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
Versions of package abinit
ReleaseVersionArchitectures
bullseye9.2.2-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie7.8.2-2amd64,armel,armhf,i386
stretch8.0.8-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster8.8.4-2amd64,arm64,armhf,i386
sid9.10.4-3amd64,arm64,mips64el,ppc64el,riscv64,s390x
bookworm9.6.2-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream10.3.3
Debtags of package abinit:
fieldchemistry, physics
roleprogram
Popcon: 15 users (18 upd.)*
Newer upstream!
License: DFSG free
Git

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
Versions of package ase
ReleaseVersionArchitectures
trixie3.23.0-1all
bookworm3.22.1-3all
bullseye3.21.1-2all
buster3.17.0-2all
sid3.23.0-1all
Popcon: 8 users (8 upd.)*
Versions and Archs
License: DFSG free
Git

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
Molecular Graphics and Modelling System
Versions of package avogadro
ReleaseVersionArchitectures
bullseye1.93.0-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm1.97.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie1.99.0-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
sid1.99.0-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
buster1.2.0-4amd64,arm64,armhf,i386
stretch1.2.0-1+deb9u1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie1.0.3-10.1amd64,armel,armhf,i386
Debtags of package avogadro:
fieldchemistry
roleprogram
uitoolkitqt
useviewing
Popcon: 56 users (37 upd.)*
Versions and Archs
License: DFSG free
Git

Avogadro is a molecular graphics and modelling system targeted at molecules and biomolecules. It can visualize properties like molecular orbitals or electrostatic potentials and features an intuitive molecular builder.

Features include:

  • Molecular modeller with automatic force-field based geometry optimization
  • Molecular Mechanics including constraints and conformer searches
  • Visualization of molecular orbitals and general isosurfaces
  • Visualization of vibrations and plotting of vibrational spectra
  • Support for crystallographic unit cells
  • Input generation for the Gaussian, GAMESS and MOLPRO quantum chemistry packages
  • Flexible plugin architecture and Python scripting

File formats Avogadro can read include PDB, XYZ, CML, CIF, Molden, as well as Gaussian, GAMESS and MOLPRO output.

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 
binoculars
Surface X-ray diffraction 2D detector data reduction
Versions of package binoculars
ReleaseVersionArchitectures
buster0.0.4-1all
bookworm-backports0.0.19-1~bpo12+1all
trixie0.0.19-1all
sid0.0.19-1all
bullseye0.0.6-1all
bookworm0.0.13-1all
Popcon: 5 users (1 upd.)*
Versions and Archs
License: DFSG free
Git

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
??? missing short description for package cadabra :-(
Versions of package cadabra
ReleaseVersionArchitectures
stretch1.46-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bookworm1.46-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye1.46-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster1.46-5amd64,arm64,armhf,i386
jessie1.39-0.2amd64,armel,armhf,i386
Debtags of package cadabra:
fieldmathematics
roleprogram
Popcon: 1 users (9 upd.)*
Versions and Archs
License: DFSG free
Git
cbflib-bin
utilities to manipulate CBF files
Versions of package cbflib-bin
ReleaseVersionArchitectures
jessie0.9.2.2-1amd64,armel,armhf,i386
bullseye0.9.6+dfsg1-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster0.9.5.18+dfsg1-1amd64,arm64,armhf,i386
trixie0.9.7+dfsg1-4amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bookworm0.9.7+dfsg1-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid0.9.7+dfsg1-4amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
stretch0.9.2.2-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package cbflib-bin:
roleprogram
Popcon: 2 users (9 upd.)*
Versions and Archs
License: DFSG free
Git

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.

cif-linguist
transform CIF data among CIF formats and dialects
Versions of package cif-linguist
ReleaseVersionArchitectures
trixie0.4.2-5amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bullseye0.4.2-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm0.4.2-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid0.4.2-5amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
Popcon: 0 users (6 upd.)*
Versions and Archs
License: DFSG free
Git

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
tools for manipulating CIF format files
Versions of package cod-tools
ReleaseVersionArchitectures
sid3.10.0+dfsg-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bullseye3.1.0+dfsg-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm3.7.0+dfsg-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie3.10.0+dfsg-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
buster2.3+dfsg-3amd64,arm64,armhf,i386
Popcon: 2 users (8 upd.)*
Versions and Archs
License: DFSG free
Git

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
Versions of package cp2k
ReleaseVersionArchitectures
stretch4.1-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bookworm2023.1-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid2023.2-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x
jessie2.5.1-3amd64,armel,armhf,i386
buster6.1-2amd64,arm64,armhf,i386
bullseye8.1-9amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream2024.3
Popcon: 10 users (9 upd.)*
Newer upstream!
License: DFSG free
Git

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

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

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

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

Ab-initio Molecular Dynamics:

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

Mixed quantum-classical (QM/MM) simulations:

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

Further Features include:

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

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

drawxtl
crystal structure viewer
Versions of package drawxtl
ReleaseVersionArchitectures
bookworm5.5-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid5.5-6.1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
trixie5.5-6.1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bullseye5.5-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster5.5-3amd64,arm64,armhf,i386
stretch5.5-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie5.5-3amd64,armel,armhf,i386
Debtags of package drawxtl:
interfacex11
roleprogram
uitoolkitglut
x11application
Popcon: 10 users (8 upd.)*
Versions and Archs
License: DFSG free
Git

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

Four forms of graphics are produced:

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

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

Please cite: Larry W. Finger, Martin Kroeker and Brian H. Toby: DRAWxtl, an open-source computer program to produce crystal-structure drawings. (eprint) J. Appl. Cryst. 40:188-192 (2007)
Screenshots of package drawxtl
etsf-io
Binary tools to check, merge and read ETSF files
Versions of package etsf-io
ReleaseVersionArchitectures
trixie1.0.4-5amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
jessie1.0.3-4amd64,armel,armhf,i386
stretch1.0.4-1.1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster1.0.4-4amd64,arm64,armhf,i386
bullseye1.0.4-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm1.0.4-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid1.0.4-5amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
Popcon: 3 users (7 upd.)*
Versions and Archs
License: DFSG free
Git

The European Theoretical Spectroscopy Facility (ETSF) is a European network dedicated to providing support and services for ongoing research in academic, government and industrial laboratories.

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

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

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

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

  • check file conformance to the specifications;
  • extract data from files;
  • merge multiple files from parallel runs, as specified in the specifications.
feynmf
set of LaTeX macros for creating Feynman diagrams
Maintainer: Thorsten Alteholz
Versions of package feynmf
ReleaseVersionArchitectures
stretch1.08-10all
buster1.08-11all
trixie1.08-14all
bullseye1.08-12all
bookworm1.08-14all
jessie1.08-9all
sid1.08-14all
Debtags of package feynmf:
fieldphysics
made-oftex
works-withtext
works-with-formattex
Popcon: 235 users (206 upd.)*
Versions and Archs
License: DFSG free
Git

FeynMF is a LaTeX package for easy drawing of professional-quality Feynman diagrams, illustrations that depict the fundamental interactions of subatomic particles. The diagrams may be created using either the Metafont or MetaPost programs. FeynMF lays out most diagrams satisfactorily from the structure of the graph without any need for manual intervention. Nevertheless all the power of Metafont or MetaPost is available for more obscure cases.

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

finalcif
editor for Crystallographic Information Format
Versions of package finalcif
ReleaseVersionArchitectures
bookworm113+dfsg-2all
trixie137+dfsg-2all
sid137+dfsg-2all
upstream144
Popcon: 2 users (6 upd.)*
Newer upstream!
License: DFSG free
Git

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
general-purpose nonlinear curve fitting and data analysis
Versions of package fityk
ReleaseVersionArchitectures
buster1.3.1-3amd64,arm64,armhf,i386
stretch1.3.0-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie1.2.1-0.1amd64,armel,armhf,i386
bookworm1.3.2-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid1.3.2-3amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
trixie1.3.2-3amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bullseye1.3.1-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package fityk:
fieldchemistry, physics
interfacex11
roleprogram
sciencecalculation, modelling, plotting
scopeutility
uitoolkitncurses, wxwidgets
x11application
Popcon: 22 users (17 upd.)*
Versions and Archs
License: DFSG free
Git

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
visualization program for biomolecules
Versions of package garlic
ReleaseVersionArchitectures
stretch1.6-1.1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster1.6-3amd64,arm64,armhf,i386
bullseye1.6-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm1.6-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie1.6-3amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
sid1.6-3amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
jessie1.6-1.1amd64,armel,armhf,i386
Debtags of package garlic:
fieldbiology, chemistry
interfacex11
roleprogram
scopeutility
uitoolkitxlib
useviewing
x11application
Popcon: 12 users (20 upd.)*
Versions and Archs
License: DFSG free
Git

Garlic is written for the investigation of membrane proteins. It may be used to visualize other proteins, as well as some geometric objects. This version of garlic recognizes PDB format version 2.1. Garlic may also be used to analyze protein sequences.

It only depends on the X libraries, no other libraries are needed.

Features include:

  • The slab position and thickness are visible in a small window.
  • Atomic bonds as well as atoms are treated as independent drawable objects.
  • The atomic and bond colors depend on position. Five mapping modes are available (as for slab).
  • Capable to display stereo image.
  • Capable to display other geometric objects, like membrane.
  • Atomic information is available for atom covered by the mouse pointer. No click required, just move the mouse pointer over the structure!
  • Capable to load more than one structure.
  • Capable to draw Ramachandran plot, helical wheel, Venn diagram, averaged hydrophobicity and hydrophobic moment plot.
  • The command prompt is available at the bottom of the main window. It is able to display one error message and one command string.
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)
Registry entries: Bio.tools 
gdis
molecular and crystal model viewer
Versions of package gdis
ReleaseVersionArchitectures
stretch0.90-5amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster0.90-5amd64,arm64,armhf,i386
jessie0.90-5amd64,armel,armhf,i386
bullseye0.90-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm0.90-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid0.90-6amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
Debtags of package gdis:
fieldchemistry
interface3d, x11
roleprogram
uitoolkitgtk
useediting, learning, viewing
works-with3dmodel
x11application
Popcon: 13 users (16 upd.)*
Versions and Archs
License: DFSG free
Git

A GTK+ based program for the display and manipulation of isolated molecules, periodic systems and crystalline habits. It is in development, but is nonetheless fairly functional. It has the following features:

  • Support for several file types (CIF, BIOSYM, XYZ, XTL, MARVIN, and GULP)
  • A simple molecular creation and manipulation tool
  • A dialogue for creating starting configurations for molecular dynamics simulations
  • Assorted tools for visualization (geometry information, region highlighting, etc.)
  • Animation of BIOSYM files (also rendered animations, see below)

GDIS also allows you to perform the following functions through other packages:

  • Model rendering (courtesy of POVRay)
  • Energy minimization (courtesy of GULP)
  • Morphology calculation (courtesy of cdd)
  • Space group processing (courtesy of SgInfo)
  • View the Periodic Table (courtesy of GPeriodic)
  • Load additional filetypes, such as PDB (courtesy of Babel)
Screenshots of package gdis
ggobi
Data visualization system for high-dimensional data
Maintainer: Dirk Eddelbuettel
Versions of package ggobi
ReleaseVersionArchitectures
jessie2.1.11-1amd64,armel,armhf,i386
stretch2.1.11-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster2.1.11-2amd64,arm64,armhf,i386
bullseye2.1.11-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm2.1.11-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie2.1.12-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
sid2.1.12-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
Debtags of package ggobi:
fieldstatistics
roleprogram
uitoolkitgtk
useviewing
works-with-formatxml
Popcon: 35 users (9 upd.)*
Versions and Archs
License: DFSG free
Git

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
GNOME molecular modelling environment
Versions of package ghemical
ReleaseVersionArchitectures
buster3.0.0-4amd64,arm64,armhf,i386
bullseye3.0.0-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid3.0.0-5amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x
bookworm3.0.0-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
stretch3.0.0-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package ghemical:
fieldchemistry
interface3d, x11
roleprogram
suitegnome
uitoolkitgtk
useediting, learning, viewing
works-with3dmodel
x11application
Popcon: 11 users (20 upd.)*
Versions and Archs
License: DFSG free
Git

Ghemical is a computational chemistry software package written in C++. It has a graphical user interface and it supports both quantum- mechanics (semi-empirical) models and molecular mechanics models. Geometry optimization, molecular dynamics and a large set of visualization tools using OpenGL are currently available.

Ghemical relies on external code to provide the quantum-mechanical calculations. Semi-empirical methods MNDO, MINDO/3, AM1 and PM3 come from the MOPAC7 package (Public Domain), and are included in the package. The MPQC package is used to provide ab initio methods: the methods based on Hartree-Fock theory are currently supported with basis sets ranging from STO-3G to 6-31G**.

Registry entries: Bio.tools  SciCrunch 
Screenshots of package ghemical
gnuplot
Command-line driven interactive plotting program.
Versions of package gnuplot
ReleaseVersionArchitectures
jessie4.6.6-2all
stretch5.0.5+dfsg1-6+deb9u1all
sid6.0.0+dfsg1-3all
trixie6.0.0+dfsg1-3all
jessie-security4.6.6-2+deb8u1all
buster5.2.6+dfsg1-1+deb10u1all
bookworm5.4.4+dfsg1-2all
bullseye5.4.1+dfsg1-1+deb11u1all
upstream6.0.2-prerelease-test
Debtags of package gnuplot:
fieldmathematics
interfacecommandline
roledummy, metapackage
useconverting
works-withimage, image:vector
Popcon: 220 users (63 upd.)*
Newer upstream!
License: DFSG free
Git

Gnuplot is a portable command-line driven interactive data and function plotting utility that supports lots of output formats, including drivers for many printers, (La)TeX, (x)fig, Postscript, and so on. The X11-output is packaged in gnuplot-x11.

Data files and self-defined functions can be manipulated by the internal C-like language. Can perform smoothing, spline-fitting, or nonlinear fits, and can work with complex numbers.

This metapackage is to install a full-featured gnuplot (-qt, -x11 or -nox).

gpaw
DFT and beyond within the projector-augmented wave method
Versions of package gpaw
ReleaseVersionArchitectures
bookworm22.8.0-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster1.5.1-1amd64,arm64,armhf,i386
bullseye21.1.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid24.6.0-1amd64,arm64,mips64el,ppc64el,riscv64,s390x
stretch1.1.0-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Popcon: 13 users (8 upd.)*
Versions and Archs
License: DFSG free
Git

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
periodic table application
Versions of package gperiodic
ReleaseVersionArchitectures
bookworm3.0.3-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye3.0.3-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie3.0.3-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
stretch2.0.10-7amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie2.0.10-7amd64,armel,armhf,i386
sid3.0.3-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
buster3.0.3-1amd64,arm64,armhf,i386
Debtags of package gperiodic:
fieldchemistry
interfacex11
roleprogram
scopeutility
uitoolkitgtk
uselearning, viewing
x11application
Popcon: 35 users (34 upd.)*
Versions and Archs
License: DFSG free
Git

GPeriodic is a small X/GTK+-based program which allows you to browse through a periodic table of chemical elements, and view somewhat detailed information on each of the elements. 118 elements are currently listed.

grace
XY graphing and plotting tool
Maintainer: Nicholas Breen
Versions of package grace
ReleaseVersionArchitectures
jessie5.1.24-3amd64,armel,armhf,i386
sid5.1.25-17amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
trixie5.1.25-17amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
stretch5.1.25-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye5.1.25-9amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster5.1.25-6amd64,arm64,armhf,i386
bookworm5.1.25-13amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package grace:
fieldmathematics
interfacex11
roleprogram
scopeapplication
uitoolkitmotif
useediting, learning, printing
works-withimage, image:vector, text
works-with-formatpostscript
x11application
Popcon: 162 users (40 upd.)*
Versions and Archs
License: DFSG free
Git

Grace is a point-and-click tool that allows the user to draw X-Y plots. This is the program formerly known as Xmgr.

A few of its features are: User defined scaling, tick marks, labels, symbols, line styles, colors, polynomial regression, splines, running averages, DFT/FFT, cross/auto-correlation, batch mode for unattended plotting, and hardcopy support for PostScript, FrameMaker and several image formats.

graphviz
rich set of graph drawing tools
Versions of package graphviz
ReleaseVersionArchitectures
bookworm2.42.2-7+deb12u1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie2.42.4-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bullseye2.42.2-5+deb11u1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie2.38.0-7amd64,armel,armhf,i386
stretch2.38.0-17amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch-security2.38.0-17+deb9u1amd64,arm64,armel,armhf,i386
buster2.40.1-6+deb10u1amd64,arm64,armhf,i386
buster-security2.40.1-6+deb10u1amd64,arm64,armhf,i386
sid2.42.4-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
experimental12.2.1-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
upstream12.2.1
Debtags of package graphviz:
fieldmathematics
interfacecommandline, x11
roleprogram
sciencevisualisation
scopeutility
uitoolkitathena, tk
useviewing
works-withgraphs, image, image:raster, image:vector
x11application
Popcon: 14488 users (7984 upd.)*
Newer upstream!
License: DFSG free

Graph drawing addresses the problem of visualizing structural information by constructing geometric representations of abstract graphs and networks. Automatic generation of graph drawings has important applications in key technologies such as database design, software engineering, VLSI and network design and visual interfaces in other domains. Situations where these tools might be particularly useful include:

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

This package contains the command-line tools.

Screenshots of package graphviz
gsl-bin
GNU Scientific Library (GSL) -- binary package
Maintainer: Dirk Eddelbuettel
Versions of package gsl-bin
ReleaseVersionArchitectures
trixie2.8+dfsg-5amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
jessie1.16+dfsg-2amd64,armel,armhf,i386
stretch2.3+dfsg-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster2.5+dfsg-6amd64,arm64,armhf,i386
buster-security2.5+dfsg-6+deb10u1amd64,arm64,armhf,i386
bullseye2.6+dfsg-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye-security2.6+dfsg-2+deb11u1amd64,arm64,armhf,i386
bookworm2.7.1+dfsg-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm-proposed-updates2.7.1+dfsg-5+deb12u1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid2.8+dfsg-5amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
Debtags of package gsl-bin:
devellang:c
fieldmathematics
interfacecommandline
roleprogram
scopeutility
suitegnu
Popcon: 28 users (99 upd.)*
Versions and Archs
License: DFSG free
Git

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.

This package provides several example binaries.

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

gwyddion
Scanning Probe Microscopy visualization and analysis tool
Versions of package gwyddion
ReleaseVersionArchitectures
bookworm2.62-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
stretch2.47-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye2.57-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster2.52-1amd64,arm64,armhf,i386
jessie2.38-2amd64,armel,armhf,i386
sid2.67-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
trixie2.67-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
Debtags of package gwyddion:
fieldphysics
interfacex11
roleprogram
sciencevisualisation
scopeapplication
uitoolkitgtk
useanalysing, viewing
works-withimage, image:raster
x11application
Popcon: 26 users (29 upd.)*
Versions and Archs
License: DFSG free
Git

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

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

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

Please cite: David Nečas and Petr Klapetek: Gwyddion: an open-source software for SPM data analysis. (eprint) Central European Journal of Physics 10(1):181-188 (2012)
Registry entries: SciCrunch 
Screenshots of package gwyddion
libblas3
Basic Linear Algebra Reference implementations, shared library
Versions of package libblas3
ReleaseVersionArchitectures
jessie1.2.20110419-10amd64,armel,armhf,i386
buster3.8.0-2amd64,arm64,armhf,i386
bullseye3.9.0-3+deb11u1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie3.12.0-4amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bookworm3.11.0-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid3.12.0-4amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
stretch3.7.0-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package libblas3:
roleshared-lib
Popcon: 14459 users (4840 upd.)*
Versions and Archs
License: DFSG free
Git

BLAS (Basic Linear Algebra Subroutines) is a set of efficient routines for most of the basic vector and matrix operations. They are widely used as the basis for other high quality linear algebra software, for example lapack and linpack. This implementation is the Fortran 77 reference implementation found at netlib.

This package contains a shared version of the library.

Please cite: E. Anderson, Z. Bai, C. Bischof, S. Blackford, J. Demmel, J. Dongarra, J. Du Croz, A. Greenbaum, S. Hammarling, A. McKenney and D. Sorensen: LAPACK Users' Guide (1999)
libgsl0ldbl
??? missing short description for package libgsl0ldbl :-(
Maintainer: Dirk Eddelbuettel
Versions of package libgsl0ldbl
ReleaseVersionArchitectures
jessie1.16+dfsg-2amd64,armel,armhf,i386
Debtags of package libgsl0ldbl:
fieldmathematics
roleshared-lib
suitegnu
works-withsoftware:running
Popcon: 1 users (0 upd.)*
Versions and Archs
License: DFSG free
liblapack3
Library of linear algebra routines 3 - shared version
Versions of package liblapack3
ReleaseVersionArchitectures
jessie3.5.0-4amd64,armel,armhf,i386
sid3.12.0-4amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bookworm3.11.0-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye3.9.0-3+deb11u1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster3.8.0-2amd64,arm64,armhf,i386
stretch3.7.0-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
trixie3.12.0-4amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
Debtags of package liblapack3:
roleshared-lib
Popcon: 9741 users (2496 upd.)*
Versions and Archs
License: DFSG free
Git

LAPACK version 3.X is a comprehensive FORTRAN library that does linear algebra operations including matrix inversions, least squared solutions to linear sets of equations, eigenvector analysis, singular value decomposition, etc. It is a very comprehensive and reputable package that has found extensive use in the scientific community.

This package contains a shared version of the library.

Please cite: E. Anderson, Z. Bai, C. Bischof, S. Blackford, J. Demmel, J. Dongarra, J. Du Croz, A. Greenbaum, S. Hammarling, A. McKenney and D. Sorensen: LAPACK Users' Guide (1999)
libssm-bin
macromolecular superposition library - binaries
Versions of package libssm-bin
ReleaseVersionArchitectures
bullseye1.4.0-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm1.4.0-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid1.4.0-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
buster1.4.0-1amd64,arm64,armhf,i386
trixie1.4.0-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
Popcon: 0 users (6 upd.)*
Versions and Archs
License: DFSG free
Git

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
Versions of package mayavi2
ReleaseVersionArchitectures
buster4.5.0-1amd64,arm64,armhf,i386
jessie4.3.1-3.1amd64,armel,armhf,i386
sid4.8.2-4amd64,arm64,mips64el,ppc64el,riscv64,s390x
trixie4.8.2-4amd64,arm64,mips64el,ppc64el,riscv64,s390x
bookworm4.8.0-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
stretch4.5.0-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye4.7.1-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package mayavi2:
develexamples, lang:python
roleprogram
useviewing
Popcon: 21 users (33 upd.)*
Versions and Archs
License: DFSG free
Git

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.

Screenshots of package mayavi2
mpich
Implementation of the MPI Message Passing Interface standard
Versions of package mpich
ReleaseVersionArchitectures
sid4.2.1-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bookworm4.0.2-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie3.1-5amd64,armel,armhf,i386
stretch3.2-7amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
trixie4.2.0-14amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
experimental4.2.1-3amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bullseye3.4.1-5~deb11u1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster3.3-3amd64,arm64,armhf,i386
upstream4.2.3
Debtags of package mpich:
adminbenchmarking, monitoring
networkhiavailability, load-balancing, scanner
scopeutility
usetransmission
Popcon: 70 users (45 upd.)*
Newer upstream!
License: DFSG free
Git

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
Versions of package mpqc
ReleaseVersionArchitectures
stretch2.3.1-18+deb9u1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bookworm2.3.1-22amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie2.3.1-16amd64,armel,armhf,i386
sid2.3.1-22amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
buster2.3.1-19amd64,arm64,armhf,i386
bullseye2.3.1-21amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package mpqc:
fieldchemistry, physics
interfacecommandline, x11
roleprogram
scopeutility
uitoolkitgtk
x11application
Popcon: 13 users (21 upd.)*
Versions and Archs
License: DFSG free
Git

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
Versions of package nco
ReleaseVersionArchitectures
jessie4.4.2-1amd64,armel,armhf,i386
bookworm5.1.4-1+deb12u1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye4.9.7-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster4.7.9-1amd64,arm64,armhf,i386
stretch-backports4.7.9-1~bpo9+1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
trixie5.2.9-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
sid5.2.9-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
stretch4.6.3-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package nco:
fieldmeteorology
interfacecommandline
roleprogram
scopeutility
Popcon: 27 users (17 upd.)*
Versions and Archs
License: DFSG free
Git

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
Versions of package ncview
ReleaseVersionArchitectures
buster2.1.8+ds-3amd64,arm64,armhf,i386
bullseye2.1.8+ds-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid2.1.11+ds-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
jessie1.93g-1amd64,armel,armhf,i386
bookworm2.1.8+ds-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie2.1.11+ds-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
stretch2.1.7+ds-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package ncview:
fieldmeteorology
interfacex11
roleprogram
uitoolkitathena
useviewing
x11application
Popcon: 37 users (18 upd.)*
Versions and Archs
License: DFSG free
Git

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.

Screenshots of package ncview
netcdf-bin
Programs for reading and writing NetCDF files
Versions of package netcdf-bin
ReleaseVersionArchitectures
trixie4.9.2-7amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
stretch4.4.1.1-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie4.1.3-7.2amd64,armel,armhf,i386
sid4.9.2-7amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
buster4.6.2-1amd64,arm64,armhf,i386
bullseye4.7.4-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
experimental4.9.3~rc2-1~exp1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bookworm4.9.0-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream4.9.3~rc2
Debtags of package netcdf-bin:
interfacecommandline
roleprogram
scopeutility
Popcon: 89 users (37 upd.)*
Newer upstream!
License: DFSG free
Git

Contains the programs ncdump and ncgen which convert NetCDF files to ASCII and back, respectively. 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.

nexus-tools
NeXus scientific data file format - applications
Versions of package nexus-tools
ReleaseVersionArchitectures
trixie4.4.3-6amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bookworm4.4.3-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye4.4.3-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie4.3.2-svn1921-2amd64,armel,armhf,i386
sid4.4.3-6amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
Popcon: 1 users (6 upd.)*
Versions and Archs
License: DFSG free
Git

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
GNU Octave language for numerical computations
Versions of package octave
ReleaseVersionArchitectures
bullseye6.2.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie3.8.2-4amd64,armel,armhf,i386
stretch4.0.3-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch-backports4.4.0-3~bpo9+1s390x
stretch-backports4.4.1-4~bpo9+1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el
buster4.4.1-5amd64,arm64,armhf,i386
buster-backports5.2.0-3~bpo10+1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm7.3.0-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie9.2.0-3amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
sid9.2.0-3amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
Debtags of package octave:
fieldmathematics
roleprogram
suitegnu
Popcon: 712 users (159 upd.)*
Versions and Archs
License: DFSG free
Git

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

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

The package is enhanced by the following packages: liboctave-dev octave-dev octave-doc texmacs-bin
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 
openkim-models
Models and model-drivers for KIM-API
Versions of package openkim-models
ReleaseVersionArchitectures
bookworm2021.01.28-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster-backports2021.01.28-2~bpo10+1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye2021.01.28-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid2021.01.28-2.1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
trixie2021.01.28-2.1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
Popcon: 0 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

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

openmpi-bin
high performance message passing library -- binaries
Versions of package openmpi-bin
ReleaseVersionArchitectures
trixie5.0.6-3amd64,arm64,mips64el,ppc64el,riscv64,s390x
bullseye4.1.0-10amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm4.1.4-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid5.0.6-3amd64,arm64,mips64el,ppc64el,riscv64,s390x
jessie1.6.5-9.1+deb8u1amd64,armel,armhf,i386
buster3.1.3-11amd64,arm64,armhf,i386
stretch2.0.2-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package openmpi-bin:
admincluster
fieldbiology, chemistry, mathematics, physics
interfacecommandline
roleprogram
scopeutility
Popcon: 1017 users (772 upd.)*
Versions and Archs
License: DFSG free
Git

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.

Features:

  • Full MPI-3.1 standards conformance
  • Thread safety and concurrency
  • Dynamic process spawning
  • High performance on all platforms
  • Reliable and fast job management
  • Network and process fault tolerance
  • Support network heterogeneity
  • Single library supports all networks
  • Run-time instrumentation
  • Many job schedulers supported
  • Internationalized error messages
  • Component-based design, documented APIs

This package contains the Open MPI utility programs.

openmx
package for nano-scale material simulations
Versions of package openmx
ReleaseVersionArchitectures
stretch3.7.6-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie3.7.6-1amd64,armel,armhf,i386
buster3.8.5+dfsg1-1amd64,arm64,armhf,i386
Debtags of package openmx:
fieldchemistry, physics
Popcon: 1 users (6 upd.)*
Versions and Archs
License: DFSG free
Git

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.

Screenshots of package openmx
psi3
Quantum Chemical Program Suite
Versions of package psi3
ReleaseVersionArchitectures
jessie3.4.0-5amd64,armel,armhf,i386
sid3.4.0-6amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bookworm3.4.0-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye3.4.0-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster3.4.0-6amd64,arm64,armhf,i386
stretch3.4.0-6amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package psi3:
fieldchemistry, physics
interfacecommandline
roleprogram
sciencecalculation
scopesuite
usecalculating
Popcon: 8 users (7 upd.)*
Versions and Archs
License: DFSG free
Svn

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
Screenshots of package psi3
python3-lmfit
Least-Squares Minimization with Constraints (Python 3)
Versions of package python3-lmfit
ReleaseVersionArchitectures
bullseye1.0.1-6all
jessie0.8.0+dfsg.1-1all
sid1.2.2-3all
trixie1.2.2-3all
bookworm1.1.0-1all
stretch0.9.5+dfsg-2all
buster0.9.11+dfsg-2all
upstream1.3.2
Popcon: 34 users (21 upd.)*
Newer upstream!
License: DFSG free
Git

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
scientific tools for Python 3
Versions of package python3-scipy
ReleaseVersionArchitectures
sid1.14.1-3amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
jessie0.14.0-2amd64,armel,armhf,i386
bullseye1.6.0-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm1.10.1-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie1.13.1-6amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
buster1.1.0-7amd64,arm64,armhf,i386
stretch0.18.1-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Popcon: 15965 users (2794 upd.)*
Versions and Archs
License: DFSG free
Git

SciPy supplements the popular NumPy module (python-numpy package), gathering a variety of high level science and engineering modules together as a single package.

SciPy is a set of Open Source scientific and numeric tools for Python. It currently supports special functions, integration, ordinary differential equation (ODE) solvers, gradient optimization, genetic algorithms, parallel programming tools, an expression-to-C++ compiler for fast execution, and others.

Registry entries: SciCrunch 
python3-sympy
Computer Algebra System (CAS) in Python (Python 3)
Versions of package python3-sympy
ReleaseVersionArchitectures
stretch1.0-3all
bullseye1.7.1-3all
bookworm1.11.1-1all
buster1.3-2all
trixie1.13.3-1all
sid1.13.3-1all
Popcon: 15964 users (2627 upd.)*
Versions and Archs
License: DFSG free
Git

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.

The package is enhanced by the following packages: texmacs-bin
pyxplot
data plotting program producing publication-quality output
Maintainer: Stuart Prescott
Versions of package pyxplot
ReleaseVersionArchitectures
stretch0.9.2-6amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
trixie0.9.2-14amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bookworm0.9.2-13amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie0.9.2-5amd64,armel,armhf,i386
bullseye0.9.2-12amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster0.9.2-8amd64,arm64,armhf,i386
sid0.9.2-14amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
Debtags of package pyxplot:
interfacecommandline, text-mode
roleprogram
scienceplotting, visualisation
useconverting, viewing
works-withtext
works-with-formatpdf, plaintext, postscript
Popcon: 4 users (7 upd.)*
Versions and Archs
License: DFSG free
Git

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
Electronic-Structure and Ab-Initio Molecular Dynamics Suite
Versions of package quantum-espresso
ReleaseVersionArchitectures
bookworm6.7-2amd64,arm64,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie5.1+dfsg-3amd64,armel,armhf,i386
stretch6.0-3amd64,arm64,armhf,i386,mips,mipsel,ppc64el,s390x
buster6.3-4amd64,arm64,armhf,i386
bullseye6.7-2amd64,arm64,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid6.7-3amd64,arm64,armhf,i386,mips64el,ppc64el,riscv64,s390x
Debtags of package quantum-espresso:
roleprogram
Popcon: 23 users (10 upd.)*
Versions and Archs
License: DFSG free
Git

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)
sasview
Small Angle Scattering Analysis suite
Versions of package sasview
ReleaseVersionArchitectures
bullseye5.0.3-3all
bookworm5.0.5-5all
experimental5.0.5-2all
trixie5.0.6-4all
sid5.0.6-5all
buster4.2.1-1all
upstream6.0.0
Popcon: 3 users (8 upd.)*
Newer upstream!
License: DFSG free
Git

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.

science-numericalcomputation
Debian Science Numerical Computation packages
Versions of package science-numericalcomputation
ReleaseVersionArchitectures
jessie1.4all
buster1.10all
trixie1.14.7all
bullseye1.14.2all
stretch1.7all
sid1.14.7all
bookworm1.14.5all
Debtags of package science-numericalcomputation:
devellang:lisp
rolemetapackage, shared-lib
Popcon: 0 users (17 upd.)*
Versions and Archs
License: DFSG free
Git

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
Scientific software package for numerical computations
Versions of package scilab
ReleaseVersionArchitectures
bookworm6.1.1+dfsg2-6all
buster6.0.1-10+deb10u1all
stretch-security5.5.2-4+deb9u1all
stretch5.5.2-4all
jessie5.5.1-7all
trixie2024.1.0+dfsg-6all
sid2024.1.0+dfsg-6all
bullseye6.1.0+dfsg1-7all
upstream2025.0.0
Debtags of package scilab:
fieldelectronics, mathematics, physics, statistics
interfacex11
roleprogram
scopeutility
uitoolkittk
useanalysing, learning
works-withimage
x11application
Popcon: 82 users (29 upd.)*
Newer upstream!
License: DFSG free
Git

Scilab is a matrix-based scientific software package. Scilab contains hundreds of built-in mathematical functions, rich data structures (including polynomials, rationals, linear systems, lists, etc...) and comes with a number of specific toolboxes for control, signal processing, ...

This package also provides Xcos, a graphical editor to design hybrid dynamical systems models. Models can be designed, loaded, saved, compiled and simulated. Stable and efficient solution for industrial and academics needs, Xcos provides functionalities for modeling of mechanical systems (automotive, aeronautics...), hydraulic circuits (dam, pipe modeling...), control systems, etc. Modelica capabilities are also provided.

For a minimum version of scilab, install package "scilab-cli".

The package is enhanced by the following packages: texmacs-bin
udav
library for scientific graphs (window interface)
Versions of package udav
ReleaseVersionArchitectures
jessie2.2.2.1-3amd64,armel,armhf,i386
buster2.4.2.1-5amd64,arm64,armhf,i386
bullseye2.4.4-7amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid8.0.2-3amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bookworm8.0.1-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
stretch2.3.4-1.1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package udav:
fieldmathematics
interfacex11
roleprogram
scopeutility
uitoolkitqt
x11application
Popcon: 7 users (12 upd.)*
Versions and Archs
License: DFSG free
Git

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
Versions of package v-sim
ReleaseVersionArchitectures
sid3.7.2-9amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
stretch3.7.2-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye3.7.2-8amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm3.7.2-9amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package v-sim:
fieldchemistry, physics
interfacex11
roleprogram
sciencevisualisation
scopeapplication
uitoolkitgtk
useviewing
x11application
Popcon: 12 users (11 upd.)*
Versions and Archs
License: DFSG free
Git

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.

Screenshots of package v-sim
voronota
Voronoi diagram-based tool to find atom contacts
Versions of package voronota
ReleaseVersionArchitectures
bookworm1.22.3149-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie1.22.3149-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
buster1.19.2352-1amd64,arm64,armhf,i386
sid1.22.3149-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bullseye1.22.3149-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream1.27.3834
Popcon: 0 users (6 upd.)*
Newer upstream!
License: DFSG free
Git

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.

Please cite: Kliment Olechnovič and Česlovas Venclovas: Voronota: A Fast and Reliable Tool for Computing the Vertices of the Voronoi Diagram of Atomic Balls. Journal of Computational Chemistry 35:672-681 (2014)

Official Debian packages with lower relevance

axiom
General purpose computer algebra system: main binary and modules
Maintainer: Camm Maguire
Versions of package axiom
ReleaseVersionArchitectures
trixie20170501-13amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
sid20170501-13amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bullseye20170501-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
stretch20140801-12amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie20140801-6amd64,armel,armhf,i386
buster20170501-4amd64,arm64,armhf,i386
bookworm20170501-12amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package axiom:
develcompiler, interpreter
fieldmathematics
interfacetext-mode
roleprogram
scopeutility
Popcon: 10 users (11 upd.)*
Versions and Archs
License: DFSG free

Axiom is useful for research and development of mathematical algorithms. It defines a strongly typed, mathematically correct type hierarchy. It has a programming language and a built-in compiler.

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

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

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

The package is enhanced by the following packages: texmacs-bin
dx
OpenDX (IBM Visualization Data Explorer) - main package
Versions of package dx
ReleaseVersionArchitectures
jessie4.4.4-7amd64,armel,armhf,i386
stretch4.4.4-9amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid4.4.4-18amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
trixie4.4.4-18amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bookworm4.4.4-15amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye4.4.4-13amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster4.4.4-12amd64,arm64,armhf,i386
Debtags of package dx:
interfacex11
roleprogram
scopeutility
uitoolkitmotif
useviewing
works-withimage
x11application
Popcon: 19 users (16 upd.)*
Versions and Archs
License: DFSG free
Git

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.
dx-doc
OpenDX (IBM Visualization Data Explorer) - documentation
Versions of package dx-doc
ReleaseVersionArchitectures
buster4.4.4-12all
jessie4.4.4-7all
bookworm4.4.4-15all
sid4.4.4-18all
bullseye4.4.4-13all
stretch4.4.4-9all
trixie4.4.4-18all
Debtags of package dx-doc:
made-ofhtml
roledocumentation
uitoolkitmotif
useviewing
works-withimage
Popcon: 0 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

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
Versions of package dxsamples
ReleaseVersionArchitectures
stretch4.4.0-3all
sid4.4.0-5all
trixie4.4.0-5all
bookworm4.4.0-5all
bullseye4.4.0-5all
buster4.4.0-4all
jessie4.4.0-1all
Debtags of package dxsamples:
develexamples
interfacecommandline
roledocumentation, program
scopeutility
useviewing
works-withimage
Popcon: 8 users (3 upd.)*
Versions and Archs
License: DFSG free
Git

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
??? missing short description for package feel++-apps :-(
Versions of package feel++-apps
ReleaseVersionArchitectures
jessie0.99.0-final.1-1amd64,i386
Popcon: 0 users (0 upd.)*
Versions and Archs
License: DFSG free
Svn
gpiv
??? missing short description for package gpiv :-(
Versions of package gpiv
ReleaseVersionArchitectures
jessie0.6.1-2.3amd64,armel,armhf,i386
Debtags of package gpiv:
uitoolkitgtk
Popcon: 0 users (0 upd.)*
Versions and Archs
License: DFSG free
Screenshots of package gpiv
gpivtools
??? missing short description for package gpivtools :-(
Versions of package gpivtools
ReleaseVersionArchitectures
jessie0.6.0-3.1amd64,armel,armhf,i386
Debtags of package gpivtools:
interfacecommandline
roleprogram
Popcon: 0 users (0 upd.)*
Versions and Archs
License: DFSG free
hdf5-helpers
HDF5 - Helper tools
Maintainer: Gilles Filippini
Versions of package hdf5-helpers
ReleaseVersionArchitectures
buster1.10.4+repack-10amd64,arm64,armhf,i386
jessie1.8.13+docs-15+deb8u1amd64,armel,armhf,i386
buster-security1.10.4+repack-10+deb10u1amd64,arm64,armhf,i386
sid1.14.5+repack-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bullseye1.10.6+repack-4+deb11u1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie1.10.10+repack-5amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
jessie-security1.8.13+docs-15+deb8u1amd64,armel,armhf,i386
stretch1.10.0-patch1+docs-3+deb9u1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bookworm1.10.8+repack1-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 416 users (379 upd.)*
Versions and Archs
License: DFSG free
Git

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.

hdf5-tools
HDF5 - Runtime tools
Maintainer: Gilles Filippini
Versions of package hdf5-tools
ReleaseVersionArchitectures
stretch1.10.0-patch1+docs-3+deb9u1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye1.10.6+repack-4+deb11u1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm1.10.8+repack1-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie-security1.8.13+docs-15+deb8u1amd64,armel,armhf,i386
jessie1.8.13+docs-15+deb8u1amd64,armel,armhf,i386
trixie1.10.10+repack-5amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
sid1.14.5+repack-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
buster-security1.10.4+repack-10+deb10u1amd64,arm64,armhf,i386
buster1.10.4+repack-10amd64,arm64,armhf,i386
Debtags of package hdf5-tools:
interfacecommandline
roledocumentation, program
scopeutility
useconverting
Popcon: 107 users (180 upd.)*
Versions and Archs
License: DFSG free
Git

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.

libgraphviz-perl
Perl interface to the GraphViz graphing tool
Versions of package libgraphviz-perl
ReleaseVersionArchitectures
jessie2.16-1all
stretch2.22-1all
buster2.22-1all
bullseye2.24-1all
bookworm2.24-1all
trixie2.24-1all
sid2.24-1all
upstream2.26
Debtags of package libgraphviz-perl:
devellang:perl, library
works-withimage, image:raster, image:vector
Popcon: 88 users (33 upd.)*
Newer upstream!
License: DFSG free
Git

This module provides an interface to layout and image generation of directed and undirected graphs in a variety of formats (PostScript, PNG, etc.) using the "dot", "neato", "twopi", "circo" and "fdp" programs from the GraphViz project (http://www.graphviz.org/ or http://www.research.att.com/sw/tools/graphviz/).

maxima
Computer algebra system -- base system
Maintainer: Camm Maguire
Versions of package maxima
ReleaseVersionArchitectures
stretch5.38.1-8amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster5.42.1-1amd64,arm64,armhf,i386
bullseye5.44.0-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm5.46.0-11amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid5.47.0-5amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
jessie5.34.1-2amd64,armel,armhf,i386
trixie5.47.0-5amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
Debtags of package maxima:
fieldmathematics
roleprogram
Popcon: 231 users (80 upd.)*
Versions and Archs
License: DFSG free

Maxima is a fully symbolic computation program. It is full featured doing symbolic manipulation of polynomials, matrices, rational functions, integration, Todd-coxeter methods for finite group analysis, graphing, multiple precision floating point computation. It has a symbolic source level debugger for maxima code. Maxima is based on the original Macsyma developed at MIT in the 1970s. It is quite reliable, and has good garbage collection, and no memory leaks. It comes with hundreds of self tests.

This package contains the main executables and base system files.

The package is enhanced by the following packages: texmacs-bin
mpich-doc
Documentation for MPICH
Versions of package mpich-doc
ReleaseVersionArchitectures
stretch3.2-7all
bullseye3.4.1-5~deb11u1all
experimental4.2.1-3all
sid4.2.1-2all
jessie3.1-5all
trixie4.2.0-14all
bookworm4.0.2-3all
buster3.3-3all
upstream4.2.3
Debtags of package mpich-doc:
networkhiavailability, load-balancing, service
roledocumentation
works-withnetwork-traffic
Popcon: 0 users (0 upd.)*
Newer upstream!
License: DFSG free
Git

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
Versions of package netcdf-doc
ReleaseVersionArchitectures
bullseye4.7.4-1all
jessie4.1.3-7.2all
buster4.6.2-1all
bookworm4.9.0-3all
trixie4.9.2-7all
sid4.9.2-7all
experimental4.9.3~rc2-1~exp1all
stretch4.4.1.1-2all
upstream4.9.3~rc2
Debtags of package netcdf-doc:
made-ofhtml, info, postscript
roledocumentation
Popcon: 0 users (0 upd.)*
Newer upstream!
License: DFSG free
Git

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
Versions of package openmpi-doc
ReleaseVersionArchitectures
sid5.0.5-6all
stretch2.0.2-2all
bookworm4.1.4-3all
bullseye4.1.0-10all
jessie1.6.5-9.1+deb8u1all
sid5.0.6-3all
buster3.1.3-11all
trixie5.0.6-3all
Debtags of package openmpi-doc:
develdoc, examples
made-ofman
roledocumentation
Popcon: 0 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

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
Versions of package pymca
ReleaseVersionArchitectures
jessie4.7.4+dfsg-1amd64,armel,armhf,i386
stretch5.1.3+dfsg-1all
bullseye5.6.3+dfsg-1all
sid5.9.3+dfsg-1all
bookworm5.8.0+dfsg-2all
trixie5.9.3+dfsg-1all
bookworm-backports5.8.7+dfsg-2~bpo12+1all
buster5.4.3+dfsg-1all
Popcon: 9 users (7 upd.)*
Versions and Archs
License: DFSG free
Git

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.

Screenshots of package pymca
python3-pygraphviz
Python interface to the Graphviz graph layout and visualization package (Python 3)
Versions of package python3-pygraphviz
ReleaseVersionArchitectures
bullseye1.7-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie1.14-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
sid1.14-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
buster1.5-1amd64,arm64,armhf,i386
stretch1.4~rc1-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bookworm1.7-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 311 users (659 upd.)*
Versions and Archs
License: DFSG free
Git

Pygraphviz is a Python interface to the Graphviz graph layout and visualization package.

With Pygraphviz you can create, edit, read, write, and draw graphs using Python to access the Graphviz graph data structure and layout algorithms.

This package contains the Python 3 version of python-pygraphviz.

qtiplot
data analysis and scientific plotting
Versions of package qtiplot
ReleaseVersionArchitectures
buster0.9.8.9-18amd64,arm64,armhf,i386
stretch0.9.8.9-15amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie0.9.8.9-9amd64,armel,armhf,i386
Debtags of package qtiplot:
interfacex11
roleprogram
uitoolkitqt
x11application
Popcon: 11 users (1 upd.)*
Versions and Archs
License: DFSG free
Git

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
Screenshots of package qtiplot
scidavis
??? missing short description for package scidavis :-(
Maintainer: Georges Khaznadar
Versions of package scidavis
ReleaseVersionArchitectures
stretch1.D13-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package scidavis:
interfacex11
roleprogram
scopeapplication
uitoolkitqt
uselearning, viewing
x11application
Popcon: 6 users (0 upd.)*
Versions and Archs
License: DFSG free
Screenshots of package scidavis
science-mathematics
Debian Science Mathematics packages
Versions of package science-mathematics
ReleaseVersionArchitectures
buster1.10all
stretch1.7all
jessie1.4all
sid1.14.7all
trixie1.14.7all
bookworm1.14.5all
bullseye1.14.2all
Debtags of package science-mathematics:
fieldmathematics
rolemetapackage
suitedebian
Popcon: 1 users (13 upd.)*
Versions and Archs
License: DFSG free
Git

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
Versions of package science-statistics
ReleaseVersionArchitectures
buster1.10all
stretch1.7all
sid1.14.7all
jessie1.4all
trixie1.14.7all
bullseye1.14.2all
bookworm1.14.5all
Debtags of package science-statistics:
rolemetapackage
suitedebian
Popcon: 2 users (16 upd.)*
Versions and Archs
License: DFSG free
Git

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.

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

fdmnes
calculates spectra of different spectroscopies
Versions of package fdmnes
ReleaseVersionArchitectures
VCS0.0.20120607-1all
Versions and Archs
License: To-be-clarified
Git
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)
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 247275