[Ifeffit] idealized 95-atom Pt cluster

Bruce Ravel bravel at anl.gov
Mon May 16 16:19:40 CDT 2005

On Monday 16 May 2005 15:47, Charles Chusuei wrote:
> Hi,,,
> I'm a new user to Artemis and Atoms. I would like to generate a simulated
> EXAFS spectrum of an idealized bare 95-atom cluster of Pt (with no ligands
> attached to it).  Looking at Cambridge data files, the largest cluster
> documented is 18, so I would have to make one up.  I would like to arrange
> the 95 atoms into an idealized sphere with the standard geometry for bulk
> Pt-Pt bonding that can be predicted from the crystal structure (e.g.
> metallic radius = 139nm, metallic separation = 277.5nm separation, etc.)
> I understand this can be done using Artemis and Atoms.  I'm relatively new
> to using the software (prodominantly know how to use Athena for plotting
> the experimental EXAFS data , not much more).
> Could anyone provide suggestions on how to get started on this task? E.g.
> Generating the crystal data and displaying the EXAFS of the resulting bare
> cluster?


When you asked me this in private email last week, I did not
completely understand the question.

One (simple) solution to your question is to run Atoms on crystalline
Pt and have it write out a cluster of the approximate size.  For
instance, a 7 angstrom cluster contains 87 atoms.  I am guessing that
the exafs from that will be pretty similar to the cluster you are
looking for.

Of course, there are truncation effects.  The cluster you are
interested in will have some geometry which may not be well
approximated by a sphere.  Also, one must worry about the attenuation
of coordination numbers due to absorption by atoms at the perifery of
the cluster.

Also, remember that Atoms is a crystallography code.  If you are
interested in a cluster of atoms that is not a crystal, then you will
need some other mechanism for generating the list of atomic
coordinates needed by Feff.

Many people, including some some of the frequent contributors to this
mailing list, have done considerable work on exafs of metallic
nanoparticles.  You should look up papers by Anatoly Frenkel and by
Scott Calvin (and probably others as well) to see how some of the
exafs experts who have already done work in this field have addressed
your problem.


 Bruce Ravel  ----------------------------------- bravel at anl.gov  -or-
						  ravel at phys.washington.edu
 Environmental Research Division, Building 203, Room E-165
 Argonne National Laboratory         phone and voice mail: (1) 630 252 5033
 Argonne IL 60439, USA                                fax: (1) 630 252 9793

 My homepage:    http://feff.phys.washington.edu/~ravel 
 EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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