June 2007 - Ifeffit - millenia.cars.aps.anl.gov

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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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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2007 APS XAFS School
by Julie Olmsted Cross 04 Apr '08

04 Apr '08

The on-line application for the 2007 APS XAFS School is now available at xafs.org http://www.xafs.org/Workshops/APS2007 ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~ Julie O. Cross Advanced Photon Source Argonne National Lab 9700 South Cass Ave., Bldg. 401/B4204 Argonne IL 60439 tel: 630 327 7825 fax: 630 252 0580 ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~

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gifeffit installation issue on ubuntu feisty fawn
by Emiliano Fonda 02 Jul '07

02 Jul '07

Hi, I would like to use gifeffit on the beamline where I work for fast extraction of EXAFS data during scans and so on. But I have a problem even before starting to code: horae and ifeffit works well, I compiled and installed the python wrapper, but gifeffit refuse to work and I cannot import the Ifeffit module in python. The error message is: fonda@nemotele:~$ gifeffit Traceback (most recent call last): File "/usr/local/bin/gifeffit", line 2, in <module> import GIFeffit, sys File "/usr/lib/python2.5/site-packages/Ifeffit/GIFeffit.py", line 27, in <module> from Ifeffit import Ifeffit File "/usr/lib/python2.5/site-packages/Ifeffit/Ifeffit.py", line 46, in <module> import _ifeffit, types, cmd, os, sys ImportError: /usr/lib/python2.5/site-packages/Ifeffit/_ifeffit.so: undefined symbol: pgclos_ The linux distro is ubuntu feisty fawn and I got the libpgplot5 package installed... ... may anyone help me, please? Thanks, E. Fonda SAMBA beamline SOLEIL synchrotron

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Meaning of sigma^2 and real space resolution in XAFS
by Moneeb Shatnawi 30 Jun '07

30 Jun '07

Hello, Thanks Bruce and Matt for the previous comments� I have the following questions and I would appreciate comments about them: My Questions are: 1- Can we consider sigma^2 of a single scattering path to be a measure of Debey Waller factor? 2- Is sigma^2 a measure of �or directly proportional to� strain in a bond? 3- When doing first shell fitting in Artemis, The actual bond length is: r_eff + dr +- delta �dr�� Are the error bars associated with dr values �delta�dr� of about 0�001 A� realistic? �i�e� 0�001 A is too small to detect by XAFS�� 4- What determines the real space resolution in XAFS measurements other than K_max? Thanks, Moneeb -- Moneeb T� Shatnawi Physics and Astronomy Department 4256 Biomed� Phys� Sciences Building Michigan State University East Lansing, MI 48824 Tel: +1-517-355-9200 ext�2325 E-mail: mtshatnawi@pa�msu�edu

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Re: [Ifeffit] Fwd: scattering amplitude by FEFF and Artemis
by Feng Wang 29 Jun '07

29 Jun '07

Thank you, Dr. Ravel, Could you please just simply tell me the expression for the magnitude of chi (q) (labelled as |chi(q)|)? Thank you. Feng > Feng, > > I am forwarding this to the Ifeffit mailing list since I am in the > middle of an experiment and don't have much time to devote to an > answer. > > > Dear Dr. Ravel, > > > I am now learning to use your Artemis program to calculate the scattering > > amplitude from each paths (shells). It seems your Artemis can give the > > scattering amplitude of each path, as done by EXAFS calculations in FEFF. I > > think the results from both program should be same or comparable, but it > > looks much different, as attached for a result of diamond-K. Is anything > > wrong with my calculations? > > It's really hard to tell. The figure you sent does not convey any > sense of how it was made. Without a clear explanation of what you > did or, better yet, an artemis project file to inspect, I am not sure > how I can possibly answer your question. > > > I have been wondering how big a cluster we should use for FEFF calculations, > > or the contributions of the atoms far from the central atom (e.g. > 1nm) > > since so big clusters (such as 400 atoms and even more) are used for FEFF > > calculations in several recent publications. I hope to get some ideas from > > the scattering amplitude of the paths involved by the atoms far from the > > central atoms. Do you also have any suggestions? > > The nice thing about feff is that it is very easy to use to answer > this sort of question without having to rely on an "expert". What > happens if you run feff with clusters ranging from very small to very > large and compare the chi(k) functions generated for the first few > coordination shells? > > B > > > Feng > > > ==================================== > > EM group, NINT > > 11421 Saskatachewan Drive > > Edmonton, Canada T6G 2M9 > > -- > Bruce Ravel ---------------------------------------------- bravel(a)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/ ==================================== EM group, NINT 11421 Saskatachewan Drive Edmonton, Canada T6G 2M9

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Fwd: average first shell position and width
by Bruce Ravel 28 Jun '07

28 Jun '07

Moneeb, I'm in the middle of beam run, so I am forwarding this along to the Ifeffit mailing list for commentary. B ---------- Forwarded Message from Moneeb Shatnawi <Moneeb Shatnawi <mtshatnawi(a)pa.msu.edu>> ---------- Subject: average first shell position and width Date: Wednesday 27 June 2007 From: Moneeb Shatnawi <mtshatnawi(a)pa.msu.edu> To: Bruce Ravel <bravel(a)anl.gov> Dear Dr. Ravel, Hello, I am Moneeb Shatnawi from physics department at Michigan State University, I have a PDF and XAFS data on GeSe system, and I would like to check if the PDF and XAFS results are consistent with each other in terms of the first PDF peak position and width. The first PDF peak in this system is a mixed shell of Se-Se bonds as well as Ge-Se bonds. The PDF data gave a width of the first PDF peak of about 0.06 A, and the XAFS data gave sigma^2 for Ge-Se bond is 0.006 A^2, and for Se-Se bond is 0.003 A^2. How is sigma in XAFS results (I was using Artemis program) related to the width of the first PDF peak? Also, when obtaining the XAFS fits to the data, I was using: Theory ---> first shell fit. In this, I was giving r_eff for Se-Se bond to be 2.32 A and that for Ge-Se to be 2.368 A. Through the XAFS refinement, I obtained r, dr as well as r_eff. which of these should be considered as the actual bond length (r or r_eff)? and how are these related to the average position that I get from fitting the first PDF peak in this system? I appreciate your help, Thanks, Moneeb ------------------------------------------------------- -- Bruce Ravel ---------------------------------------------- bravel(a)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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Fwd: scattering amplitude by FEFF and Artemis
by Bruce Ravel 28 Jun '07

28 Jun '07

Feng, I am forwarding this to the Ifeffit mailing list since I am in the middle of an experiment and don't have much time to devote to an answer. > Dear Dr. Ravel, > I am now learning to use your Artemis program to calculate the scattering > amplitude from each paths (shells). It seems your Artemis can give the > scattering amplitude of each path, as done by EXAFS calculations in FEFF. I > think the results from both program should be same or comparable, but it > looks much different, as attached for a result of diamond-K. Is anything > wrong with my calculations? It's really hard to tell. The figure you sent does not convey any sense of how it was made. Without a clear explanation of what you did or, better yet, an artemis project file to inspect, I am not sure how I can possibly answer your question. > I have been wondering how big a cluster we should use for FEFF calculations, > or the contributions of the atoms far from the central atom (e.g. > 1nm) > since so big clusters (such as 400 atoms and even more) are used for FEFF > calculations in several recent publications. I hope to get some ideas from > the scattering amplitude of the paths involved by the atoms far from the > central atoms. Do you also have any suggestions? The nice thing about feff is that it is very easy to use to answer this sort of question without having to rely on an "expert". What happens if you run feff with clusters ranging from very small to very large and compare the chi(k) functions generated for the first few coordination shells? B > Feng > ==================================== > EM group, NINT > 11421 Saskatachewan Drive > Edmonton, Canada T6G 2M9 -- Bruce Ravel ---------------------------------------------- bravel(a)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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XAFS postdoc position at HASYLAB
by Welter, Edmund 27 Jun '07

27 Jun '07

Dear colleagues, at the Hamburger Synchrotron Strahlungslabor (HASYLAB) a postdoc position in the XAFS business is available. If you or one of your colleagues is interested please contact me by e-mail or phone (address at the bottom of this mail). The main task will be the operation of our new XAFS-beamline (beamline C). As a postdoc you will have the opportunity to use HASYLAB's facilities for your own research. Moreover, you will be a live witness of the construction and commissioning of the new high brilliance source PETRA III (user operation at PETRA III will start in 2009) and of the start phase of the XFEL project. If you have questions about this mail or the available position please do not reply to the mailing list, but contact me directly instead. Best regards, Edmund Welter

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weighting multi-data fit
by Jörg Haug 25 Jun '07

25 Jun '07

Dear all, I have a question regarding the weighting for a multiple data set fitting. I found that there is the parameter Epsilon to do this in Artemis. But in the help file there is no description how to use this parameter. Which value did I have to use to set the weighting to (for example) double or half? Best regards Jörg -- Dr. Jörg Haug Martin-Luther-Universität Halle-Wittenberg Institut für Physik Anorganisch-Nichtmetallische Materialien Friedemann-Bach-Platz 6 D-06108 Halle Telefon: 0345 55 25 529 Fax: 0345 55 27 159 e-mail: joerg.haug(a)physik.uni-halle.de http://www.physik.uni-halle.de/Fachgruppen/Glas/arbeitsgruppen/anw.htm

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