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

Looking for reviewers for data reduction chapter
by Scott Calvin 06 Sep '11

06 Sep '11

Hi all, Once again, I have a draft of a chapter of my textbook ready for review. This chapter is on data reduction, including normalization, background subtraction, and Fourier transforms. This will be Chapter 4 in the book, so it should be suitable for near-beginners as well as those with more experience. This is also a chapter where I had to make a lot of decisions on nomenclature and presentation, so experts might be interested as well, particularly if you have strong opinions on that kind of thing! It is a bit more than 40 pages long, which makes it the longest so far. If you are interested in reviewing the chapter and can get feedback to me by 29 September, please contact me directly at SCalvin(a)slc.edu . As always, repeat reviewers are welcome! --Scott Calvin Sarah Lawrence College

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Regarding the execution of Demos in PGPLOT
by Rajesh Kumar 06 Sep '11

06 Sep '11

I recently installed 1. PGPLOT 5 (ver: 5.2.2-15) through Synaptic Package Manager from ubuntu - MOTU-Developers (Mathematics, Multiverse) 2. IFEFFIT from Carlo Segre < segre(a)debian.org>, (version 2:1.2.11d-6~lucid0 ) and 3. Horae-07-1 through Synaptic Package Manager from ubuntu - developers (Science, Multiverse) I am not able to run the demo programs. So I started running demo programs for PGPLOT first. My examples are in directory: /usr/share/doc/pgplot5/examples/pgdemo2.f.gz When I compile the program "depgplot10.f" and executed the file, the interaction on the console is attached in the file attached herewith. I need help in this regard and I am very very new to "xafs" as well as ubuntu. Wishing you best of life and time, With regards Rajesh Kumar

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Worm in SixPack
by Abhijeet Gaur 05 Sep '11

05 Sep '11

Hi all, I have been encountering this problem each time when I run SIXPACK on my sytem. Every time I run SIXPACK it shows the infection due to a worm* * * SIXPACK\MULTIARRAY.PYD,WORM.Z040709.0486.9.* * * Thus, after some time SIXPACK stops running and I have to download it again. I am sorry if I am asking a question already asked on this list but I had searched this on ifeffit mail archieve, but unable to find a similar problem. Kindly help. With thanks Abhijeet Gaur

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Re: [Ifeffit] settings tab in Artemis
by Matt Newville 05 Sep '11

05 Sep '11

Hi Morgan, Sorry, somehow your legitimate message got lost in the spam box. > From: Morgan Scott <msco001(a)aucklanduni.ac.nz> > To: ifeffit(a)millenia.cars.aps.anl.gov > Date: Mon, 5 Sep 2011 12:04:45 +1200 > Subject: settings tab in Artemis > Hello; > > I have changed some settings in my plot display (legend position, gridlines) in Athena. > I wish to do the same thing in Artemis, but there is no settings tab in the menu. > Is it possible to change the display in Artemis? > If so how? > > regards; > -- > Morgan Scott > Ph.D. candidate > School of Chemical Sciences > University of Auckland Yes, these preferences can be set, it's just in a different place. Use Edit -> Edit Preferences (at very bottom) which will bring up a panel to set and save such options. --Matt

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LCF with different scales
by Hana 03 Sep '11

03 Sep '11

Hi list, I'm looking for a way to make LCF with standards that were measured at different occasions and beam-lines. I did read previous comments regarding this issue, but still need to clarify: 1. Does limiting the range to the smallest range help in this case (if spectra were measured with the same steps size, and a calibration standard was used)? 2. For harder situation; when different steps were used - I found that sixpack (according to its manual) interpolating all spectra to the same energy grid - does this solve the problem? I will be happy to be advised. Thanks, Hana

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A simple question regardng the 'chi' in the xmu.dat file (FEFF8)
by Deok-Yong Cho 02 Sep '11

02 Sep '11

Dear Ifeffit users: Hello, I have a simple question regarding the 'chi' in the xmu.dat, an output file of FEFF8. I wish I could get helps from you to resolve this. As far as I know... in the xmu.dat file from Feff6, mu=mu0*(1+'chi') as it should be, but in the xmu.dat file from Feff 8, the 'chi' written in the xmu.dat is a rescaled one by mu0/(mu0 at edge+tens eV) so that mu should be equal to mu0+'chi'. I checked up for FEFF8.4 by turning on and off the FMS card, and found that with the FMS card, mu = mu0+'chi', while without the FMS card, mu is quite close to or same as mu0*(1+'chi') instead of mu0+'chi'. Please help me to find which one is correct. Attached are the Feff.inp and the resultant xmu.dat for ZnO. Thank you all. Best Regards, Deok-Yong Cho Post-doctoral researcher at RWTH Aachen, Germany

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Athena in Demeter
by Amitava D Roy 30 Aug '11

30 Aug '11

Bruce, Is it possible to put back the "negate" button into the Demeter version of Athena? You have it in the classic version. The button is very useful. Thanks very much, Amitava Roy Amitava Roy J. Bennett, Sr., Center for Advanced Microstructures and Devices 6980 Jefferson Highway Louisiana State University Baton Rouge, LA 70806 225-578-6706 (O) 225-578-6954 (Fax)

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Re: [Ifeffit] Regarding Demeter
by Bruce Ravel 29 Aug '11

29 Aug '11

On Monday, August 29, 2011 03:48:26 pm you wrote: > Dear Bruce, > I have been struggling to install the any of the demeter or horae. I have > tried so many things but not able to install. > I have installed PGPLOT, IFEFTIT already on my computer (Ubuntu 10.04, > intel i686). > There are so many different version available and I have tried many of > them. > I need your help and word of guidance. Let me know the more straight > forward way of doing it. > I would be using it in my research on edge spectroscopy. Rajesh, I am CCing this to the Ifeffit mailing list, which is the proper venue for a question of this sort. If you are not subscribed to the Ifeffit mailing list, here is the info: http://cars9.uchicago.edu/mailman/listinfo/ifeffit In the future, please make use of the list. First off, you should know that "horae" is the version of the codes that has been out for years. "Demeter" is the new version which is under development. Demeter is better than horae in almost every way, but, like all software under development, it's not guaranteed to work as advertised. That said, I use Demeter for all my own work and many others have begun using it. If something stable is more to your liking, Carlo Segre has built installation packages for horae. Use your package manager to install it. If a search for "horae" turns up nothing, add the appropriate repository (I think 10.04 == Lucid) from: http://debian-xray.iit.edu/ to your package manager. If you have never done this before, consult https://help.ubuntu.com/community/Repositories/Ubuntu Once you have done that, you should be able to simply install "horae" and have all the dependencies met. If you want to use the newer, fancier, but not-yet-stable code, follow the instructions at: http://cars9.uchicago.edu/ifeffit/Demeter/InstallDemeterOnUnixWithGit Follow these instructions to the letter. Don't improvise unless you know what you are doing. It will take you a while to get all the dependencies built. Be patient -- once you are set up, updating is quick and easy. 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 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter

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Job Vacancy in UK
by fred.mosselmans＠diamond.ac.uk 26 Aug '11

26 Aug '11

Because of an internal promotion, there is now a vacancy for a beamline scientist on the microfocus spectroscopy beamline at Diamond. The details can be found at http://www.diamond.ac.uk/Home/Jobs/Current/DIA0638-TH.html Thanks Fred Prof. J F W Mosselmans Principal Beamline Scientist I18 Diamond Light Source Diamond House Harwell Campus Didcot Oxon OX11 ODE UK -- 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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PhD position in Lausanne/Villigen (Switzerland)
by Chergui Majed 26 Aug '11

26 Aug '11

PHD POSITION IN ULTRAFAST X-RAY ABSORPTION SPECTROSCOPY A PhD position is available in the group of Professor M. Chergui to carry out steady-state and time resolved (ps/fs) X-ray absorption spectroscopy studies on metalloproteins in physiological solutions. The experiments involve the use of ultrashort pulse lasers to excite the sample, while the probing is done by the pulsed X-rays from a synchrotron. Involvement with experiments at the X-ray Free Electron Laser at LCLS-Stanford is also envisioned. The research is carried out in collaboration with the Swiss Light Source (Paul-Scherrer Institut, Villigen) and the candidate will be based there. For more information about the methodology and results, see: Picosecond and femtosecond X-ray absorption spectroscopy of molecular systems M. Chergui, Acta Crystallografica A66 (2010) 229-239 Light-induced spin crossover in Fe(II)-based complexes: the full photocycle unravelled by ultrafast optical and X-ray spectroscopies A. Cannizzo et al, Coordination Chemistry Reviews 254 (2010) 2677-2686 experiments on chemical and biological systems in solution F. A. Lima, et al, Review of Scientific Instruments 82 (2011) 063111 Probing the transition from hydrophilic to hydrophobic solvation with atomic scale resolution V.-T. Pham, et al, Journal of the American Chemical Society, 2011, 133, 12740-12748 For information and applications (letter of motivation, recommendations, CV and list of publications, if any), please contact: Dr. Chris Milne Chergui Group Swiss Light Source, PSI CH-5232 Villigen PSI Tel: +41 (0)56 310 5477 Fax: +41 (0)56 310 4413 Email: chris.milne(a)psi.ch<mailto:chris.milne@psi.ch> Or Professor Majed CHERGUI Ecole Polytechnique Fédérale de Lausanne Laboratoire de Spectroscopie Ultrarapide ISIC, Faculté des Sciences de Base Station 6 CH-1015 Lausanne, Switzerland tel: xx 41 21 6930447 / 0457 fax: xx 41 21 6930365 email: Majed.Chergui(a)epfl.ch<mailto:Majed.Chergui@epfl.ch> http://lsu.epfl.ch/ P<http://lsu.epfl.ch/P> Please consider the environment before printing this email - Considérez svp l'environnement avant d'imprimer ce courriel

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