On Wednesday 05 January 2005 02:23 pm, Carlo U. Segre wrote:
Bruce:
Occasionally, I don't know or don't care what the extended crystallographic environment of the absorber. All I want to do is apply single scattering analysis and I need some simple paths from FEFF. At this time, I can't see how to do this within Artemis since the Atoms page requires a space group and more information than I have available.
Would it be possible to have the option for a simpler interface which just allows me to generate single scattering paths between two atoms at a specific distance from each other? Perhaps, I could even specify a coordination geometry (tetrahedral, octahedral, etc.)?
First off, I should mention that I was off yesterday afternoon judging an elementary school science fair, so I did not see this very interesting thread until this morning. I am going to have a lot to say in response to everything Carlo, Scott, Anatoly, Dave, and Mike said. In this post, I am going to address the issue in the least interesting way. That is, I am going to suggest a strategy for doing this analysis that is fairly simple and works within the framework of the existing code. Later today I'll comment on what new functionality should be put into Artemis. Before I start, I do want to point out that this is a topic that Sam has already addressed in SixPack and is yet another reason that you should give SixPack a look if you haven't already. Scott pointed this out: "Isn't a symmetric octahedral arrangment just the single-scattering path with a degeneracy of 6; a tetrahedral a degeneracy of 4; etc.?" I agree. If you are in the situation where you know almost nothing beyond the species of the absorber and a guess for the species of the scatterer, then you really don't need to be fretting the details. Just do the simplest possible thing. To my mind, the simplest possible thing is rocksalt. I always keep this atoms.inp file lying around somewhere where I can find it quickly: title FeO, rocksalt structure space f m 3 m a = 3.3108 core = Fe atoms Fe 0.00000 0.00000 0.00000 O 0.50000 0.50000 0.50000 Import it into Artemis, change the atomic species to your absorber and scatterer and run Atoms. This will give you 6 scatterers at 1.655 A. That's not an unreasonable number for a transition metal oxide, which is likely what we are talking about. You might choose to make "a" a bit bigger for other things. After Feff finishes, Artemis asks about how many paths you want to import. Choose to import 1 path. On the path page, change the value for N from 6 to 1. At this point you can click the big, green button. The "amp" parameter will be a measure of the coordination multiplied by S_0^2. One could criticize this scheme by saying that a rocksalt crystal is not a good representation of a messy unknown. I agree with Scott that it is close enough, that it is sufficient at this stage of the game to just multiply a reasonable scattering path by a coordination number. Ultimately, I sense that Carlo and some others are suggesting that Artemis should have a one-click solution for a basic first shell analysis problem. What I have written here is certainly not that solution. This will be the topic of my next posting to the list. All that said, my suggestion isn't really that complicated conceptually and it is not so difficult to do with Artemis. It is, in my opinion, pretty much as defensible as any other simple approach to first-shell, cumulant-y analysis, including all of the suggestions made in this thread. B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/