VESTA_Manual

VESTA:aThree-DimensionalVisualizationSystemforElectronicandStructuralAnalysisKoichiMOMMA1andFujioIZUMI2NationalInstituteforMaterialsScience,1-1Namiki,Tsukuba,Ibaraki305-0044,JapanOctober6,20111Currentaliation:NationalMuseumofNatureandScience,Tokyo,3-23-1Hyakunincho,Shinjuku-ku,Tokyo169-0073.E-mail:[e-mail]2E-mail:[e-mail]NTxi1INTRODUCTIONANDBACKGROUND11.1UnderstandingCrystalandElectronicStructuresinThreeDimensions......11.2CircumstancesbehindtheDevelopmentofVESTA.................11.3What'sNewinVESTA3...............................21.4NotesonthisManual.................................32OVERVIEWOFTHEPROGRAM42.1GeneralFeatures....................................42.2VisualizationofStructuralModels..........................42.2.1Avarietyofstructuralinformationderivedonselectionofobjects.....92.3VisualizationofVolumetricData...........................92.4VisualizationofCrystalMorphologies........................112.5CooperationwithExternalPrograms.........................132.6InputandOutputFiles................................132.7ProgrammingConcept.................................132.7.1Graphicaluserinterface............................142.7.2Corelibraries..................................143GETTINGSTARTED153.1Minimumrequirementsofhardware.........................153.2Windows........................................153.3MacOSX........................................163.4Linux..........................................163.4.132-bitversion..................................163.4.264-bitversion..................................173.5TroubleShooting....................................183.6LoadingFiles......................................184MAINWINDOW194.1ComponentsoftheMainWindow...........................194.2Menus..........................................204.2.1Filemenu....................................204.2.2Editmenu....................................214.2.3Viewmenu...................................214.2.4Objectsmenu..................................214.2.5Utilitiesmenu..................................22ii4.2.6Helpmenu...................................234.3ToolsintheHorizontalToolbar............................234.3.1Alignment....................................234.3.2Rotation.....................................234.3.3Translation...................................244.3.4Scaling.....................................244.4ToolsintheVerticalToolbar.............................244.5TextArea........................................254.5.1Outputtab...................................254.5.2Commenttab..................................255DISPLAYSTYLES275.1StructuralModels...................................275.1.1Objectstobedisplayed............................275.1.2Styles......................................285.2VolumetricData....................................295.3CrystalShapes.....................................305.3.1Styles......................................306GIVINGPHASEDATA316.1DeningPhases.....................................326.2SymmetryandUnitCell................................326.2.1Crystalsystemsandspacegroups.......................326.2.2Behaviorwhenchangingaspace-groupsetting...............346.2.3Latticeparameters...............................356.2.4Customizationofsymmetryoperations....................356.2.5Reducingsymmetry..............................356.2.6Transformationoftheunitcell........................366.3StructureParameters..................................406.3.1SymbolsandLabels..............................416.3.2Formalcharge..................................416.3.3Fractionalcoordinates.............................426.3.4Occupancy...................................426.3.5Atomicdisplacementparameters.......................426.3.6Importingstructureparameters........................446.3.7Removingduplicateatoms...........................446.4VolumetricData....................................456.4.1Volumetricdatatodrawisosurfaces.....................456.4.2Volumetricdataforsurfacecoloring.....................476.5CrystalShape......................................476.5.1Examples....................................487OVERLAYINGMULTIPLEDATA507.1PositioningofPhases..................................507.2RelativeOrientationofPhases............................517.3Examples........................................51iii8CREATINGBONDSANDPOLYHEDRA538.1SpecicationsofSearchingforBonds.........................548.1.1Searchmode..................................548.1.2Boundarymode.................................548.1.3Options.....................................548.1.4Apairofatoms.................................558.2OperatingInstructions.................................558.2.1Creatingcoordinationpolyhedra.......................558.2.2Searchingformoleculesandclusters.....................568.2.3Applicationsofthe\Searchmoleculesmodetoinorganiccrystals.....568.2.4Searchingforhydrogenbonds.........................578.2.5Visualizingcage-likestructures............