Debian Science Nanoscale Physics Development packages

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

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

This package contains the documentation and tutorials.

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/

This package is a binary incompatible upgrade to the blas-dev package. Several minor changes to the C interface have been incorporated.

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 static version of the library.

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. The CBFLIB API is loosely based on the CIFPARSE API for mmCIF files. CBFLIB does not perform any semantic integrity checks and simply provides functions to create, read, modify and write CBF binary data files and imgCIF ASCII data files.

This package contains libraries and header files for program development.

The CCP4 software suite is based around a library of routines which cover common tasks, such as file opening, parsing keyworded input, reading and writing of standard data formats, applying symmetry operations, etc. Programs in the suite call these routines which, as well as saving the programmer some effort, ensure that the varied programs in the suite have a similar look-and-feel.

The library contains several sub components:

• CMTZ library -- Contains a variety of functions for manipulating the data structure, for example adding crystals, datasets or columns. The data structure can be dumped to an output MTZ data file.

• CMAP library -- Functions defining the C-level API for accessing CCP4 map files.

• CSYM library -- a collection of functions centered around a data file syminfo.lib which is auto-generated from sgtbx (the Space Group Toolbox of cctbx).

• CCP4 utility library -- many utility functions which either give specific CCP4 or platform independent functionality.

• CCP4 Parser library -- provides CCP4-style parsing, as used for processing keywords of CCP4 programs, MTZ header records, etc.

• CCP4 resizable arrays -- defines an object and methods which looks just like a simple C array, but can be resized at will without incurring excessive overheads.

Computational Crystallography Toolbox contains following modules:

• annlib_adaptbx:
• boost_adaptbx: wrappers for Boost functionality in CCTBX
• cbflib_adaptbx:
• ccp4io_adaptbx:
• cctbx: Libraries for general crystallographic applications, useful for both small-molecule and macro-molecular crystallography.
• cma_es:
• crys3d: Modules for the display of molecules, electron density, and reciprocal space data.
• dxtbx: The Diffraction Image Toolbox, a library for handling X-ray detector data of arbitrary complexity from a variety of standard formats.
• fable: Fortran EMulation library for porting Fortran77 to C++.
• gltbx: Python bindings for OpenGL
• iotbx: Working with common crystallographic file formats.
• libtbx: The build system common to all other modules. This includes a very thin wrapper around the SCons software construction tool. It also contains many useful frameworks and utilities to simplify application development, including tools for regression testing, parallelization across multiprocessor systems and managed clusters, and a flexible, modular configuration syntax called PHIL (Python Hierarchial Interface Language) used throughout the CCTBX.
• mmtbx: Functionality specific to macromolecular crystallography. This includes all of the machinery required for setup of geometry restraints, bulk solvent correction and scaling, analysis of macromolecular diffraction data, calculation of weighted map coefficients, and most of the methods implemented in phenix.refine. The majority of infrastructure for the MolProbity validation server (and Phenix equivalent) is also located here.
• omptbx: OpenMP interface.
• rstbx: A reciprocal space toolbox to autoindex small molecule Bragg diffraction, given the reciprocal space vectors.
• scitbx: General scientific calculations. his includes a family of high-level C++ array types, a fast Fourier transform library, and a C++ port of the popular L-BFGS quasi-Newton minimizer.
• smtbx: Small-Molecule crystallography.
• spotfinder:
• tbxx:
• wxtbx: wxPython controls used in the Phenix GUI and various utilities

This package provide everythings needed to link against the cctbx libraries.

Wrappers for C functions, allowing usage of try ... catch ... blocks in C language. Wrapped functions include memory allocation, standard I/O and strdup.

This package contains static library and header files.

The aim of the clipper project is to produce a set of object-oriented libraries for the organisation of crystallographic data and the performance of crystallographic computation.

This package contains development environment for programs which will use the clipper libraries.

COD::Precision, module for handling precision in Crystallographic Information Format (CIF) notation, expressed as standard uncertainties in parentheses next to the value.

This package provides the Open Source release of Schroedinger's routines for the 2D coordinate representation of chemical compounds.

This package provides header files for developing against the API of that library.

ETSF_IO is a library of F90 routines to read/write the ETSF file format.

This package contains the static libraries provided by ETSF_IO to let electronic structure codes read and write ETSF files. It also contains the module file used by the Fortran compiler.

ETSF_IO is a library of F90 routines to read/write the ETSF file format.

This Package contains the HTML documentation of the API and some tutorials on how to use the library in electronic structure codes.

The FFTW library computes Fast Fourier Transforms (FFT) in one or more dimensions. It is extremely fast. This package contains the statically linked library, header files and test programs.

This package contains the header files and static libraries. For documentation, see libfftw3-doc.

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 development files for serial platforms.

The HepMC package is an object oriented event record written in C++ for High Energy Physics Monte Carlo Generators.

Many extensions from HEPEVT, the Fortran HEP standard, are supported: the number of entries is unlimited, spin density matrices can be stored with each vertex, flow patterns (such as color) can be stored and traced, integers representing random number generator states can be stored, and an arbitrary number of event weights can be included. Particles and vertices are kept separate in a graph structure, physically similar to a physics event.

The added information supports the modularisation of event generators. Event information is accessed by means of iterators supplied with the package.

This package provides development files for HepMC3.

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 the development files (headers and documentation) for KIM-API.

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 static version of the library.

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:

• manpages of BLAS and LAPACK routines,
• the Lapack User's Guide manual (in HTML),
• the manual for the LAPACKE C interface to LAPACK (in PDF).

This package provides header files to develop one's own software that uses a library wth an Open Source parser for Maestro (.mae) files.

Common tool chain for working with molecular structure data in various applications. This library provides a unified way to perform operations on molecular structure data, like reading and writing to common geometry file formats.

This package contains development files.

MMDB is designed to assist developers in working with macromolecular coordinate files. The library handles both PDB and mmCIF format files.

The Library also features an internal binary format, portable between different platforms. This is achieved at uniformity of the Library's interface functions, so there is no difference in handling different formats.

MMDB provides various high-level tools for working with coordinate files, including reading and writing, orthogonal-fractional transforms, generation of symmetry mates, editing the molecular structure and more.

This package contains library and header files needed for program development.

This is a source distribution of NCrystal, a library and associated tools which enables calculations for Monte Carlo simulations of thermal neutrons in crystals.

This package contains the development files.

NetCDF (network Common Data Form) is a set of interfaces for array-oriented data access and a freely distributed collection of data access libraries for C, Fortran, C++, Java, and other languages. The netCDF libraries support a machine-independent format for representing scientific data. Together, the interfaces, libraries, and format support the creation, access, and sharing of scientific data.

This package provides headers.

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 the development libraries.

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 the java 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-3 compliant implementation, Open MPI offers advantages for system and software vendors, application developers and computer science researchers.

This package contains the header files and compiler wrappers which are needed to compile and link programs against libopenmpi.

ScaLAPACK is the parallel version of LAPACK used on clusters.

There are packages for the shared libraries, for the static libraries and the development files (this one) and for test programs.

Also included:

• PBLAS, Parallel Basic Linear Algebra Subprograms
• BLACS, Basic Linear Algebra Communication Subprograms

This is a dummy package which depends on the scalapack development package supporting the default implementation of MPI on this architecture.

SpFFT was originally intended for transforms of data with spherical cutoff in frequency domain, as required by some computational material science codes. For distributed computations, SpFFT uses a slab decomposition in space domain and pencil decomposition in frequency domain (all sparse data within a pencil must be on one rank). If desired, the library can be compiled without any parallelization (MPI, OpenMP, CUDA / ROCm).

This package contains development files.

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 libraries and header files needed for program development.

Spglib is a C library for crystal symmetry determination. Symmetry operations, space groups and other data can be obtained using this symmetry finder.

Features include:

• Identify space-group type
• Find symmetry operations
• Find a primitive cell
• Search irreducible k-points
• Refine crystal structure
• Wyckoff position assignment

This package contains static library and header files.

The UFO data processing framework is a C library suited to build general purpose streams data processing on heterogeneous architectures such as CPUs, GPUs or clusters. It is extensively used at the Karlsruhe Institute of Technology for Ultra-fast X-ray Imaging (radiography, tomography and laminography).

A gobject-instrospection binding is also provided to write scripts or user interfaces.

This package contain the development files for libufo.

LibXC is a library of exchange-correlation (XC) functionals for density-functional theory (DFT). The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals that can be used by other codes.

This package contains the static library, the C headers and the Fortran modules necessary for developers.

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.

PyFAI is a Python library for azimuthal integration; it allows the conversion of diffraction images taken with 2D detectors like CCD cameras into X-Ray powder patterns that can be used by other software like Rietveld refinement tools (i.e. FullProf), phase analysis or texture analysis.

As PyFAI is a library, its main goal is to be integrated in other tools like PyMca, LiMa or EDNA. To perform online data analysis, the precise description of the experimental setup has to be known. This is the reason why PyFAI includes geometry optimization code working on "powder rings" of reference samples. Alternatively, PyFAI can also import geometries fitted with other tools like Fit2D.

PyFAI has been designed to work with any kind of detector with any geometry (transmission, reflection, off-axis, ...). It uses the Python library FabIO to read most images taken by diffractometer.

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.

This is the Python 3 version of the package.

Computational Crystallography Toolbox contains following modules:

• annlib_adaptbx:
• boost_adaptbx: wrappers for Boost functionality in CCTBX
• cbflib_adaptbx:
• ccp4io_adaptbx:
• cctbx: Libraries for general crystallographic applications, useful for both small-molecule and macro-molecular crystallography.
• cma_es:
• crys3d: Modules for the display of molecules, electron density, and reciprocal space data.
• dxtbx: The Diffraction Image Toolbox, a library for handling X-ray detector data of arbitrary complexity from a variety of standard formats.
• fable: Fortran EMulation library for porting Fortran77 to C++.
• gltbx: Python bindings for OpenGL
• iotbx: Working with common crystallographic file formats.
• libtbx: The build system common to all other modules. This includes a very thin wrapper around the SCons software construction tool. It also contains many useful frameworks and utilities to simplify application development, including tools for regression testing, parallelization across multiprocessor systems and managed clusters, and a flexible, modular configuration syntax called PHIL (Python Hierarchial Interface Language) used throughout the CCTBX.
• mmtbx: Functionality specific to macromolecular crystallography. This includes all of the machinery required for setup of geometry restraints, bulk solvent correction and scaling, analysis of macromolecular diffraction data, calculation of weighted map coefficients, and most of the methods implemented in phenix.refine. The majority of infrastructure for the MolProbity validation server (and Phenix equivalent) is also located here.
• omptbx: OpenMP interface.
• rstbx: A reciprocal space toolbox to autoindex small molecule Bragg diffraction, given the reciprocal space vectors.
• scitbx: General scientific calculations. his includes a family of high-level C++ array types, a fast Fourier transform library, and a C++ port of the popular L-BFGS quasi-Newton minimizer.
• smtbx: Small-Molecule crystallography.
• spotfinder:
• tbxx:
• wxtbx: wxPython controls used in the Phenix GUI and various utilities

This package provide a selected collection of python modules from the cctbx project.

cif2cell is a tool to generate the geometrical setup for various electronic structure codes from a CIF (Crystallographic Information Framework) file. The code will generate the crystal structure for the primitive cell or the conventional cell.

FabIO is an I/O library for images produced by 2D X-ray detectors and written in Python. FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, ...), for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers an unified interface to their headers (as a Python dictionary) and datasets (as a numpy ndarray of integers or floats)

This is the Python 3 version of the package.

This python wrapper is designed to tightly integrate with PyOpenCL. It consists of a low-level Cython based wrapper with an interface similar to the underlying C library. On top of that it offers a high-level interface designed to work on data contained in instances of pyopencl.array.Array, a numpy work-alike array class for GPU computations. The high-level interface takes some inspiration from pyFFTW. For details of the high-level interface see fft.py.

This package installs the library for Python 3.

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 the Python 3 bindings.

This package provides a periodic table of the elements with support for mass, density and xray/neutron scattering information.

Masses, densities and natural abundances come from the NIST Physics Laboratory, but do not represent a critical evaluation by NIST scientists.

Neutron scattering calculations use values collected by the Atomic Institute of the Austrian Universities. These values do corresponding to those from other packages, though there are some differences depending to the tables used. Bound coherent neutron scattering for gold in particular is significantly different from older value: 7.63(6) as measured in 1974 compared to 7.90(7) as measured in 1990.

X-ray scattering calculations use a combination of empirical and theoretical values from the LBL Center for X-ray Optics. These values differ from those given in other sources such as the International Tables for Crystallography, Volume C, and so may give different results from other packages.

This package installs the library for Python 3.

Python bindings for Crystallographic Information Format (CIF) v1.1 and v2.0 parser, which is written in C language, and developed by the Crystallography Open Database. A CIF format file is represented by a list of data blocks, where each data block is represented by a dictionary.

This package installs the library for Python 3.

Pythonic wrapper around FFTW, the speedy FFT library. The ultimate aim is to present a unified interface for all the possible transforms that FFTW can perform.

Both the complex DFT and the real DFT are supported, as well as arbitrary axes of abitrary shaped and strided arrays, which makes it almost feature equivalent to standard and real FFT functions of numpy.fft (indeed, it supports the clongdouble dtype which numpy.fft does not).

pyFFTW is BSD-licensed and should not be confused with python-fftw, a GPL-licensed python module with the same aim of providing python bindings to FFTW3. Or python3-gpyfft, which provides bindings to the OpenCL FFT library clFFT.

This package provides the Python 3 bindings.

QuTiP is open-source software for simulating the dynamics of open quantum systems. The QuTiP library depends on the excellent Numpy, Scipy, and Cython numerical packages. In addition, graphical output is provided by Matplotlib. QuTiP aims to provide user-friendly and efficient numerical simulations of a wide variety of Hamiltonians, including those with arbitrary time-dependence, commonly found in a wide range of physics applications such as quantum optics, trapped ions, superconducting circuits, and quantum nanomechanical resonators.

This package installs the library for Python 3.

The sasdata Python module provides utilities for importing and operating on reduced small angle scattering data. The module may be used in standalone code to build custom fitters, in conjunction with the sasmodels modules to analyse data from custom scripts, or as part of the sasview analysis package.

This package contains the Python 3 module.

sasmodels is a Python module for calculating theoretical Small Angle Scattering patterns. The models provided are usable directly in the bumps fitting package and in the sasview analysis package.

This package contains the Python 3 version of the module.

This package provides an R interface to Unidata's NetCDF library functions. NetCDF (network Common Data Form) is a set of interfaces for array-oriented data access. In addition to the interface to the NetCDF library functions, R interfaces are provided to access Unidata's UDUNITS calendar conversions.

ScaLAPACK is the parallel version of LAPACK. It depends on PVM or MPI.

This package provides the man pages for the routines in the ScaLAPACK library (see package scalapack1-pvm, scalapack1-mpich or scalapack1-lam) and a quick reference for PBLAS and ScaLAPACK. PBLAS is the library for Parallel Basic Linear Algebra Subprograms included in ScaLAPACK.

Also included: ScaLAPACK Users' Guide (SLUG) and the FAQ on ScaLAPACK.

This metapackage will install Debian Science packages which might be helpful for development of applications for Mathematics.

You might also be interested in the science-mathematics metapackage.

The UFO data processing framework is a C library suited to build general purpose streams data processing on heterogeneous architectures such as CPUs, GPUs or clusters. It is extensively used at the Karlsruhe Institute of Technology for Ultra-fast X-ray Imaging (radiography, tomography and laminography).

This package contains average',backproject', bin',blur', buffer',calculate', camera',clip', contrast',crop', denoise',duplicate', fftmult',fft', filter',flatten', flip',forwardproject', gemm',ifft', interpolate',loop', measure',merge', metaballs',monitor', null',opencl', ordfilt',pad', read',reduce', refeed',replicate', rescale',ringwriter', sleep',slice', stack',stdin', stdout',subtract', transpose',write' and `zeropad' plugins

VecGeom is a vectorized geometry modeller library with hit-detection features as needed by particle detector simulation at the LHC and beyond.

This package includes the development files for VecGeom.

The FFTW library computes Fast Fourier Transforms (FFT) in one or more dimensions. It is extremely fast. This package contains the documentation for the fftw3 library.

HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.

From a Python programmer's perspective, HDF5 provides a robust way to store data, organized by name in a tree-like fashion. You can create datasets (arrays on disk) hundreds of gigabytes in size, and perform random-access I/O on desired sections. Datasets are organized in a filesystem-like hierarchy using containers called "groups", and accessed using the tradional POSIX /path/to/resource syntax.

H5py provides a simple, robust read/write interface to HDF5 data from Python. Existing Python and Numpy concepts are used for the interface; for example, datasets on disk are represented by a proxy class that supports slicing, and has dtype and shape attributes. HDF5 groups are presented using a dictionary metaphor, indexed by name.

This is a simple dependency package which depends on the serial or MPI build of h5py and provides test data files.

NetCDF version 4 has many features not found in earlier versions of the library and is implemented on top of HDF5. This module can read and write files in both the new netCDF 4 and the old netCDF 3 format, and can create files that are readable by HDF5 clients. The API is modelled after Scientific.IO.NetCDF, and should be familiar to users of that module.

Most new features of netCDF 4 are implemented, such as multiple unlimited dimensions, groups and zlib data compression. All the new numeric data types (such as 64 bit and unsigned integer types) are implemented. Compound and variable length (vlen) data types are supported, but the enum and opaque data types are not. Mixtures of compound and vlen data types (compound types containing vlens, and vlens containing compound types) are not supported.

This package contains the netCDF 4 module for Python 3.

Thread-pool Controls provides Python helpers to limit the number of threads used in the threadpool-backed of common native libraries used for scientific computing and data science (e.g. BLAS and OpenMP).

Fine control of the underlying thread-pool size can be useful in workloads that involve nested parallelism so as to mitigate oversubscription issues.

This package provides info files with the reference manual for the GNU Scientific Library (GSL), a collection of routines for numerical analysis.

The reference manual is also available in postscript and html formats in the packages gsl-ref-psdoc and gsl-ref-html, respectively.

This package provides a pdf file with the reference manual for the GNU Scientific Library (GSL), a collection of routines for numerical analysis.

The reference manual is also available in postscript and html formats in the packages gsl-ref-psdoc and gsl-ref-html, respectively.

This package provides html files with the reference manual for the GNU Scientific Library (GSL), a collection of routines for numerical analysis.

This package provides a ps file with the reference manual for the GNU Scientific Library (GSL), a collection of routines for numerical analysis.

This package is a binary incompatible upgrade to the blas-dev package. Several minor changes to the C interface have been incorporated.

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 implementation of the library belongs to the CLAPACK distribution.

This package contains a static version of the library.

Pseudopotentials consist in atomic data used for atomic-scale electronic structure calculations. Libpspio is a library to read and write pseudopotentials in various formats, allowing as well for conversion in some cases.

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 package contains the development files needed to interface other software with Wannier90.