June 2002 - Ifeffit - millenia.cars.aps.anl.gov

Ifeffit 1.0072 released
by Matt Newville 18 Jul '02

18 Jul '02

Hi Everyone, I figured that it had been long enough for version 1.0071, so posted version 1.0072 today. This version has several small feature improvements and bug fixes. There is also a fairly substantial changes to the 'configure ; make ' on Unix, so that the perl and python extensions are no longer built during this process, but have to be built after installation of the library, with the 'normal method' for these languages: cd wrappers/python python setup.py install cd wrappers/perl perl Makefile.PL ; make install This change greatly simplifies the work of the configuration script and is much more reliable. The other major change is that the internals of macro handling were largely rewritten so that nested macros work correctly in all cases (including on windows). Related to that, macros that are run by feffit() and minimize() at each iteration of the fitting loop now run correctly as well. I have a Windows dll ready, but am having difficulty making standalone executables from the ravelware perl scripts. Hopefully that will get worked out soon so that a new Windows installer with the latest athena, artemis, and tkatoms, as well as gifeffit and samxas will be possible. I've also started (but haven't gotten very far on) an annoted collection of ifeffit scripts, intended to be something of a 'how-to' or 'cookbook' for ifeffit commands that will complement the documents and FAQ. Any suggestions or comments on this would be very welcome. Finally, I am really expecting that 1.0072 represents a nearly complete version of Ifeffit 1.0. I believe the XAFS analysis functionality is more-or-less complete at this point. I'm willing to fix bugs, and add small features, but would like to try to leave this version stable and to start working (even if slowly!) on much more significant changes that would eventually become Ifeffit 2. Thanks, --Matt

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my programs on OSX
by Bruce Ravel 24 Jun '02

24 Jun '02

Hi folks, I received an email from a new user last week praising Francois on his helpful pages (http://www.univ-mlv.fr/~farges/atomsX/) explaining how to get Atoms up and running on OSX. Now I have a question for you OSX gurus on this list. Can someone write up a web page to supplement this explaining how to get Ifeffit (and, by extension, Athena and Artemis) up and running on OSX? Or perhaps this exists, in which case I need the URL so I can make a link on my web pages. Eventually, I would like there to be some kind of (Fink-based, I suppose) installer package for OSX, but for the moment it would be nice to at least give some guidance to the inspired and dedicated OSX users. Thanks, 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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(no subject)
by Bruce Ravel 24 Jun '02

24 Jun '02

Hi, I fixed several bugs in Artemis last week and today I posted a new source code tarball. The changes include: 1. fixed several bugs in displaying and using different FT window choices 2. fixed some bugs affecting deletion and rereading of feff calculation. 3. added the ability to turn on and off the "include this path in fit" button for the set of selected paths (i.e. all the paths highlighted in orange in the list on the right). I also reorganized the pull-down menus for including/excluding paths from the fit. 4. paths included in the fit are listed in black text, paths excluded from the fit are listed in a different color. also things not intended for plotting (such as the GSD listing) are printed in italics. this all gives some visual cues to help use the contents of the list effectively. 5. fixed (I hope!) a serious problem which manifested itself by having the data appear as a bizarre starburst-like plot in k-space. Several people had noticed this already. These are all pretty significant usability improvements. Special thanks this week go to Paul Fons for helping me track down several of these problems. As always, grab the latest from http://feff.phys.washington.edu/~ravel/software/exafs/ 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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artemis source code update
by Bruce Ravel 18 Jun '02

18 Jun '02

Hi, I fixed the following four problems with artemis reported to me last week: 1. a really bad bug triggered by using capital letters in parameter names 2. a strange end-of-line problem when artemis was run on unix using feffNNNN.dat files made on windows 3. the "View paths.dat" button will look for "paths.dat" or "path00.dat", i.e. it will find the paths file from feff6 or feff8 4. several related bugs in how the functional form of the FT windows were chosen and displayed on the screen I updated the source tarball and posted it on my web site. http://feff.phys.washington.edu/~ravel/software/exafs/ Artemis currently has the unfortunate, complimetary problems of lacking documentation while being a complex and unintuitive program. The best suggestion I can make for now for learning to use it is to check out the two project files in the examples/Cu/ directory. They are the ones with the .apj extensions. If you are a feffit user, you can import your `feffit.inp' files. If you have never used feffit before, I would recommend reading Chapters 2 and 4 of the `notes.pdf' file found on the web page for my "EXAFS Analysis Using FEFF and FEFFIT" course: http://leonardo.phys.washington.edu/~ravel/course/ Between that and examining the project files, hopefully Artemis will make some kind of sense. Thanks especially to Mark Jensen and Michael DeLeon for their email in the last few days. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu 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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Mark Jensen's artemis bug report
by Bruce Ravel 14 Jun '02

14 Jun '02

Hi, Yesterday, Mark Jensen alerted me to two problems in the current version of artemis. The first is a situation wherein artemis ignores certain guess parameters. The second is a situation in which artemis fails to display the header information from the feffNNNN.dat file as in this screenshot: http://leonardo.phys.washington.edu/~ravel/software/exafs/images/artemis/ar… The first problem is due to the fact that artemis gets confused by capital letters in parameter names. That is, "deltar" is ok, but "deltaR" is not. This will be fixed in the next release. The work-around for this problem is to avoid capital letters in parameter names. The second problem was for the somewhat strange situation of running artemis on a unix machine and having made the feffNNNN.dat files on a windows machine. Because of a mistake that I made in the code that fills in the text box in the picture above, artemis got confused by the different end-of-line conventions on windows and unix. How embarassing! This will also be fixed soon. The work-around is to run feff and artemis on the same kind of computer. I want to thank Mark for the excellent bug report and for his help in troubleshooting. Regards, 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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XAS GUIs
by Webb, Samuel M. 14 Jun '02

14 Jun '02

Hi All... Just wanted to post this to the audience here. I've been working on a set of GUIs for XAS preprocessing and fitting and I think they are just about ready for testing by a broader audience. The first program is SamView and performs basic averaging of scans, energy calibration, deadtime correction and viewing of raw data. At this point, it is specialized to read only certain file formats, but the capability will be expanded in the future. Since my focus has been at SSRL recently, it will read binary and ASCII formats from SSRL, as well as from DND-CAT at the APS. In summary, it is essentially a graphical version of MAVE, MCALIB, and MDEAD for those who have used EXAFSPAK at SSRL. The second program (SamXAS) is a XAS fitting routine. It has a GUI interface to IFEFFIT for FEFF fitting of XAS, a linear combination fitting routine for XAS and XANES, and an interface for creating FEFF single scattering paths (if Feff8 is installed on your system). It also has a fitting routine to account for fluoresence self absorption with out prior knowledge of the sample composition. These are all in their infancy, but I'm looking for feedback on how to improve them, with out replicating the magnificnet work of other contributors. The documentation for both is essentially non-existent, but there are a few sample workspaces and data files included to get you started. Familiarity with IFEFFIT is definitely a plus. The programs can be downloaded from www.stanford.edu/~swebb. Thanks! Sam Webb SSRL samwebb(a)slac.stanford.edu

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First attempts to use Artemis
by Mark Jensen 13 Jun '02

13 Jun '02

Dear Everyone: I'm not sure if this is a bug report or a dopey user report for Artemis, but I am having a problem with Artemis on two Red Hat 7.3 systems with Feff8. The data files load and are displayed in the PGPlot window. I can load and display FEFF paths in the windows too. (Nice touch Bruce. Ravel-ware is great!). However, :( , the path information is not displayed in the path text box like the last picture in Bruce's poster shows. That's not a killer problem in my mind. The real problem is that I can only fit 0 or 1 variable, no matter how many I set as guessed. It appears that Artemis/ifeffit is only varying the guessed variable associated with the first path variable on whichever tab (Basic parameters or Other parameters) is visible (i.e. S02, OR the third cummulant). It won't vary both S02 and the 3rd cummulant and it won't vary any guessed variables that appear in the other path parameters. It doesn;t appear to matter how many different paths I include. If there isn't a guessed variable in either the S02 or third cummulant path, none of the guessed variables is varied. The values of all guessed variables that are not varied always return from ifeffit as 0.0. Any thoughts Mark Jensen ------------------------------ Mark P. Jensen Chemistry Division Argonne National Laboratory 9700 South Cass Avenue Argonne, Illinois 60439-4831 USA 630-252-3670 630-252-7501 FAX mjensen(a)anl.gov

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rendering problem with Athena
by Carlo U. Segre 08 Jun '02

08 Jun '02

hello Bruce: I have noticed a rendering problem with Athena in Linux. I am attaching a PNG screenshot of the offending screen. As you can see, the lowest part of the "Background Removal" subwindow is showing only the top and it is impossible to read it. Since the window will not resize, it is not just a question of enlarging it. I use a Debian testing system and I would be happy to tell you what libraries are installed if you let me know which ones are relevant. Carlo -- Carlo U. Segre -- Professor of Physics 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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