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

Installation Problem
by William Diebel 05 Jan '10

05 Jan '10

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Problems with Ifeffit installation
by William Diebel 05 Jan '10

05 Jan '10

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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 04 Jan '10

04 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 04 Jan '10

04 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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installing IFeffit, etc on user accounts
by Elizabeth J. Biddinger 30 Dec '09

30 Dec '09

I recently installed the IFeffit package on a multi-user computer that uses Windows XP Pro. Athena and all of the other programs open and work fine on the administrator account but do not work on the user accounts. If I change one of the users to administrator it also works, but as soon as I change them back to user it again does not work. The Athena version we are using is 0.8.56 if that helps. Network security reasons require that our general users are on "user" not "administrator" logins. Any suggestions on how to get the programs to work in "user" mode? Thanks, Elizabeth Biddinger

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Silver oxide Standard
by Chris Patridge 21 Dec '09

21 Dec '09

hello everyone, I am asking if anyone might have any oxygen K near edge data for silver oxide standards? We forgot to collect the sample at our last beamline time. Thank you in advance, Chris Patridge

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Re: [Ifeffit] spline clamps in ifeffit code
by Bruce Ravel 15 Dec '09

15 Dec '09

On Monday 07 December 2009 05:37:41 am you wrote: > Hi Bruce, > > I have a question concerning the spline clamps in ifeffit. Is there > any possibility to set them directly in the spline() command? I tried > to do it with spline(..., clamp1=0, clamp2=24,...) but it did not work > and by default both spline clamps seem to be zero. Unfortunately I > found nothing about it in the reference guide either. So how can I > configure the clamps in the Ifeffit code? > > Thanks and kind regards, Hi Jan, I am CCing this to the Ifeffit mailing list, which is the better place to ask a question of this sort. I was out of town all of last week -- had you sent this to the mailing list rather than to me directly, you probably would already have received an answer. You seem to have the syntax correct. That is, if you follow along in Athena's Ifeffit buffer, you see that "spline(..., clamp1=0, clamp2=24,...)" is exactly what she does. Anything you see in the Ifeffit buffer should be directly transplantable to an Ifeffit script. Indeed, that is the very purpose of making the Ifeffit buffer available to the user. So, what do you mean that the clamps both seem to be zero? How do you know that? Can you show us an example data file and a short example ifeffit script that demonstrates the problem? It is quite possible that changing the clamp strength will have no significant impact of the background removal. To refresh my memory as I am writing this email, I loaded an iron foil spectrum into Athena. Indeed, changing clamp 2 has little impact on the background removal. But I know from experience that, in general, it does. Just to tell the whole story, I'll point out that the numeric values of the clamp strengths in Athena are configurable. If you go to Edit preferences, then open the clamp group, you will be able to assign new values to the 5 named clamp strengths. HTH, 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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Athena linux version problem
by Nelson Lobo 14 Dec '09

14 Dec '09

Dear Sir I have installed the latest version of Horae 070 in Ubuntu using synaptic package manager. The problem is that I don't see the 'OK' button in Athena 0.8.059 ( ifeffit1.2.11d), after I open a data file. scrolling to bottom of page, dragging the bottom of the page doesn't help either. Please let me know what should be done. My laptop resolution is 1280x800. Attached is a screen shot of the problem. Thanks Nelson

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