DEMO_febio_0022_multigen_interface_band

Below is a demonstration for:

Contents

Keywords

clear; close all; clc;

Plot settings

fontSize=15;
faceAlpha1=0.8;
faceAlpha2=0.3;
markerSize=40;
lineWidth=3;
plotColors=gjet(9);
lineWidth1=2;
markerSize1=25;

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_strainEnergy=[febioFebFileNamePart,'_energy_out.txt']; %Log file name for exporting strain energy density

%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

%Multi-generational properties of band
c1_g=[c1/1000 c1*100];
k_g=c1_g*k_factor;

% FEA control settings
numTimeSteps=6; %Number of time steps desired
max_refs=25; %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

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

appliedPressure=3e-3; %pressure value

% Geometry parameters
tissueRadius=35;
tissueHeight=150;
boneRadius=10;
wrapHeight=24;
wrapThickness=5;
pointSpacing=6; % Aproximate node spacing

Build tissue skin surface top

%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
h=(tissueHeight/2)-wrapHeight/2;
cPar.numSteps=round(h/pointSpacing);
cPar.numSteps=cPar.numSteps+iseven(cPar.numSteps);
cPar.depth=h;
cPar.patchType='tri';
cPar.dir=-1;
cPar.closeLoopOpt=1;
[Fg1,Vg1]=polyExtrude(Vc,cPar);
Vg1(:,3)=Vg1(:,3)+tissueHeight/2;

[T,R] = cart2pol(Vg1(:,1),Vg1(:,2));
R=R-(tissueRadius/2*((Vg1(:,3)-(wrapHeight/2))/(tissueHeight/2)).^2);
[Vg1(:,1),Vg1(:,2)] = pol2cart(T,R);

Vg1b=Vg1(cPar.numSteps:cPar.numSteps:end,:);
Vg1t=Vg1(1:cPar.numSteps:end,:);

Build tissue skin surface bottom

Fg2=Fg1;
Fg2=fliplr(Fg2);
Vg2=Vg1;
Vg2(:,3)=-Vg2(:,3);
Vg2b=Vg2(cPar.numSteps:cPar.numSteps:end,:);
Vg2t=Vg2(1:cPar.numSteps:end,:);

Build tissue skin surface middle

% Extruding model
h=wrapHeight;
cPar.numSteps=round(h/pointSpacing);
cPar.numSteps=cPar.numSteps+iseven(cPar.numSteps);
cPar.depth=h;
cPar.patchType='tri';
cPar.closeLoopOpt=1;

Vc_start=Vg1b;
Vc_end=Vg2b;
[Fg3,Vg3]=polyLoftLinear(Vc_start,Vc_end,cPar);

% Vg3(:,3)=Vg3(:,3)+tissueHeight/2;
Vg3b=Vg3(cPar.numSteps:cPar.numSteps:end,:);
Vg3t=Vg3(1:cPar.numSteps:end,:);

Build wrap outer surface

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

x=(tissueRadius+wrapThickness)*cos(t);
y=(tissueRadius+wrapThickness)*sin(t);
z=zeros(size(x));
Vc=[x(:) y(:) z(:)];
np=ceil(max(pathLength(Vc))./pointSpacing);
[Vwt]=evenlySampleCurve(Vc,np,'pchip',1);
Vwt(:,3)=mean(Vg3t(:,3));
Vwb=Vwt;
Vwb(:,3)=Vwt(:,3)-wrapHeight;

h=wrapHeight;
cPar.numSteps=round(h/pointSpacing);
cPar.numSteps=cPar.numSteps+iseven(cPar.numSteps);
cPar.depth=h;
cPar.patchType='tri';
cPar.closeLoopOpt=1;

Vc_start=Vwt;
Vc_end=Vwb;
[Fw1,Vw1]=polyLoftLinear(Vc_start,Vc_end,cPar);

Build bone surface

x=boneRadius*cos(t);
y=boneRadius*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.numSteps=cPar.numSteps+iseven(cPar.numSteps);
cPar.depth=tissueHeight;
cPar.patchType='tri';
cPar.dir=-1;
cPar.closeLoopOpt=1;
[Fb,Vb]=polyExtrude(Vc,cPar);
Fb=fliplr(Fb);
Vb(:,3)=Vb(:,3)+tissueHeight/2;

Vbb=Vb(cPar.numSteps:cPar.numSteps:end,:);
Vbt=Vb(1:cPar.numSteps:end,:);

Capping tissue top

regionCell={Vg1t(:,[1 2]),Vbt(:,[1 2])};
[Ft,Vt]=regionTriMesh2D(regionCell,pointSpacing,0,0);
Vt(:,3)=mean(Vg1t(:,3));
Ft=fliplr(Ft);

Capping tissue bottom

regionCell={Vg2t(:,[1 2]),Vbb(:,[1 2])};
[Fgb,Vgb]=regionTriMesh2D(regionCell,pointSpacing,0,0);
Vgb(:,3)=mean(Vg2t(:,3));

Capping wrap top

regionCell={Vwt(:,[1 2]),Vg1b(:,[1 2])};
[Fwtt,Vwtt]=regionTriMesh2D(regionCell,pointSpacing,0,0);
Vwtt(:,3)=mean(Vwt(:,3));
Fwtt=fliplr(Fwtt);

Capping wrap bottom

regionCell={Vwb(:,[1 2]),Vg2b(:,[1 2])};
[Fwbb,Vwbb]=regionTriMesh2D(regionCell,pointSpacing,0,0);
Vwbb(:,3)=mean(Vwb(:,3));

Visualizing surface geometry

cFigure;
xlabel('X','FontSize',fontSize); ylabel('Y','FontSize',fontSize); zlabel('Z','FontSize',fontSize)
hold on;

gpatch(Fg1,Vg1,plotColors(1,:),'k');
patchNormPlot(Fg1,Vg1);
plotV(Vg1t,'r.-','lineWidth',lineWidth1,'MarkerSize',markerSize1);
plotV(Vg1b,'y.-','lineWidth',lineWidth1,'MarkerSize',markerSize1);

gpatch(Fg2,Vg2,plotColors(2,:),'k');
patchNormPlot(Fg2,Vg2);
plotV(Vg2t,'r.-','lineWidth',lineWidth1,'MarkerSize',markerSize1);
plotV(Vg2b,'y.-','lineWidth',lineWidth1,'MarkerSize',markerSize1);

gpatch(Fg3,Vg3,plotColors(3,:),'k');
patchNormPlot(Fg3,Vg3);
plotV(Vg3t,'r.-','lineWidth',lineWidth1,'MarkerSize',markerSize1);
plotV(Vg3b,'y.-','lineWidth',lineWidth1,'MarkerSize',markerSize1);

gpatch(Fw1,Vw1,plotColors(4,:),'k');
patchNormPlot(Fw1,Vw1);
plotV(Vwt,'g.-','lineWidth',lineWidth1,'MarkerSize',markerSize1);
plotV(Vwb,'g.-','lineWidth',lineWidth1,'MarkerSize',markerSize1);

gpatch(Fb,Vb,plotColors(5,:),'k');
patchNormPlot(Fb,Vb);
plotV(Vbt,'r.-','lineWidth',lineWidth1,'MarkerSize',markerSize1);
plotV(Vbb,'y.-','lineWidth',lineWidth1,'MarkerSize',markerSize1);

gpatch(Ft,Vt,plotColors(6,:),'k');
patchNormPlot(Ft,Vt);

gpatch(Fgb,Vgb,plotColors(7,:),'k');
patchNormPlot(Fgb,Vgb);

gpatch(Fwtt,Vwtt,plotColors(8,:),'k');
patchNormPlot(Fwtt,Vwtt);

gpatch(Fwbb,Vwbb,plotColors(9,:),'k');
patchNormPlot(Fwbb,Vwbb);

axisGeom;
colormap(plotColors); colorbar;
drawnow;

Joining and merging geometry sets

%Joining sets

%Creating color information
Cg1=1*ones(size(Fg1,1),1); %Tissue top cylinder
Cg2=2*ones(size(Fg2,1),1); %Tissue bottom cylinder
Cg3=3*ones(size(Fg3,1),1); %Tissue middle cylinder
Cw1=4*ones(size(Fw1,1),1); %Wrap outer cylinder
Cb=5*ones(size(Fb,1),1); %Bone cylinder
Ct=6*ones(size(Ft,1),1); %Tissue top
Cgb=7*ones(size(Fgb,1),1); %Tissue bottom
Cwtt=8*ones(size(Fwtt,1),1); %Wrap top
Cwbb=9*ones(size(Fwbb,1),1); %Wrap bottom

[F,V,C]=joinElementSets({Fg1,Fg2,Fg3,Fw1,Fb,Ft,Fgb,Fwtt,Fwbb},{Vg1,Vg2,Vg3,Vw1,Vb,Vt,Vgb,Vwtt,Vwbb},{Cg1,Cg2,Cg3,Cw1,Cb,Ct,Cgb,Cwtt,Cwbb}); %joining sets together

%merging sets
[F,V]=mergeVertices(F,V);

cFigure;
xlabel('X','FontSize',fontSize); ylabel('Y','FontSize',fontSize); zlabel('Z','FontSize',fontSize)
hold on;

gpatch(F,V,C,'none',0.5);
% patchNormPlot(F,V);

axisGeom;
colormap(plotColors); icolorbar;
drawnow;

Find solid mesh region interior points

logicRegion=ismember(C,[3 4 8 9]);
[V_in_1]=getInnerPoint(F(logicRegion,:),V);

logicRegion=ismember(C,[1 2 3 5 6 7 ]);
[V_in_2]=getInnerPoint(F(logicRegion,:),V);

V_regions=[V_in_1;V_in_2];

cFigure;
xlabel('X','FontSize',fontSize); ylabel('Y','FontSize',fontSize); zlabel('Z','FontSize',fontSize)
hold on;

gpatch(F,V,C,'none',0.2);
plotV(V_in_1,'r.','MarkerSize',25);
plotV(V_in_2,'b.','MarkerSize',25);

axisGeom;
colormap(plotColors); colorbar;
drawnow;

Mesh solid using tetgen

% Create tetgen meshing input structure
modelName=fullfile(savePath,'tempModel');

% Regional mesh volume parameter
[regionA]=tetVolMeanEst(F,V); %Volume for a regular tet based on edge lengths
volumeFactors=(regionA.*ones(size(V_regions,1),1));

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

Mesh model using tetrahedral elements using tetGen (see: http://wias-berlin.de/software/tetgen/)

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

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- TETGEN Tetrahedral meshing --- 20-Apr-2023 10:44:35
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Writing SMESH file --- 20-Apr-2023 10:44:35
----> Adding node field
----> Adding facet field
----> Adding holes specification
----> Adding region specification
--- Done --- 20-Apr-2023 10:44:35
--- Running TetGen to mesh input boundary--- 20-Apr-2023 10:44:35
Opening /mnt/data/MATLAB/GIBBON/data/temp/tempModel.smesh.
Delaunizing vertices...
Delaunay seconds:  0.014849
Creating surface mesh ...
Surface mesh seconds:  0.002311
Recovering boundaries...
Boundary recovery seconds:  0.00435
Removing exterior tetrahedra ...
Spreading region attributes.
Exterior tets removal seconds:  0.001671
Recovering Delaunayness...
Delaunay recovery seconds:  0.002409
Refining mesh...
  1956 insertions, added 1569 points, 47341 tetrahedra in queue.
  651 insertions, added 477 points, 56522 tetrahedra in queue.
  868 insertions, added 552 points, 62664 tetrahedra in queue.
  1157 insertions, added 444 points, 40125 tetrahedra in queue.
  1542 insertions, added 162 points, 1308 tetrahedra in queue.
Refinement seconds:  0.087088
Smoothing vertices...
Mesh smoothing seconds:  0.130497
Improving mesh...
Mesh improvement seconds:  0.005233

Writing /mnt/data/MATLAB/GIBBON/data/temp/tempModel.1.node.
Writing /mnt/data/MATLAB/GIBBON/data/temp/tempModel.1.ele.
Writing /mnt/data/MATLAB/GIBBON/data/temp/tempModel.1.face.
Writing /mnt/data/MATLAB/GIBBON/data/temp/tempModel.1.edge.

Output seconds:  0.049115
Total running seconds:  0.297754

Statistics:

  Input points: 1468
  Input facets: 3010
  Input segments: 4478
  Input holes: 0
  Input regions: 2

  Mesh points: 4712
  Mesh tetrahedra: 24781
  Mesh faces: 50919
  Mesh faces on exterior boundary: 2714
  Mesh faces on input facets: 3010
  Mesh edges on input segments: 4478
  Steiner points inside domain: 3244

--- Done --- 20-Apr-2023 10:44:36
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Importing TetGen files --- 20-Apr-2023 10:44:36
--- Done --- 20-Apr-2023 10:44:36

Visualizing mesh

meshView(meshOutput);

Access model element and patch data

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

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

cFigure;
xlabel('X','FontSize',fontSize); ylabel('Y','FontSize',fontSize); zlabel('Z','FontSize',fontSize)
hold on;

gpatch(Fb,V,Cb);

axisGeom;
colormap(plotColors)
drawnow;

Define boundary condition node sets

logicRigid=ismember(Cb,[5 6 7]);
bcSupportList=Fb(logicRigid,:);
bcSupportList=unique(bcSupportList(:));

Define pressure surface

F_pressure=fliplr(Fb(Cb==3,:));

Plot boundary condition nodes

cFigure;
xlabel('X','FontSize',fontSize); ylabel('Y','FontSize',fontSize); zlabel('Z','FontSize',fontSize)
hold on;

gpatch(Fb,V,Cb,'none',0.5);
plotV(V(bcSupportList,:),'k.','lineWidth',lineWidth1,'MarkerSize',markerSize1);
gpatch(F_pressure,V,0.5*ones(1,3),'k');

axisGeom;
colormap(plotColors);
drawnow;

Create element sets and material indices

%Create material indices
elementMaterialIndices=CE;
elementMaterialIndices(elementMaterialIndices==-3)=1;
elementMaterialIndices(elementMaterialIndices==-2)=2;

%Order material sets
E1=E(elementMaterialIndices==1,:); %Tissue material
E2=E(elementMaterialIndices==2,:); %Wrap material
E=[E1;E2];

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';

%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.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='Normal_material';
febio_spec.Material.material{1}.ATTR.name=materialName1;
febio_spec.Material.material{1}.ATTR.id=1;
febio_spec.Material.material{1}.ATTR.type='Ogden unconstrained';
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}.cp=k;

materialName2='Multigen_material';
febio_spec.Material.material{2}.ATTR.name=materialName2;
febio_spec.Material.material{2}.ATTR.id=2;
febio_spec.Material.material{2}.ATTR.type='multigeneration';

febio_spec.Material.material{2}.generation{1}.ATTR.id=1;
febio_spec.Material.material{2}.generation{1}.start_time=0;
febio_spec.Material.material{2}.generation{1}.solid{1}.ATTR.type='Ogden unconstrained';
febio_spec.Material.material{2}.generation{1}.solid{1}.c1=c1_g(1);
febio_spec.Material.material{2}.generation{1}.solid{1}.m1=m1;
febio_spec.Material.material{2}.generation{1}.solid{1}.c2=c1_g(1);
febio_spec.Material.material{2}.generation{1}.solid{1}.m2=-m1;
febio_spec.Material.material{2}.generation{1}.solid{1}.cp=k_g(1);

febio_spec.Material.material{2}.generation{2}.ATTR.id=2;
febio_spec.Material.material{2}.generation{2}.start_time=1;
febio_spec.Material.material{2}.generation{2}.solid{1}.ATTR.type='Ogden unconstrained';
febio_spec.Material.material{2}.generation{2}.solid{1}.c1=c1_g(2);
febio_spec.Material.material{2}.generation{2}.solid{1}.m1=m1;
febio_spec.Material.material{2}.generation{2}.solid{1}.c2=c1_g(2);
febio_spec.Material.material{2}.generation{2}.solid{1}.m2=-m1;
febio_spec.Material.material{2}.generation{2}.solid{1}.cp=k_g(2);

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

% -> Elements
partName1='Part1';
febio_spec.Mesh.Elements{1}.ATTR.name=partName1; %Name of this part
febio_spec.Mesh.Elements{1}.ATTR.type='tet4'; %Element type
febio_spec.Mesh.Elements{1}.elem.ATTR.id=(1:1:size(E1,1))'; %Element id's
febio_spec.Mesh.Elements{1}.elem.VAL=E1;

partName2='Part2';
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;

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

% -> Surfaces
surfaceName1='LoadedSurface';
febio_spec.Mesh.Surface{1}.ATTR.name=surfaceName1;
febio_spec.Mesh.Surface{1}.tri3.ATTR.id=(1:1:size(F_pressure,1))';
febio_spec.Mesh.Surface{1}.tri3.VAL=F_pressure;

%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;

%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;

%Loads section
% -> Surface load
febio_spec.Loads.surface_load{1}.ATTR.type='pressure';
febio_spec.Loads.surface_load{1}.ATTR.surface=surfaceName1;
febio_spec.Loads.surface_load{1}.pressure.ATTR.lc=1;
febio_spec.Loads.surface_load{1}.pressure.VAL=appliedPressure;
febio_spec.Loads.surface_load{1}.symmetric_stiffness=1;

%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; 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.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=',';

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 10:44:43
FEBio path: /home/kevin/FEBioStudio2/bin/febio4
# Attempt removal of existing log files                20-Apr-2023 10:44:43
 * Removal succesful                                   20-Apr-2023 10:44:43
# Attempt removal of existing .xplt files              20-Apr-2023 10:44:43
 * Removal succesful                                   20-Apr-2023 10:44:43
# Starting FEBio...                                    20-Apr-2023 10:44:43
  Max. total analysis time is: Inf s
 * Waiting for log file creation                       20-Apr-2023 10:44:43
   Max. wait time: 30 s
 * Log file found.                                     20-Apr-2023 10:44:43
# Parsing log file...                                  20-Apr-2023 10:44:43
    number of iterations   : 4                         20-Apr-2023 10:44:45
    number of reformations : 4                         20-Apr-2023 10:44:45
------- converged at time : 0.166667                   20-Apr-2023 10:44:45
    number of iterations   : 4                         20-Apr-2023 10:44:45
    number of reformations : 4                         20-Apr-2023 10:44:45
------- converged at time : 0.333333                   20-Apr-2023 10:44:45
    number of iterations   : 5                         20-Apr-2023 10:44:46
    number of reformations : 5                         20-Apr-2023 10:44:46
------- converged at time : 0.5                        20-Apr-2023 10:44:46
    number of iterations   : 6                         20-Apr-2023 10:44:48
    number of reformations : 6                         20-Apr-2023 10:44:48
------- converged at time : 0.666667                   20-Apr-2023 10:44:48
    number of iterations   : 6                         20-Apr-2023 10:44:49
    number of reformations : 6                         20-Apr-2023 10:44:49
------- converged at time : 0.833333                   20-Apr-2023 10:44:49
    number of iterations   : 4                         20-Apr-2023 10:44:50
    number of reformations : 4                         20-Apr-2023 10:44:50
------- converged at time : 1                          20-Apr-2023 10:44:50
    number of iterations   : 4                         20-Apr-2023 10:44:51
    number of reformations : 4                         20-Apr-2023 10:44:51
------- converged at time : 1.16667                    20-Apr-2023 10:44:51
    number of iterations   : 4                         20-Apr-2023 10:44:52
    number of reformations : 4                         20-Apr-2023 10:44:52
------- converged at time : 1.33333                    20-Apr-2023 10:44:52
    number of iterations   : 4                         20-Apr-2023 10:44:53
    number of reformations : 4                         20-Apr-2023 10:44:53
------- converged at time : 1.5                        20-Apr-2023 10:44:53
    number of iterations   : 3                         20-Apr-2023 10:44:53
    number of reformations : 3                         20-Apr-2023 10:44:53
------- converged at time : 1.66667                    20-Apr-2023 10:44:53
    number of iterations   : 3                         20-Apr-2023 10:44:54
    number of reformations : 3                         20-Apr-2023 10:44:54
------- converged at time : 1.83333                    20-Apr-2023 10:44:54
    number of iterations   : 3                         20-Apr-2023 10:44:55
    number of reformations : 3                         20-Apr-2023 10:44:55
------- converged at time : 2                          20-Apr-2023 10:44:55
 Elapsed time : 0:00:12                                20-Apr-2023 10:44:55
 N O R M A L   T E R M I N A T I O N
# Done                                                 20-Apr-2023 10:44:55
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Import FEBio results

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

Importing nodal displacements from a log file

    dataStruct=importFEBio_logfile(fullfile(savePath,febioLogFileName_disp),0,1);

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

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

Importing element stress from a log file

    dataStruct=importFEBio_logfile(fullfile(savePath,febioLogFileName_strainEnergy),0,1);

    %Access data
    E_energy=dataStruct.data;

Plotting the simulated results using anim8 to visualize and animate deformations

    c1_plot=c1*ones(size(timeVec));
    cg_plot=c1_g(1)*ones(size(timeVec));
    cg_plot(timeVec>=1)=c1_g(2);

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

    % Create basic view and store graphics handle to initiate animation
    hf=cFigure; %Open figure
    gtitle([febioFebFileNamePart,': Press play to animate']);

    subplot(1,2,1); hold on;
    title('Ogden parameter c_1');
    xlabel('Time'); ylabel('c_1');
    plot(timeVec,c1_plot,'b-','lineWidth',2);
    plot(timeVec,cg_plot,'r-','lineWidth',2);
    hp1=plot(timeVec(1),c1_plot(1),'b.','MarkerSize',50);
    hp2=plot(timeVec(1),cg_plot(1),'r.','MarkerSize',50);
    legend([hp1 hp2],'Material 1','Material 2');
    axis tight; axis square; set(gca,'fontsize',fontSize);
    grid on;

    subplot(1,2,2); hold on;
    hp3=gpatch(Fb,V_DEF(:,:,end),CV,'k',1); %Add graphics object to animate
    hp3.FaceColor='interp';
    colormap(gjet(250)); hc=colorbar;
    caxis([0 max(E_energy(:))]/10);
    axisGeom(gca,fontSize);
    axis(axisLim(V_DEF)); %Set axis limits statically
    axis manual;
    camlight headlight;
    drawnow;

    % Set up animation features
    animStruct.Time=timeVec; %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

        [CV]=faceToVertexMeasure(E,V,E_energy(:,:,qt));

        %Set entries in animation structure
        animStruct.Handles{qt}=[hp3 hp3 hp1 hp1 hp2 hp2]; %Handles of objects to animate
        animStruct.Props{qt}={'Vertices','CData','XData','YData','XData','YData'}; %Properties of objects to animate
        animStruct.Set{qt}={V_DEF(:,:,qt),CV,timeVec(qt),c1_plot(qt),timeVec(qt),cg_plot(qt)}; %Property values for to set in order to animate
    end
    anim8(hf,animStruct); %Initiate animation feature
    drawnow;

end

GIBBON www.gibboncode.org

Kevin Mattheus Moerman, [email protected]

GIBBON footer text

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

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

Copyright (C) 2006-2022 Kevin Mattheus Moerman and the GIBBON contributors

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

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

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

Published with MATLAB® R2022b