Tutorialonprocessingofsinglecrystaldiffractiondataathigh

pressureusingATREXIDLandRSV

ByPrzemyslawDera,
HawaiiInstituteofGeophysicsandPlanetology(pdera@hawaii.edu)

DevelopmentofthissoftwareissupportedbyNSFGeoInformaticsawardEAR1440005

TableofContents
Initialsetup...................................................................................................................................................2
Detectorcalibration......................................................................................................................................3
Goniometersettings.....................................................................................................................................8
Peaksearch.................................................................................................................................................12
Peakindexinganddeterminationoforientation(UB)matrix....................................................................14
Peakprediction...........................................................................................................................................16
Peakfitting..................................................................................................................................................18
Pealpredictionandfittingforimageseries................................................................................................21
Mergingofpeaksfromdifferentdetectorpositions..................................................................................23
ScalingandrotationdependentintensitycorrectionsinATREX................................................................24
ExportingSHELXhklfilewithstructurefactoramplitudes.........................................................................26

Initialsetup
StarttheprogrambydoubleclickingontheGSE_ADAicon(assumingthatIDLVMhasbeeninstalled
correctly).
ThedemodatasetwascollectedwithaMAR165CCDdetector,andthediffractionimagesweresavedas
tifffiles.Selectthecorrect(default)imageformat:

Onmycomputer,afterdownloadingfromGitHub,thedemodataislocatedinthefollowingdirectory:
C:\Users\przemyslaw\Documents\GitHub\GSE_ADA\Demo_data
Selectoutputdirectory.Forthepurposeofthisdemowewillcreateanalysisfolderinthediffraction
imagedirectory:

Detectorcalibration
Openoneofthecalibrationimages.ForthisexperimentcalibrationdatawasrecordedforLaB6powder
sample.Forthisdetectorthepixelsizeis0.079mm.Thewavelengthfortheexperimentwas0.3344A,
andthedetectorwasplacedatanapproximatedistanceof200mm.


Thediffractiondataforthesamplewascollectedatthreedetectorpositions.Thefirstposition(file
namescontainingD1)hastheincidentbeamhittingthedetectorclosetothegeometriccenterofthe
image.TheremainingtwopositionsdifferedfromD1bytranslationofthedetectorinhorizontalplane,
approximatelyperpendiculartotheincidentbeam,byabut70mmtotheright(filenamescontainingD2)
andtotheleft(filenamescontainingD1).
Youhavetocalibratethedetectorgeometryateachofthesethreedetectorpositionsfirst,inorderto
beabletoanalyzethesinglecrystaldata.Afteryouopenadiffractionimage,theprogramchecksif
thereisacalibration.calfileassociatewithit.Ifyouareopeningtheimageforthefirsttime,thereisno
calibrationyet,sotheprogramwilldisplayadialogaskingyoutoselectoneandsaveitintheimage
directory.Youcandothisafteryoucompletethecalibration.

GototheCalibrationtab.Setthecorrectstartingvaluesofthedetectorparameter(pixelsize,
wavelength,approximatedistance).TheTestbuttonallowsyoutoadjustandtestthesignaltonoise
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ratioforautomatedselectionofpointsalongtheDebyeScherrerrings.Theprogramrequiresatleast8
pointsalongaring,fortheringtobeusedintherefinement.Theimagebelowwasobtainedwiths/n
ratioof2.0(thismeansthatpointswithintensity2xhigherthanlocalbackgroundwillbeused).Pixels
thatsatisfythesignaltonoisearemarkedwithpurple,whereaspixelsthatbelongtoacceptablerings
aremarkedwithblue.

Thisshouldbesufficient,butifyouwanttousemorepoints,adjustthenumberbelowtheTestbutton
to1.0,andclickTestagain.Therearemorepointsselectedforrefinementnow,asshownbelow.


ClicktheRefinecalbutton.Theprogramgoesthroughthecalibrationcalculationsandwilldisplaythe
dialogbelow,whenitisfinished.

Afterthecalibrationrefinementiscompleted,theprogramdisplaysstandarddeviationsofallrefined
parametersingreyboxesnexttotheparametervalues.ATREXcanuseoneoftwodefinitionsofthe
calibrationparameters.Oneofthemisconsistentwithfit2d,thesecondusesanalternativedefinitionof
therotationparameter.Thedefinitionoftheparametercanbeswitchedwithradiobuttons.Make
surethatyoucalibrateanduseforfurthercalculationsconsistentlythesametypeofcalibration
parameters.
TocheckifthecalibrationworkedwellyoucanoverlaythecalculatedDebyeScherrerringsontothe
diffractionimageofthecalibrantusingtheshowringscheckbox.Theavailablecalibrantsinclude
CeO2andLaB6.


SavethecalibrationbypressingtheSavebuttoninCalibration.
RepeatthecalibrationprocedurefortheD2andD3detectorpositions.Thewavelength,pixelsizeand
approximatedistancearethesameforallthreedetectorpositons.ResultsofthecalibrationfortheD2
detectorpostionareshowninthefiguresbelow.

Goniometersettings
Itistimetolookatthediffractionimagesofthesamplenow.Beforeyoudothat,telltheprogramabout
thesettingofthegoniometeryouused.Differentinstrumentsusedifferentdefinitionofpositive
rotationdirection,anddifferentoffsets.AttheAPSsynchrotronbeamlines13IDDand13BMDhavethe
rotationdirectionconsistentwithATREX,butuseanoffsetof90deg.16IDBand166BMDuseinverted
rotationand0offset.13BMChasinvertedrotationand90degor90degoffset.Inputthecorrect
settingsundertheGoniotabbeforeproceedingfurtherwiththeanalysis.


ATREXallowstoadjustthecontrastoftheimagedisplaybyselectingtwoparameters,minIandmaxI.In
thedefaultinvertedgreyscalecolorschemeallintensitiesabovemaxIaredisplayedasblackandall
intensitiesbelowminIarewhite,whereaseverythinginbetweenisanappropriateshadeofgray.

Theimageaboveisalittledark.AdjustmaxIfrom1000to2000forbettervisibility.Theresultisshown
below.

Eachimageseries(seriesofimagefileswherethenamescontainconsecutive3digitsequencenumbers)
sharesthesamedetectorcalibration.Toassigncalibrationtoanimageseriesmakesurethatthecorrect
calibrationisloadedandsimplysaveit(usingSavebuttonintheCalibrationtab)withdefaultname
proposedbytheprogram(itwillbesavedintheimagedirectory).Ifyouopenanyimagebelongingto
thesameseriesagain,ATREXwillknowwhichcalibrationtouse.Youwillhavetodoitseparatelyfor
eachindividualimageseries.
Duringthedemoexperiment,weusedadiamondanvilcellequippedwithBoehler/Almaxdiamonds,
with66deg.totalopeningangle.Thepressurewas7.8GPa,andthepressuretransmittingmediumwas
He.Wecollecteddatainaseriesof1deg.stepsatdetectorpositionD1(filenames
B1_Om_P4_C1_D1s_006.tiftoB1_Om_P4_C1_D1s_071.tif),onewiderotationimage,coveringthe
whole66deg.atdetectorpositionD1(B1_Om_P4_C1_D1w_005.tif),andtwosetsoffour16.5deg.wide
stepsfordetectorpositionsD2(B1_Om_P4_C1_D2s_140.tiftoB1_Om_P4_C1_D2s_143.tif)andD3
(B1_Om_P4_C1_D3s_150.tiftoB1_Om_P4_C1_D3s_153.tif).Thesampleinthisexperimentwasa
naturalcrystalofomphacitepyroxenefromtheRRUFFcollection:
http://rruff.info/omphacite/display=default/R061129
Startbyassigningappropriatedetectorcalibrationstoeachoftheseries(itisenoughtoassign
calibrationtojustoneimagebelongingtotheseries).

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Duringthedatacollection,witheachdiffractionimagethedatacollectionprogramsavesanASCIIfile
withimagesetting,thatcontainthestartrotationangle,rotationrange,exposuretime,etc.Youcansee
intheScantabthatATREXreadsthesefilesandentersforyoutheappropriateinformation.This
informationisalsoautomaticallypassedtothePredicttab,wherethesettingforcalculatingpeak
positionsfromtheorientationmatrixaredefined.

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Ifyourdatadoesnothavesettingfiles,ATREXwillallowyoutogeneratethemforeachimageseries,if
youspecifytheappropriateinformationyourself.

Peaksearch
OpenoneofthestepimagesfordetectorpositionD1.InSearchtabselectthefitpeaksbutton.Click
thePSSeriesbutton.Theprogramwillgothroughalloftheimagesbelongingtothestepscanseries
andperformpeaksearchandfittinginindividualimages.Apeaktable.pksfilewillbesavedforeach
individualimageoftheseries.AttheendofthisprocessATREXwillmergeallofthepeaktablesintoone
andalsosavetheresultingpeaktable.

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Attheendofpeaksearchtheimageshouldlookssimilartotheoneinthefigurebelow.Peaksmarked
withgreencoloraretheonesforwhichATREXcouldnotdoasatisfactorypeakfit.Startbyremoving
thesepeaksbyclickingtheDeletebuttoninPeaks.

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Theresultingmergedpeaktableisautomaticallyshouldbesavedinafile
B1_Om_P4_C1_D1s__merge.pks

Peakindexinganddeterminationoforientation(UB)matrix
YoucandothepeakindexingandorientationmatrixdeterminationinRSV,likeinthepreviousversion
ofthisIDLsoftware,GSE_ADA/RSV,butATREXnowalsohasaninterfacewhichallowstolaunch
cell_nowdirectly.TodothatgotoPredictandclicktheSimulatebutton.Indexingisavailableby
clickingtheIndexbuttonintheDiffractionimagesimulationwindow.
YouwillhavetotellATREXwhatisthelocationofthecell_now.exeexecutableonyourcomputer
(cell_nowcanbeobtainedfromBrukerAXSorfromprof.GeorgeSheldrick).UsetheBrowsebuttonin
thewindowbelowtoselectthefilelocation,andthenclickOK.

ATREXlaunchescell_nowinthebackgroundandtakescareoftheinternaldialogs.Theresults(choices
oftheunitcells)arecapturedanddisplayedinanewwindow,shownbelow.

Thedemosample,omphacitehasamonoclinicbasecentered(Ctype)unitcell,soselectsolution
number2fromthelist.Whenyoumaketheselection,ATREXrecognizesthemostlikelysymmetry
(monoclinicwithbuniqueinourcase),butyoucanoverridetheautomatedselection.ClicktheSelect
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button.Theprogramperformsasimplerefinementoftheorientationmatrixandselects(markedwith
greencolor)peaksthatdonotconformtotheorientationmatrix.Theresultsareshowninthefigure
below.Therearequitealotofpeaksthatwerenotindexedcorrectly,butitisok.Werunthepeak
searchwithhighsensitivitysoinadditiontothesamplepeaks,therearediamondpeaksandafewdark
currentnoisepeaksaswell.

TheorientationmatrixandlatticetypeyouselectedwerepassedtotheSimulationwindow:

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Peakprediction
OpenthewiderotationimagefordetectorpositionD1.Ithasallofthesamplepeaksaccumulated,and
youcanuseittoverifyifyourorientationmatrixissatisfactory.ChangetheDownstr.DACopeningto
33deg.,whichwasthecaseforthisdemoexperiment.Deleteallthepeaks(ClearbuttoninPeaks
tab),andclickGenerateinthesimulationwindow.Theresultshouldlooklikeinthefigurebelow.

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Allsamplepeaksarecorrectlypredictedusingtheorientationmatrixwehave.Insomecaseswithlarge
unitcellssomepredictedpeaksaresoclosetogetherintheimagethatreliablefittingisnotpossible.
ATREXwillidentifysuchcasesandselecttheoffendingpeaks(withgreen)foryou.Ifanypeaksare
markedwithgreen,afterexecutingthegeneratefunction,removethembeforeproceedingfurther
(forthisdemodatasetthereshouldnotbeanytooclosespecialoverlaps).
WewillusethewiderotationimageatD1insteadofthesmall1deg.stepsfordeterminationofpeak
intensities,becausethesignaltonoiseishigh,therearenoproblemswithspatialoverlaps,andthewide
imageisfreefromthesynchronizationerrorsthatstepimagescollectedquicklysometimessuffer.
Thenextstepistofilteroutunobservedpeaks.ThisisdoneinthePeakstabbyclickingthe
Observedbutton.Thenumbertotherightofthebuttondeterminestheminimumintensitycount
abovebackgroundwithin5x5pixelregionaroundthepredictedpeakpositionthathastobesatisfiedfor
thepeaktoberecognizedasobserved.Thisdatawascollectedwithgoodstatistics,soletsusea50
countthreshold.Theresultoffilteringofunobservedpeaksisshownbelow.Removetheselectedpeaks
(DeletebuttoninPeaks).

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Peakfitting
Thenextstepispeakfitting.Makesurethatthefittingboxsize(numbertotherightofBoxlabelin
peaks)isappropriate.Forthedemodatathedefaultboxsizeof8(thisparameterisaboxradius,so
therealfittingboxis17x17pixels)isok,thoughforotherdatasets,particularlycollectedathigher
pressures,wherepeaksarebroaderyoumayneedtomakethisnumberlarger.Clickoncoupleofpeaks
inthepeaklist,andseeifthepeakprofilesfitwellwithinthefittingbox.Youcanseetheresultofthe
fittinginthethreegraphicalwindowsonthebottomrightsideofthePeakstab.Theycorrespondto
thezoomoftheactualimage,fittedprofileandtheresidualintensity(imagefittedprofile).

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ATREXoffersabuiltincBNbackingplateabsorptioncorrection,butthedemodatasetwascollectedina
DACwithoutacBNseat,sowehavetodisablethiscorrectioninIntegrate/Corrections,likeshown
below.

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Ifyouaresatisfiedwiththeboxsize,selectthecorrectLaueclassforyourcrystal(2/mforomphacite)
andclickthePeakfitbuttoninPeaks.Fittingofthe~300peaksonmydesktopcomputertakes
about30seconds.AttheendATREXselectsagainwithgreenthepeaksforwhichaconvincingfitting
convergencewasnotachieved.Removethesepeaks(DeletebuttoninPeaks).

Afterthefittingandremovalofbadpeakstheinternalconsistencyfactorforallthepeaksinthisimage
shouldbearound11%(beforeweremoveoutliersandapplycorrectionforthecrystalmotioninthe
beam).

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Savetheresultsofthefittingina.pksfile(IjustoverwritetheB1_Om_P4_C1_D1s__merge.pksfile).We
havetoprocesstheremainingtwodetectorposition.OpenoneofthewidestepimagesatD2.Make
surethecorrectcalibrationissavedforthisfileseries.

Peakpredictionandfittingforimageseries
TheorientationofthecrystalforthisdetectorpositionisjustthesameasforD1.Wewilluseafeature
ofATREXwhichpredictspeaksinafileseriesandprocessesthewholeseriesautomatically.Totrigger
thisfunctiongotoScanandclickthePredictwholeseriesbutton.ATREXdoespredictionofpeakin
eachimage,filteringofunobservedpeaks,peakfittingandremovalofbadfits,aswellasmergesthe
peaksfromallstepsattheend.ThefinalresultforD2isshownbelow.Theresultsarewrittenintoafile
.pksB1_Om_P4_C1_D2s__merge.pks.

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RepeatthisoperationfortheD3images.TheresultsforD3areshownbelow.

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Mergingofpeaksfromdifferentdetectorpositions
Nextstepismergingofthepeaksfromallthreedetectorpositions,whichisdoneinRSV.
DuringthedatacollectionatD1thesamplerotationwastwotimesfasterthanatD2andD3because
theoffsetdetectorpositionscontainmainlyweaker,highanglepeaks.Tomergethedatacorrectlyyou
havetoopenthethree.pksfileandselectappropriatescalefactorsinRSV.Makesurethatthescale
factorissetto1andopentheD1file.Changescalefactorto0.5(thespeedwasslower,sothe
intensitieshavetobedividedby2tobringthemtothesamelevelasD1).Selecttheappendoption.
Keepscalefactorat0.5andopentheD3file.Again,selectAppend.

Thereshouldbeabout790peaksinthethreecombinedfiles.GotoIndex/IndexandclickRecalc.
UB.ThiswillcalculatetheorientationmatrixfromtheMillerindicesandCartesiancoordinatesof
reciprocalvectors.

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GotoRefineandselectappropriatesymmetryconstraint(monoclinicbuniqueforthiscrystal).Click
onRefinew/dspcseveraltimes.GotoFilterandlookattheerrorplot.Therearefewpeaksthat
clearlyseemtobeoutliers.Thedefaultlimitsindspacingforrecognizingoutliersarespecifiednextto
Dd/dbutton.Youcanchangethese,ifnecessary,andclickonDd/dtomakeanewselection.Forthe
demodatasetthedefaultvaluesshouldbeOK.Deletetheoutlayerpeaks(DeleteselectedinView).
Savetheresultingmergedpeaktable(SaveasinFile).Youwillneedtocreateanew.pksfileforthis.
IcalledmyfileB1_Om_P4_C1_D123s__merge.pks.

ScalingandrotationdependentintensitycorrectionsinATREX
OpenthenewfileinATREX(OpeninthePeakstab).Thereshouldbe~779peaksshowingR_intof
12.5%.
GotoIntegrate/Scaleandclickthescalebutton.Theplotbelowshowsrotationangledependence
ofindividualmeasurementofpeakintensityvs.averageintensityforeachgroupofsymmetry
dependentpeaks.Thereareclearlyfewoutlier.Clicktheselectbutton,andadjusttheselectionlimits
(textboxesbelowSelectifnecessary).Deletetheselectedoutliers.

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ClickScaleagain.Youcanseethatthereisaslightslopeofthedependenceandtheprogramfitsa
polynomialcurvethataccountsforthecrystalmovinginthebeam.ClickApplyscaleandScaleagain.
TheslopedependencehasbeencorrectedandtheR_intdroppedto0.0646.

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ExportingSHELXhklfilewithstructurefactoramplitudes
Savetheresultingpeaktable(e.g.overwritethepreviousfile).OpenthefileinRSV.Save.hklSHELXfile
usingExporthklbuttoninFile.Ifyouaregoingtorefinethestructureusingamodelthatyou
downloadedfromadatabase,youhavetomakesurethatthesettingoftheunitcellinRSVisconsistent
withthesettingofyourmodel.Foromphacitethisshouldbethecase(theaunitcellparameteris
>9A,theLatticetypeisCandthebetaangleis~106deg.).Thestructurerefinementprocedureis
describedinaseparatetutorial.

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