# Computer Physics Communications

Published by Elsevier

Print ISSN: 0010-4655

Published by Elsevier

Print ISSN: 0010-4655

Publications

Program summary:
Program title: MH(2)c (MH helix curves) Catalogue identifier: AELX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AELX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 327 565 No. of bytes in distributed program, including test data, etc.: 17 433 656 Distribution format: tar.gz Programming language: Matlab Computer: Personal computer architectures Operating system: Windows, Linux, Mac (all systems on which Matlab can be installed) RAM: Depends on the trajectory size, min. 1 GB (Matlab) Classification: 2.1, 4.9, 4.14 External routines: Curve Fitting Toolbox and Statistic Toolbox of Matlab Nature of problem: Major histocompatibility (MH) proteins share a similar overall structure. However, identical MH alleles which present different peptides differ by subtle conformational alterations. One hypothesis is that such conformational differences could be another level of T cell regulation. By this software package we present a reliable and systematic way to compare different MH structures to each other. Solution method: We tested several fitting approaches on all available experimental crystal structures of MH to obtain an overall picture of how to describe MH helices. For this purpose we transformed all complexes into the same space and applied splines and polynomials of several degrees to them. To draw a general conclusion which method fits them best we employed the "corrected Akaike Information Criterion". The software is applicable for all kinds of helices of biomolecules. Running time: Depends on the data, for a single stationary structure the runtime should not exceed a few seconds.

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Fluorescence Correlation Spectroscopy (FCS) is widely used to quantitate reaction rates and concentrations of molecules in vitro and in vivo. We recently reported Fluorescence Triple Correlation Spectroscopy (F3CS), which correlates three signals together instead of two. F3CS can analyze the stoichiometries of complex mixtures and detect irreversible processes by identifying time-reversal asymmetries. Here we report the computational developments that were required for the realization of F3CS and present the results as the Triple Correlation Toolbox suite of programs. Triple Correlation Toolbox is a complete data analysis pipeline capable of acquiring, correlating and fitting large data sets. Each segment of the pipeline handles error estimates for accurate error-weighted global fitting. Data acquisition was accelerated with a combination of off-the-shelf counter-timer chips and vectorized operations on 128-bit registers. This allows desktop computers with inexpensive data acquisition cards to acquire hours of multiple-channel data with sub-microsecond time resolution. Off-line correlation integrals were implemented as a two delay time multiple-tau scheme that scales efficiently with multiple processors and provides an unprecedented view of linked dynamics. Global fitting routines are provided to fit FCS and F3CS data to models containing up to ten species. Triple Correlation Toolbox is a complete package that enables F3CS to be performed on existing microscopes.

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Analytical ultracentrifugation allows one to measure in real-time the concentration gradients arising from the application of a centrifugal force to macromolecular mixtures in solution. In the last decade, the ability to efficiently solve the partial differential equation governing the ultracentrifugal sedimentation and diffusion process, the Lamm equation, has spawned significant progress in the application of sedimentation velocity analytical ultracentrifugation for the study of biological macromolecules, for example, the characterization of protein oligomeric states and the study of reversible multi-protein complexes in solution. The present work describes a numerical algorithm that can provide an improvement in accuracy or efficiency over existing algorithms by more than one order of magnitude, and thereby greatly facilitate the practical application of sedimentation velocity analysis, in particular, for the study of multi-component macromolecular mixtures. It is implemented in the public domain software SEDFIT for the analysis of experimental data.

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A Fortran program package is introduced for rapid evaluation of the electrostatic potentials and forces in biomolecular systems modeled by the linearized Poisson-Boltzmann equation. The numerical solver utilizes a well-conditioned boundary integral equation (BIE) formulation, a node-patch discretization scheme, a Krylov subspace iterative solver package with reverse communication protocols, and an adaptive new version of fast multipole method in which the exponential expansions are used to diagonalize the multipole to local translations. The program and its full description, as well as several closely related libraries and utility tools are available at http://lsec.cc.ac.cn/lubz/afmpb.html and a mirror site at http://mccammon.ucsd.edu/. This paper is a brief summary of the program: the algorithms, the implementation and the usage.

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We present an order N method for calculating electrostatic interactions that has been integrated into the molecular dynamics portion of the TINKER Molecular Modeling package. This method, introduced in a previous paper [J. Chem. Phys. 131 (2009) 154103] and termed the Image-Charge Solvation Model (ICSM), is a hybrid electrostatic approach that combines the strengths of both explicit and implicit representations of the solvent. A multiple-image method is used to calculate reaction fields due to the implicit part while the Fast Multipole Method (FMM) is used to calculate the Coulomb interactions for all charges, including the explicit part. The integrated package is validated through test simulations of liquid water. The results are compared with those obtained by the Particle Mesh Ewald (PME) method that is built in the TINKER package. Timing performance of TINKER with the integrated ICSM is benchmarked on bulk water as a function of the size of the system. In particular, timing analysis results show that the ICSM outperforms the PME for sufficiently large systems with the break-even point at around 30,000 particles in the simulated system.

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In the functional approach to quantum chromodynamics, the properties of hadronic bound states are accessible via covariant integral equations, e.g. the Bethe-Salpeter equation for mesons. In particular, one has to deal with linear, homogeneous integral equations which, in sophisticated model setups, use numerical representations of the solutions of other integral equations as part of their input. Analogously, inhomogeneous equations can be constructed to obtain off-shell information in addition to bound-state masses and other properties obtained from the covariant analogue to a wave function of the bound state. These can be solved very efficiently using well-known matrix algorithms for eigenvalues (in the homogeneous case) and the solution of linear systems (in the inhomogeneous case). We demonstrate this by solving the homogeneous and inhomogeneous Bethe-Salpeter equations and find, e.g. that for the calculation of the mass spectrum it is as efficient or even advantageous to use the inhomogeneous equation as compared to the homogeneous. This is valuable insight, in particular for the study of baryons in a three-quark setup and more involved systems.

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The recently developed high-order accurate multiple image approximation to the reaction field for a charge inside a dielectric sphere [J. Comput. Phys., 223 (2007) 846-864] is compared favorably to other commonly employed reaction field schemes. These methods are of particular interest because they are useful in the study of biological macromolecules by the Monte Carlo and Molecular Dynamics methods.

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A recent article by Deng and Cai (Extending the fast multipole method for charges inside a dielectric sphere in an ionic solvent: High-order image approximations for reaction fields, to appear in J. Comput. Phys.) introduced two fourth-order image approximations to the reaction field for a charge inside a dielectric sphere immersed in a solvent of low ionic strength. To represent such a reaction field, the image approximations employ a point charge at the classical Kelvin image point and two line charges that extend from this Kelvin image point along the radial direction to infinity, with one decaying to zero and the other growing to infinity. In this paper, alternative versions of the fourth-order image approximations are presented, using the same point charge but three different line charges, all decaying to zero along the radial direction. Similar discussions on how to approximate the line charges by discrete image charges and how to apply the resulting multiple discrete image approximations together with the fast multipole method are also included.

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An implementation of the Hirshfeld (HD) and Hirshfeld-Iterated (HD-I) atomic charge density partitioning schemes is described. Atomic charges and atomic multipoles are calculated from the HD and HD-I atomic charge densities for arbitrary atomic multipole rank l(max) on molecules of arbitrary shape and size. The HD and HD-I atomic charges/multipoles are tested by comparing molecular multipole moments and the electrostatic potential (ESP) surrounding a molecule with their reference ab initio values. In general, the HD-I atomic charges/multipoles are found to better reproduce ab initio electrostatic properties over HD atomic charges/multipoles. A systematic increase in precision for reproducing ab initio electrostatic properties is demonstrated by increasing the atomic multipole rank from l(max) = 0 (atomic charges) to l(max) = 4 (atomic hexadecapoles). Both HD and HD-I atomic multipoles up to rank l(max) are shown to exactly reproduce ab initio molecular multipole moments of rank L for L ≤ l(max). In addition, molecular dipole moments calculated by HD, HD-I, and ChelpG atomic charges only (l(max) = 0) are compared with reference ab initio values. Significant errors in reproducing ab initio molecular dipole moments are found if only HD or HD-I atomic charges used.

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By utilizing a novel three-layer dielectric model for the interface between a spherical quantum dot and the surrounding matrix, a robust numerical method for calculating the self-polarization energy of a spherical quantum dot with a finite confinement barrier is presented in this paper. The proposed numerical method can not only overcome the inherent mathematical divergence in the self-polarization energy which arises for the simplest and most widely used step-like model of the dielectric interface, but also completely eliminate the potential numerical divergence which may occur in the Bolcatto-Proetto's formula [J. Phys.: Condens. Matter 13, 319-334 (2001)], an approximation method commonly employed for more realistic three-layer dielectric models such as the linear and the cosine-like models frequently mentioned in the literature. Numerical experiments have demonstrated the convergence of the proposed numerical method as the number of the steps used to discretize the translation layer in a three-layer model goes to infinity, an important property that the Bolcatto-Proetto's formula appears not necessarily to possess.

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A new software package, Browndye, is presented for simulating the diffusional encounter of two large biological molecules. It can be used to estimate second-order rate constants and encounter probabilities, and to explore reaction trajectories. Browndye builds upon previous knowledge and algorithms from software packages such as UHBD, SDA, and Macrodox, while implementing algorithms that scale to larger systems.

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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: HFOLD
Catalogue identifier: AEJG_v1_0
Program summary URL:
http://cpc.cs.qub.ac.uk/summaries/AEJG_v1_0.html
Program obtainable from: CPC Program Library, Queenʼs University, Belfast, N. Ireland
Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html
No. of lines in distributed program, including test data, etc.: 340 621
No. of bytes in distributed program, including test data, etc.: 1 760 051
Distribution format: tar.gz
Programming language: Fortran 77
Computer: Workstation, PC
Operating system: Linux
RAM: 524 288 000 Bytes
Classification: 11.1
External 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.

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We test a recent proposal to use approximate trivializing maps in a field
theory to speed up Hybrid Monte Carlo simulations. Simulating the CP^{N-1}
model, we find a small improvement with the leading order transformation, which
is however compensated by the additional computational overhead. The scaling of
the algorithm towards the continuum is not changed. In particular, the effect
of the topological modes on the autocorrelation times is studied.

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Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves
and bond-rebridging moves combined) we have determined the density of states
and thermodynamic properties for a short sequence of the HP protein model. For
free chains these proteins are known to first undergo a collapse "transition"
to a globule state followed by a second "transition" into a native state. When
placed in the proximity of an attractive surface, there is a competition
between surface adsorption and folding that leads to an intriguing sequence of
"transitions". These transitions depend upon the relative interaction strengths
and are largely inaccessible to "standard" Monte Carlo methods.

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The treatment of van der Waals interactions in density functional theory is an important field of ongoing research. Among different approaches developed recently to capture these non-local interactions, the van der Waals density functional (vdW-DF) developed in the groups of Langreth and Lundqvist is becoming increasingly popular. It does not rely on empirical parameters, and has been successfully applied to molecules, surface systems, and weakly-bound solids. As the vdW-DF requires the evaluation of a six-dimensional integral, it scales, however, unfavorably with system size. In this work, we present a numerically efficient implementation based on the Monte-Carlo technique for multi-dimensional integration. It can handle different versions of vdW-DF. Applications range from simple dimers to complex structures such as molecular crystals and organic molecules physisorbed on metal surfaces.

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The Cellular Potts Model (CPM) has been used in a wide variety of biological simulations. However, most current CPM implementations use a sequential modified Metropolis algorithm which restricts the size of simulations. In this paper we present a parallel CPM algorithm for simulations of morphogenesis, which includes cell-cell adhesion, a cell volume constraint, and cell haptotaxis. The algorithm uses appropriate data structures and checkerboard subgrids for parallelization. Communication and updating algorithms synchronize properties of cells simulated on different processor nodes. Tests show that the parallel algorithm has good scalability, permitting large-scale simulations of cell morphogenesis (10(7) or more cells) and broadening the scope of CPM applications. The new algorithm satisfies the balance condition, which is sufficient for convergence of the underlying Markov chain.

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New methods based on surfaces or beads have allowed measurement of properties of single DNA molecules in very accurate ways. Theoretical coarse grained models have been developed to understand the behavior of single stranded and double stranded DNA. These models have been shown to be accurate and relatively simple for very short systems of 6-8 base pairs near surfaces. Comparatively less is known about the influence of a surface on the secondary structures of longer molecules important to many technologies. Surface fields due to either applied potentials and/or dielectric boundaries are not in current surface mounted coarse grained models. To gain insight into longer and surface mounted sequences we parameterized a discretized worm-like chain model. Each link is considered a sphere of 6 base pairs in length for dsDNA, and 1.5 bases for ssDNA (requiring an always even number of spheres). For this demonstration of the model, the chain is tethered to a surface by a fixed length, non-interacting 0.536 nm linker. Configurational sampling was achieved via Monte-Carlo simulation. Our model successfully reproduces end to end distance averages from experimental results, in agreement with polymer theory and all atom simulations. Our average tilt results are also in agreement with all atom simulations for the case of dense systems.

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Multipole expansions offer a natural path to coarse-graining the electrostatic potential. However, the validity of the expansion is restricted to regions outside a spherical enclosure of the distribution of charge and, therefore, not suitable for most applications that demand accurate representation at arbitrary positions around the molecule. We propose and demonstrate a distributed multipole expansion approach that resolves this limitation. We also provide a practical algorithm for the computational implementation of this approach. The method allows the partitioning of the charge distribution into subsystems so that the multipole expansion of each component of the partition, and therefore of their superposition, is valid outside an enclosing surface of the molecule of arbitrary shape. The complexity of the resulting coarse-grained model of electrostatic potential is dictated by the area of the molecular surface and therefore, for a typical three-dimensional molecule, it scale as N(2/3) with N, the number of charges in the system. This makes the method especially useful for coarse-grained studies of biological systems consisting of many large macromolecules provided that the configuration of the individual molecules can be approximated as fixed.

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This paper deals with accurate numerical simulation of two-dimensional time-domain Maxwell's equations in materials with curved dielectric interfaces. The proposed fully second-order scheme is a hybridization between the immersed interface method (IIM), introduced to take into account curved geometries in structured schemes, and the Lax-Wendroff scheme, usually used to improve order of approximations in time for partial differential equations. In particular, the IIM proposed for two-dimensional acoustic wave equations with piecewise constant coefficients [C. Zhang, R.J. LeVeque, The immersed interface method for acoustic wave equations with discontinuous coefficients, Wave Motion 25 (1997) 237-263] is extended through a simple least squares procedure to such Maxwell's equations. Numerical results from the simulation of electromagnetic scattering of a plane incident wave by a dielectric circular cylinder appear to indicate that, compared to the original IIM for the acoustic wave equations, the augmented IIM with the proposed least squares fitting greatly improves the long-time stability of the time-domain solution. Semi-discrete finite difference schemes using the IIM for spatial discretization are also discussed and numerically tested in the paper.

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We present a new numerical technique to solve large-scale eigenvalue problems. It is based on the projection technique, used in strongly correlated quantum many-body systems, where first an effective approximate model of smaller complexity is constructed by projecting out high energy degrees of freedom and in turn solving the resulting model by some standard eigenvalue solver.
Here we introduce a generalization of this idea, where both steps are performed numerically and which in contrast to the standard projection technique converges in principle to the exact eigenvalues. This approach is not just applicable to eigenvalue problems encountered in many-body systems but also in other areas of research that result in large-scale eigenvalue problems for matrices which have, roughly speaking, mostly a pronounced dominant diagonal part. We will present detailed studies of the approach guided by two many-body models.

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We consider the question of how the cardiac rhythm spontaneously self-regulates and propose a new mechanism as a possible answer. We model the neuroautonomic regulation of the heart rate as a stochastic feedback system and find that the model successfully accounts for key characteristics of cardiac variability, including the 1/f power spectrum, the functional form and scaling of the distribution of variations of the interbeat intervals, and the correlations in the Fourier phases which indicate nonlinear dynamics.

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NASA
In the present paper, an algorithm for HZE (High Charge and Energy) fragmentation based upon a combination of a two step abrasion/ablation model and electromagnetic dissociation is presented. Development of the model and detailed comparison with available experimental data are given elsewhere. The abrasion process accounts for the removal of nuclear matter in the overlap region of the colliding ions. An average transmission factor is used for the projectile and target nuclei at a given impact parameter to account for the finite mean free path in nuclear matter. The ions are treated otherwise on a geometric basis assuming uniform spheres. The ablation process is treated as a single nucleon-evaporation for every 10 MeV of excitation energy as used by Bowman in the original form of the model. The charge distribution of final fragments are calculated according to the Rudstam formula, except for some correction in mass 5, 8 and 9 fragments which show strong structure effects and correspondingly significant deviation from Rudstam's values. The nuclear electromagnetic dissociation is based on the Weizsacker-Williams (WW) method of virtual quanta where due to its simplicity, the virtual photon spectrum for individual multipoles, and finite extent of the charge distribution are not included. Comparisons of the model are made with the available experimental data here and more extensively elsewhere.

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This document describes the first proof-of-concept version of the Pythia7 program.Pythia7 is a complete re-write of the Pythia program in C++. It is mainly intended to be a replacement for the ‘Lund’ family of event generators, but is also a framework with a structure suitable for implementing any event generator model.In this document, the structure of the program is presented both from the user and the developer point of view. It is not intended to be a complete manual, but together with the documentation provided in the distribution, it should be sufficient to start working with the program.

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Magnetism at the nanoscale has been a very active research area in the past
decades, because of its novel fundamental physics and exciting potential
applications. We have recently performed an {\it ab intio} study of the
structural, electronic and magnetic properties of all 3$d$ transition metal
(TM) freestanding atomic chains and found that Fe and Ni nanowires have a giant
magnetic anisotropy energy (MAE), indicating that these nanowires would have
applications in high density magnetic data storages. In this paper, we perform
density functional calculations for the Fe, Co and Ni linear atomic chains on
Cu(001) surface within the generalized gradient approximation, in order to
investigate how the substrates would affect the magnetic properties of the
nanowires. We find that Fe, Co and Ni linear chains on Cu(001) surface still
have a stable or metastable ferromagnetic state. When spin-orbit coupling (SOC)
is included, the spin magnetic moments remain almost unchanged, due to the
weakness of SOC in 3$d$ TM chains, whilst significant orbital magnetic moments
appear and also are direction-dependent. Finally, we find that the MAE for Fe,
and Co remains large, i.e., being not much affected by the presence of Cu
substrate.

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The paper describes two Monte Carlo codes dedicated to muon simulations: MUSIC (MUon SImulation Code) and MUSUN (MUon Simulations UNderground). MUSIC is a package for muon transport through matter. It is particularly useful for propagating muons through large thickness of rock or water, for instance from the surface down to underground/underwater laboratory. MUSUN is designed to use the results of muon transport through rock/water to generate muons in or around underground laboratory taking into account their energy spectrum and angular distribution.

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The Monte Carlo generator MERADGEN 1.0 for the simulation of radiative events in parity conserving doubly-polarized Møller scattering has been developed. Analytical integration wherever it is possible provides rather fast and accurate generation. Some numerical tests and histograms are presented.Program summaryProgram title: MERADGEN 1.0Catalogue identifier:ADYM_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYM_v1_0Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandLicensing provisions: noneProgramming language: FORTRAN 77Computer(s) for which the program has been designed: allOperating system(s) for which the program has been designed: LinuxRAM required to execute with typical data: 1 MBNo. of lines in distributed program, including test data, etc.:2196No. of bytes in distributed program, including test data, etc.:23 501Distribution format:tar.gzHas the code been vectorized or parallelized?: noNumber of processors used: 1Supplementary material: noneExternal routines/libraries used: noneCPC Program Library subprograms used: noneNature of problem: Simulation of radiative events in parity conserving doubly-polarized Møller scattering.Solution method: Monte Carlo method for simulation within QED, analytical integration wherever it is possible that provides rather fast and accurate generation.Restrictions: noneUnusual features: noneAdditional comments: noneRunning time: The simulation of 108 radiative events for itest:=1 takes up to 45 seconds on AMD Athlon 2.80 GHz processor.

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WPHACT (W W and Higgs Physics with PHACT) is a MC program and unweighted event generator which computes all Standard Model processes with four fermions in the final state at e+e− colliders. It is based on an helicity amplitude method which allows precise and fast evaluations of the matrix elements both for massless and massive fermions. Fermion masses for b quarks are exactly taken into account. QED initial state and Coulomb corrections are evaluated, while QCD final state corrections are included in an approximate formulation. Cuts can be easily introduced and distributions for any variable at parton level can be implemented. The contributions to the processes of neutral Standard Model or Susy Higgs can be included. Anomalous couplings effects for the triple coupling can be computed. An interface to hadronization is provided and Jetset can be directly called from the program.

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The AcerMC Monte Carlo Event Generator is dedicated for the generation of Standard Model background processes at pp LHC collisions. The program itself provides a library of the massive matrix elements and phase space modules for generation of a set of selected processes: , , , , and complete electroweak process. The hard process event, generated with one of these modules, can be completed by the initial and final state radiation, hadronization and decays, simulated with either PYTHIA or HERWIG Monte Carlo event generator. Interfaces to both of these generators are provided in the distribution version. The matrix element codes have been derived with the help of the MADGRAPH package. The phase-space generation is based on the multi-channel self-optimizing approach as proposed in NEXTCALIBUR event generator. Eventually, additional smoothing of the phase space was obtained by using a modified ac-VEGAS routine in order to improve the generation efficiency.

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The first version of a computer program "eett6f" for calculating cross sections of e+e- -> 6 fermions processes relevant for a t\bar{t}-pair production and decay at centre of mass energies typical for linear colliders is presented. "eett6f v.~1.0" allows for calculating both the total and differential cross sections at tree level of the Standard Model. The program can be used as the Monte Carlo generator of unweighted events as well. Comment: 19 pages, submitted to Comput. Phys. Commun

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A Monte Carlo program solving the Boltzmann equation for partons via the cascade method is presented. At presented, only gluon-gluon elastic scattering is included. The scattering cross section is regulated by a medium generated screening mass. Three different geometric modes (3-dimensional expansion, 1-d expansion, and scattering inside a box) are provided for both the theoretical study of parton transport and the application of the cascade method. Space cell division is available to save the number of computer operations. This improves the speed of the calculation by a large factor and makes the code best optimized for simulation of parton cascade in ultrarelativistic heavy ion collisions.

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In this article we have summarized the status of the system SANC version 1.00. We have implemented theoretical predictions for many high energy interactions of fundamental particles at the one-loop precision level for up to 4-particle processes. In the present part of our SANC description we place emphasis on an extensive discussion of an important first step of calculations of the one-loop amplitudes of 3- and 4-particle processes in QED, QCD and EW theories.Program summaryTitle of program:SANCCatalogue identifier: ADXK_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXK_v1_0Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandDesigned for: platforms on which Java and FORM3 are availableTested on: Intel-based PC'sOperating systems: Linux, WindowsProgramming languages used: Java, FORM3, PERL, FORTRANMemory required to execute with typical data: 10 MbNo. of bytes in distributed program, including test data, etc.: 3 658 844No. of bits in a word: 32No. of processors used: 1 on SANC server, 1 on SANC clientDistribution format: tar.gzNature of physical problem: Automatic calculation of pseudo- and realistic observables for various processes and decays in the Standard Model of Electroweak interactions, QCD and QED at one-loop precision level. Form factors and helicity amplitudes free of UV divergences are produced. For exclusion of IR singularities the soft photon emission is included.Method of solution: Numerical computation of analytical formulae of form factors and helicity amplitudes. For simulation of two fermion radiative decays of Standard Model bosons (W±,Z) and the Higgs boson a Monte Carlo technique is used.Restrictions on the complexity: In the current version of SANC there are 3 and 4 particle processes and decays available at one-loop precision level.Typical running time: The running time depends on the selected process. For instance, the symbolic calculation of form factors (with precomputed building blocks) of Bhabha scattering in the Standard Model takes about 15 s, helicity amplitudes—about 30 s, and bremsstrahlung—10 s. The numerical computation of cross-section for this process takes about 5 s (CPU 3 GHz IP4, RAM 512 Mb, L2 1024 KB).

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A description of the Fortran program HECTOR for a variety of semi-analytical calculations of radiative QED, QCD, and electroweak corrections to the double-differential cross sections of NC and CC deep inelastic charged lepton proton (or lepton deuteron) scattering is presented. HECTOR originates from the substantially improved and extended earlier programs HELIOS and TERAD91. It is mainly intended for applications at HERA or LEPxLHC, but may be used also for muon scattering in fixed target experiments. The QED corrections may be calculated in different sets of variables: leptonic, hadronic, mixed, Jaquet-Blondel, double angle etc. Besides the leading logarithmic approximation up to order O(alpha^2), exact order O(alpha) corrections and inclusive soft photon exponentiation are taken into account. The photoproduction region is also covered.

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The general-purpose self-adapting Monte Carlo (MC) event generator/simulator mFOAM (standing for mini-FOAM) is a new compact version of the FOAM program, with a slightly limited functionality with respect to its parent version. On the other hand, mFOAM is easier to use for the average user. This new version is fully integrated with the ROOT package, the C++ utility library used widely in the particle physics community. The internal structure of the code is simplified and the very valuable feature of the persistency of the objects of the mFOAM class is improved. With the persistency at hand, it is possible to record very easily the complete state of a MC simulator object based on MFOAM and ROOT into a disk-file at any stage of its use: just after object allocation, after full initialization (exploration of the distribution), or at any time during the generation of the long series of MC! events. Later on the MC simulator object can be easily restored from the disk-file in the "ready to go" state. Objects of the TFoam class can be used as a stand-alone solution to many everyday problems in the area of the Monte Carlo simulation, or as building blocks in large-scale MC projects, taking full advantage of the object-oriented technology and persistency.

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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 summaryProgram 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.

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JetViP is a computer program for the calculation of inclusive single- and dijet cross sections in eP- and e gamma-scattering in NLO QCD, The virtuality of the photon, radiated by the incoming electron, can be chosen in a continuous range, reaching from photoproduction into deep inelastic scattering. The various contributions to the full jet cross section, including the resolved photon contributions, are implemented. The calculation is based on the phase-space-slicing method. (C) 1999 Elsevier Science B.V.

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GRAPE-Dilepton is a Monte Carlo event generator for dilepton production in ep collisions. The cross-section calculation is based on the exact matrix elements in the electroweak theory at tree level. The dilepton productions via γγ, , collisions and via photon internal conversion are taken into account. In addition, the effects of the on/off-shell production are also included. The relevant Feynman amplitudes are generated by the automatic calculation system GRACE. The calculation of the proton vertex covers the whole kinematical region. This generator has an interface to PYTHIA and SOPHIA to obtain complete hadronic final states. This program can be downloaded from the CPC Program Library under catalogue identifies http://www-zeus.desy.de/~abe/grape/.

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A FORTRAN package containing parametrizations of parton distribution functions (PDFs) in the proton is described. It allows an easy access to PDFs provided by several recent parametrizations and to some parameters characterizing particular parametrization. Some comments about the use of various parametrizations are also included.

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A neural net program for pattern classification is presented. The neural net architecture is based on an improved version of Kohonen's learning vector organization: learning vector quantization with training count. The number of times a neuron is trained by input patterns of each class is stored in newly introduced training counters. This information, together with other which is collected during training, is used at the end of each training epoch for pruning, merging and creating neurons, and also in the classification process to estimate the reliability of the classification. Initially, neurons are automatically allocated to classes in proportion to the volumes and linear sizes of the corresponding distributions of input patterns in the pattern space, as estimated from the class covariance matrices. As an aside, pattern classification according to Mahalanobis distance and Fisher linear discrimination is also provided

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We present the Monte Carlo event generator YFSWW3 version 1.16 for theprocess of W-pair production and decay in electron-positron collisions. It includes ${\cal O}(\alpha)$ electroweak radiative corrections in the WW production stage together with the ${\cal O}(\alpha^3)$ initial-state-radiation (ISR) corrections in the leading-logarithmic (LL) approximation, implemented within the Yennie-Frautschi-Suura (YFS) exclusive exponentiation framework. The photon radiation in the W decays is generated by the dedicated program PHOTOS up to ${\cal O}(\alpha^2)$ LL, normalised to the W branching ratios. The program is interfaced with the $\tau$ decay library TAUOLA and the quark fragmentation/hadronization package JETSET. The semi-analytical code KORWAN for the calculations of the differential and total cross-sections at the Born level and in the ISR approximation is included. Comment: submitted to Comput. Physics Commun

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Theoretical predictions in high energy physics are routinely provided in the
form of Monte Carlo generators. Comparisons of predictions from different
programs and/or different initialization set-ups are often necessary. MC-TESTER
can be used for such tests of decays of intermediate states (particles or
resonances) in a semi-automated way.
Since 2002 new functionalities were introduced into the package. In
particular, it now works with the HepMC event record, the standard for C++
programs. The complete set-up for benchmarking the interfaces, such as
interface between tau-lepton production and decay, including QED bremsstrahlung
effects is shown. The example is chosen to illustrate the new options
introduced into the program. From the technical perspective, our paper
documents software updates and supplements previous documentation.
As in the past, our test consists of two steps. Distinct Monte Carlo programs
are run separately; events with decays of a chosen particle are searched, and
information is stored by MC-TESTER. Then, at the analysis step, information
from a pair of runs may be compared and represented in the form of tables and
plots.
Updates introduced in the progam up to version 1.24.3 are also documented. In
particular, new configuration scripts or script to combine results from
multitude of runs into single information file to be used in analysis step are
explained.

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We present the latest version of micrOMEGAs, a code that calculates the relic density of the lightest supersymmetric particle (LSP) in the minimal supersymmetric standard model (MSSM). All tree-level processes for the annihilation of the LSP are included as well as all possible coannihilation processes with neutralinos, charginos, sleptons, squarks and gluinos. The cross-sections extracted from CalcHEP are calculated exactly using loop-corrected masses and mixings as specified in the SUSY Les Houches Accord. Relativistic formulae for the thermal average are used and care is taken to handle poles and thresholds by adopting specific integration routines. The input parameters can be either the soft SUSY parameters in a general MSSM or the parameters of a SUGRA model specified at the GUT scale. In the latter case, a link with Suspect, SOFTSUSY, Spheno and Isajet allows one to calculate the supersymmetric spectrum, Higgs masses, as well as mixing matrices. Higher-order corrections to Higgs couplings to quark pairs including QCD as well as some SUSY corrections ( ) are implemented. Routines calculating , and are also included. In particular the routine includes an improved NLO for the SM and the charged Higgs while the SUSY large effects beyond leading-order are included. This new version also provides cross-sections for any process as well as partial decay widths for two-body final states in the MSSM allowing for easy simulation at colliders.

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We have written the Exclusive Hadronic Monte Carlo Event (ExHuME) generator. ExHuME is based around the perturbative QCD calculation of Khoze, Martin and Ryskin of the process pp→p+X+p, where X is a centrally produced colour singlet system.Program summaryTitle of program:ExHuMECatalogue identifier:ADYA_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYA_v1_0Program obtainable from:CPC Program Library, Queen's University of Belfast, N. IrelandLicensing provisions:NoneProgramming language used:C++, some FORTRANComputer:Any computer with UNIX capability. Users should refer to the README file distributed with the source code for further detailsOperating system:Linux, Mac OS XNo. of lines in distributed program, including test data, etc.:111 145No. of bytes in distributed program, including test data, etc.: 791 085Distribution format:tar.gzRAM:60 MBExternal routines/libraries:LHAPDF [http://durpdg.dur.ac.uk/lhapdf/], CLHEP v1.8 or v1.9 [L. Lönnblad, Comput. Phys. Comm. 84 (1994) 307; http://wwwinfo.cern.ch/asd/lhc++/clhep/]Subprograms used:Pythia [T. Sjostrand et al., Comput. Phys. Comm. 135 (2001) 238], HDECAY [A. Djouadi, J. Kalinowski, M. Spira, HDECAY: A program for Higgs boson decays in the standard model and its supersymmetric extension, Comput. Phys. Comm. 108 (1998) 56, hep-ph/9704448]. Both are distributed with the source codeNature of problem:Central exclusive production offers the opportunity to study particle production in a uniquely clean environment for a hadron collider. This program implements the KMR model [V.A. Khoze, A.D. Martin, M.G. Ryskin, Prospects for New Physics observations in diffractive processes at the LHC and Tevatron, Eur. Phys. J. C 23 (2002) 311, hep-ph/0111078], which is the only fully perturbative model of exclusive production.Solution method:Monte Carlo techniques are used to produce the central exclusive parton level system. Pythia routines are then used to develop a realistic hadronic system.Restrictions:The program is, at present, limited to Higgs, di-gluon and di-quark production. However, in principle it is not difficult to include more.Running time:Approximately 10 minutes for 10000 Higgs events on an Apple 1 GHz G4 PowerPC.

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The Monte Carlo program KoralW version 1.42 is presented. It generates all four-fermion final states with multibranch dedicated Monte Carlo pre-samplers and complete, massive, Born matrix elements. The presamplers cover the entire phase space. Multiphoton bremsstrahlung is implemented in the ISR approximation within the YFS formulation with the O(alpha**3) leading-log matrix element. The anomalous WWV couplings are implemented in CC03 approximation. The standard decay libraries (JETSET, PHOTOS, TAUOLA) are interfaced. The semi-analytical CC03-type code KorWan for differential and total cross-sections is included.

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The Monte Carlo generator {\sc Major} 1.5 simulates the production and decay of heavy Majorana neutrinos via lepton mixing or exchange of `light' right-handed $W$-bosons in deep inelastic scattering, i.e. $e^{\pm} p \rightarrow {N} X \rightarrow{e}^{\pm} W^{\mp} X$ or $\nu_e Z X$. Physics and programming aspects are described in this manual. Comment: 13 pages LaTeX, 2 PostScript figures

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The version 1.51 of the Monte Carlo (MC) program KoralW for all processes is presented. The most important change from the previous version 1.42 is the facility for writing MC events on the mass storage device and reprocessing them later on. In the reprocessing parameters of the Standard Model may be modified in order to fit them to experimental data. Another important new feature is the possibility of including complete corrections to double-resonant W-pair component-processes in addition to all background (non-WW) graphs. The inclusion is done with the help of the YFSWW3 MC event generator for fully exclusive differential distributions (event per event). Technically, it is done in such a way that YFSWW3 runs concurrently with KoralW as a separate slave process, reading momenta of the MC event generated by KoralW and returning the correction weight to KoralW. The latter introduces the correction using this weight, and finishes processing the event (rejection due to total MC weight, hadronization, etc.). The communication between KoralW and YFSWW3 is done with the help of the FIFO facility of the UNIX/Linux operating system. This does not require any modifications of the FORTRAN source codes. From the user's point of view, the resulting Concurrent MC event generator KoralW&YFSWW3 looks as a regular single MC event generator with all the standard features.

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Two ESOP processors using information from proportional chambers, scintillation hodoscopes and calorimeter ADCs have been used in a second stage trigger to improve the sensitivity and decrease the tape handling problems of an experiment to study the hadronic production of charmed particles. Details of the trigger and the results obtained are given.

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This article discusses an efficient implementation of tensors of arbitrary
rank by using some of the idioms introduced by the recently published C++ ISO
Standard (C++11). With the aims at providing a basic building block for
high-performance computing, a single Array class template is carefully crafted,
from which vectors, matrices, and even higher-order tensors can be created. An
expression template facility is also built around the array class template to
provide convenient mathematical syntax. As a result, by using templates, an
extra high-level layer is added to the C++ language when dealing with algebraic
objects and their operations, without compromising performance. The
implementation is tested running on both CPU and GPU.

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Coincidence intensities of the cascade decay 31D → 21P → 11S of helium excited by electron impact are computed using the symbolic manipulation package Mathematica. The formulation requires the calculation of a few thousand Clebsch-Gordan coefficients and rotation matrices, which would be extremely tedious to carry out by hand. A scheme is presented as an illustrative example of a lengthy and cumbersome calculation handled by Mathematica with ease.

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The study of phase transitions in concentrated solutions and melts of flexible or stiff polymers is a computational challenge for computer simulations, since already a single polymer coil exhibits nontrivial structure from the scale of a chemical bond (1 Å) to the coil radius (100 Å), and for the simulation of collective phenomena huge simulation boxes containing many polymers are required. A strategy to deal with this problem is the use of highly coarse-grained models on a lattice, such as the bond fluctuation model. Several studies employing such models will be briefly reviewed, e.g.: temperature-driven isotropic-nematic phase transition in concentrated solutions of semiflexible polymers, unmixing of polymer blends in the bulk and in a geometry confined between walls which prefer one component. It is shown that the finite-size scaling techniques previously developed for Ising-type models are useful in this context, too. Simulation of unmixed polymer blends between competing walls allows a study of an interface localization–delocalization transition and the observations of anomalous interfacial broadening (depending on thin film thickness). These simulations have also elucidated experiments.

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