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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.