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

ZHAN Fei zhanfei at ihep.ac.cn
Wed Nov 12 03:21:55 CST 2014

Dear Bruce:
    I am really sorry that I lost this mail you send,because the mechanism of my mail address.
Thanks a lot for your patience to give me detailed advise and strategy about my problems.I will 
take a step back and gain a deeper understanding of my sample and method itself.

> -----原始邮件-----
> 发件人: "Bruce Ravel" <bravel at bnl.gov>
> 发送时间: 2014年11月11日 星期二
> 收件人: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
> 抄送: 
> 主题: Re: [Ifeffit] Fwd: Re:  Re:  problem about negative
> On 11/11/2014 10:19 AM, Bruce Ravel wrote:
> > 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?
> Zhanfei,
> As I said yesterday, I don't know anything about your sample, so it is 
> hard for me to know what the "right" answer is to your problem.  But I 
> can make some observations and some suggestions.
>   * Your data range is really short.  As you seem to have noticed 
> (judging from the very short k-range in your project file), your data 
> has serious systematic problems starting at 9 or 10 inverse Angstroms. 
> I cannot quite tell, but your data appear to be transmission data.  Well 
> it is possible that you have some instability or nonlinearity at the 
> beamline, I would guess that your sample is not very homogeneous.  It is 
> possible that more disciplined sample preparation might help extend that 
> range of the interpretable data.
>   * You are right that slightly increasing the Rbkg value seems to make 
> a positive difference in the extracted chi(k) data.  Your data seem to 
> be an example of the sort of data I was alluding to yesterday.  The 
> background subtraction is difficult because it is difficult to 
> distinguish the Fourier components of the background function from the 
> Fourier components of the data.  I think that the background subtraction 
> with Rbkg=1.1 looks much better than with Rbkg=1.0, but given how 
> different they are, you have to be concerned about the correlations 
> between the background and the parameters of the data.
> It is clear that your data are of the sort for which background 
> subtraction is difficult.  So how do you know what is an acceptable 
> background subtraction?
> Well, using only Fourier methods, I think we have demonstrated that you 
> cannot know the right answer without some kind of prior knowledge.
> So, how do you get that prior knowledge?
> Well, my advice is to first solve some simpler problems.  Measure your 
> standards.
> Measure the common forms of moly oxide and moly sulfide.  Measure moly 
> metal.  Analyze all of them.  The advantage of the standards is that you 
> know what the answer should be.  Do the data processing and data 
> analysis.  Make sure that, when you do the analysis, you get the right 
> answers.
> Having done that exercise, you will then have a lot more knowledge about 
> what the various forms of moly oxide look like and what the challenges 
> are when doing the data processing and data analysis.
> Some questions:
>    - Are there any forms of moly oxide for which the bond length is as 
> short as 1.6?  If so, do the conditions of formation exist in your 
> system?  Is your sample of a valence consistent with the valence of the 
> Mo when it has such a short bond?
>   - If you convince yourself that it is possible for moly to have an 
> oxygen atom at 1.6 or 1.7, what did you have to do with your standard to 
> get a sensible analysis of the EXAFS data?  Hopefully, that will guide 
> you to doing a sensible analysis of your unknown sample.
>   - If none of your moly oxide standards have an O atom at 1.6 or 1.7, 
> why do you think it is chemically reasonable for your unknown sample to 
> have such a short bond?  If, in fact, that short bond doesn't exist 
> elsewhere in nature, why would your sample magically have such a short bond?
>   - If you do not believe in such a short bond, then does your 
> experience with the standards give you the confidence to increase Rbkg 
> such that the low-R signal is removed by the background function?
> I completely understand that you have a compelling reason to understand 
> your unknown sample and that I am suggesting that you spend a good chunk 
> of time measuring and analyzing a bunch of standards that are not your 
> actual research project.  That might seem like time that takes you away 
> from your real goal, but you have already demonstrated that you are 
> stumped by your real goal.  I am saying the only way to get over your 
> current hurdle is to take a step back and gain a deeper understanding of 
> the data, the physics of EXAFS, the methods of EXAFS analysis, and the 
> intricacies of your current problem.
> B
> -- 
>   Bruce Ravel  ------------------------------------ bravel at bnl.gov
>   National Institute of Standards and Technology
>   Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
>   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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