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

Hephaestus crash
by Darren Dale 17 Feb '13

17 Feb '13

Hello all, I'm working on getting my ifeffit/demeter environment together, following the instructions at http://bruceravel.github.com/demeter/pods/installation.pod.html . When I run hephaestus, select F'/F'', and then select any element in the table, the program bails and I get some feedback in the terminal: Can't use string ("Demeter") as a HASH ref while "strict refs" in use at accessor Demeter::devflag (defined at /home/darren/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter.pm line 100) line 8. Sometimes, "<F> line 29." is appended to that error message. I'm running the forthcoming kubuntu 13.04. Any ideas how I can improve my install? Thanks, Darren

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demeter windows download
by Darren Dale 17 Feb '13

17 Feb '13

Hello Bruce, All, I wanted to install Demeter on my windows computer this morning. I followed links to instructions at http://cars9.uchicago.edu/ifeffit/Demeter/WindowsUpdater , which in turns links to https://github.com/bruceravel/demeter/downloads . Unfortunately, github recently discontinued the downloads service, so that is not a functioning link anymore. Is there a new location available to find the installer? Thanks, Darren

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problem of paths calculation
by wangshaofeng＠iae.ac.cn 17 Feb '13

17 Feb '13

Hello Bruce, I am using demeter-atoms to calculate paths using a cif file (see attachment). When I run feff to calculate paths, there is a dialog box saying "You have defined ipot #1 but not used it in the atoms list". If I change the core atom from Ni to S, the calculation can be done. So how to solve this problem. Shaofeng

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Athena doesn't start - Larch server not running
by Ivan Stijepovic 16 Feb '13

16 Feb '13

Dear Bruce and other people in the list, I have just installed Demeter from the git on Ubuntu 12.04 using instructions given by Dave Hughes ( https://gist.github.com/waveform80/3959252) Everything went fine during installation but then I tried to start Athena using *dathena* command from the terminal and I got this message: Demeter says: Uh oh! You have requested using Larch, but there is no Larch server running! Then I installed Larch (with some problems during installation, but that is different story) and again tried starting Athena with the same result. When I tried starting Larch in a server mode with *larch -r* command it didn't offer a possibility to start Athena in the same terminal window. Then I opened a new tab in the terminal and just typed *dathena* and the GUI appeared. Now, I have two questions: 1. Do I have to start Larch server every time like this before using Athena or is there some other solution for this? 2. I tried Artemis without Larch server running and didn't get the error message. Is Artemis independent from Larch or are there some problems that might occur later? -- Best wishes, Dr Ivan Stijepović Department of Materials Engineering Faculty of Technology University of Novi Sad Bul. cara Lazara 1 21000 Novi Sad Serbia tel: +381 21 485 3750 fax: +381 21 450 413 e-mail: ivan.stijepovic(a)gmail.com

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Re: [Ifeffit] Demeter administator mode.
by Bruce Ravel 13 Feb '13

13 Feb '13

On Tuesday, February 12, 2013 04:19:55 PM you wrote: > Dear Bruce, > I am researcher from ICIQ, Spain and we produced some data at ALBA > synchrotron light facility in Barcelona ,Spain. My question is about > Demeter software in administrator mode. It works in only admin mode so it > can’t be used to normal users in our institute workgroup. Is there any > solution to this problem ? Atul, First off, I am CCing my answer to the Ifeffit mailing list, which is the appropriate venue for questions about the software. You can join the mailing list at http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Secondly, I provide instructions for submitting a useful and actionable bug report at http://bruceravel.github.com/demeter/pods/bugs.pod.html The advantage of following those instructions is that, including sending the log file with the initial report, it expedites my ability to understand the problem you are having. Finally, I think I recognize the problem you are having. Demeter attempts to write to "%APPDAtA%\demeter" where %APPDATA% is typically C:\Users\<username>\AppData\Roaming\ on Win 7 and C:\Documents and Settings\<username>\Application Data\ on Win XP. In the last release, I attempted to fix a problem whereby "%APPDAtA%\demeter" was not created at the time of installation. Athena or Artemis would then try to write to that location and fail because that folder did not exist. My "solution" in the last release was not correct and I hope to fix that in the upcoming release. The likliest solution to your problem is to create that folder by hand for each user, then try running the programs again. If that does not work, then please report back *to* *the* *mailing* *list* and I will again try to figure out what the problem is. Regards, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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Molybdenum nitride spectrum for Mo k and/or Mo L3 edge
by Soma Chattopadhyay 12 Feb '13

12 Feb '13

Hello Was wondering if anybody has a Mo k edge and/or L3 edge exafs spectra/spectrum (preferable with Mo foil in reference) for the compound molybdenum Nitride and can send me data. Will appreciate very much. Thanks Soma

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Basic question in normalization and background removal
by Bajamundi Cyril 08 Feb '13

08 Feb '13

Hello, I have here a very basic XANES data processing. I am but a novice in this XANES analysis. In Bruce's lecture "Athena: Data processing I<mms://diamstream02.diamond.ac.uk/xafs-2011-2>" posted in the Diamond Light Source website, he used the Fe_lepidocrocite.000 example to show how background removal and normalization is done. For the normalization range he used the range 150 - 742.610 because his original photon energy scan range is quite long [ Emin: -200 and Emax: 800]. However, say that your original scan range is only short e.g. within the range Emin : -30 to Emax: 80, such that you don't see the non-wiggly range and you only see the a short portion of the post edge range, how does one set the normalization range for this data? Since I'm very new to XANES analysis, I keep second-guessing my choice of normalization range. Your patience for answering this simple question will definitely help me in moving to the actual fingerprinting analysis that I need to do with my sample. Many thanks. Warm regards, Cyril [cid:image004.jpg@01CE05DE.B8F89320] [cid:image007.jpg@01CE05DE.B8F89320]

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XAS position in Industry
by Shelly Kelly 06 Feb '13

06 Feb '13

Dear XAS Community, We have a position open at UOP LLC, A Honeywell Company to support our XAS/tomography group. The position description can be found under Req number 00213183 at http://www.careersathoneywell.com/en/home. Please apply through the web site. Thank-you, Shelly Kelly

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Open post-doc position in Korea
by Deok-Yong Cho 03 Feb '13

03 Feb '13

Dear Ifeffit users: To whom interested in post-doc position in Korea: A two-year contract post-doc position is open in the Center for Functional Interfaces of Correlated Electron Systems (CFI-CES), Institute for Basic Science (IBS), located in Seoul National University, Seoul, Korea. We expect he/she will perform spectroscopic analysis including IR spectroscopy (Spectroscopic ellipsometry and FT-IR) at the institute and synchrotron experiments such as soft/hard x-ray absorption spectroscopy and XAFS analysis for new functional oxide materials (mainly strongly-correlated electron system). Please find enclosed document for more details. Best Regards, Deok-Yong Cho Spectroscopy team in CFI-CES, Institute for Basic Science (IBS), Seoul National University

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Re: [Ifeffit] Help with importing binary files from NSLS BM X15B in athena (Bruce Ravel)
by Raoul-Marie Couture 30 Jan '13

30 Jan '13

Dear Bruce, The patch worked, I was able to configure the plugin and import the binary data. I changed the default columns, otherwise some files were imported scrambled: Energy :1 (that one was ok) I0 : 6 (that one was ok) Narrow (I imported I_Trans instead): column 7 Trans (I imported Total_fluo instead): column 8 Wide (I imported S K-alpha fluo instead): column 9. Thanks for the quick and helpful reply. Raoul ________________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov [ifeffit-request(a)millenia.cars.aps.anl.gov] Sent: January 30, 2013 1:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 119, Issue 31 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Look for paper about WL (Gudrun Lisa Bovenkamp) 2. Re: Help with importing binary files from NSLS BM X15B in athena (Bruce Ravel) 3. Re: Look for paper about WL (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Wed, 30 Jan 2013 04:27:35 +0100 From: "Gudrun Lisa Bovenkamp" <bovenkamp(a)physik.uni-bonn.de> To: <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Look for paper about WL Message-ID: <web-12374983(a)be2.uni-bonn.de> Content-Type: text/plain;charset=iso-8859-1; format="flowed" Dear all, I need reference (paper) to say that WL refers to anti-bonding orbitals and in the same context that pre-edge refers to bonding orbitals. Is there any paper that can help me? Thanks, Lisa ------------------------------ Message: 2 Date: Wed, 30 Jan 2013 10:03:49 -0500 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Help with importing binary files from NSLS BM X15B in athena Message-ID: <1855179.1CSfgNSBKa(a)lachesis.bnl.gov> Content-Type: text/plain; charset="us-ascii" On Wednesday, January 30, 2013 02:17:35 AM Raoul-Marie Couture wrote: > I'm trying to import binary files generated at BM X15B of NSLS, at the S > K-edge. I selected the corresponding plugin, and Athena (Demeter 0.9.14) > does not import the columns 7-10 containing the Io, It, IF and S > Kalpha-fluo. It only imports the first few columns and they don't contain > the information I need. If I ask Athena to import more columns it crashes > and exit. When I use the utility at BM X15B to convert the binary files in > simple text files, Athena does not recognize the text files as data file. > I'm I doing something wrong ? Any idea how to solve this problem ? I have > attached a binary file, its text translation (using the utility available > at BM X15B), and a screenshot of what happens when I import a binary file. The problem seems to be one of column selection. I am suspicious that a detail of how the data are saved to the binary files may have changed since I wrote the X15B plugin many years ago. Attached are two file that you should be able to drop in place on top of your current installation. Put both files in C:\strawberry\perl\site\lib\Demeter\Plugins The file "X15B.pm" wil replace the version of the file that is already there. The file "x15b.demeter_conf" is new. Make sure that you save them with filenames *exactly* as written above. For instance, if you let Outlook save "X15B.pm" as "X15B.pm.txt", it won't be recognized by Athena and everything I say below won't work. The new file will allow you configure the X15B plugin. In the Plugin Registry page, rightt click on the X15B entry. See: http://bruceravel.github.com/demeter/aug/other/plugin.html#athena%27splugin… The variables set using that configuration file, tell Athena which columns from the original data file (also which columns from the text conversion using the beamlilne tool) should be preserved when Athena converts the binary blob to an ascii column file. Most of the columns are filled with zeros, which is why the plugin wants to discard those columns. Side note: Athena deals very pooly with ascii data file that don't have the energy in the first column, which is why it has trouble reading the text file from the beamline tool. I would like to hear back from you about how this works out. If it works well for you, then it will be included in the next release of the software. If there are still problems -- then I need to know. B PS: It is possible that the "x15b.demeter_conf" file has the columns for narrow and wide backwards. Let me know if you think that's the case. I am writing this email without wandering down to X15B to ask Paul the details. -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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