Extension of HPL to complex arguments

In this paper we describe the extension of the Mathematica package HPL to treat harmonic polylogarithms of complex arguments. The harmonic polylogarithms have been introduced by Remiddi and Vermaseren [E. Remiddi, J.A.M. Vermaseren, Int. J. Modern Phys. A 15 (2000) 725, hep-ph/9905237] and have many applications in high energy particle physics.New version program summaryProgram title: HPLCatalogue identifier: ADWX_v2_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADWX_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.: 13 610No. of bytes in distributed program, including test data, etc.: 1 055 706Distribution format: tar.gzProgramming language: Mathematica 7/8.Computer: All computers running Mathematica.Operating system: Operating systems running Mathematica.Supplementary material: Additional “high weight” MinimalSet files available.Classification: 4.7.Catalogue identifier of previous version: ADWX_v1_0Journal reference of previous version: Comput. Phys. Comm. 174 (2006) 222Does the new version supersede the previous version?: YesNature of problem: Computer algebraic treatment of the harmonic polylogarithms which appear in the evaluation of Feynman diagrams.Solution method: Mathematica implementation.Reasons for new version: Added treatment of complex arguments. Details in arXiv:hep-ph/0703052.Summary of revisions: Added treatment of complex arguments. Details in arXiv:hep-ph/0703052.Running time: A few seconds for each function.     

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.     

STRINGVACUA. A Mathematica package for studying vacuum configurations in string phenomenology

We give a simple tutorial introduction to the Mathematica package STRINGVACUA, which is designed to find vacua of string-derived or inspired four-dimensional N=1 supergravities. The package uses powerful algebro-geometric methods, as implemented in the free computer algebra system Singular, but requires no knowledge of the mathematics upon which it is based. A series of easy-to-use Mathematica modules are provided which can be used both in string theory and in more general applications requiring fast polynomial computations. The use of these modules is illustrated throughout with simple examples.

Program summary

Program title: STRINGVACUACatalogue identifier: AEBZ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBZ_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: GNU GPLNo. of lines in distributed program, including test data, etc.: 31 050No. of bytes in distributed program, including test data, etc.: 163 832Distribution format: tar.gzProgramming language: “Mathematica” syntaxComputer: Home and office spec desktop and laptop machines, networked or stand aloneOperating system: Windows XP (with Cygwin), Linux, Mac OS, running Mathematica V5 or aboveRAM: Varies greatly depending on calculation to be performedClassification: 11.1External routines: Linux: The program “Singular” is called from Mathematica. Windows: “Singular” is called within the Cygwin environment from Mathematica.Nature of problem: A central problem of string-phenomenology is to find stable vacua in the four-dimensional effective theories which result from compactification.Solution method: We present an algorithmic method, which uses techniques of algebraic geometry, to find all of the vacua of any given string-phenomenological system in a huge class.Running time: Varies greatly depending on calculation requested.     

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.     

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.     

SusyMath: A Mathematica package for quantum superfield calculations

SusyMath is a Mathematica package for quantum superfield calculations. It defines a standard form to translate the correction to the effective action corresponding to a given supergraph into a Mathematica expression, which is then evaluated and simplified. Several functions for manipulations of these expressions are provided, and the package also has the ability to save the outcomes of its calculations in form.

Program summary

Title of program: SusyMathCatalogue identifier:ADYQ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYQ_v1_0Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland, also at http://fma.if.usp.br/~alysson/SusyMathLicensing provisions: LGPL, CPC non-profit use licenseProgramming language: MathematicaPlatform: Any platform supporting Mathematica 4.0 or higherComputer tested on: PC (Athlon64 X2 +3800); 1 GB RAMOperating system under which the program has been tested: Linux (Debian 4.0); XOrg 7.0.22; Mathematica 5.2No. of lines in distributed program, including test data, etc.:42 472No. of bytes in distributed program, including test data, etc.:471 596Distribution format:tar.gzNature of the problem: Evaluate quantum corrections to the effective action of supersymmetric field theories, formulated in the superfield formalism, both in three- and four-spacetime dimensions.Solution method: A set of procedures for integration by parts, application of the algebra of covariant derivatives and Grassman integration, along with several auxiliary functions, is introduced.Restrictions: At the moment, the background field method is not implemented, but the system is designed to be further generalized.Running time: Depends on the complexity of the problem. From seconds for simpler one-loop diagrams to several hours for simple two-loop graphs.     

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

     

Beam-plasma dielectric tensor with Mathematica

We present a Mathematica notebook allowing for the symbolic calculation of the 3×3 dielectric tensor of an electron-beam plasma system in the fluid approximation. Calculation is detailed for a cold relativistic electron beam entering a cold magnetized plasma, and for arbitrarily oriented wave vectors. We show how one can elaborate on this example to account for temperatures, arbitrarily oriented magnetic field or a different kind of plasma.

Program summary

Title of program: TensorCatalog identifier: ADYT_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYT_v1_0Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandComputer for which the program is designed and others on which it has been tested: Computers: Any computer running Mathematica 4.1. Tested on DELL Dimension 5100 and IBM ThinkPad T42. Installations: ETSI Industriales, Universidad Castilla la Mancha, Ciudad Real, SpainOperating system under which the program has been tested: Windows XP ProProgramming language used: Mathematica 4.1Memory required to execute with typical data: 7.17 MbytesNo. of bytes in distributed program, including test data, etc.: 33 439No. of lines in distributed program, including test data, etc.: 3169Distribution format: tar.gzNature of the physical problem: The dielectric tensor of a relativistic beam plasma system may be quite involved to calculate symbolically when considering a magnetized plasma, kinetic pressure, collisions between species, and so on. The present Mathematica notebook performs the symbolic computation in terms of some usual dimensionless variables.Method of solution: The linearized relativistic fluid equations are directly entered and solved by Mathematica to express the first-order expression of the current. This expression is then introduced into a combination of Faraday and Ampère-Maxwell's equations to give the dielectric tensor. Some additional manipulations are needed to express the result in terms of the dimensionless variables.Restrictions on the complexity of the problem: Temperature effects are limited to small, i.e. non-relativistic, temperatures. The kinetic counterpart of the present Mathematica will usually not compute the required integrals.Typical running time: About 1 minute on a Intel Centrino 1.5 GHz Laptop with 512 MB of RAM.Unusual features of the program: None.     

HypExp, a Mathematica package for expanding hypergeometric functions around integer-valued parameters

We present the Mathematica package HypExp which allows to expand hypergeometric functions around integer parameters to arbitrary order. At this, we apply two methods, the first one being based on an integral representation, the second one on the nested sums approach. The expansion works for both symbolic argument z and unit argument. We also implemented new classes of integrals that appear in the first method and that are, in part, yet unknown to Mathematica.

Program summary

Title of program:HypExpCatalogue identifier:ADXF_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXF_v1_0Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandLicence:noneComputers:Computers running Mathematica under Linux or WindowsOperating system:Linux, WindowsProgram language:MathematicaNo. of bytes in distributed program, including test data, etc.:739 410No. of lines in distributed program, including test data, etc.:89 747Distribution format:tar.gzOther package needed:the package HPL, included in the distributionExternal file required:noneNature of the physical problem:Expansion of hypergeometric functions around integer-valued parameters. These are needed in the context of dimensional regularization for loop and phase space integrals.Method of solution:Algebraic manipulation of nested sums and integral representation.Restrictions on complexity of the problem:Limited by the memory availableTypical running time:Strongly depending on the problem and the availability of libraries.     

Kranc: a Mathematica package to generate numerical codes for tensorial evolution equations

We present a suite of Mathematica-based computer-algebra packages, termed “Kranc”, which comprise a toolbox to convert certain (tensorial) systems of partial differential evolution equations to parallelized C or Fortran code for solving initial boundary value problems. Kranc can be used as a “rapid prototyping” system for physicists or mathematicians handling very complicated systems of partial differential equations, but through integration into the Cactus computational toolkit we can also produce efficient parallelized production codes. Our work is motivated by the field of numerical relativity, where Kranc is used as a research tool by the authors. In this paper we describe the design and implementation of both the Mathematica packages and the resulting code, we discuss some example applications, and provide results on the performance of an example numerical code for the Einstein equations.

Program summary

Title of program: KrancCatalogue identifier: ADXS_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXS_v1_0Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandDistribution format: tar.gzComputer for which the program is designed and others on which it has been tested: General computers which run Mathematica (for code generation) and Cactus (for numerical simulations), tested under LinuxProgramming language used: Mathematica, C, Fortran 90Memory required to execute with typical data: This depends on the number of variables and gridsize, the included ADM example requires 4308 KBHas the code been vectorized or parallelized: The code is parallelized based on the Cactus framework.Number of bytes in distributed program, including test data, etc.: 1 578 142Number of lines in distributed program, including test data, etc.: 11 711Nature of physical problem: Solution of partial differential equations in three space dimensions, which are formulated as an initial value problem. In particular, the program is geared towards handling very complex tensorial equations as they appear, e.g., in numerical relativity. The worked out examples comprise the Klein-Gordon equations, the Maxwell equations, and the ADM formulation of the Einstein equations.Method of solution: The method of numerical solution is finite differencing and method of lines time integration, the numerical code is generated through a high level Mathematica interface.Restrictions on the complexity of the program: Typical numerical relativity applications will contain up to several dozen evolution variables and thousands of source terms, Cactus applications have shown scaling up to several thousand processors and grid sizes exceeding 500³.Typical running time: This depends on the number of variables and the grid size: the included ADM example takes approximately 100 seconds on a 1600 MHz Intel Pentium M processor.Unusual features of the program: based on Mathematica and Cactus     

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.     

Algorithmic derivation of Dyson-Schwinger equations

We present an algorithm for the derivation of Dyson-Schwinger equations of general theories that is suitable for an implementation within a symbolic programming language. Moreover, we introduce the Mathematica package DoDSE¹ which provides such an implementation. It derives the Dyson-Schwinger equations graphically once the interactions of the theory are specified. A few examples for the application of both the algorithm and the DoDSE package are provided.

Program summary

Program title: DoDSECatalogue identifier: AECT_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECT_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.: 105 874No. of bytes in distributed program, including test data, etc.: 262 446Distribution format: tar.gzProgramming language: Mathematica 6 and higherComputer: all on which Mathematica is availableOperating system: all on which Mathematica is availableClassification: 11.1, 11.4, 11.5, 11.6Nature of problem: Derivation of Dyson-Schwinger equations for a theory with given interactions.Solution method: Implementation of an algorithm for the derivation of Dyson-Schwinger equations.Unusual features: The results can be plotted as Feynman diagrams in Mathematica.Running time: Less than a second to minutes for Dyson-Schwinger equations of higher vertex functions.     

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.     

The MATHSCOUT Mathematica package to postprocess the output of other scientific programs

mathscout is a mathematica¹ package to postprocess the output of other programs for scientific calculations. We wrote mathscout to import data from a major program for ab initio computational chemistry into mathematica, so that we could postprocess the chemical results. It can be used to import the output of many other packages that are used, e.g. in molecular dynamics, crystallography, spectroscopic analysis, metabolic and physiological modeling, meteorology and other areas of environmental science, cosmology and particle physics. mathscout assigns a name to each table and non-tabular datum that it extracts. This name is constructed mechanically from the identifier or phrase that precedes or follows or embeds the item in the output that mathscout processes. A selection of non-contiguous items, or all the items in a section of the file, or in the entire file are extracted using simple commands. So far, we have focused on our immediate needs to postprocess the output of the Gaussian² program. Calculations on several molecules that illustrate the usage of the package are presented here and in the Supplementary Information. mathscout is shortened to msct in the software.

Program summary

Program title: msct.mCatalogue identifier: ADZQ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZQ_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.: 30 396No. of bytes in distributed program, including test data, etc.: 1 799 469Distribution format: tar.gzProgramming language: MathematicaComputer: Any computer running unix and MathematicaOperating system: UnixSupplementary material: The Development guideClassification: 4.14, 5, 16.1, 20Nature of problem: Import data from output files of scientific computing packages, such as Gaussian, into Mathematica for symbolic calculation and production of publication quality tables and plots.Solution method: Provision of mnemonic top-down parsing procedures, functional programming.Running time: The complete extraction of data from a small basis density functional calculation on the water molecule, and from a larger basis density functional calculation on the zinc hydrate ion, that ran to 33 iterations, took 1 second and 23 seconds, respectively, on a Dell Poweredge 1750.     

Gaussian quadrature rule for arbitrary weight function and interval

A program for calculating abscissas and weights of Gaussian quadrature rules for arbitrary weight functions and intervals is reported. The program is written in Mathematica. The only requirement is that the moments of the weight function can be evaluated analytically in Mathematica. The result is a FORTRAN subroutine ready to be utilized for quadrature.

Program summary

Title of program: AWGQCatalogue identifier:ADVBProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVBProgram obtained from: CPC Program Library, Queens University, Belfast, N. IrelandComputer for which the program is designed and others on which it has been tested:Computers: Pentium IV 1.7 GHz processorInstallations: 512 MB RAMOperating systems or monitors under which the program has been tested: Windows XPProgramming language used: Mathematica 4.0No. of processors used: 1Has the code been vectorized or parallelized?: NoNo. of lines in distributed program, including test data, etc.:1076No. of bytes in distributed program, including test data, etc.: 32 681Operating systems under which program has been tested: FORTRANDistribution format: tar.gzNature of physical problem: Integration of functions.Method of solution: The recurrence relations defining the orthogonal polynomials for arbitrary weight function and integration interval are written in matrix form. The abscissas and weights for the corresponding Gaussian quadrature are found from the solution of the eigenvalue equation for the tridiagonal symmetric Jacobi matrix.Restrictions on the complexity of the problem: The program is applicable if the moments of the weight function can be evaluated analytically in Mathematica. For our test example the degree of the Gaussian quadrature cannot not be larger than 96.Typical running time: The running time of the test run is about 1 [s] with a Pentium IV 1.7 GHz processor.     

Symbolic computation of hyperbolic tangent solutions for nonlinear differential-difference equations

A new algorithm is presented to find exact traveling wave solutions of differential-difference equations in terms of tanh functions. For systems with parameters, the algorithm determines the conditions on the parameters so that the equations might admit polynomial solutions in tanh. Examples illustrate the key steps of the algorithm. Through discussion and example, parallels are drawn to the tanh-method for partial differential equations. The new algorithm is implemented in Mathematica. The package DDESpecialSolutions.m can be used to automatically compute traveling wave solutions of nonlinear polynomial differential-difference equations. Use of the package, implementation issues, scope, and limitations of the software are addressed.

Program summary

Title of program: DDESpecialSolutions.mCatalogue identifier:ADUJProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUJProgram obtainable from:CPC Program Library, Queen's University of Belfast, N. IrelandDistribution format: tar.gzComputers: Created using a PC, but can be run on UNIX and Apple machinesOperating systems under which the program has been tested: Windows 2000 and Windows XPProgramming language used: Mathematica, version 3.0 or higherMemory required to execute with typical data: 9 MBNumber of processors used: 1Has the code been vectorised or parallelized?: NoNumber of lines in distributed program, including test data, etc.: 3221Number of bytes in distributed program, including test data, etc.: 23 745Nature of physical problem: The program computes exact solutions to differential-difference equations in terms of the tanh function. Such solutions describe particle vibrations in lattices, currents in electrical networks, pulses in biological chains, etc.Method of solution: After the differential-difference equation is put in a traveling frame of reference, the coefficients of a candidate polynomial solution in tanh are solved for. The resulting traveling wave solutions are tested by substitution into the original differential-difference equation.Restrictions on the complexity of the program: The system of differential-difference equations must be polynomial. Solutions are polynomial in tanh.Typical running time: The average run time of 16 cases (including the Toda, Volterra, and Ablowitz-Ladik lattices) is 0.228 seconds with a standard deviation of 0.165 seconds on a 2.4 GHz Pentium 4 with 512 MB RAM running Mathematica 4.1. The running time may vary considerably, depending on the complexity of the problem.     

AFMM: A molecular mechanics force field vibrational parametrization program

AFMM (Automated Frequency Matching Method) is a program package for molecular mechanics force field parametrization. The method used fits the molecular mechanics potential function to both vibrational frequencies and eigenvector projections derived from quantum chemical calculations. The program optimizes an initial parameter set (either pre-existing or using chemically-reasonable estimation) by iteratively changing them until the optimal fit with the reference set is obtained. By implementing a Monte Carlo-like algorithm to vary the parameters, the tedious task of manual parametrization is replaced by an efficient automated procedure. The program is best suited for optimization of small rigid molecules in a well-defined energy minimum, for which the harmonic approximation to the energy surface is appropriate for describing the intra-molecular degrees of freedom.

Program summary

Title of program: AFMMCatalogue identifier: ADUZProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUZProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandComputer: x86 PC, SGI, Sun MicrosystemsOperating system: GNU/Linux, BSD, IRIX, SolarisProgramming language used: PythonMemory required: 10 MbytesNo. of bits in a word: 32 or 64No. of processors used: 1Parallelized?: NoNo. of lines in distributed program, including test data, etc.:13 127No. of bytes in distributed program, including test data, etc.: 182 550Distribution format: tar.gzTypical running time: 24 hNature of the physical problem: Molecular mechanics force field parametrization.Method of solution:Fitting of the molecular mechanics potential to normal modes derived from quantum chemical calculations. The missing force field parameters are optimized via a merit function to obtain the optimal fit with the reference quantum mechanical set.     

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.