[Ifeffit] The degeneracy and the coordination number

[Matt Newville]

Hi Zhaomo,

On Wed, Dec 26, 2012 at 5:23 AM, Zhaomo Tian <zhaomo1989 at postech.ac.kr> wrote:
>
> Dear all,
>
> I am confused about the degeneracy and the coordination number used in the Artemis program.
> I want to get the coordination number of 1st shell of my copper sample, so I set a guess number N1=12(initial guess) as the coordination number which will vary during the fitting iteration, but when I am looking at the 1st path's parameters, there is another N appear which may stand for the degeneracy.The 1st path of copper model is single scattering, so the degeneracy N equals coordination number . But when I set N=12, the guessed N1 will have a value which is closed to 1, only when I set N=1, the guessed N1 will have a value which is closed to 12. It seems that N and N1 are reciprocals. But I think N actually equals N1 in the single scattering case.
>
> So I am really confused, If I want to get coordination number of a shell in a fitting, how can I deal with floated coordination number and its path degeneracy N?
>
> Thanks so much.
>
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I don't know what "N" and "N1" mean in your model.  It would be
helpful to know what you're setting the Path Parameters to.

This topic can be sort of confusing.  The way Feff/Ifeffit/Artemis
models EXAFS, there are 3 separate values that scale the EXAFS
amplitude.  These are:

   degen: the "path degeneracy" built into the Feff.dat file.  This is
the value for coordination number from the cluster of atoms used in
the Feff calculation.
   S02: the "amplitude reduction factor", a number (generally)
slightly less than 1.0 meant to cover over mediocre amplitudes from
Feff, and really, imperfect experimental amplitudes.
   N:       The coordination number for the structure.

In the EXAFS equation used by Artemis, these are all multiplied together.

   Amplitude  =  degen*N*S02

There are few common scenarios:
  A: "I know the coordination number and want to refine S02".  This is
useful for well-defined structures and standards, where a single
cluster of atoms put into a single Feff calculation models the
spectrum well.  Here, you generally use the "degen" values from the
Feff.dat files, set N to 1, and refine a value for S02.

  B: "I know S02, and want to refine N".  This would be the more
common situation for "unknown structures".  Here, you ***SET degen to
1***, set S02 to the "known value" ( presumably determined with a
standard and scenario A).  Then you Guess a value for N and refine it.
 The "N*S02" entry in Artemis should then contain the expression for
the product of the variables holding S02 and N.  For example:

     set     S02_Cu = 0.87
     guess N_1st_Shell = 12.0

     Path 1: 'N*S02' =  S02_Cu * N_1st_Shell

Hope that helps,

--Matt