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Abstract Here we present a new approach to search for first order invariants (first integrals) of rational second order ordinary differential equations. This method is an alternative to the Darbouxian and symmetry approaches. Our procedure can succeed in many cases where these two approaches fail. We also present here a Maple implementation of the theoretical results and methods, hereby introduced, in a computational package — InSyDE. The package is designed, apart from materializing the algorithms presented, to provide a set of tools to allow the user to analyse the intermediary steps of the process. Computer programs in physics Program Title: InSyDE — Invariants and Symmetries of (racional second order ordinary) Differential Equations. Program Files doi: http://dx.doi.org/10.17632/4ytft6zgk7.1 Licensing provisions: GPLv3 Programming language: Maple 17. Nature of problem Search for first integrals of rational 2ODEs. Solution method: The method of solution is based on an algorithm described in this paper. Restrictions: If the rational 2ODE that is being analysed presents a very high degree in (x , y , z), then the method may not work well. Unusual features: Our implementation can find first integrals in many cases where the rational 2ODE under study cannot be reduced by other powerful solvers. Besides that, the package presents some useful research commands. [ABSTRACT FROM AUTHOR]

Abstract: Parallel code presents a non-trivial problem of load balancing computational workload throughout a system of hardware and software resources. The task of load balancing is further complicated when the number of allowable processors changes through time. This paper presents a two-component load-balancing mechanism using optimal initial workload distribution and dynamic load maintenance. The initial guess is provided by inversion of the workload distribution function. Workload distribution inversion enables efficient domain decomposition for arbitrary workloads and easily compensates for changes in system resources. Dynamic load balancing is provided by process feedback control as used, for example, in control mechanisms of physical processes. Proportional, integral, and differential (PID) feedback readily allows controls to compensate for runtime-changes of the workload distribution function. This paper demonstrates a one-dimensional realization of the ideas presented here. We apply this load-balancing technique to our gridless direct simulation Monte Carlo algorithm. We demonstrate that the method does indeed maintain uniform workload distribution across available resources as the workload and usable system resources undergo change through time. [ABSTRACT FROM AUTHOR]

Abstract: The objectives of this paper are twofold. First, the paper developed an improved algorithm to perform light scattering calculations by coated spheres. The improved algorithm was implemented in FORTRAN90 as a subroutine to allow flexible application of the code. Second, the new program was applied to the characterization of composite aluminum nanoparticles. In this application, multiple elements of the Mueller scattering matrix were measured at multiple angles to infer the properties of the nanoparticles, including the size distribution function and the thickness of the coating. The new program played a key role in the fitting of the measured data, and this application demonstrated the advantages of the new program in situations that demand high efficiency and reliability. Program summary: Program title: CMIE Catalogue identifier: AEFX_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEFX_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.: 1065 No. of bytes in distributed program, including test data, etc.: 12 933 Distribution format: tar.gz Programming language: FORTRAN90/95 Computer: Any machine running standard FORTRAN90/95 Operating system: Windows XP (Intel FORTRAN compiler 9.1) RAM: 1–100 Mbyte Classification: 16.7, 18 Nature of problem: Among various scientific and engineering applications, it is highly desirable to have an efficient, reliable, and flexible program to perform scattering calculations for coated spherical particles. Though several programs are publicly available and can perform such calculations, they are designed for more complicated scatterers (non-spherical, multilayered particles, etc.). As a result, their efficiency and reliability are usually not satisfactory when applied to coated spheres. Therefore, this paper aims at developing an improved program to provide efficient and reliable scattering calculations for coated spheres. Such virtues were demonstrated to be invaluable in applications where scattering calculations need to be performed for a great number of times over a wide range of conditions. Solution method: A new algorithm is developed to directly calculate the pre-factor of the scattering coefficients. This new technique provides reliable calculation of the pre-factor for arbitrarily large size parameters, and offers better control of the termination of the calculation. Based on this algorithm, an improved program was developed to perform light scattering calculations by coated spheres. Restrictions: Only applicable to single scattering, single layer coating, and unity permeability Running time: Several seconds–several minutes [Copyright &y& Elsevier]

We present an implementation of explicit solvent particle mesh Ewald (PME) classical molecular dynamics (MD) within the PMEMD molecular dynamics engine, that forms part of the AMBER v14 MD software package, that makes use of Intel Xeon Phi coprocessors by offloading portions of the PME direct summation and neighbor list build to the coprocessor. We refer to this implementation as pmemd MIC offload and in this paper present the technical details of the algorithm, including basic models for MPI and OpenMP configuration, and analyze the resultant performance. The algorithm provides the best performance improvement for large systems ( > 400,000 atoms), achieving a ∼35% performance improvement for satellite tobacco mosaic virus (1,067,095 atoms) when 2 Intel E5-2697 v2 processors (2 ×12 cores, 30M cache, 2.7 GHz) are coupled to an Intel Xeon Phi coprocessor (Model 7120P—1.238/1.333 GHz, 61 cores). The implementation utilizes a two-fold decomposition strategy: spatial decomposition using an MPI library and thread-based decomposition using OpenMP. We also present compiler optimization settings that improve the performance on Intel Xeon processors, while retaining simulation accuracy. [ABSTRACT FROM AUTHOR]

Abstract: The development of a new parallel framework for integrated modeling of tokamak plasmas is a primary objective of the SciDAC Framework Architecture for Core-Edge Transport Simulations (FACETS) project. The FACETS code will be used to predict the performance of tokamak discharges and to optimize tokamak discharge scenarios. Novel parallel numerical algorithms and solvers have been developed in the FACETS project in order to simulate the multi-scale dynamics of tokamak plasmas. The status of development of modules for anomalous transport in the FACETS code is described in this paper. Mechanisms that are used for coupling 1D anomalous transport in the plasma core together with 2D transport in the plasma edge (in near separatrix and scrape-off-layer regions) are considered. Results of the first verification studies based on predictive modeling of several analytical and experimental equilibria are presented. [Copyright &y& Elsevier]

Abstract: Various extensions of the tanh-function method and their implementations for finding explicit travelling wave solutions to nonlinear partial differential equations (PDEs) have been reported in the literature. However, some solutions are often missed by these packages. In this paper, a new algorithm and its implementation called TWS for solving single nonlinear PDEs are presented. TWS is implemented in Maple 10. It turns out that, for PDEs whose balancing numbers are not positive integers, TWS works much better than existing packages. Furthermore, TWS obtains more solutions than existing packages for most cases. Program summary: Program title:TWS Catalogue identifier:AEAM_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEAM_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.:1250 No. of bytes in distributed program, including test data, etc.:78 101 Distribution format:tar.gz Programming language:Maple 10 Computer:A laptop with 1.6 GHz Pentium CPU Operating system:Windows XP Professional RAM:760 Mbytes Classification:5 Nature of problem:Finding the travelling wave solutions to single nonlinear PDEs. Solution method:Based on tanh-function method. Restrictions:The current version of this package can only deal with single autonomous PDEs or ODEs, not systems of PDEs or ODEs. However, the PDEs can have any finite number of independent space variables in addition to time t. Unusual features:For PDEs whose balancing numbers are not positive integers, TWS works much better than existing packages. Furthermore, TWS obtains more solutions than existing packages for most cases. Additional comments:It is easy to use. Running time:Less than 20 seconds for most cases, between 20 to 100 seconds for some cases, over 100 seconds for few cases. References: [1] E.S. Cheb-Terrab, K. von Bulow, Comput. Phys. Comm. 90 (1995) 102. [2] S.A. Elwakil, S.K. El-Labany, M.A. Zahran, R. Sabry, Phys. Lett. A 299 (2002) 179. [3] E. Fan, Phys. Lett. 277 (2000) 212. [4] W. Malfliet, Amer. J. Phys. 60 (1992) 650. [5] W. Malfliet, W. Hereman, Phys. Scripta 54 (1996) 563. [6] E.J. Parkes, B.R. Duffy, Comput. Phys. Comm. 98 (1996) 288. [Copyright &y& Elsevier]

Alignment for tomography using a transmission electron microscopy frequently uses colloidal gold particles as fiducial reference marks. Typically, there is an implicit assumption that the tilt axis of the tomographic series is orthogonal to the beam direction. However, this may not be true, either intentionally, if a tilt-rotate stage is used, or unintentionally, because of mechanical errors in the rotation stage or the sample fixture. Here, we provide a computer code which takes as input a set of two-dimensional (2D) observations of fiducial reference marks at various tilt angles and the values of those tilt angles. It produces as output a three-dimensional model of the observations, 2D shifts for each view, and the tilt axis direction. [2] Commercial organizations identified in this paper are for the purpose of identification only and are not endorsed by NIST. The associated equipment or software identified is not necessarily the best available for the purpose. Program summary: Title of program: particleTilt Catalogue identifier: ADYW_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADYW_v1_0 Program obtainable from: CPC Program Library, Queen''s University of Belfast, N. Ireland Computers: IBM 2 compatible desktop PC; SGI 2 Octane Operating system: Red Hat 2 WS 3 Linux (with 2.4.21-40.EL kernel); IRIX 6.5 IP30 Program language used: Fortran 90 No. of bits in a word: 32 No. of processors used: one Has the code been vectorized: no No. of lines in distributed program, including test data, etc.: 2397 No. of bytes in distributed program, including test data, etc.: 47 017 Distribution format: tar.gz Peripherals used: one Typical running time: 350 ms (larger included example, on 2.8 GHz 32-bit PC) Nature of problem: The program is used to assist the alignment step in tomography. The samples should be prepared with spherical particles (typically gold beads) which are observed in several views. (Not every particle need be observed in every view.) The program reports coordinates of a 3D model of the particles as well as the direction of the tilt axis as a point on the unit sphere. Method of solution: Our package minimizes an objective function whose free variables are a set of 3D model points and 2D shifts of the views as well as two parameters characterizing of tilt axis as a point on the unit sphere. The objective function is decomposed into a pure quadratic form which encompasses the model points and shifts, and a more complicated form which has only two degrees of freedom. The Broyden–Fletcher–Goldfarb–Shanno algorithm is applied alternately and iteratively to minimize the objective function with respect to the two sets. [Copyright &y& Elsevier]

The Cellular Potts Model (CPM) has been used in a wide variety of biological simulations. However, most current CPM implementations use a sequential modified Metropolis algorithm which restricts the size of simulations. In this paper we present a parallel CPM algorithm for simulations of morphogenesis, which includes cell–cell adhesion, a cell volume constraint, and cell haptotaxis. The algorithm uses appropriate data structures and checkerboard subgrids for parallelization. Communication and updating algorithms synchronize properties of cells simulated on different processor nodes. Tests show that the parallel algorithm has good scalability, permitting large-scale simulations of cell morphogenesis (107 or more cells) and broadening the scope of CPM applications. The new algorithm satisfies the balance condition, which is sufficient for convergence of the underlying Markov chain. [Copyright &y& Elsevier]

Abstract: We describe an algorithm and a C++ implementation that we have written and made available for calculating the fully nonlinear evolution of 5D braneworld models with scalar fields. Bulk fields allow for the stabilization of the extra dimension. However, they complicate the dynamics of the system, so that analytic calculations (performed within an effective 4D theory) are usually only reliable for static bulk configurations or when the evolution of the extra dimension is negligible. In the general case, the nonlinear 5D dynamics can be studied numerically, and the algorithm and code we describe are the first ones of that type designed for this task. The program and its full documentation are available on the Web at http://www.cita.utoronto.ca/~jmartin/BRANECODE/. 1 [1] We also maintain a mirror of the BRANECODE website at http://www.cita.utoronto.ca/~kofman/BRANECODE/. In this paper we provide a brief overview of what the program does and how to use it. Program summary: Title of program: BRANECODE Catalogue identifier: ADVX Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADVX Program obtainable from: CPC Program Library, Queen''s University of Belfast, N. Ireland Licensing provisions: none Operating systems under which the program has been tested: Linux Programming language used: C++ Memory required to execute with typical data: less than 1 MB Has the code been vectorized?: no Peripherals used: none No. of lines in distributed program, including test data, etc.: 8277 No. of bytes in distributed program, including test data, etc.: 74 939 CPC Program Library subprograms used: none Nature of physical problem: Dynamics of two co-dimension one branes in a five-dimensional spacetime with a bulk scalar field and arbitrary potentials. The dynamics is governed by the five dimensional Einstein equations of gravity and the junction conditions at the position of the branes. Method of solution: Leapfrog algorithm to solve system of -dimensional partial differential equations; Initial and boundary value problem. Restrictions on the complexity of the problem: Assumption of homogeneity along three spatial dimensions parallel to the branes. Typical running time: Depending on the grid size and length of the time evolution: from ∼1 s to ∼1 h or longer. Unusual features of the program:none [Copyright &y& Elsevier]