July 2021 - Ifeffit - millenia.cars.aps.anl.gov

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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