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EXAFS fitting - noisy data
by Hu, Yang (HIU) 01 Sep '21

01 Sep '21

Dear Ifeffit members, I have some fundamental questions regarding noisy data, and I am wondering how to tell whether the data quality worth doing Fourier transformation/EXAFS fitting or not. For example, the attached MnO chi(k) data becomes noisy from 7 Å-1 when it was measured up to 12 Å-1. The deglitching (left: red -> blue) mitigated the strong dips but the high-k end still has too much noise. I practiced the FT and fitting the 1st and 2nd shells by using the lower part. But My questions here are: 1) How noisy would be too noisy? Like the data between 8 and 10 Å-1 in the attached file, can they still be included for the FT? 2) We can choose the high-k end based on the signal-to-noise ratio, but to what extend? With data being noisy from even 5 or 6 Å-1, can they still be used? 3) For fitting the 1st and 2nd shells, I still lack of clear understanding how the high-k portion can influence. If I measure a set of samples, and one of them has much noisy data so a shorter k-range is picked up for background subtraction and FT. In this case, can I still consider the change or evolution in the fitted parameters systematic? Thank you in advance, Best regards, Yang

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Manuscript comments regarding EXAFS modeling
by Peng Liu 30 Aug '21

30 Aug '21

Dear Ifeffit members, I received the following two comments. " Comment 1: Authors have fixed the amplitude reduction factor (SO2) to a fixed value (0.85). This factor is specific to particular chemical compound and sample preparation and quality (mostly homogeneity), measurement method (e.g. absorption, fluorescence). Authors can find in literature [e.g. Rehr2000] that SO2 for ideal samples (having no other effects) represent multielectron effects, which by definition depend on valence and ligands. Even more, SO2 is correlated with Debye-Waller factor (σ²) and coordination number (CN), so any chosen value will be compensated by CN and σ². As coordination numbers are used as quantitative indicators in discussion and following conclusions. I would request to clarify the selection criteria for SO2 values and advise to revise this approach (i.e. not to fix SO2 as the same value for all samples). I do not expect drastic changes in obtained CN values, but this should be tested. Comment 2: As I mentioned previously, coordination number (CN) is correlated with Debye-Waller factor (σ²). My question is: how this correlation is managed (eliminated)? Most probably (in FEFFIT) this is done by using 3 separate values for n (1,2,3), where n is a power in expression chi(k)*(k^n). " I used Artemis for the calculation. 1) Because S02 and CN are multiplication relations in the EXAFS equation, as we usually do, we fixed S02 to obtain CN for unknown samples. 2) there are outputs regarding the correlation between different fitting parameters from Artemis. Is there a way to manage or eliminate the correlation as the reviewer mentioned using Artemis or Larch? If you also could give me some suggestions to answer the comments, that would also be greatly appreciated. -- Best Regards, Peng Liu School of Environmental Studies China University of Geosciences, Wuhan, Hubei Province, PR China https://scholar.google.com/citations?user=qUtyvokAAAAJ&hl=en http://grzy.cug.edu.cn/049121/zh_CN/index.htm

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Re: [Ifeffit] [EXT] Ifeffit Digest, Vol 222, Issue 6
by Christopher Chantler 28 Aug '21

28 Aug '21

Just a little comment. If you propagate uncertainties, there is mathematically no difference between the weightings and expected fits for k powers times chi, so differences will mainly be in correlated parameters. Without propagating uncertainties you can get different answers in different regions of k fitting but the differences do not reflect physical parameters. -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS; CIT, CCN IPP, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> chantler(a)me.com<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/home.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Sunday, 29 August 2021 3:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [EXT] Ifeffit Digest, Vol 222, Issue 6 External email: Please exercise caution 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. Manuscript comments regarding EXAFS modeling (Peng Liu) 2. Re: Manuscript comments regarding EXAFS modeling (Matthew Marcus) ---------------------------------------------------------------------- Message: 1 Date: Sat, 28 Aug 2021 10:40:37 +0800 From: Peng Liu <liupeng5182(a)gmail.com> To: Ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Manuscript comments regarding EXAFS modeling Message-ID: <CAJniE5J7VBPfTkKjU01fWUUzYoFR-DqarJmwNuLuDfK5GO2Niw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear Ifeffit members, I received the following two comments. " Comment 1: Authors have fixed the amplitude reduction factor (SO2) to a fixed value (0.85). This factor is specific to particular chemical compound and sample preparation and quality (mostly homogeneity), measurement method (e.g. absorption, fluorescence). Authors can find in literature [e.g. Rehr2000] that SO2 for ideal samples (having no other effects) represent multielectron effects, which by definition depend on valence and ligands. Even more, SO2 is correlated with Debye-Waller factor (??) and coordination number (CN), so any chosen value will be compensated by CN and ??. As coordination numbers are used as quantitative indicators in discussion and following conclusions. I would request to clarify the selection criteria for SO2 values and advise to revise this approach (i.e. not to fix SO2 as the same value for all samples). I do not expect drastic changes in obtained CN values, but this should be tested. Comment 2: As I mentioned previously, coordination number (CN) is correlated with Debye-Waller factor (??). My question is: how this correlation is managed (eliminated)? Most probably (in FEFFIT) this is done by using 3 separate values for n (1,2,3), where n is a power in expression chi(k)*(k^n). " I used Artemis for the calculation. 1) Because S02 and CN are multiplication relations in the EXAFS equation, as we usually do, we fixed S02 to obtain CN for unknown samples. 2) there are outputs regarding the correlation between different fitting parameters from Artemis. Is there a way to manage or eliminate the correlation as the reviewer mentioned using Artemis or Larch? If you also could give me some suggestions to answer the comments, that would also be greatly appreciated. -- Best Regards, Peng Liu School of Environmental Studies China University of Geosciences, Wuhan, Hubei Province, PR China https://scholar.google.com/citations?user=qUtyvokAAAAJ&hl=en http://grzy.cug.edu.cn/049121/zh_CN/index.htm

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Global XAS seminar on Thursday: Ultrafast x-rays...
by Gerald T. Seidler 23 Aug '21

23 Aug '21

Dear ifeffit mailing list recipients, See seminar details below, and please send recommendations for speakers. Jerry Seidler (seidler(a)uw.edu) ------------------------------------ *Deciphering the Dynamics of the Ferrous Cytochrome c Photodissociative State Using Ultrafast X-ray Spectroscopy and Scattering Methods* Prof. Michael Mara (Northwestern University) Thursday August 26: 9 am Seattle (PDT), 12 noon NY, 5 pm London, 6 pm Berlin, 7 pm Moscow link: https://washington.zoom.us/j/92742942089 password: EXAFS *Abstract*: The femtosecond X-ray pulses provided by X-ray free electron lasers enable tracking of electronic and structural dynamics in metalloprotein active sites immediately following photoexcitation. Here, we decipher the evolution of the photodissociated state of ferrous cytochrome c using Fe K-edge X-ray absorption and emission spectroscopies, as well as X-ray solution scattering. By absorption and emission methods, we track the rebinding of the cleaved ligand and identify an electronic intermediate state involved in ligand dissociation. X-ray scattering further defines the early-time active site structure while following heat dissipation from the hot ground state of the active site into the solvent. By relating the active site temperature to the kinetics of ligand recombination, we quantify the protein bulk contribution to stabilizing the protein iron-methionine bond; this is the first direct measurement of the protein entatic state, whereby the protein regulates activity through modest tuning of the energetics of the active site. *Suggested reading:* [1] Mara, M. W. et al., Metalloprotein entatic control of ligand-metal bonds quantified by ultrafast x-ray spectroscopy, Science, 2017, 356, 1276-1280. https://science.sciencemag.org/content/356/6344/1276.full [2] Reinhard, M. E. et al, Short-lived metal-centered excited state initiates iron-methionine photodissociation in ferrous cytochrome c, Nature Communications, 2021, 12, 1086. https://doi.org/10.1038/s41467-021-21423-w -- *Gerald Seidler* *Professor, Physics Department* *University of Washington* *http://faculty.washington.edu/seidler/index.html <http://faculty.washington.edu/seidler/index.html>* *seidler(a)uw.edu <seidler(a)uw.edu>*

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XAS/MEX workshop at the Australian Synchrotron 26-27 August - Registrations closing soon! [SEC=OFFICIAL]
by MITCHELL, Valerie 23 Aug '21

23 Aug '21

[https://mcusercontent.com/50e44d7c99f0bcbe3f66cb4e9/images/3527f043-2633-a6…] Registrations closing soon! XAS & MEX Workshop [https://cdn-images.mailchimp.com/template_images/gallery/ribbon_bottom.png] [https://cdn-images.mailchimp.com/template_images/gallery/icon_clock2.gif] Thursday 26 & Friday 27 August, 2021 [https://cdn-images.mailchimp.com/template_images/gallery/icon_info2.gif] [https://mcusercontent.com/50e44d7c99f0bcbe3f66cb4e9/images/da939b82-7a45-84…] The Australian Synchrotron will be hosting a two day workshop designed for new XAS users and those interested in the capabilities of the soon-to-come MEX beamline. Registrations close at 24:00 AEST, 24 August, 2021. Program: Day 1 On the first day, talks from beamline scientists and experts in the field will highlight the capabilities of the XAS and MEX beamlines, discuss how to get the most out of beamtime, and present case studies illustrating how these techniques can help solve questions in earth, biological and chemical sciences. Day 2 Day two will feature a hands-on tutorial in XANES data analysis led by Dr. Ryo Sekine of the University of the Sunshine Coast. Opportunities will be available to discuss common data issues with beamline scientists. Presenters Dr. Niloofar Karimian, Southern Cross University Assoc. Prof. Neeraj Sharma, University of New South Wales Prof. Peter Kopittke, University of Queensland Dr. Mark Hackett, Curtin University Dr. Rosalie Hocking, Swinburne University of Technology Dr. Ryo Sekine, University of the Sunshine Coast XAS Beamline Scientists: Dr. Bernt Johannessen, Dr. Valerie Mitchell, Dr. Jessica Hamilton MEX Beamline Scientists: Dr. Chris Glover, Dr. Jeremy Wykes, Dr. Simon James, Dr. Emily Finch, Dr. Krystina Lamb Program<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> [https://cdn-images.mailchimp.com/template_images/gallery/icon_locator2.gif] Free Virtual Event [https://cdn-images.mailchimp.com/template_images/gallery/icon_share2.png] Registration is essential Click to register <https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> [Facebook]<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> Facebook<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> [Twitter]<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> Twitter<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> [Website]<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> Website<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> [YouTube]<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> YouTube<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> You are receiving this email because you are an ANSTO User. Edit Subscription Preferences<https://ansto.us17.list-manage.com/profile?u=50e44d7c99f0bcbe3f66cb4e9&id=0…> Unsubscribe<https://ansto.us17.list-manage.com/unsubscribe?u=50e44d7c99f0bcbe3f66cb4e9&…> [https://cdn-images.mailchimp.com/template_images/gallery/icon_contact2.gif] ANSTO New Illawarra Rd LUCAS HEIGHTS, NSW 2234 Australia [Email Marketing Powered by Mailchimp]<http://www.mailchimp.com/email-referral/?utm_source=freemium_newsletter&utm…> OFFICIAL

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Re: [Ifeffit] Ifeffit Digest, Vol 222, Issue 2
by Vitova, Tonya (INE) 17 Aug '21

17 Aug '21

Hi everybody, I would like to draw your attention to the following postdoc position: https://www.pse.kit.edu/karriere/joboffer.php?id=85889&language=en It will be great if you forward it to suitable candidates. Thank you in advance and best from me, 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: Montag, 16. August 2021 23:46 An: ifeffit(a)millenia.cars.aps.anl.gov Betreff: Ifeffit Digest, Vol 222, 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. Re: Problem Importing CIF files into Larch (Matt Newville) 2. Re: Problem Importing CIF files into Larch (Vincent Wu) 3. Re: Problem Importing CIF files into Larch (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Mon, 16 Aug 2021 15:21:13 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Problem Importing CIF files into Larch Message-ID: <CA+7ESbrWMTGYTa+T+2u+++Qz92JQyTJFDqsFkhVZCCqMQfiXhw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Amol, Sorry for the delay, I was offline most of last week. Thanks for posting these CIF files. I think these should be usable -- the basic "cif2feffinp()" function works on these to generate a valid Feff.inp, but the GUI CIF Browser is currently expecting additional fields such as publication information. I guess those fields should be optional. I think there is another issue with using multi-site CIF structures that I want to look into. So, I hope to get this fixed soon, but I also want to tackle a few other issues before posting a completely new version. --Matt On Tue, Aug 10, 2021 at 4:12 PM <amolagarwal2025(a)u.northwestern.edu> wrote: > Hi, > > I hope you are doing well. I am writing regarding some issues that I > am having with opening my CIF files in Larch. I have used these same > CIF files in the past in Artemis to run feff calculations. When I open > these files in the Larch open feff tab, it shows a dialog box saying > that there is an error opening the CIF file. This is happening with > all my CIF files and I am not sure why. I am attaching a couple of > these CIF files. I would really appreciate some help on this. > > > > Amol Agarwal > > PhD Student > > Materials Science & Engineering | Northwestern University > > > _______________________________________________ > 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 >

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Problem Importing CIF files into Larch
by amolagarwal2025＠u.northwestern.edu 16 Aug '21

16 Aug '21

Hi, I hope you are doing well. I am writing regarding some issues that I am having with opening my CIF files in Larch. I have used these same CIF files in the past in Artemis to run feff calculations. When I open these files in the Larch open feff tab, it shows a dialog box saying that there is an error opening the CIF file. This is happening with all my CIF files and I am not sure why. I am attaching a couple of these CIF files. I would really appreciate some help on this. Amol Agarwal PhD Student Materials Science & Engineering | Northwestern University

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XAFS short course at BNL: Nov. 17-19
by Anatoly Frenkel 30 Jul '21

30 Jul '21

Dear subscribers: As it does every year in the Fall, Synchrotron Catalysis Consortium at Brookhaven National Laboratory will run a short course from November 17 to 19 at BNL. As in the last year, when it gathered 80 participants, it will be virtual, and the course will be limited to 80 registered participants again. The course application deadline is August 15. It will be an introductory course, gearing at the beginner level. The link with the course information and application instructions is here: https://www.bnl.gov/xafs2021/ Please share this information with your group members and anyone else who may be interested. Thank you very much, Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794, Ph: 631-632-2751 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Joint Appointment: Chemistry Department, 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 Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

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Larch 0.9.55
by Matt Newville 18 Jul '21

18 Jul '21

Hi Folks, Larch 0.9.55 is now available for download. This comes only two weeks after the announcement for 0.9.53, but there have been several important improvements especially for Windows users outside of the US, and based on bugs found or features requested during the Larch for XAFS Analysis Workshop at the Virtual XAFS 2021 conference (there was a 0.9.54, but a few things were fixed since then too!). If you have installed a recent version of Larch and are on a machine connected to the internet, you should see a notice that version 0.9.55 is available, and can use that notice to automatically install the update. That will be much faster than installing from the full installer. A series of instructional videos made for this workshop on using Larch's XAS Viewer application for various aspects of XANES and EXAFS analysis are now publicly available at https://www.youtube.com/playlist?list=PLgNIl_xwV_vK4V6CmrsEsahNCAsjt8_Be. Comments, questions, suggestions on these are most welcome, either on youtube or here. For folks without access to youtube.com, these videos are also at https://millenia.cars.aps.anl.gov/videos/XrayLarch/ The changes here are relatively minor compared to the changes made in 0.9.53 (see https://millenia.cars.aps.anl.gov/pipermail/ifeffit/2021-July/010251.html) The most important changes and fixes since 0.9.53 are: - Larch's GUI applications should again work without problems on non-US Windows 10 machines. There was a serious bug (possibly since Larch 0.9.52) for using wxPython applications with Python>=3.8 and wxPython>=4.1.0. I believe we have a workaround, at least for now. - Fixes for turning CIF structures into Feff inputs and running Feff: -- more external CIF files from Crystallography Open Database and Materials Project can be converted to Feff.inp. -- external Feff.inp files can be loaded and run. -- the name of the folder created for any Feff calculation can be renamed before running Feff. - the plot selection choice in the XAS normalization panel for "one group" and "selected groups" are no longer reset each time a data set is selected. - A reference spectrum can now be set for any XAFS spectrum. When aligning or energy-shifting XAFS data, you can now easily select all of the spectra that share a reference and apply the same energy shift to those spectra. You can also easily select a reference group for one XAS spectrum and copy that to a set of other "selected spectra". There is not (yet?) a way to select a reference channel from a file when importing data, so these must be read separately and assigned. - a bug was fixed on the EXAFS / background subtraction panel on "copied groups" to ensure that processing parameters (kweight, rbkg, etc) are kept separate. - For linear combination fitting, a single energy shift can be varied during the fit, shifting the unknown data to match the combination of a (presumably aligned) set of standards. - For pre-edge peak fitting and Feff Path fitting, entries in the "fit history" can have user-specified labels which can be more meaningful than the default "Fit #1", "Fit #2", etc. - testing is now done only with Github Actions, not with the appveyor service. I want to thank all the people who took part in the workshop and gave feedback -- XAS Viewer is a lot better than it was a week ago. Thanks to Monica Bairagi and Nengchuan Tian for help, and special thanks to Klemen Bucar for helping track down and solving the Locale issue and working on the testing tools. And also thanks to Mauro Rovezzi for continued suggestions and fixes. If you have any questions, problems, or suggestions, please let me know. --Matt

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Position available: Postdoc (f/m/d) specialization in chemistry or physics
by Zimina, Anna (IKFT) 15 Jul '21

15 Jul '21

Dear all, we are looking for a chemist or physicist with a doctorate and several years of experience in the fields of catalysis, laboratory support, synchrotron radiation source, commissioning of in situ cells for X-ray absorption spectroscopy, material characterization, modelling of spectra and detailed EXAFS analysis. The main tasks include the scientific supervision of a beamline for X-ray absorption spectroscopy at the Karlsruhe synchrotron (CAT-ACT) and structural investigations of mono- and bimetallic nanoparticles for various catalytic processes. Further information can be found here: https://www.pse.kit.edu/karriere/joboffer.php?id=86224&language=en ______________________________________________________________________________________ Karlsruhe Institute of Technology (KIT) Institute of Catalysis Research and Technology (IKFT) Dr. Anna Zimina Beamline scientist Hermann-von-Helmholtz-Platz 1 Building 345 Office 304 76344 Eggenstein-Leopoldshafen Phone: +49 721 608 28673 Fax: +49 721 608 26789 E-Mail <mailto:anna.zimina@kit.edu> anna.zimina(a)kit.edu

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Position available: NSLS-II Quick Absorption and Scattering (QAS) Lead Beamline Scientist
by Stavitski, Eli 14 Jul '21

14 Jul '21

Dear all, NSLS-II is seeking high-profile candidates for the lead scientist position of the QAS beamline. The lead beamline scientist has a vision, defines the strategy to advance the science program, enhances the beamline capabilities and proposes facility improvements and upgrades. The lead beamline scientist develops, monitors, and maintains safe operating conditions at the beamline and provides oversight of all staff and users of the beamline. The lead beamline scientist is responsible for the operation of the beamline in support of the NSLS-II facility users, supervises a group of scientific and technical staff, reaches out effectively to the relevant scientific and industrial user communities, develops collaborative programs, and liaises with vendors. The lead beamline scientist works closely with users, oversees the design, implementation, maintenance and upgrade of the beamline equipment, provides guidance and oversees progress in advanced data management and analysis. https://jobs.bnl.gov/job/upton/lead-beamline-scientist-quick-x-ray-absorpti… ____________________________________ Eli Stavitski, PhD, Physicist Inner Shell Spectroscopy (ISS) Lead Beamline Scientist National Synchrotron Light Source-II Bldg. 743, Brookhaven National Laboratory Upton, NY 11973-5000 631 344 8641 istavitski(a)bnl.gov<mailto:istavitski@bnl.gov>

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July 15 seminar: X-ray Spectroscopy of Light-induced Chemical Reactions -- A New Universal Probe of Photoexcited Molecular Dynamics
by Gerald T. Seidler 12 Jul '21

12 Jul '21

Dear Colleagues, The Global XAS Journal club is an ongoing virtual seminar series. The seminar for this week in the Americas/Europe time window is below -- you can forward this to interested persons in the XAS community but *please do not make any public posting *(we've had problems with zoom-bombing). Please email me seidler(a)uw.edu to be added to the direct mailing list, where you would get this information for both the Americas/Europe and also Asia-Oceania/Europe timed seminars. About 70 prior lectures are available at the youtube channel https://www.youtube.com/channel/UCwtkyiTV4BltKTQ7tS0CltQ/videos Looking to August and the autumn term I am particularly interested in finding: (1) XAS speakers who are early career scientists, such as postdocs, assistant professors, or new staff scientists at facilities and national labs, and (2) beamline scientists to speak about capabilities and science outcomes/goals at their beamlines. Please send suggestions! Cheers, Jerry Seidler (seidler(a)uw.edu) ---------------------------------------------------------------------------------- *X-ray Spectroscopy of Light-induced Chemical Reactions -- A New Universal Probe of Photoexcited Molecular Dynamics * Prof. Aditi Bhattacherjee (University of Iowa) Thursday July 15: 9 am Seattle (PDT), 12 noon NY, 5 pm London, 6 pm Berlin, 7 pm Moscow link: https://washington.zoom.us/j/96246359168 password: EXAFS *Abstract*: Photochemical reactions of small organic molecules are prevalent in the atmosphere, in biological machineries and photocatalytic materials. Recent laboratory breakthroughs have enabled access to ultrafast X-ray spectroscopy at the carbon K-edge (1s absorption edge of carbon, at 284 electron volts). This has opened new avenues to explore ultrafast reaction mechanisms in a host of photochemical reactions in small molecules with high temporal resolution.[1] In this talk, I will discuss experiments that show how the excitation of 1s-core electrons of the constituent carbon atoms in organic molecules is a key spectroscopic probe of photoinduced molecular dynamics. First, I will present the mechanistic details that emerge in the ultrafast ring-opening reactions of hydrocarbon as well as heteronuclear organic molecules from the direct orbital sensitivity of time-resolved X-ray absorption spectroscopy at the near edge.[2,3] Second, I will also show that in favorable cases, ultrafast intersystem crossing in molecules can be identified even though X-ray absorption spectroscopy is not directly sensitive to spin states.[4] Our work reveals that future chemical applications of this method at multiple absorption edges may provide new universal spectroscopic probes of photoinduced molecular dynamics. *Suggested reading*: [1] Bhattacherjee and Leone AccChemRes 21, 3203, 2018. https://pubs.acs.org/doi/10.1021/acs.accounts.8b00462 [2] Attar, Bhattacherjee, Das, Schnorr, Closser, Prendergast, and Leone Science 356, 54, 2017. https://science.sciencemag.org/content/356/6333/54 [3] Bhattacherjee, Schnorr, Oesterling, Yang, Xue, Vivie-Riedle and Leone JAmChemSoc 140, 39, 12538, 2018. https://pubs.acs.org/doi/10.1021/jacs.8b07155 [4] Bhattacherjee, Das, Schnorr, Attar and Leone JAmChemSoc 139, 46, 2017. https://pubs.acs.org/doi/abs/10.1021/jacs.7b07532 -- *Gerald Seidler* *Professor, Physics Department* *University of Washington* *http://faculty.washington.edu/seidler/index.html <http://faculty.washington.edu/seidler/index.html>* *seidler(a)uw.edu <seidler(a)uw.edu>*

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Another Mac OS install question
by Jilbert, Tom 07 Jul '21

07 Jul '21

Hi Ifeffit folks, I am attempting installation via macports on Mac OS Big Sur, and there are problems to build demeter. Before I send around a log file, I wanted to check if anyone is still maintaining/solving macports issues (Joe Fowler?). ie is it worth it to keep trying. From the archive it seems that installing a virtual machine is a recommended alternative. Cheers, Tom

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Farrel Lytle database
by Monica Bairagi 06 Jul '21

06 Jul '21

Hello all: I am looking forward to standard metal foil data of titanium. I downloaded the data from the Farrel Lytle database but I can not import it into Athena. I looked into the data, it looked wired for me. As Athena expects data to be in columns of energy but this data is not recorded by energy but by steps of the monochromator rotation stage. I am wondering if anyone has any idea how to import or transfer the data. I am attached herewith the data file. Thanks Monica Bairagi Ph.D. Student, Ujjain, India

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Larch 0.9.53
by Matt Newville 03 Jul '21

03 Jul '21

Hi Folks, Larch 0.9.53 is now available for download and use. Although the last announcement here was in April for version 0.9.51, there have been several improvements especially to the XAS Viewer application since the last release, mostly in anticipation of upcoming workshops and short courses. - There are important fixes for reading Spec/Bliss HDF5 files from ESRF - thanks to Mauro Rovezzi for this. You can now import multiple XAS spectra from Spec/HDF5 files. - XAS Viewer now supports doing Feff6l or Feff8l calculations and has a GUI interface for doing a Feffit fit to a sum of Feff paths. In the current GUI frame, this is limited to analyzing one dataset at a time. This brings up a related feature: - A database (sqlite3) of CIF structures from the American Mineralogist Crystal Structure Database (http://rruff.geo.arizona.edu/AMS/amcsd.php) is included. The version of this database in the source code contains about 9000 structures. If your machine is well-connected to the internet and can reach https:/millenia.cars.aps.anl.gov, a more complete version (~30 Mb) with 20,000 structures will be downloaded and used. To be clear, the 9000 structures in the smaller set are probably sufficient -- what is removed is some CIFs from publications with many similar structures (T or P dependence) or structures so large and complex that they will be hard to make into single Feff files. - The CIF files from this DB or other CIF files (well, CIF is notoriously variable!) can be automatically converted to Feff input files (using python tools from the Materials Project, modified a bit). Because many of these CIF structures contain fractional occupancy, that is handled (probably poorly, but at least not failing) by randomly selecting atoms based on the site occupancy. - XAS Viewer has a CIF Browser (from the Feff menu) where you can browse by mineral name, included atoms, etc. From that you can generate a Feff6l or Feff8l input file, potentially edit that input file, and run Feff to generate path files. These will be organized in your home folder (C:\Users\Name\larch\feff for most Windows users, $HOME/.larch/feff for Linux/MacOS). There is also a Feff browser to select Feffnnnn.dat files from your previous Feff runs and bring them into the "Feffit" tab in XAS Viewer to use in the sum of paths fitting of EXAFS spectra. Of course, all of this Feff and Feff fitting interface should be viewed as "initial release" and comments, suggestions, and bug reports are welcome. The notes above are approximately the extent of the documentation, though some videos of using this will be publicly available in a few weeks. There are updated binary installers for Windows, MacOSX, and Linux. There are also updated "GetLarch.sh" and "GetLarch.bat" scripts that also hopefully fix any earlier problems. If you have any questions, problems, or suggestions, please let me know. --Matt

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Beamline Scientist position
by Kelly, Shelly D. 01 Jul '21

01 Jul '21

Hello XAFS community: I'm excited to let you know that we have an opening for beamline scientist within the Spectroscopy group at the Advanced Photon Source. Please help spread the word. https://bit.ly/3iN7Ehe Kind Regards, Shelly Kelly Spectroscopy Group Leader Advanced Photon Source

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Question about CsNO3 L3 edge
by 田能全 01 Jul '21

01 Jul '21

Hi everyone, My colleague sent me data of liquid CsNO3 sample measured using fluorescence model. According to the attached figure, I don't understand why mu(E) increased with increasing energy before and after the L3 edge. Does it make sense for cesium? Thanks. Nengchuan [image: image.png]

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Postdoc position for XAFS analysis
by 이국승(에너지환경소재연구팀) 30 Jun '21

30 Jun '21

Dear Ifeffit members, We are looking for a postdoc candidate for XAFS analysis in PAL. Tasks will be 1. XAFS analysis of electrochemical energy materials 2. Beamline management at Nano-probe XAFS beamline (BL8C) 3. One's own research The position requires PhD degree in Electrochemistry, Chemistry, Materials science or Physics, Excellent writing and communication skills in English, Experience in XAFS analysis. The position begins at any time in this year but earlier is better. If you are interested in this position, please send your CV including list of publications to Dr. Kug-Seung Lee. (lks3006(a)postech.ac.kr) Additional documents can be required including references. Kind regards, Kug-Seung Lee Kug-Seung Lee, Ph.D. Staff Scientist Manager, 8C Nano Probe XAFS Beamline Pohang Accelerator Laboratory Pohang 790-784, Republic of Korea Office: +82-54-279-1522 Fax: +82-54-279-1599 C. P.: +82-10-6419-7801 Scopus : https://www.scopus.com/authid/detail.uri?authorId=56953635300 Researcher ID: http://www.researcherid.com/rid/D-7088-2011

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Bi L3 standards
by Schlesinger, Danielle R. 29 Jun '21

29 Jun '21

Hi everyone, Does anyone have a set of Bi L3 edge standards that they would be willing to share? Thank you! Danielle Danielle R. Schlesinger, Ph.D. Post Doctoral Fellow – AOS/QPC Johns Hopkins University – Applied Physics Laboratory Tel: (240) 592-5243

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Cannon start larch on ubuntu 20.04.2 LTS
by Don Baker, Dr. 29 Jun '21

29 Jun '21

Hi Folks, I think I am missing something obvious and am hoping that you can quickly tell me my mistake, so let me begin my story: I downloaded xraylarch-2021-060Linux-x86_64.sh into downloads on a Asus Zenbook using ubuntu 20.04.2 LTS I ran the command bash ./xraylarch-2021-060Linux-x86_64.sh Larch appears to have been correctly installed, but because I am using a gnome desktop no shortcuts appeared on my desktop (as promised) and there were no files that I could identify as shortcuts in my Downloads directory (which was set to display hidden files) I then moved to the /xraylarch/bin and tried to launch larch using python and this is what happened: python larch Traceback (most recent call last): File "larch", line 5, in <module> from larch.apps import run_larch File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/__init__.py", line 52, in <module> from . import builtins File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/builtins.py", line 27, in <module> from . import xrd File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/xrd/__init__.py", line 25, in <module> from .amscifdb import CifStructure, get_amscifdb, get_cif, find_cifs File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/xrd/amscifdb.py", line 40, in <module> from pymatgen.io.cif import CifParser File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/io/cif.py", line 25, in <module> from pymatgen.core.composition import Composition File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/core/__init__.py", line 21, in <module> from .lattice import Lattice # noqa File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/core/lattice.py", line 23, in <module> from pymatgen.util.coord import pbc_shortest_vectors File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/util/coord.py", line 17, in <module> from . import coord_cython as cuc File "pymatgen/util/coord_cython.pyx", line 1, in init pymatgen.util.coord_cython ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject I also tried to use python to start larch_server and xas_viewer and had the same results. I also have the same results if I try to launch larch using ./larch This is the information on the version of Python that I am running: Python 3.8.10 (default, Jun 4 2021, 15:09:15) [GCC 7.5.0] :: Anaconda, Inc. on linux Type "help", "copyright", "credits" or "license" for more information. Any suggestions anyone has to offer will be appreciated. Wishing you all the best, Don -- Melting rocks today for a better tomorrow . . . Don R. Baker, Professor of Geochemistry, McGill University

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Cannot start larch on ubuntu 20.04.2 LTS
by Don Baker, Dr. 28 Jun '21

28 Jun '21

Hi Folks, I think I am missing something obvious and am hoping that you can quickly tell me my mistake, so let me begin my story: I downloaded xraylarch-2021-060Linux-x86_64.sh into downloads on a Asus Zenbook using ubuntu 20.04.2 LTS I ran the command bash ./xraylarch-2021-060Linux-x86_64.sh Larch appears to have been correctly installed, but because I am using a gnome desktop no shortcuts appeared on my desktop (as promised) ,and there were no files that I could identify as shortcuts in my Downloads directory (which was set to display hidden files) I then moved to the /xraylarch/bin and tried to launch larch using python and this is what happened: python larch Traceback (most recent call last): File "larch", line 5, in <module> from larch.apps import run_larch File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/__init__.py", line 52, in <module> from . import builtins File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/builtins.py", line 27, in <module> from . import xrd File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/xrd/__init__.py", line 25, in <module> from .amscifdb import CifStructure, get_amscifdb, get_cif, find_cifs File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/xrd/amscifdb.py", line 40, in <module> from pymatgen.io.cif import CifParser File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/io/cif.py", line 25, in <module> from pymatgen.core.composition import Composition File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/core/__init__.py", line 21, in <module> from .lattice import Lattice # noqa File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/core/lattice.py", line 23, in <module> from pymatgen.util.coord import pbc_shortest_vectors File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/util/coord.py", line 17, in <module> from . import coord_cython as cuc File "pymatgen/util/coord_cython.pyx", line 1, in init pymatgen.util.coord_cython ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject I also tried to use python to start larch_server and xas_viewer and had the same results. I also have the same results if I try to launch larch using ./larch This is the information on the version of Python that I am running: Python 3.8.10 (default, Jun 4 2021, 15:09:15) [GCC 7.5.0] :: Anaconda, Inc. on linux Type "help", "copyright", "credits" or "license" for more information. Any suggestions anyone has to offer will be appreciated. Wishing you all the best, Don -- Melting rocks today for a better tomorrow . . . Don R. Baker, Professor of Geochemistry, McGill University

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Re: [Ifeffit] Ifeffit Digest, Vol 220, Issue 2
by Danilo Oliveira de Souza 15 Jun '21

15 Jun '21

Hi Teresa and Matt, Concerning the SPOIL function, some months ago I digged on that and I found the first paper (I guess) on this topic, which is from Edmund R. Malinowski in an Analytical Chimica Acta, 1978 ( 10.1016/S0003-2670(01)83099-3 <https://doi.org/10.1016/S0003-2670(01)83099-3> ). Instead of reproducing this paper here (it is not just a couple of lines), I let to you read the precise definition of such a function. I have the copy on pdf of the paper if any of you is interested in it. Cheers, Danilo *Danilo OLIVEIRA DE SOUZA* *Research Fellow @ ELETTRA Sincrotrone, XAFS beamline* * Strada Statale 14 - km 163,5 in AREA Science Park* * 34149 Basovizza, Trieste ITALY* *http://www.elettra.trieste.it/elettra-beamlines/xafs.html <http://www.elettra.trieste.it/elettra-beamlines/xafs.html>* * e-mail: danilo.oliveiradesouza(a)elettra.eu <danilo.oliveiradesouza(a)elettra.eu> * * mobile: (+39) 351 50.30.731 bureau: (+39) 040-375-8604* Em qui., 10 de jun. de 2021 às 19:00, < ifeffit-request(a)millenia.cars.aps.anl.gov> escreveu: > 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: PCA Sixpack results compared to Athena (etc.) (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 10 Jun 2021 07:08:19 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] PCA Sixpack results compared to Athena (etc.) > Message-ID: > <CA+7ESbq= > J9fZ3Y0PPuyjShk+XNFOGjOTktX4m7oyu6PFfTwM5w(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Teresa, > > I'm sorry that I cannot give you a definitive answer. I should admit that > when adding PCA methods to Larch and XAS Viewer (which I invite you to try > out), I tried to follow the scikit-learn approach but also to follow the > Athena implementation. I think I never tried to test against the results > from SixPack. FWIW, Larch only does (easily) PCA on normalized mu(E) or > its derivative. I suppose PCA on chi(k) could be added, but I'm a bit sort > of skeptical of this. > > In fact, the code at > https://github.com/xraypy/xraylarch/blob/master/larch/math/pca.py (and, > just to be clear, having this both in Python and publicly available is > motivated by having these conversations of "what does it do?") has a few > different methods to train a PCA set: one directly from scikit-learn, one > basically reproducing Demeter's PCA.pm (modulo slight differences in > underlying math libraries, which should be insignificant), one that aims to > use only non-negative components (not really worth in my opinion), and one > that is sort of hand-coded and including the IND statistic. I don't know > what SixPack does. > > I cannot really explain why, but the default "readily exposed in Larch XAS > Viewer" is to use the hand-coded version of `pca_train`. In fact, they > should be all more or less interchangeable. I did some tests with these > but that was now several years ago, but it might be worth trying that > again. If you're up for that, please do try. If not and would like to > send your project and an outline of what you get, I might be able to look > at this too. > > For "target transformation", this is implemented as `pca_fit`: how well can > a data set be explained by the first N components of a training model? > > For fit statistics: I have seen "SPOIL" used several places in the EXAFS > literature but am afraid I do not actually know of a definition for this. > If anyone can explain what these are, that would be helpful. Larch can > calculate the F1 and IND statistics that are more common in the PCA > literature. XAS Viewer exposes and automatically plots IND - it's a very > useful way to select how many components are significant. > > I'm pretty sure that does not answer your actual question, but maybe it > will be helpful. If you or anyone else has suggestions for additions, > improvements, or other optional methods or statistics for PCA and/or > related methods, please let me know. > > --Matt > > > On Tue, Jun 8, 2021 at 7:43 AM <t.zahoransky(a)mineralogie.uni-hannover.de> > wrote: > > > > > Dear XAS Community, > > > > I stumbled over the issue that a PCA on 20 EXAFS spectra (k?, k = > > 2.0-11.0 ?-1) perfomed in Sixpack does not give the same results > > (Eigenvalues, variance) as in Athena. However, when I use other > > statistical programs (i.e., TIBCO Statistica or SPSS), I get the same > > results as reported in Athena. I tested this with another EXAFS > > dataset of over 30 samples and the problem persited. > > > > An old entry from 2017 in the ifeffit mailing list ("[Ifeffit] > > Calculation of SPOIL value for the reconstruction of standard > > spectra"), told me that as of Sixpack version 1.4 on, a new/different > > PCA algorithm from the scikit-learn Python package is used. > > > > So I downloaded older versions of Sixpack (i.e. 1.3) and used "Use Old > > PCA"-selection in the "Rotation" menu bar, which actually gave > > different results. However, they are still different from the > > Athena/Statistical program results. > > > > My question is: What is behind this? Is there some sort of > > normalization or axis rotation, that leads to the different values? Is > > there any way to change this so that the results are comparable to > > other programs? > > > > As I need to use the Target Transform option after PCA, which is not > > yet possible in Athena, I am at a loss as to how to deal with these > > different results and where they come from. > > > > > > Thank you very much for your help, > > > > Teresa > > > > > > -- > > Teresa Zahoransky > > > > Soil Mineralogy > > > > Gottfried Wilhelm Leibniz Universit?t Hannover > > > > Institute of Mineralogy > > > > Callinstr. 3, Room 325 > > > > D-30167 Hannover, Germany > > > > > > > > Phone: +49 (0)511 762-8058 > > > > Email: t.zahoransky(a)mineralogie.uni-hannover.de > > > > _______________________________________________ > > 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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TiFe EXELFS Two Phase Co-Refinement Question
by Wilson, Catrina 10 Jun '21

10 Jun '21

Hello, I am using Artemis to fit EXELFS data on a TiFe alloy. There are multiple interfaces between two phases (Im-3m, and P63/mmc) present in the data. I am attempting to co-refine using both phases to create a path list and using paths from both phases in the fit. My understanding of this process is that the software uses a linear combination of each path. However, that would imply that there is a weighting factor applied to each phase that would be correlated to the phase weight for that region. I was wondering if there is a way to determine what the weighting factors during a co-refinement to multiple phases are in Artemis, assuming my initial understanding of the co-refinement process is correct? Thanks for your time, Catrina Wilson Ph.D. Candidate The Ohio State University Doan-Nguyen Group and McComb Group Materials Science and Engineering Center for Electron Microscopy, 1305 Kinnear Rd., Columbus, OH 43212 (614) 643-3110 Office wilson.3981(a)osu.edu<mailto:wilson.3981@osu.edu> / osu.edu<http://osu.edu/> Pronouns: she/her/hers

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PCA Sixpack results compared to Athena (etc.)
by t.zahoransky＠mineralogie.uni-hannover.de 10 Jun '21

10 Jun '21

Dear XAS Community, I stumbled over the issue that a PCA on 20 EXAFS spectra (k², k = 2.0-11.0 Å-1) perfomed in Sixpack does not give the same results (Eigenvalues, variance) as in Athena. However, when I use other statistical programs (i.e., TIBCO Statistica or SPSS), I get the same results as reported in Athena. I tested this with another EXAFS dataset of over 30 samples and the problem persited. An old entry from 2017 in the ifeffit mailing list ("[Ifeffit] Calculation of SPOIL value for the reconstruction of standard spectra"), told me that as of Sixpack version 1.4 on, a new/different PCA algorithm from the scikit-learn Python package is used. So I downloaded older versions of Sixpack (i.e. 1.3) and used "Use Old PCA"-selection in the "Rotation" menu bar, which actually gave different results. However, they are still different from the Athena/Statistical program results. My question is: What is behind this? Is there some sort of normalization or axis rotation, that leads to the different values? Is there any way to change this so that the results are comparable to other programs? As I need to use the Target Transform option after PCA, which is not yet possible in Athena, I am at a loss as to how to deal with these different results and where they come from. Thank you very much for your help, Teresa -- Teresa Zahoransky Soil Mineralogy Gottfried Wilhelm Leibniz Universität Hannover Institute of Mineralogy Callinstr. 3, Room 325 D-30167 Hannover, Germany Phone: +49 (0)511 762-8058 Email: t.zahoransky(a)mineralogie.uni-hannover.de

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Analyzing EXAFS data on Artemis
by Alexandros Deltsidis 28 May '21

28 May '21

Dear mailing list, I am currently analyzing some EXAFS data. I am studying a Lix(C5H5N)FeSe system in a temperature grid that extends from 20 K to 300 K and I have 4 such datasets which correspond to different amount of doping (x). Right now, im focusing on fitting the 1st coordination cell, in Artemis for the Se K-edge. My starting model is the simple P4/nmm FeSe. So, in my system the 1st coordination cell, in the Se K-edge, corresponds to the Se (absorber) - Fe (backscatterer) pair. I have 2 questions: 1) I realize now, that I have a certain impurity in the high doping range on my system, namely Li2Se. I try to include a scattering path from the respective Li2Se crystal model in my fits, since a Se (absorber) - Li (backscatterer) pair is present in the R-range of my fit in the Forward Fourier Transform. My question here is if this makes sense since Li is much smaller scatterer compared to Se. In other words, does it make sense to look for physical parameters (Li-Se bond length and DW factor respectively) of a signal (Se-Li) that is "tucked" in below the main peak coming from the "majority" Se-Fe signal in the FFT? 2)Also, I'm attempting to extract an Einstein temperature for each of those datasets, by utilizing the "eins(T, thetae)" function implemented in Artemis. What is the equation that is parametrized here? Does it include the s0^2 offset term that accounts for the overall configuration disorder in the system? And if that is the case is there same way to separate it from the temperature dependent s^2 term? Thank you in advance, Deltsidis Alexandros PS:I am attaching a png. file exported from Artemis that is relative to my question 1) Ph.D candidate, Institute of Electronic Structure and Laser (IESL), Foundation for Research and Technology - Hellas (FORTH)

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