April 2009 - Ifeffit - millenia.cars.aps.anl.gov

Got Athena data plotted
by abhijeet gaur 27 Oct '09

27 Oct '09

Thanks a lot kicaj, I followed the procedure step by step and I got the data plotted in Excel. Thanks again Kicaj. Abhijeet

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Fitting procedure
by abhijeet gaur 01 May '09

01 May '09

Hello Matt Sir, Thanks a lot. I will include the error bars in fitted value for sure. with regards Abhijeet Gaur

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Inviting you to Multiply
by kaswat nano (via Multiply) 27 Apr '09

27 Apr '09

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Fitting procedure
by abhijeet gaur 24 Apr '09

24 Apr '09

Hello Matt Sir, Thanks a lot for your valuable sugestions. I had fitted the Cu foil spectra as you suggested. I had taken same SO2 value for all the paths and after fitting the first shell , making its parameter fix when fitting second shell I changed the fit R range 2.9- 3.7 in order to make the contribution of first shell negligible. I got a nice fit. The values of different parameters I got are as follows : E 0=2.90 eV , SO2= 0.72 1st shell R = 2.54, delR= -0.011, SS2=0.0083 2nd shell R= 3.69, delR= 0.080, SS2=0.0088 The experimental data is taken at room temperature. Are these parameters within the experimental error limit. Please tell me with regards Abhijeet Gaur

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Can't locate Ifeffit.pm
by Silvio Levy 21 Apr '09

21 Apr '09

Hi, I've installed horae on a new laptop after a hiatus. When I try to run athena or artemis I get the message Can't locate Ifeffit.pm in @INC (@INC contains: ... Setup: ifeffit-1.2.11c horae-069 Ubuntu 8.04.1 There is an Ifeffit.pm (in fact two) in the ifeffit-1.2.11c source directory, so I added it to the PERL5LIB path. But this didn't solve the problem; it just pushed it a few yards further. Now I get Can't locate loadable object for module Ifeffit in @INC (@INC contains: ... Anybody know the solution? Note to Bruce: the instructions in 0INSTALL still say 'perl Makefile.PL; make; make install' but the correct thing seems to be 'perl Build.PL; Build; Build install' as I found on one of your web pages. Thanks in advance Silvio

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Fitting procedure
by abhijeet gaur 20 Apr '09

20 Apr '09

I want to add some more things I have done 1) E0 is kept same for all the shells 2) All other parameters like SO2 , del r , SS2 are calculated separately for different shells. So. is there problem with taking different SO2 for different shells. Surely del r and SO2 will be different for different shells , If I got it right. Abhijeet

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NLEG
by Eugenio Otal 19 Apr '09

19 Apr '09

Hi, I am performing some XANES simulation with feff. I want to know somethings about an extra shoulder so I am using NLEG card. I have no problem with NLEG = 1 - 3, but NLEG > 3, I found a error: Eliminating path degeneracies... Plane wave chi amplitude filter 2.50% WARNING!! Two non-degenerate paths, hashed to the same hash key!! 0.12036490409027290344E+09 0.12042092980933572352E+09 3 3 npat0, npat iat, ipot0, ipot, ipat0, ipat 1 1 1 2 2 2 0 0 0 0 3 1 1 2 1 ileg, rx0,ry0,rz0, rx1,ry1,rz1 1 0.0000000000E+00 -1.3877787808E-16 1 0.0000000000E+00 0.0000000000E+00 1 1.9402260780E+00 1.9402260780E+00 2 0.0000000000E+00 0.0000000000E+00 2 0.0000000000E+00 0.0000000000E+00 2 0.0000000000E+00 0.0000000000E+00 3 0.0000000000E+00 1.7760854959E+00 3 0.0000000000E+00 0.0000000000E+00 3 1.9402260780E+00 -7.8094518185E-01 hash error that is what I found in output file and the simulation crashed. Is there somehow to solve this and continue the job? Thanks in advanced, euG

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Fitting procedure
by abhijeet gaur 19 Apr '09

19 Apr '09

Hi all, I think there is a lot of confusion over the method that i used for fitting, So I should make it clear here. In this method I fit the first shell by taking into account only first shell R range i.e. 1.5 - 2.7. Then after getting a nice fit for the first shell, I extract its parameters and make them set in Artemis. Then I include the second shell by increasing R range to 1.5 - 3.6. In the same manner I fit the first three shells of copper foil and the parameters I got for them are reasonably good. The problem of high SO2 only lies with one of my foil data which is not as good as other data. For other good data I got SO2 value for second shell within the exceptable limit. One more thing I want to say is that we can check the corelation between different parameters of shells by making them guess during any step of the fitting e.g. during the fitting of second shell we can make any parameter of the first shell to vary and check its corelation with them. But if I am counting the first shell data twice, I will include only second shell R range after first shell fit.I think it will not make any difference to results. If yes please tell me the reasons. with thanks Abhijeet gaur

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Re: [Ifeffit] Fitting procedure
by Chappell, Mark A ERDC-EL-MS 18 Apr '09

18 Apr '09

Oops, please ignore my message - sent it to the wrong address!!! --------- Message sent via my BlackBerry Wireless Device ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Sat Apr 18 14:56:35 2009 Subject: Re: [Ifeffit] Fitting procedure They're on theur way back to Vicksburg. I yried to guide them from home but couldn't figure out where she was. By 230, she hung it up and turned back --------- Message sent via my BlackBerry Wireless Device ----- Original Message ----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Sat Apr 18 12:57:18 2009 Subject: Re: [Ifeffit] Fitting procedure Hi Adam, I am confused by this thread too! As you say, the original issue involved using S02 for individual shells of data on Cu foil. Of course, having separate S02 for each shell is not usually necessary to model Cu foil -- in fact I can't think of a case where it is needed. But since S02 is 100% with N, and ~95% correlated with sigma2, it is easy to have S02 vary per shell if one allows it to happen. Whether that's a good idea or not depends on how you interpret the results. Most people choose to fix a single S02 and vary N. Lots of people fit spectra with one S02 and an N for each shell, so I don't think the number of free parameters is necessarily a big issue. In a follow-up message, Scott seemed (to me) to be more concerned about whether it was reasonable to "fix parameters for the first shell" when fitting a second or higher shells, not so much with the issue of what parameters were being refined. There weren't explicit details on what was fixed or what fitting ranges or parameters were used for the higher shells. Scott suggested (I believe) that "fixing the first shell" and fitting the second shell was not a good idea, and asked to hear differing views. I find the approach of "fit the first shell, then fix those parameters and fit the second shell" to be a reasonable way to start, so I responded. I would not call this approach "acceptable, but generally not preferred" -- I would say it has actual merit. Yes, it is often a good idea to check a fit to the whole spectrum toward the end of an analysis. But in a fit to the whole spectrum, the quality of the fit to the more subtle features (the finer structure) can often get lost in the fit to the more dominant features of the spectra. That is why we subtract mu0(E), after all. I don't see Fourier filtering as a bad idea for analyzing higher shells. But perhaps I am just not understanding what Scott and Shelly recommend??? --Matt _______________________________________________ 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] Fitting procedure
by Chappell, Mark A ERDC-EL-MS 18 Apr '09

18 Apr '09

They're on theur way back to Vicksburg. I yried to guide them from home but couldn't figure out where she was. By 230, she hung it up and turned back --------- Message sent via my BlackBerry Wireless Device ----- Original Message ----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Sat Apr 18 12:57:18 2009 Subject: Re: [Ifeffit] Fitting procedure Hi Adam, I am confused by this thread too! As you say, the original issue involved using S02 for individual shells of data on Cu foil. Of course, having separate S02 for each shell is not usually necessary to model Cu foil -- in fact I can't think of a case where it is needed. But since S02 is 100% with N, and ~95% correlated with sigma2, it is easy to have S02 vary per shell if one allows it to happen. Whether that's a good idea or not depends on how you interpret the results. Most people choose to fix a single S02 and vary N. Lots of people fit spectra with one S02 and an N for each shell, so I don't think the number of free parameters is necessarily a big issue. In a follow-up message, Scott seemed (to me) to be more concerned about whether it was reasonable to "fix parameters for the first shell" when fitting a second or higher shells, not so much with the issue of what parameters were being refined. There weren't explicit details on what was fixed or what fitting ranges or parameters were used for the higher shells. Scott suggested (I believe) that "fixing the first shell" and fitting the second shell was not a good idea, and asked to hear differing views. I find the approach of "fit the first shell, then fix those parameters and fit the second shell" to be a reasonable way to start, so I responded. I would not call this approach "acceptable, but generally not preferred" -- I would say it has actual merit. Yes, it is often a good idea to check a fit to the whole spectrum toward the end of an analysis. But in a fit to the whole spectrum, the quality of the fit to the more subtle features (the finer structure) can often get lost in the fit to the more dominant features of the spectra. That is why we subtract mu0(E), after all. I don't see Fourier filtering as a bad idea for analyzing higher shells. But perhaps I am just not understanding what Scott and Shelly recommend??? --Matt _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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