%       Copyright (c) 2000 Bruce Ravel
%       Permission is granted to copy, distribute and/or modify this
%       document under the terms of the GNU Free Documentation License,
%       Version 1.0 or any later version published by the Free Software
%       Foundation; with the Invariant Sections being "EXAFS Analysis
%       Using FEFF and FEFFIT, Part 1: Presentation", "EXAFS Analysis
%       Using FEFF and FEFFIT, Part 2: Commentary", and all related
%       analysis examples, with no Front-Cover Texts, and with no
%       Back-Cover Texts.  A copy of the license is included in the
%       section entitled "GNU Free Documentation License".
% 
% 
% This file (and all files associated with `EXAFS Analysis Using FEFF
% and FEFFIT') are free documentation; you can redistribute it and/or
% modify it under the terms of the GNU Free Documentation License as
% published by the Free Software Foundation; either version 1, or (at
% your option) any later version.
% 
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% along with `EXAFS Analysis Using FEFF and FEFFIT'; see the file
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title =  Copper example,  four shells
data = data/cu10kk.chi
out = fits/cu10k
kmin = 2	kmax = 18	dk = 1	kw = 1
rmin = 1	rmax = 6

%% Note the value of rmax for this multishell fit

format = ascii  all = no
rspout = yes	qspout = no	kspout = yes

%% Background refinement in feffit:
%%    Feffit allows you the option of refining a background spline at 
%%  the same time that it refines structural parameters.  This spline
%%  is of exactly the same sort as used in autobk and a number of
%%  knots corresponding to the k-range and the value of rmin is used.
%%  You should choose as large a value of rmin as possible without
%%  introducing significant correlations between the spline and the
%%  structural parameters.
%%    The background spline refinement is enabled by setting "bkg" to
%%  true and leaving bkgfile commented out.  Once you have found a
%%  background spline that you like, you may want to fix the
%%  background and not refine it further.  This is a handy thing to do
%%  while playing with the fitting model as refining the spline adds a
%%  lot of parameters and time to the fit.
%%    To fix the spline, set "bkg" to false and set "bkgfile" to the
%%  name of the file containing the background spline fit by feffit in
%%  k space.  This was probably written to STEMk.bkg, where STEM is
%%  the value of "out".  You need that "kspout" be set to true in
%%  order to have that file written.  (Note: bkgfile should NOT be the
%%  background file in energy written by autobk!)
%%    WARNING: There is a bug in feffit.  If you do not rename the
%%  file STEMk.bkg to something else, it will be overwritten by a file
%%  of zeros with the next fit.  To avoid loosing the file you want to
%%  use as the value of "bkgfile", it is wise to rename STEMk.bkg to
%%  something else.

% bkg = true
% bkgfile = fits/cu10kk.background




%% The following is a simple multi-shell fit which considers single
%% and multiple scattering contributions.  The correlated Debye model
%% and an isotropic expansion coefficient is used.  Copper metal is
%% the simplest possible example of a fit that goes beyond normal
%% first shell analysis and is a good introduction to the syntax and
%% construction of feffit's input files.
%%
%% The isotropic expansion coefficient is a generalization of what
%% what done with the delr path parameters in feffit_2.inp.  The
%% relationship between alpha in this input file and deltaR in
%% feffit_2.inp is 
%%          alpha = deltaR / 2.5527
%%
%% Some things to try:
%%
%%   1.  Set all=true and look at each individual path.  You will see
%%       that a lot of them are very tiny.  How do your fit results
%%       change if you remove all the tiny paths from the fit?
%%   2.  Play around with the background function.  Familiarize
%%       yourself with how it works.  Notice that refining the
%%       background adds a lot of parameters to the fit.  So play
%%       around with the bkgfile keyword.  Be careful not to overwrite
%%       your background function.
%%   3.  Play around with the {krq}pout keywords and the all keyword.
%%       Check out all the different kinds of output files feff can
%%       write. 
%%   4.  Play around with the {krq}spfit keywords.  For a problem this
%%       simple, the fit should be pretty insensitive to the fitting
%%       space. 
%%   5.  What other sigma^2 models might you use?  How does the fit
%%       change if you allow the each shell to use a single vibration
%%       frequency model (i.e. an Einstein model, i.e. allow each
%%       shell its own sigma^2 fitting parameter)

%==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==
guess	amp	0.9
guess	e0	0.0
guess	thetad	350
guess	alpha	0.0
set	temp	10
set	sigmm	0.00052 
%==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==


%% some things to note:  individual deltaR's and sigma^2's for each
%% path have been dropped in favor of isotropic expansion and a Debye
%% model.  This demonstrates the utility of defining fitting
%% parameters above and using them in the exafs equation below.  In
%% this way we are able to build interesting constraints into our
%% fitting model.


path	1	feff/feff0001.dat
id	1	First shell SS, deg=12.000, r_eff=2.5527
delr	1	alpha*reff
sigma2	1	debye(temp, thetad) + sigmm
s02	1	amp
e0	1	e0

path	2	feff/feff0002.dat
id	2	Second shell SS, deg=6.000, r_eff=3.6100
delr	2	alpha*reff
sigma2	2	debye(temp, thetad) + sigmm
s02	2	amp
e0	2	e0

path	3	feff/feff0005.dat
id	3	Third shell SS, deg=24.000, r_eff=4.4213
delr	3	alpha*reff
sigma2	3	debye(temp, thetad) + sigmm
s02	3	amp
e0	3	e0

%% note that there need be no correspondance between path index and
%% the value of NNNN in feffNNNN.dat
%%
%% Is the lack of correspondance between path indeces and NNNN a
%% needless level of abstraction and confusion, or can you imagine a
%% situation where this might be needed and desirable?  (Hint,
%% consider the copper edge in YBa2Cu3O7, which has copper in two
%% distinct crystallographic environments.)

path	4	feff/feff0003.dat
id	4	amp=10.585, deg=48.000, nleg=3, r_eff=3.8290
delr	4	alpha*reff
sigma2	4	debye(temp, thetad) + sigmm
s02	4	amp
e0	4	e0

%% Where do those id lines come from?  Look at the `files.dat', one of
%% the outputs from the feff run.  Much of this input file was
%% generated by a program whose purpose is to convert `files.dat' into
%% a `feffit.inp' skeleton.

path	5	feff/feff0004.dat
id	5	amp=8.649, deg=48.000, nleg=3, r_eff=4.3577
delr	5	alpha*reff
sigma2	5	debye(temp, thetad) + sigmm
s02	5	amp
e0	5	e0

path	6	feff/feff0006.dat
id	6	amp=10.625, deg=48.000, nleg=3, r_eff=4.7633
delr	6	alpha*reff
sigma2	6	debye(temp, thetad) + sigmm
s02	6	amp
e0	6	e0

path	7	feff/feff0007.dat
id	7	amp=21.819, deg=96.000, nleg=3, r_eff=4.7633
delr	7	alpha*reff
sigma2	7	debye(temp, thetad) + sigmm
s02	7	amp
e0	7	e0

%% here come the paths at the fourth shell distance

path	8	feff/feff0008.dat
id	8	amp=18.935, deg=12.000, nleg=2, r_eff=5.1053
delr	8	alpha*reff
sigma2	8	debye(temp, thetad) + sigmm
s02	8	amp
e0	8	e0

path	9	feff/feff0009.dat
id	9	amp=8.459, deg=12.000, nleg=3, r_eff=5.1053
delr	9	alpha*reff
sigma2	9	debye(temp, thetad) + sigmm
s02	9	amp
e0	9	e0

path	10	feff/feff0010.dat
id	10	amp=43.714, deg=24.000, nleg=3, r_eff=5.1053
delr	10	alpha*reff
sigma2	10	debye(temp, thetad) + sigmm
s02	10	amp
e0	10	e0

path	11	feff/feff0011.dat
id	11	amp=8.208, deg=12.000, nleg=4, r_eff=5.1053
delr	11	alpha*reff
sigma2	11	debye(temp, thetad) + sigmm
s02	11	amp
e0	11	e0

path	12	feff/feff0012.dat
id	12	amp=3.565, deg=12.000, nleg=4, r_eff=5.1053
delr	12	alpha*reff
sigma2	12	debye(temp, thetad) + sigmm
s02	12	amp
e0	12	e0

%% notice that paths 13, 16, and 17 are missing.  They fell below
%% feff's pathfinder cutoff

path	13	feff/feff0014.dat
id	13	amp=32.795, deg=12.000, nleg=4, r_eff=5.1053
delr	13	alpha*reff
sigma2	13	debye(temp, thetad) + sigmm
s02	13	amp
e0	13	e0

path	14	feff/feff0015.dat
id	14	amp=3.260, deg=48.000, nleg=4, r_eff=5.1053
delr	14	alpha*reff
sigma2	14	debye(temp, thetad) + sigmm
s02	14	amp
e0	14	e0

path	15	feff/feff0018.dat
id	15	amp=4.141, deg=48.000, nleg=3, r_eff=5.2920
delr	15	alpha*reff
sigma2	15	debye(temp, thetad) + sigmm
s02	15	amp
e0	15	e0

path	16	feff/feff0019.dat
id	16	amp=4.091, deg=48.000, nleg=3, r_eff=5.2920
delr	16	alpha*reff
sigma2	16	debye(temp, thetad) + sigmm
s02	16	amp
e0	16	e0

path	17	feff/feff0020.dat
id	17	amp=2.735, deg=96.000, nleg=3, r_eff=5.6977
delr	17	alpha*reff
sigma2	17	debye(temp, thetad) + sigmm
s02	17	amp
e0	17	e0

path	18	feff/feff0021.dat
id	18	amp=4.796, deg=48.000, nleg=3, r_eff=5.6977
delr	18	alpha*reff
sigma2	18	debye(temp, thetad) + sigmm
s02	18	amp
e0	18	e0

path	19	feff/feff0022.dat
id	19	amp=27.856, deg=24.000, nleg=2, r_eff=5.7079
delr	19	alpha*reff
sigma2	19	debye(temp, thetad) + sigmm
s02	19	amp
e0	19	e0

path	20	feff/feff0023.dat
id	20	amp=8.656, deg=48.000, nleg=3, r_eff=5.9353
delr	20	alpha*reff
sigma2	20	debye(temp, thetad) + sigmm
s02	20	amp
e0	20	e0

path	21	feff/feff0024.dat
id	21	amp=7.112, deg=48.000, nleg=3, r_eff=5.9353
delr	21	alpha*reff
sigma2	21	debye(temp, thetad) + sigmm
s02	21	amp
e0	21	e0

path	22	feff/feff0025.dat
id	22	amp=7.696, deg=48.000, nleg=3, r_eff=5.9353
delr	22	alpha*reff
sigma2	22	debye(temp, thetad) + sigmm
s02	22	amp
e0	22	e0

path	23	feff/feff0026.dat
id	23	amp=5.079, deg=96.000, nleg=3, r_eff=6.0396
delr	23	alpha*reff
sigma2	23	debye(temp, thetad) + sigmm
s02	23	amp
e0	23	e0

path	24	feff/feff0027.dat
id	24	amp=5.497, deg=96.000, nleg=3, r_eff=6.0396
delr	24	alpha*reff
sigma2	24	debye(temp, thetad) + sigmm
s02	24	amp
e0	24	e0

path	25	feff/feff0028.dat
id	25	amp=5.279, deg=96.000, nleg=4, r_eff=6.0396
delr	25	alpha*reff
sigma2	25	debye(temp, thetad) + sigmm
s02	25	amp
e0	25	e0

path	26	feff/feff0029.dat
id	26	amp=5.387, deg=96.000, nleg=4, r_eff=6.0396
delr	26	alpha*reff
sigma2	26	debye(temp, thetad) + sigmm
s02	26	amp
e0	26	e0

path	27	feff/feff0035.dat
id	27	amp=7.168, deg=8.000, nleg=2, r_eff=6.2527
delr	27	alpha*reff
sigma2	27	debye(temp, thetad) + sigmm
s02	27	amp
e0	27	e0

path	28	feff/feff0036.dat
id	28	amp=4.406, deg=96.000, nleg=3, r_eff=6.3409
delr	28	alpha*reff
sigma2	28	debye(temp, thetad) + sigmm
s02	28	amp
e0	28	e0

path	29	feff/feff0037.dat
id	29	amp=5.993, deg=96.000, nleg=3, r_eff=6.3409
delr	29	alpha*reff
sigma2	29	debye(temp, thetad) + sigmm
s02	29	amp
e0	29	e0

path	30	feff/feff0038.dat
id	30	amp=4.922, deg=96.000, nleg=3, r_eff=6.3409
delr	30	alpha*reff
sigma2	30	debye(temp, thetad) + sigmm
s02	30	amp
e0	30	e0



!!&& Local Variables:
!!&& input-out-path: "fits/"
!!&& input-feff-path: "feff/"
!!&& input-data-path: "data/"
!!&& input-program-name: "feffit"
!!&& End:
%# Input-mode Time-stamp: <2000/06/11 09:56:45 bruce>