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

questions concerning paper
by s440697＠stud.uni-goettingen.de 23 May '08

23 May '08

Hello, i have some questions concerning the xafs-formula in this paper (attached): "Theoretical approaches to x-ray absorption fine structure" (July 2000). The author explained on page 625 and 626 the parameters of this formula. I think, most of you have read this paper. I don't understand the meaning of lambda(k), the author wrote "... and lambda(k) is the energy-dependent XAFS mean free path (not to be confused with the de Broglie wavelength)." My question is, the mean free path whereof? The propagating photoelektron(wave) or the (back)scattered waves? In the next sentence, what is the overall amplitude factor S_0^2? How is it defined? In conjunction with question one i don't understand the expression in the next paragraph for the term e^{-2R/lambda}. The author wrote: "The decay of the wave (which wave does he mean?) due to the mean free path or finite lifetime (what does he mean?, finite lifetime of the emitted and propagating photoelektron wave?) [including core-hole lifetime] of the photoelectron is captured by ..." Is it right, that the emitted photoelektron is detectable outside the sample? Another parameter is the phase factor phi = arg f(k) "...reflects the quantum-mechanical wavelike nature of the backscattering." Please explain me the meaning of this parameter. At the bottom of this page the author wrote: "...the Debye-Waller factor, which is given to a good approximation by e^{-2 sigma^2 k^2}." In this context he refers to figure 8, where k^2 chi(k) vs. k is plotted. I don't understand this context because there is no chi in the approximation for the Debye-Waller factor. Where comes the chi here? I would be very grateful for any help you would offer to me. Thank you very much for your help and time. sincerely yours, E.Bosman --------------------------------- Eckhard Bosman e.bosman(a)stud.uni-goettingen.de +49 (0)551-39-14441 Raum: E0.104 Institut für Röntgenphysik Friedrich-Hund-Platz 1 37077 Göttingen Germany

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Re: [Ifeffit] questions concerning paper
by Frenkel, Anatoly 22 May '08

22 May '08

We should ask John Rehr to rename FEFF to Odysseus. It makes both physical and mythological sense. Anatoly ----- Original Message ----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: Ravel, Bruce; XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Thu May 22 14:30:38 2008 Subject: Re: [Ifeffit] questions concerning paper I loved it also, thanks Matt :-) May i cite your Odysseus explanation in my diploma thesis? ;) -------- Original-Nachricht -------- > Datum: Thu, 22 May 2008 12:40:01 -0400 > Von: Bruce Ravel <bravel(a)bnl.gov> > An: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Betreff: Re: [Ifeffit] questions concerning paper > > Matt, > > That was awesome! I **loved** the Odysseus explanation of the exafs > equation. Quite possibly the best Ifeffit mailing list post ever. > > B > > > > -- > 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/ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- GMX startet ShortView.de. Hier findest Du Leute mit Deinen Interessen! Jetzt dabei sein: http://www.shortview.de/?mc=sv_ext_mf@gmx _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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2008 APS XAFS School
by Matt Newville 16 May '08

16 May '08

Hi Everyone, The application form for the 2008 APS XAFS School is now open: http://cars9.uchicago.edu/xafs_school/2008 Details about this year's APS XAFS School are at http://xafs.org/Workshops/APS2008 --Matt PS: Starting sometime yesterday (and currently), mail from outside APS to this list is being bounced by an APS firewall. If you have sent mail to this list and had it bounce, please be patient. I'll post a message when the mailing list is back up.

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iron L edges
by Bruce Ravel 16 May '08

16 May '08

Hi everyone, I have just spent a fruitless half hour with google scholar trying to find a paper that publishes Fe L2,3 edge spectra (not K -- I have those!) of the FeOOH species goethite and lepidocrocite. Can anyone point me in the right direction? Thanks a million! B -- 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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feff8.4 LDOS number of energy points
by Rajmund Bacewicz 12 May '08

12 May '08

Hi all, In a Windows version of FEFF8.4, LDOS is calculated in 401 energy points, that is extremely time consuming. Is it possible to change it to a smaller number of points (e.g. 101 points like in FEFF8.2)? Regards Rajmund -- List przeskanowano programem ArcaMail, ArcaVir 2006 przeskanowano 2008-05-12 10:29:02, silnik: 2005.12.01 12:00:00, bazy: 2008.05.04 14:32:29 This message has been scanned by ArcaMail, ArcaVir 2006 scanned 2008-05-12 10:29:02, engine: 2005.12.01 12:00:00, base: 2008.05.04 14:32:29 http://www.arcabit.com

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XANES Background removal and Normalization
by Jens Kruse 10 May '08

10 May '08

Hi there, I have some P L2/L3-edge XANES spectra. I am not sure how to remove the background and normalize these data. Due to the fact that the pre edge and the post edge region is not very flat the the edge-step normalization using AUTOBK dose not work very well. CLNORM background subtraction seems to work better in some case. But some spectra get partly negative values after CLNORM (see .prj attached). So my questions are: 1:Is CLNORM the best choice in my case, especially when I plan to do linear combination fitting with these data? 2: Athena needs the knowledge of the absorbing atom an the edge to use CLNNORM, but the spectra contain both L3 an L2. So, which edge do I have to choose L3 or L2? 3: Would it be also correct to use a Victoreen-Fit for the pre edge without any further normalization and than do the linear combination fitting? Or do I have to normalize spectra in general when I am doing linear combination fitting, to eliminate effects of different concentrations of the absorbing atom in the mixtures? thanks, a lot for your help jens

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Dodgy Edge Steps
by LACHLAN MACLEAN 03 May '08

03 May '08

Hi All Long-term lurker, first time poster. I've recently collected some EXAFS data with a large edge step (~3.4) and for some reason didn't pick up on it until it was too late. I've been told that ideally we would want an edge step of 1 and anything above ~1.5-2 is too high. I'm wondering if there is a way to salvage the dataset in order to compare it with EXAFS data that I collected from two other samples (all three are supposed to be synthetic goethite). The first two samples that I want to compare have edge steps of about 0.35. I know Athena allows one to adjust the edge step but wonder how appropriate this is and how much change this would cause the EXAFS data? Trying to adjust the edge step from 3.4 down to ~1 or so seems to be quite a jump. I'm curious whether there is a way to salvage this data rather than wait until the next beamrun. Any help would be appreciated. Cheers Lachlan

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job posting: beamline scientist at GSECARS / APS
by Matt Newville 03 May '08

03 May '08

Hi Folks, GSECARS is looking for a beamline scientist with a good background in x-ray absorption / related spectroscopies to work at the APS. See the posting at http://xafs.org/Jobs (or read below) for more details, including how to apply for this position. --Matt Job Posting: Beamline Scientist, Center for Advanced Radiation Sources (CARS), The University of Chicago University of Chicago Job Requistion # 079054 The Center for Advanced Radiation Sources (CARS) of the University of Chicago has a Beamline Scientist position available at the GeoSoilEnviroCARS (GSECARS) synchrotron research facility at the Advanced Photon Source (APS), Argonne National Laboratory, in Argonne, Illinois. This full-time position requires a Ph.D. in geology, environmental science, chemistry, physics or a related field and synchrotron radiation experience applying x-ray absorption spectroscopy and x-ray fluorescence techniques in earth and environmental science research. The successful candidate will (1) conduct research on the chemical properties of earth and environmental materials using large sample instruments and x-ray microprobes; (2) participate in the development of analytical instrumentation and techniques; and (3) provide partial support for and collaborate with scientific users from the earth and environmental communities who conduct research using the GSECARS synchrotron beamlines. The successful candidate will have excellent relevant computer, organizational, verbal and written communication skills, and must be able to work effectively both independently and as a team member. Candidates must be able to satisfy requirements for access to Argonne National Laboratory. Applications must be made on-line: Go to http://jobopportunities.uchicago.edu/ and search for Job Requistion # 079054. Applications must include a curriculum vitae, cover letter, statement of research interests, and list of publications, along with three professional references. This posting will be closed when the position is filled. The University of Chicago is an Equal Opportunity/Affirmative Action Employer.

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Re: [Ifeffit] Using the amplitude reduction factor as a linearcombination fitting parameter
by Frenkel, Anatoly 01 May '08

01 May '08

There are a few points in your description that puzzle me. Have you collected not one but a series of spectra where some external condition (e.g., temperature, concentration, time, pH etc) were varied? If not, PCA cannot be used if only one spectrum was collected containing a mixture of two species. Such spectrum would have only one component, of course - itself. Next, assuming you did use PCA for a series of spectra, without having XANES and/or EXAFS data of test compounds how were you able to deconvolute abstract components that PCA generates into the two species that have meening of XANES or EXAFS data? Without test compounds such deconvolution is not possible unless you used not PCA but a linear combination fit of some sort... And, finally, if you used test compounds that could be reliably reproduced by your 2 principal components, why do you need to do anything else? They are your two species. Please clarify. Anatoly ----- Original Message ----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Tue Apr 29 03:06:28 2008 Subject: [Ifeffit] Using the amplitude reduction factor as a linearcombination fitting parameter I have recently collected EXAFS spectra of uranium on a FeS2 surface. Using principal component analysis of the XANES and k3-weighted EXAFS spectra, I have found that there are two uranium species which compose the spectra. As a first tentative guess, I believe these two uranium species are uraninite (UO2(c)) and a uranyl species. I would like now to fit the fourier transform functions (real parts and magnitudes) using the theoretical paths and path degeneracies created by feff, and use the amplitude reduction factor S02 as a fitting parameter to derive the relative amounts of the two uranium species in my samples. Normally, this S02 is taken as a constant (between 0.7 and 1.0), and the path degeneracies are fitted. So normally, S02 is not really a fitting parameter (some papers derive it even with theoretical functions). However, given the fact that S02 and N are completely correlated, I think it is justified to use this approach. Can someone comment on this? Many thanks in advance, Christophe SCK·CEN Disclaimer http://www.sckcen.be/emaildisclaimer.html

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LDOS calculations
by Rajdeep Saha 30 Apr '08

30 Apr '08

Hi All, This question concerns the Feff8 program. So this may not be the appropriate site, however I would greatly appreciate if I could get some feedback. I calculate the DOS of TiO_2 anatase system using FEFF8 and then compare the results with benchmark calculations done using VASP. Apparently, the FEFF results are no where near the VASP results. I was wondering if somebody could take a look at my input file and suggest some improvements. I am absolutely new to EXAFS, and anybody's help would be greatly appreciated. Thanks, Rajdeep Saha. The input file is as follows; TITLE anatase HOLE 1 1.0 CONTROL 1 1 1 0 0 0 PRINT 0 0 0 0 0 0 RPATH 5.5 LDOS -18 0 0.01 SCF 6.21 POTENTIALS 0 8 O 1 22 Ti 2 8 O ATOMS 5.67630000 5.67630000 14.27190000 1 Ti 5.67630000 5.67630000 4.75730000 1 Ti 5.67630000 3.78420000 16.65055000 1 Ti 5.67630000 3.78420000 7.13595000 1 Ti 5.67630000 1.89210000 14.27190000 1 Ti 5.67630000 1.89210000 4.75730000 1 Ti 5.67630000 0.00000000 16.65055000 1 Ti 5.67630000 0.00000000 7.13595000 1 Ti 3.78420000 5.67630000 11.89325000 1 Ti 3.78420000 5.67630000 2.37865000 1 Ti 3.78420000 3.78420000 9.51460000 1 Ti 3.78420000 3.78420000 0.00000000 1 Ti 3.78420000 1.89210000 11.89325000 1 Ti 3.78420000 1.89210000 2.37865000 1 Ti 3.78420000 0.00000000 9.51460000 1 Ti 3.78420000 0.00000000 0.00000000 1 Ti 1.89210000 5.67630000 14.27190000 1 Ti 1.89210000 5.67630000 4.75730000 1 Ti 1.89210000 3.78420000 16.65055000 1 Ti 1.89210000 3.78420000 7.13595000 1 Ti 1.89210000 1.89210000 14.27190000 1 Ti 1.89210000 1.89210000 4.75730000 1 Ti 1.89210000 0.00000000 16.65055000 1 Ti 1.89210000 0.00000000 7.13595000 1 Ti 0.00000000 5.67630000 11.89325000 1 Ti 0.00000000 5.67630000 2.37865000 1 Ti 0.00000000 3.78420000 9.51460000 1 Ti 0.00000000 3.78420000 0.00000000 1 Ti 0.00000000 1.89210000 11.89325000 1 Ti 0.00000000 1.89210000 2.37865000 1 Ti 0.00000000 0.00000000 9.51460000 1 Ti 0.00000000 0.00000000 0.00000000 1 Ti 5.67630000 5.67630000 16.25188826 2 O 5.67630000 5.67630000 12.29191174 2 O 5.67630000 5.67630000 6.73728826 2 O 5.67630000 5.67630000 2.77731174 2 O 5.67630000 3.78420000 18.63053826 2 O 5.67630000 3.78420000 14.67056174 2 O 5.67630000 3.78420000 9.11593826 2 O 5.67630000 3.78420000 5.15596174 2 O 5.67630000 1.89210000 16.25188826 2 O 5.67630000 1.89210000 12.29191174 2 O 5.67630000 1.89210000 6.73728826 2 O 5.67630000 1.89210000 2.77731174 2 O 5.67630000 0.00000000 18.63053826 2 O 5.67630000 0.00000000 14.67056174 2 O 5.67630000 0.00000000 9.11593826 2 O 5.67630000 0.00000000 5.15596174 2 O 3.78420000 5.67630000 13.87323826 2 O 3.78420000 5.67630000 9.91326174 2 O 3.78420000 5.67630000 4.35863826 2 O 3.78420000 5.67630000 0.39866174 2 O 3.78420000 3.78420000 17.04921174 2 O 3.78420000 3.78420000 11.49458826 2 O 3.78420000 3.78420000 7.53461174 2 O 3.78420000 3.78420000 1.97998826 2 O 3.78420000 1.89210000 13.87323826 2 O 3.78420000 1.89210000 9.91326174 2 O 3.78420000 1.89210000 4.35863826 2 O 3.78420000 1.89210000 0.39866174 2 O 3.78420000 0.00000000 17.04921174 2 O 3.78420000 0.00000000 11.49458826 2 O 3.78420000 0.00000000 7.53461174 2 O 3.78420000 0.00000000 1.97998826 2 O 1.89210000 5.67630000 16.25188826 2 O 1.89210000 5.67630000 12.29191174 2 O 1.89210000 5.67630000 6.73728826 2 O 1.89210000 5.67630000 2.77731174 2 O 1.89210000 3.78420000 18.63053826 2 O 1.89210000 3.78420000 14.67056174 2 O 1.89210000 3.78420000 9.11593826 2 O 1.89210000 3.78420000 5.15596174 2 O 1.89210000 1.89210000 16.25188826 2 O 1.89210000 1.89210000 12.29191174 2 O 1.89210000 1.89210000 6.73728826 2 O 1.89210000 1.89210000 2.77731174 2 O 1.89210000 0.00000000 18.63053826 2 O 1.89210000 0.00000000 14.67056174 2 O 1.89210000 0.00000000 9.11593826 2 O 1.89210000 0.00000000 5.15596174 2 O 0.00000000 5.67630000 13.87323826 2 O 0.00000000 5.67630000 9.91326174 2 O 0.00000000 5.67630000 4.35863826 2 O 0.00000000 5.67630000 0.39866174 2 O 0.00000000 3.78420000 17.04921174 2 O 0.00000000 3.78420000 11.49458826 2 O 0.00000000 3.78420000 7.53461174 2 O 0.00000000 3.78420000 1.97998826 2 O 0.00000000 1.89210000 13.87323826 2 O 0.00000000 1.89210000 9.91326174 2 O 0.00000000 1.89210000 4.35863826 2 O 0.00000000 1.89210000 0.39866174 2 O 0.00000000 0.00000000 17.04921174 2 O 0.00000000 0.00000000 11.49458826 2 O 0.00000000 0.00000000 7.53461174 2 O 0.00000000 0.00000000 1.97998826 0 O

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