DEMO_febio_0066_clamp_tension_test_friction

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
Define rigid clamping surfaces
Join node sets
Get logic for middle elements (to help investigate strain in the middle)
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
Compute grimp implied strain

Keywords

febio_spec version 4.0
febio, FEBio
tension, tensile
displacement control, displacement boundary condition
Hexahedral hex8
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_strain=[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;
appliedLinearStrain=0.3;
clampCompressiveLinearStrain=0.3;

pointSpacingClamp=pointSpacing;
clampExtendAmount=sampleWidth/2;

initialSpacing=0;%pointSpacing/10;

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

% FEA control settings
numTimeSteps=20; %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=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'

%Contact parameters
contactPenalty=10;
contactType='sliding-elastic'; % 'sticky'
laugon=0;
minaug=1;
maxaug=10;
fric_coeff=1;

Computing derived parameters

sampleHeight=sampleGripGripHeight+2*sampleClampedHeight;

numElementsWidthStrip=ceil(sampleWidth/pointSpacing);
numElementsWidthStrip=numElementsWidthStrip+iseven(numElementsWidthStrip); %Force uneven so there is a middle element
numElementsThicknessStrip=ceil(round(sampleThickness/pointSpacing));
numElementsHeightStrip=ceil(round(sampleHeight/pointSpacing));
numElementsHeightStrip=numElementsHeightStrip+iseven(numElementsHeightStrip); %Force uneven so there is a middle element

clampWidth=sampleWidth+(2*clampExtendAmount);
clampHeight=sampleClampedHeight+(clampExtendAmount);
numElementsWidthClamp=ceil(clampWidth/pointSpacingClamp);
numElementsHeightClamp=ceil(clampHeight/pointSpacingClamp);

clampCompressiveDisplacement=((sampleThickness.*clampCompressiveLinearStrain)/2)+initialSpacing;
clampTensionDisplacement=(sampleGripGripHeight.*appliedLinearStrain);

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 sampleHeight]; %Dimensions
boxElem=[numElementsWidthStrip numElementsThicknessStrip numElementsHeightStrip]; %Number of elements
[boxMesh]=hexMeshBox(boxDim,boxElem);
E=boxMesh.E;
V=boxMesh.V;
F=boxMesh.F;
Fb=boxMesh.Fb;
faceBoundaryMarker=boxMesh.faceBoundaryMarker;

% R1=euler2DCM([0 (8/180)*pi 0]);
% V=V*R1;

Plotting surface models

cFigure; hold on;
title('The strip mesh','FontSize',fontSize);
gpatch(Fb,V,faceBoundaryMarker);
axisGeom(gca,fontSize);
colormap(gca,gjet(250)); icolorbar;
drawnow;

Define rigid clamping surfaces

[Fc,Vc]=quadPlate([clampWidth clampHeight],[numElementsWidthClamp numElementsHeightClamp]);
R=euler2DCM([-pi/2 0 0]);
Vc=Vc*R;


Fc1=Fc;
Vc1=Vc;
Vc1(:,2)=Vc1(:,2)+sampleThickness/2+initialSpacing;
Vc1(:,3)=Vc1(:,3)-min(Vc1(:,3))+sampleGripGripHeight/2;

Vc2=Vc1;
Vc2(:,2)=-Vc2(:,2);
Fc2=fliplr(Fc);

Fc3=fliplr(Fc2);
Vc3=-Vc2;

Fc4=fliplr(Fc1);
Vc4=-Vc1;

Visualize clamping surfaces

cFigure; hold on;
title('Clamping surfaces','FontSize',fontSize);
gpatch(Fb,V,'kw','none',0.25);
gpatch(Fc1,Vc1,'rw','k',1);
patchNormPlot(Fc1,Vc1);
gpatch(Fc2,Vc2,'gw','k',1);
patchNormPlot(Fc2,Vc2);
gpatch(Fc3,Vc3,'bw','k',1);
patchNormPlot(Fc3,Vc3);
gpatch(Fc4,Vc4,'yw','k',1);
patchNormPlot(Fc4,Vc4);
axisGeom(gca,fontSize);
camlight headlight;
drawnow;

Join node sets

Fc1=Fc1+size(V,1);
Fc2=Fc2+size(V,1)+1*size(Vc1,1);
Fc3=Fc3+size(V,1)+2*size(Vc1,1);
Fc4=Fc4+size(V,1)+3*size(Vc1,1);

V=[V;Vc1;Vc2;Vc3;Vc4];

Fc=[Fc1;Fc2;Fc3;Fc4];
Cc=repmat(1:4,size(Fc1,1),1);
Cc=Cc(:);

Fb1=Fb(faceBoundaryMarker==3,:);
Fb2=Fb(faceBoundaryMarker==4,:);

Visualize boundary conditions

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

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

gpatch(Fb1,V,'cw','k',1);
patchNormPlot(Fb1,V);

gpatch(Fb2,V,'kw','k',1);
patchNormPlot(Fb2,V);

gpatch(Fc1,V,'rw','k',1);
patchNormPlot(Fc1,V);

gpatch(Fc2,V,'gw','k',1);
patchNormPlot(Fc2,V);

gpatch(Fc3,V,'bw','k',1);
patchNormPlot(Fc3,V);

gpatch(Fc4,V,'yw','k',1);
patchNormPlot(Fc4,V);

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

Get logic for middle elements (to help investigate strain in the middle)

searchTol=pointSpacing/1000;
VE=patchCentre(E,V);
logicMiddleElements= VE(:,3)<searchTol & VE(:,3)>-searchTol;

[FM]=element2patch(E(logicMiddleElements,:),[],'hex8');

cFigure; hold on;
gpatch(Fb,V,'kw','k',0.25);

gpatch(FM,V,'rw','k',1);

% hp(1)=plotV(V(bcPrescribeList1,:),'r.','MarkerSize',25);
% legend(hp,{'Node set 1','Node set 2','Node set 3','Node set 4'})
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='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;
stepStruct.Control.solver.symmetric_stiffness=symmetric_stiffness;

%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.id=1;
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;

materialName2='Material2';
febio_spec.Material.material{2}.ATTR.name=materialName2;
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=mean(Vc1,1);

materialName3='Material3';
febio_spec.Material.material{3}.ATTR.name=materialName3;
febio_spec.Material.material{3}.ATTR.type='rigid body';
febio_spec.Material.material{3}.ATTR.id=3;
febio_spec.Material.material{3}.density=1;
febio_spec.Material.material{3}.center_of_mass=mean(Vc2,1);

materialName4='Material4';
febio_spec.Material.material{4}.ATTR.name=materialName4;
febio_spec.Material.material{4}.ATTR.type='rigid body';
febio_spec.Material.material{4}.ATTR.id=4;
febio_spec.Material.material{4}.density=1;
febio_spec.Material.material{4}.center_of_mass=mean(Vc3,1);

materialName5='Material5';
febio_spec.Material.material{5}.ATTR.name=materialName5;
febio_spec.Material.material{5}.ATTR.type='rigid body';
febio_spec.Material.material{5}.ATTR.id=5;
febio_spec.Material.material{5}.density=1;
febio_spec.Material.material{5}.center_of_mass=mean(Vc4,1);

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

% -> Elements
partName1='Part1_strip';
febio_spec.Mesh.Elements{1}.ATTR.name=partName1; %Name of the element set
febio_spec.Mesh.Elements{1}.ATTR.type='hex8'; %Element type of this set
febio_spec.Mesh.Elements{1}.ATTR.mat=1; %material index for this set
febio_spec.Mesh.Elements{1}.elem.VAL=E;
febio_spec.Mesh.Elements{1}.elem.ATTR.id=mcol(1:size(E,1)); %Element material id's

partName2='Part2_Grip1';
febio_spec.Mesh.Elements{2}.ATTR.name=partName2; %Name of the element set
febio_spec.Mesh.Elements{2}.ATTR.type='quad4'; %Element type of this set
febio_spec.Mesh.Elements{2}.ATTR.mat=2; %material index for this set
febio_spec.Mesh.Elements{2}.elem.VAL=Fc1;
febio_spec.Mesh.Elements{2}.elem.ATTR.id=size(E,1)+mcol(1:size(Fc1,1)); %Element material id's

partName3='Part3_Grip2';
febio_spec.Mesh.Elements{3}.ATTR.name=partName3; %Name of the element set
febio_spec.Mesh.Elements{3}.ATTR.type='quad4'; %Element type of this set
febio_spec.Mesh.Elements{3}.ATTR.mat=3; %material index for this set
febio_spec.Mesh.Elements{3}.elem.VAL=Fc2;
febio_spec.Mesh.Elements{3}.elem.ATTR.id=size(E,1)+size(Fc1,1)+mcol(1:size(Fc2,1)); %Element material id's

partName4='Part4_Grip3';
febio_spec.Mesh.Elements{4}.ATTR.name=partName4; %Name of the element set
febio_spec.Mesh.Elements{4}.ATTR.type='quad4'; %Element type of this set
febio_spec.Mesh.Elements{4}.ATTR.mat=4; %material index for this set
febio_spec.Mesh.Elements{4}.elem.VAL=Fc3;
febio_spec.Mesh.Elements{4}.elem.ATTR.id=size(E,1)+2*size(Fc1,1)+mcol(1:size(Fc3,1)); %Element material id's

partName5='Part5_Grip4';
febio_spec.Mesh.Elements{5}.ATTR.name=partName5; %Name of the element set
febio_spec.Mesh.Elements{5}.ATTR.type='quad4'; %Element type of this set
febio_spec.Mesh.Elements{5}.ATTR.mat=5; %material index for this set
febio_spec.Mesh.Elements{5}.elem.VAL=Fc4;
febio_spec.Mesh.Elements{5}.elem.ATTR.id=size(E,1)+3*size(Fc1,1)+mcol(1:size(Fc4,1)); %Element material id's

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

febio_spec.MeshDomains.ShellDomain{1}.ATTR.name=partName2;
febio_spec.MeshDomains.ShellDomain{1}.ATTR.mat=materialName2;

febio_spec.MeshDomains.ShellDomain{2}.ATTR.name=partName3;
febio_spec.MeshDomains.ShellDomain{2}.ATTR.mat=materialName3;

febio_spec.MeshDomains.ShellDomain{3}.ATTR.name=partName4;
febio_spec.MeshDomains.ShellDomain{3}.ATTR.mat=materialName4;

febio_spec.MeshDomains.ShellDomain{4}.ATTR.name=partName5;
febio_spec.MeshDomains.ShellDomain{4}.ATTR.mat=materialName5;

% -> Surfaces
febio_spec.Mesh.Surface{1}.ATTR.name='contact_secondary1';
febio_spec.Mesh.Surface{1}.quad4.ATTR.id=mcol(1:1:size(Fc1,1));
febio_spec.Mesh.Surface{1}.quad4.VAL=Fc1;

febio_spec.Mesh.Surface{2}.ATTR.name='contact_secondary2';
febio_spec.Mesh.Surface{2}.quad4.ATTR.id=mcol(1:1:size(Fc2,1));
febio_spec.Mesh.Surface{2}.quad4.VAL=Fc2;

febio_spec.Mesh.Surface{3}.ATTR.name='contact_secondary3';
febio_spec.Mesh.Surface{3}.quad4.ATTR.id=mcol(1:1:size(Fc3,1));
febio_spec.Mesh.Surface{3}.quad4.VAL=Fc3;

febio_spec.Mesh.Surface{4}.ATTR.name='contact_secondary4';
febio_spec.Mesh.Surface{4}.quad4.ATTR.id=mcol(1:1:size(Fc4,1));
febio_spec.Mesh.Surface{4}.quad4.VAL=Fc4;

febio_spec.Mesh.Surface{5}.ATTR.name='contact_primary1';
febio_spec.Mesh.Surface{5}.quad4.ATTR.id=mcol(1:1:size(Fb1,1));
febio_spec.Mesh.Surface{5}.quad4.VAL=Fb1;

febio_spec.Mesh.Surface{6}.ATTR.name='contact_primary2';
febio_spec.Mesh.Surface{6}.quad4.ATTR.id=mcol(1:1:size(Fb2,1));
febio_spec.Mesh.Surface{6}.quad4.VAL=Fb2;

% -> Surface pairs
for q=1:1:4
    if iseven(q)
        indStrip=5;
    else
        indStrip=6;
    end
    febio_spec.Mesh.SurfacePair{q}.ATTR.name=['Contact_',num2str(q)];
    febio_spec.Mesh.SurfacePair{q}.primary=febio_spec.Mesh.Surface{indStrip}.ATTR.name;
    febio_spec.Mesh.SurfacePair{q}.secondary=febio_spec.Mesh.Surface{q}.ATTR.name;
end

%Rigid section

rbIds=[2 3 4 5]; %Rigid body ids
s=[-1 1 -1 1]; %sign/multiplier
bcId=0;
for q=1:1:numel(rbIds)

    bcId=bcId+1;

    % ->Rigid body fix boundary conditions
    febio_spec.Step.step{1}.Rigid.rigid_bc{bcId}.ATTR.name=['RigidFix_rb',num2str(rbIds(q)),'_01'];
    febio_spec.Step.step{1}.Rigid.rigid_bc{bcId}.ATTR.type='rigid_fixed';
    febio_spec.Step.step{1}.Rigid.rigid_bc{bcId}.rb=rbIds(q);
    febio_spec.Step.step{1}.Rigid.rigid_bc{bcId}.Rx_dof=1;
    %febio_spec.Step.step{1}.Rigid.rigid_bc{bcId}.Ry_dof=1;
    febio_spec.Step.step{1}.Rigid.rigid_bc{bcId}.Rz_dof=1;
    febio_spec.Step.step{1}.Rigid.rigid_bc{bcId}.Ru_dof=1;
    febio_spec.Step.step{1}.Rigid.rigid_bc{bcId}.Rv_dof=1;
    febio_spec.Step.step{1}.Rigid.rigid_bc{bcId}.Rw_dof=1;

    bcId=bcId+1;

    % ->Rigid body prescribe boundary conditions
    febio_spec.Step.step{1}.Rigid.rigid_bc{bcId}.ATTR.name=['RigidPrescribe_rb',num2str(rbIds(q)),'_01'];
    febio_spec.Step.step{1}.Rigid.rigid_bc{bcId}.ATTR.type='rigid_displacement';
    febio_spec.Step.step{1}.Rigid.rigid_bc{bcId}.rb=rbIds(q);
    febio_spec.Step.step{1}.Rigid.rigid_bc{bcId}.dof='y';
    febio_spec.Step.step{1}.Rigid.rigid_bc{bcId}.value.ATTR.lc=1;
    febio_spec.Step.step{1}.Rigid.rigid_bc{bcId}.value.VAL=s(q).*clampCompressiveDisplacement;
    febio_spec.Step.step{1}.Rigid.rigid_bc{bcId}.relative=0;

end

rbIds=[2 3 4 5]; %Rigid body ids
s=[1 1 0 0]; %sign/multiplier
bcId=0;
for q=1:1:numel(rbIds)

    bcId=bcId+1;

    % ->Rigid body fix boundary conditions
    febio_spec.Step.step{2}.Rigid.rigid_bc{bcId}.ATTR.name=['RigidFix_rb',num2str(rbIds(q)),'_02'];
    febio_spec.Step.step{2}.Rigid.rigid_bc{bcId}.ATTR.type='rigid_fixed';
    febio_spec.Step.step{2}.Rigid.rigid_bc{bcId}.rb=rbIds(q);
    febio_spec.Step.step{2}.Rigid.rigid_bc{bcId}.Rx_dof=1;
    febio_spec.Step.step{2}.Rigid.rigid_bc{bcId}.Ry_dof=1;
    %febio_spec.Step.step{2}.Rigid.rigid_bc{bcId}.Rz_dof=1;
    febio_spec.Step.step{2}.Rigid.rigid_bc{bcId}.Ru_dof=1;
    febio_spec.Step.step{2}.Rigid.rigid_bc{bcId}.Rv_dof=1;
    febio_spec.Step.step{2}.Rigid.rigid_bc{bcId}.Rw_dof=1;

    bcId=bcId+1;

    % ->Rigid body prescribe boundary conditions
    febio_spec.Step.step{2}.Rigid.rigid_bc{bcId}.ATTR.name=['RigidPrescribe_rb',num2str(rbIds(q)),'_02'];
    febio_spec.Step.step{2}.Rigid.rigid_bc{bcId}.ATTR.type='rigid_displacement';
    febio_spec.Step.step{2}.Rigid.rigid_bc{bcId}.rb=rbIds(q);
    febio_spec.Step.step{2}.Rigid.rigid_bc{bcId}.dof='z';
    febio_spec.Step.step{2}.Rigid.rigid_bc{bcId}.value.ATTR.lc=2;
    febio_spec.Step.step{2}.Rigid.rigid_bc{bcId}.value.VAL=s(q).*clampTensionDisplacement;
    febio_spec.Step.step{2}.Rigid.rigid_bc{bcId}.relative=1;

end

%Contact section
for q=1:1:4
    %Contact section
    switch contactType
        case 'sliding-elastic'
            febio_spec.Contact.contact{q}.ATTR.type=contactType;
            febio_spec.Contact.contact{q}.ATTR.surface_pair=febio_spec.Mesh.SurfacePair{q}.ATTR.name;
            febio_spec.Contact.contact{q}.two_pass=0;
            febio_spec.Contact.contact{q}.laugon=laugon;
            febio_spec.Contact.contact{q}.tolerance=0.2;
            febio_spec.Contact.contact{q}.gaptol=0;
            febio_spec.Contact.contact{q}.minaug=minaug;
            febio_spec.Contact.contact{q}.maxaug=maxaug;
            febio_spec.Contact.contact{q}.search_tol=0.01;
            febio_spec.Contact.contact{q}.search_radius=0.1*sqrt(sum((max(V,[],1)-min(V,[],1)).^2,2));
            febio_spec.Contact.contact{q}.symmetric_stiffness=0;
            febio_spec.Contact.contact{q}.auto_penalty=1;
            febio_spec.Contact.contact{q}.update_penalty=1;
            febio_spec.Contact.contact{q}.penalty=contactPenalty;
            febio_spec.Contact.contact{q}.fric_coeff=fric_coeff;
        case 'sticky'
            febio_spec.Contact.contact{q}.ATTR.type=contactType;
            febio_spec.Contact.contact{q}.ATTR.surface_pair=febio_spec.Mesh.SurfacePair{q}.ATTR.name;

            febio_spec.Contact.contact{q}.penalty=contactPenalty;

            febio_spec.Contact.contact{q}.laugon=laugon;
            febio_spec.Contact.contact{q}.minaug=minaug;
            febio_spec.Contact.contact{q}.maxaug=maxaug;
            febio_spec.Contact.contact{q}.tolerance=0.2;

            febio_spec.Contact.contact{q}.search_tolerance=0.01;
            febio_spec.Contact.contact{q}.max_traction=0;
            febio_spec.Contact.contact{q}.snap_tol=0.01;
    end
end

%LoadData section
% -> load_controller
febio_spec.LoadData.load_controller{1}.ATTR.name='LC_1';
febio_spec.LoadData.load_controller{1}.ATTR.id=1;
febio_spec.LoadData.load_controller{1}.ATTR.type='loadcurve';
febio_spec.LoadData.load_controller{1}.interpolate='LINEAR';
%febio_spec.LoadData.load_controller{1}.extend='CONSTANT';
febio_spec.LoadData.load_controller{1}.points.pt.VAL=[0 0; 1 1; 2 1];

%LoadData section
% -> load_controller
febio_spec.LoadData.load_controller{2}.ATTR.name='LC_2';
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}.extend='CONSTANT';
febio_spec.LoadData.load_controller{2}.points.pt.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.element_data{1}.ATTR.file=febioLogFileName_strain;
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);

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

Quick viewing of the FEBio input file structure

The febView function can be used to view the xml structure in a MATLAB figure window.

febView(febio_spec); %Viewing the febio file

Exporting the FEBio input file

Exporting the febio_spec structure to an FEBio input file is done using the febioStruct2xml function.

febioStruct2xml(febio_spec,febioFebFileName); %Exporting to file and domNode

Running the FEBio analysis

To run the analysis defined by the created FEBio input file the runMonitorFEBio function is used. The input for this function is a structure defining job settings e.g. the FEBio input file name. The optional output runFlag informs the user if the analysis was run succesfully.

febioAnalysis.run_filename=febioFebFileName; %The input file name
febioAnalysis.run_logname=febioLogFileName; %The name for the log file
febioAnalysis.disp_on=1; %Display information on the command window
febioAnalysis.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!!!!!!!!

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-------->    RUNNING/MONITORING FEBIO JOB    <-------- 30-Apr-2023 08:48:11
FEBio path: /home/kevin/FEBioStudio/bin/febio4
# Attempt removal of existing log files                30-Apr-2023 08:48:11
 * Removal succesful                                   30-Apr-2023 08:48:11
# Attempt removal of existing .xplt files              30-Apr-2023 08:48:11
 * Removal succesful                                   30-Apr-2023 08:48:11
# Starting FEBio...                                    30-Apr-2023 08:48:11
  Max. total analysis time is: 1e+99 s
 * Waiting for log file creation                       30-Apr-2023 08:48:11
   Max. wait time: 10 s
 * Log file found.                                     30-Apr-2023 08:48:11
# Parsing log file...                                  30-Apr-2023 08:48:11
    number of iterations   : 4                         30-Apr-2023 08:48:11
    number of reformations : 4                         30-Apr-2023 08:48:11
------- converged at time : 0.05                       30-Apr-2023 08:48:11
    number of iterations   : 4                         30-Apr-2023 08:48:11
    number of reformations : 4                         30-Apr-2023 08:48:11
------- converged at time : 0.1                        30-Apr-2023 08:48:11
    number of iterations   : 4                         30-Apr-2023 08:48:11
    number of reformations : 4                         30-Apr-2023 08:48:11
------- converged at time : 0.15                       30-Apr-2023 08:48:11
    number of iterations   : 5                         30-Apr-2023 08:48:12
    number of reformations : 5                         30-Apr-2023 08:48:12
------- converged at time : 0.2                        30-Apr-2023 08:48:12
    number of iterations   : 7                         30-Apr-2023 08:48:12
    number of reformations : 7                         30-Apr-2023 08:48:12
------- converged at time : 0.25                       30-Apr-2023 08:48:12
    number of iterations   : 4                         30-Apr-2023 08:48:12
    number of reformations : 4                         30-Apr-2023 08:48:12
------- converged at time : 0.296328                   30-Apr-2023 08:48:12
    number of iterations   : 4                         30-Apr-2023 08:48:12
    number of reformations : 4                         30-Apr-2023 08:48:12
------- converged at time : 0.343391                   30-Apr-2023 08:48:12
    number of iterations   : 4                         30-Apr-2023 08:48:13
    number of reformations : 4                         30-Apr-2023 08:48:13
------- converged at time : 0.391041                   30-Apr-2023 08:48:13
    number of iterations   : 4                         30-Apr-2023 08:48:13
    number of reformations : 4                         30-Apr-2023 08:48:13
------- converged at time : 0.439161                   30-Apr-2023 08:48:13
    number of iterations   : 4                         30-Apr-2023 08:48:13
    number of reformations : 4                         30-Apr-2023 08:48:13
------- converged at time : 0.487657                   30-Apr-2023 08:48:13
    number of iterations   : 4                         30-Apr-2023 08:48:13
    number of reformations : 4                         30-Apr-2023 08:48:13
------- converged at time : 0.536453                   30-Apr-2023 08:48:13
    number of iterations   : 5                         30-Apr-2023 08:48:13
    number of reformations : 5                         30-Apr-2023 08:48:13
------- converged at time : 0.585491                   30-Apr-2023 08:48:13
    number of iterations   : 11                        30-Apr-2023 08:48:14
    number of reformations : 11                        30-Apr-2023 08:48:14
------- converged at time : 0.63462                    30-Apr-2023 08:48:14
    number of iterations   : 4                         30-Apr-2023 08:48:14
    number of reformations : 4                         30-Apr-2023 08:48:14
------- converged at time : 0.671035                   30-Apr-2023 08:48:14
    number of iterations   : 5                         30-Apr-2023 08:48:14
    number of reformations : 5                         30-Apr-2023 08:48:14
------- converged at time : 0.710167                   30-Apr-2023 08:48:14
    number of iterations   : 4                         30-Apr-2023 08:48:14
    number of reformations : 4                         30-Apr-2023 08:48:14
------- converged at time : 0.750337                   30-Apr-2023 08:48:14
    number of iterations   : 6                         30-Apr-2023 08:48:15
    number of reformations : 6                         30-Apr-2023 08:48:15
------- converged at time : 0.792472                   30-Apr-2023 08:48:15
    number of iterations   : 5                         30-Apr-2023 08:48:15
    number of reformations : 5                         30-Apr-2023 08:48:15
------- converged at time : 0.834608                   30-Apr-2023 08:48:15
    number of iterations   : 5                         30-Apr-2023 08:48:15
    number of reformations : 5                         30-Apr-2023 08:48:15
------- converged at time : 0.877494                   30-Apr-2023 08:48:15
    number of iterations   : 5                         30-Apr-2023 08:48:15
    number of reformations : 5                         30-Apr-2023 08:48:15
------- converged at time : 0.921059                   30-Apr-2023 08:48:15
    number of iterations   : 6                         30-Apr-2023 08:48:16
    number of reformations : 6                         30-Apr-2023 08:48:16
------- converged at time : 0.965238                   30-Apr-2023 08:48:16
    number of iterations   : 6                         30-Apr-2023 08:48:16
    number of reformations : 6                         30-Apr-2023 08:48:16
------- converged at time : 1                          30-Apr-2023 08:48:16
    number of iterations   : 4                         30-Apr-2023 08:48:16
    number of reformations : 4                         30-Apr-2023 08:48:16
------- converged at time : 1.05                       30-Apr-2023 08:48:16
    number of iterations   : 6                         30-Apr-2023 08:48:16
    number of reformations : 6                         30-Apr-2023 08:48:16
------- converged at time : 1.1                        30-Apr-2023 08:48:16
    number of iterations   : 10                        30-Apr-2023 08:48:17
    number of reformations : 10                        30-Apr-2023 08:48:17
------- converged at time : 1.15                       30-Apr-2023 08:48:17
    number of iterations   : 5                         30-Apr-2023 08:48:17
    number of reformations : 5                         30-Apr-2023 08:48:17
------- converged at time : 1.18884                    30-Apr-2023 08:48:17
    number of iterations   : 4                         30-Apr-2023 08:48:17
    number of reformations : 4                         30-Apr-2023 08:48:17
------- converged at time : 1.22875                    30-Apr-2023 08:48:17
    number of iterations   : 4                         30-Apr-2023 08:48:17
    number of reformations : 4                         30-Apr-2023 08:48:17
------- converged at time : 1.27068                    30-Apr-2023 08:48:17
    number of iterations   : 3                         30-Apr-2023 08:48:18
    number of reformations : 3                         30-Apr-2023 08:48:18
------- converged at time : 1.31422                    30-Apr-2023 08:48:18
    number of iterations   : 3                         30-Apr-2023 08:48:18
    number of reformations : 3                         30-Apr-2023 08:48:18
------- converged at time : 1.35905                    30-Apr-2023 08:48:18
    number of iterations   : 3                         30-Apr-2023 08:48:18
    number of reformations : 3                         30-Apr-2023 08:48:18
------- converged at time : 1.40492                    30-Apr-2023 08:48:18
    number of iterations   : 3                         30-Apr-2023 08:48:18
    number of reformations : 3                         30-Apr-2023 08:48:18
------- converged at time : 1.45161                    30-Apr-2023 08:48:18
    number of iterations   : 3                         30-Apr-2023 08:48:18
    number of reformations : 3                         30-Apr-2023 08:48:18
------- converged at time : 1.49896                    30-Apr-2023 08:48:18
    number of iterations   : 3                         30-Apr-2023 08:48:18
    number of reformations : 3                         30-Apr-2023 08:48:18
------- converged at time : 1.54685                    30-Apr-2023 08:48:18
    number of iterations   : 3                         30-Apr-2023 08:48:18
    number of reformations : 3                         30-Apr-2023 08:48:18
------- converged at time : 1.59515                    30-Apr-2023 08:48:18
    number of iterations   : 3                         30-Apr-2023 08:48:19
    number of reformations : 3                         30-Apr-2023 08:48:19
------- converged at time : 1.6438                     30-Apr-2023 08:48:19
    number of iterations   : 3                         30-Apr-2023 08:48:19
    number of reformations : 3                         30-Apr-2023 08:48:19
------- converged at time : 1.69271                    30-Apr-2023 08:48:19
    number of iterations   : 4                         30-Apr-2023 08:48:19
    number of reformations : 4                         30-Apr-2023 08:48:19
------- converged at time : 1.74185                    30-Apr-2023 08:48:19
    number of iterations   : 4                         30-Apr-2023 08:48:19
    number of reformations : 4                         30-Apr-2023 08:48:19
------- converged at time : 1.79115                    30-Apr-2023 08:48:19
    number of iterations   : 4                         30-Apr-2023 08:48:19
    number of reformations : 4                         30-Apr-2023 08:48:19
------- converged at time : 1.8406                     30-Apr-2023 08:48:19
    number of iterations   : 4                         30-Apr-2023 08:48:20
    number of reformations : 4                         30-Apr-2023 08:48:20
------- converged at time : 1.89016                    30-Apr-2023 08:48:20
    number of iterations   : 4                         30-Apr-2023 08:48:20
    number of reformations : 4                         30-Apr-2023 08:48:20
------- converged at time : 1.9398                     30-Apr-2023 08:48:20
    number of iterations   : 4                         30-Apr-2023 08:48:20
    number of reformations : 4                         30-Apr-2023 08:48:20
------- converged at time : 1.98952                    30-Apr-2023 08:48:20
    number of iterations   : 4                         30-Apr-2023 08:48:20
    number of reformations : 4                         30-Apr-2023 08:48:20
------- converged at time : 2                          30-Apr-2023 08:48:20
 Elapsed time : 0:00:09                                30-Apr-2023 08:48:20
 N O R M A L   T E R M I N A T I O N
# Done                                                 30-Apr-2023 08:48:20
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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 strain data from a log file

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

    %Access data
    E_strain=dataStruct.data;

    [F,CF]=element2patch(E,E_strain(:,:,end));
    CV=faceToVertexMeasure(F,V,CF);

    E_strain_middle_mean=squeeze(mean(E_strain(logicMiddleElements,:,:),1));

Compute grimp implied strain

    gripStrainLinear=double(timeVec>1).*(timeVec-1).*appliedLinearStrain;
    gripStrain=1/2*((gripStrainLinear+1).^2-1); %Green-Lagrange strain
    maxGridStrain=max(abs(gripStrain));

Plotting the simulated results using anim8 to visualize and animate deformations

    % Create basic view and store graphics handle to initiate animation
    hf=cFigure; hold on;%Open figure
    gtitle([febioFebFileNamePart,': Press play to animate']);
    title('$E_{zz}$','Interpreter','Latex')
    hp1=gpatch(Fb,V_DEF(:,:,end),CV,'k',1);
    hp1.FaceColor='interp';
    hp2=gpatch(Fc,V_DEF(:,:,end),'w','none',0.5);

    axisGeom(gca,fontSize);
    colormap(warmcold(250)); hc=colorbar;
    caxis([-maxGridStrain maxGridStrain]);
    hc.Ticks=linspace(-maxGridStrain,maxGridStrain,7);
    axis(axisLim(V_DEF)); %Set axis limits statically

    camlight headlight; axis off;

    % Set up animation features
    animStruct.Time=timeVec; %The time vector
    for qt=1:1:size(N_disp_mat,3) %Loop over time increments

        CV=faceToVertexMeasure(E,V,E_strain(:,:,qt));

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

Plotting the simulated results using anim8 to visualize and animate deformations

    % Create basic view and store graphics handle to initiate animation
    hf=cFigure;
    subplot(1,2,1); hold on;
    title('$E_{zz}$','Interpreter','Latex');
    gtitle([febioFebFileNamePart,': Press play to animate']);
    hp1=gpatch(Fb,V_DEF(:,:,end),CV,'none',1,0.5); hp1.FaceColor='interp';
    hp2=gpatch(Fc,V_DEF(:,:,end),'w','none',0.5);
    hp3=gpatch(FM,V_DEF(:,:,end),CV,'k',1,2); hp3.FaceColor='interp';

    colormap(warmcold(250)); hc=colorbar;
    caxis([-maxGridStrain maxGridStrain]);
    hc.Ticks=linspace(-maxGridStrain,maxGridStrain,7);
    axisGeom(gca,fontSize); camlight headlight;
    axis(axisLim(V_DEF)); %Set axis limits statically
    view(0,0); axis off;

    subplot(1,2,2); hold on;
    xlabel('Time (s)'); ylabel('$E_{zz}$','Interpreter','Latex');
    hpl4=plot(timeVec,E_strain_middle_mean,'g.-','LineWidth',3);
    hpl5=plot(timeVec,gripStrain,'r.-','LineWidth',3);
    hp4=plot(timeVec(end),E_strain_middle_mean(end),'g.','MarkerSize',50);
    hp5=plot(timeVec(end),gripStrain(end),'r.','MarkerSize',50);
    legend([hpl4 hpl5],{'True strain $E_{zz}$','"Intended applied" strain $E_{zz}$'},'Location','NorthOutside','Interpreter','Latex');
    axis tight; box on; grid on; set(gca,'FontSize',fontSize);

    % Set up animation features
    animStruct.Time=timeVec; %The time vector
    for qt=1:1:size(N_disp_mat,3) %Loop over time increments
        % [F,CF]=element2patch(E,E_strain(:,:,qt));
        % CV=faceToVertexMeasure(F,V,CF);
        CV=faceToVertexMeasure(E,V,E_strain(:,:,qt));

        %Set entries in animation structure
        animStruct.Handles{qt}=[hp1 hp1 hp2 hp3 hp3 hp4 hp4 hp5 hp5]; %Handles of objects to animate
        animStruct.Props{qt}={'Vertices','CData','Vertices','Vertices','CData','XData','YData','XData','YData'}; %Properties of objects to animate
        animStruct.Set{qt}={V_DEF(:,:,qt),CV,V_DEF(:,:,qt),V_DEF(:,:,qt),CV,timeVec(qt),E_strain_middle_mean(qt),timeVec(qt),gripStrain(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.

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/.