March 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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DWF's for amorphous InP
by Claudia Schnohr 05 Apr '07

05 Apr '07

Hello everyone. I am a PhD student and I have encountered a problem with analysing the EXAFS of amorphous InP. For amorphous InP the first shell around an In atom is comprised of both P and In atoms. The In leads to a small peak in the R-spectrum that strongly overlaps with the bigger peak due to scattering from P. If I use two different Debye-Waller-factors, one for each scatterer, and let them both float during the fit I get weird values since the coordination numbers for both peaks have to be floated as well. Therefore, some restraint is needed for the DWF's. Is there any correlation between the two DWF's following from theory or experiment that I could use to restrain my fitting parameters ? Are there other possibilities to handle such a situation ? Many thanks in advance for your help, Claudia -- Claudia S. Schnohr Department of Electronic Materials Engineering Research School of Physical Sciences and Engineering The Australian National University Canberra, ACT 0200 AUSTRALIA

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Correlation between SO2 and sigma^2
by Ricardo Faccio 30 Mar '07

30 Mar '07

Hi Bruce and Scott for your valuable comments I am performing refinenments over a serie of cuprates. In this case La2CuO4 should work as a theoretical standard. This is why I wrote to you, but my "interesting" samples don't have much problems. The theoretical standard is the problem! quite crazy! Thanks again I will try Bruce's comments. Best regards Ricardo ------------------------------------------------------------------------- ----- Ing. Quím. Ricardo Faccio Mail: Cryssmat-Lab., Cátedra de Física, DETEMA Facultad de Química, Universidad de la República Av. Gral. Flores 2124, C.C. 1157 C.P. 11800, Montevideo, Uruguay. E-mail: rfaccio(a)fq.edu.uy Phone: 598 2 9241860 Int. 109 598 2 9290705 Fax: 598 2 9241906 Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm

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Fitting EXAFS with out any atomic coordinates?
by Mario Gomez 30 Mar '07

30 Mar '07

Hi Bruce my name is Mario and I was just wondering if your program can fir the EXAFS spectra without any atomic positions. Obviously the answer is no if you use atoms to create the FEFF file but what does one do when we have a semi-crystalline material for which no one has attempted the fractional coordinates. I mean the XRD pattern shows some crystalline but due to the high background I would think it would be very hard to do the Rietveld analysis. So what can one do, can we fit the EXAFS spectra knowing only the chemical composition and perhaps the lattice geometry(orthorhombic or hexagonal)? thanks

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Re: [Ifeffit] Ifeffit Digest, Vol 49, Issue 20
by Ricardo Faccio 29 Mar '07

29 Mar '07

Dear Iffefit users I am performing a refinement for a La2CuO4 in powder. I followed Bruce's course, and I tried determine S02 hopping its correlation with sigma^2. I am attaching a graph of this determination. Please see enclosed the file. My question is: Is common to obtain a S02 of 0.625? and is common to obtain a nearly sigma^2=0? I didn't fit E0, alpha and degeneracy for the first single shell. What is the best strategy to fix this bad result? Thanks in advance Ricardo ------------------------------------------------------------------------- ----- Ing. Quím. Ricardo Faccio Mail: Cryssmat-Lab., Cátedra de Física, DETEMA Facultad de Química, Universidad de la República Av. Gral. Flores 2124, C.C. 1157 C.P. 11800, Montevideo, Uruguay. E-mail: rfaccio(a)fq.edu.uy Phone: 598 2 9241860 Int. 109 598 2 9290705 Fax: 598 2 9241906 Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm

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Re: [Ifeffit] problem with running feff while working your ZnO example file
by Scott Calvin 29 Mar '07

29 Mar '07

Hi Soma, I am cc'ing this to the ifeffit list, as they may have a better answer than I do. The ZnO tutorial does currently have some problems having to do with variable names that became reserved after it was written. Those problems, though, do not cause the symptom you describe. The output of your feff run is "strange"--it claims to have an Rmax of 0, for instance. I'm not sure what could cause that particular problem; hopefully someone else on the list could help you. To start with, information on your operating system, version of Artemis, etc. might be helpful. --Scott Calvin Sarah Lawrence College At 06:29 PM 3/28/2007, soma(a)agni.phys.iit.edu wrote: >Hi Scott > >I work as a beamline scientist at MRCAT, sector 10 in APS where Bruce and >Shelly do their expts and I am trying to learn EXAFS analysis. Bruce >showed me your worked out example on ZnO and I was trying to follow it. > >I followed your notes till where it says to click the button "Run Feff". >When I do that ARtemis palatte gives the following message with red error >message at the end. I have copied that below. When I try putting RMAx 5 >instead of 6, it still keeps on giving the same message. i checked that >nleg was 4 and did not change it. > >I closed all programs in my linux based computer but message keeps on >appearing. Could you please let me know what I should do to proceed. > >Thank you. >Soma > >Soma Chattopadhyay >Beamline Scientist >MRCAT Sector 10 Building 433B >Advanced Photon Source >Argonne National Laboratory >9700 South Cass Avenue, Argonne >IL 60439, USA. >Phone: 1-630 252 0348 >FAX: 1-630 252 0358 >Email: soma(a)agni.phys.iit.edu > >************************************************************************** > >Scott Calvin's ZnO project > Calculating potentials and phases... > free atom potential and density for atom type 0 > free atom potential and density for atom type 1 > free atom potential and density for atom type 2 > overlapped potential and density for unique potential 0 > overlapped potential and density for unique potential 1 > overlapped potential and density for unique potential 2 > muffin tin radii and interstitial parameters > phase shifts for unique potential 0 > phase shifts for unique potential 1 > phase shifts for unique potential 2 > Preparing plane wave scattering amplitudes... > nncrit in prcrit 9 > Searching for paths... > Rmax 0.0000 keep and heap limits 0.0000000 0.0000000 > Preparing neighbor table > nfound nheap nheapx nsc r > Internal path finder limit exceeded -- path list may be incomplete. > Paths found 0 (nheapx, nbx 1 0) > Eliminating path degeneracies... > Plane wave chi amplitude filter 2.31% > > > Feff's path finder warned of reaching a memory limitation which > caused it not to compute the complete list of paths for your > cluster. There are two ways to avoid this problem when running > Feff. One is to decrease the size of the RMAX parameter in the > Feff input data. The other is to have the Feff calculation not > consider high order multiple scattering paths. Putting "NLEG 4" > in the Feff input data will limit Feff to compute only up to > four-legged (triple scattering) paths. > >**********************************************************************

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Re: [Ifeffit] Fitting EXAFS with out any atomic coordinates?
by Scott Calvin 28 Mar '07

28 Mar '07

Hi Mario, There are a couple of different ways to approach the kind of problem you describe, although you must be willing to guess at what the local environment looks like. For example, maybe the chemical composition tells you that you have an iron oxide. At a minimum, you could use Atoms to make a crystal structure for, say, hematite, and then only fit the nearest-neighbor paths, perhaps with an unknown coordination number. This can give you some information. Or, following the same example, maybe you think your material might be like a disordered hematite. Then you could try to fit the hematite structure out for several shells, but with free parameters to account for disorder (e.g. you could include vacancies). The key questions that you should not lose track of: --What would you like to know about your material? --What do you think your material might be like? I think sometimes people forget in particular about the first question. EXAFS doesn't answer generic questions very well ("tell me all about my sample"), but it often answers particular questions quite effectively ("are my iron atoms bonded to oxygen, or sulfur?"). So if you know what your particular questions are you've got a good chance of getting help using Bruce's and Matt's software. --Scott Calvin Sarah Lawrence College At 02:15 PM 3/28/2007, you wrote: >Content-class: urn:content-classes:message >Content-Type: multipart/alternative; > boundary="----_=_NextPart_001_01C77165.0DE07268" > >Hi Bruce my name is Mario and I was just wondering if your program >can fir the EXAFS spectra without any atomic positions. Obviously >the answer is no if you use atoms to create the FEFF file but what >does one do when we have a semi-crystalline material for which no >one has attempted the fractional coordinates. > >I mean the XRD pattern shows some crystalline but due to the high >background I would think it would be very hard to do the Rietveld analysis. > >So what can one do, can we fit the EXAFS spectra knowing only the >chemical composition and perhaps the lattice geometry(orthorhombic >or hexagonal)? > > > >thanks >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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[howto] configurational average in EXAFS with FEFF
by Mauro Rovezzi 28 Mar '07

28 Mar '07

Dear all, I would like your point of view on how to approach configurational average in EXAFS analysis with FEFF (let's not consider GNXAS for the moment). In particular, I'm trying to combine ab-initio DFT numerical simulations with EXAFS for doped semiconductors where in the minimized cluster there are N absorbing atoms. Usually I don't use the CFAVERAGE card because fractional degeneracies are not taken into account and, to have a qualitative analysis, I calculate an "extended"-XANES (up to 8.0 A^-1) for each cluster - where each absorbing atom is shifted to (0,0,0) - and then I average over all single-cluster signals. Well, at this point my question is: how to proceed in the quantitative analysis with Ifeffit? In fact, considering only single-scattering expansion for all the clusters the result could be seen as a radial distribution for each scattering pair where the integral gives the coordination number and the FWHM a structural Debye-Waller factor. How to combine these informations? Thanks for the answers, Mauro -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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the ifeffit wiki
by Bruce Ravel 26 Mar '07

26 Mar '07

Hi everyone, I just finished cleaning some really distasteful vandalism off of the Ifefift wiki. Several pages had been edited to add dozens of links to pages that have .... ummmm .... very little to do with XAS. Such vandalism is unwelcome on the ifeffit wiki and is most certainly not what Matt and I intended when we started it. I check for this sort of thing fairly often, but much of the latest crop of vandalism had been there for 24 hours without my noticing. If you ever see content on a wiki page that is clearly the work of a wiki vandal, feel free to clean it up or to drop me a private email and I will do so. In any event, please do not be mad at those of us who administer the wiki. We really intend the ifeffit wiki to be a place where you can bring your children to learn about XAS ;-) 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/

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