March 2017 - Ifeffit - millenia.cars.aps.anl.gov

Data export and coordination number
by Abhinav Prabhakar 13 Mar '17

13 Mar '17

Hello, As a new user, I have some questions related to the use of Athena and Artemis: i) Is it possible to extract the normalized/background corrected data from Athena (in E-,k- and R- space) and export it as numbers (to Excel perhaps)? ii) Using Artemis, how can coordination numbers (N) be expressed as 'guess' parameters (Artemis allows only numerical values for N)? Thank you. Regards, Abhinav Prabhakar (Mr.)

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Space group type in Artemis
by Abhinav Prabhakar 13 Mar '17

13 Mar '17

Hello, I have a question about the working of Artemis as a new user. Artemis does not recognize the space group B11b. When importing a cif file of a crystal with this symmetry, it sends a prompt message that the space group symbol cannot be recognized. As a result, I changed it to P11b and it works. But would this change any crystal information (for eg. Degen, Reff values) significantly? Thank you. Regards, Abhinav Prabhakar (Mr)

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APS/IIT Summer XAFS School
by Carlo Segre 06 Mar '17

06 Mar '17

Greetings: The 2017 APS/IIT SUmmer XAFS School will be held on July 9-13, 2017 in Chicago. This XAFS summer school is a continuation of the week-long summer school offered previously at the Advanced Photon Source; the venue will again be at IIT in Chicago, but will run Sunday-Thursday. Course material will cover fundamental and practical aspects of X-ray Absorption Fine Structure Spectroscopy: basics, sample preparation, experiment, theory, data analysis. One day of hands-on experiments will be carried out by participants at several APS beamlines, followed by a guided data analysis laboratory using Athena/iFEFFIT and other programs. Computers will be available for those participants attending without their own laptops. The target audience is graduate students, postdocs, and experienced scientists who are new to XAFS and want to use it in their own research. Space is available for up to 40 students. Instructors include: Dr. Steve Heald (ANL), Dr. Matt Newville (UChicago), Prof. Bruce Bunker (U. Notre Dame), Prof. Carlo Segre (IIT), Prof. Grant Bunker (IIT), and a number (positive, integer) of other experienced XAFS researchers also will participate. The cost of the course is $500 USD, which covers most but not all meals via an IIT meal card. Students will be responsible for their own housing (available on and off IIT campus) and travel to/from their home institutions. IIT is readily accessible by car, cab, and CTA train from O’Hare and Midway airports. Free time will be available most evenings for participants to visit Chicago attractions such as Grant Park, the Loop, Millennium Park, Lake Michigan; music, architecture, art, theater; Chinatown, White Sox, Field Museum, Shedd Aquarium, Adler Planetarium, and Navy Pier, restaurants, and pubs. Please email bunker(a)iit.edu with subject line “2017 XAFS School” for more information. -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim Chair, Department of Chemistry Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

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Relatively reduced ionization edge as opposed to oxidized !
by Ganesh Subramanian 01 Mar '17

01 Mar '17

Dear all, I have been running the FEFF to simulate for XANES spectra for the cobalamins (Vitamin B12 cofactors). The issue of interest is between three compounds - Methylcobalamin (Me-Cbl), Cyanocobalamin (CN-Cbl) and Hydroxocobalamin (OH-Cbl). Experimentally, Me-Cbl is supposed to the most reduced (in terms of the energy of onset of the rising absorption edge). OH-Cbl and CN-Cbl are supposed to be oxidized wrt Me-Cbl. (The official oxidation state of Cobalt for all the above three systems is +3). However, the simulations do no reflect this and it consistently seems to predict a reduced absorption edge for both OH-Cbl and CN-Cbl, in comparison to Me-Cbl. I checked the literature to confirm that the molecular coordinates that we are using as input (obtained after structure optimization using DFT - Gaussian09) is consistent with prior literature. I am wondering if there is anything related to FEFF that I miss understanding, to note why this is occurring. I am attaching the input files for the three models (these are all truncated to reduce the computational expense on DFT optimization) and the experimental and FEFF simulated spectra that I had obtained. Any help in understanding this seeming discrepancy is much appreciated. Thanking you, Ganesh

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downloading Demeter
by Bruce Ravel 01 Mar '17

01 Mar '17

To those who have noticed that Demeter has not been available for download in the last day or so: I use Amazon's S3 service to distribute the large installer files. You may have seen the news in the last 12 hours about a massive outage of that service, or you may have noticed that other internet resources that you use are unresponsive. There is nothing I can do to resolve this problem. Eventually Amazon S3 will come back on line and you will again be able to download Demeter. Please be patient and try again later. Regards, B Example news article: https://techcrunch.com/2017/02/28/amazon-aws-s3-outage-is-breaking-things-f… -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Limitations of maximum number of points in a data file in Athena
by Harishchandra Singh 01 Mar '17

01 Mar '17

Hi All, I have a query regarding limitation of maximum number of data points (or maximum size) of data file in to be imported in Athena. It would be great to hear form you all. Harish

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