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

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/

1 0

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

1 0

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/

1 0

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/

1 0

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/

2 1

(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/

1 0

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/

2 2

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/

1 0

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

1 0

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

1 0