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

artemis and athena updates
by Bruce Ravel 17 Jul '02

17 Jul '02

Hi folks, So, today I tried to actually analyze some data that is long overdue for some attention. I didn't get much analysis done, but I did find and fix lots of bugs in Artemis and Athena. Artemis: ** fixed a bug which precluded using third or fourth cumulants in fits (that was rather serious!) ** clicking buttons in the plot options section does redisplay ** data gets plotted in R when reading data files, project files, or feffit.inp files ** fixed a bug which made every item in the "select paths for fitting" menu fail ** title lines now get correctly restored from project files ** a few internal changes that affect how fits get run and results get displayed Athena: ** now using the sort argument to read_data, as was discussed in some mail earlier today ** disable "save as" menu items for spaces that do not make sense for the current record ** fixed a bug in how markers get displayed in energy plots ** fixed a few other minor bugs, see CHANGES file for details New source tarballs are now on my website. Regards, B P.S. I have been working pretty hard lately on the codes and making lots of releases. Indeed, this is my fourth tarball announcement during July! That's the open-source philosophy -- "release early and often". I don't really expect everyone to update their system everytime I announce a new tarball. Therefore, I am trying to make it clear what the major changes are so you can decide if you need to upgrade. Athena and Atoms are pretty stable these days -- you probably only need to upgrade if a change addresses a bug that you have noticed yourself. Artemis, on the other hand, is changing pretty dramatically. Each release lately has addressed some serious usability issues. It may even be useful soon ;-) -- 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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new source tarball for Artemis
by Bruce Ravel 16 Jul '02

16 Jul '02

Hi folks, I posted a new source tarball for Artemis on my website. Lots of improvements this time, including: ** a check to see that all guess parameters are used and that all math expressions use parameters that have been defined ** rearrangement and improvement (I hope!) of the page for defining guess, def, and set parameters ** fixed more problems that cropped up after deleting individual feff paths or entire feff calculations. I know I said I had fixed this in the last release, but this time I think I mean it!! ** many more features of Artemis can operate on the group of selected paths, including deletion of paths, exporting path parameter values, and editing path parameter values ** fixed a problem where, in certain situations, the array containing the background function refined during a fit was overwritten by another array. This resulted in messed up plots after doing fits with background refinements. ** and a bunch of minor things -- see the CHANGES file for details A windows update will follow soon. 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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new releases of Atoms, Athena, and Artemis
by Bruce Ravel 11 Jul '02

11 Jul '02

Hi all, I just wanted to follow up Matt's announcement of the Windows preview release yesterday. It includes versions of my programs that have been updated in the last two weeks. For those of you who are linux, unix, or OSX users, source code tarballs of the latest versions can be found on my web site. For Atoms the big changes are mostly in the parts of the code that compute absorption cross sections from the McMaster, Elam, or other tables. Several bugs were fixed, including some severe problems in the McMaster tables and a bug which resulted in negative (i.e. unphysical) normalization corrections in some situations. For Athena the changes are fairly numerous and include bug fixes, changes to the column selection dialog, changes to the behavior of the groups list, and a few other things. For Artemis, I have squashed a lot of bugs which lead to strange behavior or crashes. Many of the problems had to do with deletion of feff paths. That is now fixed and should work as expected. As always, poke at them and let me know what needs fixing. Special thanks this time to Simon Bare and Paul Fons for very helpful bug reports. 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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Test Windows Installer for Ifeffit++
by Matt Newville 09 Jul '02

09 Jul '02

Hi Everyone, There's a new version of the ifeffit windows installer available at http://cars.uchicago.edu/ifeffit/src/iffsetup_jul09.exe This installer uses ifeffit 1.0072 and includes the latest versions of atoms, athena, and gifeffit, and now includes artemis, sixpack, and a few other applications. The main point of this release is to check the installation process and the running of all the newly available programs. I'm expecting that we'll need to make some minor changes to some of the applications, but I'd like to get a release that can be stable for several months, so would greatly appreciate as much testing of these versions as possible. So, all you Windows users out there, here's your chance to help out! Please try this installer out, and trying running all the programs. If any of them don't run or crash immediately, please let us know. The installer is now 20Mb, and expands to a directory that uses about 50Mb. If this is a problem, please let us know: we could probably split the distribution into separate installers for different programs. Thanks, --Matt

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The so-called ravelware packages
by Bruce Ravel 05 Jul '02

05 Jul '02

Hey, Today Matt asked me why I don't make one big tarball with Atoms, Athen, and Artemis all in it. Apparently a few people have complained to him about problems upgrading them one at a time. I think that having one big tarball is a great idea and, in fact, I have been looking forward to the day when all three would be basically stable and ready for real work. Atoms and Athena are there. Artemis should be soon. I'll probably keep with the separate tarballs thing for my own convenience for a short while longer, but I suspect that in the next couple of months I'll start doing one huge tarball. If anyone has a compelling reason for me *not* to do so, speak up! 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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New source code releases for Atoms and Athena
by Bruce Ravel 05 Jul '02

05 Jul '02

Hi Folks, I just uploaded new source tarballs for Atoms and Athena to my web pages. For Athena, I corrected two small and somewhat obscure bugs that I found last week. One had to do with the behaviour of the "fix step" button and the other with how Cromer-Liberman normalizion parameters were handled internally. For Atoms, most of the reason for the new release was to correct mistakes in the absorption library. 1. The McMaster tables now have a correct entry for the element Re 2. The McMaster tables now corectly handle energy ranges between the L2 and L3 edges 3. The function that computes the normalization correction has much more error checking and has a few little bugs corrected. It should never return a negative normalization correction any more 4. A few small changes to WebAtoms, which also benefits by the items above. 5. A new item in the TkAtoms File menu -- a submenu labeled "Recent files". The idea here is that you can easily return to an atoms.inp file you had been looking at earlier in your TkAtoms session. As currently implemented it is functional, but behaves a little oddly. The order of the entries is backwards of what you may expect (i.e. most recent file is last in the list) and the list never gets truncated. I got tired of fiddling with it, so I declared it "functional enough";-) Check out http://feff.phys.washington.edu/~ravel/software/exafs/ for the latest. Next week I hope to build new Windows binaries of all three of my programs based on Matt's most recent release of Ifeffit, so keep you eyes on this mailing list for that announcement. As always, comments, suggestions, feature requests, and bug reports are very welcome. 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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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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