Alain Michalowicz, Karine Provost, Jacques Moscovici, Diane Muller Institut de Chimie et des Materiaux Paris Est, CNRS and UPEC
MAX (Multiplatform Applications for XAFS) is a new EXAFS data analysis package inspired by and replacing the old "EXAFS pour le Mac".
The main difference is that it is no more "pour le Mac" but Multi-platform : MacOSX (Universal), Windows (XP, Vista, and 7), Linux.
MAX includes all the EXAFS data analysis functions from reading raw data files to fitting single and mulitple scattering paths models. NEW : XANES normalization, FEFF mutiple scattering paths analysis, self absorption corrections in XANES and EXAFS,...and more.
Absorbix reminds you the country origin of MAX package.
Cherokee is not only an Indian people. It is also one of the favorite tunes of Charlie Parker, the Be-Bop alto sax genius.
RoundMidnight is also a famous jazz tune, written by my favorite jazzman, the pianist and composer Thelonius Sphere Monk. If you haven't understood that my favorite music is Jazz, I probalby missed something !!!
MAX is the first name of a very important Jazzman, the drummer Max Roach who passed in 2007. His music will never.
Giving the chemical formula and stoechiometry of a sample, calculates the X-Ray absorbtion spectrum and optimize the quantity of matter (thickness, specific mass
Now includes solid and liquid mixing and solutions. Also absorbance of the reagent for reactive liquid media.
Self-Absorption corrections for EXAFS and XANES fluorescence spectra available.
1) Reads any raw data file and transform it to absorption spectrum.
2) Performs all the steps of EXAFS Data Analysis :
- - Choice of E0 - Preedge removal - Atomic background removal (3 different methods : single polynomials, cubic splines least squares fitting, splines smoothing)
- Choice of 4 EXAFS normalization modes : atomic background extrapolation, McMaster's energy dependent deltamu0, constant deltamu0, Eisenberger-Lengeler limited developpment
- - Standard k^n*chi(k) FFT with Kaiser-Bessel window
- - Fourier Filtering functions : peak filtering, experimental phase and amplitude extraction, residual background removal, average EXAFS noise estimator.
- Other tools : mutiple data files average, Monochromator calibration correction, deglitching, Fourier analysis of the background removal (amplitude systematic error estimation). Improved users interface and tools : printable and recordable (as .jpg or .txt) graphic windows, zoom for each graphic window, custom graphical options, calculation and settings browser (easier to use than menus), manual or automatic modes, recording and batch playing EXAFS calculations scripts, Online help pages.
3) Background removal and Normalization of XANES data.
Fitting program based on the standard EXAFS formula for single and multiple scattering paths, using the CERNLIB code MINUIT
Differences and improvements from previous versions :
- improved interface with feffxxx.dat phases and amplitude files
- improved parameters constrains (especcially for multishell numbers of neighbours and Debye Waller constrains from Molecular dynamics).
- improved experimental error, qualitiy of fit factor (in k and R space) and parameters uncertainties estimators. Correlation matrix available
-improved user's interface : Online help pages, including a statisics and error course based on the IXS Standard and Criteria subcommitte error report (version 2000).
-NEW : comparison and fits between experimental EXAFS and FEFF chi.dat , chipxxxx.dat : global and partial scattering paths analysis and fit.
-Now available : Batch File driven automatic multiple fits (with automated constrains) and statistics analysis.
CRYSTALFFREV : From crystal structure to FEFF input files
Similar to Bruce Ravel's ATOMS. But with many additional options :
- Contains all the International tables of Crystallography space groups. Improved space group search by alternate full and short names and lists of symetry operations. But you can also edit custom special groups
- Import/export : CIF and PDB files
- Re-orientation of the cluster (very useful for biomolecular complexes, especcially macrocycles with axial ligands)
- Partially filled (vacancies) and shared crytallographic sites => random distribution of atoms in the cluster.
- FEFF7 (for those who need only single and multiple scattering paths phases and amplitudes) and FEFF8 formats, including XANES, SCF and Full Multiple Scattering cards.
In progress : FEFF9 cards
NEW : Straight_no-Chaser
This new member of the MAX family is a linear combinaison fit program in order to decompose a mixed spectrum in its model components.
Works on normalized XANES, complete normalized absorption or EXAFS spectra.
Linear Least Squares Fit is performed by Gauss-Jordan matrix inversion or by Single Value Decomposition
Provide statistical QF, error bars and correlation matrix.
Tools to check and minimize the correlations and improve the fit accuracy.
Two very useful options :
1) Progressive linear least squares method in order to find the best composition using three criteria : Positive coefficients, Error less than x% of the value, Lowest QF. Useful when the actual number of components among the possible model compounds spectra is unknown and some of the model spectra are highly correlated.
2) Fit of a series of N spectra (N only limited by the computer memory). Useful to fit automatically spectra issued from a Quick EXAFS experiment.
Strength and Weakness
- - Easy-to-use User's interface, tested (HERCULES at SOLEIL, LNLS and Sao Carlos Institute of Physics Brazil, University of Montpellier France ) and very convenient for EXAFS schools.
- - Automatic mode, convenient for online fast data treatment.
- - Various background removal options for "difficult" and special cases (when the standard automatic method fails).
- - Complete and easy to use statistical error, parameter correlations, and QF analysis.
- - background removal systematic error analysis
- - Online tutorial
- - Same code and stricktly identical functions on all platforms
- - Absorbix now complete : dilute solid and liquid sample absorbance and fluorescence self-absorption calculations.
- - Interface with FEFF
Weakness : missing options, for the moment ( in progress ).
- - Store and compare multiple Cherokee analysis : - Perform automatic series of EXAFS extractions for Quick EXAFS data analysis
- - Multi-edges fitting
- - Disordered systems g(r) (others than cumulants and sum of Gaussians)
- - More complex and customizable parameters constrains
- - R-space fitting (but NEW : R-space QF estimator)
- - interface to other ab-initio codes
- - No Principal Component Ananlysis in Straight_No Chaser. In progress.
- - ?
- Windows, Mac OSX, Linux
Mainly Runtime Revolution Transcript, Roundmidnight's code, partly in Transcript, partly in Fortran
- free of charge. Standalones are downloadable on our webpage.
The use of source codes needs Runtime Revolution (http://www.runrev.com). They are available on demand.
http://www.icmpe.cnrs.fr(including a free downloading page)
Alain Michalowicz - University <firstname.lastname@example.org>
Alain Michalowicz - ICMPE CNRS <email@example.com>
MAX: Multiplatform Applications for XAFS Michalowicz Alain, Moscovici Jacques, Muller-Bouvet Diane and Provost Karine, Journal of Physics: Conference Series 190 (2009) 012034-012035