Hi Prof. Bruce， Thanks for your reply. In the picture you recommended,it says "The variations in functional form allow Z to be determined (±5or so) from analysis of the EXAFS".But I don't find any publication use it. I simply try an example.I choose the second shell of MoS2 which is the Mo-Mo shell in R-space in Athena,then do the back FT to get amplitude of the second coordination shell,then I compare to amp described in paper http://pubs.acs.org/doi/abs/10.1021/ja00505a003.The peak is at the almost same wave number when q-space use k2 weight(when use higher kweight,q space peak shifts to high wavenumber ),see pic attached. I only get a peak without the vally described in paper when use kweight,but can see a vally without k weight,maybe stress the contribution in high k make the vally obscure.Can this method works in element determination correct to +-5 Z number? And is there any method to determine whether a coordination peak in R space have one element contribution or more? For example ([Ifeffit] path contribution to fit in low R-space position, but the fit bond length is much longer than that ):a cluster we expected it has both Ni-O Ni-S(normally Ni-S peak is in high position),and when spectrum has a peak between regular Ni-O and Ni-S and a shouler near Ni-O,can I ensure the expection of both Ni-O Ni-S？OR just maybe because of the multiplicity of EXAFS. Sincerely, Zhanfei

-----原始邮件----- 发件人: "Bruce Ravel" 发送时间: 2014年7月3日 星期四 收件人: "XAFS Analysis using Ifeffit" 抄送: 主题: Re: [Ifeffit] How to distinguish whether the coordination element is heavy or light

On 07/02/2014 01:06 PM, ZHAN Fei wrote:

...

Dear all,

when I try to solve my question{*[Ifeffit] path contribution to fit in low R-space position, but the fit bond length is much longer than that*},I find a method from Prof.Calvin to distinguish whether coordination shell is composed by light or heavy element:

http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2007-December/007983.html

A clue can perhaps be obtained by noting the relative height of the peak near 2.3 angstroms compared with the large peak you've fit. As k- weight is raised from 0 to 1 to 2 to 3, the peak at 2.3 angstroms does not grow relative to the first peak. That suggests the scattering may be from another low-Z element like oxygen.

But I still don't know ,why it works.

Hi Zhanfei,

First off, I am very pleased to see that you are using the archive of the mailing list as a learning resource. Well done! Lots of questions have been answered here over the years!

On this page, http://xafs.org/Tutorials, you will find a link to a document by Matt called "The Fundamentals of XAFS". Look at figure 3.3 on page 15. It's a plot of the back-scattering amplitudes of three different elements.

As you can see, they have very different behavior as a function of k. Light things don't scatter very strongly at high k whereas heavy element do.

When you change the k-weight, you change how strongly the different regions contribute to the Fourier transform. If you have different elements contributing to the spectrum, then changing the k-weight may give you a way of emphasizing one contribution over another.

HTH, B

-- Bruce Ravel ------------------------------------ bravel@bnl.gov

National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973

Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Hi Zhanfei, A few more words to add to Bruce's answer on the +/- 5 "rule." It refers to cases where the bond length is treated as a free parameter. There's a gradual change of phase shift due to scattering with Z which looks a bit like a change in bond length. So if you're fitting bond length, the fit can compensate for an incorrect choice of scatterer by also returning an incorrect bond length. If you don't know what the bond length should be and your comparing two fits with scattering atoms of similar Z, then you don't know which reported bond length is incorrect and thus which fit is more valid. But some people (Joe Woicik comes to mind) have pointed out that sometimes you do know what bond length would correspond to which Z. As an example, you might be trying to determine which of two possible known structures is found in a nanoparticulate sample. Each candidate structure might have bond lengths that are well known. In that case, bond length would not be a free parameter, but would be fixed to the appropriate value for each fit. In a case like that, a change in Z of 1 is often distinguishable; i.e., there is no +/- 5 rule. --Scott Calvin Sarah Lawrence College On Jul 4, 2014, at 9:06 AM, Bruce Ravel wrote:

On 07/04/2014 03:51 AM, ZHAN Fei wrote:

...

In the picture you recommended,it says "The variations in functional form allow Z to be determined (±5or so) from analysis of the EXAFS".But I don't find any publication use it.

Hi Zhanfei,

The figure I referred you to was a plot of the scattering amplitude (the bottom panel had the phase shift) for three different scattering elements. I don't know what's plotted in the figure you attached because there are no labels on the axes. In any case, the scattering amplitude is the F(k) term in the EXAFS equation. As such, it's relationship to chi(R) or chi(q) is subtle. And, of course, in real data, all the different scattering paths interfere with one another.

As for the Z+/-5 rule, I don't know who first stated that. Perhaps Teo and Lee...?

In any case, it is easy to test. Measure, say, a NiO standard. Try replacing O in the feff.inp by N or F and do the analysis. Try again with C or Ne. Try again with B or Na. You will find that the fit using F is basically indistinguishable of the fit with O. Ne will be a bit worse, but not much. Na a bit worse, but not much. Eventually, you will get far enough away from O that you can clearly see the difference in the fit.

Some years ago, I tried to work on a FeGa alloy. Although 5 apart, I could not distinguish Fe scatterers from Ga scatterers well enough to say anything about how the dopant was distributed in the lattice.

Hi Zhanfei, Bruce, Scott, Sorry for jumping in to this conversation a bit late. Like Bruce said, there is no magic trick for determining whether a part of the R-space spectrum comes from one or more scatterers. And while XAFS is sensitive to Z, the sensitivity is weak. Because it's XAFS School week here in Chicago, I thought I'd go through a test of the Z dependence, and also try out a "trick" (I believe I first heard this from Mali Balasubramanian, but I suspect others may know this trick too) that relies on phase-corrected Fourier transforms, and is somewhat related to Scott's description of Joe Woicik's comments. The phase-correction "trick": If you correct for the phase-shift, the peak in |chi(R)| should be at the interatomic distance (ignoring subtleties in the XAFS equation). Turning this around, the peak in the phase-corrected |chi(R)| will be at the interatomic distance if and only if the phase-shift applied was correct... which means that Z is correct (to within some uncertainty). How well does this actually work on real data? To work through these two related ideas, I used ZnSe as a test case -- a very simple structure with a well-isolated first shell, and I have some decent data on it lying around. This also seemed like a useful enough category of analysis, that I thought it would be useful to better document. Scripts and results are at http://xraypy.github.io/xraylarch/xafs/feffit.html#example-6-testing-exafs-s... (turning this into an Artemis project is left as an exercise for the interested reader). The results of just changing scatterer in the fits are pretty clear, and suggest that Z +/- 2 might be a reasonable rule-of-thumb even when refining, R and S02, at least in this case of a well-isolated first shell. The results might be different for lighter backscatterers, but there are claims, especially in the bio-XAFS literature, that one can distinguish N and O ligands at least in some cases. Still, given that the ZnSe case is so clear, it seems reasonable to stick with the more pessimistic "Z +/- 5" rule-of-thumb, as long as the possibility that one can do better in certain cases (and may do much worse in others!). The phase-correction approach is interesting in that it asks "is this particular fit self-consistent?" instead of "which of these fits is best?". This independent of the fit quality could make it a useful secondary check of Z and R (much like a bond valence sum can be an independent check on the consistency of N, R, and valence). It does not seem highly accurate on its own -- also suggesting Z +/- 2 or 3 is about as well as one can do without further knowledge of the scatterers. That might be partially related to how well one can actually determine the peak position for chi(R) on a grid of 0.03 Ang, and partly related to the fact that other terms in the EXAFS equation alter the phase. In principle, those could be accounted for -- another exercise for the interested reader. I don't think the phase-correction "trick" would help Zhanfei -- it will NOT work on a mixed coordination shell. But the approaches described might be useful and/or inspiring to others. --Matt

Hi Zhan, On Mon, Jul 7, 2014 at 3:40 AM, ZHAN Fei wrote:

Hi Matti， Thanks for your attention and patience. The back fourier transform of the specific peak (use window)of Chi(R) gives the amplitude,donated by amp_bft。As in previous mails,I ask whether the compare the amp_bft and the amplitude of specific Z number element can determine the Z.

Sorry, I'm not sure I understand this. I didn't understand the figure you attached in your earlier mail. Generally speaking, I find back-transformed data to be not very useful -- making any sense of these requires very well isolated shells of atoms. The amplitude of the back-transformed chi(k) (is that what you mean by amp_bft??) has many contributions, and is not simply f(k). It will have Z dependence, but it will have other dependencies too.

And thanks for telling me the useful trick using the total phase shift of the specific element.

The discrepancy between R and Rphcor is below,the Zn and Br is close to Se(the best fit)'s 0.013,

Yes, Ge actually gives the closest match, and Se the second closest match, and I left Ga out of the test. I would probably say that anything closer that 0.015 Ang (and, really, maybe 0.02 Ang) is pretty darn close. So the phase-correction approach appears to be (in this case) not as sensitive to Z as the reduced chi-square, but does provides a check on self-consistency. The fits with Zn and Rb are noticeably worse than the fit with Se... hence Z +/- 3 or perhaps 5 seems like a reasonable rule of thumb, and sometimes one might be able to do better.

should the enot also be important criterion in this trick?and dose the plus or minus of enot indicate the lighter or higher element relative to the specific coordination shell?

Well, an E0 shift > 10 eV probably indicating that something is off .... but that could be just the selection of E0 for the experimental data. I wouldn't put much meaning of the absolute value of E0 though for any single fit. "a bond valence sum can be an independent check on the consistency of N,

R, and valence",can your give the ref. paper of this method? Thanks

http://en.wikipedia.org/wiki/Bond_valence_method The idea is that N, R, and valence are not independent. --Matt