August 2011 - Ifeffit - millenia.cars.aps.anl.gov

Fitting on Athena
by Niken Wijaya 08 Sep '11

08 Sep '11

Hi Everyone, I am facing a lot of problems when I am trying to fit my sample's spectra with my standards one. Initially, I used Athena to do the background subtraction, but the fitting results are just too "funny". The fitting does not really fit the actual spectra. Since I am analyzing Sulphur and many papers has reported how it is prone to self-absorption effect, I thought, probably if I am using a better background subtraction such as MBACK, I would get a better results. So I decided to use it for the normalization and unlike in Athena, the normalized intensity of the spectra does not equal to 1. By saying this, the intensity of my standard models is way higher than the actual samples. Hence, when I use Athena to fit my real spectra, I would not get a good results. I have also tried using the 3rd derivative of my absorption spectra, but the fitting results are even worse. The intensity of the "fit" spectra is way higher than the actual spectra of my samples that I am trying to fit it with. In fact, when I stack the spectra from the standards and the sample together, the 3rd derivative peak of the samples is almost completely flat due to the very high intensity of the standards themselves. What did I do wrong? and what can I do to fix it? I have also attached my samples and standards spectra. Thank you very much for the assistance. Niken

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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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dementer Artemis crashing on XP
by Christopher Patridge 22 Aug '11

22 Aug '11

Hello all, I recently (yesterday) installed the new Dementer package with Strawberry perl on a freshly installed XP Pro SP3. I have tried to open a couple different old Artemis projects (.apj) and once chosen, (D) Artemis shuts down immediately with no warnings messages. The message line reads something like - "converting data to Dementer fit serialization" and then everything disappears. I have attached one of the projects I attempted to open. I can open data from previous Athena projects with no problem. Any help would be appreciated. buena salud, Chris Patridge

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New software being developed
by Bruce Ravel 18 Aug '11

18 Aug '11

Hi everyone, I suppose I should say a few words about this Demeter thing that got mentioned a couple of times today. As some of you may know, I have been working on replacements for Athena, Artemis, and Hephaestus for a while now. The new programs involve better and prettier GUIs, improved plotting capabilities, 100% re-written source code, and lots of new fitting capabilities. I expect that the new codes will be better in almost every way than what we are all currently using. I am getting very close to releasing the new codes for everybody to use. A couple months ago, I asked a small group of people to try out the new programs and to help me find bugs and other problems. This small-scale beta-testing period has been very productive and I have made good progress towards the day when I can begin transitioning everyone from the musty old software to the shiny new software. If beta-testing buggy software sounds like something you might want to try, you can find information about Demeter -- including installation instructions, documentation, source code, and other goodies -- at http://cars9.uchicago.edu/ifeffit/Demeter Be mindful that this is new software. It continues to need testing and it remains likely to crash. If that sounds like fun to you, great! But you then need to be responsible about sending me prompt and useful bug reports. If that sounds like hell to you, you should probably wait for the first stable release. 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 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter

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LCF E0
by Pieter-Jan Sabbe 18 Aug '11

18 Aug '11

Dear All I am trying to do a linear combination fit with Athena. To do that i want to first prepare my standard spectra. My unknown sample is (I presume) a combination of Cu and Cu(I)O (cuprite) and Cu(II)O (tenorite). I started with calibrating the Cu to 8979 eV as how the Athena manual say how to do it (I use the zero crossing point at the second derivative). This provided me an E0 and Eshift. I am doubting now for what I should do next: Cuprite and Tenorite have different oxidation states, meanin that the binding energies of the inner electrons will shift and in that way shifting the absorption edge of the compound. Should I look somewhere in a database (does that exist, or articles) for the absorption edge of cuprite and tenorite and set it like that or should I use the same E0 as i did for Cu? Another important thing for me, I have found some old data with some standard reference (powder spectra) measured in fluorescence mode, but my guess they are from different beamtimes, can I use data from different beamtimes/beamlines as standards in a linear combination fit? thank you in advance Pieter-Jan

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Athena: problems with LCF
by Nina Siebers 15 Aug '11

15 Aug '11

Dear All, I acquired Cd L3-edge spectra of some binary and ternary mixtures in varying proportions and for the individual components. The mixtures were created on Cd-mass basis. Then, I tried to fit the reference spectra to the spectra of the mixtures using linear combination fitting of Athena to get their abundance. However, the results were disappointing despite all spectra were carefully energy calibrated and normalized, so I decided to create simple mathematical binary and ternary mixtures by summing up the spectra of the individual reference spectra. After that I did an edge-step normalization in excel and imported the normalized calculated mixtures into Athena. Then, I tried the fitting again to exclude mixing-failures and check sensitivity of LCF with the idealized spectra. Even though the results of the LCF of the mathematical mixtures were better compared to the real mixtures, LCF was also not able to reliable deconvolute these spectra into the individual reference spectra. Does anybody have an explanation for that? It would be nice if somebody could give me information about the mathematical fitting algorithm implemented in Athena. Attached is a data file of three mixtures (two ternary and one binary mixture) including the mathematical mixture created in excel (named calculated at the end). Mixing ratios are named 1to1to1 (meaning 1:1:1 of the components in the same order). For the 1:1:1 ternary mathematical mixture the deconvolution was very good, but the others need improvement. I hope I made my problem clear this time. Thanks a lot! Wishes, Nina

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