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.     

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.     

HFOLD - A program package for calculating two-body MSSM Higgs decays at full one-loop level

HFOLD (Higgs Full One Loop Decays) is a Fortran program package for calculating all MSSM Higgs two-body decay widths and the corresponding branching ratios at full one-loop level. The package is done in the SUSY Parameter Analysis convention and supports the SUSY Les Houches Accord input and output format.

Program summary

Program title: HFOLDCatalogue identifier: AEJG_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJG_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.: 340 621No. of bytes in distributed program, including test data, etc.: 1 760 051Distribution format: tar.gzProgramming language: Fortran 77Computer: Workstation, PCOperating system: LinuxRAM: 524 288 000 BytesClassification: 11.1External routines: LoopTools 2.2 (http://www.feynarts.de/looptools/), SLHALib 2.2 (http://www.feynarts.de/slha/). The LoopTools code is included in the distribution package.Nature of problem: A future high-energy e⁺e⁻ linear collider will be the best environment for the precise measurements of masses, cross sections, branching ratios, etc. Experimental accuracies are expected at the per-cent down to the per-mile level. These must be matched from the theoretical side. Therefore higher order calculations are mandatory.Solution method: This program package calculates all MSSM Higgs two-body decay widths and the corresponding branching ratios at full one-loop level. The renormalization is done in the DR scheme following the SUSY Parameter Analysis convention. The program supports the SUSY Les Houches Accord input and output format.Running time: The example provided takes only a few seconds to run.     

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     

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.     

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.     

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.

     

QUBIT4MATLAB V3.0: A program package for quantum information science and quantum optics for MATLAB

A program package for MATLAB is introduced that helps calculations in quantum information science and quantum optics. It has commands for the following operations: (i) Reordering the qudits of a quantum register, computing the reduced state of a quantum register. (ii) Defining important quantum states easily. (iii) Formatted input and output for quantum states and operators. (iv) Constructing operators acting on given qudits of a quantum register and constructing spin chain Hamiltonians. (v) Partial transposition, matrix realignment and other operations related to the detection of quantum entanglement. (vi) Generating random state vectors, random density matrices and random unitaries.

Program summary

Program title:QUBIT4MATLAB V3.0Catalogue identifier:AEAZ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAZ_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.:5683No. of bytes in distributed program, including test data, etc.: 37 061Distribution format:tar.gzProgramming language:MATLAB 6.5; runs also on OctaveComputer:Any which supports MATLAB 6.5Operating system:Any which supports MATLAB 6.5; e.g., Microsoft Windows XP, LinuxClassification:4.15Nature of problem: Subroutines helping calculations in quantum information science and quantum optics.Solution method: A program package, that is, a set of commands is provided for MATLAB. One can use these commands interactively or they can also be used within a program.Running time:10 seconds-1 minute     

FracMAP: A user-interactive package for performing simulation and orientation-specific morphology analysis of fractal-like solid nano-agglomerates

Computer simulation techniques have found extensive use in establishing empirical relationships between three-dimensional (3d) and two-dimensional (2d) projected properties of particles produced by the process of growth through the agglomeration of smaller particles (monomers). In this paper, we describe a package, FracMAP, that has been written to simulate 3d quasi-fractal agglomerates and create their 2d pixelated projection images by restricting them to stable orientations as commonly encountered for quasi-fractal agglomerates collected on filter media for electron microscopy. Resulting 2d images are analyzed for their projected morphological properties.

Program summary

Program title: FracMAPCatalogue identifier: AEDD_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDD_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.: 4722No. of bytes in distributed program, including test data, etc.: 27 229Distribution format: tar.gzProgramming language: C++Computer: PCOperating system: Windows, LinuxRAM: 2.0 MegabytesClassification: 7.7Nature of problem: Solving for a suitable fractal agglomerate construction under constraints of typical morphological parameters.Solution method: Monte Carlo approximation.Restrictions: Problem complexity is not representative of run-time, since Monte Carlo iterations are of a constant complexity.Additional comments: The distribution file contains two versions of the FracMAP code, one for Windows and one for Linux.Running time: 1 hour for a fractal agglomerate of size 25 on a single processor.     

Gauss-Legendre and Chebyshev quadratures for singular integrals

Exact expressions are presented for efficient computation of the weights in Gauss-Legendre and Chebyshev quadratures for selected singular integrands. The singularities may be of Cauchy type, logarithmic type or algebraic-logarithmic end-point branching points. We provide Fortran 90 routines for computing the weights for both the Gauss-Legendre and the Chebyshev (Fejér-1) meshes whose size can be set by the user.

New program summary

Program title: SINGQUADCatalogue identifier: AEBR_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBR_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.: 4128No. of bytes in distributed program, including test data, etc.: 25 815Distribution format: tar.gzProgramming language: Fortran 90Computer: Any with a Fortran 90 compilerOperating system: Linux, Windows, MacRAM: Depending on the complexity of the problemClassification: 4.11Nature of problem: Program provides Gauss-Legendre and Chebyshev (Fejér-1) weights for various singular integrands.Solution method: The weights are obtained from the condition that the quadrature of order N must be exact for a polynomial of degree?(N−1). The weights are expressed as moments of the singular kernels associated with Legendre or Chebyshev polynomials. These moments are obtained in analytic form amenable for computation.Additional comments: If the NAGWare f95 compiler is used, the option, “-kind = byte”, must be included in the compile command lines of the Makefile.Running time: The test run supplied with the distribution takes a couple of seconds to execute.     

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.     

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.     

PETAG01: A program for the direct simulation of a pellet target

We describe a numerical model of an internal pellet target to study the beam dynamics in storage rings, where the nuclear experiments with such type of target are planned. In this model the Monte Carlo algorithm is applied to evaluate the particle coordinates and momentum deviation depending on time and parameters of the target. One has to mention that due to statistical character of the pellet distribution in the target the analytical techniques are not applicable. This is also true for the particle distribution in the stored beam, which is influenced by various effects (such as a cooling process, intra-beam scattering, betatron oscillation, space charge effect). In this case only the Monte Carlo technique to model energy straggling in combination with the pellet distribution in the target should be considered.

Program summary

Program title: PETAG01Catalogue identifier: ADZV_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZV_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.: 1068No. of bytes in distributed program, including test data, etc.: 11 314Distribution format: tar.gzProgramming language: Fortran 77, C/C++Computer: Platform independentOperating system: MS Windows 95/2000/XP, Linux (Unix)RAM: 128 MBClassification: 11.10Nature of problem: Particle beam dynamics with use of the pellet target.Solution method: Monte Carlo with analytical approximation.Running time: dozens of seconds     

Monte Carlo event generator for black hole production and decay in proton-proton collisions - QBH version 1.02

We describe the Monte Carlo event generator for black hole production and decay in proton-proton collisions - QBH version 1.02. The generator implements a model for quantum black hole production and decay based on the conservation of local gauge symmetries and democratic decays. The code in written entirely in C++ and interfaces to the PYTHIA 8 Monte Carlo code for fragmentation and decays.

Program summary

Program title: QBHCatalogue identifier: AEGU_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGU_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 048No. of bytes in distributed program, including test data, etc.: 118 420Distribution format: tar.gzProgramming language: C++Computer: x86Operating system: Scientific Linux, Mac OS XRAM: 1 GBClassification: 11.6External routines: PYTHIA 8130 (http://home.thep.lu.se/~torbjorn/pythiaaux/present.html) and LHAPDF (http://projects.hepforge.org/lhapdf/)Nature of problem: Simulate black hole production and decay in proton-proton collision.Solution method: Monte Carlo simulation using importance sampling.Running time: Eight events per second.     

JuNoLo - Jülich nonlocal code for parallel post-processing evaluation of vdW-DF correlation energy

Nowadays the state of the art Density Functional Theory (DFT) codes are based on local (LDA) or semilocal (GGA) energy functionals. Recently the theory of a truly nonlocal energy functional has been developed. It has been used mostly as a post-DFT calculation approach, i.e. by applying the functional to the charge density calculated using any standard DFT code, thus obtaining a new improved value for the total energy of the system. Nonlocal calculation is computationally quite expensive and scales as N² where N is the number of points in which the density is defined, and a massively parallel calculation is welcome for a wider applicability of the new approach. In this article we present a code which accomplishes this goal.

Program summary

Program title: JuNoLoCatalogue identifier: AEFM_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFM_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 980No. of bytes in distributed program, including test data, etc.: 2 126 072Distribution format: tar.gzProgramming language: Fortran 90Computer: any architecture with a Fortran 90 compilerOperating system: Linux, AIXHas the code been vectorised or parallelized?: Yes, from 1 to 65536 processors may be used.RAM: depends strongly on the problem's size.Classification: 7.3External routines:• FFTW (http://www.tw.org/)• MPI (http://www.mcs.anl.gov/research/projects/mpich2/ or http://www.lam-mpi.org/)Nature of problem: Obtaining the value of the nonlocal vdW-DF energy based on the charge density distribution obtained from some Density Functional Theory code.Solution method: Numerical calculation of the double sum is implemented in a parallel F90 code. Calculation of this sum yields the required nonlocal vdW-DF energy.Unusual features: Binds to virtually any DFT program.Additional comments: Excellent parallelization features.Running time: Depends strongly on the size of the problem and the number of CPUs used.     

Generating relativistic pseudo-potentials with explicit incorporation of semi-core states using APE, the Atomic Pseudo-potentials Engine

We present a computer package designed to generate and test norm-conserving pseudo-potentials within Density Functional Theory. The generated pseudo-potentials can be either non-relativistic, scalar relativistic or fully relativistic and can explicitly include semi-core states. A wide range of exchange-correlation functionals is included.

Program summary

Program title: Atomic Pseudo-potentials Engine (APE)Catalogue identifier: AEAC_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAC_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.: 88 287No. of bytes in distributed program, including test data, etc.: 649 959Distribution format: tar.gzProgramming language: Fortran 90, CComputer: any computer architecture, running any flavor of UNIXOperating system: GNU/LinuxRAM: <5 MbClassification: 7.3External routines: GSL (http://www.gnu.org/software/gsl/)Nature of problem: Determination of atomic eigenvalues and wave-functions using relativistic and nonrelativistic Density-Functional Theory. Construction of pseudo-potentials for use in ab-initio simulations.Solution method: Grid-based integration of the Kohn-Sham equations.Restrictions: Relativistic spin-polarized calculations are not possible. The set of exchange-correlation functionals implemented in the code does not include orbital-dependent functionals.Unusual features: The program creates pseudo-potential files suitable for the most widely used ab-initio packages and, besides the standard non-relativistic Hamann and Troullier-Martins potentials, it can generate pseudo-potentials using the relativistic and semi-core extensions to the Troullier-Martins scheme. APE also has a very sophisticated and user-friendly input system.Running time: The example given in this paper (Si) takes 10 s to run on a Pentium IV machine clocked at 2 GHz.     

HRMC: Hybrid Reverse Monte Carlo method with silicon and carbon potentials

Fortran 77 code is presented for a hybrid method of the Metropolis Monte Carlo (MMC) and Reverse Monte Carlo (RMC) for the simulation of amorphous silicon and carbon structures. In additional to the usual constraints of the pair correlation functions and average coordination, the code also incorporates an optional energy constraint. This energy constraint is in the form of either the Environment Dependent Interatomic Potential (applicable to silicon and carbon) and the original and modified Stillinger-Weber potentials (applicable to silicon). The code also allows porous systems to be modeled via a constraint on porosity and internal surface area using a novel restriction on the available simulation volume.

Program summary

Program title: HRMC version 1.0Catalogue identifier: AEAO_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAO_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.: 200 894No. of bytes in distributed program, including test data, etc.: 907 557Distribution format: tar.gzProgramming language: FORTRAN 77Computer: Any computer capable of running executables produced by the g77 Fortran compilerOperating system: Unix, WindowsRAM: Depends on the type of empirical potential use, number of atoms and which constraints are employedClassification: 7.7Nature of problem: Atomic modeling using empirical potentials and experimental dataSolution method: Monte CarloAdditional comments: The code is not standard FORTRAN 77 but includes some additional features and therefore generates errors when compiled using the Nag95 compiler. It does compile successfully with the GNU g77 compiler (http://www.gnu.org/software/fortran/fortran.html).Running time: Depends on the type of empirical potential use, number of atoms and which constraints are employed. The test included in the distribution took 37 minutes on a DEC Alpha PC.     

Scilab software package for the study of dynamical systems

This work presents a new software package for the study of chaotic flows and maps. The codes were written using Scilab, a software package for numerical computations providing a powerful open computing environment for engineering and scientific applications. It was found that Scilab provides various functions for ordinary differential equation solving, Fast Fourier Transform, autocorrelation, and excellent 2D and 3D graphical capabilities. The chaotic behaviors of the nonlinear dynamics systems were analyzed using phase-space maps, autocorrelation functions, power spectra, Lyapunov exponents and Kolmogorov-Sinai entropy. Various well known examples are implemented, with the capability of the users inserting their own ODE.

Program summary

Program title: ChaosCatalogue identifier: AEAP_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAP_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.: 885No. of bytes in distributed program, including test data, etc.: 5925Distribution format: tar.gzProgramming language: Scilab 3.1.1Computer: PC-compatible running Scilab on MS Windows or LinuxOperating system: Windows XP, LinuxRAM: below 100 MegabytesClassification: 6.2Nature of problem: Any physical model containing linear or nonlinear ordinary differential equations (ODE).Solution method: Numerical solving of ordinary differential equations. The chaotic behavior of the nonlinear dynamical system is analyzed using Poincaré sections, phase-space maps, autocorrelation functions, power spectra, Lyapunov exponents and Kolmogorov-Sinai entropies.Restrictions: The package routines are normally able to handle ODE systems of high orders (up to order twelve and possibly higher), depending on the nature of the problem.Running time: 10 to 20 seconds for problems that do not involve Lyapunov exponents calculation; 60 to 1000 seconds for problems that involve high orders ODE and Lyapunov exponents calculation.     

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.