DEMO_febio_0047_cylinder_embedded_probe_01

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 tissue
Cap ends
Merge model components
Mesh solid using tetgen
Define boundary condition node sets
Defining the FEBio input structure
Quick viewing of the FEBio input file structure
Exporting the FEBio input file
Running the FEBio analysis
Import FEBio results

Keywords

febio_spec version 3.0
febio, FEBio
probe
contact, sliding, sticky, friction
rigid body constraints
hexahedral elements, hex8
triangular elements, tri3
slab, block, rectangular
sphere
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=[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

probeHeight=75;

probeRadius=2; % The radius of the hemi-spher portion
nRefine=0; % Number of |subtri| refinements for icosahedron

pointSpacing=3;
dAdd=7;
tissueRadius=probeRadius+dAdd;
tissueHeight=probeHeight+dAdd;
volumeFactor=5;

displacementMagnitude=-1;

%Material parameter set
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

% FEA control settings
numTimeSteps=10; %Number of time steps desired
max_refs=25; %Max reforms
max_ups=0; %Set to zero to use full-Newton iterations
opt_iter=6; %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

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';

[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,:);

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

Build tissue

%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(F,V); %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 --- 18-Dec-2020 14:29:09
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Writing SMESH file --- 18-Dec-2020 14:29:09
----> Adding node field
----> Adding facet field
----> Adding holes specification
----> Adding region specification
--- Done --- 18-Dec-2020 14:29:09
--- Running TetGen to mesh input boundary--- 18-Dec-2020 14:29:09
Opening /mnt/data/MATLAB/GIBBON/data/temp/temp.smesh.
Delaunizing vertices...
Delaunay seconds:  0.06748
Creating surface mesh ...
Surface mesh seconds:  0.002073
Recovering boundaries...
Boundary recovery seconds:  0.004778
Removing exterior tetrahedra ...
Spreading region attributes.
Exterior tets removal seconds:  0.00175
Recovering Delaunayness...
Delaunay recovery seconds:  0.004578
Refining mesh...
Refinement seconds:  0.022011
Optimizing mesh...
Optimization seconds:  0.001842

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:  0.028042
Total running seconds:  0.132692

Statistics:

  Input points: 1164
  Input facets: 2324
  Input segments: 3486
  Input holes: 0
  Input regions: 1

  Mesh points: 2231
  Mesh tetrahedra: 10409
  Mesh faces: 21980
  Mesh faces on exterior boundary: 2324
  Mesh faces on input facets: 2324
  Mesh edges on input segments: 3486
  Steiner points inside domain: 1067

--- Done --- 18-Dec-2020 14:29:09
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Importing TetGen files --- 18-Dec-2020 14:29:09
--- Done --- 18-Dec-2020 14:29:09

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;

Define boundary condition node sets

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

logicIndentor= Cb==4;
bcPrescribeList=Fb(logicIndentor,:);
bcPrescribeList=unique(bcPrescribeList(:));

Visualize boundary conditions

cFigure; hold on;
gpatch(Fb,V,'bw','none',0.5);
hp(1)=plotV(V(bcSupportList,:),'k.','lineWidth',lineWidth1,'MarkerSize',markerSize1);
hp(2)=plotV(V(bcPrescribeList,:),'r.','lineWidth',lineWidth1,'MarkerSize',markerSize1);
legend(hp,{'BC Full support','BC Prescribed displacement'});
axisGeom(gca,fontSize);
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
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.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;
% Mesh section
% -> Nodes
febio_spec.Mesh.Nodes{1}.ATTR.name='Object1'; %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

% -> NodeSets
nodeSetName1='bcSupportList';
nodeSetName2='bcPrescribeList';

febio_spec.Mesh.NodeSet{1}.ATTR.name=nodeSetName1;
febio_spec.Mesh.NodeSet{1}.node.ATTR.id=bcSupportList(:);

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

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

%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';

% -> Prescribe boundary conditions
%STEP 1 Up/down
febio_spec.Step.step{1}.Boundary.bc{1}.ATTR.type='prescribe';
febio_spec.Step.step{1}.Boundary.bc{1}.ATTR.node_set=nodeSetName2;
febio_spec.Step.step{1}.Boundary.bc{1}.dof='z';
febio_spec.Step.step{1}.Boundary.bc{1}.scale.ATTR.lc=1;
febio_spec.Step.step{1}.Boundary.bc{1}.scale.VAL=displacementMagnitude;
febio_spec.Step.step{1}.Boundary.bc{1}.relative=1;

febio_spec.Step.step{1}.Boundary.bc{2}.ATTR.type='fix';
febio_spec.Step.step{1}.Boundary.bc{2}.ATTR.node_set=nodeSetName2;
febio_spec.Step.step{1}.Boundary.bc{2}.dofs='x,y';

%STEP 2 Sideways
febio_spec.Step.step{2}.Boundary.bc{1}.ATTR.type='prescribe';
febio_spec.Step.step{2}.Boundary.bc{1}.ATTR.node_set=nodeSetName2;
febio_spec.Step.step{2}.Boundary.bc{1}.dof='x';
febio_spec.Step.step{2}.Boundary.bc{1}.scale.ATTR.lc=2;
febio_spec.Step.step{2}.Boundary.bc{1}.scale.VAL=displacementMagnitude;
febio_spec.Step.step{2}.Boundary.bc{1}.relative=1;

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

%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; 0.25 1; 0.5 0; 0.75 -1; 1 0];

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=[1 0; 1.25 1; 1.5 0; 1.75 -1; 2 0];

%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{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.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=',';

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='external';%'internal' or 'external';

[runFlag]=runMonitorFEBio(febioAnalysis);%START FEBio NOW!!!!!!!!

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-------->    RUNNING/MONITORING FEBIO JOB    <-------- 18-Dec-2020 14:29:13
FEBio path: /home/kevin/FEBioStudio/bin/febio3
# Attempt removal of existing log files                18-Dec-2020 14:29:13
 * Removal succesful                                   18-Dec-2020 14:29:13
# Attempt removal of existing .xplt files              18-Dec-2020 14:29:13
 * Removal succesful                                   18-Dec-2020 14:29:13
# Starting FEBio...                                    18-Dec-2020 14:29:13
  Max. total analysis time is: Inf s
 * Waiting for log file creation                       18-Dec-2020 14:29:13
   Max. wait time: 30 s
 * Log file found.                                     18-Dec-2020 14:29:14
# Parsing log file...                                  18-Dec-2020 14:29:14
    number of iterations   : 3                         18-Dec-2020 14:29:14
    number of reformations : 3                         18-Dec-2020 14:29:14
------- converged at time : 0.1                        18-Dec-2020 14:29:14
    number of iterations   : 3                         18-Dec-2020 14:29:14
    number of reformations : 3                         18-Dec-2020 14:29:14
------- converged at time : 0.2                        18-Dec-2020 14:29:14
    number of iterations   : 1                         18-Dec-2020 14:29:15
    number of reformations : 1                         18-Dec-2020 14:29:15
------- converged at time : 0.3                        18-Dec-2020 14:29:15
    number of iterations   : 3                         18-Dec-2020 14:29:15
    number of reformations : 3                         18-Dec-2020 14:29:15
------- converged at time : 0.4                        18-Dec-2020 14:29:15
    number of iterations   : 3                         18-Dec-2020 14:29:15
    number of reformations : 3                         18-Dec-2020 14:29:15
------- converged at time : 0.5                        18-Dec-2020 14:29:15
    number of iterations   : 3                         18-Dec-2020 14:29:15
    number of reformations : 3                         18-Dec-2020 14:29:15
------- converged at time : 0.6                        18-Dec-2020 14:29:15
    number of iterations   : 3                         18-Dec-2020 14:29:16
    number of reformations : 3                         18-Dec-2020 14:29:16
------- converged at time : 0.7                        18-Dec-2020 14:29:16
    number of iterations   : 1                         18-Dec-2020 14:29:16
    number of reformations : 1                         18-Dec-2020 14:29:16
------- converged at time : 0.8                        18-Dec-2020 14:29:16
    number of iterations   : 3                         18-Dec-2020 14:29:16
    number of reformations : 3                         18-Dec-2020 14:29:16
------- converged at time : 0.9                        18-Dec-2020 14:29:16
    number of iterations   : 3                         18-Dec-2020 14:29:16
    number of reformations : 3                         18-Dec-2020 14:29:16
------- converged at time : 1                          18-Dec-2020 14:29:16
    number of iterations   : 3                         18-Dec-2020 14:29:17
    number of reformations : 3                         18-Dec-2020 14:29:17
------- converged at time : 1.1                        18-Dec-2020 14:29:17
    number of iterations   : 3                         18-Dec-2020 14:29:17
    number of reformations : 3                         18-Dec-2020 14:29:17
------- converged at time : 1.2                        18-Dec-2020 14:29:17
    number of iterations   : 1                         18-Dec-2020 14:29:17
    number of reformations : 1                         18-Dec-2020 14:29:17
------- converged at time : 1.3                        18-Dec-2020 14:29:17
    number of iterations   : 3                         18-Dec-2020 14:29:17
    number of reformations : 3                         18-Dec-2020 14:29:17
------- converged at time : 1.4                        18-Dec-2020 14:29:17
    number of iterations   : 3                         18-Dec-2020 14:29:18
    number of reformations : 3                         18-Dec-2020 14:29:18
------- converged at time : 1.5                        18-Dec-2020 14:29:18
    number of iterations   : 3                         18-Dec-2020 14:29:18
    number of reformations : 3                         18-Dec-2020 14:29:18
------- converged at time : 1.6                        18-Dec-2020 14:29:18
    number of iterations   : 3                         18-Dec-2020 14:29:18
    number of reformations : 3                         18-Dec-2020 14:29:18
------- converged at time : 1.7                        18-Dec-2020 14:29:18
    number of iterations   : 1                         18-Dec-2020 14:29:18
    number of reformations : 1                         18-Dec-2020 14:29:18
------- converged at time : 1.8                        18-Dec-2020 14:29:18
    number of iterations   : 3                         18-Dec-2020 14:29:19
    number of reformations : 3                         18-Dec-2020 14:29:19
------- converged at time : 1.9                        18-Dec-2020 14:29:19
    number of iterations   : 3                         18-Dec-2020 14:29:19
    number of reformations : 3                         18-Dec-2020 14:29:19
------- converged at time : 2                          18-Dec-2020 14:29:19
 Elapsed time : 0:00:05                                18-Dec-2020 14:29:19
 N O R M A L   T E R M I N A T I O N
# Done                                                 18-Dec-2020 14:29:19
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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_data,~]=importFEBio_logfile(fullfile(savePath,febioLogFileName_strain)); %Element data

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

    E_data=sqrt(0.5*( (E_data(:,1,:)-E_data(:,2,:)).^2 + (E_data(:,2,:)-E_data(:,3,:)).^2 + (E_data(:,3,:)-E_data(:,1,:)).^2 ));

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

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

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

    CV=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']);
%     subplot(1,2,1);
    hp1=gpatch(Fb,V_def,'kw','none',0.25); %Add graphics object to animate
    hp2=gpatch(F_cut(indBoundary,:),V_def,CV,'k',1); %Add graphics object to animate
    hp2.FaceColor='interp';
%     gpatch(Fb,V,0.5*ones(1,3),'k',0.25); %A static graphics object
    colormap(gjet(250)); colorbar;
    caxis([0 max(E_data(:))/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_def]=vertexToFaceMeasure(Fb,DN_magnitude); %Current color data to use

        [~,CF_cut_data]=element2patch(E(logicCutElements,:),E_data(logicCutElements,:,qt));
        CV=faceToVertexMeasure(F_cut(indBoundary,:),V,CF_cut_data(indBoundary,:));

        %Set entries in animation structure
        animStruct.Handles{qt}=[hp1 hp2 hp2]; %Handles of objects to animate
        animStruct.Props{qt}={'Vertices','Vertices','CData'}; %Properties of objects to animate
        animStruct.Set{qt}={V_def,V_def,CV}; %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]

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License: https://github.com/gibbonCode/GIBBON/blob/master/LICENSE

GIBBON: The Geometry and Image-based Bioengineering add-On. A toolbox for image segmentation, image-based modeling, meshing, and finite element analysis.

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

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

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