TimeSeriesStreaming.vi: LabVIEW program for reliable data streaming of large analog time series

With modern data acquisition devices that work fast and very precise, scientists often face the task of dealing with huge amounts of data. These need to be rapidly processed and stored onto a hard disk. We present a LabVIEW program which reliably streams analog time series of MHz sampling. Its run time has virtually no limitation. We explicitly show how to use the program to extract time series from two experiments: For a photodiode detection system that tracks the position of an optically trapped particle and for a measurement of ionic current through a glass capillary. The program is easy to use and versatile as the input can be any type of analog signal. Also, the data streaming software is simple, highly reliable, and can be easily customized to include, e.g., real-time power spectral analysis and Allan variance noise quantification.

Program summary

Program title: TimeSeriesStreaming.VICatalogue identifier: AEHT_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHT_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.: 250No. of bytes in distributed program, including test data, etc.: 63 259Distribution format: tar.gzProgramming language: LabVIEW (http://www.ni.com/labview/)Computer: Any machine running LabVIEW 8.6 or higherOperating system: Windows XP and Windows 7RAM: 60–360 MbyteClassification: 3Nature of problem: For numerous scientific and engineering applications, it is highly desirable to have an efficient, reliable, and flexible program to perform data streaming of time series sampled with high frequencies and possibly for long time intervals. This type of data acquisition often produces very large amounts of data not easily streamed onto a computer hard disk using standard methods.Solution method: This LabVIEW program is developed to directly stream any kind of time series onto a hard disk. Due to optimized timing and usage of computational resources, such as multicores and protocols for memory usage, this program provides extremely reliable data acquisition. In particular, the program is optimized to deal with large amounts of data, e.g., taken with high sampling frequencies and over long time intervals. The program can be easily customized for time series analyses.Restrictions: Only tested in Windows-operating LabVIEW environments, must use TDMS format, acquisition cards must be LabVIEW compatible, driver DAQmx installed.Running time: As desirable: microseconds to hours     

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.     

COOL: A code for dynamic Monte Carlo simulation of molecular dynamics

COOL is a program to simulate evaporative and sympathetic cooling for a mixture of two gases co-trapped in a harmonic potential. The collisions involved are assumed to be exclusively elastic, and losses are due to evaporation from the trap. Each particle is followed individually in its trajectory, consequently properties such as spatial densities or energy distributions can be readily evaluated. The code can be used sequentially, by employing one output as input for another run. The code can be easily generalised to describe more complicated processes, such as the inclusion of inelastic collisions, or the possible presence of more than two species in the trap.

Program summary

Program title: COOLCatalogue identifier: AEHJ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHJ_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.: 1 111 674No. of bytes in distributed program, including test data, etc.: 18 618 045Distribution format: tar.gzProgramming language: C++Computer: DesktopOperating system: LinuxRAM: 500 MbytesClassification: 16.7, 23Nature of problem: Simulation of the sympathetic process occurring for two molecular gases co-trapped in a deep optical trap.Solution method: The Direct Simulation Monte Carlo method exploits the decoupling, over a short time period, of the inter-particle interaction from the trapping potential. The particle dynamics is thus exclusively driven by the external optical field. The rare interparticle collisions are considered with an acceptance/rejection mechanism, that is by comparing a random number to the collisional probability defined in terms of the inter-particle cross section and centre-of-mass energy. All particles in the trap are individually simulated so that at each time step a number of useful quantities, such as the spatial densities or the energy distributions, can be readily evaluated.Restrictions: The in-trap motion of the particles is treated classically.Running time: The running time is relatively short, 1–2 hours. However it is convenient to replicate each simulation several times with different initialisations of the random sequence.     

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.     

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.     

A MATLAB program to calculate translational and rotational diffusion coefficients of a single particle

We developed a graphical user interface, MATLAB based program to calculate the translational diffusion coefficients in three dimensions for a single diffusing particle, suspended inside a fluid. When the particles are not spherical, in addition to their translational motion also a rotational freedom is considered for them and in addition to the previous translational diffusion coefficients a planar rotational diffusion coefficient can be calculated in this program. Time averaging and ensemble averaging over the particle displacements are taken to calculate the mean square displacement variations in time and so the diffusion coefficients. To monitor the random motion of non-spherical particles a reference frame is used that the particle just have translational motion in it. We call it the body frame that is just like the particle rotates about the z-axis of the lab frame.Some statistical analysis, such as velocity autocorrelation function and histogram of displacements for the particle either in the lab or body frames, are available in the program. Program also calculates theoretical values of the diffusion coefficients for particles of some basic geometrical shapes; sphere, spheroid and cylinder, when other diffusion parameters like temperature and fluid viscosity coefficient can be adjusted.

Program summary

Program title: KOJACatalogue identifier: AEHK_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHK_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.: 48 021No. of bytes in distributed program, including test data, etc.: 1 310 320Distribution format: tar.gzProgramming language: MatLab (MathWorks Inc.) version 7.6 or higher. Statistics Toolbox and Curve Fitting Toolbox required.Computer: Tested on windows and linux, but generally it would work on any computer running MatLab (MathWorks Inc.). There is a bug in windows 7, if the user is not the administrator sometimes the program was not able to overwrite some internal files.Operating system: Any supporting MatLab (MathWorks Inc.) v7.6 or higher.RAM: About eight times that of loaded dataClassification: 12Nature of problem: In many areas of physics, knowing diffusion coefficients is vital and gives useful information about the physical properties of diffusive particles and the environment. In many cases a diffusive particle is not a sphere and has rotation during its movements. In these cases information about a particle's trajectory both in lab and body frame would be useful. Also some statistical analysis is needed to obtain more information about a particle's motion.Solution method: This program tries to gather all required tools to analyse raw data from the Brownian motion of a diffusing particle. Ability to switch between different methods of calculation of mean square displacement to find diffusion coefficients depends on the correlations between data points. There are three methods in the program: time average, ensemble average and their combinations. A linear fit is done to measure Diffusion Coefficient (D), the weight and fraction of data points is controllable. Given physical properties of the system, the program can calculates D theoretically for some basic geometrical shapes; sphere, spheroid and cylinder. In the case of non-spherical particles if data of rotation is available, the code can calculate trajectory and diffusion also in body frame. There are more statistical tools available in the program, such as histogram and autocorrelation function to obtain more information e.g. relaxation time to ideal diffusion motion. Code uses log–log diagram of mean square displacement (MSD) to calculate the amount of deviation from normal diffusion to sub- or super-diffusion.Running time: It is dependent on the input data, but for typical data in the order of mega bytes, it would take tens of minutes.     

spinney: A Form library for helicity spinors

In this work, the library spinney is presented, which provides an implementation of helicity spinors and related algorithms for the symbolical manipulation program Form. The package is well suited for symbolic amplitude calculations both in traditional, Feynman diagram based approaches and unitarity-based techniques.

Program summary

Program title: spinneyCatalogue identifier: AEJQ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJQ_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.: 21 128No. of bytes in distributed program, including test data, etc.: 377 589Distribution format: tar.gzProgramming language: FormComputer: Any supporting the Form languageOperating system: Any supporting the Form languageClassification: 4.4, 5, 11.1Nature of problem: Implementation of the spinor-helicity formalismSolution method: Form implementationRunning time: From actual calculations of all six-point one-loop diagrams of the process bounds of 50 ms<t?71 s for the simplest and the most complicated diagram respectively have been derived on an Intel Xeon 3.20 GHz using Form 3.3.     

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.     

A Fortran program for calculating electron or hole mobility in disordered semiconductors from first-principles

A Fortran program is developed to calculate charge carrier (electron or hole) mobility in disordered semiconductors from first-principles. The method is based on non-adiabatic ab initio molecular dynamics and static master equation, treating dynamic and static disorder on the same footing. We have applied the method to calculate the hole mobility in disordered poly(3-hexylthiophene) conjugated polymers as a function of temperature and electric field and obtained excellent agreements with experimental results. The program could be used to explore structure–mobility relation in disordered semiconducting polymers/organic semiconductors and aid rational design of these materials.

Program summary

Program title: FPMuCatalogue identifier: AEJV_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJV_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.: 788 580No. of bytes in distributed program, including test data, etc.: 8 433 024Distribution format: tar.gzProgramming language: Fortran 90Computer: Any architecture with a Fortran 90 compilerOperating system: Linux, WindowsRAM: Proportional to the system size, in our example, 1.2 GBClassification: 7.9Nature of problem: Determine carrier mobility from first-principles in disordered semiconductors as a function of temperature, electric field and carrier concentration.Solution method: Iteratively solve master equation with carrier state energy and transition rates determined from first-principles.Restrictions: Mobility for disordered semiconductors where the carrier wave-functions are localized and the carrier transport is due to phonon-assisted hopping mechanism.Running time: Depending on the system size (about an hour for the example here).     

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.     

Milne, a routine for the numerical solution of Milne's problem

The routine Milne provides accurate numerical values for the classical Milne's problem of neutron transport for the planar one speed and isotropic scattering case. The solution is based on the Case eigen-function formalism. The relevant X functions are evaluated accurately by the Double Exponential quadrature. The calculated quantities are the extrapolation distance and the scalar and the angular fluxes. Also, the H function needed in astrophysical calculations is evaluated as a byproduct.

Program summary

Program title: MilneCatalogue identifier: AEGS_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGS_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.: 701No. of bytes in distributed program, including test data, etc.: 6845Distribution format: tar.gzProgramming language: Fortran 77Computer: PC under Linux or WindowsOperating system: Ubuntu 8.04 (Kernel version 2.6.24-16-generic), Windows-XPClassification: 4.11, 21.1, 21.2Nature of problem: The X functions are integral expressions. The convergence of these regular and Cauchy Principal Value integrals are impaired by the singularities of the integrand in the complex plane. The DE quadrature scheme tackles these singularities in a robust manner compared to the standard Gauss quadrature.Running time: The test included in the distribution takes a few seconds to run.     

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.     

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     

A Breit–Pauli distorted wave implementation for autostructure

We describe the Breit–Pauli distorted wave (BPDW) approach for the electron-impact excitation of atomic ions that we have implemented within the autostructure code.

Program summary

Program title:autostructureCatalogue identifier: AEIV_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIV_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.: 130 987No. of bytes in distributed program, including test data, etc.: 1 031 584Distribution format: tar.gzProgramming language: Fortran 77/95Computer: GeneralOperating system: UnixHas the code been vectorized or parallelized?: Yes, a parallel version, with MPI directives, is included in the distribution.RAM: From several kbytes to several GbytesClassification: 2, 2.4Nature of problem: Collision strengths for the electron-impact excitation of atomic ions are calculated using a Breit–Pauli distorted wave approach with the optional inclusion of two-body non-fine-structure and fine-structure interactions.Solution method: General multi-configuration Breit–Pauli atomic structure. A jK-coupling partial wave expansion of the collision problem. Slater state angular algebra. Various model potential non-relativistic or kappa-averaged relativistic radial orbital solutions — the continuum distorted wave orbitals are not required to be orthogonal to the bound.Additional comments: Documentation is provided in the distribution file along with the test-case.Running time: From a few seconds to a few 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.     

ppohDEM: Computational performance for open source code of the discrete element method

We investigate performance improvements for the discrete element method (DEM) used in ppohDEM. First, we use OpenMP and MPI to parallelize DEM for efficient operation on many types of memory, including shared memory, and at any scale, from small PC clusters to supercomputers. We also describe a new algorithm for the descending storage method (DSM) based on a sort technique that makes creation of contact candidate pair lists more efficient. Finally, we measure the performance of ppohDEM using the proposed improvements, and confirm that computational time is significantly reduced. We also show that the parallel performance of ppohDEM can be improved by reducing the number of OpenMP threads per MPI process.Program summaryProgram title: ppohDEMCatalogue identifier: AESI_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AESI_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.: 39007No. of bytes in distributed program, including test data, etc.: 2482843Distribution format: tar.gzProgramming language: Fortran.Computer: CPU based workstations and parallel computers.Operating system: Linux, Windows.Has the code been vectorized or parallelized?: Yes, using MPI. Tested with up to 8 processors.RAM: Dependent upon the numbers of particles and contact particle pairs (1 GB for the example program supplied with the package)Classification: 6.5, 13.External routines: MPI-2, OpenMPNature of problem:Collision dynamics of viscoelastic particles with friction in powder engineering and soil mechanics.Solution method:Parallelized DEM running on shared and/or distributed systems is the solution method based particle model in which geometrical size and shape attributes are provided for each element. In the DEM, the Voigt model and Coulomb friction model are considered at each contact point between particles.Running time:10 min for the example program supplied with the package using 2 CPU (each with 10 cores) of Intel Xeon E7-4870.