DEMO_febio_0021_bone_three_point_bending

Below is a demonstration for:

Building geometry for a bone
Defining the boundary conditions
Coding the febio structure
Running the model
Importing and visualizing the displacement results

Keywords
Plot settings
Control parameters
Prepare bone geometry
Create and position cylinder geometry
Get interior point
Visualizing mesh using meshView, see also anim8
Joining node sets
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
indentation
contact, sliding, sticky, friction
rigid body constraints
tetrahedral elements, tet4
triangular elements, tri3
three point bending
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=fullfile(savePath,[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

%
nSub=0;
nBlur=1;
numMaterials=25;
volumeFactor=2;

runMode='internal';

%Material parameter set
c1=18000; %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=10; %Number of time steps desired
max_refs=25; %Max reforms
max_ups=0; %Set to zero to use full-Newton iterations
opt_iter=10; %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
min_residual=1e-60;
symmetric_stiffness=0;

%Contact parameters
contactInitialOffset=0.1;
contactAlg=1;
contactPenalty=100000;
switch contactAlg
    case 1
        contactType='sticky';
    case 2
        contactType='facet-to-facet sliding';
    case 3
        contactType='sliding_with_gaps';
    case 4
        contactType='sliding2';
    case 5
        contactType='sliding-elastic';
end

zDisp=-6-contactInitialOffset;

Prepare bone geometry

[Fs,Vs]=graphicsModels(5); %Get femur model
Vs=Vs*1000; %Scale to mm
[Fs,Vs]=triSurfRemoveThreeConnect(Fs,Vs); %remove 3 edge connected nodes and triangles

%Reorient
V_mean=mean(Vs,1);
Vs=Vs-V_mean(ones(size(Vs,1),1),:); %Center around origin
[R]=pointSetPrincipalDir(Vs); %Get rotation matrix
Vs=Vs*R; %Rotate

%Refine
[Fs,Vs]=subtri(Fs,Vs,nSub);

%Smooth
cPar.Method='HC';
cPar.n=25;
V_ini=Vs;
F_ini=Fs;
[Vs]=patchSmooth(Fs,Vs,[],cPar);

[D]=patchEdgeLengths(Fs,Vs);
voxelSize=mean(D);

Plotting surface geometry

cFigure;
subplot(1,2,1);
hold on;
gpatch(Fs,Vs,'gw','k',1);
axisGeom;
camlight headlight;

subplot(1,2,2);
hold on;
hl(1)=gpatch(F_ini,V_ini,'g','none',0.5);
hl(2)=gpatch(Fs,Vs,'r','none',0.5);
axisGeom;
camlight headlight;
legend(hl,{'Original','Smoothed'});

drawnow;

Create and position cylinder geometry

pointSpacing=mean(D)/2;

inputStruct.cylRadius=10;
inputStruct.numRadial=round((2*pi*inputStruct.cylRadius)./pointSpacing);
inputStruct.cylHeight=max(Vs(:,2))-min(Vs(:,2));
nh=round(inputStruct.cylHeight./pointSpacing);
nh=nh+double(iseven(nh));
inputStruct.numHeight=nh;
inputStruct.meshType='tri';
inputStruct.closeOpt=0;

% Derive patch data for a cylinder
[Fc,Vc,Cc]=patchcylinder(inputStruct);
R=euler2DCM([0.5*pi 0 0]);
Vc=Vc*R;
Vc1=Vc;
Vc2=Vc;
Vc2(:,1)=Vc2(:,1)-60;
Vc3=Vc;
Vc3(:,1)=Vc3(:,1)+60;

logicSelect=min(Vc1(:,1))<Vs(:,1) & max(Vc1(:,1))>Vs(:,1);
zOffset=max(Vs(logicSelect,3));
Vc1(:,3)=Vc1(:,3)-min(Vc1(:,3))+zOffset+contactInitialOffset;

logicSelect=min(Vc2(:,1))<Vs(:,1) & max(Vc2(:,1))>Vs(:,1);
zOffset=min(Vs(logicSelect,3));
Vc2(:,3)=Vc2(:,3)-max(Vc2(:,3))+zOffset-contactInitialOffset;

logicSelect=min(Vc3(:,1))<Vs(:,1) & max(Vc3(:,1))>Vs(:,1);
zOffset=min(Vs(logicSelect,3));
Vc3(:,3)=Vc3(:,3)-max(Vc3(:,3))+zOffset-contactInitialOffset;

Plotting surface geometry

cFigure;
hold on;
gpatch(Fs,Vs,'kw','k',1);
gpatch(Fc,Vc1,'gw','g',1);
gpatch(Fc,Vc2,'rw','r',1);
gpatch(Fc,Vc3,'bw','b',1);

axisGeom;
camlight headlight;
drawnow

% Defining the full set of possible control parameters
imOrigin=min(Vs,[],1)-voxelSize;
imMax=max(Vs,[],1)+voxelSize;
imSiz=round((imMax-imOrigin)/voxelSize);
imSiz=imSiz([2 1 3]); %Image size (x, y corresponds to j,i in image coordinates, hence the permutation)

% Using |triSurf2Im| function to convert patch data to image data
[M,~]=triSurf2Im(Fs,Vs,voxelSize,imOrigin,imSiz);

Create inner surface

L_model=(M==2); %Interior&Boundary choosen here

%Defining erosion/dilation kernel
kk=3;
p=kk-round(kk./2);
hb=zeros(3,3);
hb(2,2,2)=1;
hb(2,2,1)=1;
hb(2,2,3)=1;
hb(1,2,2)=1;
hb(3,2,2)=1;
hb(2,3,2)=1;
hb(2,1,2)=1;

for q=1:1:nBlur
    L_model_rep=zeros(size(L_model)+(2.*p));
    L_model_rep(p+(1:size(L_model,1)),p+(1:size(L_model,2)),p+(1:size(L_model,3)))=L_model;
    L_model_blur = convn(double(L_model_rep),hb,'valid');
    L_model=L_model_blur>=(sum(hb(:)));
end

[Fs2,Vs2,~]=im2patch(L_model,L_model,'vb',voxelSize*ones(1,3));
Fs2=[Fs2(:,[1 2 3]); Fs2(:,[3 4 1])];
Vs2=Vs2+imOrigin(ones(size(Vs2,1),1),:);

cPar.Method='HC';
cPar.n=25;
[Vs2]=patchSmooth(Fs2,Vs2,[],cPar);

Visualize

cFigure;
hold on;
gpatch(Fs,Vs,'gw','none',0.5);
gpatch(Fs2,Vs2,'bw','k',1);
axisGeom;
camlight headlight;
drawnow;

Get interior point

[M2,~]=triSurf2Im(Fs2,Vs2,voxelSize,imOrigin,imSiz);
L=M>0 & M2==0;

[indInternal]=getInnerVoxel(L,6,0);

[ii,jj,kk]=ind2sub(size(L),indInternal);
V_in1=nan(1,3);
[V_in1(:,1),V_in1(:,2),V_in1(:,3)]=im2cart(ii,jj,kk,voxelSize);
V_in1=V_in1+imOrigin;

[V_in2]=getInnerPoint(Fs2,Vs2,[],[],1);

Visualize

cFigure;
hold on;
gpatch(Fs,Vs,'gw','none',0.5);
gpatch(Fs2,Vs2,'bw','none',0.5);
plotV(V_in1,'k.','MarkerSize',25);
axisGeom;
camlight headlight;
drawnow;

Join geometries together

[F,V,C]=joinElementSets({Fs,Fs2},{Vs,Vs2});

Visualize

cFigure;
hold on;
gpatch(F,V,C,'k',0.5);
colormap(gjet(2)); icolorbar;
axisGeom;
camlight headlight;
drawnow;

Mesh using tetgen

[regionA]=tetVolMeanEst(F,V); %Volume estimate for regular tets

stringOpt='-pq1.2AaY'; %tetgen options

inputStruct.stringOpt=stringOpt;
inputStruct.Faces=F;
inputStruct.Nodes=V;
inputStruct.holePoints=V_in2;
inputStruct.faceBoundaryMarker=C; %Face boundary markers
inputStruct.regionPoints=V_in1; %region points
inputStruct.regionA=regionA*volumeFactor;
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 12:51:13
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Writing SMESH file --- 04-Jun-2019 12:51:13
----> Adding node field
----> Adding facet field
----> Adding holes specification
----> Adding region specification
--- Done --- 04-Jun-2019 12:51:13
--- Running TetGen to mesh input boundary--- 04-Jun-2019 12:51:13
Opening /mnt/data/MATLAB/GIBBON/data/temp/temp.smesh.
Delaunizing vertices...
Delaunay seconds:  0.029687
Creating surface mesh ...
Surface mesh seconds:  0.008184
Recovering boundaries...
Boundary recovery seconds:  0.016573
Removing exterior tetrahedra ...
Spreading region attributes.
Exterior tets removal seconds:  0.009469
Recovering Delaunayness...
Delaunay recovery seconds:  0.008438
Refining mesh...
Refinement seconds:  0.066248
Optimizing mesh...
Optimization seconds:  0.005909

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:  0.07574
Total running seconds:  0.220599

Statistics:

  Input points: 4768
  Input facets: 9532
  Input segments: 14296
  Input holes: 1
  Input regions: 1

  Mesh points: 6915
  Mesh tetrahedra: 28842
  Mesh faces: 62450
  Mesh faces on exterior boundary: 9532
  Mesh faces on input facets: 9532
  Mesh edges on input segments: 14296
  Steiner points inside domain: 2147

--- Done --- 04-Jun-2019 12:51:14
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Importing TetGen files --- 04-Jun-2019 12:51:14
--- Done --- 04-Jun-2019 12:51:14

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

meshView(meshOutput);

% D=minDist(V,Vs);
% D=vertexToFaceMeasure(E,D);
% D=D-min(D(:));
% D=D./max(D(:));
% D=abs(D-1);
% D=round(1+(D*(numMaterials-1)));
%
% meshOutput2=meshOutput;
% meshOutput2.elementMaterialID=D;
%
% %%
% meshView(meshOutput2);

Joining node sets

[E_F,V,C]=joinElementSets({E,Fc,Fc,Fc},{V,Vc1,Vc2,Vc3});
% E=E_F{1};
% Fb
Fc1=E_F{2};
Fc2=E_F{3};
Fc3=E_F{4};

Visualize

Fb_slave=Fb(Cb==1,:);

cFigure;
hold on;

gpatch(Fb_slave,V,'kw','k',0.5);
gpatch(Fc1,V,'rw','r',1);
gpatch(Fc2,V,'gw','g',1);
gpatch(Fc3,V,'bw','b',1);

axisGeom;
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.title='Cube analysis';
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 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{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=mean(Vc1,1);

febio_spec.Material.material{3}.ATTR.type='rigid body';
febio_spec.Material.material{3}.ATTR.id=3;
febio_spec.Material.material{3}.density=1;
febio_spec.Material.material{3}.center_of_mass=mean(Vc2,1);

febio_spec.Material.material{4}.ATTR.type='rigid body';
febio_spec.Material.material{4}.ATTR.id=4;
febio_spec.Material.material{4}.density=1;
febio_spec.Material.material{4}.center_of_mass=mean(Vc3,1);

%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='bone'; %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;

febio_spec.Geometry.Elements{2}.ATTR.type='tri3'; %Element type of this set
febio_spec.Geometry.Elements{2}.ATTR.mat=2; %material index for this set
febio_spec.Geometry.Elements{2}.ATTR.name='bar1'; %Name of the element set
febio_spec.Geometry.Elements{2}.elem.ATTR.id=size(E,1)+(1:1:size(Fc1,1))'; %Element id's
febio_spec.Geometry.Elements{2}.elem.VAL=Fc1;

febio_spec.Geometry.Elements{3}.ATTR.type='tri3'; %Element type of this set
febio_spec.Geometry.Elements{3}.ATTR.mat=3; %material index for this set
febio_spec.Geometry.Elements{3}.ATTR.name='bar2'; %Name of the element set
febio_spec.Geometry.Elements{3}.elem.ATTR.id=size(E,1)+(1:1:size(Fc2,1))'; %Element id's
febio_spec.Geometry.Elements{3}.elem.VAL=Fc2;

febio_spec.Geometry.Elements{4}.ATTR.type='tri3'; %Element type of this set
febio_spec.Geometry.Elements{4}.ATTR.mat=4; %material index for this set
febio_spec.Geometry.Elements{4}.ATTR.name='bar3'; %Name of the element set
febio_spec.Geometry.Elements{4}.elem.ATTR.id=size(E,1)+(1:1:size(Fc3,1))'; %Element id's
febio_spec.Geometry.Elements{4}.elem.VAL=Fc3;

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

% -> Surfaces
febio_spec.Geometry.Surface{1}.ATTR.name='contact_master1';
febio_spec.Geometry.Surface{1}.tri3.ATTR.lid=(1:1:size(Fc1,1))';
febio_spec.Geometry.Surface{1}.tri3.VAL=Fc1;

febio_spec.Geometry.Surface{2}.ATTR.name='contact_master2';
febio_spec.Geometry.Surface{2}.tri3.ATTR.lid=(1:1:size(Fc2,1))';
febio_spec.Geometry.Surface{2}.tri3.VAL=Fc2;

febio_spec.Geometry.Surface{3}.ATTR.name='contact_master3';
febio_spec.Geometry.Surface{3}.tri3.ATTR.lid=(1:1:size(Fc3,1))';
febio_spec.Geometry.Surface{3}.tri3.VAL=Fc3;

febio_spec.Geometry.Surface{4}.ATTR.name='contact_slave';
febio_spec.Geometry.Surface{4}.tri3.ATTR.lid=(1:1:size(Fb_slave,1))';
febio_spec.Geometry.Surface{4}.tri3.VAL=Fb_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{4}.ATTR.name;

febio_spec.Geometry.SurfacePair{2}.ATTR.name='Contact2';
febio_spec.Geometry.SurfacePair{2}.master.ATTR.surface=febio_spec.Geometry.Surface{2}.ATTR.name;
febio_spec.Geometry.SurfacePair{2}.slave.ATTR.surface=febio_spec.Geometry.Surface{4}.ATTR.name;

febio_spec.Geometry.SurfacePair{3}.ATTR.name='Contact3';
febio_spec.Geometry.SurfacePair{3}.master.ATTR.surface=febio_spec.Geometry.Surface{3}.ATTR.name;
febio_spec.Geometry.SurfacePair{3}.slave.ATTR.surface=febio_spec.Geometry.Surface{4}.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;

% -> Prescribed boundary conditions on the rigid body
febio_spec.Boundary.rigid_body{1}.ATTR.mat=2;
febio_spec.Boundary.rigid_body{1}.fixed{1}.ATTR.bc='x';
febio_spec.Boundary.rigid_body{1}.fixed{2}.ATTR.bc='y';
febio_spec.Boundary.rigid_body{1}.fixed{3}.ATTR.bc='Rx';
febio_spec.Boundary.rigid_body{1}.fixed{4}.ATTR.bc='Ry';
febio_spec.Boundary.rigid_body{1}.fixed{5}.ATTR.bc='Rz';
febio_spec.Boundary.rigid_body{1}.prescribed.ATTR.bc='z';
febio_spec.Boundary.rigid_body{1}.prescribed.ATTR.lc=1;
febio_spec.Boundary.rigid_body{1}.prescribed.VAL=zDisp;

febio_spec.Boundary.rigid_body{2}.ATTR.mat=3;
febio_spec.Boundary.rigid_body{2}.fixed{1}.ATTR.bc='x';
febio_spec.Boundary.rigid_body{2}.fixed{2}.ATTR.bc='y';
febio_spec.Boundary.rigid_body{2}.fixed{3}.ATTR.bc='z';
febio_spec.Boundary.rigid_body{2}.fixed{4}.ATTR.bc='Rx';
febio_spec.Boundary.rigid_body{2}.fixed{5}.ATTR.bc='Ry';
febio_spec.Boundary.rigid_body{2}.fixed{6}.ATTR.bc='Rz';

febio_spec.Boundary.rigid_body{3}.ATTR.mat=4;
febio_spec.Boundary.rigid_body{3}.fixed{1}.ATTR.bc='x';
febio_spec.Boundary.rigid_body{3}.fixed{2}.ATTR.bc='y';
febio_spec.Boundary.rigid_body{3}.fixed{3}.ATTR.bc='z';
febio_spec.Boundary.rigid_body{3}.fixed{4}.ATTR.bc='Rx';
febio_spec.Boundary.rigid_body{3}.fixed{5}.ATTR.bc='Ry';
febio_spec.Boundary.rigid_body{3}.fixed{6}.ATTR.bc='Rz';

for qc=1:1:3

    %Contact section
    switch contactType
        case 'sticky'
            febio_spec.Contact.contact{qc}.ATTR.surface_pair=febio_spec.Geometry.SurfacePair{qc}.ATTR.name;
            febio_spec.Contact.contact{qc}.ATTR.type='sticky';
            febio_spec.Contact.contact{qc}.penalty=contactPenalty;
            febio_spec.Contact.contact{qc}.laugon=0;
            febio_spec.Contact.contact{qc}.tolerance=0.2;
            febio_spec.Contact.contact{qc}.minaug=1;
            febio_spec.Contact.contact{qc}.maxaug=10;
            febio_spec.Contact.contact{qc}.snap_tol=0;
            febio_spec.Contact.contact{qc}.max_traction=0;
            febio_spec.Contact.contact{qc}.search_tolerance=0.01;
        case 'facet-to-facet sliding'
            febio_spec.Contact.contact{qc}.ATTR.surface_pair=febio_spec.Geometry.SurfacePair{qc}.ATTR.name;
            febio_spec.Contact.contact{qc}.ATTR.type='facet-to-facet sliding';
            febio_spec.Contact.contact{qc}.penalty=contactPenalty;
            febio_spec.Contact.contact{qc}.auto_penalty=1;
            febio_spec.Contact.contact{qc}.two_pass=1;
            febio_spec.Contact.contact{qc}.laugon=1;
            febio_spec.Contact.contact{qc}.tolerance=0.1;
            febio_spec.Contact.contact{qc}.gaptol=0;
            febio_spec.Contact.contact{qc}.minaug=1;
            febio_spec.Contact.contact{qc}.maxaug=10;
            febio_spec.Contact.contact{qc}.search_tol=0.01;
            febio_spec.Contact.contact{qc}.search_radius=mean(pointSpacing)/2;
        case 'sliding_with_gaps'
            febio_spec.Contact.contact{qc}.ATTR.surface_pair=febio_spec.Geometry.SurfacePair{qc}.ATTR.name;
            febio_spec.Contact.contact{qc}.ATTR.type='sliding_with_gaps';
            febio_spec.Contact.contact{qc}.penalty=contactPenalty;
            febio_spec.Contact.contact{qc}.auto_penalty=1;
            febio_spec.Contact.contact{qc}.two_pass=0;
            febio_spec.Contact.contact{qc}.laugon=0;
            febio_spec.Contact.contact{qc}.tolerance=0.1;
            febio_spec.Contact.contact{qc}.gaptol=0;
            febio_spec.Contact.contact{qc}.minaug=0;
            febio_spec.Contact.contact{qc}.maxaug=10;
            febio_spec.Contact.contact{qc}.fric_coeff=0;
            febio_spec.Contact.contact{qc}.fric_penalty=0;
            febio_spec.Contact.contact{qc}.ktmult=1;
            febio_spec.Contact.contact{qc}.seg_up=0;
            febio_spec.Contact.contact{qc}.search_tol=0.01;
        case 'sliding2'
            febio_spec.Contact.contact{qc}.ATTR.surface_pair=febio_spec.Geometry.SurfacePair{qc}.ATTR.name;
            febio_spec.Contact.contact{qc}.ATTR.type='sliding2';
            febio_spec.Contact.contact{qc}.penalty=contactPenalty;
            febio_spec.Contact.contact{qc}.auto_penalty=1;
            febio_spec.Contact.contact{qc}.two_pass=0;
            febio_spec.Contact.contact{qc}.laugon=0;
            febio_spec.Contact.contact{qc}.tolerance=0.1;
            febio_spec.Contact.contact{qc}.gaptol=0;
            febio_spec.Contact.contact{qc}.symmetric_stiffness=0;
            febio_spec.Contact.contact{qc}.search_tol=0.01;
            febio_spec.Contact.contact{qc}.search_radius=mean(pointSpacings)/2;
        case 'sliding-elastic'
            febio_spec.Contact.contact{qc}.ATTR.surface_pair=febio_spec.Geometry.SurfacePair{qc}.ATTR.name;
            febio_spec.Contact.contact{qc}.ATTR.type='sliding-elastic';
            febio_spec.Contact.contact{qc}.two_pass=1;
            febio_spec.Contact.contact{qc}.laugon=1;
            febio_spec.Contact.contact{qc}.tolerance=0.2;
            febio_spec.Contact.contact{qc}.gaptol=0;
            febio_spec.Contact.contact{qc}.minaug=1;
            febio_spec.Contact.contact{qc}.maxaug=10;
            febio_spec.Contact.contact{qc}.search_tol=0.01;
            febio_spec.Contact.contact{qc}.search_radius=1;
            febio_spec.Contact.contact{qc}.symmetric_stiffness=0;
            febio_spec.Contact.contact{qc}.auto_penalty=1;
            febio_spec.Contact.contact{qc}.penalty=contactPenalty;
            febio_spec.Contact.contact{qc}.fric_coeff=0.5;
    end
end
%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.node_data{2}.ATTR.file=febioLogFileName_force;
febio_spec.Output.logfile.node_data{2}.ATTR.data='Rx;Ry;Rz';
febio_spec.Output.logfile.node_data{2}.ATTR.delim=',';
febio_spec.Output.logfile.node_data{2}.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=runMode;
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 12:51:20
===========================================================================
         ________    _________   _________     __     _________            
        |        |\ |        |\ |        |\   |  |\  /         \\          
        |    ____|| |    ____|| |    __  ||   |__|| |    ___    ||         
        |   |\___\| |   |\___\| |   |\_| ||    \_\| |   //  \   ||         
        |   ||      |   ||      |   || | ||    __   |  ||    |  ||         
        |   ||__    |   ||__    |   ||_| ||   |  |\ |  ||    |  ||         
        |       |\  |       |\  |         \\  |  || |  ||    |  ||         
        |    ___||  |    ___||  |    ___   || |  || |  ||    |  ||         
        |   |\__\|  |   |\__\|  |   |\__|  || |  || |  ||    |  ||         
        |   ||      |   ||      |   ||  |  || |  || |  ||    |  ||         
        |   ||      |   ||___   |   ||__|  || |  || |   \\__/   ||         
        |   ||      |        |\ |          || |  || |           ||         
        |___||      |________|| |__________|| |__||  \_________//          
                                                                           
      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 ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791614

 1
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 1
	step from line search         = 0.500000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.716673e-12    9.795402e+10    0.000000e+00 
	   energy              6.864002e-19    4.652521e-10    6.864002e-21 
	   displacement        8.747765e-24    2.186941e-24    2.186941e-30 
 *************************************************************************
 *                               WARNING                                 *
 *                                                                       *
 * Problem is diverging. Stiffness matrix will now be reformed           *
 *************************************************************************
Reforming stiffness matrix: reformation #2

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791620

 2
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            9.795402e+10    6.021190e+06    0.000000e+00 
	   energy              4.652521e-10    1.117513e+01    4.652521e-12 
	   displacement        8.747765e-24    1.540154e+03    1.540154e-03 
 *************************************************************************
 *                               WARNING                                 *
 *                                                                       *
 * Problem is diverging. Stiffness matrix will now be reformed           *
 *************************************************************************
Reforming stiffness matrix: reformation #3

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791620

 3
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 6
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            6.021190e+06    3.027803e-04    0.000000e+00 
	   energy              1.117513e+01    2.631089e-05    1.117513e-01 
	   displacement        8.747765e-24    2.612110e-03    1.540068e-03 
Reforming stiffness matrix: reformation #4

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791620

 4
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 7
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            6.021190e+06    5.713388e-12    0.000000e+00 
	   energy              1.117513e+01    4.192780e-16    1.117513e-01 
	   displacement        8.747765e-24    3.741413e-13    1.540068e-03 

------- 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

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791620

 1
 Nonlinear solution status: time= 0.2
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 1
	step from line search         = 0.500000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.219575e+12    2.091541e+14    0.000000e+00 
	   energy              6.736496e+05    6.726732e+07    6.736496e+03 
	   displacement        1.170922e+06    2.927306e+05    2.927306e-01 
 *************************************************************************
 *                               WARNING                                 *
 *                                                                       *
 * Problem is diverging. Stiffness matrix will now be reformed           *
 *************************************************************************
Reforming stiffness matrix: reformation #2

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 2
 Nonlinear solution status: time= 0.2
	stiffness updates             = 0
	right hand side evaluations   = 6
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            2.091541e+14    2.901907e+11    0.000000e+00 
	   energy              6.726732e+07    3.352957e+05    6.726732e+05 
	   displacement        1.170922e+06    1.711411e+04    4.086778e-01 
Reforming stiffness matrix: reformation #3

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 3
 Nonlinear solution status: time= 0.2
	stiffness updates             = 0
	right hand side evaluations   = 8
	stiffness matrix reformations = 3
	step from line search         = 0.502246
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            2.091541e+14    8.960940e+10    0.000000e+00 
	   energy              6.726732e+07    2.607925e+04    6.726732e+05 
	   displacement        1.170922e+06    9.511214e+03    3.957675e-01 
Reforming stiffness matrix: reformation #4

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 4
 Nonlinear solution status: time= 0.2
	stiffness updates             = 0
	right hand side evaluations   = 9
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            2.091541e+14    9.815179e+08    0.000000e+00 
	   energy              6.726732e+07    9.390240e+03    6.726732e+05 
	   displacement        1.170922e+06    2.921068e+03    3.983133e-01 
Reforming stiffness matrix: reformation #5

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 5
 Nonlinear solution status: time= 0.2
	stiffness updates             = 0
	right hand side evaluations   = 10
	stiffness matrix reformations = 5
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            2.091541e+14    6.869699e+09    0.000000e+00 
	   energy              6.726732e+07    6.299644e+03    6.726732e+05 
	   displacement        1.170922e+06    6.300442e+03    3.709624e-01 
Reforming stiffness matrix: reformation #6

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 6
 Nonlinear solution status: time= 0.2
	stiffness updates             = 0
	right hand side evaluations   = 11
	stiffness matrix reformations = 6
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            2.091541e+14    1.675504e+07    0.000000e+00 
	   energy              6.726732e+07    8.765876e+02    6.726732e+05 
	   displacement        1.170922e+06    3.840007e+02    3.628465e-01 
Reforming stiffness matrix: reformation #7

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 7
 Nonlinear solution status: time= 0.2
	stiffness updates             = 0
	right hand side evaluations   = 12
	stiffness matrix reformations = 7
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            2.091541e+14    1.811651e+08    0.000000e+00 
	   energy              6.726732e+07    1.790250e+02    6.726732e+05 
	   displacement        1.170922e+06    1.307053e+03    3.447739e-01 
Reforming stiffness matrix: reformation #8

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 8
 Nonlinear solution status: time= 0.2
	stiffness updates             = 0
	right hand side evaluations   = 13
	stiffness matrix reformations = 8
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            2.091541e+14    6.907086e+03    0.000000e+00 
	   energy              6.726732e+07    2.915145e+00    6.726732e+05 
	   displacement        1.170922e+06    8.592492e+00    3.433671e-01 
Reforming stiffness matrix: reformation #9

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 9
 Nonlinear solution status: time= 0.2
	stiffness updates             = 0
	right hand side evaluations   = 14
	stiffness matrix reformations = 9
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            2.091541e+14    1.201173e+02    0.000000e+00 
	   energy              6.726732e+07    2.146474e-03    6.726732e+05 
	   displacement        1.170922e+06    1.127701e+00    3.428329e-01 
Reforming stiffness matrix: reformation #10

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 10
 Nonlinear solution status: time= 0.2
	stiffness updates             = 0
	right hand side evaluations   = 15
	stiffness matrix reformations = 10
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            2.091541e+14    4.813931e-09    0.000000e+00 
	   energy              6.726732e+07    1.916410e-09    6.726732e+05 
	   displacement        1.170922e+06    6.535280e-06    3.428317e-01 

------- 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

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 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            5.077753e+12    5.867459e+07    0.000000e+00 
	   energy              2.669921e+06    1.243968e+02    2.669921e+04 
	   displacement        5.421481e+03    5.421481e+03    5.421481e-03 
Reforming stiffness matrix: reformation #2

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 2
 Nonlinear solution status: time= 0.3
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.077753e+12    6.878774e-01    0.000000e+00 
	   energy              2.669921e+06    9.834997e-03    2.669921e+04 
	   displacement        5.421481e+03    3.087803e-01    5.496794e-03 
Reforming stiffness matrix: reformation #3

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 3
 Nonlinear solution status: time= 0.3
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.077753e+12    8.012236e-06    0.000000e+00 
	   energy              2.669921e+06    4.096435e-09    2.669921e+04 
	   displacement        5.421481e+03    6.107608e-04    5.500219e-03 

------- 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

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 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            5.077753e+12    6.167407e+07    0.000000e+00 
	   energy              2.670386e+06    1.259974e+02    2.670386e+04 
	   displacement        5.579895e+03    5.579895e+03    5.579895e-03 
Reforming stiffness matrix: reformation #2

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 2
 Nonlinear solution status: time= 0.4
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.077753e+12    7.259262e-01    0.000000e+00 
	   energy              2.670386e+06    1.042612e-02    2.670386e+04 
	   displacement        5.579895e+03    3.157089e-01    5.657107e-03 
Reforming stiffness matrix: reformation #3

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 3
 Nonlinear solution status: time= 0.4
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.077753e+12    1.000937e-05    0.000000e+00 
	   energy              2.670386e+06    4.699737e-09    2.670386e+04 
	   displacement        5.579895e+03    6.833103e-04    5.660784e-03 

------- 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

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 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            5.077753e+12    6.486728e+07    0.000000e+00 
	   energy              2.670866e+06    1.272485e+02    2.670866e+04 
	   displacement        5.742623e+03    5.742623e+03    5.742623e-03 
Reforming stiffness matrix: reformation #2

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 2
 Nonlinear solution status: time= 0.5
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.077753e+12    7.656699e-01    0.000000e+00 
	   energy              2.670866e+06    1.104574e-02    2.670866e+04 
	   displacement        5.742623e+03    3.225860e-01    5.821738e-03 
Reforming stiffness matrix: reformation #3

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 3
 Nonlinear solution status: time= 0.5
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.077753e+12    1.246394e-05    0.000000e+00 
	   energy              2.670866e+06    5.379997e-09    2.670866e+04 
	   displacement        5.742623e+03    7.631537e-04    5.825681e-03 

------- 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

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 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            5.077753e+12    6.826624e+07    0.000000e+00 
	   energy              2.671360e+06    1.281130e+02    2.671360e+04 
	   displacement        5.909702e+03    5.909702e+03    5.909702e-03 
Reforming stiffness matrix: reformation #2

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 2
 Nonlinear solution status: time= 0.6
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.077753e+12    8.071825e-01    0.000000e+00 
	   energy              2.671360e+06    1.169446e-02    2.671360e+04 
	   displacement        5.909702e+03    3.294038e-01    5.990721e-03 
Reforming stiffness matrix: reformation #3

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 3
 Nonlinear solution status: time= 0.6
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.077753e+12    1.547009e-05    0.000000e+00 
	   energy              2.671360e+06    6.145577e-09    2.671360e+04 
	   displacement        5.909702e+03    8.508507e-04    5.994947e-03 

------- 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

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 1
 Nonlinear solution status: time= 0.7
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 1
	step from line search         = 0.635786
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.077753e+12    2.409442e+12    0.000000e+00 
	   energy              2.671869e+06    1.307488e+05    2.671869e+04 
	   displacement        6.081165e+03    2.458153e+03    2.458153e-03 
Reforming stiffness matrix: reformation #2

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 2
 Nonlinear solution status: time= 0.7
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.077753e+12    1.851585e+09    0.000000e+00 
	   energy              2.671869e+06    2.505544e+03    2.671869e+04 
	   displacement        6.081165e+03    3.976290e+03    3.277161e-03 
Reforming stiffness matrix: reformation #3

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 3
 Nonlinear solution status: time= 0.7
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.077753e+12    2.387218e+03    0.000000e+00 
	   energy              2.671869e+06    4.033266e+00    2.671869e+04 
	   displacement        6.081165e+03    1.959233e+00    3.418865e-03 
Reforming stiffness matrix: reformation #4

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 4
 Nonlinear solution status: time= 0.7
	stiffness updates             = 0
	right hand side evaluations   = 6
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.077753e+12    7.295710e+02    0.000000e+00 
	   energy              2.671869e+06    1.587028e-03    2.671869e+04 
	   displacement        6.081165e+03    8.093909e-01    3.510621e-03 
Reforming stiffness matrix: reformation #5

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 5
 Nonlinear solution status: time= 0.7
	stiffness updates             = 0
	right hand side evaluations   = 7
	stiffness matrix reformations = 5
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.077753e+12    6.581283e-10    0.000000e+00 
	   energy              2.671869e+06    1.563810e-09    2.671869e+04 
	   displacement        6.081165e+03    6.651528e-07    3.510704e-03 

------- 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

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 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            5.077753e+12    1.520618e+08    0.000000e+00 
	   energy              2.649684e+06    1.302418e+02    2.649684e+04 
	   displacement        2.142671e+03    2.142671e+03    2.142671e-03 
Reforming stiffness matrix: reformation #2

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 2
 Nonlinear solution status: time= 0.8
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.077753e+12    2.619650e+00    0.000000e+00 
	   energy              2.649684e+06    3.407697e-02    2.649684e+04 
	   displacement        2.142671e+03    3.402911e-01    2.191137e-03 
Reforming stiffness matrix: reformation #3

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 3
 Nonlinear solution status: time= 0.8
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.077753e+12    6.228440e-05    0.000000e+00 
	   energy              2.649684e+06    2.411924e-08    2.649684e+04 
	   displacement        2.142671e+03    8.257510e-04    2.193606e-03 

------- 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

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 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            5.077753e+12    1.622973e+08    0.000000e+00 
	   energy              2.650495e+06    1.227027e+02    2.650495e+04 
	   displacement        2.245440e+03    2.245440e+03    2.245440e-03 
Reforming stiffness matrix: reformation #2

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 2
 Nonlinear solution status: time= 0.9
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.077753e+12    2.803349e+00    0.000000e+00 
	   energy              2.650495e+06    3.633823e-02    2.650495e+04 
	   displacement        2.245440e+03    3.488948e-01    2.295665e-03 
Reforming stiffness matrix: reformation #3

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 3
 Nonlinear solution status: time= 0.9
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.077753e+12    7.566199e-05    0.000000e+00 
	   energy              2.650495e+06    2.746909e-08    2.650495e+04 
	   displacement        2.245440e+03    9.231313e-04    2.298339e-03 

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

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

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 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            5.077753e+12    1.732408e+08    0.000000e+00 
	   energy              2.651327e+06    1.134660e+02    2.651327e+04 
	   displacement        2.352157e+03    2.352157e+03    2.352157e-03 
Reforming stiffness matrix: reformation #2

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 2
 Nonlinear solution status: time= 1
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.077753e+12    2.999441e+00    0.000000e+00 
	   energy              2.651327e+06    3.871980e-02    2.651327e+04 
	   displacement        2.352157e+03    3.575541e-01    2.404168e-03 
Reforming stiffness matrix: reformation #3

===== reforming stiffness matrix:
	Nr of equations ........................... : 20746
	Nr of nonzeroes in stiffness matrix ....... : 791638

 3
 Nonlinear solution status: time= 1
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.077753e+12    9.149132e-05    0.000000e+00 
	   energy              2.651327e+06    3.120518e-08    2.651327e+04 
	   displacement        2.352157e+03    1.030740e-03    2.407061e-03 

------- 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 ............ : 40

	Average number of equilibrium iterations .......... : 4

	Total number of right hand evaluations ............ : 57

	Total number of stiffness reformations ............ : 40

	Time in linear solver: 0:00:08


 Elapsed time : 0:00:18


 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 12:51:39
------- 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 12:51:39

Import FEBio results

if runFlag==1 || runFlag==0 %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(:,3).^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,:);
    [CF]=vertexToFaceMeasure(Fb,DN_magnitude);

    %
    % 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,CF,'k',1); %Add graphics object to animate
    hp2=gpatch([Fc1;Fc2;Fc3],V_def,'kw','none',0.5);

    gpatch(Fb,V,0.5*ones(1,3),'none',0.25); %A static graphics object

    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
        [CF]=vertexToFaceMeasure(Fb,DN_magnitude); %Current color data to use

        %Set entries in animation structure
        animStruct.Handles{qt}=[hp1 hp1 hp2]; %Handles of objects to animate
        animStruct.Props{qt}={'Vertices','CData','Vertices'}; %Properties of objects to animate
        animStruct.Set{qt}={V_def,CF,V_def}; %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/.

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.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

DEMO_febio_0021_bone_three_point_bending

Contents

Keywords

Plot settings

Control parameters

Prepare bone geometry

Create and position cylinder geometry

Get interior point

Visualizing mesh using meshView, see also anim8

Joining node sets

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

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