %Material parameter setting degree of non-linearity
k_rim=c1_rim*10; %Bulk modulus

% FEA control settings
numTimeSteps=15; %Number of time steps desired
max_refs=35; %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;
runMode='external';

%Boundary condition parameters
initialOffset=0;
displacementMagnitude_z=-2-initialOffset; %Displacement applied

%Contact parameters
contactPenalty=10;
laugon=0;
minaug=1;
maxaug=10;
fric_coeff=0.5;

Load face geometry

testCase=1;
switch testCase
    case 1
        %Load surface model
        [Ff,Vf]=graphicsModels(9);

        %Surface markers
        V_markers=[65.51,49.94,217.14;... %Tip of the nose
            66.44,54.79,259.81;... %Nose between eyes
            53.81,115,263.39;... %Right eye outer corner
            126.5,46.62,269.75;... %Left eye outer corner
            85.67,69.44,194.1;... %Middle of mounth
            98.39,80.38,158]; %Bottom of chin
    case 2
        %Load surface model
        [Ff,Vf]=graphicsModels(13);

        %Surface markers
        V_markers=[3.50162,-181.107,-8.09110;...  %Tip of the nose
                   1.51627,-159.171,30.4679;... %Nose between eyes
                   -43.2473,-139.003,24.6407;... %Right eye outer corner
                   48.4245,-136.490,25.3913;... %Left eye outer corner
                   4.11905,-167.594,-36.9600;... %Middle of mounth
                   2.85290,-161.802,-73.4644]; %Bottom of chin
end

distEyes=sqrt(sum((V_markers(3,:)-V_markers(4,:)).^2,2));

Remeshing surface

optionStruct_remesh.pointSpacing=pointSpacingTissue; %Set desired point spacing
optionStruct_remesh.disp_on=0; % Turn off command window text display
[Ff,Vf]=ggremesh(Ff,Vf,optionStruct_remesh);

ny=vecnormalize(V_markers(2,:)-V_markers(6,:));
nx=vecnormalize(V_markers(4,:)-V_markers(3,:));
nz=vecnormalize(cross(nx,ny));
nx=vecnormalize(cross(ny,nz));

Q=[nx;ny;nz]';

cFigure; hold on;
gpatch(Ff,Vf,'w','none',0.5);
plotV(V_markers,'r.','MarkerSize',35);
text(V_markers(:,1)+4,V_markers(:,2),V_markers(:,3),{'1','2','3','4','5','6'},'FontSize',25);
quiverTriad(V_markers(1,:),Q,100);
axisGeom; camlight headlight;
colormap(spectral(250))
gdrawnow;

Centre on nose and rotate to face face looking down Z-axis

Vf=Vf-V_markers(1,:);
Vf=Vf*Q;
V_markers=V_markers-V_markers(1,:);
V_markers=V_markers*Q;
nz=[0 0 1];%nz*Q;

cFigure; hold on;
gpatch(Ff,Vf,'w','none',0.5);
plotV(V_markers,'r.','MarkerSize',35);
text(V_markers(:,1)+6,V_markers(:,2),V_markers(:,3)+15,{'1','2','3','4','5','6'},'FontSize',25);
axisGeom; camlight headlight;
colormap(spectral(250))
gdrawnow;

Construct mask rim curve

V1=V_markers(1,[1 2]);
V2=V_markers(2,[1 2]);
V3=V_markers(3,[1 2]);
V4=V_markers(4,[1 2]);
V5=V_markers(5,[1 2]);
V6=V_markers(6,[1 2]);

pp1=0.4*V1+0.6*V2;
pp2=0.6*V1+0.4*V3;
pp3=V3-[0 V3(2)]+[0 0.5*V5(2)+0.5*V1(2)];
pp4=[0.3*V2(1)+0.8*V3(1) 0.5*V5(2)+0.5*V6(2)];
pp5=V6;
pp6=[0.3*V2(1)+0.8*V4(1) 0.5*V5(2)+0.5*V6(2)];
pp7=V4-[0 V4(2)]+[0 0.5*V5(2)+0.5*V1(2)];
pp8=0.6*V1+0.4*V4;

V_rim_points=[pp1;pp2;pp3;pp4;pp5;pp6;pp7;pp8];
V_rim_points(:,3)=0;

[V_rim_points,indFaceIntersect]=traceToSurf(V_rim_points,-nz,Ff,Vf,optionStructRayTrace);
numRimControlPoints=size(V_rim_points,1);

V_rim_curve=evenlySpaceCurve(V_rim_points,pointSpacingMask,'pchip',1);
V_rim_curve=traceToSurf(V_rim_curve,-nz,Ff,Vf,optionStructRayTrace);
numPointsRimCurve=size(V_rim_curve,1);


Ne1=vecnormalize([V_rim_points(2:end,:); V_rim_points(1,:)]-V_rim_points(1:end,:));
Ne2=vecnormalize(V_rim_points - [V_rim_points(end,:); V_rim_points(1:end-1,:)]);
Ne=vecnormalize(0.5*Ne1+0.5*Ne2);

Nf=patchNormal(Ff,Vf); %Normal directions
Nff=Nf(indFaceIntersect(:,2),:);
N_rim_points=vecnormalize(cross(Nff,Ne));

V_rim_points1=V_rim_points-N_rim_points.*maskRimWidth/2;
V_rim_points2=V_rim_points+N_rim_points.*maskRimWidth/2;

cFigure; hold on;
gpatch(Ff,Vf,'w','none',0.5);
plotV(V_markers,'r.','MarkerSize',25);
text(V_markers(:,1)+4,V_markers(:,2),V_markers(:,3),{'1','2','3','4','5','6'},'FontSize',25);

plotV(V_rim_points,'k.','MarkerSize',25);
plotV(V_rim_points1,'b.','MarkerSize',25);
plotV(V_rim_points2,'g.','MarkerSize',25);

quiverVec(V_rim_points,N_rim_points,maskRimWidth/2,'y');
quiverVec(V_rim_points,-N_rim_points,maskRimWidth/2,'y');
axisGeom; camlight headlight;
view(2);
gdrawnow;

[~,indClose]=minDist(V_markers,Vf);
d=meshDistMarch(Ff,Vf,indClose([1 5]));

[~,indClose]=minDist(V_rim_curve,Vf);
d_rim_curve=meshDistMarch(Ff,Vf,indClose);
d_markers_max=max(d(indClose));

logicCloseVertices= d<=d_markers_max | d_rim_curve<distInclude;

logicCloseFaces= any(logicCloseVertices(Ff),2);
logicCloseFaces=triSurfLogicSharpFix(Ff,logicCloseFaces);

[Fs,Vs]=patchCleanUnused(Ff(logicCloseFaces,:),Vf);

ns=vecnormalize(mean(patchNormal(Fs,Vs)));

[Q]=pointSetPrincipalDir(Vs);
nz=Q(:,3)';
if dot(nz,ns)<1
    nz=-nz;
end

ny=vecnormalize(V_markers(2,:)-V_markers(1,:));
nx=cross(ny,nz);
ny=cross(nz,nx);
Q=[nx;ny;nz]';

Ffc=Ff(~logicCloseFaces,:);

cFigure;  hold on;
gpatch(Ff,Vf,d,'k',0.5);
gpatch(Ff(logicCloseFaces,:),Vf,'none','b',1,2);
plotV(V_markers,'r.','MarkerSize',25);
plotV(V_rim_points,'k.','MarkerSize',15);
plotV(V_rim_curve,'k-','LineWidth',3);

axisGeom; camlight headlight;
colormap(spectral(250))
gdrawnow;

cFigure;  hold on;
gpatch(Ff,Vf,'w','none');
gpatch(Fs,Vs,'w','b');
% patchNormPlot(Fs,Vs);
plotV(V_markers,'r.','MarkerSize',25);
% quiverTriad(V_markers(1,:),Q,50);
axisGeom;
camlight headlight;
% colormap(viridis(2)); icolorbar;
gdrawnow;

Ebs=patchBoundary(Fs);
indBoundaryCurve=edgeListToCurve(Ebs);
indBoundaryCurve=indBoundaryCurve(1:end-1)';

[~,~,Ns]=patchNormal(Fs,Vs);

Vs2=Vs-Ns*faceTissueThickness;
Fs2=Fs;

Vsc=Vs2(indBoundaryCurve,:);%-Ns(indBoundaryCurve,:)*layerThickness;
[Fs2t,Vs2t]=regionTriMesh3D({Vsc},pointSpacingMask,0,'natural');
Vs2t_ori=Vs2t;
indBoundary=unique(patchBoundary(Fs2t));

[~,indMap]=minDist(Vsc,Vs2t(indBoundary,:));
indBoundaryCurve_2t=indBoundary(indMap);
indBoundaryCurve_2t=indBoundaryCurve_2t(:);

Vs2t=traceToSurf(Vs2t,-nz,Fs2,Vs2,optionStructRayTrace);

cParSmooth.n=3;
cParSmooth.Method='HC';
cParSmooth.RigidConstraints=indBoundaryCurve_2t;
Vs2t=patchSmooth(Fs2t,Vs2t,[],cParSmooth);

numNodesThickness=ceil(faceTissueThickness./pointSpacingTissue);
if numNodesThickness<2
    numNodesThickness=2;
end

cParLoft.numSteps=numNodesThickness;
cParLoft.closeLoopOpt=1;
cParLoft.patchType='tri';
[Fss,Vss,ind1,ind2]=polyLoftLinear(Vs(indBoundaryCurve,:),Vs2t(indBoundaryCurve_2t,:),cParLoft);

[Fb,Vb,Cb]=joinElementSets({Fs,Fs2t,Fss},{Vs,Vs2t,Vss});
[Fb,Vb]=mergeVertices(Fb,Vb);

cFigure; hold on;
gpatch(Ffc,Vf,'w','none',0.5);
gpatch(Fb,Vb,Cb,'k',0.5);

% gpatch(Fs,Vs,'bw','none',0.5);
% gpatch(Fs2t,Vs2t_ori,'gw','g',0.5);
% gpatch(Fs2t,Vs2t,'rw','g',0.5);

% patchNormPlot(Fb,Vb);
axisGeom; camlight headlight;
colormap(spectral); icolorbar;
gdrawnow;

Get inner mesh point between top and bottom at nose

Pn=triSurfRayTrace(V_markers(1,:),-nz,Fb,Vb,optionStructRayTrace);
Pn=mean(Pn,1);

cFigure; hold on;
%gpatch(Ffc,Vf,'w','none',0.5);
gpatch(Fb,Vb,Cb,'none',0.5);
plotV(Pn,'r.','MarkerSize',25);

% patchNormPlot(Fb,Vb);
axisGeom; camlight headlight;
colormap(spectral); icolorbar;
gdrawnow;

%Create tetgen input structure
inputStruct.stringOpt='-pq1.2AaY'; %Options for tetgen
inputStruct.Faces=Fb; %Boundary faces
inputStruct.Nodes=Vb; %Nodes of boundary
inputStruct.faceBoundaryMarker=Cb;
inputStruct.regionPoints=Pn; %Interior points for regions
inputStruct.holePoints=[]; %Interior points for holes
inputStruct.regionA=tetVolMeanEst(Fb,Vb); %Desired tetrahedral volume for each region

% Mesh model using tetrahedral elements using tetGen
[meshOutput]=runTetGen(inputStruct); %Run tetGen

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- TETGEN Tetrahedral meshing --- 25-Feb-2022 15:49:24
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Writing SMESH file --- 25-Feb-2022 15:49:24
----> Adding node field
----> Adding facet field
----> Adding holes specification
----> Adding region specification
--- Done --- 25-Feb-2022 15:49:24
--- Running TetGen to mesh input boundary--- 25-Feb-2022 15:49:24
Opening /mnt/data/MATLAB/GIBBON/data/temp/temp.smesh.
Delaunizing vertices...
Delaunay seconds:  0.016786
Creating surface mesh ...
Surface mesh seconds:  0.006195
Recovering boundaries...
Boundary recovery seconds:  0.011554
Removing exterior tetrahedra ...
Spreading region attributes.
Exterior tets removal seconds:  0.005045
Recovering Delaunayness...
Delaunay recovery seconds:  0.006379
Refining mesh...
  4110 insertions, added 300 points, 10101 tetrahedra in queue.
  1368 insertions, added 73 points, 8679 tetrahedra in queue.
  1824 insertions, added 85 points, 5761 tetrahedra in queue.
  2431 insertions, added 89 points, 694 tetrahedra in queue.
  3241 insertions, added 264 points, 7054 tetrahedra in queue.
  4320 insertions, added 234 points, 998 tetrahedra in queue.
Refinement seconds:  0.157903
Smoothing vertices...
Mesh smoothing seconds:  0.080483
Improving mesh...
Mesh improvement seconds:  0.005482

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:  0.059011
Total running seconds:  0.349115

Statistics:

  Input points: 3084
  Input facets: 6164
  Input segments: 9246
  Input holes: 0
  Input regions: 1

  Mesh points: 4425
  Mesh tetrahedra: 17502
  Mesh faces: 38086
  Mesh faces on exterior boundary: 6164
  Mesh faces on input facets: 6164
  Mesh edges on input segments: 9246
  Steiner points inside domain: 1341

--- Done --- 25-Feb-2022 15:49:24
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Importing TetGen files --- 25-Feb-2022 15:49:24
--- Done --- 25-Feb-2022 15:49:24

Access mesh output structure

E_face=meshOutput.elements; %The elements
V=meshOutput.nodes; %The vertices or nodes
F=meshOutput.faces; %Element faces (all)
CE=meshOutput.elementMaterialID; %Element material or region id
Fb=meshOutput.facesBoundary; %The boundary faces
Cb=meshOutput.boundaryMarker; %The boundary markers

Visualization

hf=cFigure;
subplot(1,2,1); hold on;
title('Input boundaries','FontSize',fontSize);
hp(1)=gpatch(Fb,V,Cb,'k',faceAlpha1);
hp(2)=plotV(Pn,'r.','MarkerSize',markerSize1);
legend(hp,{'Input mesh','Interior point(s)'},'Location','NorthWestOutside');
axisGeom(gca,fontSize); camlight headlight;
colormap(cMap); icolorbar;

hs=subplot(1,2,2); hold on;
title('Tetrahedral mesh','FontSize',fontSize);

% Visualizing using |meshView|
optionStruct.hFig=[hf,hs];

meshView(meshOutput,optionStruct);

axisGeom(gca,fontSize);
gdrawnow;

pp9=V_markers(5,:);% (0.1*V_markers(1,:)+0.9*V_markers(5,:));

t=linspace(0.5*pi,2.5*pi,numPointsRimCurve+1)';
t=t(1:end-1);
Vcd1=maskDiscRadius1*[cos(t) sin(t) zeros(size(t))];
Vcd1=Vcd1+pp9;
Vcd1(:,3)=maskDiscOffset;

Vcd2=maskDiscRadius2*[cos(t) sin(t) zeros(size(t))];
Vcd2=Vcd2+pp9;
Vcd2(:,3)=maskDiscOffset;

%
cFigure; hold on;
gpatch(Fb,V,'w','none',0.5);
plotV(V_markers,'r.','MarkerSize',50);
text(V_markers(:,1)+4,V_markers(:,2),V_markers(:,3)+50,{'1','2','3','4','5','6'},'FontSize',65);

plotV(V_rim_points,'k.','MarkerSize',35);
plotV(V_rim_curve,'k-','LineWidth',6);
plotV(Vcd1,'b-','LineWidth',6);
plotV(Vcd2,'b-','LineWidth',6);
axisGeom;
camlight headlight;
view(2);
drawnow;

V_rim_curve1=evenlySampleCurve(V_rim_points1,numPointsRimCurve,'pchip',1);
V_rim_curve2=evenlySampleCurve(V_rim_points2,numPointsRimCurve,'pchip',1);

V_rim_curve1=traceToSurf(V_rim_curve1,[0 0 -1],Fb(Cb==1,:),V,optionStructRayTrace);
V_rim_curve2=traceToSurf(V_rim_curve2,[0 0 -1],Fb(Cb==1,:),V,optionStructRayTrace);

cFigure; hold on;
gpatch(Fb(Cb==1,:),Vb,'w','none',0.5);

% patchNormPlot(Fm,Vm);
plotV(V_markers,'r.','MarkerSize',50);
text(V_markers(:,1)+4,V_markers(:,2),V_markers(:,3),{'1','2','3','4','5','6'},'FontSize',25);
plotV(V_rim_points,'k.','MarkerSize',35,'LineWidth',3);
plotV(V_rim_curve,'k-','LineWidth',3);

plotV(V_rim_points1,'g.','MarkerSize',35,'LineWidth',3);
plotV(V_rim_curve1,'g-','LineWidth',3);

plotV(V_rim_points2,'b.','MarkerSize',35,'LineWidth',3);
plotV(V_rim_curve2,'b-','LineWidth',3);

axisGeom; camlight headlight;
view(2);
drawnow;

pointSpacingNow=mean(diff(pathLength(V_rim_curve1)));
numNodStrip=ceil(maskRimWidth./pointSpacingNow);
if numNodStrip<2
    numNodStrip=2;
end
if iseven(numNodStrip)
    numNodStrip=numNodStrip+1;
end

cParLoft.numSteps=numNodStrip;
cParLoft.closeLoopOpt=1;
cParLoft.patchType='tri';
[Fm,Vm,indStart_Vm,indEnd_Vm]=polyLoftLinear(V_rim_curve1,V_rim_curve2,cParLoft);
Fm=fliplr(Fm);
indStart_Vm=fliplr(indStart_Vm);
indEnd_Vm=fliplr(indEnd_Vm);

[~,~,Nm]=patchNormal(Fm,Vm);
Vm=traceToSurf(Vm,Nm,Fb(Cb==1,:),V,optionStructRayTrace);

cFigure; hold on;
gpatch(Fb(Cb==1,:),Vb,'w','none',0.5);
gpatch(Fm,Vm,'rw','k',1,1);
% patchNormPlot(Fm,Vm);
plotV(V_markers,'r.','MarkerSize',50);
text(V_markers(:,1)+4,V_markers(:,2),V_markers(:,3),{'1','2','3','4','5','6'},'FontSize',25);
plotV(V_rim_points,'k.','MarkerSize',35,'LineWidth',3);
plotV(Vm(indStart_Vm,:),'g-','LineWidth',3);
plotV(Vm(indEnd_Vm,:),'b-','LineWidth',3);
axisGeom; camlight headlight;
view(2);
drawnow;

[~,~,Nm]=patchNormal(Fm,Vm);

pointSpacingNow=mean(diff(pathLength(Vm(indStart_Vm,:))));
nRim=ceil((pi/2*maskRimFilletRadius)/pointSpacingNow)+1;
if nRim<4
    nRim=4;
end

[Fr1,Vr1]=roundMesh(indStart_Vm,Vm,Nm,nRim,maskRimFilletRadius);
[Fr2,Vr2]=roundMesh(indEnd_Vm,Vm,Nm,nRim,maskRimFilletRadius);
indEnd_Vr1=size(Vr1)-numPointsRimCurve+1:1:size(Vr1);
indEnd_Vr2=fliplr(indEnd_Vr1);
[Fr1,Vr1]=quad2tri(Fr1,Vr1,'a');
[Fr2,Vr2]=quad2tri(Fr2,Vr2,'a');

cFigure; hold on;
gpatch(Fb,V,'w','none',0.5);
gpatch(Fm,Vm,'rw','k',1,1);
gpatch(Fr1,Vr1,'gw','k',1,1);
gpatch(Fr2,Vr2,'bw','k',1,1);
plotV(Vr1(indEnd_Vr1,:),'r-','LineWidth',3);
plotV(Vr2(indEnd_Vr2,:),'b-','LineWidth',3);
axisGeom; camlight headlight;
view(2);
drawnow;

pointSpacingNow=mean(diff(pathLength(Vr1(indEnd_Vr1,:))));
numNodStripTop=ceil((maskRimWidth+2*maskRimFilletRadius)./pointSpacingNow);
if numNodStripTop<2
    numNodStripTop=2;
end
if iseven(numNodStripTop)
    numNodStripTop=numNodStripTop+1;
end

cParLoft.numSteps=numNodStripTop;
cParLoft.closeLoopOpt=1;
cParLoft.patchType='tri';
[Ft,Vt,indCurve1_Vt,indCurve2_Vt]=polyLoftLinear(Vr1(indEnd_Vr1,:),Vr2(indEnd_Vr2,:),cParLoft);
Ft=fliplr(Ft);
indCurve1_Vt=flipud(indCurve1_Vt(:));
% indCurve2_Vt=flipud(indCurve2_Vt(:));
[~,~,Nt]=patchNormal(Ft,Vt);

cFigure; hold on;
gpatch(Fb,V,'w','none',0.5);
gpatch(Fm,Vm,'y','k',0,1);
gpatch(Ft,Vt,'gw','k',1,1);
gpatch(Fr1,Vr1,'rw','k',1,1);
gpatch(Fr2,Vr2,'bw','k',1,1);
plotV(Vr1(indEnd_Vr1,:),'r-','LineWidth',3);
plotV(Vr2(indEnd_Vr1,:),'b-','LineWidth',3);
axisGeom; camlight headlight;
view(2);
drawnow;

Join and merge rim surfaces

[F_rim,V_rim,C_rim]=joinElementSets({Fm,Fr1,Fr2,Ft},{Vm,Vr1,Vr2,Vt});
[F_rim,V_rim]=mergeVertices(F_rim,V_rim);
[F_rim,V_rim]=patchCleanUnused(F_rim,V_rim);

cFigure; hold on;
gpatch(Fb(Cb==1,:),V,'w','none',1);
gpatch(F_rim,V_rim,C_rim,'none',1);
% patchNormPlot(F_rim,V_rim);
axisGeom; camlight headlight;
colormap spectral; icolorbar;
drawnow;

V_loft1=Vt(indCurve1_Vt,:);
V_loft2=Vcd2;

V_loft3=Vt(indCurve2_Vt,:);
V_loft4=Vcd1;

[~,indMax]=max(V_loft4(:,1));
if indMax<numPointsRimCurve/2
    V_loft4=flipud(V_loft4);
end

[~,indMax]=max(V_loft2(:,1));
if indMax<numPointsRimCurve/2
    V_loft2=flipud(V_loft2);
end

N1=Nt(indCurve1_Vt,:);
N3=Nt(indCurve2_Vt,:);
N4=ones(size(V_loft4,1),1)*[0 0 1];

N2e=vecnormalize([V_loft2(2:end,:); V_loft2(1,:)]-V_loft2(1:end,:));
N2=vecnormalize(cross(N4,N2e));

[Fd1,Vd1,X,Y,Z]=bezierLoft(V_loft1,V_loft2,N1,N2,pointSpacingMask,bezierTangency);
[Fd1,Vd1]=quad2tri(Fd1,Vd1);
[Fd2,Vd2,X,Y,Z]=bezierLoft(V_loft3,V_loft4,N3,N4,pointSpacingMask,bezierTangency);
[Fd2,Vd2]=quad2tri(Fd2,Vd2);

pointSpacingNow=mean(diff(pathLength(V_loft2)));
n=ceil((maskDiscRadius2-maskDiscRadius1)./pointSpacingNow);
if n<2
    n=2;
end
if iseven(n)
    n=n+1;
end

cParLoft.numSteps=n;
cParLoft.closeLoopOpt=1;
cParLoft.patchType='tri';
[Fdt,Vdt]=polyLoftLinear(V_loft2,V_loft4,cParLoft);

[Fc,Vc]=regionTriMesh2D({V_loft4(:,[1 2])},pointSpacingNow,0,0);
Vc(:,3)=maskDiscOffset;

cFigure; hold on;
gpatch(Fb(Cb==1,:),V,'w','none',0.5);
gpatch(F_rim,V_rim,'kw','none',1);

gpatch(Fd1,Vd1,'rw','k',0.5);
gpatch(Fd2,Vd2,'bw','k',0.5);
gpatch(Fdt,Vdt,'gw','k',0.5);
gpatch(Fc,Vc,'yw','k',1);

plotV(V_loft1,'r-','LineWidth',3);
quiverVec(V_loft1,N1,5,'k');

plotV(V_loft4,'b-','LineWidth',2);
quiverVec(V_loft4,N4,5,'k');

plotV(V_loft3,'b-','LineWidth',3);
quiverVec(V_loft3,N3,5,'k');

plotV(V_loft2,'r-','LineWidth',2);

quiverVec(V_loft2,N2,5,'k');

axisGeom; camlight headlight;
drawnow;

Join and merge mask body components

[F_mask,V_mask,C_mask]=joinElementSets({Ft,Fd1,Fd2,Fdt,Fc},{Vt,Vd1,Vd2,Vdt,Vc});
[F_mask,V_mask]=mergeVertices(F_mask,V_mask);
[F_mask,V_mask]=patchCleanUnused(F_mask,V_mask);

cFigure; hold on;
gpatch(Ff,Vf,'w','none',1);
% gpatch(Fb,V,'w','none',1);
gpatch(F_mask,V_mask,'bw','none',1);
gpatch(F_rim,V_rim,'kw','none',1);
axisGeom; camlight headlight;
view(2);
% colormap spectral; icolorbar;
drawnow;

cFigure; hold on;
gpatch(Ff,Vf,'w','none',1);
% gpatch(Fb,V,'w','none',1);
% gpatch(F_mask,V_mask,'gw','none',0.5);
gpatch(F_rim,V_rim,'kw','none',1);
axisGeom; camlight headlight;
drawnow;

cFigure; hold on;
% gpatch(Fp1,V,'w','none',1);
gpatch(F_mask,V_mask,'bw','none',1);
gpatch(F_rim,V_rim,'gw','none',1);
axisGeom;
camlight headlight;
view(2);
drawnow;

cFigure; hold on;
% gpatch(Fb,V,'w','none',0.9);
gpatch(F_rim,V_rim,C_rim,'k',1);
% patchNormPlot(F_rim,V_rim);
axisGeom;
camlight headlight;
view(2);
colormap gjet; icolorbar;
drawnow;

[V_regions]=getInnerPoint(F_rim,V_rim); % Define region points

cFigure; hold on;
gpatch(F_rim,V_rim,C_rim,'k',1);
% plotV(V_regions,'r.','MarkerSize',markerSize1)
axisGeom;
camlight headlight; view(2);
drawnow;

[regionA]=tetVolMeanEst(F_rim,V_rim); %Volume for regular tets

inputStruct.stringOpt='-pq1.2AaY';
inputStruct.Faces=F_rim;
inputStruct.Nodes=V_rim;
inputStruct.holePoints=[];
inputStruct.faceBoundaryMarker=C_rim; %Face boundary markers
inputStruct.regionPoints=V_regions; %region points
inputStruct.regionA=regionA;

% Mesh model using tetrahedral elements using tetGen
[meshOutput]=runTetGen(inputStruct); %Run tetGen

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- TETGEN Tetrahedral meshing --- 25-Feb-2022 15:49:37
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Writing SMESH file --- 25-Feb-2022 15:49:37
----> Adding node field
----> Adding facet field
----> Adding holes specification
----> Adding region specification
--- Done --- 25-Feb-2022 15:49:37
--- Running TetGen to mesh input boundary--- 25-Feb-2022 15:49:37
Opening /mnt/data/MATLAB/GIBBON/data/temp/temp.smesh.
Delaunizing vertices...
Delaunay seconds:  0.00778
Creating surface mesh ...
Surface mesh seconds:  0.002173
Recovering boundaries...
Boundary recovery seconds:  0.003202
Removing exterior tetrahedra ...
Spreading region attributes.
Exterior tets removal seconds:  0.002172
Recovering Delaunayness...
Delaunay recovery seconds:  0.002353
Refining mesh...
  1727 insertions, added 483 points, 6669 tetrahedra in queue.
  575 insertions, added 27 points, 34 tetrahedra in queue.
  766 insertions, added 36 points, 734 tetrahedra in queue.
Refinement seconds:  0.022672
Smoothing vertices...
Mesh smoothing seconds:  0.022443
Improving mesh...
Mesh improvement seconds:  0.001715

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:  0.025064
Total running seconds:  0.089744

Statistics:

  Input points: 1296
  Input facets: 2592
  Input segments: 3888
  Input holes: 0
  Input regions: 1

  Mesh points: 1849
  Mesh tetrahedra: 6812
  Mesh faces: 14920
  Mesh faces on exterior boundary: 2592
  Mesh faces on input facets: 2592
  Mesh edges on input segments: 3888
  Steiner points inside domain: 553

--- Done --- 25-Feb-2022 15:49:37
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Importing TetGen files --- 25-Feb-2022 15:49:37
--- Done --- 25-Feb-2022 15:49:37

Access model element and patch data

Fb_rim=meshOutput.facesBoundary;
Cb_rim=meshOutput.boundaryMarker;
V_rim=meshOutput.nodes;
E_rim=meshOutput.elements;

% Visualizing mesh using |meshView|, see also |anim8|
meshView(meshOutput);

Join node sets

V_rim(:,3)=V_rim(:,3)+initialOffset;
Fb_rim=Fb_rim+size(V,1);
E_rim=E_rim+size(V,1);
V=[V;V_rim];

cFigure;
gpatch(F,V,'w','k',1);
gpatch(Fb_rim,V,Cb_rim,'k',1);
axisGeom;
colormap gjet; icolorbar;
camlight headlight;
drawnow;

Define contact surfaces

% The rigid primary surface of the sphere
F_contact_primary=fliplr(Fb_rim(Cb_rim~=4,:));

% The deformable secondary surface of the slab
Fb_contact=Fb(Cb==1,:);
V_Fb_centre=patchCentre(Fb_contact,V);
D=minDist(V_Fb_centre,V_rim);
logicSecondary=D<=(2*pointSpacingTissue);
logicSecondary=triSurfLogicSharpFix(Fb_contact,logicSecondary,3);
F_contact_secondary=fliplr(Fb_contact(logicSecondary,:));

Visualize contact surfaces

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

gpatch(Fb,V,'w','none',0.5);

hl(1)=gpatch(F_contact_primary,V,'gw','k',1);
patchNormPlot(F_contact_primary,V);
hl(2)=gpatch(F_contact_secondary,V,'rw','k',1);
patchNormPlot(F_contact_secondary,V);

legend(hl,{'Primary','secondary'});

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

Define boundary conditions

%Supported nodes
bcSupportList=unique(Fb(Cb==2,:));

%Prescribed displacement nodes
bcPrescribeList=unique(Fb_rim(Cb_rim==4,:));

Visualize BC's

hf=cFigure; hold on;
title('Boundary conditions model','FontSize',fontSize);
gpatch(Fb,V,'w','none',faceAlpha2);
gpatch(Fb_rim,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='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 unconstrained';
febio_spec.Material.material{1}.ATTR.id=1;
febio_spec.Material.material{1}.c1=c1_tissue;
febio_spec.Material.material{1}.m1=m1_tissue;
febio_spec.Material.material{1}.c2=c1_tissue;
febio_spec.Material.material{1}.m2=-m1_tissue;
febio_spec.Material.material{1}.cp=k_tissue;

materialName2='Material2';
febio_spec.Material.material{2}.ATTR.name=materialName2;
febio_spec.Material.material{2}.ATTR.type='Ogden unconstrained';
febio_spec.Material.material{2}.ATTR.id=2;
febio_spec.Material.material{2}.c1=c1_rim;
febio_spec.Material.material{2}.m1=m1_rim;
febio_spec.Material.material{2}.c2=c1_rim;
febio_spec.Material.material{2}.m2=-m1_rim;
febio_spec.Material.material{2}.cp=k_rim;

% Mesh section
% -> Nodes
febio_spec.Mesh.Nodes{1}.ATTR.name='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_face,1))'; %Element id's
febio_spec.Mesh.Elements{1}.elem.VAL=E_face; %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_face,1)+(1:1:size(E_rim,1))'; %Element id's
febio_spec.Mesh.Elements{2}.elem.VAL=E_rim; %The element matrix

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

nodeSetName2='bcPrescribeList';
febio_spec.Mesh.NodeSet{2}.ATTR.name=nodeSetName2;
febio_spec.Mesh.NodeSet{2}.node.ATTR.id=bcPrescribeList(:);

%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;

% -> Surfaces
surfaceName1='contactSurface1';
febio_spec.Mesh.Surface{1}.ATTR.name=surfaceName1;
febio_spec.Mesh.Surface{1}.tri3.ATTR.id=(1:1:size(F_contact_primary,1))';
febio_spec.Mesh.Surface{1}.tri3.VAL=F_contact_primary;

surfaceName2='contactSurface2';
febio_spec.Mesh.Surface{2}.ATTR.name=surfaceName2;
febio_spec.Mesh.Surface{2}.tri3.ATTR.id=(1:1:size(F_contact_secondary,1))';
febio_spec.Mesh.Surface{2}.tri3.VAL=F_contact_secondary;

% -> Surface pairs
contactPairName='Contact1';
febio_spec.Mesh.SurfacePair{1}.ATTR.name=contactPairName;
febio_spec.Mesh.SurfacePair{1}.primary=surfaceName1;
febio_spec.Mesh.SurfacePair{1}.secondary=surfaceName2;

%Boundary condition section
% -> Fix boundary conditions
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';

febio_spec.Boundary.bc{2}.ATTR.type='fix';
febio_spec.Boundary.bc{2}.ATTR.node_set=nodeSetName2;
febio_spec.Boundary.bc{2}.dofs='x,y';

febio_spec.Boundary.bc{3}.ATTR.type='prescribe';
febio_spec.Boundary.bc{3}.ATTR.node_set=nodeSetName2;
febio_spec.Boundary.bc{3}.dof='z';
febio_spec.Boundary.bc{3}.scale.ATTR.lc=1;
febio_spec.Boundary.bc{3}.scale.VAL=displacementMagnitude_z;
febio_spec.Boundary.bc{3}.relative=0;

%Contact section
febio_spec.Contact.contact{1}.ATTR.type='sliding-elastic';
febio_spec.Contact.contact{1}.ATTR.surface_pair=contactPairName;
febio_spec.Contact.contact{1}.two_pass=0;
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*sqrt(sum((max(V,[],1)-min(V,[],1)).^2,2));
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;

%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.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_face,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;%'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!!!!!!!!

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-------->    RUNNING/MONITORING FEBIO JOB    <-------- 25-Feb-2022 15:49:48
FEBio path: /home/kevin/FEBioStudio/bin/febio3
# Attempt removal of existing log files                25-Feb-2022 15:49:48
 * Removal succesful                                   25-Feb-2022 15:49:48
# Attempt removal of existing .xplt files              25-Feb-2022 15:49:48
 * Removal succesful                                   25-Feb-2022 15:49:48
# Starting FEBio...                                    25-Feb-2022 15:49:48
  Max. total analysis time is: 1e+99 s
 * Waiting for log file creation                       25-Feb-2022 15:49:48
   Max. wait time: 10 s
 * Log file found.                                     25-Feb-2022 15:49:48
# Parsing log file...                                  25-Feb-2022 15:49:48
    number of iterations   : 5                         25-Feb-2022 15:49:51
    number of reformations : 5                         25-Feb-2022 15:49:51
------- converged at time : 0.0666667                  25-Feb-2022 15:49:51
    number of iterations   : 4                         25-Feb-2022 15:49:52
    number of reformations : 4                         25-Feb-2022 15:49:52
------- converged at time : 0.133333                   25-Feb-2022 15:49:52
    number of iterations   : 4                         25-Feb-2022 15:49:53
    number of reformations : 4                         25-Feb-2022 15:49:53
------- converged at time : 0.2                        25-Feb-2022 15:49:53
    number of iterations   : 4                         25-Feb-2022 15:49:54
    number of reformations : 4                         25-Feb-2022 15:49:54
------- converged at time : 0.266667                   25-Feb-2022 15:49:54
    number of iterations   : 4                         25-Feb-2022 15:49:55
    number of reformations : 4                         25-Feb-2022 15:49:55
------- converged at time : 0.333333                   25-Feb-2022 15:49:55
    number of iterations   : 4                         25-Feb-2022 15:49:56
    number of reformations : 4                         25-Feb-2022 15:49:56
------- converged at time : 0.4                        25-Feb-2022 15:49:56
    number of iterations   : 4                         25-Feb-2022 15:49:57
    number of reformations : 4                         25-Feb-2022 15:49:57
------- converged at time : 0.466667                   25-Feb-2022 15:49:57
    number of iterations   : 4                         25-Feb-2022 15:49:58
    number of reformations : 4                         25-Feb-2022 15:49:58
------- converged at time : 0.533333                   25-Feb-2022 15:49:58
    number of iterations   : 4                         25-Feb-2022 15:49:59
    number of reformations : 4                         25-Feb-2022 15:49:59
------- converged at time : 0.6                        25-Feb-2022 15:49:59
    number of iterations   : 4                         25-Feb-2022 15:50:00
    number of reformations : 4                         25-Feb-2022 15:50:00
------- converged at time : 0.666667                   25-Feb-2022 15:50:00
    number of iterations   : 5                         25-Feb-2022 15:50:01
------- converged at time : 0.733333                   25-Feb-2022 15:50:01
    number of iterations   : 4                         25-Feb-2022 15:50:02
    number of reformations : 4                         25-Feb-2022 15:50:02
------- converged at time : 0.8                        25-Feb-2022 15:50:02
    number of iterations   : 4                         25-Feb-2022 15:50:03
    number of reformations : 4                         25-Feb-2022 15:50:03
------- converged at time : 0.866667                   25-Feb-2022 15:50:03
    number of iterations   : 4                         25-Feb-2022 15:50:04
    number of reformations : 4                         25-Feb-2022 15:50:04
------- converged at time : 0.933333                   25-Feb-2022 15:50:04
    number of iterations   : 5                         25-Feb-2022 15:50:05
    number of reformations : 5                         25-Feb-2022 15:50:05
 Elapsed time : 0:00:18                                25-Feb-2022 15:50:06
 N O R M A L   T E R M I N A T I O N
# Done                                                 25-Feb-2022 15:50:06
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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));

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_face,E_energy(1:size(E_face,1),:,end),'tet4');
    [CV]=faceToVertexMeasure(FE_face,V,C_energy_face);

Plotting the simulated results using anim8 to visualize and animate deformations

    cMap_c=gjet(250);
    cMap=[linspacen([1 1 1],cMap_c(1,:),50)'; cMap_c];

%     cMap=cMap(4:end,:);

    % Create basic view and store graphics handle to initiate animation
    hf=cFigure; %Open figure
    gtitle([febioFebFileNamePart,': Press play to animate']);

    gpatch(Ffc,Vf,cMap(1,:),'none',1)
    hp1=gpatch(Fb(Cb==1,:),V_def,CV,'none',1); %Add graphics object to animate
    hp1.FaceColor='Interp';
    hp2=gpatch(Fb_rim,V_def,'kw','none',0.5); %Add graphics object to animate
    hp3=gpatch(F_mask,V_mask,'k','none',0.2);

    axisGeom(gca,fontSize); camlight headlight;
    colormap(cMap); colorbar;
    caxis([0 max(C_energy_face)/10]);
    axis([min(X_DEF(:)) max(X_DEF(:)) min(Y_DEF(:)) max(Y_DEF(:)) min(Z_DEF(:)) max(Z_DEF(:))]);
    axis tight;

    % 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
        [FE_face,C_energy_face]=element2patch(E_face,E_energy(1:size(E_face,1),:,qt),'tet4');
        [CV]=faceToVertexMeasure(FE_face,V,C_energy_face);

        u=mean(DN(bcPrescribeList,:),1);
        V_mask_def=V_mask+u(ones(size(V_mask,1),1),:);

        %Set entries in animation structure
        animStruct.Handles{qt}=[hp1 hp1 hp2 hp3]; %Handles of objects to animate
        animStruct.Props{qt}={'Vertices','CData','Vertices','Vertices'}; %Properties of objects to animate
        animStruct.Set{qt}={V_def,CV,V_def,V_mask_def}; %Property values for to set in order to animate
    end
    anim8(hf,animStruct); %Initiate animation feature
    drawnow;

end

function [varargout]=traceToSurf(V1,N1,F2,V2,optionStructRayTrace)

if size(N1,1)==1
    N1=N1(ones(size(V1,1),1),:);
end

numPoints=size(V1,1);
indFacesIntersect=nan(size(V1,1),2);
for q=1:1:numPoints
    [P,indFaceIntersect,~,~]=triSurfRayTrace(V1(q,:),N1(q,:),F2,V2,optionStructRayTrace);
    if size(P,1)>1
        [~,indMin]=minDist(V1(q,:),P);
        %         [~,indMin]=min(d);
        P=P(indMin,:);
        indFaceIntersect=indFaceIntersect(indMin,:);
    end
    V1(q,:)=P;
    indFacesIntersect(q,:)=indFaceIntersect;
end

varargout{1}=V1;
varargout{2}=indFacesIntersect;

end

function [Fr,Vr]=roundMesh(indCurve,Vm,Nm,nc,stripRadius)

E=[indCurve(1:end)' [indCurve(2:end) indCurve(1)]'];
ind1=indCurve(1:end)';
ind2=[indCurve(2:end) indCurve(1)]';
ind3=[indCurve(end) indCurve(1:end-1)]';

N1f=Vm(ind2,:)-Vm(ind1,:);
N1b=Vm(ind1,:)-Vm(ind3,:);
Ne=vecnormalize((N1f+N1b)/2);

% Ne=vecnormalize(edgeVec(E,Vm));
Nf=-Nm(E(:,1),:);% -vecnormalize((Nm(E(:,1),:)+Nm(E(:,2),:))/2);
Ne2=vecnormalize(cross(Nf,Ne));

X=repmat(Vm(E(:,1),1),1,nc);
Y=repmat(Vm(E(:,1),2),1,nc);
Z=repmat(Vm(E(:,1),3),1,nc);

t=repmat(linspace(0,pi/2,nc),size(Z,1),1);

X=X+stripRadius.*sin(t).*repmat(Ne2(:,1),1,nc)-stripRadius.*cos(t).*repmat(Nf(:,1),1,nc)+stripRadius.*repmat(Nf(:,1),1,nc);
Y=Y+stripRadius.*sin(t).*repmat(Ne2(:,2),1,nc)-stripRadius.*cos(t).*repmat(Nf(:,2),1,nc)+stripRadius.*repmat(Nf(:,2),1,nc);
Z=Z+stripRadius.*sin(t).*repmat(Ne2(:,3),1,nc)-stripRadius.*cos(t).*repmat(Nf(:,3),1,nc)+stripRadius.*repmat(Nf(:,3),1,nc);

for q=2:1:size(X,2)
   v=evenlySampleCurve([X(:,q) Y(:,q) Z(:,q)],size(X,1),'pchip',1);
   X(:,q)=v(:,1);
   Y(:,q)=v(:,2);
   Z(:,q)=v(:,3);
end

[Fr,Vr]=grid2patch(X,Y,Z,[],[1 0 0]);

end

function [F,V,X,Y,Z]=bezierLoft(P1,P4,N1,N4,pointSpacing,f)

D12=sqrt(sum((P1-P4).^2,2));
numPoints=ceil(max(D12)./pointSpacing);
if numPoints<2
    numPoints=2;
end

P2=P1+D12.*f.*N1;
P3=P4-D12.*f.*N4;

X=zeros(numPoints,size(P1,1));
Y=zeros(numPoints,size(P1,1));
Z=zeros(numPoints,size(P1,1));
for q=1:1:size(P1,1)
    p=[P1(q,:); P2(q,:); P3(q,:); P4(q,:)]; %Control points
    V_bezier=bezierCurve(p,numPoints*2); %Compute bezier curve
    V_bezier=evenlySampleCurve(V_bezier,numPoints,'pchip'); %resample evenly
    X(:,q)=V_bezier(:,1);
    Y(:,q)=V_bezier(:,2);
    Z(:,q)=V_bezier(:,3);
end

%Create quad patch data
[F,V] = surf2patch(X,Y,Z);
I=[(1:size(Z,1)-1)' (1:size(Z,1)-1)' (2:size(Z,1))' (2:size(Z,1))' ];
J=[size(Z,2).*ones(size(Z,1)-1,1) ones(size(Z,1)-1,1) ones(size(Z,1)-1,1) size(Z,2).*ones(size(Z,1)-1,1)];
F_sub=sub2ind(size(Z),I,J);
F=[F;F_sub];
F=fliplr(F);

end

GIBBON www.gibboncode.org

Kevin Mattheus Moerman, [email protected]

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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/.