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

Writing a paper
by mattie.peck＠huskers.unl.edu 07 May '12

07 May '12

Hello Everyone, I am in the process of fitting XAFS data for a paper and I was wondering what type of information should should be included. I remember coming across a website that had this information on it awhile ago but I can't seem to find my way back. We would like to publish a qualitative XANES paper and an EXAFS paper. Any suggestions on the type of information (plots, tables, R-factor, etc.) that should be included in each paper separately would be appreciated. Thanks, Matthea Peck

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third cumulant
by JeongEunSuk 07 May '12

07 May '12

Hello I measured temperature-dependent EXAFS at Pt L3 edge with Pt nanoparticles in room and high temperature(400 C). I have some questions about thermal vibration in EXAFS fit. I read that third and fourth culmulants related with phase and amplitude in anharmonic term, respectively. especially, I concerned third culmulant to relate with phase. As you know, the phase also relates with bonding length. So that, the bonding length between Pt-Pt pair considerably correlated with third culmulant. So I can't decide exact bonding length and third culmulant because their correlation. I think that the relation of both bonding length and third culmulant is similar to that of number and debye-waller factor. Is it right to find bonding length and third culmulant like finding number and debye-waller factor using k-weight?

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Re: [Ifeffit] (no subject)
by Anatoly I Frenkel 07 May '12

07 May '12

It sounds like a good idea but you will still need to know whether the best fit results for the bond length and third cumulant are correct. Since they are expected to vary widely for different cluster sizes and different substrates and different atmospheres, you should first try to see if your method will work for a more simple system where you know what the bond length and third cumulant should be, i.e. bulk Pt. Besides, you may find something similar to what you are proposing in Bus and v.Bokhoven's article. Anatoly Sent from my mobile phone, please forgive typos -----Original message----- From: JeongEunSuk <eunsuk1986(a)hotmail.com> To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Mon, May 7, 2012 04:02:06 GMT+00:00 Subject: [Ifeffit] (no subject) Hello I measured temperature-dependent EXAFS at Pt L3 edge with Pt nanoparticles in room and high temperature(400 C). I have some questions about thermal vibration in EXAFS fit. I read that third and fourth culmulants related with phase and amplitude in anharmonic term, respectively. especially, I concerned third culmulant to relate with phase. As you know, the phase also relates with bonding length. So that, the bonding length between Pt-Pt pair considerably correlated with third culmulant. So I can't decide exact bonding length and third culmulant because their correlation. I think that the relation of both bonding length and third culmulant is similar to that of number and debye-waller factor. Is it right to find bonding length and third culmulant like finding number and debye-waller factor using k-weight?

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(no subject)
by JeongEunSuk 06 May '12

06 May '12

Hello I measured temperature-dependent EXAFS at Pt L3 edge with Pt nanoparticles in room and high temperature(400 C). I have some questions about thermal vibration in EXAFS fit. I read that third and fourth culmulants related with phase and amplitude in anharmonic term, respectively. especially, I concerned third culmulant to relate with phase. As you know, the phase also relates with bonding length. So that, the bonding length between Pt-Pt pair considerably correlated with third culmulant. So I can't decide exact bonding length and third culmulant because their correlation. I think that the relation of both bonding length and third culmulant is similar to that of number and debye-waller factor. Is it right to find bonding length and third culmulant like finding number and debye-waller factor using k-weight?

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How to use ATOM on this file?
by Wei Li 06 May '12

06 May '12

Hello, Bruce, I have a *.cif, in which structure contains Zn and Al in the same site but diferent ratio. I cannot use ATOM to build a cluster for Feff. I am wonder if you could figure this out. Thanks in advance! best wishes yours Wei Li -- Wei Li Postdoc researcher Environmental Soil Chemistry Group Delaware Environmental Institute University of Delaware, Newark,19713 Tel:631-949-0663 http://ag.udel.edu/soilchem/li.html <http://ag.udel.edu/soilchem/>

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mailing list spam
by Bruce Ravel 04 May '12

04 May '12

Hi everyone, As you saw, a bit of unwanted email slipped through the various layers of spam filtration that protect the Ifeffit mailing list. It is a bit of a mystery how this one got through. Most messages from companies with spam-generation business models do, in fact, get discarded. Happily, this sort of thing has been a relatively rare event. Matt has done an amazing job over the years of keeping the signal to noise ratio very high on the this mailing list. Hopefully that bit of noise won't be repeated. Regards, Bruce -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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Invitation to connect on LinkedIn
by Jun LIN via LinkedIn 04 May '12

04 May '12

LinkedIn ------------ Jun LIN requested to add you as a connection on LinkedIn: ------------------------------------------ Ifeffit, I'd like to add you to my professional network on LinkedIn. - Jun Accept invitation from Jun LIN http://www.linkedin.com/e/o6ijfu-h1t9l58n-2b/qduvo2QRI4F0un7ciuz8AHbr3EkWav… View invitation from Jun LIN http://www.linkedin.com/e/o6ijfu-h1t9l58n-2b/qduvo2QRI4F0un7ciuz8AHbr3EkWav… ------------------------------------------ Why might connecting with Jun LIN be a good idea? Jun LIN's connections could be useful to you: After accepting Jun LIN's invitation, check Jun LIN's connections to see who else you may know and who you might want an introduction to. Building these connections can create opportunities in the future. -- (c) 2012, LinkedIn Corporation

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related to previous mail
by John Farell 26 Apr '12

26 Apr '12

Hi, Related to previous mail that I sent, my question is which one I have to chose i.e., "guess" option or "set" option. Or is there any mistake I did?, Procedure that I have followed was not right ?. Suggest me....

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APS / IIT XAFS Summer School
by Matt Newville 26 Apr '12

26 Apr '12

Hi Folks, Several people have asked, so I'd like to announce here that there will be an XAFS Summer School in Chicago this summer, July 9 - 13, on the IIT Campus and at APS. Grant Bunker is organizing, and more details are at http://xafs.org/Workshops/IIT2012 Cheers, --Matt

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Fwd: P-EXAFS fitting results and multiple scattering
by Bruce Ravel 24 Apr '12

24 Apr '12

Hi Dalton, I am CCing this to you and to the ifeffit mailing list, which is, of course, the appropriate venue for asking questions about the software and about XAS fitting in general. Please use the mailing list in the future. First off, kudos for measuring EXAFS data of this quality on a phosphorous surface complex. That is a non-trivial measurement. All of your problems (O MS paths, uncertainties, fit quality) are all inter-related and, I think, could be addressed, at least in part, by considering a somewhat more sophisticated approach to the data analysis problem. For those who haven't opened up Dalton's project file, you'll find that Dalton has used Artemis' "quick first shell theory" tool to generate a Feff path for the phosphorous-oxygen path. He then rather abused that tool to try to get it to make MS paths involving the P and O atoms. I am not a big fan of trying to overuse the QFS tool beyond the intention implicit in its name. If you need to model an unknown species, you are much better off trying to find a more elaborate starting model. That is a topic that Shelly wrote about extensively in her papers from her days as a uranium biogeochemist. Her concept is that, while you don't necessarily know quite what your sample looks like, you can make some informed guesses. Her strategy, then, is to pick a crystal structure that resembles what you expect to find in the real sample and run Feff on that. Then parameterize those paths from the Feff calculation that you think represent your real structure. Here is one example of this http://dx.doi.org/10.1016/S0016-7037(02)00947-X In that paper, she models, for example, a uranyl-phosphoryl bond using some kind of uranyl phosphate mineral. She doesn't use every path from the mineral -- just the ones that describe the monodentate U-O-P ligand and its associated SS and MS paths. One big advantage of this approach is that you will have well formed potentials for all of your scatterers. Abusing the quick first shell tool from Artemis pretty pretty much guarantees that you will have a poorly formed potential surface. That is certainly true for the 5-atom cluster you ended up with in your Feff calculation. I also think that you need to examine your data rather more critically. Although your data are impressively good for phosphorous EXAFS, they are still pretty noisy data. Plot your chi(R) out to 10 Angstroms. Do you see how big the peaks are between 6 and 10 Ang? That indicates the level of noise in your data. The peaks between 1.5 and 3.5 Ang are not much bigger than the level of the noise. Regardless of how well you pick your starting model in Feff, there will be a limit to how much you can say about these data beyond the first coordination shell. I am not really clear quite what you did to fit your data. What you sent to me had all the parameters either set or skipped. Given that it is not clear how much signal between 1.5 and 3.5 is above the level of the noise, it is almost certainly not reasonable to think that you have anywhere near the 14 independent points your k- and R-range settings would suggest. You say that your colleagues tend to get smaller uncertainties than you are seeing. I imagine that is because their data are considerably less noisy that these P edge data. That might not be what you were hoping to hear. But data are what data are. Yours are of limited quality and there will be severe limits on how much information you will be able to extract from them. B ---------- Forwarded Message ---------- Subject: P-EXAFS fitting results and multiple scattering Date: Sunday, April 22, 2012, 05:08:14 pm From: "daltonabdala(a)gmail.com" <daltonabdala(a)gmail.com> To: bravel(a)bnl.gov Dear Bruce, I'm a Ph D student in Dr. Sparks group and currently doing my research work on P-EXAFS. I'm particularly interested in examining the surface load, pH and time effects on the formation of P surface complexes at the goethite/water interface. My EXAFS experiments have been carried out at the X15B beamline at BNL. I've employed Athena and Artemis to do data analysis and fitting. I've come across some issues that I would like to share with you and, perhaps, you could give me some advices or come up with a different procedure that I could use in order to fix some of the issues that have raised me some skepticism about my fitting results and hampered me drawing conclusions. First, I couldn't find a way to get a better fit for Oxygen multiple scattering. Second, the uncertainties found for all fitting parameters are way too high if I am to compare uncertainties for other systems that my co-workers are used to deal with. I'm attaching an Artemis project file so you can take a look at it. Thank you very much, - Dalton -- Dalton Belchior Abdala Ph D. Candidate Environmental Soil Chemistry University of Delaware 152 Townsend Hall, 19716 Newark, DE "Not everything that counts can be counted, and not everything that can be counted counts." Albert Einstein ----------------------------------------- -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter

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