XiangyunQiu
email:xiangyun@pa.msu.eduSimonBillinge
email:billinge@pa.msu.edu
DepartmentofPhysicsandAstronomy,MichiganStateUniversity,
EastLansing,Michigan,48824-2320,USA
Documentcreated:July22,2004
Preface
PDFgetX2SoftwareLicenseAgreement
BydownloadingandinstallingacopyofthePDFgetX2SoftwareandDocumentation,youagreetothefollowingterms.
NotificationofCopyright:PDFgetX2isaproprietaryproductofMichiganStateUniversity(\"MSU\")andisprotectedbycopyrightlawsandinternationaltreaty.You(as\"EndUser\")musttreatPDFgetX2likeanyothercopyrightedmaterials.CopyrightlawsprohibitmakingcopiesoftheSoftwareforanyreason.YoumaymakecopiesoftheDocumentationforusewithalicensedversionoftheSoftware;however,MSUnotificationsofcopyrightmustbeleftintact.Ifyouhaveanyquestionsconcerningthisagreement,pleasecontacttheCopyrightLicensingOffice,MSU,EastLansing,Michigan48824U.S.A.(517)355-2186.
License:MSUgrantsEndUsertheroyalty-free,non-exclusive,non-transferablerighttousePDFgetX2softwareforresearchoreducationalpurposes.Youmaynotredistribute,transfer,rent,lease,sell,lend,sub-license,preparederivativeworks,decompile,orreverse-engineerthePDFgetX2SoftwarewithoutpriorexpresswrittenconsentofMSUattheaboveaddress.
MSUretainstitletoPDFgetX2,includingwithoutlimitationtheSoftwareandDocumentation.EndUseragreestousereasonableeffortstoprotecttheSoftwareandDocumentationfromunauthorizeduse,reproduction,distribution,orpublication.AllrightsnotspecificallygrantedinthisAgreementarereservedbyMSU.
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Contents
1
Introduction
1.1WhatisPDFgetX2?1.2Whatisnew?...
1.2.1Version1.01.2.2Betarelease1.3UsingPDFgetX2.1.4Usingthismanual.1.5Acknowledgments
667777101010101112131415151717171820202121
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2
QuickStartTutorial
2.1Installationandstart-up............2.2Copytutorialdata...............
2.2.1Descriptionofthetutorialexperiment2.3PreprocessSPECformatdata.........
2.3.1Objective...............2.3.2LoadSPECdatafile.........2.3.3Overviewofscansinformation....2.3.4SetupSPECcolumns........2.3.5Setupdeadtimecorrection......2.3.6Setupdetector(s)merging......2.3.7Actionsandvisualization.......2.3.8Savemergeddataandthehistory..2.4GetX-rayPDF................
2.4.1Objective...............2.4.2Setupworkingdirectory.......2.4.3Inputdatafiles............2.4.4Experimentsetup...........2.4.5Sampleinformation..........2.4.6Setupcorrections........
.
..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
CONTENTSPDFgetX2v1.0UsersGuide
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ListofFigures
2.12.22.32.42.52.62.72.82.92.102.112.122.132.142.152.162.172.182.19
ThewelcomeinterfacewhenstartingPDFgetX2........................ClickthePreprocessSPECFormatDatabuttontoswitchtotheGUIinFig.2.3......ThemainpreprocessSPECformatdataGUI.........................TheGUIportiondisplayingscansinformationintheSPECdata................TheGUIsectiontosetupSPECcolumns...........................TheGUItosetupdeadtimecorrectionsformonitor(left)anddetectorcolumns(right)...TheGUIsectiontoplot/savedataandprocessdata.......................VisualizationoftherawSPECdata(left)andthecorrectedSPECdata(right)........VisualizationofthemergeddataobtainedfrompreprocessSPECformatdata........ClicktheGetX-rayPDFbuttontoswitchtotheGUIinFig.2.11..............ThemainGetX-rayPDFGUI.................................Readinthesampleandsamplebackgroundfiles........................Theexperimentconfiguration..................................TheGUItoinputsamplechemicalinformation........................TheGUItosetupcorrections..............................theGUIforFouriertransformsettings...........................theGUIforsettingupexperimentaldata............................Frombottom,theUserMessagedisplay,theactionbuttons,thedatavisualizationselectionsThe(a)andthe(b)foryourreference.......................
9
111213141516171819192021222324242526
A.1Thewindowsself-installerGUI.................................40A.2ThewelcomeinterfacewhenstartingPDFgetX2........................40
ListofTables
3.13.23.33.43.53.63.73.83.93.103.113.123.133.14
Explanationofthewidgettypes...................DescriptionsoftopGUIportionofthepreprocessSPECformatdataDescriptionsoftheGUIdisplayingscansinformation........DescriptionsoftheGUItosetupSPECcolumns..........DescriptionsoftheGUItosetcolumnsforeachdetector......DescriptionsoftheGUItosetupdeadtimecorrection.......DescriptionsoftheGUItosetupmergingdetectors.........DescriptionsoftheGUIforactionandvisualization.........DescriptionsoftheGUItopframeofGetX-rayPDF........DescriptionsoftheGUItoinputandeditdatafiles.........DescriptionsoftheGUItosetupsampleinformation........
corrections(I).......DescriptionsoftheGUItosetup
DescriptionsoftheGUItosetupcorrections(II).......DescriptionsoftheGUItovisualizedataandprocessdata.....
......................................................................................................................................................................................2728292930303132333334343536
Chapter1
Introduction
1.1WhatisPDFgetX2?
PDFgetX2isauserfriendlyprogramtoobtaintheatomicpairdistributionfunction(PDF)fromX-raypowderscatteringdata.Theinteractionbetweenusersanddataisfacilitatedbyaratherextensivegraphicaluserinterface(GUI).ThesupportedplatformsincludeLinux,Windows,andMacOSs.PleaserefertoAppendixAfordetailedinstallationinstructions.ThesupportedfileformatsincludeSPEC,CHI,andfreedataformat.PleaserefertoAppendixBfordetails.
,isarealspacefunctiontellingtheprobabilityoffindingpairsofatomsseparatedbyThePDF,
distanceinthematerial.TheexperimentalPDFcanbethoughtofasthesumofsnapshotsoftheinstan-taneousatomicarrangementsoverthedatacollectiontime.Accordingly.thePDFcantellusaboutboththelocalstructure(lowregion)andaveragestructure(highregion).ThePDFmethodhasbeenusedasearlyas1931byDebye[1]tostudyliquidmercury,andhasmostlyfocusedonglassandamorphousmaterials[2;3].Notuntilrecently,thePDFanalysishasbeensuccessfullyappliedtocrystallineandnano-crystallinematerials[4].WewouldliketodirectyoutoarecentbookbyEgamiandBillinge(2003)[5]formoretechniquedetailsandrecentPDFapplications.
,isobtainedbyadirectsineFouriertransformationofthestructurefunction,whereThePDF,
isthemagnitudeofthescatteringvector.However,thecollectedrawdataduringX-rayscatteringexper-imentssubjecttovariousinstrumentandsampleeffects,whichhavetobeproperlycorrectedtoextractthe
.Thisprogram,PDFgetX2,livestoservethispurpose.Standardcorrections[5;6;7]implementedincludesubtractionofbackgroundscattering,sampleabsorption,X-raypolarization,unwantedComptonin-tensity,andnormalizationbytheaverageatomicscatteringpower.ParticularlyfortheRA-PDFexperimentsrecentlydevelopedbyChupasetal.[8]utilizingtheimageplateareadetector,additionalcorrectionsduetoobliqueincidentangledependence[9]andthedetectorenergydependence[10]arealsoimplemented.StatisticaluncertaintiesduetolimitedintensitycountsareestimatedandarepropagateduptothePDF,
,whichbecomesveryimportantwhenastheanddataareincreasinglybeingmodeledusingregressionalgorithms.Inaddition,simpledatasmoothinganddampingarealsopossible.
CHAPTER1.INTRODUCTIONUsersGuide
1
IDLisaregisteredtrademarkofResearchSystems,Inc.fortheirInteractiveDataLanguagesoftware
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Chapter2
QuickStartTutorial
Pleasenotethatthedatacorrectionscarriedoutonthedataarenotdescribedinthismanual,justtheuseoftheprogram.Foradetaileddescriptionofthecorrections,pleaseseeEgamiandBillinge[5].
2.1Installationandstart-up
DetailedinformationaboutwhereandhowtoobtaintheprogramPDFgetX2canbefoundinAppendixA.Beforeyoustart,itmightbeagoodideatocheckforupdatesand/orbugfixes.WaystoinvokePDFgetX2onfordifferentplatformsarealsoexplainedinAppendixA.
Nowlet’sstarttheprogram,andthewelcomewindowshouldappearasshowninFig.2.1.ThelookandfeeloftheGUIsvariesslightlyondifferentplatforms.
Figure2.1:ThewelcomeinterfacewhenstartingPDFgetX2
CHAPTER2.QUICKSTARTTUTORIALPDFgetX2v1.0UsersGuide
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CHAPTER2.QUICKSTARTTUTORIALPDFgetX2v1.0UsersGuide
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Chapter3
GUIWidgetsReference
QuiteafewtableswillbeshowntodescribetheGUIwidgets.Theyallcontainthreecolumns.Thefirstcolumnisthenameofthewidget,whichisusuallythetextdisplayedonthewidgetorthelabelinitsfront.Thesecondcolumnindicatesthewidgettype.Thethirdcolumnexplainsthefunctionofthewidget.Table3explainswhateachtypemeansinthiscontext.
Name
acontainerofonegroupofnextlevelwidgets,mouseclickusuallydisplayssubmenus.Thedescriptionsofitssubmenusareshownrightafterbelow,andprecededby
action
atextobjectusuallyforthesolepurposetodisplayusefulinformationlist
amultipleitemuserselectablefield,howevertheselectableitemsneedtobeactivatedbyclickingonitfirsttoseeavailablechoices
checkbox
agroupofexclusivechoices,selectionofonewilldeselectallothers
text/edit
PDFgetX2v1.0Page:27
CHAPTER3.GUIWIDGETSREFERENCETypemenuactionactionactionactionmenumenuactionactionactionaction
UsersGuide
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CHAPTER3.GUIWIDGETSREFERENCETypelabellist
UsersGuide
actiondroplist
Typedroplist
droplist
droplist
actionaction
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CHAPTER3.GUIWIDGETSREFERENCETypecheckbox
UsersGuide
droplistdroplistdroplist
Typedroplist
radioboxradioboxradioboxdroplistdroplisttextdroplist
PDFgetX2v1.0Page:30
CHAPTER3.GUIWIDGETSREFERENCETypecheckboxdroplistdroplistcheckbox
UsersGuide
texttextaction
GUItext
text
actionaction
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CHAPTER3.GUIWIDGETSREFERENCETyperadiobox
UsersGuide
radiobox
radioboxradioboxradiobox
checkboxdroplistdroplistcheckboxdroplistactionactionaction
actionactionmenu
PDFgetX2v1.0Page:32
CHAPTER3.GUIWIDGETSREFERENCETypetexttextmenuactionactiondroplistdroplistaction
UsersGuide
Typecheckboxdroplistdroplistdroplist
texttexttexttexttext
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CHAPTER3.GUIWIDGETSREFERENCEUsersGuide
Typeactiondroplist
texttexttexttexttext
Typecheckboxcheckbox
checkbox
checkbox
checkbox
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CHAPTER3.GUIWIDGETSREFERENCETypecheckbox
UsersGuide
droplistcheckbox
checkbox
checkbox
checkbox
checkboxcheckboxcheckbox
checkboxcheckboxcheckbox
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CHAPTER3.GUIWIDGETSREFERENCEUsersGuide
Typeactionaction
action
action
actionaction
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AppendixA
InstallationandStart-up
A.1
ObtainPDFgetX2andIDL
TherecommendedwaytoobtainprogramPDFgetX2istodownloaditdirectlyfromitshomepageat
http://www.pa.msu.edu/cmp/billinge-group/programs/PDFgetX2/
Recentupdates,bugfixes,andotherrelatedinformationarealsopostedon-line.Pleasecheckbackfromtimetotime.Ifthewebisnotaccessible,pleasesendusemail(billinge@pa.msu.edu)toarrangealternativeshipment.
AcommercialIDLlicenseddistribution(version6.0orhigher),orthefreelydownloadableIDLVir-tualMachine(IDL),istheonlyprerequisitetorunPDFgetX2.TheIDLisavailablefromthedownloadsectionoftheIDLwebsitehttp://www.rsinc.com/download/.SupportedplatformsbyIDLincludeLinux/UNIX,WINDOWS,andMACINTOSH.NospecifichardwareisusedbyPDFgetX2.Inprinciple,PDFgetX2canrunonanyplatformwhereIDLcanbeinstalledandwidgetsaresupported.
A.2Howtoinstall
PDFgetX2takesabout17MBharddiskspaceincludingthismanual,whileatypicalinstallationofIDLmaytakeupto200MBdiskspaceforeitherthelicenseddistributionorthevirtualmachine.
A.2.1Linux/UNIXsystem
Thefileyoushoulddownloadispdfgetx2-xxxx-yymmdd-linux.sh.Afteracompletedownload,gotothesaveddirectory,andruncommandshpdfgetx2-xx-yymmdd-linux.shtoinitializetheinstallation.Youwillbeaskedwheretoputthesourceandtheexecutable,justbesurethatyouhavetherightpermission.Forexample,withmycomputerrunningRedHatLinux9.0,IgotthefollowingwheninstallingthePDFgetX2intoalocaldirectory.
APPENDIXA.INSTALLATIONANDSTART-UPPDFgetX2v1.0UsersGuide
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APPENDIXA.INSTALLATIONANDSTART-UPPDFgetX2v1.0UsersGuide
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APPENDIXA.INSTALLATIONANDSTART-UPPDFgetX2v1.0UsersGuide
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APPENDIXA.INSTALLATIONANDSTART-UPPDFgetX2v1.0UsersGuide
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AppendixB
SupportedFileFormats
DatafileshavetobeinASCIIformat.Theprogramdoesn’tsetthesinglelinelengthlimit,whichwoulddependonyoursystem.Forallsupportedfileformats,youcanfirstspecifythenumberoflinestoskipfromthebeginning.Youcanalsospecifythecommentidentifierwhichstartsacommentlineinsteadofdata.ChangingthefileformatisdonebyclickingoneithertheEditFormat(Fig.2.3)orCustomize...(Fig.2.11)button,aGUIisprovidedtofacilitateformatselection.
B.1SPECfileformat
TheSPECfileformatherereferstoonewithcompatibledataformatwiththeoutputfilefromthecommondiffractometercontrolanddataacquisitionprogramSPEC.First,let’sshowanexampleSPECfile.
#S1ascanpmQ1136001
#LpmQerealeliveEpochSecondsIC1IC3I_CESRPULSERTOTALCOMPTONIC2ELASTIC12.071.967759312.11758556914396634394.3954162866233317186061.022.071.968759342.11849558523396548394.1594323000217317916101.042.061.962759362.102555188394768392.3244143030253315695911.062.071.969759392.118865533396616394.02341731382403177671.082.071.977759422.11559126396636393.919419292324631839639#S2ascanpmQ1136001
#LpmQerealeliveEpochSecondsIC1IC3I_CESRPULSERTOTALCOMPTONIC2ELASTIC12.071.999776062.118790517396566353.6118239718627129533
1.022.0691.997776092.118074908723938353.3194152486194271675581.042.071.9776122.118844377396583353.4194162672177270455361.062.071.996776142.11884492200396585353.4144282551195272185511.082.061.9776172.108688500394682351.707419245819926993550
APPENDIXB.SUPPORTEDFILEFORMATSPDFgetX2v1.0UsersGuide
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AppendixC
PDFgetX2HistoryFile
AnyPDFgetX2sessionatanystagecanbesavedintoahistoryfile,andloadingofthehistoryfilewillrestorethesavedsession.Eachinternalparameterisgivenakeyidentifiedbyalogicalkeywordinthehistoryfile.Youcouldedittheparametervalues,butthisshouldrarelyhappensinceallessentialparametersareaccessiblefromtheGUI.
Foryourreference,ahistoryfileisincludedbelow.Somelinesaretruncatedforreadability.#Format:#Twosectionsareinthishistoryfile:#1)PreprocessSPECData,2)GetX-rayPDF#Firstdelimiteris#######(7)whichseparatesthetwo,
#secondis#####(5)whichstartseachsubsectionfollowing.#Note:#Youmaymodifythishistoryfileusingatexteditor,however,#extremecautionmustbepaidtopreservetheformat.Thereshould#noblankbeforeorafter\"=\"sign,exceptnoinfoavailable,please#donnotchangethenumberofstringsineachlineeventhatlineis#toolongortooshort!#
Historywritten:SunJan1815:53:292004Producedbyxiangyun
#######SPECData_Reduction############ScansData_SetupViewSelect_Isa=0SpecFile=ingaas_tutorial.specNum_Scans=5#LNO.ScannumValidSelectHighlightHas_MCA
011110121110231110
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APPENDIXC.PDFGETX2HISTORYFILEPDFgetX2v1.0UsersGuide
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Bibliography
[1]P.DebyeandH.Menke,Ergeb.Tech.Röntgenk.2,1(1931).[2]L.P.TarasovandB.E.Warren,J.Chem.Phys.4,236(1936).
[3]B.E.Warren,H.Krutter,andO.Morningstar,Fourieranalysisofx-raypatternsofvitreousSiO
andBO.,J.Am.Ceram.Soc.19,202–6(1936).
[4]S.J.L.BillingeandM.G.Kanatzidis,BeyondCrystallography:thestudyofdisorder,nanocrys-tallinityandcrystallographicallychallengedmaterials,Chem.Commun.,749–760(2004).[5]T.EgamiandS.J.L.Billinge,UnderneaththeBraggPeaks:Structuralanalysisofcomplex
materials,UnderneaththeBraggPeaks:Structuralanalysisofcomplexmaterials,PergamonPress,Elsevier,Oxford,England,2003.[6]I.-K.Jeong,J.Thompson,A.M.P.Turner,andS.J.L.Billinge,PDFgetX:aprogramfordetermin-ingtheatomicpairdistributionfunctionfromx-raypowderdiffractiondata,J.Appl.Crystallogr.34,536(2001).[7]B.J.Thijsse,Theaccuracyofexperimentalradialdistributionfunctionsformetallicglasses,J.
Appl.Crystallogr.17,61(1984).[8]P.J.Chupas,X.Qiu,J.C.Hanson,P.L.Lee,C.P.Grey,andS.J.L.Billinge,RapidAcquisitionPair
DistributionFunctionAnalysis(RA-PDF),J.Appl.Crystallogr.36,1342–1347(2003).[9]J.Zaleski,G.Wu,andP.Coppens,Onthecorrectionofreflectionintensitiesrecordedonimaging
platesforincompleteabsorptioninthephosphorlayer,J.Appl.Crystallogr.31,302(1998).[10]M.ItoandY.Amemiya,X-Ray-EnergyDependenceAndUniformityOfAnImagingPlateDe-tector,NuclearInstruments&MethodsInPhysicsResearchSectionA-AcceleratorsSpectrometersDetectorsAndAssociatedEquipment310,369–372(1991).[11]W.Ruland,TheseparationofcoherentandincoherentComptonx-rayscattering,Brit.J.Appl.
Phys.15,1301(19).
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