Debian Science Project
Summary
Physics
Debian Science - Physik-Pakete

Dieses Metapaket installiert Debian-Science-Pakete für Physik. Vielleicht interessiert Sie auch das »Debtag« field::physics und, abhängig von Ihrem Schwerpunkt, das Metapaket education-physics.

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
Paket für elektronische Strukturberechnungen
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Das Hauptprogramm des Pakets ABINIT ermöglicht dem Benutzer, die Gesamtenergie, Ladungsdichte und elektronische Struktur eines Systems aus Elektronen und Kernen (Moleküle und periodische Festkörper) zu bestimmen, innerhalb der Dichtefunktionstheorie (DFT), mit Hilfe von Pseudopotentialen und ebenen Wellen.

ABINIT enthält auch Optionen zum Optimieren der Geometrie gemäß DFT-Kräften und -Beanspruchungen oder um molekulardynamische Simulationen mit diesen Kräften durchzuführen oder um dynamische Matrizen, effektive Born-Ladungen und dielektrische Tensoren zu generieren. Anregungszustände können mit der zeitabhängigen Dichtefunktionstheorie (für Moleküle) oder mit der Vielkörper-Störungstheorie (die GW-Näherung) berechnet werden. Zusätzlich zum Hauptcode von ABINIT werden verschiedene Werkzeuge mitgeliefert.

Dieses Paket enthält die erforderlichen ausführbaren Dateien zur Durchführung von Berechnungen. (Pseudopotentiale werden jedoch nicht bereitgestellt.) Installieren Sie für eine Reihe von Pseudopotentialen das Paket abinit-data.

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
Allzweck-Computeralgebrasystem: Hauptprogramme und Module
Maintainer: Camm Maguire
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Axiom ist für die Erforschung und Entwicklung von mathematischen Algorithmen nützlich. Es definiert eine stark typisierte, mathematisch korrekte Typenhierarchie. Es hat eine Programmiersprache und einen eingebauten Compiler.

Axiom wird seit 1973 entwickelt und wurde als kommerzielles Produkt verkauft. Es wurde als Freie Software veröffentlicht.

Es laufen Bemühungen zur Erweiterung der Software:

 (a) Entwicklung einer besseren Nutzerschnittstelle
 (b) Nutzbarmachung als Lehrwerkzeug
 (c) Entwicklung eines Algebra-Serverprotokolls
 (d) Integration weiterer Mathematik
 (e) Neuaufbau der Algebra im »literate programming«-Stil
 (f) Integration logischer Programmierung
 (g) Entwicklung eines Axiom-Journals mit begutachteten Einreichungen.

Dieses Paket enthält das Hauptprogramm und alle vorkompilierten Algebra- und automatisch ladbaren Module.

The package is enhanced by the following packages: texmacs-bin
cadabra
Durch Feldtheorie motiviertes Computeralgebrasystem
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Cadabra ist ein Computeralgebrasystem, das speziell zum Lösen von Problemen aus der Feldtheorie entwickelt wurde. Es besitzt umfangreiche Funktionalitäten für die Vereinfachung von Tensorpolynomen inklusive Multiterm-Symmetrien, Fermione und antikommutative Variablen, Clifford-Algebren und Fierz-Transformationen, implizite Koordinatenabhängigkeit, mehrere Indextypen und vieles mehr. Das Eingabeformat ist eine Teilmenge von TeX.

cernlib
CERNLIB Datenanalyse-Suite - Allgemeines Metapaket
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CERNLIB ist eine Sammlung von Werkzeugen und Bibliotheken zur Datenanalyse, entworfen zur Anwendung bei physikalischen Experimenten. Es ist allerdings auch in anderen Anwendungsbereichen wie der Biologie einsetzbar.

Dieses Metapaket stellt fast alle Programme und Bibliotheken zur Verfügung, die in CERNLIB enthalten sind. Die meisten Nutzer werden nur einen Teil davon installieren wollen. Einige zusätzliche CERNLIB-Programme, die nicht für viele Nutzer von Interesse sein dürften, erhalten Sie mit dem Metapaket cernlib-extras.

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
Sammlung von LaTeX-Makros zum Erzeugen von Feynman-Diagrammen
Maintainer: Thorsten Alteholz
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FeynMF ist ein LaTeX-Paket, um einfach Feynman-Diagramme in professioneller Qualität zu zeichnen. Feynman-Diagramme sind Illustrationen, welche die fundamentalen Wechselwirkungen subatomarer Teilchen anschaulich darstellen. Die Diagramme lassen sich entweder mit dem Programmen Metafont oder MetaPost zeichnen. FeynMF ordnet die meisten Diagramme anhand ihrer Struktur zufriedenstellend an, ohne dass manuelle Eingriffe nötig sind. Nichtsdestoweniger stehen für ungewöhnliche Fälle alle Möglichkeiten von Metafont oder MetaPost zur Verfügung.

Beachten Sie, dass Sie das Paket texlive-metapost benötigen, um die auf MetaPost basierende FeynMF-Variante verwenden zu können.

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
Löst Strömungsprobleme von Flüssigkeiten
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Gerris ist ein System für die Lösung partieller Differentialgleichungen, die strömende Flüssigkeiten beschreiben.

Eine kurze Zusammenfassung der (derzeit) wichtigsten Möglichkeiten:

  • Löst die zeitabhängigen, nicht komprimierbaren Euler-, Stokes- oder Navier-Stokes-Gleichungen mit variabler Dichte
  • Adaptive Gitterverfeinerung: die Auflösung wird dynamisch der Strömung angepasst
  • Komplett automatische Erstellung von Gittern in komplexer Geometrie
  • Zweiter Ordnung in Raum und Zeit
  • Unbeschränkte Anzahl von advektierten/diffundierten passiven Markern
  • Flexible Spezifikation von zusätzlichen Quelltermen
  • Portable Unterstützung für parallele Berechnungen durch die MPI-Bibliothek
  • Mehrphasenströmungs-Methode (Volume-of-Fluid) für Strömungen zwischen zwei Flächen

Dieses Paket besitzt eingebaute MPI-Unterstützung.

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
??? missing short description for package gpiv :-(
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gpivtools
??? missing short description for package gpivtools :-(
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gwyddion
Werkzeug zur Visualisierung und Analyse von Daten der Rastersondenmikroskopie
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Gwyddion ist ein modular aufgebautes Programm zur Visualisierung und Analyse von Daten der Rastersondenmikroskopie (Scanning Probe Microscopy - SPM). Es ist vor allem zur Analyse von Höhenfelddaten gedacht, welche durch Mikroskopietechniken wie

  • Rasterkraftmikroskopie (Atomic Force Microscopy - AFM),
  • Magnetkraftmikroskopie (Magnetic Force Microscopy - MFM),
  • Rastertunnelmikroskopie (Scanning Tunneling Microscopy - STM),
  • Optische Rasternahfeldmikroskopie (Near-field Scanning Optical Microscopy - SNOM oder NSOM) oder andere erhalten wurden. Es kann jedoch zur Analyse beliebiger Höhenfeld- und Bilddaten genutzt werden.

Dieses Paket beinhaltet das Hauptprogramm und seine Module. Es umfasst außerdem ein Programm für GNOME (und Xfce), welches Vorschauansichten für alle Gwyddion bekannten Dateitypen erstellt.

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)
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libroot-math-mlp-dev
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maxima
Computer-Algebra-System -- grundlegendes System
Maintainer: Camm Maguire
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Maxima ist ein Programm für Symbolisches Rechnen. Es bietet alle Möglichkeiten der symbolischen Manipulation von Polynomen, Matrizen, rationalen Funktionen, Integration, Todd-Coxeter-Methoden zur Analyse von finiten Gruppen, Zeichnen von Graphen und Berechnung von Fließkommazahlen mehrfacher Genauigkeit. Es enthält einen symbolischen Debugger auf Quellcode-Ebene für Maxima-Programmcode. Maxima beruht auf dem in den 1970ern am MIT entwickelten Macsyma. Es ist weitgehend verlässlich, verfügt über eine gute Speicherbereinigung und ist frei von Speicherlecks. Es ist mit Hunderten von Selbsttests ausgestattet.

Dieses Paket enthält die Hauptprogramme und die grundlegenden Systemdateien.

The package is enhanced by the following packages: texmacs-bin
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
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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
Physics Analysis Workstation - ein grafisches Analyseprogramm
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CERNLIB ist eine Sammlung von Datenanalysewerkzeugen und -bibliotheken für den Einsatz in physikalischen Experimenten, aber auch mit Anwendungen für andere Felder wie den Biowissenschaften.

PAW ist ein interaktives Programm, das interaktive grafische Präsentationen sowie statistische und mathematische Analysewerkzeuge bereitstellt. Es ist dafür gedacht, um mit Objekten zu arbeiten, die Physikern geläufig sind; etwa Histogramme, Ntuple, Vektoren, usw.

Das Programm ist gegen die CERN-Bibliotheken der 64-bit Architekturen statisch gelinkt, um dort die Funktion des Programms zu gewährleisten, da PAW nicht für 64-bit entwickelt wurde.

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paw++
Physics Analysis Workstation (verbesserte Lesstif-Version)
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CERNLIB ist eine Sammlung von Werkzeugen und Bibliotheken zur Datenanalyse, entworfen zur Anwendung bei physikalischen Experimenten. Es ist allerdings auch in anderen Anwendungsbereichen wie der Biologie einsetzbar.

Diese Paket enthält Paw++, ein interaktives Programm zur Analyse und grafischen Präsentation. Paw++ ist das gleiche Programm wie PAW (im Paket »paw«), aber mit einer benutzerfreundlicheren grafischen Oberfläche auf Basis von Motif (in Debian gegen Lesstif kompiliert).

Auf 64-Bit-Architekturen ist das Programm statisch gegen die CERN-Bibliotheken gelinkt, um eine ordnungsgemäße Funktion zu gewährleisten, obwohl es nicht sehr sauber für 64-Bit entworfen wurde.

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
Verteilte evolutionäre Algorithmen in Python3
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DEAP ist ein neuartiges evolutionäres rechnergestütztes Rahmenwerk für Rapid Prototyping und zum Testen von Ideen. Es versucht Algorithmen klar zu formulieren und Datenstrukturen transparent zu machen. Es arbeitet in perfekter Harmonie mit Parallelisierungsmechanismen wie Multiprocessing und SCOOP.

Dieses Paket enthält die Module für Python3.

python3-sympy
Python-3-Computeralgebrasystem (CAS)
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SymPy ist eine Python-Bibliothek für symbolische Mathematik (Manipulation). Das Ziel ist ein komplett ausgestattetes Computeralgebrasystem (CAS) zu werden, während der Code so einfach wie möglich gehalten werden soll, um verständlich und einfach erweiterbar zu sein. SymPy wurde ausschließlich in Python geschrieben und benötigt keine externen Bibliotheken, außer für die optionale Unterstützung von Plots.

Dieses Paket enthält die Python-3-Version von sympy.

The package is enhanced by the following packages: texmacs-bin
quantum-espresso
Electronic-Structure and Ab-Initio Molecular Dynamics Suite
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Quantum ESPRESSO (formerly known as PWscf) is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving, ultrasoft, and PAW).

Features include:

  • Ground-state single-point and band structure calculations using plane-wave self-consistent total energies, forces and stresses
  • Separable norm-conserving and ultrasoft (Vanderbilt) pseudo-potentials, PAW (Projector Augmented Waves)
  • Various exchange-correlation functionals, from LDA to generalized-gradient corrections (PW91, PBE, B88-P86, BLYP) to meta-GGA, exact exchange (HF) and hybrid functionals (PBE0, B3LYP, HSE)
  • Car-Parrinello and Born-Oppenheimer Molecular Dynamics
  • Structural Optimization including transition states and minimum energy paths
  • Spin-orbit coupling and noncollinear magnetism
  • Response properties including phonon frequencies and eigenvectors, effective charges and dielectric tensors, Infrared and Raman cross-sections, EPR and NMR chemical shifts
  • Spectroscopic properties like K- and L1-edge X-ray Absorption Spectra (XAS) and electronic excitations
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
??? missing short description for package root-system :-(
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science-electronics
Debian Science - Elektronik-Übergangspaket
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Debian-Electronics ist jetzt ein separates Debian Pure Blend und ermöglicht eine detaillierte Steuerung der zu installierenden Themenfelder. Um den Übergang zu erleichtern, werden mit diesem Paket alle benutzerbezogenen Tasks von Debian-Electronics installiert.

science-numericalcomputation
Debian Science - Pakete für numerische Berechnungen
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Dieses Metapaket installiert nützliche Pakete für numerische Berechnungen. Die Pakete bieten ein Array-orientiertes Berechnungs- und Visualisierungssystem für wissenschaftliches Rechnen und Datenanalyse. Sie ähneln kommerziellen Systemen wie Matlab und IDL.

siconos
modeling and simulation of nonsmooth dynamical systems (simulation runner tool)
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Siconos is an open-source scientific software primarily targeted at modeling and simulating nonsmooth dynamical systems in C++ and in Python:

  • Mechanical systems (rigid or solid) with unilateral contact and Coulomb friction and impact (nonsmooth mechanics, contact dynamics, multibody systems dynamics or granular materials).
  • Switched Electrical Circuit such as electrical circuits with ideal and piecewise linear components: power converter, rectifier, Phase-Locked Loop (PLL) or Analog-to-Digital converter.
  • Sliding mode control systems.
  • Biology (Gene regulatory network). Other applications are found in Systems and Control (hybrid systems, differential inclusions, optimal control with state constraints), Optimization (Complementarity systems and Variational inequalities), Fluid Mechanics, and Computer Graphics.

This package contains the 'siconos' tool allowing to compile and run Siconos programs/scripts in a single command.

Please cite: Vincent Acary and Bernard Brogliato: The SICONOS Platform :443-488 (2008)
siconos-mechanics-tools
modeling and simulation of nonsmooth dynamical systems (mechanics tools)
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Siconos is an open-source scientific software primarily targeted at modeling and simulating nonsmooth dynamical systems in C++ and in Python:

  • Mechanical systems (rigid or solid) with unilateral contact and Coulomb friction and impact (nonsmooth mechanics, contact dynamics, multibody systems dynamics or granular materials).
  • Switched Electrical Circuit such as electrical circuits with ideal and piecewise linear components: power converter, rectifier, Phase-Locked Loop (PLL) or Analog-to-Digital converter.
  • Sliding mode control systems.
  • Biology (Gene regulatory network). Other applications are found in Systems and Control (hybrid systems, differential inclusions, optimal control with state constraints), Optimization (Complementarity systems and Variational inequalities), Fluid Mechanics, and Computer Graphics.

This package contains tools to allow running, analysing, manipulating, exporting, and viewing the output of mechanical simulations.

Please cite: Vincent Acary and Bernard Brogliato: The SICONOS Platform :443-488 (2008)
tessa
??? missing short description for package tessa :-(
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tessa-mpi
??? missing short description for package tessa-mpi :-(
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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
Visualisiert Atomstrukturen
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V_Sim visualisiert Atomstrukturen wie Kristalle, Korngrenzen, Moleküle und so weiter (sowohl im binären Format oder auch im Textformat ASCII).

Die Darstellung erfolgt in »pseudo-3D« mit Kugeln (Atome) oder Pfeilen (Spins). Der Benutzer kann durch viele Funktionen eingreifen, um die Ansicht oder die Bindungen zu ändern, die Schnittebenen darzustellen, Oberflächen aus skalaren Feldern zu erstellen, Knoten zu duplizieren, die Geometrie zu vermessen… Mehr noch, V_Sim ermöglicht das Exportieren der Ansichten als Bild im PNG-, JPG-, PDF-Format (Bitmap), als SVG (Entwurf) und in andere Formate. Es sind auch einige Werkzeuge zum Einfärben von Atomen mittels Datenwerten oder zur Animation vieler Positionsdateien auf dem Bildschirm vorhanden.

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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
??? missing short description for package feel++-apps :-(
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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
Physics Analysis Workstation Beispiele und Tests
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CERNLIB ist eine Sammlung von Werkzeugen und Bibliotheken zur Datenanalyse, entworfen zur Anwendung bei physikalischen Experimenten. Es ist allerdings auch in anderen Anwendungsbereichen wie der Biologie einsetzbar.

Dieses Paket enthält Beispielskripte für PAW oder Paw++ und Testskripte zur Überprüfung der Programmfunktionalität. Die Beispiele und Tests können mit dem enthaltenem Programm paw-demos abgespielt werden.

science-mathematics
Debian Science: Mathematik-Pakete
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Dieses Metapaket installiert Debian-Science-Pakete mit Bezug zur Mathematik. Vielleicht ist auch das Debtag field::mathematics und, je nach Ihrem Fokus, das Metapaket education-mathematics für Sie von Interesse.

science-statistics
»Debian Science« Statistik-Pakete
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Dieses Metapaket ist Teil des Debian Pure Blend »Debian Science« und installiert Pakete im Zusammenhang zum Begriff Statistiken. Dieser Task ist ein allgemeiner Task, welcher nützlich ist für alle wissenschaftlichen Arbeiten. Das Paket hängt von einer Reihe von R-Paketen ab, genau so wie von anderen Werkzeugen, die nützlich für die Anwendung von Statistik sind. Des weiteren ist der Task Mathematik-Wissenschaften empfohlen, um optionale Mathematik-Software zu installieren.

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

fdmnes
calculates spectra of different spectroscopies
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Version: 0.0.20120607-1

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
physics simulation toolkit
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Version: 11.0.1+ds-1

Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.

This is a metapackage depending on all libraries.

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 247866