May 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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Phase transformation and space group
by 益豪 29 May '08

29 May '08

To Dear authors: We have complex perovskites, the series of La(2-x)/3 Nax Mg0.5 W0.5 O3 where x=0,0.1,0.2,0.3,0.4,0.5. I would like to fit the EXAFS data, and according as ICSD to build the atom list by using TkAtoms. However these samples might have phase transformation with the increase in x-value. First, I use the same structure which the x=0 atom coordinates from ICSD to fit the data of x=0-0.2, and use the x=0.5 atom coordinates to fit the data of x=0.3-0.5. But the trend of the distance between the central atom(W) and the six neighboring oxygen atoms with Na concentration is very strange! The distance of O-W with x=0-0.2 is increasing, x=0.2-0.3 is decreasing, and x=0.3-0.5 is increasing. I conjecture that the result is so strange because we use the different space group. I would like to ask how to choose the atom coordinates x=0 and x=0.5 from ICSD to build the theoretical model of x=0.1-0.4. Thanks for your time and help! Yi-Hao, Chang ______________________________________________________________________________________________________ 付費才容量無上限？Yahoo!奇摩電子信箱2.0免費給你，信件永遠不必刪！ http://tw.mg0.mail.yahoo.com/dc/landing

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Re: [Ifeffit] Ifeffit Digest, Vol 63, Issue 13
by Pooja Gupta 29 May '08

29 May '08

On 5/28/08, 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. Re: IXAFS for Mac OSX - Problem launching Artemis > (Dean Hesterberg) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 28 May 2008 10:27:58 -0400 > From: Dean Hesterberg <sscdlh(a)unity.ncsu.edu> > Subject: Re: [Ifeffit] IXAFS for Mac OSX - Problem launching Artemis > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <BE32E4C8-D3F7-4570-B3FB-065A114A828D(a)unity.ncsu.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Jeff, > > Thank you for your prompt advice. Sorry, I meant to say that I re- > installed "iXAFS 2 ?1 ? IFEFFIT and the Horae suite for the Mac > (universal binary for Tiger and Leopard)" from your website. I had > removed the program last Friday, re-installed it this morning, and > this time everything seems to be working fine. If I experience the > problem again, I will try your suggestion of adding (or changing) the > directory in the main "iXAFS" window. > > Dean > > > On May 23, 2008, at 4:54 PM, Jeff Terry wrote: > > > Hi Dean, > > > > I am not sure what you mean by reinstalling x11 from the mrcat > > site. I didn't know it was posted there. > > Anyway, I see this behavior on occasion when Artemis is having > > trouble opening a file. The Aquaterm > > window pops up with the normal splash screen. > > > > I work around this by just putting a directory in the project or > > directory window. For me it doesn't occur often, > > but always with the same files. > > > > This is under 10.5.2 on an intel mac. > > > > Jeff > > > > > > On May 23, 2008, at 2:50 PM, Dean Hesterberg wrote: > >> Hello, > >> > >> For months, I have been happily using IXAFS for Mac OSX - > >> excellent program! I am now having problems launching Artemis. > >> An Aquaterm graphics window opens, but the actual Artemis program > >> does not. If I keep trying, periodically Artemis appears as if it > >> will launch, but the message about cleaning up extra sessions > >> comes up, and whether I "clean up" or "keep" the sessions and/or > >> close the Aquaterm windows beforehand, the Artemis program quits > >> without opening. > >> > >> The only unusual action today was that I was working with several > >> Athena windows opened at once, but had quit all Athena sessions > >> before trying to launch Artemis. I tried downloading and re- > >> installing "X11 1.1.3 - XFree86 4.4.0" from http://mrcat.iit.edu, > >> restarted the computer, etc., but to no avail. Athena seems to > >> run fine. Even after re-installing and restarting, I sometimes > >> receive the multiple sessions cleanup message, so perhaps I need > >> to delete certain files before cleanly re-installing IXAFS. I did > >> remove (trashed) IXAFS from the Applications folder before re- > >> installing. > >> > >> I'm using a Mac Pro Dual Core Intel with > >> Mac OSX version 10.4.11 > >> X11 version 1.1.3 > >> > >> I appreciate any suggestions for fixing this problem, or a lead to > >> a previous posting if this problem has already been discussed here. > >> > >> Dean > >> > >> > >> > >> DEAN HESTERBERG > >> Professor > >> Dept. of Soil Science > >> College of Agriculture and Life Sciences > >> Box 7619 > >> 3235 Williams Hall > >> NC State University > >> Raleigh, NC 27695-7619 > >> > >> voice: (919) 513-3035 > >> fax: (919) 515-2167 > >> email: dean_hesterberg(a)ncsu.edu > >> > >>>> 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 > >>>> > >>>> _______________________________________________ > >>>> 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 > >> > >> _______________________________________________ > >> 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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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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questions concerning paper
by s440697＠stud.uni-goettingen.de 23 May '08

23 May '08

Hello, i have some questions concerning the xafs-formula in this paper (attached): "Theoretical approaches to x-ray absorption fine structure" (July 2000). The author explained on page 625 and 626 the parameters of this formula. I think, most of you have read this paper. I don't understand the meaning of lambda(k), the author wrote "... and lambda(k) is the energy-dependent XAFS mean free path (not to be confused with the de Broglie wavelength)." My question is, the mean free path whereof? The propagating photoelektron(wave) or the (back)scattered waves? In the next sentence, what is the overall amplitude factor S_0^2? How is it defined? In conjunction with question one i don't understand the expression in the next paragraph for the term e^{-2R/lambda}. The author wrote: "The decay of the wave (which wave does he mean?) due to the mean free path or finite lifetime (what does he mean?, finite lifetime of the emitted and propagating photoelektron wave?) [including core-hole lifetime] of the photoelectron is captured by ..." Is it right, that the emitted photoelektron is detectable outside the sample? Another parameter is the phase factor phi = arg f(k) "...reflects the quantum-mechanical wavelike nature of the backscattering." Please explain me the meaning of this parameter. At the bottom of this page the author wrote: "...the Debye-Waller factor, which is given to a good approximation by e^{-2 sigma^2 k^2}." In this context he refers to figure 8, where k^2 chi(k) vs. k is plotted. I don't understand this context because there is no chi in the approximation for the Debye-Waller factor. Where comes the chi here? I would be very grateful for any help you would offer to me. Thank you very much for your help and time. sincerely yours, E.Bosman --------------------------------- Eckhard Bosman e.bosman(a)stud.uni-goettingen.de +49 (0)551-39-14441 Raum: E0.104 Institut für Röntgenphysik Friedrich-Hund-Platz 1 37077 Göttingen Germany

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Re: [Ifeffit] questions concerning paper
by Frenkel, Anatoly 22 May '08

22 May '08

We should ask John Rehr to rename FEFF to Odysseus. It makes both physical and mythological sense. Anatoly ----- Original Message ----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: Ravel, Bruce; XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Thu May 22 14:30:38 2008 Subject: Re: [Ifeffit] questions concerning paper I loved it also, thanks Matt :-) May i cite your Odysseus explanation in my diploma thesis? ;) -------- Original-Nachricht -------- > Datum: Thu, 22 May 2008 12:40:01 -0400 > Von: Bruce Ravel <bravel(a)bnl.gov> > An: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Betreff: Re: [Ifeffit] questions concerning paper > > Matt, > > That was awesome! I **loved** the Odysseus explanation of the exafs > equation. Quite possibly the best Ifeffit mailing list post ever. > > B > > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- GMX startet ShortView.de. Hier findest Du Leute mit Deinen Interessen! Jetzt dabei sein: http://www.shortview.de/?mc=sv_ext_mf@gmx _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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2008 APS XAFS School
by Matt Newville 16 May '08

16 May '08

Hi Everyone, The application form for the 2008 APS XAFS School is now open: http://cars9.uchicago.edu/xafs_school/2008 Details about this year's APS XAFS School are at http://xafs.org/Workshops/APS2008 --Matt PS: Starting sometime yesterday (and currently), mail from outside APS to this list is being bounced by an APS firewall. If you have sent mail to this list and had it bounce, please be patient. I'll post a message when the mailing list is back up.

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