December 2023 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Ifeffit Digest, Vol 250, Issue 5
by Ryan Parmenter 18 Dec '23

18 Dec '23

Hi Matt, Thank you for your detailed response. Given my limited expertise in this area, I'm currently grappling with the intricacies of Python scripts, and I wouldn't typically enter the Larch buffer. I recognise that this is a current limitation on my part and am actively addressing it by attending Python workshops to enhance my understanding soon. When I input print(peakresult.result.fit_report()), the Larch command doesn't yield any values. Additionally, the box at the bottom of the GUI, where the command can be entered, transitions from'>Larch' to '...>' in red text. However, the fit statistic report can be exported/saved through the pre-edge results. Following this, the 'uvars' commands yield the area of the sum of the two Gaussians - thanks! :) Regarding your suggestion for improving the software's functionality, including a "peaks_area" parameter within the fit variables window may be valuable. I am currently comparing the areas among 15 datasets and having a 'peaks_area' parameter would facilitate the straightforward extraction and comparison of these values. Interestingly, another user expressed interest in this feature and reached out to me via email. I may have additional suggestions, but I will note them down during the next round of fits. Best regards, Ryan -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Friday, December 15, 2023 6:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 250, Issue 5 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: Larix Pre-edge Statistics (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Thu, 14 Dec 2023 20:29:38 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larix Pre-edge Statistics Message-ID: <CA+7ESboeUMm6iH9JmEfie9AuajYwDBvtYp8GrtLBSCegdkM=Fg(a)mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Hi Ryan, Yeah, this could be a little richer. For clarity, the "amplitude" Parameters will be the area of each peak. Well, it's the amplitude factor for the unit-normalized lineshape (Gaussian, Lorentzian, Voigt, etc), so it will be the area under that curve from -Inf to Inf. Those Infinities probably have small effects, here anyway ;). As you say, the centroid of multiple peaks is given, but not the total area under the sum of non-background peaks. That would not be too hard to add. But it might also fall into the category of "the sorts of calculations we should allow the user to do after a fit" without having to bake them all in. That is, if you open a Larch buffer after a pre-edge peak fit, you could get the most recent best-fit Parameters from lmfit with: pars = peakresult.result.params But also, you can get "uvars" as uvars = peakresult.result.uvars which is a dictionary of name:"ufloat" values for all Parameters (variables and "constrained values"). These "ufloat" values come from the `uncertainties` package and include uncertainties that know about the correlations between the Parameters. You can use these for simple calculations that will propagate the uncertainties (including correlations). As an example, if I do a pre-edge peak fit, with 2 Gaussian peaks (plus Line+Lorentzian for the background), I might get a good fit and a resulting report (from the larch buffer, do `print(peakresult.result.fit_report()`) that looks like this: [[Model]] (((Model(lorentzian, prefix='bpeak_') + Model(linear, prefix='bpoly_')) + Model(gaussian, prefix='gauss1_')) + Model(gaussian, prefix='gauss2_')) [[Fit Statistics]] # fitting method = leastsq # function evals = 355 # data points = 162 # variables = 11 chi-square = 4.5237e-04 reduced chi-square = 2.9958e-06 Akaike info crit = -2049.75462 Bayesian info crit = -2015.79106 R-squared = 0.99953048 [[Variables]] bpeak_amplitude: 1.82988250 +/- 0.04372160 (2.39%) (init = 2.462209) bpeak_center: 7118.44625 +/- 0.02812082 (0.00%) (init = 7120.091) bpeak_sigma: 1.36103880 +/- 0.01273292 (0.94%) (init = 2.121656) bpeak_fwhm: 2.72207761 +/- 0.02546583 (0.94%) == '2.0000000*bpeak_sigma' bpeak_height: 0.42795967 +/- 0.00701416 (1.64%) == '0.3183099*bpeak_amplitude/max(1e-15, bpeak_sigma)' bpoly_intercept: -6.37404087 +/- 0.65831626 (10.33%) (init = 2.467005) bpoly_slope: 8.9825e-04 +/- 9.2664e-05 (10.32%) (init = -0.000347) gauss1_amplitude: 0.10390560 +/- 0.00363058 (3.49%) (init = 0.14991) gauss1_center: 7111.52424 +/- 0.02714092 (0.00%) (init = 7112.452) gauss1_sigma: 0.75932812 +/- 0.02151410 (2.83%) (init = 1.315216) gauss1_fwhm: 1.78808103 +/- 0.05066183 (2.83%) == '2.3548200*gauss1_sigma' gauss1_height: 0.05459081 +/- 7.8147e-04 (1.43%) == '0.3989423*gass1_amplitude/max(1e-15, gauss1_sigma)' gauss2_amplitude: 0.03945700 +/- 0.00329914 (8.36%) (init = 0.116005) gauss2_center: 7113.18957 +/- 0.04258439 (0.00%) (init = 7113.403) gauss2_sigma: 0.57985874 +/- 0.03338641 (5.76%) (init = 0.556759) gauss2_fwhm: 1.36546297 +/- 0.07861898 (5.76%) == '2.3548200*gauss2_sigma' gauss2_height: 0.02714638 +/- 0.00110204 (4.06%) == '0.3989423*gauss2_amplitude/max(1e-15, gauss2_sigma)' fit_centroid: 7111.98258 +/- 0.01448240 (0.00%) == '(gauss1_amplitude*gauss1_center +gauss2_amplitude*gauss2_center )/(gauss1_amplitude+gauss2_amplitude)' [[Correlations]] (unreported correlations are < 0.100) C(bpoly_intercept, bpoly_slope) = -1.0000 C(bpeak_amplitude, bpeak_center) = +0.9722 C(gauss1_amplitude, gauss1_sigma) = +0.9186 .... C(gauss1_amplitude, gauss2_amplitude) = -0.7900 So there are 2 "gaussN_amplitude" Parameters for the area under each Gaussian, with a strong negative correlation. If you do >>> uvars = peakresult.result.uvars >>> print(uvars['gauss1_amplitude'], uvars['gauss2_amplitude']) >>> print(uvars['gauss1_amplitude'] + uvars['gauss2_amplitude']) You'll get the area of the sum of the two Gaussians as 0.104+/-0.004 0.0395+/-0.0033 0.1434+/-0.0023 That is, one might expect the uncertainties in 'gauss1_amplitude' and 'gauss2_amplitude' should add in quadrature, but that would overestimate the uncertainty in the sum by almost ~2x because the parameters are highly (and negatively) correlated. The uncertainty in the reported peak heights and the centroid of the two peaks also takes the correlations into account. Such calculations are not too hard to do from the Larch buffer or Python script, but we might think about how that could be exposed more flexibly. I can be persuaded to just add a Parameter "peaks_area" = the sum of the amplitudes, which would then have this value and uncertainty. Any suggestions for what should be exposed here? Cheers, --Matt On Thu, Dec 14, 2023 at 10:47?AM Ryan Parmenter <rap35(a)kent.ac.uk> wrote: > > Hello, > > > > I successfully fitted Gaussian curves to my pre-edge peaks using Larix (XAS Viewer), yielding the centroid energy for indicating Fe oxidation state. The expected trends are observed, however, in reviewing articles, I noticed they report the area and integrated intensities of Gaussian curves, often automated with Peakfit software. Can Larix generate these values in its statistical report? If not, how can I calculate the area and integrated intensity using Larix's provided values, considering the absence of standard deviation? > > > > Thanks, > > Ryan > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ------------------------------ Subject: Digest Footer _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ------------------------------ End of Ifeffit Digest, Vol 250, Issue 5 ***************************************

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Larix Pre-edge Statistics
by Ryan Parmenter 15 Dec '23

15 Dec '23

Hello, I successfully fitted Gaussian curves to my pre-edge peaks using Larix (XAS Viewer), yielding the centroid energy for indicating Fe oxidation state. The expected trends are observed, however, in reviewing articles, I noticed they report the area and integrated intensities of Gaussian curves, often automated with Peakfit software. Can Larix generate these values in its statistical report? If not, how can I calculate the area and integrated intensity using Larix's provided values, considering the absence of standard deviation? Thanks, Ryan

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by Vlog and Love birds 10 Dec '23

10 Dec '23

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Ref. XAS Data for Fe K-edge (Fe3C Iron Carbide)
by Esmael Balaghi 05 Dec '23

05 Dec '23

Dear All, Does anyone by chance have the Fe K-edge XAS data for Iron Carbide (Fe3C)? Best regards, Esmael

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O K-edge energy shift in feff8
by Otal Eugenio 05 Dec '23

05 Dec '23

Dear all, I am simulating O K-edge from LiNi0.5Mn1.5O4 with partial fluoride substitution. I am starting from a DFT simulated cif file with 30 different oxygen atoms, so I am simulating each Oxygen for a later average and comparing them with experimental results. I am using these flags: * O K edge energy = ##.## eV EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 * ixc [ Vr Vi ] EXCHANGE 0 * r_scf [ l_scf n_scf ca ] SCF 6.50 * kmax [ delta_k delta_e ] XANES 4.0 0.05 0.3 * r_fms l_fms FMS 6.50 0 * emin emax eimag LDOS -30 20 0.1 RPATH 0.1 *EXAFS 20 POTENTIALS * IPOT Z Tag 0 8 O 1 8 O 2 25 Mn 3 28 Ni 4 3 Li 5 9 F ATOMS * x y z ipot tag distance site_info 0.00000 0.00000 0.00000 0 O 0.00000 * O_25 (...) I just finished some simulations and I found the energy limits are shifted in xmu.dat for the different oxygen sites, just in absolute (omega) and relative (e) energy. As I want to see the relative intensities in the pre-edge, I am worried about normalizing the energy before averaging all the spectra. Is this ok? Is there a way to normalize the energies or am I making any mistakes? I m attaching a plot of three spectra. Best regards. (^ㅇᆽㅇ^)(=˃ᆺ˂=)(=🝦 ༝ 🝦=) Eugenio H. OTAL Assistant Professor Dept. of Materials Chemistry Shinshu University 4-17-1 Wakasato, Nagano 380-8553, JAPAN eugenio_otal(a)shinshu-u.ac.jp https://sites.google.com/view/zettsu-laboratory/news-updates ¯\_(ツ)_/¯¯\_(ツ)_/¯ Who is John Galt? ¯\_(ツ)_/¯¯\_(ツ)_/¯

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