DEMO_febio_0036_sphere_branches_slide_body_force

Below is a demonstration for:

Contents

Keywords

clear; close all; clc;

Plot settings

fontSize=15;
faceAlpha1=0.8;
faceAlpha2=0.3;
markerSize=40;
lineWidth=3;
cMap=blood(250);

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
% febioLogFileName_force=[febioFebFileNamePart,'_force_out.txt']; %Log file name for exporting force

numElementsMantel=5;
sphereRadius=3;
pointSpacing=(sphereRadius/6);
voxelSize=pointSpacing*ones(1,3);
w=sphereRadius*1.5;
reduceFactor=2.75;
contourLevel=1;

% Material parameter set
materialType=1;
c1=1e-3; %Shear-modulus-like parameter
m1=2; %Material parameter setting degree of non-linearity
k_factor=10; %Bulk modulus factor
k=c1*k_factor; %Bulk modulus
g1=2; %Viscoelastic QLV proportional coefficient
t1=150; %Viscoelastic QLV time coefficient

%Setting material density (set artificially high in effort to dampen
%oscilations and increase body force).
materialDensity=1e-9*20000; %Density

% FEA control settings
timeTotal=2; %Total simulation time
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=15; %Optimum number of iterations
max_retries=5; %Maximum number of retires
dtmin=(timeTotal/numTimeSteps)/100; %Minimum time step size
dtmax=timeTotal/(numTimeSteps); %Maximum time step size
symmetric_stiffness=0;
min_residual=1e-20;
analysisType='DYNAMIC';

runMode='external';%'internal';

%Contact parameters
contactPenalty=25;
fric_coeff=0.25;
laugon=0;
minaug=1;
maxaug=10;

%Specifying load
sphereVolume=4/3*(pi*sphereRadius^3); %Sphere Volume in mm^3
sphereMass=sphereVolume.*materialDensity; %Sphere mass in tonne
sphereSectionArea=pi*sphereRadius^2;
bodyLoadMagnitude=9.81*sphereMass*1000;

forceBodyLoad=sphereMass.*bodyLoadMagnitude;
stressBodyLoad=forceBodyLoad/sphereSectionArea;

Define branch curves

n=100;

V1=[0 0 0; -2*sphereRadius 0 0];
V1=evenlySampleCurve(V1,n,'linear',0);

x=linspace(1,-1,n)';
xx=nan(size(x));
f=4;
if f==0
    xx=x;
else
    xx(x>=0) =(exp(-f*abs(x(x>0)))-1)./(exp(-f)-1);
    xx(x<0)  =-(exp(-f*abs(x(x<0)))-1)./(exp(-f)-1);
end
xx=w/2.*xx;
xx=-xx+w/2;

x=x.*w;
x=x+(min(V1(:,1)))+(-w);

V2=[x zeros(size(x)) xx];
V2=evenlySampleCurve(V2,n,'linear',0);

x=linspace(2,-2,n)';
xx=nan(size(x));
f=4;
if f==0
    xx=x;
else
    xx(x>=0) =(exp(-f*abs(x(x>0)))-1)./(exp(-f)-1);
    xx(x<0)  =-(exp(-f*abs(x(x<0)))-1)./(exp(-f)-1);
end
xx=w/4.*xx;
xx=-xx+w/4;

x=x.*w/2;
x=x+(-w/2);

V3=[x zeros(size(x)) xx];
V3=V3-V3(1,:);
V4=V3;
V3=V3+V2(end,:);
V3=evenlySampleCurve(V3,n,'linear',0);

V4(:,3)=-V4(:,3)/3;
V4=V4+V2(end,:);
V4=evenlySampleCurve(V4,n,'linear',0);

V5=V2;
V5(:,3)=-V5(:,3)/3;

V6=V4;
V6=V6-V6(1,:);
V6(:,3)=-V6(:,3);
V6=V6+V5(end,:);

V7=V3;
V7=V7-V7(1,:);
V7(:,3)=-V7(:,3);
V7=V7+V5(end,:);

cFigure; hold on;
plotV(V1,'r.-','MarkerSize',15);
plotV(V2,'g.-','MarkerSize',15);
plotV(V3,'y.-','MarkerSize',15);
plotV(V4,'k.-','MarkerSize',15);

plotV(V5,'b.-','MarkerSize',15);
plotV(V6,'c.-','MarkerSize',15);
plotV(V7,'m.-','MarkerSize',15);
axisGeom;
drawnow;

r1=sphereRadius; %Inlet radius
A1=r1^2*pi; %Inlet area

A2=(A1*0.8); %First bifurcation inlet area
r2=sqrt(A2/pi); %First bifurcation inlet radius

A3=(A2/2); %area
r3=sqrt(A3/pi); %radius

A4=(A3/3); %area
r4=sqrt(A4/pi); %radius

E1=[(1:size(V1,1)-1)' (2:size(V1,1))'];
E2=[(1:size(V2,1)-1)' (2:size(V2,1))'];
E3=[(1:size(V3,1)-1)' (2:size(V3,1))'];
E4=[(1:size(V4,1)-1)' (2:size(V4,1))'];
E5=[(1:size(V5,1)-1)' (2:size(V5,1))'];
E6=[(1:size(V6,1)-1)' (2:size(V6,1))'];
E7=[(1:size(V7,1)-1)' (2:size(V7,1))'];

C=[linspace(r1,r2,size(V1,1))';...
   linspace(r2,r3,size(V2,1))';...
   linspace(r3,r4,size(V3,1))';...
   linspace(r3,r4,size(V4,1))';...
   linspace(r2,r3,size(V5,1))';...
   linspace(r3,r4,size(V6,1))';...
   linspace(r3,r4,size(V7,1))'];

[E,V]=joinElementSets({E1,E2,E3,E4,E5,E6,E7},{V1,V2,V3,V4,V5,V6,V7});

[E,V,ind1]=mergeVertices(E,V);
C=C(ind1);

% cPar.n=25;
% [C]=patchSmooth(E,C,[],cPar);

cFigure;
gpatch(E,V,'none',C,0,3);
axisGeom;
drawnow;

x=min(V(:,1)):voxelSize:max(V(:,1));
y=min(V(:,2))-1.5*sphereRadius:voxelSize:max(V(:,2))+1.5*sphereRadius;
z=min(V(:,3))-1.5*sphereRadius:voxelSize:max(V(:,3))+1.5*sphereRadius;
[X,Y,Z]=ndgrid(x,y,z);
V_grid=[X(:) Y(:) Z(:)];

[M_grid,indMin]=minDist(V_grid,V);

M_grid=M_grid./C(indMin);

M=reshape(M_grid,size(X));

vizStruct.colormap=warmcold(250);
vizStruct.clim=[0 contourLevel*2];
sv3(M,voxelSize,vizStruct);
camlight headlight;

imOrigin=min(V_grid,[],1)-voxelSize/2;

controlPar_isosurface.nSub=[1 1 1];%round(max(v)/2./v);
controlPar_isosurface.capOpt=0; %Option to cap open ended surfaces
controlPar_isosurface.voxelSize=voxelSize;
controlPar_isosurface.contourLevel=contourLevel;
[Fi,Vi]=levelset2isosurface(M,controlPar_isosurface); %Get iso-surface
% Fi=fliplr(Fi); %Invert face orientation
Fi_sorted=sort(Fi,2);
logicInvalid=any(diff(Fi_sorted,1,2)==0,2);
Fi=Fi(~logicInvalid,:);
[Fi,Vi]=patchCleanUnused(Fi,Vi);
Vi=Vi(:,[2 1 3]);
Vi=Vi+imOrigin;
[Fi,Vi]=triSurfRemoveThreeConnect(Fi,Vi);
[Fi,Vi]=patchCleanUnused(Fi,Vi);

Remesh using geomgram

optionStructGG.pointSpacing=pointSpacing*2;
[Fi,Vi]=ggremesh(Fi,Vi,optionStructGG);

optionStruct.maxAngleDeviation=10;
optionStruct.triangleConvert=1;
[Fi,Vi]=tri2quadGroupSplit(Fi,Vi,optionStruct);

Eb=patchBoundary(Fi);
controlPar_smooth.Method='HC';
controlPar_smooth.Alpha=0.1;
controlPar_smooth.Beta=0.5;
controlPar_smooth.n=150;
controlPar_smooth.RigidConstraints=unique(Eb(:));
[Vi]=patchSmooth(Fi,Vi,[],controlPar_smooth);

Vi=Vi-imOrigin;
Vi=Vi(:,[2 1 3]);
Eb=patchBoundary(Fi);

gpatch(Fi,Vi,'w','k',1,2);

cFigure;
gpatch(Fi,Vi,'w','k');
patchNormPlot(Fi,Vi);
axisGeom;
view(-90,0);
camlight headlight;
drawnow;

%Control settings
cPar.sphereRadius=sphereRadius;
cPar.coreRadius=sphereRadius.*0.75;
cPar.numElementsCore=ceil(sphereRadius/pointSpacing);
cPar.numElementsMantel=ceil((sphereRadius-cPar.coreRadius)/pointSpacing);
cPar.makeHollow=0;
cPar.outputStructType=2;

%Creating sphere
[meshStruct]=hexMeshSphere(cPar);

%Access ouput
E_blob=meshStruct.elements; %The elements
V_blob=meshStruct.nodes; %The vertices
Fb_blob=meshStruct.facesBoundary; %The boundary faces

%Create cut view

hFig=cFigure;
subplot(1,2,1); hold on;
title('The hexahedral mesh sphere','FontSize',fontSize);
gpatch(Fb_blob,V_blob,'r');
axisGeom(gca,fontSize);
camlight headlight;

hs=subplot(1,2,2); hold on;
title('Cut view of solid mesh','FontSize',fontSize);
optionStruct.hFig=[hFig hs];
gpatch(Fb_blob,V_blob,'kw','none',0.25);
meshView(meshStruct,optionStruct);
axisGeom(gca,fontSize);
drawnow;

drawnow;

Shift branch set

Vi=Vi(:,[2 1 3]);
Vi=Vi+imOrigin;

Join model node sets

V=[V_blob; Vi; ];
F_tube=Fi+size(V_blob,1);
F_tube=fliplr(F_tube);

center_of_mass_tube=mean(Vi,1);

Visualizing model

cFigure; hold on;
gtitle('Model components',fontSize);
hl(1)=gpatch(Fb_blob,V,'rw','k',0.8);
hl(2)=gpatch(F_tube,V,'bw','k',0.8);
patchNormPlot(F_tube,V);
legend(hl,{'Clot','Vessel'}); clear hl;
axisGeom(gca,fontSize);
camlight headlight;
drawnow;

Get contact surfaces

F_contact_blob=Fb_blob;

Visualize contact surfaces

cFigure; hold on;
title('Tube blob contact pair','fontsize',fontSize);
hl(1)=gpatch(F_tube,V,'rw','k',1);
patchNormPlot(F_tube,V);
hl(2)=gpatch(F_contact_blob,V,'gw','k',1);
patchNormPlot(F_contact_blob,V);
legend(hl,{'Secondary','Primary'}); clear hl;
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=analysisType;
febio_spec.Control.time_steps=numTimeSteps;
febio_spec.Control.step_size=timeTotal/numTimeSteps;
febio_spec.Control.solver.max_refs=max_refs;
febio_spec.Control.solver.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;
switch materialType
    case 0
        febio_spec.Material.material{1}.ATTR.type='Ogden unconstrained';
        febio_spec.Material.material{1}.ATTR.id=1;
        febio_spec.Material.material{1}.c1=c1;
        febio_spec.Material.material{1}.m1=m1;
        febio_spec.Material.material{1}.c2=c1;
        febio_spec.Material.material{1}.m2=-m1;
        febio_spec.Material.material{1}.cp=k;
        febio_spec.Material.material{1}.density=materialDensity;
    case 1
        %Viscoelastic part
        febio_spec.Material.material{1}.ATTR.type='viscoelastic';
        febio_spec.Material.material{1}.ATTR.id=1;
        febio_spec.Material.material{1}.g1=g1;
        febio_spec.Material.material{1}.t1=t1;
        febio_spec.Material.material{1}.density=materialDensity;

        %Elastic part
        febio_spec.Material.material{1}.elastic{1}.ATTR.type='Ogden unconstrained';
        febio_spec.Material.material{1}.elastic{1}.c1=c1;
        febio_spec.Material.material{1}.elastic{1}.m1=m1;
        febio_spec.Material.material{1}.elastic{1}.c2=c1;
        febio_spec.Material.material{1}.elastic{1}.m2=-m1;
        febio_spec.Material.material{1}.elastic{1}.cp=k;
        febio_spec.Material.material{1}.elastic{1}.density=materialDensity;
end

materialName2='Material2';
febio_spec.Material.material{2}.ATTR.name=materialName2;
febio_spec.Material.material{2}.ATTR.type='rigid body';
febio_spec.Material.material{2}.ATTR.id=2;
febio_spec.Material.material{2}.density=1;
febio_spec.Material.material{2}.center_of_mass=center_of_mass_tube;


%Mesh section
% -> Nodes
febio_spec.Mesh.Nodes{1}.ATTR.name='nodeSet_all'; %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_blob,1))'; %Element id's
febio_spec.Mesh.Elements{1}.elem.VAL=E_blob; %The element matrix

partName2='Part2';
febio_spec.Mesh.Elements{2}.ATTR.name=partName2; %Name of this part
febio_spec.Mesh.Elements{2}.ATTR.type='quad4'; %Element type
febio_spec.Mesh.Elements{2}.elem.ATTR.id=size(E_blob,1)+(1:1:size(F_tube,1))'; %Element id's
febio_spec.Mesh.Elements{2}.elem.VAL=F_tube; %The element matrix

% -> Surfaces
surfaceName1='contactSurface1';
febio_spec.Mesh.Surface{1}.ATTR.name=surfaceName1;
febio_spec.Mesh.Surface{1}.quad4.ATTR.id=(1:1:size(F_tube,1))';
febio_spec.Mesh.Surface{1}.quad4.VAL=F_tube;

surfaceName2='contactSurface2';
febio_spec.Mesh.Surface{2}.ATTR.name=surfaceName2;
febio_spec.Mesh.Surface{2}.quad4.ATTR.id=(1:1:size(F_contact_blob,1))';
febio_spec.Mesh.Surface{2}.quad4.VAL=F_contact_blob;

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

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

febio_spec.MeshDomains.ShellDomain.ATTR.name=partName2;
febio_spec.MeshDomains.ShellDomain.ATTR.mat=materialName2;

%Loads section
% -> Body load
febio_spec.Loads.body_load.ATTR.type='const';
febio_spec.Loads.body_load.x.ATTR.lc=1;
febio_spec.Loads.body_load.x.VAL=bodyLoadMagnitude;


%Rigid section
% -> Prescribed rigid body boundary conditions
febio_spec.Rigid.rigid_constraint{1}.ATTR.name='RigidFix_1';
febio_spec.Rigid.rigid_constraint{1}.ATTR.type='fix';
febio_spec.Rigid.rigid_constraint{1}.rb=2;
febio_spec.Rigid.rigid_constraint{1}.dofs='Rx,Ry,Rz,Ru,Rv,Rw';

%Contact section
febio_spec.Contact.contact{1}.ATTR.type='sliding-elastic';
febio_spec.Contact.contact{1}.ATTR.surface_pair=contactPairName;
febio_spec.Contact.contact{1}.two_pass=0;
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.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=runMode;

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

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-------->    RUNNING/MONITORING FEBIO JOB    <-------- 25-Feb-2022 15:33:48
FEBio path: /home/kevin/FEBioStudio/bin/febio3
# Attempt removal of existing log files                25-Feb-2022 15:33:48
 * Removal succesful                                   25-Feb-2022 15:33:48
# Attempt removal of existing .xplt files              25-Feb-2022 15:33:48
 * Removal succesful                                   25-Feb-2022 15:33:48
# Starting FEBio...                                    25-Feb-2022 15:33:48
  Max. total analysis time is: Inf s
 * Waiting for log file creation                       25-Feb-2022 15:33:48
   Max. wait time: 30 s
 * Log file found.                                     25-Feb-2022 15:33:48
# Parsing log file...                                  25-Feb-2022 15:33:48
    number of iterations   : 4                         25-Feb-2022 15:33:49
    number of reformations : 4                         25-Feb-2022 15:33:49
------- converged at time : 0.2                        25-Feb-2022 15:33:49
    number of iterations   : 6                         25-Feb-2022 15:33:49
    number of reformations : 6                         25-Feb-2022 15:33:49
    number of iterations   : 6                         25-Feb-2022 15:33:50
    number of reformations : 6                         25-Feb-2022 15:33:50
------- converged at time : 0.6                        25-Feb-2022 15:33:50
    number of iterations   : 7                         25-Feb-2022 15:33:51
    number of reformations : 7                         25-Feb-2022 15:33:51
------- converged at time : 0.8                        25-Feb-2022 15:33:51
    number of iterations   : 7                         25-Feb-2022 15:33:52
    number of reformations : 7                         25-Feb-2022 15:33:52
------- converged at time : 1                          25-Feb-2022 15:33:52
    number of iterations   : 9                         25-Feb-2022 15:33:53
    number of reformations : 9                         25-Feb-2022 15:33:53
------- converged at time : 1.2                        25-Feb-2022 15:33:53
    number of iterations   : 8                         25-Feb-2022 15:33:54
    number of reformations : 8                         25-Feb-2022 15:33:54
------- converged at time : 1.33333                    25-Feb-2022 15:33:54
    number of iterations   : 7                         25-Feb-2022 15:33:56
    number of reformations : 7                         25-Feb-2022 15:33:56
------- converged at time : 1.38222                    25-Feb-2022 15:33:56
    number of iterations   : 7                         25-Feb-2022 15:33:58
    number of reformations : 7                         25-Feb-2022 15:33:58
------- converged at time : 1.44815                    25-Feb-2022 15:33:58
    number of iterations   : 7                         25-Feb-2022 15:33:59
    number of reformations : 7                         25-Feb-2022 15:33:59
------- converged at time : 1.52543                    25-Feb-2022 15:33:59
    number of iterations   : 6                         25-Feb-2022 15:34:01
    number of reformations : 6                         25-Feb-2022 15:34:01
------- converged at time : 1.57635                    25-Feb-2022 15:34:01
    number of iterations   : 7                         25-Feb-2022 15:34:02
    number of reformations : 7                         25-Feb-2022 15:34:02
------- converged at time : 1.64362                    25-Feb-2022 15:34:02
    number of iterations   : 7                         25-Feb-2022 15:34:03
    number of reformations : 7                         25-Feb-2022 15:34:03
------- converged at time : 1.72181                    25-Feb-2022 15:34:03
    number of iterations   : 5                         25-Feb-2022 15:34:05
    number of reformations : 5                         25-Feb-2022 15:34:05
------- converged at time : 1.75599                    25-Feb-2022 15:34:05
    number of iterations   : 6                         25-Feb-2022 15:34:05
    number of reformations : 6                         25-Feb-2022 15:34:05
------- converged at time : 1.82333                    25-Feb-2022 15:34:05
    number of iterations   : 6                         25-Feb-2022 15:34:06
    number of reformations : 6                         25-Feb-2022 15:34:06
------- converged at time : 1.90156                    25-Feb-2022 15:34:06
    number of iterations   : 5                         25-Feb-2022 15:34:08
    number of reformations : 5                         25-Feb-2022 15:34:08
------- converged at time : 1.93438                    25-Feb-2022 15:34:08
    number of iterations   : 5                         25-Feb-2022 15:34:09
    number of reformations : 5                         25-Feb-2022 15:34:09
------- converged at time : 1.96719                    25-Feb-2022 15:34:09
    number of iterations   : 5                         25-Feb-2022 15:34:10
    number of reformations : 5                         25-Feb-2022 15:34:10
------- converged at time : 2                          25-Feb-2022 15:34:10
 Elapsed time : 0:00:22                                25-Feb-2022 15:34:10
 N O R M A L   T E R M I N A T I O N
# Done                                                 25-Feb-2022 15:34:10
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Import FEBio results

if 1%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; hold on;
    gtitle([febioFebFileNamePart,': Press play to animate']);
    hp=gpatch(Fb_blob,V_DEF(:,:,end),DN_magnitude,'k',1); %Add graphics object to animate
    hp.FaceColor='interp';
    gpatch(F_tube,V,'w','none',0.5); %Add graphics object to animate

    axisGeom(gca,fontSize);
    colormap(gjet(250)); colorbar;
    caxis([0 max(DN_magnitude)]/3);
    axis(axisLim(V_DEF)); %Set axis limits statically
    camlight headlight;
    drawnow;

    % 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 magnitue

        %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

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) 2006-2022 Kevin Mattheus Moerman and the GIBBON contributors

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/.

Published with MATLAB® R2021a