On Tue, Aug 19, 2014 at 9:55 AM, <huyanyun@physics.utoronto.ca> wrote:
Hi Dr. Newville,

I had similar situation and questions as with choosing Path Parameters. My goal is to identify the occupancy sites for a doped element in my sample. We have a rough guess of two possible sites, part of the doped atoms are filling a void site of the unit cell, the other part is to substitute an existing atom sites.

I was being able to writing two ATOM files and run FEFF twice to calculate all possible PATH. But when I was going to define/guess the parameters ('N','amp', 'enot', 'delr','ss')for EACH path, I totally lost idea how to group all those paths, or how to guess all those five parameters for each path. Of course, I couldn't get a good fit as I don't know how to build the model and to refine parameters in this step.

Here I post my understanding of the five parameters: 'N', path degeneracy, or coordination number; 'amp', usually close to 1, but as I have doping elements, I am expecting small partial numbers in some of the 'amp' to adjust for partial occupancy; 'enot', I think it is just the energy shift of your spectra, and as I believe my spectra are well aligned, I will SET 'enot' to zero. 'delr' is the variation of the real atom-atom distances from the calculated ones (I think I need to group paths to refine 'delr' but I don't know what's the criteria to group paths). 'ss' is to consider about the disorder effect and typically I use the Debye model.  Let me know if I am wrong in any way.

Could you please give me some suggestion how did you get started? I am looking forward to hearing from you.


For each Path in a model, you need
    a) a Feff.dat file -- this can be read from any Feff calculation, and those can be generated from a crystal structure
    b) a set of Path Parameters -- the physically meaningful quantities N*S02, E0, deltaR, sigma2, etc from the EXAFS Equation.
 
Each of the Path Parameters is given as an equation in terms of the set of Fit Parameters.  Often times, the equations are very simple.    That is, sigma2 for Path1 may simply be defined to be evaluated from 'ss'.  You could make it 'ss*2', or something else.

There is also a set of Fit Parameters -- named quantities that may be adjusted in the fit to make the sum of Paths best match your data.  These can be "set", in which case they are frozen -- not varied in the fit.    In Artemis, the Fit Parameters are shown in the Guess/Set/Def  page.   The quantities like "enot", "delr", "ss", etc are Fit Parameters.  You need to fill out an expression for each Path Parameter you want changed in the fit in terms of the set of Fit Parameters.   

Artemis will help you by complaining if some of the Fit Parameters defined are not used in any Path Parameters -- changing these values won't alter the fit, so you should not have them defined as a variable Fit Parameter.

The system is designed to be very flexible.  But this means that before you do a fit you need to understand what each of the Fit Parameters does to the Path Parameters for the Paths you are using in the fit.   We could guess that by "enot", you mean the value for the Path Parameter 'E0', and that you want to make sure that the E0 Path Parameter is given as "enot" for all Paths.   But this would be only a guess.   You are setting up the model, so you have to ask yourself why you have a variable 'enot', and what that means for your model.

--Matt