DEMO_febio_0065_clamp_tension_test

Below is a demonstration for: 1) The creation of an FEBio model for clamped tensile testing 2) The use of multiple steps 4) Running an FEBio job with MATLAB 5) Importing FEBio results into MATLAB

Keywords
Plot settings
Control parameters
Computing derived parameters
Creating strip region
Merging box sets
Define clamping surfaces
Define BC's
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
compression, tension, compressive, tensile
displacement control, displacement boundary condition
pentahedral penta6
tetrahedral tet4
cube, box, rectangular
Lattice
static, solid
hyperelastic, Ogden
displacement logfile
stress logfile

clear; close all; clc;

Plot settings

fontSize=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=fullfile(savePath,[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

%Specifying dimensions and number of elements
pointspacing=1;
sampleWidth=10;
sampleThickness=2;
sampleClampedHeight=sampleWidth;
sampleGripGripHeight=sampleWidth.*2;
tensileStrain=0.3;
clampCompressiveStrain=0.3;

%Initial material parameter set
c1=1e-3;
m1=2;
k_factor=100;
k=c1*k_factor;

% 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=12; %Optimum number of iterations
max_retries=25; %Maximum number of retires
dtmin=(1/numTimeSteps)/100; %Minimum time step size
dtmax=1/numTimeSteps; %Maximum time step size

min_residual=1e-20;
symmetric_stiffness=0;
runMode='external'; %'internal' or 'external'

Computing derived parameters

numElementsWidth=round(sampleWidth/pointspacing);
numElementsWidth=numElementsWidth+iseven(numElementsWidth); %Force uneven so there is a middle element
numElementsThickness=round(sampleThickness/pointspacing)+1;
numElementsGripGripHeight=round(sampleGripGripHeight/pointspacing);
numElementsGripGripHeight=numElementsGripGripHeight+iseven(numElementsGripGripHeight); %Force uneven so there is a middle element
numElementsClampedHeight=round(sampleClampedHeight/pointspacing);

clampCompressiveDisplacement=(sampleThickness.*clampCompressiveStrain)/2;
clampTensionDisplacement=(sampleGripGripHeight.*tensileStrain);

Creating strip region

The region consists of three "boxes" which define the upper and lower clamped regions as well as the central region.

%Create box 1
boxDim=[sampleWidth sampleThickness sampleClampedHeight]; %Dimensions
boxEl=[numElementsWidth numElementsThickness numElementsClampedHeight]; %Number of elements
[box1]=hexMeshBox(boxDim,boxEl);
E1=box1.E;
V1=box1.V;
F1=box1.F;
Fb1=box1.Fb;
faceBoundaryMarker1=box1.faceBoundaryMarker;

%Create box 3 by copying the first
E3=E1;
V3=V1;
F3=F1;
Fb3=Fb1;
faceBoundaryMarker3=faceBoundaryMarker1;

%Shift first box up
V1(:,3)=V1(:,3)+sampleGripGripHeight/2+sampleClampedHeight/2;

%Shift third box down
V3(:,3)=V3(:,3)-sampleGripGripHeight/2-sampleClampedHeight/2;

%Create box 2
boxDim=[sampleWidth sampleThickness sampleGripGripHeight]; %Dimensions
boxEl=[numElementsWidth numElementsThickness numElementsGripGripHeight]; %Number of elements
[box2]=hexMeshBox(boxDim,boxEl);
E2=box2.E;
V2=box2.V;
F2=box2.F;
Fb2=box2.Fb;
faceBoundaryMarker2=box2.faceBoundaryMarker;

Merging box sets

%Join color data
faceBoundaryMarker_all=[faceBoundaryMarker1; faceBoundaryMarker2; faceBoundaryMarker3;];
faceBoundaryMarker_ind=[ones(size(Fb1,1),1);2*ones(size(Fb2,1),1); 3*ones(size(Fb3,1),1);];

%Join nodes, elements, and faces
V=[V1;V2;V3];
E=[E1;E2+size(V1,1);E3+size(V1,1)+size(V2,1)];
F=[F1;F2+size(V1,1);F3+size(V1,1)+size(V2,1)];
Fb=[Fb1;Fb2+size(V1,1);Fb3+size(V1,1)+size(V2,1)];

%Merge nodes
[F,V,ind1,ind2]=mergeVertices(F,V);
E=ind2(E);
Fb=ind2(Fb);

Plotting surface models

cFigure;
subplot(1,2,1); hold on;
title('Merged box sets','FontSize',fontSize);
gpatch(Fb,V,faceBoundaryMarker_all);
axisGeom(gca,fontSize);
colormap(gca,gjet(250)); icolorbar;

subplot(1,2,2); hold on;
title('Merged box sets','FontSize',fontSize);
gpatch(Fb,V,faceBoundaryMarker_ind);
axisGeom(gca,fontSize);
colormap(gca,gjet(250)); icolorbar;
drawnow;

Define clamping surfaces

logicContactSurf1=faceBoundaryMarker_all==3 & faceBoundaryMarker_ind==1;
Fc1=Fb(logicContactSurf1,:);

logicContactSurf2=faceBoundaryMarker_all==4 & faceBoundaryMarker_ind==1;
Fc2=Fb(logicContactSurf2,:);

logicContactSurf3=faceBoundaryMarker_all==4 & faceBoundaryMarker_ind==3;
Fc3=Fb(logicContactSurf3,:);

logicContactSurf4=faceBoundaryMarker_all==3 & faceBoundaryMarker_ind==3;
Fc4=Fb(logicContactSurf4,:);

Visualize clamping surfaces

cFigure; hold on;
title('Clamping surfaces','FontSize',fontSize);
gpatch(Fb,V,'kw','none',0.25);
gpatch(Fc1,V,'rw','k',1);
gpatch(Fc2,V,'gw','k',1);
gpatch(Fc3,V,'bw','k',1);
gpatch(Fc4,V,'yw','k',1);
axisGeom(gca,fontSize);
camlight headlight;
drawnow;

Define BC's

bcPrescribeList1=unique(Fc1(:));
bcPrescribeMagnitudes11=zeros(numel(bcPrescribeList1),3);
bcPrescribeMagnitudes11(:,2)=clampCompressiveDisplacement; %In step 1
bcPrescribeMagnitudes12=zeros(numel(bcPrescribeList1),3);
bcPrescribeMagnitudes12(:,3)=clampTensionDisplacement; %In step 2

bcPrescribeList2=unique(Fc2(:));
bcPrescribeMagnitudes21=zeros(numel(bcPrescribeList2),3);
bcPrescribeMagnitudes21(:,2)=-clampCompressiveDisplacement; %In step 1
bcPrescribeMagnitudes22=zeros(numel(bcPrescribeList2),3);
bcPrescribeMagnitudes22(:,3)=clampTensionDisplacement; %In step 2

bcPrescribeList3=unique(Fc3(:));
bcPrescribeMagnitudes31=zeros(numel(bcPrescribeList3),3);
bcPrescribeMagnitudes31(:,2)=-clampCompressiveDisplacement; %In step 1
bcPrescribeMagnitudes32=zeros(numel(bcPrescribeList3),3);

bcPrescribeList4=unique(Fc4(:));
bcPrescribeMagnitudes41=zeros(numel(bcPrescribeList4),3);
bcPrescribeMagnitudes41(:,2)=clampCompressiveDisplacement; %In step 1
bcPrescribeMagnitudes42=zeros(numel(bcPrescribeList4),3); %In step 2

Visualize boundary conditions

cFigure; hold on;
title('Complete model','FontSize',fontSize);

gpatch(Fb,V,'kw','none',0.25);

plotV(V(bcPrescribeList1,:),'r.','MarkerSize',25);
plotV(V(bcPrescribeList2,:),'g.','MarkerSize',25);
plotV(V(bcPrescribeList3,:),'b.','MarkerSize',25);
plotV(V(bcPrescribeList4,:),'y.','MarkerSize',25);

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';

%Create control structure for use by all steps
stepStruct.Control.analysis.ATTR.type='static';
stepStruct.Control.time_steps=numTimeSteps;
stepStruct.Control.step_size=1/numTimeSteps;
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;
stepStruct.Control.max_refs=max_refs;
stepStruct.Control.max_ups=max_ups;
stepStruct.Control.symmetric_stiffness=symmetric_stiffness;
stepStruct.Control.min_residual=min_residual;

%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{1}.ATTR.id=1;
febio_spec.Step{1}.Control=stepStruct.Control;
febio_spec.Step{2}.ATTR.id=2;
febio_spec.Step{2}.Control=stepStruct.Control;

%Material section
febio_spec.Material.material{1}.ATTR.id=1;
febio_spec.Material.material{1}.ATTR.name='Normal material';
febio_spec.Material.material{1}.ATTR.type='Ogden';
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;

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

% -> Elements
febio_spec.Geometry.Elements{1}.ATTR.type='hex8'; %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='Strip'; %Name of the element set
febio_spec.Geometry.Elements{1}.elem.VAL=E;
febio_spec.Geometry.Elements{1}.elem.ATTR.id=(1:size(E,1))'; %Element material id's

% -> NodeSets
febio_spec.Geometry.NodeSet{1}.ATTR.name='bcPrescribeList1';
febio_spec.Geometry.NodeSet{1}.node.ATTR.id=bcPrescribeList1(:);
febio_spec.Geometry.NodeSet{2}.ATTR.name='bcPrescribeList2';
febio_spec.Geometry.NodeSet{2}.node.ATTR.id=bcPrescribeList2(:);
febio_spec.Geometry.NodeSet{3}.ATTR.name='bcPrescribeList3';
febio_spec.Geometry.NodeSet{3}.node.ATTR.id=bcPrescribeList3(:);
febio_spec.Geometry.NodeSet{4}.ATTR.name='bcPrescribeList4';
febio_spec.Geometry.NodeSet{4}.node.ATTR.id=bcPrescribeList4(:);

%Boundary condition section
% -> Prescribe boundary conditions
%STEP 1 Clamp compression

%Set 1
febio_spec.Step{1}.Boundary.prescribe{1}.ATTR.bc='x';
febio_spec.Step{1}.Boundary.prescribe{1}.ATTR.node_set=febio_spec.Geometry.NodeSet{1}.ATTR.name;
febio_spec.Step{1}.Boundary.prescribe{1}.scale.ATTR.lc=1;
febio_spec.Step{1}.Boundary.prescribe{1}.scale.VAL=1;
febio_spec.Step{1}.Boundary.prescribe{1}.relative=1;
febio_spec.Step{1}.Boundary.prescribe{1}.value=bcPrescribeMagnitudes11(:,1);

febio_spec.Step{1}.Boundary.prescribe{2}.ATTR.bc='y';
febio_spec.Step{1}.Boundary.prescribe{2}.ATTR.node_set=febio_spec.Geometry.NodeSet{1}.ATTR.name;
febio_spec.Step{1}.Boundary.prescribe{2}.scale.ATTR.lc=1;
febio_spec.Step{1}.Boundary.prescribe{2}.scale.VAL=1;
febio_spec.Step{1}.Boundary.prescribe{2}.relative=1;
febio_spec.Step{1}.Boundary.prescribe{2}.value=bcPrescribeMagnitudes11(:,2);

febio_spec.Step{1}.Boundary.prescribe{3}.ATTR.bc='z';
febio_spec.Step{1}.Boundary.prescribe{3}.ATTR.node_set=febio_spec.Geometry.NodeSet{1}.ATTR.name;
febio_spec.Step{1}.Boundary.prescribe{3}.scale.ATTR.lc=1;
febio_spec.Step{1}.Boundary.prescribe{3}.scale.VAL=1;
febio_spec.Step{1}.Boundary.prescribe{3}.relative=1;
febio_spec.Step{1}.Boundary.prescribe{3}.value=bcPrescribeMagnitudes11(:,3);

%Set 2
febio_spec.Step{1}.Boundary.prescribe{4}.ATTR.bc='x';
febio_spec.Step{1}.Boundary.prescribe{4}.ATTR.node_set=febio_spec.Geometry.NodeSet{2}.ATTR.name;
febio_spec.Step{1}.Boundary.prescribe{4}.scale.ATTR.lc=1;
febio_spec.Step{1}.Boundary.prescribe{4}.scale.VAL=1;
febio_spec.Step{1}.Boundary.prescribe{4}.relative=1;
febio_spec.Step{1}.Boundary.prescribe{4}.value=bcPrescribeMagnitudes21(:,1);

febio_spec.Step{1}.Boundary.prescribe{5}.ATTR.bc='y';
febio_spec.Step{1}.Boundary.prescribe{5}.ATTR.node_set=febio_spec.Geometry.NodeSet{2}.ATTR.name;
febio_spec.Step{1}.Boundary.prescribe{5}.scale.ATTR.lc=1;
febio_spec.Step{1}.Boundary.prescribe{5}.scale.VAL=1;
febio_spec.Step{1}.Boundary.prescribe{5}.relative=1;
febio_spec.Step{1}.Boundary.prescribe{5}.value=bcPrescribeMagnitudes21(:,2);

febio_spec.Step{1}.Boundary.prescribe{6}.ATTR.bc='z';
febio_spec.Step{1}.Boundary.prescribe{6}.ATTR.node_set=febio_spec.Geometry.NodeSet{2}.ATTR.name;
febio_spec.Step{1}.Boundary.prescribe{6}.scale.ATTR.lc=1;
febio_spec.Step{1}.Boundary.prescribe{6}.scale.VAL=1;
febio_spec.Step{1}.Boundary.prescribe{6}.relative=1;
febio_spec.Step{1}.Boundary.prescribe{6}.value=bcPrescribeMagnitudes21(:,3);

%Set 3
febio_spec.Step{1}.Boundary.prescribe{7}.ATTR.bc='x';
febio_spec.Step{1}.Boundary.prescribe{7}.ATTR.node_set=febio_spec.Geometry.NodeSet{3}.ATTR.name;
febio_spec.Step{1}.Boundary.prescribe{7}.scale.ATTR.lc=1;
febio_spec.Step{1}.Boundary.prescribe{7}.scale.VAL=1;
febio_spec.Step{1}.Boundary.prescribe{7}.relative=1;
febio_spec.Step{1}.Boundary.prescribe{7}.value=bcPrescribeMagnitudes31(:,1);

febio_spec.Step{1}.Boundary.prescribe{8}.ATTR.bc='y';
febio_spec.Step{1}.Boundary.prescribe{8}.ATTR.node_set=febio_spec.Geometry.NodeSet{3}.ATTR.name;
febio_spec.Step{1}.Boundary.prescribe{8}.scale.ATTR.lc=1;
febio_spec.Step{1}.Boundary.prescribe{8}.scale.VAL=1;
febio_spec.Step{1}.Boundary.prescribe{8}.relative=1;
febio_spec.Step{1}.Boundary.prescribe{8}.value=bcPrescribeMagnitudes31(:,2);

febio_spec.Step{1}.Boundary.prescribe{9}.ATTR.bc='z';
febio_spec.Step{1}.Boundary.prescribe{9}.ATTR.node_set=febio_spec.Geometry.NodeSet{3}.ATTR.name;
febio_spec.Step{1}.Boundary.prescribe{9}.scale.ATTR.lc=1;
febio_spec.Step{1}.Boundary.prescribe{9}.scale.VAL=1;
febio_spec.Step{1}.Boundary.prescribe{9}.relative=1;
febio_spec.Step{1}.Boundary.prescribe{9}.value=bcPrescribeMagnitudes31(:,3);

%Set 4
febio_spec.Step{1}.Boundary.prescribe{10}.ATTR.bc='x';
febio_spec.Step{1}.Boundary.prescribe{10}.ATTR.node_set=febio_spec.Geometry.NodeSet{4}.ATTR.name;
febio_spec.Step{1}.Boundary.prescribe{10}.scale.ATTR.lc=1;
febio_spec.Step{1}.Boundary.prescribe{10}.scale.VAL=1;
febio_spec.Step{1}.Boundary.prescribe{10}.relative=1;
febio_spec.Step{1}.Boundary.prescribe{10}.value=bcPrescribeMagnitudes41(:,1);

febio_spec.Step{1}.Boundary.prescribe{11}.ATTR.bc='y';
febio_spec.Step{1}.Boundary.prescribe{11}.ATTR.node_set=febio_spec.Geometry.NodeSet{4}.ATTR.name;
febio_spec.Step{1}.Boundary.prescribe{11}.scale.ATTR.lc=1;
febio_spec.Step{1}.Boundary.prescribe{11}.scale.VAL=1;
febio_spec.Step{1}.Boundary.prescribe{11}.relative=1;
febio_spec.Step{1}.Boundary.prescribe{11}.value=bcPrescribeMagnitudes41(:,2);

febio_spec.Step{1}.Boundary.prescribe{12}.ATTR.bc='z';
febio_spec.Step{1}.Boundary.prescribe{12}.ATTR.node_set=febio_spec.Geometry.NodeSet{4}.ATTR.name;
febio_spec.Step{1}.Boundary.prescribe{12}.scale.ATTR.lc=1;
febio_spec.Step{1}.Boundary.prescribe{12}.scale.VAL=1;
febio_spec.Step{1}.Boundary.prescribe{12}.relative=1;
febio_spec.Step{1}.Boundary.prescribe{12}.value=bcPrescribeMagnitudes41(:,3);

%STEP 2 Tension
%Set 1
febio_spec.Step{2}.Boundary.prescribe{1}.ATTR.bc='x';
febio_spec.Step{2}.Boundary.prescribe{1}.ATTR.node_set=febio_spec.Geometry.NodeSet{1}.ATTR.name;
febio_spec.Step{2}.Boundary.prescribe{1}.scale.ATTR.lc=2;
febio_spec.Step{2}.Boundary.prescribe{1}.scale.VAL=1;
febio_spec.Step{2}.Boundary.prescribe{1}.relative=1;
febio_spec.Step{2}.Boundary.prescribe{1}.value=bcPrescribeMagnitudes12(:,1);

febio_spec.Step{2}.Boundary.prescribe{2}.ATTR.bc='y';
febio_spec.Step{2}.Boundary.prescribe{2}.ATTR.node_set=febio_spec.Geometry.NodeSet{1}.ATTR.name;
febio_spec.Step{2}.Boundary.prescribe{2}.scale.ATTR.lc=2;
febio_spec.Step{2}.Boundary.prescribe{2}.scale.VAL=1;
febio_spec.Step{2}.Boundary.prescribe{2}.relative=1;
febio_spec.Step{2}.Boundary.prescribe{2}.value=bcPrescribeMagnitudes12(:,2);

febio_spec.Step{2}.Boundary.prescribe{3}.ATTR.bc='z';
febio_spec.Step{2}.Boundary.prescribe{3}.ATTR.node_set=febio_spec.Geometry.NodeSet{1}.ATTR.name;
febio_spec.Step{2}.Boundary.prescribe{3}.scale.ATTR.lc=2;
febio_spec.Step{2}.Boundary.prescribe{3}.scale.VAL=1;
febio_spec.Step{2}.Boundary.prescribe{3}.relative=1;
febio_spec.Step{2}.Boundary.prescribe{3}.value=bcPrescribeMagnitudes12(:,3);

%Set 2
febio_spec.Step{2}.Boundary.prescribe{4}.ATTR.bc='x';
febio_spec.Step{2}.Boundary.prescribe{4}.ATTR.node_set=febio_spec.Geometry.NodeSet{2}.ATTR.name;
febio_spec.Step{2}.Boundary.prescribe{4}.scale.ATTR.lc=2;
febio_spec.Step{2}.Boundary.prescribe{4}.scale.VAL=1;
febio_spec.Step{2}.Boundary.prescribe{4}.relative=1;
febio_spec.Step{2}.Boundary.prescribe{4}.value=bcPrescribeMagnitudes22(:,1);

febio_spec.Step{2}.Boundary.prescribe{5}.ATTR.bc='y';
febio_spec.Step{2}.Boundary.prescribe{5}.ATTR.node_set=febio_spec.Geometry.NodeSet{2}.ATTR.name;
febio_spec.Step{2}.Boundary.prescribe{5}.scale.ATTR.lc=2;
febio_spec.Step{2}.Boundary.prescribe{5}.scale.VAL=1;
febio_spec.Step{2}.Boundary.prescribe{5}.relative=1;
febio_spec.Step{2}.Boundary.prescribe{5}.value=bcPrescribeMagnitudes22(:,2);

febio_spec.Step{2}.Boundary.prescribe{6}.ATTR.bc='z';
febio_spec.Step{2}.Boundary.prescribe{6}.ATTR.node_set=febio_spec.Geometry.NodeSet{2}.ATTR.name;
febio_spec.Step{2}.Boundary.prescribe{6}.scale.ATTR.lc=2;
febio_spec.Step{2}.Boundary.prescribe{6}.scale.VAL=1;
febio_spec.Step{2}.Boundary.prescribe{6}.relative=1;
febio_spec.Step{2}.Boundary.prescribe{6}.value=bcPrescribeMagnitudes22(:,3);

%Set 3
febio_spec.Step{2}.Boundary.prescribe{7}.ATTR.bc='x';
febio_spec.Step{2}.Boundary.prescribe{7}.ATTR.node_set=febio_spec.Geometry.NodeSet{3}.ATTR.name;
febio_spec.Step{2}.Boundary.prescribe{7}.scale.ATTR.lc=2;
febio_spec.Step{2}.Boundary.prescribe{7}.scale.VAL=1;
febio_spec.Step{2}.Boundary.prescribe{7}.relative=1;
febio_spec.Step{2}.Boundary.prescribe{7}.value=bcPrescribeMagnitudes32(:,1);

febio_spec.Step{2}.Boundary.prescribe{8}.ATTR.bc='y';
febio_spec.Step{2}.Boundary.prescribe{8}.ATTR.node_set=febio_spec.Geometry.NodeSet{3}.ATTR.name;
febio_spec.Step{2}.Boundary.prescribe{8}.scale.ATTR.lc=2;
febio_spec.Step{2}.Boundary.prescribe{8}.scale.VAL=1;
febio_spec.Step{2}.Boundary.prescribe{8}.relative=1;
febio_spec.Step{2}.Boundary.prescribe{8}.value=bcPrescribeMagnitudes32(:,2);

febio_spec.Step{2}.Boundary.prescribe{9}.ATTR.bc='z';
febio_spec.Step{2}.Boundary.prescribe{9}.ATTR.node_set=febio_spec.Geometry.NodeSet{3}.ATTR.name;
febio_spec.Step{2}.Boundary.prescribe{9}.scale.ATTR.lc=2;
febio_spec.Step{2}.Boundary.prescribe{9}.scale.VAL=1;
febio_spec.Step{2}.Boundary.prescribe{9}.relative=1;
febio_spec.Step{2}.Boundary.prescribe{9}.value=bcPrescribeMagnitudes32(:,3);

%Set 4
febio_spec.Step{2}.Boundary.prescribe{10}.ATTR.bc='x';
febio_spec.Step{2}.Boundary.prescribe{10}.ATTR.node_set=febio_spec.Geometry.NodeSet{4}.ATTR.name;
febio_spec.Step{2}.Boundary.prescribe{10}.scale.ATTR.lc=2;
febio_spec.Step{2}.Boundary.prescribe{10}.scale.VAL=1;
febio_spec.Step{2}.Boundary.prescribe{10}.relative=1;
febio_spec.Step{2}.Boundary.prescribe{10}.value=bcPrescribeMagnitudes42(:,1);

febio_spec.Step{2}.Boundary.prescribe{11}.ATTR.bc='y';
febio_spec.Step{2}.Boundary.prescribe{11}.ATTR.node_set=febio_spec.Geometry.NodeSet{4}.ATTR.name;
febio_spec.Step{2}.Boundary.prescribe{11}.scale.ATTR.lc=2;
febio_spec.Step{2}.Boundary.prescribe{11}.scale.VAL=1;
febio_spec.Step{2}.Boundary.prescribe{11}.relative=1;
febio_spec.Step{2}.Boundary.prescribe{11}.value=bcPrescribeMagnitudes42(:,2);

febio_spec.Step{2}.Boundary.prescribe{12}.ATTR.bc='z';
febio_spec.Step{2}.Boundary.prescribe{12}.ATTR.node_set=febio_spec.Geometry.NodeSet{4}.ATTR.name;
febio_spec.Step{2}.Boundary.prescribe{12}.scale.ATTR.lc=2;
febio_spec.Step{2}.Boundary.prescribe{12}.scale.VAL=1;
febio_spec.Step{2}.Boundary.prescribe{12}.relative=1;
febio_spec.Step{2}.Boundary.prescribe{12}.value=bcPrescribeMagnitudes42(:,3);


%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=[0 0; 1 1];

febio_spec.LoadData.loadcurve{2}.ATTR.id=2;
febio_spec.LoadData.loadcurve{2}.ATTR.type='linear';
febio_spec.LoadData.loadcurve{2}.point.VAL=[0 0; 1 0; 2 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.node_data{1}.VAL=1:size(V,1);

febio_spec.Output.logfile.element_data{1}.ATTR.file=febioLogFileName_strainEnergy;
febio_spec.Output.logfile.element_data{1}.ATTR.data='Ez';
febio_spec.Output.logfile.element_data{1}.ATTR.delim=',';
febio_spec.Output.logfile.element_data{1}.VAL=1:1: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;
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 --- 27-Jul-2020 12:03:37
Waiting for log file...
Proceeding to check log file...27-Jul-2020 12:03:38
------- converged at time : 0.1
------- converged at time : 0.2
------- converged at time : 0.3
------- converged at time : 0.4
------- converged at time : 0.5
------- converged at time : 0.6
------- converged at time : 0.7
------- converged at time : 0.8
------- converged at time : 0.9
------- converged at time : 1
------- converged at time : 1.1
------- converged at time : 1.2
------- converged at time : 1.3
------- converged at time : 1.4
------- converged at time : 1.5
------- converged at time : 1.6
------- converged at time : 1.7
------- converged at time : 1.8
------- converged at time : 1.9
------- converged at time : 2
--- Done --- 27-Jul-2020 12:03:44

Import FEBio results

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

Importing nodal displacements from a log file

    [time_mat, N_disp_mat,~]=importFEBio_logfile(fullfile(savePath,febioLogFileName_disp)); %Nodal displacements
    time_mat=[0; time_mat(:)]; %Time

    N_disp_mat=N_disp_mat(:,2:end,:);
    sizImport=size(N_disp_mat);
    sizImport(3)=sizImport(3)+1;
    N_disp_mat_n=zeros(sizImport);
    N_disp_mat_n(:,:,2:end)=N_disp_mat;
    N_disp_mat=N_disp_mat_n;
    DN=N_disp_mat(:,:,end);
    DN_magnitude=sqrt(sum(DN(:,3).^2,2));
    V_DEF=N_disp_mat+repmat(V,[1 1 size(N_disp_mat,3)]);

Importing element strain energies from a log file

    [~,E_energy,~]=importFEBio_logfile(fullfile(savePath,febioLogFileName_strainEnergy)); %Element strain energy

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

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

    [F,CF]=element2patch(E,E_energy(:,:,1));
    CF_V=faceToVertexMeasure(F,V,CF);

Plotting the simulated results using anim8 to visualize and animate deformations

    axLim=[min(min(V_DEF,[],3),[],1); max(max(V_DEF,[],3),[],1)];
    indBc=[bcPrescribeList1;bcPrescribeList2;bcPrescribeList3;bcPrescribeList4;];

    % Create basic view and store graphics handle to initiate animation
    hf=cFigure; hold on;%Open figure
    gtitle([febioFebFileNamePart,': Press play to animate']);
    hp1=gpatch(Fb,V_DEF(:,:,end),CF_V,'k',1);
    hp1.FaceColor='interp';
    hp2=plotV(V(indBc,:),'k.','MarkerSize',25);

    axisGeom(gca,fontSize);
    colormap(warmcold(250)); colorbar;
    caxis([-tensileStrain tensileStrain]);
    axis(axLim(:)'); %Set axis limits statically

    camlight headlight; axis off;

    % Set up animation features
    animStruct.Time=time_mat; %The time vector
    for qt=1:1:size(N_disp_mat,3) %Loop over time increments
        V_def=V+N_disp_mat(:,:,qt); %Current nodal coordinates

        [~,CF]=element2patch(E,E_energy(:,:,qt));
        CF_V=faceToVertexMeasure(F,V,CF);

        %Set entries in animation structure
        animStruct.Handles{qt}=[hp1 hp1 hp2 hp2 hp2]; %Handles of objects to animate
        animStruct.Props{qt}={'Vertices','CData','XData','YData','ZData'}; %Properties of objects to animate
        animStruct.Set{qt}={V_def,CF_V,V_def(indBc,1),V_def(indBc,2),V_def(indBc,3)}; %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]

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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/.