[Ifeffit] Ifeffit Digest, Vol 90, Issue 21

Jatinkumar Rana jatinkumar.rana at helmholtz-berlin.de
Mon Aug 30 06:43:07 CDT 2010


Dear Dominik,

Thank you so much for your reply. However, i am not able to understand 
the logic behind removal of following atoms from Feff.inp file as 
mentioned by you

**In principle, after running ATOMS, you just need to remove atoms from
the generated feff.inp file so that the occupancy is correct. I.e., in
this case, you need to remove roughly 1/4 of the Fe7, 1/2 of the Cr1,
1/3 of the P61, 2/3 of the P62, and 1/3 of the O614 atoms. Try finding
those which are too close to other atoms. The FEFF output might help, so
try deleting preferentially those causing FEFF to fail.**

can you please give me the idea behind doing that and is it physically defendable to do such changes ??

Looking forward to your reply..

Best regards,
Jatin




On 27.08.2010 14:00, ifeffit-request at millenia.cars.aps.anl.gov wrote:
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>     1. Re: Help with cif file (Dominik Samuelis)
>     2. catalysis workshop at the karlsruher synchrotron ANKA
>        (Matthias Bauer)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 27 Aug 2010 10:09:05 +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:<4C7772A1.2000307 at fkf.mpg.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear Jatin,
>
> in your original cif file, you have site occupancies as low as 0.5 (Cr1
> site) and 0.358 (P62). Just setting them to 1 will not help, because
> ATOMS assumes them to be unity anyway.
>
> For such a complicated unit cell, the typical recipe with using
> prototypical structures of course does not help, just because there is
> not a simple prototype structure for arrojadite.
>
> In principle, after running ATOMS, you just need to remove atoms from
> the generated feff.inp file so that the occupancy is correct. I.e., in
> this case, you need to remove roughly 1/4 of the Fe7, 1/2 of the Cr1,
> 1/3 of the P61, 2/3 of the P62, and 1/3 of the O614 atoms. Try finding
> those which are too close to other atoms. The FEFF output might help, so
> try deleting preferentially those causing FEFF to fail.
>
> Another solution might be loading the structure's cif file into a
> structure editor such as DIAMOND. There, you can then check the bond
> distance histograms and delete atoms accordingly. At the end, just
> export the data in xyz format and use this as the atom positions list in
> the feff.inp file.
>
> Regards,
> Dominik
>
>
>
> On 20.08.2010 09:30, Jatinkumar Rana wrote:
>    
>> 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
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>>> When replying, please edit your Subject line so it is more specific
>>> than "Re: Contents of Ifeffit digest..."
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>>> 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>_______________________________________________
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>>>> Ifeffit at millenia.cars.aps.anl.gov
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>>>>          
>>
>>
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