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

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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Low amp results
by Joji Kuniya 29 May '07

29 May '07

I analyzed EXAFS spectra of trace of Fe in lithium tantalate crystals. At first, I created the feff.inp file of LiTaO3. Then I changed central Li atom to Fe atom and added Fe atom at the Ta site. So that, the fitted results is good except amp(amp results is 0.3). I think that the model structure is good, but I can not understand why amp is too low. How do you think about this results? And, I tried to fitting treatment using GDS parameters. But, I do not know that the general method how to use the GDS parameters. Please tell me the general way of GDS manipulation. My PC runs under Win XP, and My Artemis runs under feff8 conditions. Thank you. Joji Kuniya

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Re: [Ifeffit] Using FEFF8 with Artemis
by Richard Mayes 24 May '07

24 May '07

Scott, When I started using FEFF8.2 with Artemis (on a WinXP laptop), it took a day or two to get everything situated where Artemis would read the input file. For my ease of use, I finally created a separate folder under My Documents that I dedicated to FEFF calculations. At that point, every file generated by FEFF was written into that folder (provided that's where the FEFF executable is located) and Artemis became happy again and started accepting my input files. There is only one downside (so far), when Atoms generates an input file, I have to go into Artemis and copy that input file into the folder where FEFF is located before I can do the FEFF calculation. I tried the input file you sent to the list, and this method gives the needed files in one folder. I can send you a copy of the folder containing all the generated files if you would like (I would attach it to this message, but that would put me over the message size limit for the list). Attached is the Artemis file where I checked to see if Artemis imported the paths properly. Rich Mayes Barnes Group 450/452 Buehler Hall Dept. of Chemistry Univ. of Tennessee Knoxville, TN 37996

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white line intensity v. edge position in determining oxidation state of Re
by Edward L. Kunkes 22 May '07

22 May '07

Hi everyone, I am trying to determine the oxidation state of Re in PtRe nanoparticles catalysts supported on carbon. The ReLIII edge was measured before and after an in-situ reduction in hydrogen. Can anyone suggest Which characteristic of the edge is more related to oxidation state ? Is it the integrated white-line intensity or the position of the edge(point of maximum derivative). The edge position of the ReLIII edge of my particles is the same as that of Re foil, however the white line instensity is significanty higher. For the non-reduced PtRe particles, the edge position is similar to that of ReO2 (with a larger white line intensity). Also, does anyone have any Data on Re-foil, HReO4 and ReO2 so that i can compare it to the data i measured for my standards ? Thank you very much for your help -Edward Kunkes

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Re: [Ifeffit] An Ifeffit question.
by Bruce Ravel 21 May '07

21 May '07

On Friday 18 May 2007, Christian Lange wrote: > I am using "your" Athena and so on-software package for the evaluation > of my XAS-measurements. So far everything is working fine, but i have > one problem. The plots of this "graphics window" are a bit inconvenient > if it comes to a publication, because I cannot change line styles, > colors and so on. Or at least I don't know how to do this. > > That's why I want to ask you, whether it is possible to get the data for > the fourier transform plots in some sort of ASCII-format to import it in > Origin. Maybe with some file jiggling at the DOS prompt level? Hi Christian, This is a good question for the Ifeffit mailing list, so I am taking the liberty of CCing my answer there. This should be answered in the FAQ -- it certainly is frequently asked in my email! I completely agree that the plots made by pgplot are not pretty enough for publication and I suspect that Matt would not argue either. We use pgplot because it works well within the context of Ifeffit, because it is free and redistributable, and because it works equivalently on Windows, Unix, and the Mac. Matt and I both prefer to spend our limited time making good XAS software -- neither of us really felt particularly inclined to make and maintain publication quality plotting software. There are, after all, plenty of excellent packages out there for making beautiful plots. The trick, then, is the link between Athena and your favorite plotting package. In the File menu, there are a number of option for exporting data into plain-text, column-data files. These can then be imported easily into your favorite plotting program. The File menu options from "Save mu(E)" through "Save chi(q)" will save the current data group (i.e. the one highlighted in the groups list and the one whose parameters are currently on display in the main window). The mu(E) file, for instance, contains columns for energy data, background, I0, pre-edge line, and post-edge polynomial. You can import these columns into your favorite plotting program and have your way with them. The chi(R) file, as another example, has columns of R, real part, imaginary part, magnitude, phase, and back-transform window in R. Below those options is a submenu labeled "Save marked groups as data". The idea there is to save column data file where each column contains the data from a marked group (i.e. the ones with the little purple button in the groups list clicked). There are options for saving data in this way in each of the plotting spaces. Finally, it is possible to have some control over how the plots are made. In the Settings menu, select "Edit preferences". Then open up the Plot branch by clicking on its little plus sign. The options c0 through c9 and the linetypes option might be of interest to your. Nothing among the preferences will magically make pgplot prettier, but it may help you visualize your data. HTH, B P.S. You can join the Ifeffit mailing list at http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ It tends to be high quality conversation (except the parts written by me, of course) and high signal-to-noise. -- 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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Open post-doctoral position - please, advertise
by Michel Meyer 16 May '07

16 May '07

Dear colleagues, Bruce Ravel has suggested me to contact you in order to post the following announcement on the IFEFFIT website. Thank you very much for considering this offer. The position will stay open until the end of the year 2007. With all my best regards, Michel Meyer Post-doctoral fellowship The Institut de Chimie Moléculaire de l'Université de Bourgogne (Dijon, France) is seeking a motivated candidate for a one-year funded postdoctoral position with a strong background in X-ray Absorption Spectroscopy (XAS). In collaboration with the Rossendorf Beamline scientists at ESRF, the successful candidate will be involved both in the acquisition and interpretation of XANES and EXAFS data in order to unravel the coordination scheme of U(VI), Pu(IV) and Eu(III) on surface-modified mesoporous hybrid materials obtained by covalent grafting of functionalized macrocyclic ligands onto silica gel. These materials have found applications as solid/liquid extracting agents of actinides in an ultrapufication process of radioactive wastewaters. The following points are considered mandatory: * The applicant should have a well-established experience in X-ray absorption spectroscopy. * The applicant should hold a Ph.D. for less than 5 years. ....* Only candidates that have never been employed in France are eligible. Additional Information can be found at http://www.icmub.fr/ Please send your application including a CV, list of publications and at least 3 references to: Dr Michel MEYER LIMRES Institut de Chimie Moléculaire de l'Université de Bourgogne UMR 5260 du CNRS 9, Avenue Alain Savary BP 47870 21078 DIJON Cedex - FRANCE Tel : (33) 03 80 39 37 16 Fax : (33) 03 80 39 61 17 e-mail : Michel.Meyer(a)u-bourgogne.fr ****************************************************************** Michel MEYER Chargé de Recherche LIMRES Institut de Chimie Moléculaire de l'Université de Bourgogne UMR 5260 du CNRS 9, Avenue Alain Savary BP 47870 21078 DIJON Cedex - FRANCE Tel : (33) 03 80 39 37 16 Fax : (33) 03 80 39 61 17 e-mail : Michel.Meyer(a)u-bourgogne.fr site web http://www.u-bourgogne.fr/LIMSAG/ ******************************************************************

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How to select important MS paths in wurtzite?
by Mauro Rovezzi 16 May '07

16 May '07

Dear all, Do you know if in literature there are studies on the important multiple scattering (MS) paths in fitting wurtzite XAFS spectra? I mean which are the important paths to properly fit a wurtzite structure up to 6 A in a elegant way (<20 paths)? I'm asking this question thinking at old works by Filipponi et al. on the fcc and bcc structures explaining very well the importance of some specific triangular and collinear paths to fit the EXAFS spectrum... Well, this was my coffee-break question :) Mauro -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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Re: [Ifeffit] how to recognize element with a difference of Z<2?
by Bruce Ravel 15 May '07

15 May '07

Sebastiano, You are correct that EXAFS is relatively insensitive to atoms that are nearby on the periodic table. This is because the backscattering amplitudes and phase shifts are functions of, in part, Z number. In the case of stochastic replacement of a host atom by a dopant on the exact position of the lattice site, it can be difficult or impossible to distinguish nearby atoms. However, if the introduction of the dopant is accompanied by a distortion to the lattice, the situation might be a lot friendlier. In that case, you may be able to notice two (or more) distances in the neighboring shells, one of which can be explained by the host atom and the other(s) by the dopant. Even better, you can measure data at the edges of both host and dopant and corefine the data. That additional information might be enough to figure out what's going on. I also think that your case -- an alloy -- might be a good candidate for high energy diffraction using PDF analysis methods. PDF, or PDF combined with EXAFS, might help for your problem. Good luck, B On Tuesday 15 May 2007, Cammelli Sebastiano wrote: > Dear > > I am Sebastiano and I am working on some metallic alloy composed by > several diluted elements in a Fe matrix. The main elements are: Cu, Cr < > 0.5at%; Mn, Ni < 1.5at%, I collected some spectra at different K edge > (Mn, Ni, Cu). Submitting this alloy by annealing treatment (775K) and > neutron irradiation, some clusters are expected mainly composed by Cu; > Ni and Mn play an important role but it is not so clear. Some problems > rise when I try to analyze these data: > > "It is known" that it is not so easy to recognize by EXAFS the > difference from near elements as Fe and Mn (Z=26,25) and Cu, Ni (29,28) > because these elements has a similar electronic distribution. Performing > the analysis by Artemis I found some 'realistic' value of Mn Fe and Ni > in the first and second shell (Cu K edge), have these values any > physical meaning since I cannot distinguish element as Fe and Mn? > > Do you know any tricks that could help me? Maybe the right answer is > that EXAFS is not enough to investigate these alloys, but if I cannot > distinguish the different atoms, which kind of quantitative information > could I get? The interatomic distances are important but which is the > meaning of distance between the absorber (Cu) and an unknown atom (Fe or > Mn, Cr or Mn, Cu or Ni?)? > > Thank you help and for your time. > > Sebastiano > > > > Sebastiano.cammelli(a)psi.ch > > Paul Scherrer Institute, Villigen 5232 (CH) -- 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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Document Bug?
by Annette.Koo＠csiro.au 15 May '07

15 May '07

Not sure if this is the right place to report bugs, but upon opening either Artemis or Athena, and clicking 'Help - Document' I get the following error message, along with an empty 'pod'. Tk::Error: image "fileopen16" doesn't exist at /Per1App/Tk.pm line 228. Tk callback for image5 [\&main::_ANON_] <menu invoke> main::_ANON_<'Tk::Error: image "fileopen16" doesn\'t exist at /Per1App...... and so on for several more lines. It was working alright last month so not sure what happened. Do I need to re-install? Thanks for your help, Annette

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care and feeding of Athena
by Bruce Ravel 09 May '07

09 May '07

Hi, This week I received a bug report from an Athena user here at the APS. The problem is a bit complicated to explain, but the executive summary is that two different ways of moving chi(k) data from an Athena project file into Artemis resulted in two different spectra even though they should have been identical. I spent a bit of time trying to track down the exact nature of the bug, but it has proven a bit elusive. I can say this, the Athena project file which demonstrates the problem has 148 groups in the group list. This problem cannot be replicated in a project file with a few (or even a couple dozen) groups in the group list. Many of you will recognize the nature of the problem. 148 is more groups than Athena can comfortably handle. I'll explain this issue in some detail below. Before I do, I'll give a good rule of thumb that will help keep Athena happy with you and you happy with her: =*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*= Don't import too much data into your Athena project! About 50 or 60 data groups in the group list is a good upper limit. With fewer groups, Athena should work reliably. With more, Athena will eventually become unstable. If you need more than 60 data groups, you need to split your ensemble of data into two or more subsets and process each subset individually. =*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*= Why is that? Well, to answer, I need to explain a bit about how Athena works. All of the hard work (Fourier transforms, background removal, normalization, and so on) is done by a library of numerical and exafs-related functions called Ifeffit, which is the thing written by Matt. Athena is really just a glorified bookkeeper. She keeps track of your data and of the values of all your parameters. When it comes time to do any of the actual numerical work, she organizes the problem, then asks the Ifeffit library to take care of it. When it comes time to make a plot, Athena organizes how the plot should be made, then asks Ifeffit to take care of it. In the case of plotting, Ifeffit, in turn, asks another library called Pgplot to actually make the plot on the screen. This stack of software tools is actually quite more complicated than that. Ifeffit and Pgplot are written in a programming language called Fortran. Athena is written in a different language called Perl. There is a small piece of code written in C which allows the Perl program to talk to the Fortran libraries. Additionally, Athena uses a graphical toolkit called Tk, which is written in C, to draw buttons and sliders and text boxes and such on the screen. The point here is that Athena is something of a house of cards. Lots of different software components need to be working together correctly in order for you to do your data analysis. (One might be astonished that Athena works in the first place. Ssshhhh!!! If you lose faith, everything will come tumbling down!) Because Athena requires so many concurrently functioning pieces, it has some weak spots. One of these weak spots is quite serious. The Fortran programming language (the one used to write Ifeffit) is quite old -- early versions of Fortran date back to the mid 60s, a time when RAM was measured in kilobytes rather than gigabytes. One feature of modern programming languages that Fortran lacks is the ability to claim and release memory. Consequently, a Fortran program has to allocate enough memory to run at the moment that it starts running. If, during the course of operation, the Fortran program moves to a state in which it needs more memory -- it's out of luck. What's worse, Fortran does not even provide particularly good tools for failing gracefully when it attempts to exceed its memory limit. Ifeffit, then, allocates some large amount of memory up front and then uses some clever heap management techniques written by Matt himself to make the most effective use of the available memory. It works well, up to a point. If you attempt to import too much data into Athena, Ifeffit will run into its memory limit and begin to behave erratically. Obviously, when Ifeffit behaves erratically, so does Athena. It would seem that having 148 data groups triggers a bug in the heap management scheme. Drat! And that is why you should not have too many data groups in your Athena project file. So, should Ifeffit be rewritten in some language that does dynamic memory allocation? Probably, but that would be a lot of work and Matt has both a daughter and a day job. 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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Coordination of ball-milled alloys
by Alejandro Fernandez-Martinez 09 May '07

09 May '07

Dear all, I am quite new to XAS data analysis, maybe you can help me with a little problem I have. I am trying to fit EXAFS data at Cr K-edge of a bcc Fe30Cr70 alloy synthesized by ball-milling. For those who don't know it, this technique is very effective in alloying metals but introduces a lot of structural defects in the structure. This is clearly seen in neutron diffraction data (with DW 2 times larger than DWs of a Cr reference and larger FWHMs). When fitting the EXAFS data without any specific constrain (only for distances) I get DWs on the same order of magnitude for the Cr-foil than for the alloy, and a very reduced coordination of N1=2.3 (compare with N1=8 for the Cr-foil) for the first neighbour (without physical sense?). In order to take into account the larger DWs for the alloyed sample (as found in diffraction data) I have constrained the minimum value of the DWs to a value double than the DWs of the Cr-foil. This gives me an increase of the N for the first shell, but at the same time, I have to refine lambda (photoelectron mean free path) in order to correct the excesive decay introduced by the DW exponential in the EXAFS formula, and to get a good fit. Then I get a more physically understandable N1=5.5. - The 1st question is: do you think the logical discourse that I have followed until now is correct? I don't have idea on how much some quantities as lambda should or not be refined. - 2nd question: what dou you think about the use of diffraction data as constraint for EXAFS data analysis? Many thanks in advance! cheers, Alex -- Alejandro Fernandez-Martinez Institut Laue-Langevin 6, rue Jules Horowitz - B.P. 156 38042 Grenoble Cedex 9, France Tel: +33 (0)4.76.20.75.71 Fax: +33 (0)4 76.20.76.48 fernande(a)ill.fr -- Geochimie de l'Environnement LGIT - UJF BP 53 38041 Grenoble Cedex France

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How to use "OVERLAP" card?
by Jun Lin 09 May '07

09 May '07

I have read some references of Kelly Shelly, and I have got some idea of how to construct a structure without difinite crystalline structure. But when I try to apply to my own question, meet some difficulties. In my case, four nitrogen atoms is surrounding a iron atom. So I use OVERLAP and SS card as to define such system as described in the FEFF manual: -------------------------------------------------- POTENTIALS * ipot Z element 0 26 Fe 1 7 N * Determine approximate overlap for central and 1st nn in Cu OVERLAP 0 *determine overlap for central atom of Fe *iphovr novr rovr * ipot, number in shell, distance 1 4 2.15 OVERLAP 1 *determine approximate overlap for 1st shell N *iphovr novr rovr * ipot, number in shell, distance 0 1 2.15 *SS index ipot deg rss SS 1 1 4 2.15 -------------------------------------------------- but feff8 stopped and said: Absorbing atom coords not specified. Cannot find multiple scattering paths. since the OVERLAP does't need ATOMES card, where can I define the coordination of absorbing atom? Is there any other CARD needed for such situation? ========================================= Hi Jun, That keyword is explained here: http://feff.phys.washington.edu/feff/wiki/index.php?title=OVERLAP I think the problem is that you have not specified the SS keyword: http://feff.phys.washington.edu/feff/wiki/index.php?title=SS I use the overlap/ss thing in feff very infrequently. My preference is to start from a known structure that is somehow similar to the material I am investigating. For example, if I were to look at amorphous germanium, I would use crystalline germanium as my starting point. I would then construct the model in such a way that I parameterize the differences between the starting structure and what I expect to find in the data. I'd recommend reading papers by Scott Calvin or Anatoly Frenkel on nanoparticles or by Shelly Kelly on uranium in biogeochemical systems for excellent examples of how that sort of analysis is done. Hope that helps, B -- Shanghai Institute of Applied Physics, Chinese Academy of Sciences No. 2019, Baojia Road, Jiading District, Shanghai,China 201800

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How to use "OVERLAP" card?
by Jun Lin 08 May '07

08 May '07

Hi everybody: It is the first time I send mail to this list. I wanna use OVERLAP of Feff8.4 to design a structure for my analysis, but the program give error message as followed: > Feff 8.40 > OVERLAP: > Expert option, please read documentation carefully and check your results. > OVERLAP: > Expert option, please read documentation carefully and check your results. > My test for OVERLAP > Absorbing atom coords not specified. > Cannot find multiple scattering paths. > RDINP > STOP statement executed in my feff.inp, I wrote like this: TITLE My test for OVERLAP * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 0 0 0 0 0 0 POTENTIALS * ipot Z element * l_scmt l_fms stoichiometry 0 26 Fe 1 7 N OVERLAP 0 0 1 0.00 1 4 1.15 END Is there anyone give me some suggestion? Thanks! Lin Jun -- Shanghai Institute of Applied Physics, Chinese Academy of Sciences No. 2019, Baojia Road, Jiading District, Shanghai,China 201800

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Ru input file - a question and a problem
by Vivek Murthi 02 May '07

02 May '07

Hi Bruce/Matt/Scott I am trying to fit some Ru based catalysts using Ifeffit - 0.8.007. 1. Does anyone have an atoms input file for Ruthenium that they can share with me? _ The problem:_ 1. I got the crystallographic data for Ru from "database.iem.ac.ru/*mincryst*/" which I used inside atoms to generate FEFF a input file. However, FEFF returns an error saying that my atoms list might be wrong and that two atoms are separated by less than an 0.93 angstroms. I also checked the 5 digit precision in the input file to make sure that wasn't creating the problem. The FEFF input file generated by atoms definitely has atoms bizarrely close to each other. I do not understand why a standard crystallographic data would give such results. I have attached the "Ru.inp" input file I used and the error buffer from FEFF below for your convenience. 2. So I tried playing around with the atoms input file. I set all the xyz co-ordinates to 0, then the FEFF runs without any error but that however gives me 2 Ru paths with two separate R eff ( 2.14 and 2.70 A) but very close to each other in the first shell. Is this a possible scenario? Thank you for your time/comments/solutions. Vivek # Artemis version 0.8.007 # This file created at 16:41:31 on 2 May, 2007 # using Windows XP, perl 5.006001, Tk 800.024, and Ifeffit 1.2.9 # IFEFFIT_DIR is C:\Program Files\Ifeffit # Workspace: C:\Program Files\Ifeffit\horae\stash\artemis.project.1\ Feff 6L.02 WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 1 2 1 0.00000 0.00000 0.00000 2 0.00000 0.00018 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 3 9 3 -1.56108 0.00014 2.14100 9 -1.56116 0.00009 2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 4 5 4 0.78066 -1.35186 2.14100 5 0.78058 -1.35191 2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 6 10 6 -1.56108 0.00014 -2.14100 10 -1.56116 0.00009 -2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 7 8 7 0.78066 -1.35186 -2.14100 8 0.78058 -1.35191 -2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 11 13 11 0.78058 1.35209 2.14100 13 0.78066 1.35214 2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 12 14 12 0.78058 1.35209 -2.14100 14 0.78066 1.35214 -2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 15 23 15 0.00000 -2.70382 0.00000 23 0.00000 -2.70400 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 16 21 16 2.34173 -1.35182 0.00000 21 2.34173 -1.35200 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 17 22 17 -2.34173 -1.35182 0.00000 22 -2.34173 -1.35200 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 18 24 18 2.34173 1.35200 0.00000 24 2.34173 1.35218 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 19 25 19 -2.34173 1.35200 0.00000 25 -2.34173 1.35218 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 20 26 20 0.00000 2.70400 0.00000 26 0.00000 2.70418 0.00000 Run continues... ... Calculating potentials and phases... free atom potential and density for atom type 0 free atom potential and density for atom type 1 overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 muffin tin radii and interstitial parameters phase shifts for unique potential 0 This warning indicates a problem in the Atoms list. For some reason you have atoms that are separated by than 0.93 Angstroms (or 1.75 Rydberg). This may be due to the presence of hydrogen atoms in your feff.inp file, in which case this is an innocuous warning and may be ignored. However, this may indicate a problem constructing the Atoms list. The most common cause of this problem is a mistake in the crystallographic data used on the Atoms page. You may have incorrect values for lattice constants or angles or incorrect values for site coordinates. You may need a shift vector to move the lattice into its standard setting. Please be aware that Atoms works with 5 digits of precision. Thus, if you have a site with a coordinate of 1/3, you should use either "1/3" or "0.33333" on the Atoms page. Using insufficient precision, say "0.333" is a common cause of this error message. Artemis has continued on the possibility that the warning is caused by hydrogen atoms, but be warned that the feff.inp may require your attention. ! This atoms input file was generated by Artemis 0.8.007 ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 title = ... space = P63/MMC a = 2.7040 b = 2.7040 c = 4.2820 alpha = 90.0 beta = 90.0 gamma = 120.0 core = Ru edge = K rmax = 3.0 shift 0.00000 0.00000 0.00000 atoms ! elem x y z tag occ. Ru 0.33330 0.66670 0.25000 Ru 1.00000

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large Eo's and neg. D-W factors
by Richard Mayes 02 May '07

02 May '07

Greetings! I have inherited a vanadium EXAFS data set (due to a group member graduating - lucky dog!) that is giving me major fits. I am getting consistent numbers with all my fits which visually look fantastic, that is until I look at the numbers...one Debye-Waller factor is negative (a V-O path) and the Eo's are large, the V-Cl path is on the order of -20 eV, the V=O path is on the order of 17 eV, and the V-O path falling at -11 eV. ARe there any "tricks" outside of restraints or constraints that I can attempt to get more realistic values? (I understand that a large Eo can be realistic, but a negative Debye-Waller factor doesn't make sense.) I can restrain the V-O Debye-Waller factor and get a positive value, but then the V=O D-W factor is negative. If I restrain both D-W factors, the fit falls apart, suggesting something else is wrong that I just can't find. Another issue I'm having involves something in Artemis that's confusing me. Sometimes after a fit, the Artemis Pallet shows the V=O feature as the one at 1.8 Angstroms and the V-O feature at 1.6 Angstroms, completely reversed to the FEFF model. I have seen this when I separated the chlorides as well (I attempted to model the Cl at different distances as reported by Deguns, et. al. (attached) due to the immediate environment around the V in our sample being similar to the one they report in scheme 1-(I), p5008). Attached is a text file that shows an Artemis Pallet output illustrating what I'm trying to describe for the V=O and V-O paths. The Artemis project that generated the output is also attached. At this point, I'm wandering what I'm missing. Any help is greatly appreciated!! Many thanks in advance! Rich Mayes Barnes Group 450/452 Buehler Hall Dept. of Chemistry Univ. of Tennessee Knoxville, TN 37996 Project title : Fitting SA_162deglitch-merge.chi Comment : Fit #1 Prepared by : Contact : Started : 15:46:44 on 17 April, 2007 This fit at : 15:58:01 on 18 April, 2007 Environment : Artemis 0.8.007 using Windows XP, perl 5.006001, Tk 800.024, and Ifeffit 1.2.9 Figure of merit : 3 ============================================================ Independent points = 14.027343750 Number of variables = 9.000000000 Chi-square = 45.640992098 Reduced Chi-square = 9.078550099 R-factor = 0.012557807 Measurement uncertainty (k) = 0.000687372 Measurement uncertainty (R) = 0.023895029 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): enot = 17.1999060 +/- 3.4058600 (0.0000) delr = 0.1588460 +/- 0.0081480 (0.0000) ss = -0.0022720 +/- 0.0007180 (0.0030) enot_O2 = -11.0384940 +/- 9.8688920 (guessed as enot) delr_O2 = -0.2214820 +/- 0.0356500 (0.0000) ss_O2 = 0.0027560 +/- 0.0021290 (0.0030) enot_Cl = -16.0026700 +/- 3.5982940 (guessed as enot) delr_Cl = -0.0118230 +/- 0.0104780 (0.0000) ss_Cl = 0.0016470 +/- 0.0004220 (0.0030) Set parameters: amp = 0.93 CN_O1 = 1 CN_O2 = 1 CN_Cl = 2 Correlations between variables: enot_Cl and delr_Cl --> 0.9479 enot_O2 and delr_O2 --> 0.9104 enot and enot_Cl --> 0.8766 enot and enot_O2 --> -0.8755 ss and delr_Cl --> 0.8737 delr_O2 and enot_Cl --> -0.8655 ss and enot_Cl --> 0.8469 enot_O2 and enot_Cl --> -0.8220 ss and delr_O2 --> -0.8025 enot and delr_Cl --> 0.7864 enot and delr_O2 --> -0.7825 delr_O2 and delr_Cl --> -0.7817 enot_O2 and ss_O2 --> 0.7535 delr_O2 and ss_O2 --> 0.7259 enot_O2 and delr_Cl --> -0.7080 ss and enot_O2 --> -0.6872 enot and ss --> 0.6795 delr_O2 and ss_Cl --> -0.6271 delr and ss_Cl --> -0.6217 ss_O2 and enot_Cl --> -0.6173 ss and ss_Cl --> 0.5740 ss_O2 and ss_Cl --> -0.5640 enot and ss_O2 --> -0.5314 enot_Cl and ss_Cl --> 0.5264 ss and ss_O2 --> -0.5084 enot_O2 and ss_Cl --> -0.4750 ss_O2 and delr_Cl --> -0.4747 delr_Cl and ss_Cl --> 0.4701 delr and ss_O2 --> 0.4134 enot and delr --> 0.3090 enot and ss_Cl --> 0.2693 All other correlations are below 0.25 ===== Data set >>SA 162deglitch-merge<< ======================================== file: C:\Program Files\Ifeffit\horae\stash\artemis.project.2\chi_data\SA_162deglitch-merge.chi title lines: Self absorption correction of 162deglitch-merge using method of Troger et al. + V K edge + Formula=H24.75 C8.25 O21.48 Si12.125 Cl4.7 V1.48 Merge in e space of: ** D:/200600603/Barnes-lab/EXAFS/NSLS/EXAFS/MYL-JULY-2006/all-VOCl3/162-Me2SiCl2+V5/162.001 ** D:/200600603/Barnes-lab/EXAFS/NSLS/EXAFS/MYL-JULY-2006/all-VOCl3/162-Me2SiCl2+V5/162.002 ** D:/200600603/Barnes-lab/EXAFS/NSLS/EXAFS/MYL-JULY-2006/all-VOCl3/162-Me2SiCl2+V5/162.003 k-range = 2.388 - 15.000 dk = 2.000 k-window = hanning k-weight = 2 R-range = 1.200 - 3.000 dR = 0.200 R-window = hanning fitting space = R background function = none phase correction = none R-factor for this data set = 0.01256 ===== Paths used to fit SA 162deglitch-merge FEFF1: Path 1: [O] .. feff = C:\Program Files\Ifeffit\horae\stash\artemis.project.2\data0.feff1\feff0001.dat id = reff= 1.6819, nlegs= 2, path= V<->O label = r = 1.840746 degen = 1.000000 s02 = 0.930000 e0 = 17.199906 dr = 0.158846 ss2 = -0.002272 3rd = 0.000000 4th = 0.000000 ei = 0.000000 FEFF1: Path 2: [O] .. feff = C:\Program Files\Ifeffit\horae\stash\artemis.project.2\data0.feff1\feff0002.dat id = reff= 1.8269, nlegs= 2, path= V<->O label = r = 1.605418 degen = 1.000000 s02 = 0.930000 e0 = -11.038494 dr = -0.221482 ss2 = 0.002756 3rd = 0.000000 4th = 0.000000 ei = 0.000000 FEFF1: Path 3: [Cl] .. feff = C:\Program Files\Ifeffit\horae\stash\artemis.project.2\data0.feff1\feff0003.dat id = reff= 2.1121, nlegs= 2, path= V<->Cl label = r = 2.100277 degen = 1.000000 s02 = 1.860000 e0 = -16.002670 dr = -0.011823 ss2 = 0.001647 3rd = 0.000000 4th = 0.000000 ei = 0.000000

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Athena and Artemis reference
by IONESCU, Mihail 02 May '07

02 May '07

Dear Bruce, What reference we can give in our papers for using Athena and Artemis packages, which you guys have been provided so generously to the user community? Thanks, Mihail ----------------------------------------------------------------- Dr Mihail Ionescu Senior Research Scientist Ion Beam Accelerator Applications Australian Nuclear Science and Technology Organisation ANSTO Bld. 53, New Illawarra Rd, Lucas Heights, NSW 2234 Australia PMB1, Menai, NSW 2234 Ph: +612 9717 3301 Fax: +612 9717 3257 -----------------------------------------------------------------

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Potential Postdoctoral Position in XAFS
by Bare, Simon R 30 Apr '07

30 Apr '07

POSTDOCTORAL POSITION in XAFS and XRD UOP LLC There is a potential opening for a postdoctoral position in synchrotron radiation research of catalysts and adsorbents with UOP LLC. The successful candidate with work with UOP LLC research scientists and will support UOP LLC exploratory and fundamental industrial research activities primarily at the Advanced Photon Source (APS) at Argonne National Laboratory. UOP LLC, a Honeywell Company, located in northwest suburban Chicago, is an international leader in technology, products, and services for the petroleum processing and separation industries (www.uop.com <http://www.uop.com/> ). The successful candidate will participate in all aspects of experiments related to operating a beamline, collecting, analyzing and interpreting the data. This position requires expertise in techniques of XAFS (preferably with knowledge of Athena/Artemis or Iffeffit software) and XRD, together with hands-on experience with electronic control and measuring equipment and beamline components. A CV with publications list, and the names and addresses of two references, should be sent via e-mail to Dr. Simon Bare at: simon.bare(a)uop.com.

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sum path NAN?
by Mauro Rovezzi 27 Apr '07

27 Apr '07

Dear all, Do you have any idea of what means NAN (Not A Number?) in "sum path" Ifeffit output during the fit? I've already posted this issue in a post dated 2006/10/04 and Bruce asked to me to give him something to reproduce this issue on his computer but this behavior is very unstable and I don't understand how to exactly reproduce it. I would like to know in your opinion what could bring a variable during the minimization process to NAN. In addition, what exactly means the four numbers visible in the "sum path #1 #2 #3 #4" output? It seems to me that, for each path, #2 = delr and #3 = sigma2, isn't it? M. -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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