[Ifeffit] Fitting EXAFS simulation to experimental
Anatoly I Frenkel
afrenke2 at yu.edu
Thu May 29 09:58:11 CDT 2014
Yes, it is possible to vary atomic positions in the fitting process and evaluate their effect on the fit, or just use them as adjustable parameters in the fit as any other fitting variables.
This process was historically started by Yizhak Yacoby (see papers from his group in the 1990s), who introduced structural distortions into the fit.
We had a somewhat similar approach in this work:
where we have parameterized the fractional coordinates of oxygen atoms in the perovskite structure and traced their effect on EXAFS equation (most non-trivially, on the scattering amplitude of multiple scattering (Equations 6,7) paths, the rest was pretty trivial: Equations 4,5).
I think Bruce also had done such parameterization in some of his papers and in his Thesis.
From: ifeffit-bounces at millenia.cars.aps.anl.gov [ifeffit-bounces at millenia.cars.aps.anl.gov] on behalf of Scott Calvin [scalvin at sarahlawrence.edu]
Sent: Thursday, May 29, 2014 10:40 AM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Fitting EXAFS simulation to experimental
I'm not sure what level you were asking your question from. Bruce provided an answer to one interpretation of the question.
If the question is, however, "has anyone written an automated script that allows the user to choose parameters given to ATOMS as fitting parameters for all space groups," then my answer is that I'm not aware of that having been done.
For example, it is very easy to make the lattice parameter for a cubic space group be a fitting parameter, as changes to it will result in a uniform fractional change to the length of all paths, and the reff keyword makes it easy to implement a uniform fractional change. Plenty of people have computed the relationship between ATOMS parameters and path parameters for specific geometries (including more complicated ones), and used that for fitting.
But in each case that requires some effort to think about the geometry involved. That's different from having a script that allows you to designate a shift in, say, the x-coordinate in fractional coordinates of one kind of atom in the input file and automatically have that result in the generation of the correct function of that fitting parameter in each of the paths used in FEFF, including multiple-scattering paths. And that's the thing that I don't think currently exists.
Sarah Lawrence College
On May 29, 2014, at 9:04 AM, Bruce Ravel <bravel at bnl.gov> wrote:
> On 05/28/2014 06:58 PM, Carl Brozek wrote:
>> Dear listhost,
>> I'm using Artemis as a front end for ATOMS and FEFF and I would like to
>> build a simulated EXAFS spectrum based on experimental data I have. I
>> know how to generate a simulation based on a .cif or .xyz file, but is
>> it possible to vary parameters in these input geometries to best match
>> the experimental?
>> Has someone implemented this in artemis or matlab?
> In Artemis, this is called a VPath.
> You will need to import data of some sort because a VPath is created
> from paths that have been associated with a data set.
> Run Feff. Drag and drop any number of paths from the Path tab in the
> Feff window onto your data Window. Mark the paths paths you want to
> include in your VPath by clicking their little check buttons. From
> the Actions menu, select "Make VPath from marked". This will prompt
> you for a name for the VPath and insert the VPath into the plotting
> list, as described in the page whose URL is given above.
> As for varying structural parameters, that is what we call a "fit".
> You can parameterize the various Delta R parameters to represent
> changes in lattice positions. There are plenty of examples of this
> using Ifeffit -- Daniel Haskel's papers on cuprate superconductors, my
> own papers on titanate perovskites, lots of work buy Anatoly Frenkel
> on various catalyst materials, Sam Webb's work on manganites, just to
> name a few.
> Bruce Ravel ------------------------------------ bravel at bnl.gov
> National Institute of Standards and Technology
> Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
> Building 535A
> Upton NY, 11973
> Homepage: http://xafs.org/BruceRavel
> Software: https://github.com/bruceravel
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
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