[Ifeffit] Artemis: Error in laoding additional FEFF paths?
Carlo U. Segre
segre at iit.edu
Thu Jun 10 23:43:18 CDT 2004
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 at agni.phys.iit.edu http://www.iit.edu/~segre
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