DEMO_febio_0032_sphere_tube_slide
Below is a demonstration for:
- Building geometry for a spherical blob with tetrahedral elements which is being pushed 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 4.0
- febio, FEBio
- indentation
- contact, sliding, friction
- rigid body constraints
- tetrahedral elements, tet4
- triangular elements, tri3
- 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 % 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; runMode='external';% 'internal' or 'external' 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,{'Secondary','Primary'}); clear hl; axisGeom(gca,fontSize); camlight headlight; drawnow;
Visualize BC's
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='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.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; 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}.VAL=mrow(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=surfaceName2; febio_spec.Mesh.SurfacePair{1}.secondary=surfaceName1; %Boundary condition section % -> Fix boundary conditions febio_spec.Boundary.bc{1}.ATTR.name='zero_displacement_yz'; 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=0; febio_spec.Boundary.bc{1}.y_dof=1; febio_spec.Boundary.bc{1}.z_dof=1; febio_spec.Boundary.bc{2}.ATTR.name='prescibed_displacement_z'; febio_spec.Boundary.bc{2}.ATTR.type='prescribed displacement'; febio_spec.Boundary.bc{2}.ATTR.node_set=nodeSetName1; febio_spec.Boundary.bc{2}.dof='x'; febio_spec.Boundary.bc{2}.value.ATTR.lc=1; febio_spec.Boundary.bc{2}.value.VAL=displacement_X; febio_spec.Boundary.bc{2}.relative=0; %Rigid section % ->Rigid body fix boundary conditions febio_spec.Rigid.rigid_bc{1}.ATTR.name='RigidFix_1'; febio_spec.Rigid.rigid_bc{1}.ATTR.type='rigid_fixed'; febio_spec.Rigid.rigid_bc{1}.rb=2; febio_spec.Rigid.rigid_bc{1}.Rx_dof=1; febio_spec.Rigid.rigid_bc{1}.Ry_dof=1; febio_spec.Rigid.rigid_bc{1}.Rz_dof=1; febio_spec.Rigid.rigid_bc{1}.Ru_dof=1; febio_spec.Rigid.rigid_bc{1}.Rv_dof=1; febio_spec.Rigid.rigid_bc{1}.Rw_dof=1; %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=0; 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*sqrt(sum((max(V,[],1)-min(V,[],1)).^2,2)); 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.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=','; % Plotfile section febio_spec.Output.plotfile.compression=0;
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=runMode; [runFlag]=runMonitorFEBio(febioAnalysis);%START FEBio NOW!!!!!!!!
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--------> RUNNING/MONITORING FEBIO JOB <-------- 20-Apr-2023 17:56:50
FEBio path: /home/kevin/FEBioStudio2/bin/febio4
# Attempt removal of existing log files 20-Apr-2023 17:56:50
* Removal succesful 20-Apr-2023 17:56:50
# Attempt removal of existing .xplt files 20-Apr-2023 17:56:50
* Removal succesful 20-Apr-2023 17:56:50
# Starting FEBio... 20-Apr-2023 17:56:50
Max. total analysis time is: Inf s
* Waiting for log file creation 20-Apr-2023 17:56:50
Max. wait time: 30 s
* Log file found. 20-Apr-2023 17:56:51
# Parsing log file... 20-Apr-2023 17:56:51
number of iterations : 4 20-Apr-2023 17:56:51
number of reformations : 4 20-Apr-2023 17:56:51
------- converged at time : 0.05 20-Apr-2023 17:56:51
number of iterations : 6 20-Apr-2023 17:56:52
number of reformations : 6 20-Apr-2023 17:56:52
------- converged at time : 0.1 20-Apr-2023 17:56:52
number of iterations : 8 20-Apr-2023 17:56:53
number of reformations : 8 20-Apr-2023 17:56:53
------- converged at time : 0.15 20-Apr-2023 17:56:53
number of iterations : 7 20-Apr-2023 17:56:54
number of reformations : 7 20-Apr-2023 17:56:54
------- converged at time : 0.2 20-Apr-2023 17:56:54
number of iterations : 6 20-Apr-2023 17:56:55
number of reformations : 6 20-Apr-2023 17:56:55
------- converged at time : 0.25 20-Apr-2023 17:56:55
number of iterations : 8 20-Apr-2023 17:56:56
number of reformations : 8 20-Apr-2023 17:56:56
------- converged at time : 0.3 20-Apr-2023 17:56:56
number of iterations : 9 20-Apr-2023 17:57:01
number of reformations : 9 20-Apr-2023 17:57:01
------- converged at time : 0.318182 20-Apr-2023 17:57:01
number of iterations : 6 20-Apr-2023 17:57:02
number of reformations : 6 20-Apr-2023 17:57:02
------- converged at time : 0.342727 20-Apr-2023 17:57:02
number of iterations : 6 20-Apr-2023 17:57:03
number of reformations : 6 20-Apr-2023 17:57:03
------- converged at time : 0.372364 20-Apr-2023 17:57:03
number of iterations : 6 20-Apr-2023 17:57:04
number of reformations : 6 20-Apr-2023 17:57:04
------- converged at time : 0.406073 20-Apr-2023 17:57:04
number of iterations : 11 20-Apr-2023 17:57:08
number of reformations : 11 20-Apr-2023 17:57:08
------- converged at time : 0.436319 20-Apr-2023 17:57:08
number of iterations : 10 20-Apr-2023 17:57:12
number of reformations : 10 20-Apr-2023 17:57:12
------- converged at time : 0.454624 20-Apr-2023 17:57:12
number of iterations : 6 20-Apr-2023 17:57:13
number of reformations : 6 20-Apr-2023 17:57:13
------- converged at time : 0.479268 20-Apr-2023 17:57:13
number of iterations : 6 20-Apr-2023 17:57:14
number of reformations : 6 20-Apr-2023 17:57:14
------- converged at time : 0.508984 20-Apr-2023 17:57:14
number of iterations : 7 20-Apr-2023 17:57:15
number of reformations : 7 20-Apr-2023 17:57:15
------- converged at time : 0.542756 20-Apr-2023 17:57:15
number of iterations : 7 20-Apr-2023 17:57:16
number of reformations : 7 20-Apr-2023 17:57:16
------- converged at time : 0.579774 20-Apr-2023 17:57:16
number of iterations : 7 20-Apr-2023 17:57:17
number of reformations : 7 20-Apr-2023 17:57:17
------- converged at time : 0.619388 20-Apr-2023 17:57:17
number of iterations : 6 20-Apr-2023 17:57:18
number of reformations : 6 20-Apr-2023 17:57:18
------- converged at time : 0.661079 20-Apr-2023 17:57:18
number of iterations : 6 20-Apr-2023 17:57:19
number of reformations : 6 20-Apr-2023 17:57:19
------- converged at time : 0.704432 20-Apr-2023 17:57:19
number of iterations : 5 20-Apr-2023 17:57:20
number of reformations : 5 20-Apr-2023 17:57:20
------- converged at time : 0.749115 20-Apr-2023 17:57:20
number of iterations : 5 20-Apr-2023 17:57:20
number of reformations : 5 20-Apr-2023 17:57:20
------- converged at time : 0.794861 20-Apr-2023 17:57:20
number of iterations : 5 20-Apr-2023 17:57:21
number of reformations : 5 20-Apr-2023 17:57:21
------- converged at time : 0.841458 20-Apr-2023 17:57:21
number of iterations : 5 20-Apr-2023 17:57:22
number of reformations : 5 20-Apr-2023 17:57:22
------- converged at time : 20-Apr-2023 17:57:22
number of iterations : 5 20-Apr-2023 17:57:23
number of reformations : 5 20-Apr-2023 17:57:23
------- converged at time : 0.936557 20-Apr-2023 17:57:23
number of iterations : 5 20-Apr-2023 17:57:24
number of reformations : 5 20-Apr-2023 17:57:24
------- converged at time : 0.984815 20-Apr-2023 17:57:24
number of iterations : 5 20-Apr-2023 17:57:25
number of reformations : 5 20-Apr-2023 17:57:25
------- converged at time : 1 20-Apr-2023 17:57:25
Elapsed time : 0:00:34 20-Apr-2023 17:57:25
N O R M A L T E R M I N A T I O N
# Done 20-Apr-2023 17:57:25
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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),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; 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]
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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
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