[Ifeffit] error in ATOMS

Robert Gordon ragordon at alumni.sfu.ca
Wed Nov 13 12:14:49 CST 2013


  X, Y, and Z coordinates

     Specify the fractional coordinate of a site in one of the cell axis 
directions. You may use simple fractions such as "1/2".

Space group  P 21 21 21

Are your axes in Angstroms?

On 11/13/2013 11:58 AM, Julius Campecino wrote:
> Hi Chris,
>
> Same problem:
> Can't call method "attributes" on an undefined value at /usr/local/lib/perl5/site_perl/5.10.0/Xray/ATP.pm line 342.
> Can you try running this input and see if it works for you or not? 
> Maybe there is something at my end that is causing this error.
>
> ! This atoms input file was generated by WebAtoms 1.8 (Atoms 3.0beta10)
> ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001
> title = WT NiSOD
> space = P212121
> a =	112.260	b =	113.810	c =	128.60
> alpha =	 90.0	beta =	 90.0	gamma =	 90.0
> core =	Ni	edge =	K	rmax =	  5.0
> atoms
> ! elem   x          y          z     tag           occ.
>    Ni    3.10300   27.70100    6.07300  Ni            1.00000
>    S     4.02900   29.69700    6.64700  S             1.00000
>    S     1.59500   28.53900    4.74300  S             1.00000
>    N     2.45400   25.74800    5.82600  N             1.00000
>    N     3.74200   25.63100    2.96500  N             1.00000
>    N     4.55400   26.84200    7.01300  N             1.00000
> Thanks for your help!
>
> Julius
>
> On Wed, Nov 13, 2013 at 9:23 AM, Christopher Patridge 
> <patridge at buffalo.edu <mailto:patridge at buffalo.edu>> wrote:
>
>     Julius,
>
>     I again did not find answer to the error but you could also try
>     the following entity of ATOMS on the web which easily allows a
>     huge number of sites
>
>     http://cars9.uchicago.edu/cgi-bin/atoms/atoms.cgi
>
>     Chris
>
>     ********************************************
>     Dr. Christopher Patridge
>     Assistant Professor of Chemistry
>     Dept of Math and Natural Science
>     D'youville College
>     320 Porter Ave., Buffalo, NY 14201
>     Phone: 716-829-8096 <tel:716-829-8096>
>     Email:_patridgc at dyc.edu <mailto:patridgc at dyc.edu>_
>
>
>
>     On Nov 13, 2013, at 12:19 PM, Julius Campecino
>     <jcampecino at gmail.com <mailto:jcampecino at gmail.com>> wrote:
>
>>     Hi everyone,
>>
>>     Did anyone figure out how to fix "Can't call method tag" error
>>     and adding sites? Really a novice on fitting and I badly need
>>     help on this to get going. Sorry to bother everyone.
>>
>>     Thanks!
>>
>>     Julius
>>
>>
>>     On Mon, Nov 11, 2013 at 8:48 AM, Julius Campecino
>>     <jcampecino at gmail.com <mailto:jcampecino at gmail.com>> wrote:
>>
>>         Hi Chris,
>>
>>         Yeah, I did try "add a site" but it is not responding. Does
>>         anyone else experience this problem? Thank you, Chris.
>>
>>         Julius
>>
>>
>>         On Mon, Nov 11, 2013 at 9:51 AM, Christopher Patridge
>>         <patridge at buffalo.edu <mailto:patridge at buffalo.edu>> wrote:
>>
>>             Julius,
>>
>>             While I am not certain what the error means, there is a
>>             button displayed right above the atom list which says
>>             "ADD A SITE."  I would suggest that having a unit cell as
>>             large as you do, along with rather weak scatterers such
>>             as N, C, O, and I assume H, it is probably unnecessary to
>>             have sites beyond the 3rd shell or so since these
>>             contribute negligibly to the EXAFS.
>>
>>             Chris
>>
>>             ********************************************
>>             Dr. Christopher Patridge
>>             Assistant Professor of Chemistry
>>             Dept of Math and Natural Science
>>             D'youville College
>>             320 Porter Ave., Buffalo, NY 14201
>>             Phone: 716-829-8096 <tel:716-829-8096>
>>             Email:_patridgc at dyc.edu <mailto:patridgc at dyc.edu>_
>>
>>
>>
>>             On Nov 10, 2013, at 1:26 PM, Julius Campecino
>>             <jcampecino at gmail.com <mailto:jcampecino at gmail.com>> wrote:
>>
>>>             Hi Bruce,
>>>
>>>             Here's the screen shot of my work in ATOMS. It's
>>>             supposed to be more than 7 atoms in the core column but
>>>             that's also one thing I do not know how to add change
>>>             and add more atoms.
>>>
>>>             When I click "Run Atoms", it gives me this error "Can't
>>>             call method "tag" on an undefined value at
>>>             C:/strawberry/perl/site/lib/Demeter/Atoms.pm line 668.''
>>>             I am using the recent version 0.9.18.2 of the Demeter
>>>             installer.
>>>
>>>             Thank you for your help!
>>>
>>>             Julius
>>>             <Atoms.png>_______________________________________________
>>>             Ifeffit mailing list
>>>             Ifeffit at millenia.cars.aps.anl.gov
>>>             <mailto:Ifeffit at millenia.cars.aps.anl.gov>
>>>             http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>
>>
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>>
>>
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>
>
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-- 
Dr. Robert Gordon
Staff Scientist, PNCSRF
APS Sector 20 (PNC/XSD)
9700 S Cass Ave. 435E
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