DEMO_febio_0039_nut_bolt_ring

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;
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;

%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);
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
------>  Geogram/vorpalite for resmeshing  <------ 17-Dec-2020 15:30:25
# Export mesh input file.                          17-Dec-2020 15:30:25
# Run Geomgram/vorpalite.                          17-Dec-2020 15:30:25
 ______________________________________________________________________________ 
|                                                                              |
| o-[config      ] Configuration file name:geogram.ini                         |
|                  Home directory:/root                                        |
| o-[I/O         ] Output = /mnt/data/MATLAB/GIBBON/data/temp/temp_out.obj     |
|                  Loading file /mnt/data/MATLAB/GIBBON/data/temp/temp.obj...  |
|                  (FP64) nb_v:1354 nb_e:0 nb_f:2720 nb_b:1 tri:1 dim:3        |
|                  Attributes on vertices: point[3]                            |
| o-[Load        ] Elapsed time: 0 s                                           |
   ___________________________
 _/ =====[preprocessing]===== \________________________________________________
|                                                                              |
| o-[CmdLine     ] using pre:epsilon=0(0%)                                     |
| o-[Validate    ] Detected 2 duplicate and 5 degenerate facets                |
|                  Detected non-manifold vertices                              |
|                     (fixed by generating 16 new vertices)                    |
|                  (FP64) nb_v:1370 nb_e:0 nb_f:2713 nb_b:23 tri:1 dim:3       |
|                  Attributes on vertices: point[3]                            |
| o-[CmdLine     ] using pre:min_comp_area=3.4132(3%)                          |
| o-[Components  ] Nb connected components=4                                   |
|                  Removed 3 connected components(9 facets)                    |
| o-[CmdLine     ] using pre:epsilon=0(0%)                                     |
| o-[Validate    ] Removed 3 duplicated vertices                               |
|                  (FP64) nb_v:1352 nb_e:0 nb_f:2704 nb_b:0 tri:1 dim:3        |
|                  Attributes on vertices: point[3]                            |
| o-[CmdLine     ] using pre:max_hole_area=100                                 |
| o-[Validate    ] Mesh does not have 0-area facets (good)                     |
| o-[CmdLine     ] using pre:margin=0(0%)                                      |
| o-[Pre         ] Elapsed time: 0 s                                           |
   _______________________
 _/ =====[remeshing]===== \____________________________________________________
|                                                                              |
||| o-[Newton      ] Elapsed time: 0.22s                                         |
| o-[Remesh      ] Computing RVD...                                            |
| o-[Validate    ] (FP64) nb_v:5819 nb_e:0 nb_f:11638 nb_b:0 tri:1 dim:3       |
|                  Attributes on vertices: point[3]                            |
| o-[Remesh      ] Elapsed time: 0.29 s                                        |
   ____________________________
 _/ =====[postprocessing]===== \_______________________________________________
|                                                                              |
| o-[CmdLine     ] using post:min_comp_area=3.21932(3%)                        |
| o-[Components  ] Nb connected components=1                                   |
|                  Mesh does not have small connected component (good)         |
| o-[CmdLine     ] using post:max_hole_area=100                                |
|                  using post:max_deg3_dist=0.00872519(0.10000000000000001%)   |
| o-[Degree3     ] Does not have any degree 3 vertex (good)                    |
| o-[Post        ] Elapsed time: 0 s                                           |
   ____________________
 _/ =====[result]===== \_______________________________________________________
|                                                                              |
| o-[FinalMesh   ] (FP64) nb_v:5819 nb_e:0 nb_f:11638 nb_b:0 tri:1 dim:3       |
|                  Attributes on vertices: point[3]                            |
| o-[I/O         ] Saving file /mnt/data/MATLAB/GIBBON/data/temp/temp_out.obj. |
|                  ..                                                          |
| o-[Total time  ] Elapsed time: 0.81 s                                        |
\______________________________________________________________________________/
# Importing remeshed geometry.                     17-Dec-2020 15:30:26
# Removing temporary files.                        17-Dec-2020 15:30:26
# Done!                                            17-Dec-2020 15:30:26
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
------>  Geogram/vorpalite for resmeshing  <------ 17-Dec-2020 15:30:26
# Export mesh input file.                          17-Dec-2020 15:30:26
# Run Geomgram/vorpalite.                          17-Dec-2020 15:30:26
 ______________________________________________________________________________ 
|                                                                              |
| o-[config      ] Configuration file name:geogram.ini                         |
|                  Home directory:/root                                        |
| o-[I/O         ] Output = /mnt/data/MATLAB/GIBBON/data/temp/temp_out.obj     |
|                  Loading file /mnt/data/MATLAB/GIBBON/data/temp/temp.obj...  |
|                  (FP64) nb_v:2469 nb_e:0 nb_f:4970 nb_b:24 tri:1 dim:3       |
|                  Attributes on vertices: point[3]                            |
| o-[Load        ] Elapsed time: 0 s                                           |
   ___________________________
 _/ =====[preprocessing]===== \________________________________________________
|                                                                              |
| o-[CmdLine     ] using pre:epsilon=0(0%)                                     |
| o-[Validate    ] Detected 0 duplicate and 36 degenerate facets               |
|                  (FP64) nb_v:2469 nb_e:0 nb_f:4934 nb_b:0 tri:1 dim:3        |
|                  Attributes on vertices: point[3]                            |
| o-[CmdLine     ] using pre:min_comp_area=4.61829(3%)                         |
| o-[Components  ] Nb connected components=1                                   |
|                  Mesh does not have small connected component (good)         |
| o-[CmdLine     ] using pre:max_hole_area=100                                 |
| o-[Validate    ] Mesh does not have 0-area facets (good)                     |
| o-[CmdLine     ] using pre:margin=0(0%)                                      |
| o-[Pre         ] Elapsed time: 0 s                                           |
   _______________________
 _/ =====[remeshing]===== \____________________________________________________
|                                                                              |
||| o-[Newton      ] Elapsed time: 0.37s                                         |
| o-[Remesh      ] Computing RVD...                                            |
| o-[Validate    ] (FP64) nb_v:7848 nb_e:0 nb_f:15692 nb_b:0 tri:1 dim:3       |
|                  Attributes on vertices: point[3]                            |
| o-[Remesh      ] Elapsed time: 0.46 s                                        |
   ____________________________
 _/ =====[postprocessing]===== \_______________________________________________
|                                                                              |
| o-[CmdLine     ] using post:min_comp_area=4.27901(3%)                        |
| o-[Components  ] Nb connected components=1                                   |
|                  Mesh does not have small connected component (good)         |
| o-[CmdLine     ] using post:max_hole_area=100                                |
|                  using post:max_deg3_dist=0.011076(0.10000000000000001%)     |
| o-[Degree3     ] Does not have any degree 3 vertex (good)                    |
| o-[Post        ] Elapsed time: 0 s                                           |
   ____________________
 _/ =====[result]===== \_______________________________________________________
|                                                                              |
| o-[FinalMesh   ] (FP64) nb_v:7848 nb_e:0 nb_f:15692 nb_b:0 tri:1 dim:3       |
|                  Attributes on vertices: point[3]                            |
| o-[I/O         ] Saving file /mnt/data/MATLAB/GIBBON/data/temp/temp_out.obj. |
|                  ..                                                          |
| o-[Total time  ] Elapsed time: 1.18 s                                        |
\______________________________________________________________________________/
# Importing remeshed geometry.                     17-Dec-2020 15:30:27
# Removing temporary files.                        17-Dec-2020 15:30:28
# Done!                                            17-Dec-2020 15:30:28
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 --- 17-Dec-2020 15:30:28
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Writing SMESH file --- 17-Dec-2020 15:30:28
----> Adding node field
----> Adding facet field
----> Adding holes specification
----> Adding region specification
--- Done --- 17-Dec-2020 15:30:28
--- Running TetGen to mesh input boundary--- 17-Dec-2020 15:30:28
Opening /mnt/data/MATLAB/GIBBON/data/temp/temp.smesh.
Delaunizing vertices...
Delaunay seconds:  0.036393
Creating surface mesh ...
Surface mesh seconds:  0.002305
Recovering boundaries...
Boundary recovery seconds:  0.003665
Removing exterior tetrahedra ...
Spreading region attributes.
Exterior tets removal seconds:  0.000849
Recovering Delaunayness...
Delaunay recovery seconds:  0.001169
Refining mesh...
Refinement seconds:  0.018766
Optimizing mesh...
Optimization seconds:  0.001577

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:  0.023749
Total running seconds:  0.088624

Statistics:

  Input points: 1091
  Input facets: 2182
  Input segments: 3273
  Input holes: 0
  Input regions: 1

  Mesh points: 2066
  Mesh tetrahedra: 9308
  Mesh faces: 19707
  Mesh faces on exterior boundary: 2182
  Mesh faces on input facets: 2182
  Mesh edges on input segments: 3273
  Steiner points inside domain: 975

--- Done --- 17-Dec-2020 15:30:28
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Importing TetGen files --- 17-Dec-2020 15:30:28
--- Done --- 17-Dec-2020 15:30:28

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='3.0';

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

%Control section
febio_spec.Control.analysis='STATIC';
febio_spec.Control.time_steps=numTimeSteps;
febio_spec.Control.step_size=1/numTimeSteps;
febio_spec.Control.solver.max_refs=max_refs;
febio_spec.Control.solver.max_ups=max_ups;
febio_spec.Control.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}.node.ATTR.id=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.type='fix';
febio_spec.Boundary.bc{1}.ATTR.node_set=nodeSetName1;
febio_spec.Boundary.bc{1}.dofs='x,y';

%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';

febio_spec.Rigid.rigid_constraint{2}.ATTR.name='RigidFix_1';
febio_spec.Rigid.rigid_constraint{2}.ATTR.type='fix';
febio_spec.Rigid.rigid_constraint{2}.rb=3;
febio_spec.Rigid.rigid_constraint{2}.dofs='Rx,Ry,Ru,Rv';

febio_spec.Rigid.rigid_constraint{3}.ATTR.name='RigidPrescribe';
febio_spec.Rigid.rigid_constraint{3}.ATTR.type='prescribe';
febio_spec.Rigid.rigid_constraint{3}.rb=3;
febio_spec.Rigid.rigid_constraint{3}.dof='Rz';
febio_spec.Rigid.rigid_constraint{3}.value.ATTR.lc=1;
febio_spec.Rigid.rigid_constraint{3}.value.VAL=prescribedDisplacement_Z;
febio_spec.Rigid.rigid_constraint{3}.relative=0;

febio_spec.Rigid.rigid_constraint{4}.ATTR.name='RigidPrescribe';
febio_spec.Rigid.rigid_constraint{4}.ATTR.type='prescribe';
febio_spec.Rigid.rigid_constraint{4}.rb=3;
febio_spec.Rigid.rigid_constraint{4}.dof='Rw';
febio_spec.Rigid.rigid_constraint{4}.value.ATTR.lc=1;
febio_spec.Rigid.rigid_constraint{4}.value.VAL=prescribedRotation_Z;
febio_spec.Rigid.rigid_constraint{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;
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.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=',';

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;

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    <-------- 17-Dec-2020 15:30:37
FEBio path: /home/kevin/FEBioStudio/bin/febio3
# Attempt removal of existing log files                17-Dec-2020 15:30:37
 * Removal succesful                                   17-Dec-2020 15:30:37
# Attempt removal of existing .xplt files              17-Dec-2020 15:30:37
 * Removal succesful                                   17-Dec-2020 15:30:37
# Starting FEBio...                                    17-Dec-2020 15:30:37
  Max. total analysis time is: Inf s
 * Waiting for log file creation                       17-Dec-2020 15:30:37
   Max. wait time: 30 s
 * Log file found.                                     17-Dec-2020 15:30:38
# Parsing log file...                                  17-Dec-2020 15:30:38
    number of iterations   : 12                        17-Dec-2020 15:30:40
    number of reformations : 12                        17-Dec-2020 15:30:40
------- converged at time : 0.05                       17-Dec-2020 15:30:40
    number of iterations   : 9                         17-Dec-2020 15:30:42
    number of reformations : 9                         17-Dec-2020 15:30:42
------- converged at time : 0.1                        17-Dec-2020 15:30:42
    number of iterations   : 14                        17-Dec-2020 15:30:46
    number of reformations : 14                        17-Dec-2020 15:30:46
------- converged at time : 0.15                       17-Dec-2020 15:30:46
    number of iterations   : 27                        17-Dec-2020 15:31:20
    number of reformations : 27                        17-Dec-2020 15:31:20
------- converged at time : 0.183333                   17-Dec-2020 15:31:20
    number of iterations   : 22                        17-Dec-2020 15:31:25
    number of reformations : 22                        17-Dec-2020 15:31:25
------- converged at time : 0.212092                   17-Dec-2020 15:31:25
    number of iterations   : 21                        17-Dec-2020 15:31:30
    number of reformations : 21                        17-Dec-2020 15:31:30
------- converged at time : 0.239535                   17-Dec-2020 15:31:30
    number of iterations   : 25                        17-Dec-2020 15:31:37
    number of reformations : 25                        17-Dec-2020 15:31:37
------- converged at time : 0.266329                   17-Dec-2020 15:31:37
    number of iterations   : 12                        17-Dec-2020 15:31:40
    number of reformations : 12                        17-Dec-2020 15:31:40
------- converged at time : 0.290347                   17-Dec-2020 15:31:40
    number of iterations   : 17                        17-Dec-2020 15:31:44
    number of reformations : 17                        17-Dec-2020 15:31:44
------- converged at time : 0.319562                   17-Dec-2020 15:31:44
    number of iterations   : 11                        17-Dec-2020 15:31:46
    number of reformations : 11                        17-Dec-2020 15:31:46
------- converged at time : 0.350536                   17-Dec-2020 15:31:46
    number of iterations   : 9                         17-Dec-2020 15:31:49
    number of reformations : 9                         17-Dec-2020 15:31:49
------- converged at time : 0.385315                   17-Dec-2020 15:31:49
    number of iterations   : 9                         17-Dec-2020 15:31:51
    number of reformations : 9                         17-Dec-2020 15:31:51
------- converged at time : 0.423138                   17-Dec-2020 15:31:51
    number of iterations   : 8                         17-Dec-2020 15:31:53
    number of reformations : 8                         17-Dec-2020 15:31:53
------- converged at time : 0.463397                   17-Dec-2020 15:31:53
    number of iterations   : 9                         17-Dec-2020 15:31:55
    number of reformations : 9                         17-Dec-2020 15:31:55
------- converged at time : 0.505604                   17-Dec-2020 15:31:55
    number of iterations   : 9                         17-Dec-2020 15:31:57
    number of reformations : 9                         17-Dec-2020 15:31:57
------- converged at time : 0.54937                    17-Dec-2020 15:31:57
    number of iterations   : 10                        17-Dec-2020 15:31:59
    number of reformations : 10                        17-Dec-2020 15:31:59
------- converged at time : 0.594382                   17-Dec-2020 15:31:59
    number of iterations   : 10                        17-Dec-2020 15:32:01
    number of reformations : 10                        17-Dec-2020 15:32:01
------- converged at time : 0.640392                   17-Dec-2020 15:32:01
    number of iterations   : 9                         17-Dec-2020 15:32:03
    number of reformations : 9                         17-Dec-2020 15:32:03
------- converged at time : 0.6872                     17-Dec-2020 15:32:03
    number of iterations   : 10                        17-Dec-2020 15:32:05
    number of reformations : 10                        17-Dec-2020 15:32:05
------- converged at time : 0.734646                   17-Dec-2020 15:32:05
    number of iterations   : 9                         17-Dec-2020 15:32:07
    number of reformations : 9                         17-Dec-2020 15:32:07
------- converged at time : 0.782603                   17-Dec-2020 15:32:07
    number of iterations   : 10                        17-Dec-2020 15:32:10
    number of reformations : 10                        17-Dec-2020 15:32:10
------- converged at time : 0.830969                   17-Dec-2020 15:32:10
    number of iterations   : 10                        17-Dec-2020 15:32:12
    number of reformations : 10                        17-Dec-2020 15:32:12
------- converged at time : 0.879662                   17-Dec-2020 15:32:12
    number of iterations   : 12                        17-Dec-2020 15:32:15
    number of reformations : 12                        17-Dec-2020 15:32:15
------- converged at time : 0.928616                   17-Dec-2020 15:32:15
    number of iterations   : 10                        17-Dec-2020 15:32:17
    number of reformations : 10                        17-Dec-2020 15:32:17
------- converged at time : 0.977779                   17-Dec-2020 15:32:17
    number of iterations   : 8                         17-Dec-2020 15:32:19
    number of reformations : 8                         17-Dec-2020 15:32:19
------- converged at time : 1                          17-Dec-2020 15:32:19
 Elapsed time : 0:01:42                                17-Dec-2020 15:32:19
 N O R M A L   T E R M I N A T I O N
# Done                                                 17-Dec-2020 15:32:19
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Import FEBio results

if runFlag==1 %i.e. a succesful run

Importing nodal displacements from a log file

    dataStruct=importFEBio_logfile(fullfile(savePath,febioLogFileName_disp),1,1);

    %Access data
    N_disp_mat=dataStruct.data; %Displacement
    timeVec=dataStruct.time; %Time
    %Create deformed coordinate set
    V_DEF=N_disp_mat+repmat(V,[1 1 size(N_disp_mat,3)]);

Importing element stress from a log file

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

    %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([min(E_energy(:)) max(E_energy(:))]);
    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, gibbon.toolbox@gmail.com

GIBBON footer text

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

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

Copyright (C) 2006-2020 Kevin Mattheus Moerman

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

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

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