[Ifeffit] Fitting EXAFS simulation to experimental

Matt Newville newville at cars.uchicago.edu
Thu May 29 14:16:12 CDT 2014

Hi Matthew,

On Thu, May 29, 2014 at 11:18 AM, Matthew Marcus <mamarcus at lbl.gov> wrote:

> I wonder if what he was asking about is an automated way of mapping the
> position parameters for a given space group, that is, fractional atomic
> coordinates as listed in a .cif, onto
> the various path distances.  As it is now, it's impractically hard to do
> it except for very simple cases.

I completely agree.

>  Maybe what is needed is a language for specifying local structures in
> which
> atom positions and occupancies can be given by variables, and the program
> would automatically parameterize the paths.  As a hypothetical toy example,
> consider a simple model of
> a substitutional model of Fe in bcc W (atoms chosen more or less at
> random).  Here, we suspect that since Fe is a smaller atom than W, the
> first neighbors would be
> displaced inward.

This is an excellent suggestion...

>  Thus, we might have a specification something like
> SET a0 = 3.165  /* lattice parameter of pure W */
> CENTRAL Fe 0 0 0
> ATOM W          /* 1st NN */
>         POS a0*(1-dist1)*(sqrt(3),sqrt(3),sqrt(3))/2
>         OCC 1
>         SS SS1
>         POS a0*(1-dist1)*(-sqrt(3),sqrt(3),sqrt(3))/2
>         OCC 1
>         SS SS1
> ... add the other 6
> ATOM W          /* 2nd NN */
>         POS a0*(1-dist2)*(1,0,0)
>         OCC 1
>         SS SS2
> ... add the other 5
> The program would then automatically compute not only the distances for
> the SS paths, but those for the MS paths as well,
> and perhaps even estimate the ss values based on the ss's for the shells.
>  This is a relatively trivial example in which the scripting isn't needed.
> However, it gets bigger.  For instance, suppose that some of the 1NN atoms
> might have Fe on them.  Then, the W sites would have
>         OCC 1-xFe
> and there would be ATOM Fe sites specifications like:
>         POS a0*(1-dist1Fe)*(sqrt(3),sqrt(3),sqrt(3))/2
>         OCC xFe
>         SS SS1Fe
> and the program would automatically work up MS paths with the proper
> weighting for the number of W and Fe atoms involved.
> Now, consider an octahedral cage in which the central atom may be
> off-center:
> SET a0 = <appropriate value>
> CENTRAL Ti a0*(d_off,d_off,d_off)/sqrt(3)
>         POS (a0/2)*(1+d1,d2,d2)
>         OCC 1
>         SS SS1
>         POS (a0/2)*(d2,1+d1,d2)
>         OCC 1
>         SS SS1
>         POS (a0/2)*(d2,d2,1+d1)
>         OCC 1
>         SS SS1
>         POS (a0/2)*(-1+d1,d2,d2)
>         OCC 1
>         SS SS1
> ...
> The distortions shown are intended to keep the 3-fold symmetry about 111.
>  Now, when you consider the higher shells, you can see that it could get
> pretty messy to work out what the distances would be as a function of
> d_off, even if you don't allow displacements of higher neighbors.
> This sort of specification only becomes sort of practical because
> computers can now handle the multitudes of paths which will appear.  Funny
> that the Vpath thing should have just got discussed; that tool would be
> extra-important for distorted structures.
> For the POS parameters, the above are given in Cartesian coords, but it
> would be good to have the option to do it in crystal coords, invoking
> the crystal symmetry.  I'm not sure how to do that for impurities.
> I realize that this would be a HUGE job, but whoever does it would win the
> hearts of EXAFS people everywhere :-)
>         mam
Yes, that's a very nice way to do it, and I think such a distortion
language would be a great way to map the problem to EXAFS.  I think such
ideas have been kicked around for a long time, and I'm pretty sure
something like this was part of Bruce's motivation for Virtual Paths.

A confounding, persistent issue for many years was that Feff's pathfinder
(purposely?) loses all information about the atomic positions for a path.
Basically, the pathfinder needs to be able to retain the full path in order
to model distortions in the way you're talking about.  I believe Bruce's
pathfinder in Artemis does this.

I agree it's real work, but would be highly useful.

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