DEMO_febio_0032_sphere_tube_slide

Below is a demonstration for:

Contents

Keywords

clear; close all; clc;

Plot settings

fontSize=15;
faceAlpha1=0.8;
faceAlpha2=0.3;
markerSize=40;
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_force=[febioFebFileNamePart,'_force_out.txt']; %Log file name for exporting force

% Sphere parameters
sphereRadius1=1;
sphereRadius2=sphereRadius1/4;
numElementsMantel=6;
numElementsCore=7;

% Ground plate parameters
tubeRadius=0.8*sphereRadius1;
inletRadius=tubeRadius/3;
tubeLength=4;

% Material parameter set
c1=1e-3; %Shear-modulus-like parameter
m1=2; %Material parameter setting degree of non-linearity
k_factor=10; %Bulk modulus factor
k=c1*k_factor; %Bulk modulus

% 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=15; %Optimum number of iterations
max_retries=10; %Maximum number of retires
dtmin=(1/numTimeSteps)/100; %Minimum time step size
dtmax=1/(numTimeSteps); %Maximum time step size
symmetric_stiffness=0;

displacement_X=-2;

%Contact parameters
contactPenalty=10;
laugon=0;
minaug=1;
maxaug=10;
fric_coeff=0.01;
max_traction=0;

Creating model geometry and mesh

%Control settings
optionStruct.sphereRadius=sphereRadius1;
optionStruct.coreRadius=sphereRadius2;
optionStruct.numElementsMantel=numElementsMantel;
optionStruct.numElementsCore=numElementsCore;
optionStruct.makeHollow=1;
optionStruct.outputStructType=2;

%Creating sphere
[meshStruct]=hexMeshSphere(optionStruct);

% Access model element and patch data
Fb_blob=meshStruct.facesBoundary;
Cb_blob=meshStruct.boundaryMarker;
V_blob=meshStruct.nodes;
E_blob=meshStruct.elements;

Visualize mesh

hFig=cFigure;
subplot(1,2,1); hold on;
title('Boundary surfaces','FontSize',fontSize);
gpatch(Fb_blob,V_blob,Cb_blob,'k',0.5);
% patchNormPlot(Fb,V);
axisGeom(gca,fontSize);
colormap(gjet); icolorbar;
camlight headlight;

hs=subplot(1,2,2); hold on;
title('Cut view of solid mesh','FontSize',fontSize);
optionStruct.hFig=[hFig hs];
gpatch(Fb_blob,V_blob,'kw','none',0.25);
meshView(meshStruct,optionStruct);
axisGeom(gca,fontSize);
drawnow;

Creating tube model

pointSpacingTube=mean(patchEdgeLengths(Fb_blob(Cb_blob==1,:),V_blob))/2;
t=linspace(-0.1*pi,pi,100);
x=inletRadius*sin(t);
y=inletRadius*cos(t);
V_curve_tube=[x(:) y(:) zeros(size(x(:)))];
V_curve_tube(:,1)=V_curve_tube(:,1)-inletRadius;
V_curve_tube(:,2)=V_curve_tube(:,2)+inletRadius+tubeRadius;
V_curve_tube(end+1,:)=[-tubeLength tubeRadius 0];
nResample=ceil(max(pathLength(V_curve_tube))./pointSpacingTube);
V_curve_tube=evenlySampleCurve(V_curve_tube,nResample,'pchip',0);

cPar.closeLoopOpt=1;
cPar.numSteps=[]; %If empty the number of steps is derived from point spacing of input curve
cPar.w=[1 0 0];
[F_tube,V_tube]=polyRevolve(V_curve_tube,cPar);
V_tube(:,1)=V_tube(:,1)-sphereRadius1;

[Fd,Vd]=patchCleanUnused(Fb_blob(Cb_blob==1,:),V_blob);
c=1;
while 1
    [D,indMin]=minDist(V_tube,Vd);
    [~,indMinMin]=min(D);
    d=V_tube(indMinMin,1)-Vd(indMin(indMinMin),1);
    V_tube(:,1)=V_tube(:,1)-d(1);
    if c>1
        if abs(d-dp)<0.001
            break
        end
    end
    c=c+1;
    dp=d;
end
center_of_mass_tube=mean(V_tube,1);

Visualizing plate mesh

cFigure; hold on;
gtitle('The plate surface mesh',fontSize);
gpatch(Fb_blob,V_blob,'kw','none',0.5);
gpatch(F_tube,V_tube,'bw','k',0.5);
% patchNormPlot(F_tube,V_tube);
axisGeom(gca,fontSize);
camlight headlight;
drawnow;

Join model node sets

V=[V_blob; V_tube; ];
F_tube=F_tube+size(V_blob,1);

Visualizing model

cFigure; hold on;
gtitle('Model components',fontSize);
hl(1)=gpatch(Fb_blob,V,'rw','k',0.8);
hl(2)=gpatch(F_tube,V,'bw','k',0.8);
legend(hl,{'Blob','Tube'}); clear hl;
axisGeom(gca,fontSize);
camlight headlight;
drawnow;

Get contact surfaces

F_contact_secondary=Fb_blob(Cb_blob==1,:);

Visualize contact surfaces

cFigure; hold on;
title('Tube blob contact pair','fontsize',fontSize);
hl(1)=gpatch(F_tube,V,'rw','k',1);
patchNormPlot(F_tube,V);
hl(2)=gpatch(F_contact_secondary,V,'gw','k',1);
patchNormPlot(F_contact_secondary,V);
legend(hl,{'Master','Slave'}); clear hl;
axisGeom(gca,fontSize);
camlight headlight;
drawnow;

Visualize contact surfaces

bcPrescribeList=unique(Fb_blob(Cb_blob==2,:));

cFigure; hold on;
title('Tube blob contact pair','fontsize',fontSize);
hl(1)=gpatch(F_tube,V,'rw','none',0.25);
hl(2)=gpatch(Fb_blob,V,'gw','none',0.25);
hl(3)=plotV(V(bcPrescribeList,:),'k.','MarkerSize',15);
legend(hl,{'Tube','Blob','Prescribed nodes'}); clear hl;
axisGeom(gca,fontSize);

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.solver.symmetric_stiffness=0;
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 unconstrained';
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}.cp=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=center_of_mass_tube;

%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(E_blob,1))'; %Element id's
febio_spec.Mesh.Elements{1}.elem.VAL=E_blob; %The element matrix

partName2='Part2';
febio_spec.Mesh.Elements{2}.ATTR.name=partName2; %Name of this part
febio_spec.Mesh.Elements{2}.ATTR.type='quad4'; %Element type
febio_spec.Mesh.Elements{2}.elem.ATTR.id=size(E_blob,1)+(1:1:size(F_tube,1))'; %Element id's
febio_spec.Mesh.Elements{2}.elem.VAL=F_tube; %The element matrix

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

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

febio_spec.MeshDomains.ShellDomain.ATTR.name=partName2;
febio_spec.MeshDomains.ShellDomain.ATTR.mat=materialName2;

% -> Surfaces
surfaceName1='contactSurface1';
febio_spec.Mesh.Surface{1}.ATTR.name=surfaceName1;
febio_spec.Mesh.Surface{1}.quad4.ATTR.id=(1:1:size(F_tube,1))';
febio_spec.Mesh.Surface{1}.quad4.VAL=F_tube;

surfaceName2='contactSurface2';
febio_spec.Mesh.Surface{2}.ATTR.name=surfaceName2;
febio_spec.Mesh.Surface{2}.quad4.ATTR.id=(1:1:size(F_contact_secondary,1))';
febio_spec.Mesh.Surface{2}.quad4.VAL=F_contact_secondary;

% -> Surface pairs
contactPairName='Contact1';
febio_spec.Mesh.SurfacePair{1}.ATTR.name=contactPairName;
febio_spec.Mesh.SurfacePair{1}.primary=surfaceName1;
febio_spec.Mesh.SurfacePair{1}.secondary=surfaceName2;

%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='y';

febio_spec.Boundary.bc{2}.ATTR.type='fix';
febio_spec.Boundary.bc{2}.ATTR.node_set=nodeSetName1;
febio_spec.Boundary.bc{2}.dofs='z';

febio_spec.Boundary.bc{3}.ATTR.type='prescribe';
febio_spec.Boundary.bc{3}.ATTR.node_set=nodeSetName1;
febio_spec.Boundary.bc{3}.dof='x';
febio_spec.Boundary.bc{3}.scale.ATTR.lc=1;
febio_spec.Boundary.bc{3}.scale.VAL=displacement_X;
febio_spec.Boundary.bc{3}.relative=0;

%Rigid section
% -> Prescribed rigid body boundary conditions
febio_spec.Rigid.rigid_constraint{1}.ATTR.name='RigidFix_1';
febio_spec.Rigid.rigid_constraint{1}.ATTR.type='fix';
febio_spec.Rigid.rigid_constraint{1}.rb=2;
febio_spec.Rigid.rigid_constraint{1}.dofs='Rx,Ry,Rz,Ru,Rv,Rw';

%Contact section
febio_spec.Contact.contact{1}.ATTR.type='sliding-elastic';
febio_spec.Contact.contact{1}.ATTR.surface_pair=contactPairName;
febio_spec.Contact.contact{1}.two_pass=1;
febio_spec.Contact.contact{1}.laugon=laugon;
febio_spec.Contact.contact{1}.tolerance=0.2;
febio_spec.Contact.contact{1}.gaptol=0;
febio_spec.Contact.contact{1}.minaug=minaug;
febio_spec.Contact.contact{1}.maxaug=maxaug;
febio_spec.Contact.contact{1}.search_tol=0.01;
febio_spec.Contact.contact{1}.search_radius=0.1;
febio_spec.Contact.contact{1}.symmetric_stiffness=0;
febio_spec.Contact.contact{1}.auto_penalty=1;
febio_spec.Contact.contact{1}.penalty=contactPenalty;
febio_spec.Contact.contact{1}.fric_coeff=fric_coeff;

%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=',';

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.runMode='external';%'internal';

[runFlag]=runMonitorFEBio(febioAnalysis);%START FEBio NOW!!!!!!!!
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-------->    RUNNING/MONITORING FEBIO JOB    <-------- 15-Dec-2020 13:08:24
FEBio path: /home/kevin/FEBioStudio/bin/febio3
# Attempt removal of existing log files                15-Dec-2020 13:08:24
 * Removal succesful                                   15-Dec-2020 13:08:24
# Attempt removal of existing .xplt files              15-Dec-2020 13:08:24
 * Removal succesful                                   15-Dec-2020 13:08:24
# Starting FEBio...                                    15-Dec-2020 13:08:24
  Max. total analysis time is: Inf s
 * Waiting for log file creation                       15-Dec-2020 13:08:24
   Max. wait time: 30 s
 * Log file found.                                     15-Dec-2020 13:08:24
# Parsing log file...                                  15-Dec-2020 13:08:24
    number of iterations   : 5                         15-Dec-2020 13:08:25
    number of reformations : 5                         15-Dec-2020 13:08:25
------- converged at time : 0.05                       15-Dec-2020 13:08:25
    number of iterations   : 7                         15-Dec-2020 13:08:26
    number of reformations : 7                         15-Dec-2020 13:08:26
------- converged at time : 0.1                        15-Dec-2020 13:08:26
    number of iterations   : 7                         15-Dec-2020 13:08:27
    number of reformations : 7                         15-Dec-2020 13:08:27
------- converged at time : 0.15                       15-Dec-2020 13:08:27
    number of iterations   : 8                         15-Dec-2020 13:08:28
    number of reformations : 8                         15-Dec-2020 13:08:28
------- converged at time : 0.2                        15-Dec-2020 13:08:28
    number of iterations   : 6                         15-Dec-2020 13:08:29
    number of reformations : 6                         15-Dec-2020 13:08:29
------- converged at time : 0.25                       15-Dec-2020 13:08:29
    number of iterations   : 8                         15-Dec-2020 13:08:33
    number of reformations : 8                         15-Dec-2020 13:08:33
------- converged at time : 0.290909                   15-Dec-2020 13:08:33
    number of iterations   : 8                         15-Dec-2020 13:08:35
    number of reformations : 8                         15-Dec-2020 13:08:35
------- converged at time : 0.333636                   15-Dec-2020 13:08:35
    number of iterations   : 6                         15-Dec-2020 13:08:36
    number of reformations : 6                         15-Dec-2020 13:08:36
------- converged at time : 0.377818                   15-Dec-2020 13:08:36
    number of iterations   : 9                         15-Dec-2020 13:08:38
    number of reformations : 9                         15-Dec-2020 13:08:38
------- converged at time : 0.419041                   15-Dec-2020 13:08:38
    number of iterations   : 9                         15-Dec-2020 13:08:40
    number of reformations : 9                         15-Dec-2020 13:08:40
------- converged at time : 0.46202                    15-Dec-2020 13:08:40
    number of iterations   : 7                         15-Dec-2020 13:08:41
    number of reformations : 7                         15-Dec-2020 13:08:41
------- converged at time : 0.506403                   15-Dec-2020 13:08:41
    number of iterations   : 10                        15-Dec-2020 13:08:43
    number of reformations : 10                        15-Dec-2020 13:08:43
------- converged at time : 0.551909                   15-Dec-2020 13:08:43
    number of iterations   : 7                         15-Dec-2020 13:08:44
    number of reformations : 7                         15-Dec-2020 13:08:44
------- converged at time : 0.598314                   15-Dec-2020 13:08:44
    number of iterations   : 6                         15-Dec-2020 13:08:45
    number of reformations : 6                         15-Dec-2020 13:08:45
------- converged at time : 0.645438                   15-Dec-2020 13:08:45
    number of iterations   : 6                         15-Dec-2020 13:08:46
    number of reformations : 6                         15-Dec-2020 13:08:46
------- converged at time : 0.693137                   15-Dec-2020 13:08:46
    number of iterations   : 5                         15-Dec-2020 13:08:47
    number of reformations : 5                         15-Dec-2020 13:08:47
------- converged at time : 0.741296                   15-Dec-2020 13:08:47
    number of iterations   : 5                         15-Dec-2020 13:08:48
    number of reformations : 5                         15-Dec-2020 13:08:48
------- converged at time : 0.789824                   15-Dec-2020 13:08:48
    number of iterations   : 5                         15-Dec-2020 13:08:48
    number of reformations : 5                         15-Dec-2020 13:08:48
------- converged at time : 0.838646                   15-Dec-2020 13:08:48
    number of iterations   : 5                         15-Dec-2020 13:08:49
    number of reformations : 5                         15-Dec-2020 13:08:49
------- converged at time : 0.887704                   15-Dec-2020 13:08:49
    number of iterations   : 5                         15-Dec-2020 13:08:50
    number of reformations : 5                         15-Dec-2020 13:08:50
------- converged at time : 0.93695                    15-Dec-2020 13:08:50
    number of iterations   : 5                         15-Dec-2020 13:08:51
    number of reformations : 5                         15-Dec-2020 13:08:51
------- converged at time : 0.986346                   15-Dec-2020 13:08:51
    number of iterations   : 5                         15-Dec-2020 13:08:52
    number of reformations : 5                         15-Dec-2020 13:08:52
------- converged at time : 1                          15-Dec-2020 13:08:52
 Elapsed time : 0:00:27                                15-Dec-2020 13:08:52
 N O R M A L   T E R M I N A T I O N
# Done                                                 15-Dec-2020 13:08:52
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Import FEBio results

if 1%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; hold on;
    gtitle([febioFebFileNamePart,': Press play to animate']);
    hp=gpatch(Fb_blob,V_DEF(:,:,end),DN_magnitude,'k',1); %Add graphics object to animate
    hp.FaceColor='interp';
    gpatch(F_tube,V,'w','none',0.5); %Add graphics object to animate

    axisGeom(gca,fontSize);
    colormap(gjet(250)); colorbar;
    caxis([0 max(DN_magnitude)]/3);
    axis(axisLim(V_DEF)); %Set axis limits statically
    camlight headlight;
    drawnow;

    % 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 magnitue

        %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;
end

GIBBON www.gibboncode.org

Kevin Mattheus Moerman, gibbon.toolbox@gmail.com

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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/.