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.     

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.     

Improved Invariant Generation for Tvoc

The NYU Tvoc project applies the method of translation validation to verify that optimized code is semantically equivalent to the unoptimized code, by establishing, for each run of the optimizing compiler, a set of verification conditions (VCs) whose validity implies the correctness of the optimized run. The core of Tvoc is Tvoc-sp, that handles structure preserving optimizations, i.e., optimizations that do not alter the inner loop structures. The underlying proof rule, Val, on whose soundness Tvoc-sp is based, requires, among other things, to generating invariants at each “cutpoint” of the control graph of both source and target codes. The current implementation of Tvoc-sp employs somewhat naïve fix-point computations to obtain the invariants. In this paper, we propose an alternative method to compute invartiants which is based on simple data-flow analysis techniques.     

Pomwig: Herwig for diffractive interactions

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

Range and Roots: Two common patterns for specifying and propagating counting and occurrence constraints

We propose Range and Roots which are two common patterns useful for specifying a wide range of counting and occurrence constraints. We design specialised propagation algorithms for these two patterns. Counting and occurrence constraints specified using these patterns thus directly inherit a propagation algorithm. To illustrate the capabilities of the Range and Roots constraints, we specify a number of global constraints taken from the literature. Preliminary experiments demonstrate that propagating counting and occurrence constraints using these two patterns leads to a small loss in performance when compared to specialised global constraints and is competitive with alternative decompositions using elementary constraints.     

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.     

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.     

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.     

A combinatorial algorithm for max csp

We consider the problem max csp over multi-valued domains with variables ranging over sets of size s_i?s and constraints involving k_j?k variables. We study two algorithms with approximation ratios A and B, respectively, so we obtain a solution with approximation ratio max(A,B).The first algorithm is based on the linear programming algorithm of Serna, Trevisan, and Xhafa [Proc. 15th Annual Symp. on Theoret. Aspects of Comput. Sci., 1998, pp. 488-498] and gives ratio A which is bounded below by s^1−k. For k=2, our bound in terms of the individual set sizes is the minimum over all constraints involving two variables of , where s₁ and s₂ are the set sizes for the two variables.We then give a simple combinatorial algorithm which has approximation ratio B, with B>A/e. The bound is greater than s^1−k/e in general, and greater than s^1−k(1−(s−1)/2(k−1)) for s?k−1, thus close to the s^1−k linear programming bound for large k. For k=2, the bound is if s=2, 1/2(s−1) if s?3, and in general greater than the minimum of 1/4s₁+1/4s₂ over constraints with set sizes s₁ and s₂, thus within a factor of two of the linear programming bound.For the case of k=2 and s=2 we prove an integrality gap of . This shows that our analysis is tight for any method that uses the linear programming upper bound.     

ris3: A program for relativistic isotope shift calculations

An atomic spectral line is characteristic of the element producing the spectrum. The line also depends on the isotope. The program ris3 (Relativistic Isotope Shift) calculates the electron density at the origin and the normal and specific mass shift parameters. Combining these electronic quantities with available nuclear data, isotope-dependent energy level shifts are determined.     

-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.     

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.     

Muse: Multi-algorithm collaborative crystal structure prediction

The algorithm and testing of the Multi-algorithm-collaborative Universal Structure-prediction Environment (Muse) are detailed. Presently, in Muse I combined the evolutionary, the simulated annealing, and the basin hopping algorithms to realize high-efficiency structure predictions of materials under certain conditions. Muse is kept open and other algorithms can be added in future. I introduced two new operators, slip and twist, to increase the diversity of structures. In order to realize the self-adaptive evolution of structures, I also introduced the competition scheme among the ten variation operators, as is proved to further increase the diversity of structures. The symmetry constraints in the first generation, the multi-algorithm collaboration, the ten variation operators, and the self-adaptive scheme are all key to enhancing the performance of Muse. To study the search ability of Muse, I performed extensive tests on different systems, including the metallic, covalent, and ionic systems. All these present tests show that Muse has very high efficiency and 100% success rate.     

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.     

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.