[Ifeffit] tracking atom positions

Matt Newville newville at cars.uchicago.edu
Wed Aug 7 23:08:06 CDT 2013

Hi Matthew,

On Wed, Aug 7, 2013 at 5:10 PM, Matthew Marcus <mamarcus at lbl.gov> wrote:
> Funny, I thought I did start a new thread...
> YES!  Management of inequivalent sites would be very nice indeed!  As it is
> now, you have to manually make multiple FEFF files, keeping
> track of the stoichiometry, and setting up multiple FEFF calculations,
> keeping track yourself of what parameters should be in common.
> The common thread here is a tighter integration of the structure description
> (ATOMS, feff.inp) with the FEFF calculation and fitting.
> Good catch about the degeneracy; I hadn't thought of that, but you're right.
> I wonder if it would make sense to put in a kludge which,
> for small enough breaking of the degeneracy, pretends that they're still
> degenerate but adjusts ss accordingly.  I guess the S02 and
> dr would also get small adjusts because the nearer atoms would be slightly
> over-represented compared to the farther ones.  This
> kludge would shorten the path list, making it less confusing, and also
> perhaps save computation time.  There would have to be an alarm
> set for when k*(distance splitting) is too big to allow this approximation.
> An intermediate case would bring in C3 and C4, in a
> fixed relation to the distortion parameters.  All of this adjusting would,
> prefereably, be 'behind the scenes', invisible to the user
> unless he asks to see it.

It might be possible to re-cast the Sum in the EXAFS Equation to be a
sum over atom positions around a central atom,  each of which has
"Atom Parameters"  of E0, S02, x, y, z, sigma_x, sigma_y, and sigma_z.

That would require accounting for each atom in the cluster (no
degeneracy), and would still have incomplete accounting of disorder
for MS paths (but we really have that now anyway).  It would also
require a fair amount of work on Feff (and some on Larch/Feffit).
Probably the best approach (and useful for other reasons) would be to
allow calculations of XAFS contributions from Paths of arbitrary
geometry to happen "inside the fitting loop".

But with that approach, one could set up and model distortions in
crystals much more easily than currently be done.   Again, I think the
analysis  side would not be that hard.   Now that Feff8.5 for EXAFS
has been released as Free Software (as of June 2013), it's worth
thinking about doing this and how to do it well.

This would make a great project for a grad student or post-doc, and
allow for a nice series of papers.  I think it would be greatly
appreciated by many people modeling EXAFS in crystals.     I think it
could be done and would be happy to help.... Any one interested?


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