basics of data processing - brookhaven national … experiment, and advanced applications 1 basics...

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September 30, 2005 2005 NSLS EXAFS Course:Theory, Experiment, and Advanced Applications

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Basics of Data Processing

Scott CalvinSarah Lawrence College


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Importing Raw Data in Athena

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What This Talk Is

• An overview of some of the generalfeatures of Artemis and Athena

• A highlight of a few areas where novicesoften go astray


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What This Talk Is Not

• An exhaustive documentation of everyfeature in Artemis and Athena

• A detailed tutorial• A discussion of EXAFS theory

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“Groups” includeindividual scans

Groups in Athena


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This is the “current” group

Checks indicate“marked” groups

Note that these buttonsplot the current group

These buttons plot allthe marked groups

“Marked” and “Current” Groups

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These options affectplots of the current group

These options affect plotsof all marked groups

“Marked” and “Current” Groups


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Vertical translation betweenscans will not affect EXAFS

But a closer look…

Compare Scans

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…reveals other problems.

Scans 38 and 39 appearinconsistent with the rest

Energy calibration appearsto have drifted

Compare Scans


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Under the “align”menu, you can haveAthena attempt toshift scans for you,or you can do it “byhand”

Alignment in Athena

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The scans are now aligned

If we had not alignedthem, the average wouldshow considerabledifferences:

Note missing shoulderon unaligned version

Alignment Matters


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alignment is very important

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This informationapplies to thecurrent scan

Right clicking bringsup a menu that lets

you apply thesesettings to all scans,

or to all marked scans

Background Removal in Athena


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Choose Eo at firstpeak in the

derivative spectrum

Click here to see aplot of the

derivative spectrum

Choosing Eo in Athena

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Choosing Eo carefully is of lowimportance for EXAFS, as long as it

is done consistently for all scans


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Choose pre-edge andnormalization ranges

Normalizing in Athena

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These pre- and post-edge lines look OK

This post-edge line goestoo high near edge

Good and Bad Normalization


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Merge aligned andnormalized scans here

Merging Data in Athena

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Normalization may be very important insome cases, such as determining

coordination number when you think youknow So

2, but if you are fitting So2 it is

relatively unimportant


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Rbkg controls how far up in theFourier transform the background

will try to suppress; i.e. how“wiggly” the background can be

Rbkg

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Rbkg of 2.0 _ wiggles toomuch in energy space andthus kills off low-R peak

in Fourier transform

Energy plot k-space plot Magnitude ofFourier transform

Rbkg

Rbkg of 0.2 Å “misses” inenergy space and thus

introduces spurious low-Rpeak in Fourier transform


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Rbkg is fairly important

Ideally, small changes in Rbkg should notsignificantly change the parameters you

find via your fits

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Fourier Transforms in Athena


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This data appears consistent for allscans. If there is trouble at high-k,it is systematic and reproducible.

Choosing kmax

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Choice of kmax should be of low importanceIdeally, small changes in choice of kmaxshould not change parameters you find

via your fits


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Choose kmin where backgroundstops being strongly dependent onsmall changes in backgroundparameters

Choosing kmin

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Choice of kmin should be of low importanceIdeally, small changes in choice of kminshould not change parameters you findvia your fits. In practice, fit is often

more sensitive to kmin than kmax


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Unweighted

k-weight 1

k-weight 2

k-weight 3

k-weight

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This affects theFourier transform

This affects thek-space plot

Athena Reminder!


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Effect of k-weight on Fourier Transform

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k-weight should be of low importanceIdeally, different k-weights should notchange parameters you find via your fits.


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Entering a Crystal ModelGet here fromthe Theory menuLattice parameters

are given inAngstroms

Artemis givescoordinates of atomsin fractionalcoordinates; i.e.multiply by latticeparameters to getAngstroms

This is the maximumdistance from theabsorbing atom (inAngstroms) that youwant feff to calculate.Make it a few Angstromslarger than the largestpath you plan to use, sothat feff can calculatepotentials properly

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What if the Sample Isn’t Crystalline?

• Short-Range Amorphous (e.g. glasses): Use acrystal structure which is locally similar on theAtoms page, but only use the inner paths foranalysis

• Macromolecular: Use the space group P 1 andlattice parameters A=B=C=100. Then entercoordinates of atoms in units of hundredths ofan Angstrom.


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This list of potentials can bechanged, but the absorbermust be 0 and you cannot skipnumbers

This file is generatedautomatically when you runAtoms, but you should look at itto see if it makes sense

Atoms Generates a feff.inp File

These coordinates anddistances are given inAngstroms; you shouldalways check that first-shell distances andcoordination numbers makesense to you

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The left part ofthe screenchangesdepending onwhat ishighlighted in…

The Artemis Main Screen

…the “Data &Paths” panel.

The right side ofthe screenmostly controlsthe plots……and the biggreen Fit buttonmakes it go!


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Interpretation shows you a listof paths:

Feff Screen

Black non-italicised paths areincluded in the fit

Paths with the text in brown arenot currently included in the fit

Italicised black paths are notcurrently in the path list at all

Paths with brown backgrounds aredirect scattering

Paths with blue backgrounds arefocused

Right-clicking allows you to addpaths to the list, include them inthe fit, and more…

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Clicking on a data set brings upa screen where you can choosek- and R-ranges for fit, k-weights, etc..

Data Screen


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This screen allows you todefine various kinds ofparameters:

Guess, Def, Set Screen

Guess parameters are optimizedduring fittingDef parameters are calculatedduring fittingSet parameters are calculatedbefore fittingAfter parameters are calculatedafter fittingSkip parameters are not used

Restraints force a parameter tobe close to a specified value“reff” is a special parameter equalto half of the nominal path length

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Clicking on a path lets youspecify path parameters interms of Guess, Def, Setparameters

Guess, Def, Set Screen


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Clicking on Fit in the Data &Paths screen brings up ascreen that lets you viewresults from previous fits andcompare them graphically

Log Files Screen

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