Debian Science Numerical Computation packages

Currently, ADMesh only reads the STL file format that is used for rapid prototyping applications, although it can write STL, VRML, OFF, and DXF files. Some features of admesh are: Fill holes in the mesh by adding facets. Repair facets by connecting nearby facets. Repair normal directions (i.e. facets should be CCW) Remove degenerate facets (i.e. facets with 2 or more vertices equal)

Algotutor to interaktywny program do obserwacji pośrednich kroków algorytmów ("animacji algorytmów"). Algotutor przeznaczony jest dla studentów informatyki oraz badaczy algorytmów i/lub struktur danych. Osoby takie mogą tworzyć pliki danych w formacie zwykłego tekstu (właściwie anonimowe skróty Perla, ale nie trzeba się tym przejmować) i umożliwiać temu programowi przejście przez jakikolwiek predefiniowany algorytm. Następnie można cofnąć się i ponowić sekwencję wykonywania algorytmu na różnych poziomach szczegółowości.

CalculiX to bezpłatna, otwartoźródłowa aplikacja do analizy elementów skończonych, która wykorzystuje format wejściowy podobny do Abaqusa. Posiada niejawny i jawny solwer oraz procesor wstępny i końcowy (CGX). Pakiet zawiera solwer 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.

Cbc (Coin-or branch and cut) to otwartoźródłowy program do rozwiązywania mieszanych liczb całkowitych, napisany w języku C++. Może być używany w roli nadającej się do wywoływania biblioteki lub niezależnego pliku wykonywalnego (programu).

Pakiet zawiera plik wykonywalny cbc.

Clp (Coin-or linear programming) to otwartoźródłowy solwer programowania liniowego napisany w języku C++. Jest on przeznaczony przede wszystkim do użytku jako biblioteka wywoływalna, ale dostępna jest też podstawowa, samodzielna wersja wykonywalna. Jego zadaniem jest wyszukiwanie rozwiązań problemów liniowej optymalizacji matematycznej z graniczeniami.

Pakiet zawiera plik wykonywalny clp.

SYMPHONY is an open-source generic mixed-integer linear programs (MILP) solver, callable library, and extensible framework for implementing customized solvers SYMPHONY has a number of advanced capabilities, including the ability to solve multi-objective MILPs, the ability to warm start its solution procedure, and the ability to perform basic sensitivity analyses.

SYMPHONY is part of the larger COIN-OR initiative (Computational Infrastructure for Operations Research).

This package contains the symphony executable.

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.

GNU Data Language (GDL) to darmowy kompilator przyrostowy zgodny z IDL (Interactive Data Language) czyli z językiem programowania wykorzystywanym do analizy danych. Jego składnia jest w pełni zgodna z IDL 7.1. IDL jest zastrzeżonym znakiem towarowym firmy ITT Visual Information Solutions. Od wersji IDL 8.0 obsługiwane są następujące elementy językowe:

• pętle FOREACH
• ujemne indeksy tablicy
• wskaźniki i obiekty do zbierania śmieci
• wywoływanie metody na obiekcie za pomocą operatora kropki "." (np. 'object.aMemberProcedure,arg1')

System plików wejściowych i wyjściowych jest w pełni zaimplementowany. Oficjalnie udostępniono obsługę GUI (widżetów), ale nie jest ona jeszcze ukończona.

Pakiet udostępnia główną linię poleceń oraz interfejs interpretera.

Pyzo is a cross-platform Python IDE focused on interactivity and introspection, which makes it very suitable for scientific computing. Its practical design is aimed at simplicity and efficiency.

It consists of two main components, the editor and the shell, and uses a set of pluggable tools to help the programmer in various ways. Some example tools are source structure, project manager, interactive help, workspace...

Pyzo is written in (pure) Python 3 and uses the Qt GUI toolkit. Binaries are provided for all major operating system. After installing Pyzo, it can be used to execute code on any Python version available on your system (Python 2.4 - 3.x, including Pypy).

This is a transitional dummy package enabling the upgrade from IEP to Pyzo. It can safely be removed.

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 actual terminal shell for Python 3.

Julia jest wysokopoziomowym, dynamicznym językiem programowania o wysokiej wydajności, stworzonym dla obliczeń technicznych, o składni przypominającej języki używane w innych technicznych środowiskach obliczeniowych. Julia dostarcza rewelacyjny kompilator, umożliwia rozproszone równoległe wykonywanie programów, zapewnia numeryczną dokładność i zawiera obszerną bibliotekę funkcji matematycznych. Biblioteka, w większości napisana w samej Julii, zawiera również dojrzałe, najlepszej jakości biblioteki w C oraz Fortranie służące do przeprowadzania obliczeń algebry liniowej, generowania liczb losowych, wyznaczania transformacji Fouriera oraz przetwarzania tekstu. Programy w Julii opierają się o definiowanie funkcji oraz przeciążanie ich dla różnych kombinacji typów argumentów (które również mogą być definiowane przez użytkownika).

Ten pakiet dostarcza pełną instalację środowiska Julia (kompilator JIT, bibliotekę standardową, interfejs tekstowy).

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.

The ADOLC system automatically calculates exact derivatives of a C/C++ function. It uses C++ overloading to record arithmetic operations, which it plays back later in various ways to calculate the requested values.

This package contains the development library, header files, and user's manual.

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.

This library provides an implementation of the Basic Linear Algebra Subprograms levels 1, 2 and 3, using OpenCL and optimized for AMD GPU hardware.

This package provides the development files.

The clFFT library is an open source OpenCL library implementation of discrete Fast Fourier Transforms, which:

• Provides a fast and accurate platform for calculating discrete FFTs.
• Works on CPU or GPU backends.
• Supports in-place or out-of-place transforms.
• Supports 1D, 2D, and 3D transforms with a batch size that can be greater than 1.
• Supports planar (real and complex components in separate arrays) and interleaved (real and complex components as a pair contiguous in memory) formats.
• Supports dimension lengths that can be any mix of powers of 2, 3, and 5.
• Supports single and double precision floating point formats.

This package provides the development files.

ColPack is a package comprising of implementation of algorithms for specialized vertex coloring problems that arise in sparse derivative computation. It is written in an object-oriented fashion heavily using the Standard Template Library (STL). It is designed to be simple, modular, extenable and efficient. Its primary application has been for use in automatic differentiation.

This package contains the development library, header files, and documentation.

DUNE, the Distributed and Unified Numerics Environment is a modular toolbox for solving partial differential equations (PDEs) with grid-based methods. It supports the easy implementation of methods like Finite Elements (FE), Finite Volumes (FV), and also Finite Differences (FD).

This package contains the development files for the grid interface.

The Parma Polyhedra Library (PPL) is a C++ library for the manipulation of (not necessarily closed) convex polyhedra and other numerical abstractions. The applications of convex polyhedra include program analysis, optimized compilation, integer and combinatorial optimization and statistical data-editing. The Parma Polyhedra Library is user friendly (you write `x + 2y + 5z <= 7' when you mean it), fully dynamic (available virtual memory is the only limitation to the dimension of anything), written in standard C++, exception-safe, rather efficient and thoroughly documented.

This package provides the header files and static libraries for the C and C++ interfaces.

QSopt-ex is an implementation of a simplex-based algorithm that returns exact rational solutions, taking advantage of the speed of floating-point calculations and attempting to minimize the operations performed in rational arithmetic.

This package contains the header files and static library.

This is a library for sparse matrix computations featuring the Recursive Sparse Blocks (RSB) matrix format. This format allows cache efficient and multi-threaded (that is, shared memory parallel) operations on large sparse matrices. It provides the most common operations necessary to iterative solvers, like matrix-vector multiplication, triangular solution, rows/columns scaling, diagonal extraction / setting, blocks extraction, norm computation, formats conversion. The RSB format is especially well suited for symmetric and transposed multiplication variants.

This package contains the static libraries for development with librsb, including examples.

SLEEF stands for SIMD Library for Evaluating Elementary Functions. It implements vectorized versions of all C99 real floating point math functions. It can utilize SIMD instructions of modern processors. SLEEF is designed to fully utilize SIMD computation by reducing the use of conditional branches and scatter/gather memory access.

The library contains subroutines for all C99 real FP math functions in double precision and single precision. SLEEF also includes subroutines for discrete Fourier transform(DFT).

This package ships development files.

Suitesparse is a collection of libraries for computations involving sparse matrices. This package includes the following libraries:

AMD approximate minimum degree ordering

CAMD symmetric approximate minimum degree

BTF permutation to block triangular form (beta)

COLAMD column approximate minimum degree ordering

CCOLAMD constrained column approximate minimum degree ordering

CHOLMOD sparse Cholesky factorization

CXSparse a concise sparse matrix package

KLU sparse LU factorization, primarily for circuit simulation

LDL a simple LDL' factorization

UMFPACK sparse LU factorization

ParU unsymmetric multifrontal multithreaded sparse LU factorization

RBio read/write sparse matrices in Rutherford/Boeing format

SPQR sparse QR factorization

Mongoose graph partitioning library that can quickly compute edge cuts

SPEX solves sparse linear systems in exact arithmetic

SuiteSparse_config configuration routines for all the above packages.

This package contains the static libraries and header files.

This package contains all development files necessary to build applications using SUNDIALS (SUite of Nonlinear and DIfferential/ALgebraic equation Solvers). All examples and documentation links live in this package as well.

TooN is a C++ numerics library which is designed to operate efficiently on large numbers of small matrices, and provides easy access to a number of algorithms including matrix decompositions and optimizations.

TooN is type generic and works well with a variety of numeric types including double, float and automatic differentiation types.

It is designed to integrate very will with the libCVD computer vision library and GVars3 configuration library.

TooN is a C++ numerics library which is designed to operate efficiently on large numbers of small matrices, and provides easy access to a number of algorithms including matrix decompositions and optimizations.

TooN is type generic and works well with a variety of numeric types including double, float and automatic differentiation types.

It is designed to integrate very will with the libCVD computer vision library and GVars3 configuration library.

TaG is the TooN Algorithm Library, it contains a mixed bag of algorithms including estimation, 3D geoometry and standard library enhancements.

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.

METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. The package contains some binaries for graph analyzing.

Octave to (głównie kompatybilny z MATLAB®) język wysokiego poziomu, przeznaczony zwłaszcza do obliczeń numerycznych. Zapewnia on wygodny interfejs wiersza poleceń do rozwiązywania liniowych oraz nieliniowych zadań metodami numerycznymi.

Octave może być dynamicznie rozszerzony o dostarczone przez użytkownika pliki C++.

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.

Psurface is a C++ library that handles piecewise linear bijections between triangulated surfaces. These surfaces can be of arbitrary shape and need not even be manifolds.

This package contains several utilities for working with psurface.

Bitstring is a pure Python module designed to help make the creation and analysis of binary data as simple and natural as possible.

Bitstrings can be constructed from integers (big and little endian), hex, octal, binary, strings or files. They can be sliced, joined, reversed, inserted into, overwritten, etc. with simple functions or slice notation. They can also be read from, searched and replaced, and navigated in, similar to a file or stream.

This package provides the Python 3 version of the module.

The CSA library provides elementary connection-sets and operators for combining them. It also provides an iteration interface to such connection-sets enabling efficient iteration over existing connections with a small memory footprint also for very large networks. The CSA can be used as a component of neuronal network simulators or other tools.

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 both OpenMP threading and MPI multiprocess support.

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.

This is the Python 3 version of the package.

The lmfit Python package provides a simple, flexible interface to non-linear optimization or curve fitting problems. The package extends the optimization capabilities of scipy.optimize by replacing floating pointing values for the variables to be optimized with Parameter objects. These Parameters can be fixed or varied, have upper and/or lower bounds placed on its value, or written as an algebraic expression of other Parameters.

The principal advantage of using Parameters instead of simple variables is that the objective function does not have to be rewritten to reflect every change of what is varied in the fit, or what relationships or constraints are placed on the Parameters. This means a scientific programmer can write a general model that encapsulates the phenomenon to be optimized, and then allow user of that model to change what is varied and fixed, what range of values is acceptable for Parameters, and what constraints are placed on the model. The ease with which the model can be changed also allows one to easily test the significance of certain Parameters in a fitting model.

The lmfit package allows a choice of several optimization methods available from scipy.optimize. The default, and by far best tested optimization method used is the Levenberg-Marquardt algorithm from MINPACK-1 as implemented in scipy.optimize.leastsq. This method is by far the most tested and best support method in lmfit, and much of this document assumes this algorithm is used unless explicitly stated. An important point for many scientific analysis is that this is only method that automatically estimates uncertainties and correlations between fitted variables from the covariance matrix calculated during the fit.

A few other optimization routines are also supported, including Nelder-Mead simplex downhill, Powell's method, COBYLA, Sequential Least Squares methods as implemented in scipy.optimize.fmin, and several others from scipy.optimize. In their native form, some of these methods setting allow upper or lower bounds on parameter variables, or adding constraints on fitted variables. By using Parameter objects, lmfit allows bounds and constraints for all of these methods, and makes it easy to swap between methods without hanging the objective function or set of Parameters.

Finally, because the approach derived from MINPACK-1 usin the covariance matrix to determine uncertainties is sometimes questioned (and sometimes rightly so), lmfit supports methods to do a brute force search of the confidence intervals and correlations for sets of parameters.

This is the Python 3 version of the package.

Matplotlib to biblioteka napisana w czystym Pythonie do kreślenia wykresów, zaprojektowana tak, aby zapewnić odpowiednią jakość wydruku w Pythonie ze składnią znaną użytkownikom Matlaba. Matplotlib umożliwia uzyskanie dostępu do wszystkich poleceń rysowania wykresów w interfejsie pylab za pośrednictwem funkcjonalnego interfejsu znanego użytkownikom Matlaba lub interfejsu obiektowego znanego użytkownikom Pythona.

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.

This package installs NumPy for Python 3.

A Python interface to the C++ Parma Polyhedra Library (PPL), which allows computations with polyhedra and grids, like mixed integer linear programming.

This package installs the library for Python 3.

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.

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.

Implements band-limited sinc interpolation method for sampling rate conversion.

rioxarray is an extension to the xarray package that

• supports multidimensional datasets such as netCDF
• stores the CRS as a WKT, which is the recommended format
• loads in the CRS, transform, and nodata metadata in standard CF & GDAL locations
• supports masking and scaling data with the masked and mask_and_scale kwargs
• adds the coordinate axis CF metadata
• loads in raster metadata into the attributes

This package provides the Python 3 library

SciPy uzupełnia popularny moduł NumPy (pakiet python-numpy), gromadząc w jednym pakiecie różnorodne moduły naukowe i inżynieryjne wysokiego poziomu.

SciPy to zestaw otwartoźródłowych narzędzi naukowych i numerycznych dla języka Python. Obecnie obsługuje funkcje specjalne, integrację, rozwiązywanie równań różniczkowych zwyczajnych (ODE), optymalizację gradientów, algorytmy genetyczne, narzędzia programowania równoległego, kompilator wyrażeń dla C++ zapewniający szybkie wykonywanie i inne.

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.

This package implements sparse multidimensional arrays on top of NumPy and scipy.sparse. It generalizes the scipy.sparse.coo_matrix layout but extends beyond just rows and columns to an arbitrary number of dimensions. The original motivation is for machine learning algorithms, but it is intended for somewhat general use.

It supports:

• NumPy ufuncs (where zeros are preserved)
• Arithmetic with scalars (where zeros are preserved)
• Reductions (sum, max)
• Reshape
• Transpose
• Tensordot
• Slicing with integers, lists, and slices (with no step value)
• Concatenation and stacking
• Addition with other sparse arrays of the same shape

This package provides the modules for Python 3.

PyTables is a package for managing hierarchical datasets and designed to efficiently cope with extremely large amounts of data.

It is built on top of the HDF5 library and the NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively save and retrieve very large amounts of data. One important feature of PyTables is that it optimizes memory and disk resources so that they take much less space (between a factor 3 to 5, and more if the data is compressible) than other solutions, like for example, relational or object oriented databases.

• Compound types (records) can be used entirely from Python (i.e. it is not necessary to use C for taking advantage of them).
• The tables are both enlargeable and compressible.
• I/O is buffered, so you can get very fast I/O, specially with large tables.
• Very easy to select data through the use of iterators over the rows in tables. Extended slicing is supported as well.
• It supports the complete set of NumPy objects.

Theano is a Python library that allows one to define and evaluate mathematical expressions involving multi-dimensional arrays efficiently. It provides a high-level Numpy like expression language for functional description of calculation, rearranges expressions for speed and stability, and generates native machine instructions for fast calculation. Optionally, highly accelerated computations could be carried out on graphics cards processors.

This package contains Theano for Python 3.

xarray (formerly xray) is an open source project and Python package that aims to bring the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the core pandas data structures.

It provides a pandas-like and pandas-compatible toolkit for analytics on multi-dimensional arrays, rather than the tabular data for which pandas excels.

This package provides the Python 3 library

Pyzo is a cross-platform Python IDE focused on interactivity and introspection, which makes it very suitable for scientific computing. Its practical design is aimed at simplicity and efficiency.

It consists of two main components, the editor and the shell, and uses a set of pluggable tools to help the programmer in various ways. Some example tools are source structure, project manager, interactive help, workspace...

Pyzo is written in (pure) Python 3 and uses the Qt GUI toolkit. Binaries are provided for all major operating system. After installing Pyzo, it can be used to execute code on any Python version available on your system (Python 2.4 - 3.x, including Pypy).

This package provides the Pyzo IDE.

QSopt-ex is an implementation of a simplex-based algorithm that returns exact rational solutions, taking advantage of the speed of floating-point calculations and attempting to minimize the operations performed in rational arithmetic.

This package contains the command-line utilities.

R to system do obliczeń statystycznych i prezentacji danych w formie graficznej. Składa się on z języka oraz środowiska wykonawczego z grafiką, debuggerem, dostępem do niektórych funkcji systemowych oraz możliwością uruchamiania programów zapisanych w plikach skryptów.

Na pojawienie się R duży wpływ miały dwa istniejące języki: S (Becker, Chambers & Wilks) i Scheme (Sussman). Rezultatem jest język bardzo podobny do S z implementacją i semantyką odziedziczoną po Scheme.

Rdzeniem R jest interpretowany język komputerowy, umożliwiający tworzenie rozgałęzień i pętli oraz programowanie modułowe z użyciem funkcji. Większość funkcji R dostępnych dla użytkowników została napisana w R. R pozwala użytkownikom wywoływać procedury napisane w C, C++ lub Fortran w celu poprawy wydajności, a większość podstawowych funkcji R pozwala to zrobić. Rozkład R zawiera funkcje dla dużej liczby procedur statystycznych i leżących u ich podstaw obliczeń matematycznych. Ponadto, zawiera duży zestaw funkcji zapewniających elastyczne środowisko do graficznej prezentacji danych i wyników obliczeń.

Dodatkowo w CRAN (Comprehensive R Archive Network) dostępnych jest kilka tysięcy pakietów rozszerzeń, z których wiele to także pakiety Debiana o nazwie "r-cran-".

Ten pakiet jest pakietem zbiorczym ułatwiającym przejście z instalacji pakietu wcześniejszego niż 1.5.0 do większego pakietu r-base. Po jego zainstalowaniu można go bezpiecznie usunąć, a apt-get automatycznie zaktualizuje jego komponenty podczas przyszłych aktualizacji. Po zainstalowaniu tego pakietu użytkownicy będą mogli, jeśli będą sobie tego życzyć, zainstalować pakiet r-base-core.

This R package solves a system of nonlinear equations using a Broyden or a Newton method with a choice of global strategies such as line search and trust region. There are options for using a numerical or user supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a singular or ill-conditioned Jacobian.

Scilab to oparty na macierzach pakiet oprogramowania naukowego. Scilab zawiera setki wbudowanych funkcji matematycznych, bogate struktury danych (w tym: wielomiany, wymierne, systemy liniowe, listy itp.) oraz szereg specjalistycznych zestawów narzędzi do sterowania, przetwarzania sygnałów, itd.

Ten pakiet zawiera również Xcos, edytor graficzny do projektowania hybrydowych modeli układów dynamicznych. Modele można projektować, ładować, zapisywać, kompilować i symulować. Xcos stanowi stabilne i wydajne rozwiązanie dla potrzeb przemysłu i środowiska akademickiego. Xcos zapewnia funkcje do modelowania układów mechanicznych (motoryzacja, aeronautyka ...), obwodów hydraulicznych (modelowanie zapór, rur ...), układów sterowania itp.

Aby korzystać z minimalnej wersji scilab należy zainstalować pakiet "scilab-cli".

SDPB is an open-source, arbitrary-precision, parallelized semidefinite program solver, designed for the conformal bootstrap. SDPB significantly outperforms less specialized solvers and should enable many new computations.

For more information, see "A Semidefinite Program Solver for the Conformal Bootstrap" at http://arxiv.org/abs/1502.02033.

Spyder is a powerful interactive development environment for Python providing many features and facilities, including advanced editing facilities (including tooltips and completion facilities), issue highlighting, interactive testing, debugging and introspection facilities, an embedded console (IPython) supporting graphics and much more.

This package provides the application.

There is one plugin currently available in Debian: spyder-unittest, in the package python3-spyder-unittest.

Toulbar2 is an exact discrete optimization tool for Graphical Models such as Cost Function Networks, Markov Random Fields, Weighted Constraint Satisfaction Problems and Bayesian Nets.

ViTables is a component of the PyTables family. It is a graphical tool for browsing and editing files in both PyTables and HDF5 formats.

ViTables capabilities include easy navigation through the data hierarchy, displaying of real data and its associated metadata, a simple, yet powerful, browsing of multidimensional data and much more.

One of the greatest strengths of ViTables is its ability to display very large tables. Tables with one thousand millions of rows (and beyond) are navigated stunningly fast and with very low memory requirements. So, if you ever need to browse very large tables, don't hesitate, ViTables is your choice.

xtensor is a C++ library meant for numerical analysis with multi-dimensional array expressions.

This is a dummy package transitioning to libxtensor-dev.

YADE (Yet Another Dynamic Engine - Jeszcze inny dynamiczny silnik).

Rozszerzalne środowisko otwartoźródłowe dla dyskretnych modeli numerycznych, skoncentrowane na metodzie elementów dyskretnych. Części obliczeniowe napisano w języku C++ przy użyciu elastycznego modelu obiektowego, umożliwiając niezależną implementację nowych algorytmów i interfejsów. Python służy do szybkiego i zwięzłego tworzenia scen, kontroli symulacji, przetwarzania końcowego i debugowania.

Ten pakiet zawiera zoptymalizowaną pod kątem szybkości kompilację yade.

Yorick to skryptowy język programowania służący do:

• naukowych symulacji i obliczeń;
• obróbki danych i sterowania dużymi symulacjami;
• tworzenia interaktywnych, naukowych wizualizacji;
• odczytywania, zapisywania i tłumaczenia plików zawierających duże ilości liczb.

Zaletą tego języka jest spójna składnia dla operacji na macierzach, co pozwala na bardzo szybkie i efektywne obliczenia tego typu. Na pierwszy rzut oka składnia Yoricka przypomina C, ale zmienne nigdy nie są wyraźnie deklarowane, a zasięg ich ważności jest dynamiczny podobnie jak w niektórych odmianach języka Lisp. Yorick został zaprojektowany zarówno do używania go w sposób interaktywny z poziomu klawiatury, jak i do tworzenia skryptów, które później zostaną uruchomione.

Pakiet zawiera środowisko programistyczne oparte na edytorze Emacs, które można uruchomić poprzez naciśnięcie kombinacji klawiszy M-x i wpisanie polecenia yorick.

Dostępnych jest wiele dodatkowych pakietów i wtyczek do Yoricka (nazwy pakietów zaczynają się od "yorick-"). Warto zainstalować metapakiet yorick-full, który zależy od zdecydowanej większości z nich.

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 to biblioteka C++ o otwartym kodzie źródłowym, służąca do modelowania i rozwiązywania dużych, skomplikowanych problemów optymalizacyjnych. Jest to bogata w funkcje, dojrzała i wydajna biblioteka, która jest używana w procesie produkcyjnym Google od 2010 roku.

Ceres Solver może rozwiązać dwa rodzaje problemów:

• Nieliniowe problemy najmniejszych kwadratów z ograniczeniem granic.
• Ogólne problemy optymalizacji bez ograniczeń.

Pakiet zawiera dokumentację znalezioną na stronie http://ceres-solver.org/ oraz przykłady dołączone do tego wydania.

The Coin-MP optimizer is an open source solver, it is part of the COIN-OR project which is an initiative to spur the development of open-source software for the operations research community.

CoinMP is a C-API library that supports most of the functionality of CLP (Coin LP), CBC (Coin Branch-and-Cut), and CGL (Cut Generation Library) projects.

This package contains the files needed to build applications using libCoinMP.

Surface Evolver to interaktywny program do modelowania powierzchni cieczy, kształtowanej pod wpływem różnych sił i napięć.

Pakiet zawiera warianty evolver-a skompilowane z różnymi formatami zmiennoprzecinkowymi (double, long double, quadruple), ale bez obsługi X.

Surface Evolver to interaktywny program do modelowania powierzchni cieczy, kształtowanej pod wpływem różnych sił i napięć.

Pakiet zawiera warianty evolver-a skompilowane z różnymi formatami zmiennoprzecinkowymi (double, long double, quadruple), i z wyświetlaczem opartym na OpenGL/GLUT.

Test porównawczy dotyczący wysokiej wydajności obliczeniowej (HPC) uruchamia zestaw 7 testów mierzących wydajność procesora, pamięci i sieci dla klastrów HPC. Obejmuje on między innymi test wydajnościowy LINPACK (HPL), stosowany w rankingu Top500 (http://www.top500.org/).

Neartree is an API and a library for finding nearest neighbors among points in spaces of arbitrary dimensions. This package provides a C++ template, TNear.h, and C library and header files for compiling programs using Neartree.

The library uses the Nearest Neighbor algorithm after Kalantari and McDonald, (IEEE Transactions on Software Engineering, v. SE-9, pp. 631-634,1983) modified to use recursion instead of a double-linked tree and simplified so that it does less checking for things like is the distance to the right less than the distance to the left; it was found that these checks make little to no difference.

A lightweight C++ library of numerical optimization methods for nonlinear functions, including L-BFGS-B for TensorFlow

This is a simple C package for adaptive multidimensional integration (cubature) of vector-valued integrands over hypercubes. Of course, it can handle scalar integrands as the special case where f is a one-dimensional vector: the dimensionalities of f and x are independent. The integrand can be evaluated for an array of points at once to enable easy parallelization.

This package contains the development files.

LBFGS++ is a header-only C++ library that implements the Limited-memory BFGS algorithm (L-BFGS) for unconstrained minimization problems, and a modified version of the L-BFGS-B algorithm for box-constrained ones.

Psurface is a C++ library that handles piecewise linear bijections between triangulated surfaces. These surfaces can be of arbitrary shape and need not even be manifolds.

There are two main uses for psurface. When doing adaptive finite element simulations on grids with parametrized boundaries, psurface can store the parametrization. Boundary parametrizations are practically mappings from the coarse grid boundary to the actual boundary, and if that actual boundary is a triangulated surface then psurface can handle it. This is implemented, for example, in the dune-grid module of Dune.

Secondly, when doing domain decomposition methods with nonconforming interfaces, you need to relate the two interface grids to each other. Psurface can do this for you, even if your interfaces do not match geometrically. Such is the case, e.g., in contact problems. This second functionality is also available for 1d surfaces in 2d space.

The easiest way to use psurface for domain decomposition is to get the dune-grid-glue module and use it to drive psurface.

This package contains the development files.

libquantum is a C library for the simulation of a quantum computer. Based on the principles of quantum mechanics, it provides an implementation of a quantum register. Basic operations for register manipulation such as the Hadamard gate or the Controlled-NOT gate are available through an easy-to-use interface. Measurements can be performed on either single qubits or the whole quantum register.

Features:

• Simulation of arbitrary quantum algorithms is possible
• High performance and low memory consumption
• Decoherence support for realistic quantum computation
• Interface for quantum error correction (QEC)
• Supports the density operator formalism
• Implementations of Shor's factoring algorithm and Grover's search algorithm are included

This package contains the header files and static libraries which are needed to develop applications based on libquantum.

The STochastic OPTimization library (StOpt) aims at providing tools in C++ for solving some stochastic optimization problems encountered in finance or in the industry. Different methods are available:

• dynamic programming methods based on Monte Carlo with regressions (global, local, kernel and sparse regressors), for underlying states following some uncontrolled Stochastic Differential Equations;
• dynamic programming with a representation of uncertainties with a tree: transition problems are here solved by some discretizations of the commands, resolution of LP with cut representation of the Bellman values;
• Semi-Lagrangian methods for Hamilton Jacobi Bellman general equations for underlying states following some controlled Stochastic Differential Equations;
• Stochastic Dual Dynamic Programming methods to deal with stochastic stock management problems in high dimension. Uncertainties can be given by Monte Carlo and can be represented by a state with a finite number of values (tree);
• Some branching nesting methods to solve very high dimensional non linear PDEs and some appearing in HJB problems. Besides some methods are provided to solve by Monte Carlo some problems where the underlying stochastic state is controlled. For each method, a framework is provided to optimize the problem and then simulate it out of the sample using the optimal commands previously computed. Parallelization methods based on OpenMP and MPI are provided in this framework permitting to solve high dimensional problems on clusters. The library should be flexible enough to be used at different levels depending on the user's willingness.

This package contains the headers and the static libraries (libstopt-mpi which allows for multithreading, and libstopt which does not).

Agate is a Python data analysis library that is optimized for humans instead of machines. It is an alternative to numpy and pandas that solves real-world problems with readable code.

Why agate?

• A readable and user-friendly API.
• A complete set of SQL-like operations.
• Unicode support everywhere.
• Decimal precision everywhere.
• Exhaustive user documentation.
• Pluggable extensions that add SQL integration, Excel support, and more.
• Designed with iPython, Jupyter and atom/hydrogen in mind.
• Pure Python. No C dependencies to compile.
• Exhaustive test coverage.
• MIT licensed and free for all purposes.
• Zealously zen.
• Made with love.

This package provides the modules for Python 3.