May 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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Using windows apj files on linux
by joshua jason kas 30 May '07

30 May '07

Hi, I recently updated to redhat 4. I am running: artemis 0.8.009 IFEFFIT 1.2.9 Tk-804.027 perl 5.8.5 I have an artemis project file that I started on my win xp machine and would like to use on the linux machine. When I open the apj file on linux, some of the information about the fits seems to be scrambled. Here are some of the symptoms. 1) The raw logs seem to have aquired the following escape character at the end of each line: \x{d} This shows up as a carriage return or end of line on this screen. 2) Quick summary of selected fits gives 0 for all reported values (chisq, rfactor, nidp, etc) and does not report any guessed parameters. Here is one of the quick summaries. Note that the \x{d} do not show up here, but they do in the artemis message palette. I am also attatching the project file. Thanks for any help, Josh Kas Project title : Fitting pt1_amine_165_he_573.chi Comment : fer dw, constant delr, ei=0, kw=1, kmin=2.0, rmin=1.2 Figure of merit : 17 Fitting statistics Number of independent points : 0 Number of variables : 0 Chi-square : 0 Reduced chi-square : 0 R-factor : 0 Measurement uncertainty (k) : 0 Measurement uncertainty (R) : 0 Guess parameters =*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*=

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the brand new Athena User's Guide
by Bruce Ravel 30 May '07

30 May '07

Hi! The last few months have been a pretty quiet period for me in terms of software development because I have been working on new documentation for Athena. As such things often do, it took longer than planned. But I am very pleased with the results and I am hopeful that you will find it useful. The html version is on line at http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/ A (rather large) PDF version of the document is at http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/athena.pdf For those interested in contributing to or packaging the document, the source files can be found at or downloaded via svn from http://cars9.uchicago.edu/svn/aug/ This is a first draft and a large project. It will certainly require updates. If you find anything missing or anything incorrectly or poorly explained, please let me know. Now that this document is finished, I will work on the next release of the codes. I have a long list of bugs fixes and improvements that I hope to roll out for all platforms before the APS XAFS summer school in July. 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/

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Re: [Ifeffit] Ifeffit Digest, Vol 51, Issue 26
by Jun Lin 30 May '07

30 May '07

I guess the problem lies in the different "end line character" for Linux and Windows. Before you load "dos style"(Windows use it) apj file, you should translate it into "Linux style". It is easy in Linux system by using "dos2unix". On 5/30/07, ifeffit-request(a)millenia.cars.aps.anl.gov < ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Using windows apj files on linux (joshua jason kas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 29 May 2007 10:13:06 -0700 (PDT) > From: joshua jason kas <hebhop(a)u.washington.edu> > Subject: [Ifeffit] Using windows apj files on linux > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <Pine.LNX.4.64.0705290956010.21265(a)dante01.u.washington.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi, > I recently updated to redhat 4. I am running: > artemis 0.8.009 > IFEFFIT 1.2.9 > Tk-804.027 > perl 5.8.5 > > I have an artemis project file that I > started on my win xp machine and would like to use on the linux machine. > When I open the apj file on linux, some of the information about the fits > seems to be scrambled. Here are some of the symptoms. > > 1) The raw logs seem to have aquired the following > escape character at the end of each line: \x{d} > This shows up as a carriage return or end of line on this > screen. > > 2) Quick summary of selected fits gives 0 for all reported values > (chisq, rfactor, nidp, etc) and does not report any guessed > parameters. > > Here is one of the quick summaries. Note that the \x{d} do not show up > here, but they do in the artemis message palette. I am also attatching the > project file. > Thanks for any help, > Josh Kas > > Project title : Fitting pt1_amine_165_he_573.chi > > Comment : fer dw, constant delr, ei=0, kw=1, kmin=2.0, rmin=1.2 > > Figure of merit : 17 > > > Fitting statistics > Number of independent points : 0 > Number of variables : 0 > Chi-square : 0 > Reduced chi-square : 0 > R-factor : 0 > Measurement uncertainty (k) : 0 > Measurement uncertainty (R) : 0 > > Guess parameters > > =*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*= > > >

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Plotting problem
by Clement Mbudi 29 May '07

29 May '07

Hi there, Can somebody tell how to get rid of the " all marked groups" default title when plotting several groups together within Athena environment. The " change group label" seems to only work for a single group. Similarly, how to change titles of both Y and X axes within Athena ? Thanks. Clement Edmonton, AB _________________________________________________________________ Windows Live Hotmail with drag and drop, you can easily move and organize your mail in one simple step. Get it today! www.newhotmail.ca?icid=WLHMENCA153

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Low amp results
by Joji Kuniya 28 May '07

28 May '07

I analyzed EXAFS spectra of trace of Fe in lithium tantalate crystals. At first, I created the feff.inp file of LiTaO3. Then I changed central Li atom to Fe atom and added Fe atom at the Ta site. So that, the fitted results is good except amp(amp results is 0.3). I think that the model structure is good, but I can not understand why amp is too low. How do you think about this results? And, I tried to fitting treatment using GDS parameters. But, I do not know that the general method how to use the GDS parameters. Please tell me the general way of GDS manipulation. My PC runs under Win XP, and My Artemis runs under feff8 conditions. Thank you. Joji Kuniya

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Re: [Ifeffit] Using FEFF8 with Artemis
by Richard Mayes 24 May '07

24 May '07

Scott, When I started using FEFF8.2 with Artemis (on a WinXP laptop), it took a day or two to get everything situated where Artemis would read the input file. For my ease of use, I finally created a separate folder under My Documents that I dedicated to FEFF calculations. At that point, every file generated by FEFF was written into that folder (provided that's where the FEFF executable is located) and Artemis became happy again and started accepting my input files. There is only one downside (so far), when Atoms generates an input file, I have to go into Artemis and copy that input file into the folder where FEFF is located before I can do the FEFF calculation. I tried the input file you sent to the list, and this method gives the needed files in one folder. I can send you a copy of the folder containing all the generated files if you would like (I would attach it to this message, but that would put me over the message size limit for the list). Attached is the Artemis file where I checked to see if Artemis imported the paths properly. Rich Mayes Barnes Group 450/452 Buehler Hall Dept. of Chemistry Univ. of Tennessee Knoxville, TN 37996

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white line intensity v. edge position in determining oxidation state of Re
by Edward L. Kunkes 22 May '07

22 May '07

Hi everyone, I am trying to determine the oxidation state of Re in PtRe nanoparticles catalysts supported on carbon. The ReLIII edge was measured before and after an in-situ reduction in hydrogen. Can anyone suggest Which characteristic of the edge is more related to oxidation state ? Is it the integrated white-line intensity or the position of the edge(point of maximum derivative). The edge position of the ReLIII edge of my particles is the same as that of Re foil, however the white line instensity is significanty higher. For the non-reduced PtRe particles, the edge position is similar to that of ReO2 (with a larger white line intensity). Also, does anyone have any Data on Re-foil, HReO4 and ReO2 so that i can compare it to the data i measured for my standards ? Thank you very much for your help -Edward Kunkes

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