Debian Science Simulations packages

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 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 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 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

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

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 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.

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 is a simulation environment for modeling individual neurons and networks of neurons. It provides tools for conveniently building, managing, and using models in a way that is numerically sound and computationally efficient. It is particularly well-suited to problems that are closely linked to experimental data, especially those that involve cells with complex anatomical and biophysical properties.

NEURON offers

• "natural syntax", which allows one to specify model properties in familiar idioms
• efficient and painless spatial and temporal discretization
• several different, user-selectable numerical integration methods
• convenient user interface (interpreters + GUI)
• user-extendable library of biophysical mechanisms

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 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 resource files.

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.

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.

QuTiP is open-source software for simulating the dynamics of open quantum systems. The QuTiP library depends on the excellent Numpy, Scipy, and Cython numerical packages. In addition, graphical output is provided by Matplotlib. QuTiP aims to provide user-friendly and efficient numerical simulations of a wide variety of Hamiltonians, including those with arbitrary time-dependence, commonly found in a wide range of physics applications such as quantum optics, trapped ions, superconducting circuits, and quantum nanomechanical resonators.

This package installs the library for Python 3.

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.

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 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 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 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 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.

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.

This is a transitional package. It can safely be removed.

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).

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 Python wrappers for reading, parsing, and writing files in Eclipse format, a format widely used in the reservoir simulation community.

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 Python wrappers for the simulators.

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.