Dear Matt,
I still have questions about Artemis concerning the S0^2. In your book/summary called XAFS-Fundamentals there is a section at the beginning of chapter six that says:
“Starting with this structure, we can calculate the scattering amplitude and phaseshifts
and theoretically. The complete calculation is beyond the scope of this treatment,
but don’t worry too much by that phrase “we’ll calculate these theoretically”! These
functions are actually fairly easy to calculate using one of a few different computer
programs – for the calculations here, the FEFF program was used. The results of the
FEFF calculation are stored in simple files containing the scattering factors and meanfree-
path for a given coordination shell. The calculations in these files can be used
directly in a number of analysis programs.”
Are these somewhere listed in Artemis?
The calculations stored in the feffNNNN.dat files can be accessed from Larch, but I think they're not readily exposed by Artemis. The point is that you don't have to worry about these scattering factors, but only about the Path Parameters (S02, E0, deltaR, sigma2, etc) that modify these scattering terms.
Because if I start fitting the value in GDS is always guessed to be one, for any element in the sample. If I go and look at the FEFF calculation it tells me:
TITLE LiPF6
HOLE 1 1.0 * FYI: (F K edge @ 696.7 eV, 2nd number is S0^2)
* mphase,mpath,mfeff,mchi
CONTROL 1 1 1 1
PRINT 1 0 0 0
I don’t really understand which is the second number and why all S0^2 then are either 0 or 1.
Best, Julian
One can set an S02 value during the Feff calculation. That is what goes as the second number in the HOLE entry in feff.inp (The first value is an integer indicating the edge type -- 1 for 'K', and so on). Setting that value will apply the S02 value to all paths calculated by that run of Feff. You can also set values for sigma2 from Feff too,
Artemis/Ifeffit/Larch etc use the Feff calculations stored in feffNNNN.dat (or equivalent) and build a model from a collection of paths from Feff. If S02 or sigma2 is set in the original Feff calculation(s), it is difficult to track during the analysis (neither S02 nor sigma2 are written to the individual feffNNNN.dat files).
In some sense Artemis/Ifeffit/Larch etc only use part of Feff -- the calculation of the EXAFS contribution of a single, idealized path. They do not use the sum-of-paths module(s) of Feff, but instead replace that with its own sum-of-paths implementation that is richer (allowing feffNNNN.dat from different feff runs, allowing parameters like S02, sigma2, E0, deltaR, etc to be varied, etc).
So, the recommendation (more like an expectation, really) is to NOT set S02 to any value except 1.0 and to NOT set any parameters that will calculate sigma2 in feff.inp if the intention is to use those paths for fitting. Let the fitting program adjust S02 and/or disorder terms.