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The IFEFFIT Reference Guide

Matthew Newville
Consortium for Advanced Radiation Sources
University of Chicago, Chicago, IL

Version 1.2.5
Feb 09, 2004

This Reference Guide is also available in the following formats:
[ PDF | Postscript ]

Important Note:
This Reference Guide is incomplete and may contain bugs!
Suggestions for improvements are welcome.
Thanks for your patience!

Matt

Contents
License
1 Introduction

Acknowledgements

2 The Basics of IFEFFIT

2.1 Starting the program
2.2 A Sample Run
2.3 The show() and print() Commands

3 Structure and Syntax of IFEFFIT

3.1 Commands
3.2 Scalars, Arrays, and Strings
3.3 Dynamic Variables: set(), def(), and sync()
3.4 Fitting Variables: guess()
3.5 Mathematical Syntax and Operations

3.5.1 Common Math Operations
3.5.2 Common Math Functions
3.5.3 Array-Specific Operations
3.5.4 Functions for Smoothing and Interpolating Data
3.5.5 XAFS-specific Functions for $\sigma^{2}_{}$

3.6 Commands, Arguments, and Keyword/Values
3.7 Getting information back from IFEFFIT
3.8 Log Files, echo(), show(), and print()

4 Input and Output Files

4.1 Reading ASCII Column Files
4.2 Sorting Data with read_data()
4.3 Writing ASCII Column Files
4.4 The PAD Format for Save and Restore Files

5 Plotting with IFEFFIT

5.1 Specifying Data for Plotting
5.2 Error Bars
5.3 Colors, Line Styles, and Other Attributes
5.4 Text Strings and Labels
5.5 Markers and Arrows
5.6 Cursor and Zooming
5.7 Graphics Devices

5.7.1 X-Windows Graphics
5.7.2 GrWin Graphics for Win32 systems
5.7.3 Aquaterm Graphics for Mac OS X
5.7.4 PostScript, GIF and PNG Graphics Files

6 Basic XAFS Data Processing

6.1 Data Manipulation and Corrections
6.2 De-glitching
6.3 Pre-Edge Subtraction, Finding E₀, and Normalization
6.4 Simple XANES spectral analysis
6.5 Post-Edge Background Subtraction: isolating $\chi$ (k)
6.6 XAFS Fourier Transforms

6.6.1 Forward Fourier Transforms with fftf()
6.6.2 BackTransforms with fftr()
6.6.3 Phase-Corrected XAFS Fourier Transforms

7 Fitting XAFS Data with FEFF Calculations

7.1 Defining and Using Paths
7.2 Creating $\chi$ (k) data with ff2chi()
7.3 Building a Fitting Model
7.4 Executing a Fit
7.5 Estimating the uncertainties in fitted variables
7.6 Goodness of Fit Parameters
7.7 Post-Fitting Tasks
7.8 Additional Fitting Features of feffit()

7.8.1 Including Background Refinement
7.8.2 Constraints and Restraints in Fitting
7.8.3 Multiple-k-Weighting
7.8.4 Simultaneous Fitting of Multiple Data Sets

8 Fitting Non-XAFS Data with IFEFFIT
9 Commands

9.1 bkg_cl()
9.2 chi_noise()
9.3 color()
9.4 comment()
9.5 correl()
9.6 cursor()
9.7 def()
9.8 echo()
9.9 erase()
9.10 exit()
9.11 feffit()
9.12 ff2chi()
9.13 fftf()
9.14 fftr()
9.15 f1f2()
9.16 get_path()
9.17 guess()
9.18 history()
9.19 linestyle()
9.20 load()
9.21 log()
9.22 macro()
9.23 minimize()
9.24 newplot()
9.25 path()
9.26 pause()
9.27 plot()
9.28 plot_arrow()
9.29 plot_marker()
9.30 plot_text()
9.31 pre_edge()
9.32 print()
9.33 quit()
9.34 random()
9.35 read_data()
9.36 rename()
9.37 reset()
9.38 restore()
9.39 save()
9.40 set()
9.41 show()
9.42 spline()
9.43 sync()
9.44 unguess()
9.45 window()
9.46 write_data()
9.47 zoom()

10 Macros in IFEFFIT
11 Scripting and Programming with IFEFFIT

11.1 Which language to use?
11.2 Controlling screen outputs: The echo buffer
11.3 The Fortran interface to IFEFFIT

11.3.1 integer function ifeffit()
11.3.2 integer function iffputsca()
11.3.3 integer function iffgetsca()
11.3.4 integer function iffputarr()
11.3.5 integer function iffgetarr()
11.3.6 integer function iffputstr()
11.3.7 integer function iffgetstr()
11.3.8 integer function iffgetecho()

11.4 The C interface to IFEFFIT

11.4.1 function ifeffit()
11.4.2 function iff_put_scalar()
11.4.3 function iff_get_scalar() and iff_scaval()
11.4.4 function put_string()
11.4.5 function get_string()
11.4.6 function put_array()
11.4.7 function get_array()
11.4.8 function get_echo()

11.5 The IFEFFIT Perl Module
11.6 Using IFEFFIT from Python
11.7 Using IFEFFIT from Tcl

A. Glossary of Program Variables

A..1 Scalar Naming Conventions
A..2 Array Naming Conventions

B. Fourier Transforms in IFEFFIT

B..1 Fourier transform Conventions
B..2 Fourier transform window functions

Bibliography
Index
About this document ...

Matt Newville
2004-02-09