Just to make things more mysterious, I tried the same procedure just now on a notebook computer (running the same version of Mac OS X as on my desktop at work) ... and had the uninitialized string problem (at 7313 in artemis). To the best of my knowledge, the two systems are nominally identical. Weird. Well at least I have something to track down now. Paul On Jun 11, 2004, at 1:43 PM, Carlo U. Segre wrote:
Paul:
Thanks for the details.
I tried reverting back to previous versions until the ZnO tutorial "worked". I found that version 035 freezes like version 036 but version 034 seems to work OK.
However, when I looked at the echo buffer, I noticed that despite apparently loading the new paths without any problem, there was a trapped error. It is a bit different than the one I get from v035 and v036 and it is a warning that does not crash the program, however, it does indicate that something is not quite right. Not that in the echo buffer, the loading of a path eventually reports an "Adding FEFF0 ... done!". This did not seem to be in Paul's file.
Finally, just to remove doubt about my Debian packages, I did a local install of v036 and the crash that I reported earlier still occurs albeit with a slightly different message than the original one I reported. In this case the error happened in the "main::add_a_path" routine, just like the non-fatal error in v034 reported below whereas in my Debian package version, the error is in "main::read_feff".
Clearly there is some inconsistency here.
Carlo
--------------- Echo Buffer -------------------- Running fit (this could take a few minutes, please be patient) ... amp = 0.906536 +/- 0.109976 Writing log file ... Running fit ... done! Artemis trapped a warning! Message dumped to /home/segre/.horae/stash/ARTEMIS.TRAP Artemis trapped a warning! Message dumped to /home/segre/.horae/stash/ARTEMIS.TRAP Adding FEFF0 ... "/home/segre/.horae/stash/artemis.project.0/data0.feff0/feff0025.dat" had Macintosh EOL characters and was fixed. Adding FEFF0 ... done! Artemis trapped a warning! Message dumped to /home/segre/.horae/stash/ARTEMIS.TRAP Artemis trapped a warning! Message dumped to /home/segre/.horae/stash/ARTEMIS.TRAP Adding FEFF0 ... "/home/segre/.horae/stash/artemis.project.0/data0.feff0/feff0028.dat" had Macintosh EOL characters and was fixed. Adding FEFF0 ... done!
and
------------------ ARTEMIS.TRAP ----------------- # Artemis 0.7.004 # This file created at 23:11:44 on 10 June, 2004 # using linux, perl 5.008004, Tk 800.025, and Ifeffit 1.2.5 # Workspace: /home/segre/.horae/stash/artemis.project.0/
The following message was trapped by Artemis on a SIGWARN:
Artemis0.7.004warn/home/segre/.horae/stash/ ARTEMIS.TRAPCODE(0x963f3dc)/home/segre/.horae/stash/artemis.project.0/ at /usr/bin/artemis line 1551 main::__ANON__('Use of uninitialized value in string eq at /usr/bin/artemis l...') called at /usr/bin/artemis line 5895
main::add_a_path('/home/segre/.horae/stash/artemis.project.0/ data0.feff0/feff00...', 1, 0) called at /usr/bin/artemis line 3917 main::__ANON__() called at /usr/lib/perl5/Tk.pm line 225 eval {...} called at /usr/lib/perl5/Tk.pm line 225 Tk::__ANON__('Tk::Menu=HASH(0x9b2acac)', 'active') called at /usr/lib/perl5/Tk/Menu.pm line 531 Tk::Menu::Invoke('Tk::Menu=HASH(0x9b2acac)', 1) called at /usr/lib/perl5/Tk.pm line 347 eval {...} called at /usr/lib/perl5/Tk.pm line 347 Tk::MainLoop() called at /usr/bin/artemis line 1695 ------------------------------------------------------------------
On Fri, 11 Jun 2004, Paul Fons wrote:
I thought I would add some more confusion to the issue and mention that on my system (Mac 10.3.4 with perl 5.008001, Artemis 0.7.006, Tk804.027, and Ifeffit 1.2.5 -- as reported in the properties window of artemis) I am *not* having any problems opening the ZnO3.apj project under horae-036/Examples. The specific procedure I used was to start artemis, load the project ZnO3.apj. I then plotted the FT os some of the loaded paths and did a fit. I then loaded the additional paths 10 & 11 did a fit without error and finally loaded paths 25 and 28 and also did a fit without error (or a Trap file being generated). Note I loaded the additional files from the ...horae/stash/artemis.project.1/data0.feff0 folder which was the current directory when I selected add a feff path from the FEFF menu as the journal entry said. This would seem to imply that the problems that was being reported by Stefano and Carlo are not unavoidable but may stem from some detail of the library being used or some other fixable entity. Since it works on my machine without error, perhaps we can track things down by looking at the details... I have tacked on the echo buffer as well as the results buffer from the ZnO3.apj after I followed the tutorial's advice and added the additional single scattering paths. Note I added the feff paths from the .horae/stash folder. Is there any obvious difference that might help track down the problem -- e.g. the path names or somesuch?
Paul
Here is a copy of the echo buffer:
Showing new GDS page Using Ifeffit 1.2.5 Copyright (c) 2004 Matt Newville, Univ of Chicago Artemis may be freely redistributed under the terms of its license. Artemis comes with absolutely NO WARRANTY. HINT: A def parameter's math expression is stored and updated throughout a fit. Opening project zipfile /Users/paulfons/Ports/horae-036/examples/artemis/ZnO/ZnO3.apj ... Opening project zipfile ZnO3.apj ... done! Importing atoms.inp file ... Importing atoms.inp file ... done! Doing intrp for FEFF0 ... Doing intrp for FEFF0 ... done! amp: Plotting in r space ... Plotting in r space ... done! Opened project file `/Users/paulfons/.horae/stash/artemis.project.1/descriptions/artemis'. Plotting in r space ... Plotting in r space ... done! Running fit (this could take a few minutes, please be patient) ... amp = 1.102200 +/- 0.222995 Writing log file ... Running fit ... done! Plotting in r space ... Plotting in r space ... done! Running fit (this could take a few minutes, please be patient) ... amp = 0.907452 +/- 0.110477 Writing log file ... Running fit ... done! Plotting in r space ... Plotting in r space ... done! "/Users/paulfons/.horae/stash/artemis.project.1/data0.feff1/ feff0025.dat" had Macintosh EOL characters and was fixed. "/Users/paulfons/.horae/stash/artemis.project.1/data0.feff1/ feff0028.dat" had Macintosh EOL characters and was fixed. Running fit (this could take a few minutes, please be patient) ... amp = 0.911856 +/- 0.106227 Writing log file ... Running fit ... done!
-- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@agni.phys.iit.edu http://www.iit.edu/~segre _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons@aist.go.jp The lines below are in a Japanese font 〒３０５−８５６８ 茨城県つくば市東１−１−1 つくば中央第４ 近接場光応用工学センター ポール・フォンス主任研究官