August 2005 - 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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Artemis- Loading up error
by Zohair Hussain 16 Apr '06

16 Apr '06

Hi! I recently had to install ifeffit software package on our network computer. The first time I ran Artemis I was asked to update which I did. However, Artemis did not start after that. The error message that I got is shown in the attached figures artemis-error1a and 1b. Please note that only Artemis doesn't work, all the other softwares (Athena, Hephaestus, TKAtoms etc.) work fine. I tried running the .bat file from the Ifeffit folder but that didn't work either. I also tried to run the artemis.exe file and received the error shown in figure "artemis-error2". Later I unisntalled and re-installed Ifeffit and chose not to do the updates and Artemis is now running fine. I was wondering if anyone has any idea why this is so or if there is a way around installing the updates and still being able to use Artemis??? Thanks, Zohair

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RE: [Ifeffit] R-factor
by Scott Calvin 20 Sep '05

20 Sep '05

Hi Alison, I agree entirely with Victor and Anatoly. In addition, I'd say that in my work an R-factor of above 0.1 is pretty sketchy. How sketchy depends on the complexity of the fit, of course; you're going over a big r-range, so if it takes you only two or three parameters to get an R-factor of 0.11, I guess that's not too bad. But if you have more parameters than that and it's still not fitting so well, I'd be concerned. As a referee, for example, that would be a much larger warning flag to me than the little discrepancy between the R-factors for the k- and q-space fits. Just to echo Victor and Anatoly again: it's quite easy for me to believe that the fitting algorithm just happened to find a somewhat different minimum in the fitting space in the two cases. They both suggested ways to test if that is the case. Although I've never fit in q-space, I've seen something that on the face of it is equally baffling: sometimes I've added an additional fitting parameter, changing nothing else, and seen the R-factor <italic>increase </italic>slightly. In some ideal sense, that shouldn't be--the fitting routine (this one happened to be Ifeffit) "should" at worst get the identical fit as to when the new parameter was constrained. But it is impossible to write a fitting routine that is guaranteed to find the closest possible fit, so all routines will occasionally generate those kinds of results. --Scott Calvin Sarah Lawrence College >-------------- Original message -------------- > >> Bruce, >> >> I've looked, and my R-factors for the back-transformed >> space are not necessarily twice the value of the R-factors >> for the k-space fits. In fact, they are often quite >> close. For example, just recently I had a k-space >> R-factor of 0.102 and a q-space R-factor of 0.113. Now, I >> realize those numbers are very close, but I'm afraid if I >> try to publish this, then I will get criticism for the >> q-space R-factors being larger. If I can explain it, then >> maybe it won't be a problem. >

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Ifeffit Wiki
by Matt Newville 02 Sep '05

02 Sep '05

Hi Folks, I've created and started a wiki for Ifeffit and related topics. Currently, this is at http://cars9.uchicago.edu/iffwiki At this point, this should be considered experimental. I'm still ambivalent about the whole thing, but we definitely need *something* to allow outside people to add content. Please feel free to play with this wiki, and let me know what you think. If this is something we decide we want to keep, I'll have this become part of the main set of Ifeffit and XAFS pages. I'd like to give it a trial run first, and hear some feedback. For those who aren't familar with wikis, these are set of web pages that are editable and expandable by users. There are all sorts of features for adding content -- too many to explain here. The basic idea is that you log onto the system, and edit the web pages using a web browser in a simplified structured text -- NOT directly editing HTML. Anyway, it's pretty easy to use, and there's plenty of documentation on how to use it. --Matt

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Re: Fitting an Extended R-range
by Michel Jaouen 31 Aug '05

31 Aug '05

>Shelly wrote: > >I was hoping that you could help me put together a list of EXAFS papers >that fit the R-space data out to at least 5 Angstroms. Hi Shelly, You can add to Scott's list the following entry: Mutiple-scattering EXAFS and EXELFS of titanium alloys T. Sikora, G. Hug, M. Jaouen, and J.J. Rehr, PRB 32, n°3, 1723 (2000) Best regards, M. Jaouen -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

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RE: [Ifeffit] Fitting an Extended R-range
by Kelly, Shelly D. 30 Aug '05

30 Aug '05

Hi Scott, Thank you for the help. Have a good one. Shelly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin Sent: Monday, August 29, 2005 10:10 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Fitting an Extended R-range Sorry, the first one should have been: > >"Estimating crystallite size in polydispersed samples using EXAFS," S. >Calvin, C. J. Riedel, E. E. Carpenter, S. A. Morrison, R. M. Stroud, & V. >G. Harris, Physica Scripta, T115, 744 (2005). >> --Scott Calvin Sarah Lawrence College _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Fitting an Extended R-range
by Kelly, Shelly D. 29 Aug '05

29 Aug '05

Hello Friends, I was hoping that you could help me put together a list of EXAFS papers that fit the R-space data out to at least 5 Angstroms. Thank you Shelly

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RE: [Ifeffit] Fitting an Extended R-range
by Kelly, Shelly D. 29 Aug '05

29 Aug '05

Hi Michel, Since I'm not getting a huge list of papers from anyone, I will take all that you think might be appropriate. SK -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Michel Schlegel Sent: Monday, August 29, 2005 2:24 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Fitting an Extended R-range Hello Shelly, >Hello Friends, > >I was hoping that you could help me put together a list of EXAFS papers >that fit the R-space data out to at least 5 Angstroms. > >Thank you >Shelly Does comparison of fourier transforms count as well ? (or are you just interested in the accuracy/uncertainty on the fitting parameters?) Best regards, Michel -- Michel Schlegel Commissariat à l'énergie atomique CEN de Saclay, DEN/DPC/SCP/LRSI Bat 391 - Piece 205B F91 191 Gif-sur-Yvette Cedex, France Ph: +33 (0)1 69 08 93 84 Fax: +33 (0)1 69 08 54 11 _______________________________________________ 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 an Extended R-range
by Kelly, Shelly D. 26 Aug '05

26 Aug '05

Hi Scott, Thanks for the help. I'm not picky about how it was done....Well, as long as it is reasonable. Shelly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin Sent: Friday, August 26, 2005 4:27 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Fitting an Extended R-range Hi Shelly, Does fitting to empirical standards count, or do you want only fits to theoretical standards (e.g. FEFF)? --Scott Calvin Sarah Lawrence College > >Hello Friends, > >I was hoping that you could help me put together a list of EXAFS >papers that fit the R-space data out to at least 5 Angstroms. > _______________________________________________ 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] A basic question about data collection
by Frenkel, Anatoly 26 Aug '05

26 Aug '05

I am probably missing the point, but it is not immediately obvious to me why the following is equivalent in terms of improving the signal to noise: a) constant E-space increment and b) constant k-space increment combined with k-dependent integration time. In a), the data cluster at high E, but each data point in E corresponds to a different final state and thus is unique. Averaging over E-space data in the small interval Delta E, (1/Delta E)*Int [xmu(E) dE] is not equivalent to the time average of xmu(E) collected at a fixed E: (1/T)*Int [xmu(E) dt]. Thus, k^n-weighted integration time, to my mind, is the only proper way of reducing statistical noise. Anatoly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Carlo Segre Sent: Thu 8/25/2005 5:13 PM To: XAFS Analysis using Ifeffit Cc: Subject: Re: [Ifeffit] A basic question about data collection Matt and Scott: On Thu, 25 Aug 2005, Matt Newville wrote: > This is important for QEXAFS (which typically does sample at a > very fine energy grid). I've been told by people doing QEXAFS > that a simple box-car average is good enough for binnning QEXAFS > data. That's what Ifeffit's rebin() function does. I'd think > that a more sophisticated rolling average (convolution) would > be better (and not screw up energy resolution), but apparantly > it's not an issue. > I have ben playing with the athena smoothing and rebinning funcionalities and I think that I prefer the rebinning because smoothing tends to attenuate sharp peaked structure. A rolling average might be good too but I haven't tried it too much. My guess is that for gentle features such as in the EXAFS region, rebinning, rolling averages and smoothing will all give statistically indistiguishable results. I amy be wrong. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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