Contents

clear; close all; clc;

Plot settings

markerSize=10;
markerSize2=10;
fontSize=15;
faceAlpha1=0.3;
faceAlpha2=0.5;
cMap=gjet(4);

Control parameters

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

% Defining file names
febioFebFileNamePart='tempModel';
febioFebFileName=fullfile(savePath,[febioFebFileNamePart,'.feb']); %FEB file name
febioLogFileName=[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_sed=[febioFebFileNamePart,'_stress_out.txt']; %Log file name for exporting strain energy density

tireWidth = 120;
tireRadius = 150;
tireThickness = 8;
threadHeight = 8;
tireBulge=tireWidth/8;
pointSpacing = 8;
tireCircumference = 2*pi.*tireRadius;

numFeatures = 20;
groveWidth = 8;

distKeep=75; %Distance after which model is cropped, empty = full model
displacementVert=0.8*tireThickness;
displacementHor=-tireRadius/20;
contactInitialOffset=0.1;

%Material parameter set
c1=1e-3; %Shear-modulus-like parameter
m1=2; %Material parameter setting degree of non-linearity
k_factor=100; %Bulk modulus factor
k=c1*k_factor; %Bulk modulus

% FEA control settings
numTimeSteps=20; %Number of time steps desired
max_refs=40; %Max reforms
max_ups=0; %Set to zero to use full-Newton iterations
opt_iter=25; %Optimum number of iterations
max_retries=5; %Maximum number of retires
dtmin=(1/numTimeSteps)/100; %Minimum time step size
dtmax=1/numTimeSteps; %Maximum time step size
runMode='external';%'internal';
min_residual=1e-20;

%Contact parameters
contactPenalty=5;
laugon=0;
minaug=1;
maxaug=10;
fric_coeff=0.5;
tireHalfWidth=tireWidth/2;
featureHeight = (tireCircumference-(numFeatures*groveWidth))./numFeatures;
featureWidth = tireHalfWidth-2*groveWidth;

% Coordinates of 1x1 square
v=[-1 -1 0;...
    1 -1 0;...
    1  1 0;...
    -1  1 0]/2;

% Deformation gradient tensor for shear
f=eye(3,3);
f(1,2)=1;

%Create boundary coordinates
V1=v; %Copy square
V1(:,1)=V1(:,1).*tireCircumference+tireCircumference/2; %Stretch to create circumference
V1(:,2)=V1(:,2).*tireHalfWidth+tireHalfWidth/2; %Stretch to get desired width
V1=evenlySpaceCurve(V1,pointSpacing,'linear',1,1:1:size(v,1)); %Evenly sample
V1=(f*V1')'; %Shear

%Create thread feature
Vf=v; %Copy square
Vf(:,1)=Vf(:,1).*featureHeight; %Stretch to create circumference
Vf(:,2)=Vf(:,2).*(featureWidth+groveWidth/2)+tireHalfWidth/2-groveWidth/4; %Stretch to get desired width
Vf=evenlySpaceCurve(Vf,pointSpacing,'linear',1,1:1:size(v,1)); %Evenly sample
Vf(:,1)=Vf(:,1)+featureHeight/2+groveWidth/2;

VF=cell(1,numFeatures);
for q=1:1:numFeatures
    Vff=Vf;
    Vff(:,1)=Vf(:,1)+(q-1).*(featureHeight+groveWidth); %Shift
    VF{q}=(f*Vff')'; %Shear and store
end
%Defining 4 regions
regionSpec{1}={V1(:,[1 2])};
for q=1:1:numFeatures
    regionSpec{1}{q+1}=VF{q}(:,[1 2]);
end

for q=1:1:numFeatures
    regionSpec{q+1}{1}=VF{q}(:,[1 2]);
end

[Ft,Vt,Ct]=multiRegionTriMesh2D(regionSpec,pointSpacing,0,0);
Vt(:,3)=0;

Fb=fliplr(Ft);
Vb=Vt;
Vb(:,2)=-Vb(:,2);

Cb=Ct;
Cb(Cb>1)=Cb(Cb>1)-1+max(Ct);

[F,V,C]=joinElementSets({Ft,Fb},{Vt,Vb},{Ct,Cb});
[F,V]=mergeVertices(F,V);
cFigure; hold on;
plotV(V1,'r.-','MarkerSize',markerSize);
plotV(VF,'b.-','MarkerSize',markerSize);
gpatch(F,V,C);

axisGeom(gca,fontSize); view(2);
colormap spectral; icolorbar;
gdrawnow;
cMax=max(C);
numVert=size(V,1);
F2=F(C>1,:);
C2=C(C>1,:)+cMax;
Eb1=patchBoundary(F2);

Eb2=Eb1+numVert;
F=[F(C==1,:);F2+numVert];
V=[V;V];
C=[C(C==1,:);C2+max(C(:))];
if tireBulge>eps(0)
    w=tireWidth;
    h=tireBulge;
    r=h/2+(w^2/(8*h));
    a=atan((w/2)./(r-h));

    TH = (V(:,2)./tireHalfWidth)*a;
    R = r.*ones(size(V,1),1);
    R(numVert+1:end)=R(numVert+1:end)+threadHeight;
    Z = V(:,1);
    [V(:,1),V(:,2),V(:,3)] = pol2cart(TH,R,Z);
    V=V(:,[3 2 1]);

    V(:,3)=V(:,3)-r+h;
else
    V(numVert+1:end,3)=V(numVert+1:end,3)+threadHeight;
end
cFigure; hold on;
plotV(V1,'r.-','MarkerSize',markerSize);
plotV(VF,'b.-','MarkerSize',markerSize);
gpatch(F,V,C);

axisGeom(gca,fontSize); view(2);
colormap spectral; icolorbar;
gdrawnow;
TH = V(:,1)./tireRadius;
R = tireRadius+V(:,3);

Z = V(:,2);
[V(:,1),V(:,2),V(:,3)] = pol2cart(TH,R,Z);
V=V(:,[1 3 2]); F=fliplr(F);

[Eb1,V1]=patchCleanUnused(Eb1,V);
[Eb2,V2]=patchCleanUnused(Eb2,V);

[F,V,~,indFix]=mergeVertices(F,V);

numSteps=ceil(threadHeight./pointSpacing)+1;


%Create quadrilateral faces
X=linspacen(V1(:,1),V2(:,1),numSteps);
Y=linspacen(V1(:,2),V2(:,2),numSteps);
Z=linspacen(V1(:,3),V2(:,3),numSteps);

Vn=[X(:) Y(:) Z(:)]; %Vertex set
Fn=repmat([fliplr(Eb1) Eb2],numSteps-1,1);
q=repmat(0:(numSteps-2),size(Eb1,1),1);
q=q(:);
Q=[q q q+1 q+1]*size(V1,1);
Fn=Fn+Q;

[Fn,Vn]=quad2tri(Fn,Vn,'a');
[F,V]=patchCleanUnused(F,V);
C(C>1)=2; %Switch to use 2 for all thread profile parts
[F_out,V_out,C_out]=joinElementSets({F,Fn},{V,Vn},{C,max(C(:))+1*ones(size(Fn,1),1)});
[F_out,V_out]=patchCleanUnused(F_out,V_out);
[F_out,V_out]=mergeVertices(F_out,V_out);
Eb_out=patchBoundary(F_out);
cFigure; hold on;
gpatch(F_out,V_out,C_out);
% patchNormPlot(Fq,Vq);
axisGeom(gca,fontSize); camlight headlight;
colormap spectral; icolorbar;
gdrawnow;

Create inner cylinder

inputStructCyl.cylRadius=tireRadius-tireThickness;
inputStructCyl.numRadial=ceil((2*pi*inputStructCyl.cylRadius)/pointSpacing);
inputStructCyl.cylHeight=tireWidth;
numheight=ceil(tireWidth./pointSpacing);
numheight=numheight+iseven(numheight); %Force uneven
inputStructCyl.numHeight=numheight;
inputStructCyl.meshType='tri';

Derive patch data for a cylinder

[F_in,V_in]=patchcylinder(inputStructCyl);
V_in=V_in(:,[1 3 2]);
Eb_in=patchBoundary(F_in);
C_in=(max(C_out)+1)*ones(size(F_in,1),1);
inputStructGroup.outputType='label';
G_out=tesgroup(Eb_out,inputStructGroup);
G_in=tesgroup(Eb_in,inputStructGroup);

yMean_out=nan(2,1);
yMean_in=nan(2,1);
for q=1:1:2
    ind_out=Eb_out(G_out==q,:);
    yMean_out(q)=mean(V_out(ind_out(:),2));

    ind_in=Eb_in(G_in==q,:);
    yMean_in(q)=mean(V_in(ind_in(:),2));
end

[~,ind1_out]=min(yMean_out);
[~,ind2_out]=max(yMean_out);
indCurve1_out=edgeListToCurve(Eb_out(G_out==ind1_out,:));
indCurve1_out=indCurve1_out(1:end-1);
indCurve2_out=edgeListToCurve(Eb_out(G_out==ind2_out,:));
indCurve2_out=indCurve2_out(1:end-1);

[~,ind1_in]=min(yMean_in);
[~,ind2_in]=max(yMean_in);
indCurve1_in=edgeListToCurve(Eb_in(G_in==ind1_in,:));
indCurve1_in=indCurve1_in(1:end-1);
indCurve2_in=edgeListToCurve(Eb_in(G_in==ind2_in,:));
indCurve2_in=indCurve2_in(1:end-1);

[Fs1,Vs1]=regionTriMesh2D({V_out(indCurve1_out,[1 3]),V_in(indCurve1_in,[1 3])},pointSpacing,0);
Vs1(:,3)=-tireWidth/2;
Vs1=Vs1(:,[1 3 2]);
Cs1=(max(C_in)+1)*ones(size(Fs1,1),1);

[Fs2,Vs2]=regionTriMesh2D({V_out(indCurve2_out,[1 3]),V_in(indCurve2_in,[1 3])},pointSpacing,0);
Vs2(:,3)=tireWidth/2;
Vs2=Vs2(:,[1 3 2]);
Fs2=fliplr(Fs2);
Cs2=(max(Cs1)+1)*ones(size(Fs2,1),1);
[FT,VT,CT]=joinElementSets({F_out,F_in,Fs1,Fs2},{V_out,V_in,Vs1,Vs2},{C_out,C_in,Cs1,Cs2});
[FT,VT]=patchCleanUnused(FT,VT);
[FT,VT]=mergeVertices(FT,VT);
cFigure; hold on;

gpatch(FT,VT,CT,'none');
patchNormPlot(FT,VT);

axisGeom(gca,fontSize); camlight headlight;
colormap spectral; icolorbar;
gdrawnow;
V_regions=getInnerPoint(FT,VT); %Define region points
V_holes=[]; %Define hole points
[regionTetVolumes]=tetVolMeanEst(FT,VT); %Volume estimate for regular tets
stringOpt='-pq1.2AaY'; %Options for tetgen

Mesh using TetGen

%Create tetgen input structure
inputStruct.stringOpt=stringOpt; %Tetgen options
inputStruct.Faces=FT; %Boundary faces
inputStruct.Nodes=VT; %Nodes of boundary
inputStruct.faceBoundaryMarker=CT;
inputStruct.regionPoints=V_regions; %Interior points for regions
inputStruct.holePoints=V_holes; %Interior points for holes
inputStruct.regionA=regionTetVolumes; %Desired tetrahedral volume for each region

% Mesh model using tetrahedral elements using tetGen
[meshOutput]=runTetGen(inputStruct); %Run tetGen
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- TETGEN Tetrahedral meshing --- 21-Nov-2022 16:54:26
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Writing SMESH file --- 21-Nov-2022 16:54:26
----> Adding node field
----> Adding facet field
----> Adding holes specification
----> Adding region specification
--- Done --- 21-Nov-2022 16:54:26
--- Running TetGen to mesh input boundary--- 21-Nov-2022 16:54:26
Opening /mnt/data/MATLAB/GIBBON/data/temp/temp.smesh.
Delaunizing vertices...
Delaunay seconds:  0.217484
Creating surface mesh ...
Surface mesh seconds:  0.007777
Recovering boundaries...
Boundary recovery seconds:  0.022495
Removing exterior tetrahedra ...
Spreading region attributes.
Exterior tets removal seconds:  0.006895
Recovering Delaunayness...
Delaunay recovery seconds:  0.013661
Refining mesh...
  6409 insertions, added 4064 points, 103362 tetrahedra in queue.
  2134 insertions, added 615 points, 88720 tetrahedra in queue.
  2844 insertions, added 386 points, 9791 tetrahedra in queue.
  3791 insertions, added 274 points, 5489 tetrahedra in queue.
Refinement seconds:  0.249418
Smoothing vertices...
Mesh smoothing seconds:  0.391893
Improving mesh...
Mesh improvement seconds:  0.011337

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:  0.113535
Total running seconds:  1.03492

Statistics:

  Input points: 4808
  Input facets: 9616
  Input segments: 14424
  Input holes: 0
  Input regions: 1

  Mesh points: 10225
  Mesh tetrahedra: 47884
  Mesh faces: 100576
  Mesh faces on exterior boundary: 9616
  Mesh faces on input facets: 9616
  Mesh edges on input segments: 14424
  Steiner points inside domain: 5417

--- Done --- 21-Nov-2022 16:54:27
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Importing TetGen files --- 21-Nov-2022 16:54:27
--- Done --- 21-Nov-2022 16:54:27

Access mesh output structure

E=meshOutput.elements; %The elements
V=meshOutput.nodes; %The vertices or nodes
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(V_regions,'r.','MarkerSize',markerSize);
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;
if ~isempty(distKeep)
    Fb_full=Fb;
    V_full=V;
    [Fb_full,V_full]=patchCleanUnused(Fb_full,V_full);

    VE=patchCentre(E,V);
    logicKeepElements = VE(:,3) <= (min(VE(:,3))+distKeep);
    E=E(logicKeepElements,:);
    indKeepNodes=unique(E);
    logicKeep_Fb=all(ismember(Fb,indKeepNodes),2);
    Fb=Fb(logicKeep_Fb,:);
    Cb=Cb(logicKeep_Fb,:);

    logicKeep_F=all(ismember(F,indKeepNodes),2);
    F=F(logicKeep_F,:);

    [E,V,indFix]=patchCleanUnused(E,V);
    Fb=indFix(Fb);
    F=indFix(F);
    meshOutput.nodes=V;
    meshOutput.facesBoundary=Fb;
    meshOutput.boundaryMarker=Cb;
    meshOutput.faces=F;
    meshOutput.elements=E;
    meshOutput.elementMaterialID=ones(size(E,1),1);
else
    Fb_full=Fb;
    V_full=V;
end
hf=cFigure;
subplot(1,2,1); hold on;
title('Input boundaries','FontSize',fontSize);
hp(1)=gpatch(Fb,V,Cb,'k',faceAlpha1);
hp(2)=plotV(V_regions,'r.','MarkerSize',markerSize);
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;
plateDim=[2*tireRadius tireWidth];
plateEl=ceil(plateDim./pointSpacing);
[Eg,Vg]=quadPlate(plateDim,plateEl);
Vg(:,3)=Vg(:,3)+min(VT(:,3))-contactInitialOffset;
center_of_mass=mean(Vg,1);

Joining node sets

Eg=Eg+size(V,1); %Fixed element indices
V=[V;Vg;]; %Combined node sets
cFigure; hold on;
hp(1)=gpatch(Fb,V,Cb,'k',faceAlpha1);
hp(2)=gpatch(Eg,V,'kw','k',faceAlpha1);
% legend(hp,{'Input mesh','Interior point(s)'},'Location','NorthWestOutside');
axisGeom(gca,fontSize); camlight headlight;
colormap(cMap); icolorbar;
gdrawnow;

Define contact surfaces

% The rigid master surface of the sphere
F_contact_secondary=Eg;

% The deformable slave surface of the slab
logicContactSurf1=Cb==2;
F_contact_primary=fliplr(Fb(logicContactSurf1,:));

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

gpatch(Fb,V,'kw','none',faceAlpha2);
hl(1)=gpatch(F_contact_secondary,V,'g','k',1);
patchNormPlot(F_contact_secondary,V);
hl(2)=gpatch(F_contact_primary,V,'b','k',1);
patchNormPlot(F_contact_primary,V);

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

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

Define boundary conditions

%Supported nodes
bcSupportList=unique(Fb(Cb==4,:));

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,'w','none',faceAlpha2);

hl2(1)=gpatch(Eg,V,'gw','k',1);
hl2(2)=plotV(V(bcSupportList,:),'k.','MarkerSize',markerSize);

legend(hl2,{'Rigid body plate','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';

%Create control structure for use by all steps
febio_spec.Control.analysis='STATIC';
stepStruct.Control.time_steps=numTimeSteps;
stepStruct.Control.step_size=1/numTimeSteps;
stepStruct.Control.solver.max_refs=max_refs;
stepStruct.Control.solver.max_ups=max_ups;
stepStruct.Control.solver.symmetric_stiffness=0;
febio_spec.Control.solver.min_residual=min_residual;
stepStruct.Control.time_stepper.dtmin=dtmin;
stepStruct.Control.time_stepper.dtmax=dtmax;
stepStruct.Control.time_stepper.max_retries=max_retries;
stepStruct.Control.time_stepper.opt_iter=opt_iter;

%Add template based default settings to proposed control section
[stepStruct.Control]=structComplete(stepStruct.Control,febio_spec.Control,1); %Complement provided with default if missing

%Remove control field (part of template) since step specific control sections are used
febio_spec=rmfield(febio_spec,'Control');

febio_spec.Step.step{1}.Control=stepStruct.Control;
febio_spec.Step.step{1}.ATTR.id=1;
febio_spec.Step.step{2}.Control=stepStruct.Control;
febio_spec.Step.step{2}.ATTR.id=2;

%Material section
materialName1='Material1';
febio_spec.Material.material{1}.ATTR.name=materialName1;
febio_spec.Material.material{1}.ATTR.type='Ogden';
febio_spec.Material.material{1}.ATTR.id=1;
febio_spec.Material.material{1}.c1=c1;
febio_spec.Material.material{1}.m1=m1;
febio_spec.Material.material{1}.c2=c1;
febio_spec.Material.material{1}.m2=-m1;
febio_spec.Material.material{1}.k=k;

materialName2='Material2';
febio_spec.Material.material{2}.ATTR.name=materialName2;
febio_spec.Material.material{2}.ATTR.type='rigid body';
febio_spec.Material.material{2}.ATTR.id=2;
febio_spec.Material.material{2}.density=1;
febio_spec.Material.material{2}.center_of_mass=center_of_mass;

%Mesh section
% -> Nodes
febio_spec.Mesh.Nodes{1}.ATTR.name='nodeSet_all'; %The node set name
febio_spec.Mesh.Nodes{1}.node.ATTR.id=(1:size(V,1))'; %The node id's
febio_spec.Mesh.Nodes{1}.node.VAL=V; %The nodel coordinates

% -> Elements
partName1='Part1';
febio_spec.Mesh.Elements{1}.ATTR.name=partName1; %Name of this part
febio_spec.Mesh.Elements{1}.ATTR.type='tet4'; %Element type
febio_spec.Mesh.Elements{1}.elem.ATTR.id=(1:1:size(E,1))'; %Element id's
febio_spec.Mesh.Elements{1}.elem.VAL=E; %The element matrix

partName2='Part2';
febio_spec.Mesh.Elements{2}.ATTR.name=partName2; %Name of this part
febio_spec.Mesh.Elements{2}.ATTR.type='quad4'; %Element type
febio_spec.Mesh.Elements{2}.elem.ATTR.id=size(E,1)+(1:1:size(Eg,1))'; %Element id's
febio_spec.Mesh.Elements{2}.elem.VAL=Eg; %The element matrix

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

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

febio_spec.MeshDomains.ShellDomain.ATTR.name=partName2;
febio_spec.MeshDomains.ShellDomain.ATTR.mat=materialName2;

% -> Surfaces
surfaceName1='contactSurface1';
febio_spec.Mesh.Surface{1}.ATTR.name=surfaceName1;
febio_spec.Mesh.Surface{1}.quad4.ATTR.id=(1:1:size(F_contact_secondary,1))';
febio_spec.Mesh.Surface{1}.quad4.VAL=F_contact_secondary;

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

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

%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';

%Rigid section
% -> Prescribed rigid body boundary conditions
febio_spec.Step.step{1}.Rigid.rigid_constraint{1}.ATTR.name='RigidFix_1';
febio_spec.Step.step{1}.Rigid.rigid_constraint{1}.ATTR.type='fix';
febio_spec.Step.step{1}.Rigid.rigid_constraint{1}.rb=2;
febio_spec.Step.step{1}.Rigid.rigid_constraint{1}.dofs='Rx,Ry';

febio_spec.Step.step{1}.Rigid.rigid_constraint{2}.ATTR.name='RigidPrescribe';
febio_spec.Step.step{1}.Rigid.rigid_constraint{2}.ATTR.type='prescribe';
febio_spec.Step.step{1}.Rigid.rigid_constraint{2}.rb=2;
febio_spec.Step.step{1}.Rigid.rigid_constraint{2}.dof='Rz';
febio_spec.Step.step{1}.Rigid.rigid_constraint{2}.value.ATTR.lc=1;
febio_spec.Step.step{1}.Rigid.rigid_constraint{2}.value.VAL=(displacementVert+contactInitialOffset);
febio_spec.Step.step{1}.Rigid.rigid_constraint{2}.relative=0;

febio_spec.Step.step{2}.Rigid.rigid_constraint{1}.ATTR.name='RigidFix_1';
febio_spec.Step.step{2}.Rigid.rigid_constraint{1}.ATTR.type='fix';
febio_spec.Step.step{2}.Rigid.rigid_constraint{1}.rb=2;
febio_spec.Step.step{2}.Rigid.rigid_constraint{1}.dofs='Ry,Rz,Ru,Rv,Rw';

febio_spec.Step.step{2}.Rigid.rigid_constraint{2}.ATTR.name='RigidPrescribe';
febio_spec.Step.step{2}.Rigid.rigid_constraint{2}.ATTR.type='prescribe';
febio_spec.Step.step{2}.Rigid.rigid_constraint{2}.rb=2;
febio_spec.Step.step{2}.Rigid.rigid_constraint{2}.dof='Rx';
febio_spec.Step.step{2}.Rigid.rigid_constraint{2}.value.ATTR.lc=2;
febio_spec.Step.step{2}.Rigid.rigid_constraint{2}.value.VAL=displacementHor;
% febio_spec.Step.step{2}.Rigid.rigid_constraint{2}.relative=1;

%Contact section
febio_spec.Contact.contact{1}.ATTR.type='sliding-elastic';
febio_spec.Contact.contact{1}.ATTR.surface_pair=febio_spec.Mesh.SurfacePair{1}.ATTR.name;
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; 2 1];

febio_spec.LoadData.load_controller{2}.ATTR.id=2;
febio_spec.LoadData.load_controller{2}.ATTR.type='loadcurve';
febio_spec.LoadData.load_controller{2}.interpolate='LINEAR';
febio_spec.LoadData.load_controller{2}.points.point.VAL=[0 0; 1 0; 2 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_sed;
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,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.runMode=runMode;

[runFlag]=runMonitorFEBio(febioAnalysis);%START FEBio NOW!!!!!!!!
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-------->    RUNNING/MONITORING FEBIO JOB    <-------- 21-Nov-2022 16:54:40
FEBio path: /home/kevin/FEBioStudio/bin/febio3
# Attempt removal of existing log files                21-Nov-2022 16:54:40
 * Removal succesful                                   21-Nov-2022 16:54:40
# Attempt removal of existing .xplt files              21-Nov-2022 16:54:40
 * Removal succesful                                   21-Nov-2022 16:54:40
# Starting FEBio...                                    21-Nov-2022 16:54:40
  Max. total analysis time is: Inf s
 * Waiting for log file creation                       21-Nov-2022 16:54:40
   Max. wait time: 30 s
 * Log file found.                                     21-Nov-2022 16:54:40
# Parsing log file...                                  21-Nov-2022 16:54:40
    number of iterations   : 4                         21-Nov-2022 16:54:41
    number of reformations : 4                         21-Nov-2022 16:54:41
------- converged at time : 0.05                       21-Nov-2022 16:54:41
    number of iterations   : 4                         21-Nov-2022 16:54:41
    number of reformations : 4                         21-Nov-2022 16:54:41
------- converged at time : 0.1                        21-Nov-2022 16:54:41
    number of iterations   : 5                         21-Nov-2022 16:54:42
    number of reformations : 5                         21-Nov-2022 16:54:42
------- converged at time : 0.15                       21-Nov-2022 16:54:42
    number of iterations   : 4                         21-Nov-2022 16:54:42
    number of reformations : 4                         21-Nov-2022 16:54:42
------- converged at time : 0.2                        21-Nov-2022 16:54:42
    number of iterations   : 4                         21-Nov-2022 16:54:43
    number of reformations : 4                         21-Nov-2022 16:54:43
------- converged at time : 0.25                       21-Nov-2022 16:54:43
    number of iterations   : 4                         21-Nov-2022 16:54:43
    number of reformations : 4                         21-Nov-2022 16:54:43
------- converged at time : 0.3                        21-Nov-2022 16:54:43
    number of iterations   : 4                         21-Nov-2022 16:54:44
    number of reformations : 4                         21-Nov-2022 16:54:44
------- converged at time : 0.35                       21-Nov-2022 16:54:44
    number of iterations   : 5                         21-Nov-2022 16:54:44
    number of reformations : 5                         21-Nov-2022 16:54:44
------- converged at time : 0.4                        21-Nov-2022 16:54:44
    number of iterations   : 4                         21-Nov-2022 16:54:45
    number of reformations : 4                         21-Nov-2022 16:54:45
------- converged at time : 0.45                       21-Nov-2022 16:54:45
    number of iterations   : 5                         21-Nov-2022 16:54:46
    number of reformations : 5                         21-Nov-2022 16:54:46
------- converged at time : 0.5                        21-Nov-2022 16:54:46
    number of iterations   : 4                         21-Nov-2022 16:54:46
    number of reformations : 4                         21-Nov-2022 16:54:46
------- converged at time : 0.55                       21-Nov-2022 16:54:46
    number of iterations   : 4                         21-Nov-2022 16:54:47
    number of reformations : 4                         21-Nov-2022 16:54:47
------- converged at time : 0.6                        21-Nov-2022 16:54:47
    number of iterations   : 4                         21-Nov-2022 16:54:48
    number of reformations : 4                         21-Nov-2022 16:54:48
------- converged at time : 0.65                       21-Nov-2022 16:54:48
    number of iterations   : 4                         21-Nov-2022 16:54:48
    number of reformations : 4                         21-Nov-2022 16:54:48
------- converged at time : 0.7                        21-Nov-2022 16:54:48
    number of iterations   : 4                         21-Nov-2022 16:54:49
    number of reformations : 4                         21-Nov-2022 16:54:49
------- converged at time : 0.75                       21-Nov-2022 16:54:49
    number of iterations   : 4                         21-Nov-2022 16:54:49
    number of reformations : 4                         21-Nov-2022 16:54:49
------- converged at time : 0.8                        21-Nov-2022 16:54:49
    number of iterations   : 4                         21-Nov-2022 16:54:50
    number of reformations : 4                         21-Nov-2022 16:54:50
------- converged at time : 0.85                       21-Nov-2022 16:54:50
    number of iterations   : 4                         21-Nov-2022 16:54:50
    number of reformations : 4                         21-Nov-2022 16:54:50
------- converged at time : 0.9                        21-Nov-2022 16:54:50
    number of iterations   : 4                         21-Nov-2022 16:54:51
    number of reformations : 4                         21-Nov-2022 16:54:51
------- converged at time : 0.95                       21-Nov-2022 16:54:51
    number of iterations   : 5                         21-Nov-2022 16:54:51
    number of reformations : 5                         21-Nov-2022 16:54:51
------- converged at time : 1                          21-Nov-2022 16:54:51
    number of iterations   : 5                         21-Nov-2022 16:54:52
    number of reformations : 5                         21-Nov-2022 16:54:52
------- converged at time : 1.05                       21-Nov-2022 16:54:52
    number of iterations   : 5                         21-Nov-2022 16:54:54
    number of reformations : 5                         21-Nov-2022 16:54:54
------- converged at time : 1.1                        21-Nov-2022 16:54:54
    number of iterations   : 4                         21-Nov-2022 16:54:54
    number of reformations : 4                         21-Nov-2022 16:54:54
------- converged at time : 1.15                       21-Nov-2022 16:54:54
    number of iterations   : 4                         21-Nov-2022 16:54:55
    number of reformations : 4                         21-Nov-2022 16:54:55
------- converged at time : 1.2                        21-Nov-2022 16:54:55
    number of iterations   : 5                         21-Nov-2022 16:54:55
    number of reformations : 5                         21-Nov-2022 16:54:55
------- converged at time : 1.25                       21-Nov-2022 16:54:55
    number of iterations   : 5                         21-Nov-2022 16:54:56
    number of reformations : 5                         21-Nov-2022 16:54:56
------- converged at time : 1.3                        21-Nov-2022 16:54:56
    number of iterations   : 5                         21-Nov-2022 16:54:57
    number of reformations : 5                         21-Nov-2022 16:54:57
------- converged at time : 1.35                       21-Nov-2022 16:54:57
    number of iterations   : 5                         21-Nov-2022 16:54:57
    number of reformations : 5                         21-Nov-2022 16:54:57
------- converged at time : 1.4                        21-Nov-2022 16:54:57
    number of iterations   : 5                         21-Nov-2022 16:54:58
    number of reformations : 5                         21-Nov-2022 16:54:58
------- converged at time : 1.45                       21-Nov-2022 16:54:58
    number of iterations   : 5                         21-Nov-2022 16:54:59
    number of reformations : 5                         21-Nov-2022 16:54:59
------- converged at time : 1.5                        21-Nov-2022 16:54:59
    number of iterations   : 5                         21-Nov-2022 16:55:00
    number of reformations : 5                         21-Nov-2022 16:55:00
------- converged at time : 1.55                       21-Nov-2022 16:55:00
    number of iterations   : 5                         21-Nov-2022 16:55:00
    number of reformations : 5                         21-Nov-2022 16:55:00
------- converged at time : 1.6                        21-Nov-2022 16:55:00
    number of iterations   : 5                         21-Nov-2022 16:55:01
    number of reformations : 5                         21-Nov-2022 16:55:01
------- converged at time : 1.65                       21-Nov-2022 16:55:01
    number of iterations   : 5                         21-Nov-2022 16:55:02
    number of reformations : 5                         21-Nov-2022 16:55:02
------- converged at time : 1.7                        21-Nov-2022 16:55:02
    number of iterations   : 5                         21-Nov-2022 16:55:02
    number of reformations : 5                         21-Nov-2022 16:55:02
------- converged at time : 1.75                       21-Nov-2022 16:55:02
    number of iterations   : 6                         21-Nov-2022 16:55:03
    number of reformations : 6                         21-Nov-2022 16:55:03
------- converged at time : 1.8                        21-Nov-2022 16:55:03
    number of iterations   : 6                         21-Nov-2022 16:55:04
    number of reformations : 6                         21-Nov-2022 16:55:04
------- converged at time : 1.85                       21-Nov-2022 16:55:04
    number of iterations   : 6                         21-Nov-2022 16:55:04
    number of reformations : 6                         21-Nov-2022 16:55:04
------- converged at time : 1.9                        21-Nov-2022 16:55:04
    number of iterations   : 5                         21-Nov-2022 16:55:05
    number of reformations : 5                         21-Nov-2022 16:55:05
------- converged at time : 1.95                       21-Nov-2022 16:55:05
    number of iterations   : 6                         21-Nov-2022 16:55:06
    number of reformations : 6                         21-Nov-2022 16:55:06
------- converged at time : 2                          21-Nov-2022 16:55:06
 Elapsed time : 0:00:26                                21-Nov-2022 16:55:06
 N O R M A L   T E R M I N A T I O N
# Done                                                 21-Nov-2022 16:55:06
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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_sed),1,1);

    %Access data
    E_sed_mat=dataStruct.data;
    E_sed_mat(isnan(E_sed_mat))=0;

Plotting the simulated results using anim8 to visualize and animate deformations

    [CV]=faceToVertexMeasure(E,V,E_sed_mat(:,:,end));

    % Create basic view and store graphics handle to initiate animation
    hf=cFigure; %Open figure
    gtitle([febioFebFileNamePart,': Press play to animate']);
    title('Strain energy density','Interpreter','Latex')
    gpatch(Fb_full,V_full,'w','none',0.25);
    hp=gpatch(Fb,V_DEF(:,:,end),CV,'none',1); %Add graphics object to animate
%     hp.Marker='.';
%     hp.MarkerSize=markerSize2;
    hp.FaceColor='interp';

    hp2=gpatch(Eg,V_DEF(:,:,end),'w','none',0.5); %Add graphics object to animate
    Ebb=patchBoundaryLabelEdges(Fb,V,Cb);
    hp3=gpatch(Ebb,V_DEF(:,:,end),'none','k',1,3);
    hp4=gpatch(patchBoundary(Eg),V_DEF(:,:,end),'none','kw',1,3);

    axisGeom(gca,fontSize);
    colormap(spectral(250)); colorbar;
    caxis([0 0.25*max(E_sed_mat(:))]);
    axis(axisLim(V_DEF,V_full)); %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_sed_mat(:,:,qt));

        %Set entries in animation structure
        animStruct.Handles{qt}=[hp hp hp2 hp3 hp4]; %Handles of objects to animate
        animStruct.Props{qt}={'Vertices','CData','Vertices','Vertices','Vertices'}; %Properties of objects to animate
        animStruct.Set{qt}={V_DEF(:,:,qt),CV,V_DEF(:,:,qt),V_DEF(:,:,qt),V_DEF(:,:,qt)}; %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) 2006-2022 Kevin Mattheus Moerman and the GIBBON contributors

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/.