[Ifeffit] Artemis: Error in loading additional FEFF paths?

Paul Fons paul-fons at aist.go.jp
Fri Jun 11 12:35:10 CDT 2004 

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 at agni.phys.iit.edu    http://www.iit.edu/~segre
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>
>

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 at aist.go.jp

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