[Ifeffit] Fitting using Experimental standard

[Frenkel, Anatoly]

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 at millenia.cars.aps.anl.gov <ifeffit-bounces at millenia.cars.aps.anl.gov> 
To: XAFS Analysis using Ifeffit <ifeffit at 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 at bnl.gov>  
	To: ifeffit at 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 at millenia.cars.aps.anl.gov <ifeffit-bounces at millenia.cars.aps.anl.gov>
	To: XAFS Analysis using Ifeffit <ifeffit at 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 at bnl.gov>
	To: "XAFS Analysis using Ifeffit" <ifeffit at 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 at 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)
	
	
	
	
	
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