DEMO_febio_0045_tentacle_active_contraction_01.m

Creating geometry for a basic tentacle model
Assigning fiber directions
Defining the boundary conditions
Coding the febio structure
Running the model
Importing and visualizing results

Keywords
Control parameters
Creating a loft feature
Tetrahedral meshing using tetgen (see also runTetGen)
Visualizing mesh using meshView, see also anim8
Split into two materials
Joining node sets
Define contact surfaces
Defining the FEBio input structure
Quick viewing of the FEBio input file structure
Exporting the FEBio input file
Running the FEBio analysis
Import FEBio results

Keywords

febio_spec version 4.0
febio, FEBio
pressure loading
tetrahedral elements,
tetgen
static, solid
hyperelastic, Ogden
displacement logfile
stress logfile

clear; close all; clc;

Plot settings

figColor='w';
figColorDef='white';
fontSize=25;
markerSize1=25;
lineWidth1=3;
faceAlpha=0.5;
faceAlpha2=0.25;
vectorPlotSize=0.5;
markerSize=25;

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
k_factor=10; %Bulk modulus factor
c1=1e-3; %Shear-modulus-like parameter
m1=2; %Material parameter setting degree of non-linearity of ground matrix
ksi=c1*1000;
k=c1*k_factor; %Bulk modulus
T0=5e-3; %Active stress

k_factor=100; %Bulk modulus factor
c1p=c1*10; %Shear-modulus-like parameter
m1p=m1; %Material parameter setting degree of non-linearity
kp=c1p*k_factor; %Bulk modulus

% FEA control settings
numTimeSteps=25; %Number of time steps desired
max_refs=40; %Max reforms
max_ups=0; %Set to zero to use full-Newton iterations
opt_iter=10; %Optimum number of iterations
max_retries=5; %Maximum number of retires
dtmin=(1/numTimeSteps)/100; %Minimum time step size
dtmax=1/numTimeSteps; %Maximum time step size
symmetric_stiffness=0;

runMode='external';% 'internal' or 'external'

tentacleHeight=70;

% Bar
barRadius=9;
barLocation=30;

%Contact parameters
contactPenalty=1;
laugon=0;
minaug=1;
maxaug=10;
fric_coeff=0.5;

Creating a loft feature

% Sketching profile 1
ns=15;
t=linspace(0,2*pi,ns);
t=t(1:end-1);
r1=5;
x=r1*cos(t);
y=r1*sin(t);
z=zeros(size(x));
V_bottom=[x(:) y(:) z(:)];
V_bottom(x>(r1/2))=(r1/2);
% V_bottom=evenlySampleCurve(V_bottom,ns,'pchip',1);
V_bottom(:,1)=V_bottom(:,1)-max(V_bottom(:,1));

% Sketching profile 2
t=linspace(0,2*pi,ns);
t=t(1:end-1);
r2=2;
x=r2*cos(t);
y=r2*sin(t);
z=zeros(size(x));
V_top=[x(:) y(:) z(:)];
V_top(x>(r2/2))=(r2/2);
V_top(:,3)=V_top(:,3)+tentacleHeight;
% V_top=evenlySampleCurve(V_top,ns,'pchip',1);
V_top(:,1)=V_top(:,1)-max(V_top(:,1));

% Create loft
% cPar.numSteps=17;
cPar.closeLoopOpt=1;
cPar.patchType='tri';
[F,V]=polyLoftLinear(V_bottom,V_top,cPar);

[Ft,Vt]=regionTriMesh2D({V_top(:,[1 2])},[],0,0);
Vt(:,3)=mean(V_top(:,3));

[Fb,Vb]=regionTriMesh2D({V_bottom(:,[1 2])},[],0,0);
Fb=fliplr(Fb);
Vb(:,3)=mean(V_bottom(:,3));

[F,V,C]=joinElementSets({F,Ft,Fb},{V,Vt,Vb});
[F,V]=mergeVertices(F,V);

indRigid=F(C==3,:);

cPar.Method='HC';
cPar.n=10;
cPar.RigidConstraints=unique(indRigid);
[V]=patchSmooth(F,V,[],cPar);

Plotting results

cFigure; hold on;
title('The lofted feature','FontSize',fontSize);

gpatch(F,V,C,'k',1);
% patchNormPlot(F,V);

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

Tetrahedral meshing using tetgen (see also `runTetGen`)

% Create tetgen input structure
inputStruct.stringOpt='-pq1.2AaY';
inputStruct.Faces=F;
inputStruct.Nodes=V;
inputStruct.holePoints=[];
inputStruct.faceBoundaryMarker=C; %Face boundary markers
inputStruct.regionPoints=getInnerPoint(F,V); %region points
inputStruct.regionA=2*tetVolMeanEst(F,V);
inputStruct.minRegionMarker=2; %Minimum region marker

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

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

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- TETGEN Tetrahedral meshing --- 20-Apr-2023 18:09:38
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Writing SMESH file --- 20-Apr-2023 18:09:38
----> Adding node field
----> Adding facet field
----> Adding holes specification
----> Adding region specification
--- Done --- 20-Apr-2023 18:09:38
--- Running TetGen to mesh input boundary--- 20-Apr-2023 18:09:38
Opening /mnt/data/MATLAB/GIBBON/data/temp/temp.smesh.
Delaunizing vertices...
Delaunay seconds:  0.00409
Creating surface mesh ...
Surface mesh seconds:  0.00117
Recovering boundaries...
Boundary recovery seconds:  0.001809
Removing exterior tetrahedra ...
Spreading region attributes.
Exterior tets removal seconds:  0.000901
Recovering Delaunayness...
Delaunay recovery seconds:  0.00076
Refining mesh...
Refinement seconds:  0.010967
Smoothing vertices...
Mesh smoothing seconds:  0.016331
Improving mesh...
Mesh improvement seconds:  0.000924

Writing /mnt/data/MATLAB/GIBBON/data/temp/temp.1.node.
Writing /mnt/data/MATLAB/GIBBON/data/temp/temp.1.ele.
Writing /mnt/data/MATLAB/GIBBON/data/temp/temp.1.face.
Writing /mnt/data/MATLAB/GIBBON/data/temp/temp.1.edge.

Output seconds:  0.01118
Total running seconds:  0.048247

Statistics:

  Input points: 710
  Input facets: 1416
  Input segments: 2124
  Input holes: 0
  Input regions: 1

  Mesh points: 1146
  Mesh tetrahedra: 4558
  Mesh faces: 9824
  Mesh faces on exterior boundary: 1416
  Mesh faces on input facets: 1416
  Mesh edges on input segments: 2124
  Steiner points inside domain: 436

--- Done --- 20-Apr-2023 18:09:38
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Importing TetGen files --- 20-Apr-2023 18:09:38
--- Done --- 20-Apr-2023 18:09:38

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

meshView(meshOutput);

Split into two materials

[VE]=patchCentre(E,V); %Compute element centre coordinates

logicActive=VE(:,1)>=-r2;

E1=E( logicActive,:);
E2=E(~logicActive,:);
E=[E1; E2];

[VE1]=patchCentre(E1,V);

%Define fibers as going from one face center to the other
v_fib=[0 0 1];
e1_dir=v_fib(ones(size(E1,1),1),:);
[e2_dir,e3_dir]=vectorOrthogonalPair(e1_dir); %Get orthogonal vector pair

%Get boundary directions faces to set-up support
F_bottom=Fb(Cb==3,:); %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,'kw','none',0.25);
hl(2)=quiverVec(VE1,e1_dir,vectorPlotSize,'k');

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;

clear hl;

w=4*r1; %Width measure

pointSpacing=mean(patchEdgeLengths(Fb,V));

optionStruct.cylRadius=barRadius;
optionStruct.numRadial=round((2*pi*barRadius)/(pointSpacing/2));
optionStruct.cylHeight=w/2;
% optionStruct.numHeight=optionStruct.numRadial;
optionStruct.meshType='tri';
optionStruct.closeOpt=0;
[Fc,Vc]=patchcylinder(optionStruct);
Fc=fliplr(Fc);

Vc=Vc(:,[1 3 2]);

% %Shift bar
Vc(:,1)=Vc(:,1)+barRadius+0.1*pointSpacing;
Vc(:,3)=Vc(:,3)+barLocation;

center_of_mass=mean(Vc,1);

cFigure; hold on;
gtitle('Boundary conditions and fiber directions',fontSize);
gpatch(Fb,V,'kw','none',0.25);

gpatch(Fc,Vc,'rw','k',1);
patchNormPlot(Fc,Vc);
axisGeom(gca,fontSize);
camlight headlight;
drawnow;

Joining node sets

Fc=Fc+size(V,1); %Fixed element indices
V=[V;Vc;]; %Combined node sets

Define contact surfaces

% The rigid primary surface of the sphere
F_contact_primary=Fc;

% The deformable secondary surface of the slab
F_contact_secondary=fliplr(Fb);

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

gpatch(Fb,V,'kw','none',faceAlpha2);
hl(1)=gpatch(F_contact_primary,V,'gw','k',1);
patchNormPlot(F_contact_primary,V);
hl(2)=gpatch(F_contact_secondary,V,'bw','k',1);
patchNormPlot(F_contact_secondary,V);

legend(hl,{'primary','secondary'});

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='4.0';

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

%Control section
febio_spec.Control.analysis='STATIC';
febio_spec.Control.time_steps=numTimeSteps;
febio_spec.Control.step_size=1/numTimeSteps;
febio_spec.Control.solver.max_refs=max_refs;
febio_spec.Control.solver.qn_method.max_ups=max_ups;
febio_spec.Control.solver.symmetric_stiffness=symmetric_stiffness;
febio_spec.Control.time_stepper.dtmin=dtmin;
febio_spec.Control.time_stepper.dtmax=dtmax;
febio_spec.Control.time_stepper.max_retries=max_retries;
febio_spec.Control.time_stepper.opt_iter=opt_iter;

%Material section
materialName1='Material1';
febio_spec.Material.material{1}.ATTR.name=materialName1;
febio_spec.Material.material{1}.ATTR.type='solid mixture';
febio_spec.Material.material{1}.ATTR.id=1;

%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 active fiber component
febio_spec.Material.material{1}.solid{2}.ATTR.type='prescribed uniaxial active contraction';
febio_spec.Material.material{1}.solid{2}.T0.VAL=T0;
febio_spec.Material.material{1}.solid{2}.T0.ATTR.lc=1;

%The passive material
materialName2='Material2';
febio_spec.Material.material{2}.ATTR.name=materialName2;
febio_spec.Material.material{2}.ATTR.type='Ogden';
febio_spec.Material.material{2}.ATTR.id=2;
febio_spec.Material.material{2}.c1=c1p;
febio_spec.Material.material{2}.m1=m1p;
febio_spec.Material.material{2}.c2=c1p;
febio_spec.Material.material{2}.m2=-m1p;
febio_spec.Material.material{2}.k=kp;

materialName3='Material3';
febio_spec.Material.material{3}.ATTR.name=materialName3;
febio_spec.Material.material{3}.ATTR.type='rigid body';
febio_spec.Material.material{3}.ATTR.id=3;
febio_spec.Material.material{3}.density=1e-9;
febio_spec.Material.material{3}.center_of_mass=mean(Vc,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='tet4'; %Element type
febio_spec.Mesh.Elements{1}.elem.ATTR.id=(1:1:size(E1,1))'; %Element id's
febio_spec.Mesh.Elements{1}.elem.VAL=E1; %The element matrix

partName2='Part2';
febio_spec.Mesh.Elements{2}.ATTR.name=partName2; %Name of this part
febio_spec.Mesh.Elements{2}.ATTR.type='tet4'; %Element type
febio_spec.Mesh.Elements{2}.elem.ATTR.id=size(E1,1)+(1:1:size(E2,1))'; %Element id's
febio_spec.Mesh.Elements{2}.elem.VAL=E2; %The element matrix

partName3='Part3';
febio_spec.Mesh.Elements{3}.ATTR.name=partName3; %Name of this part
febio_spec.Mesh.Elements{3}.ATTR.type='tri3'; %Element type
febio_spec.Mesh.Elements{3}.elem.ATTR.id=size(E1,1)+size(E2,1)+(1:1:size(Fc,1))'; %Element id's
febio_spec.Mesh.Elements{3}.elem.VAL=Fc; %The element matrix

% -> NodeSets
nodeSetName1='bcSupportList';
febio_spec.Mesh.NodeSet{1}.ATTR.name=nodeSetName1;
febio_spec.Mesh.NodeSet{1}.VAL=mrow(bcSupportList);

%MeshDomains section
febio_spec.MeshDomains.SolidDomain{1}.ATTR.name=partName1;
febio_spec.MeshDomains.SolidDomain{1}.ATTR.mat=materialName1;

febio_spec.MeshDomains.SolidDomain{2}.ATTR.name=partName2;
febio_spec.MeshDomains.SolidDomain{2}.ATTR.mat=materialName2;

febio_spec.MeshDomains.ShellDomain{1}.ATTR.name=partName3;
febio_spec.MeshDomains.ShellDomain{1}.ATTR.mat=materialName3;

% -> Surfaces
surfaceName1='contactSurface1';
febio_spec.Mesh.Surface{1}.ATTR.name=surfaceName1;
febio_spec.Mesh.Surface{1}.tri3.ATTR.id=(1:1:size(F_contact_primary,1))';
febio_spec.Mesh.Surface{1}.tri3.VAL=F_contact_primary;

surfaceName2='contactSurface2';
febio_spec.Mesh.Surface{2}.ATTR.name=surfaceName2;
febio_spec.Mesh.Surface{2}.tri3.ATTR.id=(1:1:size(F_contact_secondary,1))';
febio_spec.Mesh.Surface{2}.tri3.VAL=F_contact_secondary;

% -> Surface pairs
surfacePairName='Contact1';
febio_spec.Mesh.SurfacePair{1}.ATTR.name=surfacePairName;
febio_spec.Mesh.SurfacePair{1}.primary=surfaceName1;
febio_spec.Mesh.SurfacePair{1}.secondary=surfaceName2;

%MeshData section
% -> ElementData
febio_spec.MeshData.ElementData{1}.ATTR.elem_set=partName1;
febio_spec.MeshData.ElementData{1}.ATTR.type='mat_axis';

for q=1:1:size(E1,1)
    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.name='zero_displacement_xyz';
febio_spec.Boundary.bc{1}.ATTR.type='zero displacement';
febio_spec.Boundary.bc{1}.ATTR.node_set=nodeSetName1;
febio_spec.Boundary.bc{1}.x_dof=1;
febio_spec.Boundary.bc{1}.y_dof=1;
febio_spec.Boundary.bc{1}.z_dof=1;

%Rigid section
% ->Rigid body fix boundary conditions
febio_spec.Rigid.rigid_bc{1}.ATTR.name='RigidFix_1';
febio_spec.Rigid.rigid_bc{1}.ATTR.type='rigid_fixed';
febio_spec.Rigid.rigid_bc{1}.rb=3;
febio_spec.Rigid.rigid_bc{1}.Rx_dof=1;
febio_spec.Rigid.rigid_bc{1}.Ry_dof=1;
febio_spec.Rigid.rigid_bc{1}.Rz_dof=1;
febio_spec.Rigid.rigid_bc{1}.Ru_dof=1;
febio_spec.Rigid.rigid_bc{1}.Rv_dof=1;
febio_spec.Rigid.rigid_bc{1}.Rw_dof=1;

%Contact section
febio_spec.Contact.contact{1}.ATTR.surface_pair=surfacePairName;
febio_spec.Contact.contact{1}.ATTR.type='sliding-elastic';
febio_spec.Contact.contact{1}.two_pass=1;
febio_spec.Contact.contact{1}.laugon=laugon;
febio_spec.Contact.contact{1}.tolerance=0.2;
febio_spec.Contact.contact{1}.gaptol=0;
febio_spec.Contact.contact{1}.minaug=minaug;
febio_spec.Contact.contact{1}.maxaug=maxaug;
febio_spec.Contact.contact{1}.search_tol=0.01;
febio_spec.Contact.contact{1}.search_radius=0.1*sqrt(sum((max(V,[],1)-min(V,[],1)).^2,2));
febio_spec.Contact.contact{1}.symmetric_stiffness=0;
febio_spec.Contact.contact{1}.auto_penalty=1;
febio_spec.Contact.contact{1}.penalty=contactPenalty;
febio_spec.Contact.contact{1}.fric_coeff=fric_coeff;

%LoadData section
% -> load_controller
febio_spec.LoadData.load_controller{1}.ATTR.name='LC_1';
febio_spec.LoadData.load_controller{1}.ATTR.id=1;
febio_spec.LoadData.load_controller{1}.ATTR.type='loadcurve';
febio_spec.LoadData.load_controller{1}.interpolate='LINEAR';
%febio_spec.LoadData.load_controller{1}.extend='CONSTANT';
febio_spec.LoadData.load_controller{1}.points.pt.VAL=[0 0; 1 1];

%Output section
% -> log file
febio_spec.Output.logfile.ATTR.file=febioLogFileName;
febio_spec.Output.logfile.node_data{1}.ATTR.file=febioLogFileName_disp;
febio_spec.Output.logfile.node_data{1}.ATTR.data='ux;uy;uz';
febio_spec.Output.logfile.node_data{1}.ATTR.delim=',';

% Plotfile section
febio_spec.Output.plotfile.compression=0;

Quick viewing of the FEBio input file structure

The febView function can be used to view the xml structure in a MATLAB figure window.

febView(febio_spec); %Viewing the febio file

Exporting the FEBio input file

Exporting the febio_spec structure to an FEBio input file is done using the febioStruct2xml function.

febioStruct2xml(febio_spec,febioFebFileName); %Exporting to file and domNode

Running the FEBio analysis

To run the analysis defined by the created FEBio input file the runMonitorFEBio function is used. The input for this function is a structure defining job settings e.g. the FEBio input file name. The optional output runFlag informs the user if the analysis was run succesfully.

febioAnalysis.run_filename=febioFebFileName; %The input file name
febioAnalysis.run_logname=febioLogFileName; %The name for the log file
febioAnalysis.disp_on=1; %Display information on the command window
febioAnalysis.runMode=runMode;

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

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-------->    RUNNING/MONITORING FEBIO JOB    <-------- 20-Apr-2023 18:09:48
FEBio path: /home/kevin/FEBioStudio2/bin/febio4
# Attempt removal of existing log files                20-Apr-2023 18:09:48
 * Removal succesful                                   20-Apr-2023 18:09:48
# Attempt removal of existing .xplt files              20-Apr-2023 18:09:48
 * Removal succesful                                   20-Apr-2023 18:09:48
# Starting FEBio...                                    20-Apr-2023 18:09:48
  Max. total analysis time is: Inf s
 * Waiting for log file creation                       20-Apr-2023 18:09:48
   Max. wait time: 30 s
 * Log file found.                                     20-Apr-2023 18:09:49
# Parsing log file...                                  20-Apr-2023 18:09:49
    number of iterations   : 14                        20-Apr-2023 18:09:50
    number of reformations : 14                        20-Apr-2023 18:09:50
------- converged at time : 0.04                       20-Apr-2023 18:09:50
    number of iterations   : 12                        20-Apr-2023 18:09:51
    number of reformations : 12                        20-Apr-2023 18:09:51
------- converged at time : 0.0738681                  20-Apr-2023 18:09:51
    number of iterations   : 11                        20-Apr-2023 18:09:52
    number of reformations : 11                        20-Apr-2023 18:09:52
------- converged at time : 0.10482                    20-Apr-2023 18:09:52
    number of iterations   : 10                        20-Apr-2023 18:09:52
    number of reformations : 10                        20-Apr-2023 18:09:52
------- converged at time : 0.13435                    20-Apr-2023 18:09:52
    number of iterations   : 10                        20-Apr-2023 18:09:53
    number of reformations : 10                        20-Apr-2023 18:09:53
------- converged at time : 0.163881                   20-Apr-2023 18:09:53
    number of iterations   : 10                        20-Apr-2023 18:09:54
    number of reformations : 10                        20-Apr-2023 18:09:54
------- converged at time : 0.193411                   20-Apr-2023 18:09:54
    number of iterations   : 10                        20-Apr-2023 18:09:55
    number of reformations : 10                        20-Apr-2023 18:09:55
------- converged at time : 0.222941                   20-Apr-2023 18:09:55
    number of iterations   : 10                        20-Apr-2023 18:09:55
    number of reformations : 10                        20-Apr-2023 18:09:55
------- converged at time : 0.252471                   20-Apr-2023 18:09:55
    number of iterations   : 10                        20-Apr-2023 18:09:56
    number of reformations : 10                        20-Apr-2023 18:09:56
------- converged at time : 0.282002                   20-Apr-2023 18:09:56
    number of iterations   : 9                         20-Apr-2023 18:09:57
    number of reformations : 9                         20-Apr-2023 18:09:57
------- converged at time : 0.311532                   20-Apr-2023 18:09:57
    number of iterations   : 9                         20-Apr-2023 18:09:57
    number of reformations : 9                         20-Apr-2023 18:09:57
------- converged at time : 0.341629                   20-Apr-2023 18:09:57
    number of iterations   : 9                         20-Apr-2023 18:09:58
    number of reformations : 9                         20-Apr-2023 18:09:58
------- converged at time : 0.372261                   20-Apr-2023 18:09:58
    number of iterations   : 9                         20-Apr-2023 18:09:59
    number of reformations : 9                         20-Apr-2023 18:09:59
------- converged at time : 0.4034                     20-Apr-2023 18:09:59
    number of iterations   : 8                         20-Apr-2023 18:09:59
    number of reformations : 8                         20-Apr-2023 18:09:59
------- converged at time : 0.435018                   20-Apr-2023 18:09:59
    number of iterations   : 8                         20-Apr-2023 18:10:00
    number of reformations : 8                         20-Apr-2023 18:10:00
------- converged at time : 0.467626                   20-Apr-2023 18:10:00
    number of iterations   : 8                         20-Apr-2023 18:10:00
    number of reformations : 8                         20-Apr-2023 18:10:00
------- converged at time : 0.501106                   20-Apr-2023 18:10:00
    number of iterations   : 8                         20-Apr-2023 18:10:01
    number of reformations : 8                         20-Apr-2023 18:10:01
------- converged at time : 0.535356                   20-Apr-2023 18:10:01
    number of iterations   : 8                         20-Apr-2023 18:10:02
    number of reformations : 8                         20-Apr-2023 18:10:02
------- converged at time : 0.570284                   20-Apr-2023 18:10:02
    number of iterations   : 8                         20-Apr-2023 18:10:02
    number of reformations : 8                         20-Apr-2023 18:10:02
------- converged at time : 0.605811                   20-Apr-2023 18:10:02
    number of iterations   : 7                         20-Apr-2023 18:10:03
    number of reformations : 7                         20-Apr-2023 18:10:03
------- converged at time : 0.641866                   20-Apr-2023 18:10:03
    number of iterations   : 7                         20-Apr-2023 18:10:03
    number of reformations : 7                         20-Apr-2023 18:10:03
------- converged at time : 0.678692                   20-Apr-2023 18:10:03
    number of iterations   : 6                         20-Apr-2023 18:10:04
    number of reformations : 6                         20-Apr-2023 18:10:04
------- converged at time : 0.716137                   20-Apr-2023 18:10:04
    number of iterations   : 6                         20-Apr-2023 18:10:04
    number of reformations : 6                         20-Apr-2023 18:10:04
------- converged at time : 0.754093                   20-Apr-2023 18:10:04
    number of iterations   : 6                         20-Apr-2023 18:10:05
    number of reformations : 6                         20-Apr-2023 18:10:05
------- converged at time : 0.792457                   20-Apr-2023 18:10:05
    number of iterations   : 6                         20-Apr-2023 18:10:05
    number of reformations : 6                         20-Apr-2023 18:10:05
------- converged at time : 0.831149                   20-Apr-2023 18:10:05
    number of iterations   : 6                         20-Apr-2023 18:10:06
    number of reformations : 6                         20-Apr-2023 18:10:06
------- converged at time : 0.870103                   20-Apr-2023 18:10:06
    number of iterations   : 6                         20-Apr-2023 18:10:06
    number of reformations : 6                         20-Apr-2023 18:10:06
------- converged at time : 0.909266                   20-Apr-2023 18:10:06
    number of iterations   : 5                         20-Apr-2023 18:10:06
    number of reformations : 5                         20-Apr-2023 18:10:06
------- converged at time : 0.948596                   20-Apr-2023 18:10:06
    number of iterations   : 5                         20-Apr-2023 18:10:07
    number of reformations : 5                         20-Apr-2023 18:10:07
------- converged at time : 0.98806                    20-Apr-2023 18:10:07
    number of iterations   : 5                         20-Apr-2023 18:10:07
    number of reformations : 5                         20-Apr-2023 18:10:07
------- converged at time : 1                          20-Apr-2023 18:10:07
 Elapsed time : 0:00:18                                20-Apr-2023 18:10:07
 N O R M A L   T E R M I N A T I O N
# Done                                                 20-Apr-2023 18:10:07
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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),0,1);

    %Access data
    N_disp_mat=dataStruct.data; %Displacement
    timeVec=dataStruct.time; %Time

    %Create deformed coordinate set
    V_DEF=N_disp_mat+repmat(V,[1 1 size(N_disp_mat,3)]);

Plotting the simulated results using anim8 to visualize and animate deformations

    DN_magnitude=sqrt(sum(N_disp_mat(:,:,end).^2,2)); %Current displacement magnitude

    % Create basic view and store graphics handle to initiate animation
    hf=cFigure; %Open figure
    gtitle([febioFebFileNamePart,': Press play to animate']);
    title('$u_{mag}$ [mm]','Interpreter','Latex')
    hp1=gpatch(Fb,V_DEF(:,:,end),DN_magnitude,'k',1); %Add graphics object to animate
    hp1.FaceColor='interp';

    hp2=gpatch(Fc,V_DEF(:,:,end),'w','none',1); %Add graphics object to animate

    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}=[hp1 hp1 hp2]; %Handles of objects to animate
        animStruct.Props{qt}={'Vertices','CData','Vertices'}; %Properties of objects to animate
        animStruct.Set{qt}={V_DEF(:,:,qt),DN_magnitude,V_DEF(:,:,qt)}; %Property values for to set in order to animate
    end
    anim8(hf,animStruct); %Initiate animation feature
    drawnow;

end

GIBBON www.gibboncode.org

Kevin Mattheus Moerman, [email protected]

GIBBON footer text

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

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

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

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

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