- Ifeffit - millenia.cars.aps.anl.gov

Ab initio calculations
by Luanga Nchari 06 Apr '09

06 Apr '09

I would like to do ab initio calculations to get a theoretical XANES spectra. I have XYZ coordinates..... Could somebody remind me how I can run this on my PC. Cheers, Luanga

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Mixed Multiple scattering shell
by Joseph Washington 01 Apr '09

01 Apr '09

Hello all, I was wondering if anyone can send any useful hints or tips for parameterizing a mixed multiple scattering shell comprised of two NaCl type strucutres, like the AgBr(1-x)Cl(x) example. Has anyone worked on fitting the third shell in that example? I am looking for examples of nacl rocksalt-like FEFF calculations that have successfully parametrized multiple scattering path contributions. Right now, after running feff, I'm using a different delr / ss term for each multiple scattering path I include. Does anyone have any clever ways of representing these in terms of the delr/ss in the first shell? Also, FEFF is telling me that the amp and mixing terms are almost completely correlated and this cause the amp term to blow up. Thanks all, I really appreciate the assistance! Joseph

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Re: [Ifeffit] Ifeffit Digest, Vol 73, Issue 25
by Zuzaan, Damdinsuren 31 Mar '09

31 Mar '09

Hi Matt, >From the raw data I can recognize columns with dead time information. Also I am waiting reply from beamline scientists. Anyway, could you give me some detailed information how to do this dead time correction with Ifeffit commands or within Athena. Thank you in advance. Cheers, Damdin ------------------------------ Message: 2 Date: Mon, 30 Mar 2009 10:18:43 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 73, Issue 24 To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <b8522e3d0903300818w355650dfub735bf29165fc0a1(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Damdin, > I checked my spectra and found that I forgot to do the dead time correction (measurement were in fluorescence mode). > So I think the small S02 and N are due to deadtime effect. Yes, a slightly saturated detector can cause an S02 that is a little smaller than normal. > It is possible to do it in Athena? In general, athena doesn't have buttons or a page to do dead time corrections. This is because there isn't a single, consistent way to store the dead time information. You might want to consult with the beamline scientist for how to make these corrections. If you know what columns in your data file hold the dead time information (and what the columns are holding), it's possible to do this with Ifeffit commands (within athena, even). Cheers, --Matt Newville <newville at cars.uchicago.edu>

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New Method for Normalization?
by Barton, David (DG) 30 Mar '09

30 Mar '09

XANES Aficionados, I know most users on this list are hard-core EXAFS analysts, but some of us use XANES analysis to decipher mixed phases or use it to get structural clues when data quality isn't sufficient for EXAFS analysis. Anyway, I have a question for those interested in quantitative analysis of XANES or those that are willing to offer an opinion on methods to normalize raw spectra to get reliable, repeatable comparisons of near-edge features. Has anyone considered using the methods of Penner-Hahn to normalize their data to get reliable intensities of near-edge features? The reference to their method of normalization is below: J. Synchrotron Rad. (2005). 12, 506-510 [doi:10.1107/S0909049504034193] "A method for normalization of X-ray absorption spectra" T.-C. Weng, G. S. Waldo and J. E. Penner-Hahn It is my understanding the Ifeffit uses a linear function to remove the pre-edge and a quadratic for the post-edge and that the Athena's flatten is a subtraction of these functions. This is an excellent method under most scenarios since the background is usually fairly smooth and can be well approximated by a quadratic equation. Personally, I have had only a few rare cases where the quadratic function on the post-edge was not sufficient to reliably normalize the data and in those cases a third-order polynomial was sufficient. Does anyone else have an opinion on using alternative normalization routines? Dave _________________________________ David Barton The Dow Chemical Company

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Re: [Ifeffit] Ifeffit Digest, Vol 73, Issue 24
by Zuzaan, Damdinsuren 30 Mar '09

30 Mar '09

Hello everyone, Shelly, Matt, Scott many thanks for your reply. I checked my spectra and found that I forgot to do the dead time correction (measurement were in fluorescence mode). So I think the small S02 and N are due to deadtime effect. It is possible to do it in Athena? Damdin -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Saturday, March 28, 2009 6:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 73, Issue 24 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: About S02 (Matt Newville) 2. Re: About S02 (Scott Calvin) ---------------------------------------------------------------------- Message: 1 Date: Fri, 27 Mar 2009 16:28:46 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> Subject: Re: [Ifeffit] About S02 To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <b8522e3d0903271428i7c6ea611l325443292de87b45(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Damdin, An XAFS book or theory that says "S02 must be between 0.8 and 1" overstates the case. In simplest terms, S02 is a fudge factor. There is a theoretical basis for it (passive electron overlap), but much of this can also be folded into other "loss terms" that are due to inelastic scattering events for the photo-electron. These should be part of the EXAFS calculation from, say, Feff, but are hard to do well to high precision. When using Feff, Ifeffit, Artemis, it does turn out that, in most cases, the calculated amplitudes tend to overestimate the experimental amplitudes, and that applying a constant S02 between 0.8 and 1.0 works reasonably well. That is hardly a "must be" between 0.8 and 1. In addition to the theoretical issues of Feff not-quite-correctly calculating S02, there are experimental factors that affect the XAFS amplitude: the estimate of the edge step being the most important, but also the energy resolution of the incident x-rays and sample-dependent issues such as pinholes, and for fluorescence measurements detector deadtime and self-absorption. There is an understandable desire to turn these observation into a rule-of-thumb and then into some sort of rule that can be pointed to as if to say "this analysis is wrong" or "this analysis is correct". As is normal for such rules-of-thumb, it is sometimes broken. Of course the main trouble with the uncertainty of which S02 to use is that for a single-shell analysis, one cannot distinguish S02 from the coordination number. That is, the EXAFS amplitude for S02=1, N=4 is the same as for S02=0.8, N=5, and for S02=0.67, N=6. Distinguishing these cases is hard (don't let anyone tell you they aren't or that there is a button in Artemis that fixes this problem). If you need to distinguish N=5 from N=6, you better be pretty confident that your data and analysis have a good value for S02. The classic approach to this is to measure a data on a "standard" is free from amplitude-reducing artifacts and for which the coordination number is well-defined as easy to extract from the data, measure this at the same beamline conditions (energy resolution, harmonic content) as your unknown sample, and then work to be highly consistent in setting the edge step. The S02 applied to the standard to get the correct coordination number is then applied to the unknown data to get its coordination number. There are many ways for such an analysis to fall short of perfect, but it is generally the best we can do. --Matt On Fri, Mar 27, 2009 at 8:19 AM, Zuzaan, Damdinsuren <zuzaan(a)uni-mainz.de> wrote: > Hello everyone, > > I am graduate student and doing EXAFS in my research. > > My question is about S02. From the XAFS books or theory it says that > this value must be between 0.8 to 1, but in the literature some people > used different values like 0.25 or 1.4. In my case I fitted > experimental RDF of my standard sample by holding the known r and n > values for each path, while varying E0, S02 and sigma2. Obtained E0 > and S02 values were holded for unknown sample and rest were floated > freely. S02 were 0.64. So my question is that this relatively small > S02 value could affect the mineralogical interpretations made in my > study. Should I refit it using high value? Thanks in advance > > Regards, > > Damdin > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > ------------------------------ Message: 2 Date: Fri, 27 Mar 2009 19:23:29 -0400 From: Scott Calvin <SCalvin(a)slc.edu> Subject: Re: [Ifeffit] About S02 To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <E7658A83-0512-4A17-ACC0-1CC7A2A7F831(a)slc.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Hi Damdin, Matt and Shelly have answered this very well, but I have one more thought to add. You have a mineralogical sample and apparently have a pretty good idea what the mineral is, since you're not varying r or n. Under those circumstances, you probably have a hypothesis as to the structure beyond the nearest-neighbor. If you include more than one path in your fit, the inability to distinguish coordination number from S02 is reduced, and more importantly for your purposes, the correlation between S02 and sigma2 is also reduced. If it stays the same when you add more paths, it can help increase your confidence that the low S02 in your fit is appropriate. --Scott Calvin Sarah Lawrence College On Mar 27, 2009, at 9:19 AM, Zuzaan, Damdinsuren wrote: > Hello everyone, > > I am graduate student and doing EXAFS in my research. > > My question is about S02. From the XAFS books or theory it says that > this value must be between 0.8 to 1, but in the literature some people > used different values like 0.25 or 1.4. In my case I fitted > experimental RDF of my standard sample by holding the known r and n > values for each path, while varying E0, S02 and sigma2. Obtained E0 > and S02 values were holded for unknown sample and rest were floated > freely. S02 were 0.64. So my question is that this relatively small > S02 value could affect the mineralogical interpretations made in my > study. Should I refit it using high value? Thanks in advance > > Regards, > > Damdin ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 73, Issue 24 ***************************************

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About S02
by Zuzaan, Damdinsuren 27 Mar '09

27 Mar '09

Hello everyone, I am graduate student and doing EXAFS in my research. My question is about S02. From the XAFS books or theory it says that this value must be between 0.8 to 1, but in the literature some people used different values like 0.25 or 1.4. In my case I fitted experimental RDF of my standard sample by holding the known r and n values for each path, while varying E0, S02 and sigma2. Obtained E0 and S02 values were holded for unknown sample and rest were floated freely. S02 were 0.64. So my question is that this relatively small S02 value could affect the mineralogical interpretations made in my study. Should I refit it using high value? Thanks in advance Regards, Damdin

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Accepting applications for 2009 APS XAFS School, July 6-10, 2009
by Julie Olmsted Cross 23 Mar '09

23 Mar '09

FYI: The application form for the 2009 APS XAFS School is now live at: http://xafs.org/Workshops/APS2009 ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~ Dr. Julie O. Cross User Technical Interface APS Engineering Support Division Argonne National Laboratory 9700 South Cass Ave., Bldg. 401/B4204 Argonne IL 60439 tel: 630 252 0592 fax: 630 252 7187 ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~

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Lattice distortion
by Eugenio Otal 23 Mar '09

23 Mar '09

Hi, I am trying to simulate the XANES spectra of erbium in a interstitial site of ZnO, now I am looking for the changes if the erbium atom is not in the center of the site. I done some simulations but I don´t get any change in the spectra with the distortion of the site. Is this possible? I attach the figure of the simulations and the inp files. Thanks, euG --

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Lattice distortion
by Eugenio Otal 19 Mar '09

19 Mar '09

Hi, I am trying to simulate the XANES spectra of erbium in a interstitial site of ZnO, now I am looking for the changes if the erbium atom is not in the center of the site. I done some simulations but I don´t get any change in the spectra with the distortion of the site. Is this possible? I attach the figure of the simulations and the inp files. Thanks, euG

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Athena data
by abhijeet gaur 18 Mar '09

18 Mar '09

Hi Price, Now I got my data imported into Origin. Thanks with regards Abhijeet Gaur Vikram University Ujjain M.P. ( India )

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