DEMO_febio_0039_nut_bolt_ring

Below is a demonstration for:

Building geometry for a slab with hexahedral elements, and a triangulated sphere.
Defining the boundary conditions
Coding the febio structure
Running the model
Importing and visualizing the displacement results

Keywords
Plot settings
Control parameters
Import STL file as patch data
Mesh ring
Visualizing mesh using meshView, see also anim8
Join geometries
Create 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
indentation
contact, sliding, sticky, friction
rigid body constraints
hexahedral elements, hex8
triangular elements, tri3
slab, block, rectangular
sphere
static, solid
hyperelastic, Ogden
displacement logfile
stress logfile

clear; close all; clc;

Plot settings

fontSize=15;
faceAlpha1=0.8;
faceAlpha2=0.3;
markerSize=40;
lineWidth=3;
markerSize2=25;

Control parameters

% Path names
defaultFolder = fileparts(fileparts(mfilename('fullpath')));
savePath=fullfile(defaultFolder,'data','temp');
stlPath=fullfile(defaultFolder,'data','STL');

% STL files for parts
fileName_1=fullfile(stlPath,'M3_nut.stl');
fileName_2=fullfile(stlPath,'M3_bolt.stl');

pointSpacing=0.3;

% 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_strainEnergy=[febioFebFileNamePart,'_energy_out.txt']; %Log file name for exporting strain energy density

%Define prescribed rotation
prescribedRotation_Z=-(pi/2);
prescribedDisplacement_Z=-1;

%Material parameters (MPa if spatial units are mm)
E_youngs1=17000; %Youngs modulus
nu1=0.25; %Poissons ratio
materialDensity=1e-9; %Density

% FEA control settings
numTimeSteps=20; %Number of time steps desired
max_refs=35; %Max reforms
max_ups=0; %Set to zero to use full-Newton iterations
opt_iter=20; %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;
min_residual=1e-20;

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

%Contact parameters
contactPenalty=5;
laugon=0;
minaug=1;
maxaug=10;
fric_coeff=0.2;

Import STL file as patch data

[stlStruct] = import_STL(fileName_1);
F_nut=stlStruct.solidFaces{1}; %Faces
V_nut=stlStruct.solidVertices{1}; %Vertices
[F_nut,V_nut]=mergeVertices(F_nut,V_nut,3); % Merging nodes
V_nut=V_nut*10; %Scale size
meanV1=mean(V_nut,1);
V_nut=V_nut-meanV1;
% V_nut(:,[1 2])=V_nut(:,[1 2]).*1.01;
V_nut=V_nut+meanV1;
V_nut(:,3)=V_nut(:,3)+4.06;

[stlStruct] = import_STL(fileName_2);
F_bolt=stlStruct.solidFaces{1}; %Faces
V_bolt=stlStruct.solidVertices{1}; %Vertices
[F_bolt,V_bolt]=mergeVertices(F_bolt,V_bolt,3); % Merging nodes
V_bolt=V_bolt*10;  %Scale size

optionStruct.pointSpacing=pointSpacing/2; %Set desired pointSpacing

[F_nut,V_nut]=ggremesh(F_nut,V_nut,optionStruct);

[F_bolt,V_bolt]=ggremesh(F_bolt,V_bolt,optionStruct);

r1=3;
n=round((2*pi*r1)/pointSpacing);
t=linspace(0,2*pi,n);t=t(1:end-1);
x=r1*cos(t);
y=r1*sin(t);
V1c=[x(:) y(:)];

r2=3.2/2;
n=round((2*pi*r2)/pointSpacing);
t=linspace(0,2*pi,n);t=t(1:end-1);
x=r2*cos(t);
y=r2*sin(t);
V2c=[x(:) y(:)];

[F1,V1]=regionTriMesh2D({V1c,V2c},pointSpacing,0,0);
F1=fliplr(F1);
V1(:,3)=0;
V1c(:,3)=0;
V2c(:,3)=0;

F2=F1;
F2=fliplr(F2);
V2=V1;
V2(:,3)=V2(:,3)+2;

V1c2=V1c;
V1c2(:,3)=V1c2(:,3)+2;

V2c2=V2c;
V2c2(:,3)=V2c2(:,3)+2;

cPar.closeLoopOpt=1;
cPar.patchType='tri';
[F3,V3]=polyLoftLinear(V1c,V1c2,cPar);
[F4,V4]=polyLoftLinear(V2c,V2c2,cPar);
F4=fliplr(F4);

[Fw,Vw,Cw]=joinElementSets({F1,F2,F3,F4},{V1,V2,V3,V4});
[Fw,Vw]=mergeVertices(Fw,Vw);

Mesh ring

[V_regions]=getInnerPoint(Fw,Vw); % Define region points
V_holes=[]; % Define hole points
[regionA]=tetVolMeanEst(Fw,Vw); %Volume for regular tets

stringOpt='-pq1.2AaY';

inputStruct.stringOpt=stringOpt;
inputStruct.Faces=Fw;
inputStruct.Nodes=Vw;
inputStruct.holePoints=V_holes;
inputStruct.faceBoundaryMarker=Cw; %Face boundary markers
inputStruct.regionPoints=V_regions; %region points
inputStruct.regionA=regionA*2;
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=fliplr(meshOutput.facesBoundary);
V=meshOutput.nodes;
Cwb=meshOutput.boundaryMarker;
CE=meshOutput.elementMaterialID;
E=meshOutput.elements;
V(:,3)=V(:,3)+2;

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- TETGEN Tetrahedral meshing --- 20-Apr-2023 18:03:45
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Writing SMESH file --- 20-Apr-2023 18:03:45
----> Adding node field
----> Adding facet field
----> Adding holes specification
----> Adding region specification
--- Done --- 20-Apr-2023 18:03:45
--- Running TetGen to mesh input boundary--- 20-Apr-2023 18:03:45
Opening /mnt/data/MATLAB/GIBBON/data/temp/temp.smesh.
Delaunizing vertices...
Delaunay seconds:  0.029761
Creating surface mesh ...
Surface mesh seconds:  0.001773
Recovering boundaries...
Boundary recovery seconds:  0.004365
Removing exterior tetrahedra ...
Spreading region attributes.
Exterior tets removal seconds:  0.000998
Recovering Delaunayness...
Delaunay recovery seconds:  0.001219
Refining mesh...
Refinement seconds:  0.020568
Smoothing vertices...
Mesh smoothing seconds:  0.040713
Improving mesh...
Mesh improvement seconds:  0.00206

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:  0.020907
Total running seconds:  0.122485

Statistics:

  Input points: 1097
  Input facets: 2194
  Input segments: 3291
  Input holes: 0
  Input regions: 1

  Mesh points: 2071
  Mesh tetrahedra: 9120
  Mesh faces: 19337
  Mesh faces on exterior boundary: 2194
  Mesh faces on input facets: 2194
  Mesh edges on input segments: 3291
  Steiner points inside domain: 974

--- Done --- 20-Apr-2023 18:03:45
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Importing TetGen files --- 20-Apr-2023 18:03:45
--- Done --- 20-Apr-2023 18:03:45

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

meshView(meshOutput);

Join geometries

F_nut=F_nut+size(V,1);
F_bolt=F_bolt+size(V,1)+size(V_nut,1);

V=[V; V_nut; V_bolt];

R=euler2DCM([pi 0 0]);
V=V*R;

Visualize

cFigure; hold on;
gpatch(F_nut,V,'rw','k',1);
gpatch(F_bolt,V,'gw','k',1);
gpatch(Fb,V,Cwb,'k',1);
colormap(gjet(4)); icolorbar;
axisGeom;
camlight headlight;
drawnow;

bcSupportList=unique(Fb(Cwb==4,:));

Visualize contact surfaces

cFigure; hold on;
gpatch(F_nut,V,'w','none',0.5);
gpatch(F_bolt,V,'w','none',0.5);
gpatch(Fb,V,'w','none',0.5);

hl=plotV(V(bcSupportList,:),'k.','MarkerSize',markerSize);

legend(hl,{'BC support XY'});

axisGeom;
camlight headlight;
drawnow;

Create contact surfaces

VF_nut=patchCentre(F_nut,V);
VF_bolt=patchCentre(F_bolt,V);

F_secondary1=Fb(Cwb==1,:);
F_secondary2=Fb(Cwb==2,:);

zWasherTop=mean(V(unique(F_secondary1),3));
zWasherBottom=mean(V(unique(F_secondary2),3));

logicBoltBottom=VF_bolt(:,3)>zWasherTop & VF_bolt(:,3)<zWasherTop+pointSpacing;
logicBoltBottom=triSurfLogicSharpFix(F_bolt,logicBoltBottom,2);
F_primary1=F_bolt(logicBoltBottom,:);

logicNutTop=VF_nut(:,3)<zWasherBottom & VF_nut(:,3)>zWasherBottom-pointSpacing;
logicNutTop=triSurfLogicSharpFix(F_nut,logicNutTop,2);
F_primary2=F_nut(logicNutTop,:);

Visualize contact surfaces

cFigure; hold on;
gpatch(F_nut,V,'w','none',0.5);
gpatch(F_bolt,V,'w','none',0.5);
gpatch(Fb,V,'w','none',0.5);

gpatch(F_secondary1,V,'rw','k',1);
patchNormPlot(F_secondary1,V);

gpatch(F_secondary2,V,'gw','k',1);
patchNormPlot(F_secondary2,V);

gpatch(F_primary1,V,'bw','k',1);
patchNormPlot(F_primary1,V);

gpatch(F_primary2,V,'cw','k',1);
patchNormPlot(F_primary2,V);

axisGeom;
camlight headlight;
drawnow;

Defining the FEBio input structure

See also febioStructTemplate and febioStruct2xml and the FEBio user manual.

%Get a template with default settings
[febio_spec]=febioStructTemplate;

%febio_spec version
febio_spec.ATTR.version='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='neo-Hookean';
febio_spec.Material.material{1}.ATTR.id=1;
febio_spec.Material.material{1}.E=E_youngs1;
febio_spec.Material.material{1}.v=nu1;

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=1e-9;
febio_spec.Material.material{2}.center_of_mass=mean(V_nut,1);

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(V_bolt,1);

%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='tet4'; %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

partName2='Part2';
febio_spec.Mesh.Elements{2}.ATTR.name=partName2; %Name of this part
febio_spec.Mesh.Elements{2}.ATTR.type='tri3'; %Element type
febio_spec.Mesh.Elements{2}.elem.ATTR.id=size(E,1)+(1:1:size(F_nut,1))'; %Element id's
febio_spec.Mesh.Elements{2}.elem.VAL=F_nut; %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(E,1)+size(F_nut,1)+(1:1:size(F_bolt,1))'; %Element id's
febio_spec.Mesh.Elements{3}.elem.VAL=F_bolt; %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.ATTR.name=partName1;
febio_spec.MeshDomains.SolidDomain.ATTR.mat=materialName1;

febio_spec.MeshDomains.ShellDomain{1}.ATTR.name=partName2;
febio_spec.MeshDomains.ShellDomain{1}.ATTR.mat=materialName2;

febio_spec.MeshDomains.ShellDomain{2}.ATTR.name=partName3;
febio_spec.MeshDomains.ShellDomain{2}.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_primary1,1))';
febio_spec.Mesh.Surface{1}.tri3.VAL=F_primary1;

surfaceName2='contactSurface2';
febio_spec.Mesh.Surface{2}.ATTR.name=surfaceName2;
febio_spec.Mesh.Surface{2}.tri3.ATTR.id=(1:1:size(F_primary2,1))';
febio_spec.Mesh.Surface{2}.tri3.VAL=F_primary2;

surfaceName3='contactSurface3';
febio_spec.Mesh.Surface{3}.ATTR.name=surfaceName3;
febio_spec.Mesh.Surface{3}.tri3.ATTR.id=(1:1:size(F_secondary1,1))';
febio_spec.Mesh.Surface{3}.tri3.VAL=F_secondary1;

surfaceName4='contactSurface4';
febio_spec.Mesh.Surface{4}.ATTR.name=surfaceName4;
febio_spec.Mesh.Surface{4}.tri3.ATTR.id=(1:1:size(F_secondary2,1))';
febio_spec.Mesh.Surface{4}.tri3.VAL=F_secondary2;

% -> Surface pairs
contactPairName1='Contact1';
febio_spec.Mesh.SurfacePair{1}.ATTR.name=contactPairName1;
febio_spec.Mesh.SurfacePair{1}.primary=surfaceName1;
febio_spec.Mesh.SurfacePair{1}.secondary=surfaceName3;

contactPairName2='Contact2';
febio_spec.Mesh.SurfacePair{2}.ATTR.name=contactPairName2;
febio_spec.Mesh.SurfacePair{2}.primary=surfaceName2;
febio_spec.Mesh.SurfacePair{2}.secondary=surfaceName4;

%Boundary condition section
% -> Fix boundary conditions
febio_spec.Boundary.bc{1}.ATTR.name='zero_displacement_xy';
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=0;

%Rigid section
% ->Rigid body fix boundary conditions
febio_spec.Rigid.rigid_bc{1}.ATTR.name='RigidFix_RB2';
febio_spec.Rigid.rigid_bc{1}.ATTR.type='rigid_fixed';
febio_spec.Rigid.rigid_bc{1}.rb=2;
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;

febio_spec.Rigid.rigid_bc{2}.ATTR.name='RigidFix_RB3';
febio_spec.Rigid.rigid_bc{2}.ATTR.type='rigid_fixed';
febio_spec.Rigid.rigid_bc{2}.rb=3;
febio_spec.Rigid.rigid_bc{2}.Rx_dof=1;
febio_spec.Rigid.rigid_bc{2}.Ry_dof=1;
febio_spec.Rigid.rigid_bc{2}.Ru_dof=1;
febio_spec.Rigid.rigid_bc{2}.Rv_dof=1;

% ->Rigid body prescribe boundary conditions
febio_spec.Rigid.rigid_bc{3}.ATTR.name='RigidPrescribed_disp_RB3';
febio_spec.Rigid.rigid_bc{3}.ATTR.type='rigid_displacement';
febio_spec.Rigid.rigid_bc{3}.rb=3;
febio_spec.Rigid.rigid_bc{3}.dof='z';
febio_spec.Rigid.rigid_bc{3}.value.ATTR.lc=1;
febio_spec.Rigid.rigid_bc{3}.value.VAL=prescribedDisplacement_Z;
febio_spec.Rigid.rigid_bc{3}.relative=0;

febio_spec.Rigid.rigid_bc{4}.ATTR.name='RigidPrescribed_rot_RB3';
febio_spec.Rigid.rigid_bc{4}.ATTR.type='rigid_rotation';
febio_spec.Rigid.rigid_bc{4}.rb=3;
febio_spec.Rigid.rigid_bc{4}.dof='Rw';
febio_spec.Rigid.rigid_bc{4}.value.ATTR.lc=1;
febio_spec.Rigid.rigid_bc{4}.value.VAL=prescribedRotation_Z;
febio_spec.Rigid.rigid_bc{4}.relative=0;

%Contact section
febio_spec.Contact.contact{1}.ATTR.surface_pair=contactPairName1;
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;
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;

febio_spec.Contact.contact{2}.ATTR.surface_pair=contactPairName2;
febio_spec.Contact.contact{2}.ATTR.type='sliding-elastic';
febio_spec.Contact.contact{2}.two_pass=1;
febio_spec.Contact.contact{2}.laugon=laugon;
febio_spec.Contact.contact{2}.tolerance=0.2;
febio_spec.Contact.contact{2}.gaptol=0;
febio_spec.Contact.contact{2}.minaug=minaug;
febio_spec.Contact.contact{2}.maxaug=maxaug;
febio_spec.Contact.contact{2}.search_tol=0.01;
febio_spec.Contact.contact{2}.search_radius=0.1*sqrt(sum((max(V,[],1)-min(V,[],1)).^2,2));
febio_spec.Contact.contact{2}.symmetric_stiffness=0;
febio_spec.Contact.contact{2}.auto_penalty=1;
febio_spec.Contact.contact{2}.penalty=contactPenalty;
febio_spec.Contact.contact{2}.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=',';

febio_spec.Output.logfile.element_data{1}.ATTR.file=febioLogFileName_strainEnergy;
febio_spec.Output.logfile.element_data{1}.ATTR.data='sed';
febio_spec.Output.logfile.element_data{1}.ATTR.delim=',';
febio_spec.Output.logfile.element_data{1}.ATTR.elem_set=partName1;

% 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;%'internal';

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

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-------->    RUNNING/MONITORING FEBIO JOB    <-------- 20-Apr-2023 18:03:54
FEBio path: /home/kevin/FEBioStudio2/bin/febio4
# Attempt removal of existing log files                20-Apr-2023 18:03:54
 * Removal succesful                                   20-Apr-2023 18:03:54
# Attempt removal of existing .xplt files              20-Apr-2023 18:03:54
 * Removal succesful                                   20-Apr-2023 18:03:54
# Starting FEBio...                                    20-Apr-2023 18:03:54
  Max. total analysis time is: Inf s
 * Waiting for log file creation                       20-Apr-2023 18:03:54
   Max. wait time: 30 s
 * Log file found.                                     20-Apr-2023 18:03:55
# Parsing log file...                                  20-Apr-2023 18:03:55
    number of iterations   : 12                        20-Apr-2023 18:03:57
    number of reformations : 12                        20-Apr-2023 18:03:57
------- converged at time : 0.05                       20-Apr-2023 18:03:57
    number of iterations   : 9                         20-Apr-2023 18:03:59
    number of reformations : 9                         20-Apr-2023 18:03:59
------- converged at time : 0.1                        20-Apr-2023 18:03:59
    number of iterations   : 15                        20-Apr-2023 18:04:04
    number of reformations : 15                        20-Apr-2023 18:04:04
------- converged at time : 0.15                       20-Apr-2023 18:04:04
    number of iterations   : 26                        20-Apr-2023 18:04:24
    number of reformations : 26                        20-Apr-2023 18:04:24
------- converged at time : 0.191667                   20-Apr-2023 18:04:24
    number of iterations   : 30                        20-Apr-2023 18:04:32
    number of reformations : 30                        20-Apr-2023 18:04:32
------- converged at time : 0.228272                   20-Apr-2023 18:04:32
    number of iterations   : 20                        20-Apr-2023 18:04:38
    number of reformations : 20                        20-Apr-2023 18:04:38
------- converged at time : 0.258252                   20-Apr-2023 18:04:38
    number of iterations   : 26                        20-Apr-2023 18:04:45
    number of reformations : 26                        20-Apr-2023 18:04:45
------- converged at time : 0.288232                   20-Apr-2023 18:04:45
    number of iterations   : 16                        20-Apr-2023 18:04:49
    number of reformations : 16                        20-Apr-2023 18:04:49
------- converged at time : 0.314588                   20-Apr-2023 18:04:49
    number of iterations   : 13                        20-Apr-2023 18:04:52
    number of reformations : 13                        20-Apr-2023 18:04:52
------- converged at time : 0.343735                   20-Apr-2023 18:04:52
    number of iterations   : 16                        20-Apr-2023 18:04:56
    number of reformations : 16                        20-Apr-2023 18:04:56
------- converged at time : 0.377052                   20-Apr-2023 18:04:56
    number of iterations   : 14                        20-Apr-2023 18:04:59
    number of reformations : 14                        20-Apr-2023 18:04:59
------- converged at time : 0.412338                   20-Apr-2023 18:04:59
    number of iterations   : 13                        20-Apr-2023 18:05:02
    number of reformations : 13                        20-Apr-2023 18:05:02
------- converged at time : 0.450497                   20-Apr-2023 18:05:02
    number of iterations   : 9                         20-Apr-2023 18:05:04
    number of reformations : 9                         20-Apr-2023 18:05:04
------- converged at time : 0.491024                   20-Apr-2023 18:05:04
    number of iterations   : 10                        20-Apr-2023 18:05:07
    number of reformations : 10                        20-Apr-2023 18:05:07
------- converged at time : 0.533446                   20-Apr-2023 18:05:07
    number of iterations   : 10                        20-Apr-2023 18:05:09
    number of reformations : 10                        20-Apr-2023 18:05:09
------- converged at time : 0.577383                   20-Apr-2023 18:05:09
    number of iterations   : 13                        20-Apr-2023 18:05:12
    number of reformations : 13                        20-Apr-2023 18:05:12
------- converged at time : 0.622533                   20-Apr-2023 18:05:12
    number of iterations   : 10                        20-Apr-2023 18:05:14
    number of reformations : 10                        20-Apr-2023 18:05:14
------- converged at time : 0.668653                   20-Apr-2023 18:05:14
    number of iterations   : 11                        20-Apr-2023 18:05:16
    number of reformations : 11                        20-Apr-2023 18:05:16
------- converged at time : 0.7                        20-Apr-2023 18:05:16
    number of iterations   : 12                        20-Apr-2023 18:05:20
    number of reformations : 12                        20-Apr-2023 18:05:20
------- converged at time : 0.763066                   20-Apr-2023 18:05:20
    number of iterations   : 10                        20-Apr-2023 18:05:23
    number of reformations : 10                        20-Apr-2023 18:05:23
------- converged at time : 0.811079                   20-Apr-2023 18:05:23
    number of iterations   : 11                        20-Apr-2023 18:05:26
    number of reformations : 11                        20-Apr-2023 18:05:26
------- converged at time : 0.85949                    20-Apr-2023 18:05:26
    number of iterations   : 10                        20-Apr-2023 18:05:29
    number of reformations : 10                        20-Apr-2023 18:05:29
------- converged at time : 0.908218                   20-Apr-2023 18:05:29
    number of iterations   : 10                        20-Apr-2023 18:05:32
    number of reformations : 10                        20-Apr-2023 18:05:32
------- converged at time : 0.957201                   20-Apr-2023 18:05:32
    number of iterations   : 11                        20-Apr-2023 18:05:37
    number of reformations : 11                        20-Apr-2023 18:05:37
------- converged at time : 1                          20-Apr-2023 18:05:37
 Elapsed time : 0:01:42                                20-Apr-2023 18:05:37
 N O R M A L   T E R M I N A T I O N
# Done                                                 20-Apr-2023 18:05:37
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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)]);

Importing element stress from a log file

    dataStruct=importFEBio_logfile(fullfile(savePath,febioLogFileName_strainEnergy),0,1);

    %Access data
    E_energy=dataStruct.data;

Plotting the simulated results using anim8 to visualize and animate deformations

    [CV]=faceToVertexMeasure(E,V,E_energy(:,:,end));

    % Create basic view and store graphics handle to initiate animation
    hf=cFigure; %Open figure
    gtitle([febioFebFileNamePart,': Press play to animate']);
    title('$\Psi$','Interpreter','Latex')
    hp=gpatch(Fb,V_DEF(:,:,end),CV,'k',1); %Add graphics object to animate
    hp.Marker='.';
    hp.MarkerSize=markerSize2;
    hp.FaceColor='interp';

    hp2=gpatch([F_nut;F_bolt],V_DEF(:,:,end),'w','none',0.5); %Add graphics object to animate

    axisGeom(gca,fontSize);
    colormap(gjet(250)); colorbar;
    caxis([0 max(E_energy(:))/4]);
    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

        [CV]=faceToVertexMeasure(E,V,E_energy(:,:,qt));

        %Set entries in animation structure
        animStruct.Handles{qt}=[hp hp hp2]; %Handles of objects to animate
        animStruct.Props{qt}={'Vertices','CData','Vertices'}; %Properties of objects to animate
        animStruct.Set{qt}={V_DEF(:,:,qt),CV,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/.