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

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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*****SPAM*****Acess download Athena sofware
by Joyce Ribeiro de Paula Santos 28 Feb '17

28 Feb '17

Hi folks My name is Joyce and I'm PhD' student in the Universidade de São Paulo, Brazil. Today, I tried to make a download of Athena software in the web site: http://bruceravel.github.io/demeter/ , but I couldn't make it. Could you provide me the link to download the athena software? Or give instructions how to make a download? Thanks -- Joyce Ribeiro de P Santos Graduada em Bacharelado em Ciências Biológicas - UFSCar Mestre em Microbiologia Agrícola - ESALQ/USP Doutoranda em Ciências Química na Agricultura e Ambiente - CENA/USP

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Units for various parameters of ‘feffNNNN.dat’ file
by Samy Ould-Chikh 28 Feb '17

28 Feb '17

Dear Ifeffit mailing list, I have a question which concern units and I can’t find the answer in the Feff manual. In a FeffNNN.dat output file, what are the unit of the numbers (if any) corresponding to φc, |Feff|, φeff, the reduction factor, λ, Re(p) Thanks for the help. Best Regards, Samy Ould-Chikh KAUST Catalysis Center Bldg.3,Level 4, #4231 4700 King Abdullah University of Science & Technology Thuwal 23955-6900 Kingdom of Saudi Arabia Tel: +966 12 8084486 E-mail: samy.ouldchikh(a)kaust.edu.sa<mailto:eman.ahmedbahjri@kaust.edu.sa> Website: http://kcc.kaust.edu.sa/Pages/Home.aspx From: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Ritimukta Sarangi Sent: Thursday, February 23, 2017 11:17 PM To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] SSRL EXAFS Summer School 2017 Hello everyone, Responding to popular demand, the SSRL summer school will be held during the last week of June in 2017. More information will be available on the SSRL website soon and I will send a link to the school webpage to this list (when its available). Stay tuned! Best, -Riti Sarangi SSRL ________________________________ This message and its contents including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Calculation of metal concentration (and hence density) from Edge Jump
by pushkar shejwalkar 27 Feb '17

27 Feb '17

Dear All, First of all, is it possible to calculate the concentration of metal (loading, therefore) from just the edge jump? Is there a simpler equation like knowing the Flux values or some basic instrumental information we can calculate the concentration term using Io and It values of beamline (the simplest form of Beer-lambert law)? if so what formula should we use. I searched in the mailing list archive and have found one such archive but it discusses how to use calculation to find out how much sample would be needed to get the edge jump. I am rather interested in the reverse way. I have an experimental edge jump and want to calculate (if possible with as much accuracy as possible) the concentration of metal. I know with only edge jump it will be difficult and XRF will be a better and more reliable way. But for better understanding and cross checking between different samples, I wish to do such calculations. Can anyone guide me to the right direction and equations to do such calculations? Thank you all in advance Warmest regards Pushkar -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Tokyo-to Japan

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SSRL EXAFS Summer School 2017
by Ritimukta Sarangi 23 Feb '17

23 Feb '17

Hello everyone, Responding to popular demand, the SSRL summer school will be held during the last week of June in 2017. More information will be available on the SSRL website soon and I will send a link to the school webpage to this list (when its available). Stay tuned! Best, -Riti Sarangi SSRL

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EXAFS and XANES Summer School at SSRL
by Ritimukta Sarangi 23 Feb '17

23 Feb '17

Hello folks, I have received several queries over the last 6 months about hosting an EXAFS Summer School in 2017 at SSRL. Typically we host it every other year, so we would have offered the School in 2018. However, if there is very high interest, we would certainly consider hosting a school in 2017. Please reply to me directly at ritis(a)slac.stanford.edu if you or your group will benefit from a school in 2017. Please note that we if go ahead with it, the school will be in the June-July 2017 timeframe. Best wishes, -Riti Sarangi SSRL

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Bond length and Coordination number problems from EXAFS
by Fuxiang Zhang 21 Feb '17

21 Feb '17

Dear All, I met a problem in fitting my sample. The sample is a very simple crystalline Ni (fcc) with minor Pd. I measured both the K-edge of Ni and Pd and fit with a 55 randomly distributed cluster model (from calculations). The model suggested that there are 1 Pd in the first and second-shell, 6-Pd in the 3rd-shell and 2-Pd in the 4th shell. I have attached the FPJ file here, can anyone help me to have a look. 1. In fitting the K-edge of Pd, most paths are single scattering, but I always get a shorter Pd-Pd length than Pd-Ni, even I tried to include all the paths. Not sure if I made any mistakes in the path parameters settings. 2. If including the minor contribution paths, I use the same parameters for the path: @Ni1.1 Ni1.1@ (acute triangle) and the path: @N1.1 Ni1.1@ (obtuse triangle), as well as single scattering path @Ni1.1@. I know there's a problem (though no much effect on the results), but don't know how to set the first two paths' parameters 3. If the result is correct, which may suggest there is no Pd in the 1st-shell, but how to fit the coordination number of Pd is a problem. Since Pd is only 1/12 in the first shell, while the uncertainty of CN from EXAFS fitting is pretty large. Does it make a sense to refine the CN? FPJ file is attached Thank you very much Fuxiang Zhang

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