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

upcoming EXAFS course at NSLS
by Bruce Ravel 12 May '03

12 May '03

Hi folks, It occurs to me that not everyone who reads this list is or ever has been a user of NSLS, so you may not be aware of an upcoming event. This summer, Simon Bare and I are running a course on EXAFS Data Collection and Analysis at the NSLS. The course will be July 14-17 and will include lectures, beamline practicals, and lots of time in front of computers using atoms, feff, ifeffit, athena, and artemis. The speaker list includes eight 75 minute lectures on a variety of topics covering most aspects of XAS measurement and EXAFS analysis. The speaker list is really great this year and includes some familiar names from our little list, including Matt, Simon, Shelly Kelly, Scott Calvin, and John Rehr. Last year's course was lots of fun for everyone involved. Here is the URL: http://nslsweb.nsls.bnl.gov/nsls/org/workshops/exafs/exafs_workshop.htm We have limited space and received about a factor of two too many application last year. Still, it would be great to see some of you folks this summer at the NSLS! Or you might pass the URL along to someone else in your research group who is looking for an intense but fun introduction to XAFS. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Re: [Ifeffit] Re: ifeffit_1.0077 compilation problem
by Carlo U. Segre 09 May '03

09 May '03

Matt: I very much like the idea of a "stable" and "testing" line for the programs. I could keep both of them updated in my Debian packages. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Research, Armour College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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RE: [Ifeffit] Re: ifeffit_1.0077 compilation problem
by SCHLEGEL Michel 177447 09 May '03

09 May '03

Dear Everybody, > I can then start a beta series for new features and build > systems, and expect only beta testers to be affected. Any > comments on this? Just a suggestion (discard it right away if it looks like it will take too much time): Why not copying the well-proved Linux bumbering of versions, and reserve odd numbers for test versions, and even numbers for "stable" versions? This would allow simple laymen to benefit from the outstanding capabilities of Ifeffit, while allowing the "clergy" to summon the debugging deities on well-iddntified newborn versions... Best regards, Michel Schlegel

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Re: ifeffit_1.0077 compilation problem
by Matt Newville 08 May '03

08 May '03

Hi Paul, I'm responding to this one on the mailing list. As many people have noticed, there are several problems with the 1.0077 distribution of Ifeffit. It seems that it should be treated as a 'test' version. Most of the problems are small from my end (that is, easy to fix, even if show-stoppers for functionality or building). I'll be changing the links to ifeffit.tar.gz to point to versions ifeffit-1.0077a.tar.gz, ifeffit-1.0077b.tar.gz, .... over the next few days for testing. If you're brave, you can try the latest test version and let me know what's not working. Otherwise, we should have a stable, working 1.0078 sometime next week, possibly with some of the wrappers using some of the new features. As more people are using Ifeffit/Athena/Sixpack for real work, it seems that having a stable version is good idea. So I'm leaning toward calling the next release (ie, 1.0078) Ifeffit-1.100 and only fixing bugs, and build problem for this version so that this can be the 'stable, recommended' version, and can get better tests and documentation to really reflect this stable version. I can then start a beta series for new features and build systems, and expect only beta testers to be affected. Any comments on this? On Thu, 8 May 2003, Paul Fons wrote: > In attempting to compile 1.0077 of ifeffit, I encountered some > unresolved symbols. A grep search seems to indicate that atomic.f has > the definitions, but it doesn't seem to be in the macosx makefile. > Any suggestions? Yes, two suggestions: 1. Run 'configure; make ' work from the base ifeffit directory. If this doesn't work, please let me know what fails. I'd much refer this to work, and it seems close. 2. Change line 134 of src/macosx/makefile.in to read $(srcdir)/iff_unguess.o $(srcdir)/iff_window.o $(srcdir)/atomic.o and re-run 'configure ; make'. > I am doing the build using the Makefile in src/macosx. One more thing, > under 10.2 I had some problems with overlapping definitions in multiple > libraries (in Apple's and Fink). The solution was to delete the "-l > termcap" as well as the "-L/usr/lib" from the library options in the > makefile. As I have yet to get things to link successfully, I will > send you the final modifications when I resolve the symbols (at_kedge, > etc.) problem. Which is the preferred version: Apple's or Fink's? Is there any hope of getting a binary distribution for Mac OS X or at least clear and complete instructions for how to do a complete installation using Fink? --Matt

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ooops!
by Bruce Ravel 05 May '03

05 May '03

Hi all, Matt pointed out to me that I forgot to increment the version numbers of Athena and Artemis in their source codes. Thus, when the splash screens appear at start up, they each report a version number that is 1 too small. For instance, the current version of Athena is 0.8.018, but the splash screen says 0.8.017. Silly me. Rather than fix this problem, I'll just make a new release at the end of the week that makes use of some of the nifty news features of Ifeffit 1.0077 which Matt released today. And this time I'll try **really really** hard to get the version numbers correct.... ;-) B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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ifeffit 1.0077
by Matt Newville 05 May '03

05 May '03

Hi Everyone, I've just posted Ifeffit version 1.0077. It's been a while since the last release, and there have been several changes and improvements. The highlights are: - The spline() and bkg_cl() now uses a new rebinning/interpolation algorithm to convert data from chi(E) to chi(k). For finely-spaced energy data such as from QEXAFS measurements, this averages over all energy points within the corresponding k range. For data that isn't finely-spaced, a three-point interpolation is used (as before). There is also a rebin() function that works like other interpolation functions: new.y = rebin(old.x, old.y, new.x) which will use the the same algorithm. Again, this is not normally needed, as spline() and bkg_cl() do this as well. - feffit() now supports multiple-k-weights in a single fit: feffit(..., kweight=2, kweight=0, kweight=4,...) That is, listing multiple values of 'kweight' will use all of them (up to the first 5). Each portion of the fit will be properly weighted, but the error bars reported for such fits always reflect the fact that only 1 data set is really is used (and if 'bkg=true' is used, only 1 set of bkg parameters will be used). The output arrays generated for this form of multiple-k-weight fits will use the FIRST kweight listed. Other outputs will have to be created explicitly. - other improvements to feffit: feffit(bkg=true) now works with multiple-data-set fits. feffit() and minimize() now list 'bad variables' after a fit for which error bars could not be estimated. feffit() now produces correct chi(R) data when input chi(k) data is not on a k=0.05Ang^-1 grid. feffit() with multiple-data-set fits now looks closely to see if repeated data is used, to avoid 'double counting' for N_idp. - f1f2() now looks up and uses the 'known core-width of an edge' by default. That is, if the atom given has an edge energy in the supplied energy range, the corresponding core-width is used. Of course, you can still supply a value for 'width'. Other improvements to f1f2() were made in the Lorentzian convolution, and the precision of the Cromer-Libermann data. - read_data() no longer sorts on the first column by default. - plotting improvements: plot() now interprets 'key=""' correctly (ie, 'no legend') plot(reset) now works to reset the color/style tables. Notes on the windows installation: - I included the latest versions of athena, artemis, and sixpack as of this morning (05/05/2003). - Source and binary installers for the Ifeffit Python module are included in wrappers/python. - I tried (briefly) to build sixpack with python2.2, but ended up installing the binary sixpack from Sam's' web page. Sixpack uses python2.1, which is fine, but clashes with python2.2. To avoid version conflicts, I put sixpack in a completely separate directory 'sixpack'. The batch file and icons point to that version. This means some duplication of files, so we may eventually want to move uniformly to python2.2. - The executables for feffit.exe and autobk.exe have been updated. These should a) write output files more reliably, and b) auto-sense RDF files better. This last feature is not extensively tested. There are lots of changes in this version, and so plenty of room for mistakes. Please give this version and these new features a try and let me know if there are any problems. And, as always, suggestions for what to include in the next version are welcome. Thanks, --Matt

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Fwd: problem in executing programs
by Bruce Ravel 05 May '03

05 May '03

Hi folks, I received the email below from a new Ifeffit user. Apparently he is having sporadic problems trying to run the programs on Windows ME. Given that he is able to run Athena but not Artemis, I am confused. And I do not have a machine running ME on which I can try to fin a solution. Do any of you have a suggestion for him? (Although "upgrade to Windows XP" and "run linux instead" are both valid suggestions, I am guessing he is looking for a way to actually run the codes on ME.) Thanks, Bruce ---------- Forwarded Message ---------- Subject: problem in executing programs Date: Mon, 05 May 2003 17:20:20 +0100 From: Yuni Krisnandi <y.krisnandi(a)abdn.ac.uk> To: ravel(a)phys.washington.edu Hi Bruce, I just downloaded IFFEFIT and followed instructions for Windows ME. So far, I couldn't run the programs by clicking the icons in the start up. However, I managed to execute iffefit.bat and athena.bat. I still couldn't run artemis, although I've tried another way by typing the path c:\Iffefit\artemis.bat . it always gave message: bad command or file name. I understand this is such a trivial question for you. But I have no clue at all. Thanks, Yuni "Anyone can become angry - that is easy, but to be angry with the right person, to the right degree, at the right time, for the right purpose, and the right way - that is not easy." Aristotle ------------------------------------------------------- -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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athena 0.8.018 and artemis 0.6.003
by Bruce Ravel 04 May '03

04 May '03

Hi Folks, I made new versions of both Athena and Artemis today. There are no new features but I fixed a number of bugs that came to my attention in the last two weeks. You can check the change logs on the web site for the details. As always, the new source code tarball as well as new Windows executables of Athena and Artemis are available on my web site. Much gratitude this time goes to Carlo Segre, Paul Fons, and Markus Janousch for useful bug reports. Thanks, guys! Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Athena - resetting working directory
by Carlo U. Segre 28 Apr '03

28 Apr '03

Hello Bruce: I am using the latest version of Athena on Linux and I have noticed a strange behavior. I cd to the directory where my data is located and run athena form the command line. When I want to open my first file, the dialog puts me in the same directory with no problem. However, any time I try to do another file operation (reading, writing, etc), the dialog starts at the filesystem root "/". Even if I move back to the initial directory the next time it is back at the root. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Research, Armour College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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Re: ifeffit window
by Matt Newville 25 Apr '03

25 Apr '03

Hi Frank, I Hope it's OK that I CC: this to the ifeffit mailing list. On Thu, 24 Apr 2003, Frank Haass wrote: > Hi Matt! > > I have worked on my data with the IFEFFIT for a few days now, and I think it > is quite a very good improvement from the autobk and feffit-Versions I used > bevor. Great! But, I have a question concerning the windows for FT which can > be used in IFEFFIT. > > In the "old" FEFFIT, the keyword ikwindo could be used to change the window > function from Hanning to Gau� etc. > > Using the keyword kwindow (kwindow = 1 etc.) in IFEFFIT, it was not possible > to do this. Have I taken the wrong keyword? Are the numbers uses for the > separate window-functions in IFEFFIT the same like in FEFFIT? The 'ikwindo' flags in Feffit were too hard for most of to remember, so Ifeffit uses character strings for the name of the window function as with fftf(data.chi, kmin=2,kmax=12,dk=1, kwindow='hanning') The feffit() and window() command use this keyword too, or it can set with the string $kwindow: set $kwindow = 'hanning' I'm not sure that's easier than it was in Feffit, but it doesn't seem worse. For back-transforms, use 'rwindow' in place of 'kwindow'. The supported window types are: hanning fhanning kaiser parzen welch sine gaussian Only the first 3 letters of these namew are really needed. The default is 'hanning', but 'kaiser' is often a good choice. Of course, the GUIs have drop-down lists for this. I see that this information is not in the on-line docs. Eeek! I would have sworn it was.... I'll be sure to add this when I post the next version. The good news is that I am actually working on this these days, and even though I keep finding more to add and fix, I'm optimistic that 1.0077 will be ready next week. --Matt

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