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Manuscript comments regarding EXAFS modeling
by Peng Liu 29 Aug '21

29 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 22 Aug '21

22 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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