Re: [Ifeffit] can sigma square ever be less than zero?
Hi Chris, On Mon, Jun 28, 2010 at 3:10 PM, Chris Patridge wrote: > Hello all, > > I am working on W L3 edge data. W is acting as a substitution dopant in > vanadium dioxide at rather low concentration. In a past mailing > conversation discussing Feff6 overestimation of E0 for heavier elements it > was mentioned that the E0 could be past the rising edge due to the white > line from W data. Well using this comment I aligned data using the theory > method well explained by Shelly Kelly SnO2 example. Literature suggests W > approximates WO2 cubic structure locally instead of the VO2 unit structure. > Then fitting the first oxygen coordination shell paths which are well > isolated from the other paths, it gives reasonable values for amplitude and > enot of 0.77 (0.17) and -1.14 (3.06) respectively. delr is -0.067 (0.028) > and then ss comes out to -0.00036 (0.00414). Can ss be negative if the > uncertainty brings it above 0? Well, this sigma^2 is not *very* negative, is it? By itself, that might be an OK place to start as an initial fit. But I would probably take the combined results of sigma^2 being approximately zero (never mind it being slightly negative) and delr being far from zero (-0.07 +/- 0.03) as a suggestion that the starting model is not really the story the data wants to tell you. My understanding is that tungsten oxides can be challenging to model. See Moscovici et al J Chem Phys 125, 124505 (2006), for a discussion of what can go wrong. That paper does focus on trivalent tungsten, but it might give useful pointers. --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] can sigma square ever be less than zero?
On Monday 28 June 2010 04:10:12 pm Chris Patridge wrote: > Hello all, > > I am working on W L3 edge data. W is acting as a substitution dopant in > vanadium dioxide at rather low concentration. In a past mailing > conversation discussing Feff6 overestimation of E0 for heavier elements > it was mentioned that the E0 could be past the rising edge due to the > white line from W data. Well using this comment I aligned data using > the theory method well explained by Shelly Kelly SnO2 example. > Literature suggests W approximates WO2 cubic structure locally instead > of the VO2 unit structure. Then fitting the first oxygen coordination > shell paths which are well isolated from the other paths, it gives > reasonable values for amplitude and enot of 0.77 (0.17) and -1.14 (3.06) > respectively. delr is -0.067 (0.028) and then ss comes out to -0.00036 > (0.00414). Can ss be negative if the uncertainty brings it above 0? In a numerical sense -- the sense in which the covarience matrix of the fit is evaluated -- there is no problem at all with a negative sigma squared. In that case, a negative value is what was required to find the best fit, in the numerical sense. Of course, this just emphasizes a point often repeated on this mailing list. A fit requires a human to make an interpretation. In a physical sense, sigma^2 cannot be negative. Just look at it -- it is the square of soemthing! sigma is a real-valued quantity, the square of a real number cannot be negative. So, how should we interpret a fit that gives a negative sigma^2? Well, you have to think about what sigma^2 is correlated with. It is certainly correlated with amplitude. If the amplitude is much too small for some reason (say, because you, for some reason, fixed N*S02 to some value that is too small), then the fit will have to make sigma^2 smaller to compensate. But the negative sigma^2 might also be telling you something about the amount of disroder in the strutucral model you used in your Feff calculation. You might use some crystallography as the starting point for the Feff calculation and that crystallography might result in a very disrodered shell. Well, if the local structure is much less disordered than that but you retain that amount of structural disorder by using all those slightly different paths, then the fit has to somehow compensate for the excess structural disorder in the fitting model. It may do so by making sigma^2 really small, even negative. So, in general a negative sigma^2 is probably trying to tell you something about the assumptions that went into your fit. A negative sigma^2 is unphysical, so a defensible interpretation of the fitting result cannot include a negative sigma^2. However, obtaining such a thing at some point during the analysis might be a useful hint about how to modify your fitting model. HTH, B -- Bruce Ravel bra...@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/~ravel/software/exafs/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] can sigma square ever be less than zero?
Hi Chris, Not to be picky, but I think we have to consider the semantics of what you're asking very carefully. "Can ss be negative," as in, can the physical quantity which is the variance in the absorber-scatterer distance be negative? No, since variances are the square of a real number. "Can ss be negative," as in, can ifeffit output a negative best-fit value for ss? Yes, as you've seen. "Can ss be negative," as in, can a fit with a negative best-fit value for ss be considered a valid fit? That's really what you're asking, I think, and the answer is that it could be, depending on what you are trying to claim. Since the uncertainty in your case is quite large, it's certainly possible that your fit is consistent with believable values. But it also means that your fit gives you very little idea of what ss should actually be. The twin facts that the uncertainty is large and that the best-fit value is very close to 0 make the fit less convincing. The simplest explanation in your case is that Ifeffit is finding a fit with an S02 and a ss that are both a bit low. Since they tend to correlate highly, that's not uncommon. Have you tried fitting using different k-weights, or, better yet, several k-weights simultaneously? At any rate, I'd say your fit is a promising preliminary fit. As far as a publication-quality fit, it would be nice to get the nearest- neighbor ss pinned down a bit better. --Scott Calvin Sarah Lawrence College On Jun 28, 2010, at 4:10 PM, Chris Patridge wrote: Hello all, I am working on W L3 edge data. W is acting as a substitution dopant in vanadium dioxide at rather low concentration. In a past mailing conversation discussing Feff6 overestimation of E0 for heavier elements it was mentioned that the E0 could be past the rising edge due to the white line from W data. Well using this comment I aligned data using the theory method well explained by Shelly Kelly SnO2 example. Literature suggests W approximates WO2 cubic structure locally instead of the VO2 unit structure. Then fitting the first oxygen coordination shell paths which are well isolated from the other paths, it gives reasonable values for amplitude and enot of 0.77 (0.17) and -1.14 (3.06) respectively. delr is -0.067 (0.028) and then ss comes out to -0.00036 (0.00414). Can ss be negative if the uncertainty brings it above 0? Thank you all, Chris Patridge PhD Candidate Department of Chemistry NSC 405 SUNY Buffalo 315-529-0501 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] can sigma square ever be less than zero?
Hello all, I am working on W L3 edge data. W is acting as a substitution dopant in vanadium dioxide at rather low concentration. In a past mailing conversation discussing Feff6 overestimation of E0 for heavier elements it was mentioned that the E0 could be past the rising edge due to the white line from W data. Well using this comment I aligned data using the theory method well explained by Shelly Kelly SnO2 example. Literature suggests W approximates WO2 cubic structure locally instead of the VO2 unit structure. Then fitting the first oxygen coordination shell paths which are well isolated from the other paths, it gives reasonable values for amplitude and enot of 0.77 (0.17) and -1.14 (3.06) respectively. delr is -0.067 (0.028) and then ss comes out to -0.00036 (0.00414). Can ss be negative if the uncertainty brings it above 0? Thank you all, Chris Patridge PhD Candidate Department of Chemistry NSC 405 SUNY Buffalo 315-529-0501 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Postdoctoral position open
Dear Members, I have an opening for a postdoctoral position in my research group and center starting in August of 2010. The position will be for two years with renewal option at the end of the first. Qualification for this position is a recent Ph.D in physics or chemistry in the field related to synchrotron spectroscopy. Most important would be to have good experience conducting in situ x-ray absorption studies including EXAFS data analysis. We will train the person on other more specific aspects of the spectroscopy as conducted by the research group. Proficiency in basic electrochemistry including classical methods are a must. Please apply with resume and one or two key publications to me personally as soon as possible. We promise a very vibrant research environment and opportunity to develop a portfolio for future career options such as academic positions. This includes training in proposal writing and teaching graduate level courses. In addition this position carries competitive salary and benefits. Sincerely Sanjeev Mukerjee (Professor) Department of Chemistry and Chemical Biology Director of the Northeastern University Center for Renewable Energy Technology (NUCRET) Northeastern University, 360 Huntington Avenue, Boston, MA 02115 Phone (617) 373 2382 Fax (617) 373 8949 URL: www.northeastern.edu/nucret www.northeastern.edu/leap ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
