Codes


XFIT GitHub links

xfit source code : https://github.com/AustralianSynchrotron/xfit
average-wxwin : https://github.com/AustralianSynchrotron/average-wxwin

The XFIT package of codes (AVERAGE, SPLINE, XFIT, GRAPH) was written in Sydney the 1990s by Dr Paul Ellis under the supervision of Prof. Hans Freeman. The package contains some useful functionality for data reduction (WSIWYG aspects) and especially for curve-fitting of EXAFS data including geometrical constraints/restraints and two-site modelling. However the code for most parts has not been supported for many years and some parts (SPLINE) cannot run on later than Windows XP service pack 1. In addition, XFIT only supports the use of FEFF4 and FEFF6.

The code is now released into the public domain through the following GitHub links. Rather than wishing for an updated version of XFIT, instead we hope that active programmers in the community will co-opt useful sections of code to incorporate the most treasured aspects of the software into their own packages.

Please let us know if you are doing so by emailing Hugh Harris ( ) with XFIT in the title. James Hester has some experience with the code and has agreed to answer some questions at .

 

 

GNXAS and GNXAS2

http://gnxas.unicam.it/
The GNXAS package is and advanced software for EXAFS data analysis based on multiple-scattering (MS) calculations and a rigorous fitting procedure of the raw experimental data.

http://gnxas2.unicam.it/
GNXAS2: A web environment for advanced XAS data-analysis

The main characteristic of the software are:
atomic phase shifts calculations in the muffin-tin approximation based on atom self-consistent relativistic calculations. Account for the neighbors is taken.
Inclusion of inelastic losses through complex Hedin-Lundqvist potential.
Calculation of MS signals associated with two, three, and four atom configurations using advanced algorithms.

Use of an advanced fitting procedure that allows:
to fit simultaneously any number of spectra containing any number of edges, to use directly the raw data without any pre-analysis, to account for complex background multi-electron excitation features, to use various model peaks for the pair, triplet and quadruplet distribution functions, including non Gaussian models and extremal cases.

In all cases absolute parameters can be fitted,to treat liquid phase or disordered systems and extract reliable g(r) functions in the short range, to perform a rigorous statistical error analysis and plot two-dimensional correlation maps, To provide a flexible scientific tool for EXAFS data analysis where the user has access to every stage of the calculation. GNXAS is not a black box. Full modularity than makes easy to interface parts of the GNXAS software with other available software.

Its flexibility and advanced characteristics are essential to perform a modern EXAFS data-analysis and to extract accurately all the valuable information contained in your data.

 

 

Fitit

http://nano.sfedu.ru/fitit.html

FitIt is a free software to fit spectra using multidimensional interpolation approximation. It works under 32-bit Microsoft Windows operation systems. The main field of applications is quantitative determination of the local atomic structure parameters on the basis of fitting of X-ray absorption near edge structure (XANES). The algorithm of multidimensional interpolation of the spectrum as a function of structural parameters allows to minimize the number of time-consuming calculations required to find optimal values of the parameters.
The main program FitIt.exe has visual interface and consist of two main parts:

  • Tool to construct multidimensional interpolation of the spectrum as a function of a few parameters.
  • Subroutine for multidimensional fitting of the spectrum. It allows to find the set of parameters which corresponds to the minimal discrepancy between interpolated and experimental spectra

The program allows to use any external program for calculations of the spectrum and only small converters are needed to generate input files and read output files of any program of the user. At the moment converters for compatibility with FEFF8 and FDMNES are distributed in the FitIt package.

Also you can use any program for transformation of the geometry of your cluster. In the FitIt distributive you will find program Prot2005, which allows to perform lots of types of geometry transformations.

 

FEFF

http://leonardo.phys.washington.edu/feff/

FEFF is an automated program for ab initio multiple scattering calculations of X-ray Absorption Fine Structure (XAFS) and X-ray Absorption Near-Edge Structure (XANES) spectra for clusters of atoms. The code yields scattering amplitudes and phases used in many modern XAFS analysis codes, as well as various other properties.

  • FEFF 9: New Release Info Here
  • FEFF 8: The newest version is FEFF8 (Version 8.40). FEFF 8 improves over previous versions of FEFF by including self consistent calculation of potentials to provide charge transfer and a more accurate estimate of the Fermi level. It also includes full multiple scattering calculations to improve XANES calculations, where multiple scattering expansions can fail to converge. FEFF 8 can output the angular momentum projected density of states, x-ray emission spectra and x-ray scattering amplitudes. The improvements in FEFF 8.40 simplify spin-dependent calculations and can include improved treatment of core-hole and local field effects. FEFF8 now includes JFEFF, a graphical front-end for FEFF 8.4.
  • FEFF 7: Relativistic version of FEFF 6 including polarization.
  • FEFF 6: High-order multiple-scattering EXAFS/XANES code.
  • ATOMS: Generates input files, feff.inp, for crystalline materials which are suitable for FEFF5 and higher (included with FEFF).

 


 

Books:Nonfiction

 


 

Synchrotron Radiation Applications

Edited by Xinyi Zhang
2018, World Scientific Pub Co Inc
ISBN-10: 9813227664
ISBN-13: 978-9813227668

This is a research-level review volume. It presents both the fundamentals and the advanced research results, covering most part of important aspects of synchrotron radiation applications. Among the broad subjects of synchrotron radiation applications, as the main content of this book we have applications in VUV, soft X-rays, hard X-rays and XFEL (X-ray free electron laser) and important applications by various synchrotron-based techniques and methods, such as ARPES (angle-resolved photoemission spectroscopy), VUV photo-ionization spectroscopy, X-ray absorption/emission spectroscopy and X-ray absorption fine structure, X-ray diffraction, small angle X-ray scattering, X-ray excited optical luminescence, imaging and high pressure techniques.


Modern Techniques for Circular Dichroism and Synchrotron Radiation Circular Dichroism Spectroscopy

Bonnie A. Wallace and Robert W. Janes
2009, IOS Press,US
ISBN:1607500000
ISBN-13:9781607500001

The first monograph published that focuses on the emerging technique of synchrotron radiation circular dichroism (SRCD), a technique in which the editors are recognised world experts.


Introduction to XAFS
A Practical Guide to X-ray Absorption Fine Structure Spectroscopy

Grant Bunker, Illinois Institute of Technology
ISBN-13: 9780521767750

A coherent introduction for researchers (e.g. chemistry and physics graduate students) who are just starting XAFS-based research. It covers the basics of experiment, theory, and data analysis, with concise examples in Mathematica 7, a good quantity of new and previously unpublished material, and pointers to more detailed treatments where such things are available. Companion material such as data analysis examples using various programs, and source code in Mathematica 7 will be posted on the companion web site.

 

Concept of Nanochemistry

Cademartiri, Ludovico / Ozin, Geoffrey A.
ISBN-10: 3-527-32626-X
ISBN-13: 978-3-527-32626-6 - Wiley-VCH, Weinheim

A new approach as a textbook, ideal for interdisciplinary courses, bridging chemistry, materials science, physics and biology.


PLASTIC FANTASTIC:How the Biggest Fraud in Physics Shook The Scientific World

Eugene Samuel Reich
Macmillan Science
ISBN 0-230-22467-9

 

PAGE TOP

Books and Codes

Books

Codes

Tutorial Materials

 


Fundamentals of XAFS

a ~40 page introduction to XAFS, aimed at the advanced undergraduate level
(Revision 1.7 July 23, 2004).

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

[Detail] Downloadable pdf

 


Principles of X-ray Absorption Spectroscopy and Applications to Environmental Science

Advanced school on Synchrotron Techniques In Environmental Scientific Projects
(Trieste – Italy, 15-26 April 2013)

Giuliana Aquilanti

[Detail] Downloadable pdf

 


IUCr 2014 XAFS Tutorial for crystallographers and beginners
      (Montreal, August 5, 2014)

A one-­day, free Tutorial Workshop on XAFS titled "IUCr 2014 XAFS Tutorial for crystallographers and beginners" was held on August 5, 2014, in Montreal as a satellite event for the XXIII International Congress and General Assembly of the International Union of Crystallography (IUCr2014, Montreal, August 6-­14, 2014, http://www.iucr2014.org).

[Detail] http://www.iucr.org/resources/commissions/xafs/iucr-2014-xafs-tutorial2

 


EXCURVE tutorial

Martin C. Feiters
Dept. Synthetic Organic Chemistry, Institute for Molecules and Materials, Faculty of Science, Radboud University Nijmegen

Based on Feiters & Meyer-Klaucke (2013) BioXA Chapter 6. Practical Approaches to Biological Inorganic Chemistry (R.R. Crinchton and R. Louro, Editors, 2013).

* About EXCURVE(downloadable pdf)

* C2-EXAFS (an easy-to-use interface to the Excurve program)
http://www.esi.umontreal.ca/accelrys/life/cerius46/analytical/bk4_EXAFS.doc.html

 


The following materials are downloadable by the courtesy of the author, Prof. Paolo Fornasini, Dipartimento di Fisica - Universita' di Trento, Via Sommarive 14, 38123 Povo (Trento), Italy

X-ray absorption spectroscopy Part 1& Part 2
Paolo Fornasini, XII International School on Synchrotron Radiation, Grado, Sep. 16-27, 2013

 


The following materials are downloadable by the courtesy of the author, Prof. Grant Bunker, Illinois Institute of Technology, Chicago, Illinois
(http://www.iit.edu/csl/phy/faculty/bunker_grant.shtml)

Preparation of XAFS Samples

Interpreting XANES



Documents concerning the IUCr 2011 XAFS Tutorial for crystallographers
and beginners held in Madrid on August 22, 2011 are available on the
website of the IUCr Commission on XAFS.

http://www.iucr.org/resources/commissions/xafs/iucr-2011-xafs-tutorial

 


These materials are kindly provided by the courtesy of by F. d'Acapito
ESRF-GILDACRG CNR-INFM-OGG 6, Rue Jules Horowitz F-38043 Grenoble.

Introduction to ab-initio methods for EXAFS data analysis

Hercules
(http://www.esrf.eu/events/conferences/HSC/AboutHERCULES)

a. Introduction to the X-ray Absorption Spectroscopy (XAS)
b. Exercise on InAs EXAFS data

 


GNXAS tutorial materials

The following materials are provided by the courtesy of the XAS group at Camerino University.

Documentation, downloading and data-analysis examples of the multiple-scattering GNXAS data-analysis method can be found at the site http://gnxas.unicam.it .

Full data-analysis examples:
http://gnxas.unicam.it/XASLABwww/pag_gnxas/gnxas_examp.html

Documentation and manuals:
http://gnxas.unicam.it/XASLABwww/pag_gnxas.html#documentation

GNXAS School: http://gnxas.unicam.it/w/school/