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! For reference here are the results from the fitting as well: Project title : Fitting ZnO.chi Comment : Prepared by : Contact : Started : 14:30:05 on 1 November, 2003 This fit at : 11:51:37 on 11 June, 2004 Environment : Artemis 0.7.006 using darwin, perl 5.008001, Tk 804.027, and Ifeffit 1.2.5 ============================================================ Independent points = 10.044921875 Number of variables = 4.000000000 Chi-square = 8182.854180122 Reduced Chi-square = 1353.674100233 R-factor = 0.025528340 Measurement uncertainty (k) = 0.000496786 Measurement uncertainty (R) = 0.000798106 Number of data sets = 1.000000000 Guess parameters +/- uncertainties: amp = 0.9118560 +/- 0.1062270 (1.0000) e0 = 5.4996840 +/- 0.7722610 (0.0000) ss = 0.0073380 +/- 0.0017720 (0.0030) delscale = 0.0031830 +/- 0.0037480 (0.0000) Def parameters: delr = 0.0145400 Correlations between variables: amp and ss --> 0.8234 e0 and delscale --> 0.8012 All other correlations are below 0.25 ===== Data set >>ZnO.chi<< ======================================== file: /Users/paulfons/.horae/stash/artemis.project.1/chi_data/ZnO.chi title lines: Merge in n space of: ** C:/Documents and Settings/Scott/My Documents/Projects/ZnO/Data/011113.032 (_013_032) ** C:/Documents and Settings/Scott/My Documents/Projects/ZnO/Data/011113.033 (_013_033) ** C:/Documents and Settings/Scott/My Documents/Projects/ZnO/Data/011113.034 (_013_034) ** C:/Documents and Settings/Scott/My Documents/Projects/ZnO/Data/011113.035 (_013_035) ** C:/Documents and Settings/Scott/My Documents/Projects/ZnO/Data/011113.036 (_013_036) ** C:/Documents and Settings/Scott/My Documents/Projects/ZnO/Data/011113.037 (_013_037) k-range = 3.000 - 10.000 dk = 2.000 k-window = kaiser-bessel k-weight = 1 R-range = 1.000 - 3.300 dR = 0.100 R-window = kaiser-bessel fitting space = R background function = none phase correction = none R-factor for this data set = 0.02553 ===== Paths used to fit ZnO.chi FEFF0: feff0001.dat (ifeffit group = feff0_1) .. feff = /Users/paulfons/.horae/stash/artemis.project.1/data0.feff0/feff0001.dat id = reff= 1.9593, degen= 3.0, path: Zn->O->Zn r = 1.965537 reff = 1.959300 degen = 3.000000 s02 = 0.911856 e0 = 5.499684 dr = 0.006237 ss2 = 0.007338 FEFF0: feff0002.dat .. feff = /Users/paulfons/.horae/stash/artemis.project.1/data0.feff0/feff0002.dat id = reff= 2.0396, degen= 1.0, path: Zn->O->Zn r = 2.046093 reff = 2.039600 degen = 1.000000 s02 = 0.911856 e0 = 5.499684 dr = 0.006493 ss2 = 0.007338 FEFF0: feff0003.dat .. feff = /Users/paulfons/.horae/stash/artemis.project.1/data0.feff0/feff0003.dat id = reff= 3.1675, degen= 1.0, path: Zn->O->Zn r = 3.177583 reff = 3.167500 degen = 1.000000 s02 = 0.911856 e0 = 5.499684 dr = 0.010083 ss2 = 0.007338 FEFF0: feff0004.dat .. feff = /Users/paulfons/.horae/stash/artemis.project.1/data0.feff0/feff0004.dat id = reff= 3.2093, degen= 6.0, path: Zn->Zn->Zn r = 3.219516 reff = 3.209300 degen = 6.000000 s02 = 0.911856 e0 = 5.499684 dr = 0.010216 ss2 = 0.007338 FEFF0: feff0005.dat .. feff = /Users/paulfons/.horae/stash/artemis.project.1/data0.feff0/feff0005.dat id = reff= 3.2501, degen= 6.0, path: Zn->Zn->Zn r = 3.260446 reff = 3.250100 degen = 6.000000 s02 = 0.911856 e0 = 5.499684 dr = 0.010346 ss2 = 0.007338 FEFF0: feff0011.dat (ifeffit group = feff0_6) .. feff = /Users/paulfons/.horae/stash/artemis.project.1/data0.feff0/feff0011.dat id = reff= 3.7950, degen= 3.0, path: Zn->O->Zn r = 3.807081 reff = 3.795000 degen = 3.000000 s02 = 0.911856 e0 = 5.499684 dr = 0.012081 ss2 = 0.007338 FEFF0: feff0012.dat .. feff = /Users/paulfons/.horae/stash/artemis.project.1/data0.feff0/feff0012.dat id = reff= 3.8371, degen= 6.0, path: Zn->O->Zn r = 3.849315 reff = 3.837100 degen = 6.000000 s02 = 0.911856 e0 = 5.499684 dr = 0.012215 ss2 = 0.007338 FEFF0: feff0025.dat .. feff = /Users/paulfons/.horae/stash/artemis.project.1/data0.feff0/feff0025.dat id = reff= 4.5383, degen= 6.0, path: Zn->O->Zn r = 4.552747 reff = 4.538300 degen = 6.000000 s02 = 0.911856 e0 = 5.499684 dr = 0.014447 ss2 = 0.007338 FEFF0: feff0028.dat .. feff = /Users/paulfons/.horae/stash/artemis.project.1/data0.feff0/feff0028.dat id = reff= 4.5675, degen= 6.0, path: Zn->Zn->Zn r = 4.582040 reff = 4.567500 degen = 6.000000 s02 = 0.911856 e0 = 5.499684 dr = 0.014540 ss2 = 0.007338 On 2004/06/11, at 5:11, Stefano Ciurli wrote:
Carlo,
I have been having consistent problems running the tutorials on my MacOSX G4 portable PC. I have posted several times the tect of the trap files I am getting. .Apparently, there is no definitve answer (yet). I am sure Bruce will try to clean up things whenever he has time. But, if for some reason, some of you out there knows a way out, I'll be one of the many to be happy to read it.
Stefano.
One of my students is just trying Scott's ZnO tutorial and we are finding a consistent problem when trying to work with the third project file.
When we get to the point of adding an additional path, (feff0011.dat), artemis crashes with the following message:
---------------------------------
The following message was trapped by Artemis:
Artemis0.7.006warn/home/segre/.horae/stash/ ARTEMIS.TRAPCODE(0x9652e54)/home/segre/.horae/stash/ artemis.project.2/ at /usr/bin/artemis line 1562 main::__ANON__('Use of uninitialized value in string eq at /usr/bin/artemis l...') called at /usr/bin/artemis line 7313 main::read_feff('^^') called at /usr/lib/perl5/Tk.pm line 225 eval {...} called at /usr/lib/perl5/Tk.pm line 225 Tk::__ANON__('Tk::Menu=HASH(0x974a060)', 'active') called at /usr/lib/perl5/Tk/Menu.pm line 531 Tk::Menu::Invoke('Tk::Menu=HASH(0x974a060)', 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 1707
--------------------------------
This is happening on all of my Linux machines. They are using my Debian packages and so I have not tried with the tarball installation.
Has anyone else had this problem? I hesitate to report it as a bug until it is confirmed. In a previous version of horae, it worked fine.
Carlo
-- 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 Carlo.Segre@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
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Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203
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