Debian Science Simulations packages

CalculiX est une application d'analyse d'éléments finis libre qui utilise un format d'entrée similaire à celui d'Abaqus. Il a un solveur implicite et explicite, un préprocesseur et un postprocesseur (CGX). Ce paquet fournit le solveur CalculiX CrunchiX (cxx).

CalculiX GraphiX (cgx) est un pré et postprocesseur tridimensionnel pour les éléments finis. Des modèles à éléments finis de CalculiX CrunchiX peuvent être compilés, calculés et post-traités. Le pré et postprocesseur est un outil 3D interactif utilisant l'API openGL.

En plus des fichiers de résultats de CalculiX CrunchiX, les résultats d'OpenFoam, Duns (2D et 3D), Isaac (2D et 3D) et Nastran (f06) peuvent être lus. Pour prétraiter le format natif Netgen, STEP et STL peuvent être importés.

ESyS-Particle is Open Source software for particle-based numerical modelling. The software implements the Discrete Element Method (DEM), a widely used technique for modelling processes involving large deformations, granular flow and/or fragmentation. ESyS-Particle is designed for execution on parallel supercomputers, clusters or multi-core PCs running a Linux-based operating system. The C++ simulation engine implements spatial domain decomposition via the Message Passing Interface (MPI). A Python wrapper API provides flexibility in the design of numerical models, specification of modelling parameters and contact logic, and analysis of simulation data. ESyS-Particle has been utilised to simulate earthquake nucleation, comminution in shear cells, silo flow, rock fragmentation, and fault gouge evolution, to name but a few applications.

Gazebo est un simulateur de plusieurs robots pour des environnements de plein air. Comme Stage (faisant partie de Player Project), il peut simuler une population de robots, capteurs et objets, mais le fait dans un monde à trois dimensions. Il génère à la fois des retours réalistes de capteur et des interactions physiques plausibles entre objets (il intègre une simulation précise des propriétés physiques de solide rigide).

Ce paquet fournit les exécutables principaux de l’application.

GetDP est un solveur général d’éléments finis utilisant des éléments mélangés pour rendre discrets des complexes différentiels de type De Rham en une, deux ou trois dimensions.

La principale caractéristique de GetDP est la proximité entre les données d’entrée définissant les problèmes d’éléments finis (écrites par l’utilisateur dans des fichiers de données en ASCII) et les expressions mathématiques symboliques de ces problèmes.

Consulter le manuel de référence de GetDP pour un aperçu plus approfondi des possibilités de GetDP : http://www.geuz.org/getdp

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

Ceres Solver est une bibliothèque libre en C++ pour modéliser et résoudre des problèmes d'optimisation de grande taille et complexes. Il s'agit d'une bibliothèque riche en fonctionnalités, mûre et performante qui est utilisée en production par Google depuis 2010.

Ceres Solver peut résoudre deux types de problèmes :

 — les problèmes de moindres carrés non linéaires avec contraintes de
   bornes ;
 — les problèmes d'optimisation génériques sans contrainte.

Ce paquet fournit les en-têtes de développement.

DART is a collaborative, cross-platform, open source library created by the Georgia Tech Graphics Lab and Humanoid Robotics Lab. The library provides data structures and algorithms for kinematic and dynamic applications in robotics and computer animation. DART is distinguished by it's accuracy and stability due to its use of generalized coordinates to represent articulated rigid body systems and computation of Lagrange's equations derived from D.Alembert's principle to describe the dynamics of motion. For developers, in contrast to many popular physics engines which view the simulator as a black box, DART gives full access to internal kinematic and dynamic quantities, such as the mass matrix, Coriolis and centrifugal forces, transformation matrices and their derivatives. DART also provides efficient computation of Jacobian matrices for arbitrary body points and coordinate frames. Contact and collision are handled using an implicit time-stepping, velocity-based LCP (linear-complementarity problem) to guarantee non-penetration, directional friction, and approximated Coulomb friction cone conditions. For collision detection, DART uses FCL developed by Willow Garage and the UNC Gamma Lab. DART has applications in robotics and computer animation because it features a multibody dynamic simulator and tools for control and motion planning. Multibody dynamic simulation in DART is an extension of RTQL8, an open source software created by the Georgia Tech Graphics Lab.

This package contains main headers and other tools for development.

The KIM API is an Application Programming Interface for atomistic simulations. The API provides a standard for exchanging information between atomistic simulation codes (molecular dynamics, molecular statics, lattice dynamics, Monte Carlo, etc.) and interatomic models (potentials or force fields). It also includes a set of library routines for using the API with bindings for:

FORTRAN 77, Fortran 90/95, Fortran 2003 C, C++

Atomistic simulation codes that support the KIM API work seamlessly with the KIM-compliant interatomic models (KIM Models) distributed on this website. The interface is computationally efficient and often requires relatively minor changes to existing codes.

This package contains models and model-drivers for KIM-API

The Open Porous Media (OPM) software suite provides libraries and tools for modeling and simulation of porous media processes, especially for simulating CO2 sequestration and improved and enhanced oil recovery.

The Eclipse file format is widely used in the reservoir simulation community. This package provides utility programs to process files in this format, like for comparing two files, converting between binary version and formatted text file format, etc.

The Open Porous Media (OPM) software suite provides libraries and tools for modeling and simulation of porous media processes, especially for simulating CO2 sequestration and improved and enhanced oil recovery.

opm-grid provides implementations of grids for reservoir simulation, corner point or more general pillar grids, following the DUNE grid interface: CpGrid, a parallel corner point grid, and PolyhedralGrid a more general serial grid implementation of an unstructured, legacy, grid.

A standard grid type in the petroleum industry, corner-point grids fills the domain with a relatively low number of cells while still providing sufficient flexibility to model faults, fractures and erosion. The grid format was originally designed with an eye towards geological modeling rather than numerical simulation, but is still suitable for e.g. low order finite volume discretizations.

This package provides programs to mirror corner point grids specified in Eclipse file format and convert the corner point grid representation of an Eclipse together with permeability/porosity to file suitable for visualization with Paraview.

The Open Porous Media (OPM) software suite provides libraries and tools for modeling and simulation of porous media processes, especially for simulating CO2 sequestration and improved and enhanced oil recovery.

opm-simulators provides a research (ebos) and a production (flow) fully implicit black-oil simulators, supporting one to three phases and supporting solvent and polymer options. It uses cell centered finite volume schemes with two point flux approximation and automatic differentiation for the discretization and uses state of the art linear and nonlinear solvers. It supports standard and multi segment well models and reading and writing file in Eclipse format, a defacto industry standard in the oil reservoir simulation community.

Package provides the simulation programs.

The Open Porous Media (OPM) software suite provides libraries and tools for modeling and simulation of porous media processes, especially for simulating CO2 sequestration and improved and enhanced oil recovery.

opm-upscaling provides tools for single phase and relative permeability upscaling. During upscaling effective parameters (like porosity, permeability, and capillary pressure) for a simulation on a coarser scale are computed from properties of a simulation on a fine scale.

Package provides the upscaling applications.

LIGGGHTS stands for LAMMPS improved for general granular and granular heat transfer simulations.

LAMMPS is a classical molecular dynamics simulator. It is widely used in the field of Molecular Dynamics. Thanks to physical and algorithmic analogies, LAMMPS is a very good platform for DEM simulations. LAMMPS offers a GRANULAR package to perform these kind of simulations. LIGGGHTS aims to improve those capability with the goal to apply it to industrial applications. Development version.

mbpoll uses libmodbus (http://libmodbus.org/). Although the syntax of these options is very close modpoll proconX program, it is a completely independent project.

mbpoll can:

• read discrete inputs
• read and write binary outputs (coil)
• read input registers
• read and write output registers (holding register)

The reading and writing registers may be in decimal, hexadecimal or floating single precision.

MUSIC allows spike events and continuous time series to be communicated between parallel applications within the same MPI job in a cluster computer. Typical usage cases are connecting models developed for different simulators and connecting a parallel simulator to a post-processing tool.

This package contains the MUSIC launch utility.

NEURON est un environnement de simulation pour modéliser des neurones individuels et des réseaux de neurones. Il fournit des outils pour construire, gérer et utiliser commodément des modèles, d'une manière qui ressemble à des nombres et qui soit efficace du point de vue du calcul. C'est particulièrement adapté pour des problèmes fortement liés à des données expérimentales, en particulier ceux impliquant des cellules aux propriétés anatomiques et biophysiques complexes.

NEURON offre

 –⋅une « syntaxe naturelle », qui permet de spécifier les
   propriétés d'un modèle dans des langages courants ;
 –⋅une discrétisation spatiale et temporelle efficace et facile ;
 –⋅plusieurs méthodes d'intégration numérique au choix de
   l'utilisateur ;
 –⋅une interface utilisateur commode (interpréteur et
   interface graphique) ;
 –⋅une bibliothèque, extensible par l'utilisateur, de mécanismes
   biophysiques.

Open CASCADE Technology 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.

Draw is a command interpreter based on Tcl and a graphical system used to test and demonstrate Open CASCADE Technology modeling libraries.

Open CASCADE Technology est une suite de modélisation de solide et de surface en 3D, de visualisation, d’échange de données et développement rapide d’applications. C’est une plateforme performante de développement de logiciels de simulation numérique incluant CAD/CAM/CAE, AEC et GIS, ainsi que des applications PDM.

Ce paquet fournit les fichiers de ressources.

OpenFOAM is the free, open source CFD software released and developed primarily by OpenCFD Ltd since 2004. It has a large user base across most areas of engineering and science, from both commercial and academic organisations. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics.

Package contains binaries.

It is implemented in Python and the performance critical parts are implemented in Cython.

PySPH is implemented in a way that allows a user to specify the entire SPH simulation in pure Python. High-performance code is generated from this high-level Python code, compiled on the fly and executed. PySPH also features optional automatic parallelization using mpi4py and Zoltan.

The package contains viewer for PySPH.

DEAP is a novel evolutionary computation framework for rapid prototyping and testing of ideas. It seeks to make algorithms explicit and data structures transparent. It works in perfect harmony with parallelisation mechanism such as multiprocessing and SCOOP.

This package contains the modules for Python3.

Escript is a programming tool for implementing mathematical models in Python using the finite element method (FEM). Because users do not access the data structures it is very easy to use and scripts can run on desktop computers as well as highly parallel supercomputer without changes. Application areas for escript include earth mantle convection, geophysical inversion, earthquakes, porous media flow, reactive transport, plate subduction, erosion, and tsunamis.

Scripts can be executed in parallel (on varying numbers of threads or nodes) without any special modifications.

Escript now includes the esys.downunder module for 3D inversion of geophysical data sets. The current version supports gravity, magnetic and joint inversion.

This package contains the commands and libraries for Python3 with OpenMP threading and MPI multiprocess support.

Escript is a programming tool for implementing mathematical models in Python using the finite element method (FEM). Because users do not access the data structures it is very easy to use and scripts can run on desktop computers as well as highly parallel supercomputer without changes. Application areas for escript include earth mantle convection, geophysical inversion, earthquakes, porous media flow, reactive transport, plate subduction, erosion, and tsunamis.

Scripts can be executed in parallel (on varying numbers of threads or nodes) without any special modifications.

Escript now includes the esys.downunder module for 3D inversion of geophysical data sets. The current version supports gravity, magnetic and joint inversion.

This package contains the commands and libraries for Python3 with both OpenMP threading and MPI multiprocess support.

Ce cadriciel est implémenté en Python et les parties critiques pour la performance sont implémentées en Cython.

PySPH est implémenté d'une telle façon que l'utilisateur puisse spécifier l'entièreté de la simulation SPH en pur Python. Le code de haute performance est généré à partir de ce code Python de haut niveau, compilé à la volée et exécuté. PySPH fournit aussi facultativement la parallélisation automatique à l'aide de mpi4py et Zoltan.

QuTiP est logiciel au code source ouvert pour simuler des systèmes quantiques ouverts. La bibliothèque QuTiP dépend des paquets de calcul excellents Numpy, Scipy et Cython. De plus, une sortie graphique est fournie par Matplotlib. QuTiP vise à fournir des simulations numériques efficaces et conviviales d’une grande diversité d’hamiltoniens, incluant ceux avec une dépendance temporelle arbitraire couramment trouvés dans une large tranche d’applications physiques, telles que l’optique quantique, les pièges à ions, les circuits supraconducteurs et les résonateurs quantiques nanométriques.

Ce paquet installe la bibliothèque pour Python 3.

SfePy est un logiciel pour résoudre des systèmes d’équations aux dérivées partielles couplées (EDP) par la méthode des éléments finis en 1D, 2D et 3D. Il peut être vu comme une boite noire de solveur d’EDP ou comme un paquet de Python pouvant être utilisé pour construire des applications personnelles. Le mot « simple » signifie que les problèmes de MEF peuvent être codés très facilement et rapidement.

Siconos is an open-source scientific software primarily targeted at modeling and simulating nonsmooth dynamical systems in C++ and in Python:

• Mechanical systems (rigid or solid) with unilateral contact and Coulomb friction and impact (nonsmooth mechanics, contact dynamics, multibody systems dynamics or granular materials).
• Switched Electrical Circuit such as electrical circuits with ideal and piecewise linear components: power converter, rectifier, Phase-Locked Loop (PLL) or Analog-to-Digital converter.
• Sliding mode control systems.
• Biology (Gene regulatory network). Other applications are found in Systems and Control (hybrid systems, differential inclusions, optimal control with state constraints), Optimization (Complementarity systems and Variational inequalities), Fluid Mechanics, and Computer Graphics.

This package contains the 'siconos' tool allowing to compile and run Siconos programs/scripts in a single command.

Siconos is an open-source scientific software primarily targeted at modeling and simulating nonsmooth dynamical systems in C++ and in Python:

• Mechanical systems (rigid or solid) with unilateral contact and Coulomb friction and impact (nonsmooth mechanics, contact dynamics, multibody systems dynamics or granular materials).
• Switched Electrical Circuit such as electrical circuits with ideal and piecewise linear components: power converter, rectifier, Phase-Locked Loop (PLL) or Analog-to-Digital converter.
• Sliding mode control systems.
• Biology (Gene regulatory network). Other applications are found in Systems and Control (hybrid systems, differential inclusions, optimal control with state constraints), Optimization (Complementarity systems and Variational inequalities), Fluid Mechanics, and Computer Graphics.

This package contains tools to allow running, analysing, manipulating, exporting, and viewing the output of mechanical simulations.

SUMO is an open source, highly portable, microscopic road traffic simulation package designed to handle large road networks. Main binary.

TkGate is a digital circuit editor and simulator with a Tcl/Tk based interface. TkGate includes a large number of built-in devices including basic gates, memories, ttys and modules for hierarchical design. The simulator can be controlled either interactively or through a simulation script. Memory contents can be loaded from files, and a microcode/macrocode compiler (gmac) is included to create tkgate memory files from a high-level description. The simulator supports continuous simulation, single step simulation (by clock or epoch) and breakpoints. Save files are in a Verilog-like format.

TkGate also includes a number of tutorial and example circuits which can be loaded through the "Help" menu. The examples range from a simple gate-level 3-bit adder to a 16-bit CPU programmed to play the "Animals" game.

TkGate has a multi-language interface with support for English, Japanese, French and Spanish.

Yet Another Dynamic Engine.

Extensible open-source framework for discrete numerical models, focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, allowing independent implementation of new algorithms and interfaces. Python is used for rapid and concise scene construction, simulation control, postprocessing and debugging.

This package contains speed-optimized build of yade.

CalculiX est une application d'analyse d'éléments finis libre qui utilise un format d'entrée similaire à celui d'Abaqus. Il a un solveur implicite et explicite, un préprocesseur et un postprocesseur (CGX).

Ce paquet fournit la documentation au format HTML pour CalculiX CrunchiX.

CalculiX est une application d'analyse d'éléments finis libre qui utilise un format d'entrée similaire à celui d'Abaqus. Il a un solveur implicite et explicite, un préprocesseur et un postprocesseur (CGX).

Ce paquet fournit les fichiers d'exemple pour CalculiX CrunchiX.

CalculiX GraphiX (cgx) est un pré et postprocesseur tridimensionnel pour les éléments finis. Des modèles à éléments finis de CalculiX CrunchiX peuvent être compilés, calculés et post-traités. Le pré et postprocesseur est un outil 3D interactif utilisant l'API openGL.

En plus des fichiers de résultats de CalculiX CrunchiX, les résultats d'OpenFoam, Duns (2D et 3D), Isaac (2D et 3D) et Nastran (f06) peuvent être lus. Pour prétraiter le format natif Netgen, STEP et STL peuvent être importés.

Ce paquet fournit les exemples.

Ceres Solver est une bibliothèque libre en C++ pour modéliser et résoudre des problèmes d'optimisation de grande taille et complexes. Il s'agit d'une bibliothèque riche en fonctionnalités, mûre et performante qui est utilisée en production chez Google depuis 2010.

Ceres Solver peut résoudre deux types de problèmes :

 — les problèmes de moindres carrés non linéaires avec contraintes de
   bornes ;
 — les problèmes d'optimisation génériques sans contrainte.

Ce paquet fournit la documentation disponible sur http://ceres-solver.org/ et les exemples fournis avec la distribution.

OpenSurgSim is C++ toolkit for developing real-time surgical simulations. It lets you build simulators using the included building blocks, such as input device support, haptic feedback, graphics, collision detection and physics simulation.

This package contains the development files needed to build your own OpenSurgSim applications.

The Open Porous Media (OPM) software suite provides libraries and tools for modeling and simulation of porous media processes, especially for simulating CO2 sequestration and improved and enhanced oil recovery.

This package contains the shared buildsystem of all OPM modules, the headers for input, parsing, and output of files in Eclipse format, a format widely used in the reservoir simulation community, and generic utilities used in other OPM modules.

The Open Porous Media (OPM) software suite provides libraries and tools for modeling and simulation of porous media processes, especially for simulating CO2 sequestration and improved and enhanced oil recovery.

opm-grid provides implementations of grids for reservoir simulation, corner point or more general pillar grids, following the DUNE grid interface: CpGrid, a parallel corner point grid, and PolyhedralGrid a more general serial grid implementation of an unstructured, legacy, grid.

A standard grid type in the petroleum industry, corner-point grids fills the domain with a relatively low number of cells while still providing sufficient flexibility to model faults, fractures and erosion. The grid format was originally designed with an eye towards geological modeling rather than numerical simulation, but is still suitable for e.g. low order finite volume discretizations.

This package provides the development files for the grid implementations, i.e. the headers and shared library links.

Il s'agit d'un paquet de transition qui peut être supprimé sans danger.

The Open Porous Media (OPM) software suite provides libraries and tools for modeling and simulation of porous media processes, especially for simulating CO2 sequestration and improved and enhanced oil recovery.

opm-models is a header-only simulation framework which is primary focused on fully implicit models for flow and transport in porous media. It uses finite volume schemes for discretization and automatic differentiation for calculating the Jacobians. Its main objectives is to provide an easily usable, well maintainable, high performance framework which is capable of capturing all macro-scale scenarios relevant for academic research and industrial applications involving flow and transport processes in porous media.

This package provides the development files (headers) needed to build applications based on opm-models.

The Open Porous Media (OPM) software suite provides libraries and tools for modeling and simulation of porous media processes, especially for simulating CO2 sequestration and improved and enhanced oil recovery.

opm-simulators provides a research (ebos) and a production (flow) fully implicit black-oil simulators, supporting one to three phases and supporting solvent and polymer options. It uses cell centered finite volume schemes with two point flux approximation and automatic differentiation for the discretization and uses state of the art linear and nonlinear solvers. It supports standard and multi segment well models and reading and writing file in Eclipse format, a very common format used in the oil reservoir simulation community.

Package provides the development files (headers and shared library links).

The Open Porous Media (OPM) software suite provides libraries and tools for modeling and simulation of porous media processes, especially for simulating CO2 sequestration and improved and enhanced oil recovery.

opm-upscaling provides tools for single phase and relative permeability upscaling. During upscaling effective parameters (like porosity, permeability, and capillary pressure) for a simulation on a coarser scale are computed from properties of a simulation on a fine scale.

Package provides the development files (headers and shared library links).

La suite OPM (Open Porous Media) fournit des bibliothèques et des outils pour la modélisation et la simulation de milieux poreux, particulièrement pour la simulation de capture de CO2 et une meilleure récupération du pétrole.

Ce paquet fournit les enveloppes de Python pour lire, analyser et éditer des fichiers au format Eclipse, un format largement utilisé dans le domaine des réservoirs pétroliers.

La suite OPM (Open Porous Media) fournit des bibliothèques et des outils pour la modélisation et la simulation de milieux poreux, particulièrement pour la simulation de capture de CO2 et une meilleure récupération du pétrole.

opm-simulators fournit des simulateurs de produits pétroliers totalement continus pour la recherche (ebos) et la production (flow), prenant en charge de une à trois phases et prenant en charge les options solvants et polymères. Il utilise les schémas de volumes finis centrés sur les mailles avec approximation de flux à deux points et la différentiation automatique pour la discrétisation, et utilise des solveurs linéaires et non linéaires à la pointe de l’art. Il prend en charge les modèles de puits standard et multi segment et la lecture et l’écriture de fichier au format Eclipse, un format largement utilisé dans le domaine de simulation des réservoirs pétroliers.

Ce paquet fournit les enveloppes de Python pour les simulateurs.

PySwarms is an extensible research toolkit for particle swarm optimization (PSO) in Python.

It is intended for swarm intelligence researchers, practitioners, and students who prefer a high-level declarative interface for implementing PSO in their problems. PySwarms enables basic optimization with PSO and interaction with swarm optimizations.

Features:

• High-level module for Particle Swarm Optimization
• Built-in objective functions to test optimization algorithms
• Plotting environment for cost histories and particle movement
• Hyperparameter search tools to optimize swarm behaviour

This package contains the Python 3.x version of PySwarms.

FDMNES calculates the spectra of different spectroscopies related to the real or virtual absorption of x-ray in material. It gives the absorption cross sections of photons around the ionization edge, that is in the energy range of XANES in the EXAFS. The calculation is performed with all conditions of rectilinear or circular polarization. In the same way, it calculates the structure factors and intensities of anomalous or resonant diffraction spectra (DAFS or RXD). FDMNES also allows the comparison of the simulated spectra to experimental ones with the help of objective criteria.

G+Smo (Geometry + Simulation Modules, pronounced "gismo") is a new open-source C++ library that brings together mathematical tools for geometric design and numerical simulation. This package contains inlude headers, cmake configuration files and other development utils.