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-boun...@millenia.cars.aps.anl.gov
<ifeffit-boun...@millenia.cars.aps.anl.gov>
To: XAFS Analysis using Ifeffit <ifeffit@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:fren...@bnl.gov>
To: ifeffit@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-boun...@millenia.cars.aps.anl.gov
<ifeffit-boun...@millenia.cars.aps.anl.gov>
To: XAFS Analysis using Ifeffit <ifeffit@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" <fren...@bnl.gov>
To: "XAFS Analysis using Ifeffit" <ifeffit@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-boun...@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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