Re: [Ifeffit] [SPAM] Re: problem about negative

Hi Bruce： Thanks a lot for your advise. I reconsider the path I used in my fit,I found Mo-O 1.7A and Mo-O 1.6A，though has 0.1A difference，but has big gap in phase of Chi,it may cause using the false path lead to negative N to numerically correct it.0.1A diatance can cause such big difference,Why we usually use path just "reff not far from bond length "?Picture of two path is atached. My sample is a cluster(Mo K edge,has been attached) which has Mo-O Mo-S,maybe Mo-Mo bond.I am not sure whether the first peak in R space is real coordiantion shell or not,but I also fit it use a Mo-O 1.5A path,delr of bond length and enot is a little bigger. ssO = 0.01240260 # +/- 0.00124076 [0.00300] delrO = 0.17825404 # +/- 0.02825020 [0] enot = -13.42877449 # +/- 1.98759165 [0] Rbkg>1.1 can avoid the first peak,but the remaining curve is somewhat not smooth.How to distinguish whether a long wavelength oscillation appear as a real peak or false one?I am confused about it. I find when I avoid the first scattering peak after white line(kmin=4.8 maybe too large),the first peak of R space disappeared.Because usually the first scatering peak is related to the first coordiantion shell,can I think the first peak in R space less 1A is a real peak instead of noise？ Thanks Sincerely,

-----原始邮件----- 发件人: "Bruce Ravel" 发送时间: 2014年11月10日 星期一 收件人: "XAFS Analysis using Ifeffit" 抄送: 主题: [SPAM] Re: [Ifeffit] problem about negative

Hi Zhanfei,

When I present the interpretation of fitting results in one of my training courses, I spend a quite bit of time on the problem of interpreting fitting results, including the results that are somehow surprising of unphysical.

You are right that a negative coordination number is troubling. So is a coordination number with an error bar of about the same size as the best fit value. Your "NO" parameter is certainly troubling.

Since I do not know anything about the sample you are measuring, how it was prepared, or how it was measured, I don't know the resolution to your problem. However, I want to suggest that you take a broader view of what the problem might be.

When you come upon a weird value like a coordination number of -1.9, there are at least 5 broad categories of things that might be going wrong:

1. You may be misusing the software in some obvious way or you may have uncovered a previously unknown bug in the software. This seems to be your assumption, but I suspect that it's not the problem here.

2. You may have made a mistaken assumption about the species of the scatterer. The first plot is the result of a couple of quick first shell theory calculation made with Artemis for Ni bound to oxygen and sulfur, each at the same distance. Notice how the two are almost perfectly out of phase. Where you to use the wrong one, the fit would correct that by using a negative amplitude. (I made the calculation for a Ni absorber, but the same thing would happen with a Mo absorber.)

3. You may have run the theory incorrectly. I occasionally run Atoms with the wrong edge by accident. Attached is the result for a first neighbor oxygen scatterer around Mo with the Feff calculation done for the K and L3 edges. These are not quite as far out of phase as the first example, but they are pretty far out of phase. With a large enough E0, they would get far enough out of phase that a negative amplitude could numerically correct the fit.

4. There are a number of experimental artifact that can yield spurious oscillations in your data. These sorts of things are discussed in many places in the literature and on the Tutorials page at xafs.org. Scott gives a nice summary of many of them in section 5.9 of his recent book (ww.amazon.com/XAFS-Everyone-Scott-Calvin/dp/1439878633/).

5. Some materials with big white lines and short near neighbor distances are simply difficult to deal with. With a big white line, the background function needs to have a lot of freedom to follow the data properly at low k. However, giving the background spline a lot of freedom gives it Fourier components that are associated with the near neighbor scatterer. Shelly discusses this problem somewhat in her tutorials at http://xafs.org/Tutorials.

I often tell people that weird fitting values are valuable information becasue they force you to reconsider all of your assumptions and all of your experiment. #2 suggests that you should think very hard about what you expect to find. #3 suggests that you may have made a silly -- but easily fixed -- mistake. #4 suggests that there was a problem with the sample or with the beamline and you may need to try the measurement again, this time being more careful about everything in the experiment. #5 is the scariest -- some materials simply defy the standard algorithms used in the software and require extraordinary care in processing and interpretation.

As I said, I have no way of knowing how to advise you, but I am fairly confident that some or all of your problem relates to something I've said in this email.

Good luck, B

PS: If #5 turns out to be the culprit, then you should think hard about how you ask your question. You provided a plot of chi(R) in your original question, which is helpful. But if the problem is difficulty in removing the background, a plot of mu(E) and the background function would be useful. In fact, a small Athena project file containing the data in question might be even more helpful.

Good questions get good answers. Vague or incomplete questions get vague or incomplete answers.

On 11/09/2014 08:53 AM, ZHAN Fei wrote:

...

Dear all: When I get a wrong fit about Mo-O and Mo-S fit of first two shells. ssO = 0.00729812 # +/- 0.00961052 [0.00300] delrO = -0.02968655 # +/- 0.03378397 [-0.05765] enot = -5.30590978 # +/- 7.08310376 [-16.71557] NO = -1.88450657 # +/- 1.59438947 [0.5] NS = 1.71281926 # +/- 1.08552732 [1.00000] delrS = 0.00418341 # +/- 0.04904499 [-0.05647] ssS = 0.00329415 # +/- 0.00688491 [0.00300] name N S02 sigma^2 e0 delr Reff R ========================================================================== S1.1 1.000 1.456 0.00329 -5.306 0.00418 2.41350 2.41768 O7.1 1.000 -1.602 0.00730 -5.306 -0.02969 1.54660 1.51691

name ei third fourth ========================================== S1.1 0.00000 0.00000 0.00000 O7.1 0.00000 0.00000 0.00000

ssO with a negative coordiantion number NO.I searched the mailist there is only information about negative ss http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg02326.htm... ss to compensate small amp).but here I even get a negative amp.What's wrong can cause a negative amp? Thanks for help. Sincerely,

-----原始邮件----- *发件人:* "ZHAN Fei" *发送时间:* 2014年11月9日 星期日 *收件人:* ifeffit@millenia.cars.aps.anl.gov *抄送:* *主题:* [Ifeffit] too small bond length in R space

Dear all： I encounter a problem of exafs fit in an example of Mo which have Mo-O Mo-S Mo-Mo bond.The problem is that the Mo-O peak in R space has too small bond length (less than 1.4A(+0.5A for phase correction) ).Because when 1.2>rbkg>0.68 there is little change in spectrum of R and k space,and when I increase the value of rmin of forward Fourier transform the peak changes little,so I think it's not a noise.But when I try to fit it use the 1.35A path of Mo-O,I can't fit it well. Could you give me some advise about fit too small bond length,or recommend papers of similar situation? picture of R space is attached. Thanks Sincerely, zhanfei ihep of China R space of spectrum

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

National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973

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