Debian Science Nanoscale Physics packages

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.

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.

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.

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.

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.

The CIF API provides a standard C interface for reading, writing, and manipulating Crystallographic Information Files (CIFs). It is targeted in particular at CIF 2.0, but it provides support for CIF 1.1 and earlier as well.

This package contains cif_linguist, an experimental program for converting data between various versions of the CIF format.

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

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 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.

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 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.

Finalcif is a full-featured CIF file editor to make editing and validation of CIF files easy. It collects all the information from a work folder needed in order to finalize a CIF file for publication. In any case, one can also import a valid CIF file to complete the information. In ideal cases, it takes one click to have a publication-ready file.

Essentially, one should have the corresponding CIF file for FinalCif in its original 'work' folder, which contains all other files such as SAINT list files, SADABS list file, SHELX list files, etc. that led to this CIF file.

Checking the final CIF file with the IUCr CheckCIF server is a one-click problem in FinalCif. One gets a web and PDF report or just a local PLATON CIF check for computers without internet.

FinalCif generates beautiful CIF reports in seconds for publication as MS Word files (also compatible with Openoffice etc.). The report includes tables of structure properties like R-values or atom parameters and a report text about the experiment conditions.

The button "save cif file" saves the current file under 'name'-finalcif.cif. FinalCif will never make changes to the original CIF file.

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.

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.

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)

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 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**.

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).

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.

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.

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.

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.

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 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.

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.

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.

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

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.

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 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.

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.

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.

NeXus is a common data format for neutron, X-ray, and muon science. It is being developed as an international standard by scientists and programmers representing major scientific facilities in Europe, Asia, Australia, and North America in order to facilitate greater cooperation in the analysis and visualization of neutron, X-ray, and muon data.

This is the package containing some applications for reading and writing NeXus files.

Octave is a (mostly MATLAB® compatible) high-level language, primarily intended for numerical computations. It provides a convenient command-line interface for solving linear and nonlinear problems numerically.

Octave can be dynamically extended with user-supplied C++ files.

The KIM API is an Application Programming Interface for atomistic simulations. The API provides a standard for exchanging information between atomistic simulation codes (molecular dynamics, molecular statics, lattice dynamics, Monte Carlo, etc.) and interatomic models (potentials or force fields). It also includes a set of library routines for using the API with bindings for:

FORTRAN 77, Fortran 90/95, Fortran 2003 C, C++

Atomistic simulation codes that support the KIM API work seamlessly with the KIM-compliant interatomic models (KIM Models) distributed on this website. The interface is computationally efficient and often requires relatively minor changes to existing codes.

This package contains models and model-drivers for KIM-API

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 (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.

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

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.

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.

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

This package contains the Python 3 version of sympy.

Pyxplot is a multi-purpose graph plotting tool, scientific scripting language, vector graphics suite, and data processing package. Its interface is designed to make common tasks -- e.g., plotting labelled graphs of data -- accessible via short, simple, intuitive commands.

Pyxplot produces publication-quality figures. To this end, text is rendered with all of the beauty and flexibility of the LaTeX typesetting environment.

Extensive documentation and examples can be found in the pyxplot-doc package. A gallery of sample plots is available from the project's web site.

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

SasView is software for the analysis of Small-Angle Scattering (SAS) data.

It fits analytic functions describing different types of material microstructure to experimental data in order to determine the shape, size and degree of ordering.

SasView also includes tools for calculating scattering length densities, slit sizes, resolution, fringe thicknesses/d-spacings, the (Porod) invariant ('total scattering'), and distance distribution functions.

SasView is a Small Angle Scattering Analysis Software Package, originally developed as part of the NSF DANSE project under the name SansView, now managed by an international collaboration of facilities.

This package installs the sasview executable script.

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 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“.

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 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.

The analysis of macromolecular structures often requires a comprehensive definition of atomic neighborhoods. Such a definition can be based on the Voronoi diagram of balls, where each ball represents an atom of some van der Waals radius. Voronota is a software tool for finding all the vertices of the Voronoi diagram of balls. Such vertices correspond to the centers of the empty tangent spheres defined by quadruples of balls. Voronota is especially suitable for processing three-dimensional structures of biological macromolecules such as proteins and RNA.

Since version 1.2 Voronota also uses the Voronoi vertices to construct inter-atom contact surfaces and solvent accessible surfaces. Voronota provides tools to query contacts, generate contacts graphics, compare contacts and evaluate quality of protein structural models using contacts.

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.

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.

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.

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.

Hierarchical Data Format 5 (HDF5) is a file format and library for storing scientific data. HDF5 was designed and implemented to address the deficiencies of HDF4.x. It has a more powerful and flexible data model, supports files larger than 2 GB, and supports parallel I/O.

This package contains helper tools for HDF5.

Hierarchical Data Format 5 (HDF5) is a file format and library for storing scientific data. HDF5 was designed and implemented to address the deficiencies of HDF4.x. It has a more powerful and flexible data model, supports files larger than 2 GB, and supports parallel I/O.

This package contains runtime tools for HDF5.

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 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.

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.

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 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.

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 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

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.

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.