Debian Science Project
Summary
Nanoscale physics
Debian Science Nanoscale Physics packages

This metapackage will install Debian Science packages related to Nanoscale Physics, which corresponds to the study of physical systems typically ranging from 1 to 100 nm in size. The properties of such systems usually depend on the number of atoms they are made of, while this number is still relatively large for an accurate description.

The nanoscale is the meeting point of classical and quantum physics. Previous research efforts were considering either smaller systems, for which everybody could develop their own methods and software independently, or much bigger systems, for which it was clearly impossible to provide a fine-grained description. Addressing the issues raised by the nanoscale requires however cooperative and coordinated efforts in a multidisciplinary context. This metapackage is part of such an endeavor.

You might also be interested in the debtag field::physics and, depending on your focus, in the physics and education-physics metapackages.

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 Nanoscale 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)
Ase
Atomic Simulation Environment
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ASE is an Atomic Simulation Environment written in the Python programming language with the aim of setting up, stearing, and analyzing atomic simulations. ASE is part of CAMPOS, the CAMP Open Source project.

ASE contains Python interfaces to several different electronic structure codes including Abinit, Asap, Dacapo, Elk, GPAW and SIESTA.

This package provides the executable scripts.

Please cite: S. R. Bahn and K. W. Jacobsen: An object-oriented scripting interface to a legacy electronic structure code. (2002)
Avogadro
systém molekulárnej grafiky a modelovania
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Avogadro je systém molekulárnej grafiky a modelovania cielený na molekuly a biomolekuly. Dokáže vizualizovať vlastnosti ako molekulárne orbitály alebo elektrostatické potenciály a obsahuje inovatívny nástroj na tvorbu molekúl.

Medzi jeho vlastnosti patrí:

  • modelovač molekúl s automatickou optimalizáciou geometrie založenou na silovom poli
  • molekulárna mechanika vrátane obmedzení a hľadaní vyhovujúcich
  • vizualizácia molekulárnych orbitálov a všeobecných isopovrchov
  • vizualizácia vibrácií a kreslenie vibračného spektra
  • podpora jednotiek kryštalografických buniek
  • generovanie vstupu pre balíky kvantovej chémie Gaussian, GAMESS a MOLPRO
  • flexibilná architektúra zásuvných modulov a skriptovanie v Pythone

Avogadro dokáže čítať súborové formáty PDB, XYZ, CML, CIF, Molden a tiež zapisovať výstup do Gaussian, GAMESS a MOLPRO.

Please cite: Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek and Geoffrey R Hutchison: Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. (eprint) J. Cheminf. 4:17 (2012)
Registry entries: Bio.Tools  SciCrunch  OMICtools 
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Binoculars
Surface X-ray diffraction 2D detector data reduction
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BINoculars is a tool for data reduction and analysis of large sets of surface diffraction data that have been acquired with a two-dimensional X-ray detector. The intensity of each pixel of a two-dimensional detector is projected onto a three-dimensional grid in reciprocal-lattice coordinates using a binning algorithm. This allows for fast acquisition and processing of high-resolution data sets and results in a significant reduction of the size of the data set. The subsequent analysis then proceeds in reciprocal space. It has evolved from the specific needs of the ID03 beamline at the ESRF, but it has a modular design and can be easily adjusted and extended to work with data from other beamlines or from other measurement techniques.

Cadabra
field-theory motivated computer algebra system
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Cadabra is a computer algebra system designed specifically for the solution of problems encountered in field theory. It has extensive functionality for tensor polynomial simplification including multi-term symmetries, fermions and anti-commuting variables, Clifford algebras and Fierz transformations, implicit coordinate dependence, multiple index types and many more. The input format is a subset of TeX.

Cbflib-bin
utilities to manipulate CBF files
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CBFlib is a library of ANSI-C functions providing a simple mechanism for accessing Crystallographic Binary Files (CBF files) and Image-supporting CIF (imgCIF) files.

This package contains various utility programs.

Cod-tools
tools for manipulating CIF format files
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cod-tools is a set of Perl modules and command line tools for manipulating Crystallographic Information Format (CIF) v1.1 and v2.0 files.

Please cite: Saulius Gražulis, Andrius Merkys, Antanas Vaitkus and Mykolas Okulič-Kazarinas: Computing stoichiometric molecular composition from crystal structures. Journal of Applied Crystallography 48:85-91 (2015)
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)

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.

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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.
Extrema
powerful visualization and data analysis tool
Maintainer: Christine Spang
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Extrema is a mature and robust data analysis application, originally developed at the TRIUMF particle physics laboratory. It is designed to be of great practical use to researchers and aims to be both powerful and easy to use.

Extrema features a rich graphical user interface, as well as an intuitive command language. It provides well-documented tools for both 2D and 3D graphing, data reduction and analysis, and data input/output.

Feynmf
sada makier LaTeXu na tvorbu Feynmannovych diagramov
Maintainer: Thorsten Alteholz
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FeynMF je balík LaTeXu na jednoduché kreslenie Feynmannovych diagramov v profesionálnej kvalite. Sú to ilustrácie zobrazujúce interakcie fundamentálnych subatomických častíc. Je možné ich tvoriť buď pomocou programu Metafont alebo MetaPost. FeynMF väčšinu diagramov rozloží uspokojivo na základe štruktúry grafu bez potrebu manuálneho zásahu. V obskúrnejších prípadoch je ale k dispozícii všetka sila programu Metafont alebo MetaPost.

Pamätajte, že ak chcete používať verziu FeynMF založenú na MetaPost, budete potrebovať balík texlive-metapost.

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)
Garlic
program na vizualizáciu biomolekúl
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Garlic je napísaný na vyšetrovanie membránových bielkovín. Je možné ho použiť na vizualizáciu iných bielkovín a tiež niektorých geometrických objektov. Táto verzia Garlic pozná formát PDB verzie 2.1. Garlic je možné použiť na analýzu bielkovinových sekvencií.

Závisí iba od knižníc X, nie sú potrebné žiadne iné knižnice.

Medzi jeho vlastnosti patria:

  • Pozícia a hrúbka platničiek (slab) sú viditeľné v malom okne.
  • Atómové väzby a farby väzieb v závislosti od polohy. Je dostupných päť režimov mapovania (ako pri platničkách).

  • Schopný zobraziť stereoskopický obraz.

  • Schopný zobraziť iné geometrické objekty ako membrány.
  • Atómové informácie sú dostupné pre atóm, na ktorom sa nachádza kurzor myši. Nie je potrebné klikať, len presunúť kurzor nad štruktúru.

  • Schopný načítať viac ako jednu štruktúru.

  • Schopný nakresliť Ramachandranov diagram, závitnicové koleso, Vennov diagram, spriemerovanú hydrofóbnosť a hydrofobický moment.

  • Naspodku hlavného okna je k dispozícii príkazový riadok. Dokáže zobraziť jednu chybovú správu a jeden reťazec príkazov.

Please cite: Damir Zucic and Davor Juretic: Precise Annotation of Transmembrane Segments with Garlic - a Free Molecular Visualization Program (eprint) Croatica Chemica Acta 77(1-2):397-401 (2004)
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Gdis
prehliadač modelov molekúl a kryštálov
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Program založený na GTK+ na zobrazovanie a manipuláciu s izolovanými molekulami, periodickými systémami a kryštalickými štruktúrami. Program je síce vo vývoji, ale dostatočne použiteľný. Má nasledovné rysy:

  • Podpora viacerých typov súborov (CIF, BIOSYM, XYZ, XTL, MARVIN a GULP)
  • Nástroj na jednoduchú tvorbu a manipuláciu s molekulami
  • Dialóg na tvorbu štartovacích konfigurácií pre molekulárne dynamické simulácie
  • Rôzne nástroje na vizualizáciu (informácia o geometrii, zvýrazňovanie oblastí, atď.)
  • Animácie BIOSYM súborov (tiež vykresľované animácie, pozri ďalej)

GDIS taktiež umožňuje vykonávať nasledujúce funkcie pomocou ďalších balíkov:

  • Vykresľovanie modelov (vďaka POVRay)
  • Minimalizácia energie (vďaka GULP)
  • Kalkulácia morfológie (vďaka cdd)
  • Spracovanie priestorových grúp (vďaka SgInfo)
  • Zobrazenie Periodickej tabuľky (vďaka GPeriodic)
  • Načítanie prídavných typov súborov, ako napríklad PDB (vďaka Babel)
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Ggobi
Data visualization system for high-dimensional data
Maintainer: Dirk Eddelbuettel
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GGobi is an open source visualization program for exploring high-dimensional data. It provides highly dynamic and interactive graphics such as tours, as well as familiar graphics such as the scatterplot, barchart and parallel coordinates plots. Plots are interactive and linked with brushing and identification.

See http://www.ggobi.org for more information.

Ghemical
prostredie GNOME na modelovanie molekúl
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Ghemical je balík softvéru na výpočtovú chémiu napísaný v C++. Má grafické používateľské prostredie a podporuje modely kvantovej mechaniky (semi-empirické) aj modely molekulárnej mechaniky. Momentálne sú dostupné funkcie optimalizácie geometrie, dynamiky molekúl a veľká množina vizualizačných nástrojov používajúcich OpenGL.

Ghemical využíva na kvantovo-mechanické výpočty externý kód. Semi-empirické metódy MNDO, MINDO/3, AM1 a PM3 pochádzajú z balíka MOPAC7 (voľné dielo) a sú súčasťou balíka. Balík MPQC poskytuje metódy ab initio: metódy založené na teórii Hartree-Fock sú momentálne podporované so základnými sadami od STO-3G do 6-31G**.

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Gnuplot
program na interaktívne kreslenie riadený z príkazového riadka
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Gnuplot je portabilný nástroj na interaktívne kreslenie dát a funkcií riadený z príkazového riadka, podporujúci mnoho výstupných formátov vrátane ovládačov mnohých tlačiarní, (La)TeX, (x)fig, Postscript atď. Výstup do X11 nájdete v balíku gnuplot-x11.

S dátovými súbormi a funkciami je možné pracovať pomocou jazyka podobného jazyku C. Dokáže vyhladzovať, prekladať krivkou, nelineárne prekladanie krivkou a pracovať s komplexnými číslami.

Tento balík slúži na inštaláciu plnohodnotného gnuplot (-qt, -x11 or -nox).

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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)
Gperiodic
aplikácia periodickej tabuľky
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GPeriodic je malý program založený na X/GTK+, ktorý vám umožňuje prehliadať periodickú tabuľku chemických prvkov a zobrazovať pomerne podrobné informácie o každom z prvkov. Momentálne obsahuje 118 prvkov.

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Grace
nástroj na tvorbu a vykresľovanie v dvoch rozmeroch
Maintainer: Nicholas Breen
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Grace je nástroj na vykresľovanie v dvoch rozmeroch pomocou myši. Toto je program, ktorý bol v minulosti známy ako Xmgr.

Niektoré z jeho vlastností: používateľom definované škálovanie, zaškrtávanie, menovky, symboly, štýly čiar, polynomiálna regresia, krivky, pohyblivé priemery, DFT/FFT, krážová- a auto-korelácia, dávkový režime na bezobslužné vykresľovanie a podpora tlačenia do PostScript, FrameMaker a niekoľkých formátov obrázkov.

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Graphviz
sada bohatých nástrojov na kreslenie grafov
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Kreslenie grafov sa zaoberá problémom vizualizácie štrukturálnych informácií zostavením geometrických reprezentácií abstraktných grafov a sietí. Automatická tvorba kresieb grafov má dôležité aplikácie v kľúčových technológiách ako návrh databáz, softvérové inžinierstvo, VLSI a návrh sietí a vizuálnych rozhraní v iných doménach. Medzi situácie, kde tieto nástroje môžu byť obzvlášť užitočné patrí:

  • chcete reštrukturalizovať program a najprv chcete pochopiť vzťahy medzi jeho typmi, procedúrami a zdrojovými súbormi,
  • potrebujete nájsť úzke miesta na chrbticovej internetovej sieti - nielen jednotlivé spojenia, ale aj ich vzťahy,
  • ladíte protokol alebo mikroarchitektúru reprezentovanú konečným stavovým automatom a potrebujete zistiť, ako nastáva istý chybový stav,
  • chcete prehliadať schému databázy, bázy znalostí alebo grafickú reprezentáciu distribuovaného programu,
  • chcete vidieť prehľad kolekcie navzájom prepojených dokumentov,
  • chcete objaviť vzory a záujmové komunity v databáze telefónnych hovorov alebo emailových správ.

Tento balík obsahuje nástroje pre príkazový riadok.

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Gsl-bin
GNU Scientific Library (GSL) - binárny balík
Maintainer: Dirk Eddelbuettel
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Vedecká knižnica GNU - GNU Scientific Library (GSL) je zbierka funkcií na numerickú analýzu. Funkcie vytvoril od začiatku tím GSL v jazyku C. Predstavujú moderné API pre programátorov v jazyku C a zároveň umožňujú písanie väzieb pre jazyky vyššej úrovne.

Balík poskytuje niekoľko binárnych súborov s príkladmi.

URL: http://www.gnu.org/software/gsl/

Gwyddion
nástroj na vizualizáciu a analýzu mikroskopie skenovacej sondy
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Gwyddion je modulárny program na vizualizáciu a analýzu dát mikroskopie skenujúcej sondou (SPM - Scanning Probe Microscopy). Je primárne určený na analýzu výškových dát získaných mikroskopickými technikami ako sú

  • atómová silová mikroskopia (AFM - Atomic Force Microscopy)
  • magnetická silová mikroskopia (MFM - Magnetic Force Microscopy)
  • mikroskopia skenujúca tunelovaním (STM - Scanning Tunneling Microscopy)
  • optická mikroskopia skenovania blízkym poľom (SNOM alebo NSOM - Near-field Scanning Optical Microscopy)

a ďalšie. Možno ju však použiť na analýzu ľubovoľne hlboké pole a analýzu obrazu.

Tento balík obsahuje hlavnú aplikáciu a jej moduly. Tiež obsahuje tvorbu náhľadov pre GNOME (a Xfce) pre všetky typy súborov, ktoré Gwyddion pozná.

Tiež obsahuje Pygwy, rozhranie Gwyddionu na tvorbu skriptov v Pythone.

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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Libblas3
referenčné implementácie základnej lineárnej algebry - zdieľaná knižnica
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BLAS (Basic Linear Algebra Subroutines - podprogramy základnej lineárnej algebry) je sada efektívnych rutín pre väčšinu základných vektorových a maticových operácií. Široko sa využívajú ako základ ďalšieho kvalitného softvéru na lineárnu algebru, napr. lapack a linpack. Táto implementácia je referenčná implementácia vo Fortrane 77, ktorá sa nachádza na netlib.

Tento balík obsahuje zdieľanú verziu knižnice.

Libgsl0ldbl
GNU Scientific Library (GSL) -- library package
Maintainer: Dirk Eddelbuettel
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The GNU Scientific Library (GSL) is a collection of routines for numerical analysis. The routines are written from scratch by the GSL team in C, and present a modern API for C programmers, while allowing wrappers to be written for very high level languages.

GSL includes data types and routines for complex numbers, vectors, matrices, basic linear algebra subroutines (BLAS), eigensystems, simulated annealing, minimization, root finding, pseudo-random numbers, least-squares fitting, fast Fourier transforms (FFT), differential equations, quadrature, Monte Carlo integration, special functions, physical constants, and much more.

This package provides the shared libraries required to run programs compiled with GNU GSL. To compile your own programs you also need to install libgsl0-dev.

Liblapack3
knižnica rutín lineárnej algebry, verzia 3 - zdieľaná knižnica
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LAPACK verzia 3.X je vyčerpávajúca knižnica FORTRANu na operácie lineárnej algebry vrátane inverzie matice, riešení sústavy lineárnych rovníc metódou najmenších štvorcov, analýzy vlastných vektorov, dekompozície singulárnych hodnôt atď. Je to veľmi vyčerpávajúci balík s dobrou povesťou, ktorý našiel rozsiahle využitie vo vedeckej komunite.

Tento balík obsahuje zdieľanú verziu knižnice.

Libssm-bin
macromolecular superposition library - binaries
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SSM is a macromolecular coordinate superposition library, written by Eugene Krissinel of the EBI.

The library implements the SSM algorithm of protein structure comparison in three dimensions, which includes an original procedure of matching graphs built on the protein's secondary-structure elements, followed by an iterative three-dimensional alignment of protein backbone Calpha atoms.

This package contains the binaries of the libraries

Please cite: E. Krissinel and K. Henrick: Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. (PubMed,eprint) Acta Crystallogr D Biol Crystallogr. 60(1):2256-68 (2004)
Mayavi2
scientific visualization package for 2-D and 3-D data
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MayaVi2 is a cross-platform tool for 2-D and 3-D scientific data visualization. Its features include:

  • Visualization of scalar, vector and tensor data in 2 and 3 dimensions
  • Easy scriptability using Python
  • Easy extendability via custom sources, modules, and data filters
  • Reading several file formats: VTK (legacy and XML), PLOT3D, etc.
  • Saving of visualizations
  • Saving rendered visualization in a variety of image formats.

MayaVi2 has been designed with scriptability and extensibility in mind. While the mayavi2 application is usable by itself, it may be used as an Envisage plugin which allows it to be embedded in user applications natively. Alternatively, it may be used as a visualization engine for any application.

This package also provides TVTK, which wraps VTK objects to provide a convenient, Pythonic API, while supporting Traits attributes and NumPy/SciPy arrays. TVTK is implemented mostly in pure Python, except for a small extension module.

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Mpich
Implementation of the MPI Message Passing Interface standard
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MPICH is a high-performance and widely portable implementation of the MPI-3.1 standard from the Argonne National Laboratory. It efficiently supports different computation and communication platforms including commodity clusters, SMPs, massively parallel systems, and high-speed networks. This release has all MPI 3.1 functions and features required by the standard with the exception of support for the "external32" portable I/O format and user-defined data representations for I/O.

This package includes the program binaries necessary to run MPICH programs.

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).

Nco
Command-line operators to analyze netCDF files
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NCO is a suite of programs known as operators. The operators are stand-alone, command-line programs executable in a POSIX shell. Operators take one or more netCDF files as input, perform operations (e.g., averaging, hyperslabbing), and produce a netCDF output file. NCO was originally designed to manipulate and analyze climate data, though it works on any netCDF format datasets.

Please cite: Charles S. Zender: Analysis of Self-describing Gridded Geoscience Data with netCDF Operators (NCO). (eprint) Environmental Modelling & Software 23(10):1338-1342 (2008)
Ncview
X11 visual browser for NetCDF format files
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You would use ncview to get a quick and easy, push-button look at your NetCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data and other simple visual operations.

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Netcdf-bin
programy na čítanie a zapisovanie súborov NetCDF
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Obsahuje programy ncdump a ncgen, ktoré konvertujú súbory NetCDF na ASCII a späť. NetCDF (network Common Data Form) je rozhranie na prístup k vedeckým dátam a voľne šírená knižnica softvéru poskytujúca implementáciu tohto rozhrania. Knižnica netCDF tiež definuje strojovo nezávislý formát na reprezentáciu vedeckých dát. Rozhranie, knižnica a formát spolu podporujú tvorbu, prístup k vedeckým dátam a ich a zdieľanie.

Octave
jazyk GNU Octave na numerické výpočty
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Octave je vysokoúrovňový jazyk (prevažne kompatibilný s Matlab(R)) primárne určený na numerické výpočty. Poskytuje pohodlné rozhranie príkazového riadka na numerické riešenie lineárnych a nelineárnych problémov.

Octave je možné dynamicky rozšíriť pomocou používateľských súborov C++.

The package is enhanced by the following packages: liboctave-dev octave-doc texmacs
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)
Registry entries: SciCrunch 
Openmpi-bin
knižnica na vyskokovýkonné odovzdávanie správ - spustiteľné súbory
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Open MPI je projekt kombinujúci technológie a zdroje z niekoľkých ďalších projektov (FT-MPI, LA-MPI, LAM/MPI a PACX-MPI), aby zostavil tú najlepšiu dostupnú knižnicu MPI. Celkom nová implementácia MPI-3.1, Open MPI ponúka výhody dodávateľom systémov a softvéru, vývojárom aplikácií a výskumníkom oblasti informatiky.

Vlastnosti:

  • plne v súlade so štandardmi MPI-3.1
  • reentrantná, podporujúca paralelizáciu
  • dynamické spúšťanie procesov
  • vysoký výkon na všetkých platformách
  • spoľahlivá a rýchla správa úloh
  • tolerancia voči sieťovým chybám a chybám v procesoch
  • podpora heterogénnej siete
  • jediná knižnica podporuje všetky siete
  • dynamická implementácia
  • podpora mnohých plánovačov úloh
  • internacionalizované chybové hlásenia
  • dizajn založený na komponentoch, zdokumentované API

Tento balík obsahuje pomocné programy Open MPI.

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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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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Python3-lmfit
Least-Squares Minimization with Constraints (Python 3)
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The lmfit Python package provides a simple, flexible interface to non-linear optimization or curve fitting problems. The package extends the optimization capabilities of scipy.optimize by replacing floating pointing values for the variables to be optimized with Parameter objects. These Parameters can be fixed or varied, have upper and/or lower bounds placed on its value, or written as an algebraic expression of other Parameters.

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

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

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

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

This is the Python 3 version of the package.

Python3-scipy
vedecké nástroje pre Python 3
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SciPy dopĺňa populárny modul NumPy (balík python-numpy) a v rámci jedného balíka poskytuje rozličné vysokoúrovňové vedecké a inžinierske moduly.

SciPy je sada open source vedeckých a numerických nástrojov pre Python. Momentálne podporuje špeciálne funkcie, integrály, riešenie obyčajných diferenciálnych rovníc (ODR), optimalizáciu gradientov, genetické algoritmy, nástroje na paralelné programovanie, kompilátor výrazov do C++ na rýchly beh a ďalšie.

Tento balík poskytuje verziu pre Python 3.

Python3-sympy
systém počítačovej algebry pre jazyk Python 3
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SymPy je knižnica jazyka Python na symbolické výpočty. Jej cieľom je stať sa plnohodnotným systémom počítačovej algebry (CAS - Computer Algebra System) a zachovať si čo najprehľadnejší kód, aby bol jednoducho pochopiteľný a rozšíriteľný. SymPy je napísaná čisto v jazyku Python a nevyžaduje žiadne externé knižnice s výnimkou voliteľnej podpory vykresľovania.

Tento balík obsahuje verziu sympy pre Python 3.

Pyxplot
program na vykresľovanie dát tvoriaci výstup v publikačnej kvalite
Maintainer: Stuart Prescott
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Pyxplot je viacúčelový nástroj na kreslenie grafov, vedecký skriptovací jazyk, balík vektorovej grafiky a balík na spracovanie dát. Jeho rozhranie umožňuje prístup k bežným úlohám, napr. vykresľovaniu grafov dát s označením, pomocou krátkych, jednoduchých a intuitívnych príkazov.

Pyxplot tvorí obrázky v publikačnej kvalite. Preto sa text vykresľuje s krásou a flexibilitou sadzacieho prostredia LaTeX.

V balíku pyxplot-doc nájdete rozsiahlu dokumentáciu a príklady. Galériu vzorových grafov nájdete na webovej stránke projektu.

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)
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.

Scilab
balík vedeckého softvéru na numerické výpočty
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Scilab je balík maticového vedeckého softvéru. Scilab obsahuje stovky zabudovaných matematických funkcií, bohaté údajové štruktúry (vrátane polynómov, racionálnych funkcií, lineárnych systémov, zoznamov atď.) a dodáva sa s množstvom konkrétnych sád nástrojov na riadenie, spracovanie signálov atď.

Tento balík poskytuje Xcos, grafický editor na návrh hybridných modelov dynamických systémov.Modely možno navrhovať, načítať, ukladať, kompilovať a simulovať. Xcos je stabilné a výkonné riešenie priemyselných a akademických potrieb, poskytujúce funkcie na modelovanie mechanických systémov (automobilový a letecký priemysel, ...), hydraulických okruhov (priehrady, modelovanie rúr, ...), riadiacich systémov atď. Tiež obsahuje možnosti Modelica.

Minimálnu verziu Scilabu môžete nainštalovať z balíka „scilab-cli“.

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Udav
library for scientific graphs (window interface)
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A free cross-platform library of fast C++ routines for plotting data in up to 3 dimensions. It can export plots to bitmaps and vector EPS, SVG, IDTF files. There are simple window interfaces based on GLUT, FLTK and/or Qt. MathGL can also be used in the console. There are interfaces to a set of languages, such as, C, Fortran, Pascal, Forth, Python, Octave.

This package contains the udav window environment based on mathgl.

V-sim
Visualize atomic structures
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V_Sim visualizes atomic structures such as crystals, grain boundaries, molecules and so on (either in binary format, or in plain text format).

The rendering is done in pseudo-3D with spheres (atoms) or arrows (spins). The user can interact through many functions to choose the view, set the bindings, draw cutting planes, compute surfaces from scalar fields, duplicate nodes, measure geometry... Moreover V_Sim allows one to export the view as images in PNG, JPG, PDF (bitmap), SVG (scheme) and other formats. Some tools are also available to colorize atoms from data values or to animate on screen many position files.

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Official Debian packages with lower relevance

Axiom
počítačový algebraický systém na všeobecné účely - hlavný binárny súbor a moduly
Maintainer: Camm Maguire
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Axiom sa hodí na výskum a vývoj matematických algoritmov. Definuje silne typovú, matematicky korektnú hierarchiu typov. Obsahuje programovací jazyk a zabudovaný kompilátor.

Axiom sa vyvíja od roku 1973 a predával sa ako komerčný produkt. Bol uvoľnený ako slobodný softvér.

Prebiehajú snahy rozšíriť tento softvér:

 a) vyvinúť lepšie používateľské rozhranie
 b) urobiť ho užitočným ako nástroj pri výuke
 c) vyvinúť serverový protokol pre algebru
 d) integrovať ďalšiu matematiku
 e) prebudovať algebru v štýle gramotného programovania (literate
    programming)
 f) integrovať logické programovanie
 g) vyvinúť recenzovaný časopis Axiom Journal

Tento balík obsahuje hlavný binárny súbor programu a všetky predkompilované algebraické a automaticky načítateľné moduly.

The package is enhanced by the following packages: texmacs
Dx
OpenDX (IBM Visualization Data Explorer) - main package
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Data Explorer is a system of tools and user interfaces for visualizing data. In general terms the visualization of data can be considered a 3-stage process:

   1. Describing and importing data
   2. Processing the data through a visualization program
   3. Presenting the resulting image.
This is the main package.
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OpenDX (IBM Visualization Data Explorer) - documentation
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Data Explorer is a system of tools and user interfaces for visualizing data. In general terms the visualization of data can be considered a 3-stage process:

   1. Describing and importing data
   2. Processing the data through a visualization program
   3. Presenting the resulting image.
This is the documentation package. It includes online help and html

documentation.

Dxsamples
Sample programs for the OpenDX Data Explorer
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This package contains examples of scripts and networks for the OpenDX Data Explorer. They are referenced in the OpenDX tutorial, but can also be used stand-alone to browse and investigate.

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

Gpiv
GUI program for Particle Image Velocimetry
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Gpiv is a Graphic User Interface program using the GTK/GNOME libraries for Particle Image Velocimetry (PIV). The program gives a quick overview of the parameter settings of the processes and allows to change them easy, running the processes, individually or in a chain, visualizes and displays the results. The processes that may be invoked by Gpiv are:

Image processing: typical image manipulations that might be needed for PIV interrogation.

Image interrogation, resulting into estimators of particle image displacements.

Data validation to test on outliers, peak-locking effect and velocity gradients over the interrogation area's.

Data post-processing: data manipulation, spatial and time scaling to obtain a velocity field from the PIV data, calculation of spatial averages, vorticity and strain.

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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.

Hdf5-helpers
HDF5 (Hierarchical Data Format 5) - pomocné nástroje
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HDF5 je formát súborov a knižnica na ukladanie vedeckých dát. HDF5 bol navrhnutý a implementovaný s ohľadom na odstránenie nedostatkov HDF4.x. Má mocnejší a flexibilnejší dátový model, podporuje súbory väčšie ako 2 GB a podporuje paralelný V/V.

Tento balík obsahuje pomocné nástroje pre HDF5.

Hdf5-tools
HDF5 (Hierarchical Data Format 5) - nástroje
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HDF5 je formát súborov a knižnica na ukladanie vedeckých dát. HDF5 bol navrhnutý a implementovaný s ohľadom na odstránenie nedostatkov HDF4.x. Má mocnejší a flexibilnejší dátový model, podporuje súbory väčšie ako 2 GB a podporuje paralelný V/V.

Tento balík obsahuje pre HDF5 nástroje na použitie počas behu.

Libgraphviz-perl
rozhranie jazyka Perl k nástroju GraphViz na tvorbu grafov
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Tento modul poskytuje rozhranie na tvorbu rozloženia a obrázkov smerových a nesmerových grafov v rôznych formátoch (PostScript, PNG, atď.) pomocou programov „dot“, „neato“, „twopi“, „circo“ a „fdp“ z projektu GraphViz (http://www.graphviz.org/ alebo http://www.research.att.com/sw/tools/graphviz/).

Maxima
počítačový algebraický systém - základný systém
Maintainer: Camm Maguire
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Maxima je plne symbolický výpočtový program. Obsahuje plnú podporu symbolickej manipulácie polynómov, matíc, racionálnych funkcií, integrálov, Todd-Coxeterových metód na analýzu konečných grúp, grafov, výpočtov s pohyblivou desatinnou čiarkou. Obsahuje ladenie na úrovni symbolov zdrojového kódu Maxima. Maxima je založená na originálnom programe Macsyma, vyvinutom na MIT v 70-tych rokoch. Je spoľahlivý, má dobrú správu pamäte a žiadne úniky pamäte. Obsahuje stovky vlastných testov.

Tento balík obsahuje hlavný spustiteľný súbor a základné systémové súbory.

The package is enhanced by the following packages: texmacs
Mpich-doc
Documentation for MPICH
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MPICH is a high-performance and widely portable implementation of the MPI-3.1 standard from the Argonne National Laboratory. It efficiently supports different computation and communication platforms including commodity clusters, SMPs, massively parallel systems, and high-speed networks. This release has all MPI 3.1 functions and features required by the standard with the exception of support for the "external32" portable I/O format and user-defined data representations for I/O.

This package includes the MPICH documentation.

Netcdf-doc
Documentation for NetCDF
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NetCDF (network Common Data Form) is an interface for scientific data access and a freely-distributed software library that provides an implementation of the interface. The netCDF library also defines a machine-independent format for representing scientific data. Together, the interface, library, and format support the creation, access, and sharing of scientific data.

This package contains documentation for the NetCDF library in a variety of formats.

Openmpi-doc
high performance message passing library -- man pages
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Open MPI is a project combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-3.1 compliant implementation, Open MPI offers advantages for system and software vendors, application developers and computer science researchers.

This package contains man pages describing the Message Passing Interface standard.

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-pygraphviz
rozhranie jazyka Python k balíku Graphviz na rozloženie a vizualizáciu grafov - Python 3
Maintainer: Sandro Tosi
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Pygraphviz je rozhranie jazyka Python k balíku Graphviz na rozloženie a vizualizáciu grafov.

Pomocou Pygraphviz môžete vytvárať, čítať, upravovať a vykresľovať grafy pomocou jazyka Python a prístupu k algoritmom Graphviz na rozloženie a vizualizáciu grafov.

Tento balík obsahuje verziu python-pygraphviz pre Python 3.

Qtiplot
data analysis and scientific plotting
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Qtiplot is a fully fledged plotting software similar to the OriginLab Origin software (See http://www.originlab.com for more information about Origin).

It can make two and three dimensional plots of publication quality, both from datasets and functions. It can do non-linear fitting and multi-peak fitting.

Some Features:

  • Cross platform: works natively on Windows, Mac OS X and Linux/Unix systems
  • Fully Python scriptable
  • OpenGL based 3D plotting
  • Publication quality plots and easy export to various image formats (EMF, EPS, PS, PDF, SVG, BMP, JPG, PNG, TIFF, etc ...)
  • Easy integration with LaTeX typesetting system
  • Powerful and versatile spreadsheets with column-logic calculations and easy import/export of multiple files
  • One-click access to extensive built-in data analysis routines
  • Advanced statistical analysis: Student's t-Test, ANOVA, chi-square test for variance, normality test (Shapiro-Wilk)
  • Linear and nonlinear curve fitting with weighting and estimation of statistical errors of the fit-parameters
  • Multi-peak fitting
  • Image analysis tools
  • Templates support: all settings for plots, tables and matrices can be saved and restored later on for a fast editing process
  • Project files based on folders, a powerful project explorer with built-in drag and drop and searching facilities
  • Full import of Excel workbooks and Open Document Format spreadsheets, dBase, SQLite and Microsoft Access databases
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Scidavis
application for scientific data analysis and visualization
Maintainer: Georges Khaznadar
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SciDAVis is a free interactive application aimed at data analysis and publication-quality plotting. It combines a shallow learning curve and an intuitive, easy-to-use graphical user interface with powerful features such as scriptability and extensibility.

SciDAVis is similar in its field of application to proprietary Windows applications like Origin and SigmaPlot as well as free applications like QtiPlot, Labplot and Gnuplot.

What sets SciDAVis apart from the above is its emphasis on providing a friendly and open environment for new and experienced users alike.

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Science-mathematics
Debian Science Mathematics packages
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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.

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.

Debian packages in contrib or non-free

Horae
interactive graphical processing and analysis of EXAFS data
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ATHENA is an interactive graphical utility for processing EXAFS data. It handles most of the common data handling chores of interest, including deglitching, aligning, merging, background removal, and Fourier transforms.

ARTEMIS is an interactive graphical utility for fitting EXAFS data using theoretical standards from FEFF and sophisticated data modelling along with flexible data visualization and statistical analysis.

HEPHAESTUS is a souped up periodic table for the x-ray absorption spectroscopist. It provides a number of utilities involving tables of absorption coefficients and other chemical data.

Ifeffit
Interactive XAFS analysis program
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IFEFFIT is an interactive program for XAFS analysis. It combines the high-quality analysis algorithms of AUTOBK and FEFFIT with graphical display of XAFS data and general data manipulation.

IFEFFIT comes as a command-line program, but the underlying functionality is available as a programming library. The IFEFFIT library can be used from C, Fortran, Tcl, Perl, and Python. This allows a variety of user interfaces (both graphical and non-graphical) to be written around IFEFFIT. Currently, three graphical user interfaces: G.I.FEFFIT, ATHENA/ARTEMIS, and SIXPACK are built on the underlying IFEFFIT library. IFEFFIT and all three GUIs are under active development, but are fairly well tested and ready for use.

Sixpack
full-featured package for XAS analysis
Maintainer: Carlo Segre
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Sam's Interface for XAS Package, or SIXPack for short, is the unification of the previously named SamXAS and SamView programs into a single analysis package. Thus the package can guide the user through data averaging and calibration, background removal, and many aspects of fitting.

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.

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)

Exciting - wnpp
All-electron full-potential electronic-structure code
Responsible: Yann Pouillon
License: GPL
Debian package not available

exciting is a full-potential all-electron Density-Functional-Theory (DFT) package based on the Linearized Augmented Plane-Wave (LAPW) method.

It can be applied to all kinds of materials, irrespective of the atomic species involved, and also allows for the investigation of the atomic-core region.

We particularly focus on excited state properties, within the framework of time-dependent DFT (TDDFT) as well as within many-body perturbation theory (MBPT).

No known packages available

Ape
Atomic pseudopotential generator
Responsible: Yann Pouillon
License: GPL
Debian package not available

APE (Atomic Pseudopotential Engine) is a tool for generating atomic pseudopotentials within the Density-Functional Theory framework. It produces pseudopotential files suitable for use with SIESTA, OCTOPUS and ABINIT.

Atompaw
PAW atomic dataset generator
Responsible: Yann Pouillon
License: GPL
Debian package not available

The computer program atompaw generates projector and basis functions which are needed for performing electronic structure calculations based on the Projector-Augmented Wave (PAW) method. The program is applicable to materials throughout the periodic table. It produces an output file containing the projector and basis functions and the corresponding matrix elements in a form which can be read be the PWPAW and ABINIT codes. Additional data files are also produced which can be used to help evaluate the accuracy and efficiency of the generated functions.

Bigdft
Wavelet-based electronic-structure calculations
Responsible: Damien Caliste
License: GPL
Debian package not available

BigDFT is a DFT-based massively parallel electronic structure code using a wavelet basis set. Wavelets constitute a real space basis set distributed on an adaptive mesh (two levels of resolution in our implementation).

Thanks to our Poisson solver based on a Green function formalism, periodic systems, surfaces and isolated systems can be simulated with the proper boundary conditions. GTH or HGH pseudopotentials are used to remove the core electrons.

The Poisson solver is also integrated in ABINIT, OCTOPUS and CP2K.

Please cite: L. Genovese, A. Neelov, S. Goedecker, T. Deutsch, S. A. Ghasemi, A. Willand, D. Caliste, O. Zilberberg, M. Rayson, A. Bergman, R. Schneider: Daubechies wavelets as a basis set for density functional pseudopotential calculations. (2008)
Liblevmar-2-6
Levenberg-Marquardt nonlinear least squares algorithms
Responsible: Yann Pouillon
License: GPL
Debian package not available

The Levenberg-Marquardt (LM) algorithm is an iterative technique that finds a local minimum of a function that is expressed as the sum of squares of nonlinear functions. It has become a standard technique for nonlinear least-squares problems and can be thought of as a combination of steepest descent and the Gauss-Newton method.

This library provides native ANSI C implementations of the Levenberg-Marquardt optimization algorithm, usable also from C++, Matlab, Perl, Python, Haskell and Tcl. Both unconstrained and constrained (under linear equations, inequality and box constraints) Levenberg-Marquardt variants are included.

Remark of Debian Science team: packaging efforts can be found at https://launchpad.net/levmar
Octopus
Real-space TDDFT-based electronic-structure code
Responsible: Miguel Marques
License: LGPL
Debian package not available

Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within Density-Functional Theory (DFT), in its Time-Dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation.

Please cite: A. Castro, H. Appel, M. Oliveira, C.A. Rozzi, X. Andrade, F. Lorenzen, M. A. L. Marques, E. K. U. Gross, A. Rubio: octopus: a tool for the application of time-dependent density functional theory. (2006)
Wannier90-1
Maximally Localized Wannier Functions
Responsible: Arash Mostofi
License: GPL
Debian package not available

Wannier90 is an electronic-structure software computing maximally-localized Wannier functions (MLWF). It works on top of other electronic-structure software, such as Abinit, FLEUR, and PwSCF.

This is an old version still used by several packages. A patched version compatible with the ETSF Software Suite is available from https://launchpad.net/wannier90.

Please cite: A. A. Mostofi, J. R. Yates, Y.-S. Lee, I. Souza, D. Vanderbilt, N. Marzari: A Tool for Obtaining Maximally-Localised Wannier Functions. (2008)
Remark of Debian Science team: packaging efforts can be found at https://launchpad.net/wannier90
Wannier90-2
Maximally Localized Wannier Functions
Responsible: Arash Mostofi
License: GPL
Debian package not available

Wannier90 is an electronic-structure software computing maximally-localized Wannier functions (MLWF). It works on top of other electronic-structure software, such as Abinit, FLEUR, and PwSCF.

Please cite: A. A. Mostofi, J. R. Yates, Y.-S. Lee, I. Souza, D. Vanderbilt, N. Marzari: A Tool for Obtaining Maximally-Localised Wannier Functions. (2008)
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