[Ifeffit] Generating Atom lists using Artemis

Kelly, Shelly D. SKelly at anl.gov
Mon Jan 8 14:05:18 CST 2007



---------------------------
Shelly Kelly
Argonne National Laboratory
Bldg 203, RM E113
> 
> On Saturday 06 January 2007 10:53, Kelly, Shelly D. wrote:
> > Hello Artemis users,
> >
> > I found an interesting feature in Artemis when generating a list of
> atoms
> > from the attached cif file worth sharing on the list.  In the
attached
> cif
> > file for Pd2Si the position of the Si2 atoms are at x,y,z = 0.3333,
> 0.6667,
> > 0 with a space group of p -6 2 m. Using this cif file and choosing
> either
> > Pd1 or Pd2 as the core atom results in errors in the atom list.  For
> > example for the Pd2 site there are 4 Si neighbors with the 1st and
3rd
> and
> > the 2nd and 4th on top of each other.  If you edit the atomic
positions
> so
> > that the Si2 atoms are correct to an additional digit x,y,z =
0.33333,
> > 0.66667,0 then the atom list is fixed with only two Pd2-Si neighbors
at
> > each of the unique positions.  The interesting feature is that the
> > coordinates on the atoms page need to be correct to the 5 decimal
place.
> 
> 
> This has been discussed many, many times on the mailing list and is
> explained in question 3 at
>    http://cars9.uchicago.edu/iffwiki/FAQ/RunningFeff
> 
> The version of Feff that ships with Ifeffit (and, I believe, all
> others) uses 5 significant figures in the path finder.  Since Atoms
> main purpose is to interact with Feff, it interprets the 5 digit thing
> quite strictly.
> 
> B
> 
> 

[sdk] Hi Bruce,

Well, I thought that I had skipped your "here is a link describing that
response" by searching the Ifeffit wiki.  I didn't run FEFF, so I missed
the description of the problem under the FEFF error message of
overlapping atoms.   

I think that it would be helpful for the ATOMS page within Artemis to
contain a note of some sort indicating that the 5th digit is
significant.  Now that I have had additional time to ponder this
problem, I realize that I have learned it several times only to forget
it again....:)

Cheers,
Shelly




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