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?
Charles, 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. HTH, B -- Bruce Ravel ----------------------------------- bravel@anl.gov -or- ravel@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/