DEMO_febio_0043_lego_brick_attach.m

Below is a demonstration for:

Building geometry for a lego block with tetrahedral elements%
Defining the boundary conditions
Coding the febio structure
Running the model
Importing and visualizing the results

Keywords
Plot settings
Control parameters
Creating model geometry and mesh
Mesh using tetrahedral elements
Visualizing mesh using meshView, see also |anim8|dsfaasdfs
Joining node and element sets
Define contact surfaces
Define boundary conditions
Defining the FEBio input structure
Quick viewing of the FEBio input file structure
Exporting the FEBio input file
Running the FEBio analysis
Import FEBio results

Keywords

febio_spec version 2.5
febio, FEBio% *
contact, sliding, sticky, friction
tetrahedral elements, tet4
triangular elements, tri3
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');
surfaceModelPath=fullfile(defaultFolder,'data','libSurf');
surfaceModelName='lego_block_2x4_035.mat';

volumeFactor=500;

% 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

% Material parameter set
c1=1e-3; %Shear-modulus-like parameter
m1=2; %Material parameter setting degree of non-linearity
k_factor=25; %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=12; %Optimum number of iterations
max_retries=5; %Maximum number of retires
dtmin=(1/numTimeSteps)/500; %Minimum time step size
dtmax=(1/numTimeSteps); %Maximum time step size
symmetric_stiffness=0;
min_residual=1e-20;

% Contact parameters
contactPenalty=0.1;
laugon=0;
minaug=1;
maxaug=10;
fric_coeff=0.1;

% Boundary condition parameters
initialOffset=2;
displacementMagnitude=-1.6973-initialOffset; %1.6973

Creating model geometry and mesh

% Import surface model
surfaceData=load(fullfile(surfaceModelPath,surfaceModelName));

%Access model data
F_brick=surfaceData.F;
V_brick=surfaceData.V;
C_brick=surfaceData.C;

% Merging nodes
[F_brick,V_brick]=mergeVertices(F_brick,V_brick);

% Smooth mesh
logicBoundaryNodes=false(size(V_brick,1),1);
for q=unique(C_brick)'
    Eb=patchBoundary(F_brick(C_brick==q,:),V_brick);
    logicBoundaryNodes(Eb(:))=1;
end

cPar.Method='HC';
cPar.n=10;
cPar.RigidConstraints=find(logicBoundaryNodes);
[V_brick]=patchSmooth(F_brick,V_brick,[],cPar);

% Get mesh point spacing
pointSpacing=mean(patchEdgeLengths(F_brick,V_brick));

% Rotate model
R=euler2DCM([-0.5*pi 0 0]);
V_brick=V_brick*R;

% Center model
V_brick=V_brick-mean(V_brick,1); %Center on mean
V_brick(:,3)=V_brick(:,3)-min(V_brick(:,3)); %Shift so bottom is at 0 in z-dir

Plotting model boundary surfaces and a cut view

cFigure; hold on;
title('Model boundary surfaces and labels','FontSize',fontSize);
gpatch(F_brick,V_brick,C_brick,'k',faceAlpha1);
plotV(V_brick(logicBoundaryNodes,:),'r.','MarkerSize',25);
colormap(gjet(250)); icolorbar;
axisGeom(gca,fontSize);
camlight headlight;
drawnow;

colorIndicesTop=[1:3 32:35 37];
colorIndicesBottom=[4:11];

cFigure;
title('Model boundary surfaces and labels','FontSize',fontSize);
gpatch(F_brick,V_brick,C_brick,'none',0.25);

logicPlot1=ismember(C_brick,colorIndicesBottom);
gpatch(F_brick(logicPlot1,:),V_brick,C_brick(logicPlot1,:),'k',1);

colormap(gjet(250)); icolorbar;
axisGeom(gca,fontSize);
camlight headlight;

drawnow;

cFigure;
title('Model boundary surfaces and labels','FontSize',fontSize);
gpatch(F_brick,V_brick,C_brick,'none',0.25);

logicPlot1=ismember(C_brick,colorIndicesTop);
gpatch(F_brick(logicPlot1,:),V_brick,C_brick(logicPlot1,:),'k',1);

colormap(gjet(250)); icolorbar;
axisGeom(gca,fontSize);
camlight headlight;

drawnow;

Mesh using tetrahedral elements

stringOpt='-pq1.2AaY';

inputStruct.stringOpt=stringOpt;
inputStruct.Faces=F_brick;
inputStruct.Nodes=V_brick;
inputStruct.holePoints=[];
inputStruct.faceBoundaryMarker=C_brick; %Face boundary markers
inputStruct.regionPoints=getInnerPoint(F_brick,V_brick); %region points
inputStruct.regionA=tetVolMeanEst(F_brick,V_brick)*volumeFactor; %Volume for regular tets
inputStruct.minRegionMarker=2; %Minimum region marker

% Mesh model using tetrahedral elements using tetGen
[meshOutput]=runTetGen(inputStruct); %Run tetGen

% Access model element and patch data
Fb=meshOutput.facesBoundary;
Cb=meshOutput.boundaryMarker;
V=meshOutput.nodes;
CE=meshOutput.elementMaterialID;
E=meshOutput.elements;

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- TETGEN Tetrahedral meshing --- 04-Jun-2019 13:18:11
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Writing SMESH file --- 04-Jun-2019 13:18:11
----> Adding node field
----> Adding facet field
----> Adding holes specification
----> Adding region specification
--- Done --- 04-Jun-2019 13:18:12
--- Running TetGen to mesh input boundary--- 04-Jun-2019 13:18:12
Opening /mnt/data/MATLAB/GIBBON/data/temp/temp.smesh.
Delaunizing vertices...
Delaunay seconds:  0.225523
Creating surface mesh ...
Surface mesh seconds:  0.073514
Recovering boundaries...
Boundary recovery seconds:  0.236563
Removing exterior tetrahedra ...
Spreading region attributes.
Exterior tets removal seconds:  0.122273
Recovering Delaunayness...
Delaunay recovery seconds:  0.072991
Refining mesh...
Refinement seconds:  0.665434
Optimizing mesh...
Optimization seconds:  0.046929

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:  0.544164
Total running seconds:  1.98946

Statistics:

  Input points: 35422
  Input facets: 70840
  Input segments: 106260
  Input holes: 0
  Input regions: 1

  Mesh points: 51324
  Mesh tetrahedra: 208983
  Mesh faces: 453386
  Mesh faces on exterior boundary: 70840
  Mesh faces on input facets: 70840
  Mesh edges on input segments: 106260
  Steiner points inside domain: 15902

--- Done --- 04-Jun-2019 13:18:15
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Importing TetGen files --- 04-Jun-2019 13:18:15
--- Done --- 04-Jun-2019 13:18:15

Visualizing mesh using `meshView`, see also |anim8|dsfaasdfs

meshView(meshOutput);

Fb1=Fb;
Fb2=Fb;
V1=V;
V2=V;
V2(:,3)=V2(:,3)+max(V2(:,3))+initialOffset;

Plotting joined geometry

cFigure;
title('Joined node sets','FontSize',fontSize);
hold on;
gpatch(Fb1,V1,Cb,'k',faceAlpha1);
gpatch(Fb2,V2,Cb,'k',faceAlpha1);

colormap(gjet(6)); icolorbar;
axisGeom(gca,fontSize);
camlight headlight;
drawnow;

Joining node and element sets

V=[V1;V2;]; %Combined node sets
Fb2=Fb2+size(V1,1);
E1=E;
E2=E+size(V1,1);
E=[E1;E2];
Fb=[Fb1;Fb2];
% Cb=[Cb;Cb_max(Cb(:))];

Plotting joined geometry

cFigure;
title('Joined node sets','FontSize',fontSize);
hold on;
gpatch(Fb1,V,'rw','k');
gpatch(Fb2,V,'bw','k');
axisGeom(gca,fontSize);
camlight headlight;
drawnow;

Define contact surfaces

% The rigid master surface of the sphere
F_contact_master=fliplr(Fb2(ismember(Cb,colorIndicesTop),:));

% The deformable slave surface of the slab
F_contact_slave=fliplr(Fb1(ismember(Cb,colorIndicesBottom),:));

% Plotting surface models
cFigure; hold on;
title('Contact sets and normal directions','FontSize',fontSize);

gpatch(Fb1,V,'kw','none',0.5);
gpatch(Fb2,V,'kw','none',0.5);

hl(1)=gpatch(F_contact_master,V,'gw','k',1);
patchNormPlot(F_contact_master,V);
hl(2)=gpatch(F_contact_slave,V,'bw','k',1);
patchNormPlot(F_contact_slave,V);

legend(hl,{'Master','Slave'});

axisGeom(gca,fontSize);
camlight headlight;
drawnow;

Define boundary conditions

% Supported nodes
F_base=Fb1(ismember(Cb,37),:);
bcSupportList=unique(F_base);

% Prescribed displacement nodes
F_top=Fb2(ismember(Cb,12),:);
bcPrescribeList=unique(F_top);

Visualize BC's

hf=cFigure;
title('Boundary conditions model','FontSize',fontSize);
hold on;

gpatch(Fb1,V,'kw','none',faceAlpha2);
gpatch(Fb2,V,'kw','none',faceAlpha2);
gpatch(F_base,V,'rw','k',1);
gpatch(F_top,V,'gw','k',1);

clear hl;
hl(1)=plotV(V(bcSupportList,:),'r.','MarkerSize',markerSize);
hl(2)=plotV(V(bcPrescribeList,:),'g.','MarkerSize',markerSize);
legend(hl,{'BC support','BC prescribe'});

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='2.5';

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

%Control section
febio_spec.Control.analysis.ATTR.type='static';
febio_spec.Control.time_steps=numTimeSteps;
febio_spec.Control.step_size=1/numTimeSteps;
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;
febio_spec.Control.max_refs=max_refs;
febio_spec.Control.max_ups=max_ups;
febio_spec.Control.symmetric_stiffness=symmetric_stiffness;
febio_spec.Control.min_residual=min_residual;

%Material section
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;

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

% -> Elements
febio_spec.Geometry.Elements{1}.ATTR.type='tet4'; %Element type of this set
febio_spec.Geometry.Elements{1}.ATTR.mat=1; %material index for this set
febio_spec.Geometry.Elements{1}.ATTR.name='Propeller'; %Name of the element set
febio_spec.Geometry.Elements{1}.elem.ATTR.id=(1:1:size(E,1))'; %Element id's
febio_spec.Geometry.Elements{1}.elem.VAL=E;

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

febio_spec.Geometry.NodeSet{2}.ATTR.name='bcPrescribeList';
febio_spec.Geometry.NodeSet{2}.node.ATTR.id=bcPrescribeList(:);

% -> Surfaces
febio_spec.Geometry.Surface{1}.ATTR.name='contact_master';
febio_spec.Geometry.Surface{1}.tri3.ATTR.lid=(1:1:size(F_contact_master,1))';
febio_spec.Geometry.Surface{1}.tri3.VAL=F_contact_master;

febio_spec.Geometry.Surface{2}.ATTR.name='contact_slave';
febio_spec.Geometry.Surface{2}.tri3.ATTR.lid=(1:1:size(F_contact_slave,1))';
febio_spec.Geometry.Surface{2}.tri3.VAL=F_contact_slave;

% -> Surface pairs
febio_spec.Geometry.SurfacePair{1}.ATTR.name='Contact1';
febio_spec.Geometry.SurfacePair{1}.master.ATTR.surface=febio_spec.Geometry.Surface{1}.ATTR.name;
febio_spec.Geometry.SurfacePair{1}.slave.ATTR.surface=febio_spec.Geometry.Surface{2}.ATTR.name;

%Boundary condition section
% -> Fix boundary conditions
febio_spec.Boundary.fix{1}.ATTR.bc='x';
febio_spec.Boundary.fix{1}.ATTR.node_set=febio_spec.Geometry.NodeSet{1}.ATTR.name;
febio_spec.Boundary.fix{2}.ATTR.bc='y';
febio_spec.Boundary.fix{2}.ATTR.node_set=febio_spec.Geometry.NodeSet{1}.ATTR.name;
febio_spec.Boundary.fix{3}.ATTR.bc='z';
febio_spec.Boundary.fix{3}.ATTR.node_set=febio_spec.Geometry.NodeSet{1}.ATTR.name;

febio_spec.Boundary.fix{4}.ATTR.bc='x';
febio_spec.Boundary.fix{4}.ATTR.node_set=febio_spec.Geometry.NodeSet{2}.ATTR.name;
febio_spec.Boundary.fix{5}.ATTR.bc='y';
febio_spec.Boundary.fix{5}.ATTR.node_set=febio_spec.Geometry.NodeSet{2}.ATTR.name;

% -> Prescribe boundary conditions
febio_spec.Boundary.prescribe{1}.ATTR.bc='z';
febio_spec.Boundary.prescribe{1}.ATTR.node_set=febio_spec.Geometry.NodeSet{2}.ATTR.name;
febio_spec.Boundary.prescribe{1}.scale.ATTR.lc=1;
febio_spec.Boundary.prescribe{1}.scale.VAL=1;
febio_spec.Boundary.prescribe{1}.relative=1;
febio_spec.Boundary.prescribe{1}.value=displacementMagnitude;

% %Contact section
% febio_spec.Contact.contact{1}.ATTR.surface_pair=febio_spec.Geometry.SurfacePair{1}.ATTR.name;
% febio_spec.Contact.contact{1}.ATTR.type='sliding-elastic';
% 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
febio_spec.LoadData.loadcurve{1}.ATTR.id=1;
febio_spec.LoadData.loadcurve{1}.ATTR.type='linear';
febio_spec.LoadData.loadcurve{1}.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);

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.disp_log_on=1; %Display convergence information in the command window
febioAnalysis.runMode='internal';%'internal';
febioAnalysis.t_check=0.25; %Time for checking log file (dont set too small)
febioAnalysis.maxtpi=1e99; %Max analysis time
febioAnalysis.maxLogCheckTime=3; %Max log file checking time

[runFlag]=runMonitorFEBio(febioAnalysis);%START FEBio NOW!!!!!!!!

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- STARTING FEBIO JOB --- 04-Jun-2019 13:18:35
===========================================================================
         ________    _________   _________     __     _________            
        |        |\ |        |\ |        |\   |  |\  /         \\          
        |    ____|| |    ____|| |    __  ||   |__|| |    ___    ||         
        |   |\___\| |   |\___\| |   |\_| ||    \_\| |   //  \   ||         
        |   ||      |   ||      |   || | ||    __   |  ||    |  ||         
        |   ||__    |   ||__    |   ||_| ||   |  |\ |  ||    |  ||         
        |       |\  |       |\  |         \\  |  || |  ||    |  ||         
        |    ___||  |    ___||  |    ___   || |  || |  ||    |  ||         
        |   |\__\|  |   |\__\|  |   |\__|  || |  || |  ||    |  ||         
        |   ||      |   ||      |   ||  |  || |  || |  ||    |  ||         
        |   ||      |   ||___   |   ||__|  || |  || |   \\__/   ||         
        |   ||      |        |\ |          || |  || |           ||         
        |___||      |________|| |__________|| |__||  \_________//          
                                                                           
      F I N I T E   E L E M E N T S   F O R   B I O M E C H A N I C S      
                                                                           
                 --- v e r s i o n - 2 . 9 . 0 ---                 
                                                                           
                                                                           
  http://febio.org                                                         
  FEBio is a registered trademark.                                         
  copyright (c) 2006-2019 - All rights reserved                            
                                                                           
===========================================================================


Success loading plugin NeoHookeanPi.so (version 0.0.0)
Reading file /mnt/data/MATLAB/GIBBON/data/temp/tempModel.feb ...SUCCESS!
 ]0;(0%) tempModel.feb - FEBio 2.9.0.0  
===== beginning time step 1 : 0.1 =====
Reforming stiffness matrix: reformation #1

===== reforming stiffness matrix:
	Nr of equations ........................... : 277840
	Nr of nonzeroes in stiffness matrix ....... : 10222172

 1
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            6.103681e-02    6.233186e-29    0.000000e+00 
	   energy              4.058548e+00    2.065331e-15    4.058548e-02 
	   displacement        5.323382e+03    5.323382e+03    5.323382e-03 
 *************************************************************************
 *                               WARNING                                 *
 *                                                                       *
 * No force acting on the system.                                        *
 *************************************************************************

------- converged at time : 0.1

 ]0;(10%) tempModel.feb - FEBio 2.9.0.0  
===== beginning time step 2 : 0.2 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.2
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            6.103681e-02    9.872897e-29    0.000000e+00 
	   energy              4.058548e+00    7.185498e-15    4.058548e-02 
	   displacement        5.323382e+03    5.323382e+03    5.323382e-03 
 *************************************************************************
 *                               WARNING                                 *
 *                                                                       *
 * No force acting on the system.                                        *
 *************************************************************************

------- converged at time : 0.2

 ]0;(20%) tempModel.feb - FEBio 2.9.0.0  
===== beginning time step 3 : 0.3 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.3
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            6.103681e-02    9.889987e-29    0.000000e+00 
	   energy              4.058548e+00    4.721315e-15    4.058548e-02 
	   displacement        5.323382e+03    5.323382e+03    5.323382e-03 
 *************************************************************************
 *                               WARNING                                 *
 *                                                                       *
 * No force acting on the system.                                        *
 *************************************************************************

------- converged at time : 0.3

 ]0;(30%) tempModel.feb - FEBio 2.9.0.0  
===== beginning time step 4 : 0.4 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.4
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            6.103681e-02    9.939564e-29    0.000000e+00 
	   energy              4.058548e+00    2.495893e-14    4.058548e-02 
	   displacement        5.323382e+03    5.323382e+03    5.323382e-03 
 *************************************************************************
 *                               WARNING                                 *
 *                                                                       *
 * No force acting on the system.                                        *
 *************************************************************************

------- converged at time : 0.4

 ]0;(40%) tempModel.feb - FEBio 2.9.0.0  
===== beginning time step 5 : 0.5 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.5
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            6.103681e-02    9.303451e-29    0.000000e+00 
	   energy              4.058548e+00    3.775807e-15    4.058548e-02 
	   displacement        5.323382e+03    5.323382e+03    5.323382e-03 
 *************************************************************************
 *                               WARNING                                 *
 *                                                                       *
 * No force acting on the system.                                        *
 *************************************************************************

------- converged at time : 0.5

 ]0;(50%) tempModel.feb - FEBio 2.9.0.0  
===== beginning time step 6 : 0.6 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.6
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            6.103681e-02    9.272562e-29    0.000000e+00 
	   energy              4.058548e+00    6.499990e-15    4.058548e-02 
	   displacement        5.323382e+03    5.323382e+03    5.323382e-03 
 *************************************************************************
 *                               WARNING                                 *
 *                                                                       *
 * No force acting on the system.                                        *
 *************************************************************************

------- converged at time : 0.6

 ]0;(60%) tempModel.feb - FEBio 2.9.0.0  
===== beginning time step 7 : 0.7 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.7
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            6.103681e-02    9.132290e-29    0.000000e+00 
	   energy              4.058548e+00    4.794886e-15    4.058548e-02 
	   displacement        5.323382e+03    5.323382e+03    5.323382e-03 
 *************************************************************************
 *                               WARNING                                 *
 *                                                                       *
 * No force acting on the system.                                        *
 *************************************************************************

------- converged at time : 0.7

 ]0;(70%) tempModel.feb - FEBio 2.9.0.0  
===== beginning time step 8 : 0.8 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.8
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            6.103681e-02    8.996771e-29    0.000000e+00 
	   energy              4.058548e+00    6.717857e-15    4.058548e-02 
	   displacement        5.323382e+03    5.323382e+03    5.323382e-03 
 *************************************************************************
 *                               WARNING                                 *
 *                                                                       *
 * No force acting on the system.                                        *
 *************************************************************************

------- converged at time : 0.8

 ]0;(80%) tempModel.feb - FEBio 2.9.0.0  
===== beginning time step 9 : 0.9 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.9
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            6.103681e-02    9.023336e-29    0.000000e+00 
	   energy              4.058548e+00    1.321626e-14    4.058548e-02 
	   displacement        5.323382e+03    5.323382e+03    5.323382e-03 
 *************************************************************************
 *                               WARNING                                 *
 *                                                                       *
 * No force acting on the system.                                        *
 *************************************************************************

------- converged at time : 0.9

 ]0;(90%) tempModel.feb - FEBio 2.9.0.0  
===== beginning time step 10 : 1 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 1
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            6.103681e-02    8.782676e-29    0.000000e+00 
	   energy              4.058548e+00    6.133905e-15    4.058548e-02 
	   displacement        5.323382e+03    5.323382e+03    5.323382e-03 
 *************************************************************************
 *                               WARNING                                 *
 *                                                                       *
 * No force acting on the system.                                        *
 *************************************************************************

------- converged at time : 1

 ]0;(100%) tempModel.feb - FEBio 2.9.0.0  

N O N L I N E A R   I T E R A T I O N   I N F O R M A T I O N

	Number of time steps completed .................... : 10

	Total number of equilibrium iterations ............ : 10

	Average number of equilibrium iterations .......... : 1

	Total number of right hand evaluations ............ : 20

	Total number of stiffness reformations ............ : 10

	Time in linear solver: 0:00:37


 Elapsed time : 0:01:17


 N O R M A L   T E R M I N A T I O N

Waiting for log file...
Proceeding to check log file...04-Jun-2019 13:19:53
------- converged at time : 0.1
------- converged at time : 0.2
------- converged at time : 0.3
------- converged at time : 0.4
------- converged at time : 0.5
------- converged at time : 0.6
------- converged at time : 0.7
------- converged at time : 0.8
------- converged at time : 0.9
------- converged at time : 1
--- Done --- 04-Jun-2019 13:19:54

Import FEBio results

if runFlag==1 %i.e. a succesful run

    % Importing nodal displacements from a log file
    [time_mat, N_disp_mat,~]=importFEBio_logfile(fullfile(savePath,febioLogFileName_disp)); %Nodal displacements
    time_mat=[0; time_mat(:)]; %Time

    N_disp_mat=N_disp_mat(:,2:end,:);
    sizImport=size(N_disp_mat);
    sizImport(3)=sizImport(3)+1;
    N_disp_mat_n=zeros(sizImport);
    N_disp_mat_n(:,:,2:end)=N_disp_mat;
    N_disp_mat=N_disp_mat_n;
    DN=N_disp_mat(:,:,end);
    DN_magnitude=sqrt(sum(DN.^2,2));
    V_def=V+DN;
    V_DEF=N_disp_mat+repmat(V,[1 1 size(N_disp_mat,3)]);
    X_DEF=V_DEF(:,1,:);
    Y_DEF=V_DEF(:,2,:);
    Z_DEF=V_DEF(:,3,:);

Plotting the simulated results using anim8 to visualize and animate deformations

    % Create basic view and store graphics handle to initiate animation
    hf=cFigure; %Open figure
    gtitle([febioFebFileNamePart,': Press play to animate']);
    hp1=gpatch(Fb,V_def,DN_magnitude,DN_magnitude,1); %Add graphics object to animate
    hp1.FaceColor='interp';
%     gpatch(Fb,V,'kw','none',0.5); %Add graphics object to animate

    axisGeom(gca,fontSize);
    colormap(gjet(250)); colorbar;
    caxis([0 max(DN_magnitude(:))]);
    axis([min(X_DEF(:)) max(X_DEF(:)) min(Y_DEF(:)) max(Y_DEF(:)) min(Z_DEF(:)) max(Z_DEF(:))]);
    camlight headlight;

    % Set up animation features
    animStruct.Time=time_mat; %The time vector
    for qt=1:1:size(N_disp_mat,3) %Loop over time increments
        DN=N_disp_mat(:,:,qt); %Current displacement
        DN_magnitude=sqrt(sum(DN.^2,2)); %Current displacement magnitude
        V_def=V+DN; %Current nodal coordinates

        %Set entries in animation structure
        animStruct.Handles{qt}=[hp1 hp1]; %Handles of objects to animate
        animStruct.Props{qt}={'Vertices','CData'}; %Properties of objects to animate
        animStruct.Set{qt}={V_def,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.

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/.