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GNXAS

Current versions: 11.2013/12.2006

Info and News

Full and updated GNXAS documentation: the GNXAS 'red-book'.


Latest GNXAS intensive courses: Camerino, Italy (2009), Melbourne, Australia (2011), Riberao Preto, Brasil (2013)

Latest news about the programs (29-Jul-2015)

Become a GNXAS user in 5 steps:
1) DOWNLOAD the GNXAS package
2) Fill the form for the REGISTRATION
3) Installation instructions
4) Using and downloading the related software (TopDrawer, CERN libraries, ATOMS).
5) Data-analysis examples

Info about all the GNXAS distributions:
i) 11.2013 and later versions (29-Jul-2015)
ii) 12.2006 versions (05-Dec-2006)
iii) 12.2001 versions (10-Jan-2002)
iv) 3.2001 and 9.00 versions (24-Mar-2001)
v) 2.99 and 8.99 versions (24-Aug-1999)


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INTRODUCTION to GNXAS

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. 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.


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PROGRAM DESCRIPTION

The backbone of the GNXAS package is composed of three main codes, in the logical sequence they are:

  • 1) PHAGEN, potential and phase shift generation.
  • INT
  • 2) GNXAS, signal calculation for reference geometries
  • 3) FITHEO, advanced fitting of the experimental data


Two other programs are able to prepare automatically the input for PHAGEN and GNXAS starting directly from model molecular position or crystallographic data. These are particularly useful in the case of complex structures where the configuration counting is not trivial. These programs are:

  • 4) CRYMOL, allows to treat complex molecular and crystallographic structures providing input information for PHAGEN, GNPEAK, and XANES; the program identifies prototypical phase-shift atoms and select a suitable cluster of atoms for successive XAS calculations.
  • 5) GNPEAK, is based on a general algorithm able to identify inequivalent two-body, three-body and four-body configurations in specified atomic aggregates.
  • 6) XANES is a program in which the continued fraction algorithm is fully implemented for non-symmetrized XANES calculation. For the reasons mentioned above the usage of this program for scientific applications is discouraged.
crymol gnpeak phagen gnxas fitheo

Flow chart of the various programs composing the package.
CLICK on the flow chart to obtain more information about the programs.


Several other programs were written to facilitate the output readout, in particular:

  • 7) PHAPLO, produces a graphic output for the phase-shift file generated by PHAGEN.
  • 8) READDER, converts the binary signal files generated by GNXAS into ASCII files to facilitate visualizing and checking the output.
  • 9) CONTOUR, to convert character contour plots in the FITHEO output and facilitates error analysis.

Three additional programs have been written to facilitate the analysis of disordered systems (including liquids) where the structure is described in terms of radial distribution functions g(r). These are:

  • 10) GRFIT, fitting utility of model radial distribution function data.
  • 11) GRXAS, calculates the EXAFS signal associated with a given partial radial distribution function.
  • 12) GRREC, allows reconstruction of g(r) after model refinement.

Finally the GNXAS distribution includes miscellaneous programs useful for XAS based research:

  • 13) XASAM, a program for sample thickness optimization in the transmission geometry.
  • 14) JESF, an automatic routine for EXAFS extraction, Fourier transformation, and noise evaluation. This program is useful for a qualitative data-analysis and it is routinely used at the ESRF-BM29 (now BM23) beamline for on-line data analysis and sometimes at XAFS@Elettra, for this reason it is believed that JESF has already analyzed more than 106 EXAFS spectra (without crashing)!
  • 15) DECONV, a deconvolution program suitable to deconvolve the core-hole life-time broadening in high quality spectra.

The extended GNXAS package includes also several other advanced or utility Linux programs that are available to users upon request, described in the recent Full and updated GNXAS documentation (2009): the GNXAS 'red-book'.


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DOCUMENTATION

XANES PROGRAM:

DECONVOLUTION PROGRAM:

MAIN PROGRAMS -OLD documentation (text files):


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WHO WROTE GNXAS

GNXAS is the result of nearly 10 years of research efforts in the field of x-ray absorption spectroscopy. Several scientists have contributed to its development. It contains the most up to date algorithms for EXAFS data analysis directly coded by the investigators. It was soon realized that the use of these programs could have been appreciated by scientists in various fields willing to perform advanced applications of the EXAFS technique. For this reason the programs were made available to the scientific community. We should warn the users however that as a result of this history GNXAS is not a trivial and "user proof" code.

The complexity of some of the algorithms makes the required input very cumbersome and INPUT mistakes can be sometimes hard to identify.

The research effort was coordinated by C. R. Natoli of the INFN - Laboratori Nazionali di Frascati, a pioneer of the multiple-scattering applications to the EXAFS spectroscopy. Natoli is the author of the PHAGEN program where all the theory for the potential calculation is included.

The GNXAS code was mainly written by A. Filipponi - Universita' dell'Aquila, implementing efficient codes for MS calculations with fast matrix products and continued fraction approaches. FITHEO has been mainly written by A. Di Cicco Universita' di Camerino. A complete version of GNXAS was already available in 1990.

Several algorithms and approaches implemented in the package have been jointly developed by the authors.

Other colleagues participated to major theoretical developments and/or have partly contributed to the development of the package. Among them we acknowledge the work of:

  • T. A. Tyson - Implementation of Hedin-Lundqvist potential (PHAGEN code)
  • M. Benfatto - Early developments in MS theory, disordered systems
  • K. O. Hodgson - Applications to biological systems
  • C. Brouder - Developments in MS theory
  • G. Mancini - Protection software development
  • M. Sanchez Del Rio - IDL interface
  • K. Hatada: conversion to gfortran

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WHERE TO FIND GNXAS

GNXAS was supported by the Italian Consiglio Nazionale delle Ricerche (CNR) (last contract 98.00475.ST76). Later on, INFM supported the developments in 1999-2003.

Distribution of the code is provided by the XAS group @ Camerino University working at the Dipartimento di Fisica . An alternative mirror site was maintained by A. Filipponi at L'Aquila University.

The executable codes are made available to users without charge provided that they are used for NO PROFIT scientific research and full acknowledgement is given to the authors.

GNXAS must NOT be used for military research, nuclear research, or any kind of classified research.

The authors decline any responsibility for erroneous results that can be obtained as a consequence of proper or improper use of the package.

The executable are presently available for the following operative systems:

    Current versions
  • Linux (32/64 bit) gnxas.unicam.it (Camerino)
  • Mac OS (32/64 bit) gnxas.unicam.it (Camerino)
  • Windows 7 (64 bit) gnxas.unicam.it (Camerino)
    Older versions
  • VMS (DEC VAX) gnxas.unicam.it (Camerino)
  • Open-VMS (DEC/Compaq alpha-VAX) gnxas.unicam.it (Camerino)
  • DEC OSF1 (DEC/Compaq alpha-VAX) gnxas.unicam.it (Camerino)
  • HP UNIX - L'Aquila, info on request, A. Filipponi
  • SUN OS - L'Aquila, info on request, A. Filipponi
  • Linux gnxas.unicam.it (Camerino) and L'Aquila (info on request, A. Filipponi)

Instructions for Linux/UNIX installation are also available.

The executables can be downloaded following our registration procedures. Downloading of Linux versions can be done using both links.


Last revised 28 July 2015 - Andrea Di Cicco

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URL: http://gnxas.unicam.it

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