Workstation Operating Systems Research Articles

The Ratip program for relativistic calculations of atomic transition, ionization and recombination properties

The Ratip program for relativistic calculations of atomic transition, ionization and recombination properties

An object oriented code for simulating supersymmetric Yang–Mills theories

We present SUSY_LATTICE – a C++ program that can be used to simulate certain classes of supersymmetric Yang–Mills (SYM) theories, including the well known N=4 SYM in four dimensions, on a flat Euclidean space–time lattice. Discretization of SYM theories is an old problem in lattice field theory. It has resisted solution until recently when new ideas drawn from orbifold constructions and topological field theories have been brought to bear on the question. The result has been the creation of a new class of lattice gauge theories in which the lattice action is invariant under one or more supersymmetries. The resultant theories are local, free of doublers and also possess exact gauge-invariance. In principle they form the basis for a truly non-perturbative definition of the continuum SYM theories. In the continuum limit they reproduce versions of the SYM theories formulated in terms of twisted fields, which on a flat space–time is just a change of the field variables. In this paper, we briefly review these ideas and then go on to provide the details of the C++ code. We sketch the design of the code, with particular emphasis being placed on SYM theories with N=(2,2) in two dimensions and N=4 in three and four dimensions, making one-to-one comparisons between the essential components of the SYM theories and their corresponding counterparts appearing in the simulation code. The code may be used to compute several quantities associated with the SYM theories such as the Polyakov loop, mean energy, and the width of the scalar eigenvalue distributions. Program summaryProgram title: SUSY_LATTICECatalogue identifier: AELS_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AELS_v1_0.htmlProgram obtainable from: CPC Program Library, Queenʼs University, Belfast, N. IrelandLicensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 9315No. of bytes in distributed program, including test data, etc.: 95 371Distribution format: tar.gzProgramming language: C++Computer: PCs and WorkstationsOperating system: Any, tested on Linux machinesClassification:: 11.6Nature of problem: To compute some of the observables of supersymmetric Yang–Mills theories such as supersymmetric action, Polyakov/Wilson loops, scalar eigenvalues and Pfaffian phases.Solution method: We use the Rational Hybrid Monte Carlo algorithm followed by a Leapfrog evolution and a Metropolis test. The input parameters of the model are read in from a parameter file.Restrictions: This code applies only to supersymmetric gauge theories with extended supersymmetry, which undergo the process of maximal twisting. (See Section 2 of the manuscript for details.)Running time: From a few minutes to several hours depending on the amount of statistics needed.

Algorithmic derivation of functional renormalization group equations and Dyson–Schwinger equations

We present the Mathematica application DoFun1 which allows to derive Dyson–Schwinger equations and renormalization group flow equations for n-point functions in a simple manner. DoFun offers several tools which considerably simplify the derivation of these equations from a given physical action. We discuss the application of DoFun by means of two different types of quantum field theories, namely a bosonic O(N) theory and the Gross–Neveu model. Program summaryProgram title:DoFunCatalogue identifier: AELN_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AELN_v1_0.htmlProgram obtainable from: CPC Program Library, Queenʼs 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 506No. of bytes in distributed program, including test data, etc.: 571 837Distribution format: tar.gzProgramming language: Mathematica 7 and higherComputer: PCs and workstationsOperating system: All on which Mathematica is available (Windows, Unix, MacOS)Classification: 11.1, 11.4, 11.5, 11.6Nature of problem: Derivation of functional renormalization group equations and Dyson–Schwinger equations from the action of a given theory.Solution method: Implementation of an algorithm to derive functional renormalization group and Dyson–Schwinger equations.Unusual features: The results can be plotted as Feynman diagrams in Mathematica. The output is compatible with the syntax of many other programs and is therefore suitable for further (algebraic) computations.Running time: Seconds to minutes

MEMPSODE: A global optimization software based on hybridization of population-based algorithms and local searches

We present MEMPSODE, a global optimization software tool that integrates two prominent population-based stochastic algorithms, namely Particle Swarm Optimization and Differential Evolution, with well established efficient local search procedures made available via the Merlin optimization environment. The resulting hybrid algorithms, also referred to as Memetic Algorithms, combine the space exploration advantage of their global part with the efficiency asset of the local search, and as expected they have displayed a highly efficient behavior in solving diverse optimization problems. The proposed software is carefully parametrized so as to offer complete control to fully exploit the algorithmic virtues. It is accompanied by comprehensive examples and a large set of widely used test functions, including tough atomic cluster and protein conformation problems. Program summaryProgram title: MEMPSODE (MEMetic Particle Swarm Optimization and Differential Evolution)Catalogue identifier: AELM_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AELM_v1_0.htmlProgram obtainable from: CPC Program Library, Queenʼs University, Belfast, N. IrelandLicensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 14 877No. of bytes in distributed program, including test data, etc.: 592 244Distribution format: tar.gzProgramming language: ANSI C, ANSI Fortran-77Computer: WorkstationsOperating system: Developed under the Linux operating system using the GNU compilers v.4.4.3. It has also been tested under Solaris and the Cygwin environment.RAM: The code uses O(n×N) internal storage, n being the dimension of the problem and N the maximum population size. The required memory is dynamically allocated.Word size: 64 bitsClassification: 4.9Subprograms used:Cat IdTitleReferenceAAXW_v4_0 MERLIN-3.1.1 CPC 159 (2004) 70Nature of problem: Optimization is a valuable mathematical tool for solving a plethora of scientific and engineering problems. Usually, the underlying problems are modeled with objective functions whose minimizers (or maximizers) correspond to the desired solutions of the original problem. In many cases, there is a multitude of such minimizers that correspond to solutions either locally, i.e., in their close neighborhood, or globally, i.e., with respect to the whole search space. There is a significant number of efficient algorithms for addressing optimization problems. One can distinguish two main categories, based on their adequacy in performing better global (exploration) or local (exploitation) search. Standard local optimization algorithms have the ability to rapidly converge towards local minimizers but they are also prone to get easily trapped in their vicinity. These algorithms usually exploit local information of the objective function, including first- and second-order derivatives. On the other hand, global optimization algorithms are designed to perform better exploration, although at the cost of questionable convergence properties. Typically, these approaches integrate stochastic operations. The form of the optimization problem at hand plays a crucial role in the selection of the most appropriate algorithm. Objective functions that lack nice mathematical properties (such as differentiability, continuity etc.) may raise applicability issues for algorithms that require derivatives. On the other hand, applications that require high accuracy may be laborious for stochastic algorithms. The existence of a multitude of local and/or global minimizers can render these problems even harder for any single optimization algorithm.Solution method: Evolutionary Algorithms and Swarm Intelligence approaches have been established as effective global optimization algorithms that make minor assumptions about the objective function. Particle Swarm Optimization (PSO) and Differential Evolution (DE) possess a salient position among the most successful algorithms of these categories. Numerous studies indicate that their performance can be radically improved when combined with efficient local optimization schemes. The resulting hybrid algorithms offer more balanced search intensification/diversification than the original ones, thereby increasing both their efficiency and effectiveness. Such hybrid schemes are called Memetic Algorithms, and they have gained a rapidly growing interest over the past few years.We present MEMPSODE (MEMetic, PSO and DE), a global optimization software that implements memetic PSO and DE within a unified framework. The software utilizes local search procedures from the established Merlin optimization environment. The performance of the implemented approaches is illustrated on several examples, including hard optimization tasks such as atomic cluster and protein conformation problems.Restrictions: The current version of the software uses double precision arithmetic. However, it can be easily adapted by the user to handle integer or mixed-integer problems.Unusual features: The software takes into account only bound constraints. General constraints may be tackled by user-defined penalty or barrier functions that can be easily incorporated in the source code of the objective function.Additional comments: The use of the Merlin Optimization Environment 3.1.1 (see subprograms above) is optional.A comprehensive user manual is provided that covers in detail the installation procedure and provides detailed examples of operation.Running time: The running time depends solely on the complexity of the objective function (and its derivatives, if used) as well as on the available computational budget (number of function evaluations). The test run provided (Rastrigin function n=10), requires 2.5×106 function evaluations (2.8 seconds on an i7-920 CPU).

Finding higher symmetries of differential equations using the MAPLE package DESOLVII

We present and describe, with illustrative examples, the MAPLE computer algebra package DESOLVII, which is a major upgrade of DESOLV. DESOLVII now includes new routines allowing the determination of higher symmetries (contact and Lie–Bäcklund) for systems of both ordinary and partial differential equations. Program summaryProgram title: DESOLVIICatalogue identifier: ADYZ_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYZ_v2_0.htmlProgram obtainable from: CPC Program Library, Queenʼs 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 858No. of bytes in distributed program, including test data, etc.: 112 515Distribution format: tar.gzProgramming language: MAPLE internal languageComputer: PCs and workstationsOperating system: Linux, Windows XP and Windows 7RAM: Depends on the type of problem and the complexity of the system (small≈MB, large≈GB)Classification: 4.3, 5Catalogue identifier of previous version: ADYZ_v1_0Journal reference of previous version: Comput. Phys. Comm. 176 (2007) 682Does the new version supersede the previous version?: YesNature of problem: There are a number of approaches one may use to find solutions to systems of differential equations. These include numerical, perturbative, and algebraic methods. Unfortunately, approximate or numerical solution methods may be inappropriate in many cases or even impossible due to the nature of the system and hence exact methods are important. In their own right, exact solutions are valuable not only as a yardstick for approximate/numerical solutions but also as a means of elucidating the physical meaning of fundamental quantities in systems.One particular method of finding special exact solutions is afforded by the work of Sophus Lie and the use of continuous transformation groups. The power of Lieʼs group theoretic method lies in its ability to unify a number of ad hoc integration methods through the use of symmetries, that is, continuous groups of transformations which leave the differential system “unchanged”. These symmetry groups may then be used to find special solutions. Solutions found in this manner are called similarity or invariant solutions.The method of finding symmetry transformations initially requires the generation of a large overdetermined system of linear, homogeneous, coupled PDEs. The integration of this system is usually reasonably straightforward requiring the (often elementary) integration of equations by splitting the system according to dependency on different orders and degrees of the dependent variable/s. Unfortunately, in the case of contact and Lie–Bäcklund symmetries, the integration of the determining system becomes increasingly more difficult as the order of the symmetry is increased. This is because the symmetry generating functions become dependent on higher orders of the derivatives of the dependent variables and this diminishes the overall resulting “separable” differential conditions derived from the main determining system. Furthermore, typical determining systems consist of tens to hundreds of equations and this, combined with standard mechanical solution methods, makes the process well suited to automation using computer algebra systems.The new MAPLE package DESOLVII, which is a major upgrade of DESOLV, now includes routines allowing the determination of higher symmetries (contact and Lie–Bäcklund) for systems of both ordinary and partial differential equations. In addition, significant improvements have been implemented to the algorithm for PDE solution. Finally, we have made some improvements in the overall automated process so as to improve user friendliness by reducing user intervention where possible.Solution method: See “Nature of problem” above.Reasons for new version: New and improved functionality.Summary of revisions:1.New functionality – can now compute generalised symmetries.2.Much improved efficiency (speed and memory use) of existing routines.Restrictions: Sufficient memory may be required for complex systems.Running time: Depends on the type of problem and the complexity of the system (small≈seconds, large≈hours).

Universal interface of TAUOLA: Technical and physics documentation

Because of their narrow width, τ decays can be well separated from their production process. Only spin degrees of freedom connect these two parts of the physics process of interest for high energy collision experiments. In the following, we present a Monte Carlo algorithm which is based on that property. The interface supplements events generated by other programs, with τ decays. Effects of spin, including transverse degrees of freedom, genuine weak corrections or of new physics may be taken into account at the time when a τ decay is generated and written into an event record. The physics content of the C++ interface is already now richer than its FORTRAN predecessor. Program summary Program title: TAUOLA++, versions 1.0.2, 1.0.3, 1.0.4, 1.0.5, 1.0.6 Catalogue identifier: AELH_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AELH_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.: 649 068 No. of bytes in distributed program, including test data, etc.: 6 544 479 Distribution format: tar.gz Programming language: C++, FORTRAN77 Computer: PCs, workstations Operating system: Linux, MacOS RAM: < 10 MB Classification: 11.2 External routines: HepMC ( http://lcgapp.cern.ch/project/simu/HepMC/), optional; PYTHIA8 ( http://home.thep.lu.se/~torbjorn/Pythia.html) Subprograms used: Cat Id Title Reference ADSM_v2_0 MC-TESTER Comput. Phys. Commun. 182 (2011) 779 Nature of problem: The code of Monte Carlo generators often has to be tuned to the needs of large HEP Collaborations and experiments. In particular τ lepton decays need to be added (or modified) to the previously generated (or measured) events encapsulated in an event record. Solution method: The new algorithm, the universal interface of TAUOLA which works with the HepMC event record of C++ applications is documented. It uses the τ decay generator as described in [2] with the updates explained in [1]. For the new interface spin treatment was improved. For example it features complete spin effects in processes mediated by Z / γ ⁎ interactions. The effects of electroweak corrections can be taken into account in this case as well. In general, the program superseeds its FORTRAN predecessor [1]. The event record analysis as well as initialization is also modernized. Restrictions: The input event record must meet the requirements described in Section 2.3.1 of the documentation. Unusual features: Two sets of installation scripts; an additional tool for calculating tables for electroweak corrections. Running time: Depends on the size and complexity of the events. Small events (<50 particles), require 1 to 7 minutes for processing 1 M events on PC/Linux with a 2.4 GHz processor.

A Fortran 90 Hartree–Fock program for one-dimensional periodic π-conjugated systems using Pariser–Parr–Pople model

Pariser–Parr–Pople (P-P-P) model Hamiltonian is employed frequently to study the electronic structure and optical properties of π-conjugated systems. In this paper we describe a Fortran 90 computer program which uses the P-P-P model Hamiltonian to solve the Hartree–Fock (HF) equation for infinitely long, one-dimensional, periodic, π-electron systems. The code is capable of computing the band structure, as also the linear optical absorption spectrum, by using the tight-binding and the HF methods. Furthermore, using our program the user can solve the HF equation in the presence of a finite external electric field, thereby, allowing the simulation of gated systems. We apply our code to compute various properties of polymers such as trans-polyacetylene, poly- para-phenylene, and armchair and zigzag graphene nanoribbons, in the infinite length limit. Program summary Program title: ppp_bulk.x Catalogue identifier: AEKW_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEKW_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.: 87 464 No. of bytes in distributed program, including test data, etc.: 2 046 933 Distribution format: tar.gz Programming language: Fortran 90 Computer: PCs and workstations Operating system: Linux, Code was developed and tested on various recent versions of 64-bit Fedora including Fedora 14 (kernel version 2.6.35.12-90). Classification: 7.3 External routines: This program needs to link with LAPACK/BLAS libraries compiled with the same compiler as the program. For the Intel Fortran Compiler we used the ACML library version 4.4.0, while for the gfortran compiler we used the libraries supplied with the Fedora distribution. Nature of problem: The electronic structure of one-dimensional periodic π-conjugated systems is an intense area of research at present because of the tremendous interest in the physics of conjugated polymers and graphene nanoribbons. The computer program described in this paper provides an efficient way of solving the Hartree–Fock equations for such systems within the P-P-P model. In addition to the Bloch orbitals, band structure, and the density of states, the program can also compute quantities such as the linear absorption spectrum, and the electro-absorption spectrum of these systems. Solution method: For a one-dimensional periodic π-conjugated system lying in the xy-plane, the single-particle Bloch orbitals are expressed as linear combinations of p z -orbitals of individual atoms. Then using various parameters defining the P-P-P Hamiltonian, the Hartree–Fock equations are set up as a matrix eigenvalue problem in the k-space. Thereby, its solutions are obtained in a self-consistent manner, using the iterative diagonalizing technique at several k points. The band structure and the corresponding Bloch orbitals thus obtained are used to perform a variety of calculations such as the density of states, linear optical absorption spectrum, electro-absorption spectrum, etc. Running time: Most of the examples provided take only a few seconds to run. For a large system, however, depending on the system size, the run time may be a few minutes to a few hours.

IONIS: Approximate atomic photoionization intensities

A program to compute relative atomic photoionization cross sections is presented. The code applies the output of the multiconfiguration Dirac–Fock method for atoms in the single active electron scheme, by computing the overlap of the bound electron states in the initial and final states. The contribution from the single-particle ionization matrix elements is assumed to be the same for each final state. This method gives rather accurate relative ionization probabilities provided the single-electron ionization matrix elements do not depend strongly on energy in the region considered. The method is especially suited for open shell atoms where electronic correlation in the ionic states is large. Program summary Program title: IONIS Catalogue identifier: AEKK_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEKK_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.: 1149 No. of bytes in distributed program, including test data, etc.: 12 877 Distribution format: tar.gz Programming language: Fortran 95 Computer: Workstations Operating system: GNU/Linux, Unix Classification: 2.2, 2.5 Nature of problem: Photoionization intensities for atoms. Solution method: The code applies the output of the multiconfiguration Dirac–Fock codes Grasp92 [1] or Grasp2K [2], to compute approximate photoionization intensities. The intensity is computed within the one-electron transition approximation and by assuming that the sum of the single-particle ionization probabilities is the same for all final ionic states. Restrictions: The program gives nonzero intensities for those transitions where only one electron is removed from the initial configuration(s). Shake-type many-electron transitions are not computed. The ionized shell must be closed in the initial state. Running time: Few seconds for a large problem with a few thousand configurations.

OneLOop: For the evaluation of one-loop scalar functions

OneLOop is a program to evaluate the one-loop scalar 1-point, 2-point, 3-point and 4-point functions, for all kinematical configurations relevant for collider-physics, and for any non-positive imaginary parts of the internal squared masses. It deals with all UV and IR divergences within dimensional regularization. Furthermore, it provides routines to evaluate these functions using straightforward numerical integration. Program summary Program title: OneLOop Catalogue identifier: AEJO_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEJO_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.: 12 061 No. of bytes in distributed program, including test data, etc.: 74 163 Distribution format: tar.gz Programming language: Fortran Computer: Workstations Operating system: Linux, Unix RAM: Negligible Classification: 4.4, 11.1 Nature of problem: In order to reach next-to-leading order precision in the calculation of cross sections of hard scattering processes, one-loop amplitudes have to be evaluated. This is done by expressing them as linear combination of one-loop scalar functions. In a concrete calculation, these functions eventually have to be evaluated. If the scattering process involves unstable particles, consistency requires the evaluation of these functions with complex internal masses. Solution method: Expressions for the one-loop scalar functions in terms of single-variable analytic functions existing in literature have been implemented. Restrictions: The applicability is restricted to the kinematics occurring in collider-physics. Running time: The evaluation of the most general 4-point function with 4 complex masses takes about 180 μs, and the evaluation of the 4-point function with 4 real masses takes about 18 μs on a 2.80 GHz Intel Xeon processor.

OPUCEM: A library with error checking mechanism for computing oblique parameters

After a brief review of the electroweak radiative corrections to gauge-boson self-energies, otherwise known as the direct and oblique corrections, a tool for calculation of the oblique parameters is presented. This tool, named OPUCEM, brings together formulas from multiple physics models and provides an error-checking machinery to improve reliability of numerical results. It also sets a novel example for an “open-formula” concept, which is an attempt to improve the reliability and reproducibility of computations in scientific publications by encouraging the authors to open-source their numerical calculation programs. Finally, we demonstrate the use of OPUCEM in two detailed case studies related to the fourth Standard Model family. The first is a generic fourth family study to find relations between the parameters compatible with the EW precision data and the second is the particular study of the flavor democracy predictions for both Dirac and Majorana-type neutrinos. Program summaryProgram title: OPUCEM (library)Catalogue identifier: AEIW_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIW_v1_0.htmlProgram obtainable from: CPC Program Library, Queenʼs 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.: 175 457No. of bytes in distributed program, including test data, etc.: 1 061 012Distribution format: tar.gzProgramming language: C/C++Computer: PCs and WorkstationsOperating system: Any Unix based system such as Linux and MacOSX, partial testing with Cygwin under WindowsRAM: GUI takes about 25 MB, the individual library calls are negligibleClassification: 11.1, 11.6External routines: ROOT library set (optional), complex number constructs from either the C99 standard or from the C++ Technical Report 1 (ISO/IEC TR 19768)Nature of problem: The calculation of Electroweak Precision variables for each point of the parameter space of a given beyond the Standard Model theory is tedious and error prone. The available formulas in the literature sometimes contain typos and most of the time they are valid only under some specific conditions, not suitable for quick comparison across different studies nor direct implementation on a computer.Solution method: One loop exact calculation of the oblique parameters are collected into a freely available C/C++ library for a number of models. One-loop exact calculation of the contributions of a number of models to the oblique parameters are collected in a freely available C/C++ library. The public availability of the implementations and the internal error checking mechanism aim the correctness of the results. Additionally, the Graphical User Interface and auxiliary tools provide the means for rapid result comparison or update when new data becomes available.Unusual features: The library computes the oblique parameters S, T and U both with exact one-loop calculations and with well-defined approximations for a number of models to establish a certain level of confidence. The comparisons between exact and approximate computations, and amongst formulas from different papers provide an error checking machinery which improves the end user reliability.Running time: Fractions of a second for each function call

MathQCDSR: A Mathematica package for QCD sum rules calculations

We present a software package written in Mathematica for standard QCD sum rules calculations. Two examples are given to demonstrate how to use the package. One is for the mass spectrum of octet baryons from two-point correlation functions; the other for the magnetic moments of octet baryons in the external-field method. The free package FeynCalc is used to handle the gamma-matrix algebra. In addition to two notebooks for the construction of the QCD sum rules, two corresponding notebooks are provided for a Monte Carlo-based numerical analysis, complete with in-line graphical display of sum rule matching, error distributions, and scatter plots for correlations. Program summaryProgram title: MathQCDSRCatalogue identifier: AEJA_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJA_v1_0.htmlProgram obtainable from: CPC Program Library, Queenʼs 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.: 93 897No. of bytes in distributed program, including test data, etc.: 631 481Distribution format: tar.gzProgramming language: MathematicaComputer: PCs and WorkstationsOperating system: Any OS that supports Mathematica. The package has been tested under Windows XP, Macintosh OS X, and LinuxClassification: 11.5External routines: FeynCalc (http://www.feyncalc.org/). It is a freely available Mathematica package for high-energy physics calculations. Here it is used primarily to handle gamma-matrix algebra.Nature of problem: The QCD sum rule method is a nonperturbative approach to solving quantum chromodynamics (QCD), the fundamental theory of the strong force. The approach establishes a direct link between hadron phenomenology and the QCD vacuum structure via a few QCD parameters called vacuum condensates and susceptibilities. It has been widely applied in nuclear and particle physics to gain insight into various aspects of strong-interaction physics.Solution method: First, QCD sum rules are constructed by evaluating correlation functions from two perspectives. On the quark level, it leads to a function of QCD parameters and the Borel mass parameter M. On the hadronic level, it leads to a function of phenomenological parameters and the same M. By numerically matching the two sides over a range in M, the phenomenological parameters can be extracted. The construction involves a large amount of gamma-matrix algebra, Fourier transform, and Borel transform. The matching usually involves searching for minimum χ2. We employ a Monte Carlo-based procedure to perform the analysis which allows for realistic error estimates.Restrictions: The package deals with only standard (SVZ) QCD sum rule calculations. It can be easily adapted to handle other variants of the method (like finite-energy sum rules). Due to the use of FeynCalc, two of the notebooks (qcdsr2pt-construction.nb and qcdsr3pt-construction.nb) only run on version 6.0 of Mathematica. The other two can run on any version.Additional comments: The package consists of the following 4 notebooks:•qcdsr2pt-construction.nb – This notebook constructs the QCD sum rules for octet baryon masses and outputs them, one particle at a time, to disk in plain text for analysis. For reference, we include all the output files (named Mass-*.txt) as part of the package, totaling 8 files in about 20 lines. The user should generate the outputs on their own computer and check against the supplied ones.•qcdsr2pt-analysis.nb – This notebook reads and analyzes the QCD sum rules produced by qcdsr2pt-construction.nb. The user can save the graphics in the analysis to disk in a variety of formats.•qcdsr3pt-construction.nb – This notebook constructs the QCD sum rules for the octet baryon magnetic moments and outputs them, one particle at a time, to disk in plain text for analysis. Again, for reference, we include all the output files (named Mag-*.txt), totaling 24 files in about 400 lines. The user should generate the outputs on their own computer and check against the supplied ones to make sure the program is running properly.•qcdsr3pt-analysis.nb – This notebook reads and analyzes the QCD sum rules produced by qcdsr3pt-construction.nb. The user can save the graphics in the analysis to disk in a variety of formats. Each notebook can be run separately, apart from the simple interface between the construction and analysis programs via plain text files written to disk.Running time: For mass calculations, qcdsr2ptconstruction.nb and qcdsr2pt-analysis.nb take about a minute each to run on a laptop. For magnetic moment calculations, qcdsr3pt-construction.nb can take up to 10 minutes for a given particle, and qcdsr3pt-analysis.nb typically a few minutes, depending on the number of Monte Carlo samples.

Gibbs2: A new version of the quasi-harmonic model code. I. Robust treatment of the static data

We describe in this article the techniques developed for the robust treatment of the static energy versus volume theoretical curve in the new version of the quasi-harmonic model code [Comput. Phys. Commun. 158 (2004) 57]. An average of strain polynomials is used to determine, as precisely as the input data allow it, the equilibrium properties and the derivatives of the static E(V) curve. The method provides a conservative estimation of the error bars associated to the fitting procedure. We have also developed the techniques required for detecting, and eventually removing, problematic data points and jumps in the E(V) curve. The fitting routines are offered as an independent octave package, called AsturFit, with an open source license. Program summaryProgram title:AsturFitCatalogue identifier: AEIY_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIY_v1_0.htmlProgram obtainable from: CPC Program Library, Queenʼs University, Belfast, N. IrelandLicensing provisions: GPL version 3No. of lines in distributed program, including test data, etc.: 21 347No. of bytes in distributed program, including test data, etc.: 620 496Distribution format: tar.gzProgramming language: GNU OctaveComputer: WorkstationsOperating system: Unix, GNU/LinuxClassification: 4.9External routines: The GSL and OPTIM packages from the octaveforge site (http://octave.sourceforge.net/).Nature of problem: Fit the total energy versus volume data of a solid to a continuous function and extract the equilibrium properties and the derivatives of the energy, with an estimation of the error introduced by the fitting procedure.Solution method: The use of averages of strain polynomials allows a robust and reliable representation of the energy curve and its derivatives, together with a statistical estimation of the goodness of the calculated properties.Additional comments: The techniques discussed have been implemented in Gibbs2, to be included with the second part of this article. Included here is the OCTAVE implementation of the routines, useful for interactive work and also for the creation of independent scripts. Some representative examples are included as test cases with a collection of data sets, test scripts, and model outputs.Running time: Seconds at most in routine uses of the program. Special tasks like the bootstrap analysis may take up to some minutes.

Computer program Neutron_CR-39 for simulation of neutrons from an Am–Be source and calculation of proton track profiles

A computer program called Neutron_CR-39.F90 for neutron simulation through a PADC detector and its detection was described and developed. In this work the neutron Am–Be source was considered for simulation. It was shown that the most intensive secondary particles, created in neutron interactions with the detector, are protons. The programming steps are outlined with detailed description of neutron simulation, determination of latent tracks of created protons, as well as, their development after detector etching in the same and opposite direction of particle motion. The outputs of the code are parameters of created protons (coordinates of starting and stopping points, direction angles of particles, initial and deposited energies) and number of visible tracks per incident neutron. Program summaryProgram title: Neutron_CR-39Catalogue identifier: AEIU_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIU_v1_0.htmlProgram obtainable from: CPC Program Library, Queenʼs 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.: 140 004No. of bytes in distributed program, including test data, etc.: 2 213 012Distribution format: tar.gzProgramming language: Fortran 90Computer: PCs and workstationsOperating system: Unix, Linux, Windows 95+RAM: 256 MBClassification: 17.5, 18External routines: For the Windows installation the entire code must be linked with the PORTLIB library.Nature of problem: The neutrons do not cause ionizations in the detector, and consequently no tracks are produced directly by them in the PADC. Due to the elastic and nonelastic interaction of neutrons with the atoms of PADC, recoil nuclei and secondary particles are created producing latent intrinsic tracks. After chemical etching in aqueous NaOH solution these tracks become visible under optical microscope and usually density of visible tracks is measured. Optical microscopes are often used for this purpose but the process is relatively tedious and time consuming. The present computer program has been written for neutron simulation through PADC detector; determination of parameters of secondary particles; calculation track profiles of secondary particles emitted in the same and opposite direction as etchant progression. The outputs of the code are parameters of secondary particles (coordinates of starting and stopping points, direction angles of particles, initial and deposited energies) and number of visible tracks per incident neutron.Solution method: A computer program is prepared to simulate neutronʼs interactions in a PADC by the Monte Carlo method using the Neutron data library ENDF/B-VII [B. Milenkovic, D. Nikezic, N. Stevanovic, Radiat. Meas. 45 (2010) 1338]. The parameters of the emitted secondary particles (emission angle, initial energy, deposited energy and starting and stopping coordinates) were stored in an enclosed file. The subroutine for calculation of track profiles by a finite difference method for particles emitted in the same direction was developed [D. Nikezic, N. Stevanovic, D. Kostic, S. Savovic, K.C.C. Tse, K.N. Yu, Radiat. Meas. 43 (2008) S76]. It was shown that there are many tracks formed in the opposite direction than the etchant progression. The method for calculation of track profiles for these particles is developed in [B. Milenkovic, N. Stevanovic, D. Krstic, D. Nikezic, Radiat. Meas. 44 (2009) 57]. It is very different than the method for track in the same direction. The separate subroutine for this purpose was developed here.Additional comments: The program distribution file contains an executable which enables the program to be run on a Windows machine. The source code is also provided, but in order to build an executable the PORTLIB must be available.Running time: Running time depends mainly on the neutron number for simulation, source and detector geometry and removed layer required by the user. Running time is several minutes.

The FermiFab toolbox for fermionic many-particle quantum systems

This paper introduces the FermiFab toolbox for many-particle quantum systems. It is mainly concerned with the representation of (symbolic) fermionic wavefunctions and the calculation of corresponding reduced density matrices (RDMs). The toolbox transparently handles the inherent antisymmetrization of wavefunctions and incorporates the creation/annihilation formalism. Thus, it aims at providing a solid base for a broad audience to use fermionic wavefunctions with the same ease as matrices in Matlab, say. Leveraging symbolic computation, the toolbox can greatly simply tedious pen-and-paper calculations for concrete quantum mechanical systems, and serves as “sandbox” for theoretical hypothesis testing. FermiFab (including full source code) is freely available as a plugin for both Matlab and Mathematica. Program summary Program title: FermiFab Catalogue identifier: AEIN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEIN_v1_0.html Program obtainable from: CPC Program Library, Queenʼs University, Belfast, N. Ireland Licensing provisions: Special license provided by the author No. of lines in distributed program, including test data, etc.: 1 165 461 No. of bytes in distributed program, including test data, etc.: 15 557 308 Distribution format: tar.gz Programming language: MATLAB 7.9, Mathematica 7.0, C Computer: PCs, Sun Solaris workstation Operating system: Any platform supporting MATLAB or Mathematica; tested with Windows (32 and 64 bit) and Sun Solaris. RAM: Case dependent Classification: 4.15 Nature of problem: Representation of fermionic wavefunctions, computation of RDMs (reduced density matrices) and handing of the creation/annihilation operator formalism. Solution method: Mapping of Slater determinants to bitfields, implementation of the creation/annihilation and RDM formalism by bit operations. Running time: Depends on the problem size; several seconds for the provided demonstration files.

SADE] a Maple package for the symmetry analysis of differential equations

We present the package SADE (Symmetry Analysis of Differential Equations) for the determination of symmetries and related properties of systems of differential equations. The main methods implemented are: Lie, nonclassical, Lie–Bäcklund and potential symmetries, invariant solutions, first-integrals, Nöther theorem for both discrete and continuous systems, solution of ordinary differential equations, order and dimension reductions using Lie symmetries, classification of differential equations, Casimir invariants, and the quasi-polynomial formalism for ODE's (previously implemented by the authors in the package QPSI) for the determination of quasi-polynomial first-integrals, Lie symmetries and invariant surfaces. Examples of use of the package are given. Program summary Program title: SADE Catalogue identifier: AEHL_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEHL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 27 704 No. of bytes in distributed program, including test data, etc.: 346 954 Distribution format: tar.gz Programming language: MAPLE 13 and MAPLE 14 Computer: PCs and workstations Operating system: UNIX/LINUX systems and WINDOWS Classification: 4.3 Nature of problem: Determination of analytical properties of systems of differential equations, including symmetry transformations, analytical solutions and conservation laws. Solution method: The package implements in MAPLE some algorithms (discussed in the text) for the study of systems of differential equations. Restrictions: Depends strongly on the system and on the algorithm required. Typical restrictions are related to the solution of a large over-determined system of linear or non-linear differential equations. Running time: Depends strongly on the order, the complexity of the differential system and the object computed. Ranges from seconds to hours.

The program LOPT for least-squares optimization of energy levels

The article describes a program that solves the least-squares optimization problem for finding the energy levels of a quantum-mechanical system based on a set of measured energy separations or wavelengths of transitions between those energy levels, as well as determining the Ritz wavelengths of transitions and their uncertainties. The energy levels are determined by solving the matrix equation of the problem, and the uncertainties of the Ritz wavenumbers are determined from the covariance matrix of the problem. Program summary Program title: LOPT Catalogue identifier: AEHM_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEHM_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.: 19 254 No. of bytes in distributed program, including test data, etc.: 427 839 Distribution format: tar.gz Programming language: Perl v.5 Computer: PC, Mac, Unix workstations Operating system: MS Windows (XP, Vista, 7), Mac OS X, Linux, Unix (AIX) RAM: 3 Mwords or more Word size: 32 or 64 Classification: 2.2 Nature of problem: The least-squares energy-level optimization problem, i.e., finding a set of energy level values that best fits the given set of transition intervals. Solution method: The solution of the least-squares problem is found by solving the corresponding linear matrix equation, where the matrix is constructed using a new method with variable substitution. Restrictions: A practical limitation on the size of the problem N is imposed by the execution time, which scales as N 3 and depends on the computer. Unusual features: Properly rounds the resulting data and formats the output in a format suitable for viewing with spreadsheet editing software. Estimates numerical errors resulting from the limited machine precision. Running time: 1 s for N = 100 , or 60 s for N = 400 on a typical PC.

Las Palmeras Molecular Dynamics: A flexible and modular molecular dynamics code

Las Palmeras Molecular Dynamics (LPMD) is a highly modular and extensible molecular dynamics (MD) code using interatomic potential functions. LPMD is able to perform equilibrium MD simulations of bulk crystalline solids, amorphous solids and liquids, as well as non-equilibrium MD (NEMD) simulations such as shock wave propagation, projectile impacts, cluster collisions, shearing, deformation under load, heat conduction, heterogeneous melting, among others, which involve unusual MD features like non-moving atoms and walls, unstoppable atoms with constant-velocity, and external forces like electric fields. LPMD is written in C++ as a compromise between efficiency and clarity of design, and its architecture is based on separate components or plug-ins, implemented as modules which are loaded on demand at runtime. The advantage of this architecture is the ability to completely link together the desired components involved in the simulation in different ways at runtime, using a user-friendly control file language which describes the simulation work-flow. As an added bonus, the plug-in API (Application Programming Interface) makes it possible to use the LPMD components to analyze data coming from other simulation packages, convert between input file formats, apply different transformations to saved MD atomic trajectories, and visualize dynamical processes either in real-time or as a post-processing step. Individual components, such as a new potential function, a new integrator, a new file format, new properties to calculate, new real-time visualizers, and even a new algorithm for handling neighbor lists can be easily coded, compiled and tested within LPMD by virtue of its object-oriented API, without the need to modify the rest of the code. LPMD includes already several pair potential functions such as Lennard-Jones, Morse, Buckingham, MCY and the harmonic potential, as well as embedded-atom model (EAM) functions such as the Sutton–Chen and Gupta potentials. Integrators to choose include Euler (if only for demonstration purposes), Verlet and Velocity Verlet, Leapfrog and Beeman, among others. Electrostatic forces are treated as another potential function, by default using the plug-in implementing the Ewald summation method. Program summary Program title: LPMD Catalogue identifier: AEHG_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEHG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 509 490 No. of bytes in distributed program, including test data, etc.: 6 814 754 Distribution format: tar.gz Programming language: C++ Computer: 32-bit and 64-bit workstation Operating system: UNIX RAM: Minimum 1024 bytes Classification: 7.7 External routines: zlib, OpenGL Nature of problem: Study of Statistical Mechanics and Thermodynamics of condensed matter systems, as well as kinetics of non-equilibrium processes in the same systems. Solution method: Equilibrium and non-equilibrium molecular dynamics method, Monte Carlo methods. Restrictions: Rigid molecules are not supported. Polarizable atoms and chemical bonds (proteins) either. Unusual features: The program is able to change the temperature of the simulation cell, the pressure, cut regions of the cell, color the atoms by properties, even during the simulation. It is also possible to fix the positions and/or velocity of groups of atoms. Visualization of atoms and some physical properties during the simulation. Additional comments: The program does not only perform molecular dynamics and Monte Carlo simulations, it is also able to filter and manipulate atomic configurations, read and write different file formats, convert between them, evaluate different structural and dynamical properties. Running time: 50 seconds on a 1000-step simulation of 4000 argon atoms, running on a single 2.67 GHz Intel processor.

SUSY_FLAVOR: A computational tool for FCNC and CP-violating processes in the MSSM

We present SUSY_FLAVOR – a Fortran 77 program that calculates important leptonic and semi-leptonic low-energy observables in the general R-parity conserving MSSM. For a set of input MSSM parameters, the code gives predictions for the K ¯ 0 K 0 , D ¯ D , B ¯ d B d and B ¯ s B s mixing parameters; B → X s γ , B s , d → l + l − , K L 0 → π 0 ν ¯ ν and K + → π + ν ¯ ν decay branching ratios; and the electric dipole moments of the leptons and the neutron. All these quantities are calculated at one-loop level (with some higher-order QCD corrections included) in the exact sfermion mass eigenbasis, without resorting to mass insertion approximations. The program can be obtained from http://www.fuw.edu.pl/susy_flavor. Program summary Program title: SUSY_FLAVOR Catalogue identifier: AEGV_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEGV_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.: 14 603 No. of bytes in distributed program, including test data, etc.: 82 126 Distribution format: tar.gz Programming language: Fortran 77 Computer: PCs and workstations Operating system: Any, tested on Linux Classification: 11.6 Nature of problem: Predicting CP-violating observables, meson mixing parameters and branching ratios for a set of rare processes in the general R-parity conserving MSSM. Solution method: We use standard quantum theoretical methods to calculate Wilson coefficients in MSSM and at one loop including QCD corrections at higher orders when this is necessary and possible. The input parameters can be read from an external file in SLHA format. Restrictions: The results apply only to the case of MSSM with R-parity conservation. Running time: For single parameter set approximately 1 s in double precision on a PowerBook Mac G4.

HepML, an XML-based format for describing simulated data in high energy physics

In this paper we describe a HepML format and a corresponding C++ library developed for keeping complete description of parton level events in a unified and flexible form. HepML tags contain enough information to understand what kind of physics the simulated events describe and how the events have been prepared. A HepML block can be included into event files in the LHEF format. The structure of the HepML block is described by means of several XML Schemas. The Schemas define necessary information for the HepML block and how this information should be located within the block. The library libhepml is a C++ library intended for parsing and serialization of HepML tags, and representing the HepML block in computer memory. The library is an API for external software. For example, Matrix Element Monte Carlo event generators can use the library for preparing and writing a header of an LHEF file in the form of HepML tags. In turn, Showering and Hadronization event generators can parse the HepML header and get the information in the form of C++ classes. libhepml can be used in C++, C, and Fortran programs. All necessary parts of HepML have been prepared and we present the project to the HEP community. Program summary Program title: libhepml Catalogue identifier: AEGL_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEGL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU GPLv3 No. of lines in distributed program, including test data, etc.: 138 866 No. of bytes in distributed program, including test data, etc.: 613 122 Distribution format: tar.gz Programming language: C++, C Computer: PCs and workstations Operating system: Scientific Linux CERN 4/5, Ubuntu 9.10 RAM: 1 073 741 824 bytes (1 Gb) Classification: 6.2, 11.1, 11.2 External routines: Xerces XML library ( http://xerces.apache.org/xerces-c/), Expat XML Parser ( http://expat.sourceforge.net/) Nature of problem: Monte Carlo simulation in high energy physics is divided into several stages. Various programs exist for these stages. In this article we are interested in interfacing different Monte Carlo event generators via data files, in particular, Matrix Element (ME) generators and Showering and Hadronization (SH) generators. There is a widely accepted format for data files for such interfaces – Les Houches Event Format (LHEF). Although information kept in an LHEF file is enough for proper working of SH generators, it is insufficient for understanding how events in the LHEF file have been prepared and which physical model has been applied. In this paper we propose an extension of the format for keeping additional information available in generators. We propose to add a new information block, marked up with XML tags, to the LHEF file. This block describes events in the file in more detail. In particular, it stores information about a physical model, kinematical cuts, generator, etc. This helps to make LHEF files self-documented. Certainly, HepML can be applied in more general context, not in LHEF files only. Solution method: In order to overcome drawbacks of the original LHEF accord we propose to add a new information block of HepML tags. HepML is an XML-based markup language. We designed several XML Schemas for all tags in the language. Any HepML document should follow rules of the Schemas. The language is equipped with a library for operation with HepML tags and documents. This C++ library, called libhepml, consists of classes for HepML objects, which represent a HepML document in computer memory, parsing classes, serializating classes, and some auxiliary classes. Restrictions: The software is adapted for solving problems, described in the article. There are no additional restrictions. Running time: Tests have been done on a computer with Intel(R) Core(TM)2 Solo, 1.4 GHz. Parsing of a HepML file: 6 ms (size of the HepML files is 12.5 Kb) Writing of a HepML block to file: 14 ms (file size 12.5 Kb) Merging of two HepML blocks and writing to file: 18 ms (file size – 25.0 Kb).

Solution of self-consistent equations for the N 3LO nuclear energy density functional in spherical symmetry. The program hosphe (v1.02)

We present solution of self-consistent equations for the N 3LO nuclear energy density functional. We derive general expressions for the mean fields expressed as differential operators depending on densities and for the densities expressed in terms of derivatives of wave functions. These expressions are then specified to the case of spherical symmetry. We also present the computer program hosphe (v1.02), which solves the self-consistent equations by using the expansion of single-particle wave functions on the spherical harmonic oscillator basis. Program summary Program title: HOSPHE (v1.02) Catalogue identifier: AEGK_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEGK_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.: 45 809 No. of bytes in distributed program, including test data, etc.: 290 514 Distribution format: tar.gz Programming language: Fortran-90 Computer: PCs and workstations Operating system: Linux RAM: 50 MB Classification: 17.22 External routines: LAPACK ( http://www.netlib.org/lapack/), BLAS ( http://www.netlib.org/blas/) Nature of problem: The nuclear mean-field methods constitute principal tools of a description of nuclear states in heavy nuclei. Within the Local Density Approximation with gradient corrections up to N 3LO [1], the nuclear mean-field is local and contains derivative operators up to sixth order. The locality allows for an effective and fast solution of the self-consistent equations. Solution method: The program uses the spherical harmonic oscillator basis to expand single-particle wave functions of neutrons and protons for the nuclear state being described by the N 3LO nuclear energy density functional [1]. The expansion coefficients are determined by the iterative diagonalization of the mean-field Hamiltonian, which depends non-linearly on the local neutron and proton densities. Restrictions: Solutions are limited to spherical symmetry. The expansion on the harmonic-oscillator basis does not allow for a precise description of asymptotic properties of wave functions. Running time: 50 seconds of CPU time for the ground-state of 208Pb described by using N 0 = 50 as the maximum harmonic-oscillator shell included in the basis.