[Ifeffit] tracking atom positions

Bruce Ravel bravel at bnl.gov
Wed Aug 7 16:12:42 CDT 2013


Matthew said:

> As it is now, if you want to describe your unknown structure as a
> distorted version of the one for which FEFF was run, you have to
> enter formulas for distances by hand.  For instance, suppose you're
> doing a substitutional dopant and you want to use Artemis to fit the
> displacement of the impurity off-site and the dilation/contraction
> of the first-neighbor shell.  As it is now, you have to do the
> algebra yourself to compute all the distances in terms of the
> distortion parameters.  It would be really nice if there were some
> syntax for describing the alteration of atom positions, from which
> Artemis would automatically compute the displacements.  This might
> have to be a new class of parameters.  Such a computation would
> cover the MS paths as well.  What it would still NOT do is account
> for the effect of leg-to-leg angles on MS paths (deviation from
> focusing/backscatter), but it would be a step.  I realize that this
> would be a big job to implement in a nice way that wouldn't break
> everything that came before, but it would be super useful and make
> the IFEFFIT team (yet again) heros to the community

It's nice to start a new thread when you start a new thread, so I'm
starting a new thread. :)

I understand exactly what you are asking for.  In short, you would
like to be able to parameterize atom positions, possibly even
crystallographic parameters, and have those propagated through to the
math expressions for delta_R for the paths.

In fact, Demeter has some of what's needed already built in.  There
are two things needed to implement that with the way things currently
work.

  1. The pathfinder needs to remember the all the scattering geometries
     that contribute to a degenerate set of paths so that a
     parameterization has the possibility of breaking degeneracies.

  2. In the case of using crystal data, Atoms needs to remember the
     symmetry operations that were done to place each atom in the
     cluster.  This would allow Demeter to propagate a change in a
     crystal parameter through to delta_R.

#1 already exists in Demeter.  #2 is something I worked on in the
past, but never got working to my satisfaction.  The point is that
most of #2 is in there, but commented out.  That is, it's reasonably
close.

As you suggest, the hard part is presenting this to the user.  I have
actually been thinking about this problem lately and am interested in
getting back to it.  I have another big feff-interface improvement to
work on first (an idea for dealing with Feff calculations over
multiple, inequivalent sites in a user-friendly and user-efficient
way), but I'll think about it.

I should mention that Shelly has implemented something like this
before for use with Matt's ancient feffit program.  You might be able
to get her to chime in....

B


-- 
  Bruce Ravel  ------------------------------------ bravel at bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
  Building 535A
  Upton NY, 11973

  Homepage:    http://xafs.org/BruceRavel
  Software:    https://github.com/bruceravel



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