Debian Science Nanoscale physics packages

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

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

This package contains all programs needed to perform calculations. For documentation and tests, install the abinit-doc package.

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.

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.

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

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-inito molecular dynamics (AIMD) simulations. Features include:

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

• Density-Functional Theory (DFT) Calculations with various Exchange- Correlation (XC) functionals
• Hartree-Fock (HF) Calculations
• Gas phase or Periodic boundary conditions (PBC)
• Basis sets include various standard Gaussian-Type Orbitals (GTOs), Pseudo- potential plane-waves (PW), augmented plane waves (APW) and a mixed Gaussian and (augmented) plane wave approach (GPW / GAPW)
• Pseudo-Potentials (PP) including the norm-conserving, seperable Goedecker-Teter-Hutter (GTH) PP
• 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
• Dispersion corrections via DFT-D2 and DFT-D3 pair-potential models
• Density-Fitting for DFT via Bloechl or Density Derived Atomic Point Charges (DDAPC) charges and for HFX via Auxiliary Density Matrix Methods (ADMM)
• 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
• Excited states via time-dependent DFT (TDDFT)

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-Parinello like Langevin Born-Oppenheimer Molecular Dynamics

Mixed quantum-classical (QM/MM) simulations:

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

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
• Semi-Empirical calculations including the AM1, RM1, PM3, MNDO, MNDO-d, PNNL and PM6 parametrizations and density-functional tight-binding (DFTB), 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
• HFX module for linear-scaling MD simulations using hybrid functionals
• Static (e.g. spectra) and dynamical (e.g. diffusion) properties

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

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

Four forms of graphics are produced:

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

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

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

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

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

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

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

• check file conformance to the specifications;
• extract data from files;
• merge multiple files from parallel runs, as specified in the specifications.

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

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

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

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

Fityk 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.

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.

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)

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 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**.

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 package is for transition and to install a full-featured gnuplot supporting the X11-output.

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 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.

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.

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.

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.

Gwyddion's Python scripting interface Pygwy is also included.

The BLACS project is an ongoing investigation whose purpose is to create a linear algebra oriented message passing interface that may be implemented efficiently and uniformly across a large range of distributed memory platforms.

You can choose between an implementation based on MPI or PVM. This package uses MPI. There are packages for the shared libraries (this one), for the static libraries and the development files, and for test programs.

Most users do not need to install this package directly because it is used as a high level driver for the communication in the ScaLAPACK packages. Therefore, it is installed when installing ScaLAPACK. ScaLAPACK is a parallel version of LAPACK and is used on Beowulf type clusters.

Several minor changes to the C interface have been incorporated. One can maintain both versions on a system simultaneously to aid in the transition.

The FFTW library computes Fast Fourier Transforms (FFT) in one or more dimensions. It is extremely fast. This package is a transitional package depending on the packages containing the single and double precision libraries.

To get the static library and the header files, you need to install libfftw3-dev. For documentation, see libfftw3-doc.

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

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

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

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 includes the shared library files used for mpich runtime.

MPICH2 is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard (both MPI-1 and MPI-2). It efficiently supports different computation and communication platforms including commodity clusters, SMPs, massively parallel systems, and high-speed networks.

This package includes the MPICH2 shared libraries.

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-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers and computer science researchers.

This package contains the Open MPI shared libraries.

ScaLAPACK is the parallel version of LAPACK and is used on Beowulf type clusters.

You can choose between an implementation based on MPI or PVM. This package uses MPI. There are packages for the shared libraries (this one), for the static libraries and the development files and for test programs.

Also included: PBLAS, Parallel Basic Linear Algebra Subprograms.

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.

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.

This package provides manual pages in both man and HTML form documenting the MPI (Message Passing Interface) parallel programming standard as implemented by MPICH, and the user's guides for the transports included in binary Debian packages (chp4, chp4mpd, chshmem).

For the MPI specification, see mpi-specs.

MPICH is a robust and flexible implementation of the MPI (Message Passing Interface). MPI is often used with parallel or distributed computing projects. MPICH is a multi-platform, configurable system (development, execution, libraries, etc) for MPI. It can achieve parallelism using networked machines or using multitasking on a single machine.

This version is compiled with ch_p4 support, which only requires installation on the master node, and starts up parallel tasks using rsh.

MPICH2 is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard (both MPI-1 and MPI-2). It efficiently supports different computation and communication platforms including commodity clusters, SMPs, massively parallel systems, and high-speed networks.

This package includes the program binaries necessary to run MPICH2 programs.

MPICH2 is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard (both MPI-1 and MPI-2). It efficiently supports different computation and communication platforms including commodity clusters, SMPs, massively parallel systems, and high-speed networks.

This package includes the MPICH2 documentation.

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 pertubation theory (MP2)

Additionally, it can compute energies for the following methods:

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

It also includes an internal coordinate geometry optimizer.

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

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

You would use ncview to get a quick and easy, push-button look at your NetCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data and other simple visual operations.

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.

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

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

Open MPI is a project combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers and computer science researchers.

Features:

• Full MPI-2 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.

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-2 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.

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

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

It can compute energies and gradients for the following methods:

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

Additionally, it can compute energies for the following methods:

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

Further features include:

• Flexible, modular and customizable input format
• Excited state calculations with the CC2/CC3, EOM-CCSD, CASSCF, MRCI and MRCCSD methods
• Internal coordinate geometry optimizer
• Harmonic frequencies calculations
• One-electron properties like dipole/quadrupole moments, natural orbitals, electrostatic potential, hyperfine coupling constants or spin density
• Utilization of molecular point-group symmetry to increase efficiency

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, AIFIRA and SupaVisio formats.

ASE is an Atomistic Simulation Environment written in the Python programming language with the aim of setting up, stearing, and analyzing atomistic 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.

https://wiki.fysik.dtu.dk/ase/

gElemental is a GTK+ periodic table viewer that provides detailed information about chemical elements. It features a table view which allows the elements to be coloured thematically by several properties, a sortable list view and an element properties dialog, displaying a variety of information, including historical, thermodynamic, electrochemical, and crystallographic properties.

The data set is available through the libelemental shared library.

This package contains the Python bindings allowing you to use libelemental from Python scripts.

ScientificPython is a collection of Python modules that are useful for scientific computing. Most modules are rather general, others belong to specific domains and will be of interest to only a small number of users (e.g. the module Scientific.IO.PDB). Almost all modules make extensive use of Numerical Python (NumPy)

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.

SciTools is a Python package containing lots of useful tools for scientific computing in Python. The package is built on top of other widely used packages such as NumPy, SciPy, ScientificPython, Gnuplot, etc.

SciTools also comes with a plotting interface called Easyviz, which is a unified interface to various packages for scientific visualization and plotting. Both curve plots and more advanced 2D/3D visualization of scalar and vector fields are supported. The Easyviz interface was designed with three ideas in mind: 1) a simple, Matlab-like syntax; 2) a unified interface to lots of visualization engines (backends): Gnuplot, Matplotlib, Grace, Veusz, Pmw.Blt.Graph, PyX, Matlab, VTK, VisIt, OpenDX; and 3) a minimalistic interface which offers only basic control of plots: curves, linestyles, legends, title, axis extent and names. More fine-tuning of plots can be done by adding backend-specific commands.

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.

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.

Besides offering an attractive front-end to GNU Octave, an environment for numerical computation highly compatible with MATLAB, QtOctave currently also features matrix data entry and display and some GUI shortcuts to frequently used Octave functions. It also offers access in place to Octave's documentation with octave-htmldoc or octave-info.

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

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.

UDAV provides a graphical environment for Data Array Visualization based on the MathGL library. It allows easy viewing, manipulation and plotting of datasets, and supports a wide range of graphical effects with a simple scripting language, MGL. It can also execute MGL scripts. Features include:

• Simple and fast plotting of data and formulas;
• One-click interface - just open the datafile in UDAV;
• Scripts and graphical output both shown at the same time;
• Rotate, pan, and zoom controls (via buttons or mouse);
• Toggleable lighting and transparency;
• GIF animation;
• Support for smoothed lighting, transparency, arbitrary curvilinear coordinates, and TeX symbols and formulas;
• Tables for data editing, with support for 3-dimensional arrays;
• Basic toolset for data handling (smoothing, resizing, cropping, filling by formula, summation, differentiation, histogram creation, and so on);
• Export to bitmap and vector formats (PNG, JPEG, EPS, or SVG).

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.

Data Explorer is a system of tools and user interfaces for visualizing data. In general terms the visualization of data can be considered a 3-stage process:

   1. Describing and importing data
   2. Processing the data through a visualization program
   3. Presenting the resulting image.
This is the main package.

Data Explorer is a system of tools and user interfaces for visualizing data. In general terms the visualization of data can be considered a 3-stage process:

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

documentation.

Gmsh is an automatic 3D finite element mesh generator (primarily Delaunay) with build-in CAD and post-processing facilities. Its design goal is to provide a simple meshing tool for academic test cases with parametric input and up to date visualization capabilities.

Gmsh is built around four modules: geometry, mesh, solver and post-processing. The specification of any input to these modules is done either interactively using the graphical user interface or in ASCII text files using Gmsh's own scripting language.

See Gmsh's reference manual for a more thorough overview of Gmsh's capabilities.

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

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

Image interrogation, resulting into estimators of particle image displacements.

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

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

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

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

All programs start with gpiv_.

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

This package provides some applications codes(source and executables) such as laplacian with cG and dG methods, stokes, heat transfer, solid mechanics(static and dynamic).

Life is a versatile finite element library to solve partial differential equations

Support 1D, 2D, 3D

Support the following basic entities: simplices (segment, triangle, tetrahedron) and product of simplices (quadrangle, hexahedron)

Support various point sets on these basic entities: equispaced points, quadrature points, interpolation points (Gauss-Lobatto, Fekete, WarpBlend?)

Support continuous and discontinuous Galerkin methods

Support various polynomial sets:

• Lagrange(continuous,discontinuous,all dimensions,all interpolation point sets)

• Dubiner(discontinuous), boundary adapted(continuous)

• Legendre(discontinuous), boundary adapted(continuous)

Provide mathematical concept for higher order abstraction (Function spaces and associated elements, forms and operators)

Provide a language embedded in C++ for variational formulations, projection and numerical integration

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

SciDAVis is a free interactive application aimed at data analysis and publication-quality plotting. It combines a shallow learning curve and an intuitive, easy-to-use graphical user interface with powerful features such as scriptability and extensibility.

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

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

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

This metapackage is part of the Debian Pure Blend "Debian Science" and installs packages related to statistics. This task is a general task which might be useful for any scientific work. It depends from a lot of R packages as well as from other tools which are useful to do statistics. Moreover the Science Mathematics task is suggested to optionally install all mathematics related software.

SIVP intends to do image and video processing tasks. SIVP is meant to be a useful, efficient, and free image and video processing toolbox for Scilab. Its goals include tasks such as filtering, blurring, edge detection, thresholding, histogram manipulation, segmentation, mathematical morphology, and color image processing.

This package also provides some functions on video processing.

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

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

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

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

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

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

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.

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.

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.

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 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.

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).

GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method. It uses real-space uniform grids and multigrid methods or atom-centered basis-functions.

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.

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.

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