PAN Blend Project
Summary
xas
photons-and-neutrons EXAFS and XANES

This metapackage will install all X-ray photons-and-neutrons PAN EXAFS and XANES absorption spectroscopy packages.

Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for PAN Blend to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the PAN Blend mailing list

Links to other tasks

PAN Blend xas packages

Official Debian packages with high relevance

ifeffit
programme interactif d’analyse de XAFS
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bookworm1.2.11d-12.5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie1.2.11d-12.7amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
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IFEFFIT est un programme interactif d’analyse de XAFS. Il combine les algorithmes de haute qualité d’analyse d’AUTOBK et FEFFIT avec l’affichage graphique de données de XAFS et la manipulation générale de données.

IFEFFIT est fourni comme programme en ligne de commande, mais la fonctionnalité sous-jacente est disponible comme bibliothèque de programmation. La bibliothèque IFEFFIT peut être utilisée à partir de programme en C, Fortran, Tcl ou Perl.

pymca
applications et boite à outils pour l’analyse de fluorescence de rayons X – scripts
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PyMca est un ensemble d’applications et de bibliothèques de Python pour l’analyse de spectre de fluorescence des rayons X.

Les applications incluses dans ce paquet sont :

 – edfviewer : affichage et inspection de fichiers de données au
               format de données ESRF ;
 – elementsinfo : affichage de données de rayons X d’élément spécifique ;
 – mca2edf : conversion des fichiers MCA SPEC vers EDF ;
 – peakidentifier : affichage de pics de fluorescence X dans une gamme
                    d’énergie donnée ;
 – pymcabatch : ajustement par lot de spectre ;
 – pymcapostbatch : post-traitement des résultats d’ajustement par lot ;
 – pymca : analyse de données interactive ;
 – pymcaroitool : outil de zone d’intérêt (ROI) d’imagerie.

La boîte à outils PyMca peut lire les fichiers de données aux formats SPEC, ESRF data file (EDF), OMNIC, HDF5, AIFIRA et SupaVisio.

Il s’agit des scripts du paquet.

Screenshots of package pymca
python3-xraylarch
spectroscopie d’absorption et de fluorescence de rayons X et analyse de données de diffraction
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Larch est une bibliothèque et un ensemble d’applications pour l’analyse et le traitement de données de spectroscopie d’absorption et de fluorescence de rayons X et de données d’image de diffraction et de fluorescence d’un rayonnement synchrotron.

Larch est principalement destiné à XAFS (X-ray absorption fine-structure spectroscopy), incluant XANES (X-ray absorption near-edge spectroscopy) et EXAFS (extended X-ray absorption fine-structure spectroscopy). Il prend en charge des outils de visualisation et d’analyse pour les spectres XRF (X-ray fluorescence) et les images XRD (X-ray diffraction) comme obtenus en analysant des flux de microsonde à rayons X.

Ce paquet installe le module larch et les scripts pour Python 3 :

 – GSE MapViewer pour des données de microsonde à rayons X GSECARS ;
 – interface en ligne de commande et graphique en GTK pour Larch ;
 – visualisateur XAS pour l’analyse et le traitement XAFS ;
 – XRF Display pour l’affichage et l’analyse de spectre XRF.

L’ILC de Larch est fournie par le paquet larch_cli dans Debian.

quantum-espresso
suite Electronic-Structure et Ab-Initio Molecular Dynamics
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ESPRESSO Quantum (anciennement connu sous le nom PWscf) est une suite intégrée de codes informatiques pour les calculs de structure électronique et de modélisation de matériaux à l'échelle nanométrique. Elle est basée sur la théorie de la densité fonctionnelle, les ondes planes et les pseudopotentiels (tous conservant les normes, ultrasoft et PAW).

Please cite: P. Giannozzi, S. Baroni, N. Bonini, M. Calandra, R. Car, C. Cavazzoni, D. Ceresoli, G. L. Chiarotti, M. Cococcioni, I. Dabo, A. Dal Corso, S. Fabris, G. Fratesi, S. de Gironcoli, R. Gebauer, U. Gerstmann, C. Gougoussis, A. Kokalj, M. Lazzeri, L. Martin-Samos, N. Marzari, F. Mauri, R. Mazzarello, S. Paolini, A. Pasquarello, L. Paulatto, C. Sbraccia, S. Scandolo, G. Sclauzero, A. P. Seitsonen, A. Smogunov, P. Umari and R. M. Wentzcovitch: QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials. J. Phys. Condens. Matter 21:395502 (2009)
quantum-espresso-data-sssp
Standard solid-state pseudopotentials (SSSP) library
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The convergence pattern of each element includes for each of the considered family:

  • the total number of electrons in the valence, Z;
  • delta value (the error in the equation of state compared with all-electron WIEN2k results, developed by Cottenier group), at full converged cutoff;
  • the largest phonon frequency, ωmax, at the zone boundary (as a number), at full cutoff;
  • and then as a function of wave function cutoff:
  • the discrepancy of all phonon frequencies, δω̄, at the zone boundary, with respect to the converged value;
  • the convergence of the pressure, δVpress, with respect to the converged value;
  • the convergence of the cohesive energy, δEcoh, with respect to the converged value;
  • the convergence of the bands structure, η10 and max η10 with respect to the converged value.

Debian packages in contrib or non-free

horae
interactive graphical processing and analysis of EXAFS data
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ATHENA is an interactive graphical utility for processing EXAFS data. It handles most of the common data handling chores of interest, including deglitching, aligning, merging, background removal, and Fourier transforms.

ARTEMIS is an interactive graphical utility for fitting EXAFS data using theoretical standards from FEFF and sophisticated data modelling along with flexible data visualization and statistical analysis.

HEPHAESTUS is a souped up periodic table for the x-ray absorption spectroscopist. It provides a number of utilities involving tables of absorption coefficients and other chemical data.

libdemeter-perl
comprehensive XAS data analysis system using Feff and Ifeffit or Larch
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Demeter provides an object oriented interface to the EXAFS data analysis capabilities of the popular and powerful Ifeffit package and its successor Larch. Given that the Ifeffit and Larch APIs involve streams of text commands, this package is, at heart, a code generator. Many methods of this package return text. All actual interaction with Ifeffit or Larch is handled through a single method, dispose, which is described below. The internal structure of this package involves accumulating text in a scalar variable through successive calls to the various code generating methods. This text is then disposed to Ifeffit, to Larch, to a file, or elsewhere. The outward looking methods organize all of the complicated interactions of your data with Ifeffit or Larch.

This package is aimed at many targets. It can be the back-end of a graphical data analysis program, providing the glue between the on-screen representation of the fit and the actual command executed by Ifeffit or Larch. It can be used for one-off data analysis chores -- indeed most of the examples that come with the package can be reworked into useful one-off scripts. It can also be the back-end to sophisticated data analysis chores such as high-throughout data processing and analysis or complex physical modeling.

No known packages available

prestopronto
Software for analysis of Quick Exafs data
License: GPL3+
Debian package not available
rixs
Sorting and visualization of 1D spectra: XAS, scan positions, etc. (Detailed specifications sent to S. Bac in April 2020)
License: ?
Debian package not available

Visualization of contextual data (energy and polarization of the line, resolution, sample and spectrometer positions) Processing of CCD images to extract RIXS spectra: application of thresholds, extraction of the curvature (by Gaussian fit) necessary to sum the CCD lines after linear interpolation. Visualization of the RIXS spectra and construction of RIXS maps in two representations: Emission Energy and Energy Loss.

*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 251901