DEMO_febio_0012_disc_pressure

Below is a demonstration for:

Contents

Keywords

clear; close all; clc;

Plot settings

fontSize=20;
faceAlpha1=0.8;
markerSize=30;
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=[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=0.5e-3;
loadType='pressure';%'traction';

%Specifying dimensions and number of elements
pointSpacing=1;
inputStruct.cylRadius=30;
inputStruct.numRadial=round((inputStruct.cylRadius*pi)/pointSpacing);
inputStruct.cylHeight=3;
inputStruct.numHeight=round(inputStruct.cylHeight/pointSpacing);
inputStruct.meshType='tri';
inputStruct.closeOpt=1;

% Derive patch data for a cylinder
[Fs,Vs,Cs]=patchcylinder(inputStruct);

%Material parameter set
c1=1e-3; %Shear-modulus-like parameter
m1=8; %Material parameter setting degree of non-linearity
k_factor=1e2; %Bulk modulus factor
k=c1*k_factor; %Bulk modulus

% 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=6; %Optimum number of iterations
max_retries=5; %Maximum number of retires
dtmin=(1/numTimeSteps)/100; %Minimum time step size
dtmax=1/numTimeSteps; %Maximum time step size

Creating model geometry and mesh

The disc is meshed using tetrahedral elements using tetgen

inputStruct.stringOpt='-pq1.2AaY';
inputStruct.Faces=Fs;
inputStruct.Nodes=Vs;
inputStruct.holePoints=[];
inputStruct.faceBoundaryMarker=Cs; %Face boundary markers
inputStruct.regionPoints=getInnerPoint(Fs,Vs); %region points
inputStruct.regionA=tetVolMeanEst(Fs,Vs); %Volume for regular tets
inputStruct.minRegionMarker=2; %Minimum region marker
[meshStruct]=runTetGen(inputStruct); % Mesh model using tetrahedral elements using tetGen
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- TETGEN Tetrahedral meshing --- 11-Dec-2020 12:20:40
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Writing SMESH file --- 11-Dec-2020 12:20:40
----> Adding node field
----> Adding facet field
----> Adding holes specification
----> Adding region specification
--- Done --- 11-Dec-2020 12:20:40
--- Running TetGen to mesh input boundary--- 11-Dec-2020 12:20:40
Opening /mnt/data/MATLAB/GIBBON/data/temp/temp.smesh.
Delaunizing vertices...
Delaunay seconds:  0.038626
Creating surface mesh ...
Surface mesh seconds:  0.005492
Recovering boundaries...
Boundary recovery seconds:  0.007175
Removing exterior tetrahedra ...
Spreading region attributes.
Exterior tets removal seconds:  0.001
Recovering Delaunayness...
Delaunay recovery seconds:  0.016216
Refining mesh...
Refinement seconds:  0.034285
Optimizing mesh...
Optimization seconds:  0.001953

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

Output seconds:  0.043402
Total running seconds:  0.14832

Statistics:

  Input points: 1830
  Input facets: 3656
  Input segments: 5484
  Input holes: 0
  Input regions: 1

  Mesh points: 2880
  Mesh tetrahedra: 11774
  Mesh faces: 25376
  Mesh faces on exterior boundary: 3656
  Mesh faces on input facets: 3656
  Mesh edges on input segments: 5484
  Steiner points inside domain: 1050

--- Done --- 11-Dec-2020 12:20:40
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Importing TetGen files --- 11-Dec-2020 12:20:40
--- Done --- 11-Dec-2020 12:20:40

Access model element and patch data

Fb=meshStruct.facesBoundary;
Cb=meshStruct.boundaryMarker;
V=meshStruct.nodes;
CE=meshStruct.elementMaterialID;
E=meshStruct.elements;

Plotting model boundary surfaces and a cut view

hFig=cFigure;
subplot(1,2,1); hold on;
title('Model boundary surfaces and labels','FontSize',fontSize);
gpatch(Fb,V,Cb,'k',faceAlpha1);
colormap(gjet(6)); icolorbar;
axisGeom(gca,fontSize);

hs=subplot(1,2,2); hold on;
title('Cut view of solid mesh','FontSize',fontSize);
optionStruct.hFig=[hFig hs];
meshView(meshStruct,optionStruct);
axisGeom(gca,fontSize);
drawnow;

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==1,:)); %Node set part of selected face

%Define pressure surface
F_pressure=fliplr(Fb(Cb==2,:)); %The top face set

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,'kw','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;
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='3.0';

%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.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=k;

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

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

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

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

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

%Boundary condition section
% -> Fix boundary conditions
febio_spec.Boundary.bc{1}.ATTR.type='fix';
febio_spec.Boundary.bc{1}.ATTR.node_set=nodeSetName1;
febio_spec.Boundary.bc{1}.dofs='x,y,z';

%Loads section
% -> Surface load
switch loadType
    case 'pressure'
        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;
    case 'traction'
        febio_spec.Loads.surface_load{1}.ATTR.type='traction';
        febio_spec.Loads.surface_load{1}.ATTR.surface=surfaceName1;
        febio_spec.Loads.surface_load{1}.scale.ATTR.lc=1;
        febio_spec.Loads.surface_load{1}.scale.VAL=appliedPressure;
        febio_spec.Loads.surface_load{1}.traction=[0 0 -1];
end

%LoadData section
% -> load_controller
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}.points.point.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);

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='external';%'internal';

[runFlag]=runMonitorFEBio(febioAnalysis);%START FEBio NOW!!!!!!!!
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-------->    RUNNING/MONITORING FEBIO JOB    <-------- 11-Dec-2020 12:20:44
FEBio path: /home/kevin/FEBioStudio/bin/febio3
# Attempt removal of existing log files                11-Dec-2020 12:20:44
 * Removal succesful                                   11-Dec-2020 12:20:45
# Attempt removal of existing .xplt files              11-Dec-2020 12:20:45
 * Removal succesful                                   11-Dec-2020 12:20:45
# Starting FEBio...                                    11-Dec-2020 12:20:45
  Max. total analysis time is: Inf s
 * Waiting for log file creation                       11-Dec-2020 12:20:45
   Max. wait time: 30 s
 * Log file found.                                     11-Dec-2020 12:20:45
# Parsing log file...                                  11-Dec-2020 12:20:45
    number of iterations   : 9                         11-Dec-2020 12:20:46
    number of reformations : 9                         11-Dec-2020 12:20:46
------- converged at time : 0.1                        11-Dec-2020 12:20:46
    number of iterations   : 5                         11-Dec-2020 12:20:47
    number of reformations : 5                         11-Dec-2020 12:20:47
------- converged at time : 0.181833                   11-Dec-2020 12:20:47
    number of iterations   : 4                         11-Dec-2020 12:20:47
    number of reformations : 4                         11-Dec-2020 12:20:47
------- converged at time : 0.2654                     11-Dec-2020 12:20:47
    number of iterations   : 4                         11-Dec-2020 12:20:47
    number of reformations : 4                         11-Dec-2020 12:20:47
------- converged at time : 0.352254                   11-Dec-2020 12:20:47
    number of iterations   : 4                         11-Dec-2020 12:20:48
    number of reformations : 4                         11-Dec-2020 12:20:48
------- converged at time : 0.441737                   11-Dec-2020 12:20:48
    number of iterations   : 4                         11-Dec-2020 12:20:48
    number of reformations : 4                         11-Dec-2020 12:20:48
------- converged at time : 0.533323                   11-Dec-2020 12:20:48
    number of iterations   : 4                         11-Dec-2020 12:20:49
    number of reformations : 4                         11-Dec-2020 12:20:49
------- converged at time : 0.626592                   11-Dec-2020 12:20:49
    number of iterations   : 4                         11-Dec-2020 12:20:49
    number of reformations : 4                         11-Dec-2020 12:20:49
------- converged at time : 0.721208                   11-Dec-2020 12:20:49
    number of iterations   : 4                         11-Dec-2020 12:20:49
    number of reformations : 4                         11-Dec-2020 12:20:49
------- converged at time : 0.8169                     11-Dec-2020 12:20:49
    number of iterations   : 3                         11-Dec-2020 12:20:50
    number of reformations : 3                         11-Dec-2020 12:20:50
------- converged at time : 0.913454                   11-Dec-2020 12:20:50
    number of iterations   : 3                         11-Dec-2020 12:20:50
    number of reformations : 3                         11-Dec-2020 12:20:50
------- converged at time : 1                          11-Dec-2020 12:20:50
 Elapsed time : 0:00:05                                11-Dec-2020 12:20:50
 N O R M A L   T E R M I N A T I O N
# Done                                                 11-Dec-2020 12:20:50
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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(:))]/3);
    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) 2006-2020 Kevin Mattheus Moerman

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/.