Debian Science High Energy Physics packages

The DIALS software is developed in a fully open-source, collaborative environment. The main development teams are based at Diamond Light Source and CCP4, in the UK, and at Lawrence Berkeley National Laboratory, USA. However, in the spirit of the open source movement, we welcome collaboration from anyone who wishes to contribute to the project.

To avoid “reinventing the wheel” as much as possible, the DIALS project builds on knowledge accumulated over many decades in the field of crystallographic data processing. We benefit greatly from the altruism of experts who contribute their ideas and advice, either directly or via their detailed publications on existing algorithms and packages such as XDS [2] and MOSFLM [3]. At the heart of the DIALS framework lies a design philosophy of hardware abstraction and a generalised model of the experiment that is inspired directly by material published on the seminal workshops on position sensitive detector software [1]. Continuing in the spirit of these workshops we held our own series of meetings, with talks from invited speakers, and code camps in which specific problems are addressed by intensive effort across the collaboration. Summaries of these meetings and copies of slides given as presentations are available here.

DIALS is written using Python and C++, making heavy use of the cctbx [4] for core crystallographic calculations and much infrastructure including a complete build system. Seamless interaction between the C++ and Python components of this hybrid system is enabled by Boost.Python. Python provides a useful ground for rapid prototyping, after which core algorithms and data structures may be transferred over to C++ for speed. High level interfaces of the hybrid system remain in Python, facilitating further development and code reuse both within DIALS and by third parties.

FeynMF to pakiet LaTeX-a umożliwiający łatwe rysowanie diagramów Feynmana * profesjonalnej jakości. Diagramy Feynmana są ilustracjami, które wyraźnie pokazują podstawowe interakcje cząstek subatomowych. Diagramy można tworzyć za pomocą programów Metafont lub MetaPost. FeynMF w zadowalający sposób porządkuje większość diagramów w oparciu o ich strukturę, bez konieczności ręcznej interwencji. Niemniej jednak w nietypowych przypadkach dostępne są wszystkie opcje Metafont lub MetaPost.

Uwaga! Aby korzystać z wersji FeynMF opartej na MetaPost należy zainstalować pakiet texlive-metapost.

LoopTools is a package for evaluation of scalar and tensor one-loop integrals based on the FF package by G.J. van Oldenborgh. It features an easy Fortran, C++, and Mathematica interface to the scalar one-loop functions of FF and in addition provides the 2-, 3-, and 4-point tensor coefficient functions.

This package provides program file, lt, of LoopTools.

NEURON is a simulation environment for modeling individual neurons and networks of neurons. It provides tools for conveniently building, managing, and using models in a way that is numerically sound and computationally efficient. It is particularly well-suited to problems that are closely linked to experimental data, especially those that involve cells with complex anatomical and biophysical properties.

NEURON offers

• "natural syntax", which allows one to specify model properties in familiar idioms
• efficient and painless spatial and temporal discretization
• several different, user-selectable numerical integration methods
• convenient user interface (interpreters + GUI)
• user-extendable library of biophysical mechanisms

SDPB is an open-source, arbitrary-precision, parallelized semidefinite program solver, designed for the conformal bootstrap. SDPB significantly outperforms less specialized solvers and should enable many new computations.

For more information, see "A Semidefinite Program Solver for the Conformal Bootstrap" at http://arxiv.org/abs/1502.02033.

CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

This metapackage provides almost all of the programs and libraries contained in CERNLIB. Most people will likely want only a subset of these. A few extra CERNLIB programs, not of interest to many people, may be obtained via the cernlib-extras metapackage.

CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

This package includes miscellaneous architecture-independent files useful for CERNLIB libraries and programs, including an example script that can generate a skeleton CERNLIB directory structure and Vim syntax highlighting macros for KUIPC CDF files and PAW "kumac" macro files.

CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

This metapackage provides the libraries and analysis tools (e.g. PAW) likely to be wanted by most users of the CERN libraries who are not interested specifically in high energy physics. It does not provide development libraries or tools; those may be obtained by installing the cernlib-core-dev metapackage or individual lib*-dev packages.

CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

This metapackage provides a few additional CERNLIB programs not included in any other CERNLIB package. Very few people are likely to be interested in them; currently they include zftp, pawserv and zserv. The latter two programs run as daemons through inetd and may raise concerns about the system's security.

Installing this package along with the 'cernlib' metapackage will supply a complete set of all CERNLIB programs and libraries, except for those not included in Debian due to licensing reasons.

CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

This metapackage provides various Monte Carlo libraries included in CERNLIB (both shared and static). Likely only physicists will be interested in these packages. Note that the GEANT 3.21 framework is not included, but it may be obtained by also installing the geant321 Debian package.

Be aware that the libraries of Ariadne, Fritiof, Jetset, Lepto, and Pythia are not available within Debian due to licensing issues; see the README.Debian file in the montecarlo-base package for information on obtaining them.

CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

DZedit is an interactive interface to the DZDOC (ZEBRA documentation) system developed at CERN. ZEBRA, part of the Packlib library, allows the creation of complex data structures in the FORTRAN 77 language; the DZDOC system helps to generate and maintain documentation for ZEBRA data structures.

GEANT is a framework for simulating the passage of subatomic particles through matter, for instance, particle detectors. For maximum flexibility, GEANT simulations are performed by linking FORTRAN code supplied by the user with the GEANT library, then running the resulting executable.

This package includes gxint, a script that makes this linking step more convenient.

GEANT is a framework for simulating the passage of subatomic particles through matter, for instance, particle detectors. For maximum flexibility, GEANT simulations are performed by linking FORTRAN code supplied by the user with the GEANT library, then running the resulting executable.

This package includes some documentation in text format about GEANT 3.21.

Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.

This is a metapackage depending on all libraries.

CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

KUIPC, the Kit for a User Interface Package Compiler, is a tool to simplify the writing of a program's user interface code. It takes a Command Definition File (CDF) as input, which describes the commands to be understood by the program, and outputs C or FORTRAN code that makes the appropriate function calls to set up the user interface. This code can then be compiled and linked with the rest of the program. Since the generated code uses KUIP routines, the program must also be linked against the Packlib library that contains them.

KUIPC is no longer actively developed, so aside from its use in the build process of CERNLIB, it is of mainly historical interest.

CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

KXterm is a terminal emulator which combines the best features from the (now defunct) Apollo DM pads (like: input and transcript pads, automatic file backup of transcript pad, string search in pads, etc.) and the Korn shell emacs-style command line editing and command line recall mechanism. It can support the command-line interface of various CERNLIB applications.

LHAPDF provides a unified and easy to use interface to modern PDF sets. It is designed to work not only with individual PDF sets but also with the more recent multiple "error" sets. It can be viewed as the successor to PDFLIB, incorporating many of the older sets found in the latter, including pion and photon PDFs. In LHAPDF the computer code and input parameters/grids are separated thus allowing more easy updating and no limit to the expansion possibilities.

This package provides a minimal PDF sets required by the test suites of LHAPDF and ThePEG.

Note: the python-lhapdf package provides lhapdf-getdata script to download other PDF sets.

CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

This package contains the Nypatchy family of programs, the successors to Patchy and Ypatchy. These programs are intended for working with sets of patches (for instance, for use on different machine architectures) meant to be applied to a source code tree. The patch sets and common source code are maintained as a single text-based Patchy Master file (PAM file). PAM files can contain C, FORTRAN, or assembly code.

Nypatchy and related utilities can perform actions on a PAM file such as updating it; comparing it to an older version; or outputting source code suitable for input to a compiler, having selected some subset of available patches to use. These utilities can be used interactively, or can run in batch mode from a "cradle" file of commands.

While Nypatchy is still used in places, mainly high-energy physics, these programs are no longer under active development. They are not recommended for use in new projects.

LHAPDF provides a unified and easy to use interface to modern PDF sets. It is designed to work not only with individual PDF sets but also with the more recent multiple "error" sets. It can be viewed as the successor to PDFLIB, incorporating many of the older sets found in the latter, including pion and photon PDFs. In LHAPDF the computer code and input parameters/grids are separated thus allowing more easy updating and no limit to the expansion possibilities.

This package provides Octave bindings for LHAPDF.

CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

PAW is an interactive program providing interactive graphical presentation and statistical and mathematical analysis tools. It is designed to work on objects familiar to physicists such as histograms, event files (Ntuples), vectors, etc.

The program is linked statically against the CERN libraries on 64-bit architectures in order to function properly, as its design is not very 64-bit clean.

CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

This package includes Paw++, an interactive program for use in analysis and graphical presentation. Paw++ is the same program as PAW (in the "paw" package), but with a more user-friendly Motif-based GUI, compiled against Lesstif in Debian.

The program is linked statically against the CERN libraries on 64-bit architectures in order to function properly, as its design is not very 64-bit clean.

CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

This package includes example scripts for use by PAW or Paw++, and test scripts to make sure that the PAW or Paw++ programs behave correctly. You may run the examples and tests with the included paw-demos program.

CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

This package contains the server daemon for remote PAW clients. PAW is the Physics Analysis Workstation, a graphical analysis program. Included in the same binary is zserv, the server daemon for the ZFTP protocol; zserv is a macro-extensible file transfer program which supports the transfer of formatted, unformatted and ZEBRA RZ files (CMZ, HBOOK, etc.). It is similar to a standard FTP daemon, although it listens on a different port. Both servers operate through inetd.

Since these servers accept passwords in clear text and do not support SSL or other encryption methods, you should probably only install this package within a trusted LAN. It should be seen as equivalent to vanilla telnetd in terms of security (or lack thereof).

PYTHIA is a program for the generation of high-energy physics events, i.e. for the description of collisions at high energies between elementary particles such as e+, e-, p and pbar in various combinations. It contains theory and models for a number of physics aspects, including hard and soft interactions, parton distributions, initial- and final-state parton showers, multiple interactions, fragmentation and decay.

This package provides interfaces to call ROOT functions in PYTHIA8 code.

Rivet is a toolkit for validation of Monte Carlo event generators. Using a computationally efficient model for observable computations, Rivet provides a set of experimental analyses useful for generator sanity checks, as well as a convenient infrastructure for adding your own analysis.

This package provides program files of Rivet.

Rivet is a toolkit for validation of Monte Carlo event generators. Using a computationally efficient model for observable computations, Rivet provides a set of experimental analyses useful for generator sanity checks, as well as a convenient infrastructure for adding your own analysis.

This package provides analysis plugins of Rivet. Note that ATLASCone and CDFCones are not supported in Debian due to license issues of FastJet.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains an import/export module for the ROOT geometry.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains a geometry builder plugin for ROOT.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains a geometry painter plugin for ROOT.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains the AfterImage plug-in for ROOT, which allows you to store output graphics in many formats, including JPEG, PNG, SVG, etc.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains the Graf2d Qt plug-in for ROOT. This plugin provides Qt interfaces of Graf2d library.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains the X11 plug-in for ROOT, which allows using an X display for showing graphics.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains the X 3D plug-in for ROOT. This plugin provides 3D rendering of volumes and shapes defined in ROOT. Included is also a low quality 3D viewer for ROOT defined geometries.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains a plug-in to show a pop-up dialog when fitting various kinds of data.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains a plug-in for editing graphical user interfaces in ROOT.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains the Qt plug-in for ROOT. This plugin provides an abstraction over a display. Windows are created via Qt.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains a plug-in browsing an interactive PROOF session in ROOT.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains the Hbook plug-in for ROOT, allowing you to access legacy Hbook files (NTuples and Histograms from PAW).

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains a painter of histograms for ROOT.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains a painter of spectra for ROOT.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains the SQL plug-in for ROOT, that allows transparent access to files data via an SQL database, using ROOT's TFile interface.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains the XML reader plug-in for ROOT. This package provide a plug-in to parse XML files with ROOT.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains the Fast Fourier Transform extension for ROOT. It uses the very fast fftw (version 3) library.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains the fumili plug-in for ROOT. This provides an alternative fitting algorithm for ROOT.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains the MINUIT version 2 plug-in for ROOT. This provides an fitting algorithm for ROOT.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains the Pythia version 8 plug-in for ROOT. This package provide the ROOT user with transparent interface to the Pythia (version 8) event generators for hadronic interactions. If the term "hadronic" does not ring any bells, this package is not for you.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains the Globus plug-in for ROOT, that allows authentication and authorization against globus.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains the Kerberos (version 5) plug-in for ROOT, that allows authentication and authorisation using Kerberos tokens.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains the MySQL plug-in for ROOT. This plugin provides a thin client (interface) to MySQL servers. Using this client, one can obtain information from a MySQL database into the ROOT environment.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains the ODBC (Open DataBase Connectivity) plug-in for ROOT, that allows transparent access to any kind of database that supports the ODBC protocol.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains the PostGreSQL plug-in for ROOT. This plugin provides a thin client (interface) to PostGreSQL servers. Using this client, one can obtain information from a PostGreSQL database into the ROOT environment.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains a plug-in for browsing a ROOT tree in ROOT.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

With the data defined as a set of objects, specialized storage methods can give direct access to the separate attributes of the selected objects, without having to touch the bulk of the data. Included are histogramming methods in 1, 2 and 3 dimensions, curve fitting, function evaluation, minimization, graphics and visualization classes to allow the easy creation of an analysis system that can query and process the data interactively or in batch mode.

The command language, the scripting (or macro) language, and the programming language are all C++, thanks to the built-in CINT C++ interpreter. This interpreter removes the time consuming compile/link cycle, allowing for fast prototyping of the macros, and providing a good environment to learn C++. If more performance is needed, the interactively developed macros can be compiled using a C++ compiler.

The system has been designed in such a way that it can query its databases in parallel on MPP machines or on clusters of workstations or high-end PCs. ROOT is an open system that can be dynamically extended by linking external libraries. This makes ROOT a premier platform on which to build data acquisition, simulation and data analysis systems.

This package is a metapackage to ensure the installation of all possible ROOT packages on a system.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

With the data defined as a set of objects, specialized storage methods can give direct access to the separate attributes of the selected objects, without having to touch the bulk of the data. Included are histogramming methods in 1, 2 and 3 dimensions, curve fitting, function evaluation, minimization, graphics and visualization classes to allow the easy creation of an analysis system that can query and process the data interactively or in batch mode.

The command language, the scripting (or macro) language, and the programming language are all C++, thanks to the built-in CINT C++ interpreter. This interpreter removes the time consuming compile/link cycle, allowing for fast prototyping of the macros, and providing a good environment to learn C++. If more performance is needed, the interactively developed macros can be compiled using a C++ compiler.

The system has been designed in such a way that it can query its databases in parallel on MPP machines or on clusters of workstations or high-end PCs. ROOT is an open system that can be dynamically extended by linking external libraries. This makes ROOT a premier platform on which to build data acquisition, simulation and data analysis systems.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains some common infrastructure files for ROOT.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains the tutorial scripts and test suite for the ROOT system, as well as the automatically generated HTML class documentation.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains the PROOF server. proofd is the core daemon of the PROOF (Parallel ROOt Facility) system for distributed parallel computing. Installing this package on a machine, makes it possible for the machine to participate in a parallel computing farm (cluster or via the Internet), either as a master or a slave, using a transparent interface.

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data efficiently.

This package contains ROOT file server. rootd is a server for ROOT files, serving files over the Internet. Using this daemon, you can access files on the machine from anywhere on the Internet, using a transparent interface.

ThePEG is a general toolkit for implementing physics models of event generation in high energy particle collisions. It defines a general structure of event generation in terms of abstract base classes for e.g. hard partonic matrix elements, parton showers and the decay of unstable particles. Different models are then implemented by creating classes which inherits from these base classes and implements sets of pre-defined virtual functions.

This package provides program files of ThePEG.

ThePEG is a general toolkit for implementing physics models of event generation in high energy particle collisions. It defines a general structure of event generation in terms of abstract base classes for e.g. hard partonic matrix elements, parton showers and the decay of unstable particles. Different models are then implemented by creating classes which inherits from these base classes and implements sets of pre-defined virtual functions.

This package provides Java GUI of ThePEG.

CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

ZFTP is a macro-extensible file transfer program which supports the transfer of formatted, unformatted and ZEBRA RZ files (CMZ, HBOOK, etc.). It provides a common interface on all systems and avoids the problems of file format conversion that occur when transferring CERNLIB files between different architectures.

Except for the special treatment of CERNLIB files and use of a different port, zftp is very similar to an FTP client. Unless you are already familiar with this program, it will almost certainly be useless to you.