January 2010 - Ifeffit - millenia.cars.aps.anl.gov

Fitting using Experimental standard
by abhijeet gaur 05 Jan '10

05 Jan '10

A very happy new year to all Generally the fitting is done using theoretical standards. For that in Artemis, we give input as crystallographic data. But If we want to use an experimental standard instead of theoretical standard, how that can be done. Is it possible to use experimental standard in Artemis? or we have to use some other method. with thanks Abhijeet Gaur School of Studies in Physics Vikram University, Ujjain (India)

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Re: [Ifeffit] Fitting using Experimental standard
by Frenkel, Anatoly 05 Jan '10

05 Jan '10

I doctored FEFF path. Not sure if Artemis offers anything better and less intrusive than this trick but I think it is still the only way to use experimental standards for fits (other than the ratio method that is implemented in athena as Bruce desribed, which is used for monoatomic shells only). A. ________________________________ 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: Mon Jan 04 22:54:30 2010 Subject: Re: [Ifeffit] Fitting using Experimental standard Ah, I see. I think Artemis has some way of putting in experimental phase and amp, but that may be just to make a "corrected" FT. Is that so? Otherwise, I suppose it should be possible to write a fake FEFF path file and read it in. I guess that's what you did. mam ----- Original Message ----- From: Frenkel, Anatoly <mailto:frenkel@bnl.gov> To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Monday, January 04, 2010 7:43 PM Subject: Re: [Ifeffit] Fitting using Experimental standard Thank you, Matthew. As they say in Russia, everything new is well forgotten old. Seriously, that paper was really how to use FEFFIT for both experimental and theoretical standards, not just theoretical. A. ----- 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: Mon Jan 04 22:34:56 2010 Subject: Re: [Ifeffit] Fitting using Experimental standard You're describing the way many of us, including me, used to analyze data before FEFF became as reliable and easy to use (courtesy of Artemis and the like) as it is now. As shown in the paper, you extract amplitude and phase from model compounds, by back-transforming filtered shells, then use those to fit data. Multiple data sets aren't new, either; I used to do that with data taken on dilute solid solutions at different temperatures. Another trick I used to use a lot was if I didn't have a standard for the right pair of atoms, I'd use FEFF to get the difference in scattering factors (phase+amp) between the pair I wanted and a nearby (in Z) pair I had data for. For instance, you can get CuAl2 as a compound and extract the phase+amp for Cu as the central atom and Al as the scatterer. You can't do that for Cu and Si because there's no Si-rich intermetallic in the CuSi system. Therefore, you can do: Amp(Cu->Si) = Amp_exp(Cu->Al)*Amp_Feff(Cu->Si)/Amp_Feff(Cu->Al) Phi(Cu->Si) = Phi_exp(Cu->Al)+Phi_Feff(Cu->Si)-Phi_Feff(Cu->Al) and get a "semi-empirical" Cu->Si "standard". Why the +- for phase and the */ for amp? You can think of it as extrapolating the log of a complex signal chi~(k) = Amp(k)*exp(i*Phi(k)), of which the measured chi is the Im(). This expresses everything in terms of relatively slowly-varying quantities and treats amp and phi as parts of the same quantity, which they really are. One of the programs available from the ALS beamline 10.3.2 website http://xraysweb.lbl.gov/uxas/Beamline/Software/Software.htm is called EXAFSfit and does this sort of fitting to amp and phase. You feed it amp and phases which come from the FT program, also available at the website. The amp and phase files are simple 2-column ASCII, thus readable anywhere. mam ----- Original Message ----- From: "Frenkel, Anatoly" <frenkel(a)bnl.gov> To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Monday, January 04, 2010 6:21 PM Subject: Re: [Ifeffit] Fitting using Experimental standard I know of one very obscure conference proceeding describing what you are looking for. It was written during pre-Artemis times but the method can be used with Artemis, of course. A. I. Frenkel, M. Vairavamurthy, and M. Newville, A study of the coordination environment in aqueous cadmium-thiol complexes by EXAFS spectroscopy: experimental vs. theoretical standards J. Synchrotron Rad., 8 , 669-771 (2001). The link to PDF is here: https://pubweb.bnl.gov/~frenkel/EXP-FEFF/thiols.pdf Anatoly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of abhijeet gaur Sent: Mon 1/4/2010 9:15 AM To: ifeffit Subject: [Ifeffit] Fitting using Experimental standard A very happy new year to all Generally the fitting is done using theoretical standards. For that in Artemis, we give input as crystallographic data. But If we want to use an experimental standard instead of theoretical standard, how that can be done. Is it possible to use experimental standard in Artemis? or we have to use some other method. with thanks Abhijeet Gaur School of Studies in Physics Vikram University, Ujjain (India) -------------------------------------------------------------------------------- > _______________________________________________ > 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] Fitting using Experimental standard
by Frenkel, Anatoly 05 Jan '10

05 Jan '10

Thank you, Matthew. As they say in Russia, everything new is well forgotten old. Seriously, that paper was really how to use FEFFIT for both experimental and theoretical standards, not just theoretical. A. ----- 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: Mon Jan 04 22:34:56 2010 Subject: Re: [Ifeffit] Fitting using Experimental standard You're describing the way many of us, including me, used to analyze data before FEFF became as reliable and easy to use (courtesy of Artemis and the like) as it is now. As shown in the paper, you extract amplitude and phase from model compounds, by back-transforming filtered shells, then use those to fit data. Multiple data sets aren't new, either; I used to do that with data taken on dilute solid solutions at different temperatures. Another trick I used to use a lot was if I didn't have a standard for the right pair of atoms, I'd use FEFF to get the difference in scattering factors (phase+amp) between the pair I wanted and a nearby (in Z) pair I had data for. For instance, you can get CuAl2 as a compound and extract the phase+amp for Cu as the central atom and Al as the scatterer. You can't do that for Cu and Si because there's no Si-rich intermetallic in the CuSi system. Therefore, you can do: Amp(Cu->Si) = Amp_exp(Cu->Al)*Amp_Feff(Cu->Si)/Amp_Feff(Cu->Al) Phi(Cu->Si) = Phi_exp(Cu->Al)+Phi_Feff(Cu->Si)-Phi_Feff(Cu->Al) and get a "semi-empirical" Cu->Si "standard". Why the +- for phase and the */ for amp? You can think of it as extrapolating the log of a complex signal chi~(k) = Amp(k)*exp(i*Phi(k)), of which the measured chi is the Im(). This expresses everything in terms of relatively slowly-varying quantities and treats amp and phi as parts of the same quantity, which they really are. One of the programs available from the ALS beamline 10.3.2 website http://xraysweb.lbl.gov/uxas/Beamline/Software/Software.htm is called EXAFSfit and does this sort of fitting to amp and phase. You feed it amp and phases which come from the FT program, also available at the website. The amp and phase files are simple 2-column ASCII, thus readable anywhere. mam ----- Original Message ----- From: "Frenkel, Anatoly" <frenkel(a)bnl.gov> To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Monday, January 04, 2010 6:21 PM Subject: Re: [Ifeffit] Fitting using Experimental standard I know of one very obscure conference proceeding describing what you are looking for. It was written during pre-Artemis times but the method can be used with Artemis, of course. A. I. Frenkel, M. Vairavamurthy, and M. Newville, A study of the coordination environment in aqueous cadmium-thiol complexes by EXAFS spectroscopy: experimental vs. theoretical standards J. Synchrotron Rad., 8 , 669-771 (2001). The link to PDF is here: https://pubweb.bnl.gov/~frenkel/EXP-FEFF/thiols.pdf Anatoly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of abhijeet gaur Sent: Mon 1/4/2010 9:15 AM To: ifeffit Subject: [Ifeffit] Fitting using Experimental standard A very happy new year to all Generally the fitting is done using theoretical standards. For that in Artemis, we give input as crystallographic data. But If we want to use an experimental standard instead of theoretical standard, how that can be done. Is it possible to use experimental standard in Artemis? or we have to use some other method. with thanks Abhijeet Gaur School of Studies in Physics Vikram University, Ujjain (India) -------------------------------------------------------------------------------- > _______________________________________________ > 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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Mackale's table
by Neetu parsai 01 Jan '10

01 Jan '10

Happy New year to all I am in need of Mackale's table for backscattering amplitude and phase shift that I want to calculate EXAFS function for some transition metals. with best wishes Mrs.Neetu Parsai Head Department of Engg.Physics Sanghvi Innovative Academy Indore. Residence: 130 Hemu colony, New G.D.C.Road, Indore-452015(M.P.) India.

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