Debian Science Project
Summary
Physics
Debian Science Physics packages

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

Official Debian packages with high relevance

Abinit
package for electronic structure calculations
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ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave basis.

ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors. Excited states can be computed within the Time-Dependent Density Functional Theory (for molecules), or within Many-Body Perturbation Theory (the GW approximation). In addition to the main ABINIT code, different utility programs are provided.

This package contains the executables needed to perform calculations (however, pseudopotentials are not supplied). For a set of pseudopotentials, install the abinit-data package.

Please cite: X. Gonze, B. Amadon, P.-M. Anglade, J.-M. Beuken, F. Bottin, P. Boulanger, F. Bruneval, D. Caliste, R. Caracas, M. Côté, T. Deutsch, L. Genovese, Ph. Ghosez, M. Giantomassi, S. Goedecker, D.R. Hamann, P. Hermet, F. Jollet, G. Jomard, S. Leroux, M. Mancini, S. Mazevet, M. J. T. Oliveira, G. Onida, Y. Pouillon, T. Rangel, G.-M. Rignanese, D. Sangalli, R. Shaltaf, M. Torrent, M. J. Verstraete, G. Zerah and J. W. Zwanziger: ABINIT: First-principles approach to material and nanosystem properties. (eprint) Comput. Phys. Commun. 180(12):2582-2615 (2009)
Axiom
汎用計算機代数システム: メインバイナリおよびモジュール
Maintainer: Camm Maguire
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axiom は数学アルゴリズムの研究や開発に便利です。強く型付され、数学的に 正確な型階層を定義します。プログラミング言語と内蔵コンパイラを備えてい ます。

axiom は 1973 年から開発が続けられ、商用製品として販売されていました。 そしてフリーソフトウェアとしてリリースされました。

以下の事項を目指すべく、本ソフトウエアを拡張するための努力が行なわれて います:

 (a) より優れたインターフェイスの開発
 (b) 教育用ツールとして便利なものにする
 (c) 代数サーバプロトコルの開発
 (d) 追加された数学分野の統合
 (e) 読み書き可能なプログラミングスタイルでの代数の再構築
 (f) 論理プログラミングの統合
 (g) 校閲者の提案による Axiom Journal の開発

本パッケージには、メインプログラムバイナリおよび全ての前もってコンパイル された代数モジュールと、自動ロード可能なモジュールが含まれます。

The package is enhanced by the following packages: texmacs
Cadabra
場の理論に動機付けられた計算機代数システム
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Cadabra は、特に場の理論に現われる問題を解くために設計された計算機代数 システムです。テンソル多項式の単純化用に広汎な機能があります。多項間 対称性、フェルミオンおよび反交換関係にある変数、クリフォード代数や フィルツ変換、暗黙の座標依存性、複数種類の添字など、他にも多くの機能が あります。入力フォーマットは TeX のサブセットです。

Cernlib
CERNLIB data analysis suite - general use metapackage
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CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

This metapackage provides almost all of the programs and libraries contained in CERNLIB. Most people will likely want only a subset of these. A few extra CERNLIB programs, not of interest to many people, may be obtained via the cernlib-extras metapackage.

Cp2k
Ab Initio Molecular Dynamics
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CP2K is a program to perform simulations of solid state, liquid, molecular and biological systems. It is especially aimed at massively parallel and linear scaling electronic structure methods and state-of-the-art ab-initio molecular dynamics (AIMD) simulations.

CP2K is optimized for the mixed Gaussian and Plane-Waves (GPW) method based on pseudopotentials, but is able to run all-electron or pure plane-wave/Gaussian calculations as well. Features include:

Ab-initio Electronic Structure Theory Methods using the QUICKSTEP module:

  • Density-Functional Theory (DFT) energies and forces
  • Hartree-Fock (HF) energies and forces
  • Moeller-Plesset 2nd order perturbation theory (MP2) energies and forces
  • Random Phase Approximation (RPA) energies
  • Gas phase or Periodic boundary conditions (PBC)
  • Basis sets include various standard Gaussian-Type Orbitals (GTOs), Pseudo- potential plane-waves (PW), and a mixed Gaussian and (augmented) plane wave approach (GPW/GAPW)
  • Norm-conserving, seperable Goedecker-Teter-Hutter (GTH) and non-linear core corrected (NLCC) pseudopotentials, or all-electron calculations
  • Local Density Approximation (LDA) XC functionals including SVWN3, SVWN5, PW92 and PADE
  • Gradient-corrected (GGA) XC functionals including BLYP, BP86, PW91, PBE and HCTH120 as well as the meta-GGA XC functional TPSS
  • Hybrid XC functionals with exact Hartree-Fock Exchange (HFX) including B3LYP, PBE0 and MCY3
  • Double-hybrid XC functionals including B2PLYP and B2GPPLYP
  • Additional XC functionals via LibXC
  • Dispersion corrections via DFT-D2 and DFT-D3 pair-potential models
  • Non-local van der Waals corrections for XC functionals including B88-vdW, PBE-vdW and B97X-D
  • DFT+U (Hubbard) correction
  • Density-Fitting for DFT via Bloechl or Density Derived Atomic Point Charges (DDAPC) charges, for HFX via Auxiliary Density Matrix Methods (ADMM) and for MP2/RPA via Resolution-of-identity (RI)
  • Sparse matrix and prescreening techniques for linear-scaling Kohn-Sham (KS) matrix computation
  • Orbital Transformation (OT) or Direct Inversion of the iterative subspace (DIIS) self-consistent field (SCF) minimizer
  • Local Resolution-of-Identity Projector Augmented Wave method (LRIGPW)
  • Absolutely Localized Molecular Orbitals SCF (ALMO-SCF) energies for linear scaling of molecular systems
  • Excited states via time-dependent density-functional perturbation theory (TDDFPT)

Ab-initio Molecular Dynamics:

  • Born-Oppenheimer Molecular Dynamics (BOMD)
  • Ehrenfest Molecular Dynamics (EMD)
  • PS extrapolation of initial wavefunction
  • Time-reversible Always Stable Predictor-Corrector (ASPC) integrator
  • Approximate Car-Parrinello like Langevin Born-Oppenheimer Molecular Dynamics (Second-Generation Car-Parrinello Molecular Dynamics (SGCP))

Mixed quantum-classical (QM/MM) simulations:

  • Real-space multigrid approach for the evaluation of the Coulomb interactions between the QM and the MM part
  • Linear-scaling electrostatic coupling treating of periodic boundary conditions
  • Adaptive QM/MM

Further Features include:

  • Single-point energies, geometry optimizations and frequency calculations
  • Several nudged-elastic band (NEB) algorithms (B-NEB, IT-NEB, CI-NEB, D-NEB) for minimum energy path (MEP) calculations
  • Global optimization of geometries
  • Solvation via the Self-Consistent Continuum Solvation (SCCS) model
  • Semi-Empirical calculations including the AM1, RM1, PM3, MNDO, MNDO-d, PNNL and PM6 parametrizations, density-functional tight-binding (DFTB) and self-consistent-polarization tight-binding (SCP-TB), with or without periodic boundary conditions
  • Classical Molecular Dynamics (MD) simulations in microcanonical ensemble (NVE) or canonical ensmble (NVT) with Nose-Hover and canonical sampling through velocity rescaling (CSVR) thermostats
  • Metadynamics including well-tempered Metadynamics for Free Energy calculations
  • Classical Force-Field (MM) simulations
  • Monte-Carlo (MC) KS-DFT simulations
  • Static (e.g. spectra) and dynamical (e.g. diffusion) properties
  • ATOM code for pseudopotential generation
  • Integrated molecular basis set optimization

CP2K does not implement conventional Car-Parrinello Molecular Dynamics (CPMD).

Drawxtl
crystal structure viewer
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DRAWxtl reads a basic description of the crystal structure, which includes unit-cell parameters, space group, atomic coordinates, thermal parameters or a Fourier map, and outputs a geometry object that contains polyhedra, planes, lone-pair cones, spheres or ellipsoids, bonds, iso-surface Fourier contours and the unit-cell boundary.

Four forms of graphics are produced:

  • an OpenGL window for immediate viewing
  • the Persistence of Vision Ray Tracer (POV-RAY) scene language for publication-quality drawings
  • the Virtual Reality Modeling Language (VRML) for dissemination across the Internet
  • a Postscript rendering of the OpenGL window for those who want high-quality output but do not have POV-RAY installed.

File formats DRAWxtl can read include CIF, FDAT, FullProf (pcr), GSAS, SCHAKAL, SHELX, DISCUS and WIEN2k.

Please cite: Larry W. Finger, Martin Kroeker and Brian H. Toby: DRAWxtl, an open-source computer program to produce crystal-structure drawings. (eprint) J. Appl. Cryst. 40:188-192 (2007)
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Etsf-io
Binary tools to check, merge and read ETSF files
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The European Theoretical Spectroscopy Facility (ETSF) is a European network dedicated to providing support and services for ongoing research in academic, government and industrial laboratories.

The ETSF is divided into 7 beamlines, each of which is concerned with a specific scientific topic:

  • Optics ;
  • Energy Loss Spectroscopy ;
  • Quantum Transport ;
  • Time-resolved Spectroscopy ;
  • Photo-emission Spectroscopy ;
  • Vibrational Spectroscopy ;
  • X-Rays Spectroscopy.

To allow the adoption of its recommendations about standardization, the ETSF proposes different libraries and tools implementing or using these specifications, as well as widely usable pieces of software.

ETSF_IO is a library of F90 routines to read/write the ETSF file format. This package contains the user tools to:

  • check file conformance to the specifications;
  • extract data from files;
  • merge multiple files from parallel runs, as specified in the specifications.
Feynmf
set of LaTeX macros for creating Feynman diagrams
Maintainer: Thorsten Alteholz
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FeynMF is a LaTeX package for easy drawing of professional-quality Feynman diagrams, illustrations that depict the fundamental interactions of subatomic particles. The diagrams may be created using either the Metafont or MetaPost programs. FeynMF lays out most diagrams satisfactorily from the structure of the graph without any need for manual intervention. Nevertheless all the power of Metafont or MetaPost is available for more obscure cases.

Note that you will need the texlive-metapost package in order to use the MetaPost-based version of FeynMF.

Fityk
general-purpose nonlinear curve fitting and data analysis
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Fityk is a flexible and portable program for nonlinear fitting of analytical functions (especially peak-shaped) to data (usually experimental data). In other words, for nonlinear peak separation and analysis.

It was developed for analyzing diffraction patterns, but can be also used in other fields, since concepts and operations specific for crystallography are separated from the rest of the program.

Fityk offers various nonlinear fitting methods, subtracting background, calibrating data, easy placement of peaks and changing peak parameters, automation of common tasks with scripts, and much more. The main advantage of the program is flexibility - parameters of peaks can be arbitrarily bound to each other, eg. the width of a peak can be an independent variable, can be the same as the width of another peak or can be given by a complicated - common to all peaks - formula.

libjs-sphinxdoc is necessary for the Javascript stuff in the documentation.

Please cite: M. Wojdyr: Fityk: a general-purpose peak fitting program. (eprint) J. Appl. Cryst. 43(5):1126-1128 (2010)
Geant321
[Physics] Particle detector description and simulation tool
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GEANT is a framework for simulating the passage of subatomic particles through matter, for instance, particle detectors. For maximum flexibility, GEANT simulations are performed by linking FORTRAN code supplied by the user with the GEANT library, then running the resulting executable.

This package includes gxint, a script that makes this linking step more convenient.

Gerris
流体ソルバ
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Gerris は、流体を表す偏微分方程式を解くためのシステムです。

(現在の) 主要機能の概要は次の通りです:

  • 時間依存の非圧縮性可変密度オイラー、ストークスまたは ナビエ・ストークス方程式を解きます
  • 適合細分化格子 (AMR) 法: 分解能は流体の特徴に動的に適応します
  • 複雑な形状の完全自動格子生成
  • 空間と時間で二次オーダー
  • 個数無制限の移流・拡散パッシブトレーサ
  • 追加のソース項を柔軟に指定できます
  • MPI ライブラリを使用した移植性の高い並列サポート
  • 界面流体の Volume of Fluid (VOF) 法による移流スキーム

本パッケージには MPI サポートが組み込まれています。

Ghkl
diffractometer computation control application
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The hkl library is a framework for diffraction computation and diffractometer control, heavily used at the SOLEIL synchrotron. It supports various types of diffractometer geometry: Eulerian 4-circle, Eulerian 6-circle, kappa 4-circle, kappa 6-circle, and z-axis geometry. For each of these it provides several numerically computed modes, such as bisector and constant psi.

This package provides a gui on top of the hkl library.

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Gpaw
DFT and beyond within the projector-augmented wave method
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A density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods, atom-centered basis-functions or plane-waves.

Please cite: J. J. Mortensen, L. B. Hansen and K. W. Jacobsen: Real-space grid implementation of the projector augmented wave method. (eprint) Physical Review B 71(3) (2005)
Gpiv
粒子画像流速測定のための GUI プログラム
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Gpiv は粒子画像流速測定 (PIV) のための GTK/GNOME ライブラリを使用したグラ フィックユーザインターフェースプログラムです。このプログラムは、処理のパラ メータ設定を素早く眺めて簡単に変更できます。処理を独立あるいは連鎖的に実行 し、可視化し、結果を表示します。Gpiv が呼び出せる処理は次の通りです:

画像処理: PIV 検査の際によく必要となる画像操作。

画像照合: 粒子画像の移動量の推定値を出力。

データ検証: 検査領域上の異常値、ピークロッキング効果や速度勾配をテスト。

データ後処理: データ操作、PIV データから速度場を得るための空間および時間ス ケーリング、空間平均の計算、渦度、ひずみ。

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Gpivtools
command line programs for Particle Image Velocimetry
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A collection of programs for images that are generated during a Particle Image Velocimetry (PIV) experiment. This is a technique to obtain the velocity field of a fluid flow quantitatively and is performed by tracking tracer particles that have been seeded to a fluid. The technique is also applied for observing deformations at surfaces of (solid) bodies. The package contains:

  • an image processing program for typical filtering and manipulation routines that may be convenient for PIV.
  • an image interrogation program resulting into estimators of particle image displacements.
  • validation programs to test on outliers, peak-locking effect and velocity gradients.
  • post-processing programs for data manipulation (flipping, rotation etc), spatial and time scaling, calculation of spatial averages and derivative quantities from the PIV data, like vorticity and strain.
  • miscellaneous programs and scripts to perform image format conversion, batch-processing, pipeline processing (image evaluation, validation and post-processing at once), calculation of time averages from a series of PIV data sets, data-visualization and data-manipulation.

All programs start with gpiv_.

This package contains all files used by gpivtools and gpivtools-mpi, like the man pages.

Gwyddion
Scanning Probe Microscopy visualization and analysis tool
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Gwyddion is a modular program for Scanning Probe Microscopy (SPM) data visualization and analysis. It is primarily intended for analysis of height field data obtained by microscopy techniques like

  • Atomic Force Microscopy (AFM),
  • Magnetic Force Microscopy (MFM),
  • Scanning Tunneling Microscopy (STM),
  • Near-field Scanning Optical Microscopy (SNOM or NSOM) and others. However, it can be used for arbitrary height field and image analysis.

This package contains the main application and its modules. It also contains a GNOME (and Xfce) thumbnailer which creates previews for all file types known to Gwyddion.

Please cite: David Nečas and Petr Klapetek: Gwyddion: an open-source software for SPM data analysis. (eprint) Central European Journal of Physics 10(1):181-188 (2012)
Registry entries: SciCrunch  OMICtools 
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Libroot-math-mlp-dev
Multi layer perceptron extension for ROOT - development files
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The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains development files of the mlp plug-in for ROOT, provides a Multi Layer Perceptron Neural Network package for ROOT.

Libroot-montecarlo-vmc-dev
Virtual Monte-Carlo library for ROOT - development files
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The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains development files of the Vmc library for ROOT.

Libroot-tmva-dev
Toolkit for multivariate data analysis - development files
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The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

The Toolkit for Multivariate Analysis (TMVA) provides a ROOT-integrated environment for the parallel processing and evaluation of MVA techniques to discriminate signal from background samples. It presently includes (ranked by complexity):

  • Rectangular cut optimisation
  • Correlated likelihood estimator (PDE approach)
  • Multi-dimensional likelihood estimator (PDE - range-search approach)
  • Fisher (and Mahalanobis) discriminant
  • H-Matrix (chi-squared) estimator
  • Artificial Neural Network (two different implementations)
  • Boosted Decision Trees

The TMVA package includes an implementation for each of these discrimination techniques, their training and testing (performance evaluation). In addition all these methods can be tested in parallel, and hence their performance on a particular data set may easily be compared.

This package provides development files of TMVA package for ROOT.

Maxima
計算機代数システム -- ベースシステム
Maintainer: Camm Maguire
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Maxima は、完全に記号化された計算プログラムです。フル機能で、多項式、行列、 有理関数、積分、有限群分析用 Todd-coxeter 法、グラフ、多倍長精度浮動小数点 演算の記号的操作を行えます。maxima コード用の記号的なソースレベルのデバッガ を備えています。Maxima は 1970 年代に MIT で開発された元祖 Macsyma に基づい ています。非常に信頼性が高く、高性能なガベージコレクション機能を持ち、また メモリリークを起こしません。何百もの自己テストコードが付属します。

本パッケージには、主要実行ファイルと基礎的なシステムファイルが 含まれます。

The package is enhanced by the following packages: texmacs
Meshlab
System for processing and editing triangular meshes
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This is an open source, portable, and extendible system for the processing and editing of unstructured 3D triangular meshes. The system is aimed to help the processing of the typical not-so-small unstructured models arising in 3D scanning, providing a set of tools for editing, cleaning, healing, inspecting, rendering and converting this kind of meshes.

Meshlab can read files in these formats: PLY, STL, OFF, OBJ, 3DS, COLLADA and PTX. It can write PLY, STL, OFF, OBJ, 3DS, COLLADA, VRML, and DXF.

Please cite: Paolo Cignoni, Marco Callieri, Massimiliano Corsini, Matteo Dellepiane, Fabio Ganovelli and Guido Ranzuglia: MeshLab: an Open-Source Mesh Processing Tool. (2008)
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Mpqc
Massively Parallel Quantum Chemistry Program
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MPQC is an ab-inito quantum chemistry program. It is especially designed to compute molecules in a highly parallelized fashion.

It can compute energies and gradients for the following methods:

  • Closed shell and general restricted open shell Hartree-Fock (HF)
  • Density Functional Theory (DFT)
  • Closed shell second-order Moeller-Plesset perturbation theory (MP2)

Additionally, it can compute energies for the following methods:

  • Open shell MP2 and closed shell explicitly correlated MP2 theory (MP2-R12)
  • Second order open shell pertubation theory (OPT2[2])
  • Z-averaged pertubation theory (ZAPT2)

It also includes an internal coordinate geometry optimizer.

MPQC is built upon the Scientific Computing Toolkit (SC).

Oce-draw
OpenCASCADE Community Edition CAE platform shared library
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OpenCASCADE is a suite for 3D surface and solid modeling, visualization, data exchange and rapid application development. It is an excellent platform for development of numerical simulation software including CAD/CAM/CAE, AEC and GIS, as well as PDM applications.

This package is based on OCE, OpenCASCADE Community Edition, which is maintained by a community of developers, and not by OpenCASCADE SAS.

This package contains the DRAW test harness.

Openfoam
Open source toolbox for Computational Fluid Dynamics (CFD) - binaries
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OpenFOAM is the free, open source CFD software released and developed primarily by OpenCFD Ltd since 2004. It has a large user base across most areas of engineering and science, from both commercial and academic organisations. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics.

Package contains binaries.

Openmx
package for nano-scale material simulations
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OpenMX (Open source package for Material eXplorer) is a program package for nano-scale material simulations based on density functional theories (DFT), norm-conserving pseudopotentials and pseudo-atomic localized basis functions. Since the code is designed for the realization of large-scale ab initio calculations on parallel computers, it is anticipated that OpenMX can be a useful and powerful tool for nano-scale material sciences in a wide variety of systems such as biomaterials, carbon nanotubes, magnetic materials, and nanoscale conductors.

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Opticalraytracer
Virtual lens/mirror design workshop
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OpticalRayTracer is an application that analyzes systems of lenses and mirrors. It uses optical principles and a virtual optical bench to predict the behavior of many kinds of ordinary and exotic lens types as well as flat and curved mirrors. OpticalRayTracer includes an advanced, easy-to-use interface that allows the user to rearrange the optical configuration by dragging objects around using the mouse.

OpticalRayTracer fully analyzes lens optical properties, including refraction and dispersion. The dispersion display uses color-coded light beams to simplify interpretation of the results.

OpticalRayTracer allows the creation of mirrors, flat and curved. In modern optical designs, mirrors often produce better results than lenses, for example in astronomical instruments. Such instruments can be roughed out in OpticalRayTracer's virtual workbench.

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Paw
物理解析ワークステーション - グラフィカルな解析プログラム
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CERNLIB は物理分野の実験で使用するために作られたデータ解析ツールおよびライ ブラリ群ですが、他のたとえば生物科学分野などにも使われています。

PAW は対話的なグラフィク表示と統計的および数学的な解析ツールを提供する 対話的なプログラムです。 物理学者が慣れ親しんでいるヒストグラム、イベントファイル (Ntuples)、ベクト ルなどといったオブジェクトに対して作業するように設計されています。

このプログラムは、設計が完全な 64 ビットクリーンではないため、 64 ビットアーキテクチャで適切に動作させるために CERN ライブラリを スタティックリンクしています。

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Paw++
物理分析ワークステーション (Lesstif による強化版)
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CERNLIB は物理実験で使うために作られたデータ解析ツールとライブラリの スイートですが、生物科学といった別分野向けのアプリケーションもあります。

本パッケージには分析やグラフィカルな表示に利用するための対話的な プログラムである paw++ が含まれます。paw++ は ("paw" パッケージに含まれる) paw と同じプログラムですが、よりユーザフレンドリーな Motif ベースの GUI を持ち、Debian では Lesstif を使ってコンパイルされています。

このプログラムは、設計が完全な 64 ビットクリーンではないため、 64 ビットアーキテクチャで適切に動作させるために CERN ライブラリを スタティックリンクしています。

Psi3
Quantum Chemical Program Suite
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PSI3 is an ab-initio quantum chemistry program. It is especially designed to accurately compute properties of small to medium molecules using highly correlated techniques.

It can compute energies and gradients for the following methods:

  • Closed shell and general restricted open shell Hartree-Fock (RHF/ROHF) (including analytical hessians for RHF)
  • Closed shell Moeller-Plesset pertubation theory (MP2)
  • Complete active space SCF (CASSCF)
  • Coupled-cluster singles doubles (CCSD)
  • Coupled-cluster singles doubles with pertubative triples (CCSD(T)) (only for unrestricted (UHF) reference wavefunctions)

Additionally, it can compute energies for the following methods:

  • Unrestricted open shell Hartree-Fock (UHF)
  • Closed/open shell Moeller-Plesset pertubation theory (MP2)
  • Closed shell explicitly correlated MP2 theory (MP2-R12) and spin-component scaled MP2 theory (SCS-MP2)
  • Multireference configuration-interaction (MRCI)
  • Coupled-cluster singles doubles with pertubative triples (CCSD(T))
  • Second/third-order approximate coupled-cluster singles doubles (CC2/CC3)
  • Multireference coupled-cluster singles doubles (MRCCSD)
  • Closed shell and general restricted open shell equation-of-motion coupled- cluster singles doubles (EOM-CCSD)

Further features include:

  • Flexible, modular and customizable input format
  • Excited state calculations with the CC2/CC3, EOM-CCSD, CASSCF, MRCI and MRCCSD methods
  • Internal coordinate geometry optimizer
  • Harmonic frequencies calculations
  • One-electron properties like dipole/quadrupole moments, natural orbitals, electrostatic potential, hyperfine coupling constants or spin density
  • Utilization of molecular point-group symmetry to increase efficiency
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Pyfr
flux reconstruction in Python
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PyFR is an open-source Python based framework for solving advection-diffusion type problems on streaming architectures using the Flux Reconstruction approach of Huynh. The framework is designed to solve a range of governing systems on mixed unstructured grids containing various element types. It is also designed to target a range of hardware platforms via use of an in-built domain specific language derived from the Mako templating engine.

This package provides the PyFR application.

Please cite: F.D. Witherden, A.M. Farrington and P.E. Vincent: PyFR: An open source framework for solving advection–diffusion type problems on streaming architectures using the flux reconstruction approach. (eprint) Computer Physics Communications 185(11):3028-3040 (2014)
Pymca
Applications and toolkit for X-ray fluorescence analysis -- scripts
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PyMca is set of applications and Python libraries for analysis of X-ray fluorescence spectra.

The applications included in this package are:

  • edfviewer - Display and inspection of data files in ESRF Data Format
  • elementsinfo - Displays element specific X-ray data
  • mca2edf - Converts files from SPEC MCA format to EDF
  • peakidentifier - Displays X-ray fluorescence peaks in a given energy range
  • pymcabatch - Batch fitting of spectra
  • pymcapostbatch - Post-processing of batch fitting results
  • pymca - Interactive data-analysis
  • pymcaroitool - Region-of-interest (ROI) imaging tool

The PyMca toolkit can read data files in SPEC, ESRF data file (EDF), OMNIC, HDF5, AIFIRA and SupaVisio formats.

This are the scripts of the package.

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Python3-deap
Distributed Evolutionary Algorithms in Python3
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DEAP is a novel evolutionary computation framework for rapid prototyping and testing of ideas. It seeks to make algorithms explicit and data structures transparent. It works in perfect harmony with parallelisation mechanism such as multiprocessing and SCOOP.

This package contains the modules for Python3.

Python3-sympy
Computer Algebra System (CAS) in Python (Python 3)
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SymPy is a Python library for symbolic mathematics (manipulation). It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries, except optionally for plotting support.

This package contains the Python 3 version of sympy.

Quantum-espresso
電子構造および第一原理分子動力学スイート
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Quantum ESPRESSO(以前は PWscf という名前でした)は、電子構造計算および ナノスケールの材料モデリング用の一連のコンピュータコードです。密度汎関数法 および平面波基底、擬ポテンシャル(ノルム保存、ウルトラソフト、PAWの全て)に 基いています。

次のような機能があります。

  • 平面波基底を用いた基底状態一点計算によるバンド構造計算、自己無撞着 エネルギー計算、力および応力
  • 分離可能型ノルム保存擬ポテンシャルおよび(Vanderbiltの)ウルトラソフト 擬ポテンシャル、PAW (Projector Augmented Waves)
  • LDA から GGA (PW91, PBE, B88-P86, BLYP) やメタ GGA、厳密交換相互作用 (HF)、ハイブリッド汎関数 (PBE0, B3LYP, HSE) に至るまでの様々な交換相関 汎関数
  • カー・パリネロ分子動力学法およびボルン・オッペンハイマー分子動力学法
  • 遷移状態および最小エネルギーパスを含む構造最適化
  • スピン軌道相互作用および非共線的磁気構造
  • フォノン周波数および固有ベクトルや、有効電荷、誘電テンソル、赤外および ラマン散乱断面積、EPR および NMR 化学シフトなどの応答特性
  • X線吸光スペクトル (XAS) におけるK吸収端およびL1吸収端や電子励起などの スペクトル特性
Please cite: P. Giannozzi, S. Baroni, N. Bonini, M. Calandra, R. Car, C. Cavazzoni, D. Ceresoli, G. L. Chiarotti, M. Cococcioni, I. Dabo, A. Dal Corso, S. Fabris, G. Fratesi, S. de Gironcoli, R. Gebauer, U. Gerstmann, C. Gougoussis, A. Kokalj, M. Lazzeri, L. Martin-Samos, N. Marzari, F. Mauri, R. Mazzarello, S. Paolini, A. Pasquarello, L. Paulatto, C. Sbraccia, S. Scandolo, G. Sclauzero, A. P. Seitsonen, A. Smogunov, P. Umari and R. M. Wentzcovitch: QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials. J. Phys. Condens. Matter 21:395502 (2009)
Root-system
metapackage to install all ROOT packages
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The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

With the data defined as a set of objects, specialized storage methods can give direct access to the separate attributes of the selected objects, without having to touch the bulk of the data. Included are histogramming methods in 1, 2 and 3 dimensions, curve fitting, function evaluation, minimization, graphics and visualization classes to allow the easy creation of an analysis system that can query and process the data interactively or in batch mode.

The command language, the scripting (or macro) language, and the programming language are all C++, thanks to the built-in CINT C++ interpreter. This interpreter removes the time consuming compile/link cycle, allowing for fast prototyping of the macros, and providing a good environment to learn C++. If more performance is needed, the interactively developed macros can be compiled using a C++ compiler.

The system has been designed in such a way that it can query its databases in parallel on MPP machines or on clusters of workstations or high-end PCs. ROOT is an open system that can be dynamically extended by linking external libraries. This makes ROOT a premier platform on which to build data acquisition, simulation and data analysis systems.

This package is a metapackage to ensure the installation of all possible ROOT packages on a system.

Science-electronics
Debian Science Electronics transitional package
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Debian-Electronics is now a separate Debian Pure Blend and allows a fine-grained control on the topics to install. To ease the transition, this package will install all user related tasks from Debian-Electronics.

Science-numericalcomputation
Debian Science Numerical Computation packages
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This metapackage will install Debian Science packages useful for numerical computation. The packages provide an array oriented calculation and visualisation system for scientific computing and data analysis. These packages are similar to commercial systems such as Matlab and IDL.

Tessa
FDTD 法を使った三次元光学システムシミュレータ
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Tessa は波長のスケールでの光学システムの三次元シミュレータであり、 finite differences time-domain method (FDTD) 法に基づいています。 大規模な共振器に焦点を置いていますが、伝搬ビームの研究用にも利用可能です。 任意の誘電体および吸収体のシミュレートが可能であり、一台のワークステーション で利用可能ですし、クラスタでも利用可能です。

Tessa はものすごく効率的であると信じられています。

URL: http://alioth.debian.org/projects/tessa/

Tessa-mpi
simulation of 3D optical systems using FDTD on MPI clusters
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Tessa is a three-dimensional simulation software for optical systems at the wavelength scale, based on the finite differences time-domain method (FDTD). It focuses on simulating large, resonating structures, but can also be used to study propagating beams. It can simulate arbitrary dielectric and absorbing materials, and can be used on single workstations as well as clusters.

This package is built with MPI support.

URL: http://alioth.debian.org/projects/tessa/

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.

V-sim
原子構造の可視化
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V_Sim は結晶、結晶粒界、分子などの原子構造 (バイナリ形式もしくは プレインテキスト形式のもの) を可視化できます。

描画は擬似 3D で、球 (原子) や矢印 (スピン) で表されます。ユーザは、多くの 関数を使って対話することでビューの選択、バインディングの設定、断面の描画、 スカラー場からの表面の計算、ノードの複製、形状測定、などができます。さらに、 V_Sim ではビューを画像として PNG, JPG, PDF (ビットマップ), SVG (図) や 他の形式でエクスポートできます。原子をデータの値から色付けしたり、多くの 位置ファイルを画面上でアニメーション表示したりできるいくつかのツールも 利用できます。

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Official Debian packages with lower relevance

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
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

Openctm-tools
Tools for compression of 3D triangle meshes
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OpenCTM — the Open Compressed Triangle Mesh file format — is a file format, a software library and a tool set for compression of 3D triangle meshes. The geometry is compressed to a fraction of comparable file formats, and the format is easily accessible through a simple, portable API.

This package contains the programs ctmconv and ctmview, used to convert and view OpenCTM files.

Paw-demos
物理分析ワークステーションのサンプルおよびテストスクリプト
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CERNLIB は物理実験で使うために作られたデータ解析ツールとライブラリの スイートですが、生物科学といった別分野向けのアプリケーションもあります。

本パッケージには、PAW または Paw++ で使うサンプルスクリプト、および PAW ま たは Paw++ プログラムが正しく動作していることを確認するためのテストスクリプ トが含まれます。このサンプルやテストスクリプトを同梱のプログラム paw-demos で実行しても構いません。

Science-mathematics
Debian Science 数学パッケージ
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このメタパッケージは、数学に関連する Debian Science パッケージ群をインス トールします。あなたの関心次第ですが、field::mathematics という debtag や、 メタパッケージ education-mathematics にも興味があるかもしれません。

Science-statistics
Debian Science 統計学パッケージ
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このメタパッケージは Debian Pure Blend "Debian Science" の一部で、統計学に 関連したパッケージをインストールします。このタスクはどんな科学的研究にも使 える一般的なタスクです。たくさんの R パッケージに加え、統計処理を行うのに便 利な他のツールに依存します。さらに、オプションで数学関連の全ソフトウェアを インストールできる Science Mathematics タスクを提案します。

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

Fdmnes
calculates spectra of different spectroscopies
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FDMNES calculates the spectra of different spectroscopies related to the real or virtual absorption of x-ray in material. It gives the absorption cross sections of photons around the ionization edge, that is in the energy range of XANES in the EXAFS. The calculation is performed with all conditions of rectilinear or circular polarization. In the same way, it calculates the structure factors and intensities of anomalous or resonant diffraction spectra (DAFS or RXD). FDMNES also allows the comparison of the simulated spectra to experimental ones with the help of objective criteria.

Geant4
toolkit for simulation of particle/nuclear physics in detectors
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Version: 4.9.4.p02-1

Geant4 is a toolkit for the simulation of the passage of particles through matter. Its application areas include high energy physics and nuclear experiments, medical, accelerator and space physics studies. The Geant4 software consists of an extensive set of libraries, fundamentally object-oriented and based in modern C++. It may be used to develop programs with command-line, Xaw-based, or Motif-based interfaces.

This package is a metapackage that depends upon all components of a Geant4 environment. Unless you know exactly what parts of Geant4 you want, it is best to install this package.

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

No known packages available but some record of interest (WNPP bug)

Blzpack - wnpp
library for solving large sparse eigenproblems
Responsible: Ondrej Certik
License: BSD
Debian package not available

BLZPACK (for Block LancZos PACKage, release 04/00) is a standard Fortran 77 implementation of the block Lanczos algorithm intended for the solution of the standard eigenvalue problem Ax=µx or the generalized eigenvalue problem Ax=µBx, where A and B are real, sparse symmetric matrices, µ an eigenvalue and x an eigenvector.

The development of this eigensolver was motivated by the need to solve large, sparse, generalized problems from free vibration analyses in structural engineering. Several upgrades were performed afterwards aiming at the solution of eigenvalues problems from a wider range of applications.

Documentation: user's guide, technical report and comprehensive bibliography.

Install this package if you need to compile or link against BLZPACK.

Clhep - wnpp
Class Library for High Energy Physics
Responsible: Lifeng Sun
License: GPL-3, LGPL-3
Debian package not available
Language: C++

The CLHEP package is a set of High Energy Physics specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra.

Gate - wnpp
Geant4 Application for Emission Tomography
Responsible: Nicolas Spalinger
License: LGPL
Debian package not available

GATE incorporates the Geant4 libraries in a modular, versatile, and scripted simulation toolkit which is adapted to the field of nuclear medicine both in PET (Positron Emission Tomography) and SPECT (Single Photon Emission Computer Tomography). It allows the accurate description of time-dependent phenomena such as source or detector movement and source decay kinetics. The ability to synchronize all time-dependent components allows a coherent description of the acquisition process. It makes it possible to perform realistic simulations of data acquisitions in time.

No known packages available

Espresso++
Extensible Simulation Package for Research on Soft matter
License: Not yet known (hopefully free)
Debian package not available

ESPResSo is a highly versatile software package for the scientific simulation and analysis of coarse-grained atomistic or bead-spring models as they are used in soft matter research, with emphasis on charged systems.

Jfreemesh
3D mesh library in Java
License: QPL
Debian package not available

JFreeMesh is a 3D mesh library written in Java and providing a high level API for mesh manipulation. JFreeMesh is based on a descending mesh data structure but simulate a full connectivity mesh by providing optimized method to access to any upper mesh element by using the global mesh methods. Therefore,

 JFreeMesh allows to load a large amount of mesh elements for a small memory
foot print. JFreeMesh comes with a default mesh loader based on the GMSH file

format and provides, through the JFreeMesh-VTK package, an exporter to VTK.

Spis
Software toolkit for spacecraft-plasma interactions modelling
License: GPL
Debian package not available

JSPIS stands for Spacecraft Plasma Interaction System. SPIS project aims at developing a software toolkit for spacecraft-plasma interactions modelling.

*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 200888