TiReX: Replica-exchange molecular dynamics using Tinker

We present a driver program for performing replica-exchange molecular dynamics simulations with the Tinker package. Parallelization is based on the Message Passing Interface, with every replica assigned to a separate process. The algorithm is not communication intensive, which makes the program suitable for running even on loosely coupled cluster systems. Particular attention is paid to the practical aspects of analyzing the program output.

Program summary

Program title: TiReXCatalogue identifier: AEEK_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEK_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 43 385No. of bytes in distributed program, including test data, etc.: 502 262Distribution format: tar.gzProgramming language: Fortran 90/95Computer: Most UNIX machinesOperating system: LinuxHas the code been vectorized or parallelized?: parallelized with MPIClassification: 16.13External routines: TINKER version 4.2 or 5.0, built as a libraryNature of problem: Replica-exchange molecular dynamics.Solution method: Each replica is assigned to a separate process; temperatures are swapped between replicas at regular time intervals.Running time: The sample run may take up to a few minutes.     

Qprop: A Schrödinger-solver for intense laser-atom interaction

The Qprop package is presented. Qprop has been developed to study laser-atom interaction in the nonperturbative regime where nonlinear phenomena such as above-threshold ionization, high order harmonic generation, and dynamic stabilization are known to occur. In the nonrelativistic regime and within the single active electron approximation, these phenomena can be studied with Qprop in the most rigorous way by solving the time-dependent Schrödinger equation in three spatial dimensions. Because Qprop is optimized for the study of quantum systems that are spherically symmetric in their initial, unperturbed configuration, all wavefunctions are expanded in spherical harmonics. Time-propagation of the wavefunctions is performed using a split-operator approach. Photoelectron spectra are calculated employing a window-operator technique. Besides the solution of the time-dependent Schrödinger equation in single active electron approximation, Qprop allows to study many-electron systems via the solution of the time-dependent Kohn-Sham equations.

Program summary

Program title:QPROPCatalogue number:ADXBProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXBProgram obtainable from:CPC Program Library, Queen's University of Belfast, N. IrelandComputer on which program has been tested:PC Pentium IV, AthlonOperating system:LinuxProgram language used:C++Memory required to execute with typical data:Memory requirements depend on the number of propagated orbitals and on the size of the orbitals. For instance, time-propagation of a hydrogenic wavefunction in the perturbative regime requires about 64 KB RAM (4 radial orbitals with 1000 grid points). Propagation in the strongly nonperturbative regime providing energy spectra up to high energies may need 60 radial orbitals, each with 30000 grid points, i.e. about 30 MB. Examples are given in the article.No. of bits in a word:Real and complex valued numbers of double precision are usedNo. of lines in distributed program, including test data, etc.:69 995No. of bytes in distributed program, including test data, etc.: 2 927 567Peripheral used:Disk for input-output, terminal for interaction with the userCPU time required to execute test data:Execution time depends on the size of the propagated orbitals and the number of time-stepsDistribution format:tar.gzNature of the physical problem:Atoms put into the strong field of modern lasers display a wealth of novel phenomena that are not accessible to conventional perturbation theory where the external field is considered small as compared to inneratomic forces. Hence, the full ab initio solution of the time-dependent Schrödinger equation is desirable but in full dimensionality only feasible for no more than two (active) electrons. If many-electron effects come into play or effective ground state potentials are needed, (time-dependent) density functional theory may be employed. Qprop aims at providing tools for (i) the time-propagation of the wavefunction according to the time-dependent Schrödinger equation, (ii) the time-propagation of Kohn-Sham orbitals according to the time-dependent Kohn-Sham equations, and (iii) the energy-analysis of the final one-electron wavefunction (or the Kohn-Sham orbitals).Method of solution:An expansion of the wavefunction in spherical harmonics leads to a coupled set of equations for the radial wavefunctions. These radial wavefunctions are propagated using a split-operator technique and the Crank-Nicolson approximation for the short-time propagator. The initial ground state is obtained via imaginary time-propagation for spherically symmetric (but otherwise arbitrary) effective potentials. Excited states can be obtained through the combination of imaginary time-propagation and orthogonalization. For the Kohn-Sham scheme a multipole expansion of the effective potential is employed. Wavefunctions can be analyzed using the window-operator technique, facilitating the calculation of electron spectra, either angular-resolved or integratedRestrictions onto the complexity of the problem:The coupling of the atom to the external field is treated in dipole approximation. The time-dependent Schrödinger solver is restricted to the treatment of a single active electron. As concerns the time-dependent density functional mode of Qprop, the Hartree-potential (accounting for the classical electron-electron repulsion) is expanded up to the quadrupole. Only the monopole term of the Krieger-Li-Iafrate exchange potential is currently implemented. As in any nontrivial optimization problem, convergence to the optimal many-electron state (i.e. the ground state) is not automatically guaranteedExternal routines/libraries used:The program uses the well established libraries blas, lapack, and f2c     

An integrated tool for loop calculations: aITALC

aITALC, a new tool for automating loop calculations in high energy physics, is described. The package creates Fortran code for two-fermion scattering processes automatically, starting from the generation and analysis of the Feynman graphs. We describe the modules of the tool, the intercommunication between them and illustrate its use with three examples.

Program summary

Title of the program:aITALC version 1.2.1 (9 August 2005)Catalogue identifier:ADWOProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADWOProgram obtainable from:CPC Program Library, Queen's University of Belfast, N. IrelandComputer:PC i386Operating system:GNU/Linux, tested on different distributions SuSE 8.2 to 9.3, Red Hat 7.2, Debian 3.0, Ubuntu 5.04. Also on SolarisProgramming language used:GNU Make, Diana, Form, Fortran77Additional programs/libraries used:Diana 2.35 (Qgraf 2.0), Form 3.1, LoopTools 2.1 (FF)Memory required to execute with typical data:Up to about 10 MBNo. of processors used:1No. of lines in distributed program, including test data, etc.:40 926No. of bytes in distributed program, including test data, etc.:371 424Distribution format:tar gzip fileHigh-speed storage required:from 1.5 to 30 MB, depending on modules present and unfolding of examplesNature of the physical problem:Calculation of differential cross sections for e⁺e⁻ annihilation in one-loop approximation.Method of solution:Generation and perturbative analysis of Feynman diagrams with later evaluation of matrix elements and form factors.Restriction of the complexity of the problem:The limit of application is, for the moment, the 2→2 particle reactions in the electro-weak standard model.Typical running time:Few minutes, being highly depending on the complexity of the process and the Fortran compiler.     

Revised and extended Utilities for the Ratip package

During the last years, the Ratip package has been found useful for calculating the excitation and decay properties of free atoms. Based on the (relativistic) multiconfiguration Dirac-Fock method, this program is used to obtain accurate predictions of atomic properties and to analyze many recent experiments. The daily work with this package made an extension of its Utilities [S. Fritzsche, Comput. Phys. Comm. 141 (2001) 163] desirable in order to facilitate the data handling and interpretation of complex spectra. For this purpose, we make available an enlarged version of the Utilities which mainly supports the comparison with experiment as well as large Auger computations. Altogether 13 additional tasks have been appended to the program together with a new menu structure to improve the interactive control of the program.

Program summary

Title of program: RATIPCatalogue identifier: ADPD_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADPD_v2_0Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandLicensing provisions: noneReference in CPC to previous version: S. Fritzsche, Comput. Phys. Comm. 141 (2001) 163Catalogue identifier of previous version: ADPDAuthors of previous version: S. Fritzsche, Department of Physics, University of Kassel, Heinrich-Plett-Strasse 40, D-34132 Kassel, GermanyDoes the new version supersede the original program?: yesComputer for which the new version is designed and others on which it has been tested: IBM RS 6000, PC Pentium II-IVInstallations: University of Kassel (Germany), University of Oulu (Finland)Operating systems: IBM AIX, Linux, UnixProgram language used in the new version: ANSI standard Fortran 90/95Memory required to execute with typical data: 300 kBNo. of bits in a word: All real variables are parameterized by a selected kind parameter and, thus, can be adapted to any required precision if supported by the compiler. Currently, the kind parameter is set to double precision (two 32-bit words) as used also for other components of the Ratip package [S. Fritzsche, C.F. Fischer, C.Z. Dong, Comput. Phys. Comm. 124 (2000) 341; G. Gaigalas, S. Fritzsche, Comput. Phys. Comm. 134 (2001) 86; S. Fritzsche, Comput. Phys. Comm. 141 (2001) 163; S. Fritzsche, J. Elec. Spec. Rel. Phen. 114-116 (2001) 1155]No. of lines in distributed program, including test data, etc.:231 813No. of bytes in distributed program, including test data, etc.: 3 977 387Distribution format: tar.gzip fileNature of the physical problem: In order to describe atomic excitation and decay properties also quantitatively, large-scale computations are often needed. In the framework of the Ratip package, the Utilities support a variety of (small) tasks. For example, these tasks facilitate the file and data handling in large-scale applications or in the interpretation of complex spectra.Method of solution: The revised Utilities now support a total of 29 subtasks which are mainly concerned with the manipulation of output data as obtained from other components of the Ratip package. Each of these tasks are realized by one or several subprocedures which have access to the corresponding modules of the main components. While the main menu defines seven groups of subtasks for data manipulations and computations, a particular task is selected from one of these group menus. This allows to enlarge the program later if technical support for further tasks will become necessary. For each selected task, an interactive dialog about the required input and output data as well as a few additional information are printed during the execution of the program.Reasons for the new version: The requirement for enlarging the previous version of the Utilities [S. Fritzsche, Comput. Phys. Comm. 141 (2001) 163] arose from the recent application of the Ratip package for large-scale radiative and Auger computations. A number of new subtasks now refer to the handling of Auger amplitudes and their proper combination in order to facilitate the interpretation of complex spectra. A few further tasks, such as the direct access to the one-electron matrix elements for some given set of orbital functions, have been found useful also in the analysis of data.Summary of revisions: extraction and handling of atomic data within the framework of Ratip. With the revised version, we now ‘add’ another 13 tasks which refer to the manipulation of data files, the generation and interpretation of Auger spectra, the computation of various one- and two-electron matrix elements as well as the evaluation of momentum densities and grid parameters. Owing to the rather large number of subtasks, the main menu has been divided into seven groups from which the individual tasks can be selected very similarly as before.Typical running time: The program responds promptly for most of the tasks. The responding time for some tasks, such as the generation of a relativistic momentum density, strongly depends on the size of the corresponding data files and the number of grid points.Unusual features of the program: A total of 29 different tasks are supported by the program. Starting from the main menu, the user is guided interactively through the program by a dialog and a few additional explanations. For each task, a short summary about its function is displayed before the program prompts for all the required input data.     

Relativistic central-field Green's functions for the Ratip package

From perturbation theory, Green's functions are known for providing a simple and convenient access to the (complete) spectrum of atoms and ions. Having these functions available, they may help carry out perturbation expansions to any order beyond the first one. For most realistic potentials, however, the Green's functions need to be calculated numerically since an analytic form is known only for free electrons or for their motion in a pure Coulomb field. Therefore, in order to facilitate the use of Green's functions also for atoms and ions other than the hydrogen-like ions, here we provide an extension to the Ratip program which supports the computation of relativistic (one-electron) Green's functions in an—arbitrarily given—central-field potential V(r). Different computational modes have been implemented to define these effective potentials and to generate the radial Green's functions for all bound-state energies E<0. In addition, care has been taken to provide a user-friendly component of the Ratip package by utilizing features of the Fortran 90/95 standard such as data structures, allocatable arrays, or a module-oriented design.

Program summary

Title of program:XgreensCatalogue number: ADWMProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADWMProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandLicensing provisions:NoneComputer for which the new version has been tested: PC Pentium II, III, IV, AthlonInstallations: University of Kassel (Germany)Operating systems: SuSE Linux 8.2, SuSE Linux 9.0Program language used in the new version: ANSI standard Fortran 90/95Memory required to execute with typical data: On a standard grid (400 nodes), one central-field Green's function requires about 50 kBytes in RAM while approximately 3 MBytes are needed if saved as two-dimensional array on some external disc spaceNo. of bits in a word: Real variables of double- and quad-precision are usedPeripheral used: Disk for input/outputCPU time required to execute test data: 2 min on a 450 MHz Pentium III processorNo. of lines in distributed program, including test data etc.: 82 042No. of bytes in distributed program, including test data etc.: 814 096Distribution format: tar.gzNature of the physical problem: In atomic perturbation theory, Green's functions may help carry out the summation over the complete spectrum of atom and ions, including the (summation over the) bound states as well as an integration over the continuum [R.A. Swainson, G.W.F. Drake, J. Phys. A 24 (1991) 95]. Analytically, however, these functions are known only for free electrons (V(r)≡0) and for electrons in a pure Coulomb field (V(r)=−Z/r). For all other choices of the potential, in contrast, the Green's functions must be determined numerically.Method of solution: Relativistic Green's functions are generated for an arbitrary central-field potential V(r)=−Z(r)/r by using a piecewise linear approximation of the effective nuclear charge function Z(r) on some grid : Zi(r)=Z0i+Z1ir. Then, following McGuire's algorithm [E.J. McGuire, Phys. Rev. A 23 (1981) 186], the radial Green's functions are constructed from the (two) linear-independent solutions of the homogeneous equation [P. Morse, H. Feshbach, Methods of Theoretical Physics, McGraw-Hill, New York 1953 (Part 1, p. 825)]. In the computation of these radial functions, the Kummer and Tricomi functions [J. Spanier, B. Keith, An Atlas of Functions, Springer, New York, 1987] are used extensively.Restrictions onto the complexity of the problem: The main restrictions of the program concern the shape of the effective nuclear charge Z(r)=−rV(r), i.e. the choice of the potential, and the allowed energies. Apart from obeying the proper boundary conditions for a point-like nucleus, namely, Z(r→0)=Znuc>0 and Z(r→∞)=Znuc−Nelectrons?0, the first derivative of the charge function Z(r) must be smaller than the (absolute value of the) energy of the Green's function, .Unusual features of the program:Xgreens has been designed as a part of the Ratip package [S. Fritzsche, J. Elec. Spec. Rel. Phen. 114-116 (2001) 1155] for the calculation of relativistic atomic transition and ionization properties. In a short dialog at the beginning of the execution, the user can specify the choice of the potential as well as the energies and the symmetries of the radial Green's functions to be calculated. Apart from central-field Green's functions, of course, the Coulomb Green's function [P. Koval, S. Fritzsche, Comput. Phys. Comm. 152 (2003) 191] can also be computed by selecting a constant nuclear charge Z(r)=Zeff. In order to test the generated Green's functions, moreover, we compare the two lowest bound-state orbitals which are calculated from the Green's functions with those as generated separately for the given potential. Like the other components of the Ratip package, Xgreens makes careful use of the Fortran 90/95 standard.     

Pomwig: Herwig for diffractive interactions

We have modified the Herwig event generator to incorporate diffractive interactions. All standard Herwig hard subprocesses are available.     

Comment on “A direct approach with computerized symbolic computation for finding a series of traveling waves to nonlinear equations” by Engui Fan and H.H. Dai: [Comput. Phys. Commun. 153 (2003) 17]

Fan and Dai [Comput. Phys. Commun. 153 (2003) 17] have found a series of traveling wave solutions for nonlinear equations by applying a direct approach with computerized symbolic computations. They have claimed that the proposed method, in comparison with most existing symbolic computation methods such as a tanh method and Jacobi function method, not only give new and more general solutions, but also provides a guideline to classify various types of the solution according to some parameters. We show that the claims by Fan and Dai are wrong since some of the solutions do not satisfy the differential equation that they have adopted for the algebraic method.     

Bandwidth on AT-free graphs

We study the classical Bandwidth problem from the viewpoint of parametrised algorithms. Given a graph G=(V,E) and a positive integer k, the Bandwidth problem asks whether there exists a bijective function β:{1,…,∣V∣}→V such that for every edge uv∈E, ∣β⁻¹(u)−β⁻¹(v)∣≤k. It is known that under standard complexity assumptions, no algorithm for Bandwidth with running time of the form f(k)n^O(1) exists, even when the input is restricted to trees. We initiate the search for classes of graphs where such algorithms do exist. We present an algorithm with running time n⋅2^O(klogk) for Bandwidth on AT-free graphs, a well-studied graph class that contains interval, permutation, and cocomparability graphs. Our result is the first non-trivial algorithm that shows fixed-parameter tractability of Bandwidth on a graph class on which the problem remains NP-complete.     

An object-oriented C++ implementation of Davidson method for finding a few selected extreme eigenpairs of a large, sparse, real, symmetric matrix

A C++ class named Davidson is presented for determining a few eigenpairs with lowest or alternatively highest values of a large, real, symmetric matrix. The algorithm described by Stathopoulos and Fischer is used. The exception mechanism is involved to report the errors. The class is written in ANSI C++, so it is fully portable. In addition a console program as well as a program with graphical user interface for Microsoft Windows is attached, which allow one to calculate the lowest eigenstates of time-independent Schrödinger equation for a given binding potential in one, two or three spatial dimensions. The package contains the classes providing often used potential functions (model atom potential, Coulomb potential, square well potential and Kramers-Henneberger well potential) as well as a possibility to use any potential stored in a file (then any dimensionality of the problem is allowed).The described code is the subject of M.Sc. thesis of T.D. prepared under the supervision of J.M.

Program summary

Program title: DavidsonCatalogue identifier: ADZM_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZM_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.: 3 037 055No. of bytes in distributed program, including test data, etc.: 20 002 609Distribution format: tar.gzProgramming language: C++Computer: AllOperating system: AnyRAM: User's parameters dependentWord size: 32 and 64 bitsSupplementary material: Test results for the 2D and 3D cases is availableClassification: 4, 4.8Nature of problem: Finding a few extreme eigenpairs of a real, symmetric, sparse matrix. Examples in quantum optics (interaction of matter with a laser field).Solution method: Davidson algorithmRunning time: The test example included in the distribution package (1D matrix) takes approximately 30 minutes to run. 2D matrix calculations can take hours and 3D, days, 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.

     

Kanga(ROO): Handling the micro-DST of the BaBar experiment with ROOT

A system based on ROOT for handling the micro-DST of the BaBar experiment is described. The purpose of the Kanga system is to have micro-DST data available in a format well suited for data distribution within a world-wide collaboration with many small sites. The design requirements, implementation and experience in practice after three years of data taking by the BaBar experiment are presented.     

fgh, a code for the calculation of Coulomb radial wave functions from series expansions

The code fgh is an up-dated version of a code coulfg (see [Seaton, Comput. Phys. Comm. 25 (1982) 87]), used for the calculation of the Coulomb functions f and g, analytic in the energy, for attractive potentials. The new code works for attractive and repulsive potentials and also gives the functions h which have simple asymptotic forms. There is an option to use either the variables (?,r) customary in atomic physics, or (for positive energies) (η,ρ) customary in nuclear physics. When (η,ρ) are used, the code also gives the functions F_?(η,ρ) and G_?(η,ρ).Use of series solutions can lead to loss of accuracy due to cancellation effects. fgh provides an indication of the number of significant figures lost due to cancellations.     

Supervised ranking in the weka environment

Software for solving the supervised ranking problem is presented. Four variants of the Ordinal Stochastic Dominance Learner (OSDL) are given, together with the space and time complexity of their implementations. It is shown that the described software, which includes two further algorithms for supervised ranking, fits seamlessly into the weka environment.     

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.     

Proofs of randomized algorithms in Coq

Randomized algorithms are widely used for finding efficiently approximated solutions to complex problems, for instance primality testing and for obtaining good average behavior. Proving properties of such algorithms requires subtle reasoning both on algorithmic and probabilistic aspects of programs. Thus, providing tools for the mechanization of reasoning is an important issue. This paper presents a new method for proving properties of randomized algorithms in a proof assistant based on higher-order logic. It is based on the monadic interpretation of randomized programs as probabilistic distributions (Giry, Ramsey and Pfeffer). It does not require the definition of an operational semantics for the language nor the development of a complex formalization of measure theory. Instead it uses functional and algebraic properties of unit interval. Using this model, we show the validity of general rules for estimating the probability for a randomized algorithm to satisfy specified properties. This approach addresses only discrete distributions and gives rules for analyzing general recursive functions.We apply this theory to the formal proof of a program implementing a Bernoulli distribution from a coin flip and to the (partial) termination of several programs. All the theories and results presented in this paper have been fully formalized and proved in the Coq proof assistant.     

udkm1Dsim—A simulation toolkit for 1D ultrafast dynamics in condensed matter

The udkm1Dsim  toolbox is a collection of matlab (MathWorks Inc.) classes and routines to simulate the structural dynamics and the according X-ray diffraction response in one-dimensional crystalline sample structures upon an arbitrary time-dependent external stimulus, e.g. an ultrashort laser pulse. The toolbox provides the capabilities to define arbitrary layered structures on the atomic level including a rich database of corresponding element-specific physical properties. The excitation of ultrafast dynamics is represented by an N$N$-temperature model which is commonly applied for ultrafast optical excitations. Structural dynamics due to thermal stress are calculated by a linear-chain model of masses and springs. The resulting X-ray diffraction response is computed by dynamical X-ray theory. The udkm1Dsim  toolbox is highly modular and allows for introducing user-defined results at any step in the simulation procedure.