DEMO_febio_0031_blob_shear_contact

Below is a demonstration for:

Building geometry for a hemi-spherical blob with tetrahedral elements which is being sheared by a rigid wall. This demo consists off:
Defining the boundary conditions
Coding the febio structure
Running the model
Importing and visualizing the displacement results

Keywords
Plot settings
Control parameters
Creating model geometry and mesh
Creating rigid body ground plate
Creating rigid body shear surface
Join model node sets
Get 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
tetrahedral elements, tet4
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;

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

% Hemi-sphere parameters
hemiSphereRadius=1;
nRefine=2;
closeOption=1;
smoothEdge=1;

% Ground plate parameters
plateRadius=2*hemiSphereRadius;

% Probe parameters
probeWidth=3*hemiSphereRadius;
filletProbe=0.25; %Fillet radius

% Define probe displacement
probeDisplacement=hemiSphereRadius*2;
probeOverlapFactor=0.4;

% Material parameter set
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

% FEA control settings
numTimeSteps=30;
max_refs=25; %Max reforms
max_ups=0; %Set to zero to use full-Newton iterations
opt_iter=10; %Optimum number of iterations
max_retries=25; %Maximum number of retires
symmetric_stiffness=0;
min_residual=1e-20;
step_size=1/numTimeSteps;
dtmin=(1/numTimeSteps)/100; %Minimum time step size
dtmax=(1/(numTimeSteps)); %Maximum time step size

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

%Contact parameters
contactPenalty=1;
laugon=0;
minaug=1;
maxaug=10;
fric_coeff=0.01;
max_traction=0;

Creating model geometry and mesh

% Create hemi-sphere mesh
[F_blob,V_blob,C_blob]=hemiSphereMesh(nRefine,hemiSphereRadius,1);
pointSpacingBlob=mean(patchEdgeLengths(F_blob,V_blob));

%Smoothen edges
if smoothEdge==1
    %Get rigid region
    ind=1:1:size(V_blob,1); %Indices for all nodes
    indRigid=find(ismember(ind,F_blob(C_blob==2,:)) & ~ismember(ind,F_blob(C_blob==1,:))); %Indices for new bottom surface nodes

    %Smoothing
    cPar.Method='HC';
    cPar.n=250;
    cPar.RigidConstraints=indRigid;
    [V_blob]=patchSmooth(F_blob,V_blob,[],cPar);

    %Fix color data with new bottom surface
    C_blob=ones(size(C_blob));
    C_blob(all(ismember(F_blob,indRigid),2))=2;

end

Visualize hemi-sphere surface

cFigure; hold on;
gtitle('The hemi-sphere surface mesh',fontSize);
gpatch(F_blob,V_blob,C_blob,'k',0.85);
patchNormPlot(F_blob,V_blob);
axisGeom(gca,fontSize);
colormap(gjet); icolorbar;
camlight headlight;
drawnow;

Using tetgen to create a tetrahedral mesh

% Tetgen input structure
inputStruct.stringOpt='-pq1.2AaY';
inputStruct.Faces=F_blob;
inputStruct.Nodes=V_blob;
inputStruct.holePoints=[];
inputStruct.faceBoundaryMarker=C_blob; %Face boundary markers
inputStruct.regionPoints=getInnerPoint(F_blob,V_blob); %region points
inputStruct.regionA=tetVolMeanEst(F_blob,V_blob);
inputStruct.minRegionMarker=2; %Minimum region marker

% Create tetrahedral mesh using tetGen
[meshOutput]=runTetGen(inputStruct); %Run tetGen

% Access model element and patch data
Fb_blob=fliplr(meshOutput.facesBoundary);
Cb_blob=meshOutput.boundaryMarker;
V_blob=meshOutput.nodes;
E_blob=meshOutput.elements;

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- TETGEN Tetrahedral meshing --- 20-Apr-2023 11:35:54
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Writing SMESH file --- 20-Apr-2023 11:35:54
----> Adding node field
----> Adding facet field
----> Adding holes specification
----> Adding region specification
--- Done --- 20-Apr-2023 11:35:54
--- Running TetGen to mesh input boundary--- 20-Apr-2023 11:35:54
Opening /mnt/data/MATLAB/GIBBON/data/temp/temp.smesh.
Delaunizing vertices...
Delaunay seconds:  0.002067
Creating surface mesh ...
Surface mesh seconds:  0.000757
Recovering boundaries...
Boundary recovery seconds:  0.000926
Removing exterior tetrahedra ...
Spreading region attributes.
Exterior tets removal seconds:  0.00028
Recovering Delaunayness...
Delaunay recovery seconds:  0.000508
Refining mesh...
  634 insertions, added 526 points, 16457 tetrahedra in queue.
  211 insertions, added 164 points, 19804 tetrahedra in queue.
  281 insertions, added 193 points, 22682 tetrahedra in queue.
  374 insertions, added 195 points, 19304 tetrahedra in queue.
  499 insertions, added 99 points, 452 tetrahedra in queue.
Refinement seconds:  0.022635
Smoothing vertices...
Mesh smoothing seconds:  0.042211
Improving mesh...
Mesh improvement seconds:  0.00171

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:  0.014534
Total running seconds:  0.085729

Statistics:

  Input points: 476
  Input facets: 948
  Input segments: 1422
  Input holes: 0
  Input regions: 1

  Mesh points: 1662
  Mesh tetrahedra: 8647
  Mesh faces: 17768
  Mesh faces on exterior boundary: 948
  Mesh faces on input facets: 948
  Mesh edges on input segments: 1422
  Steiner points inside domain: 1186

--- Done --- 20-Apr-2023 11:35:54
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Importing TetGen files --- 20-Apr-2023 11:35:54
--- Done --- 20-Apr-2023 11:35:54

Visualize blob mesh

hFig=cFigure;
subplot(1,2,1); hold on;
gpatch(Fb_blob,V_blob,Cb_blob,'k',1);
patchNormPlot(Fb_blob,V_blob);
axisGeom(gca,fontSize);
colormap(gjet); icolorbar;
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(meshOutput,optionStruct);
axisGeom(gca,fontSize);
drawnow;

Creating rigid body ground plate

%Get outer surve of ground surface
[Eb]=patchBoundary(Fb_blob(Cb_blob==2,:));
indCurveBottom=edgeListToCurve(Eb);
indCurveBottom=indCurveBottom(1:end-1);

% Derive point spacing for plate
pointSpacingPlate=pointSpacingBlob;

% Compose outer curve of the plate
nPlateCurve=ceil((2*pi*plateRadius)/pointSpacingPlate);
t=linspace(0,2*pi,nPlateCurve);
t=t(1:end-1);
x=plateRadius.*sin(t);
y=plateRadius.*cos(t);
Vp_outer_curve=[x(:) y(:)];

% Copy inner curve from the hemi-sphere
Vp_inner_curve=V_blob(indCurveBottom,[1 2]);

% Create mesh out outer region
regionCell={Vp_outer_curve,Vp_inner_curve};
[F_plate,V_plate]=regionTriMesh2D(regionCell,pointSpacingPlate,0,0);
V_plate(:,3)=0; %Add z-direction

% Copy mesh for inner region
[F_plate_inner,V_plate_inner]=patchCleanUnused(fliplr(Fb_blob(Cb_blob==2,:)),V_blob);
[F_plate,V_plate,C_plate]=joinElementSets({F_plate,F_plate_inner},{V_plate,V_plate_inner});
[F_plate,V_plate]=mergeVertices(F_plate,V_plate);

center_of_mass_plate=mean(V_plate,1);

Visualizing plate mesh

cFigure; hold on;
gtitle('The plate surface mesh',fontSize);
gpatch(Fb_blob,V_blob,'kw','none',0.5);
gpatch(F_plate,V_plate,C_plate,'k',1);
patchNormPlot(F_plate,V_plate);
axisGeom(gca,fontSize);
colormap(gjet); icolorbar;
camlight headlight;
drawnow;

Creating rigid body shear surface

pointSpacingProbe=pointSpacingBlob/2;

%Sketching side profile
x=[-hemiSphereRadius hemiSphereRadius hemiSphereRadius]-hemiSphereRadius*2;
y=[0 0 0];
z=[hemiSphereRadius*(1-probeOverlapFactor) hemiSphereRadius*(1-probeOverlapFactor) hemiSphereRadius*1.5];
V_probe_curve_sketch=[x(:) y(:) z(:)];

%Fillet sketch
np=100; %Number of points used to construct each fillet edge
[V_probe_curve]=filletCurve(V_probe_curve_sketch,filletProbe,np,0);
numPointsProbeCurve=ceil(max(pathLength(V_probe_curve))/pointSpacingProbe);
[V_probe_curve] = evenlySampleCurve(V_probe_curve,numPointsProbeCurve,'pchip',0);

% Extruding curve
% controlParametersExtrude.pointSpacing=pointSpacingProbe;
controlParametersExtrude.depth=hemiSphereRadius*2.5;
controlParametersExtrude.numSteps=ceil(controlParametersExtrude.depth/pointSpacingProbe);
controlParametersExtrude.numSteps=controlParametersExtrude.numSteps+iseven(controlParametersExtrude.numSteps); %Force uneven
controlParametersExtrude.patchType='tri';
controlParametersExtrude.dir=0;
controlParametersExtrude.n=[0 1 0];
controlParametersExtrude.closeLoopOpt=0;

[F_probe,V_probe]=polyExtrude(V_probe_curve,controlParametersExtrude);
F_probe=fliplr(F_probe); %Invert face orientation so normals point to blob

center_of_mass_probe=mean(V_probe,1);

Visualizing probe mesh

cFigure; hold on;
title('The probe surface mesh','fontSize',fontSize);
gpatch(Fb_blob,V_blob,'kw','none',0.5);
gpatch(F_plate,V_plate,'kw','none',0.5);
hl(1)=plotV(V_probe_curve_sketch,'k.-.','lineWidth',3,'MarkerSize',25);
hl(2)=plotV(V_probe_curve,'r-','lineWidth',3,'MarkerSize',25);
hl(3)=gpatch(F_probe,V_probe,'gw','k',1);
legend(hl,{'Sketched probe curve','Rounded probe curve','Probe surface mesh'}); clear hl;
axisGeom(gca,fontSize);
camlight headlight;
drawnow;

Join model node sets

V=[V_blob; V_plate; V_probe];
F_plate=F_plate+size(V_blob,1);
F_probe=F_probe+size(V_blob,1)+size(V_plate,1);
Fb_all=[Fb_blob;F_plate;F_probe];

Visualizing model

cFigure; hold on;
gtitle('Model components',fontSize);
hl(1)=gpatch(Fb_blob,V,'rw','k',0.8);
hl(2)=gpatch(F_plate,V,'bw','k',0.8);
hl(3)=gpatch(F_probe,V,'gw','k',0.8);
legend(hl,{'Blob','Plate','Probe'}); clear hl;
axisGeom(gca,fontSize);
camlight headlight;
drawnow;

Get contact surfaces

% F_contact_blob1=Fb_blob(Cb_blob==1,:);
% F_contact_blob2=Fb_blob(Cb_blob==2,:);

Visualize contact surfaces

cFigure;
subplot(1,2,1); hold on;
title('Probe blob contact pair','fontsize',fontSize);
hl(1)=gpatch(F_probe,V,'rw','k',1);
patchNormPlot(F_probe,V);
hl(2)=gpatch(Fb_blob,V,'gw','k',1);
patchNormPlot(Fb_blob,V);
legend(hl,{'secondary','primary'}); clear hl;
axisGeom(gca,fontSize);
camlight headlight;

subplot(1,2,2); hold on;
title('Plate blob contact pair','fontsize',fontSize);
hl(1)=gpatch(F_plate,V,'rw','k',1);
patchNormPlot(F_plate,V);
hl(2)=gpatch(Fb_blob,V,'gw','k',1);
patchNormPlot(Fb_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='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='Ogden';
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}.k=k;

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_plate;

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=1;
febio_spec.Material.material{3}.center_of_mass=center_of_mass_probe;

%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_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='tri3'; %Element type
febio_spec.Mesh.Elements{2}.elem.ATTR.id=size(E_blob,1)+(1:1:size(F_plate,1))'; %Element id's
febio_spec.Mesh.Elements{2}.elem.VAL=F_plate;

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_blob,1)+size(F_plate,1)+(1:1:size(F_probe,1))'; %Element id's
febio_spec.Mesh.Elements{3}.elem.VAL=F_probe;

%MeshDomains section
febio_spec.MeshDomains.SolidDomain{1}.ATTR.name=partName1;
febio_spec.MeshDomains.SolidDomain{1}.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_plate,1))';
febio_spec.Mesh.Surface{1}.tri3.VAL=F_plate;

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

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

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

% -> Surface pairs
contactPairName1='Contact1';
febio_spec.Mesh.SurfacePair{1}.ATTR.name=contactPairName1;
febio_spec.Mesh.SurfacePair{1}.primary=surfaceName2;
febio_spec.Mesh.SurfacePair{1}.secondary=surfaceName1;

contactPairName2='Contact2';
febio_spec.Mesh.SurfacePair{2}.ATTR.name=contactPairName2;
febio_spec.Mesh.SurfacePair{2}.primary=surfaceName4;
febio_spec.Mesh.SurfacePair{2}.secondary=surfaceName3;

%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=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_2';
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}.Rz_dof=1;
febio_spec.Rigid.rigid_bc{2}.Ru_dof=1;
febio_spec.Rigid.rigid_bc{2}.Rv_dof=1;
febio_spec.Rigid.rigid_bc{2}.Rw_dof=1;

% ->Rigid body prescribe boundary conditions
febio_spec.Rigid.rigid_bc{3}.ATTR.name='RigidPrescribe';
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='x';
febio_spec.Rigid.rigid_bc{3}.value.ATTR.lc=1;
febio_spec.Rigid.rigid_bc{3}.value.VAL=probeDisplacement;
febio_spec.Rigid.rigid_bc{3}.relative=0;

%Contact section
% -> Contact 1
febio_spec.Contact.contact{1}.ATTR.type='sticky';
febio_spec.Contact.contact{1}.ATTR.surface_pair=contactPairName1;
febio_spec.Contact.contact{1}.penalty=10;
febio_spec.Contact.contact{1}.laugon=0;
febio_spec.Contact.contact{1}.tolerance=0.1;
febio_spec.Contact.contact{1}.minaug=1;
febio_spec.Contact.contact{1}.maxaug=10;
febio_spec.Contact.contact{1}.snap_tol=0;
febio_spec.Contact.contact{1}.max_traction=max_traction;
febio_spec.Contact.contact{1}.search_tolerance=0.1;

febio_spec.Contact.contact{2}.ATTR.type='sliding-elastic';
febio_spec.Contact.contact{2}.ATTR.surface_pair=contactPairName2;
febio_spec.Contact.contact{2}.two_pass=0;
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=',';

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='external';%'internal';

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

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-------->    RUNNING/MONITORING FEBIO JOB    <-------- 20-Apr-2023 11:36:05
FEBio path: /home/kevin/FEBioStudio2/bin/febio4
# Attempt removal of existing log files                20-Apr-2023 11:36:05
 * Removal succesful                                   20-Apr-2023 11:36:05
# Attempt removal of existing .xplt files              20-Apr-2023 11:36:05
 * Removal succesful                                   20-Apr-2023 11:36:05
# Starting FEBio...                                    20-Apr-2023 11:36:05
  Max. total analysis time is: Inf s
 * Waiting for log file creation                       20-Apr-2023 11:36:05
   Max. wait time: 30 s
 * Log file found.                                     20-Apr-2023 11:36:05
# Parsing log file...                                  20-Apr-2023 11:36:05
    number of reformations : 1                         20-Apr-2023 11:36:06
------- converged at time : 0.0333333                  20-Apr-2023 11:36:06
    number of iterations   : 1                         20-Apr-2023 11:36:06
    number of reformations : 1                         20-Apr-2023 11:36:06
------- converged at time : 0.0666667                  20-Apr-2023 11:36:06
    number of iterations   : 1                         20-Apr-2023 11:36:06
    number of reformations : 1                         20-Apr-2023 11:36:06
------- converged at time : 0.1                        20-Apr-2023 11:36:06
    number of iterations   : 1                         20-Apr-2023 11:36:06
    number of reformations : 1                         20-Apr-2023 11:36:06
------- converged at time : 0.133333                   20-Apr-2023 11:36:06
    number of iterations   : 1                         20-Apr-2023 11:36:07
    number of reformations : 1                         20-Apr-2023 11:36:07
------- converged at time : 0.166667                   20-Apr-2023 11:36:07
    number of iterations   : 5                         20-Apr-2023 11:36:07
    number of reformations : 5                         20-Apr-2023 11:36:07
------- converged at time : 0.2                        20-Apr-2023 11:36:07
    number of iterations   : 5                         20-Apr-2023 11:36:08
    number of reformations : 5                         20-Apr-2023 11:36:08
------- converged at time : 0.233333                   20-Apr-2023 11:36:08
    number of iterations   : 5                         20-Apr-2023 11:36:08
    number of reformations : 5                         20-Apr-2023 11:36:08
------- converged at time : 0.266667                   20-Apr-2023 11:36:08
    number of iterations   : 5                         20-Apr-2023 11:36:09
    number of reformations : 5                         20-Apr-2023 11:36:09
------- converged at time : 0.3                        20-Apr-2023 11:36:09
    number of iterations   : 6                         20-Apr-2023 11:36:09
    number of reformations : 6                         20-Apr-2023 11:36:09
------- converged at time : 0.333333                   20-Apr-2023 11:36:09
    number of iterations   : 6                         20-Apr-2023 11:36:10
    number of reformations : 6                         20-Apr-2023 11:36:10
------- converged at time : 0.366667                   20-Apr-2023 11:36:10
    number of iterations   : 6                         20-Apr-2023 11:36:11
    number of reformations : 6                         20-Apr-2023 11:36:11
------- converged at time : 0.4                        20-Apr-2023 11:36:11
    number of iterations   : 6                         20-Apr-2023 11:36:12
    number of reformations : 6                         20-Apr-2023 11:36:12
------- converged at time : 0.433333                   20-Apr-2023 11:36:12
    number of iterations   : 6                         20-Apr-2023 11:36:13
    number of reformations : 6                         20-Apr-2023 11:36:13
------- converged at time : 0.466667                   20-Apr-2023 11:36:13
    number of iterations   : 6                         20-Apr-2023 11:36:13
    number of reformations : 6                         20-Apr-2023 11:36:13
------- converged at time : 0.5                        20-Apr-2023 11:36:13
    number of iterations   : 6                         20-Apr-2023 11:36:14
    number of reformations : 6                         20-Apr-2023 11:36:14
------- converged at time : 0.533333                   20-Apr-2023 11:36:14
    number of iterations   : 7                         20-Apr-2023 11:36:15
    number of reformations : 7                         20-Apr-2023 11:36:15
------- converged at time : 0.566667                   20-Apr-2023 11:36:15
    number of iterations   : 7                         20-Apr-2023 11:36:15
    number of reformations : 7                         20-Apr-2023 11:36:15
------- converged at time : 0.6                        20-Apr-2023 11:36:15
    number of iterations   : 7                         20-Apr-2023 11:36:16
    number of reformations : 7                         20-Apr-2023 11:36:16
------- converged at time : 0.633333                   20-Apr-2023 11:36:16
    number of iterations   : 7                         20-Apr-2023 11:36:17
    number of reformations : 7                         20-Apr-2023 11:36:17
------- converged at time : 0.666667                   20-Apr-2023 11:36:17
    number of iterations   : 7                         20-Apr-2023 11:36:18
    number of reformations : 7                         20-Apr-2023 11:36:18
------- converged at time : 0.7                        20-Apr-2023 11:36:18
    number of iterations   : 6                         20-Apr-2023 11:36:19
    number of reformations : 6                         20-Apr-2023 11:36:19
------- converged at time : 0.733333                   20-Apr-2023 11:36:19
    number of iterations   : 7                         20-Apr-2023 11:36:20
    number of reformations : 7                         20-Apr-2023 11:36:20
------- converged at time : 0.766667                   20-Apr-2023 11:36:20
    number of iterations   : 6                         20-Apr-2023 11:36:21
    number of reformations : 6                         20-Apr-2023 11:36:21
------- converged at time : 0.8                        20-Apr-2023 11:36:21
    number of iterations   : 6                         20-Apr-2023 11:36:21
    number of reformations : 6                         20-Apr-2023 11:36:21
------- converged at time : 0.833333                   20-Apr-2023 11:36:21
    number of iterations   : 6                         20-Apr-2023 11:36:22
    number of reformations : 6                         20-Apr-2023 11:36:22
------- converged at time : 0.866667                   20-Apr-2023 11:36:22
    number of iterations   : 6                         20-Apr-2023 11:36:23
    number of reformations : 6                         20-Apr-2023 11:36:23
------- converged at time : 0.9                        20-Apr-2023 11:36:23
    number of iterations   : 6                         20-Apr-2023 11:36:23
    number of reformations : 6                         20-Apr-2023 11:36:23
------- converged at time : 0.933333                   20-Apr-2023 11:36:23
    number of iterations   : 6                         20-Apr-2023 11:36:24
    number of reformations : 6                         20-Apr-2023 11:36:24
------- converged at time : 0.966667                   20-Apr-2023 11:36:24
    number of iterations   : 5                         20-Apr-2023 11:36:25
    number of reformations : 5                         20-Apr-2023 11:36:25
------- converged at time : 1                          20-Apr-2023 11:36:25
 Elapsed time : 0:00:19                                20-Apr-2023 11:36:25
 N O R M A L   T E R M I N A T I O N
# Done                                                 20-Apr-2023 11:36:25
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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; hold on;
    gtitle([febioFebFileNamePart,': Press play to animate']);
    hp1=gpatch(Fb_blob,V_DEF(:,:,end),DN_magnitude,'k',1); %Add graphics object to animate
    hp1.FaceColor='interp';
    hp2=gpatch(F_probe,V_DEF(:,:,end),'kw','none',0.5); %Add graphics object to animate
    hp3=gpatch(F_plate,V_DEF(:,:,end),'kw','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}=[hp1 hp1 hp2 hp3]; %Handles of objects to animate
        animStruct.Props{qt}={'Vertices','CData','Vertices','Vertices'}; %Properties of objects to animate
        animStruct.Set{qt}={V_DEF(:,:,qt),DN_magnitude,V_DEF(:,:,qt),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/.