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

Re: [Ifeffit] new release (061) of my codes
by Matt Newville 30 Mar '06

30 Mar '06

HI Stefano, > stefano% ~> /Applications/Ifeffit/bin/ifeffit -i > tcsh: /Users/stefano: Permission denied. But that's implying that you can't even run ifeffit due to permission problems. That makes it seem much more about your system than about Ifeffit. > stefano# ifeffit > stefano# ifeffit> print $&install_dir Hmm, that's weird. The banner message didn't print and the prompt is wrong (it should be "Ifeffit>"). Any ideas why that might be? > stefano# ifeffit> print $&install_dir > su: Illegal variable name. > stefano# print $&install_dir > su: Illegal variable name. Hmm, that's weird too. I'm not sure what wrote "su: Illegal variable name." I'm pretty sure that is not from the ifeffit program. --Matt

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Number of independent points: Artemis & Feffit
by Mauro Rovezzi 30 Mar '06

30 Mar '06

Hi guys, I've noticed a strange behaviour in Artemis during the calculation of N_idp; the value differs from the Feffit one. In fact, with command line feffit (ver. 2.984) N_idp=(2*delta_k*delta_R/pi)+2 but with Artemis the "+2" value disappears. Seen that the procedure is: Artemis-->Ifeffit-->feffit(), why they differs? Mauro -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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(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 29 Mar '06

29 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 24 Mar '06

24 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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GeO2
by Santiago J.A. Figueroa 21 Mar '06

21 Mar '06

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: Trying to create atoms.inp
by Bruce Ravel 10 Mar '06

10 Mar '06

Gerald, You are correct that the link you give does not provide you with enough information about the structure to use Atoms. Have you looked in the Crystal Structires series by Wyckoff? Or the Inorganic Crystal Structure Database (ICSD)? Have you tried to do a search through the crystallography literature? I am sending this to the Ifeffit Mailing List (which is probably the correct place for a question like this) in hopes that someone will have more information that I do. B On Friday 10 March 2006 04:33, Schmidt, Gerald wrote: > Dear Bruce, > > a colleague of mine attended the recent workshop at the SLS in Villigen, > Switzerland (Damdin, from Mongolia). Maybe he told you that we're currently > working on some Zr and As EXAFS data...? > > Well, the original substance used for the samples was zirconium dinitrate, > which was applied to activated charcoal. We want to find out how the > sorption of As alters the crystal structure. > > The problem seems to be that we can't find enough information about > zirconium dinitrate to create a feff model. In all the databases I have > heard of it could not be found. The only thing I found was the attached > file (from > http://www.chemexper.com/index.shtml?main=http://www.chemexper.com/search/c >as/14985-18-3.html). It contains, at least, some xyz coordinates. > But obviously the space group and the lattice constants are missing. > > Do you have any idea what we could do to find the missing parameters so we > can successfully run atoms? > > Thanks & best regards, > Gerald > > --------------------------------- > Gerald Schmidt (Dipl. Geoecologist) > Institute of Geosciences > Mineralogy Section > Johannes-Gutenberg-University Mainz > Becherweg 21 > D-55099 Mainz > Germany > Tel. +49-6131-39-24780 > Fax +49-6131-39-23070 > gschmidt(a)uni-mainz.de -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance 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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k weight in Athena
by koppolu uma mahendra kumar 08 Mar '06

08 Mar '06

Dear All, I have a doubt about k-weights while extracting the signal in ATHENA. In athena Background removal panel conatins one button called k-weight. My question is how significant k weigths at the stage of background removal. Please explain Thanking You Mahendra -- Research Student Material Science Laboratory University of Hyderabad(india) X-ray Synchrotron Radiation Laboratory University of Trento(Italy)

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Re: Tkatoms
by Bruce Ravel 08 Mar '06

08 Mar '06

Linda, I am CCing this question and my (short) answer to the Ifeffit mailing list. > I am installing atoms for the first time on my Windows XP PC. When I > download the file ifeffit.1.2.8.exe I can run the atoms command line > version but I don't find how I can run the TK version on my PC. > Thanks for your answer. http://cars9.uchicago.edu/cgi-bin/ifeffit/faqwiz?req=all#7.3 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] Amplitude in Artemis
by Barton, David (DG) 02 Mar '06

02 Mar '06

Balwant, I have done a number of LCF using Athena and have found that this error message is typically associated with the rejection of one of your standards as a possible component in the fit. This error message may be avoided in most cases if you uncheck the options of --weights between 0 &1 and --Force weights to sum to 1 AND you put in an appropriate initial guess for the fit. When you rerun the fit with these options unchecked, it should be obvious what caused the error since one or more of your standard spectra will get a negative weight. When this occurs it is probably a good sign that the standard is not appropriate in the fit and some other standard should be used. Hope this helps, Dave > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of bsin1033(a)mail.usyd.edu.au > Sent: Thursday, March 02, 2006 3:41 PM > To: XAFS Analysis using Ifeffit; Kelly, Shelly D. > Cc: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Amplitude in Artemis > > > Hi Ifeffitters, > > I was trying to use the linear combination fitting function > in Athena to quantifying Cr(VI) and Cr(III) species. I used > two endmembers of Cr species as the two standards but the > program fails and gives error message "The fit flagged a > warning--probably that error bars could not be calculated. > That is probably an indication that one or more of your > standards are inappropriate for this fit." It appears I am > either using the wrong settings or even wrong function to do > the job, any suggestions. We have additional 3 spectra with > variable combinations of Cr(VI) and > Cr(III) as well. > > Cheers, > > Balwant Singh > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging > Program. _______________________________________________ > 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] Amplitude in Artemis
by Kelly, Shelly D. 02 Mar '06

02 Mar '06

Hi Paul, Here is an edited version of the Fe project file. I believe that the first shell signal is not isolated from the 2nd and third shells. One way for the fit to look better when not enough paths are present is for the s2 value to be large to spread the signal out with an outrageous coordination number. I added a C and a Zn path to model the region from r=1 to 3.5 Å. The fit is not that great, the background needs to be fixed and I'm not sure that the C and Zn paths are the best choice. If you look at the real or imaginary parts of the fit with kweights of 1 and 2 and 3 you will see that we have done a fair job at reproducing the data. Hopefully this little bit of help will get you going in the right direction. Shelly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Tuesday, February 28, 2006 5:54 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Amplitude in Artemis Hi Shelly I've attached the artemis project files. Hopefully you get further with them than I have been able to. Cheers Paul ----- Original Message ----- From: Kelly, Shelly D. <mailto:SKelly@anl.gov> To: XAFS Analysis using Ifeffit <mailto:ifeffit@millenia.cars.aps.anl.gov> Sent: Wednesday, March 01, 2006 1:50 AM Subject: RE: [Ifeffit] Amplitude in Artemis Hi Paul, How close are the distances for the 6 ligands? It is usually not possible to fit a single peak in the EXAFS spectrum by 6 independent signals. It sound like the distribution of distances for these 6 ligands is incorrect. I suggest that you try to fit just the first peak with one and then with two different shells with unknown coordination numbers and distances. This will give you some more information about what the data indicate the structure is like. If you send me an artemis file, I'll take a peak at it. Shelly skelly(a)anl.gov ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Monday, February 27, 2006 6:31 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Amplitude in Artemis Hi Shelly Unfortunately the coordination number is 1 for all atoms present. I have the crystal structure of the complex, so I am currently including 6 ligating atoms all at distances defined by the structure in the input file. It seems to be the first shell that is causing the problems, with a quickfit first shell artemis fit giving nominally 13 ligating species (which is of course absurd). So I believe something else must be the problem. Cheers Paul ----- Original Message ----- From: Kelly, Shelly D. <mailto:SKelly@anl.gov> To: XAFS Analysis using Ifeffit <mailto:ifeffit@millenia.cars.aps.anl.gov> Sent: Tuesday, February 28, 2006 12:55 AM Subject: RE: [Ifeffit] Amplitude in Artemis Hi Paul, It seems possible that one of the other amplitude terms is also incorrect. Scott already mentioned the step height but what about the coordination number? The amplitude of the model is given by coordination number * S02. You mentioned that the S02 value was somewhere between 2 and 4. What is the value for coordination number * S02? If the coordination number is 1, then it is possible that the parameters are switched. Maybe the coordination number should be between 2 and 4 and S02 should be around 1. HTH, Shelly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Sunday, February 26, 2006 6:52 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Amplitude in Artemis I have just started a PhD and have been given alot of EXAFS data to simulate but I don't know much about artemis. I have tried to fit the data for quite some time now, but can't get any kind of good fit unless the amplitude is above 1. Is there any way amp can be above 1 and rationally explained? Cheers, Paul ________________________________ _______________________________________________ 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] Amplitude in Artemis
by Kelly, Shelly D. 28 Feb '06

28 Feb '06

Hi Paul, How close are the distances for the 6 ligands? It is usually not possible to fit a single peak in the EXAFS spectrum by 6 independent signals. It sound like the distribution of distances for these 6 ligands is incorrect. I suggest that you try to fit just the first peak with one and then with two different shells with unknown coordination numbers and distances. This will give you some more information about what the data indicate the structure is like. If you send me an artemis file, I'll take a peak at it. Shelly skelly(a)anl.gov ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Monday, February 27, 2006 6:31 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Amplitude in Artemis Hi Shelly Unfortunately the coordination number is 1 for all atoms present. I have the crystal structure of the complex, so I am currently including 6 ligating atoms all at distances defined by the structure in the input file. It seems to be the first shell that is causing the problems, with a quickfit first shell artemis fit giving nominally 13 ligating species (which is of course absurd). So I believe something else must be the problem. Cheers Paul ----- Original Message ----- From: Kelly, Shelly D. <mailto:SKelly@anl.gov> To: XAFS Analysis using Ifeffit <mailto:ifeffit@millenia.cars.aps.anl.gov> Sent: Tuesday, February 28, 2006 12:55 AM Subject: RE: [Ifeffit] Amplitude in Artemis Hi Paul, It seems possible that one of the other amplitude terms is also incorrect. Scott already mentioned the step height but what about the coordination number? The amplitude of the model is given by coordination number * S02. You mentioned that the S02 value was somewhere between 2 and 4. What is the value for coordination number * S02? If the coordination number is 1, then it is possible that the parameters are switched. Maybe the coordination number should be between 2 and 4 and S02 should be around 1. HTH, Shelly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Sunday, February 26, 2006 6:52 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Amplitude in Artemis I have just started a PhD and have been given alot of EXAFS data to simulate but I don't know much about artemis. I have tried to fit the data for quite some time now, but can't get any kind of good fit unless the amplitude is above 1. Is there any way amp can be above 1 and rationally explained? Cheers, Paul ________________________________ _______________________________________________ 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] Amplitude in Artemis
by Kelly, Shelly D. 27 Feb '06

27 Feb '06

Hi Paul, It seems possible that one of the other amplitude terms is also incorrect. Scott already mentioned the step height but what about the coordination number? The amplitude of the model is given by coordination number * S02. You mentioned that the S02 value was somewhere between 2 and 4. What is the value for coordination number * S02? If the coordination number is 1, then it is possible that the parameters are switched. Maybe the coordination number should be between 2 and 4 and S02 should be around 1. HTH, Shelly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Sunday, February 26, 2006 6:52 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Amplitude in Artemis I have just started a PhD and have been given alot of EXAFS data to simulate but I don't know much about artemis. I have tried to fit the data for quite some time now, but can't get any kind of good fit unless the amplitude is above 1. Is there any way amp can be above 1 and rationally explained? Cheers, Paul

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Amplitude in Artemis
by Paul 26 Feb '06

26 Feb '06

I have just started a PhD and have been given alot of EXAFS data to simulate but I don't know much about artemis. I have tried to fit the data for quite some time now, but can't get any kind of good fit unless the amplitude is above 1. Is there any way amp can be above 1 and rationally explained? Cheers, Paul

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SPAM score=47.4*** Fonts in document pods
by Dave Baker 22 Feb '06

22 Feb '06

-------------------- Start SpamAssassin results ---------------------- Content analysis details: (score=47.4,required=5.3) -2.6 BAYES_00 BODY: Bayesian spam probability is 0 to 1% [score: 0.0000] 50 STOCKS_APS FULL: Hot Stocks Spam -------------------- End of SpamAssassin results --------------------- The original message was not completely plain text, and may be unsafe to open with some email clients; in particular, it may contain a virus, or confirm that your address can receive spam. If you wish to view it, it may be safer to save it to a file and open it with an editor.

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Re: How to change the spline knots in Athena
by Bruce Ravel 21 Feb '06

21 Feb '06

On Tuesday 21 February 2006 03:08, you wrote: > I am using Athena (0.8.048) software for XAFS analysis. > It is greatly helpful to me for XAFS characterization. > > I have a question on the background estimation. > Spline knots is displayed by "About current group" menu. > Could you tell me how to change the spline knots, if possible. > Changing the knots is useful to suppress the long-range variation. This is the kind of question that is better sent to the mailing list, so I am CCing my answer there. The number of knots is determined by the values of the k-range of the spline fit and by the value of Rbkg. The number of knots is delta_k * Rbkg * 2 / pi and the knots are evenly spaced in k. Ifeffit (and so Athena) does not allow you to move the knots to different locations nor does it allow you add or remove knots. The AUTOBK algorithm works by making a distinction between data and background in terms of Fourier components. Consequently it *cannot* allow you to move the knots or use more knots, since doing so would change the Fourier components included in the background spline. 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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error message in help
by Bradley Roberts 21 Feb '06

21 Feb '06

With Ifeffit 1.2.8, Athena 0.8.047, Artemis 0.8.004 running on OS X and plotting correctly, I'm not able to pull up any of the help windows. In either of the GUI programs, when I click on the Help menu and choose Document (or any of the sub-menu items in Athena) X11 beeps in error, and a window opens with the title "pod" and nothing displayed within the window. I mentioned before that I could not get tk::pod to install correctly via CPAN (the response being) Installing tk::pod FAILED windows would pop up during the make test routine that said: Can't find Pod 'perl' with an OK button and that the Text::English and Tk::HistEntry modules were not installed (though they are installed, says CPAN) I recognize that this is probably more of a Perl/CPAN related question but perhaps someone has seen this problem before. -- Bradley Roberts (br2(a)u.washington.edu) Graduate Student, Department of Materials Science & Engineering Roberts Hall 302 Box 352120 University of Washington Seattle, WA 98195 206-616-7485 lab 206-543-3100 fax

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Re: [Ifeffit] pgplot+Kubuntu+/XWINDOW /XSERVE
by Bruce Ravel 21 Feb '06

21 Feb '06

On Monday 20 February 2006 23:48, Denis Testemale wrote: > I've been using Ifeffit+horae (VERY GOOD) stuff for a while on my > previous Mandrake linux distro. I've changed to Kubuntu now. I have > difficulties to install everything on this new laptop. [Please be > aware that I use Linux for quite some time now but still consider > myself as an "everyday beginner"] > > I'm stuck at the installation of PGPLOT. > I've tried then to install from Mat's PGPLOT_install script but ran > into the same kind of error. Here it is: Kubuntu is debian-based and, I think, can use any debian repository. So I think you should be able to use Carlo's debian repository to install the software. Just point kynoptic at the repositories mentioned here: http://cars9.uchicago.edu/~ravel/software/downloads.html#debian Hope that helps, 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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