DEMO_febio_0058_face_tube_loading

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');

% 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

volumeFactor=2; %Volume factor used in tetgen, larger means larger internal elements
layerThickness=5;
numSplit=1;
stripWidth=6;
stripRadius=4;
pointSpacingMask=stripWidth/2;
nRim=ceil(stripRadius/pointSpacingMask)+1;
if nRim<6
    nRim=6;
end
discRadius1=30;
discRadius2=discRadius1+5;
discNodeOffset=15;

%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*100; %Bulk modulus

% FEA control settings
numTimeSteps=10; %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=0.1;
displacementMagnitude_z=-2-initialOffset; %Displacement applied

%Contact parameters
contactPenalty=0.1;
laugon=0;
minaug=1;
maxaug=10;
fric_coeff=0.5;

optStructRayTrace.eps      = 1e-6;
optStructRayTrace.triangle = 'two sided';
optStructRayTrace.ray      = 'ray';
optStructRayTrace.border   = 'normal';

nz=[0 0 1];

Load face mesh

% [Fs,Vs]=graphicsModels(10);

[stlStruct] = import_STL(fullfile(defaultFolder,'data','STL','nefertiti_fine.stl'));
Fs=stlStruct.solidFaces{1}; %Faces
Vs=stlStruct.solidVertices{1}; %Vertices
[Fs,Vs]=mergeVertices(Fs,Vs); % Merging nodes
pointSpacing=mean(patchEdgeLengths(Fs,Vs));

cFigure;  hold on;
gpatch(Fs,Vs,'gw','k');
% gpatch(Eb,Vs,'bw','b',1,2);
% plotV(Vs(logicForce,:),'r.','MarkerSize',25);
axisGeom;
camlight headlight;
drawnow;
Vs2=Vs;
Eb=patchBoundary(Fs,Vs);
cParSmooth.n=15;
cParSmooth.Method='LAP';
cParSmooth.RigidConstraints=unique(Eb(:));
Vs2=patchSmooth(Fs,Vs2,[],cParSmooth);

[~,~,N]=patchNormal(Fs,Vs2);
Vs2=Vs2-N*layerThickness;
cParSmooth.n=5;
cParSmooth.Method='HC';
Vs2=patchSmooth(Fs,Vs2,[],cParSmooth);

V=[Vs;Vs2];
E_face=[Fs+size(Vs,1) Fs];

[E_face,V]=subPenta(E_face,V,numSplit,3);

[F]=element2patch(E_face,V,'penta6');
Fp_tri=F{1};
Fp2=Fp_tri(1:size(Fs,1),:);
Fp1=Fp_tri(end-size(Fs,1)+1:end,:);
cFigure;
gpatch(Fs,Vs,'bw','none',1);
gpatch(F,V,'w','k',0.5);
axisGeom;
camlight headlight;
drawnow;
[~,ind1_nose]=max(V(:,3));

indNoseTip=ind1_nose;

V1=V(indNoseTip,:);
V2=V1;
V2(:,2)=V2(:,2)+45;
V3=V1;
V3(:,2)=min(V(:,2));
V4=V1;
V4(:,1)=min(V(:,1))+4;
V5=V1;
V5(:,1)=max(V(:,1)-4);
V_markers=[V1;V2;V3;V4;V5];
V_markers(:,3)=max(V(:,3));

V_rim=[(0.5*V1+0.5*V2);...
    (0.2*V1+0.8*V4);...
    (0.3*V1+0.7*V4)+[0 -35 0];...
    (0.2*V1+0.8*V3)+[-25 0 0];...
    (0.1*V1+0.9*V3);...
    ];

Vcc=flipud(V_rim(2:end-1,:));
Vcc(:,1)=-Vcc(:,1);
V_rim=[V_rim;Vcc];


Vcs=evenlySampleCurve(V_rim,1000,'pchip',1);
np=ceil(max(pathLength(Vcs))/pointSpacingMask);
Vcs=evenlySampleCurve(V_rim,np,'pchip',1);

t=linspace(0.5*pi,2.5*pi,np+1)';
t=t(1:end-1);
Vcd1=discRadius1*[cos(t) sin(t)];
Vcd1(:,2)=Vcd1(:,2)+(0.5*V1(:,2)+0.5*V3(:,2));
Vcd1(:,3)=max(V(:,3))+discNodeOffset;

Vcd2=discRadius2*[cos(t) sin(t)];
Vcd2(:,2)=Vcd2(:,2)+(0.5*V1(:,2)+0.5*V3(:,2));
Vcd2(:,3)=max(V(:,3))+discNodeOffset;
cFigure; hold on;
gpatch(Fp1,V,'w','none',1);
plotV(V_markers,'r.','MarkerSize',50);
text(V_markers(:,1)+4,V_markers(:,2),V_markers(:,3),{'1','2','3','4','5'},'FontSize',25);
plotV(V_rim,'k.','MarkerSize',35,'LineWidth',3);
plotV(Vcs,'k-','LineWidth',2);
% plotV(Vcd1,'b-','LineWidth',2);
axisGeom;
camlight headlight;
view(2);
drawnow;
m=mean(Vcs,1);
r=mean(sqrt(sum((Vcs-m(ones(np,1),:)).^2,2)));
f=(r+stripWidth/2)/r;
Vcs1=(Vcs-m(ones(np,1),:)).*f+m(ones(np,1),:);
f=(r-stripWidth/2)/r;
Vcs2=(Vcs-m(ones(np,1),:)).*f+m(ones(np,1),:);

% Ecs=[(1:size(Vcs,1))' [2:size(Vcs,1) 1]'];
% ne=vecnormalize(edgeVec(Ecs,Vcs));
% ne2=cross(ne,nz(ones(size(ne,1),1),:));
%
% Vcs1=Vcs+ne2*stripWidth/2;
% Vcs2=Vcs-ne2*stripWidth/2;

[Fm,Vm]=regionTriMesh2D({Vcs1(:,[1 2]),Vcs2(:,[1 2])},pointSpacingMask,0,0);
Vm(:,3)=max(V(:,3));
N=patchNormal(Fm,Vm);
n=mean(N,1);
if dot(n,nz)>0
    Fm=fliplr(Fm);
end
cFigure; hold on;
gpatch(Fp1,V,'w','none',1);
gpatch(Fm,Vm,'gw','g',1,2);
plotV(V_markers,'r.','MarkerSize',50);
text(V_markers(:,1)+4,V_markers(:,2),V_markers(:,3),{'1','2','3','4','5'},'FontSize',25);
plotV(V_rim,'k.','MarkerSize',35,'LineWidth',3);
% plotV(Vcs,'k-','LineWidth',2);
plotV(Vcs1,'g-','LineWidth',2);
plotV(Vcs2,'g-','LineWidth',2);
% quiverVec(Vcs,ne2,stripWidth/2,'g');
% quiverVec(Vcs,-ne2,stripWidth/2,'g');
axisGeom;
camlight headlight;
view(2);
drawnow;
[~,~,Nm]=patchNormal(Fm,Vm);

[Vm2]=traceToSurf(Vm,Nm,Fp1,V,optStructRayTrace);
cFigure; hold on;
gpatch(Fp1,V,'w','none',0.9);
gpatch(Fm,Vm,'gw','g',0,1);
gpatch(Fm,Vm2,'none','k',0,2);

axisGeom;
camlight headlight;
view(2);
drawnow;
[~,~,Nm2]=patchNormal(Fm,Vm2);
Em2=patchBoundary(Fm,Vm2);

groupOpt.outputType='label';
G=tesgroup(Em2,groupOpt);

[Fr1,Vr1]=roundMesh(Em2(G==1,:),Vm2,Nm2,nRim,stripRadius);
[Fr2,Vr2]=roundMesh(Em2(G==2,:),Vm2,Nm2,nRim,stripRadius);
indEnd=size(Vr1)-np+1:1:size(Vr1);
[Fr1,Vr1]=quad2tri(Fr1,Vr1,'a');
[Fr2,Vr2]=quad2tri(Fr2,Vr2,'a');

pointSpacing=0.5; %Desired point spacing
resampleCurveOpt=1;
interpMethod='linear'; %or 'natural'
[Ft,Vt]=regionTriMesh3D({Vr1(indEnd,:),Vr2(indEnd,:)},pointSpacingMask,0,'linear');
cFigure; hold on;
gpatch(Fp1,V,'w','none',0.5);

gpatch(Fm,Vm2,'gw','none',1,2);
gpatch(Fr1,Vr1,'gw','none',1,2);
gpatch(Fr2,Vr2,'gw','none',1,2);

axisGeom;
camlight headlight;
view(2);
drawnow;
cFigure; hold on;
gpatch(Fp1,V,'w','none',0.9);
gpatch(Fm,Vm2,'none','k',0,2);
gpatch(Ft,Vt,'gw','g',1,1);
gpatch(Fr1,Vr1,'rw','r',1,2);
gpatch(Fr2,Vr2,'bw','b',1,2);
plotV(Vr1(indEnd,:),'y-','LineWidth',3);
plotV(Vr2(indEnd,:),'y-','LineWidth',3);
axisGeom;
camlight headlight;
view(2);
drawnow;
cPar.closeLoopOpt=1;
cPar.patchType='quad';
V_loft1=Vr2(indEnd,:);
V_loft2=Vcd1;
V_loft3=Vr1(indEnd,:);
V_loft4=Vcd2;
[~,indMax]=max(V_loft1(:,2));
if indMax>1
    V_loft1=V_loft1([indMax:size(V_loft1,1) 1:indMax-1],:);
end
[~,indMax]=max(V_loft1(:,1));
if indMax<np/2
    V_loft1=flipud(V_loft1);
end

[~,indMax]=max(V_loft3(:,2));
if indMax>1
    V_loft3=V_loft3([indMax:size(V_loft3,1) 1:indMax-1],:);
end
[~,indMax]=max(V_loft3(:,1));
if indMax<np/2
    V_loft3=flipud(V_loft3);
end

[Fd1,Vd1]=polyLoftLinear(V_loft1,V_loft2,cPar);
[Fd1,Vd1]=quad2tri(Fd1,Vd1,'a');

[Fd2,Vd2]=polyLoftLinear(V_loft3,V_loft4,cPar);
[Fd2,Vd2]=quad2tri(Fd2,Vd2,'a');

clear cparSmooth;
cparSmooth.Method='HC';
cparSmooth.n=5;
Eb1=patchBoundary(Fd1,Vd1);
cparSmooth.RigidConstraints=Eb1;
Vd1=patchSmooth(Fd1,Vd1,[],cparSmooth);
Eb2=patchBoundary(Fd2,Vd2);
cparSmooth.RigidConstraints=Eb2;
Vd2=patchSmooth(Fd2,Vd2,[],cparSmooth);

[Fdt,Vdt]=regionTriMesh2D({Vcd2(:,[1 2]),Vcd1(:,[1 2])},pointSpacingMask,0,0);
Vdt(:,3)=max(V(:,3))+discNodeOffset;

N=patchNormal(Fdt,Vdt);
n=mean(N,1);
if dot(n,nz)>0
    Fdt=fliplr(Fdt);
end

[Fc,Vc]=regionTriMesh2D({Vcd1(:,[1 2])},pointSpacingMask,0,0);
Vc(:,3)=max(V(:,3))+discNodeOffset;

cFigure; hold on;
gpatch(Fp1,V,'w','none',0.9);
gpatch(Fd1,Vd1,'bw','b',1);
gpatch(Fdt,Vdt,'rw','r',1);
gpatch(Fd2,Vd2,'gw','g',1);
plotV(Vr1(indEnd,:),'r-','LineWidth',3);
plotV(Vr2(indEnd,:),'g-','LineWidth',3);
plotV(Vcd1,'b-','LineWidth',3);

axisGeom;
camlight headlight;
view(2);
drawnow;
[F_rim,V_rim,C_rim]=joinElementSets({Fm,Fr1,Fr2,Ft},{Vm2,Vr1,Vr2,Vt});
[F_rim,V_rim]=mergeVertices(F_rim,V_rim);
[F_mask,V_mask,C_mask]=joinElementSets({Fd1,Fd2,Fdt,Fc},{Vd1,Vd2,Vdt,Vc});
[F_mask,V_mask]=mergeVertices(F_mask,V_mask);
cFigure; hold on;
gpatch(Fp1,V,'w','none',1);
gpatch(F_mask,V_mask,'bw','none',0.8);
gpatch(F_rim,V_rim,'gw','none',1);
axisGeom;
camlight headlight;
view(2);
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(Fp1,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
[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*volumeFactor;

% Mesh model using tetrahedral elements using tetGen
[meshOutput]=runTetGen(inputStruct); %Run tetGen
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- TETGEN Tetrahedral meshing --- 02-Jul-2020 21:04:21
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Writing SMESH file --- 02-Jul-2020 21:04:21
----> Adding node field
----> Adding facet field
----> Adding holes specification
----> Adding region specification
--- Done --- 02-Jul-2020 21:04:21
--- Running TetGen to mesh input boundary--- 02-Jul-2020 21:04:21
Opening /mnt/data/MATLAB/GIBBON/data/temp/temp.smesh.
Delaunizing vertices...
Delaunay seconds:  0.018535
Creating surface mesh ...
Surface mesh seconds:  0.00352
Recovering boundaries...
Boundary recovery seconds:  0.004724
Removing exterior tetrahedra ...
Spreading region attributes.
Exterior tets removal seconds:  0.002664
Recovering Delaunayness...
Delaunay recovery seconds:  0.002536
Refining mesh...
Refinement seconds:  0.033414
Optimizing mesh...
Optimization seconds:  0.001728

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:  0.028718
Total running seconds:  0.096012

Statistics:

  Input points: 1964
  Input facets: 3928
  Input segments: 5892
  Input holes: 0
  Input regions: 1

  Mesh points: 2224
  Mesh tetrahedra: 7355
  Mesh faces: 16674
  Mesh faces on exterior boundary: 3928
  Mesh faces on input facets: 3928
  Mesh edges on input segments: 5892
  Steiner points inside domain: 260

--- Done --- 02-Jul-2020 21:04:21
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Importing TetGen files --- 02-Jul-2020 21:04:21
--- Done --- 02-Jul-2020 21:04:21

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 master surface of the sphere
F_contact_master=fliplr(Fb_rim(Cb_rim~=4,:));

% The deformable slave surface of the slab
Vc_Fp2=patchCentre(Fp1,V);
D=minDist(Vc_Fp2,V_rim);
logicSlave=D<=(10*pointSpacing);
logicSlave=triSurfLogicSharpFix(Fp1,logicSlave,3);
F_contact_slave=Fp1(logicSlave,:);

Visualize contact surfaces

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

gpatch(F,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,'rw','k',1);
patchNormPlot(F_contact_slave,V);

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

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

Define boundary conditions

%Supported nodes
bcSupportList=unique(Fp2);

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

Visualize BC's

hf=cFigure; hold on;
title('Boundary conditions model','FontSize',fontSize);
gpatch(F,V,'kw','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='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';
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}.k=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='penta6'; %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='Face'; %Name of the element set
febio_spec.Geometry.Elements{1}.elem.ATTR.id=(1:1:size(E_face,1))'; %Element id's
febio_spec.Geometry.Elements{1}.elem.VAL=E_face;

febio_spec.Geometry.Elements{2}.ATTR.type='tet4'; %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='Tube'; %Name of the element set
febio_spec.Geometry.Elements{2}.elem.ATTR.id=size(E_face,1)+(1:1:size(E_rim,1))'; %Element id's
febio_spec.Geometry.Elements{2}.elem.VAL=E_rim;

% -> 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}.tri3.ATTR.lid=(1:1:size(F_contact_master,1))';
febio_spec.Geometry.Surface{1}.tri3.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_z;

%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_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!!!!!!!!
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- STARTING FEBIO JOB --- 02-Jul-2020 21:04:31
Waiting for log file...
Proceeding to check log file...02-Jul-2020 21:04:31
------- converged at time : 0.0666667
------- converged at time : 0.10691
------- converged at time : 0.159105
------- converged at time : 0.22086
------- converged at time : 0.290265
------- converged at time : 0.365789
------- converged at time : 0.446208
------- converged at time : 0.530543
------- converged at time : 0.618011
------- converged at time : 0.707985
------- converged at time : 0.799965
------- converged at time : 0.893549
------- converged at time : 0.988416
------- converged at time : 1
--- Done --- 02-Jul-2020 21:06:04

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),'penta6');
    [CV]=faceToVertexMeasure(FE_face,V,C_energy_face);

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(FE_face{1},V_def,CV,'k',1); %Add graphics object to animate
    hp1.FaceColor='Interp';
    hp2=gpatch(Fb_rim,V_def,'k','none',0.3); %Add graphics object to animate
    hp3=gpatch(F_mask,V_mask,'kw','none',0.3);

    axisGeom(gca,fontSize);
    colormap(gjet(250)); colorbar;
    caxis([0 max(C_energy_face{1})/5]);
    axis([min(X_DEF(:)) max(X_DEF(:)) min(Y_DEF(:)) max(Y_DEF(:)) min(Z_DEF(:)) max(Z_DEF(:))]);
    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
        [FE_face,C_energy_face]=element2patch(E_face,E_energy(1:size(E_face,1),:,qt),'penta6');
        [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[P]=traceToSurf(V1,N1,F2,V2,optStructRayTrace)

numPoints=size(V1,1);
P=nan(numPoints,3);
c=1;
% hw=waitbar(c/numPoints,['Ray tracing...',num2str(round(100.*c/numPoints)),'%']);
for q=1:1:numPoints
    v1=V1(q,:);
    n1=N1(q,:);
    [V_intersect,L_intersect,~] = triangleRayIntersection(v1(ones(size(F2,1),1),:),n1(ones(size(F2,1),1),:),V2,F2,optStructRayTrace);
    V_intersect=V_intersect(L_intersect,:);
    if nnz(L_intersect)>0
        d=min(distND(V_intersect,v1),[],2);
        [~,indMin]=min(d);
        P(q,:)=V_intersect(indMin,:);
    end
%     waitbar(c/numPoints,hw,['Ray tracing...',num2str(round(100.*c/numPoints)),'%']);
    c=c+1;
end
% close(hw);
end

function [Fr,Vr]=roundMesh(E,Vm2,Nm2,nc,stripRadius)

indCurve=edgeListToCurve(E);
indCurve=indCurve(1:end-1);
E=[indCurve(1:end)' [indCurve(2:end) indCurve(1)]'];

Ne=vecnormalize(edgeVec(E,Vm2));
Nf=-Nm2(E(:,1),:);
Ne2=vecnormalize(cross(Nf,Ne));

X=repmat(Vm2(E(:,1),1),1,nc);
Y=repmat(Vm2(E(:,1),2),1,nc);
Z=repmat(Vm2(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);

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

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/.

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) 2006-2020 Kevin Mattheus Moerman

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.