Debian Science Project
Summary
Mathematics
Debian Science Mathematics packages

This metapackage will install Debian Science packages related to Mathematics. You might also be interested in the field::mathematics debtag and, depending on your focus, in the education-mathematics metapackage.

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 Mathematics packages

Official Debian packages with high relevance

4ti2
mathematical tool suite for problems on linear spaces -- tools
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4ti2 is a mathematical software package for algebraic, geometric and combinatorial problems on linear spaces.

This package provides the 4ti2 tool suite.

agda
dependently typed functional programming language
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Agda is a dependently typed functional programming language: It has inductive families, which are like Haskell's GADTs, but they can be indexed by values and not just types. It also has parameterised modules, mixfix operators, Unicode characters, and an interactive Emacs interface (the type checker can assist in the development of your code).

Agda is also a proof assistant: It is an interactive system for writing and checking proofs. Agda is based on intuitionistic type theory, a foundational system for constructive mathematics developed by the Swedish logician Per Martin-Löf. It has many similarities with other proof assistants based on dependent types, such as Coq, Epigram and NuPRL.

This is a meta package which provides Agda's emacs mode, executable, standard library and its documentation.

auto-07p
software for continuation and bifurcation problems in ODE
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AUTO can do a limited bifurcation analysis of algebraic systems of the form

  f(u,p) = 0,  f,u in Rn
and of systems of ordinary differential equations of the form
  u'(t) = f(u(t),p),  f,u in Rn
subject to initial conditions, boundary conditions, and integral

constraints. Here p denotes one or more parameters. AUTO can also do certain continuation and evolution computations for parabolic PDEs. It also includes the software HOMCONT for the bifurcation analysis of homoclinic orbits. AUTO is quite fast and can benefit from multiple processors; therefore it is applicable to rather large systems of differential equations.

axiom
General purpose computer algebra system: main binary and modules
Maintainer: Camm Maguire
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Axiom is useful for research and development of mathematical algorithms. It defines a strongly typed, mathematically correct type hierarchy. It has a programming language and a built-in compiler.

Axiom has been in development since 1973 and was sold as a commercial product. It has been released as free software.

Efforts are underway to extend this software to (a) develop a better user interface (b) make it useful as a teaching tool (c) develop an algebra server protocol (d) integrate additional mathematics (e) rebuild the algebra in a literate programming style (f) integrate logic programming (g) develop an Axiom Journal with refereed submissions.

This package contains the main program binary and all precompiled algebra and autoloadable modules.

bliss
tool to compute graph automorphisms and labelings -- bin
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Bliss is a backtracking algorithm for computing automorphism groups and canonical forms of graphs, based on individualization and refinement. Its data structures, subroutines, and pruning heuristics are specially designed for fast handling of large and sparse graphs.

This package provides the command line tool bliss.

cohomcalg
sheaf cohomology of line bundles on toric varieties
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The algorithm for the computation of sheaf cohomologies for line bundles on toric varieties presented in "Cohomology of Line Bundles: A Computational Algorithm" by Ralph Blumenhagen, Benjamin Jurke, Thorsten Rahn, and Helmut Roschy has been implemented in a convenient and high-performance C/C++ application called cohomCalg.

The optional cohomCalg Koszul extension serves as a Mathematica 7 frontend and allows for the easy computation of hypersurface and complete intersection cohomologies, following the material presented in "Cohomology of Line Bundles: Applications" by the same authors.

Please cite: Ralph Blumenhagen, Benjamin Jurke, Thorsten Rahn and Helmut Roschy: Cohomology of Line Bundles: A Computational Algorithm. J. Math. Phys. 51 (2010)
coinor-cbc
Coin-or branch-and-cut mixed integer programming solver
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Cbc (Coin-or branch and cut) is an open-source mixed integer programming solver written in C++. It can be used as a callable library or as a stand-alone executable.

This package contains cbc executable.

coinor-csdp
Software package for semidefinite programming (binaries)
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CSDP is a library of routines that implements a predictor corrector variant of the semidefinite programming algorithm of Helmberg, Rendl, Vanderbei, and Wolkowicz. The code runs in parallel on shared memory multi-processor systems, and it makes effective use of sparsity in the constraint matrices.

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

This package contains the binaries.

Please cite: Borchers, Brian: CSDP, AC library for semidefinite programming. (eprint) Optimization methods and Software 11(1-4):612-623 (1999)
coinor-libbonmin-dev
COIN-OR mixed integer programming (developer files)
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Bonmin (Basic Open-source Nonlinear Mixed INteger programming) is an open-source code for solving general MINLP (Mixed Integer NonLinear Programming) problems.

Bonmin is part of the larger COIN-OR initiative (Computational Infrastructure for Operations Research) and can be used with other COIN-OR packages that make use of cuts, such as the mixed-integer linear programming solver Cbc.

This package contains the header files for developers.

coinor-symphony
COIN-OR solver for mixed-integer linear programs
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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.

coq
proof assistant for higher-order logic (toplevel and compiler)
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Coq is a proof assistant for higher-order logic, which allows the development of computer programs consistent with their formal specification. It is developed using Objective Caml and Camlp5.

This package provides coqtop, a command line interface to Coq.

A graphical interface for Coq is provided in the coqide package. Coq can also be used with ProofGeneral, which allows proofs to be edited using emacs and xemacs. This requires the proofgeneral package to be installed.

The package is enhanced by the following packages: libaac-tactics-ocaml libssreflect-ocaml
cryptominisat
SAT solver command line interface
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CryptoMiniSat is a modern, multi-threaded, simplifying SAT solver.

This package provides a command line interface which reads SAT formulas in conjunctive normal form in the DIMACS format with the extension of XOR clauses and decides whether they are satisfiable.

eclib-tools
Programs for modular symbols and elliptic curves over Q
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This package includes several programs to compute with elliptic curves over Q ; most notably mwrank (for 2-descent on elliptic curves over Q) and the modular symbol tools used to create the elliptic curve database.

eprover
Equational theorem prover
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This package provides tools to prove equational theorems: from a mathematical specification in many-sorted first-order logic with equality and an hypothesis/conjecture, it will look for a proof.

Remark of Debian Science team: Removed from Debian

This package was removed from Debian but some versions are available from http://snapshot.debian.org/

Reasons are given here: http://bugs.debian.org/651971

feel++-apps
A library for the finite element method
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Provides some applications codes(source and executables) such as laplacian with cG and dG methods, stokes, heat transfer, solid mechanics(static and dynamic).

Feel++ is a versatile finite element library to solve partial differential equations

Support 1D, 2D, 3D

Support the following basic entities: simplices (segment, triangle, tetrahedron) and product of simplices (quadrangle, hexahedron)

Support various point sets on these basic entities: equispaced points, quadrature points, interpolation points (Gauss-Lobatto, Fekete, WarpBlend?)

Support continuous and discontinuous Galerkin methods

Support various polynomial sets:

  • Lagrange(continuous,discontinuous,all dimensions,all interpolation point sets)

  • Dubiner(discontinuous), boundary adapted(continuous)

  • Legendre(discontinuous), boundary adapted(continuous)

Provide mathematical concept for higher order abstraction (Function spaces and associated elements, forms and operators)

Provide a language embedded in C++ for variational formulations, projection and numerical integration

fenics
Automated Solution of Differential Equations
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FEniCS is a collection of free software for automated, efficient solution of differential equations.

FEniCS has an extensive list of features, including automated solution of variational problems, automated error control and adaptivity, a comprehensive library of finite elements, high performance linear algebra and many more.

FEniCS is organized as a collection of interoperable components, including the problem-solving environment DOLFIN, the form compiler FFC, the finite element tabulator FIAT, the just-in-time compiler Instant, the code generation interface UFC, the form language UFL and a range of additional components.

This is a metapackage which depends on all FEniCS components.

This is the legacy version of FEniCS. You may want to consider installing the next-generation FEniCS-X (fenicx package).

flintqs
Program using quadratic sieve to factor integers
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This package includes William Hart's program to find prime factors of large integers (at least forty digits).

It does so using highly optimized multi-polynomial quadratic sieve.

form
Symbolic manipulation system
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This is a Symbolic Manipulation System. It reads symbolic expressions from files and executes symbolic/algebraic transformations upon them. The answers are returned in a textual mathematical representation. As its landmark feature, the size of the considered expressions in FORM is only limited by the available disk space and not by the available RAM.

fplll-tools
Tools to compute LLL-reduction of Euclidian lattices
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fpLLL is a library for computing reduced (nearly orthogonal) bases for Euclidean lattices using the floating-point LLL algorithm.

fpLLL contains multiple different implementations of the floating-point LLL reduction algorithm, offering multiple different speed/guarantees ratios.

It contains a 'wrapper' that chooses the estimated best sequence of variants in order to provide a guaranteed output as fast as possible. In the case of the wrapper, the succession of variants is oblivious to the user.

This package contains the base tools using libfplll.

freefem
PDE oriented language using Finite Element Method
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FreeFEM is a language adapted to Partial Differential equation. The underlying method used is the Finite Element Method. This tool has been successfully used as a teaching tool and even as a research tool.

freefem++
Provides the binaries of the FreeFem++ FE suite
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FreeFem++ is an implementation of a language dedicated to the finite element method. It enables you to solve Partial Differential Equations (PDE) easily.

Problems involving PDE from several branches of physics such as fluid-structure interactions require interpolations of data on several meshes and their manipulation within one program. FreeFem++ includes a fast quadtree-based interpolation algorithm and a language for the manipulation of these data on multiple meshes. It contains also a powerful mesh generation and adaption tool integrated seamlessly in FreeFem++ called bamg.

FreeFem++ is written in C++ and the FreeFem++ language is a C++ idiom allowing for a smooth learning curve.

This package contains the executables of FreeFem++.

Please cite: Hecht, F.: New development in FreeFem++. J. Numer. Math. 20(3-4):251-265 (2012)
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freefem3d
Language and solver for partial differential equations in 3D
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FreeFEM3D (aka ff3d) is a 3D solver of partial differential equations (PDE). It is a member of the familly of the freefem programs (see http://www.freefem.org).

ff3d, as well as its cousins, is a PDE solver driven by a user-friendly language. It solves many kind of problems such as elasticity, fluids (Stokes and Navier-Stokes) and a lot more. The user has to enter the equation associated with the problem, giving either the PDE in strong formulation or weak (variational) formulation.

ff3d can use either the Finite Elements method (the mesh of the geometry being provided by the user) or a Fictitious Domain like approach where the geometry is described using Constructive Solid Geometry (CSG). This description is done using the POV-Ray language but others such as VRML could be added.

The processing of the results is left to the user. One can use various graphic tools: output in the MEdit mesh format or VTK are supported. The implementation of a VTK base visualization module is underway.

The goal of ff3d is to provide a good teaching tool and a research toolbox (the code is written in C++ and its design is such that new methods can be easily implemented).

freemat
mathematics framework (mostly matlab compatible)
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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.

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frobby
Computations with monomial ideals
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Frobby is a software system and project for computations with monomial ideals. Frobby is free software and it is intended as a vehicle for computational and mathematical research on monomial ideals.

The current functionality includes Euler characteristic, Hilbert series, maximal standard monomials, combinatorial optimization on monomial ideals, primary decomposition, irreducible decomposition, Alexander dual, associated primes, minimization and intersection of monomial ideals as well as the computation of Frobenius problems (using 4ti2) with very mmlarge numbers. Frobby is also able to translate between formats that can be used with several different computer systems, such as Macaulay 2, Monos, 4ti2, CoCoA4 and Singular. Thus Frobby can be used with any of those systems.

gap
computer algebra system for Groups, Algorithms and Programming
Maintainer: Bill Allombert
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GAP is a system for computational discrete algebra, with particular emphasis on Computational Group Theory. GAP provides a programming language, a library of thousands of functions implementing algebraic algorithms written in the GAP language as well as large data libraries of algebraic objects. GAP is used in research and teaching for studying groups and their representations, rings, vector spaces, algebras, combinatorial structures, and more.

This is a dummy package that depends on the standard GAP components.

gap-character-tables
GAP Library of character tables
Maintainer: Bill Allombert
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GAP is a system for computational discrete algebra, with particular emphasis on Computational Group Theory. GAP provides a programming language, a library of thousands of functions implementing algebraic algorithms written in the GAP language as well as large data libraries of algebraic objects. GAP is used in research and teaching for studying groups and their representations, rings, vector spaces, algebras, combinatorial structures, and more.

This package contains the Character Table Library by Thomas Breuer.

gap-design
block designs for GAP
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GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas.

This package provides for GAP routines for constructing, classifying, partitioning and studying block designs.

gap-factint
advanced methods for factoring integers for GAP
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GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas.

This package brings to GAP routines for factoring integers, in particular:

  • Pollard's p-1
  • Williams' p+1
  • Elliptic Curves Method (ECM)
  • Continued Fraction Algorithm (CFRAC)
  • Multiple Polynomial Quadratic Sieve (MPQS)

It also provides access to Richard P. Brent's tables of factors of integers of the form b^k +/- 1.

gap-float
multi-precision floating-point computation for GAP
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GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas.

This GAP package brings to GAP floating-point numbers with arbitrary precision; it is based on MPFR, MPFI, MPC, CXSC, and FPLLL.

gap-grape
GRaph Algorithms using PErmutation groups for GAP
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GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas.

This package implements computing with graphs and groups for GAP. GRAPE is primarily designed for constructing and analysing graphs related to groups, finite geometries, and designs; special emphasis is placed on the determination of regularity properties and subgraph structure.

gap-guava
coding theory library for GAP
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GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas.

This GAP package brings to GAP computing with error-correcting codes.

gap-laguna
LAGUNA GAP package
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GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas.

LAGUNA stands for `Lie AlGebras and UNits of group Algebras'.

This package provides GAP with functionality for calculation of the normalized unit group of the modular group algebra of the finite p-group and for investigation of Lie algebra associated with group algebras and other associative algebras.

gap-openmath
OpenMath phrasebook for GAP
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GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas.

This package allows GAP to import and export mathematical objects encoded in OpenMath, for the purpose of exchanging them with other applications that are OpenMath enabled.

gap-prim-groups
Database of primitive groups for GAP
Maintainer: Bill Allombert
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GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas. In the example text, gap is used to analyse Rubik's Cube using group theory. A kernel implements a Pascal-like language.

This package contains the database of primitive groups.

This is a transitional package. It can be safely removed after the installation is complete.

gap-small-groups
Database of small groups for GAP
Maintainer: Bill Allombert
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GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas. In the example text, gap is used to analyse Rubik's Cube using group theory. A kernel implements a Pascal-like language.

The Small Groups Library is a catalogue of groups of `small' order. This package contains the groups data and identification routines for groups of order up to 1000 except 512, 768 and groups whose order factorises in at most 3 primes.

Note that data for order 512, 768 and between 1000 and 2000 except 1024 are available separately in the gap-small-groups-extra packages.

This is a transitional package. It can be safely removed after the installation is complete.

gap-small-groups-extra
Large database of small groups for GAP
Maintainer: Bill Allombert
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GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas. In the example text, gap is used to analyse Rubik's Cube using group theory. A kernel implements a Pascal-like language.

The Small Groups Library is a catalogue of groups of `small' order. This package contains the groups data and identification routines for groups

  • of order at most 2000 except 1024.
  • of cubefree order at most 50 000.
  • of order p^n for n <= 6 and all primes p.
  • of squarefree order.
  • whose order factorises in at most 3 primes.
  • of order q^n * p for q^n dividing 2^8, 3^6, 5^5, 7^4 and p prime different to q

The Small Groups Library provides access to these groups and a method to identify the catalogue number of a given group.

This is a transitional package. It can be safely removed after the installation is complete.

gap-sonata
Systems Of Nearrings And Their Applications for GAP
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GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas.

This package provides to GAP methods for the construction and analysis of finite nearrings.

gap-table-of-marks
GAP TomLib - The GAP Library of Tables of Marks
Maintainer: Bill Allombert
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GAP is a system for computational discrete algebra, with particular emphasis on Computational Group Theory. GAP provides a programming language, a library of thousands of functions implementing algebraic algorithms written in the GAP language as well as large data libraries of algebraic objects. GAP is used in research and teaching for studying groups and their representations, rings, vector spaces, algebras, combinatorial structures, and more.

This package contains the GAP Library of Tables of Marks by L. Naughton and G. Pfeiffer.

gap-toric
toric variety for GAP
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GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas.

This package provides for GAP routines for working with toric varieties and dealing with cones and related combinatorial geometric object.

gap-trans-groups
Database of transitive groups for GAP
Maintainer: Bill Allombert
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GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas. In the example text, gap is used to analyse Rubik's Cube using group theory. A kernel implements a Pascal-like language.

This package contains the database of transitive groups.

This is a transitional package. It can be safely removed after the installation is complete.

geneagrapher
Create tree from Mathematics Genealogy Project (executable)
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The Mathematics Genealogy Grapher (Geneagrapher) is a software tool to gather the information for building math genealogy trees with data from the Mathematics Genealogy Project. The information extracted is stored in dot file format, which can then be passed to Graphviz to generate a graph.

This package contains the command-line tool.

geogebra
Dynamic mathematics software for education
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GeoGebra is a dynamic geometry program. You can do constructions with points, vectors, segments, lines, conic sections as well as functions and change them dynamically afterwards. On the other hand, equations and coordinates can be entered directly.

Support for many geometric constructions is provided, as well as support for many calculus-based tools (derivatives, osculating circle, ...).

GeoGebra files can be exported in many different formats, or as interactive applets for web pages.

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geomview
interactive geometry viewing program
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Geomview is interactive geometry software which is particularly appropriate for mathematics research and education. In particular, geomview can display things in hyperbolic and spherical space as well as Euclidean space.

Geomview allows multiple independently controllable objects and cameras. It provides interactive control for motion, appearances (including lighting, shading, and materials), picking on an object, edge or vertex level, snapshots in SGI image file or Renderman RIB format, and adding or deleting objects is provided through direct mouse manipulation, control panels, and keyboard shortcuts. External programs can drive desired aspects of the viewer (such as continually loading changing geometry or controlling the motion of certain objects) while allowing interactive control of everything else.

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gerris
Fluid Flow Solver
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Gerris is a system for the solution of the partial differential equations describing fluid flow.

A brief summary of its main (current) features:

  • Solves the time-dependent incompressible variable-density Euler, Stokes or Navier-Stokes equations
  • Adaptive mesh refinement: the resolution is adapted dynamically to the features of the flow
  • Entirely automatic mesh generation in complex geometries
  • Second-order in space and time
  • Unlimited number of advected/diffused passive tracers
  • Flexible specification of additional source terms
  • Portable parallel support using the MPI library
  • Volume of Fluid advection scheme for interfacial flows

This package has MPI support built in.

getdp
general environment for the treatment of discrete problems
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GetDP is a general finite element solver using mixed elements to discretize de Rham-type complexes in one, two and three dimensions.

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

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

Please cite: P. Dular, C. Geuzaine, A. Genon and W. Legros: An evolutive software environment for teaching finite element methods in electromagnetism. IEEE Transactions on Magnetics 35(3):1682 - 1685 (1999)
gfan
program for computing with Groebner fans
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Gfan is a software package for computing Groebner fans and tropical varieties. These are polyhedral fans associated to polynomial ideals. The maximal cones of a Groebner fan are in bijection with the marked reduced Groebner bases of its defining ideal. The software computes all marked reduced Groebner bases of an ideal. Their union is a universal Groebner basis. The tropical variety of a polynomial ideal is a certain subcomplex of the Groebner fan. Gfan contains algorithms for computing this complex for general ideals and specialized algorithms for tropical curves, tropical hypersurfaces and tropical varieties of prime ideals. In addition to the above core functions the package contains many tools which are useful in the study of Groebner bases, initial ideals and tropical geometry. Among these are an interactive traversal program for Groebner fans and programs for graphical renderings.

For ordinary Groebner basis computations Gfan is not competitive in speed compared to programs such as CoCoA, Singular and Macaulay2.

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ginac-tools
GiNaC symbolic framework support tools
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GiNaC (which stands for "GiNaC is Not a CAS (Computer Algebra System)") is a library for doing symbolic (i.e. non-numeric) computation directly in the C++ programming language.

This package provides some additional tools, like the popular ginsh (GiNaC interactive shell) and viewgar (for inspecting GiNaC archive files).

gmsh
Three-dimensional finite element mesh generator
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Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor. Its design goal is to provide a fast, light and user-friendly meshing tool with parametric input and advanced visualization capabilities. Gmsh is built around four modules: geometry, mesh, solver and post-processing. The specification of any input to these modules is done either interactively using the graphical user interface or in ASCII text files using Gmsh's own scripting language.

See Gmsh's reference manual for a more thorough overview of Gmsh's capabilities.

Please cite: C. Geuzaine and J.-F. Remacle: Gmsh: a three-dimensional finite element mesh generator with built-in pre- and post-processing facilities. (eprint) International Journal for Numerical Methods in Engineering 79(11):1309-1331 (2009)
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graphviz
rich set of graph drawing tools
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Graph drawing addresses the problem of visualizing structural information by constructing geometric representations of abstract graphs and networks. Automatic generation of graph drawings has important applications in key technologies such as database design, software engineering, VLSI and network design and visual interfaces in other domains. Situations where these tools might be particularly useful include:

  • you would like to restructure a program and first need to understand the relationships between its types, procedures, and source files
  • you need to find the bottlenecks in an Internet backbone - not only individual links, but their relationships
  • you're debugging a protocol or microarchitecture represented as a finite state machine and need to figure out how a certain error state arises
  • you would like to browse a database schema, knowledge base, or distributed program represented graphically
  • you would like to see an overview of a collection of linked documents
  • you would like to discover patterns and communities of interest in a database of telephone calls or e-mail messages

This package contains the command-line tools.

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hol-light
HOL Light theorem prover
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HOL Light is an interactive theorem prover for Higher-Order Logic with a very simple logical core running in an OCaml toplevel. HOL Light is famous for the verification of floating-point arithmetic as well as for the Flyspeck project, which aimed at the formalization of Tom Hales' proof of the Kepler conjecture.

julia
high-performance programming language for technical computing
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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).

lcalc
program for calculating with L-functions
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lcalc is a program for computing zeros and values of L-functions. Supported L-functions include the Riemann zeta function, the L-function of the Ramanujan delta function, and L-functions of elliptic curves defined over the rationals.

libjgrapht-java
Java library of graph theory data structures and algorithms
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JGraphT is a free Java class library that provides mathematical graph-theory objects and algorithms. In JGraphT, a graph is defined as a set of vertices connected by a set of edges.

It is possible to define graphs, to modify, compare or generate them, to run many algorithms through them. One may also import or export graphs.

libmatheval1
GNU library for evaluating symbolic mathematical expressions (runtime)
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GNU libmatheval is a library comprising of several procedures that make it possible to create an in-memory tree representation of mathematical functions over single or multiple variables and later use this representation to evaluate functions for specified variable values, to create corresponding trees for function derivatives over specified variables or to print textual representations of in-memory trees to a specified string. The library supports arbitrary variable names in expressions, decimal constants, basic unary and binary operators and elementary mathematical functions.

This package contains the runtime shared library.

lp-solve
Solve (mixed integer) linear programming problems
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The linear programming (LP) problem can be formulated as: Solve A.x >= V1, with V2.x maximal. A is a matrix, x is a vector of (nonnegative) variables, V1 is a vector called the right hand side, and V2 is a vector specifying the objective function.

An integer linear programming (ILP) problem is an LP with the constraint that all the variables are integers. In a mixed integer linear programming (MILP) problem, some of the variables are integer and others are real.

The program lp_solve solves LP, ILP, and MILP problems. It is slightly more general than suggested above, in that every row of A (specifying one constraint) can have its own (in)equality, <=, >= or =. The result specifies values for all variables.

lp_solve uses the 'Simplex' algorithm and sparse matrix methods for pure LP problems. If one or more of the variables is declared integer, the Simplex algorithm is iterated with a branch and bound algorithm, until the desired optimal solution is found. lp_solve can read MPS format input files.

lrcalc
programs for calculating Littlewood-Richardson coefficients
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The "Littlewood-Richardson Calculator" is a package of C programs for computing Littlewood-Richardson coefficients, providing fast calculation of single LR coefficients, products of Schur functions, and skew Schur functions. Its interface uses the same notation as the SF package of John Stembridge, to make it easier to use both packages at the same time.

This package contains the command-line programs.

lrslib
package to enumerate vertices and extreme rays of a convex polyhedron
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A convex polyhedron is the set of points satisfying a finite family of linear inequalities. The study of the vertices and extreme rays of such systems is important and useful in e.g. mathematics and optimization. In a dual interpretation, finding the vertices of a (bounded) polyhedron is equivalent to finding the convex hull (bounding inequalities) of an (arbitrary dimensional) set of points. Lrs (lexicographic reverse search) has two important features that can be very important for certain applications: it works in exact arithmetic, and it consumes memory proportional to the input, no matter how large the output is.

macaulay2
Software system for algebraic geometry research
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Macaulay 2 is a software system for algebraic geometry research, written by Daniel R. Grayson and Michael E. Stillman. Based on Groebner bases, it provides algorithms for computing homological invariants of rings and modules.

This package contains the architecture dependent portion of Macaulay2.

Please cite: Daniel R. Grayson and Michael E. Stillman: Macaulay2, a software system for research in algebraic geometry.
magnus
Very simple screen magnifier
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Magnus is a simple screen magnifying glass. It nicely integrates with X11 desktops like MATE or Xfce (probably with others not named here, too).

Visually impaired users may find this tool helpful for zooming into certain screen areas in order to improve readability/visibilty of fonts, icons and other data.

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mathicgb
Compute Groebner bases (command line tool)
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Mathicgb is a program for computing Groebner basis and signature Groebner bases. Mathicgb is based on the fast data structures from mathic.

The paper "Practical Groebner Basis Computation" describes the algorithms in Mathicgb from a high level. It was presented at ISSAC 2012 and is available at http://arxiv.org/abs/1206.6940

This package contains the command line tool.

Please cite: Bjarke Hammersholt Roune and Michael Stillman: Practical Groebner Basis Computation. (eprint) Proceedings of the International Symposium on Symbolic and Algebraic Computation (2012)
mathomatic
portable Computer Algebra System (CAS)
Maintainer: tony mancill
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Mathomatic implements most of the rules of algebra for the mathematical operators +, -, *, /, % (modulus), and power (including roots).

Mathomatic can symbolically:

  • combine and solve equations,
  • completely simplify and compare expressions and equations,
  • do simple calculus transformations and series,
  • do standard, complex number, modular, and polynomial arithmetic,
  • generate optimized C, Java, and Python language code from simplified equations,
  • plot expressions with gnuplot in two or three dimensions,
  • do quick calculations, colorize expressions, etc.
matita
interactive theorem prover
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Matita is a graphical interactive theorem prover based on the Calculus of (Co)Inductive Constructions.

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maxima-sage
Computer algebra system -- base system
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Maxima 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. It has a symbolic source level debugger for maxima code. Maxima is based on the original Macsyma developed at MIT in the 1970s. It is quite reliable, and has good garbage collection, and no memory leaks. It comes with hundreds of self tests.

The maxima-sage packages are meant to be used together with SageMath. They contain the version of Maxima that works together with the SageMath version in Debian and use ECL instead of GCL as Lisp compiler. To use Maxima by itself, the more complete and up-to-date maxima package is recommended.

This package contains the main executables and base system files.

mcl
Markov Cluster algorithm
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The MCL package is an implementation of the MCL algorithm, and offers utilities for manipulating sparse matrices (the essential data structure in the MCL algorithm) and conducting cluster experiments.

MCL is currently being used in sciences like biology (protein family detection, genomics), computer science (node clustering in Peer-to-Peer networks), and linguistics (text analysis).

The package is enhanced by the following packages: zoem
Please cite: Stijn van Dongen and Cei Abreu-Goodger: Using MCL to extract clusters from networks. (PubMed,eprint) Methods Mol Biol. 804:281-95 (2012)
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minisat
Fast and lightweight SAT solver
Maintainer: Michael Tautschnig
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Despite the NP completeness of the satisfiability problem of Boolean formulas (SAT), SAT solvers are often able to decide this problem in a reasonable time frame. As all other NP complete problems are reducible to SAT, the solvers have become a general purpose tool for this class of problems.

MiniSat is a minimalistic, open-source SAT solver, developed to help researchers and developers alike to get started on SAT. Winning all the industrial categories of the SAT 2005 competition, MiniSat is a good starting point both for future research in SAT, and for applications using SAT.

model-builder
graphical ODE simulator
Maintainer: Varun Hiremath (Olly Betts)
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Model Builder is a graphical tool for designing, simulating and analyzing Mathematical model consisting of a system of ordinary differential equations(ODEs).

mumps-test
Example/test binaries using MUMPS
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MUMPS implements a direct solver for large sparse linear systems, with a particular focus on symmetric positive definite matrices. It can operate on distributed matrices e.g. over a cluster. It has Fortran and C interfaces, and can interface with ordering tools such as Scotch.

nauty
library for graph automorphisms -- interface and tools
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nauty (No AUTomorphisms, Yes?) is a set of procedures for computing automorphism groups of graphs and digraphs. This mathematical software suite is developed by Brendan McKay and Adolfo Piperno: http://pallini.di.uniroma1.it

nauty computes graph information in the form of a set of generators, the size of the group, and the orbits of the group; it can also produce a canonical label. The nauty suite is written in C and comes with a command-line interface, a collection of command-line tools, and an Application Programming Interface (API).

This package provides the nauty interface named dreadnaut, and a small collection of utilities called gtools.

The package is enhanced by the following packages: nauty-doc
Please cite: B.D. McKay and A. Piperno: Practical graph isomorphism, II. Journal of Symbolic Computation 60(0):94 - 112 (2014)
netgen
Automatic 3d tetrahedral mesh generator
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NETGEN is an automatic 3d tetrahedral mesh generator. It accepts input from constructive solid geometry (CSG) or boundary representation (BRep) from STL file format. NETGEN contains modules for mesh optimization and hierarchical mesh refinement.

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normaliz
math computing tools for affine monoids, rational polytopes and cones
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Normaliz is a mathematical tool for computations in affine monoids, vector configurations, lattice polytopes, and rational cones.

This dummy package provides the standard installation.

octave
GNU Octave language for numerical computations
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Octave is a (mostly MATLAB® 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.

The package is enhanced by the following packages: liboctave-dev octave-dev octave-doc
Please cite: John W. Eaton, David Bateman, Søren Hauberg and Rik Wehbring: GNU Octave version 4.2.0 manual: a high-level interactive language for numerical computations. (2016)
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palp
Package for Analyzing Lattice Polytopes
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This package contains various tools to work with lattice polytopes:

  • mori.x computes star triangulations of a polytope
  • cws.x creates weight systems and combined weight systems
  • class.x classifies reflexive polytopes
  • poly.x computes data of a polytope
  • nef.x computes Hodge numbers of nef-partitions
Please cite: Maximilian Kreuzer and Harald Skarke: PALP: A Package for Analyzing Lattice Polytopes with Applications to Toric Geometry. Computer Physics Communications 157:87-106 (2004)
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pari-gp
PARI/GP Computer Algebra System binaries
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PARI/GP is a widely used computer algebra system designed for fast computations in number theory (factorizations, algebraic number theory, elliptic curves...), but also contains a large number of other useful functions to compute with mathematical entities such as matrices, polynomials, power series, algebraic numbers etc., and a lot of transcendental functions. PARI is also available as a C library to allow for faster computations.

Originally developed by Henri Cohen and his co-workers (University Bordeaux I, France), PARI is now under the GPL and maintained by Karim Belabas with the help of many volunteer contributors.

This package contains the GP calculator.

persalys
GUI for uncertainty treatment and variabilities management
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Persalys is a graphical user interface for OpenTURNS, dedicated to the treatment of uncertainty and the management of variabilities. The software is a tool between the computer simulation, probabilistic analyses and the data sciences. The interface is available in French or in English.

Persalys allows one to:

  • create mathematical models: analytical, coupling with an external model (finite elements, ...), FMU;
  • analyse the variability of one's parameters thanks to many methods and visualisation tools;
  • statistically analyse one's measuring data, infer probability distributions or create metamodels.
phcpack
general-purpose solver for polynomial systems (command line)
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PHCpack is a software package to solve polynomial systems by homotopy continuation methods.

A polynomial system is given as a sequence of polynomials in several variables. Homotopy continuation methods operate in two stages. In the first stage, a family of polynomial systems (the so-called homotopy) is constructed. This homotopy contains a polynomial system with known solutions. In the second stage, numerical continuation methods are applied to track the solution paths defined by the homotopy, starting at the known solutions and leading to the solutions of the given polynomial system.

This package contains the command line interface to PHCpack.

Please cite: Verschelde, Jan: Algorithm 795: PHCpack: A general-purpose solver for polynomial systems by homotopy continuation ACM Trans. Math. Software 25(2):251-276 (1999)
planarity
Program for planarity-related graph algorithms
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This package contains a command-line reference implementation of the Edge Addition Planarity Algorithm, which is the best linear-time method to embed a planar graph and isolate planarity obstructions.

polylib-utils
Various tools using libpolylib
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Polylib is a free C library for doing computations on polyhedra. The library is operating on objects like vectors, matrices, lattices, polyhedra, Z-polyhedra, unions of polyhedra and other intermediary structures. It provides functions for all important operations on these structures.

This package contains various utilities to perform polyhedral operations.

proofgeneral
generic frontend for proof assistants
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Proof General is a major mode to turn Emacs into an interactive proof assistant to write formal mathematical proofs using a variety of theorem provers.

This package provides Proof General support for Coq. (There is no other proof assistant that one could sensibly support.)

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prover9
theorem prover and countermodel generator
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This package provides the Prover9 resolution/paramodulation theorem prover and the Mace4 countermodel generator.

Prover9 is an automated theorem prover for first-order and equational logic. It is a successor of the Otter prover. Prover9 uses the inference techniques of ordered resolution and paramodulation with literal selection.

The program Mace4 searches for finite structures satisfying first-order and equational statements, the same kind of statement that Prover9 accepts. If the statement is the denial of some conjecture, any structures found by Mace4 are counterexamples to the conjecture.

Mace4 can be a valuable complement to Prover9, looking for counterexamples before (or at the same time as) using Prover9 to search for a proof. It can also be used to help debug input clauses and formulas for Prover9.

pyomo
PYthon Optimization Modeling Objects
Maintainer: Daniel Stender
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Pyomo is a tool for formulating and analyzing mathematical models that represent real-world systems for complex optimization applications as applied in different areas of business, engineering, research, and administration. It's used to define symbolic problems, create concrete problem instances, and solve this instances with standard solvers. Pyomo provides a capability that is commonly associated with algebraic modeling languages (AML) and applications like AMPL, AIMMS, or GAMS, but has its modeling objects within the Python environment. Pyomo features a versatile set of modeling components, and supports concrete models (defined with data) as well as abstract models (defined without data).

For the processing of instantiated models Pyomo supports a wide range of independent solvers that could be written either in Python or other languages. Pyomo supports the general ASL (AMPL Solver Library) compatible interface, and has invidividual backends for solvers which some of them are available within Debian (GLPK, COIN-OR CPC, OPENOPT). Pyomo's solver manager could also employ the public NEOS Server to remotely optimize models if network access is available.

Pyomo was formerly released as the Coopr software library, and includes the PySP package (Pyomo Stochastic Programming) which provides generic solvers for stochastic programming.

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python3-deap
Distributed Evolutionary Algorithms in Python3
Maintainer: Miriam Ruiz (Roland Mas)
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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-dolfin
Base Python interface for DOLFIN (Python 3)
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DOLFIN is the Python and C++ interface of the FEniCS project for the automated solution of differential equations, providing a consistent PSE (Problem Solving Environment) for solving ordinary and partial differential equations. Key features include a simple, consistent and intuitive object-oriented API; automatic and efficient evaluation of variational forms; automatic and efficient assembly of linear systems; and support for general families of finite elements.

This is the base package depending on specific dolfin builds. By default the version built against the preferred version of PETSc in /usr/lib/petsc is selected (with 32-bit indexing, but the alternative version (64-bit PETSc) can be selected by setting the environment variable PETSC_DIR.

This is the legacy version of DOLFIN, you may want to install the next-generation python3-dolfinx (DOLFIN-X) instead.

python3-ffc
compiler for finite element variational forms (Python 3)
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The FEniCS Form Compiler FFC provides state-of-the-art automatic and efficient evaluation of general multilinear forms (variational formulations) for FEniCS. FFC functions as the form evaluation system for DOLFIN but can also be used to compile forms for other systems.

FFC works as a compiler for multilinear forms by generating code (C or C++) for the evaluation of a multilinear form given in mathematical notation. This new approach to form evaluation makes it possible to combine generality with efficiency; the form can be given in mathematical notation and the generated code is as efficient as hand-optimized code.

This package installs the legacy FFC library for Python 3.

You may want to consider installing python3-ffcx instead to get the next-generation FFC-X.

python3-minieigen
Wrapper of parts of the Eigen library (Python 3)
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Small wrapper for core parts of Eigen, c++ library for linear algebra. It is mainly useful for inspecting c++ code which already uses eigen and boost::python. Supported types are Vectors (2,3,6 and dynamic-sized with integer and floating-point values), Matrices (3x3, 6x6 and dynamic-sized with floating-point values) and Quaternions. Numerous methods are wrapped and the original API of Eigen is followed.

This is the Python 3 version of the package.

python3-openturns
Python3 front-end of OpenTURNS (aka TUI)
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OpenTURNS is a powerful and generic tool to treat and quantify uncertainties in numerical simulations in design, optimization and control. It allows both sensitivity and reliability analysis studies:

  • defining the outputs of interest and decision criterion;
  • quantify and model the source of uncertainties;
  • propagate uncertainties and/or analyse sensitivity and
  • rank the sources of uncertainty

Targeted users are all engineers who want to introduce the probabilistic dimension in their so far deterministic studies.

This package provides the Python3 bindings to the library.

python3-persalys
GUI for uncertainty treatment (Python bindings)
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Persalys is a graphical user interface for OpenTURNS, dedicated to the treatment of uncertainty and the management of variabilities. The software is a tool between the computer simulation, probabilistic analyses and the data sciences. The interface is available in French or in English.

Persalys allows one to:

  • create mathematical models: analytical, coupling with an external model (finite elements, ...), FMU;
  • analyse the variability of one's parameters thanks to many methods and visualisation tools;
  • statistically analyse one's measuring data, infer probability distributions or create metamodels.

This package contains the Python3 bindings.

python3-sagenb-export
Convert SageNB Notebooks (Python 3)
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This is a tool to convert SageNB notebooks to other formats, in particular IPython/Jupyter notebooks.

This package installs the library for Python 3.

python3-ufl
unified language for form-compilers (Python 3)
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UFL (Unified Form Language) is a unified language for definition of variational forms intended for finite element discretization. More precisely, it defines a fixed interface for choosing finite element spaces and defining expressions for weak forms in a notation close to mathematical notation. The form compilers FFC and SyFi use UFL as their end-user interface, producing UFC implementations as their output.

This package installs the library for Python 3.

qepcad
quantifier elimination tool
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QEPCAD is an implementation of quantifier elimination by partial cylindrical algebraic decomposition due originally to Hoon Hong, and subsequently added on to by many others. It is an interactive command-line program written in C/C++, and based on the SACLIB library. Presented here is QEPCAD B version 1.x, the "B" designating a substantial departure from the original QEPCAD and distinguishing it from any development of the original that may proceed in a different direction. QEPCAD and the SACLIB library are the result of a program of research by George Collins and his PhD students that has spanned several decades ... and continues still!

qhull-bin
calculate convex hulls and related structures (utilities)
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Qhull computes convex hulls, Delaunay triangulations, halfspace intersections about a point, Voronoi diagrams, furthest-site Delaunay triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d, and higher dimensions.

This package contains the qhull executable that gives a pipe interface to some of the functionality of the library. Also included is rbox is a useful tool in generating input for Qhull; it generates hypercubes, diamonds, cones, circles, simplices, spirals, lattices, and random points.

Qhull produces graphical output for Geomview. This helps with understanding the output (http://www.geomview.org).

qsopt-ex
Exact linear programming solver
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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.

Please cite: David L Applegate, William Cook, Sanjeeb Dash and Daniel G Espinoza: Exact solutions to linear programming problems. Operations Research Letters 35(6):693-699 (2007)
regina-normal
mathematical software for low-dimensional topology
Maintainer: Ben Burton
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Regina is a software package for 3-manifold and 4-manifold topologists, with a focus on triangulations, knots and links, normal surfaces, and angle structures.

For 3-manifolds, it includes high-level tasks such as 3-sphere recognition, connected sum decomposition and Hakenness testing, comes with a rich database of census manifolds, and incorporates the SnapPea kernel for working with hyperbolic manifolds. For 4-manifolds, it offers a range of combinatorial and algebraic tools, plus support for normal hypersurfaces. For knots and links, Regina can perform combinatorial manipulation, compute knot polynomials, and work with several import/export formats.

Regina comes with a full graphical user interface, as well as Python bindings and a low-level C++ programming interface.

This package includes the graphical user interface and the command-line Python interface. The users' handbook and the API documentation are in the separate package regina-normal-doc.

rheolef
efficient Finite Element environment
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Rheolef is a computer environment that serves as a convenient laboratory for computations in applied mathematics involving finite element-like methods. It provides a set of commands and C++ algorithms and containers.

Most basically, containers cover the classic graph data structure for sparse matrix formats and finite element meshes. At a higher level of abstraction, they can handle approximate finite element spaces, discrete fields. Flexible and powerful expressions are used to specify bilinear forms.

Current applications include:

  • massively distributed memory finite element environment, based on MPI;
  • elasticity, Stokes and Navier-Stokes problems in 2D and 3D;
  • complex fluids applications: viscoplasticity, viscoelasticity, wall slip;
  • nonlinear problems with fixed-point, Newton and continuation methods;
  • high order polynomials, mixed elements and discontinuous Galerkin methods;
  • auto-adaptive mesh approaches;
  • axisymmetric problems;
  • multi-regions and variable coefficient problems.

This package provides the rheolef commands. These support input and output in various file formats for mesh-generators and numerical data visualization systems such as paraview, and gnuplot.

Please cite: Piere Saramito: (2016)
rubiks
Small collection of Rubik's cube solvers
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This package contains several different Rubik's cube solvers, either useful directly on the command-line or through sagemath.

Michael Reid's "optimal" uses pre-computed tables to find an optimal solution to the 3x3x3 Rubik's cube.

Dik T.Winter's "dikcube" uses Kociemba's algorithm to iteratively find a short solution to the 3x3x3 cube.

Eric Dietz' "cubex" has fast non-optimal solver for the 3x3x3 cube.

sagemath
Open Source Mathematical Software
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SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. Access their combined power through a common, Python-based language or directly via interfaces or wrappers.

Mission: Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab.

This package contains the main SageMath installation.

sagemath-database-conway-polynomials
Database of Conway polynomials
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This package contains a small database of Conway polynomials, for primes up to 109987 and a various number of exponents.

It is part of the sagemath software suite.

sagemath-database-cremona-elliptic-curves
Databases of elliptic curves over the rationals
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This package contains John Cremona's database of all elliptic curves over the rationals of bounded conductor.

It is a complement to the sagemath software suite.

sagemath-database-elliptic-curves
Databases for elliptic curves
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This package contains in fact two databases: - the subset of John Cremona's database of elliptic curves up to conductor at most 10000 - William Stein's database of interesting elliptic curves

It is part of the sagemath software suite.

sagemath-database-graphs
Databases of graphs
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This package contains a database of graphs, created by Emily Kirkman based on the work of Jason Grout. It also contains the ISGCI graph database.

It is part of the sagemath software suite.

sagemath-database-mutually-combinatorial-designs
Databases of combinatorial designs
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This package contains a database of mutually orthogonal Latin squares, as found in the Handbook of Combinatorial Designs, 2ed.

It is part of the sagemath software suite.

sagemath-database-polytopes
Databases of polytopes
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This package contains a database of 2-dimension and of 3-dimensional reflexive polytopes.

It is part of the sagemath software suite.

science-statistics
Debian Science Statistics packages
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This metapackage is part of the Debian Pure Blend "Debian Science" and installs packages related to statistics. This task is a general task which might be useful for any scientific work. It depends from a lot of R packages as well as from other tools which are useful to do statistics. Moreover the Science Mathematics task is suggested to optionally install all mathematics related software.

scilab
Scientific software package for numerical computations
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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".

scilab-ann
Scilab module for artificial neural networks
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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
scotch
programs and libraries for graph, mesh and hypergraph partitioning
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Its purpose is to apply graph theory, with a divide and conquer approach, to scientific computing problems such as graph and mesh partitioning, static mapping, and sparse matrix ordering, in application domains ranging from structural mechanics to operating systems or bio-chemistry.

The SCOTCH distribution is a set of programs and libraries which implement the static mapping and sparse matrix reordering algorithms developed within the SCOTCH project.

SCOTCH has many interesting features:

  • Its capabilities can be used through a set of stand-alone programs as well as through the libSCOTCH library, which offers both C and Fortran interfaces.

  • It provides algorithms to partition graph structures, as well as mesh structures defined as node-element bipartite graphs and which can also represent hypergraphs.

  • It can map any weighted source graph onto any weighted target graph. The source and target graphs may have any topology, and their vertices and edges may be weighted. Moreover, both source and target graphs may be disconnected. This feature allows for the mapping of programs onto disconnected subparts of a parallel architecture made up of heterogeneous processors and communication links.

  • It computes amalgamated block orderings of sparse matrices, for efficient solving using BLAS routines.

  • Its running time is linear in the number of edges of the source graph, and logarithmic in the number of vertices of the target graph for mapping computations.

  • It can handle indifferently graph and mesh data structures created within C or Fortran programs, with array indices starting from 0 or 1.

  • It offers extended support for adaptive graphs and meshes through the handling of disjoint edge arrays.

  • It is dynamically parametrizable thanks to strategy strings that are interpreted at run-time.

  • It uses system memory efficiently, to process large graphs and meshes without incurring out-of-memory faults;

  • It is highly modular and documented. Since it has been released under the CeCILL-C free/libre software license, it can be used as a testbed for the easy and quick development and testing of new partitioning and ordering methods.

  • It can be easily interfaced to other programs. The programs comprising the SCOTCH project have been designed to run in command-line mode without any interactive prompting, so that they can be called easily from other programs by means of system() or popen() calls, or piped together on a single command line. Moreover, vertex labeling capabilities allow for easy renumbering of vertices.

  • It provides many tools to build, check, and display graphs, meshes and matrix patterns.

  • It is written in C and uses the POSIX interface, which makes it highly portable. PT-SCOTCH uses the MPI interface, and optionally the POSIX threads.

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singular
Computer Algebra System for Polynomial Computations
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SINGULAR is a Computer Algebra System (CAS) for polynomial computations with emphasis on the special needs of commutative algebra, algebraic geometry, and singularity theory.

This dummy package provides the standard installation.

snappea
program for creating and studying hyperbolic 3-manifolds
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SnapPea is Jeff Weeks' computational tool for mathematicians working in low-dimensional topology. It is used for creating and studying hyperbolic 3-manifolds, and is accessible via Python scripts as well as through a traditional graphical user interface.

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surf-alggeo
visualization of real algebraic geometry
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Surf is a script driven tool to visualize some real algebraic geometry: plane algebraic curves, algebraic surfaces and hyperplane sections of surfaces.

The algorithms should be stable enough not to be confused by curve/surface singularities in codimension greater than one and the degree of the surface or curve. This has been achieved quite a bit. Curves of degree up to 30 and surfaces of degree up to 20 have been drawn successfully. However, there are examples of curves/surfaces of lower degree where surf fails to produce perfect images. This happens especially if the equation of the curve/surface is not reduced. Best results are achieved using reduced equations. On the other hand, surf displays the Fermat-curves accurately for degree up to 98.

Surf is free software distributed under the GNU General Public License (GPL).

This dummy package is meant to allow multi-variant support for surf.

sympow
mathematical program for SYMmetric POWer elliptic curve L-functions -- program
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SYMPOW is a mathematical program to compute special values of symmetric power elliptic curve L-functions; it can compute up to about 64 digits of precision.

This package provides the SYMPOW program itself.

tachyon
Parallel/Multiprocessor Standalone Ray Tracer - metapackage
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Tachyon is a portable, high performance parallel ray tracing system supporting MPI and multithreaded implementations. Tachyon is built as a C callable library, which can be used within applications.

Tachyon implements all of the basic geometric primitives such as triangles, planes, spheres, cylinders, etc. Some of the goals in developing Tachyon were to make it fast and for it to parallelize well. These are what set it apart from more full-featured programs like POV-Ray, Rayshade, and others. Tachyon supports enough features to be an excellent alternative to slower programs for demanding animation and scientific visualization tasks.

This metapackage allows multi-variant support for tools built upon tachyon.

tetgen
Quality Tetrahedral Mesh Generator
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TetGen generates the Delaunay tetrahedralization, Voronoi diagram, and convex hull for three-dimensional point sets, generates the constrained Delaunay tetrahedralizations and quality tetrahedral meshes for three-dimensional domains with piecewise linear boundary.

topcom
Triangulations Of Point Configurations and Oriented Matroids
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TOPCOM is a collection of clients to compute Triangulations Of Point Configurations and Oriented Matroids, resp.

The algorithms use only combinatorial data of the point configuration as is given by its oriented matroid. Some basic commands for computing and manipulating oriented matroids can also be accessed by the user.

It was very much inspired by the maple program PUNTOS, which was written by Jesus de Loera. TOPCOM is entirely written in C++, so there is a significant speed up compared to PUNTOS.

toulbar2
Exact combinatorial optimization for Graphical Models
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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.

wxmaxima
GUI for the computer algebra system Maxima
Maintainer: Gunter Königsmann
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wxMaxima is a graphical user interface for the computer algebra system Maxima. It eases the use of Maxima by making most of its commands available through a menu system and by providing input dialogs for commands that require more than one argument. It also implements its own display engine that outputs mathematical symbols directly instead of depicting them with ASCII characters.

wxMaxima also features 2D and 3D inline plots, simple animations, mixing of text and mathematical calculations to create documents, exporting of input and output to TeX, and a browser for Maxima's manual including command index and full text searching.

xcas
Computer Algebra System - console and graphical calculator
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Giac is a computer algebra system, following the development of the CAS for HP calculators. It has fast implementation of algorithms for polynomial operations, and compatibility mode with Maple or Mupad CAS as well as TI calculators.

This package contains the user-facing giac programs: xcas, icas, and pgiac; as well as the cas_help program for providing user-oriented help.

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xmaxima
Computer algebra system -- x interface
Maintainer: Camm Maguire
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Maxima 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. It has a symbolic source level debugger for maxima code. Maxima is based on the original Macsyma developed at MIT in the 1970s. It is quite reliable, and has good garbage collection, and no memory leaks. It comes with hundreds of self tests.

This package contains an X Windows interface using the tcl/tk libraries.

xmds
eXtensible Multi-Dimensional Simulator
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XMDS is a code generator that integrates equations, from Ordinary Differential Equations (ODEs) up to stochastic Partial Differential Equations (PDEs). You write them down in human readable form in an XML file, and it goes away and writes and compiles a C++ program that integrates those equations as fast as it can possibly be done in your architecture.

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xmds2
eXtensible Multi-Dimensional Simulator
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XMDS is a code generator that integrates equations, from Ordinary Differential Equations (ODEs) up to stochastic Partial Differential Equations (PDEs). You write them down in human readable form in an XML file, and it goes away and writes and compiles a C++ program that integrates those equations as fast as it can possibly be done in your architecture.

XMDS 2 is a major upgrade rewritten in Python which is faster and far more versatile than previous versions, allowing the efficient integration of almost any initial value problem on regular domains.

Please cite: Graham R. Dennis, Joseph J. Hope and Mattias T. Johnsson: XMDS2: Fast, scalable simulation of coupled stochastic partial differential equations. Computer Physics Communications 184(1):201-208 (2013)

Official Debian packages with lower relevance

ann-tools
Approximate Nearest Neighbor Searching library (tools)
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ANN is a library written in C++, which supports data structures and algorithms for both exact and approximate nearest neighbor searching in arbitrarily high dimensions. ANN assumes that distances are measured using any class of distance functions called Minkowski metrics. These include the well known Euclidean distance, Manhattan distance, and max distance. ANN performs quite efficiently for point sets ranging in size from thousands to hundreds of thousands, and in dimensions as high as 20.

This package contains the ann2fig (display ANN output in fig format) and the ann_sample (a sample demonstration for ANN) programs.

evolver-nox
Surface Evolver - with no X support
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The Surface Evolver is an interactive program for the modelling of liquid surfaces shaped by various forces and constraints.

This package provides evolver variants built with different floating point formats (double, long double, quadruple) but with no X support.

The package is enhanced by the following packages: evolver-doc
evolver-ogl
Surface Evolver - with OpenGL display
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The Surface Evolver is an interactive program for the modelling of liquid surfaces shaped by various forces and constraints.

This package provides evolver variants built with different floating point formats (double, long double, quadruple) and with an OpenGL/GLUT display.

The package is enhanced by the following packages: evolver-doc
gap-gapdoc
GAPDoc - A Meta Package for GAP Documentation
Maintainer: Bill Allombert
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GAP is a system for computational discrete algebra, with particular emphasis on Computational Group Theory. GAP provides a programming language, a library of thousands of functions implementing algebraic algorithms written in the GAP language as well as large data libraries of algebraic objects. GAP is used in research and teaching for studying groups and their representations, rings, vector spaces, algebras, combinatorial structures, and more.

This package contains GAPDoc, "A Meta Package for GAP Documentation", by Frank Lübeck and Max Neunhöffer, which is used to manage GAP documentation.

gap-io
low level C library IO bindings for GAP
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GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas.

This package allows GAP to access UNIX I/O C-library functions.

gap-online-help
GAP computer algebra system, online help
Maintainer: Bill Allombert
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Newer upstream!
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GAP is a system for computational discrete algebra, with particular emphasis on Computational Group Theory. GAP provides a programming language, a library of thousands of functions implementing algebraic algorithms written in the GAP language as well as large data libraries of algebraic objects. GAP is used in research and teaching for studying groups and their representations, rings, vector spaces, algebras, combinatorial structures, and more.

This package contains the documentation in TeX format needed for the online help system.

gap-scscp
SCSCP protocol in GAP
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GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas.

This package implements the Symbolic Computation Software Composability Protocol (SCSCP) for GAP.

gmp-ecm
Factor integers using the Elliptic Curve Method
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gmp-ecm is a free implementation of the Elliptic Curve Method (ECM) for integer factorization.

The original purpose of the ECMNET project was to make Richard Brent's prediction true, i.e. to find a factor of 50 digits or more by ECM. This goal was attained on September 14, 1998, when Conrad Curry found a 53-digit factor of 2^677-1 c150 using George Woltman's mprime program. The new goal of ECMNET is now to find other large factors by ecm, mainly by contributing to the Cunningham project, most likely the longest, ongoing computational project in history according to Bob Silverman. A new record was set by Nik Lygeros and Michel Mizony, who found in December 1999 a prime factor of 54 digits using GMP-ECM.

See http://www.loria.fr/~zimmerma/records/ecmnet.html for more information about ecmnet.

This package provides the command line utility.

libspectra-dev
library for large scale eigenvalue problems (development files)
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Spectra stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. It is a C++ library for large scale eigenvalue problems, built on top of Eigen, an open source linear algebra library.

Spectra is implemented as a header-only C++ library, whose only dependency, Eigen, is also header-only. Hence Spectra can be easily embedded in C++ projects that require calculating eigenvalues of large matrices.

Spectra is designed to calculate a specified number of eigenvalues of a large square matrix. Usually this number of eigenvalues is much smaller than the size of the matrix, so that only a few eigenvalues and eigenvectors are computed, which in general is more efficient than calculating the whole spectral decomposition. Users can choose eigenvalue selection rules to pick the eigenvalues of interest, such as the largest k eigenvalues, or eigenvalues with largest real parts, etc.

netgen-doc
Automatic 3d tetrahedral mesh generator documentation
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NETGEN is an automatic 3d tetrahedral mesh generator. It accepts input from constructive solid geometry (CSG) or boundary representation (BRep) from STL file format. NETGEN contains modules for mesh optimization and hierarchical mesh refinement.

This package contains the user manual (in PDF format) and example files.

primesieve
fast prime number generator C/C++ library
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primesieve is a free software program and C/C++ library that generates primes using a highly optimized sieve of Eratosthenes implementation. primesieve can generate primes and prime k-tuplets up to nearly 2^64.

See http://primesieve.org/ for more information.

This dummy package provides the standard installation.

r-cran-evd
GNU R Functions for extreme value distributions
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Extends simulation, distribution, quantile and density functions to univariate and multivariate parametric extreme value distributions, and provides fitting functions which calculate maximum likelihood estimates for univariate and bivariate maxima models, and for univariate and bivariate threshold models.

Please cite: Alec G. Stephenson: evd: Extreme Value Distributions. R News 2(2):31-32 (2002)
sagetex
Embed Sage code and plots into LaTeX
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The SageTeX LaTeX package allows you to embed code, results of computations, and plots from the SageMath mathematics software suite into LaTeX documents. SageMath is an open-source Computer Algebra System (CAS).

This package provides the LaTeX package.

The package is enhanced by the following packages: sagetex-doc

Debian packages in contrib or non-free

matlab-support
distro integration for local MATLAB installations
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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.

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

isabelle
generic theorem proving environment
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Version: 2008-4

Features a choice of several ready-to-use logics (Higher Order Logic, Higher Order Logic augmented with Scott's Logic for Computable Functions, First Order Logic, Zermello-Frankel, an extensional version of Martin-Löf Type Theory, Barendregt's Lambda Cube, a few sequent calculi (including modal and linear logics), ...) or defining your own logic / deductive system, a procedural and a declarative proof style, rich automation for classical reasoning, equational logic and algebra, LaTeX and X-Symbols notational support.

This package contains the isabelle toolchain.

Remark of Debian Science team: upstream prefers Isabelle not being packaged

There is an alternative software coq which is packaged in Debian (see above).

Unofficial packages built by somebody else

octaviz
3D visualization system for Octave
License: unknown

Octaviz is a visualization system for Octave. It is a wrapper that makes all VTK classes accessible from within Octave using the same object-oriented syntax as in C++ or Python. Octaviz also provides high-level functions for 2D and 3D visualization. Using those functions, most common visualization tasks (3D surface plots, contour plots etc) can be accomplished without any knowledge about VTK.

Remark of Debian Science team: Removed from Debian

This package was removed from Debian but some versions are available from http://snapshot.debian.org/

Reasons are given here: http://bugs.debian.org/535537

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