GeodesicViewer - A tool for exploring geodesics in the theory of relativity

The GeodesicViewer realizes exocentric two- and three-dimensional illustrations of lightlike and timelike geodesics in the general theory of relativity. By means of an intuitive graphical user interface, all parameters of a spacetime as well as the initial conditions of the geodesics can be modified interactively. This makes the GeodesicViewer a useful instrument for the exploration of geodesics in four-dimensional Lorentzian spacetimes.

Program summary

Program title: GeodesicViewerCatalogue identifier: AEFP_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFP_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.: 168 868No. of bytes in distributed program, including test data, etc.: 6 076 202Distribution format: tar.gzProgramming language: C++, Qt, Qwt, OpenGLComputer: All platforms with a C++ compiler, Qt, Qwt, OpenGLOperating system: Linux, Mac OS XRAM: 24 MbytesClassification: 1.5External routines:

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Gnu Scientific Library (GSL) (http://www.gnu.org/software/gsl/)

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Motion4D (included in the package). The Motion4D library can also be downloaded from CPC. Catalogue identifier: AEEX

•

Qt (http://qt.nokia.com/downloads)

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Qwt (http://qwt.sourceforge.net/)

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OpenGL (http://www.opengl.org/)

Nature of problem: Illustrate geodesics in four-dimensional Lorentzian spacetimes.Solution method: Integration of ordinary differential equations. 3D-Rendering via OpenGL.Running time: Interactive. The examples given take milliseconds.     

A Maple package for verifying ultradiscrete soliton solutions

We present a computer algebra program for verifying soliton solutions of ultradiscrete equations in which both dependent and independent variables take discrete values. The package is applicable to equations and solutions that include the max function. The program is implemented using Maple software.

Program summary

Program title: UltdeCatalogue identifier: AEDB_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDB_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.: 3171No. of bytes in distributed program, including test data, etc.: 13 633Distribution format: tar.gzProgramming language: Maple 10Computer: PC/AT compatible machineOperating system: Windows 2000, Windows XPRAM: Depends on the problem; minimum about 1 GBWord size: 32 bitsClassification: 5Nature of problem: The existence of multi-soliton solutions strongly suggest the integrability of nonlinear evolution equations. However enormous calculation is required to verify multi-soliton solutions of ultradiscrete equations. The use of computer algebra can be helpful in such calculations.Solution method: Simplification by using the properties of max-plus algebra.Restrictions: The program can only handle single ultradiscrete equations.Running time: Depends on the complexity of the equation and solution. For the examples included in the distribution the run times are as follows. (Core 2 Duo 3 GHz, Windows XP)

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Example 1: 2725 sec.

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Example 2: 33 sec.

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Example 3: 1 sec.

     

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.

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

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

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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.

     

Markovian Monte Carlo program EvolFMC v.2 for solving QCD evolution equations

We present the program EvolFMC v.2 that solves the evolution equations in QCD for the parton momentum distributions by means of the Monte Carlo technique based on the Markovian process. The program solves the DGLAP-type evolution as well as modified-DGLAP ones. In both cases the evolution can be performed in the LO or NLO approximation. The quarks are treated as massless. The overall technical precision of the code has been established at 5×¹⁰−4. This way, for the first time ever, we demonstrate that with the Monte Carlo method one can solve the evolution equations with precision comparable to the other numerical methods.

New version program summary

Program title: EvolFMC v.2Catalogue identifier: AEFN_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFN_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 binary test data, etc.: 66 456 (7407 lines of C++ code)No. of bytes in distributed program, including test data, etc.: 412 752Distribution format: tar.gzProgramming language: C++Computer: PC, MacOperating system: Linux, Mac OS XRAM: Less than 256 MBClassification: 11.5External routines: ROOT (http://root.cern.ch/drupal/)Nature of problem: Solution of the QCD evolution equations for the parton momentum distributions of the DGLAP- and modified-DGLAP-type in the LO and NLO approximations.Solution method: Monte Carlo simulation of the Markovian process of a multiple emission of partons.Restrictions:

1.

Limited to the case of massless partons.

2.

Implemented in the LO and NLO approximations only.

3.

Weighted events only.

Unusual features: Modified-DGLAP evolutions included up to the NLO level.Additional comments: Technical precision established at 5×¹⁰−4.Running time: For the 10⁶ events at 100 GeV: DGLAP NLO: 27s; C^′-type modified DGLAP NLO: 150s (MacBook Pro with Mac OS X v.10.5.5, 2.4 GHz Intel Core 2 Duo, gcc 4.2.4, single thread).     

A new version of Scilab software package for the study of dynamical systems

This work presents a new version of a software package for the study of chaotic flows, maps and fractals [1]. 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 or iterative equations.

New version program summary

Program title: Chaos v2.0Catalogue identifier: AEAP_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAP_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.: 1275No. of bytes in distributed program, including test data, etc.: 7135Distribution format: tar.gzProgramming language: Scilab 5.1.1. Scilab 5.1.1 should be installed before running the program. Information about the installation can be found at http://wiki.scilab.org/howto/install/windows.Computer: PC-compatible running Scilab on MS Windows or LinuxOperating system: Windows XP, LinuxRAM: below 150 MegabytesClassification: 6.2Catalogue identifier of previous version: AEAP_v1_0Journal reference of previous version: Comput. Phys. Comm. 178 (2008) 788Does the new version supersede the previous version?: YesNature of problem: Any physical model containing linear or nonlinear ordinary differential equations (ODE).Solution method:

1.

Numerical solving of ordinary differential equations for the study of chaotic flows. The chaotic behavior of the nonlinear dynamical system is analyzed using Poincare sections, phase-space maps, autocorrelation functions, power spectra, Lyapunov exponents and Kolmogorov-Sinai entropies.

2.

Numerical solving of iterative equations for the study of maps and fractals.

Reasons for new version: The program has been updated to use the new version 5.1.1 of Scilab with new graphical capabilities [2]. Moreover, new use cases have been added which make the handling of the program easier and more efficient.Summary of revisions:

1.

A new use case concerning coupled predator-prey models has been added [3].

2.

Three new use cases concerning fractals (Sierpinsky gasket, Barnsley's Fern and Tree) have been added [3].

3.

The graphical user interface (GUI) of the program has been reconstructed to include the new use cases.

4.

The program has been updated to use Scilab 5.1.1 with the new graphical capabilities.

Additional comments: The program package contains 12 subprograms.

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interface.sce - the graphical user interface (GUI) that permits the choice of a routine as follows

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1.sci - Lorenz dynamical system

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2.sci - Chua dynamical system

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3.sci - Rosler dynamical system

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4.sci - Henon map

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5.sci - Lyapunov exponents for Lorenz dynamical system

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6.sci - Lyapunov exponent for the logistic map

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7.sci - Shannon entropy for the logistic map

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8.sci - Coupled predator-prey model

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1f.sci - Sierpinsky gasket

•

2f.sci - Barnsley's Fern

•

3f.sci - Barnsley's Tree

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, Lyapunov exponents calculation and fractals.References:

[1]

C.C. Bordeianu, C. Besliu, Al. Jipa, D. Felea, I. V. Grossu, Comput. Phys. Comm. 178 (2008) 788.

[2]

S. Campbell, J.P. Chancelier, R. Nikoukhah, Modeling and Simulation in Scilab/Scicos, Springer, 2006.

[3]

R.H. Landau, M.J. Paez, C.C. Bordeianu, A Survey of Computational Physics, Introductory Computational Science, Princeton University Press, 2008.

     

AutoDipole - Automated generation of dipole subtraction terms -

We present an automated generation of the subtraction terms for next-to-leading order QCD calculations in the Catani-Seymour dipole formalism. For a given scattering process with n external particles our Mathematica package generates all dipole terms, allowing for both massless and massive dipoles. The numerical evaluation of the subtraction terms proceeds with MadGraph, which provides Fortran code for the necessary scattering amplitudes. Checks of the numerical stability are discussed.

Program summary

Program title: AutoDipoleCatalogue identifier: AEGO_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGO_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.: 138 042No. of bytes in distributed program, including test data, etc.: 1 117 665Distribution format: tar.gzProgramming language: Mathematica and FortranComputer: Computers running Mathematica (version 7.0)Operating system: The package should work on every Linux system supported by Mathematica. Detailed tests have been performed on Scientific Linux as supported by DESY and CERN and on openSUSE and Debian.RAM: Depending on the complexity of the problem, recommended at least 128 MB RAMClassification: 11.5External routines: MadGraph (including HELAS library) available under http://madgraph.hep.uiuc.edu/ or http://madgraph.phys.ucl.ac.be/ or http://madgraph.roma2.infn.it/. A copy of the tar file, MG_ME_SA_V4.4.30, is included in the AutoDipole distribution package.Nature of problem: Computation of next-to-leading order QCD corrections to scattering cross sections, regularization of real emission contributions.Solution method: Catani-Seymour subtraction method for massless and massive partons [1,2]; Numerical evaluation of subtracted matrix elements interfaced to MadGraph [3-5] (stand-alone version) using helicity amplitudes and the HELAS library [6,7] (contained in MadGraph).Restrictions: Limitations of MadGraph are inherited.Running time: Dependent on the complexity of the problem with typical run times of the order of minutes.References:

[1]

S. Catani, M.H. Seymour, Nuclear Phys. B 485 (1997) 291, hep-ph/9605323.

[2]

S. Catani, et al., Nuclear Phys. B 627 (2002) 189, hep-ph/0201036.

[3]

T. Stelzer, W.F. Long, Comput. Phys. Comm. 81 (1994) 357, hep-ph/9401258.

[4]

F. Maltoni, T. Stelzer, JHEP 0302 (2003) 027, hep-ph/0208156.

[5]

J. Alwall, et al., JHEP 0709 (2007) 028, arXiv:0706.2334 [hep-ph].

[6]

K. Hagiwara, H. Murayama, I. Watanabe, Nuclear Phys. B 367 (1991) 257.

[7]

H. Murayama, I. Watanabe, K. Hagiwara, KEK-91-11.

     

yambo: An ab initio tool for excited state calculations

yambo is an ab initio code for calculating quasiparticle energies and optical properties of electronic systems within the framework of many-body perturbation theory and time-dependent density functional theory. Quasiparticle energies are calculated within the GW approximation for the self-energy. Optical properties are evaluated either by solving the Bethe-Salpeter equation or by using the adiabatic local density approximation. yambo is a plane-wave code that, although particularly suited for calculations of periodic bulk systems, has been applied to a large variety of physical systems. yambo relies on efficient numerical techniques devised to treat systems with reduced dimensionality, or with a large number of degrees of freedom. The code has a user-friendly command-line based interface, flexible I/O procedures and is interfaced to several publicly available density functional ground-state codes.

Program summary

Program title:yamboCatalogue identifier: AEDH_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDH_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: GNU General Public Licence v2.0No. of lines in distributed program, including test data, etc.: 149 265No. of bytes in distributed program, including test data, etc.: 2 848 169Distribution format: tar.gzProgramming language: Fortran 95, CComputer: any computer architecture, running any flavor of UNIXOperating system: GNU/Linux, AIX, Irix, OS/XHas the code been vectorised or parallelized?: YesRAM: 10-1000 MbytesClassification: 7.3, 4.4, 7.2External routines:

•

BLAS (http://www.netlib.org/blas/)

•

LAPACK (http://www.netlib.org/lapack/)

•

MPI (http://www-unix.mcs.anl.gov/mpi/) is optional.

•

BLACS (http://www.netlib.org/scalapack/) is optional.

•

SCALAPACK (http://www.netlib.org/scalapack/) is optional.

•

FFTW (http://www.fftw.org/) is optional.

•

netCDF (http://www.unidata.ucar.edu/software/netcdf/) is optional.

Nature of problem: Calculation of excited state properties (quasiparticles, excitons, plasmons) from first principles.Solution method: Many body perturbation theory (Dyson equation, Bethe Salpeter equation) and time-dependent density functional theory. Quasiparticle approximation. Plasmon-pole model for the dielectric screening. Plane wave basis set with norm conserving pseudopotentials.Unusual features: During execution, yambo supplies estimates of the elapsed and remaining time for completion of each runlevel. Very friendly shell-based user-interface.Additional comments:yambo was known as “SELF” prior to GPL release. It belongs to the suite of codes maintained and used by the European Theoretical Spectroscopy Facility (ETSF) [1].Running time: The typical yambo running time can range from a few minutes to some days depending on the chosen level of approximation, and on the property and physical system under study.References:[1] The European Theoretical Spectroscopy Facility, http://www.etsf.eu.     

JADAMILU: a software code for computing selected eigenvalues of large sparse symmetric matrices

A new software code for computing selected eigenvalues and associated eigenvectors of a real symmetric matrix is described. The eigenvalues are either the smallest or those closest to some specified target, which may be in the interior of the spectrum. The underlying algorithm combines the Jacobi-Davidson method with efficient multilevel incomplete LU (ILU) preconditioning. Key features are modest memory requirements and robust convergence to accurate solutions. Parameters needed for incomplete LU preconditioning are automatically computed and may be updated at run time depending on the convergence pattern. The software is easy to use by non-experts and its top level routines are written in FORTRAN 77. Its potentialities are demonstrated on a few applications taken from computational physics.

Program summary

Program title: JADAMILUCatalogue identifier: ADZT_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZT_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.: 101 359No. of bytes in distributed program, including test data, etc.: 7 493 144Distribution format: tar.gzProgramming language: Fortran 77Computer: Intel or AMD with g77 and pgf; Intel EM64T or Itanium with ifort; AMD Opteron with g77, pgf and ifort; Power (IBM) with xlf90.Operating system: Linux, AIXRAM: problem dependentWord size: real:8; integer: 4 or 8, according to user's choiceClassification: 4.8Nature of problem: Any physical problem requiring the computation of a few eigenvalues of a symmetric matrix.Solution method: Jacobi-Davidson combined with multilevel ILU preconditioning.Additional comments: We supply binaries rather than source code because JADAMILU uses the following external packages:

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MC64. This software is copyrighted software and not freely available. COPYRIGHT (c) 1999 Council for the Central Laboratory of the Research Councils.

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AMD. Copyright (c) 2004-2006 by Timothy A. Davis, Patrick R. Amestoy, and Iain S. Duff. All Rights Reserved. Source code is distributed by the authors under the GNU LGPL licence.

•

BLAS. The reference BLAS is a freely-available software package. It is available from netlib via anonymous ftp and the World Wide Web.

•

LAPACK. The complete LAPACK package or individual routines from LAPACK are freely available on netlib and can be obtained via the World Wide Web or anonymous ftp.

•

For maximal benefit to the community, we added the sources we are proprietary of to the tar.gz file submitted for inclusion in the CPC library. However, as explained in the README file, users willing to compile the code instead of using binaries should first obtain the sources for the external packages mentioned above (email and/or web addresses are provided).

Running time: Problem dependent; the test examples provided with the code only take a few seconds to run; timing results for large scale problems are given in Section 5.     

wannier90: A tool for obtaining maximally-localised Wannier functions

We present wannier90, a program for calculating maximally-localised Wannier functions (MLWF) from a set of Bloch energy bands that may or may not be attached to or mixed with other bands. The formalism works by minimising the total spread of the MLWF in real space. This is done in the space of unitary matrices that describe rotations of the Bloch bands at each k-point. As a result, wannier90 is independent of the basis set used in the underlying calculation to obtain the Bloch states. Therefore, it may be interfaced straightforwardly to any electronic structure code. The locality of MLWF can be exploited to compute band-structure, density of states and Fermi surfaces at modest computational cost. Furthermore, wannier90 is able to output MLWF for visualisation and other post-processing purposes. Wannier functions are already used in a wide variety of applications. These include analysis of chemical bonding in real space; calculation of dielectric properties via the modern theory of polarisation; and as an accurate and minimal basis set in the construction of model Hamiltonians for large-scale systems, in linear-scaling quantum Monte Carlo calculations, and for efficient computation of material properties, such as the anomalous Hall coefficient. wannier90 is freely available under the GNU General Public License from http://www.wannier.org/.

Program summary

Program title: wannier90Catalogue identifier: AEAK_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAK_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.: 556 495No. of bytes in distributed program, including test data, etc.: 5 709 419Distribution format: tar.gzProgramming language: Fortran 90, perlComputer: any architecture with a Fortran 90 compilerOperating system: Linux, Windows, Solaris, AIX, Tru64 Unix, OSXRAM: 10 MBWord size: 32 or 64Classification: 7.3External routines:

•

BLAS (http://www/netlib.org/blas).

•

LAPACK (http://www.netlib.org/lapack).

Both available under open-source licenses.Nature of problem: Obtaining maximally-localised Wannier functions from a set of Bloch energy bands that may or may not be entangled.Solution method: In the case of entangled bands, the optimally-connected subspace of interest is determined by minimising a functional which measures the subspace dispersion across the Brillouin zone. The maximally-localised Wannier functions within this subspace are obtained by subsequent minimisation of a functional that represents the total spread of the Wannier functions in real space. For the case of isolated energy bands only the second step of the procedure is required.Unusual features: Simple and user-friendly input system. Wannier functions and interpolated band structure output in a variety of file formats for visualisation.Running time: Test cases take 1 minute.References:

[1] 

N. Marzari, D. Vanderbilt, Maximally localized generalized Wannier functions for composite energy bands, Phys. Rev. B 56 (1997) 12847.

[2] 

I. Souza, N. Marzari, D. Vanderbilt, Maximally localized Wannier functions for entangled energy bands, Phys. Rev. B 65 (2001) 035109.

     

An updated version of the Motion4D-library

We present an updated version of the Motion4D-library that can be used for the newly developed GeodesicViewer application.

New version program summary

Program title: Motion4D-libraryCatalogue identifier: AEEX_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEX_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.: 153 757No. of bytes in distributed program, including test data, etc.: 5 178 439Distribution format: tar.gzProgramming language: C++Computer: All platforms with a C++ compilerOperating system: Linux, Unix, WindowsRAM: 31 MBytesCatalogue identifier of previous version: AEEX_v1_0Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 2355Classification: 1.5External routines: Gnu Scientific Library (GSL) (http://www.gnu.org/software/gsl/)Does the new version supersede the previous version?: YesNature of problem: Solve geodesic equation, parallel and Fermi-Walker transport in four-dimensional Lorentzian spacetimes.Solution method: Integration of ordinary differential equations.Reasons for new version: To be applicable for the GeodesicViewer (accepted for publication in Comput. Phys. Comm. (COMPHY) 3941, doi:10.1016/j.cpc.2009.10.010 [program AEFP_v1_0]), there were several minor adjustments to be done.Summary of revisions:

1.

Calculation of embedding diagrams are improved.

2.

Physical units can be used for some metrics.

3.

Tests for the constraint equation within the metric classes are slightly modified.

4.

New metrics: AlcubierreWarp, GoedelScaled, GoedelScaledCart, Kasner.

Running time: The test runs provided with the distribution require only a few seconds to run.     

Accelerating Monte Carlo simulations with an NVIDIA graphics processor

Modern graphics cards, commonly used in desktop computers, have evolved beyond a simple interface between processor and display to incorporate sophisticated calculation engines that can be applied to general purpose computing. The Monte Carlo algorithm for modelling photon transport in turbid media has been implemented on an NVIDIA^® 8800gt graphics card using the CUDA toolkit. The Monte Carlo method relies on following the trajectory of millions of photons through the sample, often taking hours or days to complete. The graphics-processor implementation, processing roughly 110 million scattering events per second, was found to run more than 70 times faster than a similar, single-threaded implementation on a 2.67 GHz desktop computer.

Program summary

Program title: Phoogle-C/Phoogle-GCatalogue identifier: AEEB_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEB_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.: 51 264No. of bytes in distributed program, including test data, etc.: 2 238 805Distribution format: tar.gzProgramming language: C++Computer: Designed for Intel PCs. Phoogle-G requires a NVIDIA graphics card with support for CUDA 1.1Operating system: Windows XPHas the code been vectorised or parallelized?: Phoogle-G is written for SIMD architecturesRAM: 1 GBClassification: 21.1External routines: Charles Karney Random number library. Microsoft Foundation Class library. NVIDA CUDA library [1].Nature of problem: The Monte Carlo technique is an effective algorithm for exploring the propagation of light in turbid media. However, accurate results require tracing the path of many photons within the media. The independence of photons naturally lends the Monte Carlo technique to implementation on parallel architectures. Generally, parallel computing can be expensive, but recent advances in consumer grade graphics cards have opened the possibility of high-performance desktop parallel-computing.Solution method: In this pair of programmes we have implemented the Monte Carlo algorithm described by Prahl et al. [2] for photon transport in infinite scattering media to compare the performance of two readily accessible architectures: a standard desktop PC and a consumer grade graphics card from NVIDIA.Restrictions: The graphics card implementation uses single precision floating point numbers for all calculations. Only photon transport from an isotropic point-source is supported. The graphics-card version has no user interface. The simulation parameters must be set in the source code. The desktop version has a simple user interface; however some properties can only be accessed through an ActiveX client (such as Matlab).Additional comments: The random number library used has a LGPL (http://www.gnu.org/copyleft/lesser.html) licence.Running time: Runtime can range from minutes to months depending on the number of photons simulated and the optical properties of the medium.References:

[1]

http://www.nvidia.com/object/cuda_home.html.

[2]

S. Prahl, M. Keijzer, Sl. Jacques, A. Welch, SPIE Institute Series 5 (1989) 102.

     

CADNA: a library for estimating round-off error propagation

The CADNA library enables one to estimate round-off error propagation using a probabilistic approach. With CADNA the numerical quality of any simulation program can be controlled. Furthermore by detecting all the instabilities which may occur at run time, a numerical debugging of the user code can be performed. CADNA provides new numerical types on which round-off errors can be estimated. Slight modifications are required to control a code with CADNA, mainly changes in variable declarations, input and output. This paper describes the features of the CADNA library and shows how to interpret the information it provides concerning round-off error propagation in a code.

Program summary

Program title:CADNACatalogue identifier:AEAT_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAT_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.:53 420No. of bytes in distributed program, including test data, etc.:566 495Distribution format:tar.gzProgramming language:FortranComputer:PC running LINUX with an i686 or an ia64 processor, UNIX workstations including SUN, IBMOperating system:LINUX, UNIXClassification:4.14, 6.5, 20Nature of problem:A simulation program which uses floating-point arithmetic generates round-off errors, due to the rounding performed at each assignment and at each arithmetic operation. Round-off error propagation may invalidate the result of a program. The CADNA library enables one to estimate round-off error propagation in any simulation program and to detect all numerical instabilities that may occur at run time.Solution method:The CADNA library [1] implements Discrete Stochastic Arithmetic [2-4] which is based on a probabilistic model of round-off errors. The program is run several times with a random rounding mode generating different results each time. From this set of results, CADNA estimates the number of exact significant digits in the result that would have been computed with standard floating-point arithmetic.Restrictions:CADNA requires a Fortran 90 (or newer) compiler. In the program to be linked with the CADNA library, round-off errors on complex variables cannot be estimated. Furthermore array functions such as product or sum must not be used. Only the arithmetic operators and the abs, min, max and sqrt functions can be used for arrays.Running time:The version of a code which uses CADNA runs at least three times slower than its floating-point version. This cost depends on the computer architecture and can be higher if the detection of numerical instabilities is enabled. In this case, the cost may be related to the number of instabilities detected.References:

[1]

The CADNA library, URL address: http://www.lip6.fr/cadna.

[2]

J.-M. Chesneaux, L'arithmétique Stochastique et le Logiciel CADNA, Habilitation á diriger des recherches, Université Pierre et Marie Curie, Paris, 1995.

[3]

J. Vignes, A stochastic arithmetic for reliable scientific computation, Math. Comput. Simulation 35 (1993) 233-261.

[4]

J. Vignes, Discrete stochastic arithmetic for validating results of numerical software, Numer. Algorithms 37 (2004) 377-390.

     

PHASE-OTI: A pre-equilibrium model code for nuclear reactions calculations

The present work focuses on a pre-equilibrium nuclear reaction code (based on the one, two and infinity hypothesis of pre-equilibrium nuclear reactions). In the PHASE-OTI code, pre-equilibrium decays are assumed to be single nucleon emissions, and the statistical probabilities come from the independence of nuclei decay. The code has proved to be a good tool to provide predictions of energy-differential cross sections. The probability of emission was calculated statistically using bases of hybrid model and exciton model. However, more precise depletion factors were used in the calculations. The present calculations were restricted to nucleon-nucleon interactions and one nucleon emission.

Program summary

Program title: PHASE-OTICatalogue identifier: AEDN_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDN_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.: 5858No. of bytes in distributed program, including test data, etc.: 149 405Distribution format: tar.gzProgramming language: Fortran 77Computer: Pentium 4 and Centrino DuoOperating system: MS WindowsRAM: 128 MBClassification: 17.12Nature of problem: Calculation of the differential cross section for nucleon induced nuclear reaction in the framework of pre-equilibrium emission model.Solution method: Single neutron emission was treated by assuming occurrence of the reaction in successive steps. Each step is called phase because of the phase transition nature of the theory. The probability of emission was calculated statistically using bases of hybrid model [1] and exciton model [2]. However, more precise depletion factor was used in the calculations. Exciton configuration used in the code is that described in earlier work [3].Restrictions: The program is restricted to single nucleon emission and nucleon-nucleon interactions.Running time: 5-30 minutesReferences:

[1]

M. Blann, Phys. Rev. Lett. 27 (1971) 337.

[2]

E. Gadioli, E.G. Erba, J.J. Hogan, Phys. Rev. C 16 (1977) 1404-1424.

[3]

E.K. Elmaghraby, Phys. Rev. C 78 (2008) 014601.

     

GDF v2.0, an enhanced version of GDF

An improved version of the function estimation program GDF is presented. The main enhancements of the new version include: multi-output function estimation, capability of defining custom functions in the grammar and selection of the error function. The new version has been evaluated on a series of classification and regression datasets, that are widely used for the evaluation of such methods. It is compared to two known neural networks and outperforms them in 5 (out of 10) datasets.

Program summary

Title of program: GDF v2.0Catalogue identifier: ADXC_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXC_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.: 98 147No. of bytes in distributed program, including test data, etc.: 2 040 684Distribution format: tar.gzProgramming language: GNU C++Computer: The program is designed to be portable in all systems running the GNU C++ compilerOperating system: Linux, Solaris, FreeBSDRAM: 200000 bytesClassification: 4.9Does the new version supersede the previous version?: YesNature of problem: The technique of function estimation tries to discover from a series of input data a functional form that best describes them. This can be performed with the use of parametric models, whose parameters can adapt according to the input data.Solution method: Functional forms are being created by genetic programming which are approximations for the symbolic regression problem.Reasons for new version: The GDF package was extended in order to be more flexible and user customizable than the old package. The user can extend the package by defining his own error functions and he can extend the grammar of the package by adding new functions to the function repertoire. Also, the new version can perform function estimation of multi-output functions and it can be used for classification problems.Summary of revisions: The following features have been added to the package GDF:

•

Multi-output function approximation. The package can now approximate any function . This feature gives also to the package the capability of performing classification and not only regression.

•

User defined function can be added to the repertoire of the grammar, extending the regression capabilities of the package. This feature is limited to 3 functions, but easily this number can be increased.

•

Capability of selecting the error function. The package offers now to the user apart from the mean square error other error functions such as: mean absolute square error, maximum square error. Also, user defined error functions can be added to the set of error functions.

•

More verbose output. The main program displays more information to the user as well as the default values for the parameters. Also, the package gives to the user the capability to define an output file, where the output of the gdf program for the testing set will be stored after the termination of the process.

Additional comments: A technical report describing the revisions, experiments and test runs is packaged with the source code.Running time: Depending on the train data.     

Model-Driven Development for scientific computing. An upgrade of the RHEEDGr program

Model-Driven Engineering (MDE) is the software engineering discipline, which considers models as the most important element for software development, and for the maintenance and evolution of software, through model transformation. Model-Driven Architecture (MDA) is the approach for software development under the Model-Driven Engineering framework. This paper surveys the core MDA technology that was used to upgrade of the RHEEDGR program to C++0x language standards.

New version program summary

Program title: RHEEDGR-09Catalogue identifier: ADUY_v3_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUY_v3_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.: 21 263No. of bytes in distributed program, including test data, etc.: 1 266 982Distribution format: tar.gzProgramming language: Code Gear C++ BuilderComputer: Intel Core Duo-based PCOperating system: Windows XP, Vista, 7RAM: more than 1 MBClassification: 4.3, 7.2, 6.2, 8, 14Does the new version supersede the previous version?: YesNature of problem: Reflection High-Energy Electron Diffraction (RHEED) is a very useful technique for studying growth and surface analysis of thin epitaxial structures prepared by the Molecular Beam Epitaxy (MBE). The RHEED technique can reveal, almost instantaneously, changes either in the coverage of the sample surface by adsorbates or in the surface structure of a thin film.Solution method: The calculations are based on the use of a dynamical diffraction theory in which the electrons are taken to be diffracted by a potential, which is periodic in the dimension perpendicular to the surface.Reasons for new version: Responding to the user feedback the graphical version of the RHEED program has been upgraded to C++0x language standards. Also, functionality and documentation of the program have been improved.Summary of revisions:

1.

Model-Driven Architecture (MDA) is the approach defined by the Object Management Group (OMG) for software development under the Model-Driven Engineering framework [1]. The MDA approach shifts the focus of software development from writing code to building models. By adapting a model-centric approach, the MDA approach hopes to automate the generation of system implementation artifacts directly from the model. The following three models are the core of the MDA: (i) the Computation Independent Model (CIM), which is focused on basic requirements of the system, (ii) the Platform Independent Model (PIM), which is used by software architects and designers, and is focused on the operational capabilities of a system outside the context of a specific platform, and (iii) the Platform Specific Model (PSM), which is used by software developers and programmers, and includes details relating to the system for a specific platform. Basic requirements for the calculation of the RHEED intensity rocking curves in the one-beam condition have been described in Ref. [2]. Fig. 1 shows the PIM for the present version of the program. Fig. 2 presents the PSM for the program.

2.

The TGraph2D.bpk package has been recompiled to Graph2D0x.bpl and upgraded according to C++0x language standards. Fig. 3 shows the PSM of the Graph2D component, which is manifested by the Graph2D0x.bpl package presently. This diagram is a graphic presentation of the static view, which shows a collection of declarative model elements and their relationships. Installation instructions of the Graph2D0x package can be found in the new distribution.

3.

The program requires the user to provide the appropriate parameters for the crystal structure under investigation. These parameters are loaded from the parameters.ini file at run-time. Instructions for the preparation of the .ini files can be found in the new distribution.

4.

The program enables carrying out one-dimensional dynamical calculations for the fcc lattice, with a two-atoms basis and fcc lattice, with one atom basis but yet the zeroth Fourier component of the scattering potential in the TRHEED1D::crystPotUg() function can be modified according to users' specific application requirements.

5.

A graphical user interface (GUI) for the program has been reconstructed.

6.

The program has been compiled with English/USA regional and language options.

Unusual features: The program is distributed in the form of main projects RHEEDGr_09.cbproj and Graph2D0x.cbproj with associated files, and should be compiled using Code Gear C++ Builder 2009 compilers.Running time: The typical running time is machine and user-parameters dependent.References:

[1]

OMG, Model Driven Architecture Guide Version 1.0.1, 2003, http://www.omg.org/cgi-bin/doc?omg/03-06-01.

[2]

A. Daniluk, Comput. Phys. Comm. 166 (2005) 123.

     

LCG MCDB—a knowledgebase of Monte-Carlo simulated events

In this paper we report on LCG Monte-Carlo Data Base (MCDB) and software which has been developed to operate MCDB. The main purpose of the LCG MCDB project is to provide a storage and documentation system for sophisticated event samples simulated for the LHC Collaborations by experts. In many cases, the modern Monte-Carlo simulation of physical processes requires expert knowledge in Monte-Carlo generators or significant amount of CPU time to produce the events. MCDB is a knowledgebase mainly dedicated to accumulate simulated events of this type. The main motivation behind LCG MCDB is to make the sophisticated MC event samples available for various physical groups. All the data from MCDB is accessible in several convenient ways. LCG MCDB is being developed within the CERN LCG Application Area Simulation project.

Program summary

Program title: LCG Monte-Carlo Data BaseCatalogue identifier: ADZX_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZX_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: GNU General Public LicenceNo. of lines in distributed program, including test data, etc.: 30 129No. of bytes in distributed program, including test data, etc.: 216 943Distribution format: tar.gzProgramming language: PerlComputer: CPU: Intel Pentium 4, RAM: 1 Gb, HDD: 100 GbOperating system: Scientific Linux CERN 3/4RAM: 1 073 741 824 bytes (1 Gb)Classification: 9External routines:

•

perl >= 5.8.5;

•

Perl modules

○

DBD-mysql >= 2.9004,

○

File::Basename,

○

GD::SecurityImage,

○

GD::SecurityImage::AC,

○

Linux::Statistics,

○

XML::LibXML > 1.6,

○

XML::SAX,

○

XML::NamespaceSupport;

•

Apache HTTP Server >= 2.0.59;

•

mod auth external >= 2.2.9;

•

edg-utils-system RPM package;

•

gd >= 2.0.28;

•

rpm package CASTOR-client >= 2.1.2-4;

•

arc-server (optional)

Nature of problem: Often, different groups of experimentalists prepare similar samples of particle collision events or turn to the same group of authors of Monte-Carlo (MC) generators to prepare the events. For example, the same MC samples of Standard Model (SM) processes can be employed for the investigations either in the SM analyses (as a signal) or in searches for new phenomena in Beyond Standard Model analyses (as a background). If the samples are made available publicly and equipped with corresponding and comprehensive documentation, it can speed up cross checks of the samples themselves and physical models applied. Some event samples require a lot of computing resources for preparation. So, a central storage of the samples prevents possible waste of researcher time and computing resources, which can be used to prepare the same events many times.Solution method: Creation of a special knowledgebase (MCDB) designed to keep event samples for the LHC experimental and phenomenological community. The knowledgebase is realized as a separate web-server (http://mcdb.cern.ch). All event samples are kept on types at CERN. Documentation describing the events is the main contents of MCDB. Users can browse the knowledgebase, read and comment articles (documentation), and download event samples. Authors can upload new event samples, create new articles, and edit own articles.Restrictions: The software is adopted to solve the problems, described in the article and there are no any additional restrictions.Unusual features: The software provides a framework to store and document large files with flexible authentication and authorization system. Different external storages with large capacity can be used to keep the files. The WEB Content Management System provides all of the necessary interfaces for the authors of the files, end-users and administrators.Running time: Real time operations.References:[1] The main LCG MCDB server, http://mcdb.cern.ch/.[2] P. Bartalini, L. Dudko, A. Kryukov, I.V. Selyuzhenkov, A. Sherstnev, A. Vologdin, LCG Monte-Carlo data base, hep-ph/0404241.[3] J.P. Baud, B. Couturier, C. Curran, J.D. Durand, E. Knezo, S. Occhetti, O. Barring, CASTOR: status and evolution, cs.oh/0305047.     

A new version of Visual tool for estimating the fractal dimension of images

This work presents a new version of a Visual Basic 6.0 application for estimating the fractal dimension of images (Grossu et al., 2009 [1]). The earlier version was limited to bi-dimensional sets of points, stored in bitmap files. The application was extended for working also with comma separated values files and three-dimensional images.

New version program summary

Program title: Fractal Analysis v02Catalogue identifier: AEEG_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEG_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.: 9999No. of bytes in distributed program, including test data, etc.: 4 366 783Distribution format: tar.gzProgramming language: MS Visual Basic 6.0Computer: PCOperating system: MS Windows 98 or laterRAM: 30 MClassification: 14Catalogue identifier of previous version: AEEG_v1_0Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1999Does the new version supersede the previous version?: YesNature of problem: Estimating the fractal dimension of 2D and 3D images.Solution method: Optimized implementation of the box-counting algorithm.Reasons for new version:

1.

The previous version was limited to bitmap image files. The new application was extended in order to work with objects stored in comma separated values (csv) files. The main advantages are:

a)

Easier integration with other applications (csv is a widely used, simple text file format);

b)

Less resources consumed and improved performance (only the information of interest, the “black points”, are stored);

c)

Higher resolution (the points coordinates are loaded into Visual Basic double variables [2]);

d)

Possibility of storing three-dimensional objects (e.g. the 3D Sierpinski gasket).

2.

In this version the optimized box-counting algorithm [1] was extended to the three-dimensional case.

Summary of revisions:

1.

The application interface was changed from SDI (single document interface) to MDI (multi-document interface).

2.

One form was added in order to provide a graphical user interface for the new functionalities (fractal analysis of 2D and 3D images stored in csv files).

Additional comments: User friendly graphical interface; Easy deployment mechanism.Running time: In the first approximation, the algorithm is linear.References:

[1] I.V. Grossu, C. Besliu, M.V. Rusu, Al. Jipa, C.C. Bordeianu, D. Felea, Comput. Phys. Comm. 180 (2009)  1999-2001.

[2] F. Balena, Programming Microsoft Visual Basic 6.0, Microsoft Press, US, 1999.