Demo for High Pressure X-Ray diffraction data processing with ATREX

7/23/2019 Demo for High Pressure X-Ray diffraction data processing with ATREX

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Tutorialonprocessingofsinglecrystaldiffractiondataathigh

pressureusingATREXIDLandRSV

ByPrzemyslawDera,

HawaiiInstituteofGeophysicsandPlanetology([email protected])

DevelopmentofthissoftwareissupportedbyNSFGeoInformaticsawardEAR1440005

TableofContentsInitialsetup................................................................................................................................................... 2

Detectorcalibration...................................................................................................................................... 3

Goniometersettings..................................................................................................................................... 8

Peaksearch................................................................................................................................................. 12

Peakindexinganddeterminationoforientation(UB)matrix.................................................................... 14

Peakprediction........................................................................................................................................... 16

Peakfitting.................................................................................................................................................. 18

Pealpredictionandfittingforimageseries................................................................................................ 21

Mergingofpeaksfromdifferentdetectorpositions.................................................................................. 23

ScalingandrotationdependentintensitycorrectionsinATREX................................................................ 24

ExportingSHELXhklfilewithstructurefactoramplitudes......................................................................... 26


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InitialsetupStarttheprogrambydoubleclickingontheGSE_ADAicon(assumingthatIDLVMhasbeeninstalled

correctly).

ThedemodatasetwascollectedwithaMAR165CCDdetector,andthediffractionimagesweresavedas

tifffiles.

Select

the

correct

(default)

image

format:

Onmycomputer,afterdownloadingfromGitHub,thedemodataislocatedinthefollowingdirectory:

C:\Users\przemyslaw\Documents\GitHub\GSE_ADA\Demo_data

Selectoutputdirectory.Forthepurposeofthisdemowewillcreateanalysisfolderinthediffraction

imagedirectory:


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DetectorcalibrationOpenoneofthecalibrationimages.ForthisexperimentcalibrationdatawasrecordedforLaB6powder

sample.Forthisdetectorthepixelsizeis0.079mm.Thewavelengthfortheexperimentwas0.3344A,

andthedetectorwasplacedatanapproximatedistanceof200mm.


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Thediffractiondataforthesamplewascollectedatthreedetectorpositions.Thefirstposition(file

namescontainingD1)hastheincidentbeamhittingthedetectorclosetothegeometriccenterofthe

image.TheremainingtwopositionsdifferedfromD1bytranslationofthedetectorinhorizontalplane,

approximatelyperpendiculartotheincidentbeam,byabut70mmtotheright(filenamescontainingD2)

andtotheleft(filenamescontainingD1).

Youhavetocalibratethedetectorgeometryateachofthesethreedetectorpositionsfirst,inorderto

beable

to

analyze

the

single

crystal

data.

After

you

open

adiffraction

image,

the

program

checks

if

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,

and

click

Test

again.

There

are

more

points

selected

for

refinement

now,

as

shown

below.


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ClicktheRefinecalbutton.Theprogramgoesthroughthecalibrationcalculationsandwilldisplaythe

dialogbelow,whenitisfinished.

Afterthecalibrationrefinementiscompleted,theprogramdisplaysstandarddeviationsofallrefined

parametersingreyboxesnexttotheparametervalues.ATREXcanuseoneoftwodefinitionsofthe

calibrationparameters.Oneofthemisconsistentwithfit2d,thesecondusesanalternativedefinitionof

therotationparameter.Thedefinitionoftheparametercanbeswitchedwithradiobuttons. Make

surethatyoucalibrateanduseforfurthercalculationsconsistentlythesametypeofcalibration

parameters.

TocheckifthecalibrationworkedwellyoucanoverlaythecalculatedDebyeScherrerringsontothe

diffractionimageofthecalibrantusingtheshowringscheckbox.Theavailablecalibrantsinclude

CeO2andLaB6.


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SavethecalibrationbypressingtheSavebuttoninCalibration.

RepeatthecalibrationprocedurefortheD2andD3detectorpositions.Thewavelength,pixelsizeand

approximatedistancearethesameforallthreedetectorpositons.ResultsofthecalibrationfortheD2

detectorpostionareshowninthefiguresbelow.


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GoniometersettingsItistimetolookatthediffractionimagesofthesamplenow.Beforeyoudothat,telltheprogramabout

thesettingofthegoniometeryouused.Differentinstrumentsusedifferentdefinitionofpositive

rotationdirection,anddifferentoffsets.AttheAPSsynchrotronbeamlines13IDDand13BMDhavethe

rotationdirection

consistent

with

ATREX,

but

use

an

offset

of

90

deg.

16IDB

and

166BMD

use

inverted

rotationand0offset.13BMChasinvertedrotationand90degor90degoffset.Inputthecorrect

settingsundertheGoniotabbeforeproceedingfurtherwiththeanalysis.


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ATREXallowstoadjustthecontrastoftheimagedisplaybyselectingtwoparameters,minIandmaxI.In

thedefaultinvertedgreyscalecolorschemeallintensitiesabovemaxIaredisplayedasblackandall

intensitiesbelowminIarewhite,whereaseverythinginbetween isanappropriateshadeofgray.


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Theimageaboveisalittledark.AdjustmaxIfrom1000to2000forbettervisibility.Theresultisshown

below.

Eachimageseries(seriesofimagefileswherethenamescontainconsecutive3digitsequencenumbers)

sharesthesamedetectorcalibration.Toassigncalibrationtoanimageseriesmakesurethatthecorrect

calibrationisloadedandsimplysaveit(usingSavebuttonintheCalibrationtab)withdefaultname

proposedbytheprogram(itwillbesavedintheimagedirectory).Ifyouopenanyimagebelongingto

thesame

series

again,

ATREX

will

know

which

calibration

to

use.

You

will

have

to

do

it

separately

for

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.tif toB1_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.

PeaksearchOpenoneofthestepimagesfordetectorpositionD1.InSearchtabselectthefitpeaksbutton.Click

thePSSeriesbutton.Theprogramwillgothroughalloftheimagesbelongingtothestepscanseries

andperform

peak

search

and

fitting

in

individual

images.

A

peak

table

.pks

file

will

be

saved

for

each

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)matrixYoucandothepeakindexingandorientationmatrixdeterminationinRSV,likeinthepreviousversion

ofthis

IDL

software,

GSE_ADA/RSV,

but

ATREX

now

also

has

an

interface

which

allows

to

launch

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,therearediamondpeaksand afewdark

currentnoisepeaksaswell.

TheorientationmatrixandlatticetypeyouselectedwerepassedtotheSimulationwindow:


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PeakpredictionOpenthewiderotationimagefordetectorpositionD1.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.steps fordeterminationofpeak

intensities,because

the

signal

to

noise

is

high,

there

are

no

problems

with

spatial

overlaps,

and

the

wide

imageisfreefromthesynchronizationerrorsthatstepimagescollectedquicklysometimessuffer.

Thenextstepistofilteroutunobservedpeaks.ThisisdoneinthePeakstabbyclickingthe

Observedbutton.Thenumbertotherightofthebuttondeterminestheminimumintensitycount

abovebackgroundwithin5x5pixelregionaroundthepredictedpeakpositionthathastobesatisfiedfor

thepeaktoberecognizedasobserved.Thisdatawascollectedwithgoodstatistics,soletsusea50

countthreshold.Theresultoffilteringofunobservedpeaksisshownbelow.Removetheselectedpeaks

(DeletebuttoninPeaks).


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PeakfittingThenextstepispeakfitting.Makesurethatthefittingboxsize(numbertotherightofBoxlabelin

peaks)isappropriate.Forthedemodatathedefaultboxsizeof8(thisparameterisaboxradius,so

therealfittingboxis17x17pixels)isok,thoughforotherdatasets,particularlycollectedathigher

pressures,where

peaks

are

broader

you

may

need

to

make

this

number

larger.

Click

on

couple

of

peaks

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.

PeakpredictionandfittingforimageseriesTheorientationofthecrystalforthisdetectorpositionisjustthesameasforD1.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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MergingofpeaksfromdifferentdetectorpositionsNextstepismergingofthepeaksfromallthreedetectorpositions,whichisdoneinRSV.

DuringthedatacollectionatD1thesamplerotationwastwotimesfasterthanatD2andD3because

theoffsetdetectorpositionscontainmainlyweaker,highanglepeaks.Tomergethedatacorrectlyyou

haveto

open

the

three

.pks

file

and

select

appropriate

scale

factors

in

RSV.

Make

sure

that

the

scale

factorissetto1andopentheD1file.Changescalefactorto0.5(thespeedwasslower,sothe

intensitieshavetobedividedby2tobringthemtothesamelevelasD1).Selecttheappendoption.

Keepscalefactorat0.5andopentheD3file.Again,selectAppend.

Thereshould

be

about

790

peaks

in

the

three

combined

files.

Go

to

Index/Index

and

click

Recalc.

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

Openthe

new

file

in

ATREX

(Open

in

the

Peaks

tab).

There

should

be

~779

peaks

showing

R_int

of

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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ExportingSHELXhklfilewithstructurefactoramplitudesSavetheresultingpeaktable(e.g.overwritethepreviousfile).OpenthefileinRSV.Save.hklSHELXfile

usingExporthklbuttoninFile.Ifyouaregoingtorefinethestructureusingamodelthatyou

downloadedfromadatabase,youhavetomakesurethatthesettingoftheunitcellinRSVisconsistent

withthesettingofyourmodel.Foromphacitethisshouldbethecase(theaunitcellparameteris

>9A,the

Lattice

type

is

C

and

the

beta

angle

is

~106

deg.).

The

structure

refinement

procedure

is

describedinaseparatetutorial.

Date post:	19-Feb-2018
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