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
appliedPressure=0.5;

%Material parameter set
k_factor=50; %Bulk modulus factor

c1=1; %Shear-modulus-like parameter
m1=2; %Material parameter setting degree of non-linearity
k1=c1*k_factor; %Bulk modulus

c2=50*c1; %Shear-modulus-like parameter
m2=2; %Material parameter setting degree of non-linearity
k2=c2*k_factor; %Bulk modulus

% FEA control settings
numTimeSteps=40; %Number of time steps desired
opt_iter=35; %Optimum number of iterations
max_refs=opt_iter*2; %Max reforms
max_ups=0; %Set to zero to use full-Newton 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;

periodSize=6;
numPeriods=8;
heightFactor=1.5; %To scale height wrt period size
widthFactor=1; %To scale width wrt period size

numElementsPeriod=ceil(periodSize./pointSpacing);
if numElementsPeriod<4
    numElementsPeriod=4;
end

numElementsLength=((numPeriods-1)*numElementsPeriod)+(numElementsPeriod-1);
modelLength=numElementsLength.*pointSpacing;
modelHeight_X=periodSize*heightFactor;
modelWidth_Y=periodSize*widthFactor;

numElementsHeight_X=ceil(modelHeight_X./pointSpacing);
if numElementsHeight_X<6
    numElementsHeight_X=6;
end

numElementsWidth_Y=ceil(modelWidth_Y./pointSpacing);
if numElementsWidth_Y<1
    numElementsWidth_Y=1;
end

boxDim=[modelHeight_X modelWidth_Y modelLength];
boxEl=[numElementsHeight_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.*(numElementsHeight_X-1)))+1;

CD=rem(CZ,numElementsPeriod);

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

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

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

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;

% Remove 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;
indicesInnerSurface=unique(Fb(Cb==1,:));
logicElementsInner=any(ismember(E,indicesInnerSurface),2);

E1=E(~logicElementsInner,:); %Other elements
E2=E(logicElementsInner,:); %Inner element layer
E=[E1;E2];

[F1]=element2patch(E1);
[F2]=element2patch(E2);
cFigure; hold on;
gpatch(F1,V,'bw','k',0.5);
gpatch(F2,V,'rw','k',0.5);
plotV(V(indicesInnerSurface,:),'k.','MarkerSize',markerSize);
axisGeom;
colormap(turbo(250)); icolorbar;
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='4.0';

%Module section
febio_spec.Module.ATTR.type='solid';

%Control section
febio_spec.Control.analysis='STATIC';
febio_spec.Control.time_steps=numTimeSteps;
febio_spec.Control.step_size=1/numTimeSteps;
febio_spec.Control.solver.max_refs=max_refs;
febio_spec.Control.solver.qn_method.max_ups=max_ups;
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;

%Material section
materialName1='Material1';
febio_spec.Material.material{1}.ATTR.name=materialName1;
febio_spec.Material.material{1}.ATTR.type='Ogden';
febio_spec.Material.material{1}.ATTR.id=1;
febio_spec.Material.material{1}.c1=c1;
febio_spec.Material.material{1}.m1=m1;
febio_spec.Material.material{1}.c2=c1;
febio_spec.Material.material{1}.m2=-m1;
febio_spec.Material.material{1}.k=k1;

materialName2='Material2';
febio_spec.Material.material{2}.ATTR.name=materialName2;
febio_spec.Material.material{2}.ATTR.type='Ogden';
febio_spec.Material.material{2}.ATTR.id=2;
febio_spec.Material.material{2}.c1=c2;
febio_spec.Material.material{2}.m1=m2;
febio_spec.Material.material{2}.c2=c2;
febio_spec.Material.material{2}.m2=-m2;
febio_spec.Material.material{2}.k=k2;

%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='hex8'; %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; %The element matrix

partName2='Part2';
febio_spec.Mesh.Elements{2}.ATTR.name=partName2; %Name of this part
febio_spec.Mesh.Elements{2}.ATTR.type='hex8'; %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; %The element matrix

% -> Surfaces
surfaceName1='LoadedSurface';
febio_spec.Mesh.Surface{1}.ATTR.name=surfaceName1;
febio_spec.Mesh.Surface{1}.quad4.ATTR.id=(1:1:size(F_pressure,1))';
febio_spec.Mesh.Surface{1}.quad4.VAL=F_pressure;

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

%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;
5
%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];

%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);

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

     5

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.runMode=runMode;

[runFlag]=runMonitorFEBio(febioAnalysis);%START FEBio NOW!!!!!!!!
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-------->    RUNNING/MONITORING FEBIO JOB    <-------- 01-May-2023 09:13:55
FEBio path: /home/kevin/FEBioStudio/bin/febio4
# Attempt removal of existing log files                01-May-2023 09:13:55
 * Removal succesful                                   01-May-2023 09:13:55
# Attempt removal of existing .xplt files              01-May-2023 09:13:55
 * Removal succesful                                   01-May-2023 09:13:55
# Starting FEBio...                                    01-May-2023 09:13:55
  Max. total analysis time is: Inf s
 * Waiting for log file creation                       01-May-2023 09:13:55
   Max. wait time: 30 s
 * Log file found.                                     01-May-2023 09:13:55
# Parsing log file...                                  01-May-2023 09:13:55
    number of iterations   : 20                        01-May-2023 09:13:56
    number of reformations : 20                        01-May-2023 09:13:56
------- converged at time : 0.025                      01-May-2023 09:13:56
    number of iterations   : 21                        01-May-2023 09:13:57
    number of reformations : 21                        01-May-2023 09:13:57
------- converged at time : 0.055                      01-May-2023 09:13:57
    number of iterations   : 23                        01-May-2023 09:13:58
    number of reformations : 23                        01-May-2023 09:13:58
------- converged at time : 0.089                      01-May-2023 09:13:58
    number of iterations   : 25                        01-May-2023 09:13:59
    number of reformations : 25                        01-May-2023 09:13:59
------- converged at time : 0.1262                     01-May-2023 09:13:59
    number of iterations   : 25                        01-May-2023 09:14:00
    number of reformations : 25                        01-May-2023 09:14:00
------- converged at time : 0.165745                   01-May-2023 09:14:00
    number of iterations   : 25                        01-May-2023 09:14:01
    number of reformations : 25                        01-May-2023 09:14:01
------- converged at time : 0.207206                   01-May-2023 09:14:01
    number of iterations   : 27                        01-May-2023 09:14:02
    number of reformations : 27                        01-May-2023 09:14:02
------- converged at time : 0.250231                   01-May-2023 09:14:02
    number of iterations   : 27                        01-May-2023 09:14:03
    number of reformations : 27                        01-May-2023 09:14:03
------- converged at time : 0.294223                   01-May-2023 09:14:03
    number of iterations   : 29                        01-May-2023 09:14:04
    number of reformations : 29                        01-May-2023 09:14:04
------- converged at time : 0.339047                   01-May-2023 09:14:04
    number of iterations   : 30                        01-May-2023 09:14:05
    number of reformations : 30                        01-May-2023 09:14:05
------- converged at time : 0.384381                   01-May-2023 09:14:05
    number of iterations   : 31                        01-May-2023 09:14:06
    number of reformations : 31                        01-May-2023 09:14:06
------- converged at time : 0.430089                   01-May-2023 09:14:06
    number of iterations   : 31                        01-May-2023 09:14:08
    number of reformations : 31                        01-May-2023 09:14:08
------- converged at time : 0.476066                   01-May-2023 09:14:08
    number of iterations   : 33                        01-May-2023 09:14:09
    number of reformations : 33                        01-May-2023 09:14:09
------- converged at time : 0.522294                   01-May-2023 09:14:09
    number of iterations   : 30                        01-May-2023 09:14:10
    number of reformations : 30                        01-May-2023 09:14:10
------- converged at time : 0.560912                   01-May-2023 09:14:10
    number of iterations   : 32                        01-May-2023 09:14:12
    number of reformations : 32                        01-May-2023 09:14:12
------- converged at time : 0.600441                   01-May-2023 09:14:12
    number of iterations   : 34                        01-May-2023 09:14:13
    number of reformations : 34                        01-May-2023 09:14:13
------- converged at time : 0.64045                    01-May-2023 09:14:13
    number of iterations   : 35                        01-May-2023 09:14:14
    number of reformations : 35                        01-May-2023 09:14:14
------- converged at time : 0.680605                   01-May-2023 09:14:14
    number of iterations   : 35                        01-May-2023 09:14:16
    number of reformations : 35                        01-May-2023 09:14:16
------- converged at time : 0.714068                   01-May-2023 09:14:16
    number of iterations   : 35                        01-May-2023 09:14:17
    number of reformations : 35                        01-May-2023 09:14:17
------- converged at time : 0.747531                   01-May-2023 09:14:17
    number of iterations   : 35                        01-May-2023 09:14:18
    number of reformations : 35                        01-May-2023 09:14:18
------- converged at time : 0.780993                   01-May-2023 09:14:18
    number of iterations   : 36                        01-May-2023 09:14:20
    number of reformations : 36                        01-May-2023 09:14:20
------- converged at time : 0.814456                   01-May-2023 09:14:20
    number of iterations   : 35                        01-May-2023 09:14:21
    number of reformations : 35                        01-May-2023 09:14:21
------- converged at time : 0.847454                   01-May-2023 09:14:21
    number of iterations   : 36                        01-May-2023 09:14:23
    number of reformations : 36                        01-May-2023 09:14:23
------- converged at time : 0.880452                   01-May-2023 09:14:23
    number of iterations   : 35                        01-May-2023 09:14:24
    number of reformations : 35                        01-May-2023 09:14:24
------- converged at time : 0.912992                   01-May-2023 09:14:24
    number of iterations   : 33                        01-May-2023 09:14:25
    number of reformations : 33                        01-May-2023 09:14:25
------- converged at time : 0.945532                   01-May-2023 09:14:25
    number of iterations   : 31                        01-May-2023 09:14:27
    number of reformations : 31                        01-May-2023 09:14:27
------- converged at time : 0.973083                   01-May-2023 09:14:27
    number of iterations   : 27                        01-May-2023 09:14:28
    number of reformations : 27                        01-May-2023 09:14:28
------- converged at time : 1                          01-May-2023 09:14:28
 Elapsed time : 0:00:32                                01-May-2023 09:14:28
 N O R M A L   T E R M I N A T I O N
# Done                                                 01-May-2023 09:14:28
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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)]);

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),0,1);

    %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

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.

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/.