GNXAS

Current versions: 12.2023/11.2013/12.2006

• GNXAS info and news
• Introduction to GNXAS
• Program Description
• Documentation, GNXAS 'red-book'
• Who wrote GNXAS
• Where to find GNXAS

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), Nagoya, Japan (August 2023).

Latest news and info about the programs

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). 5) Data-analysis examples Info about all the GNXAS distributions: i) 11.2013 and later 12.2024 versions (2016-) ii) 11.2013 versions (25-Jul-2015) iii) 12.2006 versions (05-Dec-2006) iv) 12.2001 versions (10-Jan-2002) v) 3.2001 and 9.00 versions (24-Mar-2001) vi) 2.99 and 8.99 versions (24-Aug-1999)

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INTRODUCTION to GNXAS

The GNXAS package is an 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.

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.
• 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'.

• a1) RMC-GNXAS (RMCXAS), this program provides Reverse Monte Carlo (RMC) refinement of XAS data using GNXAS-based calculations. Structural refinement is obtained constraining the two-dody distribution function at intermediate distances by X-ray, neutron diffraction or MD/MC computer simulations. See Phys. Rev. Letters 91, 135505 (2003) ) and J. Phys. Condens. Matter 17 S135 (2005) . The program has been written by A. Di Cicco with contributions of A. Trapananti and F. Iesari and is described in the updated GNXAS documentation (2009): the GNXAS 'red-book'.
• a2) CRYMOL_RMC (RMCXAS), this is version of the CRYMOL program specialized to provide the initial atomic configuration for the box used for RMC refinement. The program has been written by A. Di Cicco and is described in the updated GNXAS documentation (2009): the GNXAS 'red-book'.
• a3) EDXRD is a utility program able to calculate energy and angular dispersive x-ray diffraction patterns using an input file for the structure based on CRYMOL. The program has been written by A. Di Cicco and is described in the updated GNXAS documentation (2009): the GNXAS 'red-book'.
• a4) PEAKFIT is a utility program performing multiple peak-fitting refinement with different functions in presence of complex background, including Bragg peaks in x-ray diffraction . The program has been written by A. Di Cicco (using an initial version "linefit" by A. Filipponi) and is described in the updated GNXAS documentation (2009): the GNXAS 'red-book'.

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DOCUMENTATION

• Full and updated GNXAS documentation (2009): the GNXAS 'red-book'.

• Alternatively: TASK QUARTERLY Vol. 4, No 4, 575-669 (2000). (download PDF file)

• Additional documentation (Filipponi): XANES (continued fraction) program, revised May 1999 (html), Deconvolution program (DECONV) (html, 2000) pdf

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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 based on the work of C. R. Natoli (INFN - Laboratori Nazionali di Frascati), a pioneer of the multiple-scattering applications to the EXAFS spectroscopy. Natoli is the main 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 - initial conversion to gfortran and GUI interface
• F. Iesari, M. Minicucci, L. Properzi - contributions to the GUI interface
• F. Iesari - update and extension of the RMC-GNXAS program

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WHERE TO FIND GNXAS

Distribution of the code is provided by the XAS group @ Camerino University working at the Sezione di Fisica .

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:

The executables can be downloaded following our registration procedures.