[Ifeffit] Ifeffit Digest, Vol 90, Issue 21

Scott Calvin SCalvin at slc.edu
Mon Aug 30 07:31:29 CDT 2010 

Hi Dominik,

I haven't had time to look at your question in detail, but try the  
link below, and see if you find it helpful:

http://cars9.uchicago.edu/ifeffit/Doped

--Scott Calvin
Sarah Lawrence College

On Aug 30, 2010, at 7:43 AM, Jatinkumar Rana wrote:

> 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:
>> Send Ifeffit mailing list submissions to
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>> When replying, please edit your Subject line so it is more specific
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>>
>> Today's Topics:
>>
>>    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
>>>> 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
>>>>>
>>>
>>>
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>>
>>
>
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