didnt get any instruction thanks yael

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Today's Topics:

1. Re: weights data processing (Bruce Ravel) 2. Re: EXAFS question (Bruce Ravel)

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Message: 1 Date: Mon, 26 Jul 2004 09:06:13 -0400 From: Bruce Ravel Subject: Re: [Ifeffit] weights data processing To: XAFS Analysis using Ifeffit Message-ID: <200407260906.13553.ravel@phys.washington.edu> Content-Type: text/plain; charset="iso-8859-1"

I wanted to add a coupe more comments on Stafano's questions regarding k-weighting in Athena and Artemis.

Regarding k-weights in Athena: Athena's default for the k-weight using background removal is 1. I chose that pretty much for the reason that Scott gave. Ifeffit's default is 0, so this is a situation where Athena and Ifeffit have different default behavior. As for the insensitivity of your data to this value, I would say that it is situational. Sometimes, the k-weight can have a dramatic influence on the background removal. Stability of the background removal and its impact on subsequent analysis has been a frequent topic of discussion in this forum. k-weight, then, is yet another parameter that can impact the stability of your spline.

Rgearding k-weights in Artemis: Scott and Matt covered the "why" of k-weights. How k-weights are actually used by Artemis when fitting and plotting is a bit complicated. See section 5.8.4 of the (incomplete) artemis document for a detailed explanation of how k-weighting is used in Artemis. http://leonardo.phys.washington.edu/~ravel/software/exafs/doc/artemis.pdf

B

-- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642

NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973

My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Message: 2 Date: Mon, 26 Jul 2004 09:37:31 -0400 From: Bruce Ravel Subject: [Ifeffit] Re: EXAFS question To: "Norman White" Cc: XAFS Analysis using Ifeffit Message-ID: <200407260937.31266.ravel@phys.washington.edu> Content-Type: text/plain; charset="iso-8859-1"

Norman,

Your question is the sort of thing that is appropriate for the Ifeffit mailing list, so I am CCing my answer there. You should consider joining the mailing list. It is a great resource and gives you access to a large number of experts who can answer your questions.

On Friday 23 July 2004 03:38 pm, Norman White wrote: NW> In going through Matt Neville's xas_fun_slides.pdf file that was NW> included with the Athena software, I noticed on slide 36:

MN > The Fe-O distance in FeO is 2.14 � A, but the first peak is at 1.6 � A. MN > This shift in the first peak is due to the phase-shift, MN > delta(k): sin[2kR + delta(k)] . MN > A shift of -0.5 � A is typical.

NW> I asked him in an e-mail about the shift and he said (edited):

MN > For traditional XAFS analysis, we do a relatively simple Fourier MN > transform. This simple FT would give a peak in chi(r) at 'R' if MN > the oscillatory part was sin[2kR]. Since it's sin[2kR + delta(k)] MN > instead, there's a shift. MN > MN > It turns out that, to first order, delta(k) is linear and has a MN > negative slope of about 1: MN > delta(k) ~= -k ~= -2k (0.5), MN > MN > so that the shift in phase is about 0.5A.

NW> I asked if this was true for all elements and he said:

MN > It's a typical value for most bonds, but shouldn't be taken as an MN > accurate number (and it's easy enough to calculate).

NW> NW> How is an accurate shift calculated? Is this correction performed

This calculation is computed quite accurately by Feff. Indeed, getting that calculation (and the related calculation of the scattering amplitude) correct is the raison d'etre of Feff.

NW> automatically in Athena? If it is a constant, why is it not simply NW> included in the step producing the radial distribution function from NW> the k values? Can it be accurately calculated? The manual had NW> statements that seemed to imply that it could be calculated with the NW> Atoms program but did not explain how at a level I understood. NW> NW> Matt neville stated in an e-mail that: MN > The phase shift correction can be made fairly easy with MN > SixPack and with Artemis as well as Ifeffit.

It's not a constant and treating it as such would be specious at best, and it is not something that Athena intends to compute. However, since it is something that Feff computes, one can imagine using the results of Feff. How this is done is slightly different in Athena as in Artemis.

At the level of Athena, we know the absorbing atom but it is not actually necessary to know what the material is to use Athena effectively. In Artemis, on the other hand, we do have to know something about what the materials is. This difference between the two explains the rationale for how phase correction works i the two programs.

In Athena, only a central atom phase correction is supported. This is enabled by clicking the button that says "phase correction" in the forward trasform section of the mail window. With that button clicked, the central atom phase shift is subtracted from the data before the transform is made. When you plot chi(R), then, the transform will be peaked a little bit to the right of where it was peaked without that button clicked.

Artemis does a somewhat better job of this. In Artemis, you can select a path to use for pase correction. With a path selected, the central *and* scattering atom phase shifts will be subtracted before transforming. This is possible in Artemis because we have the fuill information about the material and the full feff calculation at our disposal. In Athena, in contrast, we only know about the absorber and I have never implemented (and don't really intend to do so) a way of reading in a feff path for the purpose of phase shifted transforms.

NW> NW> I could not find where it explained how to do this.

Did you read any of the documentation?

For Athena: http://leonardo.phys.washington.edu/~ravel/software/exafs/doc/Athena/athena_... isc.html The document is also available within Athena via the Help menu.

For Artemis: Section 5.8.5 of http://leonardo.phys.washington.edu/~ravel/software/exafs/doc/artemis.pdf

NW> I am looking at As adsorption on Fe-Al oxides and other minerals NW> I know what the central atom is As. NW> I can also estimate the oxygen bondlengths and the As-cation distance from NW> the "corrected" EXAFS pattern and the literature. Is it possible to NW> simulate an EXAFs pattern? NW> Is so, how?

Yes.

Have you read the Artemis manual?

B

-- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642

NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973

My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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End of Ifeffit Digest, Vol 17, Issue 23 ***************************************