[Ifeffit] How to do with diffraction peak

Anatoly I Frenkel afrenke2 at yu.edu
Wed Dec 12 12:04:00 CST 2012

(For masochists only): I still have Matthew's plastic scintillator in my cabinet at the NSLS, so if anyone is willing to try this trick with the original hardware, let me know.

From: ifeffit-bounces at millenia.cars.aps.anl.gov [ifeffit-bounces at millenia.cars.aps.anl.gov] on behalf of Matthew Marcus [mamarcus at lbl.gov]
Sent: Wednesday, December 12, 2012 12:49 PM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] How to do with diffraction peak

Here's one last trick that I used to use when I used a plastic scintillator at NSLS and didn't have a spinner.  WARNING - this is painful!
I used to tape a piece of Polaroid film to the face of the detector, run through a scan, develop the film, see where the white spots
were, and put Pb tape on the detector at those spots.  Told you it was painful!  Aside from that, I think Bruce is right - you're screwed
with 1-channel data, especially if the Bragg peaks are broad and/or come in the XANES region.  If you have to take data without a spinner or
multi-element detector, the trial-and-error method of changing the sample orientation often works to shift the Bragg peaks away from sensitive
parts of the spectrum to where you don't mind too much losing some points.

I have never tried fitting peak shapes to the Bragg peaks (say, a Lorentzian or pseudo-Voight plus a smooth polynomial; don't subtract the polynomial).
I suspect that the peak shapes aren't 'nice' enough for that to work reliably.  The shapes of the tails, for instance, would be influenced by
the angular divergence of the beam onto the sample and into the monochromator and any strain.

On 12/12/2012 7:28 AM, Bruce Ravel wrote:
> On Tuesday, December 11, 2012 04:08:03 PM Zhaomo Tian wrote:
>> I got XAFS data for Ag with CO adsorption( using Ag K edge), Ag is thin
>> film~300nm deposited on Si/SiO2 substrate. But in the original μ(E)
>> spectra, from 25894-26044eV, four obvious diffraction peaks appear( I
>> attached the file), and I guess they will influence the quality of fitting.
>> Is there anyone who knows how to deal with these diffraction peak? Will it
>> be corrected by smoothing or changing some origin data points in the
>> original file? I want the modification that will not destroy data analysis
>> later.
> You have received some decent advice on how to post-process your data
> to minimize the effect of the diffraction peak.  I think it bears
> mentioning that not all prblems are best solved after the fact in
> software.  Some problems should be addressed as the data are measured
> or even beforehand.
> I see from the data file you sent that you were at beamline 10C at
> Pohang.  It is hard to tell for certain from the data file or from the
> website, but it seems as though you were using a PIPS detector to
> measure your fluorescence XAFS.
> This is an experimental setup can be a difficult one to combine with a
> sample that diffracts.  The sort of PIPS commonly used at an XAS
> beamline tends to be of a very large surface area.  That means that
> the likelihood of some diffraction peak from the sample hitting the
> detector during the measurement is pretty high.  In fact, it happened
> 4 times for you.  That means you have a lot of data points to
> deglitch, were you to follow Kicaj's advice.  Because you used a PIPS
> rather than a multi-element detector, you don't have the option of
> following any of Matthew's (excellent) advice.
> I hate to say it, but I think you are screwed.  The best you can do is
> deglitch as best you can.  Because you will be removing so many points
> from the data, you will introduce substantial systematic error into
> the data set that remains.  I don't really see what you can do about
> that at this late date.
> So, what might you do the next time you visit the synchrotron to
> obtain better data?  In fact, there are number of things that you can
> consider at the stages of sample preparation or of data collection.
> 1. You don't say a lot about the sample or its substrate.  Perhaps you
>     have a reason that the substrate *must* be crystalline.  Perhaps
>     not.  Putting your film on an amorphous substrate would obviate the
>     problem of diffraction from the substrate.  That may be your best
>     bet.
> 2. The large size of the PIPS detector is a contributing factor to the
>     problem.  Simply using a detector with a smaller surface area
>     reduces (but certainly does not eliminate!) the likelihood of
>     diffraction peaks hiiting it.  Moving the detector farther away
>     from the sample would serve the same purpose.  Of course, doing so
>     would also serve to reduce your count rate, thus reducing the
>     quality of your data.  There is a cost to everything!
> 3. Use the 13 element Ge detector instead of the PIPS.  Then you can
>     simply eliminate channels hit by Bragg peaks or do the
>     post-processing trick Matthew described.
> 4. At my beamline, we have users almost every cycle who measure stuff
>     on crystalline substrates.  Our favorite trick is to mount the
>     sample on a spinner (e.g. http://dx.doi.org/10.1063/1.1147815) At
>     my beamline, we actually attach the sample the sort of small DC fan
>     that is used to cool electronics.  Inexpensive, simple, and
>     effective!  By keeping the sample constantly in motion, the energy
>     at which the Bragg condition is met is constantly changing.  This
>     serves to reduce the effect of the Bragg peak by a few orders of
>     magnitude by spreading it out in energy.  Usually, it can be made
>     smaller than chi(k), resulting in analyzable data.
> The bottom line is that you have the sort of problem that I think
> needs to be solved up front rather than after the fact.
> I know that's not helpful right now, but hopefully it will be the next
> time you go to the beamline.
> Cheers,
> B
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