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

GIFeffit, Athena and Artemis Installation
by Mark Jensen 21 May '02

21 May '02

Bruce, Matt, and everyone: Ever since the Windows version of Athena was released, I've been hooked. I couldn't wait for a Windows version of Artemis, so after a week of pondering the best way to re-introduce Linux to my PC, I have installed Linux, PGPlot, Ifeffit, Athena and Artemis this morning. I had a problem that others doing a "Ravel-ware" installation for the first time might run across. After an apparently successful installation, neither Athena nor Artemis ran, saying that they couldn't locate FileDialog.pm, widgets.pm, or Chemistry/Elements.pm (depending on the program). I was unsure where to get these files, or why they weren't where they were supposed to be, but the Chemistry/Elements.pm file made me wonder if that wasn't part of Atoms3.0. Indeed it is. After installing Atoms, Athena and Artemis both appear to be working correctly. So, Bruce might want to make a change in the intall.unix file to say that Athena (or Artemis) requires PGPlot, IFeffit, and Atoms. There is one other problem that I have not solved. Ifeffit runs fine, but when I try to run GIFeffit, the "splash window" pops up for a split second and then I get 2 error messages before the program shuts down. The errors are File "/usr/local/gin/gifeffit", line 3, in GIFeffit.GIFeffit (sys.argv[1]) File "/usr/lib/python1.5/site-package/Ifeffit/GIFeffit.py" line 285, in __init__ self.iff_dir = os.getenv('IFEFFIT_DIR) Attribute Error: getenv Does anyone have any thought? Have I missed something obvious in the installation? Mark Jensen ---------------------------------------- Mark Jensen Chemistry Division Argonne National Laboratory 9700 South Cass Avenue Argonne, Illinois 60439-4831 (630) 252-3670 (630) 252-7501 FAX mjensen(a)anl.gov

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New pgplot in fink unstable branch
by Dr. Paul Fons 17 May '02

17 May '02

There is a new version of pgplot in the unstable branch of fink which breaks the ifeffit install process. The only thing that needs to be changed is to include the two "library" like arguments: -framework Foundation -framework AppKit to the linking arguments (or compile arguments). The location of the pgplot library has also been changed to (the now standard location) /sw/lib/pgplot. I can see how to make the changed to the Makefile in src/macosx without trouble, but I am thrown a little by the python setup (it seems somewhat convoluted). What changes need to be made there to reflect the new link arguments and the new location of the pgplot library? Thanks.

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athena update
by Bruce Ravel 16 May '02

16 May '02

Hi folks, I guess I have been a busy boy this week. There's another release of athena on my web site. New stuff includes: 1. A couple bug fixes and several changes to the layout of the main window. 2. An automated alignment algorithm which works by varying an e0 shift to minimize the difference spectra of the derivative of two mu(E) spectra. I would not place great trust in this algorithm, but it think it will often provide a good first guess for the e0 shift. It works well for the EuTiO3 data that is included in the examples. You can use this algorithm from the alignment dialog or from the data preprocessing options in the file selection dialog. 3. Athena now checks to see if input data is monotonically increasing in energy (or wavenumber for chi(k) data). If it is not, Athena spits up an error message and refuses to read the data. This choice seems safe, but I am open to suggestions for other ways to treat the non-monotonic data. 4. A y-axis offset plotting parameter. This is most useful for stacked plots like in this screenshot: http://leonardo.phys.washington.edu/~ravel/software/exafs/images/athena/ath… This was done by setting the y-axis offset for the first data group to 0.5 and to -0.5 for the third data group. Enjoy, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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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uh oh!
by Bruce Ravel 15 May '02

15 May '02

So, has anyone downloaded the athena tarball I released yesterday and noticed that you cannot plot chi(k) with any k-weighting other than 1? Yikes! How embarassing! That bug will certainly be fixed in the next release. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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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non-monotonic data
by Bruce Ravel 14 May '02

14 May '02

Matt, Can you explain what ifeffit does when it reads a mu(E) data file which has non-monotonically increasing energy values. Specifically what happens to data like this: # energy xmu # ---------------- 1 0.1 2 0.15 2 0.15 3 0.18 4 0.2 end so on. Ifeffit throws up one of these two sets of error messages: spline: energy data appears out of order pre_edge: energy data appears out of order or spline: energy and xmu are different length? I understand that non-monotonic data will give problems in the intepolations and elsewhere, but what does ifeffit actually do in this case? FWIW, I plan to have athena check data as it is read in to verify that the energy array is monotonic up (or down, in which case the data will be reversed) before trying to do anything with it. But I remain curious about what ifeffit chooses to do. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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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new Athena, first release of Artemis
by Bruce Ravel 13 May '02

13 May '02

Howdy folks, Today I am pleased to announce a new release of Athena and the first release of Artemis. These are source code only releases -- I have not yet built Windows binaries. But those of you on unix machines can grab the latest and try them out. Get the latest from the normal spot: http://feff.phys.washington.edu/~ravel/software/exafs/ See some Artemis screenshots at the bottom of http://feff.phys.washington.edu/~ravel/software/exafs/screenshots.html Athena: The new features are: 1. An on-line document in the Help menu 2. Plotting difference spectra and making data groups containing difference spectra 3. Plot chi(E) (by which I mean k-weighted chi(k) but with the x-axis converted to energy) 4. Several minor improvements to the on-screen display and to the example files Artemis: Be kind. This is an initial release. ;-) Many features are missing. Many features that are present may not work quite right. But it does fit and plot. That's a big step! It cannot currently do multiple data sets, but it can handle feffNNNN.dat files from multiple feff calculations. Probably the best way to start using Artemis is to open the example project file for FCC copper (examples/Cu/cu.apj). Artemis can currently plot things in k, R, or q. It can do fits or simply evaluate the path parameters and do a sum of paths like ff2chi. To start a project of your own, do the following: 1. Read in a chi(k) data file by selecting "Open data" from the File menu. 2. Read in a feff calculation by selecting "Open FEFF calculation" form the File menu and selecting the feff.inp file from the relevant feff calculation. (You need to have already run feff, Artemis is expecting to find the feffNNNN.dat files.) 3. Click on "Guess, Set, Def" in the column on the right and define some fitting parameters. 4. Click on "Data' in the right column and set the fitting and FT parameters. 5. Click on all the paths that you want to include in the fits and define the path parameters. Like in FEFFIT, this is the time consuming part of the process. I am open to suggestions for helpful functionality in that part of the code. 6. Once that is all done, click on the Fit button. 7. Make plots by selecting things to plot from the right column and clicking on the appropriate plot button. The list uses extended selection, thus you can click and drag to select multiple items. You can also control-click to select multiple, disjoint items for plotting. Play around, let me know what breaks and what needs to be added. Remember that Athena changed A LOT in the first few months as Shelly and Matt and others gave me feedback. It took a while, but she went from a shaky, buggy beginning to being a useful, solid utility. Artemis will get there, too, but I need your help to get through the initial growing pains. Regards, Bruce -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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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Problems running athena/tkatoms
by Norbert Weiher 12 Apr '02

12 Apr '02

Dear friends, seems to be that I'm another guy having problems in setting up athena/tkatoms ;) I browsed the archives but found nothing that helped me to get them running. Here is the story: tkatoms worked well - then I installed the newest version and get: weiher> tkatoms.pl ...(lots of messages like the following)... Bareword found where operator expected at /usr/lib/perl5/site_perl/5.6.0/Xray/lib/atomsrc line 186, near "12 normal" (Missing operator before normal?) Unquoted string "normal" may clash with future reserved word at /usr/lib/perl5/site_perl/5.6.0/Xray/lib/atomsrc line 186, <RC> line 186. couldn't read bitmap file "/usr/lib/perl5/site_perl/5.6.0/Xray/lib/tkatoms.xbm": Datei oder Verzeichnis nicht gefundenerror reading bitmap file "/usr/lib/perl5/site_perl/5.6.0/Xray/lib/tkatoms.xbm" at /usr/lib/perl5/site_perl/5.6.0/i586-linux/Tk/Submethods.pm line 37, <RC> line 186. for athena it seems that it can't find the ifeffit.so libs - although they are installed (as well as the perl wrappers) and pass all test runs. I get: weiher> athena Can't load '/usr/lib/perl5/site_perl/5.6.0/i586-linux/auto/Ifeffit/Ifeffit.so' for module Ifeffit: /usr/lib/perl5/site_perl/5.6.0/i586-linux/auto/Ifeffit/Ifeffit.so: undefined symbol: G77_getenv_0 at /usr/lib/perl5/5.6.0/i586-linux/DynaLoader.pm line 200. at /usr/local/bin/athena line 50 Compilation failed in require at /usr/local/bin/athena line 50. BEGIN failed--compilation aborted at /usr/local/bin/athena line 57. I'd really love to get the packages on their way which has never been a real problem. I don't know why the new versions don't compile on my system. The requirements are all fulfilled (perl > 5.0, new Tk version...). Can anyone help me with my problems? The system is a SuSE linux box (V7.2) with kernel 2.4.4 compiled. Regards, Norbert -- Dipl. Chem. Norbert Weiher (norbertweiher(a)yahoo.de) Institute for Chemistry - Takustr. 3 - 14195 Berlin Phone/Fax: +49 30 838 53750 / 54792

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Reverse Monte Carlo
by Dr. Paul Fons 11 Apr '02

11 Apr '02

Athena and ifeffit are all running fine (now I am just waiting for artemis) so I thought I would ask a silly question about reverse monte carlo. I have taken multiple edge data on a (nearly amorphous) buffer layer comprised of S, O, and Zn. I was wondering about applying reverse monte carlo to look at some prototypical structures. Has anyone ever used Rmca (http://www.studsvik.uu.se/Software/rmc/rmc.htm) I found this using SINCRIS at the IUCr which stated that there were unix and vms versions of the software. On the ftp server I only found a os independent fortran program (which relies apparently on os dependent subroutines for which only vms and windows NT are available on the site). Is there a real unix version out there? Any opinions on the value of rmc for getting an idea of what is going on structure wise? Dr. Paul Fons Photonics Research Institute National Institute for Advanced Industrial Science and Technology Ministry of Economics and Trade Umezono 1-1-1 Tsukuba, Japan 305-8568 tel. 81-298-61-5636 fax. 81-298-61-5615 paul-fons(a)aist.go.jp Lines below are in Japanese 独立行政法人産業技術総合研究所光技術部門〒305-8568 茨城県つくば市梅園1-1-1 産総研つくば中央第2 E-mail: paul-fons(a)aist.go.jp, Tel. 0298-61-5636, Fax. 0298-61-5615

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online help bug in tkatoms
by Bruce Ravel 28 Mar '02

28 Mar '02

Howdy folks, Today I received a bug report regarding the on-line help feature in tkatoms. I belve that this problem only affects unix systems. The problem is that, when selecting "Help with Atoms" from the help menu, you may get an error dialog telling you, among other things "Error: Can't set -file to `tkatoms.pod' for Tk::Pod=HASH(0x8f06fe0)" The cause seems to be an error in one of my installation scripts and it should be fixed in the next release (sometime in the indeterminate future -- I am mostly working on artemis right now). If you don't feel you can live without the online help, I think you can make the problem go away by copying by hand the file `tkatoms.pod' from /usr/lib/perl5/site_perl/5.6.0/i586-linux/Xray/ (or whatever similar directory it ended up in on your system) to /usr/lib/perl5/site_perl/5.6.0/i586-linux/Xray/lib/ which is where it should have gone in the first place, except for the bug in my installation script wherein I left out the "lib/" part. Regards B Carlo, if you haven't already, you may be interested in subscribing to our mailing list http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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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Update athena problems
by Norbert Weiher 28 Mar '02

28 Mar '02

Dear friends, I tracked down the athena installation problems to the point that it's definitively a bug in the perl wrapper for ifeffit. Even re-compiling my gcc suite didn't solve this problem. All suggestions given by Matt and Bruce have not been successful so far. Maybe someone here got athena running on a linux box (I have SuSE 7.2) and experienced the same? Could it be the gcc version I use (2.95.3)? Include paths, etc seem to be okay. The build of the wrapper works, but the make test still aborts with the message I posted... gifeffit & ifeffit work fine. Any new suggestions on this issue? Regards, Norbert -- Dipl. Chem. Norbert Weiher (norbertweiher(a)yahoo.de) Institute for Chemistry - Takustr. 3 - 14195 Berlin Phone/Fax: +49 30 838 53750 / 54792

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