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

Paul Fons paul-fons at aist.go.jp
Thu Jun 10 22:04:37 CDT 2004


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 at iit.edu    http://www.iit.edu/~segre
>> _______________________________________________
>> Ifeffit mailing list
>> Ifeffit at millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
> -- 
> ____________________________________________
>
> 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
>
> "Fatti non foste a viver come bruti,
> ma per seguir virtute e canoscenza"
> Dante Alighieri - Inferno - Canto XXVI
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
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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

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
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