[Ifeffit] occupancy numbers vs stochiometry with TkAtoms

[Bruce Ravel]

 jjr> what is the recommended procedure for lattices with non-integer
 jjr> occupation? The Atoms documentation seems not very specific on
 jjr> this point, though it does emphasize the "confusing" aspects of
 jjr> the problem and the fact that it is easy to generate nonsense
 jjr> feff.inp.

I've tried really hard in my documents and in fora such as this one
and FEFFUSERS (see for example
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2002-July/000092.html)
to explain well why I think that translating non-integer
crystallographic occupancies into a sensible feff.inp file is too hard
of a problem for a computer program.  If my explanations remain
"unspecific" after all that, then I'll try harder the next time I sit
down to write on that topic.

 jjr> For example I could edit the feff.inp file that is generated and
 jjr> cut out *arbitrarily* some fraction of the atoms of a given tag,
 jjr> e.g., 2/3 of the Li1s, 1/2 of the Li2s, etc.

That *is* the standard solution, although I would do something a bit
more sophisticated that I will explain in a a few paragraphs.

The reason that removing arbitrary atoms is the only solution I
recommend is because Feff has the requirement that a point in space
either be empty or be entirely occupied by a particular atom.  Because
Feff does not allow a site to fractionally occupied, Atoms cannot do
something that is guaranteed to be sensible.

Feff could do a wieghted sum of phase shifts of different atom types
when it evaluates the elements of its t-matrix.  That may work well
for stochastic doping, but not for clustering.

The best solution I have come up with for a problem like this is to
have atoms generate the feff.inp file for the undoped (or unvacated)
cluster.  Then write yourself a little program that reads in the
feff.inp, uses a random number generator to remove the proper number
of vacated atoms, writes out the altered feff.inp file, and runs
feff.  Add up these feff runs until their sum converges.  It probably
won't take more that about 10 calculations.


 jjr> But I also must edit the stoichiometry so the potentials come
 jjr> out right.  But this procedure does seem arbitrary. Also, it
 jjr> appears that the Li atoms in this material are not all
 jjr> distinguishable so one has to take a linear combination FEFF
 jjr> runs for the different input Li sites.

 jjr> can TkAtoms take the occupancy into account in determining the
 jjr> stoichiometry?

I should use the occupancy information to compute better
stoichiometries.  Good suggestion.  Thanks!  I'll put that on the list
of things to do, but I may not get to it for a while.

As for the different Li sites, here is a tidbit from the Atoms doc
that may be of value:

  How do I change the unique potentials assignment in feff.inp files?

  There are three schemes for assigning unique potentials. They are
  assignment by atomic species, by user-supplied tag, or by
  crystallographic site. Change the value of the :ipots argument to
  the <potentials> token in 'feff.atp' to be one of species, tags, or
  sites. I welcome suggestions for new assignment schemes.

On unix, the `feff.atp' file gets installed in the site_perl space of
the perl hierarchy.  On my computer, its in:
  /usr/lib/perl5/site_perl/5.6.0/i586-linux/Xray/atp/
Copy `feff.atp' from there into your ~/.atoms/ directory and edit it
as indicated.  TkAtoms will use the personal copy rather than the
system-wdie copy.  You could even call your edited file something like
"feff_tags.atp" and that will come up in the output file types menu in
TkAtoms.

On a windows computer, it'll be at (I don't have windows booted up
right now, so this is by memory and may be slightly wrong)
  C:\Program Files\Ifeffit\perl\Xray\atp\


B

-- 
 Bruce Ravel  ----------------------------------- ravel at phys.washington.edu
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 Naval Research Laboratory                          phone: (1) 202 767 5947
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 My homepage:    http://feff.phys.washington.edu/~ravel 
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