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

Ta L3 edge and Pt L2 edge
by Natee Sirisit 29 Oct '15

29 Oct '15

Dear all Do anyone have an Ta L3 edge of TaN and Pt K and L2 edge of (1,5-Cyclooctadiene)dimethylplatinum(II). Could you share the copy to me please? Many thanks for considering my request. Sincerely yours, Natee -- Natee Sirisit Ph.D. student Graduate school of engineering and Catalyst Surface Research Division, Institute for Catalysis (ICAT) Hokkaido university Sapporo 060-8628, JAPAN Tel.: (02)1129115 Email: sirisit.n(a)cat.hokudai.ac.jp

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Athena and Artemis installation problem
by Wuhib Tamrat 27 Oct '15

27 Oct '15

Hi all, This is with regard to an installation problem that I am facing at the moment on my Mac. Sorry, if this is too basic a problem and the email is spamming your mail box. Below are specifics of three fold problems that I would be happy if I could find a solution for at least one. Problem1: I am working on El Capitan (the latest Mac Operating System) and what I guess the problem to be is compatibility issues with the different required components (X11, XQuartz and Aqua term). And may be with the required macports as well. I installed using the disk image provided on http://cars9.uchicago.edu/ifeffit/Downloads <http://cars9.uchicago.edu/ifeffit/Downloads> and had followed all the instructions given. I see that the latest OS available is for ‘Snow Leopard’ but the package works well on colleagues’ computers with latter versions of mac OS. The problem is that all get installed but when I open the software suit, the initial small window that has the three individual programs opens but what ever I do to it afterwards it does not open into anything else. There is also the option to choose a file. So I navigate and choose a file thinking it will help pushing the program to open but that leads to nowhere as well. So, I am wondering if anybody had faced similar problem installing on the latest versions of mac OS and has a solution. Problem 2: Initially I tried installing the “demeter” suit via ‘Terminal’ as specified in the site [http://bruceravel.github.io/demeter/ <http://bruceravel.github.io/demeter/>]. By writing a command on Terminal as opposed to with a disc image as in the case of Problem 1). My operating system at that time was Yosemite. All worked as explained on the website, even writing “athena” on a terminal window calls the program Athena. But that is just it, no explanation as how to call Artemis or Hephaestus exist on the site. So I am wondering if the installation procedure given on the site works also with the other two programs and if so, is there a way to open them or call them via ’Terminal'. Problem 3: My last problem was when Athena closed unexpectedly. As most programs, Athena had an auto recover option which opens when it is restarted. But this time the auto recover option always comes up and this option renders the whole program inactive; “Application Not Responding”. Every time I open Athena, “Auto recover” option comes up and Athena become unresponsive. I tried updating the software in hope of changing something but that did not change anything. Uninstalling it is also a problem because there were no files that I could find to uninstall from or delete. I could not find the location where terminal installed the “Demeter” suit. There is a way to delete on terminal by writing “Sudo rm-rf/file name” but that is not removing “demeter” either. And yes, I have consulted the IT/informatics people at my institution and they were no help. I thank you in advance for any suggestion or similar experience sharing. And also for baring with me reading this long mail. Regards Wuhib

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Magnetic EXAFS simulation using FEFF8.4
by Jerry Li 26 Oct '15

26 Oct '15

Dear All, I am trying FEFF simulation of the spin polarized spectra of single crystal Tb, see the attached Feff.inp . However, the results xmu.dat doesn't show any the mu+ and mu- as I expected, just NaN instead. Could you please help me check what is wrong with the input file? Jerry

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Unable to run Demeter on EPA computers
by Matt Noerpel 22 Oct '15

22 Oct '15

Hello Ifeffit list, I just started a post-doc position at the EPA and I will need to use Artemis and Athena. Unfortunately, nobody here is able to run Demeter on their work computers. The old version (0.8) does work. We all have new Dell computers running Windows 7 64 bit. I tried version 0.9.22 (with explicitly setting the path at the top of the batch file) and 0.9.23 prerelease 3, but neither work. The program opens the command prompt, shows the splash image briefly, and then disappears and produces the log file (shown below) in the AppData folder. This seems like it has something to do with the way our computers are set up here. An IT specialist (cc:ed here) was working on it for a while today removing user restrictions etc., but the problem didn't change. Does anyone have any idea what could be causing this problem or have you encountered a similar problem with government computers? Thanks, Matt Noerpel dathena.log: BEGIN failed--compilation aborted at C:/demeter/perl/site/lib/Demeter.pm line 54. Compilation failed in require at C:/demeter/perl/site/lib/Demeter/UI/Athena.pm line 24. BEGIN failed--compilation aborted at C:/demeter/perl/site/lib/Demeter/UI/Athena.pm line 24. Compilation failed in require at C:\demeter\perl\site\bin\dathena.bat line 43. BEGIN failed--compilation aborted at C:\demeter\perl\site\bin\dathena.bat line 43. Started at 2015-10-14T14:31:22 Win7Enterprise (64-bit) Service Pack 1 Service Pack 16176012102561 PATH is: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\demeter\c\bin;C:\demeter\perl\site\bin;C:\demeter\perl\bin;C:\demeter\c\bin\gnuplot\bin perl version: v5.18.2 backend: ifeffit @INC: C:/demeter/perl/site/lib/MSWin32-x64-multi-thread C:/demeter/perl/site/lib C:/demeter/perl/vendor/lib C:/demeter/perl/lib . Can't load 'C:/demeter/perl/site/lib/auto/Ifeffit/Ifeffit.dll' for module Ifeffit: load_file:Invalid access to memory location at C:/demeter/perl/lib/DynaLoader.pm line 190. at (eval 18) line 1. Compilation failed in require at (eval 18) line 1. BEGIN failed--compilation aborted at (eval 18) line 1. For what it's worth, some dodgy corners of the internet suggest using XSLoader instead of DynaLoader. When I do that, the error message is exactly the same except replacing DynaLoader with XSLoader.

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Demeter 0.9.23 in multi-user environments
by Godfrey, Ian 19 Oct '15

19 Oct '15

Hi All, I'm trying to install Demeter 0.9.23 on a Win 8.1 Pro x64 machine with two user accounts set up. Both user accounts on this PC need to use Demeter. Unfortunately the latest version of Demeter installs into a user specific folder, which creates two problems: 1) Users do not seem to have access to each other's folders to run Demeter 2) The shortcuts (start menu/desktop) only get installed/updated for the installing user Compounding this issue the installer automatically removes any existing installation at installation, so you can't simply install it twice. Thanks, Ian Ps. Any update on this message: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2015-August/012662.html ?

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XES calculations for hematite
by Michal.Nowakowski 19 Oct '15

19 Oct '15

Dear All, I'm PhD student from Poland. I have recently tried to calculate Kß line of XES spectrum for hematite using FeFF9.6 code but I'm unable to reproduce the spin-dependent satellite peak Kß'. I've alredy tried to use SPIN card with XES card. Is there any possibility to do it in FeFF? Thank you in advance, Michal Nowakowski -- Open WebMail Project (http://openwebmail.org)

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XAFS short course in BNL on Nov 5-7
by Anatoly I Frenkel 14 Oct '15

14 Oct '15

Dear subscribers, As a follow up to my previous message, the web page for the XAFS short course at Brookhaven and the application form are live: http://workshops.ps.bnl.gov/?w=XAFS2015 Please note the application deadline, September 20. Best regards, Anatoly Anatoly Frenkel, Ph.D. Professor and Chair, 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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Fwd: XAS tutorial videos
by Bruce Ravel 14 Oct '15

14 Oct '15

Hi Wuhib, This is a sufficiently general question that I am forwarding my answer to the mailing list. The videos are not my property, they belong to Diamond. You are correct that the manner in which they are streamed does not allow for jumping around, but there is nothing that I can do about that. You also mentioned that Shu had given you a download link (I have not included the link what I echoed blow because I do not know if Shu and the folks at Diamond want that link advertised). I have no trouble downloading or running them. Once downloaded, I can jump around as expected. If you are having "browser/network" issues, that seems like a problem for you (or your institution's IT folks) to solve. Again, there's nothing I can do about that. Final point, please use the mailing list in the future rather than writing to me directly about issues related to the software. Good luck, B -------- Forwarded Message -------- Subject: XAS tutorial videos Date: Wed, 14 Oct 2015 16:23:09 +0200 From: Wuhib Tamrat <tamrat(a)cerege.fr> To: bravel(a)bnl.gov Hello Bruce, My name is Wuhib and I am a PhD student in Aix Marseille University (France). I am recently being introduced to the world of XAS and I found your training videos from November 2011 at the Diamond Light source quite helpful. But the problem is that the streaming version does not give the flexibility to go back and forth to specific times in the lecture video. So I was wondering if you could find a way to send me the videos, if you have them and if it is not much trouble. Thank you. Regards Wuhib PS: I received a link from Dr. Shu Hayama but as he himself guessed I am having difficulty playing and downloading the .wmv files due to probably browser/network related issues. -- 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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larch xray plugin - incorrect chantler data at edges
by Dr. Johannes Zellner 14 Oct '15

14 Oct '15

Hi, the larch xraydb plugin doesn't provide correct numbers for chantler f1 data around edges. Apparently this is due to incorrect interpolation in xray/xraydb.py in line 274. Below is a plot of "delta" from xraydb_plugin.xray_delta_beta() for Silicon which is terrribly wrong. The more correct "delta" as from chantler is shown in the following plot: --> I'd recommend to replace (line 274 in plugin xray/xraydb.py): out = UnivariateSpline(te, ty, s=smoothing)(energy) by a simple linear interpolation out = np.interp(energy, te, ty) The latter yields linear segments between chantler's data, but this is still better than the totally unphysical spline interpolation. Best regards, -- Johannes

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a bug when installing demeter
by Zhenxing Feng 13 Oct '15

13 Oct '15

Hi, I am trying to install Demeter on my Mac OX X EI Capitan. After installing MacPorts properly, I run the command, “sudo port install xorg-server demeter”. However, it reports a bug when building libgcc, when the following errors: Error: org.macports.build for port libgcc returned: command execution failed Please see the log file for port libgcc for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/libgcc/main.log Error: Unable to upgrade port: 1 Error: Unable to execute port: upgrade ifeffit failed Could you help figure out how I can proceed further? Thanks, Zhenxing

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