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

bond distance resolution and correlation of parameters in MS analyses?
by MarkBondin 06 Jun '07

06 Jun '07

Hi, I would like general opinions of some EXAFS practioners in regards to the most widely accepted methods for bond distance resolution and correlation of parameters in both single scattering (SS) and multiple scattering (MS) EXAFS refinements and if these can be said to differ? 1)Does the equation for bond distance resolution (r = pi/2deltak) only apply to SS? I have held the opinion that this can be applied to MS analysis however I have recently been informed that this equation does not correctly describe distance resolution in MS analyses. The paper in Coord. Chem. Rev. 2005, 249, 141-160 describes this and is this concordant with the views of the wider EXAFS community? 2) What is the actual equation which defines the determinacy of a fitting procedure and does this differ between SS and MS analyses? For MS analyses there has been a recently published equation (Coord. Chem. Rev. 2005, 249, 141-160) which takes into acount the number of dimensions used in the analyses and is this only relevant to MS analyses of data? This has also been expressed in the paper by Binsted (Biochemistry. 1992, 31, 12117-12125) however a different equation has been detailed by Stern (Phys. Rev. B. 1993, 48, 9825-9827) which I have been using as a guide in my MS analyses. Is this acceptable? Any thoughts and opinions would be greatly appreciated as this relates directly to corrections suggested to be made to my PhD thesis! Many thanks, Mark

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help with CoCr bimetallic catalyst
by codruta.zoican＠yale.edu 06 Jun '07

06 Jun '07

I have been, working with a bimetallic Co/Cr catalyst supported on a silica template for synthesis of single wall carbon nanotubes. Recently I have performed some analysis at the NSLS. It is clear from the spectra in R space that the interatomic distances are modified compared to the monometallic catalyst therefore I am dealing with an alloy. Does anyone have or know about a model that would allow me to get a coordination nomber using Artemis. Thank you, Codruta.

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Re: [Ifeffit] Deconvolution of XANES spectra
by Gerald Seidler 03 Jun '07

03 Jun '07

Dear Jakob, Attached you will find my student's recent paper on deconvolution of XANES and EXAFS using iterative maximum-likelihood algorithms (TT Fister et al, Phys Rev B vol75, artNo.174106 ). Our software is available through EPAPS, but it is in Mathematica, which I realize isn't most convenient for many users. We will have matlab/scilab versions ready by the end of the summer which will include both the Richardson-Lucy (ratio) method from our paper and also the deCittert (linear) method previously used with good success by Babanov. The matlab/scilab package will come with a GUI so that it should be easy to use, even for experimenters with no knowledge of those programming environments. After that, we'll start working on making a stand-alone executable... but note that scilab is free (it is the shareware copy of matlab). Let me know if you'd like to talk about your particular application. We have a pretty good idea about the likely performance of our approach for different spectra, and I would be happy to run some test deconvolutions for you. Cheers, Jerry ------------------------- Gerald T. Seidler Associate Professor, Physics University of Washington ---------- Forwarded message ---------- Date: Sun, 3 Jun 2007 13:55:42 +0200 From: Frommer Jakob <jakob.frommer(a)env.ethz.ch> Reply-To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Deconvolution of XANES spectra Dear all, I would like to know whether some of you do have experience in deconvoluting XANES spectra in order to remove both, lifetime and experimental broadening. If so, what programs are you using for this purpose? Any hint would be of great help With many thanks and best wishes Jakob

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Deconvolution of XANES spectra
by Frommer Jakob 03 Jun '07

03 Jun '07

Dear all, I would like to know whether some of you do have experience in deconvoluting XANES spectra in order to remove both, lifetime and experimental broadening. If so, what programs are you using for this purpose? Any hint would be of great help With many thanks and best wishes Jakob ___________________________________________________ Jakob Frommer Soil Chemistry Group Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Universitätstrasse 16, CHN F19 CH - 8092 Zürich Tel: +41 44 632 87 58 Fax: +41 44 633 11 18 Email: jakob.frommer(a)env.ethz.ch http://www.ito.ethz.ch/SoilChem/

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programming error in Hephaestus??
by I.Reitz 01 Jun '07

01 Jun '07

Dear listmembers, I´m a student at the very beginning with synchrotron radiation and we use Hephaestus to calculate the flux through an ionisation chamber. I have some questions (sorry about my bad english): To make it short, I think I have found an error in the tool. In the tool "formulas" I took Kr, 30000 eV and get: the Absorbtion length: 15.031 cm (Resources Henke) : 14.431 cm (Resources Elam) which I also found in NIST Database then use the tool "Ion Chamber" put in Kr (only one gas), 10cm pathlength, 760 Torr, 30000 eV I got for Percentage absorbed: 48.58% (Resources Henke) which is correct I think : 39.22% (Resources Elam) which is wrong I think In my eyes the correct result for 14.431 cm Absorbtion length has to be: 49.99% absorbed photons. It is critical for me, since the correct flux measured with the ionisation chamber goes directly in my results. We investigated the detector response on monochromatic X-rays at HASYLAB of a widely used flat-panel detector in medicine. And I have also a question to you: Why do you use 30 eV/e- as ionization energy for the gases? Is there a reference for that? In addition, don´t we have to take the room temperature into account not only the pressure, that means: Density(Temperature) = (273,15K/293,15K)*0.003749g/cm^3(at 273,15K) Any help and hint is highly appreciated since I am a student at the very beginning. Thanks a lot and warm greetings from Germany Irmi Reitz -- ********************************************* I. Reitz German Cancer Research Center DKFZ, E0401 Dept. of Medical Physics in Radiation Therapy Im Neuenheimer Feld 280 D – 69120 Heidelberg Phone: +49 - 6221 42-2455 Fax: +49 - 6221 42-2572 Email: I.Reitz(a)dkfz.de *********************************************

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Windows on Vista
by Bruce Ravel 01 Jun '07

01 Jun '07

On Friday 01 June 2007, Luanga Nchari wrote: > I have tried to install Ifeffit on Windows Vista but it has failed. > Could somebody tell me how best it can be installed? Cheers, > Luanga Nchari Luanga, Check the Ifeffit mailing list archives for March: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2007-March/thread.html One of the first threads should answer your question. Mark Jensen's posts are the most useful ones. If you still have trouble, ask again. B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Using windows apj files on linux
by joshua jason kas 31 May '07

31 May '07

Hi, I recently updated to redhat 4. I am running: artemis 0.8.009 IFEFFIT 1.2.9 Tk-804.027 perl 5.8.5 I have an artemis project file that I started on my win xp machine and would like to use on the linux machine. When I open the apj file on linux, some of the information about the fits seems to be scrambled. Here are some of the symptoms. 1) The raw logs seem to have aquired the following escape character at the end of each line: \x{d} This shows up as a carriage return or end of line on this screen. 2) Quick summary of selected fits gives 0 for all reported values (chisq, rfactor, nidp, etc) and does not report any guessed parameters. Here is one of the quick summaries. Note that the \x{d} do not show up here, but they do in the artemis message palette. I am also attatching the project file. Thanks for any help, Josh Kas Project title : Fitting pt1_amine_165_he_573.chi Comment : fer dw, constant delr, ei=0, kw=1, kmin=2.0, rmin=1.2 Figure of merit : 17 Fitting statistics Number of independent points : 0 Number of variables : 0 Chi-square : 0 Reduced chi-square : 0 R-factor : 0 Measurement uncertainty (k) : 0 Measurement uncertainty (R) : 0 Guess parameters =*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*=

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the brand new Athena User's Guide
by Bruce Ravel 30 May '07

30 May '07

Hi! The last few months have been a pretty quiet period for me in terms of software development because I have been working on new documentation for Athena. As such things often do, it took longer than planned. But I am very pleased with the results and I am hopeful that you will find it useful. The html version is on line at http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/ A (rather large) PDF version of the document is at http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/athena.pdf For those interested in contributing to or packaging the document, the source files can be found at or downloaded via svn from http://cars9.uchicago.edu/svn/aug/ This is a first draft and a large project. It will certainly require updates. If you find anything missing or anything incorrectly or poorly explained, please let me know. Now that this document is finished, I will work on the next release of the codes. I have a long list of bugs fixes and improvements that I hope to roll out for all platforms before the APS XAFS summer school in July. Regards, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/

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Re: [Ifeffit] Ifeffit Digest, Vol 51, Issue 26
by Jun Lin 30 May '07

30 May '07

I guess the problem lies in the different "end line character" for Linux and Windows. Before you load "dos style"(Windows use it) apj file, you should translate it into "Linux style". It is easy in Linux system by using "dos2unix". On 5/30/07, ifeffit-request(a)millenia.cars.aps.anl.gov < ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > > 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. Using windows apj files on linux (joshua jason kas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 29 May 2007 10:13:06 -0700 (PDT) > From: joshua jason kas <hebhop(a)u.washington.edu> > Subject: [Ifeffit] Using windows apj files on linux > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <Pine.LNX.4.64.0705290956010.21265(a)dante01.u.washington.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi, > I recently updated to redhat 4. I am running: > artemis 0.8.009 > IFEFFIT 1.2.9 > Tk-804.027 > perl 5.8.5 > > I have an artemis project file that I > started on my win xp machine and would like to use on the linux machine. > When I open the apj file on linux, some of the information about the fits > seems to be scrambled. Here are some of the symptoms. > > 1) The raw logs seem to have aquired the following > escape character at the end of each line: \x{d} > This shows up as a carriage return or end of line on this > screen. > > 2) Quick summary of selected fits gives 0 for all reported values > (chisq, rfactor, nidp, etc) and does not report any guessed > parameters. > > Here is one of the quick summaries. Note that the \x{d} do not show up > here, but they do in the artemis message palette. I am also attatching the > project file. > Thanks for any help, > Josh Kas > > Project title : Fitting pt1_amine_165_he_573.chi > > Comment : fer dw, constant delr, ei=0, kw=1, kmin=2.0, rmin=1.2 > > Figure of merit : 17 > > > Fitting statistics > Number of independent points : 0 > Number of variables : 0 > Chi-square : 0 > Reduced chi-square : 0 > R-factor : 0 > Measurement uncertainty (k) : 0 > Measurement uncertainty (R) : 0 > > Guess parameters > > =*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*= > > >

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Plotting problem
by Clement Mbudi 29 May '07

29 May '07

Hi there, Can somebody tell how to get rid of the " all marked groups" default title when plotting several groups together within Athena environment. The " change group label" seems to only work for a single group. Similarly, how to change titles of both Y and X axes within Athena ? Thanks. Clement Edmonton, AB _________________________________________________________________ Windows Live Hotmail with drag and drop, you can easily move and organize your mail in one simple step. Get it today! www.newhotmail.ca?icid=WLHMENCA153

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