A web-deployed interface for performing ab initio molecular dynamics, optimization, and electronic structure in Fireball

Fireball is an ab initio technique for fast local orbital simulations of nanotechnological, solid state, and biological systems. We have implemented a convenient interface for new users and software architects in the platform-independent Java language to access Fireball's unique and powerful capabilities. The graphical user interface can be run directly from a web server or from within a larger framework such as the Computational Science and Engineering Online (CSE-Online) environment or the Distributed Analysis of Neutron Scattering Experiments (DANSE) framework. We demonstrate its use for high-throughput electronic structure calculations and a multi-100 atom quantum molecular dynamics (MD) simulation.

Program summary

Program title: FireballUICatalogue identifier: AECF_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECF_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.: 279 784No. of bytes in distributed program, including test data, etc.: 12 836 145Distribution format: tar.gzProgramming language: JavaComputer: PC and workstationOperating system: The GUI will run under Windows, Mac and Linux. Executables for Mac and Linux are included in the package.RAM: 512 MBWord size: 32 or 64 bitsClassification: 4.14Nature of problem: The set up and running of many simulations (all of the same type), from the command line, is a slow process. But most research quality codes, including the ab initio tight-binding code FIREBALL, are designed to run from the command line. The desire is to have a method for quickly and efficiently setting up and running a host of simulations.Solution method: We have created a graphical user interface for use with the FIREBALL code. Once the user has created the files containing the atomic coordinates for each system that they are going to run a simulation on, the user can set up and start the computations of up to hundreds of simulations.Running time: 3 to 5 minutes on a 2 GHz Pentium IV processor.     

A Breit–Pauli distorted wave implementation for autostructure

We describe the Breit–Pauli distorted wave (BPDW) approach for the electron-impact excitation of atomic ions that we have implemented within the autostructure code.

Program summary

Program title:autostructureCatalogue identifier: AEIV_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIV_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.: 130 987No. of bytes in distributed program, including test data, etc.: 1 031 584Distribution format: tar.gzProgramming language: Fortran 77/95Computer: GeneralOperating system: UnixHas the code been vectorized or parallelized?: Yes, a parallel version, with MPI directives, is included in the distribution.RAM: From several kbytes to several GbytesClassification: 2, 2.4Nature of problem: Collision strengths for the electron-impact excitation of atomic ions are calculated using a Breit–Pauli distorted wave approach with the optional inclusion of two-body non-fine-structure and fine-structure interactions.Solution method: General multi-configuration Breit–Pauli atomic structure. A jK-coupling partial wave expansion of the collision problem. Slater state angular algebra. Various model potential non-relativistic or kappa-averaged relativistic radial orbital solutions — the continuum distorted wave orbitals are not required to be orthogonal to the bound.Additional comments: Documentation is provided in the distribution file along with the test-case.Running time: From a few seconds to a few hours.     

One universal extra dimension in Pythia

The Universal Extra Dimensions model has been implemented in the Pythia generator from version 6.4.18 onwards, in its minimal formulation with one TeV⁻¹-sized extra dimension. The additional possibility of gravity-mediated decays, through a variable number of eV⁻¹-sized extra dimensions into which only gravity extends, is also available. The implementation covers the lowest lying Kaluza-Klein (KK) excitations of Standard Model particles, except for the excitations of the Higgs fields, with the mass spectrum calculated at one loop. 2→2 tree-level production cross sections and unpolarized KK number conserving 2-body decays are included. Mixing between iso-doublet and -singlet KK excitations is neglected thus far, and is expected to be negligible for all but the top sector.

New version summary

Program title: PYTHIA Version number: 6.420Catalogue identifier: ACTU_v2_1Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ACTU_v2_1.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 79 362No. of bytes in distributed program, including test data, etc.: 590 900Distribution format: tar.gzProgramming language: Fortran 77Computer: CERN lxplus and any other machine with a Fortran 77 compilerOperating system: Linux Red HatRAM: about 800 K wordsWord size: 32 bitsClassification: 11.2Catalogue identifier of previous version: ACTU_v2_0Journal reference of previous version: Comput. Phys. Comm. 135 (2001) 238Does the new version supersede the previous version?: YesNature of problem: At high energy collisions between elementary particles, physics beyond the Standard Model is searched for. Many models are being investigated, namely extra-dimensional models.Solution method: The Universal Extra Dimension model is implemented in the PYTHIA event generator.Reasons for new version: The Universal Extra Dimensions model has been implemented in the PYTHIA generator from version 6.4.18 onwards, in its minimal formulation with one TeV⁻¹-sized extra dimension. The additional possibility of gravity-mediated decays, through a variable number of eV⁻¹-sized extra dimensions into which only gravity extends, is also available. The implementation covers the lowest lying Kaluza-Klein (KK) excitations of Standard Model particles, except for the excitations of the Higgs fields, with the mass spectrum calculated at one loop. 2→2 tree-level production cross sections and unpolarized KK number conserving 2-body decays are included. Mixing between iso-doublet and -singlet KK excitations is neglected thus far, and is expected to be negligible for all but the top sector.Running time: 10-1000 events per second, depending on the process studied.     

ASPIN: An all spin scattering code for atom-molecule rovibrationally inelastic cross sections

We present in this work a new computational code for the quantum calculation of integral cross sections for atom-molecule (linear) scattering processes. The atom is taken to be structureless while the molecule can be in its singlet, doublet, or triplet spin states and can be treated as either a rigid rotor or a rovibrational target. All the relevant state-to-state integral cross sections, and their sums over final states, can be calculated with the present code, for which we also describe in detail the various component routines.

Program summary

Program title: ASPINCatalogue identifier: AEBO_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBO_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.: 99 596No. of bytes in distributed program, including test data, etc.: 1 267 615Distribution format: tar.gzProgramming language: Fortran/MPIComputer: AMD OPTERON COMPUTING SYSTEMS, model TYAN GX28 (B2882)Operating system: SuSE LINUX Professional 9RAM: 128 GBClassification: 2.6External routines: LAPACK/BLASNature of problem: Scattering of a diatomic molecule in its , , or spin states with an atom in its state. Partial and integral cross sections.Solution method: The coupled channel equations that describe the scattering process are solved through the propagation of the reactance K matrix employing a modification of the Variable Phase Method [1-3].Restrictions: Depending on the vib-rotational base used the problem may or may not fit into available RAM memory because all the runtime relevant quantities are stored on RAM memory instead of on disk.Additional comments: Both serial and parallel implementations of the program are provided. The CPC Librarian was not able to successfully run the parallel version.Running time: For simple and converged calculations a usual running time is in the order of a few minutes in the computer mentioned above, being shorter for the singlet and longer for the triplet.References:[1] F. Calogero, Variable Phase Approach to Potential Scattering, New York, 1967.[2] A. Degasperis, Il Nuovo Cimento 34 (1964) 1667.[3] C. Zemach, Il Nuovo Cimento 33 (1964) 939.     

OneLOop: For the evaluation of one-loop scalar functions

OneLOop is a program to evaluate the one-loop scalar 1-point, 2-point, 3-point and 4-point functions, for all kinematical configurations relevant for collider-physics, and for any non-positive imaginary parts of the internal squared masses. It deals with all UV and IR divergences within dimensional regularization. Furthermore, it provides routines to evaluate these functions using straightforward numerical integration.

Program summary

Program title: OneLOopCatalogue identifier: AEJO_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJO_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.: 12 061No. of bytes in distributed program, including test data, etc.: 74 163Distribution format: tar.gzProgramming language: FortranComputer: WorkstationsOperating system: Linux, UnixRAM: NegligibleClassification: 4.4, 11.1Nature of problem: In order to reach next-to-leading order precision in the calculation of cross sections of hard scattering processes, one-loop amplitudes have to be evaluated. This is done by expressing them as linear combination of one-loop scalar functions. In a concrete calculation, these functions eventually have to be evaluated. If the scattering process involves unstable particles, consistency requires the evaluation of these functions with complex internal masses.Solution method: Expressions for the one-loop scalar functions in terms of single-variable analytic functions existing in literature have been implemented.Restrictions: The applicability is restricted to the kinematics occurring in collider-physics.Running time: The evaluation of the most general 4-point function with 4 complex masses takes about 180 μs, and the evaluation of the 4-point function with 4 real masses takes about 18 μs on a 2.80 GHz Intel Xeon processor.     

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

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

Program summary

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

MontePython: Implementing Quantum Monte Carlo using Python

We present a cross-language C++/Python program for simulations of quantum mechanical systems with the use of Quantum Monte Carlo (QMC) methods. We describe a system for which to apply QMC, the algorithms of variational Monte Carlo and diffusion Monte Carlo and we describe how to implement theses methods in pure C++ and C++/Python. Furthermore we check the efficiency of the implementations in serial and parallel cases to show that the overhead using Python can be negligible.

Program summary

Program title: MontePythonCatalogue identifier: ADZP_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZP_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.: 49 519No. of bytes in distributed program, including test data, etc.: 114 484Distribution format: tar.gzProgramming language: C++, PythonComputer: PC, IBM RS6000/320, HP, ALPHAOperating system: LINUXHas the code been vectorised or parallelized?: Yes, parallelized with MPINumber of processors used: 1-96RAM: Depends on physical system to be simulatedClassification: 7.6; 16.1Nature of problem: Investigating ab initio quantum mechanical systems, specifically Bose-Einstein condensation in dilute gases of ⁸⁷RbSolution method: Quantum Monte CarloRunning time: 225 min with 20 particles (with 4800 walkers moved in 1750 time steps) on 1 AMD Opteron^TM Processor 2218 processor; Production run for, e.g., 200 particles takes around 24 hours on 32 such processors.     

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.     

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     

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.     

Helac-Phegas: A generator for all parton level processes

The updated version of the Helac-Phegas¹ event generator is presented. The matrix elements are calculated through Dyson-Schwinger recursive equations using color connection representation. Phase-space generation is based on a multichannel approach, including optimization. Helac-Phegas generates parton level events with all necessary information, in the most recent Les Houches Accord format, for the study of any process within the Standard Model in hadron and lepton colliders.

New version program summary

Program title: HELAC-PHEGASCatalogue identifier: ADMS_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADMS_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.: 35 986No. of bytes in distributed program, including test data, etc.: 380 214Distribution format: tar.gzProgramming language: FortranComputer: AllOperating system: LinuxClassification: 11.1, 11.2External routines: Optionally Les Houches Accord (LHA) PDF Interface library (http://projects.hepforge.org/lhapdf/)Catalogue identifier of previous version: ADMS_v1_0Journal reference of previous version: Comput. Phys. Comm. 132 (2000) 306Does the new version supersede the previous version?: Yes, partlyNature of problem: One of the most striking features of final states in current and future colliders is the large number of events with several jets. Being able to predict their features is essential. To achieve this, the calculations need to describe as accurately as possible the full matrix elements for the underlying hard processes. Even at leading order, perturbation theory based on Feynman graphs runs into computational problems, since the number of graphs contributing to the amplitude grows as n!.Solution method: Recursive algorithms based on Dyson-Schwinger equations have been developed recently in order to overcome the computational obstacles. The calculation of the amplitude, using Dyson-Schwinger recursive equations, results in a computational cost growing asymptotically as 3n, where n is the number of particles involved in the process. Off-shell subamplitudes are introduced, for which a recursion relation has been obtained allowing to express an n-particle amplitude in terms of subamplitudes, with 1-, 2-, …  up to (n−1) particles. The color connection representation is used in order to treat amplitudes involving colored particles. In the present version HELAC-PHEGAS can be used to efficiently obtain helicity amplitudes, total cross sections, parton-level event samples in LHA format, for arbitrary multiparticle processes in the Standard Model in leptonic, and pp collisions.Reasons for new version: Substantial improvements, major functionality upgrade.Summary of revisions: Color connection representation, efficient integration over PDF via the PARNI algorithm, interface to LHAPDF, parton level events generated in the most recent LHA format, k_⊥ reweighting for Parton Shower matching, numerical predictions for amplitudes for arbitrary processes for phase-space points provided by the user, new user interface and the possibility to run over computer clusters.Running time: Depending on the process studied. Usually from seconds to hours.References:

[1]

A. Kanaki, C.G. Papadopoulos, Comput. Phys. Comm. 132 (2000) 306.

[2]

C.G. Papadopoulos, Comput. Phys. Comm. 137 (2001) 247.

     

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.     

QCDMAPT: Program package for Analytic approach to QCD

A program package, which facilitates computations in the framework of Analytic approach to QCD, is developed and described in detail. The package includes both the calculated explicit expressions for relevant spectral functions up to the four-loop level and the subroutines for necessary integrals.

Program summary

Program title: QCDMAPTCatalogue identifier: AEGP_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGP_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.: 2579No. of bytes in distributed program, including test data, etc.: 180 052Distribution format: tar.gzProgramming language: Maple 9 and higherComputer: Any which supports Maple 9Operating system: Any which supports Maple 9Classification: 11.1, 11.5, 11.6Nature of problem: Subroutines helping computations within Analytic approach to QCD.Solution method: A program package for Maple is provided. It includes both the explicit expressions for relevant spectral functions and the subroutines for basic integrals used in the framework of Analytic approach to QCD.Running time: Template program running time is about a minute (depends on CPU).     

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.     

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.     

SMMP v. 3.0—Simulating proteins and protein interactions in Python and Fortran

We describe a revised and updated version of the program package SMMP. SMMP is an open-source FORTRAN package for molecular simulation of proteins within the standard geometry model. It is designed as a simple and inexpensive tool for researchers and students to become familiar with protein simulation techniques. SMMP 3.0 sports a revised API increasing its flexibility, an implementation of the Lund force field, multi-molecule simulations, a parallel implementation of the energy function, Python bindings, and more.

Program summary

Title of program:SMMPCatalogue identifier:ADOJ_v3_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADOJ_v3_0.htmlProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandLicensing provisions:Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlProgramming language used:FORTRAN, PythonNo. of lines in distributed program, including test data, etc.:52 105No. of bytes in distributed program, including test data, etc.:599 150Distribution format:tar.gzComputer:Platform independentOperating system:OS independentRAM:2 MbytesClassification:3Does the new version supersede the previous version?:YesNature of problem:Molecular mechanics computations and Monte Carlo simulation of proteins.Solution method:Utilizes ECEPP2/3, FLEX, and Lund potentials. Includes Monte Carlo simulation algorithms for canonical, as well as for generalized ensembles.Reasons for new version:API changes and increased functionality.Summary of revisions:Added Lund potential; parameters used in subroutines are now passed as arguments; multi-molecule simulations; parallelized energy calculation for ECEPP; Python bindings.Restrictions:The consumed CPU time increases with the size of protein molecule.Running time:Depends on the size of the simulated molecule.     

-XSummer- Transcendental functions and symbolic summation in Form

Harmonic sums and their generalizations are extremely useful in the evaluation of higher-order perturbative corrections in quantum field theory. Of particular interest have been the so-called nested sums, where the harmonic sums and their generalizations appear as building blocks, originating for example, from the expansion of generalized hypergeometric functions around integer values of the parameters. In this paper we discuss the implementation of several algorithms to solve these sums by algebraic means, using the computer algebra system Form.

Program summary

Title of program:XSummerCatalogue identifier:ADXQ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXQ_v1_0Program obtainable from:CPC Program Library, Queen's University of Belfast, N. IrelandLicense:GNU Public License and Form LicenseComputers:allOperating system:allProgram language:FormMemory required to execute:Depending on the complexity of the problem, recommended at least 64 MB RAMNo. of lines in distributed program, including test data, etc.:9854No. of bytes in distributed program, including test data, etc.:126 551Distribution format:tar.gzOther programs called:noneExternal files needed:noneNature of the physical problem:Systematic expansion of higher transcendental functions in a small parameter. The expansions arise in the calculation of loop integrals in perturbative quantum field theory.Method of solution:Algebraic manipulations of nested sums.Restrictions on complexity of the problem:Usually limited only by the available disk space.Typical running time:Dependent on the complexity of the problem.     

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.     

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.