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

Using larch for feff Fitting -> simple 4 parameter fit
by Mangold, Stefan (IPS) 18 Aug '22

18 Aug '22

Dear all, I try to use larch for Feff Fitting. For a first start, I liked the option of Artemis with the „simple 4 parameter fit“. Larch produces for every path an independent dear and sigma2. Is there a simple way to make this simple 4 parameter fit also in larch? best regards Stefan Mangold

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XAFS short course at BNL: November 2-4
by Anatoly Frenkel 09 Aug '22

09 Aug '22

Dear subscribers: Please spread the word to those who may be interested in our next annual short course at BNL on X-ray absorption fine structure. The dates are: November 2-4. It will be virtual. The level will be intermediate to advance (last year it was a beginner level). As in the past, lectures, discussions and software demonstration sessions will be on Wednesday and Thursday, and the full day data analysis practicum will be on Friday. More information about the course and the link to the application form will appear soon on BNL web site, and on the web site of the Synchrotron Catalysis Consortium (SCC). Regards, Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 Joint Appointment: Senior Chemist Chemistry Division, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/staff/frenkel -------------------------------------------------------------------

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Standardized Spectra
by Kyle Draim 08 Aug '22

08 Aug '22

Hello! I don't have any X-Ray data to analyze in your app, I'm just seeking a visual display of each element's standardized/accepted X-Ray spectra (instead of a table of numbers). So far, I've downloaded the application, but I'm stuck on how to find this information. I would greatly appreciate it if you would be willing to provide the necessary steps to accessing this information or if you would be willing to direct me to the right source for that info. Thanks, Kyle

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xraylarch
by Paul Fons 06 Aug '22

06 Aug '22

Hi. Due to the difficulties of getting demeter to work on the Apple M1 machines, I have started to use xraylarch and so far I like the interface as well as the possibility of scripting later on. I had a couple of observations and a question regarding xraylarch usage that I hope could be addressed here. First, one can load multiple spectra into the (feff) fitting window. It seems, however, that which paths are selected are universal (the selected paths are used for all exafs spectra). Does this mean that multiple edge fitting is not possible. If multiple edge fitting is possible, how is it done? In the fitting window, one can have several spectra loaded and one can select all or some of the spectra to be fit. The interface seems like it was designed for multiple edge fitting, but is it? Second, it is strange that whenever a parameter is changed that the fitting variable settings (fixed, vary, constrain) are reset. For complex fits, this generates a lot of unnecessary clicking (and the corresponding mistake possibilities) Third, when one reads in several different feff calculations, one would, in principle, like to have a different value of e0 (the origin of energy offset) for each feff calculation. By default when a feff calculation is read in the variable e0 is defined. When one defines alternative energy offset variables for the different feff calculations and deletes the original e0 value, something strange happens. Accessing the “Edit Parameters” window results in e0 reappearing (even though it has been manually deleted previously). Is this a feature? The same thing may happen for other “automatic” variables as well. Four. This is really a feature request. When a variable is unused (lets say some additional paths are introduced in the fitting process and a new fit without them is attempted), the choices in the parameter list are (fix, vary, and constrain). There is no option to “skip” like in Artemis. Obviously, one can choose fix, but in doing so the unused variable shows up in the fit result summary and is somewhat confusing. It would be subjectively better to have the option to “skip” a variable and not have it show up in the fit summary. Just some initial thoughts...

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VC and V(CO)6 data to share
by Ismael Graff 06 Aug '22

06 Aug '22

Dear XAFS enthusiasts, would anyone have XAFS data of crystalline vanadium carbide (VC) and vanadium hexacarbonyl (V(CO)6) to share? In the case of V(CO)6 I´m having great trouble of finding any published measurement! I found papers for Cr(CO)6, but not V(CO)6. Bibliographical references are also welcome. All the best, Ismael. -- ************************************ * Ismael Graff * * * * Universidade Federal do Paraná * * Departamento de Física, CP 19044 * * 81531-980, Curitiba, Brazil. * * Tel (office): +55 41 3361 3093 * * Tel (Lab): +55 41 3361 3427 * * Fax: +55 41 3361 3418 * * http://fisica.ufpr.br/graff * * * * "DOCENDO DISCIMUS" * ************************************

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Re: [Ifeffit] Exafs spectra Fitting of WO3 nanoparticles (Abdallah Nassereddine)
by Mosselmans, Fred (DLSLtd,RAL,SCI) 04 Aug '22

04 Aug '22

Dear Abdallah, It is often quite reasonable to fix two paths debye waller factors to be the same if they are the same atom at similar distances. However there is a slight problem with what you are trying to do. Because EXAFS is a sum of sine waves the minimum distance it can resolve between two paths of the same atom type is Pi/2*Kmax where kmax is the maximum k value in your data. Hence if you are trying to fit separate paths of the same atom type 0.06 A apart you need data out to about 26 k. I think and no one has ever told me this is completely Ok the only way to get two distances from such an analysis is to assert that the difference between the path is a fixed value and thus refine the two paths with the same delta R (and probably the same debye wller factor) this in my experience works in some cases Best regards Fred Mosselmans -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 03 August 2022 18:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 234, Issue 2 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. Exafs spectra Fitting of WO3 nanoparticles (Abdallah Nassereddine) ---------------------------------------------------------------------- Message: 1 Date: Wed, 03 Aug 2022 14:40:44 +0200 From: Abdallah Nassereddine <abdallah.nassereddine(a)esrf.fr> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Exafs spectra Fitting of WO3 nanoparticles Message-ID: <ddfc8c51f227c914d472d4115733b956(a)esrf.fr> Content-Type: text/plain; charset="utf-8"; Format="flowed" Dear all, Good morning, I try to Fit EXAFS spectra of a sample composed of supported tungsten oxide ( WO3/ZSM-5) nanoparticles obtained by operando studies under gas (CH4, He) at 750 ?C. First, and after several trials, I analyzed the WO3 reference spectrum obtained at room temperature and I succeeded in determining the amplitude (S0) by using the monoclinic structure WO3 cif file. Then, I used the value of this amplitude obtained to be able to fit the structural parameters (coordination number N, Debye-waller Factor, Interatomic distance) of WO3/ZSM-5 nanoparticles under gas, but I can't. the best result I got was by selecting the first two shells (at 1.858 and 1.919 Angstrom) of the monoclinic structure. However, with all the optimizations, the Debye-waller factor obtained for the second W-O shell (1.919 Angstrom) is always negative, and if I don't take this shell into account, I completely lose my Fit. Have any of you ever worked on this type of sample and might have an idea that would help me improve my Fit? Thank you in advance, Best regards, Abdallah Nassereddine

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Exafs spectra Fitting of WO3 nanoparticles
by Abdallah Nassereddine 03 Aug '22

03 Aug '22

Dear all, Good morning, I try to Fit EXAFS spectra of a sample composed of supported tungsten oxide ( WO3/ZSM-5) nanoparticles obtained by operando studies under gas (CH4, He) at 750 °C. First, and after several trials, I analyzed the WO3 reference spectrum obtained at room temperature and I succeeded in determining the amplitude (S0) by using the monoclinic structure WO3 cif file. Then, I used the value of this amplitude obtained to be able to fit the structural parameters (coordination number N, Debye-waller Factor, Interatomic distance) of WO3/ZSM-5 nanoparticles under gas, but I can't. the best result I got was by selecting the first two shells (at 1.858 and 1.919 Angstrom) of the monoclinic structure. However, with all the optimizations, the Debye-waller factor obtained for the second W-O shell (1.919 Angstrom) is always negative, and if I don't take this shell into account, I completely lose my Fit. Have any of you ever worked on this type of sample and might have an idea that would help me improve my Fit? Thank you in advance, Best regards, Abdallah Nassereddine

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Synchrotron geochemist position at DOE-National Energy Technology Laboratory
by Mengling Stuckman 02 Aug '22

02 Aug '22

Dear ifeffit members, Recently we are interested in hiring a synchrotron geochemist for our critical mineral sustainability program at NETL. U.S. citizens are strongly preferred. Here is the specific job posting. https://careers.leidos.com/jobs/9878648-synchrotron-geochemist Feel free to pass along this information to your coworkers or postdocs who are interested. If you have any questions related to the post, feel free to contact me at mengling.stuckman(a)netl.doe.gov Thanks and have a nice day, Mengling -- Mengling Stuckman Leidos Technical Fellow National Energy Technology Laboratory U.S. Department of Energy Pittsburgh, PA mengling.stuckman(a)netl.doe.gov Office: 412-386-7387

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Athena: the R factor for normalized mu(E)
by Jon-Petter Gustafsson 13 Jul '22

13 Jul '22

Hello all, I have been a frequent user of Athena for many years, mostly for interpreting P K-edge XANES spectra. Until last week I thought that the R factor in Athena was always defined as: sum( [data_i - fit_i]^2 ) ------------------------------- sum( data_i^2 ] This is also the definition given in the online manual, and it has been stated by me and by other colleagues in a number of papers dealing with P K-edge XANES. But well, this is not true when dealing with normalized XANES spectra! I realized this when I played around with a number of my old LC fits in Excel. While the chi-square value (or maybe more precisely, the sum of squared residuals) was reproduced perfectly, I always got "R factors" (i.e. with the above definition) between 2 and 3 times lower than what Athena gives. After that I consulted the Demeter programming documentation (https://bruceravel.github.io/demeter/pods/Demeter/LCF.pm.html) to find that, for normalized mu(E), "Demeter thus scales the R-factor to make it somewhat closer to 10^-2". However, the equation stated on this page actually reproduces the R factor even more poorly, and therefore I won't reiterate it here. After inspecting the Perl code, and trying out different alternatives in Excel, I now believe that the following equation provides a more accurate definition of the R factor (correct me if I'm wrong!): sum( [data_i - fit_i]^2 ) ------------------------------- sum( [data_i - avg data]^2 ) where "avg data" is the arithmetic mean of the data in the LC fitting range. It would be great if others could confirm this. As far as I understand, this won't affect the interpretations that any of us have made over the years, it only affects the understanding of what the R factor actually is... Kind regards, Jon Petter Jon Petter Gustafsson, Professor in Soil Chemistry Department of Soil and Environment Swedish University of Agricultural Sciences (SLU) Box 7014 750 07 Uppsala, Sweden Phone: 018-671284; e-mail: jon-petter.gustafsson(a)slu.se<mailto:jon-petter.gustafsson@slu.se> --- N?r du skickar e-post till SLU s? inneb?r detta att SLU behandlar dina personuppgifter. F?r att l?sa mer om hur detta g?r till, klicka h?r <https://www.slu.se/om-slu/kontakta-slu/personuppgifter/> E-mailing SLU will result in SLU processing your personal data. For more information on how this is done, click here <https://www.slu.se/en/about-slu/contact-slu/personal-data/>

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Literature question---FEFF-based wavelet
by Xinyu Luo 29 Jun '22

29 Jun '22

Hi everyone, I'm a graduate student interested in using wt-EXAFS to analyze LDH compounds. I've surfed the ESRF website, tried Continuous Cauchy and Morlet as mother wavelets, and am aware of their limitations. I'm inspired by previous work by Funke et al. [J. Synchrotron Radiat. 2007, 14 (5), 426–432.], that customizing the mother wavelet can strengthen the sensitivity to the path of interest. I have some questions as follows. 1)Can the FEFF-Morlet wavelet be manipulated through parameters like the Morlet or Cauchy wavelet to reach the desired Heisenberg box? 2)How to practically execute the as-mentioned four steps to construct the FEFF-Morlet wavelet? Could you suggest some software toolkit to start, perhaps Matlab? 3)I'm also curious about the 2D contour generated by FEFF-Morlet which didn't show up in the paper. Will the overview wt figure gain better general resolution simply by choosing an appropriate mother wavelet? Regards Xinyu

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