[Ifeffit] Fitting using Experimental standard
Matthew Marcus
mamarcus at lbl.gov
Mon Jan 4 23:08:55 CST 2010
I wonder if some kind soul with some programming time to spare (ha ha) could write a program to do that. It would be relatively simple,
but does need the knowledge of how to write a FEFF path. It would ask questions like where the phase and amp files are, what k-power
was used, what the distance is, which path number to use, etc. then write out the ASCII path in the appropriate directory for Artemis.
A potential problem is what to do about the data range, since a normal FEFF path goes from k=0 to k=20 (from memory) and most data doesn't.
Also, there would be a problem if the reference-compound data didn't go as far as the data one is trying to fit because Artemis would have
no obvious way of knowing that the "FEFF path" is bogus beyond a certain k-range. I guess the program would have to ask for the data
file being fitted and issue a warning, or just let the user find out the hard way :-)
mam
On 1/4/2010 8:05 PM, Frenkel, Anatoly wrote:
> 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
> <mailto: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
> <mailto:ifeffit-bounces at millenia.cars.aps.anl.gov>
> <ifeffit-bounces at millenia.cars.aps.anl.gov
> <mailto: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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