HypExp 2, Expanding hypergeometric functions about half-integer parameters

In this article, we describe a new algorithm for the expansion of hypergeometric functions about half-integer parameters. The implementation of this algorithm for certain classes of hypergeometric functions in the already existing Mathematica package HypExp is described. Examples of applications in Feynman diagrams with up to four loops are given.

New version program summary

Program title:HypExp 2Catalogue identifier:ADXF_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXF_v2_0.htmlProgram obtainable from:CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions:Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.:106 401No. of bytes in distributed program, including test data, etc.:2 668 729Distribution format:tar.gzProgramming language:MathematicaComputer:Computers running MathematicaOperating system:Linux, Windows, MacRAM:Depending on the complexity of the problemSupplementary material:Library files which contain the expansion of certain hypergeometric functions around their parameters are availableClassification:4.7, 5Does the new version supersede the previous version?:YesNature of problem:Expansion of hypergeometric functions about parameters that are integer and/or half-integer valued.Solution method:New algorithm implemented in Mathematica.Reasons for new version:Expansion about half-integer parameters.Summary of revisions:Ability to expand about half-integer valued parameters added.Restrictions:The classes of hypergeometric functions with half-integer parameters that can be expanded are listed below.Additional comments:The package uses the package HPL included in the distribution.Running time:Depending on the expansion.     

S@M, a mathematica implementation of the spinor-helicity formalism

In this paper we present the package S@M (Spinors@Mathematica) which implements the spinor-helicity formalism in Mathematica. The package allows the use of complex-spinor algebra along with the multi-purpose features of Mathematica. The package defines the spinor objects with their basic properties along with functions to manipulate them. It also offers the possibility of evaluating the spinorial objects numerically at every computational step. The package is therefore well suited to be used in the context of on-shell technology, in particular for the evaluation of scattering amplitudes at tree- and loop-level.

Program summary

Program title: S@MCatalogue identifier: AEBF_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBF_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 14 404No. of bytes in distributed program, including test data, etc.: 77 536Distribution format: tar.gzProgramming language: MathematicaComputer: All computers running MathematicaOperating system: Any system running MathematicaClassification: 4.4, 5, 11.1Nature of problem: Implementation of the spinor-helicity formalismSolution method: Mathematica implementationRunning time: The notebooks provided with the package take only a few seconds to run.     

xPerm: fast index canonicalization for tensor computer algebra

We present a very fast implementation of the Butler-Portugal algorithm for index canonicalization with respect to permutation symmetries. It is called xPerm, and has been written as a combination of a Mathematica package and a C subroutine. The latter performs the most demanding parts of the computations and can be linked from any other program or computer algebra system. We demonstrate with tests and timings the effectively polynomial performance of the Butler-Portugal algorithm with respect to the number of indices, though we also show a case in which it is exponential. Our implementation handles generic tensorial expressions with several dozen indices in hundredths of a second, or one hundred indices in a few seconds, clearly outperforming all other current canonicalizers. The code has been already under intensive testing for several years and has been essential in recent investigations in large-scale tensor computer algebra.

Program summary

Program title: xPermCatalogue identifier: AEBH_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBH_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 93 582No. of bytes in distributed program, including test data, etc.: 1 537 832Distribution format: tar.gzProgramming language: C and Mathematica (version 5.0 or higher)Computer: Any computer running C and Mathematica (version 5.0 or higher)Operating system: Linux, Unix, Windows XP, MacOSRAM:: 20 MbyteWord size: 64 or 32 bitsClassification: 1.5, 5Nature of problem: Canonicalization of indexed expressions with respect to permutation symmetries.Solution method: The Butler-Portugal algorithm.Restrictions: Multiterm symmetries are not considered.Running time: A few seconds with generic expressions of up to 100 indices. The xPermDoc.nb notebook supplied with the distribution takes approximately one and a half hours to execute in full.     

The Invar tensor package

The Invar package is introduced, a fast manipulator of generic scalar polynomial expressions formed from the Riemann tensor of a four-dimensional metric-compatible connection. The package can maximally simplify any polynomial containing tensor products of up to seven Riemann tensors within seconds. It has been implemented both in Mathematica and Maple algebraic systems.

Program summary

Program title:Invar Tensor PackageCatalogue identifier:ADZK_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZK_v1_0.htmlProgram obtainable from:CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions:Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 136 240No. of bytes in distributed program, including test data, etc.:2 711 923Distribution format:tar.gzProgramming language:Mathematica and MapleComputer:Any computer running Mathematica versions 5.0 to 5.2 or Maple versions 9 and 10Operating system:Linux, Unix, Windows XPRAM:30 MbWord size:64 or 32 bitsClassification:5External routines:The Mathematica version requires the xTensor and xPerm packages. These are freely available at http://metric.iem.csic.es/Martin-Garcia/xActNature of problem:Manipulation and simplification of tensor expressions. Special attention on simplifying scalar polynomial expressions formed from the Riemann tensor on a four-dimensional metric-compatible manifold.Solution method:Algorithms of computational group theory to simplify expressions with tensors that obey permutation symmetries. Tables of syzygies of the scalar invariants of the Riemann tensor.Restrictions:The present versions do not fully address the problem of reducing differential invariants or monomials of the Riemann tensor with free indices.Running time:Less than a second to fully reduce a monomial of the Riemann tensor of degree 7 in terms of independent invariants.     

A completely open source based computing system for computer generation of Fourier holograms

Computer generated holograms are usually generated using commercial software like MATLAB, MATHCAD, Mathematica, etc. This work is an approach in doing the same using freely distributed open source packages and Operating System. A Fourier hologram is generated using this method and tested for simulated and optical reconstruction. The reconstructed images are in good agreement with the objects chosen. The significance of using such a system is also discussed.

Program summary

Program title: FHOLOCatalogue identifier: AEDS_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDS_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 176 336No. of bytes in distributed program, including test data, etc.: 4 294 872Distribution format: tar.gzProgramming language: C++Computer: any X86 micro computerOperating system: Linux (Debian Etch)RAM: 512 MBClassification: 18Nature of problem: To generate a Fourier Hologram in micro computer only by using open source operating system and packages.Running time: Depends on the matrix size. 10 sec for a matrix of size 256×256.     

FeynRules - Feynman rules made easy

In this paper we present FeynRules, a new Mathematica package that facilitates the implementation of new particle physics models. After the user implements the basic model information (e.g., particle content, parameters and Lagrangian), FeynRules derives the Feynman rules and stores them in a generic form suitable for translation to any Feynman diagram calculation program. The model can then be translated to the format specific to a particular Feynman diagram calculator via FeynRules translation interfaces. Such interfaces have been written for CalcHEP/CompHEP, FeynArts/FormCalc, MadGraph/MadEvent and Sherpa, making it possible to write a new model once and have it work in all of these programs. In this paper, we describe how to implement a new model, generate the Feynman rules, use a generic translation interface, and write a new translation interface. We also discuss the details of the FeynRules code.

Program summary

Program title: FeynRulesCatalogue identifier: AEDI_v1_0Program summary URL::http://cpc.cs.qub.ac.uk/summaries/AEDI_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 15 980No. of bytes in distributed program, including test data, etc.: 137 383Distribution format: tar.gzProgramming language: MathematicaComputer: Platforms on which Mathematica is availableOperating system: Operating systems on which Mathematica is availableClassification: 11.1, 11.2, 11.6Nature of problem: Automatic derivation of Feynman rules from a Lagrangian. Implementation of new models into Monte Carlo event generators and FeynArts.Solution method: FeynRules works in two steps:

1. derivation of the Feynman rules directly form the Lagrangian using canonical commutation relations among fields and creation operators.

2. implementation of the new physics model into FeynArts as well as various Monte Carlo programs via interfaces.

Full-size table

     

Real-time Java simulations of multiple interference dielectric filters

An interactive Java applet for real-time simulation and visualization of the transmittance properties of multiple interference dielectric filters is presented. The most commonly used interference filters as well as the state-of-the-art ones are embedded in this platform-independent applet which can serve research and education purposes. The Transmittance applet can be freely downloaded from the site http://cpc.cs.qub.ac.uk.

Program summary

Program title: TransmittanceCatalogue identifier: AEBQ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBQ_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 5778No. of bytes in distributed program, including test data, etc.: 90 474Distribution format: tar.gzProgramming language: JavaComputer: Developed on PC-Pentium platformOperating system: Any Java-enabled OS. Applet was tested on Windows ME, XP, Sun Solaris, Mac OSRAM: VariableClassification: 18Nature of problem: Sophisticated wavelength selective multiple interference filters can include some tens or even hundreds of dielectric layers. The spectral response of such a stack is not obvious. On the other hand, there is a strong demand from application designers and students to get a quick insight into the properties of a given filter.Solution method: A Java applet was developed for the computation and the visualization of the transmittance of multilayer interference filters. It is simple to use and the embedded filter library can serve educational purposes. Also, its ability to handle complex structures will be appreciated as a useful research and development tool.Running time: Real-time simulations     

Symbolic computation of the Hartree-Fock energy from a chiral EFT three-nucleon interaction at NLO

We present the first of a two-part Mathematica notebook collection that implements a symbolic approach for the application of the density matrix expansion (DME) to the Hartree-Fock (HF) energy from a chiral effective field theory (EFT) three-nucleon interaction at N²LO. The final output from the notebooks is a Skyrme-like energy density functional that provides a quasi-local approximation to the non-local HF energy. In this paper, we discuss the derivation of the HF energy and its simplification in terms of the scalar/vector-isoscalar/isovector parts of the one-body density matrix. Furthermore, a set of steps is described and illustrated on how to extend the approach to other three-nucleon interactions.

Program summary

Program title: SymbHFNNNCatalogue identifier: AEGC_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGC_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 96 666No. of bytes in distributed program, including test data, etc.: 378 083Distribution format: tar.gzProgramming language: Mathematica 7.1Computer: Any computer running Mathematica 6.0 and later versionsOperating system: Windows Xp, Linux/UnixRAM: 256 MbClassification: 5, 17.16, 17.22Nature of problem: The calculation of the HF energy from the chiral EFT three-nucleon interaction at N²LO involves tremendous spin-isospin algebra. The problem is compounded by the need to eventually obtain a quasi-local approximation to the HF energy, which requires the HF energy to be expressed in terms of scalar/vector-isoscalar/isovector parts of the one-body density matrix. The Mathematica notebooks discussed in this paper solve the latter issue.Solution method: The HF energy from the chiral EFT three-nucleon interaction at N²LO is cast into a form suitable for an automatic simplification of the spin-isospin traces. Several Mathematica functions and symbolic manipulation techniques are used to obtain the result in terms of the scalar/vector-isoscalar/isovector parts of the one-body density matrix.Running time: Several hours     

HypExp 2, expanding hypergeometric functions about half-integer parameters

HypExp is a Mathematica package for expanding hypergeometric functions about integer and half-integer parameters.New version program summaryProgram title: HypExp 2Catalogue identifier: ADXF_v2_1Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADXF_v2_1.htmlProgram obtainable from: CPC Program Library, Queen?s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 107 274No. of bytes in distributed program, including test data, etc.: 2 690 337Distribution format: tar.gzProgramming language: Mathematica 7 and 8Computer: Computers running MathematicaOperating system: Linux, Windows, MacRAM: Depending on the complexity of the problemSupplementary material: Library files which contain the expansion of certain hypergeometric functions around their parameters are availableClassification: 4.7, 5Catalogue identifier of previous version: ADXF_v2_0Journal reference of previous version: Comput. Phys. Comm. 178 (2008) 755Does the new version supersede the previous version?: YesNature of problem: Expansion of hypergeometric functions about parameters that are integer and/or half-integer valued.Solution method: New algorithm implemented in Mathematica.Reasons for new version: Compatibility with new versions of Mathematica.Summary of revisions: Support for versions 7 and 8 of Mathematica added. No changes in the features of the package.Restrictions: The classes of hypergeometric functions with half-integer parameters that can be expanded are listed in the long write-up.Additional comments: The package uses the package HPL included in the distribution.Running time: Depending on the expansion.     

Resolution of singularities for multi-loop integrals

We report on a program for the numerical evaluation of divergent multi-loop integrals. The program is based on iterated sector decomposition. We improve the original algorithm of Binoth and Heinrich such that the program is guaranteed to terminate. The program can be used to compute numerically the Laurent expansion of divergent multi-loop integrals regulated by dimensional regularisation. The symbolic and the numerical steps of the algorithm are combined into one program.

Program summary

Program title: sector_decompositionCatalogue identifier: AEAG_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAG_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 47 506No. of bytes in distributed program, including test data, etc.: 328 485Distribution format: tar.gzProgramming language: C++Computer: allOperating system: UnixRAM: Depending on the complexity of the problemClassification: 4.4External routines: GiNaC, available from http://www.ginac.de, GNU scientific library, available from http://www.gnu.org/software/gslNature of problem: Computation of divergent multi-loop integrals.Solution method: Sector decomposition.Restrictions: Only limited by the available memory and CPU time.Running time: Depending on the complexity of the problem.     

A recursive method to calculate UV-divergent parts at one-loop level in dimensional regularization

A method is introduced to calculate the UV-divergent parts at one-loop level in dimensional regularization. The method is based on the recursion, and the basic integrals are just the scaleless integrals after the recursive reduction, which involve no other momentum scales except the loop momentum itself. The method can be easily implemented in any symbolic computer language, and a implementation in Mathematica is ready to use.Program summaryProgram title: UVPartCatalogue identifier: AELY_v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AELY_v1_0.htmlProgram obtainable from: CPC Program Library, Queen?s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 26 361No. of bytes in distributed program, including test data, etc.: 412 084Distribution format: tar.gzProgramming language: MathematicaComputer: Any computer where the Mathematica is running.Operating system: Any capable of running Mathematica.Classification: 11.1External routines: FeynCalc (http://www.feyncalc.org/), FeynArts (http://www.feynarts.de/)Nature of problem: To get the UV-divergent part of any one-loop expression.Solution method: UVPart is a Mathematica package where the recursive method has been implemented.Running time: In general it is below one second.     

QDENSITY—A Mathematica quantum computer simulation

This Mathematica 6.0 package is a simulation of a Quantum Computer. The program provides a modular, instructive approach for generating the basic elements that make up a quantum circuit. The main emphasis is on using the density matrix, although an approach using state vectors is also implemented in the package. The package commands are defined in Qdensity.m which contains the tools needed in quantum circuits, e.g., multiqubit kets, projectors, gates, etc.

New version program summary

Program title: QDENSITY 2.0Catalogue identifier: ADXH_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXH_v2_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 26 055No. of bytes in distributed program, including test data, etc.: 227 540Distribution format: tar.gzProgramming language: Mathematica 6.0Operating system: Any which supports Mathematica; tested under Microsoft Windows XP, Macintosh OS X, and Linux FC4Catalogue identifier of previous version: ADXH_v1_0Journal reference of previous version: Comput. Phys. Comm. 174 (2006) 914Classification: 4.15Does the new version supersede the previous version?: Offers an alternative, more up to date, implementationNature of problem: Analysis and design of quantum circuits, quantum algorithms and quantum clusters.Solution method: A Mathematica package is provided which contains commands to create and analyze quantum circuits. Several Mathematica notebooks containing relevant examples: Teleportation, Shor's Algorithm and Grover's search are explained in detail. A tutorial, Tutorial.nb is also enclosed.Reasons for new version: The package has been updated to make it fully compatible with Mathematica 6.0Summary of revisions: The package has been updated to make it fully compatible with Mathematica 6.0Running time: Most examples included in the package, e.g., the tutorial, Shor's examples, Teleportation examples and Grover's search, run in less than a minute on a Pentium 4 processor (2.6 GHz). The running time for a quantum computation depends crucially on the number of qubits employed.     

Solving surface structures from normal incidence X-ray standing wave data

A program is provided to determine structural parameters of atoms in or adsorbed on surfaces by refinement of atomistic models towards experimentally determined data generated by the normal incidence X-ray standing wave (NIXSW) technique. The method employs a combination of Differential Evolution Genetic Algorithms and Steepest Descent Line Minimisations to provide a fast, reliable and user friendly tool for experimentalists to interpret complex multidimensional NIXSW data sets.

Program summary

Program title: NIXSW Planewave SolverCatalogue identifier: ADZE_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZE_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 16 874No. of bytes in distributed program, including test data, etc.: 1 631 874Distribution format: tar.gzProgramming language: Borland C++ Builder 5Computer: Any Windows CompatibleOperating system: Windows 2000 and XPRAM: <10 MBClassification: 7.4Nature of problem: Using NIXSW experimental data to calculate atomic positions of adsorbates.Restrictions: Data from substrates must have cubic, tetragonal or orthorhombic crystal structures i.e. with 90° between conventional cell axes.Running time: Seconds-minutes dependant on the number of plane waves and the number of atomic sites.     

Solution of few-body problems with the stochastic variational method II: Two-dimensional systems

A computational approach is presented for efficient solution of two-dimensional few-body problems, such as quantum dots or excitonic complexes, using the stochastic variational method. The computer program can be used to calculate the energies and wave functions of various two-dimensional systems.

Program summary

Program title: svm-2dCatalogue identifier: AEBE_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBE_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 5091No. of bytes in distributed program, including test data, etc.: 130 963Distribution format: tar.gzProgramming language: Fortran 90Computer: The program should work on any system with a Fortran 90 compilerOperating system: The program should work on any system with a Fortran 90 compilerClassification: 7.3Nature of problem: Variational calculation of energies and wave functions using Correlated Gaussian basis.Solution method: Two-dimensional few-electron problems are solved by the variational method. The ground state wave function is expanded into Correlated Gaussian basis functions and the parameters of the basis states are optimized by a stochastic selection procedure. Accurate results can be obtained for 2-6 electron systems.Running time: A couple of hours for a typical system.     

GenMin: An enhanced genetic algorithm for global optimization

A new method that employs grammatical evolution and a stopping rule for finding the global minimum of a continuous multidimensional, multimodal function is considered. The genetic algorithm used is a hybrid genetic algorithm in conjunction with a local search procedure. We list results from numerical experiments with a series of test functions and we compare with other established global optimization methods. The accompanying software accepts objective functions coded either in Fortran 77 or in C++.

Program summary

Program title: GenMinCatalogue identifier: AEAR_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAR_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 35 810No. of bytes in distributed program, including test data, etc.: 436 613Distribution format: tar.gzProgramming language: GNU-C++, GNU-C, GNU Fortran 77Computer: The tool is designed to be portable in all systems running the GNU C++ compilerOperating system: The tool is designed to be portable in all systems running the GNU C++ compilerRAM: 200 KBWord size: 32 bitsClassification: 4.9Nature of problem: A multitude of problems in science and engineering are often reduced to minimizing a function of many variables. There are instances that a local optimum does not correspond to the desired physical solution and hence the search for a better solution is required. Local optimization techniques are frequently trapped in local minima. Global optimization is hence the appropriate tool. For example, solving a nonlinear system of equations via optimization, employing a least squares type of objective, one may encounter many local minima that do not correspond to solutions (i.e. they are far from zero).Solution method: Grammatical evolution and a stopping rule.Running time: Depending on the objective function. The test example given takes only a few seconds to run.     

CrasyDSE: A framework for solving Dyson–Schwinger equations

Dyson–Schwinger equations are important tools for non-perturbative analyses of quantum field theories. For example, they are very useful for investigations in quantum chromodynamics and related theories. However, sometimes progress is impeded by the complexity of the equations. Thus automating parts of the calculations will certainly be helpful in future investigations. In this article we present a framework for such an automation based on a C++ code that can deal with a large number of Green functions. Since also the creation of the expressions for the integrals of the Dyson–Schwinger equations needs to be automated, we defer this task to a Mathematica notebook. We illustrate the complete workflow with an example from Yang–Mills theory coupled to a fundamental scalar field that has been investigated recently. As a second example we calculate the propagators of pure Yang–Mills theory. Our code can serve as a basis for many further investigations where the equations are too complicated to tackle by hand. It also can easily be combined with DoFun, a program for the derivation of Dyson–Schwinger equations.¹Program summaryProgram title: CrasyDSECatalogue identifier: AEMY _v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEMY_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 49030No. of bytes in distributed program, including test data, etc.: 303958Distribution format: tar.gzProgramming language: Mathematica 8 and higher, C++.Computer: All on which Mathematica and C++ are available.Operating system: All on which Mathematica and C++ are available (Windows, Unix, Mac OS).Classification: 11.1, 11.4, 11.5, 11.6.Nature of problem: Solve (large) systems of Dyson–Schwinger equations numerically.Solution method: Create C++ functions in Mathematica to be used for the numeric code in C++. This code uses structures to handle large numbers of Green functions.Unusual features: Provides a tool to convert Mathematica expressions into C++ expressions including conversion of function names.Running time: Depending on the complexity of the investigated system solving the equations numerically can take seconds on a desktop PC to hours on a cluster.     

TiReX: Replica-exchange molecular dynamics using Tinker

We present a driver program for performing replica-exchange molecular dynamics simulations with the Tinker package. Parallelization is based on the Message Passing Interface, with every replica assigned to a separate process. The algorithm is not communication intensive, which makes the program suitable for running even on loosely coupled cluster systems. Particular attention is paid to the practical aspects of analyzing the program output.

Program summary

Program title: TiReXCatalogue identifier: AEEK_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEK_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 43 385No. of bytes in distributed program, including test data, etc.: 502 262Distribution format: tar.gzProgramming language: Fortran 90/95Computer: Most UNIX machinesOperating system: LinuxHas the code been vectorized or parallelized?: parallelized with MPIClassification: 16.13External routines: TINKER version 4.2 or 5.0, built as a libraryNature of problem: Replica-exchange molecular dynamics.Solution method: Each replica is assigned to a separate process; temperatures are swapped between replicas at regular time intervals.Running time: The sample run may take up to a few minutes.     

Program package for multicanonical simulations of U(1) lattice gauge theory

We document our Fortran 77 code for multicanonical simulations of 4D U(1) lattice gauge theory in the neighborhood of its phase transition. This includes programs and routines for canonical simulations using biased Metropolis heatbath updating and overrelaxation, determination of multicanonical weights via a Wang-Landau recursion, and multicanonical simulations with fixed weights supplemented by overrelaxation sweeps. Measurements are performed for the action, Polyakov loops and some of their structure factors. Many features of the code transcend the particular application and are expected to be useful for other lattice gauge theory models as well as for systems in statistical physics.

Program summary

Program title: STMC_U1MUCACatalogue identifier: AEET_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEET_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 18 376No. of bytes in distributed program, including test data, etc.: 205 183Distribution format: tar.gzProgramming language: Fortran 77Computer: Any capable of compiling and executing Fortran codeOperating system: Any capable of compiling and executing Fortran codeClassification: 11.5Nature of problem: Efficient Markov chain Monte Carlo simulation of U(1) lattice gauge theory close to its phase transition. Measurements and analysis of the action per plaquette, the specific heat, Polyakov loops and their structure factors.Solution method: Multicanonical simulations with an initial Wang-Landau recursion to determine suitable weight factors. Reweighting to physical values using logarithmic coding and calculating jackknife error bars.Running time: The prepared tests runs took up to 74 minutes to execute on a 2 GHz PC.     

MDVRY: a polarizable classical molecular dynamics package for biomolecules

The MDVRY classical molecular dynamics package is presented for the study of biomolecules in the gas and liquid phase. Electrostatic polarization has been implemented in the formalism of point induced dipoles following the model of Thole. Two schemes have been implemented for the calculation of induced dipoles, i.e. resolution of the self-consistent equations and a ‘Car-Parrinello’ dynamical approach. In this latter, the induced dipoles are calculated at each time step of the dynamics through the dynamics of additional degrees of freedom associated with the dipoles. This method saves computer time and allows to study polarized solvated proteins at a very low CPU cost. The program is written in C-language and runs on LINUX machines. A detailed manual of the code is given. The main features of the package are illustrated taking on examples of proteins in the gas phase or immersed in liquid water.

Program summary

Program title: MDVRYCatalogue identifier: AEBY_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBY_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 39 156No. of bytes in distributed program, including test data, etc.: 277 197Distribution format: tar.bz2Programming language: CComputer: Linux machines with FFTW Fourier Transform package installedOperating system: Linux machines, SUSE & RedHat distributionsClassification: 3, 16.13, 23External routines: FFTW (http://www.fftw.org/)Nature of problem: Molecular Dynamics Software package.Solution method: Velocity Verlet algorithm. The implemented force field is composed of intra-molecular interactions and inter-molecular interactions (electrostatics, polarization, van der Waals). Polarization is accounted through induced point dipoles at each atomic site. Supplementary degrees of freedom are associated to the induced dipoles so that a modified Hamiltonian of the dynamics is written. This allows to calculate the induced dipoles with a very fast ‘Car-Parrinello’ type of dynamics.Running time: The test run provided takes approximately 6 minutes to run.