SUSY Les Houches Accord 2 I/O made easy

A library for reading and writing data in the SUSY Les Houches Accord 2 format is presented. The implementation is in native Fortran 77. The data are contained in a single array conveniently indexed by preprocessor statements.

Program summary

Program title: SLHA2LibCatalogue identifier: AEDY_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDY_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.: 7550No. of bytes in distributed program, including test data, etc.: 160 123Distribution format: tar.gzProgramming language: FortranComputer: For the build process, a Fortran 77 compiler in a Unixish environment (make, shell) are requiredOperating system: Linux, Mac OS, Windows (Cygwin), Tru64 UnixRAM: The SLHA Record is currently 88 944 bytes longClassification: 4.14, 11.6Nature of problem: Exchange of SUSY parameters and decay information in an ASCII file format.Solution method: The SLHA2Lib provides routines for reading and writing files in the SUSY Les Houches Accord 2 format, a common interchange format for SUSY parameters and decay data.Restrictions: The fixed-sized array that holds the SLHA2 data necessarily limits the amount of decay data that can be stored. This limit can be enlarged by editing and re-running the SLHA2.m program.Unusual features: Data are transported in a single “double complex” array in Fortran, indexed through preprocessor macros. This is about the simplest conceivable container and needs neither dynamic memory allocation nor Fortran extension like structures.Running time: Both reading and writing a SLHA file are typically in the range of a few milliseconds.     

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.     

Motion4D - A library for lightrays and timelike worldlines in the theory of relativity

The Motion4D-library solves the geodesic equation as well as the parallel- and Fermi-Walker-transport in four-dimensional Lorentzian spacetimes numerically. Initial conditions are given with respect to natural local tetrads which are adapted to the symmetries or the coordinates of the spacetime. Beside some already implemented metrics like the Schwarzschild and Kerr metric, the object oriented structure of the library permits to implement other metrics or integrators in a straight forward manner.

Program summary

Program title: Motion4D-libraryCatalogue identifier: AEEX_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEX_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.: 150 425No. of bytes in distributed program, including test data, etc.: 5 139 407Distribution format: tar.gzProgramming language: C++Computer: All platforms with a C++ compilerOperating system: Linux, Unix, WindowsRAM: 39 MBytesClassification: 1.5External routines: Gnu Scientific Library (GSL) (http://www.gnu.org/software/gsl/)Nature of problem: Solve geodesic equation, parallel and Fermi-Walker transport in four-dimensional Lorentzian spacetimes.Solution method: Integration of ordinary differential equationsRunning time: The test runs provided with the distribution require only a few seconds to run.     

Object-oriented design patterns in Fortran 90/95: mazev1, mazev2 and mazev3

This paper discusses the concept, application, and usefulness of software design patterns for scientific programming in Fortran 90/95. An example from the discipline of object-oriented design patterns, that of a game based on navigation through a maze, is used to describe how some important patterns can be implemented in Fortran 90/95 and how the progressive introduction of design patterns can usefully restructure Fortran software as it evolves. This example is complemented by a discussion of how design patterns have been used in a real-life simulation of Particle-in-Cell plasma physics. The following patterns are mentioned in this paper: Factory, Strategy, Template, Abstract Factory and Facade.

Program summary

Program title: mazev1, mazev2, mazev3Catalogue identifier: AEAI_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAI_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.: 1958No. of bytes in distributed program, including test data, etc.: 17 100Distribution format: tar.gzProgramming language: Fortran 95Computer: PC/MacOperating system: Unix/Linux/Mac (FreeBSD)/Windows (Cygwin)RAM: These are interactive programs with small (KB) memory requirementsClassification: 6.5, 20Nature of problem: A sequence of programs which demonstrate the use of object oriented design patterns for the restructuring of Fortran 90/95 software. The programs implement a simple maze game similar to that described in [1].Solution method: Restructuring uses versions of the Template, Strategy and Factory design patterns.Running time: Interactive.References:

[1] 

E. Gamma, R. Helm, R. Johnson, J. Vlissides, Design Patterns: Elements of Reusable Object Oriented Software, Addison-Wesley, 1995, ISBN 0201633612.

     

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.     

A fast algorithm for voxel-based deterministic simulation of X-ray imaging

Deterministic method based on ray tracing technique is known as a powerful alternative to the Monte Carlo approach for virtual X-ray imaging. The algorithm speed is a critical issue in the perspective of simulating hundreds of images, notably to simulate tomographic acquisition or even more, to simulate X-ray radiographic video recordings. We present an algorithm for voxel-based deterministic simulation of X-ray imaging using voxel-driven forward and backward perspective projection operations and minimum bounding rectangles (MBRs). The algorithm is fast, easy to implement, and creates high-quality simulated radiographs. As a result, simulated radiographs can typically be obtained in split seconds with a simple personal computer.

Program summary

Program title: X-rayCatalogue identifier: AEAD_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAD_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.: 416 257No. of bytes in distributed program, including test data, etc.: 6 018 263Distribution format: tar.gzProgramming language: C (Visual C++)Computer: Any PC. Tested on DELL Precision 380 based on a Pentium D 3.20 GHz processor with 3.50 GB of RAMOperating system: Windows XPClassification: 14, 21.1Nature of problem: Radiographic simulation of voxelized objects based on ray tracing technique.Solution method: The core of the simulation is a fast routine for the calculation of ray-box intersections and minimum bounding rectangles, together with voxel-driven forward and backward perspective projection operations.Restrictions: Memory constraints. There are three programs in all.

•

A. Program for test 3.1(1): Object and detector have axis-aligned orientation;

•

B. Program for test 3.1(2): Object in arbitrary orientation;

•

C. Program for test 3.2: Simulation of X-ray video recordings.

1.

Program A Memory required to execute with typical data: 207 Megabytes, depending on the size of the input file. Typical running time: 2.30 s. (Tested in release mode, the same below.)

2.

Program B (the main program) Memory required to execute with typical data: 114 Megabytes, depending on the size of the input file. Typical running time: 1.60 s.

3.

Program C Memory required to execute with typical data: 215 Megabytes, depending on the size of the input file. Typical computation time: 27.26 s for cast-5, 101.87 s for cast-6.

     

HASPRNG: Hardware Accelerated Scalable Parallel Random Number Generators

The Scalable Parallel Random Number Generators library (SPRNG) supports fast and scalable random number generation with good statistical properties for parallel computational science applications. In order to accelerate SPRNG in high performance reconfigurable computing systems, we present the Hardware Accelerated SPRNG library (HASPRNG). Ported to the Xilinx University Program (XUP) and Cray XD1 reconfigurable computing platforms, HASPRNG includes the reconfigurable logic for Field Programmable Gate Arrays (FPGAs) along with a programming interface which performs integer random number generation that produces identical results with SPRNG. This paper describes the reconfigurable logic of HASPRNG exploiting the mathematical properties and data parallelism residing in the SPRNG algorithms to produce high performance and also describes how to use the programming interface to minimize the communication overhead between FPGAs and microprocessors. The programming interface allows a user to be able to use HASPRNG the same way as SPRNG 2.0 on platforms such as the Cray XD1. We also describe how to install HASPRNG and use it. For HASPRNG usage we discuss a FPGA π-estimator for a High Performance Reconfigurable Computer (HPRC) sample application and compare to a software π-estimator. HASPRNG shows 1.7x speedup over SPRNG on the Cray XD1 and is able to obtain substantial speedup for a HPRC application.

Program summary

Program title: HASPRNGCatalogue identifier: AEER_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEER_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.: 594 928No. of bytes in distributed program, including test data, etc.: 6 509 724Distribution format: tar.gzProgramming language: VHDL (XUP and Cray XD1), C++ (XUP), C (Cray XD1)Computer: PowerPC 405 (XUP) / AMD 2.2 GHz Opteron processor (Cray XD1)Operating system: LinuxFile size: 15 MB (XUP) / 22 MB (Cray XD1)Classification: 4.13Nature of problem: Many computational science applications are able to consume large numbers of random numbers. For example, Monte Carlo simulations such as π-estimation are able to consume limitless random numbers forthe computation as long as hardware resources for the computing are supported. Moreover, parallel computational science applications require independent streams of random numbers to attain statistically significant results. The SPRNG library provides this capability, but at a significant computational cost. The library presented here accelerates the generators of independent streams of random numbers.Solution method: Multiple copies of random number generators in FPGAs allow a computational science application to consume large numbers of random numbers from independent, parallel streams. HASPRNG is a random number generators library to allow a computational science application to employ the multiple copies of random number generators to boost performance. Users can interface HASPRNG with software code executing on microprocessors and/or with hardware applications executing on FPGAs.     

TIERRAS: A package to simulate high energy cosmic ray showers underground, underwater and under-ice

In this paper we present TIERRAS, a Monte Carlo simulation program based on the well-known AIRES air shower simulations system that enables the propagation of particle cascades underground, providing a tool to study particles arriving underground from a primary cosmic ray on the atmosphere or to initiate cascades directly underground and propagate them, exiting into the atmosphere if necessary. We show several cross-checks of its results against CORSIKA, FLUKA, GEANT and ZHS simulations and we make some considerations regarding its possible use and limitations. The first results of full underground shower simulations are presented, as an example of the package capabilities.

Program summary

Program title: TIERRAS for AIRESCatalogue identifier: AEFO_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFO_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.: 36 489No. of bytes in distributed program, including test data, etc.: 3 261 669Distribution format: tar.gzProgramming language: Fortran 77 and CComputer: PC, Alpha, IBM, HP, Silicon Graphics and Sun workstationsOperating system: Linux, DEC Unix, AIX, SunOS, Unix System VRAM: 22 Mb bytesClassification: 1.1External routines: TIERRAS requires AIRES 2.8.4 to be installed on the system. AIRES 2.8.4 can be downloaded from http://www.fisica.unlp.edu.ar/auger/aires/eg_AiresDownload.html.Nature of problem: Simulation of high and ultra high energy underground particle showers.Solution method: Modification of the AIRES 2.8.4 code to accommodate underground conditions.Restrictions: In AIRES some processes that are not statistically significant on the atmosphere are not simulated. In particular, it does not include muon photonuclear processes. This imposes a limitation on the application of this package to a depth of 1 km of standard rock (or 2.5 km of water equivalent). Neutrinos are not tracked on the simulation, but their energy is taken into account in decays.Running time: A TIERRAS for AIRES run of a ¹⁰²⁰ eV shower with statistical sampling (thinning) below ¹⁰¹² eV and 0.2 weight factor (see [1]) uses approximately 1 h of CPU time on an Intel Core 2 Quad Q6600 at 2.4 GHz. It uses only one core, so 4 simultaneous simulations can be run on this computer. Aires includes a spooling system to run several simultaneous jobs of any type.References:

[1]

S. Sciutto, AIRES 2.6 User Manual, http://www.fisica.unlp.edu.ar/auger/aires/.

     

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.     

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.     

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.     

Fitting sparse multidimensional data with low-dimensional terms

An algorithm that fits a continuous function to sparse multidimensional data is presented. The algorithm uses a representation in terms of lower-dimensional component functions of coordinates defined in an automated way and also permits dimensionality reduction. Neural networks are used to construct the component functions.

Program summary

Program title: RS_HDMR_NNCatalogue identifier: AEEI_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEI_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.: 19 566No. of bytes in distributed program, including test data, etc.: 327 856Distribution format: tar.gzProgramming language: MatLab R2007bComputer: any computer running MatLabOperating system: Windows XP, Windows Vista, UNIX, LinuxClassification: 4.9External routines: Neural Network Toolbox Version 5.1 (R2007b)Nature of problem: Fitting a smooth, easily integratable and differentiatable, function to a very sparse (∼2-3 points per dimension) multidimensional (D?6) large (∼¹⁰⁴-¹⁰⁵ data) dataset.Solution method: A multivariate function is represented as a sum of a small number of terms each of which is a low-dimensional function of optimised coordinates. The optimal coordinates reduce both the dimensionality and the number of the terms. Neural networks (including exponential neurons) are used to obtain a general and robust method and a functional form which is easily differentiated and integrated (in the case of exponential neurons).Running time: Depends strongly on the dataset to be modelled and the chosen structure of the approximating function, ranges from about a minute for ∼¹⁰³ data in 3-D to about a day for ∼¹⁰⁵ data in 15-D.     

PArthENoPE: Public algorithm evaluating the nucleosynthesis of primordial elements

We describe a program for computing the abundances of light elements produced during Big Bang Nucleosynthesis which is publicly available at http://parthenope.na.infn.it/. Starting from nuclear statistical equilibrium conditions the program solves the set of coupled ordinary differential equations, follows the departure from chemical equilibrium of nuclear species, and determines their asymptotic abundances as function of several input cosmological parameters as the baryon density, the number of effective neutrino, the value of cosmological constant and the neutrino chemical potential. The program requires commercial NAG library routines.

Program summary

Program title: PArthENoPECatalogue identifier: AEAV_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAV_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.: 10 033No. of bytes in distributed program, including test data, etc.: 46 002Distribution format: tar.gzProgramming language: Fortran 77Computer: PC-compatible running Fortran on Unix, MS Windows or LinuxOperating system: Windows 2000, Windows XP, LinuxClassification: 1.2, 1.9, 17.8External routines: NAG LibrariesNature of problem: Computation of yields of light elements synthesized in the primordial universe.Solution method: BDF method for the integration of the ODEs, implemented in a NAG routine.Running time: 90 sec with default parameters on a Dual Xeon Processor 2.4 GHz with 2 GB RAM.     

A cascadic monotonic time-discretized algorithm for finite-level quantum control computation

A computer package (CNMS) is presented aimed at the solution of finite-level quantum optimal control problems. This package is based on a recently developed computational strategy known as monotonic schemes.Quantum optimal control problems arise in particular in quantum optics where the optimization of a control representing laser pulses is required. The purpose of the external control field is to channel the system's wavefunction between given states in its most efficient way. Physically motivated constraints, such as limited laser resources, are accommodated through appropriately chosen cost functionals.

Program summary

Program title: CNMSCatalogue identifier: ADEB_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADEB_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.: 770No. of bytes in distributed program, including test data, etc.: 7098Distribution format: tar.gzProgramming language: MATLAB 6Computer: AMD Athlon 64 × 2 Dual, 2:21 GHz, 1:5 GB RAMOperating system: Microsoft Windows XPWord size: 32Classification: 4.9Nature of problem: Quantum controlSolution method: IterativeRunning time: 60-600 sec     

LIBERI: Library for numerical evaluation of electron-repulsion integrals

We provide a C library, called LIBERI, for numerical evaluation of four-center electron repulsion integrals, based on successive reduction of integral dimension by using Fourier transforms. LIBERI enables us to compute the integrals for numerically defined basis functions within ¹⁰−5 Hartree accuracy as well as their derivatives with respect to the atomic nuclear positions. Damping of the Coulomb interaction can also be imposed to take account of screening effect.

Program summary

Program title: LIBERICatalogue identifier: AEGG_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGG_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.: 44 091No. of bytes in distributed program, including test data, etc.: 1 692 085Distribution format: tar.gzProgramming language: CComputer: allOperating system: any Unix-like systemRAM: 5-10 MbClassification: 7.4External routines: Lapack (http://www.netlib.org/lapack/), Blas (http://www.netlib.org/blas/), FFTW3 (http://www.fftw.org/)Nature of problem: Numerical evaluation of four-center electron-repulsion integrals.Solution method: Four-center electron-repulsion integrals are computed for given basis function set, based on successive reduction of integral dimension using Fourier transform.Running time: 0.5 sec for the demo program supplied with the package.     

Visual tool for estimating the fractal dimension of images

This work presents a new Visual Basic 6.0 application for estimating the fractal dimension of images, based on an optimized version of the box-counting algorithm. Following the attempt to separate the real information from “noise”, we considered also the family of all band-pass filters with the same band-width (specified as parameter). The fractal dimension can be thus represented as a function of the pixel color code. The program was used for the study of paintings cracks, as an additional tool which can help the critic to decide if an artistic work is original or not.

Program summary

Program title: Fractal Analysis v01Catalogue identifier: AEEG_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEG_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.: 29 690No. of bytes in distributed program, including test data, etc.: 4 967 319Distribution format: tar.gzProgramming language: MS Visual Basic 6.0Computer: PCOperating system: MS Windows 98 or laterRAM: 30MClassification: 14Nature of problem: Estimating the fractal dimension of images.Solution method: Optimized implementation of the box-counting algorithm. Use of a band-pass filter for separating the real information from “noise”. User friendly graphical interface.Restrictions: Although various file-types can be used, the application was mainly conceived for the 8-bit grayscale, windows bitmap file format.Running time: In a first approximation, the algorithm is linear.     

REACH: A program for coarse-grained biomolecular simulation

REACH (Realistic Extension Algorithm viaCovariance Hessian) is a program package for residue-scale coarse-grained biomolecular simulation. The program calculates the force constants of a residue-scale elastic network model in single-domain proteins using the variance-covariance matrix obtained from atomistic molecular dynamics simulation. Secondary-structure dependence of the force constants is integrated. The method involves self-consistent, direct mapping of atomistic simulation results onto a coarse-grained force field in an efficient automated procedure without requiring iterative fits and avoiding system dependence.

Program summary

Program title: REACHCatalogue identifier: AEDA_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDA_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.: 42 244No. of bytes in distributed program, including test data, etc.: 3 682 118Distribution format: tar.gzProgramming language: FORTRAN 77Computer: x86 PCOperating system: GNU/Linux, SUSE and Red HatRAM: Depends on the system size to be calculatedWord size: 32 or 64 bitsClassification: 3External routines: LAPACK, BLASNature of problem: A direct calculation of force field for residue-scale coarse-grained biomolecular simulation derived from atomistic molecular dynamics trajectory.Solution method: A variance-covariance matrix and the associated Hessian (second-derivative) matrix are calculated from an atomistic molecular dynamics trajectory of single-domain protein internal motion and the off-diagonal Hessian matrix is fitted to that of a residue-scale elastic network model. The resulting force constants for the residue pair interactions are expressed as model functions as a function of pairwise distance.Running time: Depends on the system size and the number of MD trajectory frames used. The test run provided with the distribution takes only a few seconds to execute.     

A program for performing exact quantum dynamics calculations using cylindrical polar coordinates: A nanotube application

A program that uses the time-dependent wavepacket method to study the motion of structureless particles in a force field of quasi-cylindrical symmetry is presented here. The program utilises cylindrical polar coordinates to express the wavepacket, which is subsequently propagated using a Chebyshev expansion of the Schrödinger propagator. Time-dependent exit flux as well as energy-dependent S matrix elements can be obtained for all states of the particle (describing its angular momentum component along the nanotube axis and the excitation of the radial degree of freedom in the cylinder). The program has been used to study the motion of an H atom across a carbon nanotube.

Program summary

Program title: CYLWAVECatalogue identifier: AECL_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECL_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.: 3673No. of bytes in distributed program, including test data, etc.: 35 237Distribution format: tar.gzProgramming language: Fortran 77Computer: RISC workstationsOperating system: UNIXRAM: 120 MBytesClassification: 16.7, 16.10External routines: SUNSOFT performance library (not essential) TFFT2D.F (Temperton Fast Fourier Transform), BESSJ.F (from Numerical Recipes, for the calculation of Bessel functions) (included in the distribution file).Nature of problem: Time evolution of the state of a structureless particle in a quasicylindrical potential.Solution method: Time dependent wavepacket propagation.Running time: 50000 secs. The test run supplied with the distribution takes about 10 minutes to complete.     

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.