Debian Science Project
Summary
Simulations
Debian Science - simuleringspakker

Denne metapakke vil installere Debian Science-pakker, som bruges til at udføre simuleringer indenfor forskellige videnskabsfelter.

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
Tredimensionalt strukturelt finitte elementprogram
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Calculix er et frit finitte elementanalyseprogram, udviklet i åben kildekode, som bruger et lignende inddataformat som Abaqus. Det har en implicit og eksplicit løser og en for- og efterbrænder (CGX). Denne pakke indeholder løseren CalculiX CrunchiX (cxx).

Calculix-cgx
Calculix cgx er en 3-dimensionel for- og efterbrænder for fem
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Calculix GraphiX (cgx) er en 3-dimensionel for- og efterbrænder for finitte elementer. CalculiX CrunchiX Finite Element Models kan bygges, beregnes og efterbehandles. For- og efterbrænderen er et interaktivt 3D-værktøj, der bruger openGL API'en.

Udover Calculix CrunchiX-resultatfiler (frd) kan resultater fra OpenFoam, Duns (2D og 3D), Isaac (2D og 3D) og Nastran (f06) læses. For forbrænderens Netgen-standardformat kan STEP og STL importeres.

Esys-particle
Program til partikelbaserete numerisk modellering - MPI-version
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ESyS-Particle er et program, udviklet i åben kildekode, til partikelbaseret numerisk modellering. Programmet implementerer Discrete Element Method (DEM), en almindeligt anvendt teknik til modellering af processer, der involverer store deformationer, kornet forløb og/eller fragmentering. ESyS-Particle er designet til udførelse på parallelle supercomputere, klynger eller pc'er med flere kerner, der kører et Linux- baseret operativsystem. C++-simulationsmotoren implementerer en rumlig domænenedbrydning via Message Passing Interface (MPI). En Pythonomslags- API giver fleksibilitet i udformningen af ​​numeriske modeller, specifikation af modelleringsparametre og kontaktlogik samt analyse af simulationsdata. ESyS-Particle har været anvendt til at simulere jordskælv kimdannelse, findeling i »shear-celler«, siloforløb, stenfragmentering, og »fault gouge«-evolution, for blot at nævne nogle anvendelsesområder.

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Gazebo9
Open Source Robotics Simulator - binære filer
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Gazebo er en simulator for flere robotter i udendørsmiljøer. Som Stage (del af projektet Player), kan den simulere en population af robotter, sensorer og objekter, men gør det i en tredimensionel verden. Den opretter både realistisk sensortilbagemelding og fysisk plausible interaktioner mellem objekter (den inkluderer en præcis simulering af stift-legeme fysik).

Denne pakke indeholder hovedprogrammets binære filer.

The package is enhanced by the following packages: gazebo9-plugin-base
Getdp
Generelt miljø til behandling af discrete-problemer
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GetDP er en generel endelig elementløser der bruger blandede elementer til at discretize de Rham-type-komplekser i en, to og tre dimensioner.

Den vigtigste funktion i GetDP er nærhed mellem inddata, der definerer discrete-problemer (skrevet af brugeren i ASCII-datafiler) og de symbolske matematiske udtryk af disse problemer.

Se GetDP's referencemanual for en grundig oversigt over GetDP's funktioner: 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
Molekylær dynamisk simulator
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LAMMPS er en klassisk molekylær dynamisk kode, og et akronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

LAMMPS har potentiale for bløde materialer (biomolekyler, polymerer) og faste materialer (metaller, semikonduktører) og grovkornede eller mesoskopiske systemer. Programmet kan bruges til at opbygge atomer eller, mere generisk, som en parallel partikelsimulator på skalaerne atomar, meso eller kontinuum.

LAMMpS kører på enkelte processorer eller parallelt via teknikker for beskedfortolkning og en delvis-dekomponering af simuleringsdomænet. Koden er designet til at være nemt at ændre eller udvide med ny funktionalitet.

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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.

Libkim-api-v2-models
Models and model-drivers for KIM-API
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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

Liggghts
Open Source DEM Particle Simulation Software
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LIGGGHTS står for LAMMPS forbedret for generel granulering og granuleret varmeoverførselssimulationer (LAMMPS improved for general granular and granular heat transfer simulations).

LAMMPS er en simulator for klassisk molekylær dynamik. Den er udbredt indenfor molekylær dynamik. Takket være fysiske analogier og algoritmeanalogier er LAMMPS en særdeles god platform til DEM-simulationer. LAMMPS tilbyder en GRANULAR-pakke til at udføre denne slags simulationer. LIGGGHTS forsøger at forbedre denne evne med det mål at pakken kan bruges i industrielle programmer. Udviklingsversion.

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Music-bin
Multi-Simulation Coordinator for MPI -- Utilities
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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.

Neuron
Simuleringsmiljø for beregningsmiljøer med neuroner
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NEURON er et simuleringsmiljø til modellering af individuelle neuroner og netværk af neuroner. Det tilbyder værktøjer til nem bygning, håndtering og brug af modeller på en måde, der er numerisk fornuftig og beregningsmæssig effektiv. Det er specielt velegnet til problemer, der er tæt forbundet med eksperimentelle data, specielt dem der involverer celler med komplekse anatomiske og biofysiske egenskaber.

NEURON tilbyder

  • »naturlig syntaks«, der gør det muligt at specificere modelegenskaber i kendte idiomer
  • effektiv og smerteløs delvis og midlertidig diskretisering
  • flere forskellige, brugervalgte numeriske integreringsmetoder
  • nem brugerflade (fortolkere + grafisk brugerflade)
  • bibliotek med biofysiske mekanismer der kan udvides af brugeren
Occt-draw
Open CASCADE Technology command interpreter and graphical test system
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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.

Occt-misc
OCCT CAE-platformens delte biblioek - diverse filer
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Open CASCADE Technology er en programpakke for 3D-overflademodeller og faste modeller, visualisering, dataudveksling og hurtig programudvikling. Det er en glimrende platform til udvikling af numeriske simuleringsprogrammer inklusive CAD/CAM/CAE, AEC og GIS, samt PDM-programmer.

Denne pakke indeholder ressourcefilerne.

Openfoam
Programsæt for Computational Fluid Dynamics (CFD) - binære filer
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OpenFOAM er det førende, frie program til at beregne væskedynamik (CFD), ejet af OpenFOAM Foundation og distribueret eksklusivt under General Public Licence (GPL).

Denne pakke indeholder de binære filer.

Python3-deap
Distributed Evolutionary Algorithms in Python3
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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 Python3.

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 finitte elementer Python 3-system - OpenMP + MPI
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Escript er et programmeringsværktøj til at implementere matematiske modeller i Python via den finitte element metode (FEM). DA brugere ikke tilgår datastrukturerne er det meget nemt at bruge og skripter kan køre på skrivebordscomputere samt store parallelle supercomputere uden ændringer. Programområder for escript inkluderer jordmantelkonvektion, geofysisk inversion, jordskælv, porøse væskeløb, reaktiv transport, pladesubduktion, erosion og tsunamier.

Skripter kan køres parallelt (på varierende antal tråde eller knuder) uden nogen specielle ændringer.

Escript inkluderer nu modulet esys.downunder for 3D-inversion af geofysiske datasæt. Den nuværende version understøtter tyngdekraft, magnetisk og fælles inversion.

Denne pakke indeholder kommandoerne og bibliotekerne for Python 3 med både OpenMP-tråde og understøttelse af MPI-flerproces.

Python3-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.

Python3-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
Diskrete dynamiske beregninger, esp. granulerede mekanik - python 3
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Ramme, der kan udvides og flyttes, primært til mekanisk granulerede materialer. Beregningsdele er skrevet i C++ paralleliseret ved hjælp af OpenMP, fuldt tilgængelige og ændringsklare fra Python (ipython-konsol eller skripter). Vilkårlig kompleks scene kan opbygges med skripter. En Qt-baseret brugergrænseflade tilbydes, der byder på en fleksibel OpenGL-visning, inspektion af alle objekter og kørselstidsmodifikation. Parametriske forbrændere kan skrives i ren Python og et jobsystem kan anvendes til at drive parametriske undersøgelser. Nye materielle modeller og partikelfigurer kan tilføjes (i c++) uden at ændre eksisterende klasser.

Woo er en videreudvikling af pakken Yade (http://www.launchpad.net/yade), der sigter mod større fleksibilitet, udvidelsesmuligheder, tættere integration med Python og brugervenlighed.

Denne version er bygget med OpenMP aktiveret, og er rettet mod 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 er en mikroskopisk simuleringspakke for vejtrafik udviklet i åben kildekode og designet til at håndtere store vejnetværk. Den binære fil.

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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0.19.0+dfsg-2https://screenshots.debian.net/screenshots/000/011/525/large.png
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Yade
Platform for diskret elementmodellering
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Yet Another Dynamic Engine.

Ramme, der er udviklet i åben kildekode og som kan udvides, for diskrete numeriske modeller, fokuseret på den diskret elementmetode. Beregningsdelene er skrevet i C++ med brug af en fleksibel objektmodel, der giver mulighed for uafhængig implementering af nye algoritmer og grænseflader. Python bruges for hurtig og præcis scenekonstruktion, simuleringskontrol, efterbehandling og fejlsøgning.

Denne pakke indeholder en hastighedsoptimeret bygning af 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.),. The Yade Project, 2nd ed. (2015)
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Calculix-ccx-doc
Tredimensionalt strukturelt finitte elementprogram - dokumentationsfiler
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Calculix er et frit finitte elementanalyseprogram, udviklet i åben kildekode, som bruger et lignende inddataformat som Abaqus. Det har en implicit og eksplicit løser og en for- og efterbrænder (CGX).

Denne pakke indeholder dokumentationen i html-format for CalculiX CrunchiX.

Calculix-ccx-test
Tredimensionalt strukturelt finitte elementprogram - dokumentationsfiler
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Calculix er et frit finitte elementanalyseprogram, udviklet i åben kildekode, som bruger et lignende inddataformat som Abaqus. Det har en implicit og eksplicit løser og en for- og efterbrænder (CGX).

Denne pakke indeholder eksempelfiler for Calculix CrunchiX.

Calculix-cgx-examples
Eksempelfiler for Calculix GraphiX
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Calculix GraphiX (cgx) er en 3-dimensionel for- og efterbrænder for finitte elementer. CalculiX CrunchiX Finite Element Models kan bygges, beregnes og efterbehandles. For- og efterbrænderen er et interaktivt 3D-værktøj, der bruger openGL API'en.

Udover Calculix CrunchiX-resultatfiler (frd) kan resultater fra OpenFoam, Duns (2D og 3D), Isaac (2D og 3D) og Nastran (f06) læses. For forbrænderens Netgen-standardformat kan STEP og STL importeres.

Denne pakke indeholder eksemplerne.

Ceres-solver-doc
Dokumentation for ceres-solver
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Ceres Solver er et C++-bibliotek, udviklet i åben kildekode, for modellering og løsning af store og komplicerede optimeringsproblemer. Det er et modent og ydende bibliotek med mange funktioner, som er blevet brugt i produktionen hos Google siden 2010.

Ceres Solver kan løse to slags problemer.

  • Ikkelineær »Least Squares«-problemer med begrænsninger
  • Generelle ubegrænsede optimeringsproblemer

Denne pakke indholder dokumentationen fundet på http://ceres-solver.org/ og eksemplerne, som blev inkluderet i denne udgivelse.

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)

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.

Libgismo-dev
Geometry plus simulatiom modules development files
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Version: 0.8.3-2

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.

*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 203233