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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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data plotting
by Ofierska Weronika Lucja 28 Jun '22

28 Jun '22

Dear all, I am a new user of Athena and encountered some issues with data plotting. While plotting the uXAS data for Fe K pre-edge the quality of plotting is somehow less sharp compared to the actual data I plotted using other graphical tool (see below) [cid:4465cab9-2ae8-49e7-8253-e54ac3d22bb7] vs what I get from Athena [cid:4db817c1-78d0-4ac8-b094-12d37d055466] As you can see the resolution of the pre-edge in Athena is so poor I cannot resolve the Fe2+/Fe3+ ratio as the peak for Fe3+ is not visible. (I plotted Bruce's data from lepidocrocite to see if it's a common problem and it seems that his data look much better than mine). During my time on synchrotron we actually spent a lot of time to resolve best resolution on the pre edge, so it's not a acquisition problem. Does anyone have any idea how to fix this? I am attaching the project file and txt file (plot FluoRT2 column) with the original data. Thank you for your help, Weronika Ofierska

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new opening for high resolution X-ray spectroscopic studies of spent nuclear fuel
by Vitova, Tonya (INE) 15 Jun '22

15 Jun '22

Dear all, Please see this new job opportunity: https://www.pse.kit.edu/english/karriere/joboffer.php?id=155626 I hope that many of you will apply! Best regards, Tonya -----Ursprüngliche Nachricht----- Von: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> Im Auftrag von ifeffit-request(a)millenia.cars.aps.anl.gov Gesendet: Dienstag, 31. Mai 2022 19:00 An: ifeffit(a)millenia.cars.aps.anl.gov Betreff: Ifeffit Digest, Vol 231, Issue 22 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: Larch 0.9.61 and 60 (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Tue, 31 May 2022 07:10:28 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larch 0.9.61 and 60 Message-ID: <CA+7ESbpx-dFvXkNkL0EFXPPxsi8d3oO4vO3T3xTWeVKYNKXNzA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Kathy, Thanks and sorry for the trouble. I think I can reproduce this: changing the definitions of Path Parameters is being ignored. I have a theory of what is going wrong, but I'll have to investigate this a bit... On Tue, May 31, 2022 at 6:12 AM Kathy Dardenne <kathy.dardenne(a)kit.edu> wrote: > Hello, > > > > I was trying to use Larch 0.9.59 to fit EXAFS Data. There was no > possibility to save work in progress but it was possible to do fit, > change name of the variable used and define the expression for > amplitude (default defined as ?n*s02? in Larch where n is taken from the feff calculation). > > I have 6 slightly different Cf-O distances in my model structure and > took only one path, changing the amplitude definition ?1.0 * s02? by ?NO * s02? > . this worked perfectly. > > > > However in Larch 60 and 61 where, thanks a lot!!!, we can now save our > work, it is not possible any more to change anything in the path > parameter (neither name or expression). The added variable is not any > more varied and not taken into account. Independently of the amplitude > definition s02 get the same value as default definition and new > variables stay by start value having no influence on the fit. > > > > I join some screenshot as well ?Path parameters? and ?Fit script?. > Looking at the Path parameter I saw that the amplitude is still by > default definition so no wonder that it acts without taking into account changes. > This is the same for name changes. > > > > Am I the only one having trouble now? I worked till now with artemis, > ifeffit and previously feffit soI do not have a big experience with Larch. > The old feffit based versions stop all by Pu (Z=94) and I need Z=98 so > I changed to Larch but need to get used to. > > I am using Larch in anaconda3 on a Win10 Computer. > > > > Thanks a lot for your help. > > > > Kind regards > > > > Kathy > _______________________________________________ > 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 > -- --Matt Newville <newville at cars.uchicago.edu> 630-327-7411

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Larch 0.9.61 and 60
by Kathy Dardenne 31 May '22

31 May '22

Hello, I was trying to use Larch 0.9.59 to fit EXAFS Data. There was no possibility to save work in progress but it was possible to do fit, change name of the variable used and define the expression for amplitude (default defined as "n*s02" in Larch where n is taken from the feff calculation). I have 6 slightly different Cf-O distances in my model structure and took only one path, changing the amplitude definition "1.0 * s02" by "NO * s02" . this worked perfectly. However in Larch 60 and 61 where, thanks a lot!!!, we can now save our work, it is not possible any more to change anything in the path parameter (neither name or expression). The added variable is not any more varied and not taken into account. Independently of the amplitude definition s02 get the same value as default definition and new variables stay by start value having no influence on the fit. I join some screenshot as well "Path parameters" and "Fit script". Looking at the Path parameter I saw that the amplitude is still by default definition so no wonder that it acts without taking into account changes. This is the same for name changes. Am I the only one having trouble now? I worked till now with artemis, ifeffit and previously feffit soI do not have a big experience with Larch. The old feffit based versions stop all by Pu (Z=94) and I need Z=98 so I changed to Larch but need to get used to. I am using Larch in anaconda3 on a Win10 Computer. Thanks a lot for your help. Kind regards Kathy

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PostDoc position at BM23/ID24 beamlines of ESRF
by Kirill LOMACHENKO 30 May '22

30 May '22

Dear all, we are looking for an outstanding postdoc to do research in chemistry at BM23 and ID24 XAS beamlines of the ESRF. The prioritized fields are catalysis and electrochemistry. We expect a postdoc to run their own research exploiting their collaboration network. The ideal candidate would be a link between our cutting-edge XAS facilities and leading academic groups in the field. More details and the Apply button are here: https://esrf.gestmax.eu/1592/1/post-doc-id24-bm23/en_US Thank you for spreading the news! All the best, Kirill Lomachenko -- Dr. Kirill A. Lomachenko Scientist at BM23/ID24 beamlines European Synchrotron Radiation Facility 71 avenue des Martyrs CS 40220 38043 Grenoble Cedex 9, France Tel: +33 438 88 19 14 www.esrf.eu

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Larch 0.9.61
by Matt Newville 26 May '22

26 May '22

Hi Folks, It's only been a few days, but there were some fairly important bugs and misfeatures found with Larch 0.9.60. Rather than wait, these have mostly been fixed (details at https://github.com/xraypy/xraylarch/releases/tag/0.9.61) You can either update the code yourself with `pip install --upgrade xraylarch`, with the binary installer, or by allowing XAS Viewer to run its updater. Bug reports, comments, and suggestions are always welcome. --Matt

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