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

Bug report - autosave on mac
by Jean-Baptiste ABBE 16 Jul '15

16 Jul '15

Hi everybody, I wanted to report a really annoying problem for mac users. I’m running Athena on my laptop, on OSX 10.10 (Yosemite) with macports. I had to install also quartzX11 to be able to plot data (without it, it couldn’t find the DISPLAY value), but otherwise evrything went smoothly for a few days. Then the first bug occured. I wasn’t able anymore to select any point on the plotting area to do normalization, I had to set the value in the boxes instead. It was annoying, but I could manage that. But now I have a much more disturbing issue. Athena once crashed, (in the terminal, it was sait « Terminated 15 »), and every time I tried to launch it again, the same thing happens : 1) athena launch, a little bit longer than usual 2) a box appear to give me choice to recover data by importing it from autosave or not 3) I can’t select anaything and the rainbow wheel of death appears. After a few hours, nothing changes… and I have to terminate the programm manually. So I do some search on the internet and found thoses topics on the mailing list, and I tried thoses solutions : https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04539.html <https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04539.html> https://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg04514.h… <https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04514.html> I tried to find the autosave file : nothing I tried to uninstall and reinstall macports : nothing I tried to uninstall macports and install the demeter-devel : nothing In demeter-devel, i tried to modify the athena.demeter_config file, by changing the autosave prompt box value from true to false, and despite being admin on ma mac, I’m not able to change antything in the file. So nothing works at this moment. I will try again other solutions, but I will gladly accept any kind of help to solve my issues. Thank you ABBE J-Baptiste

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Be EXAFS and publication
by Joshua Kas 07 Jul '15

07 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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is there any ongoing effort to integrate feff and larch?
by Angel Yanguas-Gil 03 Jan '15

03 Jan '15

So far it seems from the sphinx doc that feff cannot be called from larch. Is there any ongoing effort to implement that? The simplest way would be to create a python module to generate the corresponding feff.inp file, but I'd hate to duplicate someone else's work. Thanks! Angel

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Job offer at DESY
by Edmund Welter 22 Dec '14

22 Dec '14

Dear colleagues, DESY offers a postdoc position at the new PETRA III extension EXAFS beamline P64. If you are interested in details please visit: http://www.desy.de/v2/docs/1418221001-e.pdf If you should know of a colleague who might be interested in the advertised position please feel free to forward this mail. In case you have any question please do not hesitate to contact me (preferentially not via this mail list...) Best regards, Edmund Welter

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Handling large data sets in Athena (and energy dispersive calibration)
by Godfrey, Ian 19 Dec '14

19 Dec '14

Dear All, Here's an issue I recently encountered while trying to handle some very large in situ datasets in Athena; it may be by design/an inherent limitation, rather than a bug, though: (I am running Demeter 0.9.21 pre and Demeter 0.9.20 , both x64 on Windows 8.1 x64 on separate machines). Each of my datafiles contains over 300 columns of u(E) data as space delimited plain text, however when I try and import them to Athena the import window will only display checkboxes up to column 87. I've attached an example datafile and a logfile to this email. (The data is very poor, but that shouldn't be an issue for debugging...) I've also attached a copy of the datafile as it came from the beamline - this also displays the issue, so it's nothing I've done to the file. On a related note, is it possible for the energy dispersive data calibration to be added back to Athena? To get the calibration parameters for this data I had to use the (very) old version! Thanks, Ian ---- Ian Godfrey PhD Student, UCL/JAIST Programme Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London and School of Materials Science, Japan Advanced Institute of Science and Technology i.godfrey(a)ucl.ac.uk<mailto:i.godfrey@ucl.ac.uk> i.godfrey(a)jaist.ac.jp<mailto:i.godfrey@jaist.ac.jp>

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Re: [Ifeffit] non-standard space group P 21/n
by andrea.sanson＠unipd.it 09 Dec '14

09 Dec '14

Dear Wayne, thank you very much for your enlightening answer! Best regards, Andrea Dear Andrea, To convert the atomic positions, use the following equations (starred positions are in the P21/c setting) a* = c b* = b c* = a+b To convert the unit cell,Â A* = C B* = B C* = sqrt{[Ccos(90-beta)]^2+[A-Csin(90-beta)]^2} beta* = 90 - cos-1[Ccos(90-beta)/C*] where cos-1 is the inverse cosine function If you have problems, please double check my geometry for converting the unit cell parameters. Sincerely, Wayne On Fri, Dec 5, 2014 at 9:04 AM, <andrea.sanson(a)unipd.it> wrote: Dear Gordon, thank you for your reply. I tried to use the space group P1, but the resulting local structure around the absorber atoms is completely different from that expected. Andrea HI Andrea, My suggestion, if you know where all the atoms are in the unit cell, is to use space group P1. It may be tedious and brute force in nature, but you won't have to worry about origin choices or non-standard space groups. You will still know which atoms are equivalent and can pick an appropriate one as your target atom. regards, Robert On Fri, Dec 5, 2014 at 8:07 AM, Sanson Andrea <andrea.sanson(a)unipd.it> wrote: Dear all does anyone know if is it possible to create with ATOMS the non-standard space group P 21/n ? Space group keywords are listed at the atoms website http://iffwww.iff.kfa-juelich.de/icp/atoms/atoms.sgml-7.html#ss7.4 but no keyword for P 21/n group is available. Thanks for any suggestion. Best regards, AS _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Wayne Lukens Staff Scientist Lawrence Berkeley National Lab _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Re: [Ifeffit] non-standard space group P 21/n
by andrea.sanson＠unipd.it 05 Dec '14

05 Dec '14

Dear Gordon, thank you for your reply. I tried to use the space group P1, but the resulting local structure around the absorber atoms is completely different from that expected. Andrea HI Andrea, My suggestion, if you know where all the atoms are in the unit cell, is to use space group P1. It may be tedious and brute force in nature, but you won't have to worry about origin choices or non-standard space groups. You will still know which atoms are equivalent and can pick an appropriate one as your target atom. regards, Robert On Fri, Dec 5, 2014 at 8:07 AM, Sanson Andrea <andrea.sanson(a)unipd.it> wrote: Dear all does anyone know if is it possible to create with ATOMS the non-standard space group P 21/n ? Space group keywords are listed at the atoms website http://iffwww.iff.kfa-juelich.de/icp/atoms/atoms.sgml-7.html#ss7.4 but no keyword for P 21/n group is available. Thanks for any suggestion. Best regards, AS _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars

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non-standard space group P 21/n
by Sanson Andrea 05 Dec '14

05 Dec '14

Dear all does anyone know if is it possible to create with ATOMS the non-standard space group P 21/n ? Space group keywords are listed at the atoms website http://iffwww.iff.kfa-juelich.de/icp/atoms/atoms.sgml-7.html#ss7.4 but no keyword for P 21/n group is available. Thanks for any suggestion. Best regards, AS

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Re: [Ifeffit] Launching Athena on Mountain Lion (Mac OS 10.8)
by Kyler Carroll 04 Dec '14

04 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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Regarding a fit for Fe(OTf)2
by pushkar shejwalkar 03 Dec '14

03 Dec '14

Dear All, I am experiencing problem during my fit for Fe(OTf)2 anhydrous. The problem is as follows. I collected the data and used a model to fit. The fitting values and other technical information is as below. The basic problem is Fe(OTf)2 in anhydrous condition is probably not cyrstalline because of which there are no crystal data available. Although .cif file is available for hexahydrate and tetra acetonitrile. But obviously it is not directly useful as I am looking for Fe(OTf)2 only. I used hexahydrate for fitting, and the fit information is given. Is this fit acceptable? *Now two questions* 1) Why do I not see any scattering or peak for Fe-S. I expected S to be a strong scatterer and would show a peak. Under given circumstances it looks like Fe is all surrounded by water and no triflate is present near Fe at all. Is this assumption even make sense (when the bottle said anhydrous) The bottle was not kept under inert condition (and its my fault), but does it mean Fe(OTf)2 is so hygroscopic and that it can actually form such hexahydrate to the full extent? OR there is some inherent problem with my fitting and collection itself. I used RBKG=1.0 2) Is anybody working on Fe(OTf)2 and had such or any other problem indicating that Fe(OTf)2 by itself is a bad choice of precursor because of its reactivity. Also any comments on purification method etc. does anybody know if crystal structure is available for Fe(OTf)2 anhydrous? I could not find it on the quick search or on CCDC. Any other site where I can get crystal data and .cif information? Thank you very much for all the help, I hope the question is asked appropriately and all the other information is provided, however, if anybody needs any other information please let me know. Thank you in an anticipation Best Pushkar Independent points : 16.1250000 Number of variables : 4 Chi-square : 7324.9401796 Reduced chi-square : 604.1187777 R-factor : 0.0195782 Measurement uncertainty (k) : 0.0001264 Measurement uncertainty (R) : 0.0004142 Number of data sets : 1 guess parameters: SO = 1.06525455 # +/- 0.05504541 [1.00000] delE = -2.32587026 # +/- 0.59606221 [-2.77870] delR = 0.00911122 # +/- 0.00503027 [-0.02322] ss = 0.00706809 # +/- 0.00071967 [0.00300] Correlations between variables: delr & dele --> 0.9154 ss & so --> 0.9023 All other correlations below 0.4 name N S02 sigma^2 e0 delr Reff R ========================================================================= O1.1 6.000 1.065 0.00707 -2.326 0.00911 2.09150 2.10061 -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher,JSPS Fellow Hokkaido University, Sapporo, Japan [image: Inline image 3]

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