[Ifeffit] [SPAM] Re: problem about negative
ZHAN Fei
zhanfei at ihep.ac.cn
Tue Nov 11 08:46:16 CST 2014
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" <bravel at bnl.gov>
> 发送时间: 2014年11月10日 星期一
> 收件人: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
> 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.html(negative
> > 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" <zhanfei at ihep.ac.cn>
> > *发送时间:* 2014年11月9日 星期日
> > *收件人:* ifeffit at 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
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > Ifeffit mailing list
> > Ifeffit at millenia.cars.aps.anl.gov
> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >
>
>
> --
> Bruce Ravel ------------------------------------ bravel at bnl.gov
>
> National Institute of Standards and Technology
> Synchrotron Science Group at NSLS-II
> Building 535A
> Upton NY, 11973
>
> Homepage: http://bruceravel.github.io/home/
> Software: https://github.com/bruceravel
> Demeter: http://bruceravel.github.io/demeter/
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