March 2006 - Ifeffit - millenia.cars.aps.anl.gov

(no subject)
by Emmanuelle Montarges 30 Mar '06

30 Mar '06

Hi everyone Working on MacOs10.4 computer, after several unsuccessful installations of ifeffit package....I have the following message when I try to run Athena from the Terminal window. I downloaded Tk-804.027.tar and installed it in "temp" directory, but I still have the same message...have you ever had this error? ************ Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Tk/Tk.bundle' for module Tk: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Tk/Tk.bundle, 1): Library not loaded: /usr/X11R6/lib/libX11.6.dylib Referenced from: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Tk/Tk.bundle Reason: image not found at /System/Library/Perl/5.8.6/darwin-thread-multi-2level/DynaLoader.pm line 230. at /Applications/Ifeffit/bin/athena line 52 Compilation failed in require at /Applications/Ifeffit/bin/athena line 52. BEGIN failed--compilation aborted at /Applications/Ifeffit/bin/athena line 52. ********** thanks in advance for your help Emmanuelle MONTARGES-PELLETIER

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Re: [Ifeffit] Fe B standard
by Scott Calvin 30 Mar '06

30 Mar '06

Thanks, all! That info did the trick...I ended up using an Excel spreadsheet to do the processing, which may make some of you wince, but I found it easy enough. :) --Scott Calvin Sarah Lawrence College >

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Contour plot
by Mauro Rovezzi 29 Mar '06

29 Mar '06

Hi to all, Does someone has already written an Ifeffit script calculating a contour plot? In 2003 Norbert opened this thread on "Scanning of Potential Surfaces in EXAFS": http://cars9.uchicago.edu/pipermail/ifeffit/2003-July/000398.html Do you have any "wild code" to send me? :) Thanks, Mauro -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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core hole lifetime in XANES calculation using FEFF82
by Qi Q Z 29 Mar '06

29 Mar '06

Dear all, Feff82 uses the data from K. Rahkonen and K. Krause (Atomic Data and Nuclear Data Tables, Vol 14, Number 2, 1974) to set core hole lifetime(gamach parameter). My question is if people can set gamach parameter in Feff82 by themselves? may I use a minus vi0 in EXCHANGE card to reduce broading caused by core hole lifetime? Thanks in advance. Qi

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Re: [Ifeffit] Odd feff result
by Bruce Ravel 25 Mar '06

25 Mar '06

On Friday 24 March 2006 13:01, Scott Calvin wrote: > So here's the question. These three paths are identical except for > the identity of one of the scattering atoms. The degeneracy of the > path with boron and the path with nickel is the same. Why is the feff > amplitude ratio for the boron-containing path higher than that of the > nickel-containing path? Shouldn't nickel scatter more strongly? And > yes, I double-checked...the potentials are defined correctly in the > feff.inp file. Scott, I am inclined to side with Jeremy and Feng. One might be surprised by how quick-n-dirty the amplitude calculation is. If memory serves (and who knows how likely *that* is), feff computes the complex chi(k) using plane waves, which is a very quick calculation. It then adds up the magnitude of the complex chi(k) at 4 points. That's it. The amplitude is never meant to be more than a guide to eye. As you well know, to know how each path contributes to the data, you actually need to plot them or -- better -- do a fit. 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] Odd feff result
by Feng Wang 24 Mar '06

24 Mar '06

Hi Scott and Jeremy It is interesting result, and I strongly agree with Jeremy's explanation. We also notices such a phonomenon before, a prominent postpeak, about 40 eV above iron L3 edge, even in very thin films of iron fluoride. The peak gradually disappears as fluorine is removed by electron irradiation, but appears when an iron film is oxidized.Oxygen and fluorine anions in transition-metal compounds are strong backscatters, as confirmed by the FEFF calculation, I believe boron is another strong scatter. Best regards, Feng > Scott, > > This doesn't seem like too unusual a result to me. The amp ratio from > feff is more of a qualitative than a quantitative prediction. Now I am > just making a guess; nevertheless, a boron scattering path will probably > have a significantly higher amplitude at low k compared to a Ni or Fe > scattering path. This could easily be the cause of the difference you > observe. > > Jeremy Kropf > > Chemical Engineering Division > Argonne National Laboratory > Argonne, IL 60439 > > Ph: 630.252.9398 > Fx: 630.252.9373 > kropf(a)cmt.anl.gov > > > > -----Original Message----- > > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > > Of Scott Calvin > > Sent: Friday, March 24, 2006 1:01 PM > > To: XAFS Analysis using Ifeffit > > Subject: [Ifeffit] Odd feff result > > > > Hi all, > > > > I just ran a feff calculation using feff6L and got a result > > that surprised me a little. I was modelling a ferrite with a > > nickel and boron substituted for iron in a small fraction of > > sites. Here's part of files.dat: > > > > file sig2 amp ratio deg nlegs r effective > > feff0010.dat 0.00000 2.706 2.000 3 3.7141 > > feff0011.dat 0.00000 26.472 20.000 3 3.7141 > > feff0012.dat 0.00000 4.038 2.000 3 3.7141 > > > > and the corresponding part of the paths.dat: > > > > 10 3 2.000 index, nleg, degeneracy, r= 3.7141 > > x y z ipot label rleg > > beta eta > > -3.126710 1.042240 1.042240 1 > > 'Ni ' 3.4567 150.5039 0.0000 > > -1.146460 1.146460 1.146460 3 > > 'O ' 1.9857 58.9923 0.0000 > > 0.000000 0.000000 0.000000 0 > > 'Fe ' 1.9857 150.5039 0.0000 > > 11 3 20.000 index, nleg, degeneracy, r= 3.7141 > > x y z ipot label rleg > > beta eta > > 1.042240 -3.126710 1.042240 2 > > 'Fe ' 3.4567 150.5039 0.0000 > > 1.146460 -1.146460 1.146460 3 > > 'O ' 1.9857 58.9923 0.0000 > > 0.000000 0.000000 0.000000 0 > > 'Fe ' 1.9857 150.5039 0.0000 > > 12 3 2.000 index, nleg, degeneracy, r= 3.7141 > > x y z ipot label rleg > > beta eta > > -1.042240 3.126710 1.042240 4 > > 'B ' 3.4567 150.5039 0.0000 > > -1.146460 1.146460 1.146460 3 > > 'O ' 1.9857 58.9923 0.0000 > > 0.000000 0.000000 0.000000 0 > > 'Fe ' 1.9857 150.5039 0.0000 > > > > So here's the question. These three paths are identical > > except for the identity of one of the scattering atoms. The > > degeneracy of the path with boron and the path with nickel is > > the same. Why is the feff amplitude ratio for the > > boron-containing path higher than that of the > > nickel-containing path? Shouldn't nickel scatter more > > strongly? And yes, I double-checked...the potentials are > > defined correctly in the feff.inp file. > > > > --Scott Calvin > > Sarah Lawrence College > > > > _______________________________________________ > > 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 ================================== Feng Wang fwang(a)phys.ualberta.ca Electron Microscopy Group Department of Physics University of Alberta =========================================================

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RE: [Ifeffit] Odd feff result
by Kropf, Arthur Jeremy 24 Mar '06

24 Mar '06

Scott, This doesn't seem like too unusual a result to me. The amp ratio from feff is more of a qualitative than a quantitative prediction. Now I am just making a guess; nevertheless, a boron scattering path will probably have a significantly higher amplitude at low k compared to a Ni or Fe scattering path. This could easily be the cause of the difference you observe. Jeremy Kropf Chemical Engineering Division Argonne National Laboratory Argonne, IL 60439 Ph: 630.252.9398 Fx: 630.252.9373 kropf(a)cmt.anl.gov > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Scott Calvin > Sent: Friday, March 24, 2006 1:01 PM > To: XAFS Analysis using Ifeffit > Subject: [Ifeffit] Odd feff result > > Hi all, > > I just ran a feff calculation using feff6L and got a result > that surprised me a little. I was modelling a ferrite with a > nickel and boron substituted for iron in a small fraction of > sites. Here's part of files.dat: > > file sig2 amp ratio deg nlegs r effective > feff0010.dat 0.00000 2.706 2.000 3 3.7141 > feff0011.dat 0.00000 26.472 20.000 3 3.7141 > feff0012.dat 0.00000 4.038 2.000 3 3.7141 > > and the corresponding part of the paths.dat: > > 10 3 2.000 index, nleg, degeneracy, r= 3.7141 > x y z ipot label rleg > beta eta > -3.126710 1.042240 1.042240 1 > 'Ni ' 3.4567 150.5039 0.0000 > -1.146460 1.146460 1.146460 3 > 'O ' 1.9857 58.9923 0.0000 > 0.000000 0.000000 0.000000 0 > 'Fe ' 1.9857 150.5039 0.0000 > 11 3 20.000 index, nleg, degeneracy, r= 3.7141 > x y z ipot label rleg > beta eta > 1.042240 -3.126710 1.042240 2 > 'Fe ' 3.4567 150.5039 0.0000 > 1.146460 -1.146460 1.146460 3 > 'O ' 1.9857 58.9923 0.0000 > 0.000000 0.000000 0.000000 0 > 'Fe ' 1.9857 150.5039 0.0000 > 12 3 2.000 index, nleg, degeneracy, r= 3.7141 > x y z ipot label rleg > beta eta > -1.042240 3.126710 1.042240 4 > 'B ' 3.4567 150.5039 0.0000 > -1.146460 1.146460 1.146460 3 > 'O ' 1.9857 58.9923 0.0000 > 0.000000 0.000000 0.000000 0 > 'Fe ' 1.9857 150.5039 0.0000 > > So here's the question. These three paths are identical > except for the identity of one of the scattering atoms. The > degeneracy of the path with boron and the path with nickel is > the same. Why is the feff amplitude ratio for the > boron-containing path higher than that of the > nickel-containing path? Shouldn't nickel scatter more > strongly? And yes, I double-checked...the potentials are > defined correctly in the feff.inp file. > > --Scott Calvin > Sarah Lawrence College > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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cyber-security
by Khalid, Syed 24 Mar '06

24 Mar '06

I did download the latest version Ifeffit-1.2.8a for our computers > running Windows 2000 OS. The programs work great. > To start with, I increased the 'user' privilege to 'administrator', > downloaded the program and then executed to setup. All the program 'icons' > appear on the desktop and work fine, however, they do not work if I remove > the 'administrator' privilege and login as 'user'. When you click or double > click the icons, no response what so ever. > > I went back to 'administrator' privilege, but keeping this high privilege > for users does not make our cyber-security guys happy. Any solution to this problem? > > > Syed Khalid 725 D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Phone: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov

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CORRELATION MATRIX IN IFEFFIT
by Renato Canha Ambrosio 24 Mar '06

24 Mar '06

Hi folks I'm need to explore more the correlation matrix R(ij)given by ifeffit since my fit several variables are ajusted (the number is far bellow the number of independent data points). In my MACRO, the command correl (@all, @all, print) permit to obtain the correlation matrix. So I have some questions about the calculation of correlations (rij): 1) Is the correlations(rij) calculated in ifeffit the sample linear correlation which measures the linear dependence between two vectos (in this sense, I'm thinking the term vector as a nx1 matrix in which n corresponds to the sample size - perhaps the number of fit iteractions)? If so, can I use a conventional hypothesis test like t (t = rij*sqrt[(n-1)/(1-rij**rij)] and how many degress of fredon can I consider to fint the t score on the table of t student distribution? 2) As I need to explore more the correlation matriz I would like to know if someone uses principal component analysis on Rij or some other chemometric approach. Thank you very much Renato Canha Ambrosio -- Open WebMail Project (http://openwebmail.org) ---------- Original Message ----------- From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Wed, 22 Mar 2006 12:00:17 -0600 Subject: Ifeffit Digest, Vol 37, Issue 6 > 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. GeO2 (Santiago J.A. Figueroa) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 21 Mar 2006 17:06:45 -0300 > From: "Santiago J.A. Figueroa" <figueroa(a)inifta.unlp.edu.ar> > Subject: [Ifeffit] GeO2 > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <004701c64d23$00f973a0$8c01010a@NEVERMIND> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > > Anyone out there have spectra for a GeO2 standard? > > Thanks! > > Lic. Santiago J. A. Figueroa > Instituto de Investigaciones Fisicoquímicas > Teóricas y Aplicadas (INIFTA) > Fac. de Cs. Exactas. > Universidad Nacional de La Plata > Diag. 113 y 64 > C.C.16 suc.4 (1900) La Plata > TEL: (0221) 425 7430 interno: 144 > FAX: (0221) 425 4642 > WEB: www.inifta.unlp.edu.ar > >

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Re: Fw: Doped Crystal in Artemis
by Scott Calvin 24 Mar '06

24 Mar '06

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