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

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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