DEMO_febio_0024_active_contraction_tongue

Contents

Keywords

clear; close all; clc;

Plot settings

fontSize=15;
markerSize=35;
plotColor=[1 0.5 0.4];
vectorPlotSize=10;

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

%Material parameter set
c1=1e-3; %Shear-modulus-like parameter
m1=8; %Material parameter setting degree of non-linearity
ksi=c1*100; %Fiber "modulus"
beta=3; %Fiber "nonlinearity" parameter
k_factor=1e2; %Bulk modulus factor
k=0.5.*(c1+ksi)*k_factor; %Bulk modulus
T0=10e-3; %Active stress
formulationType=1; %1=uncoupled, 2=coupled

% 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=6; %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

Set up geometry for the tongue model

% Import model geometry. This geometry was obtained with permission from the Artisynth project (https://www.artisynth.org/Demo/BiomechanicalTongueModel)
loadNameOff=fullfile(defaultFolder,'data','OFF','tongue_mesh.off'); %File name for off file
[E,V] = import_off(loadNameOff); %Import mesh data

[F,~]=element2patch(E,[]); %Get mesh faces for visualization

Visualize imported mesh

% Plotting model
cFigure; hold on;
gtitle('Tongue model geometry',fontSize);
gpatch(F,V,plotColor,'k',0.5); %Visualize mesh faces
% patchNormPlot(F,V); %Visualize normal directions
axisGeom(gca,fontSize);
camlight headlight;
drawnow;

Defining fiber directions and boundary conditions

Fiber directions are here defined as running from the bottom of elements to the top of elements, this is not physiological.

%Get boundary faces
[indBoundary]=tesBoundary(F,V); %Get boundary face indices
Fb=F(indBoundary,:); %Boundary faces

%Get top and bottom faces for boundary conditions
F_element_bottoms=E(:,[1 4 8 5]); %Get element bottom faces
F_element_tops=E(:,[2 3 7 6]); %Get element top faces

X=V(:,1); Y=V(:,2); Z=V(:,3); % Nodal coordinate components

%Compute element centre coordinates (used as fiber origins in visualization)
[VE]=patchCentre(E,V);

%Define fibers as going from one face center to the other
V_fib_bottom=patchCentre(F_element_bottoms,V); %Middle of bottom faces
V_fib_top=patchCentre(F_element_tops,V); %Middle of top faces
V_fib=vecnormalize(V_fib_top-V_fib_bottom); %Normalized fiber vectors
[a,d]=vectorOrthogonalPair(V_fib); %Get orthogonal vector pair

%Get boundary directions faces to set-up support
F_bottom=F_element_bottoms(all(ismember(F_element_bottoms,Fb),2),:); %The faces at the bottom
bcSupportList=unique(F_bottom(:)); %The node list for the bottom nodes

Visualize boundary conditions

cFigure; hold on;
gtitle('Boundary conditions and fiber directions',fontSize);
hl(1)=gpatch(Fb,V,plotColor,'none',0.25);
hl(2)=quiverVec(VE,V_fib,vectorPlotSize,'k');
quiverVec(VE,a,vectorPlotSize/2,'kw');
quiverVec(VE,d,vectorPlotSize/2,'kw');

hl(3)=gpatch(F_bottom,V,'rw','r',1);
hl(4)=plotV(V(bcSupportList,:),'r.','MarkerSize',markerSize);

legend(hl,{'Boundary faces','Fiber vectors','Bottom faces','Supported nodes'});

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;

%Material section
febio_spec.Material.material{1}.ATTR.type='solid mixture';
febio_spec.Material.material{1}.ATTR.id=1;

febio_spec.Material.material{1}.mat_axis.ATTR.type='user';

switch formulationType
    case 1
        %The gound matrix
        febio_spec.Material.material{1}.solid{1}.ATTR.type='Ogden';
        febio_spec.Material.material{1}.solid{1}.c1=c1;
        febio_spec.Material.material{1}.solid{1}.m1=m1;
        febio_spec.Material.material{1}.solid{1}.c2=c1;
        febio_spec.Material.material{1}.solid{1}.m2=-m1;
        febio_spec.Material.material{1}.solid{1}.k=k;

        %The passive fiber component
        febio_spec.Material.material{1}.solid{2}.ATTR.type='fiber-exp-pow-uncoupled';
        febio_spec.Material.material{1}.solid{2}.ksi=ksi;
        febio_spec.Material.material{1}.solid{2}.alpha=1e-20;
        febio_spec.Material.material{1}.solid{2}.beta=beta;
        febio_spec.Material.material{1}.solid{2}.theta=0;
        febio_spec.Material.material{1}.solid{2}.phi=0;
        febio_spec.Material.material{1}.solid{2}.k=k;

        %The active fiber component
        febio_spec.Material.material{1}.solid{3}.ATTR.type='uncoupled prescribed uniaxial active contraction';
        febio_spec.Material.material{1}.solid{3}.T0.VAL=T0;
        febio_spec.Material.material{1}.solid{3}.T0.ATTR.lc=1;
        febio_spec.Material.material{1}.solid{3}.theta=0;
        febio_spec.Material.material{1}.solid{3}.phi=0;
    case 2
        %The gound matrix
        febio_spec.Material.material{1}.solid{1}.ATTR.type='Ogden unconstrained';
        febio_spec.Material.material{1}.solid{1}.c1=c1;
        febio_spec.Material.material{1}.solid{1}.m1=m1;
        febio_spec.Material.material{1}.solid{1}.c2=c1;
        febio_spec.Material.material{1}.solid{1}.m2=-m1;
        febio_spec.Material.material{1}.solid{1}.cp=k;

        %The passive fiber component
        febio_spec.Material.material{1}.solid{2}.ATTR.type='fiber-exp-pow';
        febio_spec.Material.material{1}.solid{2}.ksi=ksi;
        febio_spec.Material.material{1}.solid{2}.alpha=1e-20;
        febio_spec.Material.material{1}.solid{2}.beta=beta;
        febio_spec.Material.material{1}.solid{2}.theta=0;
        febio_spec.Material.material{1}.solid{2}.phi=0;

        %The active fiber component
        febio_spec.Material.material{1}.solid{3}.ATTR.type='prescribed uniaxial active contraction';
        febio_spec.Material.material{1}.solid{3}.T0.VAL=T0;
        febio_spec.Material.material{1}.solid{3}.T0.ATTR.lc=1;
        febio_spec.Material.material{1}.solid{3}.theta=0;
        febio_spec.Material.material{1}.solid{3}.phi=0;
end
%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='hex8'; %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='Tongue'; %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(:);

% -> ElementSets
febio_spec.Geometry.ElementSet{1}.ATTR.name='elementSetTransiso';
febio_spec.Geometry.ElementSet{1}.elem.ATTR.id=(1:size(E,1))';

%MeshData section
% -> ElementData
febio_spec.MeshData.ElementData{1}.ATTR.elem_set=febio_spec.Geometry.ElementSet{1}.ATTR.name;
febio_spec.MeshData.ElementData{1}.ATTR.var='mat_axis';

for q=1:1:size(E,1)
    febio_spec.MeshData.ElementData{1}.elem{q}.ATTR.lid=q;
    febio_spec.MeshData.ElementData{1}.elem{q}.a=a(q,:);
    febio_spec.MeshData.ElementData{1}.elem{q}.d=d(q,:);
end

%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;

%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 12:53:11
===========================================================================
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      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 ........................... : 1050
	Nr of nonzeroes in stiffness matrix ....... : 31647

 1
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 1
	step from line search         = 0.195436
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            3.578681e+00    3.058119e+02    0.000000e+00 
	   energy              1.002393e+02    1.280945e+01    1.002393e+00 
	   displacement        1.902769e+04    7.267650e+02    7.267650e-04 
Reforming stiffness matrix: reformation #2

 2
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 2
	step from line search         = 0.494079
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            3.578681e+00    7.065015e+02    0.000000e+00 
	   energy              1.002393e+02    4.853562e+00    1.002393e+00 
	   displacement        1.902769e+04    9.401442e+02    2.573219e-03 
Reforming stiffness matrix: reformation #3

 3
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 7
	stiffness matrix reformations = 3
	step from line search         = 0.099559
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            3.578681e+00    5.797809e+02    0.000000e+00 
	   energy              1.002393e+02    1.554631e+00    1.002393e+00 
	   displacement        1.902769e+04    3.610776e+01    2.965313e-03 
Reforming stiffness matrix: reformation #4

 4
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 9
	stiffness matrix reformations = 4
	step from line search         = 0.061808
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            3.578681e+00    4.915819e+02    0.000000e+00 
	   energy              1.002393e+02    1.698694e-01    1.002393e+00 
	   displacement        1.902769e+04    3.008927e+01    2.992718e-03 
Reforming stiffness matrix: reformation #5

 5
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 12
	stiffness matrix reformations = 5
	step from line search         = 0.500000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            3.578681e+00    5.064640e+04    0.000000e+00 
	   energy              1.002393e+02    3.543065e+02    1.002393e+00 
	   displacement        1.902769e+04    6.241076e+03    8.960004e-03 
 *************************************************************************
 *                               WARNING                                 *
 *                                                                       *
 * Problem is diverging. Stiffness matrix will now be reformed           *
 *************************************************************************
Reforming stiffness matrix: reformation #6

 6
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 13
	stiffness matrix reformations = 6
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.064640e+04    9.984676e+01    0.000000e+00 
	   energy              3.543065e+02    4.404689e+00    3.543065e+00 
	   displacement        1.902769e+04    1.405309e+02    9.223508e-03 
Reforming stiffness matrix: reformation #7

 7
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 15
	stiffness matrix reformations = 7
	step from line search         = 0.050146
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.064640e+04    8.370548e+01    0.000000e+00 
	   energy              3.543065e+02    2.972755e+00    3.543065e+00 
	   displacement        1.902769e+04    1.343646e+02    7.754871e-03 
Reforming stiffness matrix: reformation #8

 8
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 17
	stiffness matrix reformations = 8
	step from line search         = 0.249387
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.064640e+04    3.637101e+02    0.000000e+00 
	   energy              3.543065e+02    5.591008e+00    3.543065e+00 
	   displacement        1.902769e+04    1.073987e+03    5.884595e-03 
Reforming stiffness matrix: reformation #9

 9
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 21
	stiffness matrix reformations = 9
	step from line search         = 0.071838
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.064640e+04    1.721905e+02    0.000000e+00 
	   energy              3.543065e+02    3.460791e-01    3.543065e+00 
	   displacement        1.902769e+04    8.788513e+01    5.975388e-03 
Reforming stiffness matrix: reformation #10

 10
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 23
	stiffness matrix reformations = 10
	step from line search         = 0.186462
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.064640e+04    8.407152e+01    0.000000e+00 
	   energy              3.543065e+02    2.573541e+00    3.543065e+00 
	   displacement        1.902769e+04    1.939613e+02    6.499729e-03 
Reforming stiffness matrix: reformation #11

 11
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 25
	stiffness matrix reformations = 11
	step from line search         = 0.062564
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.064640e+04    6.376154e+01    0.000000e+00 
	   energy              3.543065e+02    1.249487e+00    3.543065e+00 
	   displacement        1.902769e+04    6.176327e+01    6.343722e-03 
Reforming stiffness matrix: reformation #12

 12
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 27
	stiffness matrix reformations = 12
	step from line search         = 0.291338
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.064640e+04    1.478684e+02    0.000000e+00 
	   energy              3.543065e+02    1.817481e+00    3.543065e+00 
	   displacement        1.902769e+04    4.248722e+02    7.058470e-03 
Reforming stiffness matrix: reformation #13

 13
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 29
	stiffness matrix reformations = 13
	step from line search         = 0.143927
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.064640e+04    6.808592e+01    0.000000e+00 
	   energy              3.543065e+02    6.372276e-01    3.543065e+00 
	   displacement        1.902769e+04    3.806084e+01    7.587943e-03 
Reforming stiffness matrix: reformation #14

 14
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 30
	stiffness matrix reformations = 14
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.064640e+04    5.731627e+02    0.000000e+00 
	   energy              3.543065e+02    2.918804e+00    3.543065e+00 
	   displacement        1.902769e+04    1.588217e+03    1.199421e-02 
Reforming stiffness matrix: reformation #15

 15
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 32
	stiffness matrix reformations = 15
	step from line search         = 0.076587
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.064640e+04    4.351846e+02    0.000000e+00 
	   energy              3.543065e+02    2.244772e-01    3.543065e+00 
	   displacement        1.902769e+04    3.370531e+01    1.100715e-02 
Reforming stiffness matrix: reformation #16

 16
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 34
	stiffness matrix reformations = 16
	step from line search         = 0.375623
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.064640e+04    1.042903e+02    0.000000e+00 
	   energy              3.543065e+02    2.210132e-01    3.543065e+00 
	   displacement        1.902769e+04    1.359984e+02    1.297157e-02 
Reforming stiffness matrix: reformation #17

 17
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 36
	stiffness matrix reformations = 17
	step from line search         = 0.343569
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.064640e+04    2.878284e+01    0.000000e+00 
	   energy              3.543065e+02    2.478754e-01    3.543065e+00 
	   displacement        1.902769e+04    3.457383e+01    1.272601e-02 
Reforming stiffness matrix: reformation #18

 18
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 38
	stiffness matrix reformations = 18
	step from line search         = 0.443854
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.064640e+04    2.170420e+01    0.000000e+00 
	   energy              3.543065e+02    1.352020e-01    3.543065e+00 
	   displacement        1.902769e+04    4.334128e+01    1.325140e-02 
Reforming stiffness matrix: reformation #19

 19
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 39
	stiffness matrix reformations = 19
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.064640e+04    5.361674e+00    0.000000e+00 
	   energy              3.543065e+02    7.876295e-02    3.543065e+00 
	   displacement        1.902769e+04    5.437352e+01    1.421863e-02 
Reforming stiffness matrix: reformation #20

 20
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 40
	stiffness matrix reformations = 20
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.064640e+04    9.335125e-01    0.000000e+00 
	   energy              3.543065e+02    1.400333e-02    3.543065e+00 
	   displacement        1.902769e+04    1.494415e+01    1.476700e-02 
Reforming stiffness matrix: reformation #21

 21
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 41
	stiffness matrix reformations = 21
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.064640e+04    1.343430e-02    0.000000e+00 
	   energy              3.543065e+02    9.468536e-04    3.543065e+00 
	   displacement        1.902769e+04    1.419146e+00    1.493093e-02 
Reforming stiffness matrix: reformation #22

 22
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 42
	stiffness matrix reformations = 22
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.064640e+04    2.373922e-05    0.000000e+00 
	   energy              3.543065e+02    4.427289e-06    3.543065e+00 
	   displacement        1.902769e+04    3.500973e-02    1.495407e-02 
Reforming stiffness matrix: reformation #23

 23
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 43
	stiffness matrix reformations = 23
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.064640e+04    6.746574e-12    0.000000e+00 
	   energy              3.543065e+02    1.022690e-10    3.543065e+00 
	   displacement        1.902769e+04    1.765352e-05    1.495459e-02 

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

 ]0;(10%) tempModel.feb - FEBio 2.9.0.0  
AUTO STEPPER: decreasing time step, dt = 0.0515646


===== beginning time step 2 : 0.151565 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.151565
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 1
	step from line search         = 0.610123
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            7.824214e-01    1.743412e+02    0.000000e+00 
	   energy              1.230747e+01    1.066209e+00    1.230747e-01 
	   displacement        1.280717e+03    4.767466e+02    4.767466e-04 
Reforming stiffness matrix: reformation #2

 2
 Nonlinear solution status: time= 0.151565
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            7.824214e-01    7.632239e+01    0.000000e+00 
	   energy              1.230747e+01    4.170883e-01    1.230747e-01 
	   displacement        1.280717e+03    1.276217e+02    1.046454e-03 
Reforming stiffness matrix: reformation #3

 3
 Nonlinear solution status: time= 0.151565
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            7.824214e-01    4.854997e+00    0.000000e+00 
	   energy              1.230747e+01    2.776302e-02    1.230747e-01 
	   displacement        1.280717e+03    1.719114e+01    1.143990e-03 
Reforming stiffness matrix: reformation #4

 4
 Nonlinear solution status: time= 0.151565
	stiffness updates             = 0
	right hand side evaluations   = 6
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            7.824214e-01    4.358833e+00    0.000000e+00 
	   energy              1.230747e+01    9.364710e-03    1.230747e-01 
	   displacement        1.280717e+03    3.072389e+00    1.126744e-03 
Reforming stiffness matrix: reformation #5

 5
 Nonlinear solution status: time= 0.151565
	stiffness updates             = 0
	right hand side evaluations   = 7
	stiffness matrix reformations = 5
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            7.824214e-01    1.159930e-03    0.000000e+00 
	   energy              1.230747e+01    5.662144e-05    1.230747e-01 
	   displacement        1.280717e+03    8.448753e-02    1.127493e-03 
Reforming stiffness matrix: reformation #6

 6
 Nonlinear solution status: time= 0.151565
	stiffness updates             = 0
	right hand side evaluations   = 8
	stiffness matrix reformations = 6
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            7.824214e-01    4.426014e-07    0.000000e+00 
	   energy              1.230747e+01    3.800496e-08    1.230747e-01 
	   displacement        1.280717e+03    1.129941e-03    1.127241e-03 
Reforming stiffness matrix: reformation #7

 7
 Nonlinear solution status: time= 0.151565
	stiffness updates             = 0
	right hand side evaluations   = 9
	stiffness matrix reformations = 7
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            7.824214e-01    5.401716e-19    0.000000e+00 
	   energy              1.230747e+01    3.714505e-16    1.230747e-01 
	   displacement        1.280717e+03    1.671784e-09    1.127242e-03 

------- converged at time : 0.151565

 ]0;(15%) tempModel.feb - FEBio 2.9.0.0  
AUTO STEPPER: decreasing time step, dt = 0.0478138


===== beginning time step 3 : 0.199378 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.199378
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            6.381399e-01    3.711686e+02    0.000000e+00 
	   energy              8.163416e+00    3.936288e+00    8.163416e-02 
	   displacement        6.402336e+02    6.402336e+02    6.402336e-04 
Reforming stiffness matrix: reformation #2

 2
 Nonlinear solution status: time= 0.199378
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            6.381399e-01    6.494168e-02    0.000000e+00 
	   energy              8.163416e+00    2.037595e-02    8.163416e-02 
	   displacement        6.402336e+02    5.843704e+00    5.679038e-04 
Reforming stiffness matrix: reformation #3

 3
 Nonlinear solution status: time= 0.199378
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            6.381399e-01    7.843606e-02    0.000000e+00 
	   energy              8.163416e+00    1.327348e-05    8.163416e-02 
	   displacement        6.402336e+02    4.683135e+00    5.788850e-04 
Reforming stiffness matrix: reformation #4

 4
 Nonlinear solution status: time= 0.199378
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            6.381399e-01    3.516922e-09    0.000000e+00 
	   energy              8.163416e+00    9.922876e-08    8.163416e-02 
	   displacement        6.402336e+02    4.710421e-04    5.791173e-04 

------- converged at time : 0.199378

 ]0;(20%) tempModel.feb - FEBio 2.9.0.0  
AUTO STEPPER: increasing time step, dt = 0.058251


===== beginning time step 4 : 0.257629 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.257629
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            9.120941e-01    3.978120e+02    0.000000e+00 
	   energy              1.000444e+01    4.317817e+00    1.000444e-01 
	   displacement        6.286925e+02    6.286925e+02    6.286925e-04 
Reforming stiffness matrix: reformation #2

 2
 Nonlinear solution status: time= 0.257629
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            9.120941e-01    5.809017e-01    0.000000e+00 
	   energy              1.000444e+01    7.768295e-02    1.000444e-01 
	   displacement        6.286925e+02    1.177201e+01    5.586266e-04 
Reforming stiffness matrix: reformation #3

 3
 Nonlinear solution status: time= 0.257629
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            9.120941e-01    4.968700e-01    0.000000e+00 
	   energy              1.000444e+01    8.422652e-04    1.000444e-01 
	   displacement        6.286925e+02    1.014882e+01    5.661577e-04 
Reforming stiffness matrix: reformation #4

 4
 Nonlinear solution status: time= 0.257629
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            9.120941e-01    3.115984e-06    0.000000e+00 
	   energy              1.000444e+01    6.734583e-06    1.000444e-01 
	   displacement        6.286925e+02    8.816989e-03    5.669390e-04 
Reforming stiffness matrix: reformation #5

 5
 Nonlinear solution status: time= 0.257629
	stiffness updates             = 0
	right hand side evaluations   = 6
	stiffness matrix reformations = 5
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            9.120941e-01    2.630999e-11    0.000000e+00 
	   energy              1.000444e+01    4.596920e-11    1.000444e-01 
	   displacement        6.286925e+02    1.808040e-05    5.669708e-04 

------- converged at time : 0.257629

 ]0;(26%) tempModel.feb - FEBio 2.9.0.0  
AUTO STEPPER: increasing time step, dt = 0.0622357


===== beginning time step 5 : 0.319865 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.319865
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.003258e+00    2.567105e+02    0.000000e+00 
	   energy              9.525632e+00    2.894886e+00    9.525632e-02 
	   displacement        4.901050e+02    4.901050e+02    4.901050e-04 
Reforming stiffness matrix: reformation #2

 2
 Nonlinear solution status: time= 0.319865
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.003258e+00    2.274584e-02    0.000000e+00 
	   energy              9.525632e+00    8.248250e-03    9.525632e-02 
	   displacement        4.901050e+02    1.070113e+00    4.553130e-04 
Reforming stiffness matrix: reformation #3

 3
 Nonlinear solution status: time= 0.319865
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.003258e+00    6.206632e-02    0.000000e+00 
	   energy              9.525632e+00    2.537111e-05    9.525632e-02 
	   displacement        4.901050e+02    5.967340e-01    4.464963e-04 
Reforming stiffness matrix: reformation #4

 4
 Nonlinear solution status: time= 0.319865
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.003258e+00    3.395021e-09    0.000000e+00 
	   energy              9.525632e+00    8.842278e-08    9.525632e-02 
	   displacement        4.901050e+02    1.238183e-04    4.464974e-04 

------- converged at time : 0.319865

 ]0;(32%) tempModel.feb - FEBio 2.9.0.0  
AUTO STEPPER: increasing time step, dt = 0.0697886


===== beginning time step 6 : 0.389654 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.389654
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.221102e+00    2.153270e+02    0.000000e+00 
	   energy              1.022198e+01    2.508198e+00    1.022198e-01 
	   displacement        4.437979e+02    4.437979e+02    4.437979e-04 
Reforming stiffness matrix: reformation #2

 2
 Nonlinear solution status: time= 0.389654
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.221102e+00    5.422209e-02    0.000000e+00 
	   energy              1.022198e+01    1.580762e-02    1.022198e-01 
	   displacement        4.437979e+02    1.860105e+00    4.101481e-04 
Reforming stiffness matrix: reformation #3

 3
 Nonlinear solution status: time= 0.389654
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.221102e+00    1.281420e-01    0.000000e+00 
	   energy              1.022198e+01    9.779375e-06    1.022198e-01 
	   displacement        4.437979e+02    1.657958e+00    4.059214e-04 
Reforming stiffness matrix: reformation #4

 4
 Nonlinear solution status: time= 0.389654
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.221102e+00    4.626628e-08    0.000000e+00 
	   energy              1.022198e+01    5.049976e-07    1.022198e-01 
	   displacement        4.437979e+02    7.043919e-04    4.059933e-04 
Reforming stiffness matrix: reformation #5

 5
 Nonlinear solution status: time= 0.389654
	stiffness updates             = 0
	right hand side evaluations   = 6
	stiffness matrix reformations = 5
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.221102e+00    1.273052e-13    0.000000e+00 
	   energy              1.022198e+01    4.587549e-13    1.022198e-01 
	   displacement        4.437979e+02    1.118776e-06    4.059959e-04 

------- converged at time : 0.389654

 ]0;(39%) tempModel.feb - FEBio 2.9.0.0  
AUTO STEPPER: increasing time step, dt = 0.0726721


===== beginning time step 7 : 0.462326 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.462326
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.284044e+00    1.391528e+02    0.000000e+00 
	   energy              9.578429e+00    1.699457e+00    9.578429e-02 
	   displacement        3.578331e+02    3.578331e+02    3.578331e-04 
Reforming stiffness matrix: reformation #2

 2
 Nonlinear solution status: time= 0.462326
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.284044e+00    6.977648e-01    0.000000e+00 
	   energy              9.578429e+00    6.804499e-02    9.578429e-02 
	   displacement        3.578331e+02    7.175009e+00    3.438965e-04 
Reforming stiffness matrix: reformation #3

 3
 Nonlinear solution status: time= 0.462326
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.284044e+00    3.189647e-01    0.000000e+00 
	   energy              9.578429e+00    1.854895e-03    9.578429e-02 
	   displacement        3.578331e+02    5.052633e+00    3.306282e-04 
Reforming stiffness matrix: reformation #4

 4
 Nonlinear solution status: time= 0.462326
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.284044e+00    1.315127e-05    0.000000e+00 
	   energy              9.578429e+00    1.400178e-05    9.578429e-02 
	   displacement        3.578331e+02    1.645596e-02    3.303892e-04 
Reforming stiffness matrix: reformation #5

 5
 Nonlinear solution status: time= 0.462326
	stiffness updates             = 0
	right hand side evaluations   = 6
	stiffness matrix reformations = 5
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.284044e+00    1.474779e-10    0.000000e+00 
	   energy              9.578429e+00    2.890086e-10    9.578429e-02 
	   displacement        3.578331e+02    4.850221e-05    3.303725e-04 

------- converged at time : 0.462326

 ]0;(46%) tempModel.feb - FEBio 2.9.0.0  
AUTO STEPPER: increasing time step, dt = 0.0752804


===== beginning time step 8 : 0.537606 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.537606
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.340639e+00    9.342291e+01    0.000000e+00 
	   energy              9.035389e+00    1.200167e+00    9.035389e-02 
	   displacement        2.965571e+02    2.965571e+02    2.965571e-04 
Reforming stiffness matrix: reformation #2

 2
 Nonlinear solution status: time= 0.537606
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.340639e+00    2.574573e-03    0.000000e+00 
	   energy              9.035389e+00    2.281984e-03    9.035389e-02 
	   displacement        2.965571e+02    8.359829e-01    2.785273e-04 
Reforming stiffness matrix: reformation #3

 3
 Nonlinear solution status: time= 0.537606
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.340639e+00    4.759584e-04    0.000000e+00 
	   energy              9.035389e+00    3.982418e-06    9.035389e-02 
	   displacement        2.965571e+02    2.345815e-01    2.758247e-04 
Reforming stiffness matrix: reformation #4

 4
 Nonlinear solution status: time= 0.537606
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.340639e+00    9.120296e-14    0.000000e+00 
	   energy              9.035389e+00    4.343742e-11    9.035389e-02 
	   displacement        2.965571e+02    1.307801e-06    2.758246e-04 

------- converged at time : 0.537606

 ]0;(54%) tempModel.feb - FEBio 2.9.0.0  
AUTO STEPPER: increasing time step, dt = 0.0802244


===== beginning time step 9 : 0.617831 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.617831
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.485251e+00    7.357499e+01    0.000000e+00 
	   energy              9.136343e+00    9.886425e-01    9.136343e-02 
	   displacement        2.673061e+02    2.673061e+02    2.673061e-04 
Reforming stiffness matrix: reformation #2

 2
 Nonlinear solution status: time= 0.617831
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.485251e+00    5.016901e-04    0.000000e+00 
	   energy              9.136343e+00    4.078727e-04    9.136343e-02 
	   displacement        2.673061e+02    5.424441e-01    2.511933e-04 
Reforming stiffness matrix: reformation #3

 3
 Nonlinear solution status: time= 0.617831
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.485251e+00    3.974830e-05    0.000000e+00 
	   energy              9.136343e+00    3.596861e-07    9.136343e-02 
	   displacement        2.673061e+02    7.343689e-02    2.496291e-04 
Reforming stiffness matrix: reformation #4

 4
 Nonlinear solution status: time= 0.617831
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.485251e+00    4.624622e-17    0.000000e+00 
	   energy              9.136343e+00    2.638015e-13    9.136343e-02 
	   displacement        2.673061e+02    2.678877e-08    2.496290e-04 

------- converged at time : 0.617831

 ]0;(62%) tempModel.feb - FEBio 2.9.0.0  
AUTO STEPPER: increasing time step, dt = 0.0841795


===== beginning time step 10 : 0.70201 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.70201
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.597542e+00    5.607809e+01    0.000000e+00 
	   energy              9.026807e+00    7.917739e-01    9.026807e-02 
	   displacement        2.375426e+02    2.375426e+02    2.375426e-04 
Reforming stiffness matrix: reformation #2

 2
 Nonlinear solution status: time= 0.70201
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.597542e+00    1.644620e-04    0.000000e+00 
	   energy              9.026807e+00    6.017017e-05    9.026807e-02 
	   displacement        2.375426e+02    3.985464e-01    2.237334e-04 
Reforming stiffness matrix: reformation #3

 3
 Nonlinear solution status: time= 0.70201
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.597542e+00    4.953115e-06    0.000000e+00 
	   energy              9.026807e+00    3.401953e-08    9.026807e-02 
	   displacement        2.375426e+02    2.716076e-02    2.227750e-04 
Reforming stiffness matrix: reformation #4

 4
 Nonlinear solution status: time= 0.70201
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.597542e+00    4.866779e-20    0.000000e+00 
	   energy              9.026807e+00    1.632200e-15    9.026807e-02 
	   displacement        2.375426e+02    7.990547e-10    2.227749e-04 

------- converged at time : 0.70201

 ]0;(70%) tempModel.feb - FEBio 2.9.0.0  
AUTO STEPPER: increasing time step, dt = 0.0873436


===== beginning time step 11 : 0.789354 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.789354
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.682618e+00    4.218982e+01    0.000000e+00 
	   energy              8.788198e+00    6.276515e-01    8.788198e-02 
	   displacement        2.097285e+02    2.097285e+02    2.097285e-04 
Reforming stiffness matrix: reformation #2

 2
 Nonlinear solution status: time= 0.789354
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.682618e+00    7.388801e-05    0.000000e+00 
	   energy              8.788198e+00    1.539529e-04    8.788198e-02 
	   displacement        2.097285e+02    3.075290e-01    1.981241e-04 
Reforming stiffness matrix: reformation #3

 3
 Nonlinear solution status: time= 0.789354
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.682618e+00    8.093573e-07    0.000000e+00 
	   energy              8.788198e+00    1.229913e-09    8.788198e-02 
	   displacement        2.097285e+02    1.120427e-02    1.975251e-04 
Reforming stiffness matrix: reformation #4

 4
 Nonlinear solution status: time= 0.789354
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.682618e+00    3.545268e-21    0.000000e+00 
	   energy              8.788198e+00    4.083819e-17    8.788198e-02 
	   displacement        2.097285e+02    1.363344e-10    1.975250e-04 

------- converged at time : 0.789354

 ]0;(79%) tempModel.feb - FEBio 2.9.0.0  
AUTO STEPPER: increasing time step, dt = 0.0898749


===== beginning time step 12 : 0.879229 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.879229
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.745393e+00    3.171706e+01    0.000000e+00 
	   energy              8.475860e+00    4.974851e-01    8.475860e-02 
	   displacement        1.848383e+02    1.848383e+02    1.848383e-04 
Reforming stiffness matrix: reformation #2

 2
 Nonlinear solution status: time= 0.879229
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.745393e+00    3.914882e-05    0.000000e+00 
	   energy              8.475860e+00    1.444500e-04    8.475860e-02 
	   displacement        1.848383e+02    2.426081e-01    1.751544e-04 
Reforming stiffness matrix: reformation #3

 3
 Nonlinear solution status: time= 0.879229
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.745393e+00    1.602267e-07    0.000000e+00 
	   energy              8.475860e+00    1.033364e-09    8.475860e-02 
	   displacement        1.848383e+02    4.989770e-03    1.747765e-04 
Reforming stiffness matrix: reformation #4

 4
 Nonlinear solution status: time= 0.879229
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.745393e+00    3.037354e-21    0.000000e+00 
	   energy              8.475860e+00    8.552486e-18    8.475860e-02 
	   displacement        1.848383e+02    5.215001e-11    1.747765e-04 

------- converged at time : 0.879229

 ]0;(88%) tempModel.feb - FEBio 2.9.0.0  
AUTO STEPPER: increasing time step, dt = 0.0918999


===== beginning time step 13 : 0.971128 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.971128
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.790229e+00    2.400516e+01    0.000000e+00 
	   energy              8.126565e+00    3.966867e-01    8.126565e-02 
	   displacement        1.630437e+02    1.630437e+02    1.630437e-04 
Reforming stiffness matrix: reformation #2

 2
 Nonlinear solution status: time= 0.971128
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.790229e+00    2.256307e-05    0.000000e+00 
	   energy              8.126565e+00    1.108897e-04    8.126565e-02 
	   displacement        1.630437e+02    1.940374e-01    1.549888e-04 
Reforming stiffness matrix: reformation #3

 3
 Nonlinear solution status: time= 0.971128
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.790229e+00    3.702078e-08    0.000000e+00 
	   energy              8.126565e+00    5.225501e-10    8.126565e-02 
	   displacement        1.630437e+02    2.364943e-03    1.547494e-04 
Reforming stiffness matrix: reformation #4

 4
 Nonlinear solution status: time= 0.971128
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            1.790229e+00    2.589882e-21    0.000000e+00 
	   energy              8.126565e+00    3.562576e-18    8.126565e-02 
	   displacement        1.630437e+02    1.742368e-11    1.547494e-04 

------- converged at time : 0.971128

 ]0;(97%) tempModel.feb - FEBio 2.9.0.0  
AUTO STEPPER: increasing time step, dt = 0.0935199

MUST POINT CONTROLLER: adjusting time step. dt = 0.0288715


===== beginning time step 14 : 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            1.735414e-01    1.752241e-01    0.000000e+00 
	   energy              7.469558e-01    5.944992e-03    7.469558e-03 
	   displacement        1.399400e+01    1.399400e+01    1.399400e-05 
Reforming stiffness matrix: reformation #2

 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            1.735414e-01    1.434167e-09    0.000000e+00 
	   energy              7.469558e-01    1.367311e-07    7.469558e-03 
	   displacement        1.399400e+01    1.533648e-03    1.377933e-05 
Reforming stiffness matrix: reformation #3

 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            1.735414e-01    4.874844e-17    0.000000e+00 
	   energy              7.469558e-01    5.475029e-16    7.469558e-03 
	   displacement        1.399400e+01    9.222113e-08    1.377878e-05 

------- 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 .................... : 14

	Total number of equilibrium iterations ............ : 80

	Average number of equilibrium iterations .......... : 5.71429

	Total number of right hand evaluations ............ : 114

	Total number of stiffness reformations ............ : 80

	Time in linear solver: 0:00:00


 Elapsed time : 0:00:00


 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 12:53:13
------- converged at time : 0.1
------- converged at time : 0.151565
------- converged at time : 0.199378
------- converged at time : 0.257629
------- converged at time : 0.319865
------- converged at time : 0.389654
------- converged at time : 0.462326
------- converged at time : 0.537606
------- converged at time : 0.617831
------- converged at time : 0.70201
------- converged at time : 0.789354
------- converged at time : 0.879229
------- converged at time : 0.971128
------- converged at time : 1
--- Done --- 04-Jun-2019 12:53:13

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(:,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']);
    hp=gpatch(Fb,V_def,CF,'k',1); %Add graphics object to animate
    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}=[hp hp]; %Handles of objects to animate
        animStruct.Props{qt}={'Vertices','CData'}; %Properties of objects to animate
        animStruct.Set{qt}={V_def,CF}; %Property values for to set in order to animate
    end
    anim8(hf,animStruct); %Initiate animation feature
    drawnow;
end

Publishing GIF animation in html folder to render documentation with gif

% Uncomment to re-create gif
% [docsPath,docName,~]=fileparts(mfilename('fullpath'));
% inputStruct.defaultPath=fullfile(defaultFolder,'docs','html');
% inputStruct.imName=[docName,'_anim8'];
% exportGifAnim8(hf,inputStruct,0);

GIBBON www.gibboncode.org

Kevin Mattheus Moerman, [email protected]

GIBBON footer text

License: https://github.com/gibbonCode/GIBBON/blob/master/LICENSE

GIBBON: The Geometry and Image-based Bioengineering add-On. A toolbox for image segmentation, image-based modeling, meshing, and finite element analysis.

Copyright (C) 2019 Kevin Mattheus Moerman

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

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