manual-Diamond4使用手册

UserManualDIAMONDUserManualVersion4.1UserManualAlltitleandcopyrightsinandtotheDiamondsoftware,theaccompanyingprintedmaterials,andanycopiesoftheSoftwareProduct,areownedbyCRYSTALIMPACToritssuppliers.Allrightsreserved.Nopartofthismanualmaybereproduced,storedinaretrievalsystem,ortransmitted,inanyform,orbyanymeans,withoutthepriorwrittenpermissionofthecopyrightowner.TheDiamondsoftwareproductisprotectedbycopyrightlawsandinternationaltreatyprovisions.Therefore,youmusttreattheDiamondsoftwarelikeanyothercopyrightedmaterial,exceptthatyoumaymakeonecopyoftheDiamondsoftwaresolelyforbackuporarchivalpurposes.Thissoftwareproductisprovided”ASIS”withoutwarrantyofanykindeitherexpressedorimplied,includingbutnotlimitedtotheimpliedwarrantiesmerchantibilityandfitnessforaparticularpurpose.TheentireriskastothequalityandperformanceoftheSoftwareProductiswithyou.CRYSTALIMPACTdoesnotwarrantthatthefunctionscontainedintheSoftwareProductwillmeetyourrequirementsorthattheoperationofthesoftwarewillbeuninterruptedorerrorfree.IntelisaregisteredtrademarkofIntelCorp.,SantaClara,CA,USA.AMDisaregisteredtrademarkofAMDCorp.,Sunnyvale,CA,USA.MicrosoftandWindowsareregisteredtrademarksoftheMicrosoftCorp.,Redmond,WA,USA.Theterms”POV-Ray”and”PersistenceofVisionRaytracer”aretrademarksofPersistenceofVisionRaytracerPty.Ltd.ThePOV-RayTMpackageispresentontheDiamondCD-ROMasafreebonus;customersofDiamonddonotpayforPOV-Rayinanyway.YoucandownloadtheofficialPOV-RaypackagewithoutchargefromfilePOVLEGAL.DOC.ThePOV-Rayteamdoesnotendorsethedistributororitsproducts.ThePOV-Rayteamreceivesnocompensationforthisdistribution.FordetailedinformationaboutthePOV-Raylicense,pleasereadthe”GENERALLICENSEAGREEMENT”(alsocalled”POVLEGAL.DOC”)at::[e-mail]:flection:TheDIAMONDConcept17Task..............................................17Step-by-Step..........................................17ConnectivityandFilter....................................18ExploringUnknownCrystalStructures............................18UsingCrystalStructurePictures...............................19TutorialB:AdvancedExamples20MolecularStructures.....................................20ExploringanUnknownStructure...............................25ZeoliteFramework......................................34CreatingHighQualityPicturesUsingPOV-RayTM.....................44CreatingVideoSequences..................................51WheretogetHelp57Support58Appendix59Installation..........................................59InstallPOV-RayTM......................................60OnlineUpdate.........................................60RestoreFactorySettings...................................60What’sNewforDiamond3Users..............................61BasicSoftwareHandling...................................70References74Index75Introduction1IntroductionYouhavecrystalstructuredata(eitherspacegroup/unitcell/atomicparametersorafile(e.g.CIF))andwouldliketo...createhigh-qualitypicturesforapresentationorpublication?understandtheconstructionprinciplesofthestructure?visualizetheconstructionprinciplesinvariouswaysforyourstudents?Excellent.That’sexactlywhatyoucandowithDIAMOND,amodernsoftwarepackageforvisu-alizingcrystalstructuresattheatomiclevel.Thenewversion4hasbeenimprovedagainoverthepreviousversionstomaketheinitialstepsassimpleaspossible1.Asaresult,youcancreatebeautifulpicturesofyourcrystalstructurewithouteverreadingthismanual.Nevertheless,Diamondisareallypowerfulpackageofferingalargevarietyofoptionsfarbeyondtheseinitialsteps.InordertobeabletousethefullpowerofDiamond,westronglyrecommendtoreadthismanual,followingourrecommendations:1.Firstofall,youarecertainlyeagertogetyournewDIAMONDsoftwarepackagerunningonyourcomputerstraightawayandcreatesomepicturesfortesting.Hence,pleaseinstallthesoftwareasdescribedonp.59(ifyouhavenotalreadydoneso),andworkthroughthetutorialsessionA(p.2),followingtheinstructionsgiveninthetext.2.Onceyouhavecreatedyourfirstpictures,werecommendtoreservealittlebitoftimeforreflection,preferrablynotduringabusydaybetweenseveralphonecalls,meetingsandfre-quentlyinterruptingcolleagues.3.Haveaseatinanarmchairwiththemanualandanicecupofcoffeeortea,andreadthechapter”Reflection”onp.17.ThinkaboutyourfirststepsintutorialA,andconsiderwhatyouwouldliketodowiththesoftwareconcerningyourownresearch.4.Youmightevenwanttohaveafirstlookatthechapter”TutorialB:AdvancedExamples”(p.20)whilesittinginyourchair,inordertogetanimpressionofwhatwillhappennext.5.Afterwards,returntoyourcomputerandperfor