Bruce - thanks a lot for your post. I've encountered this bug a few times, but I thought it might be a problem with my machine; in any case I could never replicate the problem and file a bug report. I have another question to the list - how do I get rid of a spike at low k? See for instance http://www.msri.org/~levy/files/Cinnabar/cinnabar.prj If you open this file with Athena and plot in k-space, there is a big spike at low k; I haven't worried about this too much, but now that I'm starting to show other people my work, I'd like to get rid of it. Presumably my background subtraction is at fault, but how to fix it? The spike also messes the normalization. Thanks, Silvio
Hi Silvio, There are a number of ways to reduced the big spike at low k. Sometimes just tweaking E0, kmin, kmax, and k-weight are enough. My favorite approach is to use the model as a theory in the background subtraction procedure. I talk about how to do that in this presentation file that I posted on the XAFS.org page: http://www.xafs.org/Tutorials. The pdf file is called: Basics_of_XAFS_analysis.pdf. You will want to follow Example #1 Aligning data and theory. The screen shots are a bit outdated. Some of the parameters in Athena are now hidden under the "Show additional parameters" button. Good luck, Shelly --------------------------- Shelly Kelly Argonne National Laboratory Bldg 203, RM E113 9700 S. Cass Ave Argonne, IL 60439 Molecular Environmental Science Group www.mesg.anl.gov skelly@anl.gov phone: 630-252-7376
-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit- bounces@millenia.cars.aps.anl.gov] On Behalf Of Silvio Levy Sent: Wednesday, October 18, 2006 12:01 PM To: Ravel, Bruce D. Cc: XAFS Analysis using Ifeffit Subject: [Ifeffit] Athena bug and a question
Bruce - thanks a lot for your post. I've encountered this bug a few times, but I thought it might be a problem with my machine; in any case I could never replicate the problem and file a bug report.
I have another question to the list - how do I get rid of a spike at low k? See for instance http://www.msri.org/~levy/files/Cinnabar/cinnabar.prj
If you open this file with Athena and plot in k-space, there is a big spike at low k; I haven't worried about this too much, but now that I'm starting to show other people my work, I'd like to get rid of it. Presumably my background subtraction is at fault, but how to fix it? The spike also messes the normalization.
Thanks,
Silvio
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On Wednesday 18 October 2006 12:00, Silvio Levy wrote:
Bruce - thanks a lot for your post. I've encountered this bug a few times, but I thought it might be a problem with my machine; in any case I could never replicate the problem and file a bug report.
Silvio, The workaournd in the FAQ is not thoroughly tested, but I am pretty confident. If you still see the problem, let me know in personal email and I can give you a copy of the next version of Athena to try. As for the spike at low-k -- I dispute that the normalization is effected. The nromlaization is betwermined not using the background function but by regressing a line to post-edge region. That said, you most certainly have a spike at low k. I think the situation improves somewhat (without changing chi(R) significantly since the FT range starts at 2.5 in your project file) by making the lowr bound of the spline range 0 AA^-1 and making the k-weight for background removal equal to 2. And, of course, what Shelly said about using a standard is an excellent idea. B -- Bruce Ravel ---------------------------------------------- bravel@anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced 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/exafs/
participants (3)
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Bruce Ravel
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Kelly, Shelly D.
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Silvio Levy