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Inquiry About Demeter's Capabilities in Simulating Spectra from Structures
by 徐微 17 Jan '24

17 Jan '24

Dear IFEFFIT Team, I hope this message finds you well. I am writing to inquire about the capabilities of the Demeter software suite, specifically regarding its ability to simulate spectra from given structural data. I am particularly interested in understanding whether Demeter can be used to generate X-ray absorption spectra based on detailed structural information. This functionality would be extremely valuable for my work. Could you please provide information on whether Demeter includes this feature? Additionally, if there are any relevant guidelines or documentation on how to use Demeter for this purpose, I would greatly appreciate if you could point me in the right direction. Thank you for your time and assistance. I look forward to your response. Best regards, XUwei

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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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Reviews of Modo Loan
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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Post-Doc at U Minnesota and ALS
by Matt Newville 30 Nov '23

30 Nov '23

Hi Folks, Brandy Toner at the University of Minnesota is looking to hire a post-doc to be stationed at the Advanced Light Source at Lawrence Berkeley National Lab for soft and tender X-ray science work for Earth and Environmental Science. For more information, see the attached PDF, and to apply for this position, visit https://hr.umn.edu/Jobs/Find-Job and access Job Opening ID 358786 --Matt Newville

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beamline scientist position at ALS
by Matt Newville 30 Nov '23

30 Nov '23

Hi Folks, Brandy Toner at the University of Minnesota is looking to hire a beamline scientist to be stationed at the Advanced Light Source at Lawrence Berkeley National Lab to support soft and tender X-ray science work for Earth and Environmental Science. For more information, see the attached PDF, and to apply for this position, visit https://hr.umn.edu/Jobs/Find-Job and access Job Opening ID 358826 --Matt Newville

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Matt Newville and my Friends
by foxseo2023 24 Nov '23

24 Nov '23

I hope this message finds you well and thriving in your endeavors. As a fellow Vietnamese student currently pursuing education in the United States, I can't help but feel a sense of pride and excitement about the prospect of inviting you to experience the beauty and charm of my homeland, Vietnam. Vietnam is a land of captivating landscapes, rich history, and warm hospitality. From the breathtaking Ha Long Bay with its emerald waters and limestone karsts to the vibrant city life of Ho Chi Minh City, our country offers a diverse range of experiences for every traveler. Picture yourself exploring the ancient town of Hoi An, with its lantern-lit streets and traditional architecture, or hiking through the terraced rice fields of Sapa, surrounded by lush greenery. Beyond the scenic landscapes, you will discover the heart and soul of Vietnam in its people. The kindness and friendliness of the Vietnamese people create an atmosphere of warmth that is truly unique. Whether you're savoring the delicious street food in Hanoi, engaging in conversations with locals, or witnessing the traditional water puppetry shows, you'll find yourself immersed in a culture that values community and connection. Vietnam is not just a destination; it's an experience that will leave a lasting impression on your heart. I extend this invitation to you with the hope that you'll consider making Vietnam your next travel destination. Come and discover the hidden gems, the delectable cuisine, and the genuine smiles that await you in the heart of Southeast Asia. I look forward to the day when I can share the beauty of my homeland with you in person. Until then, safe travels and may your curiosity lead you to the wonders of Vietnam. Best regardshttps://vking.vn/kien-truc/biet-thu-tan-co-dien/

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Health Sciences/Specialized Reference
by Mahiyan Molla 23 Nov '23

23 Nov '23

Hello, I was speaking with someone today who is curious about the possibility of more specialized reference assistance in the cooperative. Does anyone have any health sciences libraries participating in cooperative virtual reference? Do you feel there's sufficient support within the cooperative for a health sciences or hospital library to join? We're just trying to get a sense of what might be out there already or if this is something others have tried. All best, Mahiyan Mahiyan Molla Reference & Research Services Coordinator Research Peptides <https://researchpeptides.net/> 423 E 7th St <https://www.google.com/maps/place/423+E+7th+St,+Los+Angeles,+CA+90014,+USA/…> Los Angeles, CA 90014 <https://www.google.com/maps/place/423+E+7th+St,+Los+Angeles,+CA+90014,+USA/…>

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