December 2006 - 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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Re: [Feffusers] thermal stage
by Matt Newville 05 Jan '07

05 Jan '07

Hi Igor, (and sorry for the double posting, but I thought some people on the Ifeffit list might be interested and have something to say too). I (well, GSECARS) have a Linkam TS-1500 heating stage, which can go to 1500C. It works well. We use it in our x-ray microprobe, where we're usually very concerned with contaminating signals from metals, so we run it open to air without any cover plates on it. It can easily get to 800C with this configuration (that is, no vacuum, a lot less insulation than intended), but we tend to consume the heating elements a little faster than we'd like. In fact, we just ordered some replacements. Julie (well, PNCCAT) has the Linkam THMS-600 (I think that's the model -- it goes down to LN2 temperature, and up to ~600C). The APS equipment pool also has one of these. It also works well, and really does get down to -196C. I does tend to consume LN2 and the connecting line between the stage and dewar is a little short. I think Julie had Linkam modify the basic design to open the back hole enough to allow transmission signal be measured while the stage was at 45degrees to the beam, and then also made some in-house modifications of her own (to improve the low temperature insulation, mostly). The heating element on hers also broke this fall, but she was able to repair it. Anyway, these are definitely reasonable choices, and being commercial products, probably cheaper, safer, and more reliable than anything you can build at home. I think Oxford Danfysik has (or used to have, anyway) a similar microscope heating/cooling stage that could be adapted for synchrotron work, but don't recall the details. --Matt On 12/15/06, Igor Levin <igor.levin(a)nist.gov> wrote: > Hi, > > We are considering to purchase a variable-temperature stage for the XAS > work. Linkam's THMS600 thermal stage came up as an option. Does anybody > have an experience with this stage? What are the alternatives? > > Thanks, > > Igor Levin > > Materials Research Scientist > Ceramics Division > National Institute of Standards and Technology > Gaithersburg MD 20899 > > > _______________________________________________ > Feffusers mailing list > Feffusers(a)u.washington.edu > http://mailman1.u.washington.edu/mailman/listinfo/feffusers >

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Re: [Ifeffit] CN and bond distances in Artemis
by Juan Antonio Maciá Agulló 21 Dec '06

21 Dec '06

Hi all, First of all, I would like to thanks Anatoly for his file and everybody for useful comments. I have analysed Anatoly's data and I have obtained a good value for S02 = 0.85 or 0.82 (depending on the number of variables used). So, my data is the problem, and it is not my analysis, but maybe my measurements need a more accurate analysis with Athena as Scott suggested. I was not at synchrotron measuring platinum samples and I only know that are measured in fluorescent mode. As Bruce said, I have no beamtime now for more measurements. I have more questions, related and not related to the last subject, but I am still thinking about them: The first one is easy, it is about the Nyquist theorem. I read in a paper that the formula is 2·deltak·deltaR/pi + 2. The last "+2" is new for me and I am afraid that Artemis does not consider it. I am sure that it is a silly thing. I will try to correct again Ptfoil considering self-absorption in order to obtain a spectrum similar to Anatoly's or Bruce's one. And then, I will apply the same correction for supported platinum catalysts, right? I also observed that Anatoly's Pt foil shows good signal even for large k (20 A-1). Nevertheless, obviously platinum catalysts spectra possess lower signal and specially for high values of k where the noise is big. The question is, despite Pt foil has a good signal until 20 A-1, it is usually used a smaller k-range (i.e. 3-12 A-1), right? I normally use a k-range of 3-12. And finally, how to calculate bond distances from Reff and deltaR? Thank you very much Best regards, JA

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Yttrium in alumina GBs
by Shantanu Behera 20 Dec '06

20 Dec '06

Thanks Carlo and Scott for ur response. Some numbers from my fits in this regard and some more queries. When I make a cluster based on the Alumina structure (replacing the central Al with Y with relaxed lattice parameters) I get DW 0.0025 +- 0.002, without any restraint. While I restrain the DW to 0.005, my CN jumps from 4.8 to 5.2. When I make a cluster based on Yttria structure, I get DW factor of 0.008 +- 0.002, unrestrained. While I restrain the DW to 0.01, it again jumps from 4.8 to 5.2. First query...if you can pin down on the CN change (Carlo..you wanted some numbers) Second...what are ur comments on the above 2 models and the change in DW factors. I might add that ther is no appreciable difference with k=2, 3 or 2&3 fittings. All the fits produce red-chi-sqr less than 100 (~50-70), all R-factors are <0.01 and no unphysical reports after the fit. And I have only 1 peak to worry about, there is no second shell correlation seen. I would appreciate your 2 cents on this. Warm regards Shan -- ||||||||||||||||||||||||||||||||| Shantanu Behera Center for Advanced Materials and Nanotechnology Lehigh University 5, East Packer Avenue Bethlehem, PA 18015, USA

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Re: [Ifeffit] Yttrium in alumina GBs
by Scott Calvin 20 Dec '06

20 Dec '06

Hi Shan, Nothing at all surprising here. In fact, you're getting pretty good results, in my opinion. Your CN insists on being "about" 4.8. When you push the ss, with which CN is correlated, to the top of its fitted range, the CN increases to about 5.2. To me, that says your CN is 4.8 +/ 0.4. A 10% uncertainty in CN is quite good for EXAFS! Of course, your real uncertainty is greater than that, because there are some possible systematic errors (e.g. normalization, sample effects) that might be present. But still, you're doing about as well as can be expected. Of course, that's assuming that CN's are what you're after. If finding out whether it's Alumina or Yttria is what you're after, the quality of fit and CN are not distinguishing between the two possibilities. That leaves bond distance as the best EXAFS indicator of which phase is present. --Scott Calvin Sarah Lawrence College At 05:49 PM 12/20/2006, you wrote: >Thanks Carlo and Scott for ur response. > >Some numbers from my fits in this regard and some more queries. > >When I make a cluster based on the Alumina structure (replacing the >central Al with Y with relaxed lattice parameters) I get DW 0.0025 +- >0.002, without any restraint. While I restrain the DW to 0.005, my CN >jumps from 4.8 to 5.2. > >When I make a cluster based on Yttria structure, I get DW factor of >0.008 +- 0.002, unrestrained. While I restrain the DW to 0.01, it >again jumps from 4.8 to 5.2. > >First query...if you can pin down on the CN change (Carlo..you wanted >some numbers) >Second...what are ur comments on the above 2 models and the change in >DW factors. > >I might add that ther is no appreciable difference with k=2, 3 or 2&3 >fittings. All the fits produce red-chi-sqr less than 100 (~50-70), all >R-factors are <0.01 and no unphysical reports after the fit. And I >have only 1 peak to worry about, there is no second shell correlation >seen. > >I would appreciate your 2 cents on this.

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RE: [Ifeffit] Athena problem
by Barton, David (DG) 20 Dec '06

20 Dec '06

The oddity that Jeff describes also occurs on the Windows platform (Athena 0.8.050). If you hit the "OK" button in the File-Open window a couple of times while a dataset is being loaded you will multiple instances loaded into the data group list that cannot be selected or deleted. The message trapped by Athena message can be seen in attached image. Dave >-----Original Message----- >From: ifeffit-bounces(a)millenia.cars.aps.anl.gov >[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf >Of Jeff Terry >Sent: Wednesday, December 20, 2006 12:55 PM >To: XAFS Analysis using Ifeffit >Subject: Re: [Ifeffit] Athena problem > >Since everyone is bringing up oddities in Athena, at least >under Debian, if you click on the load file button a second >time after setting up the input file parameters before it has >completed loading, you get a second group with the identical >name but it is not selectable and cannot be deleted. > >Jeff > > >On Dec 20, 2006, at 11:39 AM, Matt Newville wrote: > >> Hi, >> >> I agree that there have been several unrelated "issues" brought up >> here. Some of them are definitely reproducible, if not necessarily >> easy to capture as an isolated bug report. >> >> The "out of memory" problem that Paul Fons mentioned is >definitely due >> to ifeffit's limited, and fixed memory. This can be changed changed >> at compile time, but is (sadly) unavoidable in the current >> implementation. Someday there will be an Ifeffit 2 that eliminates >> this problem. >> >> The problem with 'clicking on the file/group area' in Athena on >> Windows is a long-standing issue. It's fairly common (for >me, anyway) >> to get an Athena session in this state, in which clicking on an >> existing group does not highlight it or make it current, and moving >> the mouse over it does not change the font. Sometimes a group can >> still be chosen as a member of a set. I don't know of an foolproof >> way to get to this state, but it seems to be more common >when reading >> in several data sets, and after a project has been open and >used for a >> while. This is definitely an irritation and it's been >like this for >> awhile. The rest of athena still runs fine. The easiest and most >> reliable workaround (that I know of) is to click into a real >widget in >> the Main Panel (so that it actually responds) and then go >back to the >> group list and click on another group. >> >> I haven't experienced very many random crashes of Athena. >> >> --Matt >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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Athena problem
by Maura H. Jordao 20 Dec '06

20 Dec '06

Dear all, Im having some problems to run Athena (Ifeffit 1.2.9) in my Windows XP (Home Edition, Version 2002), and Im writing to this list to get a help. One of them is if I plot a graph using different options (E or k for example) for many times, the graphics window freeze and I need obligatory to close the program. The other is the Pre and Post-edge lines do not appear when I marked them to plot. If somebody had experienced similar problems and know how to solve, please, write me. Ill be glad to receive some solution. Thanks, Maura ____________________________________________________________________________________ Want to start your own business? Learn how on Yahoo! Small Business. http://smallbusiness.yahoo.com/r-index

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RE: [Ifeffit] Athena problem
by Barton, David (DG) 20 Dec '06

20 Dec '06

Bruce, I believe I have a sequence of events that you can reproduce this problem of the data selection window locking up in Windows (tested in XP-SP2 and Win2000-SP4) using Athena 0.8.050. #1) Open three data sets #2) Right-click on first dataset choose Plot This Curve..In energy (Left click to choose) #3) The other datasets are now locked. Cannot select another dataset. #4) The fix: Right-click on any other dataset. Data selection begins working fine again. It appears that Athena is waiting for another Right-click after something is chosen off the popup context menu. This glitch is reproducible on WinXP and Win2000 platforms. Dave >-----Original Message----- >From: ifeffit-bounces(a)millenia.cars.aps.anl.gov >[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf >Of Bruce Ravel >Sent: Wednesday, December 20, 2006 9:06 AM >To: XAFS Analysis using Ifeffit >Subject: Re: [Ifeffit] Athena problem > > >Hi folks, > >I have been following the discussion in the last few days >about problems people are having on Windows with Athena and >Artemis. I trust that everyone appreciates that my commitment >to providing useful, usable software is strong and that I work >very hard to meet that commitment. Unfortunately, nothing in >this thread has provided me with actionable information. >While I understand that some of you are having problems, no >one has yet provided enough information for me even to begin >solving the problem (whatever it might be). >The fundamental rule of good bug reporting is that you need to >provide sufficient information that I can reproduce the >problem on my computer. If I cannot reproduce the problem, I >cannot understand it and cannot solve it. > >On my bug reporting page >(http://cars9.uchicago.edu/~ravel/software/bugs.html) >there is a box on the left side of the screen with links to >two excellent articles in how to communicate with software >developers. If you are interested in how to best help me to >understand and solve problems with my software, please read >through those articles and take the authors' suggestions to heart. > >Regards, >B > >-- > 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/ > >_______________________________________________ >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] High Correlation betn SO2 and ss
by Scott Calvin 20 Dec '06

20 Dec '06

Hi Sham, I agree with Carlo. I would also add that you should try different k-weights, including multiple k-weights at once. Since the dependence of S02 and ss on k is quite different, that can often reduce the correlation between the two. --Scott Calvin Sarah Lawrence College At 11:58 PM 12/19/2006, Shantanu Behera wrote: >Hi Folks > >I have a small doubt. I work on the structural features of Y that are >segregated to Alumina grain boundaries (very dilute amounts of Yttrium >in polycrystalline alumina). > >In some of my fits, I find a correlation ~0.85 between SO2 and ss. If >I restrain the ss, from 0.004 to 0.007, the CN changes by ~0.5 (not >considering +/-0.3). I would appreciate if someone can explain me how >to interpret the results from a structural point of view.

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