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

Phase corrected Fourier transforms
by Juan Antonio Maciá Agulló 27 Sep '06

27 Sep '06

Hi all, I have read Phase corrected Fourier transforms in Athena manual and now I have a big doubt, ¿phase correction or not in a publication? I have read also that this correction is different (more complete) in Artemis and I am not sure if I should correct also in Artemis and which path should I use and why. I saw many papers dealing with EXAFS fits and they showed a "calculated" bond distance, I think it is: d = Reff + deltaR, right? I also ask for a paper where I can find that deltaE is ok (even for high-Z backscatterers) if deltaE < 10eV. I have high correlations between ss and SO2, and deltaR and deltaE. I tried different fits but I can not eliminate them, then...is the fit wrong? Sorry for these easy questions but I am a novice in XAFS. Thank you very much. Best regards, JA

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Re: [Ifeffit] Artemis error message
by Matt Newville 20 Sep '06

20 Sep '06

Hi Stefano, Did you try using /Applications/Ifeffit/bin/feff6 as the preferred feff executable in Artemis? That's what the error message was suggesting you try. Can you verify that you have /Applications/Ifeffit/bin/feff6? --Matt

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Artemis import from the text file
by Victor.Streltsov＠csiro.au 19 Sep '06

19 Sep '06

Hi All, I have the following Artemis problem: when I export variables to text file and then read them back into new Artemis run/project (import variables from the text file), Artemis cuts parts of the expressions starting from multiplication sign '*'. I tried different text editors and character coding as well as different platforms (Windows XP, Linux FC4). It always does the same thing with imported math expressions. It doesn't like '*' character. I am puzzled. I would appreciate your help and any suggestions. Thanks Victor Dr Victor Streltsov CSIRO Molecular & Health Technologies 343 Royal Parade Parkville VIC 3052 Australia Phone: +61 3 96627311 Fax: +61 3 96627101 victor.streltsov(a)csiro.au

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Short questions
by Juan Antonio Maciá Agulló 15 Sep '06

15 Sep '06

Hi Ifeffit people, I have a couple of short questions for you. I used the "Scott Calvin's rule" (number of variables < 2/3*Nip) to calculate the maximum number of allowed free parameters but I read that some people use the Nyquist theorem, which are the differences between them? and, which one is more correct? And finally, how are errors calculated in Artemis for the parameters N (coordination number), deltaE0, S02, deltaR and sigma^2? Thanks a lot JA

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FW: PhD position@LWV/PSI
by Degueldre Claude A. 12 Sep '06

12 Sep '06

-----Original Message----- From: Bruce Ravel [mailto:bravel@anl.gov] Sent: Montag, 11. September 2006 17:22 To: Degueldre Claude A. Subject: Re: PhD position@LWV/PSI URGENT AND FOR INFORMATION COULD YOU PLEASE VENTILATE THE INFO... We have 1 position free for doctorant with main topic EXAFS. You find the job below: http://pa.web.psi.ch/pages/offenestellen/d/index_offenestellen.php?was=l iste&kategorie=doktoranden With the KS 4334 If you have any candidate, please let me know... We need to evaluate candidates on Sep. 25. All the best CLAUDE DEGUELDRE ----------------------------------------------------- On Monday 11 September 2006 10:07, you wrote: > Bruce > We have 1 position free for doctorant with main topic EXAFS. You find > the job below: > http://pa.web.psi.ch/pages/offenestellen/d/index_offenestellen.php?was > =l > iste&kategorie=doktoranden > With the KS 4334 > If you have any candidate, please let me know... > We need to evaluate candidates on Sep. 25. > All the best Hi Claude, I don't know anyone who can fill the spot in the next two weeks, unfortunately. I think you should post this job opening on the Ifeffit mailing list. Matt and I consider that an excellent use of the mailing list. 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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Installing Tk/Horae on Fedora Core 5
by Bhoopesh Mishra 12 Sep '06

12 Sep '06

Dear All, I am in the process of installing Ifeffit 1.2.9 with latest Horae package (-062) on my a new machine on which I have put Fedora core 5. I followed the instructions for installing the entire package, and had partial success in it. Ifeffit and PGPLOT seem to be working fine. I believe Tk-804.027 is also working fine, I just ran "widget" and it works. However when I tried to ./horae_update, I got error message and it aborted without compilation. To look into the problem, I manually downloaded a previous version of horae (horae-061) from another computer on which everything is working fine (Tk-800.024 with horae-061 on a Fedora Core 2). In the manual installation of horae_061, perl Makefile.PL works fine. But "make" does not complete. It terminates with the same error message as the one with which ./horae_update terminated. (attached as a screenshot) I have attached the screenshots of the error message for horae_update. I have also attached screenshots of "make install" and "make test" for Tk-804-027 just in case you would like to see that. Since Ifeffit and PGPLOT are working, I am inclined to believe that it has something to do with Fedora Core 5 and its compatibility with Tk-804.027 and horae-062. Funny part is that I tried to downgrade the Tk to Tk-800.024, but it failed to install, which indicates some issues of Tk with FC 5. I also tried the combination of Tk-804.027 with horae-060. Has anyone gone through this combination of installing Tk-804.027 with horae-062 on a Fedora Core 5? Any insight would be extremely helpful. Thanks a lot in advance. Please let me know what more information would you need if the given information is insufficient. PS: I have been successfully using all these programs on FC 2 and FC 3 for last few years but some very generous people always helped me with the installation and am now trying to be independent. Thanks again, Bhoopesh

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Re: X11 on 10.4.7
by Bruce Ravel 11 Sep '06

11 Sep '06

On Monday 11 September 2006 15:34, Kjell Bolmgren wrote: KB> KB> Bruce, KB> KB> Did you ever find out how to install X11 on 10.4.7. KB> KB> I have tried to install it from the cd and to download it but neither KB> works so far. Kjell, I am CCing this to response to the mailing list in hopes that someone will be able to lend you a helping hand. I'll restate now what I say every time I make a post about anything Apple: I don't own a Mac, I don't have a Mac at work, and my experience on the Mac in any other context is extremely limited. That Athena and Artemis work on the Mac is thanks to my choice to use cross-platform programming tools (like perl and Tk) and on the kind contributions of people like Paul, who went the final mile to make easy-to-install packages. 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] Artemis error message
by Matt Newville 11 Sep '06

11 Sep '06

Stefano, Feff6 is an executable. When it runs it needs a file named feff.inp to be in the current working directory, otherwise it will say: Feff 6L.02 Fatal Error: cannot open file "feff.inp" in module rdinp which is exactly what you got when you typed 'feff6' in a directory without a feff.inp file. That doesn't tell us a lot, but it does mean that this version of feff6 is at least not corrupted, so the Installer is probably fine. The first error message from Artemis that you sent: "The error is probably due to having Artemis configured...." and gave an "Uh-Oh" in the Echo Buffer is definitely what Artemis says when it cannot find feff6. You said you got this when the feff_executable was set to 'feff6'. Did you try setting feff_executable to '/Applications/Ifeffit/bin/feff6'? Note that spelling counts. You could open a Terminal, type 'which feff6' and paste that into the feff_executable field. Note to Bruce: How about having a "browse" button for selecting the feff_executable? > I interpret this message with the conclusion that I can just type 'feff6' in > the Artemis preferences, as the command is actually seen and of course it is > missing the feff.inp file if I run the command from the terminal. Well, it *should* work that way, but using /Applications/Ifeffit/bin/feff6 will definitely work. It does work for several of us. Hope that helps, --Matt

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Re: [Ifeffit] Demeter: my new software project
by Bruce Ravel 11 Sep '06

11 Sep '06

On Saturday 09 September 2006 11:02, Mauro Rovezzi wrote: > I really like your new project! I think it's a great idea because > Athena&Artemis are good softwares but clicking on them all the day it's > quite boring. Exactly. To my mind, the biggest problem is that it is difficult, time consuming, and error prone to encode a complex fitting model using Artemis' GUI. I forsee that one of my common uses of Demeter will be to encode a complex fitting model in a one-off script and have that script write out an Artemis project file. Then I'll get the good parts of the GUI while using something automated to deal with the tedious parts. > On the other hand, I find the Ifeffit wrapper too > low-level. In fairness, Ifeffit is great at doing its low-level thing. It's just that low-level tools tend not to scale up gracefully. > Well, Demeter seems to me the best solution as a middle-level > interface to Ifeffit, that permits to fork to user-oriented projects > written in Perl. I also appreciate the choice to move this project to a > version control system (Subversion), that is the future possibility for > users to directly contribute to the code. Thanks for all the kind words, Mauro. I am excited that you get the point of middleware and that you get the point of using Subversion. Even if you use and don't contribute, Subversion lets you always use up-to-the-minute code. 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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Demeter: my new software project
by Bruce Ravel 08 Sep '06

08 Sep '06

Hi! I think that some of you will be interested in my latest XAS software project, which I am calling Demeter. Demeter is an object-oriented programming interface to Ifeffit written in Perl. It is intended to encompass most of the current functionality of Athena and Artemis while at the same time being more generalized, lower-level, and much more robust. In short, Demeter is not a software product. Rather, it is the thing that software products can be made from. Demeter is targeted at a wide variety of XAS data analysis chores, such as * GUI's like Athena and Artemis. In fact, I intend to rewrite Artemis using Demeter once I have incorporated enough functionality into Demeter. * A parser for feffit.inp files allowing you to translate your old analysis using feffit into ifeffit scripts and Artemis projects. * The analytic component of a high-throughput system such as those presented at the XAFS13 conference by the groups of Wolfram Meyer-Klaucke and Sven Schroeder. * The backend to specialized XAS software, like Shelly Kelly's mkfit program (http://www.mesg.anl.gov/exafs.html) or for ideosyncratic analysis like that described in Physical Review B, 73, p. 184121 (2006) There is still A LOT to do, but even at this early stage Demeter is very useful. In fact, Demeter can already be used for real data processing and analysis. Demeter is available on an anonymous Subversion server, so anyone with an SVN client can check out a copy of Demeter at any time. Information about Demeter and the Subversion server is at http://cars9.uchicago.edu/~ravel/software/demeter.html You can browse the Demeter source code with your web browser at http://cars9.uchicago.edu/svn/demeter/ If this seems interesting to you, take a look at some of the short example programs demonstrating Demeter's capabilities and economy of language: http://cars9.uchicago.edu/svn/demeter/examples 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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