DEMO_febio_0024_active_contraction_tongue
- Importing geometry for a basic tongue model
- Assigning fiber directions
- Defining the boundary conditions
- Coding the febio structure
- Running the model
- Importing and visualizing results
Contents
Keywords
- febio_spec version 3.0
- febio, FEBio
- pressure loading
- hexahedral elements, hex8
- tongue
- static, solid
- Active contraction
- hyperelastic, Ogden
- displacement logfile
clear; close all; clc;
Plot settings
fontSize=15;
markerSize=25;
markerSize2=20;
plotColor='rw';
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=[febioFebFileNamePart,'.txt']; %FEBio log file name febioLogFileName_disp=[febioFebFileNamePart,'_disp_out.txt']; %Log file name for exporting displacement %Material parameter set c1=1e-3; %Shear-modulus-like parameter m1=2; %Material parameter setting degree of non-linearity ksi=c1*100; %Fiber "modulus" alphaPar=1e-20; beta=3; k_factor=1e2; %Bulk modulus factor k=0.5.*(c1+ksi)*k_factor; %Bulk modulus T0=10e-3; %Active stress % 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 e1_dir_bottom=patchCentre(F_element_bottoms,V); %Middle of bottom faces e1_dir_top=patchCentre(F_element_tops,V); %Middle of top faces e1_dir=vecnormalize(e1_dir_top-e1_dir_bottom); %Normalized fiber vectors [e2_dir,e3_dir]=vectorOrthogonalPair(e1_dir); %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); gpatch(Fb,V,plotColor,'none',0.25); hf(1)=quiverVec(VE,e1_dir,10,'r'); hf(2)=quiverVec(VE,e2_dir,5,'g'); hf(3)=quiverVec(VE,e3_dir,5,'b'); hf(4)=plotV(V(bcSupportList,:),'k.','MarkerSize',markerSize); legend(hf,{'e1-direction (fiber)','e2-direction','e3-direction','Bc fix 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='3.0'; %Module section febio_spec.Module.ATTR.type='solid'; %Control section febio_spec.Control.analysis='STATIC'; febio_spec.Control.time_steps=numTimeSteps; febio_spec.Control.step_size=1/numTimeSteps; febio_spec.Control.solver.max_refs=max_refs; febio_spec.Control.solver.max_ups=max_ups; febio_spec.Control.time_stepper.dtmin=dtmin; febio_spec.Control.time_stepper.dtmax=dtmax; febio_spec.Control.time_stepper.max_retries=max_retries; febio_spec.Control.time_stepper.opt_iter=opt_iter; %Material section materialName1='Material1'; febio_spec.Material.material{1}.ATTR.name=materialName1; febio_spec.Material.material{1}.ATTR.type='solid mixture'; febio_spec.Material.material{1}.ATTR.id=1; %Solid component 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=alphaPar; febio_spec.Material.material{1}.solid{2}.beta=beta; % febio_spec.Material.material{1}.solid{2}.mat_axis.ATTR.type='user'; %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; % Mesh section % -> Nodes febio_spec.Mesh.Nodes{1}.ATTR.name='Object1'; %The node set name febio_spec.Mesh.Nodes{1}.node.ATTR.id=(1:size(V,1))'; %The node id's febio_spec.Mesh.Nodes{1}.node.VAL=V; %The nodel coordinates % -> Elements partName1='Part1'; febio_spec.Mesh.Elements{1}.ATTR.name=partName1; %Name of this part febio_spec.Mesh.Elements{1}.ATTR.type='hex8'; %Element type febio_spec.Mesh.Elements{1}.elem.ATTR.id=(1:1:size(E,1))'; %Element id's febio_spec.Mesh.Elements{1}.elem.VAL=E; %The element matrix % -> NodeSets nodeSetName1='bcSupportList'; febio_spec.Mesh.NodeSet{1}.ATTR.name=nodeSetName1; febio_spec.Mesh.NodeSet{1}.node.ATTR.id=bcSupportList(:); %MeshDomains section febio_spec.MeshDomains.SolidDomain.ATTR.name=partName1; febio_spec.MeshDomains.SolidDomain.ATTR.mat=materialName1; %MeshData section % -> ElementData febio_spec.MeshData.ElementData{1}.ATTR.elem_set=partName1; 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=e1_dir(q,:); febio_spec.MeshData.ElementData{1}.elem{q}.d=e2_dir(q,:); end %Boundary condition section % -> Fix boundary conditions febio_spec.Boundary.bc{1}.ATTR.type='fix'; febio_spec.Boundary.bc{1}.ATTR.node_set=nodeSetName1; febio_spec.Boundary.bc{1}.dofs='x,y,z'; %LoadData section % -> load_controller febio_spec.LoadData.load_controller{1}.ATTR.id=1; febio_spec.LoadData.load_controller{1}.ATTR.type='loadcurve'; febio_spec.LoadData.load_controller{1}.interpolate='LINEAR'; febio_spec.LoadData.load_controller{1}.points.point.VAL=[0 0; 1 1]; %Output section % -> log file febio_spec.Output.logfile.ATTR.file=febioLogFileName; febio_spec.Output.logfile.node_data{1}.ATTR.file=febioLogFileName_disp; febio_spec.Output.logfile.node_data{1}.ATTR.data='ux;uy;uz'; febio_spec.Output.logfile.node_data{1}.ATTR.delim=',';
Quick viewing of the FEBio input file structure
The febView function can be used to view the xml structure in a MATLAB figure window.
febView(febio_spec); %Viewing the febio file
Exporting the FEBio input file
Exporting the febio_spec structure to an FEBio input file is done using the febioStruct2xml function.
febioStruct2xml(febio_spec,febioFebFileName); %Exporting to file and domNode
Running the FEBio analysis
To run the analysis defined by the created FEBio input file the runMonitorFEBio function is used. The input for this function is a structure defining job settings e.g. the FEBio input file name. The optional output runFlag informs the user if the analysis was run succesfully.
febioAnalysis.run_filename=febioFebFileName; %The input file name febioAnalysis.run_logname=febioLogFileName; %The name for the log file febioAnalysis.disp_on=1; %Display information on the command window febioAnalysis.runMode='internal';%'internal'; [runFlag]=runMonitorFEBio(febioAnalysis);%START FEBio NOW!!!!!!!!
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--------> RUNNING/MONITORING FEBIO JOB <-------- 11-Dec-2020 12:25:08
FEBio path: /home/kevin/FEBioStudio/bin/febio3
# Attempt removal of existing log files 11-Dec-2020 12:25:09
* Removal succesful 11-Dec-2020 12:25:09
# Attempt removal of existing .xplt files 11-Dec-2020 12:25:09
* Removal succesful 11-Dec-2020 12:25:09
# Starting FEBio... 11-Dec-2020 12:25:09
Max. total analysis time is: Inf s
===========================================================================
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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
version 3.1.0
FEBio is a registered trademark.
copyright (c) 2006-2020 - All rights reserved
===========================================================================
Default linear solver: pardiso
Reading file /mnt/data/MATLAB/GIBBON/data/temp/tempModel.feb ...SUCCESS!
Setting parameter "T0" to : 0
]0;(0%) tempModel.feb - FEBio 3.1.0
===== beginning time step 1 : 0.1 =====
Setting parameter "T0" to : 0.001
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 = 0.240343
convergence norms : INITIAL CURRENT REQUIRED
residual 3.578681e+00 2.800156e+02 0.000000e+00
energy 1.203457e+02 1.678720e+01 1.203457e+00
displacement 2.237739e+04 1.292623e+03 1.292623e-03
Reforming stiffness matrix: reformation #2
2
Nonlinear solution status: time= 0.1
stiffness updates = 0
right hand side evaluations = 4
stiffness matrix reformations = 2
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 3.578681e+00 1.984893e+03 0.000000e+00
energy 1.203457e+02 2.969599e+01 1.203457e+00
displacement 2.237739e+04 3.799826e+03 8.518954e-03
Reforming stiffness matrix: reformation #3
3
Nonlinear solution status: time= 0.1
stiffness updates = 0
right hand side evaluations = 6
stiffness matrix reformations = 3
step from line search = 0.187517
convergence norms : INITIAL CURRENT REQUIRED
residual 3.578681e+00 1.198886e+03 0.000000e+00
energy 1.203457e+02 2.100108e+00 1.203457e+00
displacement 2.237739e+04 5.741542e+01 8.586540e-03
Reforming stiffness matrix: reformation #4
4
Nonlinear solution status: time= 0.1
stiffness updates = 0
right hand side evaluations = 8
stiffness matrix reformations = 4
step from line search = 0.149900
convergence norms : INITIAL CURRENT REQUIRED
residual 3.578681e+00 7.777928e+02 0.000000e+00
energy 1.203457e+02 1.438657e+00 1.203457e+00
displacement 2.237739e+04 1.985244e+02 8.327759e-03
Reforming stiffness matrix: reformation #5
5
*************************************************************************
* ERROR *
* *
* Negative jacobian was detected. *
* *
*************************************************************************
------- failed to converge at time : 0.1
Retrying time step. Retry attempt 1 of max 5
AUTO STEPPER: retry step, dt = 0.0833333
===== beginning time step 1 : 0.0833333 =====
Setting parameter "T0" to : 0.000833333
Reforming stiffness matrix: reformation #1
1
Nonlinear solution status: time= 0.0833333
stiffness updates = 0
right hand side evaluations = 3
stiffness matrix reformations = 1
step from line search = 0.271269
convergence norms : INITIAL CURRENT REQUIRED
residual 2.485195e+00 2.542339e+02 0.000000e+00
energy 8.634345e+01 1.248693e+01 8.634345e-01
displacement 1.698566e+04 1.249921e+03 1.249921e-03
Reforming stiffness matrix: reformation #2
2
Nonlinear solution status: time= 0.0833333
stiffness updates = 0
right hand side evaluations = 4
stiffness matrix reformations = 2
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 2.485195e+00 9.824706e+02 0.000000e+00
energy 8.634345e+01 1.287378e+01 8.634345e-01
displacement 1.698566e+04 2.664550e+03 6.652439e-03
Reforming stiffness matrix: reformation #3
3
Nonlinear solution status: time= 0.0833333
stiffness updates = 0
right hand side evaluations = 6
stiffness matrix reformations = 3
step from line search = 0.217396
convergence norms : INITIAL CURRENT REQUIRED
residual 2.485195e+00 5.262433e+02 0.000000e+00
energy 8.634345e+01 9.475647e-01 8.634345e-01
displacement 1.698566e+04 2.578390e+02 6.365456e-03
Reforming stiffness matrix: reformation #4
4
Nonlinear solution status: time= 0.0833333
stiffness updates = 0
right hand side evaluations = 10
stiffness matrix reformations = 4
step from line search = 0.087740
convergence norms : INITIAL CURRENT REQUIRED
residual 2.485195e+00 4.870625e+02 0.000000e+00
energy 8.634345e+01 9.451177e-01 8.634345e-01
displacement 1.698566e+04 2.961892e+02 7.046862e-03
Reforming stiffness matrix: reformation #5
5
Nonlinear solution status: time= 0.0833333
stiffness updates = 0
right hand side evaluations = 12
stiffness matrix reformations = 5
step from line search = 0.040583
convergence norms : INITIAL CURRENT REQUIRED
residual 2.485195e+00 4.409212e+02 0.000000e+00
energy 8.634345e+01 2.645326e-02 8.634345e-01
displacement 1.698566e+04 7.892029e+00 6.971579e-03
Reforming stiffness matrix: reformation #6
6
Nonlinear solution status: time= 0.0833333
stiffness updates = 0
right hand side evaluations = 15
stiffness matrix reformations = 6
step from line search = 0.500000
convergence norms : INITIAL CURRENT REQUIRED
residual 2.485195e+00 5.152516e+03 0.000000e+00
energy 8.634345e+01 5.141664e+01 8.634345e-01
displacement 1.698566e+04 2.288505e+03 7.880917e-03
Reforming stiffness matrix: reformation #7
7
Nonlinear solution status: time= 0.0833333
stiffness updates = 0
right hand side evaluations = 18
stiffness matrix reformations = 7
step from line search = 0.500000
convergence norms : INITIAL CURRENT REQUIRED
residual 2.485195e+00 3.025771e+05 0.000000e+00
energy 8.634345e+01 4.289253e+03 8.634345e-01
displacement 1.698566e+04 5.518276e+04 5.645685e-02
*************************************************************************
* WARNING *
* *
* Problem is diverging. Stiffness matrix will now be reformed *
* *
*************************************************************************
Reforming stiffness matrix: reformation #8
8
Nonlinear solution status: time= 0.0833333
stiffness updates = 0
right hand side evaluations = 20
stiffness matrix reformations = 8
step from line search = 0.591962
convergence norms : INITIAL CURRENT REQUIRED
residual 3.025771e+05 4.087916e+04 0.000000e+00
energy 4.289253e+03 1.377149e+02 4.289253e+01
displacement 1.698566e+04 2.032838e+03 4.602504e-02
Reforming stiffness matrix: reformation #9
9
Nonlinear solution status: time= 0.0833333
stiffness updates = 0
right hand side evaluations = 22
stiffness matrix reformations = 9
step from line search = 0.346026
convergence norms : INITIAL CURRENT REQUIRED
residual 3.025771e+05 1.326551e+04 0.000000e+00
energy 4.289253e+03 7.065312e+01 4.289253e+01
displacement 1.698566e+04 1.388577e+03 3.345558e-02
Reforming stiffness matrix: reformation #10
10
Nonlinear solution status: time= 0.0833333
stiffness updates = 0
right hand side evaluations = 24
stiffness matrix reformations = 10
step from line search = 0.321231
convergence norms : INITIAL CURRENT REQUIRED
residual 3.025771e+05 5.914235e+03 0.000000e+00
energy 4.289253e+03 3.998696e+01 4.289253e+01
displacement 1.698566e+04 4.894288e+02 3.039434e-02
Reforming stiffness matrix: reformation #11
11
*************************************************************************
* ERROR *
* *
* Negative jacobian was detected. *
* *
*************************************************************************
------- failed to converge at time : 0.0833333
Retrying time step. Retry attempt 2 of max 5
AUTO STEPPER: retry step, dt = 0.0666667
===== beginning time step 1 : 0.0666667 =====
Setting parameter "T0" to : 0.000666667
Reforming stiffness matrix: reformation #1
1
Nonlinear solution status: time= 0.0666667
stiffness updates = 0
right hand side evaluations = 3
stiffness matrix reformations = 1
step from line search = 0.315230
convergence norms : INITIAL CURRENT REQUIRED
residual 1.590525e+00 2.225932e+02 0.000000e+00
energy 5.721462e+01 8.464741e+00 5.721462e-01
displacement 1.198995e+04 1.191439e+03 1.191439e-03
Reforming stiffness matrix: reformation #2
2
Nonlinear solution status: time= 0.0666667
stiffness updates = 0
right hand side evaluations = 4
stiffness matrix reformations = 2
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.590525e+00 4.085579e+02 0.000000e+00
energy 5.721462e+01 4.213348e+00 5.721462e-01
displacement 1.198995e+04 1.698109e+03 4.916117e-03
Reforming stiffness matrix: reformation #3
3
Nonlinear solution status: time= 0.0666667
stiffness updates = 0
right hand side evaluations = 6
stiffness matrix reformations = 3
step from line search = 0.061191
convergence norms : INITIAL CURRENT REQUIRED
residual 1.590525e+00 3.498493e+02 0.000000e+00
energy 5.721462e+01 5.745090e-01 5.721462e-01
displacement 1.198995e+04 3.765894e+01 5.245742e-03
Reforming stiffness matrix: reformation #4
4
Nonlinear solution status: time= 0.0666667
stiffness updates = 0
right hand side evaluations = 8
stiffness matrix reformations = 4
step from line search = 0.230912
convergence norms : INITIAL CURRENT REQUIRED
residual 1.590525e+00 2.038626e+02 0.000000e+00
energy 5.721462e+01 4.366796e-01 5.721462e-01
displacement 1.198995e+04 2.833219e+01 5.311391e-03
Reforming stiffness matrix: reformation #5
5
Nonlinear solution status: time= 0.0666667
stiffness updates = 0
right hand side evaluations = 11
stiffness matrix reformations = 5
step from line search = 0.500000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.590525e+00 1.089410e+04 0.000000e+00
energy 5.721462e+01 1.760734e+02 5.721462e-01
displacement 1.198995e+04 6.402257e+03 8.656044e-03
*************************************************************************
* WARNING *
* *
* Problem is diverging. Stiffness matrix will now be reformed *
* *
*************************************************************************
Reforming stiffness matrix: reformation #6
6
Nonlinear solution status: time= 0.0666667
stiffness updates = 0
right hand side evaluations = 12
stiffness matrix reformations = 6
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.089410e+04 2.158694e+01 0.000000e+00
energy 1.760734e+02 6.084879e-01 1.760734e+00
displacement 1.198995e+04 9.815854e+01 7.320702e-03
Reforming stiffness matrix: reformation #7
7
Nonlinear solution status: time= 0.0666667
stiffness updates = 0
right hand side evaluations = 14
stiffness matrix reformations = 7
step from line search = 0.148110
convergence norms : INITIAL CURRENT REQUIRED
residual 1.089410e+04 4.000601e+01 0.000000e+00
energy 1.760734e+02 2.512966e+00 1.760734e+00
displacement 1.198995e+04 3.176656e+02 5.886824e-03
Reforming stiffness matrix: reformation #8
8
Nonlinear solution status: time= 0.0666667
stiffness updates = 0
right hand side evaluations = 16
stiffness matrix reformations = 8
step from line search = 0.498400
convergence norms : INITIAL CURRENT REQUIRED
residual 1.089410e+04 1.688840e+02 0.000000e+00
energy 1.760734e+02 1.708471e+00 1.760734e+00
displacement 1.198995e+04 1.294535e+03 6.025381e-03
Reforming stiffness matrix: reformation #9
9
Nonlinear solution status: time= 0.0666667
stiffness updates = 0
right hand side evaluations = 18
stiffness matrix reformations = 9
step from line search = 0.056691
convergence norms : INITIAL CURRENT REQUIRED
residual 1.089410e+04 1.321143e+02 0.000000e+00
energy 1.760734e+02 1.433403e-01 1.760734e+00
displacement 1.198995e+04 1.266747e+01 6.020867e-03
Reforming stiffness matrix: reformation #10
10
Nonlinear solution status: time= 0.0666667
stiffness updates = 0
right hand side evaluations = 21
stiffness matrix reformations = 10
step from line search = 0.500000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.089410e+04 1.461494e+06 0.000000e+00
energy 1.760734e+02 1.043345e+04 1.760734e+00
displacement 1.198995e+04 4.711410e+03 8.193512e-03
*************************************************************************
* WARNING *
* *
* Problem is diverging. Stiffness matrix will now be reformed *
* *
*************************************************************************
Reforming stiffness matrix: reformation #11
11
*************************************************************************
* ERROR *
* *
* Negative jacobian was detected. *
* *
*************************************************************************
------- failed to converge at time : 0.0666667
Retrying time step. Retry attempt 3 of max 5
AUTO STEPPER: retry step, dt = 0.05
===== beginning time step 1 : 0.05 =====
Setting parameter "T0" to : 0.0005
Reforming stiffness matrix: reformation #1
1
Nonlinear solution status: time= 0.05
stiffness updates = 0
right hand side evaluations = 3
stiffness matrix reformations = 1
step from line search = 0.382209
convergence norms : INITIAL CURRENT REQUIRED
residual 8.946703e-01 1.806491e+02 0.000000e+00
energy 3.340761e+01 4.851638e+00 3.340761e-01
displacement 7.526076e+03 1.099438e+03 1.099438e-03
Reforming stiffness matrix: reformation #2
2
Nonlinear solution status: time= 0.05
stiffness updates = 0
right hand side evaluations = 4
stiffness matrix reformations = 2
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 8.946703e-01 1.385185e+02 0.000000e+00
energy 3.340761e+01 1.136196e+00 3.340761e-01
displacement 7.526076e+03 9.420664e+02 3.314635e-03
Reforming stiffness matrix: reformation #3
3
Nonlinear solution status: time= 0.05
stiffness updates = 0
right hand side evaluations = 7
stiffness matrix reformations = 3
step from line search = 0.500000
convergence norms : INITIAL CURRENT REQUIRED
residual 8.946703e-01 7.213165e+03 0.000000e+00
energy 3.340761e+01 7.930635e+01 3.340761e-01
displacement 7.526076e+03 1.600860e+03 3.931580e-03
*************************************************************************
* WARNING *
* *
* Problem is diverging. Stiffness matrix will now be reformed *
* *
*************************************************************************
Reforming stiffness matrix: reformation #4
4
Nonlinear solution status: time= 0.05
stiffness updates = 0
right hand side evaluations = 8
stiffness matrix reformations = 4
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 7.213165e+03 6.185523e+02 0.000000e+00
energy 7.930635e+01 1.823911e+01 7.930635e-01
displacement 7.526076e+03 2.981294e+02 3.083958e-03
Reforming stiffness matrix: reformation #5
5
Nonlinear solution status: time= 0.05
stiffness updates = 0
right hand side evaluations = 10
stiffness matrix reformations = 5
step from line search = 0.272600
convergence norms : INITIAL CURRENT REQUIRED
residual 7.213165e+03 2.319976e+02 0.000000e+00
energy 7.930635e+01 1.179437e+00 7.930635e-01
displacement 7.526076e+03 7.931958e+01 3.820143e-03
Reforming stiffness matrix: reformation #6
6
Nonlinear solution status: time= 0.05
stiffness updates = 0
right hand side evaluations = 14
stiffness matrix reformations = 6
step from line search = 0.085563
convergence norms : INITIAL CURRENT REQUIRED
residual 7.213165e+03 1.528933e+02 0.000000e+00
energy 7.930635e+01 1.306486e-01 7.930635e-01
displacement 7.526076e+03 2.574424e+01 3.908984e-03
Reforming stiffness matrix: reformation #7
7
*************************************************************************
* ERROR *
* *
* Negative jacobian was detected. *
* *
*************************************************************************
------- failed to converge at time : 0.05
Retrying time step. Retry attempt 4 of max 5
AUTO STEPPER: retry step, dt = 0.0333333
===== beginning time step 1 : 0.0333333 =====
Setting parameter "T0" to : 0.000333333
Reforming stiffness matrix: reformation #1
1
Nonlinear solution status: time= 0.0333333
stiffness updates = 0
right hand side evaluations = 3
stiffness matrix reformations = 1
step from line search = 0.494859
convergence norms : INITIAL CURRENT REQUIRED
residual 3.976313e-01 1.208369e+02 0.000000e+00
energy 1.546147e+01 1.921935e+00 1.546147e-01
displacement 3.791704e+03 9.285343e+02 9.285343e-04
Reforming stiffness matrix: reformation #2
2
Nonlinear solution status: time= 0.0333333
stiffness updates = 0
right hand side evaluations = 5
stiffness matrix reformations = 2
step from line search = 0.609715
convergence norms : INITIAL CURRENT REQUIRED
residual 3.976313e-01 2.059810e+01 0.000000e+00
energy 1.546147e+01 1.698197e-01 1.546147e-01
displacement 3.791704e+03 2.320285e+02 1.344860e-03
Reforming stiffness matrix: reformation #3
3
Nonlinear solution status: time= 0.0333333
stiffness updates = 0
right hand side evaluations = 7
stiffness matrix reformations = 3
step from line search = 0.362866
convergence norms : INITIAL CURRENT REQUIRED
residual 3.976313e-01 1.424090e+01 0.000000e+00
energy 1.546147e+01 3.167305e-01 1.546147e-01
displacement 3.791704e+03 2.938659e+02 2.178101e-03
Reforming stiffness matrix: reformation #4
4
Nonlinear solution status: time= 0.0333333
stiffness updates = 0
right hand side evaluations = 8
stiffness matrix reformations = 4
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 3.976313e-01 3.481186e+00 0.000000e+00
energy 1.546147e+01 4.916251e-02 1.546147e-01
displacement 3.791704e+03 1.947554e+02 3.496452e-03
Reforming stiffness matrix: reformation #5
5
Nonlinear solution status: time= 0.0333333
stiffness updates = 0
right hand side evaluations = 9
stiffness matrix reformations = 5
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 3.976313e-01 3.839852e-02 0.000000e+00
energy 1.546147e+01 1.114119e-03 1.546147e-01
displacement 3.791704e+03 6.645107e+00 3.613752e-03
Reforming stiffness matrix: reformation #6
6
Nonlinear solution status: time= 0.0333333
stiffness updates = 0
right hand side evaluations = 10
stiffness matrix reformations = 6
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 3.976313e-01 1.903321e-05 0.000000e+00
energy 1.546147e+01 8.612141e-06 1.546147e-01
displacement 3.791704e+03 2.009383e-01 3.581433e-03
Reforming stiffness matrix: reformation #7
7
Nonlinear solution status: time= 0.0333333
stiffness updates = 0
right hand side evaluations = 11
stiffness matrix reformations = 7
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 3.976313e-01 6.113976e-11 0.000000e+00
energy 1.546147e+01 5.285790e-10 1.546147e-01
displacement 3.791704e+03 9.013083e-05 3.580946e-03
convergence summary
number of iterations : 7
number of reformations : 7
------- converged at time : 0.0333333
Data Record #1
===========================================================================
Step = 1
Time = 0.0333333333
Data = ux;uy;uz
File = /mnt/data/MATLAB/GIBBON/data/temp/tempModel_disp_out.txt
]0;(3%) tempModel.feb - FEBio 3.1.0
AUTO STEPPER: decreasing time step, dt = 0.0309348
===== beginning time step 2 : 0.0642682 =====
Setting parameter "T0" to : 0.000642682
Reforming stiffness matrix: reformation #1
1
Nonlinear solution status: time= 0.0642682
stiffness updates = 0
right hand side evaluations = 2
stiffness matrix reformations = 1
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 3.087846e-01 4.907014e+02 0.000000e+00
energy 9.312529e+00 8.372926e+00 9.312529e-02
displacement 1.730467e+03 1.730467e+03 1.730467e-03
Reforming stiffness matrix: reformation #2
2
Nonlinear solution status: time= 0.0642682
stiffness updates = 0
right hand side evaluations = 3
stiffness matrix reformations = 2
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 3.087846e-01 3.338727e-01 0.000000e+00
energy 9.312529e+00 1.164293e-01 9.312529e-02
displacement 1.730467e+03 9.135860e+00 1.782077e-03
Reforming stiffness matrix: reformation #3
3
Nonlinear solution status: time= 0.0642682
stiffness updates = 0
right hand side evaluations = 4
stiffness matrix reformations = 3
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 3.087846e-01 3.374138e-01 0.000000e+00
energy 9.312529e+00 1.375186e-03 9.312529e-02
displacement 1.730467e+03 7.213673e+00 1.646950e-03
Reforming stiffness matrix: reformation #4
4
Nonlinear solution status: time= 0.0642682
stiffness updates = 0
right hand side evaluations = 5
stiffness matrix reformations = 4
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 3.087846e-01 3.109991e-06 0.000000e+00
energy 9.312529e+00 1.264540e-05 9.312529e-02
displacement 1.730467e+03 1.870843e-02 1.651437e-03
Reforming stiffness matrix: reformation #5
5
Nonlinear solution status: time= 0.0642682
stiffness updates = 0
right hand side evaluations = 6
stiffness matrix reformations = 5
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 3.087846e-01 9.788264e-11 0.000000e+00
energy 9.312529e+00 2.249798e-10 9.312529e-02
displacement 1.730467e+03 1.438450e-04 1.651795e-03
convergence summary
number of iterations : 5
number of reformations : 5
------- converged at time : 0.0642682
Data Record #1
===========================================================================
Step = 2
Time = 0.0642681832
Data = ux;uy;uz
File = /mnt/data/MATLAB/GIBBON/data/temp/tempModel_disp_out.txt
]0;(6%) tempModel.feb - FEBio 3.1.0
AUTO STEPPER: increasing time step, dt = 0.0375268
===== beginning time step 3 : 0.101795 =====
Setting parameter "T0" to : 0.00101795
Reforming stiffness matrix: reformation #1
1
Nonlinear solution status: time= 0.101795
stiffness updates = 0
right hand side evaluations = 2
stiffness matrix reformations = 1
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 4.241691e-01 4.676231e+02 0.000000e+00
energy 1.060425e+01 8.331769e+00 1.060425e-01
displacement 1.546485e+03 1.546485e+03 1.546485e-03
Reforming stiffness matrix: reformation #2
2
Nonlinear solution status: time= 0.101795
stiffness updates = 0
right hand side evaluations = 3
stiffness matrix reformations = 2
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 4.241691e-01 2.053363e-01 0.000000e+00
energy 1.060425e+01 8.722778e-02 1.060425e-01
displacement 1.546485e+03 6.181762e+00 1.564424e-03
Reforming stiffness matrix: reformation #3
3
Nonlinear solution status: time= 0.101795
stiffness updates = 0
right hand side evaluations = 4
stiffness matrix reformations = 3
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 4.241691e-01 2.042191e-01 0.000000e+00
energy 1.060425e+01 8.087356e-04 1.060425e-01
displacement 1.546485e+03 5.185187e+00 1.464999e-03
Reforming stiffness matrix: reformation #4
4
Nonlinear solution status: time= 0.101795
stiffness updates = 0
right hand side evaluations = 5
stiffness matrix reformations = 4
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 4.241691e-01 6.187509e-07 0.000000e+00
energy 1.060425e+01 4.328932e-06 1.060425e-01
displacement 1.546485e+03 7.515519e-03 1.467294e-03
Reforming stiffness matrix: reformation #5
5
Nonlinear solution status: time= 0.101795
stiffness updates = 0
right hand side evaluations = 6
stiffness matrix reformations = 5
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 4.241691e-01 4.670912e-12 0.000000e+00
energy 1.060425e+01 2.188134e-11 1.060425e-01
displacement 1.546485e+03 3.016027e-05 1.467416e-03
convergence summary
number of iterations : 5
number of reformations : 5
------- converged at time : 0.101795
Data Record #1
===========================================================================
Step = 3
Time = 0.101794964
Data = ux;uy;uz
File = /mnt/data/MATLAB/GIBBON/data/temp/tempModel_disp_out.txt
]0;(10%) tempModel.feb - FEBio 3.1.0
AUTO STEPPER: increasing time step, dt = 0.0434895
===== beginning time step 4 : 0.145285 =====
Setting parameter "T0" to : 0.00145285
Reforming stiffness matrix: reformation #1
1
Nonlinear solution status: time= 0.145285
stiffness updates = 0
right hand side evaluations = 2
stiffness matrix reformations = 1
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 5.341723e-01 3.983413e+02 0.000000e+00
energy 1.130527e+01 7.373895e+00 1.130527e-01
displacement 1.313651e+03 1.313651e+03 1.313651e-03
Reforming stiffness matrix: reformation #2
2
Nonlinear solution status: time= 0.145285
stiffness updates = 0
right hand side evaluations = 3
stiffness matrix reformations = 2
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 5.341723e-01 4.213722e-02 0.000000e+00
energy 1.130527e+01 3.209961e-02 1.130527e-01
displacement 1.313651e+03 2.098108e+00 1.287788e-03
Reforming stiffness matrix: reformation #3
3
Nonlinear solution status: time= 0.145285
stiffness updates = 0
right hand side evaluations = 4
stiffness matrix reformations = 3
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 5.341723e-01 5.071787e-02 0.000000e+00
energy 1.130527e+01 1.052171e-04 1.130527e-01
displacement 1.313651e+03 2.195729e+00 1.244634e-03
Reforming stiffness matrix: reformation #4
4
Nonlinear solution status: time= 0.145285
stiffness updates = 0
right hand side evaluations = 5
stiffness matrix reformations = 4
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 5.341723e-01 8.083798e-09 0.000000e+00
energy 1.130527e+01 2.371024e-07 1.130527e-01
displacement 1.313651e+03 9.172736e-04 1.245258e-03
convergence summary
number of iterations : 4
number of reformations : 4
------- converged at time : 0.145285
Data Record #1
===========================================================================
Step = 4
Time = 0.145284509
Data = ux;uy;uz
File = /mnt/data/MATLAB/GIBBON/data/temp/tempModel_disp_out.txt
]0;(15%) tempModel.feb - FEBio 3.1.0
AUTO STEPPER: increasing time step, dt = 0.0547916
===== beginning time step 5 : 0.200076 =====
Setting parameter "T0" to : 0.00200076
Reforming stiffness matrix: reformation #1
1
Nonlinear solution status: time= 0.200076
stiffness updates = 0
right hand side evaluations = 2
stiffness matrix reformations = 1
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 7.994922e-01 5.011811e+02 0.000000e+00
energy 1.456776e+01 9.595246e+00 1.456776e-01
displacement 1.378826e+03 1.378826e+03 1.378826e-03
Reforming stiffness matrix: reformation #2
2
Nonlinear solution status: time= 0.200076
stiffness updates = 0
right hand side evaluations = 3
stiffness matrix reformations = 2
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 7.994922e-01 4.031694e+00 0.000000e+00
energy 1.456776e+01 4.959956e-01 1.456776e-01
displacement 1.378826e+03 3.636847e+01 1.515075e-03
Reforming stiffness matrix: reformation #3
3
Nonlinear solution status: time= 0.200076
stiffness updates = 0
right hand side evaluations = 4
stiffness matrix reformations = 3
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 7.994922e-01 1.939504e+00 0.000000e+00
energy 1.456776e+01 2.152474e-02 1.456776e-01
displacement 1.378826e+03 2.947051e+01 1.303382e-03
Reforming stiffness matrix: reformation #4
4
Nonlinear solution status: time= 0.200076
stiffness updates = 0
right hand side evaluations = 5
stiffness matrix reformations = 4
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 7.994922e-01 1.031171e-03 0.000000e+00
energy 1.456776e+01 5.526879e-04 1.456776e-01
displacement 1.378826e+03 2.010791e-01 1.301577e-03
Reforming stiffness matrix: reformation #5
5
Nonlinear solution status: time= 0.200076
stiffness updates = 0
right hand side evaluations = 6
stiffness matrix reformations = 5
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 7.994922e-01 1.344883e-07 0.000000e+00
energy 1.456776e+01 1.491438e-07 1.456776e-01
displacement 1.378826e+03 2.536786e-03 1.301188e-03
Reforming stiffness matrix: reformation #6
6
Nonlinear solution status: time= 0.200076
stiffness updates = 0
right hand side evaluations = 7
stiffness matrix reformations = 6
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 7.994922e-01 8.077138e-18 0.000000e+00
energy 1.456776e+01 1.147876e-14 1.456776e-01
displacement 1.378826e+03 1.437607e-08 1.301188e-03
convergence summary
number of iterations : 6
number of reformations : 6
------- converged at time : 0.200076
Data Record #1
===========================================================================
Step = 5
Time = 0.200076145
Data = ux;uy;uz
File = /mnt/data/MATLAB/GIBBON/data/temp/tempModel_disp_out.txt
]0;(20%) tempModel.feb - FEBio 3.1.0
===== beginning time step 6 : 0.254868 =====
Setting parameter "T0" to : 0.00254868
Reforming stiffness matrix: reformation #1
1
Nonlinear solution status: time= 0.254868
stiffness updates = 0
right hand side evaluations = 2
stiffness matrix reformations = 1
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 7.535208e-01 2.634706e+02 0.000000e+00
energy 1.198306e+01 5.215163e+00 1.198306e-01
displacement 9.583917e+02 9.583917e+02 9.583917e-04
Reforming stiffness matrix: reformation #2
2
Nonlinear solution status: time= 0.254868
stiffness updates = 0
right hand side evaluations = 3
stiffness matrix reformations = 2
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 7.535208e-01 1.358551e-02 0.000000e+00
energy 1.198306e+01 1.504889e-02 1.198306e-01
displacement 9.583917e+02 1.444215e+00 9.238132e-04
Reforming stiffness matrix: reformation #3
3
Nonlinear solution status: time= 0.254868
stiffness updates = 0
right hand side evaluations = 4
stiffness matrix reformations = 3
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 7.535208e-01 1.739266e-02 0.000000e+00
energy 1.198306e+01 6.313793e-06 1.198306e-01
displacement 9.583917e+02 2.159278e+00 9.120391e-04
Reforming stiffness matrix: reformation #4
4
Nonlinear solution status: time= 0.254868
stiffness updates = 0
right hand side evaluations = 5
stiffness matrix reformations = 4
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 7.535208e-01 2.112923e-10 0.000000e+00
energy 1.198306e+01 2.119501e-08 1.198306e-01
displacement 9.583917e+02 1.525891e-04 9.121245e-04
convergence summary
number of iterations : 4
number of reformations : 4
------- converged at time : 0.254868
Data Record #1
===========================================================================
Step = 6
Time = 0.25486778
Data = ux;uy;uz
File = /mnt/data/MATLAB/GIBBON/data/temp/tempModel_disp_out.txt
]0;(25%) tempModel.feb - FEBio 3.1.0
AUTO STEPPER: increasing time step, dt = 0.0638333
===== beginning time step 7 : 0.318701 =====
Setting parameter "T0" to : 0.00318701
Reforming stiffness matrix: reformation #1
1
Nonlinear solution status: time= 0.318701
stiffness updates = 0
right hand side evaluations = 2
stiffness matrix reformations = 1
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 9.742433e-01 2.786647e+02 0.000000e+00
energy 1.380542e+01 5.634661e+00 1.380542e-01
displacement 9.650319e+02 9.650319e+02 9.650319e-04
Reforming stiffness matrix: reformation #2
2
Nonlinear solution status: time= 0.318701
stiffness updates = 0
right hand side evaluations = 3
stiffness matrix reformations = 2
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 9.742433e-01 1.657039e-02 0.000000e+00
energy 1.380542e+01 1.760321e-02 1.380542e-01
displacement 9.650319e+02 1.386903e+00 9.367273e-04
Reforming stiffness matrix: reformation #3
3
Nonlinear solution status: time= 0.318701
stiffness updates = 0
right hand side evaluations = 4
stiffness matrix reformations = 3
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 9.742433e-01 1.997622e-02 0.000000e+00
energy 1.380542e+01 1.478832e-05 1.380542e-01
displacement 9.650319e+02 2.114406e+00 9.178424e-04
Reforming stiffness matrix: reformation #4
4
Nonlinear solution status: time= 0.318701
stiffness updates = 0
right hand side evaluations = 5
stiffness matrix reformations = 4
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 9.742433e-01 3.108511e-10 0.000000e+00
energy 1.380542e+01 2.660630e-08 1.380542e-01
displacement 9.650319e+02 1.575394e-04 9.178835e-04
convergence summary
number of iterations : 4
number of reformations : 4
------- converged at time : 0.318701
Data Record #1
===========================================================================
Step = 7
Time = 0.318701089
Data = ux;uy;uz
File = /mnt/data/MATLAB/GIBBON/data/temp/tempModel_disp_out.txt
]0;(32%) tempModel.feb - FEBio 3.1.0
AUTO STEPPER: increasing time step, dt = 0.0710666
===== beginning time step 8 : 0.389768 =====
Setting parameter "T0" to : 0.00389768
Reforming stiffness matrix: reformation #1
1
Nonlinear solution status: time= 0.389768
stiffness updates = 0
right hand side evaluations = 2
stiffness matrix reformations = 1
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.151424e+00 2.495293e+02 0.000000e+00
energy 1.460520e+01 5.140450e+00 1.460520e-01
displacement 9.064664e+02 9.064664e+02 9.064664e-04
Reforming stiffness matrix: reformation #2
2
Nonlinear solution status: time= 0.389768
stiffness updates = 0
right hand side evaluations = 3
stiffness matrix reformations = 2
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.151424e+00 5.040743e-02 0.000000e+00
energy 1.460520e+01 3.363228e-02 1.460520e-01
displacement 9.064664e+02 2.460158e+00 8.863950e-04
Reforming stiffness matrix: reformation #3
3
Nonlinear solution status: time= 0.389768
stiffness updates = 0
right hand side evaluations = 4
stiffness matrix reformations = 3
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.151424e+00 5.414777e-02 0.000000e+00
energy 1.460520e+01 1.000348e-04 1.460520e-01
displacement 9.064664e+02 3.571635e+00 8.633050e-04
Reforming stiffness matrix: reformation #4
4
Nonlinear solution status: time= 0.389768
stiffness updates = 0
right hand side evaluations = 5
stiffness matrix reformations = 4
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.151424e+00 7.703645e-09 0.000000e+00
energy 1.460520e+01 2.072181e-07 1.460520e-01
displacement 9.064664e+02 6.510155e-04 8.632825e-04
convergence summary
number of iterations : 4
number of reformations : 4
------- converged at time : 0.389768
Data Record #1
===========================================================================
Step = 8
Time = 0.389767736
Data = ux;uy;uz
File = /mnt/data/MATLAB/GIBBON/data/temp/tempModel_disp_out.txt
]0;(39%) tempModel.feb - FEBio 3.1.0
AUTO STEPPER: increasing time step, dt = 0.0768533
===== beginning time step 9 : 0.466621 =====
Setting parameter "T0" to : 0.00466621
Reforming stiffness matrix: reformation #1
1
Nonlinear solution status: time= 0.466621
stiffness updates = 0
right hand side evaluations = 2
stiffness matrix reformations = 1
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.287315e+00 2.039510e+02 0.000000e+00
energy 1.470949e+01 4.267543e+00 1.470949e-01
displacement 8.214031e+02 8.214031e+02 8.214031e-04
Reforming stiffness matrix: reformation #2
2
Nonlinear solution status: time= 0.466621
stiffness updates = 0
right hand side evaluations = 4
stiffness matrix reformations = 2
step from line search = 0.403050
convergence norms : INITIAL CURRENT REQUIRED
residual 1.287315e+00 4.802204e+01 0.000000e+00
energy 1.470949e+01 1.501516e-01 1.470949e-01
displacement 8.214031e+02 3.500621e+01 8.820160e-04
Reforming stiffness matrix: reformation #3
3
Nonlinear solution status: time= 0.466621
stiffness updates = 0
right hand side evaluations = 6
stiffness matrix reformations = 3
step from line search = 0.549410
convergence norms : INITIAL CURRENT REQUIRED
residual 1.287315e+00 8.261856e+00 0.000000e+00
energy 1.470949e+01 6.220346e-02 1.470949e-01
displacement 8.214031e+02 5.987455e+01 8.014952e-04
Reforming stiffness matrix: reformation #4
4
Nonlinear solution status: time= 0.466621
stiffness updates = 0
right hand side evaluations = 7
stiffness matrix reformations = 4
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.287315e+00 9.750183e-01 0.000000e+00
energy 1.470949e+01 1.546474e-02 1.470949e-01
displacement 8.214031e+02 9.292801e+00 7.817408e-04
Reforming stiffness matrix: reformation #5
5
Nonlinear solution status: time= 0.466621
stiffness updates = 0
right hand side evaluations = 8
stiffness matrix reformations = 5
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.287315e+00 6.346602e-05 0.000000e+00
energy 1.470949e+01 3.919465e-05 1.470949e-01
displacement 8.214031e+02 1.706700e-01 7.836613e-04
Reforming stiffness matrix: reformation #6
6
Nonlinear solution status: time= 0.466621
stiffness updates = 0
right hand side evaluations = 9
stiffness matrix reformations = 6
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.287315e+00 8.149406e-10 0.000000e+00
energy 1.470949e+01 1.226672e-09 1.470949e-01
displacement 8.214031e+02 5.829135e-04 7.834990e-04
convergence summary
number of iterations : 6
number of reformations : 6
------- converged at time : 0.466621
Data Record #1
===========================================================================
Step = 9
Time = 0.466621053
Data = ux;uy;uz
File = /mnt/data/MATLAB/GIBBON/data/temp/tempModel_disp_out.txt
]0;(47%) tempModel.feb - FEBio 3.1.0
===== beginning time step 10 : 0.543474 =====
Setting parameter "T0" to : 0.00543474
Reforming stiffness matrix: reformation #1
1
Nonlinear solution status: time= 0.543474
stiffness updates = 0
right hand side evaluations = 2
stiffness matrix reformations = 1
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.234558e+00 1.264359e+02 0.000000e+00
energy 1.281352e+01 2.689527e+00 1.281352e-01
displacement 6.510432e+02 6.510432e+02 6.510432e-04
Reforming stiffness matrix: reformation #2
2
Nonlinear solution status: time= 0.543474
stiffness updates = 0
right hand side evaluations = 3
stiffness matrix reformations = 2
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.234558e+00 5.606549e-02 0.000000e+00
energy 1.281352e+01 2.517554e-02 1.281352e-01
displacement 6.510432e+02 1.256228e+00 6.347232e-04
Reforming stiffness matrix: reformation #3
3
Nonlinear solution status: time= 0.543474
stiffness updates = 0
right hand side evaluations = 4
stiffness matrix reformations = 3
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.234558e+00 8.664261e-02 0.000000e+00
energy 1.281352e+01 1.164538e-04 1.281352e-01
displacement 6.510432e+02 1.787404e+00 6.234612e-04
Reforming stiffness matrix: reformation #4
4
Nonlinear solution status: time= 0.543474
stiffness updates = 0
right hand side evaluations = 5
stiffness matrix reformations = 4
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.234558e+00 9.047457e-08 0.000000e+00
energy 1.281352e+01 9.926102e-07 1.281352e-01
displacement 6.510432e+02 1.237160e-03 6.234009e-04
Reforming stiffness matrix: reformation #5
5
Nonlinear solution status: time= 0.543474
stiffness updates = 0
right hand side evaluations = 6
stiffness matrix reformations = 5
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.234558e+00 2.484234e-13 0.000000e+00
energy 1.281352e+01 1.607765e-12 1.281352e-01
displacement 6.510432e+02 2.193900e-06 6.233965e-04
convergence summary
number of iterations : 5
number of reformations : 5
------- converged at time : 0.543474
Data Record #1
===========================================================================
Step = 10
Time = 0.543474371
Data = ux;uy;uz
File = /mnt/data/MATLAB/GIBBON/data/temp/tempModel_disp_out.txt
]0;(54%) tempModel.feb - FEBio 3.1.0
AUTO STEPPER: increasing time step, dt = 0.0790626
===== beginning time step 11 : 0.622537 =====
Setting parameter "T0" to : 0.00622537
Reforming stiffness matrix: reformation #1
1
Nonlinear solution status: time= 0.622537
stiffness updates = 0
right hand side evaluations = 2
stiffness matrix reformations = 1
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.259646e+00 9.196167e+01 0.000000e+00
energy 1.199349e+01 1.975844e+00 1.199349e-01
displacement 5.595449e+02 5.595449e+02 5.595449e-04
Reforming stiffness matrix: reformation #2
2
Nonlinear solution status: time= 0.622537
stiffness updates = 0
right hand side evaluations = 4
stiffness matrix reformations = 2
step from line search = 0.357368
convergence norms : INITIAL CURRENT REQUIRED
residual 1.259646e+00 2.500857e+01 0.000000e+00
energy 1.199349e+01 6.692348e-02 1.199349e-01
displacement 5.595449e+02 2.033266e+01 6.025975e-04
Reforming stiffness matrix: reformation #3
3
Nonlinear solution status: time= 0.622537
stiffness updates = 0
right hand side evaluations = 6
stiffness matrix reformations = 3
step from line search = 0.562745
convergence norms : INITIAL CURRENT REQUIRED
residual 1.259646e+00 4.340671e+00 0.000000e+00
energy 1.199349e+01 3.406927e-02 1.199349e-01
displacement 5.595449e+02 2.639044e+01 5.405470e-04
Reforming stiffness matrix: reformation #4
4
Nonlinear solution status: time= 0.622537
stiffness updates = 0
right hand side evaluations = 7
stiffness matrix reformations = 4
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.259646e+00 1.061715e-04 0.000000e+00
energy 1.199349e+01 4.570108e-05 1.199349e-01
displacement 5.595449e+02 1.455689e-01 5.372605e-04
Reforming stiffness matrix: reformation #5
5
Nonlinear solution status: time= 0.622537
stiffness updates = 0
right hand side evaluations = 8
stiffness matrix reformations = 5
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.259646e+00 4.378727e-08 0.000000e+00
energy 1.199349e+01 1.733351e-08 1.199349e-01
displacement 5.595449e+02 2.546243e-03 5.366428e-04
Reforming stiffness matrix: reformation #6
6
Nonlinear solution status: time= 0.622537
stiffness updates = 0
right hand side evaluations = 9
stiffness matrix reformations = 6
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.259646e+00 2.456298e-20 0.000000e+00
energy 1.199349e+01 3.146448e-16 1.199349e-01
displacement 5.595449e+02 7.828178e-10 5.366426e-04
convergence summary
number of iterations : 6
number of reformations : 6
------- converged at time : 0.622537
Data Record #1
===========================================================================
Step = 11
Time = 0.622536926
Data = ux;uy;uz
File = /mnt/data/MATLAB/GIBBON/data/temp/tempModel_disp_out.txt
]0;(62%) tempModel.feb - FEBio 3.1.0
===== beginning time step 12 : 0.701599 =====
Setting parameter "T0" to : 0.00701599
Reforming stiffness matrix: reformation #1
1
Nonlinear solution status: time= 0.701599
stiffness updates = 0
right hand side evaluations = 2
stiffness matrix reformations = 1
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.218308e+00 6.181132e+01 0.000000e+00
energy 1.071523e+01 1.338433e+00 1.071523e-01
displacement 4.615399e+02 4.615399e+02 4.615399e-04
Reforming stiffness matrix: reformation #2
2
Nonlinear solution status: time= 0.701599
stiffness updates = 0
right hand side evaluations = 3
stiffness matrix reformations = 2
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.218308e+00 2.683834e-02 0.000000e+00
energy 1.071523e+01 2.099772e-02 1.071523e-01
displacement 4.615399e+02 2.833910e+00 4.400394e-04
Reforming stiffness matrix: reformation #3
3
Nonlinear solution status: time= 0.701599
stiffness updates = 0
right hand side evaluations = 4
stiffness matrix reformations = 3
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.218308e+00 1.036914e-02 0.000000e+00
energy 1.071523e+01 1.598242e-04 1.071523e-01
displacement 4.615399e+02 1.362190e+00 4.435002e-04
Reforming stiffness matrix: reformation #4
4
Nonlinear solution status: time= 0.701599
stiffness updates = 0
right hand side evaluations = 5
stiffness matrix reformations = 4
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.218308e+00 1.681670e-09 0.000000e+00
energy 1.071523e+01 6.133057e-08 1.071523e-01
displacement 4.615399e+02 3.658549e-04 4.435969e-04
convergence summary
number of iterations : 4
number of reformations : 4
------- converged at time : 0.701599
Data Record #1
===========================================================================
Step = 12
Time = 0.701599481
Data = ux;uy;uz
File = /mnt/data/MATLAB/GIBBON/data/temp/tempModel_disp_out.txt
]0;(70%) tempModel.feb - FEBio 3.1.0
AUTO STEPPER: increasing time step, dt = 0.08325
===== beginning time step 13 : 0.78485 =====
Setting parameter "T0" to : 0.0078485
Reforming stiffness matrix: reformation #1
1
Nonlinear solution status: time= 0.78485
stiffness updates = 0
right hand side evaluations = 2
stiffness matrix reformations = 1
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.310922e+00 5.267350e+01 0.000000e+00
energy 1.071322e+01 1.136595e+00 1.071322e-01
displacement 4.276643e+02 4.276643e+02 4.276643e-04
Reforming stiffness matrix: reformation #2
2
Nonlinear solution status: time= 0.78485
stiffness updates = 0
right hand side evaluations = 3
stiffness matrix reformations = 2
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.310922e+00 5.861411e-03 0.000000e+00
energy 1.071322e+01 9.368138e-03 1.071322e-01
displacement 4.276643e+02 1.591431e+00 4.087292e-04
Reforming stiffness matrix: reformation #3
3
Nonlinear solution status: time= 0.78485
stiffness updates = 0
right hand side evaluations = 4
stiffness matrix reformations = 3
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.310922e+00 1.381984e-03 0.000000e+00
energy 1.071322e+01 3.249088e-05 1.071322e-01
displacement 4.276643e+02 5.207502e-01 4.110082e-04
Reforming stiffness matrix: reformation #4
4
Nonlinear solution status: time= 0.78485
stiffness updates = 0
right hand side evaluations = 5
stiffness matrix reformations = 4
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.310922e+00 7.793758e-12 0.000000e+00
energy 1.071322e+01 1.622342e-09 1.071322e-01
displacement 4.276643e+02 2.908302e-05 4.110390e-04
convergence summary
number of iterations : 4
number of reformations : 4
------- converged at time : 0.78485
Data Record #1
===========================================================================
Step = 13
Time = 0.784849526
Data = ux;uy;uz
File = /mnt/data/MATLAB/GIBBON/data/temp/tempModel_disp_out.txt
]0;(78%) tempModel.feb - FEBio 3.1.0
AUTO STEPPER: increasing time step, dt = 0.0866
===== beginning time step 14 : 0.87145 =====
Setting parameter "T0" to : 0.0087145
Reforming stiffness matrix: reformation #1
1
Nonlinear solution status: time= 0.87145
stiffness updates = 0
right hand side evaluations = 2
stiffness matrix reformations = 1
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.378623e+00 4.355033e+01 0.000000e+00
energy 1.049815e+01 9.299033e-01 1.049815e-01
displacement 3.889142e+02 3.889142e+02 3.889142e-04
Reforming stiffness matrix: reformation #2
2
Nonlinear solution status: time= 0.87145
stiffness updates = 0
right hand side evaluations = 3
stiffness matrix reformations = 2
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.378623e+00 2.055957e-03 0.000000e+00
energy 1.049815e+01 5.092664e-03 1.049815e-01
displacement 3.889142e+02 1.092624e+00 3.724358e-04
Reforming stiffness matrix: reformation #3
3
Nonlinear solution status: time= 0.87145
stiffness updates = 0
right hand side evaluations = 4
stiffness matrix reformations = 3
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.378623e+00 2.735604e-04 0.000000e+00
energy 1.049815e+01 9.762606e-06 1.049815e-01
displacement 3.889142e+02 2.368619e-01 3.738882e-04
Reforming stiffness matrix: reformation #4
4
Nonlinear solution status: time= 0.87145
stiffness updates = 0
right hand side evaluations = 5
stiffness matrix reformations = 4
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.378623e+00 1.411044e-13 0.000000e+00
energy 1.049815e+01 1.025009e-10 1.049815e-01
displacement 3.889142e+02 4.451933e-06 3.739006e-04
convergence summary
number of iterations : 4
number of reformations : 4
------- converged at time : 0.87145
Data Record #1
===========================================================================
Step = 14
Time = 0.871449561
Data = ux;uy;uz
File = /mnt/data/MATLAB/GIBBON/data/temp/tempModel_disp_out.txt
]0;(87%) tempModel.feb - FEBio 3.1.0
AUTO STEPPER: increasing time step, dt = 0.08928
===== beginning time step 15 : 0.96073 =====
Setting parameter "T0" to : 0.0096073
Reforming stiffness matrix: reformation #1
1
Nonlinear solution status: time= 0.96073
stiffness updates = 0
right hand side evaluations = 2
stiffness matrix reformations = 1
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.426194e+00 3.554254e+01 0.000000e+00
energy 1.015377e+01 7.446196e-01 1.015377e-01
displacement 3.495697e+02 3.495697e+02 3.495697e-04
Reforming stiffness matrix: reformation #2
2
Nonlinear solution status: time= 0.96073
stiffness updates = 0
right hand side evaluations = 3
stiffness matrix reformations = 2
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.426194e+00 9.591015e-04 0.000000e+00
energy 1.015377e+01 3.089234e-03 1.015377e-01
displacement 3.495697e+02 8.364151e-01 3.353637e-04
Reforming stiffness matrix: reformation #3
3
Nonlinear solution status: time= 0.96073
stiffness updates = 0
right hand side evaluations = 4
stiffness matrix reformations = 3
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.426194e+00 6.985931e-05 0.000000e+00
energy 1.015377e+01 3.680879e-06 1.015377e-01
displacement 3.495697e+02 1.200700e-01 3.362808e-04
Reforming stiffness matrix: reformation #4
4
Nonlinear solution status: time= 0.96073
stiffness updates = 0
right hand side evaluations = 5
stiffness matrix reformations = 4
step from line search = 1.000000
convergence norms : INITIAL CURRENT REQUIRED
residual 1.426194e+00 6.239214e-15 0.000000e+00
energy 1.015377e+01 1.129380e-11 1.015377e-01
displacement 3.495697e+02 1.022554e-06 3.362865e-04
convergence summary
number of iterations : 4
number of reformations : 4
------- converged at time : 0.96073
Data Record #1
===========================================================================
Step = 15
Time = 0.960729589
Data = ux;uy;uz
File = /mnt/data/MATLAB/GIBBON/data/temp/tempModel_disp_out.txt
]0;(96%) tempModel.feb - FEBio 3.1.0
AUTO STEPPER: increasing time step, dt = 0.091424
MUST POINT CONTROLLER: adjusting time step. dt = 0.0392704
===== beginning time step 16 : 1 =====
Setting parameter "T0" to : 0.01
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 2.689780e-01 1.058637e+00 0.000000e+00
energy 1.818592e+00 2.614896e-02 1.818592e-02
displacement 5.893627e+01 5.893627e+01 5.893627e-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 2.689780e-01 1.200151e-07 0.000000e+00
energy 1.818592e+00 4.440263e-06 1.818592e-02
displacement 5.893627e+01 1.555017e-02 5.796438e-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 2.689780e-01 5.543599e-12 0.000000e+00
energy 1.818592e+00 1.179519e-11 1.818592e-02
displacement 5.893627e+01 3.417042e-05 5.796538e-05
convergence summary
number of iterations : 3
number of reformations : 3
------- converged at time : 1
Data Record #1
===========================================================================
Step = 16
Time = 1
Data = ux;uy;uz
File = /mnt/data/MATLAB/GIBBON/data/temp/tempModel_disp_out.txt
]0;(100%) tempModel.feb - FEBio 3.1.0
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 .................... : 16
Total number of equilibrium iterations ............ : 75
Average number of equilibrium iterations .......... : 4.6875
Total number of right hand evaluations ............ : 98
Total number of stiffness reformations ............ : 75
L I N E A R S O L V E R S T A T S
Total calls to linear solver ........ : 109
Avg iterations per solve ............ : 1
Time in linear solver: 0:00:00
]0;(100%) tempModel.feb - FEBio 3.1.0
Elapsed time : 0:00:01
N O R M A L T E R M I N A T I O N
* Log file found. 11-Dec-2020 12:25:10
# Parsing log file... 11-Dec-2020 12:25:10
number of iterations : 7 11-Dec-2020 12:25:11
number of reformations : 7 11-Dec-2020 12:25:11
------- converged at time : 0.0333333 11-Dec-2020 12:25:11
number of iterations : 5 11-Dec-2020 12:25:11
number of reformations : 5 11-Dec-2020 12:25:11
------- converged at time : 0.0642682 11-Dec-2020 12:25:11
number of iterations : 5 11-Dec-2020 12:25:11
number of reformations : 5 11-Dec-2020 12:25:11
------- converged at time : 0.101795 11-Dec-2020 12:25:11
number of iterations : 4 11-Dec-2020 12:25:11
number of reformations : 4 11-Dec-2020 12:25:11
------- converged at time : 0.145285 11-Dec-2020 12:25:11
number of iterations : 6 11-Dec-2020 12:25:11
number of reformations : 6 11-Dec-2020 12:25:11
------- converged at time : 0.200076 11-Dec-2020 12:25:11
number of iterations : 4 11-Dec-2020 12:25:11
number of reformations : 4 11-Dec-2020 12:25:11
------- converged at time : 0.254868 11-Dec-2020 12:25:11
number of iterations : 4 11-Dec-2020 12:25:11
number of reformations : 4 11-Dec-2020 12:25:11
------- converged at time : 0.318701 11-Dec-2020 12:25:11
number of iterations : 4 11-Dec-2020 12:25:11
number of reformations : 4 11-Dec-2020 12:25:11
------- converged at time : 0.389768 11-Dec-2020 12:25:11
number of iterations : 6 11-Dec-2020 12:25:11
number of reformations : 6 11-Dec-2020 12:25:11
------- converged at time : 0.466621 11-Dec-2020 12:25:11
number of iterations : 5 11-Dec-2020 12:25:11
number of reformations : 5 11-Dec-2020 12:25:11
------- converged at time : 0.543474 11-Dec-2020 12:25:11
number of iterations : 6 11-Dec-2020 12:25:11
number of reformations : 6 11-Dec-2020 12:25:11
------- converged at time : 0.622537 11-Dec-2020 12:25:11
number of iterations : 4 11-Dec-2020 12:25:11
number of reformations : 4 11-Dec-2020 12:25:11
------- converged at time : 0.701599 11-Dec-2020 12:25:11
number of iterations : 4 11-Dec-2020 12:25:11
number of reformations : 4 11-Dec-2020 12:25:11
------- converged at time : 0.78485 11-Dec-2020 12:25:11
number of iterations : 4 11-Dec-2020 12:25:11
number of reformations : 4 11-Dec-2020 12:25:11
------- converged at time : 0.87145 11-Dec-2020 12:25:11
number of iterations : 4 11-Dec-2020 12:25:11
number of reformations : 4 11-Dec-2020 12:25:11
------- converged at time : 0.96073 11-Dec-2020 12:25:11
number of iterations : 3 11-Dec-2020 12:25:11
number of reformations : 3 11-Dec-2020 12:25:11
------- converged at time : 1 11-Dec-2020 12:25:11
Elapsed time : 0:00:01 11-Dec-2020 12:25:11
N O R M A L T E R M I N A T I O N
# Done 11-Dec-2020 12:25:11
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Import FEBio results
if runFlag==1 %i.e. a succesful run
Importing nodal displacements from a log file
dataStruct=importFEBio_logfile(fullfile(savePath,febioLogFileName_disp),1,1);
%Access data
N_disp_mat=dataStruct.data; %Displacement
timeVec=dataStruct.time; %Time
%Create deformed coordinate set
V_DEF=N_disp_mat+repmat(V,[1 1 size(N_disp_mat,3)]);
Plotting the simulated results using anim8 to visualize and animate deformations
DN_magnitude=sqrt(sum(N_disp_mat(:,:,end).^2,2)); %Current displacement magnitude % Create basic view and store graphics handle to initiate animation hf=cFigure; %Open figure gtitle([febioFebFileNamePart,': Press play to animate']); title('Displacement magnitude [mm]','Interpreter','Latex') hp=gpatch(Fb,V_DEF(:,:,end),DN_magnitude,'k',1); %Add graphics object to animate hp.Marker='.'; hp.MarkerSize=markerSize2; hp.FaceColor='interp'; axisGeom(gca,fontSize); colormap(gjet(250)); colorbar; caxis([0 max(DN_magnitude)]); axis(axisLim(V_DEF)); %Set axis limits statically camlight headlight; % Set up animation features animStruct.Time=timeVec; %The time vector for qt=1:1:size(N_disp_mat,3) %Loop over time increments DN_magnitude=sqrt(sum(N_disp_mat(:,:,qt).^2,2)); %Current displacement magnitude %Set entries in animation structure animStruct.Handles{qt}=[hp hp]; %Handles of objects to animate animStruct.Props{qt}={'Vertices','CData'}; %Properties of objects to animate animStruct.Set{qt}={V_DEF(:,:,qt),DN_magnitude}; %Property values for to set in order to animate end anim8(hf,animStruct); %Initiate animation feature drawnow;
end
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) 2006-2020 Kevin Mattheus Moerman
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.