Debian Science Nanoscale physics development packages

ABINIT est un paquet dont le programme principal permet de trouver l'énergie totale, la densité de charge et la structure électronique de systèmes composés d'électrons et de noyaux (molécules et solides périodiques) dans le cadre de la théorie fonctionnelle de la densité (DFT, « Density Functional Theory ») en utilisant des pseudo-potentiels et une base d'onde plane.

ABINIT inclut également des options pour optimiser la géométrie suivant les forces et stress de la DFT, pour faire des simulations de dynamique moléculaire en utilisant ces forces ou pour créer des matrices dynamiques, des charges effectives de Born et des tenseurs diélectriques. Les états excités peuvent être calculés suivant la DFT dépendante du temps (pour les molécules) ou suivant la théorie des perturbations multicorps (l'approximation GW). En plus du code principal d'ABINIT, différents utilitaires sont fournis.

Ce paquet fournit la documentation et les tutoriels.

La bibliothèque scientifique GNU (GSL, GNU Scientific Library) est une collection de routines pour l'analyse numérique. Les routines sont écrites en totalité par l'équipe GSL en C et présentent une interface de programmation (API) moderne pour les programmeurs C, tout en permettant d'écrire des adaptateurs pour des langages de très haut niveau.

Ce paquet fournit plusieurs exemples de binaires.

Page d'accueil : http://www.gnu.org/software/gsl/

Ce paquet est une mise à niveau incompatible sur le plan binaire avec le paquet blas-dev. Plusieurs modifications mineures de l'interface⋅C ont été introduites.

BLAS (Basic Linear Algebra Subroutines) est un ensemble de sous-programmes performants permettant d'effectuer la plupart des opérations de base sur les vecteurs et les matrices. Ces sous-programmes sont largement utilisés comme base par d'autres logiciels d'algèbre linéaire de haute qualité, par exemple lapack et linpack. Cette mise en œuvre est celle de référence trouvée sur netlib.org et codée en Fortran 77.

Ce paquet fournit une version statique de la bibliothèque.

CBFlib est une bibliothèque de fonctions en ANSI-C fournissant un mécanisme simple pour lire des fichiers binaires cristallographiques (CBF) et des fichiers d'images CIF (imgCIF). L'API CBFLIB est plus ou moins basée sur l'API CIFPARSE pour les fichiers mmCIF. CBFLIB ne réalise aucune vérification d'intégrité sémantique, mais fournit simplement des fonctions pour créer, lire, modifier et écrire des fichiers de données binaires CBF et des fichiers de données ASCII imgCIF.

Ce paquet fournit les bibliothèques et fichiers d'en-tête pour le développement de programme.

The CCP4 software suite is based around a library of routines which cover common tasks, such as file opening, parsing keyworded input, reading and writing of standard data formats, applying symmetry operations, etc. Programs in the suite call these routines which, as well as saving the programmer some effort, ensure that the varied programs in the suite have a similar look-and-feel.

The library contains several sub components:

• CMTZ library -- Contains a variety of functions for manipulating the data structure, for example adding crystals, datasets or columns. The data structure can be dumped to an output MTZ data file.

• CMAP library -- Functions defining the C-level API for accessing CCP4 map files.

• CSYM library -- a collection of functions centered around a data file syminfo.lib which is auto-generated from sgtbx (the Space Group Toolbox of cctbx).

• CCP4 utility library -- many utility functions which either give specific CCP4 or platform independent functionality.

• CCP4 Parser library -- provides CCP4-style parsing, as used for processing keywords of CCP4 programs, MTZ header records, etc.

• CCP4 resizable arrays -- defines an object and methods which looks just like a simple C array, but can be resized at will without incurring excessive overheads.

Wrappers for C functions, allowing usage of try ... catch ... blocks in C language. Wrapped functions include memory allocation, standard I/O and strdup.

This package contains static library and header files.

The aim of the clipper project is to produce a set of object-oriented libraries for the organisation of crystallographic data and the performance of crystallographic computation.

This package contains development environment for programs which will use the clipper libraries.

COD::Precision, module for handling precision in Crystallographic Information Format (CIF) notation, expressed as standard uncertainties in parentheses next to the value.

ETSF_IO is a library of F90 routines to read/write the ETSF file format.

This package contains the static libraries provided by ETSF_IO to let electronic structure codes read and write ETSF files. It also contains the module file used by the Fortran compiler.

ETSF_IO is a library of F90 routines to read/write the ETSF file format.

This Package contains the HTML documentation of the API and some tutorials on how to use the library in electronic structure codes.

La bibliothèque FFTW calcule les transformées de Fourier rapides (FFT) en une ou plusieurs dimensions. Elle est très rapide. Ce paquet fournit la bibliothèque statique liée, les fichiers d'en-tête et les programmes de test.

Ce paquet fournit les fichiers d'en-tête et les bibliothèques statiques. Pour la documentation, consultez libfftw3-doc.

The GNU Scientific Library (GSL) is a collection of routines for numerical analysis. The routines are written from scratch by the GSL team in C, and present a modern API for C programmers, while allowing wrappers to be written for very high level languages.

This package contains the header files, static libraries and symbolic links that developers using GNU GSL will need.

Hierarchical Data Format 5 (HDF5) is a file format and library for storing scientific data. HDF5 was designed and implemented to address the deficiencies of HDF4.x. It has a more powerful and flexible data model, supports files larger than 2 GB, and supports parallel I/O.

This package contains development files for serial platforms.

LAPACK version⋅3.x est une bibliothèque FORTRAN complète qui effectue des opérations d'algèbre linéaire, y compris l'inversion de matrice, la résolution de la méthode des moindres carrés d'ensembles linéaires d'équations, l'analyse de valeurs propres, la décomposition en valeurs singulières, etc. Ce paquet très complet et reconnu est intensivement utilisé dans la communauté scientifique.

Ce paquet fournit une version statique de la bibliothèque.

LAPACK version⋅3.x est une bibliothèque FORTRAN complète qui effectue des opérations d'algèbre linéaire, y compris l'inversion de matrice, la résolution de la méthode des moindres carrés d'ensembles linéaires d'équations, l'analyse de valeurs propres, la décomposition en valeurs singulières, etc. Ce paquet très complet et reconnu est intensivement utilisé dans la communauté scientifique.

Ce paquet fournit⋅:

 –⋅les pages de manuel des routines BLAS et LAPACK⋅;
 –⋅le guide de l'utilisateur de Lapack (en HTML)⋅;
 –⋅le manuel de l'interface LAPACKE⋅C vers LAPACK (en PDF).

MPICH is a high-performance and widely portable implementation of the MPI-3.1 standard from the Argonne National Laboratory. It efficiently supports different computation and communication platforms including commodity clusters, SMPs, massively parallel systems, and high-speed networks. This release has all MPI 3.1 functions and features required by the standard with the exception of support for the "external32" portable I/O format and user-defined data representations for I/O.

This package includes the MPICH headers and static libraries, as well as the compiler wrappers needed to build MPICH programs.

NetCDF (network Common Data Form) is a set of interfaces for array-oriented data access and a freely distributed collection of data access libraries for C, Fortran, C++, Java, and other languages. The netCDF libraries support a machine-independent format for representing scientific data. Together, the interfaces, libraries, and format support the creation, access, and sharing of scientific data.

This package provides headers.

OpenCASCADE is a suite for 3D surface and solid modeling, visualization, data exchange and rapid application development. It is an excellent platform for development of numerical simulation software including CAD/CAM/CAE, AEC and GIS, as well as PDM applications.

This package contains the headers and symlinks for libraries shipped by liboce-ocaf11.

OpenCASCADE is a suite for 3D surface and solid modeling, visualization, data exchange and rapid application development. It is an excellent platform for development of numerical simulation software including CAD/CAM/CAE, AEC and GIS, as well as PDM applications.

This package contains the headers and symlinks for libraries shipped by liboce-visualization11.

Open MPI is a project combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-3 compliant implementation, Open MPI offers advantages for system and software vendors, application developers and computer science researchers.

This package contains the header files and compiler wrappers which are needed to compile and link programs against libopenmpi.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains development files of the mlp plug-in for ROOT, provides a Multi Layer Perceptron Neural Network package for ROOT.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains development files of the Vmc library for ROOT.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

The Toolkit for Multivariate Analysis (TMVA) provides a ROOT-integrated environment for the parallel processing and evaluation of MVA techniques to discriminate signal from background samples. It presently includes (ranked by complexity):

• Rectangular cut optimisation
• Correlated likelihood estimator (PDE approach)
• Multi-dimensional likelihood estimator (PDE - range-search approach)
• Fisher (and Mahalanobis) discriminant
• H-Matrix (chi-squared) estimator
• Artificial Neural Network (two different implementations)
• Boosted Decision Trees

The TMVA package includes an implementation for each of these discrimination techniques, their training and testing (performance evaluation). In addition all these methods can be tested in parallel, and hence their performance on a particular data set may easily be compared.

This package provides development files of TMVA package for ROOT.

ScaLAPACK is the parallel version of LAPACK used on clusters.

There are packages for the shared libraries, for the static libraries and the development files (this one) and for test programs.

Also included:

• PBLAS, Parallel Basic Linear Algebra Subprograms
• BLACS, Basic Linear Algebra Communication Subprograms

This is a dummy package which depends on the scalapack development package supporting the default implementation of MPI on this architecture.

JHDF5 is a Java binding to the HDF Group library for HDF5 focusing on ease-of-use, which was developed by CISD and is now maintained by ETH SIS. The library uses HDF5 1.8 from the HDF Group and files created with JHDF5 are fully compatible with HDF5 1.6/1.8 (as you choose).

SSM is a macromolecular coordinate superposition library, written by Eugene Krissinel of the EBI.

The library implements the SSM algorithm of protein structure comparison in three dimensions, which includes an original procedure of matching graphs built on the protein's secondary-structure elements, followed by an iterative three-dimensional alignment of protein backbone Calpha atoms.

This package contains libraries and header files needed for program development.

Spglib is a C library for crystal symmetry determination. Symmetry operations, space groups and other data can be obtained using this symmetry finder.

Features include:

• Identify space-group type
• Find symmetry operations
• Find a primitive cell
• Search irreducible k-points
• Refine crystal structure
• Wyckoff position assignment

This package contains static library and header files.

LibXC is a library of exchange-correlation (XC) functionals for density-functional theory (DFT). The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals that can be used by other codes.

This package contains the static library, the C headers and the Fortran modules necessary for developers.

NetCDF (network Common Data Form) is an interface for scientific data access and a freely-distributed software library that provides an implementation of the interface. The netCDF library also defines a machine-independent format for representing scientific data. Together, the interface, library, and format support the creation, access, and sharing of scientific data.

This package contains documentation for the NetCDF library in a variety of formats.

PyFAI is a Python library for azimuthal integration; it allows the conversion of diffraction images taken with 2D detectors like CCD cameras into X-Ray powder patterns that can be used by other software like Rietveld refinement tools (i.e. FullProf), phase analysis or texture analysis.

As PyFAI is a library, its main goal is to be integrated in other tools like PyMca, LiMa or EDNA. To perform online data analysis, the precise description of the experimental setup has to be known. This is the reason why PyFAI includes geometry optimization code working on "powder rings" of reference samples. Alternatively, PyFAI can also import geometries fitted with other tools like Fit2D.

PyFAI has been designed to work with any kind of detector with any geometry (transmission, reflection, off-axis, ...). It uses the Python library FabIO to read most images taken by diffractometer.

BINoculars is a tool for data reduction and analysis of large sets of surface diffraction data that have been acquired with a two-dimensional X-ray detector. The intensity of each pixel of a two-dimensional detector is projected onto a three-dimensional grid in reciprocal-lattice coordinates using a binning algorithm. This allows for fast acquisition and processing of high-resolution data sets and results in a significant reduction of the size of the data set. The subsequent analysis then proceeds in reciprocal space. It has evolved from the specific needs of the ID03 beamline at the ESRF, but it has a modular design and can be easily adjusted and extended to work with data from other beamlines or from other measurement techniques.

This is the Python 3 version of the package.

FabIO est une bibliothèque d’E/S pour les images produites par des détecteurs de rayons X en 2D et écrite en Python. FabIO prend en charge les détecteurs d'image issus d'une douzaine d'entreprises (notamment Mar, Dectris, ADSC, Hamamatsu, Oxford…), soit un total de 20 formats de fichier différents (comme CBF, EDF, TIFF…), et il offre une interface uniforme pour leurs entêtes (comme un dictionnaire Python) et leurs jeux de données (comme une structure ndarray d'entiers ou de flottants de NumPy).

Il s'agit de la version Python⋅3 du paquet.

This python wrapper is designed to tightly integrate with PyOpenCL. It consists of a low-level Cython based wrapper with an interface similar to the underlying C library. On top of that it offers a high-level interface designed to work on data contained in instances of pyopencl.array.Array, a numpy work-alike array class for GPU computations. The high-level interface takes some inspiration from pyFFTW. For details of the high-level interface see fft.py.

This package installs the library for Python 3.

This package provides a periodic table of the elements with support for mass, density and xray/neutron scattering information.

Masses, densities and natural abundances come from the NIST Physics Laboratory, but do not represent a critical evaluation by NIST scientists.

Neutron scattering calculations use values collected by the Atomic Institute of the Austrian Universities. These values do corresponding to those from other packages, though there are some differences depending to the tables used. Bound coherent neutron scattering for gold in particular is significantly different from older value: 7.63(6) as measured in 1974 compared to 7.90(7) as measured in 1990.

X-ray scattering calculations use a combination of empirical and theoretical values from the LBL Center for X-ray Optics. These values differ from those given in other sources such as the International Tables for Crystallography, Volume C, and so may give different results from other packages.

This package installs the library for Python 3.

Python bindings for Crystallographic Information Format (CIF) v1.1 and v2.0 parser, which is written in C language, and developed by the Crystallography Open Database. A CIF format file is represented by a list of data blocks, where each data block is represented by a dictionary.

This package installs the library for Python 3.

sasmodels is a Python module for calculating theoretical Small Angle Scattering patterns. The models provided are usable directly in the bumps fitting package and in the sasview analysis package.

This package contains the Python 3 version of the module.

This package provides an R interface to Unidata's NetCDF library functions. NetCDF (network Common Data Form) is a set of interfaces for array-oriented data access. In addition to the interface to the NetCDF library functions, R interfaces are provided to access Unidata's UDUNITS calendar conversions.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

With the data defined as a set of objects, specialized storage methods can give direct access to the separate attributes of the selected objects, without having to touch the bulk of the data. Included are histogramming methods in 1, 2 and 3 dimensions, curve fitting, function evaluation, minimization, graphics and visualization classes to allow the easy creation of an analysis system that can query and process the data interactively or in batch mode.

The command language, the scripting (or macro) language, and the programming language are all C++, thanks to the built-in CINT C++ interpreter. This interpreter removes the time consuming compile/link cycle, allowing for fast prototyping of the macros, and providing a good environment to learn C++. If more performance is needed, the interactively developed macros can be compiled using a C++ compiler.

The system has been designed in such a way that it can query its databases in parallel on MPP machines or on clusters of workstations or high-end PCs. ROOT is an open system that can be dynamically extended by linking external libraries. This makes ROOT a premier platform on which to build data acquisition, simulation and data analysis systems.

This package is a metapackage to ensure the installation of all possible ROOT packages on a system.

ScaLAPACK is the parallel version of LAPACK. It depends on PVM or MPI.

This package provides the man pages for the routines in the ScaLAPACK library (see package scalapack1-pvm, scalapack1-mpich or scalapack1-lam) and a quick reference for PBLAS and ScaLAPACK. PBLAS is the library for Parallel Basic Linear Algebra Subprograms included in ScaLAPACK.

Also included: ScaLAPACK Users' Guide (SLUG) and the FAQ on ScaLAPACK.

This metapackage will install Debian Science packages which might be helpful for development of applications for Mathematics.

You might also be interested in the science-mathematics metapackage.

Provides the header files and static libraries.

Feel++ is a versatile finite element library to solve partial differential equations.

Support 1D, 2D, 3D

Support the following basic entities: simplices (segment, triangle, tetrahedron) and product of simplices (quadrangle, hexahedron)

Support various point sets on these basic entities: equispaced points, quadrature points, interpolation points (Gauss-Lobatto, Fekete, WarpBlend?)

Support continuous and discontinuous Galerkin methods

Support various polynomial sets:

• Lagrange(continuous,discontinuous,all dimensions,all interpolation point sets)

• Dubiner(discontinuous), boundary adapted(continuous)

• Legendre(discontinuous), boundary adapted(continuous)

Provide mathematical concept for higher order abstraction (Function spaces and associated elements, forms and operators)

Provide a language embedded in C++ for variational formulations, projection and numerical integration

La bibliothèque FFTW calcule les transformées de Fourier rapides (FFT) en une ou plusieurs dimensions. Elle est très rapide. Ce paquet fournit la documentation pour la bibliothèque fftw3.

OpenCASCADE is a suite for 3D surface and solid modeling, visualization, data exchange and rapid application development. It is an excellent platform for development of numerical simulation software including CAD/CAM/CAE, AEC and GIS, as well as PDM applications.

This package is based on OCE, OpenCASCADE Community Edition, which is maintained by a community of developers, and not by OpenCASCADE SAS.

This package contains the DRAW test harness.

HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.

From a Python programmer's perspective, HDF5 provides a robust way to store data, organized by name in a tree-like fashion. You can create datasets (arrays on disk) hundreds of gigabytes in size, and perform random-access I/O on desired sections. Datasets are organized in a filesystem-like hierarchy using containers called "groups", and accessed using the tradional POSIX /path/to/resource syntax.

H5py provides a simple, robust read/write interface to HDF5 data from Python. Existing Python and Numpy concepts are used for the interface; for example, datasets on disk are represented by a proxy class that supports slicing, and has dtype and shape attributes. HDF5 groups are presented using a dictionary metaphor, indexed by name.

This is a dummy package which depends on the serial or MPI build of h5py.

La version 4 de NetCDF possède de nombreuses fonctions non trouvées dans les précédentes versions de la bibliothèque et est implémentée au-dessus de HDF5. Ce module peut lire et écrire à la fois dans le nouveau format netCDF 4 et dans l’ancien netCDF 3, et il peut créer des fichiers lisibles par les clients HDF5. L’interface de programmation applicative est conçue selon le modèle de Scientific.IO.NetCDF, et devrait être familière aux utilisateurs de ce module.

La plupart des nouvelles fonctions de netCDF 4 sont mises en œuvre, telles que plusieurs dimensions illimitées, les groupes et la compression zlib des données. Tous les nouveaux types numériques de données (tels que les types d’entier 64 bits et non signé) sont implémentés. Les types de données composite et à longueur variable (vlen) sont gérés, mais les types de données énumération et opaque ne sont pas gérés. Les mélanges de types composite et vlen (types composite contenant des types vlen et inversement) ne sont pas gérés.

Ce paquet fournit le module netCDF 4 pour Python 3.

This package provides info files with the reference manual for the GNU Scientific Library (GSL), a collection of routines for numerical analysis.

The reference manual is also available in postscript and html formats in the packages gsl-ref-psdoc and gsl-ref-html, respectively.

This package provides a pdf file with the reference manual for the GNU Scientific Library (GSL), a collection of routines for numerical analysis.

The reference manual is also available in postscript and html formats in the packages gsl-ref-psdoc and gsl-ref-html, respectively.

This package provides html files with the reference manual for the GNU Scientific Library (GSL), a collection of routines for numerical analysis.

This package provides a ps file with the reference manual for the GNU Scientific Library (GSL), a collection of routines for numerical analysis.

This package is a binary incompatible upgrade to the blas-dev package. Several minor changes to the C interface have been incorporated.

BLAS (Basic Linear Algebra Subroutines) is a set of efficient routines for most of the basic vector and matrix operations. They are widely used as the basis for other high quality linear algebra software, for example lapack and linpack. This implementation is the Fortran 77 reference implementation found at netlib.

This implementation of the library belongs to the CLAPACK distribution.

This package contains a static version of the library.

Pseudopotentials consist in atomic data used for atomic-scale electronic structure calculations. Libpspio is a library to read and write pseudopotentials in various formats, allowing as well for conversion in some cases.

Wannier90 is an electronic-structure software computing maximally-localized Wannier functions (MLWF). It works on top of other electronic-structure software, such as Abinit, FLEUR, and PwSCF.

This package contains the development files needed to interface other software with Wannier90.