[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,
> 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/
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
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