[Ifeffit] Help with cif file
Jatinkumar Rana
jatinkumar.rana at helmholtz-berlin.de
Fri Aug 20 02:30:42 CDT 2010
Dear Dominic, Dear Bruce,
I am also facing the same problem as experienced by Kleper. I am working
on the EXAFS analysis of Arrojadite mineral. We have refined the
strucutre using neutron diffraction to get crystallographic information
which can be fed to ATOMS. The original .cif file contains the
fractional occupancy so ATOMS give similar error report as mentioned by
Kleper. After reading your post, i changed all site occupancy to 1 and
then run ATOMS but still it gives me the error report.
Can anybody tell me, why ATOMS report error ?
I have attached both original .cif file (with fractional occupancy) and
modified .cif file (all site occupancy = 1). I have EXAFS spectrum at Fe
and Mn K-edge.
Looking forward to your answer.
Thanks a lot in advance...
Best regards,
Jatin
On 18.08.2010 19:00, ifeffit-request at millenia.cars.aps.anl.gov wrote:
> Send Ifeffit mailing list submissions to
> ifeffit at millenia.cars.aps.anl.gov
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> or, via email, send a message with subject or body 'help' to
> ifeffit-request at millenia.cars.aps.anl.gov
>
> You can reach the person managing the list at
> ifeffit-owner at millenia.cars.aps.anl.gov
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Ifeffit digest..."
>
>
> Today's Topics:
>
> 1. Re: Help with cif file (Dominik Samuelis)
> 2. Re: Help with cif file (Bruce Ravel)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 18 Aug 2010 08:36:03 +0200
> From: Dominik Samuelis<d.samuelis at fkf.mpg.de>
> To: XAFS Analysis using Ifeffit<ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Help with cif file
> Message-ID:<01A98ED5-00FE-4875-989A-C7663E57BF97 at fkf.mpg.de>
> Content-Type: text/plain; charset=iso-8859-1
>
> Dear Kleper,
>
> even though I haven't tested it in detail, I'm sure the errors come from the fact that ATOMS cannot handle site occupancies other than unity. If you have a look in the cif file, you can see that both W (0.23) and Ti (0.54) have a fractional occupancy:
>
> loop_
> _atom_site_label
> _atom_site_type_symbol
> _atom_site_symmetry_multiplicity
> _atom_site_Wyckoff_symbol
> _atom_site_fract_x
> _atom_site_fract_y
> _atom_site_fract_z
> _atom_site_occupancy
> _atom_site_attached_hydrogens
> _atom_site_calc_flag
> W1 W4+ 4 e 0. 0. 0.0564(2) 0.23 0 d
> Ti1 Ti4+ 2 a 0. 0. 0. 0.54 0 d
> O1 O2- 4 f 0.3007(6) 0.3007(6) 0. 1. 0 d
>
> To get it working, you need to use the prototypical structure (e.g. TiO2) without mixed sites as ATOMS input. In the feff.inp file, you can then change 46 out of 100 Ti atoms to W (5 out of 10 should be ok as well for a smaller cluster). Don't forget to add the appropriate POTENTIALS line for W to the feff.inp. The small shift of the W atoms away from the Ti positions then could be handled by some additional delR parameter for the W paths during fitting.
>
> All the best,
> Dominik
>
>
> Am 17.08.2010 um 15:27 schrieb Kleper Rocha:
>
>
>> Please,
>>
>> Could someone help me with the cif file attached, get from the www.crystallographic.net shearch with the terms Ti, W, O. When I try to run the Feff the following message appears.
>>
>> "Feff 6L.02
>> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
>> atoms 1 2
>> 1 0.00000 0.00000 0.00000
>> 2 0.00000 0.00000 -0.16378
>> Run continues...
>> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
>> atoms 1 3
>> 1 0.00000 0.00000 0.00000
>> 3 0.00000 0.00000 -0.32756
>> Run continues...
>> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
>> atoms 2 3
>> 2 0.00000 0.00000 -0.16378
>> 3 0.00000 0.00000 -0.32756
>> Run continues...
>> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
>> atoms 10 11
>> 10 0.00000 0.00000 2.57634
>> 11 0.00000 0.00000 2.74012
>> Run continues...
>> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
>> atoms 10 12
>> 10 0.00000 0.00000 2.57634
>> 12 0.00000 0.00000 2.90390
>> Run continues...
>> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
>> atoms 11 12
>> 11 0.00000 0.00000 2.74012
>> 12 0.00000 0.00000 2.90390
>> Run continues...
>> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
>> atoms 13 14
>> 13 0.00000 0.00000 -2.90390
>> 14 0.00000 0.00000 -3.06768
>> Run continues...
>> Titanium tungsten oxide (0.54/0.46/2)
>> Ti.54 W.46 O2
>> O2 Ti0.54 W0.46
>> Peters, E.
>> Ueber ein niedervalentes Titan-Wolframoxid: Ti0,54 W0,46 O2
>> Calculating potentials and phases...
>> free atom potential and density for atom type 0
>> free atom potential and density for atom type 1
>> free atom potential and density for atom type 2
>> free atom potential and density for atom type 3
>> overlapped potential and density for unique potential 0
>> overlapped potential and density for unique potential 1
>> overlapped potential and density for unique potential 2
>> overlapped potential and density for unique potential 3
>> muffin tin radii and interstitial parameters
>>
>>
>> This warning indicates a problem in the Atoms list. For some
>> reason you have atoms that are separated by than 0.93 Angstroms
>> (or 1.75 Rydberg).
>>
>> This may be due to the presence of hydrogen atoms in your feff.inp
>> file, in which case this is an innocuous warning and may be ignored.
>>
>> However, this may indicate a problem constructing the Atoms
>> list. The most common cause of this problem is a mistake in the
>> crystallographic data used on the Atoms page. You may have
>> incorrect values for lattice constants or angles or incorrect
>> values for site coordinates. You may need a shift vector to move
>> the lattice into its standard setting.
>>
>> Please be aware that Atoms works with 5 digits of precision.
>> Thus, if you have a site with a coordinate of 1/3, you should use
>> either "1/3" or "0.33333" on the Atoms page. Using insufficient
>> precision, say "0.333" is a common cause of this error message.
>>
>> Artemis has continued on the possibility that the warning is
>> caused by hydrogen atoms, but be warned that the feff.inp may
>> require your attention."
>>
>> Thanks in advance.
>>
>>
>>
>> Kleper de Oliveira Rocha
>>
>> <O2 Ti0.54 W0.46.cif>_______________________________________________
>> Ifeffit mailing list
>> Ifeffit at millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>
>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: modified.cif.cif
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20100820/79b07ab1/attachment.ksh>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: original.cif.cif
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20100820/79b07ab1/attachment-0001.ksh>
More information about the Ifeffit
mailing list