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Fitting procedure
by abhijeet gaur 24 Apr '09

24 Apr '09

Hello Matt Sir, Thanks a lot for your valuable sugestions. I had fitted the Cu foil spectra as you suggested. I had taken same SO2 value for all the paths and after fitting the first shell , making its parameter fix when fitting second shell I changed the fit R range 2.9- 3.7 in order to make the contribution of first shell negligible. I got a nice fit. The values of different parameters I got are as follows : E 0=2.90 eV , SO2= 0.72 1st shell R = 2.54, delR= -0.011, SS2=0.0083 2nd shell R= 3.69, delR= 0.080, SS2=0.0088 The experimental data is taken at room temperature. Are these parameters within the experimental error limit. Please tell me with regards Abhijeet Gaur

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Can't locate Ifeffit.pm
by Silvio Levy 21 Apr '09

21 Apr '09

Hi, I've installed horae on a new laptop after a hiatus. When I try to run athena or artemis I get the message Can't locate Ifeffit.pm in @INC (@INC contains: ... Setup: ifeffit-1.2.11c horae-069 Ubuntu 8.04.1 There is an Ifeffit.pm (in fact two) in the ifeffit-1.2.11c source directory, so I added it to the PERL5LIB path. But this didn't solve the problem; it just pushed it a few yards further. Now I get Can't locate loadable object for module Ifeffit in @INC (@INC contains: ... Anybody know the solution? Note to Bruce: the instructions in 0INSTALL still say 'perl Makefile.PL; make; make install' but the correct thing seems to be 'perl Build.PL; Build; Build install' as I found on one of your web pages. Thanks in advance Silvio

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Fitting procedure
by abhijeet gaur 20 Apr '09

20 Apr '09

I want to add some more things I have done 1) E0 is kept same for all the shells 2) All other parameters like SO2 , del r , SS2 are calculated separately for different shells. So. is there problem with taking different SO2 for different shells. Surely del r and SO2 will be different for different shells , If I got it right. Abhijeet

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NLEG
by Eugenio Otal 20 Apr '09

20 Apr '09

Hi, I am performing some XANES simulation with feff. I want to know somethings about an extra shoulder so I am using NLEG card. I have no problem with NLEG = 1 - 3, but NLEG > 3, I found a error: Eliminating path degeneracies... Plane wave chi amplitude filter 2.50% WARNING!! Two non-degenerate paths, hashed to the same hash key!! 0.12036490409027290344E+09 0.12042092980933572352E+09 3 3 npat0, npat iat, ipot0, ipot, ipat0, ipat 1 1 1 2 2 2 0 0 0 0 3 1 1 2 1 ileg, rx0,ry0,rz0, rx1,ry1,rz1 1 0.0000000000E+00 -1.3877787808E-16 1 0.0000000000E+00 0.0000000000E+00 1 1.9402260780E+00 1.9402260780E+00 2 0.0000000000E+00 0.0000000000E+00 2 0.0000000000E+00 0.0000000000E+00 2 0.0000000000E+00 0.0000000000E+00 3 0.0000000000E+00 1.7760854959E+00 3 0.0000000000E+00 0.0000000000E+00 3 1.9402260780E+00 -7.8094518185E-01 hash error that is what I found in output file and the simulation crashed. Is there somehow to solve this and continue the job? Thanks in advanced, euG

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Fitting procedure
by abhijeet gaur 19 Apr '09

19 Apr '09

Hi all, I think there is a lot of confusion over the method that i used for fitting, So I should make it clear here. In this method I fit the first shell by taking into account only first shell R range i.e. 1.5 - 2.7. Then after getting a nice fit for the first shell, I extract its parameters and make them set in Artemis. Then I include the second shell by increasing R range to 1.5 - 3.6. In the same manner I fit the first three shells of copper foil and the parameters I got for them are reasonably good. The problem of high SO2 only lies with one of my foil data which is not as good as other data. For other good data I got SO2 value for second shell within the exceptable limit. One more thing I want to say is that we can check the corelation between different parameters of shells by making them guess during any step of the fitting e.g. during the fitting of second shell we can make any parameter of the first shell to vary and check its corelation with them. But if I am counting the first shell data twice, I will include only second shell R range after first shell fit.I think it will not make any difference to results. If yes please tell me the reasons. with thanks Abhijeet gaur

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Re: [Ifeffit] Fitting procedure
by Chappell, Mark A ERDC-EL-MS 18 Apr '09

18 Apr '09

Oops, please ignore my message - sent it to the wrong address!!! --------- Message sent via my BlackBerry Wireless Device ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Sat Apr 18 14:56:35 2009 Subject: Re: [Ifeffit] Fitting procedure They're on theur way back to Vicksburg. I yried to guide them from home but couldn't figure out where she was. By 230, she hung it up and turned back --------- Message sent via my BlackBerry Wireless Device ----- Original Message ----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Sat Apr 18 12:57:18 2009 Subject: Re: [Ifeffit] Fitting procedure Hi Adam, I am confused by this thread too! As you say, the original issue involved using S02 for individual shells of data on Cu foil. Of course, having separate S02 for each shell is not usually necessary to model Cu foil -- in fact I can't think of a case where it is needed. But since S02 is 100% with N, and ~95% correlated with sigma2, it is easy to have S02 vary per shell if one allows it to happen. Whether that's a good idea or not depends on how you interpret the results. Most people choose to fix a single S02 and vary N. Lots of people fit spectra with one S02 and an N for each shell, so I don't think the number of free parameters is necessarily a big issue. In a follow-up message, Scott seemed (to me) to be more concerned about whether it was reasonable to "fix parameters for the first shell" when fitting a second or higher shells, not so much with the issue of what parameters were being refined. There weren't explicit details on what was fixed or what fitting ranges or parameters were used for the higher shells. Scott suggested (I believe) that "fixing the first shell" and fitting the second shell was not a good idea, and asked to hear differing views. I find the approach of "fit the first shell, then fix those parameters and fit the second shell" to be a reasonable way to start, so I responded. I would not call this approach "acceptable, but generally not preferred" -- I would say it has actual merit. Yes, it is often a good idea to check a fit to the whole spectrum toward the end of an analysis. But in a fit to the whole spectrum, the quality of the fit to the more subtle features (the finer structure) can often get lost in the fit to the more dominant features of the spectra. That is why we subtract mu0(E), after all. I don't see Fourier filtering as a bad idea for analyzing higher shells. But perhaps I am just not understanding what Scott and Shelly recommend??? --Matt _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Re: [Ifeffit] Fitting procedure
by Chappell, Mark A ERDC-EL-MS 18 Apr '09

18 Apr '09

They're on theur way back to Vicksburg. I yried to guide them from home but couldn't figure out where she was. By 230, she hung it up and turned back --------- Message sent via my BlackBerry Wireless Device ----- Original Message ----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Sat Apr 18 12:57:18 2009 Subject: Re: [Ifeffit] Fitting procedure Hi Adam, I am confused by this thread too! As you say, the original issue involved using S02 for individual shells of data on Cu foil. Of course, having separate S02 for each shell is not usually necessary to model Cu foil -- in fact I can't think of a case where it is needed. But since S02 is 100% with N, and ~95% correlated with sigma2, it is easy to have S02 vary per shell if one allows it to happen. Whether that's a good idea or not depends on how you interpret the results. Most people choose to fix a single S02 and vary N. Lots of people fit spectra with one S02 and an N for each shell, so I don't think the number of free parameters is necessarily a big issue. In a follow-up message, Scott seemed (to me) to be more concerned about whether it was reasonable to "fix parameters for the first shell" when fitting a second or higher shells, not so much with the issue of what parameters were being refined. There weren't explicit details on what was fixed or what fitting ranges or parameters were used for the higher shells. Scott suggested (I believe) that "fixing the first shell" and fitting the second shell was not a good idea, and asked to hear differing views. I find the approach of "fit the first shell, then fix those parameters and fit the second shell" to be a reasonable way to start, so I responded. I would not call this approach "acceptable, but generally not preferred" -- I would say it has actual merit. Yes, it is often a good idea to check a fit to the whole spectrum toward the end of an analysis. But in a fit to the whole spectrum, the quality of the fit to the more subtle features (the finer structure) can often get lost in the fit to the more dominant features of the spectra. That is why we subtract mu0(E), after all. I don't see Fourier filtering as a bad idea for analyzing higher shells. But perhaps I am just not understanding what Scott and Shelly recommend??? --Matt _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Fitting procedure
by abhijeet gaur 18 Apr '09

18 Apr '09

Hi all, Thanks to all the concerned persons for having such a wonderful discussion over fitting procedure. I am able to understand the things better by going through these discussions. But what I am trying to say is that I had first applied the fitting procedure in which I make the parameters of all paths( included in the fit) to vary simultaneously, but the problem is that I am not able to get a good fit and the parameters for different paths are also coming absurd like very low amplitude etc. For days I have been trying this method of fitting but not able to get good results.I tried different models also like Debye & Einstien model, I used the relation del r= alpha* Reff but it doesn't work. Then I switch to this the method in which we fit the first shell, get the parameters fix them and then go for the next shell and in this way e fix the whole spectra. The results I got are extremely good. Thus I am using this method. Abhijeet Gaur

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Multiple data set fit
by Debora Meira 18 Apr '09

18 Apr '09

Dear all, I'd like to know a reference that has multiple set data fit as a function of temperature in nanoparticles. Is the relation of Debye Waller factor (s2 = ss2 + sd2) valid for the higher shells? In particular, can I use the Einstein model for sd2? Thanks in advance, Débora Débora M Meira Universidade Federal de São Carlos Pós-Graduação em Engenharia Química Laboratório de Catálise Tel: (16) 92461134 / (16) 34125935 _________________________________________________________________ Faça já uma busa e ganhe um wink do Messenger. Está esperando o que? É grátis! http://www.ibud.com.br/

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R quality factor in k space
by Cammelli Sebastiano 17 Apr '09

17 Apr '09

Dear iffefit user, I found on a paper (E.A. Stern et al. /Physica B 208&209 (1995) 117 120) the definition of R quality factor as: R_factor ≡ < ∆chi(R space))> = √[ ∑ |chi_C(Ri) – chi_E(Ri)|2 / ∑( chi_E(Ri))2] ----> formula 3 Where Chi(Ri) is a complex function (imaginary and real part of the XAFS spectra in the R space), C concerns the calculated XAFS spectrum, while E refers to the experimental XAFS spectrum. In the case of a linear combination fitting on the k space performed by ATHENA, the <∆chi> needs a correction. Is it correct to write: R_factor ≡ < ∆chi(k space))> = √[ ∑ (chi_C(ki) – chi_E(ki))2 / ∑( chi_E(ki))2] ? Where Chi_C(ki) = x1*chi1(k)+x2*chi2(k) : chi1 and chi2 are the EXAFS functions of the two reference samples used for the linear combination procedure and x1, x2 (with 0<x1,x2<1 and x1+x2=1) are their weight; Chi_E(k) is the EXAFS experimental function of the investigated sample. Best regards Sebastiano Cammelli

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Debye-Waller factors for metal oxides ?
by Ian James Drake 16 Apr '09

16 Apr '09

Hi, There is little discussion over the significance of fitted Debye-Waller factors (ss2) found for metal centers in metal oxides of heterogeneous catalysts. I am searching for a better way of determining how reasonable these values are in the fits I get. 1. Are phenomenological models like the correlated Debye model and Einstein model appropriate? It seems that Debye temperatures are hard to find for oxides. 2. Is there an equivalent value for ss2 in x-ray crystallography data that I can refer to for comparison in these materials? What should I look for in reviewing published x-ray crystallographic data? 3. Is the temperature dependence reported for the ss2 for some metals (like Cu and Al) similar to their respective oxides? For example, in Debye-Waller factor calculations reported for Al metal by R.C.G Killean (in J.Phys.F: Metal Phys., v. 4, pg. 1908, 1974), the ss2 changes by a factor of three between 25C and 300C. Would I expect a factor of three increase in crystalline zeolites (AlO4 structural units). 4. Specific to my work: I have studied Al containing oxides at temperatures between 25 and 300 C. I would like to quantify coordination changes by doing EXAFS fitting of the Al K-edge data. The EXAFS was taken at temperature and I observe no change in the broadening of the data. Likewise, the fitting shows no sensitivity in the Debye-Waller factor. It is nearly constant at 0.001 A over the temperatures of interest. Since ss2 and the coordination number (CN) are correlated, I would like a way to bind the error on the fitted CN by modeling real physical changes in the Debye-Waller factors. Do you have any suggestions? Looking forward to your thoughts. Ian Drake Graduate Student UC Berkeley

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Fwd: Questions about Athena & FEFF
by Bruce Ravel 15 Apr '09

15 Apr '09

Pascal, I am answering your question on the Ifeffit mailing list, which is the most appropriate venue for questions of this sort. Please read this page: http://cars9.uchicago.edu/iffwiki/BruceRavel/FormLetters/HelpRequest If I understand your question, you are asking about whether it is appropriate to run Feff with a small cluster. The canonical answer to that question is that you want to use a large cluster whenever possible so that the muffin tin potential is well constrained. Sometimes, with a very small cluster, the algorithm Feff uses to compute the muffin tin radii can result in radii that are unphysically large, resulting in an unphysical calculation. Of course, that is a somewhat hand-waving answer. It is hard to know without actually running a calculation whether the problem with muffin tin radii will actually happen. I have comfortably published results which use very small clusters indeed. In your case, as in so many cases, the best advice I can give is to try it both ways and see what happens. That is, you can try doing a XANES calculation (Are you using Feff8? You didn't say...) with the small cluster and comparing it to the Feff8 calculation which uses a large cluster to compute the potentials and small cluster to compute the full multiple scattering XANES. See the Feff document at http://leonardo.phys.washington.edu/feff/wiki/index.php?title=FEFF_Document… for details about how to set parameters in the feff.inp file to make that happen. Regards, B ---------- Forwarded Message ---------- Subject: Questions about Athena & FEFF Date: Wednesday 15 April 2009 From: "Pascal G. YOT" <pascal.yot(a)univ-montp2.fr> To: bravel(a)bnl.gov Dear Prof. Ravel, I'm working on data coming from XAFS measurements carried out at Pb-L3 edge on lead containing glassy samples. Three reducing agent are used to reduce lead(+II) inside the original glass at high temperature. Our samples contain then a fraction is in fcc lead(0) form and one other fraction of lead(+II) still remaining inside the glassy framework. EXAFS analysis show a decrease of the Pb-O coordination number from 3 (for original glass) to lower CN (1 in extreme case). My major concern is the analysis of XANES, some modifications are observed on the finger prints. I've try to fit the spectra using linear combination fitting module from Athena using lead and original glass spectrum with poor result as you have understand. I need then to generated model XANES spectra for the CN. As I'm not an expert of FEFF, I need some advices. Can I use a cluster PbOx ((d=2.23 A) with coordinate for Pb and O coming from lead oxide) containing few atoms? Is the obtained spectra reliable to give a "good" fit? I hope my questions are clear for you. Thanks in advance for your remarks. Best regards Dr. Pascal Yot ------------------------------------------------------- -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Basic questions
by haiyan 15 Apr '09

15 Apr '09

Dr. Kelly, May I get a copy about setting k-range? Thanks1 Haiyan Zhao Chemical Engineering Department Virginia Tech Blacksburg, VA 24060 Hi Andy, I have a book chapter that details how to set the k-range for a data set. It also talks about Rbkg in detail. If you want a copy just send me an email. Cheers, Shelly

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residual saving
by Guvenc Akgul 15 Apr '09

15 Apr '09

dear all, I need save residual as k^3*Chi(k) but I could not save it because it is saving only as Chi(k).how can do for this? thanks in advance guvenc

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High SO2
by abhijeet gaur 12 Apr '09

12 Apr '09

Hello Scott Sir, I got that ifeffit basically works on the principle of making the theoretical data look similar to experimental data. But what I know about fitting is that we have to first fit the first shell and then keeping the first shell parameter constant , we go for the next shell. Is it not right. Please tell me Abhijeet Gaur

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High SO2 value
by abhijeet gaur 09 Apr '09

09 Apr '09

Hi all, I am fitting a copper foil. I fit the first shell by using first ss path and got it fitted nicely. Then keeping the parameters for the first shell to be fixed , I tried to fit the second shell by taking first and second ss but it is always coming a littel displaced and not fitting well also. But when I added the the third ms path to it , the fit becomes very nice. But the problem is that parameters for third path are coming very bad. And one more problem is that the value of SO2 for second shell is coming very high around 1.5. I am not able to understand the results. Thanks in advance Abhijeet Gaur

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Linear combination fitting
by Guvenc Akgul 09 Apr '09

09 Apr '09

Dear all, I have done Ti doped ZnO EXAFS data analysis but I guess it is getting mixture structure at high concentration for example 55% Ti doped ZnO.Also I done linear combination fit , but at fitting space norm(E),ZnO weight is 0.779 and ZnTiO3 is 0.221 then I changed fitting space is chi(k) ZnO weight is getting 25.2 and ZnTiO3 is getting 74.8 and it is not same like at fitting space norm(E) why? regards guven

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huge S02 value ??
by mzhu＠udel.edu 07 Apr '09

07 Apr '09

Hello everyone, I have been fitting EXAFS of NiSO4 aqueous solution. The feff files were created from Ni(OH)2 using Feff7.00. During the fitting, coordination number was fixed as 6. The S02 derived from fitting is 1.22. I tried other materials for creating feff files, such as NiCO3 and NiPO4, and I got the similar S02 values. I also tried Feff6, it did not result in a reasonable S02 value, either. Anyone can tell me why it led to such high S02 value? The data file and feff input file (Feff 7) are attached. Thanks in advance. Best wishes, Mengqiang Zhu ----------------------- Mengqiang Zhu Ph.D Candidate Environmental Soil Chemistry Department of Plant and Soil Sciences University of Delaware 152 Townsend Hall Newark, DE 19716 http://ag.udel.edu/soilchem/zhu.html

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Basic questions
by Andy Connelly 06 Apr '09

06 Apr '09

Some really quick basic questions. I am working with EXAFS spectra of silicate glasses at various edges (including S and Fe K edges) and I am having a really difficult time pinning down the structures. Clearly with glasses I can't always be sure of the oxygen co-ordination and so I have to refine this value which is one among many problems. Just to check I have things right: 1. Are there any problems if I set the R-range min to the same value as Rbkg? 2. If I want to refine the degeneracy of a path can I write the expression "amp*N_1" in the SO2 box? (where the N box is set to 1) and then refine "amp" and/or "N_1"? where N_1 equivalent to the degeneracy and amp is effectively SO2. Clearly they will be highly correlated, but does a formula like this cause IFEFFIT any problems? 3. If, for initial fits, I am only interested in the first shell should I set R-range max to a lower value to isolate that shell and then increase it as I look at shells at longer distances? 4. If I have a calculated Fe3+-O path from a 4 and 6 co-ordinate reference are these equivalent? Obviously, they will give a different bond length and the MS paths will change but if I am only fitting a first shell is there anything different. I think the answer involves the muffin tin potentials but I'm a little out of my depth there. Any advice about solving glass structures more than welcome. Whatever I try I can't get realistic results out. Thank you for your time, Andy Connelly

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Ab initio calculations
by Luanga Nchari 06 Apr '09

06 Apr '09

I would like to do ab initio calculations to get a theoretical XANES spectra. I have XYZ coordinates..... Could somebody remind me how I can run this on my PC. Cheers, Luanga

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Mixed Multiple scattering shell
by Joseph Washington 01 Apr '09

01 Apr '09

Hello all, I was wondering if anyone can send any useful hints or tips for parameterizing a mixed multiple scattering shell comprised of two NaCl type strucutres, like the AgBr(1-x)Cl(x) example. Has anyone worked on fitting the third shell in that example? I am looking for examples of nacl rocksalt-like FEFF calculations that have successfully parametrized multiple scattering path contributions. Right now, after running feff, I'm using a different delr / ss term for each multiple scattering path I include. Does anyone have any clever ways of representing these in terms of the delr/ss in the first shell? Also, FEFF is telling me that the amp and mixing terms are almost completely correlated and this cause the amp term to blow up. Thanks all, I really appreciate the assistance! Joseph

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Re: [Ifeffit] Ifeffit Digest, Vol 73, Issue 25
by Zuzaan, Damdinsuren 31 Mar '09

31 Mar '09

Hi Matt, >From the raw data I can recognize columns with dead time information. Also I am waiting reply from beamline scientists. Anyway, could you give me some detailed information how to do this dead time correction with Ifeffit commands or within Athena. Thank you in advance. Cheers, Damdin ------------------------------ Message: 2 Date: Mon, 30 Mar 2009 10:18:43 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 73, Issue 24 To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <b8522e3d0903300818w355650dfub735bf29165fc0a1(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Damdin, > I checked my spectra and found that I forgot to do the dead time correction (measurement were in fluorescence mode). > So I think the small S02 and N are due to deadtime effect. Yes, a slightly saturated detector can cause an S02 that is a little smaller than normal. > It is possible to do it in Athena? In general, athena doesn't have buttons or a page to do dead time corrections. This is because there isn't a single, consistent way to store the dead time information. You might want to consult with the beamline scientist for how to make these corrections. If you know what columns in your data file hold the dead time information (and what the columns are holding), it's possible to do this with Ifeffit commands (within athena, even). Cheers, --Matt Newville <newville at cars.uchicago.edu>

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New Method for Normalization?
by Barton, David (DG) 30 Mar '09

30 Mar '09

XANES Aficionados, I know most users on this list are hard-core EXAFS analysts, but some of us use XANES analysis to decipher mixed phases or use it to get structural clues when data quality isn't sufficient for EXAFS analysis. Anyway, I have a question for those interested in quantitative analysis of XANES or those that are willing to offer an opinion on methods to normalize raw spectra to get reliable, repeatable comparisons of near-edge features. Has anyone considered using the methods of Penner-Hahn to normalize their data to get reliable intensities of near-edge features? The reference to their method of normalization is below: J. Synchrotron Rad. (2005). 12, 506-510 [doi:10.1107/S0909049504034193] "A method for normalization of X-ray absorption spectra" T.-C. Weng, G. S. Waldo and J. E. Penner-Hahn It is my understanding the Ifeffit uses a linear function to remove the pre-edge and a quadratic for the post-edge and that the Athena's flatten is a subtraction of these functions. This is an excellent method under most scenarios since the background is usually fairly smooth and can be well approximated by a quadratic equation. Personally, I have had only a few rare cases where the quadratic function on the post-edge was not sufficient to reliably normalize the data and in those cases a third-order polynomial was sufficient. Does anyone else have an opinion on using alternative normalization routines? Dave _________________________________ David Barton The Dow Chemical Company

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Re: [Ifeffit] Ifeffit Digest, Vol 73, Issue 24
by Zuzaan, Damdinsuren 30 Mar '09

30 Mar '09

Hello everyone, Shelly, Matt, Scott many thanks for your reply. I checked my spectra and found that I forgot to do the dead time correction (measurement were in fluorescence mode). So I think the small S02 and N are due to deadtime effect. It is possible to do it in Athena? Damdin -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Saturday, March 28, 2009 6:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 73, Issue 24 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: About S02 (Matt Newville) 2. Re: About S02 (Scott Calvin) ---------------------------------------------------------------------- Message: 1 Date: Fri, 27 Mar 2009 16:28:46 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> Subject: Re: [Ifeffit] About S02 To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <b8522e3d0903271428i7c6ea611l325443292de87b45(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Damdin, An XAFS book or theory that says "S02 must be between 0.8 and 1" overstates the case. In simplest terms, S02 is a fudge factor. There is a theoretical basis for it (passive electron overlap), but much of this can also be folded into other "loss terms" that are due to inelastic scattering events for the photo-electron. These should be part of the EXAFS calculation from, say, Feff, but are hard to do well to high precision. When using Feff, Ifeffit, Artemis, it does turn out that, in most cases, the calculated amplitudes tend to overestimate the experimental amplitudes, and that applying a constant S02 between 0.8 and 1.0 works reasonably well. That is hardly a "must be" between 0.8 and 1. In addition to the theoretical issues of Feff not-quite-correctly calculating S02, there are experimental factors that affect the XAFS amplitude: the estimate of the edge step being the most important, but also the energy resolution of the incident x-rays and sample-dependent issues such as pinholes, and for fluorescence measurements detector deadtime and self-absorption. There is an understandable desire to turn these observation into a rule-of-thumb and then into some sort of rule that can be pointed to as if to say "this analysis is wrong" or "this analysis is correct". As is normal for such rules-of-thumb, it is sometimes broken. Of course the main trouble with the uncertainty of which S02 to use is that for a single-shell analysis, one cannot distinguish S02 from the coordination number. That is, the EXAFS amplitude for S02=1, N=4 is the same as for S02=0.8, N=5, and for S02=0.67, N=6. Distinguishing these cases is hard (don't let anyone tell you they aren't or that there is a button in Artemis that fixes this problem). If you need to distinguish N=5 from N=6, you better be pretty confident that your data and analysis have a good value for S02. The classic approach to this is to measure a data on a "standard" is free from amplitude-reducing artifacts and for which the coordination number is well-defined as easy to extract from the data, measure this at the same beamline conditions (energy resolution, harmonic content) as your unknown sample, and then work to be highly consistent in setting the edge step. The S02 applied to the standard to get the correct coordination number is then applied to the unknown data to get its coordination number. There are many ways for such an analysis to fall short of perfect, but it is generally the best we can do. --Matt On Fri, Mar 27, 2009 at 8:19 AM, Zuzaan, Damdinsuren <zuzaan(a)uni-mainz.de> wrote: > Hello everyone, > > I am graduate student and doing EXAFS in my research. > > My question is about S02. From the XAFS books or theory it says that > this value must be between 0.8 to 1, but in the literature some people > used different values like 0.25 or 1.4. In my case I fitted > experimental RDF of my standard sample by holding the known r and n > values for each path, while varying E0, S02 and sigma2. Obtained E0 > and S02 values were holded for unknown sample and rest were floated > freely. S02 were 0.64. So my question is that this relatively small > S02 value could affect the mineralogical interpretations made in my > study. Should I refit it using high value? Thanks in advance > > Regards, > > Damdin > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > ------------------------------ Message: 2 Date: Fri, 27 Mar 2009 19:23:29 -0400 From: Scott Calvin <SCalvin(a)slc.edu> Subject: Re: [Ifeffit] About S02 To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <E7658A83-0512-4A17-ACC0-1CC7A2A7F831(a)slc.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Hi Damdin, Matt and Shelly have answered this very well, but I have one more thought to add. You have a mineralogical sample and apparently have a pretty good idea what the mineral is, since you're not varying r or n. Under those circumstances, you probably have a hypothesis as to the structure beyond the nearest-neighbor. If you include more than one path in your fit, the inability to distinguish coordination number from S02 is reduced, and more importantly for your purposes, the correlation between S02 and sigma2 is also reduced. If it stays the same when you add more paths, it can help increase your confidence that the low S02 in your fit is appropriate. --Scott Calvin Sarah Lawrence College On Mar 27, 2009, at 9:19 AM, Zuzaan, Damdinsuren wrote: > Hello everyone, > > I am graduate student and doing EXAFS in my research. > > My question is about S02. From the XAFS books or theory it says that > this value must be between 0.8 to 1, but in the literature some people > used different values like 0.25 or 1.4. In my case I fitted > experimental RDF of my standard sample by holding the known r and n > values for each path, while varying E0, S02 and sigma2. Obtained E0 > and S02 values were holded for unknown sample and rest were floated > freely. S02 were 0.64. So my question is that this relatively small > S02 value could affect the mineralogical interpretations made in my > study. Should I refit it using high value? Thanks in advance > > Regards, > > Damdin ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 73, Issue 24 ***************************************

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