IA-FEMesh Manual Version1

Us sersManual
IA FEMesh A-F h
Version1.0 0 MIMXLaborato ory CenterforComputerAidedDes sign EngineeringRes searchFacility TheUniversityo ofIowa IowaCity,IA www.ccad.uiow wa.edu/mimx/IA AFEMesh
August2008
IA-FEMesh
Version1.0 Users Manual
IA-FEMesh
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IA-FEMesh

CopyrightandPermissionNotice Copyright2008MIMX,TheUniversityofIowa Allrightsreserved. Permissionisherebygranted,freeofcharge,toanypersonobtainingacopyofthisdocument(the"Document"),todealinthe Documentwithoutrestriction,includingwithoutlimitationtherightstouse,copy,distribute,and/ortopermitpersonsto whomtheDocumentisfurnishedtodoso,subjecttothefollowingconditions: ThiscopyrightandpermissionnoticeshallbeincludedinallcopiesorsubstantialportionsoftheDocument. THEDOCUMENTISPROVIDED"ASIS",WITHOUTWARRANTYOFANYKIND,EXPRESSORIMPLIED,INCLUDINGBUTNOTLIMITED TOTHEWARRANTIESOFMERCHANTABILITY,FITNESSFORAPARTICULARPURPOSEANDNONINFRINGEMENTOFTHIRDPARTY RIGHTS.INNOEVENTSHALLTHEAUTHORS,CONTRIBUTORSORCOPYRIGHTHOLDERSBELIABLEFORANYCLAIM,ORANY SPECIALINDIRECTORCONSEQUENTIALDAMAGES,ORANYDAMAGESWHATSOEVERRESULTINGFROMLOSSOFUSE,DATAOR PROFITS,WHETHERINANACTIONOFCONTRACT,NEGLIGENCEOROTHERTORTIOUSACTION,ARISINGOUTOFORIN CONNECTIONWITHTHEDOCUMENTORTHEUSEOROTHERDEALINGSINTHEDOCUMENT.
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IA-FEMesh
Acknowledgements IAFEMesh was an ambitious undertaking that required the contribution of a myriad of talented and dedicated individuals.TheMusculoskeletalImaging,Modeling,andExperimentation(MIMX)ProgramatTheUniversityof Iowa consists of a multidisciplinary team of faculty, staff, and students from the Departments of Biomedical Engineering, Orthopaedics and Rehabilitation, and Radiology. Accordingly, I would like to acknowledge several individualswhoseassistanceandperseverancemadeIAFEMeshpossible.Twoindividualswereindispensiblein the development of this work. Kiran Shivanna, PhD. and VincentMagnotta, Ph.D. spentcountless hours coding andrecodingtomeetthegoalsofIAFEMesh. Iwouldalsoliketoacknowledgeseveralindividualswhoplayedvitalrolesinthedevelopmentandevaluationof thesoftware,aswellaseditingthemanualforconsistency:NicoleKallemeyn,M.S.,NicoleDeVries,M.S.,Srinivas Tadepalli, M.S., Ritesh Bafna, M.S., Anup Gandhi, B.S., Jacalyn Grosland, M.S., Mary Beth Russell, M.S., Kristin Brandt,andthestudentsenrolledintheFall2007offeringof051:157IntrotoAppliedBiomedicalFEModeling. IamindebtedtoeachoftheseindividualsfortheircontributionsandunwaveringsupportofIAFEMesh.
N.M.Grosland
TheMIMXProgramgratefullyacknowledgesfinancialsupportprovidedbyawardsR21EB001501andR01EB005973 fromtheNationalInstituteofBiomedicalImagingandBioengineering,NationalInstitutesofHealth.
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Table of Contents
TableofContents
1IntroductiontoIAFEMesh.............................................................................................................................1 1.1Overview............................................................................................................................................................. 2 1.2AboutthisManual.............................................................................................................................................. 2 1.2.1OrganizationoftheDocument.................................................................................................................... 2 1.2.2ConventionsUsedThroughouttheDocumentandSoftware...................................................................... 2 1.3InstallingandRunningIAFEMesh...................................................................................................................... 3 2InterfacingwithIAFEMesh.............................................................................................................................5 2.1Overview............................................................................................................................................................. 6 2.2TheMainToolbar................................................................................................................................................ 6 2.2.1ApplicationSettings.................................................................................................................................... 7 2.2.2ViewSettings............................................................................................................................................... 8 2.3TheViewPanel................................................................................................................................................... 9 2.4TheCommandPanel........................................................................................................................................... 9 2.5TheObjectManager......................................................................................................................................... 0 1 2.5.1Viewing/ActivatinganObject................................................................................................................... 0 1 2.5.2NamingConvention .................................................................................................................................. 0 . 1 2.5.3AdjustingtheDisplayPropertiesofanObject........................................................................................... 1 1 2.6TheTabbedPanels............................................................................................................................................ 3 1 2.6.1Loading/Saving/DeletinganObject.......................................................................................................... 3 1 2.6.2ExportingaFileinABAQUSFormat(.inp)................................................................................................. 3 1 2.6.3TheImportanceoftheCollapsedFrame................................................................................................... 3 1 2.6.4Apply/CancelanOperation..................................................................................................................... 4 1 3IAFEMeshTutorial........................................................................................................................................ 5 1 3.1Example:Creatingameshofananatomicstructure....................................................................................... 6 1 4TheImagePanel............................................................................................................................................ 9 2 4.1Overview........................................................................................................................................................... 0 3 4.2ImageTabLoad ............................................................................................................................................ 0 . 3 4.2.1SupportedImageFileFormats.................................................................................................................. 0 3 iv|I A F E M e s h
Table of Contents
4.3InteractingwiththeImage............................................................................................................................... 0 3 4.4ImageTabDelete.......................................................................................................................................... 1 3 5TheSurfacePanel.......................................................................................................................................... 2 3 5.1Overview........................................................................................................................................................... 3 3 5.2Load/Save/DeleteaSurface............................................................................................................................. 3 3 6TheBlock(s)Panel......................................................................................................................................... 4 3 6.1Overview........................................................................................................................................................... 5 3 6.2Block(s)TabCreate....................................................................................................................................... 5 3 6.2.1Createblockfromsurfacebounds, ........................................................................................................... 5 . 3 6.2.2Createblockmanually............................................................................................................................... 5 3 6.3Block(s)TabBuild/Edit.................................................................................................................................. 6 3 6.3.1BuildingBlockOperationsToolbar............................................................................................................ 7 3 6.3.2RollingBack/ForwardaBuildingBlockStructure.................................................................................... 8 3 6.3.3WorkingwithaBuildingBlockSubStructure............................................................................................ 8 3 6.4Block(s)TabDelete....................................................................................................................................... 9 3 7TheMeshPanel............................................................................................................................................. 0 4 7.1Overview........................................................................................................................................................... 1 4 7.2MeshTabAssign/EditMeshSeeds............................................................................................................... 1 4 7.2.1GlobalMeshSeedAssignment.................................................................................................................. 1 4 7.2.2LocalMeshSeedAssignment.................................................................................................................... 2 4 7.3MeshTabCreate .......................................................................................................................................... 4 . 4 7.3.1VolumetricMesh....................................................................................................................................... 4 4 7.3.2SurfaceMesh ............................................................................................................................................ 5 . 4 7.3.3Node/ElementNumberingandLabels...................................................................................................... 5 4 7.4MeshImprovement.......................................................................................................................................... 5 4 7.4.1LaplacianSmoothing................................................................................................................................. 6 4 7.4.2InteriorNodeInterpolationMethods........................................................................................................ 6 4 7.5MeshTabRenumberNodes/Elements......................................................................................................... 6 4 8TheQualityPanel.......................................................................................................................................... 7 4 8.1Overview........................................................................................................................................................... 8 4 8.2QualityTabEvaluate/DisplayMeshQuality ............................................................................................... 9 . 4 8.2.1QualityMetrics:......................................................................................................................................... 9 4
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Table of Contents
8.2.2AMeshQualitySummaryReport.............................................................................................................. 0 5 8.2.3QualityDisplayOptions............................................................................................................................. 1 5 8.3QualityTabMeshImprovement ................................................................................................................... 2 . 5 9TheMaterialsPanel....................................................................................................................................... 3 5 9.1Overview........................................................................................................................................................... 4 5 9.2MaterialsTabUserDefined.......................................................................................................................... 4 5 9.2.1EstablishingElementSetDefinitions......................................................................................................... 4 5 9.2.2ElementSetSelectionToolbarCapabilities............................................................................................... 6 5 9.3MaterialsTabImageBased.......................................................................................................................... 7 5 9.3.1BinningMaterialPropertyAssignments................................................................................................... 8 5 9.4MaterialsTabDisplayMaterialProperties................................................................................................... 9 5 10TheLoad/BCPanel...................................................................................................................................... 0 6 10.1Overview......................................................................................................................................................... 1 6 10.2Load/BCTabSTEPLoad/BCAssignments................................................................................................. 2 6 10.2.1EstablishingNodeSetDefinitions ........................................................................................................... 2 . 6 10.2.2NodeSetSelectionToolbarCapabilities.................................................................................................. 4 6 10.2.3AssigningaDescriptiveSTEPSubheading............................................................................................... 5 6 10.2.4AssigningLoad/BoundaryConditions.................................................................................................... 5 6 10.2.5DisplayingtheLoad/BoundaryConditions.............................................................................................. 5 6 10.2.6Assigning*STEPDefinitions.................................................................................................................... 6 6 10.2.7MultipleStepAnalysis............................................................................................................................. 6 6 AppendixI:BuildingBlockOperationsExamples............................................................................................. 7 6 AppendixII:Element/NodeSetSelection......................................................................................................... 6 7 AppendixIII:MeshExamples............................................................................................................................ 1 8 INDEX............................................................................................................................................................... 5 8
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Introduction to IA-FEMesh
1IntroductiontoIAFEMesh
IntroductiontoIAFEMesh
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1.1Overview Finite element (FE) analysis is a valuable tool in musculoskeletal research. The demands associated with mesh development, however, often prove daunting. In an effort to facilitate anatomic FE model development we introduceIAFEMesh(IowaFEMesh),afreelyavailablesoftwaretoolkit. IAFEMeshemploysamultiblockmeshingschemeaimedathexahedralmeshgeneration.Anemphasishasbeen placedonmakingthetoolsinteractive,inanefforttocreateauserfriendlyenvironment.Thegoalistoprovidean efficient and reliable method for model development, visualization, and mesh quality evaluation. While these toolshavebeendeveloped,initially,inthecontextofskeletalstructures,theycanbeappliedtoavirtuallyendless numberofmodelingapplications(seeAppendixIII:MeshExamples). 1.2AboutthisManual 1.2.1OrganizationoftheDocument The IAFEMesh Users Manual is divided into four distinct sections. The first section (Chapter 2) details the individualcomponentsofthegraphicaluserinterfaceandhowtheycontributetothemeshingprocess.Chapter3 steps the user through a tutorial aimed at meshing a proximal phalanx bone of the human hand (Note: a representative surface (index_proximal.stl) and the corresponding image data set (CT_hand.img.gz) may be downloaded from the IAFEMesh web site (www.ccad.uiowa.edu/mimx/IAFEMesh). Chapters 4 10 detail the individual tabbed panels (Image, Surface, Block(s), Mesh, Quality, Materials, and Load/BC) paramount to the meshingprocess.Thesepanelsweredesignedtosteptheuser,fromlefttoright,throughthemeshdevelopment process. Lastly, a series of examples are provided in the Appendices detailing some of the capabilities of IA FEMesh,namelytheBuildingBlockeditingoperationsandNode/Elementselectioncapabilities. 1.2.2ConventionsUsedThroughouttheDocumentandSoftware Thefollowingrepresenttheconventionsusedthroughoutthisdocument. ArrowsareusedtorepresentcascadingfromaTabtoaPanelmainmenuselection. Bold Tab/Panelselections,cursorselections,andactionsthroughoutthedocumentarehighlightedin boldtext. Colors ColorsareusedthroughouttheBuildingBlockeditingoperationstohighlightvariousstatesofa givencomponent(i.e.,vertex,edge,face).Weadoptedthecolorsofatrafficsignaltosignifyan activecomponent(green),astationarycomponent(red),andwiththosehighlightedinyellow, proceedwithcaution.

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1.3InstallingandRunningIAFEMesh BeforeinstallingIAFEMesh,youmustfirstdownloadeitherIAFEMeshbinariesorsourcecode.IAFEMeshis availableonmultipleplatforms.WecurrentlyofferprebuiltbinaryversionsforMicrosoftWindows,MacOSX, andLinuxbasedsystems. Windows DownloadthewindowsinstallerfromtheIAFEMeshDownloadwebsite(note:aZIParchiveisalsoavailable, thismaybepreferableforuserswhodonothaveadministrativeaccesstotheirmachine).Savetheinstallation executabletodisk.Runtheapplicationfromthedirectorytowhichitwassaved.Followthepromptsto configuretheinstallationofIAFEMesh.Oncetheinstallationiscomplete,anIAFEMeshsubmenuwillappearin theWindowStartMenu. Shouldyouchoosethearchive,simplyextractthedistributionfromthedownload;theapplicationislocatedin theIAFEMesh1.0.0/binfolder.Note,IAFEMeshisdependentonthelibraryfilesinthisdirectoryandtheTcl/Tk librariesintheIAFEMesh1.0.0/libdirectory. Linux Downloadtheprecompiledbinariesfortheappropriateplatform(versionsareavailableforboth32and64bit architectures).Oncedownloaded,extractthedistributionusingthetarcommand(e.g.,tarxzvfIAFEMesh 1.0.0Linux32.tar.gz).Note:theexecutablemaybeinstalledeitherlocallyorsystemwide.Theexecutablewill belocatedinthebindirectorycreatedduringthefileextractionprocess. Consequently,torunIAFEMeshfromthecommandprompt,youwillneedtoataddthedirectoryhousingthe IAFEMeshexecutabletoyourPATHenvironmentalvariable(i.e.,pathofthebindirectory).Forbashshell,this canbedoneusingthecommand,
% export PATH=${PATH}:/install-path/IA-FEMesh-1.0.0/bin
whereinstallpathisthedirectorywhereyouunpackedtheprogram.Thiscanbeaddedtoyour.bashrcfileto makethisadditioneachtimeyoulogin. Forthecsh,thefollowingcommandneedstoberunoraddedtoyour.cshrcfile.

% setenv PATH ${PATH}:/install-path/IA-FEMesh-1.0.0/bin
Youcanthenexecutetheprogrambytypingthefollowingatthecommandprompt:
% IA-FEMesh
Macintosh DownloadtheIAFEMEsh1.0.0.dmgfile.SimplyDoubleclickonthefilenametoextracttheinstallationpackage. Theinstallationpackagewillguideyouthroughthesoftwareinstallationprocess.Thesoftware,onceinstalled, willresideininstalldir/usr/bin.DoubleclickontheIAFEMeshapplicationinthatdirectorytostarttheprogram.
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BuildingIAFEMesh IfyouplantocompileIAFEMesh,youmustfirst,downloadandinstallCMake,thecrossplatformbuildsystem (http://www.cmake.org/HTML/Download.html).ConfigureandbuildthefollowinglibrariesusingCMake. VTK(http://www.vtk.org/getsoftware.php) version5.2 BuildwithVTK_TCL_WRAPPINGON ITK(http://www.itk.org/HTML/Download.htm) version3.6 KWWidgets(http://www.kwwidgets.org/Wiki/KWWidgets/Download) YouwillneedtodownloadthecvsversionwiththetagSlicer32 cvsd:pserver:anoncvs@www.kwwidgets.org:/cvsroot/KWWidgetscorSlicer32KWWidgets Tcl/Tk Version8.4 PrebuiltversionsofthelibrariesareavailablefromActiveState (http://www.activestate.com/downloads/index.mhtml) YoucanalsodownloadthesourcecodefromSourceforgeandbuildthisfromsource (http://sourceforge.net/project/showfiles.php?group_id=10894) Tcl/TkdoesnotbuildusingCmake.Insteadyouwillhavetofollowtheplatformspecificstepsforbuilding. ForLinuxandMacintoshbuilds,youwillruntheconfigurescriptintheunixdirectory.Thiswillgenerate makefilesforbuildingthesoftware.UnderWindows,asolutionfileexistsinthewindirectorythatcanbe usedtobuildthesoftware. Oncethesearecreated,configureIAFEMeshusingCMakeandspecifythelocationsoftheITK,VTK,and KWWidgets.Oncethemakefile,orsolutionfile,isgeneratedyouarereadytobuildthesoftware.The executableswillbelocatedinthebindirectoryofthebuildtree.
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Interfacing with IA-FEMesh
2InterfacingwithIAFEMesh
InterfacingwithIAFEMesh
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2.1Overview TheIAFEMeshinterfaceconsistsofaMainToolbar,theViewPanel,andaCommandPanelwhichconsistsofan ObjectManagerandaseriesofTabbedPanels.Thefollowingintroduceseachofthesebasiccomponents.
2.2TheMainToolbar ThemostnotablemenuontheMainToolbaristheViewMenu.TheViewMenuhousestheApplicationand ViewSettings.
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2.2.1ApplicationSettings Interface Settings Disable/enable the settings such as balloon help, etc. The userspecified settings will be retainedwhentheprogramisrestarted. TheInterfaceSettingsalsoprovideadropdownmenu(Positionofviewpanel)toassigntheViewPaneltothe leftorrightoftheinterface. IAFEMeshSettings AutosaveWorkTheobjectspopulatingtheObjectManagerwillbesavedtotheworkingdirectoryby defaultevery5minutes,unlessspecifiedotherwise.(i.e.,directory:IAFEMeshAutoSavedate). AverageElementLengthBydefault,theinitialmeshseedassignmentsarebasedonanelementedge lengthof1.Theuserisaffordedtheoptionofresettingthisdefaultlength. ABAQUSMaterialPropertyPrecisionTheusermayadjustthenumberofsignificantdigitswithwhichthe imagebasedmaterialpropertiesarewrittentothe.inpfile.
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2.2.2ViewSettings
TheColorsframeenablestheViewPanelbackgroundandtextcolortobechanged,whiletheViewframehouses acollectionoficonsusedtomanipulateorcaptureaview: Predefinedviewsbasedonthesixfacesofacube.Eachtriadindicatestheorientationofthis imaginarycubewiththeviewwindow.
Perspectiveview.
ParallelView
Rescale,orautofit,theviewtofillthewindow.
Capture/saveascreenshot
Togglesviewoftheaxes
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2.3TheViewPanel TheViewPanelfacilitatestheinteractivenatureofbuildingaBlockstructure,Meshgenerationand improvement,inadditiontoestablishingNodeandElementSetdefinitions. MouseBasedNavigation:Zoom,Rotate,andPan The following actions are available for interactively manipulating an object using themouse (assumes a right handedmouse). Tozoominandout,holdtherightmousebuttonanddragthemouseupanddown,orifavailablescroll themiddlemousewheel. Torotateanobject,holdtheleftmousebuttonanddrag Topan,holdthecentermousebutton(orwheel)anddragtheobject. 2.4TheCommandPanel The Command Panel consists of the Object Manager and a series of Tabbed Panels (i.e., Image, Surface, Block(s),Mesh,Quality,Materials,andLoad/BC).
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2.5TheObjectManager
2.5.1Viewing/ActivatinganObject Asanobjectisloaded/created,anidentifierisassignedandautomaticallypopulatestheObjectManager.The ObjectManagerfacilitatescontroloverthevisibilityandappearanceoftheindividualcomponents/objects(i.e., image,surface,blocks,andmesh).Thecheckboxprecedingtheobjectnametogglesthevisibilityoftheobject (thedefaultcheckisvisible).Asinglevisibleobjectofagiventype(e.g.,buildingblock)impliesthattheobjectis active for building/editing/manipulation. As a result, these checked objects will automatically populate the collapsibleframesthroughoutthetabbedpanelsasthedefault,oractive,object.Iftwoobjectsofthesametype are checked (i.e., visible in the view panel), the active object will be considered that listed first in the Object Manager.Ifnoobjectofaparticulartypeischecked,andisrequiredforaparticulartask(i.e.,buildingblock and/orsurfaceforameshdefinition),thenthelastobjectinthelist(forthatparticulartype)willbeassignedas the default object. This holds true throughout the program for images, surfaces, building blocks, and mesh definitions. If viewing multiple objects of a particular type, the object of interest may be directly activated within the collapsed frame (it is advisable to expand the frame to ensure that the appropriate object, or combinationthereof,isactive). 2.5.2NamingConvention ThenamingconventionusedthroughoutIAFEMeshusesasitsfoundationthesurfacefilename.Asobjectsare created/edited, their identifier assumes the following format surface filename_last operation_# times a particular operation has been performed. For example, a surface named index_proximal.stl has been loaded. Thereafter, a building block is created manually. The building block is assigned the identifier index_proximal _BBm1. A series of building block editing operations follow such that the building block is subdivided (index_proximal_Split1), a block is added (index_proximal _Add1), followed by a second subdivision (index_proximal_Split2).
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2.5.3AdjustingtheDisplayPropertiesofanObject
Clicking on the name of an object within the Object Manager will launch a window (as illustrated). This windowprovidessettingstocontroltheappearanceoftheselectedobject.
The drop down menu labeled Representation provides the options of Surface/Solid and Wireframe viewing, in addition to a combination of the two for a finite element mesh. Moreover the user has controloverboththeFillandOutlinecolors,aswellastheopacityoftheobject. Adjusts the opacity/transparency of a geometric entity. Theopacityvaluerangesbetween0and1.Anopacityof1 (the default) means the dataset is completely opaque. An opacityof0meansthedatasetiscompletelytransparent. Adjuststhelinewidthofawireframerepresentation.
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Propertyassignmentsspecifictothemeshdefinitions: Mode:AllowstheusertoswitchbetweentheCompleteMeshandspecificElementSets WhenElementSetsisselected,thewindowispopulatedbythecurrentelementsetdefinitions. Thecheckboxesareusedtotogglethevisibilityoftheset.Tochangethevisualappearanceof a given set, highlight the set label by clicking on the name. Thereafter, in addition to the aforementionedproperties,theuserhascontroloverthesizeoftheelements.
ElementSize(%):Changesthevolumeoftheelements,allowingtheusertoshrinktheelementsize throughoutthemesh.
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2.6TheTabbedPanels Theindividualpanelsweredesignedtosteptheuser,workingfromlefttoright,throughthemeshdevelopment process.Eachpanelhousesamaindropdownmenubutton,consistingofaseriesofactions(i.e.,Create,Load, Save,etc.)specifictothattab.Chapters410detailthefunctionalitiesaffordedbyeachofthetabbedpanels. 2.6.1Loading/Saving/DeletinganObject Anumberoftheactionsthroughoutthepanelsperformsimilartasksfortheirrespectiveobjects.Forexample, toloadagivenobject(Image,Surface,Block,Mesh),selectLoadfromwithinthecorrespondingpanel(e.g.,to loadanimage,selectLoadfromthedropdownmenuwithintheImagepanel).Unlessnotedotherwise,thisalso holds true for deleting and saving an object. Saving the Block Structure as well as the Mesh throughout the meshgenerationprocessishighlyadvised;namelyafterbuildingtheblockstructure,constructing/improvingthe mesh,aswellasmaterialpropertyandload/boundaryconditionassignment.Note:AllfilesaresavedinVTK format(.vtk). 2.6.2ExportingaFileinABAQUSFormat(.inp) TheMesh,Quality,Materials,andLoad/BCpanelseachaffordtheusertheabilitytoExporttheMeshdefinitionin ABAQUS file format (.inp). In addition to the input deck (filename.inp) specified by the user, an additional file (filename_input) is created to be read by the main file (i.e., *INCLUDE, INPUT=filename_input). This file accommodates the node and element definitions, in addition to the node and element sets. The imagebased materialpropertyassignmentsarealsohousedinthisfile. 2.6.3TheImportanceoftheCollapsedFrame In addition to the commonality of the main drop down menu, each tab houses a collapsed frame, which accommodates the objects contributing to a given task. For example, both a surface and building block structure contribute to a mesh definition. Consequently, within the Mesh panels Create option, resides a Surface&BuildingBlockframe.AsdescribedinViewing/ActivatinganObject,themenuswillbepopulated automaticallydependingontheobjectsdenotedasactiveviatheObjectManager.Theuseralsohastheoption ofactivatingaparticularobjectbyselectingitdirectlyfromthedropdownmenu.
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2.6.4Apply/CancelanOperation Lastly,theApplyandCancelbuttonsacttoperformthegivenactionandtoabandontheoperationandreturnto themainmenubutton,respectively.Note,whileapanelisinuse,allotherpanelsaredeactivated.Cancelmust beinvokedtochangebetweenthetabbedpanels.
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IA-FEMesh Tutorial: Proximal Phalanx Bone
3IAFEMe eshTutorial
IA-FEMesh Tutoria E al:

Proximal Phalanx Bo one
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3.1Example:Creatingameshofananatomicstructure Anatomicmodelsinitiatingwithanimagedataset(i.e.,CT/MR)areoftenprocessedtoyielda3Dtriangulated surfacerepresentationofthestructure(s)ofinterest.IAFEMeshassumesthesesurfacesformthefoundation forthestructuralgeometry,whileaseriesofbuildingblocksareusedtoestablishthemesh.Youwillinitiatethe modelbyloadingthesurfacerepresentationoftheboneofinterest.Abuildingblock,orseriesofblocks,willbe constructed,assignedadesiredmeshdensityandprojectedontothesurfacerepresentation,therebycreatinga 3DFEmodel.Thereafter,materialpropertiesandloading/boundaryconditionassignmentsmaybemade. The Command Window consists of an Objects Manager and a series of tabbed panels (i.e., Image, Surface, Block(s),Mesh,Quality,Materials,andLoad/BC).Thesepanelsweredesignedtosteptheuser,workingfrom left to right, through the mesh development process. The following example outlines the procedure for constructingawelldefinedFEmodelofaproximalphalanxbone. 1. IAFEMesh Ifyouhavenotdonesoalready,launchIAFEMesh 2. LoadinganImage To load an image, select the Image tab, from the drop down menu select Load (default). A newwindowwillbeappear,select theimagefileofinterest. 3. LoadingaSurface Toloadasurface,selecttheSurfacetab,fromthedropdownmenuselectLoad(default).Anewwindowwill belaunchedenablingyoutoopenthefileofinterest.Forthetimebeing,hidetheimagebyuncheckingthe checkboxassociatedwiththeimageintheObjectManager.
4. CreatingaBuildingBlock TocreateaBuildingBlockbasedontheboundsofthebonysurfacedefinitionselecttheBlock(s)tab,fromthe dropdownmenuselectCreate(default),andchecktheCreateblockfromsurfaceboundscheckbox(default), followedbyApply.Note:ifonlyasinglesurfacehasbeenloaded,itwillautomaticallypopulatethemenu withintheSurfaceframe.Ifmorethanonesurfaceisloaded,theactivesurfacewillbethatdisplayedviathe objectswindow.Moreover,themenuhousedwithintheSurfaceframeenablesthesurfaceofinteresttobe activatedmanually.
Note: A mesh seeding operation will be used to subdivide each face of the building block into a grid of elements.Theseelementsarethenprojectedontothe surface of interest via closest point projection. Consequently, it is advantageous to bring the vertices/facesasclosetothesurfaceaspossibletohelp provide control over the placement of the projected nodes.Anumberofinteractiveeditingcapabilitieshave beenimplementedtofacilitatethistask. 5. ManipulatingtheBuildingBlock: WithintheBlock(s)panel,fromthedropdownmenuselecttheBuild/Editoperation. ,select .Thisactivatesthe Fromthebuildingblockstoolbar abilitytorepositiontheindividualvertices,edges,and/orfacesofthebuildingblocks.Onceactivated,ared spherewillappearateachoftheBuildingBlockvertices. Tomoveabuildingblockvertexorface,simplyclickontheobjectofinterestwiththeleftmousebutton(an activeelementwillturngreen),anddragittothedesiredposition.Tomoveanedgeoftheblock,usethe middlemousebutton.
ExamplesoftheBuildingBlockeditingoperation, , whichenablestheblock(a)vertices,(b)edges,and(c) facestoberepositionedforimprovedmeshdefinitions. Note:Theradiioftheredspheresmaybescaled:
ToSavetheBuildingBlock,selectSavefromthedropdownmenu(Note:Cancelwillexittheediting operationspanel,enablingthedropdownmenutobeactivatedandSavetobeselected). 6.
AssigningMeshSeedstotheBuildingBlock. EntertheMeshpanelviatheMeshtab.FromthedropdownmenuselectAssign/EditMeshSeeds.Note,by defaultanaverageelementedgelengthof1hasbeenassignedtotheedgesofeachbuildingblock.Select to visualize the distribution of mesh seeds (i.e., Number of Divisions) throughout the structure (Note: as the blocks are manipulated, the number of divisions remains constant based on the initial element size calculations, to restore the structures average element edge length to 1, selectApply).Tochangethisassignment,anadditionaldropdownmenuprovidestheoptionofsubdividing theblockedgesviathe(1)ElementLengthor(2)NumberofElements.Onceaselectionhasbeenmade,click on the block of interest with the left mouse button. (an axis system will appear to provide additional verification of the block edges corresponding to the x, y, and z directions). Thereafter,enterthevaluesofchoiceandselectApply.Canceltoexitthemesh seedsoperation.
7.
CreatingaMesh Within the Mesh panel, from the drop downmenuselectCreate. Select Volumetric Mesh consisting of hexahedral elements using the BuildingBlockoption(Default). Thereafter, provide starting node/ element numbers (default is 1) in additiontodescriptivelabelstobeused to identify the nodes/elements associatedwiththemeshdefinition(i.e., setlabels). AssumeEllipticalInterpolation Asaninitialattempt,Uncheckthe Performsmoothingoption. SelectApplytogeneratethemesh.
8.
ACheckoftheMeshQuality Enter the Quality panel via the Quality tab. From the drop down menu select Evaluate / Display Mesh Quality. To visualize the element quality, select the Metric of Choice, followed by requesting a summary report ofthemeshforthechosenmetric.
9.
Improvemeshquality Within the Quality panel, select Mesh Improvement from the drop down menu. Check to ensure that the Surface,BlockandMeshofinterestpopulatetheMeshComponentframe. Selectaninterpolationmethod(EllipticalorTransfinite)toestablishtheinteriornodaldefinitions.Enterthe desirednumberofsmoothingiterations(Laplaciansmoothing)fortheexternalnodes,andApply.Note:Be carefultonotoversmooththemesh.Toomanyiterationsmayyieldameshofpoorquality.
Adjust the smoothing parameters, toggling between the Evaluate / Display Mesh Quality and Mesh Improvementoperationsuntilthedesiredmeshfortheassignedmeshseedingisachieved.Whiledisplaying themetricofinterest,depress toinvokeacuttingplanetoviewtheinternalelements.
10. AssigningMaterialPropertiesUserDefined SelecttheMaterialstab.WithintheMaterialspanel,selecttheUserDefinedoptionfromthemainmenu. The element set label used to identify the phalanx bone during the mesh definition step will automatically populate the Element Set menu. If additional sets are preferred, select the button. A number ofactionsareavailableforselectingtheelementsto include/exclude in/from a set (refer to Appendix II foradetaileddescriptionofeachaction). Example:ElementSetDefinitions The following outlines the procedure for defining two independent element sets: (1) the external layer of elementsand(2)theinternalelements,representativeofthecorticalandcancellousbone,respectively. Cortical_Bone Set definition: Select , hold the Ctrl button while using the left mouse buttontodragarubberbandboxaroundtheelementsofinterest.Theselectedelementswill be highlighted in green. To accept the chosen elements, click the right mouse button while hoveringoverthemesh;theacceptedelementswillturnred.Changingtheopacityviatheslider enablestheusertobettervisualize,inadditiontoworkwiththeselectedelements.Oncethe . selectionhasbeenfinalized,enteraSetLabel(e.g.,cortical_bone)andApply
Cancellous_BoneSetdefinition:Repeattheaforementionedstepsfordefiningthecorticalbone with the exception of depressing the button prior to accepting the element selection and assigninganewSetLabel(e.g.,cancellous_bone).Note:oncetheselectionhasbeenfinalized, willclose youmustreducetheopacitytovisualizetheelementsassignedtotheset.Cancel theDefineElementSet(s)window. MaterialPropertyAssignments Once the desired element sets have beendefined,usethedropdownmenu Element Set to select an element set and Enter the Modulus and Poissons Ratio in the respective text boxes, and Apply. Repeat this procedure for each material assignment. Once complete, Canceltoexittheoperation. VisualizingtheMaterialPropertyAssignments WithintheMaterialsPanel,fromthedropdownmenuselectDisplayMaterialProperties.TheElementSetto bedisplayeddefaultstoallelements.Ifaparticularsetisofinterest,usethedropdownmenutomakesuch a selection. Use definitions. to display a cutting plane which may be manipulated to view the internal element
11. AssigningMaterialPropertiesImageBased Atthispoint,youmayopttooverwritetheuserdefinedpropertieswithimagebasedmaterials,orproceedto step12. WithintheMaterialspanel,selecttheImageBasedoptionfromthemainmenu.Expandthecollapsedframe titled Mesh & Image Assignments to ensure that the appropriate Mesh and Image definitions populate the respectivemenus. Sincewepreviouslyassignedmaterialpropertiestotwoindependentelementsets,wemustoverwriteeachof them(simplyapplyingtheimagebasedpropertiestothemeshasawholeinthisscenariowillnotoverwrite theprevioususerdefineddefinitions,andhencetheelementswouldhaveconflictingmaterialassignments). Foreachelementsetdefinedpreviously(e.g.cortical_bone,cancellous_bone)dothefollowing: Select the element set of interest, assign a Poissons Ratio, select to launch a window, enablingtheconstantsforthemoduluscalculationtobeadjusted.Moreover,selectamethodofcalculating the density; via the Average, Median, or Maximum density value for a given element. Select Apply in the ImageBasedElasticModuluswindowtoconfirmthecalculationconstants,etc.SelectApplyintheMaterials Panel to commit the imagebased properties to the mesh. Repeat this procedure for all element sets for whichyouwouldliketoassignimagebasedmaterialproperties.
Note: had the userdefined properties not been assigned, the imagebased properties could have been assigneddirectlytothesetcontainingalloftheelements.
12. AssigningLoadandBoundaryConditions SelecttheLoad/BCtabandtheSTEPLoad/BCAssignmentsoptionfromthedropdownmenu.Similartothe elementsetdefinitionsdefinedpreviously,nodesareassignedtosetsfordesignatingtheloadandboundary conditions. Select . From the Node Set toolbar select (this enables the nodes associated with a face of a building block to be readily chosen). Hold the Ctrl button while using the left mousebuttontochooseanodeassociatedwiththebuildingblockfaceofinterest.Thenodesassociated withtheselectedfacewillbehighlightedingreen.Toacceptthechosennodes,clicktherightmousebutton whilehoveringoverthemesh;allnodesassociatedwiththechosenfacewillturnred.Changingtheopacity via the slider enables the user to better visualize, in addition to work with the selected nodes. Once the . Cancel will close the selection has been finalized, enter a Set Label (e.g., bounds) and Accept DefineNodeSet(s)window. IntheStepSubheadingtextbox,provideadescriptiveheadingforthecurrentstep. FromthedropdownmenusselecttheLoad/Displacementtype(Force,Displacement,Moment,Rotation),as wellastheappropriateNodeSet,andAssigntheconditionstothex,y,andzdirections,respectively.Select Apply to update the Load /BC assignments. Visual confirmation will be provided on the mesh in the View Panel.
Repeattheaforementionedprocedure ... createanadditionalnodesetforloading themodelandapplyaForce.
13. Assigning*STEPDefinitionsSelectthe*STEP Definitionsbuttontolaunchawindowhousing a number of ABAQUS STEP options such as output and print requests. Please refer to the ABAQUS manual for details regarding these parameters. All parameter requests entered into the textboxes should be delimited by commas. The following represent the default parameters included for the *STEP and Node PRINT and OUTPUT requests (a similar frame exits for Element requests). Use the NSET/ELSET drop down menus to select the set(s)ofinterest.Theselectionswithinagiven frame are committed once Apply is selected (Note: the text in the Node/Element frames will become grey once committed. To change the parameters, simply reselect the node/elementsetfromthedropdownmenu).
14. ToSavetheFEmesh.Themeshmaybesavedfromanyofthemeshrelatedpanels(i.e.,Mesh,Quality, Materials,andLoad/BCPanels)byselectingSavefromtherespectiveMainMenu.Thisenablestheuser toreadilysavethemeshthroughoutthedevelopmentprocess.ThefilewillbesavedinVTKfileformat.
RecallthattheobjectspopulatingtheObjectManagerareautomaticallysavedtotheworkingdirectory every5minutes,unlessspecifiedotherwise(referto2.2.1ApplicationSettings).
15. To Export the mesh in ABAQUS file format (*.inp). The mesh may be exported from any of the mesh relatedpanels(i.e.,Mesh,Quality,Materials,andLoad/BCPanels)byselectingExportABAQUSfilefrom therespectiveMainMenu(referto2.6.2ExportingaFileinABAQUSFormat(.inp)).
NOTES
NOTES
The Image Panel
4TheImagePanel
TheImagePanel
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The Image Panel
4.1Overview The current imaging capabilities within IAFEMesh provide visualization of the image and of a surface/mesh overlayingtheimage.Moreover,aCTimagesetprovidesfordirectmaterialpropertyassignments.Inthefuture, we plan to incorporate additional image processing capabilities for image segmentation and surface generation fromtheresultingregionsofinterest.
4.2ImageTabLoad WithintheImagePanel,selectLoad(default)fromthepanelsmaindropdownmenu. 4.2.1SupportedImageFileFormats ThefollowingimagefileformatsarecurrentlysupportedbyIAFEMesh MayoAnalyze(.hdr,.img) NifTi(.nii,.nii.gz) NRRD(.nrrd,.nhdr) META(.mha,.mhd) GIPL(.gipl,.gipl.gz) VTK(.vtk) 4.3InteractingwiththeImage
Traversing the image The image dataset may be traversed by independently translating or rotatingthecoordinateplanes.Withthemiddlemousebutton,selectaplaneanddragthemouse inthedirectionofinterest.Moreover,ifanedgeoftheplaneisselected(againwiththemiddle mousebutton),theplanewillrotate. Voxel location and intensity readings Clicking on the image with the left mouse button will providethecoordinatelocationandtheintensityvalue((x,y,z):intensity)foragivenvoxel. AdjustingtheimagecontrastThecontrastofeachplanemaybeadjustedindependentlyby draggingthemouseovertheimage/planeofinterestwhileholdingdowntherightmousebutton.
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The Image Panel
Shortcut keys: Shift, accompanied by s or w, toggles between displaying (s) and hiding (w) the image. 4.4ImageTabDelete WithintheImageTab,selectDeletefromthedropdownmenubutton,selecttheimagetoberemoved.
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The Surface Panel
5TheSurfacePanel
TheSurfacePanel
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Panels
The Surface Panel
5.1Overview Themodelingtechniquesforanatomicmodelsmayinitiatewithatriangulatedisosurface(STLorVTKformat)of the structure(s) of interest, generated directly from a segmented image data set (i.e., CT or MR). Note: the meshing techniques are applicable to geometries other than anatomic structures (refer to the Appendices for examples),solongastheycanbeloadedasSTLorVTKfileformats.
5.2Load/Save/DeleteaSurface TheSurfacePanelmainmenuaffordstheusertheabilitytoLoad,Save,andDeleteasurface.
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The Block(s) Panel
6TheBlock(s)Panel
TheBlock(s)Panel
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The Block(s) Panel
6.1Overview IAFEMesh manages thebuildings blocks via interactive building/editing techniques. For simple geometries, a single block may suffice (e.g., a phalanx bone of the hand). In such cases, the building block may be automaticallydefinedattherequestoftheoperator,thedimensionsofwhichareestablisheddirectlyfromthe boundsofthesurfaceofinterest.Theuseralsohastheoptionofmanuallycreatingabuildingblock.Regardless ofthemethod,onceablockiscreated,subsequentinteractivemanipulationsmaybeperformedonthebuilding blocktoprovidecontrolovertheresultantnodalprojections. 6.2Block(s)TabCreate
6.2.1Createblockfromsurfacebounds,followedbyApply,willautomaticallygenerateabuildingblockbased on the bounds of the surface of interest (note: the edges of the block will align with the axes of global coordinatesystem). 6.2.2CreateblockmanuallyThebuildingblockwillbe extruded perpendicular to the drawing plane; consequently, the surface should be positioned accordingly.EnteranExtrusionLength.HolddownCtrl and with the left mouse button depressed, drag the mousetodrawtheblockfacetobeextruded.Ablock will automatically be drawn based on the provided extrusion length. The block is committed once Apply (ortherightmousebutton)hasbeendepressed.Until then,theusermayredefineablock(1)byrepeatingthe aforementioned procedure or (2) by entering a new extrusionlengthfollowedbyreturn.
IftherightmousebuttonissubstitutedforApply,thecursormustbeovertheblockwhendepressed.
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The Block(s) Panel
Asanatomiccomplexityincreases,itimposesanincreaseintherequirednumberofbuildingblocksandhence, attention to their spatial orientation; this in turn requires a means to readily manipulate the building block definitions.Inordertomakethemultiblocktechniqueuserfriendly,anumberofinteractiveeditingoperations havebeendevelopedandincorporatedintoIAFEMesh.Theeditingoperationsimplementedtodateinclude: (1) positioning individual vertices/edges/faces of a building block; (2) the subdivision of a building block, or seriesofbuildingblocks;(3)theaddition/deletionofabuildingblock;(4)consolidatingtwoindependentblock structures;and(5)mirroringandmergingabuildingblockstructure. TheBuildingBlockOperationstoolbarishousedintheBlock(s)panelundertheBuild/Editmainmenu. 6.3Block(s)TabBuild/Edit
Thepagestofollowdetaileachbuildingblockoperation.Thesedetails,alongwithexamplesofeachoperation, arealsoprovidedintheAppendices;pleaserefertotheBuildingBlockOperationsToolbar .
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The Block(s) Panel
6.3.1BuildingBlockOperationsToolbar TheBuildingBlockOperationsToolbarprovidesanumberofoptionsforcreating/manipulatingablockstructure.
Move operations: Allows the constituents of a block (vertices, edges, and faces) to be repositioned independently. To activate an individual component, with the left mouse button click on the part of interest(activeelementswillbehighlightedingreen).Notethatedgeselectionrequirestheuseofthe middle,asopposedtotheleft,mousebutton.Dragthecomponenttothedesiredlocation(besureto rotatetheviewtoensuretheblockispositionedcorrectlyrelativetothesurface).Tomovemultiplefaces simultaneously,holdtheshiftbuttonwhileselecting/deselectingthefacesofinterest.
Subdivideoperation:Dividesthebuildingblockofinterestinhalf.Withtheleftmousebutton,selectthe edgealongwhichtheblockshouldbedivided(edgewillbehighlightedingreen)followedbyApply.The subdivisionwillpropagatetoadjacentblocksthroughoutthestructureautomatically.
Addoperation:Addsanewbuildingblock,orblocks,totheface(s)ofanexistingblock/structure.With theleftmousebuttonselectthefaceofinterest.Tohighlightmultiplefaces,holdtheshiftbuttonwhile selecting/deselectingthefacesofinterest.Again,theactivefaceswillbehighlightedingreen.Provide anextrusionlength,followedbyApply.1 Note:thecoincidentverticesgeneratedviatheaddoperationwillequivalenced/mergedautomatically.
Deleteoperation:Removesunwantedblocksfromabuildingblockstructure.Withtheleftmousebutton selecttheblockstoberemoved.Toremovemultipleblockssimultaneously,holdtheshiftbuttonwhile selecting/deselectingtheblocksofinterest.Theactiveblockswillbehighlightedingreen.Whenthe selectioniscomplete,selectApply.
Consolidate: Consolidates two or more independently defined building block structures into a single structural definition. To ensure that the blocks are contiguous, the vertices to be shared must be equivalenced.Note:twosphereswithintheuserspecifiedtolerancewillbehighlightedyellow.
Mirror:Mirrorsabuildingblock,orblockstructure,aboutaplane.Selecttheplaneofinterest(XY,XZ,or YZ),andpositionitasdesiredrelativetotheoriginalbuildingblockdefinition(s).
Equivalence / Merge: Merges the vertices of selected building blocks (within the specified tolerance). Required when building blocks have been mirrored, or when multiple blocks have been independently added adjacent to one another. Note: two spheres within the userspecified merge tolerance will be highlightedyellow. TherightmousebuttonmayreplacetheApplybuttonforthesplit,add,anddeleteoperations.Inorderforthis shortcuttobeused,thecursormustremainon(ornear)theactiveelement(edge,face,orblockhighlightedin green)ofinterestwhentherightmousebuttonisdepressed.
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The Block(s) Panel
6.3.2RollingBack/ForwardaBuildingBlockStructure Eachofthemoveoperationsarecommittedinteractively,theremainingoperationsrequiretheApply(orright mouse) button to take effect. Furthermore, with the exception of move, each operation may be rolled back/forwardusingtheundo/redobuttons. If,forexample,ablockisaddedtoastructureandsubsequentlymanipulatedviaasequenceofmoveoperations andtheundoactionisinvoked,thebuildingblockstructurewillreturntothestatepriortohavingaddedthe block.Theredobuttonwillreinstatethemanipulatedblockstructure. 6.3.3WorkingwithaBuildingBlockSubStructure The SubStructure button toggles between viewing/working with a selected portion (sub structure) and the completeblock structure. In order to activate the SubStructure button,disable allof the editingoperations (i.e., ensure that all editing operation buttons have been deselected). To select a single block or series of blocks,selecttheSubStructurebuttonandusetheleftmousebuttontoselecttheblockofinterest,orwith theleftmousebuttondragaboxaroundtheblocksofinterest. Note,whenthemove operationisinvokedonasubstructure,theblockfacessharedwiththeremaining structurewillbehighlightedinyellow.Thisactsareminderthatshouldthefaceand/orassociatedverticesbe moved,theywillchangethegeometryoftheneighboringblock(s).Furthermore,iftheuserattemptstoadda blocktooneofthesesharedfaces,thefacewillturnred,indicatingthatthisisnotpermissible. To reinstate the building block structure in its entirety, again deselect all editing operations, and select the CompleteStructurebutton.
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The Block(s) Panel
6.4Block(s)TabDelete IAFEMesh tracks building block development throughout the building/editing processes. As mentioned previously (Rolling Back / Forward a Building Block Structure), with the exception of move, each of the operationsiscommittedviatheApplycommand.Asaresult,BuildingBlocksarestoredsequentiallyastheyare constructed,therebylendingtotheabilitytorollback/forward.Consequently,whenaBuildingBlockisdeleted, the user is afforded the opportunity to delete the Current block, or All of the blocks contributing to its development.
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The Mesh Panel
7TheMeshPanel
TheMeshPanel
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The Mesh Panel
7.1Overview Once the building block structure has been established, the blocks are further subdivided via mesh seeds (arrangedinrows,columns,andlayers).Themeshseedsofthebuildingblockarethenprojected(viaclosest pointprojection)ontothesurfaceofinterest.Asaresult,themeshseedsaremorphedtothebonysurfaceas nodes,tolaythefoundationfortheFEmesh.Thereafter,Laplaciansmoothingmaybeperformedonthesurface nodes,followedbyinterpolationtechniques(transfinite/elliptical)toestablishtheinternalgridofnodes.Once thenodaldefinitionsareestablishedthroughout,thevolumeisfilledwithhexahedralelements. 7.2MeshTabAssign/EditMeshSeeds Onceabuildingblock,orseriesofblocks,hasbeenestablished,themeshdensitymustbeassignedthroughout themodel.Atthelevelofanindividualblock,thisisaccomplishedbysimplyspecifyingthenumberofdivisions (i.e.,elements)orthedesiredaverageelementlengthalongeachcoordinateaxisoftheblock(Rx,Gy,Bz).
7.2.1 Global Mesh Seed Assignment By default, mesh divisions (seeding) of unit length 1 are assumed throughout a building block structure (Note that these divisions are assigned based on the initial block size/shape, consequently the number of divisions will be set and therefore the element size may be altered as the block(s) are manipulated).Thiselementlengthmaybereadilyredefinedbyentering the Assign/Edit Mesh Seeds Menu and selecting Apply. Select Color CodeMeshSeedstoseethenumberofdivisionsassignedtoeachedge. The user has the option of reassigning new mesh seeds based on (1) ElementLengthor(2)theNumberofDivisionsalongablockedge.The seedsmaybeassignedgloballytothestructurebyenteringthedesired length or number of divisions along the Rx, Gy, and Bz directions (globally, these directions correspond to the x, y, and z axes respectively).
Referto2.2.1ApplicationSettingsfordetailsregardingchangingthedefaultvalueforthemeshseedlength.
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The Mesh Panel
7.2.2LocalMeshSeedAssignmentThemeshseedingmayalsobeassignedlocally.Thisisaccomplishedby selectingtheblockofinterestandassigningthemeshseedsbasedon(1)Elementlengthor(2)theNumberof Divisionsalongtheblockedge.ABuildingBlockselectedformeshseedassignmentwillbehighlightedbythe presenceofalocalaxissystem(Rx,Gy,Bz).
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The Mesh Panel
Seedsmaybeassignedinsuchawaythattheyaffectonlytheblockunderconsideration.Forexample,inthe examplebelow,themeshseedsontheGyaxiswereincreasedfrom8to16.Asaresult,thefouredgesofthe blockparalleltotheGyaxiswereassigned16subdivisions(illustratedinblue).
In this example, the edges of the block parallel to the Rx and Bz axes share edges with adjacent blocks. Consequently,thesubdivisioninformation(meshseeding)istransferredacrossblocksatthesharededges.For example,intheexamplebelow,themeshseedsontheRxaxiswereincreasedfrom10to20.Asaresult,each oftheedgesthroughthestructureparalleltotheRxaxiswereassigned20subdivisions(illustratedinblue).
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The Mesh Panel
7.3MeshTabCreate Select a Mesh/Element type: Volumetric Mesh (Hex; default) or Surface Mesh (Quad, Tri); note that tetrahedralmeshingiscurrentlydisabled.
7.3.1VolumetricMesh
ForaVolumetricMeshthedropdownmenuprovidestwomeshgenerationoptions(1)BuildingBlockProjection (default)and(2)Extrude,whichextrudesaselectsetofelementfacesauniform,userspecified,distance.Each methodgenerates8nodedhexahedralelements(ABAQUSelementtype=C3D8). Building Block Projection The grid of nodes established via the building block mesh seed assignmentsareprojectedontothesurfaceofinterestusingclosestpointprojection.Thereafter, theuserhastheoptionofusingtransfiniteorellipticalinterpolationtoestablishtheinteriornodes. Ifneedbe,theuserhastheoptionofsmoothingthemeshviaLaplacianSmoothing(referto7.4 MeshImprovement). Extrude A select set of elements may be extruded along their normals a specified distance (Extrusion Length) and Number of Divisions. When the Extrude Elements button is invoked, a window will open which houses the aforementioned parameters, accompanied by the Element
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The Mesh Panel
SelectionToolbar(refertoAppendixII).Itisrecommendedthatmaterialpropertyassignmentsare made to the underlying, or base, mesh prior to extruding a mesh, as this will ease the element selectionprocess. 7.3.2SurfaceMesh For a Surface Mesh the dropdown menu provides two mesh generation options (1) Building Block Projection (default)and(2)Extractwhichextractstheelementfacesfromavolumetricmeshforaselectsetofelements.For example,thismaybeusedtodefinearigidbodyonthebacksideofavolumetricmesh.Bothquadrilateraland triangularelementsaresupported.Thesurfacemeshdefinitionscurrentlyassumerigiddefinitions(i.e.,ABAQUS elementTYPE=R3D4andR3D3).Areferencenode(filename_RN)willautomaticallybeassignedtotherigidmesh withcoordinatesapproximatingthegeometriccenterofthemesh.Note:thisreferencenodewillautomatically populatetheNodeSetmenuwithintheLoad/BCpanel. Building Block Projection The grid of nodes established via the building block mesh seed assignmentsareprojectedontothesurfaceofinterestusingclosestpointprojection.Ifneedbe, theuserhastheoptionofsmoothingthemesh(referto7.4MeshImprovement). Extract A select set of elements may be extracted from a volumetric mesh as a surface mesh. WhentheExtractElementsbuttonisinvoked,awindowwillopenhousingtheElementSelection Toolbar (refer to Appendix II). It is recommended that material properties are assigned to the underlying, or base, mesh prior to extracting a mesh, as this will ease the element selection process.Whenameshisextracted,twomeshdefinitionswillpopulatetheObjectManager(e.g., index_proximal_Extract1 and index_proximal_Mesh_Extract1). The former will consist solely of the quadrilateral surface elements, while the latter is a mixed mesh, consisting of both the hexahedralandquadrilateralelements. 7.3.3Node/ElementNumberingandLabels Bydefaultthenode/elementnumbersstartcountingconsecutivelyfrom1unlessspecifiedotherwise.Theuser isalsopromptedtoprovidealabelfortherespectivenodes/elementssets.Aselementsareadded,thenumber picksupwheretheprevioussetended.Theuserhastheoptionofoverridingthisvalue.Moreover,theuserhas theoptionofrenumberingasetofnodes/elementsviatheRenumberNodes/Elementsactionunderthemain Meshdropdownmenu. 7.4MeshImprovement Due to variations in the curvature of the underlying surface, the distribution of the projected nodes may be suboptimal.Asaresult,LaplaciansmoothinghasbeenincorporatedintoIAFEMeshasanoptionforsmoothing theprojectedsurfacemesh.Laplaciansmoothingactstoequalizetheelementaledgelengthsbyadjustingthe locationofeachnodetothegeometriccenterofitsneighboringnodes.Duringthisprocess,thereisatendency forthenodebeingrepositionedtomoveawayfromthesurface.Toensurethatthesurfaceofthefiniteelement meshremainstruetothedesiredunderlyingimagebasedsurfacerepresentation,therepositionednodeisagain projected onto the underlying surface using closestpoint projection. Once the surface nodes are established, ellipticalortransfiniteinterpolationmaybeusedtocomputetheinteriornodes;thereafter,thevolumeisfilled withhexahedralelements.
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The Mesh Panel
7.4.1LaplacianSmoothing
BydefaultsmoothingisevokedforthemeshescreateddirectlyfromaBuildingBlockstructure.Deselectthe Perform Smoothing check box to deactivate the smoothing. The Smoothing Parameters frame houses the parameters used to control the number of Laplacian smoothing iterations to be performed (default = 1). If additional smoothing is required once the mesh is generated, these capabilities are provided in the Quality Panel,undertheMeshImprovementmenu. 7.4.2InteriorNodeInterpolationMethods The user has the option of choosing between Transfinite or Elliptical Interpolation Methods for internal node calculations. Transfinite Interpolation The interior points of the mesh are generated using transfinite interpolation. This method defines an algebraic coordinate transformation from the rectilinear grid(s) defined by the buildingblock(s)ontothephysicaldomainboundedbythesurface(Note:thecurrentnumberofdefault iterationshasbeensetto10). Elliptical Interpolation During Elliptic grid generation, the initial grid (algebraically computed using transfiniteinterpolation)isrelaxediterativelyusingaseriesofellipticpartialdifferentialequations,known asPoissongridgenerationequations.. 7.5MeshTabRenumberNodes/Elements FromthedropdownmenuselecttheNode/ElementSetlabeltoberenumberedandinthetextboxenterthe correspondingStartingNode/ElementNumber.
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The Quality Panel
8TheQualityPanel
TheQualityPanel
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The Quality Panel
8.1Overview
Regardlessofthemeshingtechnique,thesolutionofafiniteelementanalysisishighlydependentonthequality of the mesh. In addition to the mesh generation routines, algorithms have been included for evaluating and improvingtheensuingmesh.TheseoperationsarehousedintheQualityPanel.Themeshqualityapplication utilizestheopensourceVERDICTlibrarytoanalyzeelementqualityaccordingtoseveralmetrics:Volume,Edge Collapse, Jacobian, Skew, and Angle out of Bounds. These quality values are assigned per element and visualizedusingtheVTKlibrary.Sincedatasetsgenerallycontainalargenumberofelements,interactivetools have been developed that allow user to dynamically position a cutting plane within the dataset to expose internal elements. Furthermore, the elements may be scaled (via an element scaling option) for improved visualization.Theoverallobjectiveistomakethemeshgenerationprocessmoreefficientbyprovidingrapid, visualfeedbacktotheuser.
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The Quality Panel
8.2QualityTabEvaluate/DisplayMeshQuality Thefollowingdetailstheoptionsavailableforevaluatinganddisplayingtheresultingmeshquality. 8.2.1QualityMetrics:
Volume: the volume of a hexahedron is the product of the magnitude of the three principal axes.AnelementisconsideredtobevalidifitsvolumeisgreaterthanZero. EdgeCollapse:Ahexahedralelementhastwelveedges.Itisconsideredadegenerate/collapsed element if the number of edges is less than twelve. For viewing purposes, the normal and degenerateelementsareassignedvaluesof1and1,respectively. Jacobian:theJacobianisameasureofdeviationofanelementfromanideallyshapedelement. AnegativeJacobianisindicativeofsevereelementdistortion. Skew:Detectselementdistortionswhichariseduetolargeorsmallangles.Calculatestheskew angleforeachfaceofahexahedralelementandreportsthemaximum.Skewrangesfrom[0,1], where0representsadegenerateelement. AngleOutofBounds:Calculatestheangulardeviationbetweenadjacentfacesofthehexahedral element.Anelementisconsidereddistortedifananglemeasureslessthan450orgreaterthan 1350.
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The Quality Panel
8.2.2AMeshQualitySummaryReport
The Summary Report provides an overview of themeshforagivenmetric.Forexample,the illustrated summary suggests that a mesh consisting of 3978 elements yielded no distorted elements in terms of volume, while the minimum and maximum volumes were 0.014 and 2.536, respectively. Moreover, the average element volume measured 0.344with a variance of 0.092. Had there been a given numberofdistortedelements,theywouldhave been listed by Element ID and metric quality value in the window provided. The distorted element summary may be written to a file by selectingSave.
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The Quality Panel
8.2.3QualityDisplayOptions Togglesdisplayofthelegend Crosssectional view that may be manipulated by translating and rotating the cutting plane.TheInvertViewcheckboxtogglesbetweentheviewingdirectionwithrespectto thenormalofthecuttingplane.
DisplayOptionsprovidecontroloverthedisplayofmetric.Forexample,thespectrum ofthelegendmaybeassignedfromredtoblue(default),rangingfromtheminimumto the maximum metric value, respectively. It may also be changed to traverse blueto red. The limits of the scale may also be adjusted. By default, the maximum and minimum metric values are assigned. These values may be adjusted, by checking the Specify checkbox and assigning the Minimum and Maximum values of interest. Note that the elements exceeding the assigned maximum value will be colorcoded white, whilethoselessthantheminimumassumethecolorblack. Thenumberofsignificantfiguresdisplayedonthelegendandthelegendtitlemayalso bechanged.
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The Quality Panel
8.3QualityTabMeshImprovement ThemeshImprovementoptionsdetailed in7.4MeshImprovementarereiterated intheQualitypanel.Thisenablesthe meshqualitytobeevaluatedandthen improvedwithoutreturningtotheMesh Panel.Theuserhastheoptionbetween EllipticalandTransfiniteInterpolation methods,inadditiontothenumberof Laplaciansmoothingiterationsto perform.
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The Materials Panel
9TheMaterialsPanel
TheMaterialsPanel
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The Materials Panel
9.1Overview The Materials Panel affords the user the option of assigning userdefined, or imagebased, material properties. Moreover, the user has the option of displaying the resulting material definitions, as well as saving and/or exportingthemesh.
9.2MaterialsTabUserDefined UserDefinedMaterialPropertyAssignments To assign UserDefined Material Properties to a set (or sets) of elements, the elements must be grouped accordingly.Todefineindividualelementsets,selecttheElementSetDefinitionsbuttontolaunchawindow housingtheelementselectiontoolbar(describedindetailonthepagesthatfollow).Oncethesetsaredefined they will populate the drop down menu titled Element Set. From this menu select the set of interest and assigntheModulusandPoissonsratio,followedbyApply.Repeatthematerialassignmentsasneeded.Note that the Modulus and Poissons ratio text boxes will retain the assigned values for a given set for future reference.Moreover,toremoveamaterialassignment,simplyclearthetextboxandApply. 9.2.1EstablishingElementSetDefinitions Toassignmaterialpropertiesto,orrequestoutputdatafrom,aset(orsets)ofelements,theelementsmust begroupedaccordingly.Todefineindividualelementsets,selecttheElementSetDefinitionsbuttontolauncha windowhousingtheElementSelectionToolbar(describedindetailonthepagesthatfollow).Oncethesetsare definedtheywillpopulatethedropdownmenutitledElementSet.
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The Materials Panel
The Element Selection Toolbar provides a number of options for selecting/grouping elements. While making an element selection with any of these tools, hold down the Ctrl buttonandselecttheelementswiththeleftmousebutton.Theelementselectionwillbehighlightedingreen andconfirmedwithaclickoftherightmousebutton(thereaftertheelementsturnred).Elementsmaycontinue tobeadded/removedfromthesetuntilalabelisassignedandApplied.Thefollowinghighlightseachapplication. Examplesofeachareincludedonthenextpage.
AllElements:allelementsthroughoutthevolumetricmeshwithintheoutlinedfield. SurfaceElements:allsurfaceelementswithintheoutlinedfield. VisibleSurfaceElements:visiblesurfaceelementswithintheoutlinedfield. ElementsAssociatedwithaBlockFace:allelementsassociatedwithagivenblockface. SingleElement:asingleelement.
Inclusion/Exclusion:togglesbetweenincluding(+)andexcluding()theselectedentitiesfromagiven set.
The Opacity slider enables the user to readily view and work with the element selections.Theopacitylevelactstorestricttheelementsactiveforselection.Forexample,whenthemeshisfully opaque(1.00(100%)),allelementsareactiveandmaybeselectedforinclusionorexclusion.Oncetheopacityhas beenreduced,onlythehighlightedelements(selectedpreviously)remainactive.Thisenablestheusertorefinea series of elements defining a given set. The aforementioned selection methods will perform similarly on the subsetofelements,withtheexceptionofthefaceselectionoption(whichbecomesinactive). Ifneedbe,Clearstheelementselectionpriortobeingassignedanelementsetlabel.
AssignaSetLabeltotheselectedelements,followedby
.
55 | T h e Panels
The Materials Panel
9.2.2ElementSetSelectionToolbarCapabilities ExamplesofInclusion(+)
ExamplesofExclusion()
The remaining selection capabilities also function under the exclusion option, unfortunately the printed images are difficulttovisualize.Theexclusionoption was included, for the most part, as a means to readily refine an element set selection. An example is provided in Appendix II, Combining the Inclusion(+) and Exclusion () capabilities to edit an elementset.
56 | T h e
Panels
The Materials Panel
9.3MaterialsTabImageBased ImageBasedMaterialPropertyAssignments Once a mesh has been generated there is a direct correspondence between the model and the imaging data usedtogeneratethebonysurfacedefinition.Inadditiontoassigninguserspecifiedmaterialassignments(E,), IAFEMeshallowstheusertoassignelementwisematerialpropertiesuniquetoeachbone/specimenbasedon theCTnumber.ThedensityinformationprovidedbythedatasetispreservedbyconsideringalloftheCTvoxels thatfallwithintheelement.Theuserhastheoptionofaveragingthedensitiesofeachvoxelcontributingtoan element,calculatingthemediandensityvalue,orassigningthemaximumdensitycontributingtotheelement. Thereafter, the elastic moduli are calculated on an elementbyelement basis, thereby establishing the local stiffness. Subjectspecificitybasedonmaterialdefinitionsisfacilitatedbythefactthatalinearrelationshipexistsbetween digitalCTscandataandtheapparentdensityofbone.Moreover,variousmodelscanbefoundintheliterature fortherelationshipbetweenbonedensityandelasticmodulus.Forthesakeofgenerality,theelasticmodulus c has been defined according to the equation E = a + b app , where E is the elastic modulus, app the apparent density,anda,b,andcthemodelparameters.Theseparametersaretreatedasvariables,theymaybetunedby theuseraccordingtotherequirementsofthespecificproblem(defaultvalues:a=0,b=2875,andc=3).
57 | T h e
Panels
The Materials Panel
TheMesh&ImageAssignmentscollapsedframehousestheMeshandtheImagefromwhichthematerials willbeassigned.Ifmultipleobjectsareopen,ensuretheappropriateobjectidentifiersareselected.
If an element set to which the materials are to be assigned has yet to be defined, select the Element Set Definitionsbutton(refertoAppendixIIforadescriptionofthetoolsavailableforassigningelementstoaset). Otherwise,selectthedesiredelementsetfromtheElementSetmenu,andassignthecorrespondingPoissons Ratiointhetextbox. 9.3.1BinningMaterialPropertyAssignments Rather than assign unique material definitions on an elemental basis, it may be beneficial to assign a single elastic modulus to a set of elements. For example, material 1 may consist of elements with a modulus value in the range E1 E Emax, while the range for material2takestheformE2E<E1,and so on. This capability alleviates any potential restrictions imposed by some finite element modeling packages with regard to a limited number of material definitions. The Number of Bins as well as the range (check Specify Range) over which the moduli span (min and max) maybeassigned.
58 | T h e
Panels
The Materials Panel
9.4MaterialsTabDisplayMaterialProperties The Display Material Properties panel provides a means to visualize the distribution of the assigned moduli valuesthroughoutthemesh.Thefunctionalitiesaresimilartothoseprovidedforviewingthequalitymetrics. Togglesdisplayofthelegend Crosssectional view that may be manipulated by translating and rotating the cutting plane.TheInvertViewcheckboxtogglesbetweentheviewingdirectionwithrespectto thenormalofthecuttingplane.
Display Options provide control over the display of the material properties. For example, the spectrum of the legend may be assigned from redtoblue (default), rangingfromtheminimumtothemaximummetricvalue,respectively.Itmayalsobe changed to traverse bluetored. The limits of the scale may also be adjusted. By default,themaximumandminimummetricvaluesareassigned.Thesevaluesmaybe adjusted,bycheckingtheSpecifycheckboxandassigningtheMinimumandMaximum valuesofinterest.Notethattheelementsexceedingtheassignedmaximumvaluewill becolorcodedwhite,whilethoselessthantheminimumassumethecolorblack.
Thenumberofsignificantfiguresdisplayedonthelegendandthelegendtitlemayalso bechanged.
59 | T h e Panels
The Load/BC Panel
10TheLoad/BCPanel
60 | T h e Panels
TheLoad/BCPanel
The Load/BC Panel
10.1Overview TheLoading/BoundaryconditionsassignedtoameshplayanintegralroleinanFEanalysis.TheLoad/BCPanel was designed to enable the user to assign nodes to node sets which may then be assigned load and boundary conditions.Moreover,theseLoad/BCassignmentsmaybedisplayeddirectlyonthemeshforvisualconfirmation. Lastly, the user may request STEP information directly from this panel, namely from the STEPLoad/BC Assignmentsmenu).TheLoad/BCpanelalsoprovidesmenusforExportingthemodelinABAQUSFileformatas wellassavingthemesh.

61 | T h e Panels
The Load/BC Panel
10.2Load/BCTabSTEPLoad/BCAssignments Interactivetoolshavebeenimplementedtoidentifynodesforloadandboundaryconditionassignments.The user is afforded options for both single and multinode selection. Multinode selection takes several forms. Theuserhastheoptionofselectingtheseriesofnodesassociatedwithafaceofabuildingblockorbyselecting agroupofnodesviaaninteractiverubberbandboxselectiontool.Theboxselectiontoolmaybeusedtoselect all of the nodes defining the continuum mesh within the selected volume, or limit the nodes to those on the surfaceofthemesh. 10.2.1EstablishingNodeSetDefinitions To assign Load and/or Boundary Conditions to, or request output data from, a set (or sets) of nodes, the nodesmustbegroupedaccordingly.Todefineindividualnodesets,selecttheNodeSetDefinitionsbuttonto launchawindowhousingtheNodeSelectionToolbar(describedindetailonthepagesthatfollow).Oncethe setsaredefinedtheywillpopulatethedropdownmenutitledNodeSet.
62 | T h e
Panels
The Load/BC Panel
TheNodeSelectionToolbarprovidesanumberofoptionsforselecting/grouping nodes.Whilemakinganodalselectionwithanyofthesetools,holddowntheCtrlbuttonandselectthenodes with the leftmousebutton. The nodal selection will be highlighted in green and confirmed with a click of the rightmousebutton(thereafterthenodesturnred).Nodesmaycontinuetobeadded/removedfromthesetuntil alabelisassignedandApplied.Thefollowinghighlightseachapplication.Examplesofeachareincludedonthe nextpage.
AllNodes:allnodesthroughoutthevolumetricmeshwithintheoutlinedfield. SurfaceNodes:allsurfacenodeswithintheoutlinedfield. VisibleSurfaceNodes:visiblesurfacenodeswithintheoutlinedfield. Nodes associated with a block face: all nodes associated with a given block face by choosing a singlenodeonthatface. SingleNode:asinglenode.
The Opacity slider enables the user to readily view and work with the nodal selections.Theopacitylevelactstorestrictthenodesactiveforselection.Forexample,whenthemeshisfully opaque(100%), allnodes are active andmay be selected for inclusion or exclusion. Once the opacity hasbeen reduced, only the highlighted nodes (selected previously) remain active. This enables the user to view/refine a seriesofnodesdefiningagivenset.Someoftheselectionoperationsbecomeinactivewhentheopacity<1.00. Ifneedbe,Clearsthenodeselectionpriortobeingassignedanodesetlabel.
AssignaSetLabeltotheselectednodes,followedby
.
63 | T h e Panels
The Load/BC Panel
10.2.2NodeSetSelectionToolbarCapabilities Examplenodeselectionschosenviaeachofthenodalselectiontools.
64 | T h e
Panels
The Load/BC Panel
10.2.3AssigningaDescriptiveSTEPSubheading The Subheading textbox may beused toassign a descriptive subheading to the STEP. Note: ABAQUS retains onlythefirst80charactersofthesubheading. 10.2.4AssigningLoad/BoundaryConditions FromthedropdownmenubuttonchooseForce/MomentorDisplacement/Rotation.Selectapredefinednode setfromthedropdownmenu.Thereafter,assigntherespectiveLoad/BoundaryConditioninthex,y,andz textboxes,followedbyApply.Note,anappliedload/momentwillbedistributeduniformlyoverallnodeswithin an assigned set. For example, if a node set contains 10 nodes and a 10 N load is applied, the load will be distributedas1Nappliedtoeachnode.Furthermore,rotationsshouldbeenteredindegrees. Toremovealoadand/orboundaryconditionassignment,simplycleartherespectivetextboxandApply. 10.2.5DisplayingtheLoad/BoundaryConditions Once a node set has been established, it will populate the Load/BC Display window (housed in the Load/BC Display collapsed frame). Moreover, visual confirmation will be provided in the View Panel. The applied conditionsarecolorcodedwithrespecttotheglobalaxes(x:red,y:green,z:blue).Thearrowsarescaledwith respecttothelargestmagnitudeforagivencondition(load/displacement).Theoverallappearanceoftheload andboundaryconditionsmaybescaledviatheprovidedscaletextbox.Thecheckboxesenablethevisibilityof the Load/BC to be toggled on and off. The opacity may be adjusted to view forces/displacements directed withinagivenmesh.
65 | T h e
Panels
The Load/BC Panel
10.2.6Assigning*STEPDefinitions Select the *STEP Definitions button to launch a windowhousinganumberofSTEPoptionssuchas output and print requests. Please refer to the ABAQUS manuals for details regarding these parameters. As illustrated, default parameters have been provided. To accept the default step assignments, simply select Apply in the STEP frame,choosethedesiredNSETsandELSETsfrom the respective drop down menus and Apply. Note, Apply must be selected for each set assignment.Whentheoutputrequestparameters havebeencommitted,theywillbegrayedout.To reactivate the frame, select the NSET/ELSET of interestfromthedropdownmenu.Tochangea parameter,simplyuncheckacheckbox,changea drop down menu, or update the respective textbox, and Apply. All parameter requests enteredintothetextboxesshouldbedelimitedby commas. 10.2.7MultipleStepAnalysis Oftentimes it is beneficial to divide the load historyofasimulationintoanumberofsteps.As a result, the user may add/remove steps by selecting the +STEP/STEP buttons. As steps are requested, tabbed panels will be added sequentially.Usingthemethodsdescribedabove, the load and boundary conditions can then be assigned to the respective steps. Note, as additionalstepsareadded,theSTEPdefinitionsof the new step will take on the assignments from the previous step. As a result, you may need to onlyassigntheLoadandBoundaryconditionsfor thenewstep.
66 | T h e
Panels
APPENDIX I: Building Block Operations - Examples
AppendixI:BuildingBlockOperationsExamples APPENDIXI
BuildingBlockOperations
67 | A p p e n d i c e s
BuildingBlockOperationsToolbar
Move operations: Allows the constituents of a block (vertices, edges, and faces) to be repositioned independently. To activate an individual component, with the left mouse button click on the part of interest(activeelementswillbehighlightedingreen).Notethatedgeselectionrequirestheuseofthe middle,asopposedtotheleft,mousebutton.Dragthecomponenttothedesiredlocation(besureto rotatetheviewtoensuretheblockispositionedcorrectlyrelativetothesurface).Tomovemultiplefaces simultaneously,holdtheshiftbuttonwhileselecting/deselectingthefacesofinterest.
Subdivideoperation:Dividesthebuildingblockofinterestinhalf.Withtheleftmousebutton,selectthe edgealongwhichtheblockshouldbedivided(edgewillbehighlightedingreen)followedbyApply.The subdivisionwillpropagatetoadjacentblocksthroughoutthestructureautomatically.
Addoperation:Addsanewbuildingblock,orblocks,totheface(s)ofanexistingblock/structure.With theleftmousebuttonselectthefaceofinterest.Tohighlightmultiplefaces,holdtheshiftbuttonwhile selecting/deselectingthefacesofinterest.Again,theactivefaceswillbehighlightedingreen.Provide anextrusionlength,followedbyApply.2 Note:thecoincidentverticesgeneratedviatheaddoperationwillequivalenced/mergedautomatically.
Deleteoperation:Removesunwantedblocksfromabuildingblockstructure.Withtheleftmousebutton selecttheblockstoberemoved.Toremovemultipleblockssimultaneously,holdtheshiftbuttonwhile selecting/deselectingtheblocksofinterest.Theactiveblockswillbehighlightedingreen.Whenthe selectioniscomplete,selectApply.
Consolidate: Consolidates two or more independently defined building block structures into a single structural definition. To ensure that the blocks are contiguous, the vertices to be shared must be equivalenced.Note:twosphereswithintheuserspecifiedtolerancewillbehighlightedyellow.
Mirror:Mirrorsabuildingblock,orblockstructure,aboutaplane.Selecttheplaneofinterest(XY,XZ,or YZ),andpositionitasdesiredrelativetotheoriginalbuildingblockdefinition(s).
Equivalence / Merge: Merges the vertices of selected building blocks (within the specified tolerance). Required when building blocks have been mirrored, or when multiple blocks have been independently added adjacent to one another. Note: two spheres within the userspecified merge tolerance will be highlightedyellow. TherightmousebuttonmayreplacetheApplybuttonforthesplit,add,anddeleteoperations.Inorderforthis shortcuttobeused,thecursormustremainon(ornear)theactiveelement(edge,face,orblockhighlightedin green)ofinterestwhentherightmousebuttonisdepressed.
BuildingBlockModifications;ManipulatingtheBlockVertices,Edges,and/orFaces. ExamplesoftheBuildingBlockeditingoperation, definitions. 1. 2. 3. 4. Note:Eachmoveoperationiscommittedinteractively,asopposedtorequiringApply. Depressthe button.
,whichenablestheblock(a)vertices,(b)edges,and(c)facestoberepositionedforimprovedmesh
Tomoveavertex,simplyclickonthesphereofinterestwiththeleftmousebuttonanddragthevertextothedesiredlocation. Tomoveablockedge,withthecentermousebuttonselecttheedgeofinterestanddragtheedgetothedesiredlocation. Tomoveaface,usetheleftmousebutton.Ifmultiplefacesaretobemovedsimultaneously,holdtheshiftbuttonwhileselecting/deselectingthe facesofinterest,anddragthemasagrouptothedesiredlocation.
Subdividingablockintwo. Abuildingblockmaybedividedinhalfbysimplychoosingtheedgealongwhichtheblockshouldbesplit.Asameansofvisualconfirmation,theactiveedgeis highlightedbyacolorchange,andthenbisected.Thethreeedgesparalleltotheactiveedgearealsobisectedandverticesdefinedatthedivisionpoints, thereby yielding two blocks from the preexisting building block. The following provides stepbystep instructions for subdividing a block and further subdividingtheresultingstructuretoillustratehowthesubdivisionpropagatesthroughaseriesofadjacentblocks. 1. 2. Depressthe button.Withtheleftmousebuttonclickontheblockedgealongwhichtheblockistobesubdivided(asconfirmation,theedge willturngreen).Oncethedesirededgehasbeenhighlighted,selectApply(shortcut:rightmousebutton). Repeattheaforementionedsequence,thistimeselectinganedgewithparalleledgessharedbyanadjacentblock. *Note:Thesplitfunctionwillpropagatethroughtoadjacentbuildingblocks,dividingthoseblockswithedgesparalleltotheoriginalsplit edge.
AddingtoaBuildingBlockOneblockatatime. Blocksmaybeaddedindependentlyorasagroup.Thefigureaboveillustratestwoblocksbeingaddedindependently.Thefollowingprovidesstepbystep instructionsfordoingsoonceabaseblockhasbeenestablished: 1. Selectthe button.Enterthedesiredextrusionlengthandwiththeleftmousebuttonclickonthefacetowhichanewblockwillbeadded(as confirmation,thefacewillturngreen;Note:extrusionlengthassignmentandfaceselectionarenotorderdependent).Oncethedesiredfacehas beenhighlighted,selectApply(shortcut:rightmousebutton). Asillustrated,followthesamestepsoutlinedabove(step1)forasecondfacesharingacornerwiththefirst.Whenfacesareaddedindependently, eachblockisprojectedperpendiculartothechosenface.Asaresult,ifthenewblocksaretoshareanedge,therespectiveverticesmustbemerged asfollows. Select .Theverticestobemergedmustberepositionedwithincloseproximitytooneanother.(Note:theindividualcomponentsoftheblocks mayberepositionedusingthesametechniquesasthemoveoperations.)Twoverticespositionedwithintheassignedtoleranceofoneanotherwill behighlightedinyellow.Oncealloftheverticestobeequivalencedareyellow,selectapply.Iftheactioniscancelled,oranothereditingoperationis selected prior to equivalencing the vertices, all position changes will be removed and the block structure will return to the state prior to the manipulations.Anexampleofanequivalencedvertexishighlightedinthefigureabovebyanorangecircle. Refertothenextexampletoaddmultipleblockssimultaneously,therebybypassingtheneedtoequivalence.
2.
3.
AddingtoaBuildingBlockMultipleblockssimultaneously. Multipleblocksmaybeaddedtoablock/structuresimultaneously.Thefollowingprovidesstepbystepinstructionsfordoingsoonceabaseblockorstructure hasbeenestablished: 1. Depressthe button.Enterthedesiredextrusionlengthandwiththeleftmousebutton(whileholdingdowntheshiftkey)clickoneachofthe facestowhichanewblockwillbeadded(asconfirmation,thefacewillturngreen;Note:extrusionlengthassignmentandfaceselectionarenot orderdependent).Oncethedesiredfaceshavebeenhighlighted,selectApply(shortcut:rightmousebutton). Thisapplicationautomaticallyequivalencestheverticessharedbetweenadjacentblocks.
2.
RemovingaBuildingBlockorSeriesofBlocks. Blocksmayberemovedindependentlyorasagroup.Thefigureaboveillustratesasingleblockbeingremovedfromastructure.Thefollowingprovidesstep bystepinstructionsfordoingsoonceabaseblockorstructurehasbeenestablished: 1. Selectthe button.Withtheleftmousebutton,clickontheblocktoberemoved(asconfirmation,theblockwillturngreen).Ifmultipleblocks are to be removed simultaneously, hold down the shift key while making multiple block selections. Once the desired block/s has/have been highlighted,selectApply(shortcut:rightmousebutton).
ConsolidatingTwoIndependentBuildingBlockStructures. Asthemodelcomplexityincreases,theremaybeinstanceswhentwobuildingblockshave beengeneratedindependentlyandmustbemergedintoasinglestructure.Thefollowing detailsthestepsforconsolidatingtwostructuresconstructedandloadedindependently. 1. Select .Awindow,populatedbythebuildingblockstructurescurrently loadedinIAFEMesh,willopen.Checkthecheckboxofthestructure(s)tobe manipulated.Similartothemoveoperation,theverticesoftheactivestructure(s) willbehighlightedbyredspheres. SetaTolerancevalue. Repositionthevertices/edges/facestobringtheverticestobemergedwithinthe specifiedtolerance;oncewithinthespecifiedtolerance,thetwoverticeswillbe highlightedinyellow. Oncealloftheverticesofinterestarehighlightedinyellow,Apply. Note:Oncetheverticeshavebeenmerged,ifyouopt torepositionavertexfromwithintheConsolidate operationbesuretoselectApplyoncerepositioned suchthatthechangesarecommittedtothenew structure.TheotheroptionistoreturntotheMove operationandrepositionthevertices.
2. 3.
4.
Mirroringablockstructure Whenpossible,takeadvantageofsymmetry.Apreexistingbuildingblock,orseriesofblocks,maybemirroredaboutaplanepositionedrelativetothebase block structure. A plane, parallel to one of the coordinate planes may be assigned automatically, or it may be interactively repositioned to a desired orientation.Recall,neighboringblockssharevertices.Asaresult,theverticesofthenewstructuremustbemergedwiththosefromwhichitwasmirrored. Consequently, the vertices of interest are moved into close proximity to one another and merged based on a radial tolerance assigned by the user. The followingprovidesstepbystepinstructionsformirroringabaseblockorstructure: 1. Depressthe button.Selecttheplaneofinterest(xy,xz,oryz).Usetheleftmousebuttontoposition(translate/rotate)theplanewithrespectto thebasestructure.SelectApply. Theverticesalongthemirroringplanemustbemerged.Consequently,theseverticesmustbecoincident(withintolerance). Activate the Equivalence/Merge operation by selecting . Within this operation, the vertices/edges/faces may be repositioned (similar to move).Enteraradialtolerance.Whentheverticesofinterestarewithinthespecifiedtolerancetheywillbehighlightedinyellow.Onceallofthe verticesalongthemirrorplaneareallyellow,selectApplytomergethemirroredstructures.
2. 3.
APPENDIX II: Element/Node Set Selection Toolbar
AppendixII:Element/NodeSetSelection APPENDIXII
Element/NodeSetSelection
The Element Selection Toolbar provides a number of options for selecting/grouping elements. While making an element selection with any of these tools, hold down the Ctrl buttonandselecttheelementswiththeleftmousebutton.Theelementselectionwillbehighlightedingreen andconfirmedwithaclickoftherightmousebutton(thereaftertheelementsturnred).Elementsmaycontinue tobeadded/removedfromthesetuntilalabelisassignedandApplied.Thefollowinghighlightseachapplication.
AllElements:allelementsthroughoutthevolumetricmeshwithintheoutlinedfield. SurfaceElements:allsurfaceelementswithintheoutlinedfield. VisibleSurfaceElements:visiblesurfaceelementswithintheoutlinedfield. ElementsAssociatedwithaBlockFace:allelementsassociatedwithagivenblockface. SingleElement:asingleelement.
The Opacity slider enables the user to readily view and work with the element selections.Theopacitylevelactstorestricttheelementsactiveforselection.Forexample,whenthemeshisfully opaque(1.00(100%)),allelementsareactiveandmaybeselectedforinclusionorexclusion.Oncetheopacityhas beenreduced,onlythehighlightedelements(selectedpreviously)remainactive.Thisenablestheusertorefinea series of elements defining a given set. The aforementioned selection methods will perform similarly on the subsetofelements,withtheexceptionofthefaceselectionoption(whichbecomesinactive). Ifneedbe,Clearstheelementselectionpriortobeingassignedanelementsetlabel.
AssignaSetLabeltotheselectedelements,followedby
Theaboveillustrationexemplifiestheelementselectionprocess.Supposetheallelementstoolwasselected. Holding the left mouse button and the Ctrl key, drag a box around the elements of interest (the selected elementswillbehighlightedingreen).Toconfirmthisselection,withthecursoroverthemesh,clicktheright mousebutton(thehighlightedelementswillchangetored).Reducingtheopacitywillprovideaninternalview oftheselectionaswellasenabletheusertoworkwiththeelementselection. CombiningtheInclusion(+)andExclusion()capabilitiestoeditanelementset Forexample,aninitialsetofelementsareselected/included .Torefinetheselection,theopacityisfirst
decreased,andasubsetoftheelementsarethenexcludedbytogglingtheinclusion/exclusionbuttonsto . Theelementstoberemovedarechosenviatheappropriateselectionoperation(highlightedbelowingreen). Withaclickoftherightmousebuttonthehighlightedelementsareremovedfromtheelementset.
APPENDIX II: Element/Node Set Selection Toolbars
TheNodeSelectionToolbarprovidesanumberofoptionsforselecting/grouping nodes.Whilemakinganodalselectionwithanyofthesetools,holddowntheCtrlbuttonandselectthenodes with the leftmousebutton. The nodal selection will be highlighted in green and confirmed with a click of the rightmousebutton(thereafterthenodesturnred).Nodesmaycontinuetobeadded/removedfromthesetuntil alabelisassignedandApplied.Thefollowinghighlightseachapplication.
AllNodes:allnodesthroughoutthevolumetricmeshwithintheoutlinedfield. SurfaceNodes:allsurfacenodeswithintheoutlinedfield. VisibleSurfaceNodes:visiblesurfacenodeswithintheoutlinedfield. Nodes associated with a block face: all nodes associated with a given block face by choosing a singlenodeonthatface. SingleNode:asinglenode.
The Opacity slider enables the user to readily view and work with the nodal selections.Theopacitylevelactstorestrictthenodesactiveforselection.Forexample,whenthemeshisfully opaque(100%), allnodes are active andmay be selected for inclusion or exclusion. Once the opacity hasbeen reduced, only the highlighted nodes (selected previously) remain active. This enables the user to view/refine a seriesofnodesdefiningagivenset.Someoftheselectionoperationsbecomeinactivewhentheopacity<1.00. Ifneedbe,Clearsthenodeselectionpriortobeingassignedanodesetlabel.
AssignaSetLabeltotheselectednodes,followedby
APPENDIX II: Element/Node Set Selection Toolbars
CombiningtheInclusion(+)andExclusion()capabilitiestoeditanelementset Similartotheoperationsestablishedforselectingelements, For example, an initial set of nodes are selected / included . To refine the selection, the opacity is first
. decreased, and a subset of the nodes are then excluded by toggling the inclusion/exclusion buttons to Thenodestoberemovedarechosenviatheappropriateselectionoperation(highlightedingreen).Withaclick oftherightmousebuttonthehighlightednodesareremovedfromthesetdefinition.
APPENDIX III: Example Mesh Definitions
AppendixIII:MeshExamples APPENDIXIII
MeshExamples
PhalanxbonesandtheAscensionPIPTotalJointReplacement
CarpalBonesandUniversal2 TotalWristImplant
TM
HumanBrain
Aneurysm
MechanicalJoint
INDEX
A
ApplicationSettings7 ApplyButton14 Assign/EditMeshSeeds41 GlobalMeshSeedAssignment41 LocalMeshSeedAssignment42 AssigningBoundaryConditions65 AssigningLoads65 Autosave7
I
ImageBasedMaterialProperties57 InteractingwiththeImage30
L
LoadAssignments62 LoadingSeeAssigningLoads LoadinganObject13
B
BoundaryConditions62,SeeAssigningBoundary Conditions BuildingBlockOperationsToolbar36,37,68
M
MainToolbar6 MaterialProperties BinningImageBasedProperties58 ImageBased57 UserDefined54 MeshImprovement45 MultipleStepAnalysis66
C
CancelButton14 CollapsibleFrames13 CommandPanel9 CreatingaBuildingBlock35 Fromsurfacebounds35 Manually35
N
Namingconvention10 NodeNumbering45 NodeSetDefinitions63,79
D
DefiningaNodeSetSeeNodeSetDefinitions DefininganElementSetSeeElementSetDefintiions DeletinganObject13 DisplayMeshQuality49 DisplayingBoundaryConditions65 DisplayingLoads65 DisplayingMaterialProperties59
O
ObjectManager10
Q
QualityMetrics49
E
ElementNumbering45 ElementSetDefintiions55,77 ElementSize12 EvaluateMeshQuality49 ExportingaFile13 ExtractaSurfaceMesh45 ExtrudeaVolumetricMesh44
R
Referencenode45 RenumberElements46 RenumberNodes46 RollingBackaBuildingBlockStructure38 RollingForwardaBuildingBlockStructure38
85 | I n d e x
S
SavinganObject13 Shortcutkeys31 STEPDefinitions66 SurfaceMesh45
TheMaterialsPanel53 TheLoad/BCPanel60 Tutorial15
U
UserDefinedMaterialProperties54
T
TabbedPanels13 TheImagePanel29 TheSurfacePanel32 TheBlock(s)Panel34 TheMeshPanel40 TheQualityPanel47
V
ViewPanel9 ViewSettings8 Viewing/ActivatinganObject10 VolumetricMesh44
86 | I n d e x

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whereinstallpathisthedirectorywhereyouunpackedtheprogram.Thiscanbeaddedtoyour.bashrcfileto makethisadditioneachtimeyoulogin. Forthecsh,thefollowingcommandneedstoberunoraddedtoyour.cshrcfile.

Interfacing with IA-FEMesh

Interfacing with IA-FEMesh

2.1Overview TheIAFEMeshinterfaceconsistsofaMainToolbar,theViewPanel,andaCommandPanelwhichconsistsofan ObjectManagerandaseriesofTabbedPanels.Thefollowingintroduceseachofthesebasiccomponents.

2.2TheMainToolbar ThemostnotablemenuontheMainToolbaristheViewMenu.TheViewMenuhousestheApplicationand ViewSettings.

Interfacing with IA-FEMesh

Interfacing with IA-FEMesh

TheColorsframeenablestheViewPanelbackgroundandtextcolortobechanged,whiletheViewframehouses acollectionoficonsusedtomanipulateorcaptureaview: Predefinedviewsbasedonthesixfacesofacube.Eachtriadindicatestheorientationofthis imaginarycubewiththeviewwindow.

Interfacing with IA-FEMesh

Interfacing with IA-FEMesh

Interfacing with IA-FEMesh

Interfacing with IA-FEMesh

Interfacing with IA-FEMesh

Interfacing with IA-FEMesh

2.6.4Apply/CancelanOperation Lastly,theApplyandCancelbuttonsacttoperformthegivenactionandtoabandontheoperationandreturnto themainmenubutton,respectively.Note,whileapanelisinuse,allotherpanelsaredeactivated.Cancelmust beinvokedtochangebetweenthetabbedpanels.

IA-FEMesh Tutorial: Proximal Phalanx Bone

IA-FEMesh Tutoria E al:

IA-FEMesh Tutorial: Proximal Phalanx Bone

IA-FEMesh Tutorial: Proximal Phalanx Bone

IA-FEMesh Tutorial: Proximal Phalanx Bone

ExamplesoftheBuildingBlockeditingoperation, , whichenablestheblock(a)vertices,(b)edges,and(c) facestoberepositionedforimprovedmeshdefinitions. Note:Theradiioftheredspheresmaybescaled:

IA-FEMesh Tutorial: Proximal Phalanx Bone

IA-FEMesh Tutorial: Proximal Phalanx Bone

IA-FEMesh Tutorial: Proximal Phalanx Bone

IA-FEMesh Tutorial: Proximal Phalanx Bone

IA-FEMesh Tutorial: Proximal Phalanx Bone

IA-FEMesh Tutorial: Proximal Phalanx Bone

IA-FEMesh Tutorial: Proximal Phalanx Bone

Repeattheaforementionedprocedure ... createanadditionalnodesetforloading themodelandapplyaForce.

IA-FEMesh Tutorial: Proximal Phalanx Bone

14. ToSavetheFEmesh.Themeshmaybesavedfromanyofthemeshrelatedpanels(i.e.,Mesh,Quality, Materials,andLoad/BCPanels)byselectingSavefromtherespectiveMainMenu.Thisenablestheuser toreadilysavethemeshthroughoutthedevelopmentprocess.ThefilewillbesavedinVTKfileformat.

IA-FEMesh Tutorial: Proximal Phalanx Bone

IA-FEMesh Tutorial: Proximal Phalanx Bone

The Image Panel

The Image Panel

The Image Panel

The Surface Panel

The Surface Panel

The Block(s) Panel

The Block(s) Panel

The Block(s) Panel

The Block(s) Panel

Subdivideoperation:Dividesthebuildingblockofinterestinhalf.Withtheleftmousebutton,selectthe edgealongwhichtheblockshouldbedivided(edgewillbehighlightedingreen)followedbyApply.The subdivisionwillpropagatetoadjacentblocksthroughoutthestructureautomatically.

Deleteoperation:Removesunwantedblocksfromabuildingblockstructure.Withtheleftmousebutton selecttheblockstoberemoved.Toremovemultipleblockssimultaneously,holdtheshiftbuttonwhile selecting/deselectingtheblocksofinterest.Theactiveblockswillbehighlightedingreen.Whenthe selectioniscomplete,selectApply.

The Block(s) Panel

The Block(s) Panel

The Mesh Panel

The Mesh Panel

The Mesh Panel

The Mesh Panel

Seedsmaybeassignedinsuchawaythattheyaffectonlytheblockunderconsideration.Forexample,inthe examplebelow,themeshseedsontheGyaxiswereincreasedfrom8to16.Asaresult,thefouredgesofthe blockparalleltotheGyaxiswereassigned16subdivisions(illustratedinblue).

The Mesh Panel

The Mesh Panel

The Mesh Panel

The Quality Panel

The Quality Panel

The Quality Panel

8.2QualityTabEvaluate/DisplayMeshQuality Thefollowingdetailstheoptionsavailableforevaluatinganddisplayingtheresultingmeshquality. 8.2.1QualityMetrics:

The Quality Panel

The Quality Panel

The Quality Panel