[Ifeffit] Fitting EXAFS simulation to experimental

Carl Brozek brozek at mit.edu
Thu May 29 14:25:15 CDT 2014

Hi Scott,

Thanks a lot for the insight. It seems like it'll take a bit of work, but
I'm happy to hear it's doable.


On Thu, May 29, 2014 at 12:54 PM, Scott Calvin <scalvin at sarahlawrence.edu>wrote:

> Dear Carl,
> The short answer is yes, but it takes a little bit of effort.
> One method is to actually figure out how stretching the c-axis impacts the
> lengths of each path geometrically, and then use the functions determine to
> express the delr's of each path in terms of the change in c. This method is
> rigorously correct, but requires digging in to the geometry, and entering
> somewhat lengthy expressions for many of the scattering paths.
> A related method is to in effect use a first-order approximation of those
> changes. To do that, create two atoms files with slightly different values
> of c. Generate the corresponding paths, and see how the reff of those paths
> changes. For example, changing c by 0.01 might result in a certain path
> having a reff change by 0.014. Use the ratio of the change in reff to the
> change in c to scale the delr of those paths with respect to a guessed
> parameter delc. In the example I just provided the delr of the path in
> question would be chosen to be 1.4*delc.
> The second method is, of course, approximate, but for small changes in a
> parameter such as c can work pretty well, and can be easier to implement
> than the first.
> --Scott Calvin
> Sarah Lawrence College
> On May 29, 2014, at 12:33 PM, Carl Brozek <brozek at mit.edu> wrote:
> > Dear All,
> >
> > Thank you for your responses so far and I apologize for not being
> clearer.
> >
> > Here is the problem at hand: I have a material that is best thought of
> as organic, graphene-like 2-D sheets connected by infinite chains of Fe-S.
> Based on PXRD and other techniques, we know the structure of the AB plane
> (the 2-D organic part), but we aren't able to make sense of what is going
> on with the Fe-S chain. We can simulate the PXRD based on proposed .cif
> files, but it's off most likely because of the c direction (Fe-S chain).
> >
> > We collected Fe K edge XAS to tease out Fe-S bond angles and distances,
> hoping we could feed this into our simulation for the PXRD to improve the
> fit.
> >
> > Modifying the ATOMS input by hand, by constructing different reasonable
> geometries, was improving the simulation, but using a error minimization
> fitting program would be best.
> >
> > So, is it possible to vary specific angles and distances between atoms
> along the c-direction only in an error minimization program based on our
> experimental data?
> >
> > I apologize if you have already responded to this reformulated question.
> >
> > best,
> > Carl
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PhD Candidate | Chemistry | MIT
SB | 2010 | University of Chicago
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