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@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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