Re: [Ifeffit] Calculating Ce oxidation state at the L3 edge
Thanks for the response Bruce On Tue, May 16, 2017 at 2:43 PM, Bruce Ravel <bra...@bnl.gov> wrote: > On 05/16/2017 01:31 PM, Stephanie Laga wrote: > >> >> I have a (hopefully) quick question about calculating oxidation state of >> CeO2 at the L3 edge. >> >> When calculating ox state by taking the ratio of peak areas, is the >> pre-edge feature for Ce included in this calculation? This point isn't >> clear to me from looking at various papers. >> >> I've attached an image from Bernardi 2015, which shows that the %Ce III >> calculation doesn't include the fitted pre-edge feature A. I'm not sure >> why this would not be included? Is this because we only consider 2p > 5d >> transitions and the pre-edge is 2p > 4f (forbidden) transition? >> >> > > I am not sufficiently knowledgeable about CeO2 specifically to answer your > question specifically. However, there are some general principles that > apply. > > The concept here is to come up with a set of peak shapes that describe the > shapes of the end member spectra. Those two sets of peaks, taken together, > represent the contribution to the spectra from each end member. Sum the > areas of each set of peaks, that represents the contribution. > > You then fit all of both sets of peaks to an unknown spectrum and sum up > each set. You now have enough information to quantify the amount of each > end member. > > So, in general, yes, you would include the fitted peak A because that is > part of your quantification metric. So, I disagree with the formula in the > figure you attached. But peak A is small, so neglecting it has scant > impact on the result. > > Some caveats: > > 1. You must be very careful about normalization. If you do not normalize > consistently, then you will introduce systematic error in the phase > quantification. > > 2. You must use the same step-like function for both end members and for > the unknowns. If the step function changes, then the areas under the peaks > will change, introducing systematic error. > > It would be interesting to compare this to linear combination analysis to > see if you get the same answers > > HTH, > B > > -- > Bruce Ravel bra...@bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 743, Room 114 > Upton NY, 11973 > > Homepage:http://bruceravel.github.io/home/ > Software:https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Peakfitting CeO2 data in Athena
Thank you Matthew and Matt for your responses. Sorry if these are silly questions...so then does that mean arctan and gaussian shouldn't be used together? What was meant by "it does not inherently include any understanding of what that peak is"? That these functions aren't representative of the processes occuring because the single electronic assumption doesn't hold anymore...ie there are many electron effects once we get in the EXAFS region? And if I am primarily looking at XANES, I don't need to be worried about the initial EXAFS region right? On Thu, Dec 8, 2016 at 10:48 AM, Matthew Marcus <mamar...@lbl.gov> wrote: > The usual justification for using gaussians for peaks, aside from "it > works" is that there's inhomogeneous broadening over and above the > lifetime. The usual justification for using an arctan for the step is > exactly the opposite. Instrument broadening is often taken to be > gaussian. Net result: A (pseudo)Voight for peaks often works. One > issue is what to do about the post-white-line peaks, which sometimes > are viewed as the first EXAFS wiggles. Manceau has a nice paper about > S XANES (I don't have the ref handy right now) in which he goes > through peak fitting and evaluates its uniqueness. >mam > > On Thu, Dec 8, 2016 at 5:40 AM, Matt Newville > <newvi...@cars.uchicago.edu> wrote: > > Hi Stephanie, > > > > > > > > On Wed, Dec 7, 2016 at 12:33 PM, Stephanie Laga <stephanie.l...@yale.edu > > > > wrote: > >> > >> Dear all, > >> > >> I am trying to extract the % Ce(III) from some CeO2 nanoparticle XAS > data. > >> I have been using moved the peak fitting function in Athena to model the > >> XANES with an arctan background function and a series of gaussians. > >> > >> Looking through the literature I haven't seen too many specifics to > using > >> this approach (rationale for choosing the widths of peaks or how to > define > >> the background function). Similarly, doesn't seem to be much rationale > for > >> choosing a 4 vs 5 peak fit for the XANES. > >> > >> My main question is then...1) Is there a rational for picking the > >> background function, specifically the height and width (can I let the > height > >> vary or should I be keeping a constant arctan through all samples)? > >> > >> Any advice is greatly appreciated! > >> > >> Stephanie > >> > > > > Matthew answered quickly, but sort of changed the subject, suggesting a > > different analysis (LSQ) and then discussing some of the pitfalls of that > > approach. Your original question is still worth discussing. > > > > There is not a whole lot of justification in using one particular shape > for > > the background. A step broadened as arctan, error function are common > and > > seem to work well. Each has some theoretical explanation in that the > > integral of a series of Lorentzian gives an arc-tangent function while > the > > integral of a series of Gaussians will give the error function. (If this > is > > wrong, can someone please correct?). If you think as the above edge > > spectrum as a series of finely spaced individual transitions, then these > > functions have some justification.Whether it actually works well in > > detail on a particular spectrum is a separate question. FWIW, I've also > > seen people use (successfully) a single, very broad Lorentzian for the > "main > > edge". > > > > The use of Lorentzians, Gaussians, Voigts, and PseudoVoigts is somewhat > more > > justified in that those are how you would expect a single electronic > > transition to appear, especially broadened in the way(s) you'd expect a > > monochromatic X-ray beam to be energy broadened. Using such functions is > > essentially asserting that there is a single electronic transition at > that > > energy, and you want to know it's size and shape. This is not wrong, > but it > > does not inherently include any understanding of what that peak is. For > > pre-edge peaks, it's pretty well-justified, and works pretty well. For > > peaks on or after the main edge or "white line", it's less justified > because > > we know that EXAFS-like effects can be important. > > > > The biggest dangers in the peak-fitting approach are: > >1) one always gets an answer, and that is rarely "no, this is not the > > right model to use". In fairness, most linear algebra methods used for > > XANES analysis or really most other spectroscopies have the same feature. > >2) interpretation
Re: [Ifeffit] Peakfitting CeO2 data in Athena
I had started with LSQ but switched to peak fitting because I was worried about the Ce(IV) reference. I have data for bulk CeO2 and Ce(OH)4, but doesn't this have some Ce(III) impurity in it? I'm not quite sure how to account for this when I do LSQ. Another challenge I've had is in using the Ce(IV) refs for our nanoparticles, which are about 2-5 nm in diameter. Is there a good Ce(IV) ref for nanos that are in this size range? On Wed, Dec 7, 2016 at 2:37 PM, Matthew Marcus <mamar...@lbl.gov> wrote: > Instead of doing a bunch of peak fitting, try LSQ. Use CeO2 (bulk or > nanos) for one reference and some Ce(III) for the other. Consistency > check: see that the Ce(III) fraction is consistent over some set of Ce(III) > references. > Ce(III) has an assymetric white line, so it doesn't really fit a single > gaussian. CeO2, unlike other Ce(IV), has a shoulder on the first peak, and > the first peak is shifted left a little with respect to other Ce(IV). > mam > > > On 12/7/2016 10:33 AM, Stephanie Laga wrote: > >> Dear all, >> >> I am trying to extract the % Ce(III) from some CeO2 nanoparticle XAS >> data. I have been using moved the peak fitting function in Athena to model >> the XANES with an arctan background function and a series of gaussians. >> >> Looking through the literature I haven't seen too many specifics to using >> this approach (rationale for choosing the widths of peaks or how to define >> the background function). Similarly, doesn't seem to be much rationale for >> choosing a 4 vs 5 peak fit for the XANES. >> >> My main question is then...1) Is there a rational for picking the >> background function, specifically the height and width (can I let the >> height vary or should I be keeping a constant arctan through all samples)? >> >> Any advice is greatly appreciated! >> >> Stephanie >> >> >> ___ >> Ifeffit mailing list >> Ifeffit@millenia.cars.aps.anl.gov >> https://urldefense.proofpoint.com/v2/url?u=http-3A__millenia >> .cars.aps.anl.gov_mailman_listinfo_ifeffit=CwICAg=-d >> g2m7zWuuDZ0MUcV7Sdqw=UZ6LahCCy9yRGAvO8QDSWFzQq7a3vkDZfWzr2 >> SslhiE=0g-Qe_mvavdjZMlwuLL_XAVOn-Hdw7MVoGFBObqHUUA= >> y4QQn_F6Rx9uwWVg4Z7oYxHOx_7ddARSk12pRgTuM3o= Unsubscribe: >> https://urldefense.proofpoint.com/v2/url?u=http-3A__millenia >> .cars.aps.anl.gov_mailman_options_ifeffit=CwICAg=-dg >> 2m7zWuuDZ0MUcV7Sdqw=UZ6LahCCy9yRGAvO8QDSWFzQq7a3vkDZfWzr2S >> slhiE=0g-Qe_mvavdjZMlwuLL_XAVOn-Hdw7MVoGFBObqHUUA=6Tqa >> DHnrgY2yWI_fJuteI2BzDNW0fmQlifUjGkrJdHY= >> > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > https://urldefense.proofpoint.com/v2/url?u=http-3A__millenia > .cars.aps.anl.gov_mailman_listinfo_ifeffit=CwICAg=-d > g2m7zWuuDZ0MUcV7Sdqw=UZ6LahCCy9yRGAvO8QDSWFzQq7a3vkDZfWzr2 > SslhiE=0g-Qe_mvavdjZMlwuLL_XAVOn-Hdw7MVoGFBObqHUUA= > y4QQn_F6Rx9uwWVg4Z7oYxHOx_7ddARSk12pRgTuM3o= Unsubscribe: > https://urldefense.proofpoint.com/v2/url?u=http-3A__millenia > .cars.aps.anl.gov_mailman_options_ifeffit=CwICAg=-dg > 2m7zWuuDZ0MUcV7Sdqw=UZ6LahCCy9yRGAvO8QDSWFzQq7a3vkDZfWzr2S > slhiE=0g-Qe_mvavdjZMlwuLL_XAVOn-Hdw7MVoGFBObqHUUA=6Tqa > DHnrgY2yWI_fJuteI2BzDNW0fmQlifUjGkrJdHY= ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
[Ifeffit] Peakfitting CeO2 data in Athena
Dear all, I am trying to extract the % Ce(III) from some CeO2 nanoparticle XAS data. I have been using moved the peak fitting function in Athena to model the XANES with an arctan background function and a series of gaussians. Looking through the literature I haven't seen too many specifics to using this approach (rationale for choosing the widths of peaks or how to define the background function). Similarly, doesn't seem to be much rationale for choosing a 4 vs 5 peak fit for the XANES. My main question is then...1) Is there a rational for picking the background function, specifically the height and width (can I let the height vary or should I be keeping a constant arctan through all samples)? Any advice is greatly appreciated! Stephanie ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
