August 2014 - Ifeffit - millenia.cars.aps.anl.gov

Be EXAFS and publication
by Joshua Kas 08 Jul '15

08 Jul '15

Hi, This may be a long shot, but I was wondering if anyone is aware of EXAFS data on HCP Be. In particular we are looking for Debye-Waller Factors, so a publication would be great, but just data might work as well. Thanks, Josh Kas

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Re: [Ifeffit] Launching Athena on Mountain Lion (Mac OS 10.8)
by Kyler Carroll 05 Dec '14

05 Dec '14

Hello, I had posted a comment/question a few months back when I had initially installed Mountain Lion on my mac regarding iXAFS compatibility with XQuartz and the new OS not supporting X11 anymore. Since then I have received a few comments back and I found one solution to be the best. This was originally sent by Tsu-Chien Weng from SSRL (tsuchien(a)slac.stanford.edu) Please find the following solution below. Once you install XQuartz the rest will be done in the Terminal.app. This is a one time solution and I havent had any trouble thus far with the program. Hope this works as well for everyone else as it did for me. 1. Install XQuartz from <http://xquartz.macosforge.org/landing/> 2. open Terminal.app 3. cd /Applications/Utilities 4. sudo mkdir X11.app 5. cd X11.app 6. sudo ln -s ../XQuartz.app/Contents Thank you, Kyler J. Carroll, Ph.D. Assistant Project Scientist Department of NanoEngineering University of California, San Diego

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save Artemis project and cannot find Path List information when reopen
by huyanyun＠physics.utoronto.ca 27 Oct '14

27 Oct '14

Hi all, I encountered a serious problem with saving an Artermis project on my windows 8 64bit desktop. When I am ready to finish my fitting work, I click to save the log file, and go to main window to choose -File-'save project as...', and then close Artemis. But when I reopen this saved project, the Path Page lost all information for each path, and the 'Include path' button has been surprisingly unchecked for all path. The GDS page have all information there. This happened to me several times, but it seems sometime the PathPage data is saved and sometime is not, although I think I was doing the exact something. I attached one of my artemis project file and the most recent log file I saved before I close the program. Can anyone have a look and tell me what I did wrong? As my work is proceeding, this would be a very serious problem if I cannot save my 'hardwork'. Best, Yanyun ----- Attachments (links will expire on 28/02/15): 1. CoedgeforGa0.15 fitting.fpj (7.7 MB) [application/zip] Download link: https://webmail.physics.utoronto.ca/imp/attachment.php?id=53ffbffa-2424-413…

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simulating As K edge XANES using full multi scatering method
by Shaofeng Wang 24 Oct '14

24 Oct '14

Dear all, Does anyone have experience for simulating As K edge XANES using multi-scatering method or some other methods. Please introduce some papers or articles to me. Any help is appreciated. Regards, Shaofeng

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Regarding installation of demeter on Mac Mavericks system
by pushkar shejwalkar 03 Sep '14

03 Sep '14

Dear All, I am new to the mac and mac apps as well as not a techie either. I am trying to install the latest version of demeter (artemis, athena and heph) on my macbook using Mavericks OS. For this I followed the steps given on the site with Macports installation, then its activation step. and then I used terminal to connect and download the athena. However there was error which I thought might because of not having the windowing environment ( I am using all the words from site and dont know anything what it means). So I clicked to download X11 from XQuartz site. After that I logged out from terminal and logged in again. to check if anything changes but the following message was observed (the complete message is attached as word document but some part essentially the last portion talking about the error is pasted below. ---> Activating xorg-libXau @1.0.8_0 Error: org.macports.activate for port xorg-libXau returned: Image error: /opt/local/lib/libXau.6.dylib already exists and does not belong to a registered port. Unable to activate port xorg-libXau. Use 'port -f activate xorg-libXau' to force the activation. Error: Failed to install xorg-libXau Please see the log file for port xorg-libXau for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_x11_xorg-libXau/xorg-libXau/main.log Error: The following dependencies were not installed: quartz-wm xorg-libAppleWM xorg-libXext xorg-libX11 xorg-libXau xorg-libXdmcp xorg-libxcb python27 bzip2 db46 db_select gettext expat libiconv ncurses libedit openssl zlib python_select sqlite3 xorg-libpthread-stubs xorg-xcb-proto libxml2 xz xorg-xextproto xorg-libXinerama xorg-xineramaproto xorg-libXrandr xorg-randrproto xrender xorg-renderproto xinit mkfontdir mkfontscale freetype libpng xorg-libfontenc xauth xorg-libXmu xorg-libXt xorg-libsm xorg-libice xrdb xset xorg-libXfontcache xorg-fontcacheproto xorg-libXp xorg-printproto xorg-libXxf86misc xorg-xf86miscproto xkeyboard-config xkbcomp xorg-libxkbfile xorg-fonts font-adobe-100dpi fontconfig font-adobe-75dpi font-adobe-utopia-100dpi font-adobe-utopia-75dpi font-adobe-utopia-type1 font-alias font-arabic-misc font-bh-100dpi font-bh-75dpi font-bh-lucidatypewriter-100dpi font-bh-lucidatypewriter-75dpi font-bh-ttf font-bh-type1 font-bitstream-100dpi font-bitstream-75dpi font-bitstream-speedo font-bitstream-type1 font-cronyx-cyrillic font-cursor-misc font-daewoo-misc font-dec-misc font-ibm-type1 font-isas-misc font-jis-misc font-micro-misc font-misc-cyrillic font-misc-ethiopic font-misc-meltho font-misc-misc font-mutt-misc font-schumacher-misc font-screen-cyrillic font-sony-misc font-sun-misc font-winitzki-cyrillic font-xfree86-type1 xorg-encodings xorg-libXfixes xorg-fixesproto xorg-libXfont xorg-fontsproto To report a bug, follow the instructions in the guide: http://guide.macports.org/#project.tickets Error: Processing of port xorg-server failed Pushkar-Shejwalkars-MacBook:~ Pushkar$ Please help me installing it properly. Really very sorry for the long email but I thought it will be more helpful this way. Waiting for the replies. Thank you very much -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher,JSPS Fellow Hokkaido University, Sapporo, Japan

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EXAFS calculation with large RMAX and NLEG - exceeding path finder limit
by van der Veen, Renske 02 Sep '14

02 Sep '14

Dear FEFF users, Using FEFF8.4, I am trying to perform EXAFS calculations with rather large RMAX and NLEG values. The system of interest is graphite. It has been shown by Castrucci et al (J. Phys. Chem. C 2009, 113, 4848–4855), that convergence of the EXAFS modulations in the region 4-6 A-1 is only achieved for a cluster size of RMAX = 8 and including up to 8-body MS paths (NLEG = 8). I have tried to reproduce these calculations and noticed that the path finder runs into a limit when I use these parameters. I can maximally use RMAX = 7.5 and NLEG = 5. With larger RMAX or NLEG values I get the message: "Internal path finder limit exceeded -- path list may be incomplete.", and the cluster size subsequently truncated at 6-6.5 A (depending on NLEG), instead of the desired 8 A. My path filter criteria are 3% (plane-wave) and 4% (curved-wave). However, these values do not affect the appearance of the above message, which occurs before the path filter is applied. Consequently, altering the 'npx' parameter, as suggested here http://leonardo.phys.washington.edu/feff/wiki/static/c/o/d/Code_Variables_a…, does not help. Is there a way to increase this internal path limit so I can work with RMAX = 8 and NLEG = 8? P.S.1 I guess graphite is a special case for which MS can be very efficient within the graphite planes. In addition, the C-C bond length is quite short, which makes higher n-body paths more important. P.S.2 I have tried merging XANES and EXAFS using the cards: XANES, FMS 6, RPATH 8 and NLEG 8, but the same problem occurs and the agreement with experiment in the low-k region 3-6 A-1 does not become better using FMS (compared to the path expansion). Thanks in advance, Best wishes, Renske

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spline fitting
by Matthias Filez 29 Aug '14

29 Aug '14

Dear mailing list users, I am trying to fit the spline background function in a proper way to a spectrum (Ga K edge, see attached). However, it doesn't seem to work out, but I don't see why. I already tried the following: * Vary the Rbkg value * Change spline k-weight * Change k-range of spline fitting * Alter the strength of spline clamps ... and the combination of these effects. Since there is a strong white line, I suspect this causes the spline misfit. The data quality is OK. If you have any idea, please post it. Thanks in advance, Matthias _____________________ Matthias Filez Laboratory for Chemical Technology Department of Chemical Engineering Ghent University Technologiepark 914, B-9052 Zwijnaarde, Belgium +32 (0)9 33 11721 www.lct.ugent.be<http://www.lct.ugent.be/> Disclaimer: http://helpdesk.UGent.be/e-maildisclaimer.php<http://helpdesk.ugent.be/e-maildisclaimer.php>

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Demeter OS X plot button colors in Athena
by Schima, Frank 27 Aug '14

27 Aug '14

Hi Bruce, We are seeing an issue in Athena where the plot buttons are not colored correctly. According to section 2.1 of the Athena Users’s Guide, the top row of plot buttons highlighted in the image should be the same color (purple) as the plotting option widgets below them. The 2nd row of plot buttons should be yellowish. However on OS X, all plot buttons appear uncolored. By far the best way to illustrate this is with a screenshot of the Athena UI. I hope the attached image is clear enough to show the issue. I am running Demeter version 0.9.20pre10 via Macports demeter-devel on OS X 10.9.4. BTW, I am happy to work with you on other OS X issues but I am not actually a demeter user and I don’t have much data myself. But if you send me some data, I can follow steps to try to reproduce issues. [cid:F140B9BC-1ABC-4ACE-B222-A833F804F78B] Cheers! Frank

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XAFS short course at Brookhaven
by Anatoly I Frenkel 26 Aug '14

26 Aug '14

Dear subscribers: An annual short course on Methods and Applications of XAFS Spectroscopy will be run at Brookhaven National Laboratory in Nov. 13-15, 2014. The application deadline is Sep. 1. The application form is available at the course web site: http://workshops.ps.bnl.gov/?w=XAFS2014 The application form should filled out first; the 45 participants accepted to the course will be later contacted with registration information. Best regards, Anatoly Anatoly Frenkel, Professor Department of Physics, Yeshiva University 245 Lexington Avenue, New York, NY 10016 https://yu.edu/faculty-bios/frenkel/ Spokesperson, Synchrotron Catalysis Consortium http://yu.edu/scc Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.frenkel(a)yu.edu<mailto:anatoly.frenkel@yu.edu>

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math functions on GDS page
by huyanyun＠physics.utoronto.ca 21 Aug '14

21 Aug '14

Hi there, When I input math expression in the GDS page, I wonder if Artemis recognizes some general math functions, such as 'sqrt', 'cos', 'sin'. Could anyone help me find a list of all math functions covered in Artemis? Best, Yanyun

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