[Ifeffit] Help with cif file

[Bruce Ravel]

Dominik's answer sounds right to me.  See question 15 at 
http://cars9.uchicago.edu/ifeffit/FAQ/FeffitModeling

B


On Wednesday, August 18, 2010 02:36:03 am Dominik Samuelis wrote:
> 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

-- 

 Bruce Ravel  ------------------------------------ bravel at bnl.gov

 National Institute of Standards and Technology
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