Debian Science Project
Summary
Simulations
Debian Science Simulation packages

This metapackage will install Debian Science packages that are used to do simulations in different fields of science.

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 Debian Science to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Science mailing list

Links to other tasks

Debian Science Simulations packages

Official Debian packages with high relevance

Calculix-ccx
Three-Dimensional Structural Finite Element Program
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CalculiX is a free and open source finite element analysis application that uses a similar input format to Abaqus. It has an implicit and explicit solver and a pre and post processor (CGX). This package contains the solver CalculiX CrunchiX (cxx).

Calculix-cgx
Calculix cgx is a 3-dimensional pre- and post-processor for fem
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CalculiX GraphiX (cgx) is a 3-dimensional pre- and post-processor for finite elemnts. CalculiX CrunchiX Finite Element Models can be build, calculated and post-processed. The pre- and post-processor is an interactive 3D-tool using the openGL API.

In addition to the Calculix CrunchiX results files (frd) results from OpenFoam, Duns (2D and 3D), Isaac (2D and 3D) and Nastran (f06) can be read. For preprocessing Netgen nativ format, STEP and STL can be imported.

Esys-particle
Software for particle-based numerical modelling. MPI version.
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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.

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Gazebo7
Open Source Robotics Simulator - Binaries
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Gazebo is a multi-robot simulator for outdoor environments. Like Stage (part of the Player project), it is capable of simulating a population of robots, sensors and objects, but does so in a three-dimensional world. It generates both realistic sensor feedback and physically plausible interactions between objects (it includes an accurate simulation of rigid-body physics).

This package contains then main application binaries

The package is enhanced by the following packages: gazebo7-plugin-base
Getdp
general environment for the treatment of discrete problems
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GetDP is a general finite element solver using mixed elements to discretize de Rham-type complexes in one, two and three dimensions.

The main feature of GetDP is the closeness between the input data defining discrete problems (written by the user in ASCII data files) and the symbolic mathematical expressions of these problems.

See GetDP's reference manual for a more thorough overview of GetDP's capabilities: http://www.geuz.org/getdp

Please cite: P. Dular, C. Geuzaine, A. Genon and W. Legros: An evolutive software environment for teaching finite element methods in electromagnetism. IEEE Transactions on Magnetics 35(3):1682 - 1685 (1999)
Lammps
Molecular Dynamics Simulator
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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.

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Libceres-dev
nonlinear least squares minimizer (development files)
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Ceres Solver is an open source C++ library for modeling and solving large, complicated optimization problems. It is a feature rich, mature and performant library which has been used in production at Google since 2010.

Ceres Solver can solve two kinds of problems.

  • Non-linear Least Squares problems with bounds constraints.
  • General unconstrained optimization problems.

This package contains the development header files.

Liggghts
Open Source DEM Particle Simulation Software.
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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.

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Music-bin
Multi-Simulation Coordinator for MPI -- Utilities
Maintainer: Mikael Djurfeldt
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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.

Openfoam
Set of programs for Computational Fluid Dynamics (CFD). Binaries
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OpenFOAM is the leading free, open source software for computational fluid dynamics (CFD), owned by the OpenFOAM Foundation and distributed exclusively under the General Public Licence (GPL).

Package contains binaries.

Python-deap
Distributed Evolutionary Algorithms in Python
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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 Python.

Python-escript
Escript/Finley finite elements Python2 system (with OpenMP)
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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 Python2 with OpenMP threading.

Python-pysph
open source framework for Smoothed Particle Hydrodynamics
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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.

Python-sfepy
Simple Finite Elements in Python
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SfePy is a software for solving systems of coupled partial differential equations (PDEs) by the finite element method in 1D, 2D and 3D. It can be viewed both as black-box PDE solver, and as a Python package which can be used for building custom applications. The word “simple” means that complex FEM problems can be coded very easily and rapidly.

Python3-woo
Discrete dynamic compuations, esp. granular mechanics (python 3)
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Extesible and portable framework primarily for mechanics granular materials. Computation parts are written in c++ parallelized using OpenMP, fully accessible and modifiable from python (ipython console or scripts). Arbitrarily complex scene can be scripted. Qt-based user interface is provided, featuring flexible OpenGL display, inspection of all objects and runtime modification. Parametric preprocessors can be written in pure python, and batch system can be used to drive parametric studies. New material models and particle shapes can be added (in c++) without modifying existing classes.

Woo is an evolution of the Yade package (http://www.launchpad.net/yade), aiming at more flexibility, extensibility, tighter integration with python and user-friendliness.

This version is built with OpenMP enabled, and targets Python 3.x.

Radiance
Lighting Simulation and Rendering System
Maintainer: Bernd Zeimetz
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Radiance is intended to aid lighting designers and architects by predicting the light levels and appearance of a space prior to construction. The package includes programs for modeling and translating scene geometry, luminaire data and material properties, all of which are needed as input to the simulation. The lighting simulation itself uses ray tracing techniques to compute radiance values (ie. the quantity of light passing through a specific point in a specific direction), which are typically arranged to form a photographic quality image. The resulting image may be analyzed, displayed and manipulated within the package, and converted to other popular image file formats for export to other packages, facilitating the production of hard copy output.

Sumo
Simulation of Urban MObility (SUMO)
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SUMO is an open source, highly portable, microscopic road traffic simulation package designed to handle large road networks. Main binary.

Please cite: M. Behrisch, L. Bieker, J. Erdmann and D. Krajzewicz: SUMO - Simulation of Urban MObility: An Overview (eprint) SIMUL 2011, The Third International Conference on Advances in System Simulation :63-68 (2011)
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Yade
Platform for discrete element modeling
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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.

Please cite: V.ŠMilauer, E. Catalano, B. Chareyre, S. Dorofeenko, J. Duriez, A. Gladky, J. Kozicki, C. Modenese, L. Scholtès, L. Sibille, J. Stránský and K. Thoeni: Yade Documentation (V. Šmilauer, ed.), (eprint) The Yade Project, 1st ed. (2010)
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Official Debian packages with lower relevance

Calculix-ccx-doc
Three-Dimensional Structural Finite Element Program (documentation files)
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CalculiX is a free and open source finite element analysis application that uses a similar input format to Abaqus. It has an implicit and explicit solver and a pre and post processor (CGX).

This package contains the documentation in html format for CalculiX CrunchiX

Calculix-ccx-test
Three-Dimensional Structural Finite Element Program (documentation files)
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CalculiX is a free and open source finite element analysis application that uses a similar input format to Abaqus. It has an implicit and explicit solver and a pre and post processor (CGX).

This package contains example files for CalculiX CrunchiX.

Calculix-cgx-examples
Example files for Calculix GraphiX
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CalculiX GraphiX (cgx) is a 3-dimensional pre- and post-processor for finite elemnts. CalculiX CrunchiX Finite Element Models can be build, calculated and post-processed. The pre- and post-processor is an interactive 3D-tool using the openGL API.

In addition to the Calculix CrunchiX results files (frd) results from OpenFoam, Duns (2D and 3D), Isaac (2D and 3D) and Nastran (f06) can be read. For preprocessing Netgen nativ format, STEP and STL can be imported.

This package contains the examples.

Ceres-solver-doc
documentation for ceres-solver
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Ceres Solver is an open source C++ library for modeling and solving large, complicated optimization problems. It is a feature rich, mature and performant library which has been used in production at Google since 2010.

Ceres Solver can solve two kinds of problems.

  • Non-linear Least Squares problems with bounds constraints.
  • General unconstrained optimization problems.

This package contains the documentation found on http://ceres-solver.org/ and the examples that were included with the release.

Libopensurgsim-dev
Free platform for surgical simulation - development
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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.

Please cite: Timothy Kelliher, Julien Lenoir, Paul Novotny and Harald Scheirich: Open Surgical Simulation (OSS) – A Community Resource. Medicine Meets Virtual Reality 21: NextMed/MMVR21 :197-203 (2014)
Python-escript-mpi
Escript/Finley finite elements Python2 system (OpenMP + MPI)
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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 Python2 with both OpenMP threading and MPI multiprocess support.

Python-woo
Discrete dynamic computations, esp. granular mechanics (python 2)
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Extesible and portable framework primarily for mechanics granular materials. Computation parts are written in c++ parallelized using OpenMP, fully accessible and modifiable from python (ipython console or scripts). Arbitrarily complex scene can be scripted. Qt-based user interface is provided, featuring flexible OpenGL display, inspection of all objects and runtime modification. Parametric preprocessors can be written in pure python, and batch system can be used to drive parametric studies. New material models and particle shapes can be added (in c++) without modifying existing classes.

Woo is an evolution of the Yade package (http://www.launchpad.net/yade), aiming at more flexibility, extensibility, tighter integration with python and user-friendliness.

This version is built with OpenMP enabled, and targets Python 2.x

Python3-escript
Escript/Finley finite elements Python3 system (with OpenMP)
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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.

Python3-escript-mpi
Escript/Finley finite elements Python3 system (OpenMP + MPI)
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upstream5.1
Popcon: 0 users (1 upd.)*
Newer upstream!
License: DFSG free
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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.

Packaging has started and developers might try the packaging code in VCS

Fdmnes
calculates spectra of different spectroscopies
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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.

Please cite: O. Bunău and Y. Joly: Self-consistent aspects of x-ray absorption calculations. (eprint) J. Phys.: Condens. Matter 21:345501 (2009)
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