[Ifeffit] tracking atom positions

[Matthew Marcus]

I hadn't heard, nor did Kevin mention, that any part of feff8.5 was freeware.  Nice!
	mam

On 8/7/2013 9:08 PM, Matt Newville wrote:
> 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?
>
> --Matt
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