April 2008 - 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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Ifeffit Ok on BlueWhite64, ...
by Chachi Rojas 03 Feb '09

03 Feb '09

Hi Matt Ifeffit run perfectely (thanks Matt) after installed by your scripts on RC1. Now, a question for Bruce try to install horae-065, but, error message is below: ---------- === The Ifeffit wrapper, Athena, Artemis, and Hephaestus === This is linux. Checking dependencies ... Tk is not installed. Download the latest from http://search.cpan.org/search?module=Tk Failed dependencies. Not installing athena and artemis. ------ Tk modules (version 8.4.15) were installed on /usr, but perl Makefile.PL it does not recognize Some idea Ch. > Date: Wed, 22 Aug 2007 15:56:26 -0500 > From: "Matt Newville" <newville(a)cars.uchicago.edu> > Subject: [Ifeffit] Ifeffit and gfortran (was: iffefit compile on > BlueWhite64) > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0708221356y37280877v86ac576fe9b6b96c(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Chachi, all > > I believe I have a source kit that will build correctly for you using > gfortran. I've tested on three different generations of Fedora/Redhat > linux systems, one with only g77, one with only gfortran, and one with > both, and the installation now works on all of them. > > Please try > http://cars9.uchicago.edu/~ifeffit/src/ifeffit-1.2.10_rc1.tar.gz > > With this tar ball, you will need to install pgplot: > tar xvzf ifeffit-1.2.10_rc1.tar.gz > cd ifeffit-1.2.10 > sh PGPLOT_install > ./configure > make > make install > > (doing the two 'install steps' with sufficient privilege). Again, you > need to install PGPLOT with the provided script. Both the PGPLOT and > Ifeffit installations will use gfortran if available, and g77 if > gfortran is not available. I think it would not be too difficult to > attempt to use Intel's ifort compiler or g95, though I do not know > that it's needed-- all linux distribution come with gcc so have > easy-to-use packages for gfortran (and, for "legacy", g77). > > I did get horae-065 and the python wrappers to build with no trouble > (once the Tk modules were installed) on all systems, though I haven't > done much more than trivial testing. > > Since I tested only on a few linux boxes, I'd be interested in hearing > reports for other systems. > > I'll wait a few days (or more) to hear reports before uploading this > as ifeffit-1.2.10. > > --Matt >

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Questions on EXAFS
by Rajasekaran S 08 Jul '08

08 Jul '08

I have a couple of questions on the use of EXAFS: 1. How sensitive is EXAFS/XANES in determining ~ couple of ppm (up to 100ppm) of halogen content in solid content? 2. Also, are there lab-scale EXAFS/XANES equipments available towards this? Anyone working on lab-scale equipments? Thanks Raja

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Re: [Ifeffit] iXAFS 2 beta 1 released
by Hind Al-Abadleh 28 May '08

28 May '08

Hi Jeff, This is great news. I downloaded the beta version, and got the error message "Apple's X11 for Mac OSX is not installed...". So, I downloaded the latest update for X11 from Apple's website from this page: http://www.apple.com/downloads/macosx/apple/macosx_updates/x11update2006113… And when I tried to install it, an alert message came "this system doesn't need this update". So, now I'm baffled, and truly don't know where to go from here. How would I check my system (OSX 10.4.11) for the X11 already installed? Any advice will be very much appreciated. Thanks, Hind ---------------------------- Hind A. Al-Abadleh, Ph.D. Assistant Professor Chemistry Department, Wilfrid Laurier University Science Building 3020F 75 University Ave. W. Waterloo, Ontario N2L 3C5 Canada Ph.: (519) 884-0710 ext. 2873 Fax: (519) 746-0677 URL: http://www.wlu.ca/science/chemistry/halabadleh/ ---------------------------- >>> terryj(a)iit.edu 12/07/07 12:15 AM >>> Hi All, iXAFS version 2 for Mac OS X 10.4 and above has been released as a beta version. We have tested this version on ppc and intel macs running OS X 10.4 and 10.5. You must have Apple's version of X11 installed in order to use iXAFS. Ken McIvor put in yeoman's work to build the full ifeffit, horea suite as a universal binary. He packaged it as a single drag and drop installation within iXAFS. Ken wanted to post this message but had an illness in the family. Hopefully, we can all thank Ken for his work to get this built in a manner that should work on all modern Macs. A link to download this version of iXAFS can be found at the MRCAT website: http://mrcat.iit.edu We forgot to put in the documentation that the iXAFS shell allows you to run any of the programs from the command line ifeffit, feff6, etc. Jeff _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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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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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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Using the amplitude reduction factor as a linear combination fitting parameter
by Bruggeman Christophe 30 Apr '08

30 Apr '08

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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Re: [Ifeffit] Using the amplitude reduction factor as alinearcombination fitting parameter
by Frenkel, Anatoly 29 Apr '08

29 Apr '08

An option could be, if you collected just one spectrum, to construct 1st shell EXAFS data for each compound using FEFF and use a linear combination option of Athena to see if there is any value of the mixing fraction of these two theoretical compounds that resemble good fit. You will still need to know the best fit value of S02 obtained previously from standard uranium compounds and use same sigma2 for all U-O bonds. You can define your fitting range using large value of kmin to emphasize the first shell signal better, and do fititing in k space with k-weighting of 1 for the same reason. It can all be done witinin Athena. 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 10:23:10 2008 Subject: Re: [Ifeffit] Using the amplitude reduction factor as alinearcombination fitting parameter 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 _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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