DEMO_febio_0044_mammography_01.m

Below is a demonstration for:

Building geometry for a slab with hexahedral elements, and a triangulated sphere.
Defining the boundary conditions
Coding the febio structure
Running the model
Importing and visualizing the displacement results

Keywords
Plot settings
Control parameters
Create hemi-sphere
Change shape of hemi-sphere to create basic breast model
Rotate model
Get interior points
Visualizing mesh using meshView, see also anim8
Split element sets
Building plate models
Joining 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
Import rigid body reaction forces

Keywords

febio_spec version 4.0
febio, FEBio
indentation
contact, sliding, sticky, friction
rigid body constraints
tetrahedral elements, tet4
triangular elements, tri3
static, solid
hyperelastic, Ogden
displacement logfile
stress logfile

clear; close all; clc;

Plot settings

fontSize=15;
faceAlpha1=0.8;
faceAlpha2=0.3;
markerSize1=40;
markerSize2=25;
lineWidth=3;

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

%Breast geometry
r_breastNominal=40; %Breast radius
sy=1; %Y-direction radial scaling to force deviation from hemi-sphere
r1=r_breastNominal/2.5; %Radius alveola
r2=r_breastNominal/7; %Radius nipple
rm=mean([r1 r2]); %radius between outer alveola radius and outer nipple radius
w=(r1-r2)/20; %Height of alveola
h=r2; %Height of alveola
gravityShiftPercentage=0.5; %Percentage shift due to gravity
dx=r_breastNominal.*gravityShiftPercentage; %X-shift due to gravity

%Loading
quasiCompressionLevel=0.3; %Sets displacement as function of nominal breast radius
loadAngle=(0/180)*pi;
distanceChestPlate=12; %r_breastNominal/7

%Meshing parameters
nRefine=3; %Number of refine steps for hemi-sphere
volumeFactor=3;
plateHeight=r_breastNominal;

%Material parameter set
k_factor=50; %Bulk modulus factor

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

c1_2=c1_1*5; %Shear-modulus-like parameter
m1_2=m1_1; %Material parameter setting degree of non-linearity
k_2=c1_2*k_factor; %Bulk modulus

% FEA control settings
numTimeSteps=10; %Number of time steps desired
max_refs=50; %Max reforms
max_ups=0; %Set to zero to use full-Newton iterations
opt_iter=15; %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-18;

%Set run mode
runMode='external'; %'internal'

%Contact parameters
contactPenalty=15;
laugon=0;
minaug=1;
maxaug=10;
fric_coeff=0.1;

Create hemi-sphere

[F,V,C_hemiSphereLabel]=hemiSphereMesh(nRefine,r_breastNominal,1); %Construct hemi-shere mesh

Change shape of hemi-sphere to create basic breast model

%scale Y direction to deviate from hemi-sphere.
V(:,2)=V(:,2)*sy;

indExclude=unique(F(C_hemiSphereLabel==2,:));
logicExclude=false(size(V,1),1);
logicExclude(indExclude)=1;

dt=sqrt(sum(V(:,[1 2]).^2,2));
logicHigh1=dt<r1 & ~logicExclude;
logicHigh2=dt<r2 & ~logicExclude;

C_skin=double(logicHigh1);
C_skin(logicHigh2)=2;

t=linspace(0,2*pi,500);
x=rm*sin(t);
y=rm*cos(t);
vc=[x(:) y(:)];

[d]=minDist(V(C_skin==1,[1 2]),vc);
dtt=d.^3;
dtt=dtt-min(dtt);
dtt=dtt./max(dtt);
dtt=abs(dtt-1)*w;
V(C_skin==1,3)=V(C_skin==1,3)+dtt;

f=V(:,3); %Z-coordinates [min(Z) max(Z)]
f=f-min(f(:)); %Z-coordinates [0 max(Z)-min(Z)]
f=f./max(f(:)); % [0 1] %Normalized Z-coordinate parameter
V(:,1)=V(:,1)+dx.*f;

dtt=dt(C_skin==2).^3;
dtt=dtt-min(dtt);
dtt=dtt./max(dtt);
dtt=abs(dtt-1)*h;
V(C_skin==2,3)=V(C_skin==2,3)+dtt;

cFigure; hold on;
gpatch(F,V,'w','none',1);
axisGeom;
camlight headlight;
gdrawnow;

breastVolume=triSurfVolume(F,V)';

Rotate model

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

[Fs,Vs]=geoSphere(2,r_breastNominal/6);
Vs(:,1)=Vs(:,1)-r_breastNominal/2;
Vs(:,2)=Vs(:,2)-r_breastNominal/4;
Vs(:,3)=Vs(:,3)-r_breastNominal/2;

% cFigure; hold on;
% gpatch(F,V,C_skin,'none',1);
% axisGeom;
% camlight headlight;
% icolorbar;
% gdrawnow;

C=[C_hemiSphereLabel;(max(C_hemiSphereLabel(:))+1)*ones(size(Fs,1),1)];
F=[F;Fs+size(V,1)];
V=[V;Vs];

cFigure; hold on;
gpatch(F,V,C,'none',1);
axisGeom;
camlight headlight;
icolorbar;
gdrawnow;

Get interior points

[V_in1]=getInnerPoint({F,Fs},{V,Vs});
[V_in2]=getInnerPoint(Fs,Vs);

V_regions=[V_in1; V_in2];

cFigure; hold on;
gpatch(F,V,C,'none',0.5);
% gpatch(Fs,Vs,'kw','none',1);
plotV(V_regions,'k.','markerSize',50);
axisGeom;
camlight headlight;
gdrawnow;

faceBoundaryMarker=C;

[regionA]=tetVolMeanEst(F,V); %Volume for regular tets
inputStruct.stringOpt='-pq1.2AaY';
inputStruct.Faces=fliplr(F);
inputStruct.Nodes=V;
inputStruct.holePoints=[];
inputStruct.faceBoundaryMarker=faceBoundaryMarker; %Face boundary markers
inputStruct.regionPoints=V_regions; %region points
inputStruct.regionA=regionA*ones(size(V_regions,1),1)*volumeFactor;
inputStruct.minRegionMarker=2; %Minimum region marker

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

% Access model element and patch data
Fb=meshOutput.facesBoundary;
Cb=meshOutput.boundaryMarker;
V=meshOutput.nodes;
CE=meshOutput.elementMaterialID;
E=meshOutput.elements;

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- TETGEN Tetrahedral meshing --- 20-Apr-2023 18:08:19
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Writing SMESH file --- 20-Apr-2023 18:08:19
----> Adding node field
----> Adding facet field
----> Adding holes specification
----> Adding region specification
--- Done --- 20-Apr-2023 18:08:19
--- Running TetGen to mesh input boundary--- 20-Apr-2023 18:08:19
Opening /mnt/data/MATLAB/GIBBON/data/temp/temp.smesh.
Delaunizing vertices...
Delaunay seconds:  0.025983
Creating surface mesh ...
Surface mesh seconds:  0.003053
Recovering boundaries...
Boundary recovery seconds:  0.00582
Removing exterior tetrahedra ...
Spreading region attributes.
Exterior tets removal seconds:  0.001592
Recovering Delaunayness...
Delaunay recovery seconds:  0.007475
Refining mesh...
  2728 insertions, added 2696 points, 81280 tetrahedra in queue.
Refinement seconds:  0.078644
Smoothing vertices...
Mesh smoothing seconds:  0.129975
Improving mesh...
Mesh improvement seconds:  0.00538

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:  0.064965
Total running seconds:  0.323075

Statistics:

  Input points: 2047
  Input facets: 4086
  Input segments: 6129
  Input holes: 0
  Input regions: 2

  Mesh points: 5320
  Mesh tetrahedra: 26755
  Mesh faces: 55393
  Mesh faces on exterior boundary: 3766
  Mesh faces on input facets: 4086
  Mesh edges on input segments: 6129
  Steiner points inside domain: 3273

--- Done --- 20-Apr-2023 18:08:19
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Importing TetGen files --- 20-Apr-2023 18:08:19
--- Done --- 20-Apr-2023 18:08:19

Q=euler2DCM([loadAngle 0 0]);
V=V*Q;

cFigure; hold on;
hp=gpatch(Fb,V,Cb,'none',0.5);
axisGeom;
camlight headlight;
icolorbar;
gdrawnow;

Visualizing mesh using `meshView`, see also `anim8`

meshView(meshOutput);

Split element sets

E1=E(meshOutput.elementMaterialID==-2,:);
E2=E(meshOutput.elementMaterialID==-3,:);

Building plate models

%Basic side curve of plate
Vt=[0 0 0; 0 0 plateHeight; 1.5*r_breastNominal 0 plateHeight; 1.5*r_breastNominal 0 0; ];

%Fillet side curve of plate
rFillet=6; %Fillet radius
np=25; %Number of points used to construct each fillet edge
closedLoopOption=0; %Use 1 if curve represents a closed loop but containes unique points
[Vc]=filletCurve(Vt,rFillet,np,closedLoopOption);

pointSpacingPlate=mean(patchEdgeLengths(Fb,V))/2; % Get point spacing from mesh

%Extrude to form plate
cPar.pointSpacing=pointSpacingPlate;
cPar.depth=3*(r_breastNominal*sy);
cPar.patchType='quad';
cPar.dir=0;
cPar.closeLoopOpt=0;
[Fp1,Vp1]=polyExtrude(Vc,cPar);
Np1=mean(patchNormal(Fp1,Vp1),1);
if Np1(3)<0
    Fp1=fliplr(Fp1);
end

Vp1(:,3)=Vp1(:,3)-max(Vp1(:,3))+min(V(:,3));
Vp1(:,1)=Vp1(:,1)-max(Vp1(:,1))-distanceChestPlate;

%Copy to create second plate
Fp2=fliplr(Fp1);
Vp2=Vp1;
Vp2(:,3)=-Vp2(:,3);
logicNodesSetLocation=V(:,1)<=-distanceChestPlate;

max_z=max(V(logicNodesSetLocation,3));
Vp2(:,3)=Vp2(:,3)-min(Vp2(:,3))+max_z;

plateSeparation=max_z-min(V(:,3));

cFigure; hold on;
gpatch(Fb,V,'gw','k',1);
gpatch(Fp1,Vp1,'kw','bw',1);
%patchNormPlot(Fp1,Vp1);
gpatch(Fp2,Vp2,'kw','rw',1);
%patchNormPlot(Fp2,Vp2);
axisGeom;
camlight headlight;
gdrawnow;

Joining node sets

Fp1=Fp1+size(V,1); %Fixed element indices
Fp2=Fp2+size(V,1)+size(Vp1,1); %Fixed element indices
V=[V;Vp1;Vp2;]; %Combined node sets

V=V*Q';

plateDisplacement=(plateSeparation-(r_breastNominal.*(1-quasiCompressionLevel)))/2;

loadDir=[0 0 1]*Q';
plateDisplacement_XYZ=plateDisplacement.*loadDir;

V2_plate1=V;
V2_plate2=V;
V2_plate1(:,3)=V2_plate1(:,3)+plateDisplacement;
V2_plate2(:,3)=V2_plate2(:,3)-plateDisplacement;

Plotting joined geometry

cFigure;
title('Joined node sets','FontSize',fontSize);
xlabel('X','FontSize',fontSize); ylabel('Y','FontSize',fontSize); zlabel('Z','FontSize',fontSize);
hold on;
gpatch(Fb,V,'gw','k',1);
gpatch(Fp1,V,'kw','bw',1);
gpatch(Fp2,V,'kw','rw',1);

gpatch(Fp1,V2_plate1,'kw','bw',0.5);
gpatch(Fp2,V2_plate2,'kw','rw',0.5);

axisGeom;
camlight headlight;
gdrawnow;

Define contact surfaces

% The rigid primary surface of the sphere
F_contact_secondary1=Fp1;
F_contact_secondary2=Fp2;

% The deformable secondary surface of the slab
logicContactSurf1=Cb==1;
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_secondary1,V,'gw','k',1);
patchNormPlot(F_contact_secondary1,V);
hl(2)=gpatch(F_contact_secondary2,V,'rw','k',1);
patchNormPlot(F_contact_secondary2,V);
hl(3)=gpatch(F_contact_primary,V,'bw','k',1);
patchNormPlot(F_contact_primary,V);

legend(hl,{'Secondary 1','Secondary 2','Primary'});

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

Define boundary conditions

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

Visualize BC's

hf=cFigure;
title('Boundary conditions model','FontSize',fontSize);
xlabel('X','FontSize',fontSize); ylabel('Y','FontSize',fontSize); zlabel('Z','FontSize',fontSize);
hold on;

gpatch(Fb,V,'kw','none',faceAlpha2);
hl2(1)=plotV(V(bcSupportList,:),'k.','MarkerSize',markerSize1);
legend(hl2,{'BC support'});

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

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='4.0';

%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.qn_method.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';
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;

materialName2='Material2';
febio_spec.Material.material{2}.ATTR.name=materialName2;
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;

materialName3='Material3';
febio_spec.Material.material{3}.ATTR.name=materialName3;
febio_spec.Material.material{3}.ATTR.type='rigid body';
febio_spec.Material.material{3}.ATTR.id=3;
febio_spec.Material.material{3}.density=1;
febio_spec.Material.material{3}.center_of_mass=mean(Vp1,1);

materialName4='Material4';
febio_spec.Material.material{4}.ATTR.name=materialName4;
febio_spec.Material.material{4}.ATTR.type='rigid body';
febio_spec.Material.material{4}.ATTR.id=4;
febio_spec.Material.material{4}.density=1;
febio_spec.Material.material{4}.center_of_mass=mean(Vp2,1);

% 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_breast_normal';
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(E1,1))'; %Element id's
febio_spec.Mesh.Elements{1}.elem.VAL=E1; %The element matrix

partName2='Part2_tumor';
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(E1,1)+(1:1:size(E2,1))'; %Element id's
febio_spec.Mesh.Elements{2}.elem.VAL=E2; %The element matrix

partName3='Part3_plate1';
febio_spec.Mesh.Elements{3}.ATTR.name=partName3; %Name of this part
febio_spec.Mesh.Elements{3}.ATTR.type='quad4'; %Element type
febio_spec.Mesh.Elements{3}.elem.ATTR.id=size(E1,1)+size(E2,1)+(1:1:size(Fp1,1))'; %Element id's
febio_spec.Mesh.Elements{3}.elem.VAL=Fp1; %The element matrix

partName4='Part4_plate2';
febio_spec.Mesh.Elements{4}.ATTR.name=partName4; %Name of this part
febio_spec.Mesh.Elements{4}.ATTR.type='quad4'; %Element type
febio_spec.Mesh.Elements{4}.elem.ATTR.id=size(E1,1)+size(E2,1)+size(Fp1,1)+(1:1:size(Fp2,1))'; %Element id's
febio_spec.Mesh.Elements{4}.elem.VAL=Fp2; %The element matrix

%MeshDomains section
febio_spec.MeshDomains.SolidDomain{1}.ATTR.name=partName1;
febio_spec.MeshDomains.SolidDomain{1}.ATTR.mat=materialName1;

febio_spec.MeshDomains.SolidDomain{2}.ATTR.name=partName2;
febio_spec.MeshDomains.SolidDomain{2}.ATTR.mat=materialName2;

febio_spec.MeshDomains.ShellDomain{1}.ATTR.name=partName3;
febio_spec.MeshDomains.ShellDomain{1}.ATTR.mat=materialName3;

febio_spec.MeshDomains.ShellDomain{2}.ATTR.name=partName4;
febio_spec.MeshDomains.ShellDomain{2}.ATTR.mat=materialName4;

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

% -> Surfaces
surfaceName1='contactSurface1';
febio_spec.Mesh.Surface{1}.ATTR.name=surfaceName1;
febio_spec.Mesh.Surface{1}.quad4.ATTR.id=(1:1:size(F_contact_secondary1,1))';
febio_spec.Mesh.Surface{1}.quad4.VAL=F_contact_secondary1;

surfaceName2='contactSurface2';
febio_spec.Mesh.Surface{2}.ATTR.name=surfaceName2;
febio_spec.Mesh.Surface{2}.quad4.ATTR.id=(1:1:size(F_contact_secondary2,1))';
febio_spec.Mesh.Surface{2}.quad4.VAL=F_contact_secondary2;

surfaceName3='contactSurface3';
febio_spec.Mesh.Surface{3}.ATTR.name=surfaceName3;
febio_spec.Mesh.Surface{3}.tri3.ATTR.id=(1:1:size(F_contact_primary,1))';
febio_spec.Mesh.Surface{3}.tri3.VAL=F_contact_primary;

% -> Surface pairs
febio_spec.Mesh.SurfacePair{1}.ATTR.name='Contact1';
febio_spec.Mesh.SurfacePair{1}.primary=surfaceName3;
febio_spec.Mesh.SurfacePair{1}.secondary=surfaceName1;

febio_spec.Mesh.SurfacePair{2}.ATTR.name='Contact2';
febio_spec.Mesh.SurfacePair{2}.primary=surfaceName3;
febio_spec.Mesh.SurfacePair{2}.secondary=surfaceName2;

%Boundary condition section
% -> Fix boundary conditions
febio_spec.Boundary.bc{1}.ATTR.name='zero_displacement_xyz';
febio_spec.Boundary.bc{1}.ATTR.type='zero displacement';
febio_spec.Boundary.bc{1}.ATTR.node_set=nodeSetName1;
febio_spec.Boundary.bc{1}.x_dof=1;
febio_spec.Boundary.bc{1}.y_dof=1;
febio_spec.Boundary.bc{1}.z_dof=1;

%Rigid section
% ->Rigid body fix boundary conditions
febio_spec.Rigid.rigid_bc{1}.ATTR.name='RigidFixRot_RB3';
febio_spec.Rigid.rigid_bc{1}.ATTR.type='rigid_fixed';
febio_spec.Rigid.rigid_bc{1}.rb=3;
febio_spec.Rigid.rigid_bc{1}.Ru_dof=1;
febio_spec.Rigid.rigid_bc{1}.Rv_dof=1;
febio_spec.Rigid.rigid_bc{1}.Rw_dof=1;

febio_spec.Rigid.rigid_bc{2}.ATTR.name='RigidFixRot_RB4';
febio_spec.Rigid.rigid_bc{2}.ATTR.type='rigid_fixed';
febio_spec.Rigid.rigid_bc{2}.rb=4;
febio_spec.Rigid.rigid_bc{2}.Ru_dof=1;
febio_spec.Rigid.rigid_bc{2}.Rv_dof=1;
febio_spec.Rigid.rigid_bc{2}.Rw_dof=1;

% ->Rigid body prescribe boundary conditions
febio_spec.Rigid.rigid_bc{3}.ATTR.name='RigidPrescribe_X_RB3';
febio_spec.Rigid.rigid_bc{3}.ATTR.type='rigid_displacement';
febio_spec.Rigid.rigid_bc{3}.rb=3;
febio_spec.Rigid.rigid_bc{3}.dof='x';
febio_spec.Rigid.rigid_bc{3}.value.ATTR.lc=1;
febio_spec.Rigid.rigid_bc{3}.value.VAL=plateDisplacement_XYZ(1);
febio_spec.Rigid.rigid_bc{3}.relative=0;

febio_spec.Rigid.rigid_bc{4}.ATTR.name='RigidPrescribe_Y_RB3';
febio_spec.Rigid.rigid_bc{4}.ATTR.type='rigid_displacement';
febio_spec.Rigid.rigid_bc{4}.rb=3;
febio_spec.Rigid.rigid_bc{4}.dof='y';
febio_spec.Rigid.rigid_bc{4}.value.ATTR.lc=1;
febio_spec.Rigid.rigid_bc{4}.value.VAL=plateDisplacement_XYZ(2);
febio_spec.Rigid.rigid_bc{4}.relative=0;

febio_spec.Rigid.rigid_bc{5}.ATTR.name='RigidPrescribe_Z_RB3';
febio_spec.Rigid.rigid_bc{5}.ATTR.type='rigid_displacement';
febio_spec.Rigid.rigid_bc{5}.rb=3;
febio_spec.Rigid.rigid_bc{5}.dof='z';
febio_spec.Rigid.rigid_bc{5}.value.ATTR.lc=1;
febio_spec.Rigid.rigid_bc{5}.value.VAL=plateDisplacement_XYZ(3);
febio_spec.Rigid.rigid_bc{5}.relative=0;


febio_spec.Rigid.rigid_bc{6}.ATTR.name='RigidPrescribe_X_RB4';
febio_spec.Rigid.rigid_bc{6}.ATTR.type='rigid_displacement';
febio_spec.Rigid.rigid_bc{6}.rb=4;
febio_spec.Rigid.rigid_bc{6}.dof='x';
febio_spec.Rigid.rigid_bc{6}.value.ATTR.lc=1;
febio_spec.Rigid.rigid_bc{6}.value.VAL=-plateDisplacement_XYZ(1);
febio_spec.Rigid.rigid_bc{6}.relative=0;

febio_spec.Rigid.rigid_bc{7}.ATTR.name='RigidPrescribe_Y_RB4';
febio_spec.Rigid.rigid_bc{7}.ATTR.type='rigid_displacement';
febio_spec.Rigid.rigid_bc{7}.rb=4;
febio_spec.Rigid.rigid_bc{7}.dof='y';
febio_spec.Rigid.rigid_bc{7}.value.ATTR.lc=1;
febio_spec.Rigid.rigid_bc{7}.value.VAL=-plateDisplacement_XYZ(2);
febio_spec.Rigid.rigid_bc{7}.relative=0;

febio_spec.Rigid.rigid_bc{8}.ATTR.name='RigidPrescribe_Z_RB4';
febio_spec.Rigid.rigid_bc{8}.ATTR.type='rigid_displacement';
febio_spec.Rigid.rigid_bc{8}.rb=4;
febio_spec.Rigid.rigid_bc{8}.dof='z';
febio_spec.Rigid.rigid_bc{8}.value.ATTR.lc=1;
febio_spec.Rigid.rigid_bc{8}.value.VAL=-plateDisplacement_XYZ(3);
febio_spec.Rigid.rigid_bc{8}.relative=0;


%Contact section
for q=1:1:2
    febio_spec.Contact.contact{q}.ATTR.type='sliding-elastic';
    febio_spec.Contact.contact{q}.ATTR.surface_pair=febio_spec.Mesh.SurfacePair{q}.ATTR.name;
    febio_spec.Contact.contact{q}.two_pass=0;
    febio_spec.Contact.contact{q}.laugon=laugon;
    febio_spec.Contact.contact{q}.tolerance=0.2;
    febio_spec.Contact.contact{q}.gaptol=0;
    febio_spec.Contact.contact{q}.minaug=minaug;
    febio_spec.Contact.contact{q}.maxaug=maxaug;
    febio_spec.Contact.contact{q}.search_tol=0.01;
    febio_spec.Contact.contact{q}.search_radius=0.1*sqrt(sum((max(V,[],1)-min(V,[],1)).^2,2));
    febio_spec.Contact.contact{q}.symmetric_stiffness=0;
    febio_spec.Contact.contact{q}.auto_penalty=1;
    febio_spec.Contact.contact{q}.penalty=contactPenalty;
    febio_spec.Contact.contact{q}.fric_coeff=fric_coeff;
end

%LoadData section
% -> load_controller
febio_spec.LoadData.load_controller{1}.ATTR.name='LC_1';
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}.extend='CONSTANT';
febio_spec.LoadData.load_controller{1}.points.pt.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.rigid_body_data{1}.ATTR.file=febioLogFileName_force;
febio_spec.Output.logfile.rigid_body_data{1}.ATTR.data='Fx;Fy;Fz';
febio_spec.Output.logfile.rigid_body_data{1}.ATTR.delim=',';
febio_spec.Output.logfile.rigid_body_data{1}.VAL=[3 4];

% Plotfile section
febio_spec.Output.plotfile.compression=0;

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    <-------- 20-Apr-2023 18:08:32
FEBio path: /home/kevin/FEBioStudio2/bin/febio4
# Attempt removal of existing log files                20-Apr-2023 18:08:32
 * Removal succesful                                   20-Apr-2023 18:08:32
# Attempt removal of existing .xplt files              20-Apr-2023 18:08:32
 * Removal succesful                                   20-Apr-2023 18:08:32
# Starting FEBio...                                    20-Apr-2023 18:08:32
  Max. total analysis time is: Inf s
 * Waiting for log file creation                       20-Apr-2023 18:08:33
   Max. wait time: 30 s
 * Log file found.                                     20-Apr-2023 18:08:33
# Parsing log file...                                  20-Apr-2023 18:08:33
    number of iterations   : 9                         20-Apr-2023 18:08:37
    number of reformations : 9                         20-Apr-2023 18:08:37
------- converged at time : 0.1                        20-Apr-2023 18:08:37
    number of iterations   : 8                         20-Apr-2023 18:08:40
    number of reformations : 8                         20-Apr-2023 18:08:40
------- converged at time : 0.2                        20-Apr-2023 18:08:40
    number of iterations   : 9                         20-Apr-2023 18:08:44
    number of reformations : 9                         20-Apr-2023 18:08:44
------- converged at time : 0.3                        20-Apr-2023 18:08:44
    number of iterations   : 10                        20-Apr-2023 18:08:48
    number of reformations : 10                        20-Apr-2023 18:08:48
------- converged at time : 0.4                        20-Apr-2023 18:08:48
    number of iterations   : 8                         20-Apr-2023 18:08:51
    number of reformations : 8                         20-Apr-2023 18:08:51
------- converged at time : 0.5                        20-Apr-2023 18:08:51
    number of iterations   : 8                         20-Apr-2023 18:08:55
    number of reformations : 8                         20-Apr-2023 18:08:55
------- converged at time : 0.6                        20-Apr-2023 18:08:55
    number of iterations   : 9                         20-Apr-2023 18:08:59
    number of reformations : 9                         20-Apr-2023 18:08:59
------- converged at time : 0.7                        20-Apr-2023 18:08:59
    number of iterations   : 8                         20-Apr-2023 18:09:03
    number of reformations : 8                         20-Apr-2023 18:09:03
------- converged at time : 0.8                        20-Apr-2023 18:09:03
    number of iterations   : 9                         20-Apr-2023 18:09:07
    number of reformations : 9                         20-Apr-2023 18:09:07
------- converged at time : 0.9                        20-Apr-2023 18:09:07
    number of iterations   : 10                        20-Apr-2023 18:09:20
    number of reformations : 10                        20-Apr-2023 18:09:20
------- converged at time : 0.966667                   20-Apr-2023 18:09:20
    number of iterations   : 12                        20-Apr-2023 18:09:26
    number of reformations : 12                        20-Apr-2023 18:09:26
------- converged at time : 1                          20-Apr-2023 18:09:26
 Elapsed time : 0:00:53                                20-Apr-2023 18:09:26
 N O R M A L   T E R M I N A T I O N
# Done                                                 20-Apr-2023 18:09:26
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Import FEBio results

if runFlag==1 %i.e. a succesful run

    % Importing nodal displacements from a log file
    dataStructDisp=importFEBio_logfile(fullfile(savePath,febioLogFileName_disp),0,1);

    %Access data
    N_disp_mat=dataStructDisp.data; %Displacement
    timeVec=dataStructDisp.time; %Time

    %Create deformed coordinate set
    V_DEF=N_disp_mat+repmat(V,[1 1 size(N_disp_mat,3)]);

Import rigid body reaction forces

    dataStructForce=importFEBio_logfile(fullfile(savePath,febioLogFileName_force),0,1);
    forcePlate1=squeeze(dataStructForce.data(1,:,:))';
    forcePlate2=squeeze(dataStructForce.data(2,:,:))';

Visualize reaction forces

    cFigure;
    subplot(1,2,1); hold on;
    title('Bottom plate');
    xlabel('Time [s]'); ylabel('Force [N]');
    hp1=plot(timeVec,forcePlate1(:,1),'r.-','LineWidth',lineWidth,'MarkerSize',markerSize2);
    hp2=plot(timeVec,forcePlate1(:,2),'g.-','LineWidth',lineWidth,'MarkerSize',markerSize2);
    hp3=plot(timeVec,forcePlate1(:,3),'b.-','LineWidth',lineWidth,'MarkerSize',markerSize2);
    hl=legend([hp1 hp2 hp3],{'F_x','F_y','F_z'},'Location','NorthWest');
    axis tight; axis square; grid on; box on;
    set(gca,'FontSize',fontSize);

    subplot(1,2,2); hold on;
    title('Top plate');
    xlabel('Time [s]'); ylabel('Force [N]');
    hp1=plot(timeVec,forcePlate2(:,1),'r.-','LineWidth',lineWidth,'MarkerSize',markerSize2);
    hp2=plot(timeVec,forcePlate2(:,2),'g.-','LineWidth',lineWidth,'MarkerSize',markerSize2);
    hp3=plot(timeVec,forcePlate2(:,3),'b.-','LineWidth',lineWidth,'MarkerSize',markerSize2);
    hl=legend([hp1 hp2 hp3],{'F_x','F_y','F_z'},'Location','NorthWest');
    axis tight; axis square; grid on; box on;
    set(gca,'FontSize',fontSize);
    drawnow;

Visualize Z-force of top plate

    forceTop_Z=forcePlate2(:,3);

    cFigure; hold on;
    title('Top plate');
    xlabel('Time [s]'); ylabel('Force [N]');
    hp1=plot(timeVec,forceTop_Z,'b.-','LineWidth',lineWidth,'MarkerSize',markerSize2);
    hl=legend([hp1],{'F_z'},'Location','NorthWest');
    axis tight; axis square; grid on; box on;
    set(gca,'FontSize',fontSize);
    drawnow;

Plotting the simulated results using anim8 to visualize and animate deformations

    DN_magnitude=sqrt(sum(N_disp_mat(:,:,end).^2,2)); %Current displacement magnitude

    % Create basic view and store graphics handle to initiate animation
    hf=cFigure; %Open figure
    gtitle([febioFebFileNamePart,': Press play to animate']);
    hp1=gpatch(Fb,V_DEF(:,:,end),DN_magnitude,'none',0.7); %Add graphics object to animate
    hp1.FaceColor='Interp';
    hp2=gpatch(Fp1,V_DEF(:,:,end),'w','none',0.5); %Add graphics object to animate
    hp3=gpatch(Fp2,V_DEF(:,:,end),'w','none',0.5); %Add graphics object to animate

    axisGeom(gca,fontSize);
    colormap(gjet(250)); colorbar;
    caxis([0 max(DN_magnitude)]);
    axis(axisLim(V_DEF)); %Set axis limits statically
    camlight headlight;

    % Set up animation features
    animStruct.Time=timeVec; %The time vector
    for qt=1:1:size(N_disp_mat,3) %Loop over time increments
        DN_magnitude=sqrt(sum(N_disp_mat(:,:,qt).^2,2)); %Current displacement magnitude

        %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(:,:,qt),DN_magnitude,V_DEF(:,:,qt),V_DEF(:,:,qt)}; %Property values for to set in order to animate
    end
    anim8(hf,animStruct); %Initiate animation feature
    gdrawnow;

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.

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/.