[Ifeffit] Fwd: Re: why ss_2 is negative?
hw26 at njit.edu
hw26 at njit.edu
Tue Feb 27 12:48:51 CST 2007
Dear all,
Thanks million for your great advice for my EXAFS modeling! It helps me
understand more about EXAFS and I really appreciate it! But I still have some
questions to consult you.
I took your suggestion and have the amp and e0 the same for each path. In
addition, I fixed the number axial U-O as 2. For the equatorial ligand, since
the total coordination number is between 4 and 6, I guess the number of U-F as
2(that is n1), and def the number of U-O as (5-n1)(that is n2). Then I did the
fit. The result showed the ss_2 is still negative. So I set the ss_2 as 0.003,
did the fitting again. I don't know if it is ok to fix the ss_2=0.003. It
seems the dr_1 change a lot.
In addition, I tried to do fitting in Kw=2 in stead of Kw=3. At this time, the
ss_2 is positive, and from my understanding, it seems the modeling is more
resonable for dr_1 and dr_2, but the R-factor is 0.023, a little bit larger
than 0.02. How can I decide which one I should use, the Kw=3 or Kw=2? Is there
anything I can do to improve the modeling?
The attached is my modeling. I am sorry to put attachment in the email that my
bother you.
Best regards!
Hao
> Hao,
>
> A few more comments:
>
> 1. It is well advised for anyone starting to look at uranyl compounds
> with XAS to read Shelly's various publications on that topic.
> Geochem. Cosmo. Acta, 66(22) 3875-3891, (2002) is particularly
> useful. Google scholar can help you locate more of her papers.
>
> 2. I am the first to admit that Artemis and Ifeffit are difficult
> tools for the beginning exafs practitioner. These tools try to
> provide a usable face to a difficult problem. Ifeffit was written
> with enough flexibility and power to allow the so-called experts
> to do the analysis they want to do. That means that Artemis has
> enough freedom to allow the unsuspecting user to do ill-advised
> things.
>
> You really need to think about what each of the parameters means.
> For example, just because Artemis allows you to float e0 freely
> for each path does not mean that doing so is a good idea. There
> are situations where it is a very good idea to have more than one
> e0 parameter in your fit, but I suspect that yours is not one of
> them. Consequently, you should consider constraining all your
> paths to have the same e0.
>
> What do I mean by "constrain"? Well, on the Guess,Def,Set page,
> you can define a single e0 parameter as a guess parameter, then
> use that parameter on each of the path pages. In that way, you
> will have one floating parameter in your fit that is used to
> describe the e0 of all your parameters.
>
> Similarly, you should think hard about the numbers of each kind of
> path. A uranyl moiety is unlikely to have more or less than 2
> uranyl ligands. The uranyl bond is very strong, consequently it
> is energetically unfavorable in a uranyl for those two bonds to be
> over- or under-filled. Consequently, you can consider setting the
> number of yl oxygens to 2. Furthermore, the equatorial plane is
> likely to have between 4 and 6 oxygens, so you should think of
> ways to constrain the total number of equatorial oxygens to be
> something reasonable. Since the coordination number is highly
> correlated with sigma^2 in a statistical sense, thinking well
> about coordination number should help address your original
> question.
>
> 3. Scott has made a very nice Artemis tutorial which can be found at
> http://cars9.uchicago.edu/iffwiki/HoraeSoftware#contrib
> It comes in the form of a series of Artemis projects. Newcomers
> benefit by working through his tutorial before trying to analyse
> their own data with Artemis.
>
> 4. The Ifeffit web site, my home page, and especialy http://xafs.org
> are all filled with useful information for the XAS novice. If you
> haven't already looked through the resources on those sites, you
> really should budget some time to do so.
>
>
> HTH,
> B
>
>
> --
> Bruce Ravel ----------------------------------------------
> bravel at anl.gov
>
> Molecular Environmental Science Group, Building 203, Room E-165
> MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007
>
> Argonne National Laboratory phone and voice mail: (1) 630 252
> 5033
> Argonne IL 60439, USA fax: (1) 630 252
> 9793
>
> My homepage: http://cars9.uchicago.edu/~ravel
> EXAFS software: http://cars9.uchicago.edu/~ravel/software/
>
> _______________________________________________
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>
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