X-ray absorption spectroscopy (XAS) is a powerful method for obtaining electronic and structural information around a well-defined absorbing atom site of different types of matter, from biological systems to condensed materials in almost all possible thermodynamics conditions. The low energy part of the XAS spectrum, from the rising edge up to few hundreds eV, the so called XANES (X-ray absorption near-edge structure) region, is extremely rich of electronic and structural information, like, for example, the oxidation state, overall symmetry, interatomic distances and angles. In this paper we present in details the MXAN method and a new reengineered release of the code proposed in the literature some years ago which allows a complete fit of the XANES energy region in term of well-defined set of structural parameters. This approach is based on the comparison between experimental data and many theoretical calculations performed by varying selected structural parameters starting from a putative structure, i.e. from a well-defined initial geometrical configuration around the absorber. The X-ray photo-absorption cross sections are derived using full multiple-scattering theory, i.e. the scattering path operator is calculated exactly without any series expansion. In this way the analysis can start from the edge without any limitations in the energy range and polarization conditions. Here we present in detail the theoretical background behind the code and new capabilities implemented from theory in this last version of the program as the analysis of XANES data coming from time-dependent spectra. The code is provided with modern technology for rapid deployment of binaries based on Docker runtime so that, without source compiling, its execution reduces to just a command line striking for a full parallel (shared memory) run even using complex construct like memory filesystem in a transparent way to the end-user. Program summary: Program Title: MXAN CPC Library link to program files: https://doi.org/10.17632/4k9363vcvh.1 Licensing provisions: GPLv3 Programming language: FORTRAN90 External routines/libraries: MKL or OpenBLAS library Nature of problem: In MXAN (Minuit XANES) program we implemented a fitting procedure based on a full Multiple Scattering (MS) theory [1] able to extract local structural information around the absorbing atom from experimental XANES data. The MXAN method has been successfully used for studying many known and unknown molecular systems, yielding structural geometries and metrics comparable to X-ray diffraction and/or EXAFS results [2–4]. The release of this new code paves the route to new possibilities available now in the latest version of the program, as the analysis of XANES data coming from time-dependent and structural disordered systems. Solution method: MXAN program is based on the comparison between experimental data and iterative theoretical calculations performed by varying selected structural parameters starting from a well-defined initial geometrical configuration around the absorber. The calculation of XANES spectra is performed within the so-called full MS approach, i.e. the inverse of the scattering path operator is computed exactly, avoiding any “a-priori” selection of the relevant MS paths [5,6]. The fit procedure is performed in the energy space without the use of any Fourier transform algorithm; polarized spectra can be easily analyzed because the calculation is performed using the full MS approach [1]. The optimization in the space of the parameters is achieved using the CERN-library MINUIT [7] routines minimizing the square residual. Additional comments including restrictions and unusual features: Depending on the molecular system under study and on the operating runtime conditions the program may or may not fit into available host RAM memory. The present release of the code is limited to a single SMP machine by running in parallel using OpenMP and/or the multi-threaded version of MKL or OpenBLAS.

MXAN: A new program for ab-initio structural quantitative analysis of XANES experiments

Della Longa S.;Sanna N.
2021

Abstract

X-ray absorption spectroscopy (XAS) is a powerful method for obtaining electronic and structural information around a well-defined absorbing atom site of different types of matter, from biological systems to condensed materials in almost all possible thermodynamics conditions. The low energy part of the XAS spectrum, from the rising edge up to few hundreds eV, the so called XANES (X-ray absorption near-edge structure) region, is extremely rich of electronic and structural information, like, for example, the oxidation state, overall symmetry, interatomic distances and angles. In this paper we present in details the MXAN method and a new reengineered release of the code proposed in the literature some years ago which allows a complete fit of the XANES energy region in term of well-defined set of structural parameters. This approach is based on the comparison between experimental data and many theoretical calculations performed by varying selected structural parameters starting from a putative structure, i.e. from a well-defined initial geometrical configuration around the absorber. The X-ray photo-absorption cross sections are derived using full multiple-scattering theory, i.e. the scattering path operator is calculated exactly without any series expansion. In this way the analysis can start from the edge without any limitations in the energy range and polarization conditions. Here we present in detail the theoretical background behind the code and new capabilities implemented from theory in this last version of the program as the analysis of XANES data coming from time-dependent spectra. The code is provided with modern technology for rapid deployment of binaries based on Docker runtime so that, without source compiling, its execution reduces to just a command line striking for a full parallel (shared memory) run even using complex construct like memory filesystem in a transparent way to the end-user. Program summary: Program Title: MXAN CPC Library link to program files: https://doi.org/10.17632/4k9363vcvh.1 Licensing provisions: GPLv3 Programming language: FORTRAN90 External routines/libraries: MKL or OpenBLAS library Nature of problem: In MXAN (Minuit XANES) program we implemented a fitting procedure based on a full Multiple Scattering (MS) theory [1] able to extract local structural information around the absorbing atom from experimental XANES data. The MXAN method has been successfully used for studying many known and unknown molecular systems, yielding structural geometries and metrics comparable to X-ray diffraction and/or EXAFS results [2–4]. The release of this new code paves the route to new possibilities available now in the latest version of the program, as the analysis of XANES data coming from time-dependent and structural disordered systems. Solution method: MXAN program is based on the comparison between experimental data and iterative theoretical calculations performed by varying selected structural parameters starting from a well-defined initial geometrical configuration around the absorber. The calculation of XANES spectra is performed within the so-called full MS approach, i.e. the inverse of the scattering path operator is computed exactly, avoiding any “a-priori” selection of the relevant MS paths [5,6]. The fit procedure is performed in the energy space without the use of any Fourier transform algorithm; polarized spectra can be easily analyzed because the calculation is performed using the full MS approach [1]. The optimization in the space of the parameters is achieved using the CERN-library MINUIT [7] routines minimizing the square residual. Additional comments including restrictions and unusual features: Depending on the molecular system under study and on the operating runtime conditions the program may or may not fit into available host RAM memory. The present release of the code is limited to a single SMP machine by running in parallel using OpenMP and/or the multi-threaded version of MKL or OpenBLAS.
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11697/183178
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