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

iXAFS on Mountain Lion
by Weng, Tsu-Chien 22 Nov '12

22 Nov '12

Hi, I had problem launching iXAFS on Mountain Lion after the OS upgrade. It seems the path to X11 might be hard wired in the program. Here is my workaround solution by creating a symbolic link to XQuartz. It might be worth sharing the trick. 1. Install XQuartz 2.7.4 from <http://xquartz.macosforge.org/landing/> 2. Launch Terminal.app and issue the following commands: 2.1) cd /Applications/Utilities 2.2) sudo mkdir X11.app 2.3) cd X11.app 2.4) sudo ln -s ../XQuartz.app/Contents 3. Now either double-click on iXAFS.app or command line `open -a ixafs` should work -- Tsu-Chien WENG Stanford Synchrotron Radiation Lightsource 2575 Sand Hill Road, Mail Stop 69 Menlo Park, CA 94025, USA +1-650-926-4107 (office) +1-650-926-4100 (fax)

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(no subject)
by Pooja Gupta 19 Nov '12

19 Nov '12

-- "A Ship is always safe at the shore - but that is NOT what it is built for" *********************************************** Dr. Pooja Gupta Scientific Officer Material research Lab Raja Ramanna Center for Advanced Technology, Indore-452013. (M.P.) INDIA. Ph. No. (O): +91-731-2442123 (M): +91 8435718320 Fax No. (O): +91 7312442140 E-mail ID: pooja(a)rrcat.gov.in

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Calculation of a XANES spectrum
by Wei Li 18 Nov '12

18 Nov '12

Dear colleagues, If I have a structural model with geometry optimised by DFT, how do I obtain a theoretical XANES spectrum based on that model? Second questions is how to calculation the projected density of states (PDOS). Thanks! best regards Wei -- Wei Li Postdoc researcher Environmental Soil Chemistry Group Delaware Environmental Institute University of Delaware, Newark,19713 Tel:631-949-0663 http://ag.udel.edu/soilchem/li.html <http://ag.udel.edu/soilchem/>

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Re: [Ifeffit] Determining errors in R_fit
by Rana, Jatinkumar Kantilal 17 Nov '12

17 Nov '12

Dear Anatoly and Jason, Thank you so much for your feedback !! With best regards, Jatin ________________________________________ 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: Saturday, November 17, 2012 7:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 117, Issue 15 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. Determining errors in R_fit (Rana, Jatinkumar Kantilal) 2. Re: Determining errors in R_fit (Anatoly I Frenkel) 3. Re: Determining errors in R_fit (Jason Gaudet) ---------------------------------------------------------------------- Message: 1 Date: Fri, 16 Nov 2012 18:33:05 +0000 From: "Rana, Jatinkumar Kantilal" <jatinkumar.rana(a)helmholtz-berlin.de> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Determining errors in R_fit Message-ID: <F11168F9CA572049ADA84F3072DE5DB16D329DB2@didag1> Content-Type: text/plain; charset="us-ascii" Dear Ifeffit users, I have a very simple doubt about reporting the uncertainties in R_fit. In the fit, I have assumed that a bond length changes by a constant fraction, *alpha* such that Delta R = R_effective * alpha and, R_fit = R_effective +/- Delta R I can get uncertainties in the fitted value of *alpha* from artemis. But the question is how to work out the uncertainties in the R_fit. Will it be same as that of *alpha* ?? Thanks in advance !!! With best regards, Jatin ________________________________ Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

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Determining errors in R_fit
by Rana, Jatinkumar Kantilal 17 Nov '12

17 Nov '12

Dear Ifeffit users, I have a very simple doubt about reporting the uncertainties in R_fit. In the fit, I have assumed that a bond length changes by a constant fraction, *alpha* such that Delta R = R_effective * alpha and, R_fit = R_effective +/- Delta R I can get uncertainties in the fitted value of *alpha* from artemis. But the question is how to work out the uncertainties in the R_fit. Will it be same as that of *alpha* ?? Thanks in advance !!! With best regards, Jatin ________________________________ Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

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Demeter on windows 8
by George Sterbinsky 14 Nov '12

14 Nov '12

Hello, Has anyone been able to install Demeter on windows8? When I try to open Athena I get the message in attached screen shot. I tried reinstalling as suggested by the message, which did not help. One thing I noticed however was that Perl was not removed by the built in Demeter uninstaller. Any suggestions appreciated. Thank you, George

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questions about plotting old fits with demeter/artemis
by Georges Siddiqi 13 Nov '12

13 Nov '12

Hi All, I recently upgraded to the new version of demeter/athena/artemis, and while it is very nice to use, I am thoroughly lost in some areas. In the old version of Artemis, it is very easy to select old fits and plot them compared to the experimental data/new fits. I cannot figure out how to do this in the new version. The tutorial merely says "The history plotting tool is not currently working, making it difficult to write this bit of documentation!" Currently what I do is goto the "history" box of the main window, and goto the "plot tool" tab, but I can only add the 9 first fits to the plotting list. Any suggestions? am I missing something obvious? or is this (as the tutorial implies) a functionality that hasnt been added yet? thanks, georges

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About Launching Athena on Mountain Lion (Mac OS 10.8)
by 上村洋平 12 Nov '12

12 Nov '12

Dear ifeffit mailing list menbers, I'm Yohei Uemura from Hokkaido University, Japan. For Mac users, you may know the thread below about not laucning iXAFS under Maountain Lion. http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03412.html I don't know any other threads about launching iXAFS.app under Mountain Lion. I've also given up launching Athena and Artemis under Mountain Lion. But, today I found by chance how to launch Athena undr Mountain Lion. The procedure is as follows; 1) Launch XQuartz. 2) type in the xterm of XQuartz "/Applications/iXAFS.app/Contents/ Resources/iXAFS\ Shell.sh" #iXAFS.app is placed in "Application" folder. 3) type "athena" in the xterm, and then I'm able to lauch athena. Does anyone launch Athena or Artemis under Mountain Lion? I would like you who use Mountain Lion try to do my procedure. Best regards, =========================================== 上村洋平所属 : 北海道大学・触媒化学研究センター　　　朝倉研究室　博士研究員住所 : 305-0801 茨城県つくば市大穂1-1 KEK-PF 北大分室　　　 001-0021　北海道札幌市北区北21条西10丁目 Yohéi Uemura (Ph.D) Affiliation : Catalysis Research Center Hokkaido University Adress : KEK-PF, 1-1 Oho, Tsukuba-Shi, Ibaraki, Japan 305-0801 Kita21 Nishi10 Kita-Ku, Sapporo 001-0021 TEL: 029-864-5636 Email : yuemura(a)post.kek.jp ===========================================

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spinel XANES calculation by Feff
by Enyuan Hu 12 Nov '12

12 Nov '12

Dear all, I was wondering if anyone had experience in calculating XANES spectra using Feff for the spinel system. The material I was trying to investigate was ZnFe2O4. There were reports in literature that gave satisfying simulation results by Feff so I tried to follow. The feature peaks' positions from my simulation is generally right, but the intensity is definitely wrong. So I guess either someone can give me some suggestion about the getting the intensity right or share with me about his or her spinel XANES calculation experience. My background is mainly in chemistry and material science with general ideas about electronic structure. Any comment or suggestion will be greatly appreciated. Thanks! Enyuan

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Re: [Ifeffit] Demeter install for Administrator/User computer (Melissa Menard)
by fred.mosselmans＠diamond.ac.uk 11 Nov '12

11 Nov '12

I think the problem is solved by making a Demeter folder in the application data folder for each user. If you search the ifeffit mailing list you'll see this has been covered before http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03167.html Fred Prof. J F W Mosselmans Principal Beamline Scientist I18 Diamond Light Source Diamond House Harwell Campus Didcot Oxon OX11 ODE UK T 00 44 1235 778568 M 00 44 7785510211 E fred.mosselmans(a)diamond.ac.uk F 00 44 1235 778448 Never mind the W it's the tax that counts -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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