DEMO_febio_0070_pneunet_actuator_simple_01

Below is a demonstration for:

Contents

Keywords

clear; close all; clc;

Plot settings

fontSize=20;
faceAlpha1=0.8;
markerSize=40;
markerSize2=20;
lineWidth=3;

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_stress=[febioFebFileNamePart,'_stress_out.txt']; %Log file name for exporting force

%Load
pressureValue=1e-4;

%Material parameter set
c1=1e-3; %Shear-modulus-like parameter
m1=2; %Material parameter setting degree of non-linearity
k_factor=100; %Bulk modulus factor
k=c1*k_factor; %Bulk modulus

% FEA control settings
numTimeSteps=50; %Number of time steps desired
max_refs=50; %Max reforms
max_ups=0; %Set to zero to use full-Newton iterations
opt_iter=25; %Optimum number of iterations
max_retries=5; %Maximum number of retires
dtmin=(1/numTimeSteps)/100; %Minimum time step size
dtmax=(1/numTimeSteps)*2; %Maximum time step size

runMode='external';%'internal';
pointSpacing=1;

numPeriods=8;
numSteps=7;
periodSize=pointSpacing.*numSteps;

numElementsLength=((numPeriods-1)*numSteps)+(numSteps-1);
modelLength=numElementsLength.*pointSpacing;

modelWidth_X=periodSize*1.2;
numElementsWidth_X=ceil(modelWidth_X./pointSpacing);
if numElementsWidth_X<6
    numElementsWidth_X=6;
end

modelWidth_Y=periodSize*2;
numElementsWidth_Y=ceil(modelWidth_Y./pointSpacing);
if numElementsWidth_Y<3
    numElementsWidth_Y=3;
end

boxDim=[modelWidth_X modelWidth_Y modelLength];
boxEl=[numElementsWidth_X numElementsWidth_Y numElementsLength];

[meshStruct]=hexMeshBox(boxDim,boxEl);

E_bar=meshStruct.E;
V_bar=meshStruct.V;
F_bar=meshStruct.F;
Fb_bar=meshStruct.Fb;
Cb_bar=meshStruct.faceBoundaryMarker;

VE_bar=patchCentre(E_bar,V_bar);

CZ=VE_bar(:,3);
CZ=CZ-min(CZ);
CZ=CZ./max(CZ);
CZ=round((CZ.*(numElementsLength-1)))+1;

CW=VE_bar(:,1);
CW=CW-min(CW);
CW=CW./max(CW);
CW=round((CW.*(numElementsWidth_X-1)))+1;

CD=rem(CZ,numSteps);

logicKeep1=~(CD==0 & CW>3);

E1=E_bar(logicKeep1,:);
F1=element2patch(E1);
[indBoundary1]=tesBoundary(F1,V_bar);

logicKeep2=any(ismember(E1,F1(indBoundary1,:)),2);
F2=element2patch(E1(logicKeep2,:));
[indBoundary2]=tesBoundary(F2,V_bar);

Fb=F2(indBoundary2,:);
Cb=7*ones(size(Fb,1),1);

for q=1:1:6
    F_Cb1=Fb_bar(Cb_bar==q,:);
    logicNow=all(ismember(Fb,F_Cb1),2);
    Cb(logicNow)=q;
end
Cb(~any(ismember(Fb,F1(indBoundary1,:)),2))=0;

Removed unused nodes and clean up index matrices

[E,V,indFix2]=patchCleanUnused(E1(logicKeep2,:),V_bar);
Fb=indFix2(Fb);
F=indFix2(F2);
cFigure;
gpatch(Fb,V,Cb,'k',0.5);
axisGeom;
colormap(turbo(250)); icolorbar;
camlight headlight;
gdrawnow;

Defining the boundary conditions

The visualization of the model boundary shows colors for each side of the disc. These labels can be used to define boundary conditions.

%Define supported node sets
bcSupportList=unique(Fb(Cb==5,:)); %Node set part of selected face

%Get pressure faces
F_pressure=Fb(Cb==0,:);

Visualizing boundary conditions. Markers plotted on the semi-transparent model denote the nodes in the various boundary condition lists.

hf=cFigure;
title('Boundary conditions','FontSize',fontSize);
xlabel('X','FontSize',fontSize); ylabel('Y','FontSize',fontSize); zlabel('Z','FontSize',fontSize);
hold on;

gpatch(Fb,V,'w','none',0.5);

hl(1)=plotV(V(bcSupportList,:),'k.','MarkerSize',markerSize);
hl(2)=gpatch(F_pressure,V,'r','k',1);

patchNormPlot(F_pressure,V);
legend(hl,{'BC full support','Pressure surface'});

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

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';

%Control section
febio_spec.Control.analysis.ATTR.type='static';
febio_spec.Control.time_steps=numTimeSteps;
febio_spec.Control.step_size=1/numTimeSteps;
febio_spec.Control.time_stepper.dtmin=dtmin;
febio_spec.Control.time_stepper.dtmax=dtmax;
febio_spec.Control.time_stepper.max_retries=max_retries;
febio_spec.Control.time_stepper.opt_iter=opt_iter;
febio_spec.Control.max_refs=max_refs;
febio_spec.Control.max_ups=max_ups;

%Material section
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;

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

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

% -> Surfaces
febio_spec.Geometry.Surface{1}.ATTR.name='Pressure_surface';
febio_spec.Geometry.Surface{1}.quad4.ATTR.lid=(1:size(F_pressure,1))';
febio_spec.Geometry.Surface{1}.quad4.VAL=F_pressure;

%Boundary condition section
% -> Fix boundary conditions
febio_spec.Boundary.fix{1}.ATTR.bc='x';
febio_spec.Boundary.fix{1}.ATTR.node_set=febio_spec.Geometry.NodeSet{1}.ATTR.name;
febio_spec.Boundary.fix{2}.ATTR.bc='y';
febio_spec.Boundary.fix{2}.ATTR.node_set=febio_spec.Geometry.NodeSet{1}.ATTR.name;
febio_spec.Boundary.fix{3}.ATTR.bc='z';
febio_spec.Boundary.fix{3}.ATTR.node_set=febio_spec.Geometry.NodeSet{1}.ATTR.name;

%Loads
febio_spec.Loads.surface_load{1}.ATTR.type='pressure';
febio_spec.Loads.surface_load{1}.ATTR.surface=febio_spec.Geometry.Surface{1}.ATTR.name;
febio_spec.Loads.surface_load{1}.pressure.VAL=pressureValue;
febio_spec.Loads.surface_load{1}.pressure.ATTR.lc=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_stress;
febio_spec.Output.logfile.element_data{1}.ATTR.data='s1';
febio_spec.Output.logfile.element_data{1}.ATTR.delim=',';
febio_spec.Output.logfile.element_data{1}.VAL=1:size(E,1);

Quick viewing of the FEBio input file structure

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

febView(febio_spec); %Viewing the febio file

Exporting the FEBio input file

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

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

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 --- 01-Sep-2020 12:49:22
Waiting for log file...
Proceeding to check log file...01-Sep-2020 12:49:22
------- converged at time : 0.02
------- converged at time : 0.0382748
------- converged at time : 0.0565497
------- converged at time : 0.0757494
------- converged at time : 0.096322
------- converged at time : 0.118177
------- converged at time : 0.141229
------- converged at time : 0.165401
------- converged at time : 0.191014
------- converged at time : 0.217937
------- converged at time : 0.246052
------- converged at time : 0.275249
------- converged at time : 0.30543
------- converged at time : 0.336506
------- converged at time : 0.368394
------- converged at time : 0.401022
------- converged at time : 0.434136
------- converged at time : 0.467877
------- converged at time : 0.502032
------- converged at time : 0.536572
------- converged at time : 0.571344
------- converged at time : 0.60634
------- converged at time : 0.641548
------- converged at time : 0.67696
------- converged at time : 0.712568
------- converged at time : 0.748465
------- converged at time : 0.784633
------- converged at time : 0.821055
------- converged at time : 0.857712
------- converged at time : 0.894764
------- converged at time : 0.932164
------- converged at time : 0.969871
------- converged at time : 1
--- Done --- 01-Sep-2020 12:51:50

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),1,1);

    %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)]);

Plotting the simulated results using anim8 to visualize and animate deformations

    DN_magnitude=sqrt(sum(N_disp_mat(:,:,end).^2,2)); %Current displacement magnitude

    % Create basic view and store graphics handle to initiate animation
    hf=cFigure; %Open figure
    gtitle([febioFebFileNamePart,': Press play to animate']);
    title('Displacement magnitude [mm]','Interpreter','Latex')
    hp=gpatch(Fb,V_DEF(:,:,end),DN_magnitude,'k',1); %Add graphics object to animate
%     hp.Marker='.';
%     hp.MarkerSize=markerSize2;
    hp.FaceColor='interp';

    axisGeom(gca,fontSize);
    colormap(gjet(250)); colorbar;
    caxis([0 max(DN_magnitude)]);
    axis(axisLim(V_DEF)); %Set axis limits statically
    camlight headlight;

    % Set up animation features
    animStruct.Time=timeVec; %The time vector
    for qt=1:1:size(N_disp_mat,3) %Loop over time increments
        DN_magnitude=sqrt(sum(N_disp_mat(:,:,qt).^2,2)); %Current displacement magnitude

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

Importing element stress from a log file

    dataStruct=importFEBio_logfile(fullfile(savePath,febioLogFileName_stress),1,1);

    %Access data
    E_stress_mat=dataStruct.data;

    E_stress_mat(isnan(E_stress_mat))=0;

Plotting the simulated results using anim8 to visualize and animate deformations

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

    % Create basic view and store graphics handle to initiate animation
    hf=cFigure; %Open figure
    gtitle([febioFebFileNamePart,': Press play to animate']);
    title('$\sigma_{1}$ [MPa]','Interpreter','Latex')
    hp=gpatch(Fb,V_DEF(:,:,end),CV,'k',1); %Add graphics object to animate
%     hp.Marker='.';
%     hp.MarkerSize=markerSize2;
    hp.FaceColor='interp';

    axisGeom(gca,fontSize);
    colormap(gjet(250)); colorbar;
    caxis([min(E_stress_mat(:)) max(E_stress_mat(:))]);
    axis(axisLim(V_DEF)); %Set axis limits statically
    camlight headlight;

    % 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_stress_mat(:,:,qt));

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