- Ifeffit - millenia.cars.aps.anl.gov

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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iron L edges
by Bruce Ravel 16 May '08

16 May '08

Hi everyone, I have just spent a fruitless half hour with google scholar trying to find a paper that publishes Fe L2,3 edge spectra (not K -- I have those!) of the FeOOH species goethite and lepidocrocite. Can anyone point me in the right direction? Thanks a million! 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/

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feff8.4 LDOS number of energy points
by Rajmund Bacewicz 12 May '08

12 May '08

Hi all, In a Windows version of FEFF8.4, LDOS is calculated in 401 energy points, that is extremely time consuming. Is it possible to change it to a smaller number of points (e.g. 101 points like in FEFF8.2)? Regards Rajmund -- List przeskanowano programem ArcaMail, ArcaVir 2006 przeskanowano 2008-05-12 10:29:02, silnik: 2005.12.01 12:00:00, bazy: 2008.05.04 14:32:29 This message has been scanned by ArcaMail, ArcaVir 2006 scanned 2008-05-12 10:29:02, engine: 2005.12.01 12:00:00, base: 2008.05.04 14:32:29 http://www.arcabit.com

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XANES Background removal and Normalization
by Jens Kruse 10 May '08

10 May '08

Hi there, I have some P L2/L3-edge XANES spectra. I am not sure how to remove the background and normalize these data. Due to the fact that the pre edge and the post edge region is not very flat the the edge-step normalization using AUTOBK dose not work very well. CLNORM background subtraction seems to work better in some case. But some spectra get partly negative values after CLNORM (see .prj attached). So my questions are: 1:Is CLNORM the best choice in my case, especially when I plan to do linear combination fitting with these data? 2: Athena needs the knowledge of the absorbing atom an the edge to use CLNNORM, but the spectra contain both L3 an L2. So, which edge do I have to choose L3 or L2? 3: Would it be also correct to use a Victoreen-Fit for the pre edge without any further normalization and than do the linear combination fitting? Or do I have to normalize spectra in general when I am doing linear combination fitting, to eliminate effects of different concentrations of the absorbing atom in the mixtures? thanks, a lot for your help jens

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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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