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MAX: Multiplatform Applications for XAFS
This content has been downloaded from IOPscience. Please scroll down to see the full text. 2009 J. Phys.: Conf. Ser. 190 012034 (http://iopscience.iop.org/1742-6596/190/1/012034) View the table of contents for this issue, or go to the journal homepage for more
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14th International Conference on X-Ray Absorption Fine Structure (XAFS14) IOP Publishing Journal of Physics: Conference Series 190 (2009) 012034 doi:10.1088/1742-6596/190/1/012034
MAX: Multiplatform Applications for XAFS Michalowicz Alain, Moscovici Jacques, Muller-Bouvet Diane and Provost Karine Institut de Chimie et des Matériaux Paris Est (ICMPE) UMR CNRS & Université Paris 12, 2 rue H. Dunant, 94320 Thiais, France e-mail :
[email protected] Abstract. MAX is a new EXAFS and XANES analysis package, replacing our old “EXAFS pour le Mac” software suite. The major improvement is the ability to work with strictly the same code, compiled at once for Microsoft Windows, Apple MacOSX and LINUX systems, justifying the title “Multiplatform Applications for XAFS”. It is organized as four modules: ABSORBIX (X-ray absorbance and fluorescence selfabsorption calculations), CHEROKEE (EXAFS and XANES data treatment), ROUNDMIDNIGHT (EXAFS modeling and fit) and CRYSTALFFREV (from crystal structures and molecular modeling to FEFF EXAFS and XANES theoretical calculations). Most features developed in “EXAFS pour le Mac” are still available, but with much improvements in the user’s interface, data treatment algorithms and new functionalities.
1. Introduction MAX is a new EXAFS and XANES analysis package, written in order to provide totally identical XAFS data analysis functions, working with the same algorithms and codes on all computer systems commonly used, namely Microsoft Windows, Apple MacOSX and LINUX. The only difference between the three versions is the automatically adapted standard graphical interface. In order to reach this goal we have chosen an object-based software development system, RunTime Revolution with the scripting compiled language Transcript [1]. The main advantage of this development system is that we can write the code on any computer platform and get compiled standalone applications for all platforms at once. The resulting scripts are compiled, which is preferable to interpreted scripting languages. Another advantage is that each system version is a true native double-clickable application, and do not need any system emulation. MAX is organized as four modules: ABSORBIX, CHEROKEE, ROUNDMIDNIGHT and CRYSTALFFREV. Standard XAFS data analysis functions available in MAX, as in “EXAFS pour le Mac”[2] and all XAFS analysis packages listed in the software section of the xafs.org web pages [3], are briefly listed, whereas the new and original MAX features are described in more details. MAX follows all the IXS Standard and Criteria data treatment and error estimation reports recommendations [4].
c 2009 IOP Publishing Ltd
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14th International Conference on X-Ray Absorption Fine Structure (XAFS14) IOP Publishing Journal of Physics: Conference Series 190 (2009) 012034 doi:10.1088/1742-6596/190/1/012034
2. Common features All codes, either for the graphical user’s interface or for numerical algorithms are translated from “EXAFS pour le MAC“ or public Fortran sources to Runtime Revolution Transcript. The only exception is the CERN’s MINUIT function minimization Fortran code [10]. Each MAX application is organized around a principal window including all buttons and menus for the access to file management, graphics and treatment functions, and an on-line manual and tutorial. Files management and printing of texts and graphics are done with the standard file and printing windows provided in each operating system. In this way, the use of MAX applications is identical to any standard commercial software working on the same platform. Each graphical window is provided with data and figure saving and printing menus, and access to graphic and data treatments settings and functions. Most graphic windows are provided with color and plot style menus and zooms. Input and output data files are saved as text files, compatible with any system specific text processing application. They contain all the information necessary to proceed to other MAX application, import in spreadsheets and drawing applications and other XAFS data treatment and modeling codes. 3. The four MAX modules 3.1. ABSORBIX 3.1.1. ABSORBIX purpose Calculates X-ray absorbance, and optimizes samples concentrations and thickness for X-ray absorption experiments. The sample chemical composition is entered via an accessible and interactive X-ray periodic table. X-ray absorbance vs. energy calculations and plots are based on McMaster’s tables compiled in a Transcript version of Pathikrit Bandyopadhyay’s code Mucal [5]. Total absorbance can be evaluated versus the absorption jump, the sample mass/surface or thickness (if the sample density is provided). 3.1.2. ABSORBIX new features - First version could only calculate pure sample absorbance. ABSORBIX 3 calculates also the total absorbance of dilute samples. Graphical user’s interface windows are provided to edit the solid or liquid solvent and reagent chemical formulas, concentrations, densities, thickness, and the sample concentration. - Normalized fluorescence XANES or EXAFS spectra can be corrected for self-absorption systematic errors, using Haskel’s “fluo” and Booth’s formulas respectively for XANES [6] and EXAFS [7]. In ABSORBIX, the exact self-absorption formulas are solved using Brent’s numerical equation root solver algorithm [8], without any absorption length approximation. 3.2. CHEROKEE 3.2.1. CHEROKEE purpose Complete treatment of EXAFS and XANES. CHEROKEE includes the three modules separated in “EXAFS pour le Mac” [2]: “LECTURE” for reading any formatted XAFS columns data, “EXAFS” for EXAFS data processing and “GALAAD” for XANES data processing. -Edge jump determination by extrapolation of the preedge and the atomic backgrounds to E0 -Atomic background subtraction by 3 highly efficient algorithms: least squares fitting to polynomials, cubic splines least square fitting and splines smoothing [9]. An automatic optimized background removal is under development, but we underline the advantages of a manual access of different background removal options, associated with a quantitative estimation of the systematic amplitude errors by Fourier analysis, in order to allow easy switch to the most efficient algorithm.
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14th International Conference on X-Ray Absorption Fine Structure (XAFS14) IOP Publishing Journal of Physics: Conference Series 190 (2009) 012034 doi:10.1088/1742-6596/190/1/012034
-Standard energy dependent EXAFS normalization. -Fourier transform and filtering, Fourier smoothing signal/noise evaluation. Experimental or theoretical model phase and amplitude extraction. -XANES normalization by the EXAFS atomic background. Smoothed 1st and 2nd derivatives and extraction of the preedge peaks. CHEROKEE provides also many other functions, such as monochromator calibration, energy and k-spaces deglitching, switchable automatic or manual step-by-step data treatments 3.2.2. CHEROKEE new features CHEROKEE do not contain much new data analysis features yet, except a data treatment script recorder (automatic or editable manually) and player. However many numerical algorithms translated in Transcript have been largely improved by the numerical accuracy of the language. 3.3. ROUNDMIDNIGHT 3.3.1. ROUNDMIDNIGHT purpose Roundmidnight performs EXAFS modeling and fit in k-space of single and multiple scattering paths with the standard EXAFS formula, in the frame of the scattering paths expansion approximation. Fits are done by non-linear least squares refinement, based on the CERN MINUIT minimization code [10]. Phases and amplitudes are entered either by FEFF [11] files or text column format. Combined with CHEROKEE’s phase and amplitude extractor, RoundMidnight allows importing and using any phases and amplitudes from experimental models or other ab-initio codes. One can choose FEFF, or empirical mean free paths, when the FEFF ab initio mean free path is not accurate enough. - Parameters restrains and constrains: Each fitted parameter is defined by its initial guess value, initial error estimation and its limits. - Any linear combination of number of neighbors. Examples: N1+N2+N3=6, N2=2*N1, .... (new) - Debye Waller factors (new multiplier option), E0 and distances constrains (new) between shells. - Estimation of the statistical experimental noise, either by Fourier filtering of averaged spectra or by statistical estimation from several recorded spectra treated separately, with Student statistics correction for a small number of samples [12]. Compatibility of weighted fit and statistical meaning of ∆χ2 [12]. 3.3.2. ROUNDMIDNIGHT new features - Roundmidnight is organized as an easy-to-use graphical user interface (RoundMidnightRev) in front of the Fortran fitting code (RoundMidnightFit). - Possibility to fit individual or grouped scattering paths. - Tools for quality of fit estimation in restricted R-space domains. R-space fit is in progress. - Comparison and manual Debye-Waller and E0 fits of FEFF multiple scattering models (total chi.dat or selected partial sum of chipxxxx.dat) to unfiltered EXAFS spectra in k and R-spaces. - FEFF scattering paths evaluation tools. - Improved statistical treatment, error estimation, parameters correlations, and quality of fit (including F-test [13]) analysis, controlled by the user with the help of a complete tutorial based on the last Standard and Criteria Committee error report [4]. 3.4. CRYSTAFFREV 3.4.1. CRYSTAFFREV purpose From crystal structures and molecular modeling to FEFF input files [11] for EXAFS multiple scattering expansion and XANES Full Multiple Scattering (new). - Import-Export in CIF and PDB format, in order to provide a convenient interface between CRYSTALFFREV, FEFF, crystallographic and molecular modeling codes.
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14th International Conference on X-Ray Absorption Fine Structure (XAFS14) IOP Publishing Journal of Physics: Conference Series 190 (2009) 012034 doi:10.1088/1742-6596/190/1/012034
- Controlled reorientation of the cluster in order to place the central atom neighbors in desired positions (z axis, xy plane, mean plane of selected atoms (new)). 3.4.2. CRYSTAFFREV new features Compared to CRYSTALFF, the previous Fortran version [14], CRYSTALFFREV presents many extra features and is provided with a completely new interactive graphical user’s interface. - All IUCr International Tables space groups are available in a database. It is possible to import and edit external equivalent positions text files. Space groups imported from CIF files or by copy-paste from external text file can be edited, checked and compared to groups recorded in the database. - FEFF7/8 command cards, including Self Consistent Field and XANES Full Multiple Scattering. - Very useful for inorganic structures: random distributions of atoms and vacancies in the cluster for partially substituted crystal sites, according to crystal occupancy ratios. 4. Availability and services MAX is distributed by free download on the ICMPE SAX group web pages: http://www.icmpe.cnrs.fr. The downloading page includes the four applications compiled for the 3 operating systems plus a series of examples and tutorials. Users can register in a mailing list in order to be informed rapidly of the new available versions, and exchange experiences, bug reports, suggestions of new features and examples of data. 5. Conclusion Max is a new and modern improved XAFS data analysis package, in permanent evolution, written with a compiled multiplatform scripting language (Runtime Revolution’s Transcript), immediately available as native applications for MACOSX, Windows and LINUX. 6. Acknowledgements We would like to thank the MAX users who kindly accepted to suggest new options, report bugs, spent some time as beta testers and who provided XAFS data files available in the examples folder. Namely, we thank Anne Sadoc, Anne Marie Flanck, Emiliano Fonda, Christophe Denauwer, and Aymery DeMallmann. We also thank all the undergraduate students of University Paris 12 who contributed to the ABSORBIX and CRYSTALFFREV developments: Claire Charlier, El Houssine Al Waryachi, Willy Terrine, Nadhira Bennazouz, Alain Anduse and Sara Somanou. Cherokee and Roundmidnight developments were supported by a USP/COFECUB collaboration program with professor Valmor Mastelaro, Institute of Physics of Sao Carlos, Sao Paulo, Brazil. References [1] http://www.runrev.com/ [2] Michalowicz A, 1997, J.Phys. IV France 7, C2-235 [3] http://xafs.org/software/ [4] http://www.i-x-s.org/OLD/subcommittee_reports/sc/ [5] McMaster W. H. et. al. Compilation of X-ray Cross-Sections, National Bureau of Standards [6] http://www.aps.anl.gov/xfd/people/haskel/fluo.html [7] Booth C.H. and Bridges F, 2003, Lawrence Berkeley Laboratory report (LBNL-52864), pp. 1-3. [8] Brent R.P., 1973, in « Algorithms for Minimization without Derivatives », Chapter 4. PrenticeHall, Englewood Cliffs, NJ. ISBN 0-13-022335-2. [9] C. de Boor, in A Practical Guide to Splines, Springer-Verlag, 1978 [10] Minuit, CERN Program Library http://wwwasdoc.web.cern.ch/wwwasdoc/minuit/ [11] Rehr J.J. and R.C. Albers R.C., Rev. Mod. Phys. 72, 621 (2000). [12] Vlaic G,Andreatta D,Cepparo A,Colavita P.E,Fonda E,Michalowicz A,1999, J. Syn. Rad, 6, 225 [13] Michalowicz A,Provost K,Laruelle S,Mimouni A and Vlaic G,1999,J. Synchr. Rad. 6,233 [14] Provost K, Champloy F. and A. Michalowicz, 2001, J Synchr. Rad. 8, 1109-1112
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