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

FEFF6 errors?
by Carlo U. Segre 15 May '03

15 May '03

Matt: I have been having problems with the FEFF6 that is distributed with Ifeffit. If I try to run the executable with the feff.inp the TEST directory, it gives the following output ---- copper 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 phase shifts for unique potential 1 Preparing plane wave scattering amplitudes... nncrit in prcrit 9 Searching for paths... Rmax 0.0000 keep and heap limits 0.0000000 0.0000000 Preparing neighbor table nfound nheap nheapx nsc r Internal path finder limit exceeded -- path list may be incomplete. Paths found 0 (nheapx, nbx 1 0) Eliminating path degeneracies... Plane wave chi amplitude filter 2.34% STOP no input statement executed ---- It only generates the 4 files: geom.dat paths.bin paths.dat phase.bin If I look at paths.dat, I see: ---- copper Rmax 0.0000, keep limit 0.000, heap limit 0.000 ^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@ Plane wave chi amplitude filter 2.34% ------------------------------------------------------------------------------- ---- I am a bit confused about this because when building the Debian package, everything compiles properly and all the libraries seem to be there properly. Any ideas? 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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Athena - plotting limits
by Carlo U. Segre 15 May '03

15 May '03

Bruce: Why does Athena only plot from 0-15 in k-space even though there is data beyond that. Now that I look back at the mu(E) plots, they are restricted in energy too. I understand that we would normally not use data to far beyond k=15 but it still might be nice to see it. Perhaps, I am just not seeing some kind of parameter that could be set? 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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ifeffit 1.2.0
by Matt Newville 14 May '03

14 May '03

Hi Everyone, At the suggestion of several people, I've repackaged the latest version of Ifeffit and called it version 1.2.0, to indicate that this is the stable version. By this, I mean that bugs and errors will be fixed in this series, but that no new features will be added. As of now, only the source kit for ifeffit-1.2.0 is available from the Ifeffit web site. The Windows installer package should be available within a few days. In addition to this, it was recommended to start using the SourceForge.net services. This will happen, and an empty page for Ifeffit is available there at http://sourceforge.net/projects/ifeffit/ It may take much of the summer to get this working completely. This will provide multiple download sites with mirroring. In addition, the development/unstable versions will be available through Sourceforge's CVS server -- if anyone is interested in this, letting me know! There are other services (such as bug tracking) available from Sourceforge as well, and it is possible that the mailing list may eventually move to sourceforge.net as well. Thanks, --Matt

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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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