[Ifeffit] RESTRAINTS IN IFEFFIT
Renato Canha Ambrosio
rcanha at ccet.ufrn.br
Tue Jan 24 08:43:30 CST 2006
Hi Folks, this is my first message on the list. Perhaps someone could help
me. The subject is how to include restraints on exafs refinement. There is
just scanty information about this on the ifeffit reference manual.
I'm trying to refine the exafs data of a rhombohedral perovskite.
The main MS contributions to the signal at about 3.5 A (non phase correct)
arise from M – O – M interactions being M the absorber . We have a
significant SS path, a two-legged and a three-legged path. The structural
parameters of these three terms are correlated since all refers to the same
A-B-C triangle and the A-B and B-C distances must be that found for
M-O1 nearest-neighbor configurations. For these reasons
we constrained the photo electron path length for three-legged to the
M-O nearest-neighbor distance:R(three-leg = 2*RM-O). I'm trying to
intoroduce the quantity defined as delta = R(three-legged)-R(two-legged)
and thus define the SS half path length as a function of delta R(SS) = R
(three-legged) - 2*delta. I think it is a restraint not a constraint.
So I defined (def) the delta function on the line above the command FEFFIT
also delr for the SS path. I introduced the restraint in the line FEFFIT as
restraint = delrSS). The fit produce the same results as obtainde without
the definition of delta and delrSS (function of delta).
So I need to know how to introduce this restraint in the fit in order to
calculate de M - O - M bond angle (this angle should be calculated using
simple geometric relationships) - perhaps introduce the bond angle as a
restraint.
Someone can say me where I introduce the definitions of restraint parameters?
Thank you very much for your kind attention
Renato Canha
Universidade Federal do Rio Grande doNorte
Departamento de Quimica
Natal - RN - BRAZIL
Open WebMail Project (http://openwebmail.org)
---------- Original Message -----------
From: ifeffit-request at millenia.cars.aps.anl.gov
To: ifeffit at millenia.cars.aps.anl.gov
Sent: Mon, 23 Jan 2006 12:00:13 -0600
Subject: Ifeffit Digest, Vol 35, Issue 14
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> 1. Re: Re: I should be able to find this somewhere... (Bruce Ravel)
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 22 Jan 2006 16:58:07 -0600
> From: Bruce Ravel <bravel at anl.gov>
> Subject: Re: [Ifeffit] Re: I should be able to find this somewhere...
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Message-ID: <200601221658.07513.bravel at anl.gov>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> In fact, Artemis and Athena both attempt to deal correctly with input
> chi(k) data that is not on the expected grid. Both codes perform a
> test to see if the data is on the standard grid and, if not,
> front-loads the data with zeros and uses Ifeffit's boxcar rebinning
> function to put the data on the expected grid.
>
> Alas, there was a bug in the rebinning macro used by A&A which caused
> it to fail in a particular situation met by the data in Matthew's
> example. This bug will be fixed in the next release.
>
> If you import mu(E) data into Athena and then import data from the
> Athena project file into Artemis, you will never see the problem that
> Matthew reported.
>
> B
>
> On Tuesday 17 January 2006 16:09, Matt Newville wrote:
> > Hi Matthew, Bruce,
> >
> > OK, I think it's a bug. Well, maybe it's just a consequence of a
> > "known but not well advertised" problem.
> >
> > The chi(k) data you have doesn't start at k=0. By itself, this should
> > be OK, and the fit seems to be mostly fine. There seems to be a bug
> > in Ifeffit that the output fit chi(k) has the same number of data
> > points as the input chi(k) data. In this case is incorrect -- it
> > should go to the last data point in k. From looking at the code, I'm
> > pretty sure this has no effect on the fit and is only an error in the
> > output array. But the shortened chi_fit(k) will have an impact on the
> > way Bruce is calculating the residual. Even if that were fixed, the
> > residual would still be wrong, as the residual in Artemis is
> > calculated as
> > set(data0_res.k = data0.k)
> > set(data0_res.chi = data0.chi - data0_fit.chi)
> >
> > and then Fourier transforming to R-space. Since the data and fit
> > aren't aligned in k-space, the residual is incorrect. It should be
> >
> > set(data0_res.chi = data0.chi - interp(data0_fit.k, data0_fit.chi,
> > data0.k))
> >
> > or some variation on that.
> >
> > Sorry for the trouble. It's definitely a result of narrow-mindedly
> > expecting that all chi(k) data comes from Ifeffit/Athena and will
> > always start at k=0. We should get this fixed (it's mostly there!) so
> > that data from other sources can be used. Right now, the easiest
> > work-around is to pre-pack the chi(k) data with zeros (starting from
> > k=0.00)
> >
> > --Matt
> >
> > _______________________________________________
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>
> --
> Bruce Ravel ---------------------------------------------- bravel at anl.gov
>
> Molecular Environmental Science Group, Building 203, Room E-165
> MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007
>
> Argonne National Laboratory phone and voice mail: (1) 630
> 252 5033 Argonne IL 60439, USA fax:
> (1) 630 252 9793
>
> My homepage: http://cars9.uchicago.edu/~ravel
> EXAFS software: http://cars9.uchicago.edu/~ravel/software/
>
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> End of Ifeffit Digest, Vol 35, Issue 14
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