RE: [Ifeffit] RESTRAINTS IN IFEFFIT

Hi Renato, See below for some comments:

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). [Kelly, Shelly D.]

The three-leg path length is given by half the total path length. Calculated as R = (distance_AB + distance_BC + distance_AC) * 0.5 You know the distance from A-B and the distance from B-C but the distance from A-C is dependent on the angle of the triangle path. You can write an equation to determine the angle A. a^2 = b^2 + c^2 -2bc cos(A) where a=distance_AC, b=distance_AB, c=distance_BC and A is the angle opposite of the AC side of the triangle. Then the four leg path has a path length defined as R = (2*distance_AB + 2*distance_BC)*0.5 The single path from A to B has the distance R = (2*distance_AB)*0.5 The single path from A to C has the distance R = (2*distance_AC)*0.5 Which also depends on the angle A and distance_AB as defined above. So for your case you have one unknown length and one unknown bond angle to describe these path lengths. i.e. distance_AB=distance_BC is unknown and angle A is unknown. HTH Shelly 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@millenia.cars.aps.anl.gov To: ifeffit@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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Today's Topics:

1. Re: Re: I should be able to find this somewhere... (Bruce Ravel)

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Message: 1 Date: Sun, 22 Jan 2006 16:58:07 -0600 From: Bruce Ravel Subject: Re: [Ifeffit] Re: I should be able to find this

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To: XAFS Analysis using Ifeffit Message-ID: <200601221658.07513.bravel@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

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Matthew reported.

B

On Tuesday 17 January 2006 16:09, Matt Newville wrote:

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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

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output array. But the shortened chi_fit(k) will have an impact on

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way Bruce is calculating the residual. Even if that were fixed,

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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

somewhere... that the the the there!) so

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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

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- Bruce Ravel ---------------------------------------------- bravel@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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