[Ifeffit] Generating single scattering paths in Artemis

Bruce Ravel ravel at phys.washington.edu
Thu Jan 6 10:58:11 CST 2005

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

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

     title FeO, rocksalt structure
     space  f m 3 m
     a    = 3.3108
     core = Fe
       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.


 Bruce Ravel  ----------------------------------- ravel at 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/

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