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

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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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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Ifeffit: spline with a standard
by Bruce Ravel 23 May '02

23 May '02

Hi, Earlier today Michael Green asked Matt a question of the variety "How do you do ______?" Athena (and artemis) may provide some help with regards to questions like that. If you look in the Edit menu, you will see a item that says "Display Ifeffit buffer". This shows a text box which displays all text strings that have been sent by athena to ifeffit. This is useful to folks who want to learn ifeffit's syntax. To use the example that was just posted to the mailing list, one could read some data and a feff chi.dat file. Then plot the data in mu(E) and the background without a standard. Then tell athena to use the chi.dat file as a standard and replot in energy. Because the standard was changed, the spline will be redone using the newly chosen standard. All of the ifeffit commands to do this will be written to the ifeffit buffer for your examination. 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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Ifeffit: spline with a standard
by Matt Newville 23 May '02

23 May '02

Hi Michael, This seems like a question that others might have, so I hope it's OK that I'm sending this reply to the ifeffit mailing list too. On Thu, 23 May 2002, Michael Green wrote: > I can't figure out how to use a standard for background > removal in G.I.FEFFIT or IFEFFIT. Is there a way to do > this? Table 4 of the Refman lists a chi_std data type, but > I didn't find any mention of it anywhere else. Yes. In ifeffit, it would go like this: #### # background-removal using known chi(k) data read_data(file= data.xmu, label= 'energy xmu', group= dat) read_data(file= standard.chi, label= 'k chi ', group= std) # without standard spline(energy= dat.energy, xmu= dat.xmu, kweight=1,rbkg=1) # with standard spline(energy= dat.energy, xmu= dat.xmu, kweight=1,rbkg=1, k_std=std.k, chi_std = std.chi) #### That is, you read in the spectra for the standard, and use it's "k" and "chi" arrays for "k_std" and "chi_std". Hope that helps, --Matt

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divorce and OSX
by Bruce Ravel 23 May '02

23 May '02

Hi, There are two more issues that I wanted to comment on, but my last message was really long, so I am writing a new one. 1. Matt suggested an amicable divorce as a way of trying to avoid many of the installation problems that we have been having recently. I would suggest a separation rather than a divorce. Ifeffit and the apps might resolve their marital issues in the future and choose to get back together. But for now, for the sake of the kids, I think a separation is a good idea. I freely confess that many of the installation problems are either due to programming mistakes I have made or due to inherent problems in how perl modules get built. It seems imprudent that Matt and Ifeffit should suffer for those reasons. And, as Matt pointed out, my codes are evolving and releasing faster than Ifeffit itself. While it is certainly less convenient for the end user to have to install several packages than a single one, it is even less convenient if the whole kit 'n' kaboodle fails because of an error in a single app. A separation is thus a very good idea. The separation works well for unix users, where it is a simple matter to grab, say, the athena source tarball and install it on top of a functional ifeffit. It is a little less convenient for the windows users. I suppose a solution is that *I* build a new windows installer package based off of Matt most recent ifeffit release when I release new source code tarball. That's not a complete solution because Sam will certainly have a different release schedule than I will. I vote that Matt, Sam, and I put off dealing with that until dealing is unavoidable. 2. Could Paul, Francois, or Chuck summarize for us the status of ifeffit + X + perl + tk + my codes on OSX? (Although I chuckled when I read it, I cannot bring myself to actually use the word Ravelware ;-) Specifically I am interested in a clear statement of how difficult it is to get my codes up an running on a virgin system and how much time it takes. I am also interested in the prospects for providing a click-n-install package for OSX users. I just gave a poster at the NSLS users meeting on my software and showed one of Francois's pictures of Atoms running on OSX. I presume that it will spark some interest. Also, NRL's beamlines at NSLS are Mac shops (thanks to Johnny Kirkland, deacon of the church of the mac) and I'll want to be running the codes there. Thanks, 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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installation issues
by Bruce Ravel 23 May '02

23 May '02

Wow! I was gone for three days and a whole flurry of interesting issues came up. ;-) First off, I must thank Mark Jensen for these kind words: MJ> Ever since the Windows version of Athena was released, I've been MJ> hooked. I'm blushin'. Then Mark said: MJ> After an apparently successful installation, neither Athena nor MJ> Artemis ran, saying that they couldn't locate FileDialog.pm, MJ> widgets.pm, or Chemistry/Elements.pm (depending on the MJ> program). I was unsure where to get these files, or why they MJ> weren't where they were supposed to be, but the MJ> Chemistry/Elements.pm file made me wonder if that wasn't part of MJ> Atoms3.0. Indeed it is. After installing Atoms, Athena and MJ> Artemis both appear to be working correctly. So, Bruce might want MJ> to make a change in the intall.unix file to say that Athena (or MJ> Artemis) requires PGPlot, IFeffit, and Atoms. and Paul followed up with PF> Although I had "cleaned" and reinstalled several times athena and PF> Tk, I hadn't given a second thought to tkatoms -- it had no PF> relation to athena, right? wrong! Upon reintalling tkatoms, PF> athena worked. For starters, I am pleased that you both were able to solve your immediate problems. I am lucky to have such smart users. This exchange, though, underscores a serious problem. Eventually I intend to tie atoms, athena, and artemis (and a feff gui, should I or someone else ever get around to writing it) into a more cogent package. At the current stage both of the software development and of my understanding of the needs and challanges of GUI EXAFS software, it is a great convenience for them to be distinct programs. Still, as Paul pointed out, there are some ties between the codes. I use some object inheritance in athena and artemis, so they do share some code already. And one small feature of athena is only enabled if one of modules from Atoms is installed. So I have put myself in an awkward state of having neither a unified suite of programs nor three disjoint programs. Clearly what I need to do is to make a "clean room" for myself. That is, I need a place where I do not have any of my own software installed. Then I can install the tarballs individually or in any combination. If I do this, I should be able to avoid the problems that Paul and Mark reproted to this list. Thanks you both for the excellent feedback. I have said it before and I'll say it many times in the future -- this stuff is much better thanks to you guys providing feedback. Why having an out-of-date atoms resulted in the error that Paul described is a bizarre mystery to me. And why lacking atoms gave Mark an error about widget.pm is equally strange. I'll look into all of it and certainly will work on the installation scripts. 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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Athena Run Time Error Solved!
by Dr. Paul Fons 22 May '02

22 May '02

I wrote earlier that upon trying to install athena on a colleagues powerbook, I ran into problems with an undefined value in a call to the perl standard routine configure. e.g. Tk::Error: Can't call method "configure" on an undefined value at /sw/bin/athena line 1775, <R> line 9. It turns out that the problem was related to an earlier windows-related post (aka the Ravel-ware post). Although I had "cleaned" and reinstalled several times athena and Tk, I hadn't given a second thought to tkatoms -- it had no relation to athena, right? wrong! Upon reintalling tkatoms, athena worked. There must be a perl module that is installed only with tkatoms that is required by athena. Consistent with this is the observation that artemis worked out-of-the-box (e.g. a simple make) without problem. In any case all is solved. It might be a good idea however to investigate this issue further as I am fairly sure that this problem will come up again (not with me though!). In my case (on my own machines), I installed all three programs (tkatoms, athena, and artemis) and never ran into the problem. Paul

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Run time error with athena
by Dr. Paul Fons 21 May '02

21 May '02

I have been using athena and just installed the latest version (5.16) on a colleagues G4 powerbook running Mac OSX (10.1.4). This machine is ostensibly running the same set of basic software, namely same version of perl, Tk, python, and pgplot, but he gets a runtime error when he attempts to read in some data while I don't. It would help if there were some suggestions as to how to narrow down the problem. Upon opening a prj file (the example file, ga.prj in the examples folder), the following gibberish appears: Tk::Error: Can't call method "configure" on an undefined value at /sw/bin/athena line 1775, <R> line 9. main::set_properties at /sw/bin/athena line 1775 main::fill_skinny at /sw/bin/athena line 923 main::read_record at /sw/bin/athena line 4306 main::read_file at /sw/bin/athena line 1973 [\&main::read_file,0] Tk callback for .frame.menubutton2.menu Tk::__ANON__ at /Library/Perl/darwin/Tk.pm line 228 Tk::Menu::Invoke at /Library/Perl/darwin/Tk/Menu.pm line 530 (command bound to event) It seems to be referring to a perl module called configure. Any ideas? Thanks. Dr. Paul Fons Senior Research Scientist National Institute for Advanced Industrial Science and Technology Optoelectronics Institute Energy Electronics Institute Umezono 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 paul-fons(a)aist.go.jp lines below are in Japanese: 〒305-8568茨城県つくば市梅園1-1-1 主任研究官ポール・フォンス

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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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