DEMO_febio_0056_cylinder_embedded_probe_02

Below is a demonstration for:

Building geometry for a tissue segment with an embedded probe
Defining the boundary conditions
Coding the febio structure
Running the model
Importing and visualizing the displacement results

Keywords
Control parameters
Build probe
Build gel
Cap ends
Merge model components
Mesh solid using tetgen
Joining node sets
Plotting tissue and probe meshes
Define boundary condition node sets
Create contact surfaces
Defining the FEBio input structure
Quick viewing of the FEBio input file structure
Exporting the FEBio input file
Running the FEBio analysis
Import FEBio results

Keywords

febio_spec version 2.5
febio, FEBio
probe
contact, sliding, 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;
faceAlpha=1;
lineWidth1=1.5;
lineWidth2=3;
markerSize1=15;
markerSize2=30;
edgeWidth=2;
edgeColor='k';
faceAlpha1=1;

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
febioLogFileName_strain=[febioFebFileNamePart,'_strain_out.txt']; %Log file name for exporting strain
febioLogFileName_stress=[febioFebFileNamePart,'_stress_out.txt']; %Log file name for exporting strain

%Geometric parameters
probeHeight=60;
probeRadius=3; % The radius of the hemi-spher portion
nRefine=0;  % Number of |subtri| refinements for icosahedron
pointSpacingFactorTissue=2;
dAdd=3*probeRadius;
tissueRadius=probeRadius+dAdd;
tissueHeight=probeHeight+dAdd;
volumeFactor=1;

% Motion timing parameters
motionFrequency=2; %Motion frequency
cycleTime=1./motionFrequency;
numMotionCycles=8; %Number of motion cycles
timeTotal=cycleTime.*numMotionCycles; %Total simulation time
displacementMagnitude=-1; %displacement magnitude
t_load_curve=(0:cycleTime/200:timeTotal)';
a_load_curve=0.5+(0.5*sin((t_load_curve-cycleTime/4)*2*pi.*motionFrequency));
timeSetMustPoints=(0:cycleTime/2:timeTotal)';

%Material parameter set
formulationType=2; %Elastic=1 Visco=2
c1=1e-3; %Shear-modulus-like parameter
m1=2; %Material parameter setting degree of non-linearity
k_factor=1e2; %Bulk modulus factor
k=c1*k_factor; %Bulk modulus
g1=0.8; %Viscoelastic QLV proportional coefficient
t1=1; %Viscoelastic QLV time coefficient
d=1e-9; %Density (not required for static analysis)

% FEA control settings
analysisType='dynamic';
numTimeSteps=numMotionCycles.*15; %Number of time steps desired
max_refs=25; %Max reforms
max_ups=0; %Set to zero to use full-Newton iterations
opt_iter=8; %Optimum number of iterations
max_retries=6; %Maximum number of retires
dtmin=(timeTotal/numTimeSteps)/100; %Minimum time step size
dtmax=timeTotal/numTimeSteps; %Maximum time step size
symmetric_stiffness=0;
min_residual=1e-20;
runMode='external'; %'internal' or 'external';

%Contact parameters
contactPenalty=10; % Start low, study penetration, increase if needed e.g. 0.1->1->10...
laugon=0;
minaug=1;
maxaug=10;
fric_coeff=0.1;
contactType=2; %1=sticky, 2=sliding-elastic

Visualize load curve

cFigure; hold on;
title('Time curve')
xlabel('Time (s)'); ylabel('Displacement (mm)');
for q=1:1:numel(timeSetMustPoints)
    h1=plot(timeSetMustPoints(q*ones(2,1)),[0 displacementMagnitude],'r-','LineWidth',  1);
end
h2=plot(t_load_curve,a_load_curve.*displacementMagnitude,'b.-','MarkerSize',15,'LineWidth',2);
legend([h1 h2],{'Must points','Load curve'},'Location','SouthOutside');
grid on; box on; axis tight;
set(gca,'FontSize',fontSize);
drawnow;

Build probe

probeMeshInputStruct.sphereRadius=probeRadius;% => The radius of the hemi-spher portion
probeMeshInputStruct.nRefine=nRefine;% => Number of |subtri| refinements for icosahedron
probeMeshInputStruct.cylinderHeight=probeHeight-probeRadius;% => height of the cylinder part
probeMeshInputStruct.cylinderStepSize=[];% => Aproximate node spacing for cylinder portion
probeMeshInputStruct.patchType='tri_slash';

[Fp,Vp,Cp]=hemiSphereCylMesh(probeMeshInputStruct);
Fp=fliplr(Fp); %Invert face orientation

Vp(:,3)=Vp(:,3)-max(Vp(:,3));

%Get top curve
Eb=patchBoundary(Fp,Vp);
indProbeTop=edgeListToCurve(Eb);
indProbeTop=indProbeTop(1:end-1);
Vst=Vp(indProbeTop,:);

pointSpacingProbe=mean(patchEdgeLengths(Fp,Vp));

cFigure; hold on;
gpatch(Fp,Vp,'gw','k');
plotV(Vst,'b.-','lineWidth',lineWidth1,'MarkerSize',markerSize1);
patchNormPlot(Fp,Vp);
axisGeom(gca,fontSize);
drawnow;

Build gel

pointSpacing=pointSpacingProbe.*pointSpacingFactorTissue;

%Sketching profile
ns=150;
t=linspace(0,2*pi,ns);
t=t(1:end-1);

x=tissueRadius*cos(t);
y=tissueRadius*sin(t);
z=zeros(size(x));
Vc=[x(:) y(:) z(:)];
np=ceil(max(pathLength(Vc))./pointSpacing);
[Vc]=evenlySampleCurve(Vc,np,'pchip',1);

% Extruding model
cPar.numSteps=round(tissueHeight/pointSpacing);
cPar.depth=tissueHeight;
cPar.patchType='tri';
cPar.dir=-1;
cPar.closeLoopOpt=1;
[Fg,Vg]=polyExtrude(Vc,cPar);
Fg=fliplr(Fg);

Vgb=Vg(cPar.numSteps:cPar.numSteps:end,:);

Vgt=Vg(1:cPar.numSteps:end,:);

Cap ends

regionCell={Vgt(:,[1 2]),Vst(:,[1 2])};
[Ft,Vt]=regionTriMesh2D(regionCell,pointSpacing,0,0);
Vt(:,3)=mean(Vgt(:,3));

regionCell={Vgb(:,[1 2])};
[Fb,Vb]=regionTriMesh2D(regionCell,pointSpacing,0,0);
Fb=fliplr(Fb); %flip face orientation
Vb(:,3)=mean(Vgb(:,3));

Visualize

cFigure; hold on;

gpatch(Fp,Vp,'rw','k',0.5);
gpatch(Fg,Vg,'gw','k',0.5);
gpatch(Fb,Vb,'bw','k',0.5);
gpatch(Ft,Vt,'bw','k',0.5);

plotV(Vgb,'b.-','lineWidth',lineWidth1,'MarkerSize',markerSize1);
plotV(Vgt,'b.-','lineWidth',lineWidth1,'MarkerSize',markerSize1);
plotV(Vst,'b.-','lineWidth',lineWidth1,'MarkerSize',markerSize1);

axisGeom(gca,fontSize);
drawnow;

Merge model components

[F,V,C]=joinElementSets({Fg,Ft,Fb,Fp},{Vg,Vt,Vb,Vp});
[F,V]=mergeVertices(F,V);

cFigure;
subplot(1,2,1); hold on;
gpatch(F,V,C,'none',0.5);
axisGeom(gca,fontSize);
colormap gjet; icolorbar;

subplot(1,2,2); hold on;
gpatch(F,V,C);
patchNormPlot(F,V,2);
plotV(Vst,'b.-','lineWidth',lineWidth1,'MarkerSize',markerSize1);
axisGeom(gca,fontSize);
colormap gjet; icolorbar;

drawnow;

Mesh solid using tetgen

Create tetgen meshing input structure

[regionA]=tetVolMeanEst(Fg,Vg); %Volume for a regular tet based on edge lengths
V_inner=getInnerPoint(F,V); %Interior point for region

inputStruct.stringOpt='-pq1.2AaY';
inputStruct.Faces=F;
inputStruct.Nodes=V;
inputStruct.holePoints=[];
inputStruct.faceBoundaryMarker=C; %Face boundary markers
inputStruct.regionPoints=V_inner; %region points
inputStruct.regionA=regionA*volumeFactor; %Desired volume for tets
inputStruct.minRegionMarker=2; %Minimum region marker

Mesh model using tetrahedral elements using tetGen

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

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- TETGEN Tetrahedral meshing --- 24-Sep-2020 16:56:14
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Writing SMESH file --- 24-Sep-2020 16:56:14
----> Adding node field
----> Adding facet field
----> Adding holes specification
----> Adding region specification
--- Done --- 24-Sep-2020 16:56:14
--- Running TetGen to mesh input boundary--- 24-Sep-2020 16:56:14
Opening /mnt/data/MATLAB/GIBBON/data/temp/temp.smesh.
Delaunizing vertices...
Delaunay seconds:  0.044289
Creating surface mesh ...
Surface mesh seconds:  0.001612
Recovering boundaries...
Boundary recovery seconds:  0.003141
Removing exterior tetrahedra ...
Spreading region attributes.
Exterior tets removal seconds:  0.00071
Recovering Delaunayness...
Delaunay recovery seconds:  0.006846
Refining mesh...
Refinement seconds:  0.032465
Optimizing mesh...
Optimization seconds:  0.001204

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:  0.013854
Total running seconds:  0.104242

Statistics:

  Input points: 652
  Input facets: 1300
  Input segments: 1950
  Input holes: 0
  Input regions: 1

  Mesh points: 1199
  Mesh tetrahedra: 5627
  Mesh faces: 11904
  Mesh faces on exterior boundary: 1300
  Mesh faces on input facets: 1300
  Mesh edges on input segments: 1950
  Steiner points inside domain: 547

--- Done --- 24-Sep-2020 16:56:14
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Importing TetGen files --- 24-Sep-2020 16:56:14
--- Done --- 24-Sep-2020 16:56:15

Visualize mesh

meshView(meshOutput);

Access model element and patch data

F=meshOutput.faces;
V=meshOutput.nodes;
C=meshOutput.faceMaterialID;
E=meshOutput.elements;
elementMaterialID=meshOutput.elementMaterialID;

Fb=meshOutput.facesBoundary;
Cb=meshOutput.boundaryMarker;

Joining node sets

Fp=Fp+size(V,1);
V=[V; Vp];
center_of_mass_probe=mean(Vp,1);

Plotting tissue and probe meshes

cFigure; hold on;
gpatch(Fb,V,'bw','none',0.5);
gpatch(Fp,V,'rw','r',1);
axisGeom(gca,fontSize);
camlight headlight;
drawnow;

Define boundary condition node sets

logicRigid= Cb==1 | Cb==3;
bcSupportList=Fb(logicRigid,:);
bcSupportList=unique(bcSupportList(:));

Visualize boundary conditions

cFigure; hold on;
gpatch(Fb,V,'kw','none',0.25);
hp(1)=plotV(V(bcSupportList,:),'k.','lineWidth',lineWidth1,'MarkerSize',markerSize1);
hp(2)=gpatch(Fp,V,'rw','k',1);
legend(hp,{'BC Full support','Rigid body with prescribed displacement'});
axisGeom(gca,fontSize);
drawnow;

Create contact surfaces

F_contact_slave=fliplr(Fb(Cb==4,:));
F_contact_master=fliplr(Fp);

Visualize contact surfaces

cFigure;
subplot(1,2,1); hold on;
title('Contact set: Master','FontSize',fontSize);
gpatch(F_contact_master,V,'gw','k',1);
patchNormPlot(F_contact_master,V);
axisGeom(gca,fontSize);
camlight headlight;

subplot(1,2,2); hold on;
title('Contact set: Slave','FontSize',fontSize);
gpatch(Fb,V,'kw','none',0.25);
gpatch(F_contact_slave,V,'bw','k',1);
patchNormPlot(F_contact_slave,V);
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';

febio_spec.Control.time_stepper=rmfield(febio_spec.Control.time_stepper,'dtmax');

%Create control structure for use by all steps
febio_spec.Control.analysis.ATTR.type=analysisType;
febio_spec.Control.time_steps=numTimeSteps;
febio_spec.Control.step_size=timeTotal./numTimeSteps;
febio_spec.Control.time_stepper.dtmin=dtmin;
febio_spec.Control.time_stepper.dtmax.VAL=dtmax;
febio_spec.Control.time_stepper.dtmax.ATTR.lc=2;
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
switch formulationType
    case 1 %Elastic
        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}.k=k;

%         febio_spec.Material.material{1}.ATTR.type='neo-Hookean';
%         febio_spec.Material.material{1}.ATTR.id=1;
%         febio_spec.Material.material{1}.E=E_youngs1;
%         febio_spec.Material.material{1}.v=nu1;
    case 2 %Elastic

        %Elastic part
        febio_spec.Material.material{1}.elastic{1}.ATTR.type='Ogden';
        febio_spec.Material.material{1}.elastic{1}.c1=c1;
        febio_spec.Material.material{1}.elastic{1}.m1=m1;
        febio_spec.Material.material{1}.elastic{1}.k=k;
        febio_spec.Material.material{1}.elastic{1}.density=d;

        %Viscoelastic part
        febio_spec.Material.material{1}.ATTR.type='uncoupled viscoelastic';
        febio_spec.Material.material{1}.ATTR.Name='Block_material';
        febio_spec.Material.material{1}.ATTR.id=1;
        febio_spec.Material.material{1}.g1=g1;
        febio_spec.Material.material{1}.t1=t1;
        febio_spec.Material.material{1}.density=d;
end

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_probe;

%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

% -> 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;

% -> Elements
febio_spec.Geometry.Elements{1}.ATTR.type='tet4'; %Element type of this set
febio_spec.Geometry.Elements{1}.ATTR.mat=1; %material index for this set
febio_spec.Geometry.Elements{1}.ATTR.name='Tissue'; %Name of the element set
febio_spec.Geometry.Elements{1}.elem.ATTR.id=(1:1:size(E,1))'; %Element id's
febio_spec.Geometry.Elements{1}.elem.VAL=E;

febio_spec.Geometry.Elements{2}.ATTR.type='tri3'; %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='Probe'; %Name of the element set
febio_spec.Geometry.Elements{2}.elem.ATTR.id=size(E,1)+(1:1:size(Fp,1))'; %Element id's
febio_spec.Geometry.Elements{2}.elem.VAL=Fp;

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

%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;

% -> Prescribed boundary conditions on the rigid body
febio_spec.Boundary.rigid_body{1}.ATTR.mat=2;
febio_spec.Boundary.rigid_body{1}.fixed{1}.ATTR.bc='y';
febio_spec.Boundary.rigid_body{1}.fixed{2}.ATTR.bc='z';
febio_spec.Boundary.rigid_body{1}.fixed{3}.ATTR.bc='Rx';
febio_spec.Boundary.rigid_body{1}.fixed{4}.ATTR.bc='Ry';
febio_spec.Boundary.rigid_body{1}.fixed{5}.ATTR.bc='Rz';
febio_spec.Boundary.rigid_body{1}.prescribed.ATTR.bc='x';
febio_spec.Boundary.rigid_body{1}.prescribed.ATTR.lc=1;
febio_spec.Boundary.rigid_body{1}.prescribed.VAL=displacementMagnitude;

%LoadData section
febio_spec.LoadData.loadcurve{1}.ATTR.id=1;
febio_spec.LoadData.loadcurve{1}.ATTR.type='linear';
febio_spec.LoadData.loadcurve{1}.point.VAL=[t_load_curve(:) a_load_curve(:)];

febio_spec.LoadData.loadcurve{2}.ATTR.id=2;
febio_spec.LoadData.loadcurve{2}.ATTR.type='step';
febio_spec.LoadData.loadcurve{2}.point.VAL=[timeSetMustPoints dtmax.*ones(size(timeSetMustPoints))];

%Contact section
switch contactType
    case 1
        febio_spec.Contact.contact{1}.ATTR.surface_pair=febio_spec.Geometry.SurfacePair{1}.ATTR.name;
        febio_spec.Contact.contact{1}.ATTR.type='sticky';
        febio_spec.Contact.contact{1}.penalty=contactPenalty;
        febio_spec.Contact.contact{1}.laugon=laugon;
        febio_spec.Contact.contact{1}.tolerance=0.1;
        febio_spec.Contact.contact{1}.minaug=minaug;
        febio_spec.Contact.contact{1}.maxaug=maxaug;
        febio_spec.Contact.contact{1}.snap_tol=0;
        febio_spec.Contact.contact{1}.max_traction=0;
        febio_spec.Contact.contact{1}.search_tolerance=0.1;
    case 2
        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;
end

%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_strain;
febio_spec.Output.logfile.element_data{1}.ATTR.data='E1;E2;E3';
febio_spec.Output.logfile.element_data{1}.ATTR.delim=',';
febio_spec.Output.logfile.element_data{1}.VAL=1:size(E,1);

febio_spec.Output.logfile.element_data{2}.ATTR.file=febioLogFileName_stress;
febio_spec.Output.logfile.element_data{2}.ATTR.data='s1;s2;s3';%'sx;sy;sz;sxy;syz;sxz';
febio_spec.Output.logfile.element_data{2}.ATTR.delim=',';
febio_spec.Output.logfile.element_data{2}.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.disp_log_on=1; %Display convergence information in the command window
febioAnalysis.runMode=runMode;%'internal' or 'external';
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 --- 24-Sep-2020 16:56:22
Waiting for log file...
Proceeding to check log file...24-Sep-2020 16:56:23
------- converged at time : 0.0333333
------- converged at time : 0.0666667
------- converged at time : 0.1
------- converged at time : 0.133333
------- converged at time : 0.166667
------- converged at time : 0.2
------- converged at time : 0.233333
------- converged at time : 0.25
------- converged at time : 0.283333
------- converged at time : 0.316667
------- converged at time : 0.35
------- converged at time : 0.383333
------- converged at time : 0.416667
------- converged at time : 0.45
------- converged at time : 0.483333
------- converged at time : 0.5
------- converged at time : 0.533333
------- converged at time : 0.566667
------- converged at time : 0.6
------- converged at time : 0.633333
------- converged at time : 0.666667
------- converged at time : 0.7
------- converged at time : 0.733333
------- converged at time : 0.75
------- converged at time : 0.783333
------- converged at time : 0.816667
------- converged at time : 0.85
------- converged at time : 0.883333
------- converged at time : 0.916667
------- converged at time : 0.95
------- converged at time : 0.983333
------- converged at time : 1
------- converged at time : 1.03333
------- converged at time : 1.06667
------- converged at time : 1.1
------- converged at time : 1.13333
------- converged at time : 1.16667
------- converged at time : 1.2
------- converged at time : 1.23333
------- converged at time : 1.25
------- converged at time : 1.28333
------- converged at time : 1.31667
------- converged at time : 1.35
------- converged at time : 1.38333
------- converged at time : 1.41667
------- converged at time : 1.45
------- converged at time : 1.48333
------- converged at time : 1.5
------- converged at time : 1.53333
------- converged at time : 1.56667
------- converged at time : 1.6
------- converged at time : 1.63333
------- converged at time : 1.66667
------- converged at time : 1.7
------- converged at time : 1.73333
------- converged at time : 1.75
------- converged at time : 1.78333
------- converged at time : 1.81667
------- converged at time : 1.85
------- converged at time : 1.88333
------- converged at time : 1.91667
------- converged at time : 1.95
------- converged at time : 1.98333
------- converged at time : 2
------- converged at time : 2.03333
------- converged at time : 2.06667
------- converged at time : 2.1
------- converged at time : 2.13333
------- converged at time : 2.16667
------- converged at time : 2.2
------- converged at time : 2.23333
------- converged at time : 2.25
------- converged at time : 2.28333
------- converged at time : 2.31667
------- converged at time : 2.35
------- converged at time : 2.38333
------- converged at time : 2.41667
------- converged at time : 2.45
------- converged at time : 2.48333
------- converged at time : 2.5
------- converged at time : 2.53333
------- converged at time : 2.56667
------- converged at time : 2.6
------- converged at time : 2.63333
------- converged at time : 2.66667
------- converged at time : 2.7
------- converged at time : 2.73333
------- converged at time : 2.75
------- converged at time : 2.78333
------- converged at time : 2.81667
------- converged at time : 2.85
------- converged at time : 2.88333
------- converged at time : 2.91667
------- converged at time : 2.95
------- converged at time : 2.98333
------- converged at time : 3
------- converged at time : 3.03333
------- converged at time : 3.06667
------- converged at time : 3.1
------- converged at time : 3.13333
------- converged at time : 3.16667
------- converged at time : 3.2
------- converged at time : 3.23333
------- converged at time : 3.25
------- converged at time : 3.28333
------- converged at time : 3.31667
------- converged at time : 3.35
------- converged at time : 3.37857
------- converged at time : 3.40788
------- converged at time : 3.43781
------- converged at time : 3.46827
------- converged at time : 3.4993
------- converged at time : 3.5
------- converged at time : 3.53178
------- converged at time : 3.5638
------- converged at time : 3.5959
------- converged at time : 3.62801
------- converged at time : 3.66031
------- converged at time : 3.69268
------- converged at time : 3.72512
------- converged at time : 3.75
------- converged at time : 3.78267
------- converged at time : 3.81546
------- converged at time : 3.84837
------- converged at time : 3.88131
------- converged at time : 3.91427
------- converged at time : 3.94729
------- converged at time : 3.98036
------- converged at time : 4
--- Done --- 24-Sep-2020 16:57:58

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_MAG=sqrt(sum(N_disp_mat.^2,2));
    DN=N_disp_mat(:,:,end);
    DN_magnitude=sqrt(sum(DN(:,3).^2,2));
    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,:);
    [CF_def]=vertexToFaceMeasure(Fb,DN_magnitude);

    % Importing element data from a log file
    [~,E_stress,~]=importFEBio_logfile(fullfile(savePath,febioLogFileName_stress)); %Element data

    %Remove nodal index column
    E_stress=E_stress(:,2:end,:);

    %Add initial state i.e. zero
    sizImport=size(E_stress);
    sizImport(3)=sizImport(3)+1;
    E_data_mat_n=zeros(sizImport);
    E_data_mat_n(:,:,2:end)=E_stress;
    E_stress=E_data_mat_n;

    E_stress(isnan(E_stress))=0;

    E_stress1=E_stress(:,1,:);
    E_stress2=E_stress(:,2,:);
    E_stress3=E_stress(:,3,:);
    E_stress_VM=sqrt(0.5*( (E_stress1-E_stress2).^2 + (E_stress2-E_stress3).^2 + (E_stress3-E_stress1).^2 ));

    VE=patchCentre(E,V);
    logicCutElements=VE(:,2)>=0;

    [F_cut,CF_cut_data]=element2patch(E(logicCutElements,:),E_stress_VM(logicCutElements,:,1));
    [indBoundary]=tesBoundary(F_cut,V);

    CV_stress=faceToVertexMeasure(F_cut(indBoundary,:),V,CF_cut_data(indBoundary,:));

Plotting the simulated results using anim8 to visualize and animate deformations

    % Create basic view and store graphics handle to initiate animation
    hf=cFigure; %Open figure
    gtitle([febioFebFileNamePart,': Press play to animate']);
    hp1=gpatch(Fb,V_def,'kw','none',0.25); %Add graphics object to animate
    hp2=gpatch(F_cut(indBoundary,:),V_def,CV_stress,'k',1); %Add graphics object to animate
    hp2.FaceColor='interp';
    hp3=gpatch(Fp,V_def,'kw','none',1); %Add graphics object to animate
    colormap(gjet(250)); colorbar;
    caxis([0 max(E_stress_VM(:))/3]);
    axisGeom(gca,fontSize);
    axis([min(X_DEF(:)) max(X_DEF(:)) min(Y_DEF(:)) max(Y_DEF(:)) min(Z_DEF(:)) max(Z_DEF(:))]);
    axis manual;
    camlight headlight;
    drawnow;

    % 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
        DN_magnitude=sqrt(sum(DN.^2,2)); %Current displacement magnitude
        V_def=V+DN; %Current nodal coordinates
        [~,CF_cut_data]=element2patch(E(logicCutElements,:),E_stress_VM(logicCutElements,:,qt));
        CV=faceToVertexMeasure(F_cut(indBoundary,:),V,CF_cut_data(indBoundary,:));

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

    S1_mean=squeeze(mean(E_stress1,1));
    S2_mean=squeeze(mean(E_stress2,1));
    S3_mean=squeeze(mean(E_stress3,1));
    SVM_mean=squeeze(mean(E_stress_VM,1));

    t_max=(cycleTime/2:cycleTime:timeTotal)';
    t_min=(0:cycleTime:timeTotal)';
    [~,indUni]=unique(time_mat);

    S1_max=interp1(time_mat(indUni),S1_mean(indUni),t_max,'linear','extrap');
    S1_min=interp1(time_mat(indUni),S1_mean(indUni),t_min,'linear','extrap');

    S2_max=interp1(time_mat(indUni),S2_mean(indUni),t_max,'linear','extrap');
    S2_min=interp1(time_mat(indUni),S2_mean(indUni),t_min,'linear','extrap');

    S3_max=interp1(time_mat(indUni),S3_mean(indUni),t_max,'linear','extrap');
    S3_min=interp1(time_mat(indUni),S3_mean(indUni),t_min,'linear','extrap');

    SVM_max=interp1(time_mat(indUni),SVM_mean(indUni),t_max,'linear','extrap');
    SVM_min=interp1(time_mat(indUni),SVM_mean(indUni),t_min,'linear','extrap');

    cFigure; hold on;
    xlabel('Time (s)'); ylabel('Mean stress (MPa)');

    h1=plot(time_mat,S1_mean,'r-','MarkerSize',25,'LineWidth',3);
    h2=plot(time_mat,S3_mean,'b-','MarkerSize',25,'LineWidth',3);
    h3=plot(t_min,S1_min,'r.--','MarkerSize',50,'LineWidth',2);
    h4=plot(t_max,S3_max,'b.--','MarkerSize',50,'LineWidth',2);

    legend([h1 h2 h3 h4],{'Mean 1st principal stress','Mean 3rd principal stress','Maxima','Minima'},'Location','SouthOutside');

    grid on; box on; axis tight;
    set(gca,'FontSize',fontSize);
    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.

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/.