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GNXAS
Current versions: 11.2013/12.2006
Info and News
Latest GNXAS intensive courses: Camerino, Italy (2009),
Melbourne, Australia (2011), Riberao Preto, Brasil (2013), Karlsruhe, Germany (Aug 2015), Rennes, France (June 2016), Krakow, Poland (August 2018).
Latest news about the
programs
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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.
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.
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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.
- 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.
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Flow chart of the various programs composing the package.
CLICK on the flow chart to obtain more information about the programs.
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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.
- 14a,b) JESF, an automatic routine for EXAFS extraction, Fourier
transformation, and noise evaluation. This program is useful for
a qualitative data-analysis and was 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)! 14b) NEWJESF is the new version of the program producing
useful graphical outputs for gnuplot and Topdrawer.
- 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
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WHO WROTE GNXAS
Several scientists have contributed to the development of GNXAS
since 1989. 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 programs and algorithms,
like RMC-GNXAS, EDXRD (Di Cicco), and DECONV, XASAM (Filipponi) have been
developed separately 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, in chronological
order:
- 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
- P. D'Angelo - Application to liquid solutions
- A. Witkowska - Application to functional materials
- A. Trapananti - Contribution to developments of RMC-GNXAS
- M. Minicucci - Contribution to advanced Linux installations and related software maintainance
- E. Principi - GNXAS web interface (GNXAS2)
- K. Hatada - conversion to gfortran and GUI interface
- F. Iesari, M. Minicucci, L. Properzi - contributions to the GUI interface
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WHERE TO FIND GNXAS
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 (available upon request, please contact K. Hatada)
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.
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