A parallel solver for huge dense linear systems

HDSS (Huge Dense Linear System Solver) is a Fortran Application Programming Interface (API) to facilitate the parallel solution of very large dense systems to scientists and engineers. The API makes use of parallelism to yield an efficient solution of the systems on a wide range of parallel platforms, from clusters of processors to massively parallel multiprocessors. It exploits out-of-core strategies to leverage the secondary memory in order to solve huge linear systems O(100.000).The API is based on the parallel linear algebra library PLAPACK, and on its Out-Of-Core (OOC) extension POOCLAPACK. Both PLAPACK and POOCLAPACK use the Message Passing Interface (MPI) as the communication layer and BLAS to perform the local matrix operations.The API provides a friendly interface to the users, hiding almost all the technical aspects related to the parallel execution of the code and the use of the secondary memory to solve the systems. In particular, the API can automatically select the best way to store and solve the systems, depending of the dimension of the system, the number of processes and the main memory of the platform.Experimental results on several parallel platforms report high performance, reaching more than 1 TFLOP with 64 cores to solve a system with more than 200 000 equations and more than 10 000 right-hand side vectors.

New version program summary

Program title: Huge Dense System Solver (HDSS)Catalogue identifier: AEHU_v1_1Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHU_v1_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.: 87 062No. of bytes in distributed program, including test data, etc.: 1 069 110Distribution format: tar.gzProgramming language: Fortran90, CComputer: Parallel architectures: multiprocessors, computer clustersOperating system: Linux/UnixHas the code been vectorized or parallelized?: Yes, includes MPI primitives.RAM: Tested for up to 190 GBClassification: 6.5External routines: MPI (http://www.mpi-forum.org/), BLAS (http://www.netlib.org/blas/), PLAPACK (http://www.cs.utexas.edu/~plapack/), POOCLAPACK (ftp://ftp.cs.utexas.edu/pub/rvdg/PLAPACK/pooclapack.ps) (code for PLAPACK and POOCLAPACK is included in the distribution).Catalogue identifier of previous version: AEHU_v1_0Journal reference of previous version: Comput. Phys. Comm. 182 (2011) 533Does the new version supersede the previous version?: YesNature of problem: Huge scale dense systems of linear equations, Ax=B, beyond standard LAPACK capabilities.Solution method: The linear systems are solved by means of parallelized routines based on the LU factorization, using efficient secondary storage algorithms when the available main memory is insufficient.Reasons for new version: In many applications we need to guarantee a high accuracy in the solution of very large linear systems and we can do it by using double-precision arithmetic.Summary of revisions: Version 1.1

• • 

  Can be used to solve linear systems using double-precision arithmetic.

• • 

  New version of the initialization routine. The user can choose the kind of arithmetic and the values of several parameters of the environment.

Running time: About 5 hours to solve a system with more than 200 000 equations and more than 10 000 right-hand side vectors using double-precision arithmetic on an eight-node commodity cluster with a total of 64 Intel cores.     

HidSecSOFTSUSY: Incorporating effects from hidden sectors in the numerical computation of the MSSM spectrum

SOFTSUSY is a software designed to solve the RG equations of the MSSM and compute its low energy spectrum. HidSecSOFTSUSY is an extension of the SOFTSUSY package which modifies the beta functions to include contributions from light dynamic fields in the hidden sector.

Program summary

Program title: HidSecSOFTSUSYCatalogue identifier: AEHP_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHP_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.: 4167No. of bytes in distributed program, including test data, etc.: 141 411Distribution format: tar.gzProgramming language: C++, FortranComputer: Personal computerOperating system: Tested on GNU/LinuxWord size: 32 bitsClassification: 11.6External routines: Requires an installed version of SOFTSUSY (http://projects.hepforge.org/softsusy/)Nature of problem: Calculating supersymmetric particle spectrum and mixing parameters while incorporating dynamic modes from the hidden sector into the renormalization group equations. The solution to the equations must be consistent with a high-scale boundary condition on supersymmetry breaking parameters, as well as a weak-scale boundary condition on gauge couplings, Yukawa couplings and the Higgs potential parameters.Solution method: Nested iterative algorithm.Running time: A few seconds per parameter point.     

MontePython: Implementing Quantum Monte Carlo using Python

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

Program summary

Program title: MontePythonCatalogue identifier: ADZP_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZP_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 49 519No. of bytes in distributed program, including test data, etc.: 114 484Distribution format: tar.gzProgramming language: C++, PythonComputer: PC, IBM RS6000/320, HP, ALPHAOperating system: LINUXHas the code been vectorised or parallelized?: Yes, parallelized with MPINumber of processors used: 1-96RAM: Depends on physical system to be simulatedClassification: 7.6; 16.1Nature of problem: Investigating ab initio quantum mechanical systems, specifically Bose-Einstein condensation in dilute gases of ⁸⁷RbSolution method: Quantum Monte CarloRunning time: 225 min with 20 particles (with 4800 walkers moved in 1750 time steps) on 1 AMD Opteron^TM Processor 2218 processor; Production run for, e.g., 200 particles takes around 24 hours on 32 such processors.     

SLHAplus: A library for implementing extensions of the standard model

We provide a library to facilitate the implementation of new models in codes such as matrix element and event generators or codes for computing dark matter observables. The library contains an SLHA reader routine as well as diagonalisation routines. This library is available in CalcHEP and micrOMEGAs. The implementation of models based on this library is supported by LanHEP and FeynRules.

Program summary

Program title: SLHAplus_1.3Catalogue identifier: AEHX_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHX_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.: 6283No. of bytes in distributed program, including test data, etc.: 52 119Distribution format: tar.gzProgramming language: CComputer: IBM PC, MACOperating system: UNIX (Linux, Darwin, Cygwin)RAM: 2000 MBClassification: 11.1Nature of problem: Implementation of extensions of the standard model in matrix element and event generators and codes for dark matter observables.Solution method: For generic extensions of the standard model we provide routines for reading files that adopt the standard format of the SUSY Les Houches Accord (SLHA) file. The procedure has been generalized to take into account an arbitrary number of blocks so that the reader can be used in generic models including non-supersymmetric ones. The library also contains routines to diagonalize real and complex mass matrices with either unitary or bi-unitary transformations as well as routines for evaluating the running strong coupling constant, running quark masses and effective quark masses.Running time: 0.001 sec     

Code C# for chaos analysis of relativistic many-body systems

This work presents a new Microsoft Visual C# .NET code library, conceived as a general object oriented solution for chaos analysis of three-dimensional, relativistic many-body systems. In this context, we implemented the Lyapunov exponent and the “fragmentation level” (defined using the graph theory and the Shannon entropy). Inspired by existing studies on billiard nuclear models and clusters of galaxies, we tried to apply the virial theorem for a simplified many-body system composed by nucleons. A possible application of the “virial coefficient” to the stability analysis of chaotic systems is also discussed.

Program summary

Program title: Chaos Many-Body Engine v01Catalogue identifier: AEGH_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGH_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.: 30 053No. of bytes in distributed program, including test data, etc.: 801 258Distribution format: tar.gzProgramming language: Visual C# .NET 2005Computer: PCOperating system: .Net Framework 2.0 running on MS WindowsHas the code been vectorized or parallelized?: Each many-body system is simulated on a separate execution threadRAM: 128 MegabytesClassification: 6.2, 6.5External routines: .Net Framework 2.0 LibraryNature of problem: Chaos analysis of three-dimensional, relativistic many-body systems.Solution method: Second order Runge-Kutta algorithm for simulating relativistic many-body systems. Object oriented solution, easy to reuse, extend and customize, in any development environment which accepts .Net assemblies or COM components. Implementation of: Lyapunov exponent, “fragmentation level”, “average system radius”, “virial coefficient”, and energy conservation precision test.Additional comments: Easy copy/paste based deployment method.Running time: Quadratic complexity.     

Automated symbolic calculations in nonequilibrium thermodynamics

We cast the Jacobi identity for continuous fields into a local form which eliminates the need to perform any partial integration to the expense of performing variational derivatives. This allows us to test the Jacobi identity definitely and efficiently and to provide equations between different components defining a potential Poisson bracket. We provide a simple Mathematica^TM notebook which allows to perform this task conveniently, and which offers some additional functionalities of use within the framework of nonequilibrium thermodynamics: reversible equations of change for fields, and the conservation of entropy during the reversible dynamics.

Program summary

Program title: Poissonbracket.nbCatalogue identifier: AEGW_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGW_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.: 227 952No. of bytes in distributed program, including test data, etc.: 268 918Distribution format: tar.gzProgramming language: Mathematica^TM 7.0Computer: Any computer running Mathematica^TM 6.0 and later versionsOperating system: Linux, MacOS, WindowsRAM: 100 MbClassification: 4.2, 5, 23Nature of problem: Testing the Jacobi identity can be a very complex task depending on the structure of the Poisson bracket. The Mathematica^TM notebook provided here solves this problem using a novel symbolic approach based on inherent properties of the variational derivative, highly suitable for the present tasks. As a by product, calculations performed with the Poisson bracket assume a compact form.Solution method: The problem is first cast into a form which eliminates the need to perform partial integration for arbitrary functionals at the expense of performing variational derivatives. The corresponding equations are conveniently obtained using the symbolic programming environment Mathematica^TM.Running time: For the test cases and most typical cases in the literature, the running time is of the order of seconds or minutes, respectively.     

OneLOop: For the evaluation of one-loop scalar functions

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

Program summary

Program title: OneLOopCatalogue identifier: AEJO_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJO_v1_0.htmlProgram obtainable from: CPC Program Library, Queen?s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 12 061No. of bytes in distributed program, including test data, etc.: 74 163Distribution format: tar.gzProgramming language: FortranComputer: WorkstationsOperating system: Linux, UnixRAM: NegligibleClassification: 4.4, 11.1Nature of problem: In order to reach next-to-leading order precision in the calculation of cross sections of hard scattering processes, one-loop amplitudes have to be evaluated. This is done by expressing them as linear combination of one-loop scalar functions. In a concrete calculation, these functions eventually have to be evaluated. If the scattering process involves unstable particles, consistency requires the evaluation of these functions with complex internal masses.Solution method: Expressions for the one-loop scalar functions in terms of single-variable analytic functions existing in literature have been implemented.Restrictions: The applicability is restricted to the kinematics occurring in collider-physics.Running time: The evaluation of the most general 4-point function with 4 complex masses takes about 180 μs, and the evaluation of the 4-point function with 4 real masses takes about 18 μs on a 2.80 GHz Intel Xeon processor.     

[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: SADECatalogue identifier: AEHL_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHL_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's 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.: 27 704No. of bytes in distributed program, including test data, etc.: 346 954Distribution format: tar.gzProgramming language: MAPLE 13 and MAPLE 14Computer: PCs and workstationsOperating system: UNIX/LINUX systems and WINDOWSClassification: 4.3Nature 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.     

Armchair or Zigzag? A tool for characterizing graphene edge

Electronic, magnetic, and structural properties of graphene flakes depend sensitively upon the type of edge atoms. We present a simple software tool for determining the type of edge atoms in a honeycomb lattice. The algorithm is based on nearest neighbor counting. Whether an edge atom is of armchair or zigzag type is decided by the unique pattern of its nearest neighbors. Particular attention is paid to the practical aspects of using the tool, as additional features such as extracting out the edges from the lattice could help in analyzing images from transmission microscopy or other experimental probes. Ultimately, the tool in combination with density-functional theory or tight-binding method can also be helpful in correlating the properties of graphene flakes with the different armchair-to-zigzag ratios.

Program summary

Program title: edgecountCatalogue identifier: AEIA_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIA_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.: 66 685No. of bytes in distributed program, including test data, etc.: 485 381Distribution format: tar.gzProgramming language:Fortran 90/95Computer: Most UNIX-based platformsOperating system: Linux, Mac OSClassification: 16.1, 7.8Nature of problem: Detection and classification of edge atoms in a finite patch of honeycomb lattice.Solution method: Build nearest neighbor (NN) list; assign types to edge atoms on the basis of their NN pattern.Running time: Typically ∼second(s) for all examples.     

Real-time Java simulations of multiple interference dielectric filters

An interactive Java applet for real-time simulation and visualization of the transmittance properties of multiple interference dielectric filters is presented. The most commonly used interference filters as well as the state-of-the-art ones are embedded in this platform-independent applet which can serve research and education purposes. The Transmittance applet can be freely downloaded from the site http://cpc.cs.qub.ac.uk.

Program summary

Program title: TransmittanceCatalogue identifier: AEBQ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBQ_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 5778No. of bytes in distributed program, including test data, etc.: 90 474Distribution format: tar.gzProgramming language: JavaComputer: Developed on PC-Pentium platformOperating system: Any Java-enabled OS. Applet was tested on Windows ME, XP, Sun Solaris, Mac OSRAM: VariableClassification: 18Nature of problem: Sophisticated wavelength selective multiple interference filters can include some tens or even hundreds of dielectric layers. The spectral response of such a stack is not obvious. On the other hand, there is a strong demand from application designers and students to get a quick insight into the properties of a given filter.Solution method: A Java applet was developed for the computation and the visualization of the transmittance of multilayer interference filters. It is simple to use and the embedded filter library can serve educational purposes. Also, its ability to handle complex structures will be appreciated as a useful research and development tool.Running time: Real-time simulations     

CAVE: A package for detection and quantitative analysis of internal cavities in a system of overlapping balls: Application to proteins

We developed a software package (CAVE) in Fortran language to detect internal cavities in proteins which can be applied also to an arbitrary system of balls. The volume, the surface area and other quantitative characteristics of the cavities can be calculated. The code is based on the recently suggested enveloping triangulation algorithm [J. Buša et al., J. Comp. Chem. 30 (2009) 346] for computing volume and surface area of the cavity by analytical equations. Different standard sets of atomic radii can be used. The PDB compatible file containing the atomic coordinates must be stored on the disk in advance. Testing of the code on different proteins and artificial ball systems showed efficiency and accuracy of the algorithm. The program is fast. It can handle a system of several thousands of balls in the order of seconds on contemporary PC's. The code is open source and free.

Program summary

Program title: CAVECatalogue identifier: AEHC_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHC_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.: 8670No. of bytes in distributed program, including test data, etc.: 100 131Distribution format: tar.gzProgramming language: FortranComputer: PC Pentium and CoreOperating system: Linux system and Windows XP systemClassification: 16.1Nature of problem: Molecular structure analysis.Solution method: Analytical method for cavities detection, and numerical algorithm for volume and surface area calculation based on the analytical formulas, after using the stereographic transformation.Running time: Depends on the size of the molecule under consideration. The test example included in the distribution takes about 1 minute to run.     

RNGSSELIB: Program library for random number generation, SSE2 realization

The library RNGSSELIB for random number generators (RNGs) based upon the SSE2 command set is presented. The library contains realization of a number of modern and most reliable generators. Usage of SSE2 command set allows to substantially improve performance of the generators. Three new RNG realizations are also constructed. We present detailed analysis of the speed depending on compiler usage and associated optimization level, as well as results of extensive statistical testing for all generators using available test packages. Fast SSE implementations produce exactly the same output sequence as the original algorithms.

Program summary

Program title: RNGSSELIBCatalogue identifier: AEIT_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIT_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.: 4177No. of bytes in distributed program, including test data, etc.: 21 228Distribution format: tar.gzProgramming language: C.Computer: PC.Operating system: UNIX, Windows.RAM: 1 MbytesClassification: 4.13.Nature of problem: Any calculation requiring uniform pseudorandom number generator, in particular, Monte Carlo calculations.Solution method: The library contains realization of a number of modern and reliable generators: mt19937, mrg32k3a and lfsr113. Also new realizations for the method based on parallel evolution of an ensemble of dynamical systems are constructed: GM19, GM31 and GM61. The library contains both usual realizations and realizations based on SSE command set. Usage of SSE commands allows the performance of all generators to be substantially improved.Restrictions: For SSE realizations of the generators, Intel or AMD CPU supporting SSE2 command set is required. In order to use the realization lfsr113sse, CPU must support SSE4 command set.Running time: Running time is of the order of 20 sec for generating 10⁹ pseudorandom numbers with a PC based on Intel Core i7-940 CPU. Running time is analysed in detail in Section 5 of the paper.     

HASPRNG: Hardware Accelerated Scalable Parallel Random Number Generators

The Scalable Parallel Random Number Generators library (SPRNG) supports fast and scalable random number generation with good statistical properties for parallel computational science applications. In order to accelerate SPRNG in high performance reconfigurable computing systems, we present the Hardware Accelerated SPRNG library (HASPRNG). Ported to the Xilinx University Program (XUP) and Cray XD1 reconfigurable computing platforms, HASPRNG includes the reconfigurable logic for Field Programmable Gate Arrays (FPGAs) along with a programming interface which performs integer random number generation that produces identical results with SPRNG. This paper describes the reconfigurable logic of HASPRNG exploiting the mathematical properties and data parallelism residing in the SPRNG algorithms to produce high performance and also describes how to use the programming interface to minimize the communication overhead between FPGAs and microprocessors. The programming interface allows a user to be able to use HASPRNG the same way as SPRNG 2.0 on platforms such as the Cray XD1. We also describe how to install HASPRNG and use it. For HASPRNG usage we discuss a FPGA π-estimator for a High Performance Reconfigurable Computer (HPRC) sample application and compare to a software π-estimator. HASPRNG shows 1.7x speedup over SPRNG on the Cray XD1 and is able to obtain substantial speedup for a HPRC application.

Program summary

Program title: HASPRNGCatalogue identifier: AEER_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEER_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.: 594 928No. of bytes in distributed program, including test data, etc.: 6 509 724Distribution format: tar.gzProgramming language: VHDL (XUP and Cray XD1), C++ (XUP), C (Cray XD1)Computer: PowerPC 405 (XUP) / AMD 2.2 GHz Opteron processor (Cray XD1)Operating system: LinuxFile size: 15 MB (XUP) / 22 MB (Cray XD1)Classification: 4.13Nature of problem: Many computational science applications are able to consume large numbers of random numbers. For example, Monte Carlo simulations such as π-estimation are able to consume limitless random numbers forthe computation as long as hardware resources for the computing are supported. Moreover, parallel computational science applications require independent streams of random numbers to attain statistically significant results. The SPRNG library provides this capability, but at a significant computational cost. The library presented here accelerates the generators of independent streams of random numbers.Solution method: Multiple copies of random number generators in FPGAs allow a computational science application to consume large numbers of random numbers from independent, parallel streams. HASPRNG is a random number generators library to allow a computational science application to employ the multiple copies of random number generators to boost performance. Users can interface HASPRNG with software code executing on microprocessors and/or with hardware applications executing on FPGAs.     

An efficient quantum circuit analyser on qubits and qudits

This paper presents a highly efficient decomposition scheme and its associated Mathematica notebook for the analysis of complicated quantum circuits comprised of single/multiple qubit and qudit quantum gates. In particular, this scheme reduces the evaluation of multiple unitary gate operations with many conditionals to just two matrix additions, regardless of the number of conditionals or gate dimensions. This improves significantly the capability of a quantum circuit analyser implemented in a classical computer. This is also the first efficient quantum circuit analyser to include qudit quantum logic gates.

Program summary

Program title:CUGates.mCatalogue identifier: AEJM_v1_0Program summary: URL: http://cpc.cs.qub.ac.uk/summaries/AEJM_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.: 8168No. of bytes in distributed program, including test data, etc.: 173 899Distribution format: tar.gzProgramming language: MathematicaComputer: Any computer installed with Mathematica 6.0 or higher.Operating system: Any system with a copy of Mathematica 6.0 or higher installed.Classification: 4.15Nature of problem: The CUGates notebook simulates arbitrarily complex quantum circuits comprised of single/multiple qubit and qudit quantum gates.Solution method: It utilizes an irreducible form of matrix decomposition for a general controlled gate with multiple conditionals and is highly efficient in simulating complex quantum circuits.Running time: Details of CPU time usage for various example runs are given in Section 4.     

Solution of few-body problems with the stochastic variational method II: Two-dimensional systems

A computational approach is presented for efficient solution of two-dimensional few-body problems, such as quantum dots or excitonic complexes, using the stochastic variational method. The computer program can be used to calculate the energies and wave functions of various two-dimensional systems.

Program summary

Program title: svm-2dCatalogue identifier: AEBE_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBE_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 5091No. of bytes in distributed program, including test data, etc.: 130 963Distribution format: tar.gzProgramming language: Fortran 90Computer: The program should work on any system with a Fortran 90 compilerOperating system: The program should work on any system with a Fortran 90 compilerClassification: 7.3Nature of problem: Variational calculation of energies and wave functions using Correlated Gaussian basis.Solution method: Two-dimensional few-electron problems are solved by the variational method. The ground state wave function is expanded into Correlated Gaussian basis functions and the parameters of the basis states are optimized by a stochastic selection procedure. Accurate results can be obtained for 2-6 electron systems.Running time: A couple of hours for a typical system.     

Fast pulse detection algorithms for digitized waveforms from scintillators

Advanced C++ programming methods as well as fast Pulse Detection Algorithms (PDA) have been implemented in order to increase the computing speed of a LabVIEW™ data processing software developed for a Digital Pulse Shape Discrimination (DPSD) system for liquid scintillators. The newly implemented PDAs are described and compared: the most efficient method has been implemented in the data processing software, which has also been ported into C++. The comparison of the computing speeds of the new and old versions of the PDAs are presented.

Program summary

Program title: DPDS – Digital Pulse Detection SoftwareCatalogue identifier: AEHQ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHQ_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.: 454 070No. of bytes in distributed program, including test data, etc.: 20 987 104Distribution format: tar.gzProgramming language: C++ (Borland Visual C++)Computer: IBM PCOperating system: MS Windows 2000 and later…RAM: <50 Mbytes, highly depends on settingsClassification: 4.12External routines: Only standard Borland Visual C++ librariesNature of problem: A very slow pulse detection algorithm, used as standard in LABView, is preventing the ability to process achieved data during the pause between plasma discharges in modern tokamaks.Solution method: Simple yet precise pulse detection algorithms implemented and the whole data processing software translated from LABView into C++. This speeded up the elaboration up to 30 times.Restrictions: Windows system decimal separator must be “.”, not “,”.Additional comments: Processing 300 MB data file should not take longer then 10 minutes.Running time: From 1 minute to 1 hour.     

SecDec: A general program for sector decomposition

We present a program for the numerical evaluation of multi-dimensional polynomial parameter integrals. Singularities regulated by dimensional regularisation are extracted using iterated sector decomposition. The program evaluates the coefficients of a Laurent series in the regularisation parameter. It can be applied to multi-loop integrals in Euclidean space as well as other parametric integrals, e.g. phase space integrals.

Program summary

Program title: SecDecCatalogue identifier: AEIR_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIR_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.: 57 617No. of bytes in distributed program, including test data, etc.: 895 550Distribution format: tar.gzProgramming language: Wolfram Mathematica, perl, FortranComputer: From a single PC to a cluster, depending on the problemOperating system: Unix, LinuxRAM: Depends on the complexity of the problemClassification: 4.4, 5, 11.1Nature of problem: Extraction of ultraviolet and infrared singularities from parametric integrals appearing in higher order perturbative calculations in gauge theories, e.g. multi-loop Feynman integrals, Wilson loops, phase space integrals.Solution method: Algebraic extraction of singularities in dimensional regularisation using iterated sector decomposition. This leads to a Laurent series in the dimensional regularisation parameter ε, where the coefficients are finite integrals over the unit-hypercube. Those integrals are evaluated numerically by Monte Carlo integration.Restrictions: Depending on the complexity of the problem, limited by memory and CPU time. Multi-scale integrals can only be evaluated at Euclidean points.Running time: Between a few minutes and several days, depending on the complexity of the problem.     

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

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

Program summary

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