DEMO_febio_0033_sphere_tube_slide_body_force
Below is a demonstration for:
- Building geometry for a spherical blob with tetrahedral elements which is being aspirated into a tube. This demo consists off:
- Defining the boundary conditions
- Coding the febio structure
- Running the model
- Importing and visualizing the displacement results
Contents
Keywords
- febio_spec version 3.0
- febio, FEBio
- indentation
- contact, sliding, friction
- rigid body constraints
- hexahedral elements, hex8
- quadrilateral elements, quad4
- shell elements
- sphere
- static, solid
- hyperelastic, Ogden
- displacement logfile
- stress logfile
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 % Sphere parameters sphereRadius=5; pointSpacing=0.4; % Ground plate parameters tubeRadius=0.8*sphereRadius; inletRadius=tubeRadius/3; tubeLength=sphereRadius*5; % Material parameter set materialType=1; 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 g1=0.5; %Viscoelastic QLV proportional coefficient t1=12; %Viscoelastic QLV time coefficient %Setting material density (set artificially high in effort to dampen %oscilations and increase body force). materialDensity=1e-9*200000; %Density % FEA control settings timeTotal=6; %Total simulation time 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=(timeTotal/numTimeSteps)/100; %Minimum time step size dtmax=timeTotal/(numTimeSteps); %Maximum time step size symmetric_stiffness=0; min_residual=1e-20; analysisType='DYNAMIC'; %Contact parameters two_pass=1; contactPenalty=35; fric_coeff=0.1; laugon=0; minaug=1; maxaug=10; %Determine load sphereVolume=4/3*pi*sphereRadius^3; sphereWeight=(sphereVolume.*materialDensity); bodyLoadMagnitude=9.81.*sphereWeight;
Creating model geometry and mesh
Creating a solid hexahedral mesh sphere
%Control settings optionStruct.sphereRadius=sphereRadius; optionStruct.coreRadius=sphereRadius.*0.75; optionStruct.numElementsCore=ceil((sphereRadius/2)/pointSpacing); optionStruct.numElementsMantel=ceil((sphereRadius-optionStruct.coreRadius)/(2*pointSpacing)); optionStruct.makeHollow=0; optionStruct.outputStructType=2; %Creating sphere [meshOutput]=hexMeshSphere(optionStruct); % Access model element and patch data Fb_blob=meshOutput.facesBoundary; Cb_blob=meshOutput.boundaryMarker; V_blob=meshOutput.nodes; E_blob=meshOutput.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(meshOutput,optionStruct); axisGeom(gca,fontSize); drawnow;
Creating tube model
pointSpacingTube=mean(patchEdgeLengths(Fb_blob,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]; V_curve_tube(end+1,:)=[-tubeLength tubeRadius/6 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)-sphereRadius; c=1; while 1 [D,indMin]=minDist(V_tube,V_blob); [~,indMinMin]=min(D); d=V_tube(indMinMin,1)-V_blob(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);
Visualization
cFigure; hold on; gtitle('The surface meshes',fontSize); gpatch(Fb_blob,V_blob,'kw','none',0.5); gpatch(F_tube,V_tube,'bw','none',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;
Visualize contact surfaces
cFigure; hold on; title('The 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;
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=analysisType; febio_spec.Control.time_steps=numTimeSteps; febio_spec.Control.step_size=timeTotal/numTimeSteps; febio_spec.Control.solver.max_refs=max_refs; febio_spec.Control.solver.max_ups=max_ups; febio_spec.Control.solver.symmetric_stiffness=symmetric_stiffness; 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; switch materialType case 0 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; febio_spec.Material.material{1}.density=materialDensity; case 1 %Viscoelastic part febio_spec.Material.material{1}.ATTR.type='viscoelastic'; febio_spec.Material.material{1}.ATTR.id=1; febio_spec.Material.material{1}.g1=g1; febio_spec.Material.material{1}.t1=t1; febio_spec.Material.material{1}.density=materialDensity; %Elastic part febio_spec.Material.material{1}.elastic{1}.ATTR.type='Ogden unconstrained'; febio_spec.Material.material{1}.elastic{1}.c1=c1; febio_spec.Material.material{1}.elastic{1}.m1=m1; febio_spec.Material.material{1}.elastic{1}.c2=c1; febio_spec.Material.material{1}.elastic{1}.m2=-m1; febio_spec.Material.material{1}.elastic{1}.cp=k; febio_spec.Material.material{1}.elastic{1}.density=materialDensity; end 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 % -> 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; %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; %Loads section % -> Body load febio_spec.Loads.body_load.ATTR.type='const'; febio_spec.Loads.body_load.x.ATTR.lc=1; febio_spec.Loads.body_load.x.VAL=bodyLoadMagnitude; %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 <-------- 16-Dec-2020 11:29:29
FEBio path: /home/kevin/FEBioStudio/bin/febio3
# Attempt removal of existing log files 16-Dec-2020 11:29:29
* Removal succesful 16-Dec-2020 11:29:29
# Attempt removal of existing .xplt files 16-Dec-2020 11:29:29
* Removal succesful 16-Dec-2020 11:29:29
# Starting FEBio... 16-Dec-2020 11:29:29
Max. total analysis time is: Inf s
* Waiting for log file creation 16-Dec-2020 11:29:30
Max. wait time: 30 s
* Log file found. 16-Dec-2020 11:29:30
# Parsing log file... 16-Dec-2020 11:29:30
number of iterations : 1 16-Dec-2020 11:29:31
number of reformations : 1 16-Dec-2020 11:29:31
------- converged at time : 0.3 16-Dec-2020 11:29:31
number of iterations : 1 16-Dec-2020 11:29:31
number of reformations : 1 16-Dec-2020 11:29:31
------- converged at time : 0.6 16-Dec-2020 11:29:31
number of iterations : 1 16-Dec-2020 11:29:31
number of reformations : 1 16-Dec-2020 11:29:31
------- converged at time : 0.9 16-Dec-2020 11:29:31
number of iterations : 3 16-Dec-2020 11:29:32
number of reformations : 3 16-Dec-2020 11:29:32
------- converged at time : 1.2 16-Dec-2020 11:29:32
number of iterations : 5 16-Dec-2020 11:29:33
number of reformations : 5 16-Dec-2020 11:29:33
------- converged at time : 1.5 16-Dec-2020 11:29:33
number of iterations : 6 16-Dec-2020 11:29:34
number of reformations : 6 16-Dec-2020 11:29:34
------- converged at time : 1.8 16-Dec-2020 11:29:34
number of iterations : 6 16-Dec-2020 11:29:35
number of reformations : 6 16-Dec-2020 11:29:35
------- converged at time : 2.1 16-Dec-2020 11:29:35
number of iterations : 7 16-Dec-2020 11:29:36
number of reformations : 7 16-Dec-2020 11:29:36
------- converged at time : 2.4 16-Dec-2020 11:29:36
number of iterations : 6 16-Dec-2020 11:29:37
number of reformations : 6 16-Dec-2020 11:29:37
------- converged at time : 2.7 16-Dec-2020 11:29:37
number of iterations : 7 16-Dec-2020 11:29:39
number of reformations : 7 16-Dec-2020 11:29:39
------- converged at time : 3 16-Dec-2020 11:29:39
number of iterations : 7 16-Dec-2020 11:29:40
number of reformations : 7 16-Dec-2020 11:29:40
------- converged at time : 3.3 16-Dec-2020 11:29:40
number of iterations : 7 16-Dec-2020 11:29:42
number of reformations : 7 16-Dec-2020 11:29:42
------- converged at time : 3.6 16-Dec-2020 11:29:42
number of iterations : 7 16-Dec-2020 11:29:43
number of reformations : 7 16-Dec-2020 11:29:43
------- converged at time : 3.9 16-Dec-2020 11:29:43
number of iterations : 6 16-Dec-2020 11:29:45
number of reformations : 6 16-Dec-2020 11:29:45
------- converged at time : 4.2 16-Dec-2020 11:29:45
number of iterations : 6 16-Dec-2020 11:29:46
number of reformations : 6 16-Dec-2020 11:29:46
------- converged at time : 4.5 16-Dec-2020 11:29:46
number of iterations : 6 16-Dec-2020 11:29:47
number of reformations : 6 16-Dec-2020 11:29:47
------- converged at time : 4.8 16-Dec-2020 11:29:47
number of iterations : 7 16-Dec-2020 11:29:49
number of reformations : 7 16-Dec-2020 11:29:49
------- converged at time : 5.1 16-Dec-2020 11:29:49
number of iterations : 7 16-Dec-2020 11:29:50
number of reformations : 7 16-Dec-2020 11:29:50
------- converged at time : 5.4 16-Dec-2020 11:29:50
number of iterations : 8 16-Dec-2020 11:29:54
number of reformations : 8 16-Dec-2020 11:29:54
------- converged at time : 5.64545 16-Dec-2020 11:29:54
number of iterations : 7 16-Dec-2020 11:29:55
number of reformations : 7 16-Dec-2020 11:29:55
------- converged at time : 5.90182 16-Dec-2020 11:29:55
number of iterations : 5 16-Dec-2020 11:29:56
number of reformations : 5 16-Dec-2020 11:29:56
------- converged at time : 6 16-Dec-2020 11:29:56
Elapsed time : 0:00:26 16-Dec-2020 11:29:56
N O R M A L T E R M I N A T I O N
# Done 16-Dec-2020 11:29:56
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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, [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.
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/.