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

SSRL XAFS Summer School
by Ritimukta Sarangi 01 Mar '18

01 Mar '18

Hello, SSRL will host its annual summer school this year during the third week of August (13th-17th). The focus of the school will on EXAFS hands on data analysis. In addition, electronic structure determination from the XAS pre-edge analysis and advanced spectroscopies will be covered. Examples from a wide range of scientific applications will be covered, including metals in biology, chemical catalysis, heterogenous catalysis and materials. I will post more information here, as and when it becomes available (hopefully soon) and we hope that many of you can attend. Best Wishes, -Riti Sarangi

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Error message "typo in Template.pm"
by Elizabeth Tomaszewski 26 Feb '18

26 Feb '18

Hello, I keep getting the error message ""Demeter::Templates::D" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.24/Text/Template.pm line 556, <DATA> line 236.” I located the Template.pm file but can not edit the template without changing permission in the terminal, which I don’t know how to do. Line 556 reads: local *SYM = *{"$ {dest}::$name”}; Line 236 reads: $cur_item .= '\\’; Athena will open when I type in the command window but I can only see the GUI for a second before the error message comes up and it has to shut down. Please help. Thanks, Elizabeth Tomaszewski

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call for nominations for the IXAS Awards
by Matt Newville 16 Feb '18

16 Feb '18

Hi Folks, I realize that many of you will have received this from the IXAS mailing list, but I'd like to invite everyone here to consider nominations for the IXAS Awards too: The Awards Committee of the International X-ray Absorption Society (IXAS) seeks nomination for three awards. These awards will be presented at the XAFS17 Conference in Krakow, Poland. The three awards are: 1. The Edward Stern Outstanding Achievement Award: This is the highest award of the International X-ray Absorption Society. Nominations are invited across all disciplinary areas including both experimental andtheoretical studies of XAFS. Award: $1000 2. The Farrel Lytle Outstanding Young Scientist Award for Theory and Instrumentation: Nominee must have made remarkable contribution to the field of X-ray absorption spectroscopy. Nominee should be within 8 years of a Ph.D. (or equivalent) degree as of April 1, 2018. Award: $500 3. The Dale Sayers Outstanding Young Scientist Awards for Applications of XAFS: Nominee must have made remarkable contribution to the field of X-ray absorption spectroscopy. Nominee should be within 8 years of a Ph.D. (or equivalent) degree as of April 1, 2018. Award: $500 Nominations should include a CV with publications, a letter of recommendation and academic referees who can be contacted for further reference. The deadline for nomination is May 1, 2018. Please send nominations by email to IXAS vice chair Matthew Newville newville(a)cars.uchicago.edu Thanks, --Matt Newville

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Job Posting
by Frejka, Jean M 16 Feb '18

16 Feb '18

Can you please post and/or upload the attached job posting? The position is for a Data Analysis Engineer at Brookhaven National Laboratory. I have attached a two pdf files: (1) short version for posting on a bulletin board and (2) a longer version to upload or email. If you have any questions, please contact me. Thank you for your assistance. Jeannie ************************************* Jean Marie Frejka Brookhaven National Laboratory Nuclear Science and Technology Department Building 817, 33 North Renaissance Road Upton, NY 11973 Phone: 631-344-2349 Fax: 631-344-2806 frejka(a)bnl.gov<mailto:frejka@bnl.gov>

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Artemis having trouble
by Sheraz Gul 09 Feb '18

09 Feb '18

Can anyone please explain why Artemis is failing to open the fpj file I have attached? It doesn't respond anymore and screen look like the screenshot attached. It has happened to me multiple times now; I'm using Demeter version 0.9.25 on windows 10. Best regards, -- Sheraz Gul

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XAFS short course in BNL: Nov 1-3, 2017
by Anatoly Frenkel 09 Feb '18

09 Feb '18

Dear subscribers: Please share with your group members or others, who may be interested, the following information about the short course on XAFS spectroscopy: Title: *Data Analysis and Modeling of XANES and EXAFS Spectra. Applications to Nanomaterials* Dates: *November 1-3, 2017* Location: *Brookhaven National Laboratory* The course is open for applications at this web site: https://www.bnl.gov/exafs2017/ <https://mail.bnl.gov/OWA/redir.aspx?C=Cs5LzjKsiYS2QXnknBXt0VXGF6SSe4a5Kclqc…> The course will be useful for those scientists who are familiar with the foundations of XAFS experiment, theory and data analysis, and seek training in advanced methods. The course will include lectures, software demonstrations, and data analysis sessions. The emphasis will be on applications of XAFS to nanomaterials but we will welcome all participants who are interested in modern analysis methods. The course instructors will use examples from their research during presentations. The topics covered will include: -Theory of XANES, -XANES data analysis, -Structural refinement using XANES, with emphasis on the following methods: -Molecular dynamics, -Reverse Monte Carlo. -Machine Learning methods During the data analysis practicum on November 3, participants will get an opportunity to work with research projects with the help of the course instructors. The course is co-sponsored by BNL and Synchrotron Catalysis Consortium (SCC). Best regards, 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/chemistry/bio/FrenkelAnatoly.asp Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

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larch warning that I don't understand
by Ravel, Bruce 08 Feb '18

08 Feb '18

Matt, When Larch starts, what is meant by warnings like this: No handlers could be found for logger "pyFAI.opencl.common" or No handlers could be found for logger "pyFAI.gui.matplotlib" The first one went away by installing python's opencl interface -- a rather sizable prerequisite! I haven't figured out how to make the second one happy. Thanks, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter

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Demeter Mac install on High Sierra
by Alexandre Simionovici 05 Feb '18

05 Feb '18

Hi guyz, Trying to install Demeter on a Mac thru the Macports command: sudo port install xorg-server demeter neither demeter nor xorg-server is known ! Macs nowadays have XQuartz as X11 window manager so xorg is not needed but what about Zeus' wife ? Has someone managed to install it on High Sierra or even Sierra ? TIA, Alex -- _____________________________________________________________________ | Pr. Alexandre Simionovici | |Institut des Sciences de la Terre, UGA/CNRS tel. +33-(0)4.76.63.51.96 | |Observatoire des Sciences de l'Univers de Grenoble fax. +33-(0)4.76.51.40.58| |UMR 5275, Maison des Géosciences, alexandre.simionovici(a)univ-grenoble-alpes.fr| |CS 40700, 38058 Grenoble Cedex 9, FRANCE | |------------------------------------------------------------------------------------------------------------------|

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Autosave; problem with Athena crashing on mac
by Astrid Avellan 16 Jan '18

16 Jan '18

All, I recently updated my mac OSX and had to change for iXAFS on my OSX 10.8 to the demeter servers on 10.12 It was runing fine, untill Athena crashed. When I was trying to restart it, it was frozen, asking me if I want to open the autosave file, but no being able to click anywhere. All the posts online says that you want to find the file athena.autosave in your Mac in the folder $home/.horae/stash The trick is that you CANNOT see these folders by default in your Mac. To show the hidden folders in your system, you have to type into your terminal $ defaults write com.apple.finder AppleShowAllFiles YES killall Finder Once you have done that, you can find the .horae folder ONLY manually in $home/.horae/stash. A search in your folder finder will NOT work. I deleted the Athena.autosave folder, AND open the Demeter.ini file (in $home/.horae/downloads) and chance “autosave=true” for “autosave=false”. Once you are done, you can hide the folders again by typing $ defaults write com.apple.finder AppleShowAllFiles NO killall Finder Now, everything is running smoothly. But I don’t have any autosave : I autosave myself regularly! Enjoy a long life with Athena! Best Astrid

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Re: [Ifeffit] How to use Artemis with feff85L
by Bruce Ravel 12 Jan '18

12 Jan '18

Jose, I am unclear what you are sad about. The version of Feff has little to do with the quality of the analysis. See our recent paper: https://doi.org/10.1107/S1600577517011651 It is true that feff8l would simplify and streamline the code, making it easier to write and maintain. That's a bit incentive /for/ /me/ to do that work. But I think you are overstating the impact on the analysis you and others do with Artemis. B On 01/12/2018 07:15 AM, José Carlos Conesa wrote: > OK Bruce, I understand. (Sigh) > > Good luck in your actual job. > > JC > > > El 12/01/2018 a las 12:35, Bruce Ravel escribió: >> >> Yes. But I am pretty busy these with my new beamline. >> >> "Beamline scientist" is my actual job. "Software guy" is a side >> project. So the software work gets done when it gets done. >> >> B >> >> >> >> On 01/12/2018 05:25 AM, José Carlos Conesa wrote: >>> Dear Bruce, >>> >>> Do you foresee that (in a not far future) Artemis may be adapted so >>> that it can use the results of feff8.5L? >>> >>> All the best, >>> >>> >>> El 12/09/2017 a las 19:11, Bruce Ravel escribió: >>>> >>>> Feff8L is not properly integrated into Artemis yet. Sorry. I have >>>> a new beamline these days. It's hard to find time to work on the >>>> software. >>>> >>>> This is on my to do list, but it's going to take a while. >>>> >>>> B >>>> >>>> >>>> On 09/12/2017 12:54 PM, José Carlos Conesa wrote: >>>>> Hi, >>>>> >>>>> I should like to use feff85L within Artemis (from Demeter 0.9.25), >>>>> just to check in my system whether selfconsistency has a role in >>>>> unifying E0 values (with feff 6, allowing different E0 for each >>>>> scatterer leads to E0 differences >10 eV, which seems too much to >>>>> me). I find that after loading the EXAFS data (from Athena) and a >>>>> model (a .cif file containing Cu, Ce and O atoms), if I click Run >>>>> Atoms and then Run Feff with feff6 as executable I get the usual >>>>> set of paths that allow me doing a fit of the data, but if I try to >>>>> use the feff85L.exe that comes with the Demeter software (by >>>>> changing the feff executable in the File/Edit preferences menu), >>>>> after clicking the Run Feff button (without including the SCF card) >>>>> a bit of computation happens and after finishing it the path list >>>>> is empty. >>>>> >>>>> ¿Any idea of the possible reason why I get no path list? >>>>> >>>>> Thanks in advance >>>>> >>>> >>>> >>> >> >> > -- 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/ Beamline: https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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