Debian Science Numerical computation packages

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.

FreeMat is a free environment for rapid engineering and scientific prototyping and data processing. It is similar to commercial systems such as MATLAB from Mathworks, and IDL from Research Systems, but is Open Source. FreeMat is available under the GPL license.

A free IDL (Interactive Data Language) compatible incremental compiler. It has full syntax compatibility with IDL 7.1. IDL is a registered trademark of ITT Visual Information Solutions.

IPython can be used as a replacement for the standard Python shell, or it can be used as a complete working environment for scientific computing (like Matlab or Mathematica) when paired with the standard Python scientific and numerical tools. It supports dynamic object introspections, numbered input/output prompts, a macro system, session logging, session restoring, complete system shell access, verbose and colored traceback reports, auto-parentheses, auto-quoting, and is embeddable in other Python programs.

This package contains the basic terminal shell. For the qt console install ipython-qtconsole and for the html notebook install ipython-notebook.

Julia is a high-level, high-performance dynamic programming language for technical computing, with syntax that is familiar to users of other technical computing environments. It provides a sophisticated compiler, distributed parallel execution, numerical accuracy, and an extensive mathematical function library. The library, mostly written in Julia itself, also integrates mature, best-of-breed C and Fortran libraries for linear algebra, random number generation, FFTs, and string processing. Julia programs are organized around defining functions, and overloading them for different combinations of argument types (which can also be user-defined).

This package provides a complete Julia installation (JIT compiler, standard library, text-based user interface).

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.

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.

Lush is a programming language and environment that is based on the Lisp programming language. The lush language is small compared to ANSI Common Lisp and is optimized for numeric calculations. Lush includes a libraries for numerical analysis and building graphical user interfaces.

This package contains the binary executable.

Octave is a (mostly Matlab (R) compatible) high-level language, primarily intended for numerical computations. It provides a convenient command-line interface for solving linear and nonlinear problems numerically.

Octave can be dynamically extended with user-supplied C++ files.

PDL gives standard perl the ability to COMPACTLY store and SPEEDILY manipulate the large N-dimensional data arrays which are the bread and butter of scientific computing. The idea is to turn perl in to a free, array-oriented, numerical language in the same sense as commercial packages like IDL and MatLab. One can write simple perl expressions to manipulate entire numerical arrays all at once. For example, using PDL the perl variable $a can hold a 1024x1024 floating point image, it only takes 4Mb of memory to store it and expressions like $a=sqrt($a)+2 would manipulate the whole image in a few seconds.

A simple interactive shell (perldl) is provided for command line use together with a module (PDL) for use in perl scripts.

DEAP is intended to be an easy to use distributed evolutionary algorithm library in the Python language. Its two main components are modular and can be used separately. The first module is a Distributed Task Manager (DTM), which is intended to run on cluster of computers. The second part is the Evolutionary Algorithms in Python (EAP) framework.

The guiqwt Python library provides efficient 2D data-plotting features (curve/image visualization and related tools) for signal/image processing application development and interactive computing. It's based on the scientific modules NumPy and SciPy, and the PyQwt plotting widgets for PyQt4 graphical user interfaces.

Matplotlib is a pure Python plotting library designed to bring publication quality plotting to Python with a syntax familiar to Matlab users. All of the plotting commands in the pylab interface can be accessed either via a functional interface familiar to Matlab users or an object oriented interface familiar to Python users.

Numpy contains a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, and useful linear algebra, Fourier transform, and random number capabilities.

Numpy replaces the python-numeric and python-numarray modules which are now deprecated and shouldn't be used except to support older software.

SciPy supplements the popular NumPy module (python-numpy package), gathering a variety of high level science and engineering modules together as a single package.

SciPy is a set of Open Source scientific and numeric tools for Python. It currently supports special functions, integration, ordinary differential equation (ODE) solvers, gradient optimization, genetic algorithms, parallel programming tools, an expression-to-C++ compiler for fast execution, and others.

SciTools is a Python package containing lots of useful tools for scientific computing in Python. The package is built on top of other widely used packages such as NumPy, SciPy, ScientificPython, Gnuplot, etc.

SciTools also comes with a plotting interface called Easyviz, which is a unified interface to various packages for scientific visualization and plotting. Both curve plots and more advanced 2D/3D visualization of scalar and vector fields are supported. The Easyviz interface was designed with three ideas in mind: 1) a simple, Matlab-like syntax; 2) a unified interface to lots of visualization engines (backends): Gnuplot, Matplotlib, Grace, Veusz, Pmw.Blt.Graph, PyX, Matlab, VTK, VisIt, OpenDX; and 3) a minimalistic interface which offers only basic control of plots: curves, linestyles, legends, title, axis extent and names. More fine-tuning of plots can be done by adding backend-specific commands.

Besides offering an attractive front-end to GNU Octave, an environment for numerical computation highly compatible with MATLAB, QtOctave currently also features matrix data entry and display and some GUI shortcuts to frequently used Octave functions. It also offers access in place to Octave's documentation with octave-htmldoc or octave-info.

R is a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files.

The design of R has been heavily influenced by two existing languages: Becker, Chambers & Wilks' S and Sussman's Scheme. Whereas the resulting language is very similar in appearance to S, the underlying implementation and semantics are derived from Scheme.

The core of R is an interpreted computer language which allows branching and looping as well as modular programming using functions. Most of the user-visible functions in R are written in R. It is possible for the user to interface to procedures written in the C, C++, or FORTRAN languages for efficiency, and many of R's core functions do so. The R distribution contains functionality for a large number of statistical procedures and underlying applied math computations. There is also a large set of functions which provide a flexible graphical environment for creating various kinds of data presentations.

Additionally, several thousand extension "packages" are available from CRAN, the Comprehensive R Archive Network, many also as Debian packages, named 'r-cran-'.

This package is a metapackage which eases the transition from the pre-1.5.0 package setup with its larger r-base package. Once installed, it can be safely removed and apt-get will automatically upgrade its components during future upgrades. Providing this package gives a way to users to then only install r-base-core if they so desire.

Scilab is a matrix-based scientific software package. Scilab contains hundreds of built-in mathematical functions, rich data structures (including polynomials, rationals, linear systems, lists, etc...) and comes with a number of specific toolboxes for control, signal processing, ...

This package also provides Xcos, a graphical editor to design hybrid dynamical systems models. Models can be designed, loaded, saved, compiled and simulated. Stable and efficient solution for industrial and academics needs, Xcos provides functionalities for modeling of mechanical systems (automotive, aeronautics...), hydraulic circuits (dam, pipe modeling...), control systems, etc. Modelica capabilities are also provided.

For a minimum version of scilab, install package "scilab-cli".

This module implements artificial neural networks capabilities into the Scilab language. Current features are:

• Only layered feedforward networks are supported directly at the moment (for others use the "hooks" provided)
• Unlimited number of layers
• Unlimited number of neurons per each layer separately
• User defined activation function (defaults to logistic)
• User defined error function (defaults to SSE)
• Algorithms implemented so far:
• standard (vanilla) with or without bias, on-line or batch
• momentum with or without bias, on-line or batch
• SuperSAB with or without bias, on-line or batch
• Conjugate gradients
• Jacobian computation
• Computation of result of multiplication between "vector" and Hessian
• Some helper functions provided

This toolbox is providing plotting capabilities in the Scilab language. Plotlib functions matches the one from Matlab and therefor is dedicated to users switching from Matlab to Scilab.

This toolbox is providing symbolic capabilities with the Scilab languages.

It is based on Maxima which is a fully symbolic computation program. It is full featured doing symbolic manipulation of polynomials, matrices, rational functions, integration, Todd-coxeter methods for finite group analysis, graphing, multiple precision floating point computation.

SIVP intends to do image and video processing tasks. SIVP is meant to be a useful, efficient, and free image and video processing toolbox for Scilab. Its goals include tasks such as filtering, blurring, edge detection, thresholding, histogram manipulation, segmentation, mathematical morphology, and color image processing.

This package also provides some functions on video processing.

Wavelet is a powerful signal processing tool developed and developing in the last two decades. Scilab Wavelet Toolbox is a free software package to enable you using wavelet analysis tools freely in Scilab on most OSes including GNU/Linux, BSD and Windows. Scilab Wavelet Toolbox is designed to work with any Scilab Image Processing Toolbox like SIP or SIVP for displaying 2-D results.

What Scilab Wavelet Toolbox supposed to do:

• Discrete Fast Wavelet Transform, daubechies wavelets
• 1-D single level signal decomposition and reconstruction
• 1-D multi-level signal decomposition and reconstruction
• 2-D single level image decomposition and reconstruction
• 2-D multi-level image decomposition and reconstruction

Spyder (previously known as Pydee) is a free open-source Python development environment providing MATLAB-like features in a simple and light-weighted software

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.

Yorick is an interpreted programming language for:

• scientific simulations or calculations
• postprocessing or steering large simulation codes
• interactive scientific graphics
• reading, writing, and translating large files of numbers

The language features a compact syntax for many common array operations, so it processes large arrays of numbers very quickly and efficiently. Superficially, yorick code resembles C code, but yorick variables are never explicitly declared and have a dynamic scoping similar to many Lisp dialects. The yorick language is designed to be typed interactively at a keyboard, as well as stored in files for later use.

This package includes an emacs-based development environment, which you can launch by typing M-x yorick in emacs.

Many add-on packages and plug-ins are available for Yorick (the package names begin with "yorick-"). You may want to install the yorick-full metapackage which depends on the vast majority of them.

The High Performance Computing (HPC) Challenge benchmark runs a suite of 7 tests that measure the performance of CPU, memory and network for HPC clusters. Amongst others, it includes the High-Performance LINPACK (HPL) benchmark, used by the Top500 ranking (http://www.top500.org/).

This package does not provide MATLAB. Instead, it configures an existing MATLAB installation to integrate more comfortably in a Debian installation.

Currently it provides /usr/bin/matlab through the alternatives system, offers to work around incompatibilities between the libraries bundled with MATLAB and system libraries, and provides a helper utility meant to be used by other packages to compile MEX extensions.

Install this if you would like your MATLAB installation to behave more like an ordinary Debian package. Other packages may depend on this one if they install MATLAB code, for example in order to compile MEX extensions.

OctaveDE is a development environment for the Octave mathematical software package. Octave normally is run in a terminal. Octavede provides an GTK/X11 application that provides functionality similar to other mathematical software packages.