Digit: A computational package for digital system design

To facilitate the analysis and design of digital control systems, the FORTRAN IV package DIGIT[1] is developed to transform analog process models into digital transfer functions. Of interest are the impulse and step invariant filters of digital signal processing and the trapezoidal approximation of the step invariant filter. The pertinent algorithms are developed; the program is highlighted and a user's guide is included. Application of the computational package is illustrated through a sequence of examples.     

A parallel computational model for GATE simulations

GATE/Geant4 Monte Carlo simulations are computationally demanding applications, requiring thousands of processor hours to produce realistic results. The classical strategy of distributing the simulation of individual events does not apply efficiently for Positron Emission Tomography (PET) experiments, because it requires a centralized coincidence processing and large communication overheads. We propose a parallel computational model for GATE that handles event generation and coincidence processing in a simple and efficient way by decentralizing event generation and processing but maintaining a centralized event and time coordinator. The model is implemented with the inclusion of a new set of factory classes that can run the same executable in sequential or parallel mode. A Mann–Whitney test shows that the output produced by this parallel model in terms of number of tallies is equivalent (but not equal) to its sequential counterpart. Computational performance evaluation shows that the software is scalable and well balanced.     

A standard Pascal event simulation package

A package implemented using standard Pascal is described. It provides the user with basic tools for discrete event-orientated simulation, and includes facilities for scheduling and causing pending events, handling of LIFO and FIFO queues, control of periodical dumping of statistics and comprehensive initialization and error routines. Two versions of the package have been implemented, using tree and linked list structures for scheduled events. Their relative performances are compared. The tree structure proves to be more efficient except in the minority of cases where the set of scheduled events has to be searched frequently; it also provides a much more efficient scheduling algorithm than does a linked list structure. This package is primarily intended as a communication network design tool, and a simple example of this type of usage is included. It could also be used in undergraduate teaching. Coding examples are given for the main procedures, in the two implementations.     

New modalities for scientific engagement in Africa – the case for computational physics

Computational physics as a mode of studying the mathematical and physical sciences has grown world-wide over the past two decades, but this trend is yet to fully develop in Africa. The essential ingredients are there for this to happen: increasing internet connectivity, cheaper computing resources and the widespread availability of open source and freeware. The missing ingredients centre on intellectual isolation and the low levels of quality international collaborations. Low level of funding for research from local governments remains a critical issue. This paper gives a motivation for the importance of developing computational physics at the university undergraduate level, graduate level and research levels and gives suggestions on how this may be achieved within the African context. It is argued that students develop a more intuitive feel for the mathematical and physical sciences, that they learn useful, transferable skills that make our graduates well-sought after in the industrial and commercial environments, and that such graduates are better prepared to tackle research problems at the masters and doctoral levels. At the research level, the case of the African School Series on Electronic Structure Methods and Applications (ASESMA) is presented as a new multi-national modality for engaging with African scientists. There are many novel aspects to this School series, which are discussed.     

Java simulations for physics education

We discuss the use of World Wide Web-based Java simulations in teaching physics to K–12 and undergraduate students. Our work focuses on the physics of membranes and illustrating how such systems are studied. We propose that Java should be used not only to produce small versions of research simulations but also to provide models illustrating simpler concepts underlying the main subject matter. In particular, applets should be tailored to the context in which they appear and should be as intuitive to use as possible. The applets we are developing are described in the context of current client performance. We also highlight the development of collaborative systems as an area of particular interest. © 1997 John Wiley & Sons, Ltd.     

A perspective on computational intelligence education

Presents an interview with Joe Rothermich, a Vice President at Lincoln Vale, LLC, an alternative asset management firm.     

A framework for parallel computational physics algorithms on multi-core: SPH in parallel

In this paper, a simulation framework that enables distributed numerical computing in multi-core shared-memory environments is presented. Using multiple threads allows a single memory image to be shared concurrently across cores but potentially introduces race conditions. Race conditions can be avoided by ensuring each core operates on an isolated memory block. This is usually achieved by running a different operating system process on each core, such as multiple MPI processes. However, we show that in many computational physics problems, memory isolation can also be enforced within a single process by leveraging spatial sub-division of the physical domain. A new spatial sub-division algorithm is presented that ensures threads operate on different memory blocks, allowing for in-place updates of state, with no message passing or creation of local variables during time stepping. Additionally, the developed framework controls task distribution dynamically ensuring an events based load balance. Results from fluid mechanics analysis using Smoothed Particle Hydrodynamics (SPH) are presented demonstrating linear performance with number of cores.     

A computational framework for simulation of Underwater Robotic Vehicle systems

This paper presents a computational framework for efficiently simulating the dynamics and hydrodynamics of Underwater Robotic Vehicle (URV) systems. Through the use of object-oriented mechanisms, a very general yet efficient version of the Articulated-Body (AB) algorithm has been implemented. An efficient solution to branching within chains is developed in the paper so that the algorithm can be used to compute the dynamics for the entire class of open-chain, tree-structured mechanisms. By including compliant contacts with the environment, most closed-chain systems can also be modeled. URV systems with an extended set of topologies can be simulated including proposed underwater walking machines with intra-body powered articulations. Using the encapsulation inherent in C++, the hydrodynamics code has been confined to a single class, thereby explicitly defining this framework and providing an environment for readily implementing desired hydrodynamics algorithms. Resulting simulations are very efficient and can be used in a number of applications both in the development and use of URV systems.     

THERMUS—A thermal model package for ROOT

THERMUS is a package of C++ classes and functions allowing statistical-thermal model analyses of particle production in relativistic heavy-ion collisions to be performed within the ROOT framework of analysis. Calculations are possible within three statistical ensembles; a grand-canonical treatment of the conserved charges B, S and Q, a fully canonical treatment of the conserved charges, and a mixed-canonical ensemble combining a canonical treatment of strangeness with a grand-canonical treatment of baryon number and electric charge. THERMUS allows for the assignment of decay chains and detector efficiencies specific to each particle yield, which enables sensible fitting of model parameters to experimental data.

Program summary

Program title: THERMUS, version 2.1Catalogue identifier: AEBW_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBW_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.: 17 152No. of bytes in distributed program, including test data, etc.: 93 581Distribution format: tar.gzProgramming language: C++Computer: PC, Pentium 4, 1 GB RAM (not hardware dependent)Operating system: Linux: FEDORA, RedHat, etc.Classification: 17.7External routines: Numerical Recipes in C [1], ROOT [2]Nature of problem: Statistical-thermal model analyses of heavy-ion collision data require the calculation of both primordial particle densities and contributions from resonance decay. A set of thermal parameters (the number depending on the particular model imposed) and a set of thermalized particles, with their decays specified, is required as input to these models. The output is then a complete set of primordial thermal quantities for each particle, together with the contributions to the final particle yields from resonance decay. In many applications of statistical-thermal models it is required to fit experimental particle multiplicities or particle ratios. In such analyses, the input is a set of experimental yields and ratios, a set of particles comprising the assumed hadron resonance gas formed in the collision and the constraints to be placed on the system. The thermal model parameters consistent with the specified constraints leading to the best-fit to the experimental data are then output.Solution method: THERMUS is a package designed for incorporation into the ROOT [2] framework, used extensively by the heavy-ion community. As such, it utilizes a great deal of ROOT's functionality in its operation. ROOT features used in THERMUS include its containers, the wrapper TMinuit implementing the MINUIT fitting package, and the TMath class of mathematical functions and routines. Arguably the most useful feature is the utilization of CINT as the control language, which allows interactive access to the THERMUS objects. Three distinct statistical ensembles are included in THERMUS, while additional options to include quantum statistics, resonance width and excluded volume corrections are also available. THERMUS provides a default particle list including all mesons (up to the (2045)) and baryons (up to the Ω⁻) listed in the July 2002 Particle Physics Booklet [3]. For each typically unstable particle in this list, THERMUS includes a text-file listing its decays. With thermal parameters specified, THERMUS calculates primordial thermal densities either by performing numerical integrations or else, in the case of the Boltzmann approximation without resonance width in the grand-canonical ensemble, by evaluating Bessel functions. Particle decay chains are then used to evaluate experimental observables (i.e. particle yields following resonance decay). Additional detector efficiency factors allow fine-tuning of the model predictions to a specific detector arrangement. When parameters are required to be constrained, use is made of the ‘Numerical Recipes in C’ [1] function which applies the Broyden globally convergent secant method of solving nonlinear systems of equations. Since the NRC software is not freely-available, it has to be purchased by the user. THERMUS provides the means of imposing a large number of constraints on the chosen model (amongst others, THERMUS can fix the baryon-to-charge ratio of the system, the strangeness density of the system and the primordial energy per hadron). Fits to experimental data are accomplished in THERMUS by using the ROOT TMinuit class. In its default operation, the standard χ² function is minimized, yielding the set of best-fit thermal parameters. THERMUS allows the assignment of separate decay chains to each experimental input. In this way, the model is able to match the specific feed-down corrections of a particular data set.Running time: Depending on the analysis required, run-times vary from seconds (for the evaluation of particle multiplicities given a set of parameters) to several minutes (for fits to experimental data subject to constraints).References:

[1]

W.H. Press, S.A. Teukolsky, W.T. Vetterling, B.P. Flannery, Numerical Recipes in C: The Art of Scientific Computing, Cambridge University Press, Cambridge, 2002.

[2]

R. Brun, F. Rademakers, Nucl. Inst. Meth. Phys. Res. A 389 (1997) 81. See also http://root.cern.ch/.

[3]

K. Hagiwara et al., Phys. Rev. D 66 (2002) 010001.

     

An enhanced version of SMMP—open-source software package for simulation of proteins

We describe a revised and updated version of the program package SMMP (Simple Molecular Mechanics for Proteins) [F. Eisenmenger, U.H.E. Hansmann, Sh. Hayryan, C.-K. Hu, Comput. Phys. Comm. 138 (2001) 192-212]. 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. This announcement describes the first major revision of this software package and its newly added features.

Program summary

Title of program:SMMPCatalogue identifier:ADOJ₋v2₋0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADOJ_v2_0Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandOperating system under which the program has been tested:LINUX systemProgramming language used:FORTRANComputer:PC PentiumNumber of lines in distributed program, including test data, etc.:18 492Number of bytes in distributed program, including test data, etc.:278 995Distribution format:ASCIICard punching code:ASCIICatalogue Identifier of previous version:ADOJJournal Reference of previous version:F. Eisenmenger, U.H.E. Hansmann, Sh. Hayryan, C.-K. Hu, Comput. Phys. Comm. 138 (2001) 192-212Does the new version supersede the previous version?:YesNature of physical problem:Molecular mechanics computations and Monte Carlo simulation of proteinsReasons for the new version:Increased functionalitySummary of revisions:Changes in energy function and protein representation; differences in program structure and organization; new functionalities added; miscellaneous changes and additionsMethod of solution:Utilizes ECEPP2/3 and FLEX potentials. Includes Monte Carlo simulation algorithms for canonical, as well as for generalized ensemblesRestrictions on the complexity of the problem:The consumed CPU time increases with the size of protein moleculeTypical running time:Depends on the size of the molecule under simulationUnusual features of the program:No     

A Macintosh software package for simulation of human red blood cell metabolism.

We have developed a computer software package for Macintosh to simulate the metabolism and hemoglobin binding affinity of human red blood cell. The model is capable of simulating hemoglobin binding of ligands, metabolite concentrations, and metabolic fluxes at physiological steady state and in response to extracellular parameter variations, such as pH, osmolarity, glucose, and adenine concentrations. The kinetic parameters of enzymes, extracellular conditions, and initial intracellular metabolite concentrations can be specified by the user in order to model a particular situation. The software is use friendly, utilizing menu, window, and mouse to interact with the user. It also provides a pathway map of the red cell, which allows a direct access to enzyme kinetics by clicking the enzymes in the map.     

Efficient parallel algorithms for numerical simulation

COUPL+ is a programming environment for applications using unstructured and hybrid grids for numerical simulations. It automates parallelization by handling the partitioning of data and dependent data and maintaining halo interfaces and copy coherency. We explore some algorithms behind this package. A multi-level partitioning method is described which is effective in the presence of skewed data, solving the multi-set median-finding problem. Partitioning elements over a set of pre-partitioned nodes is explored and a novel method is suggested for reducing communication in the resulting distribution.     

Incorporating haptic feedback in simulation for learning physics

The purpose of this study was to investigate the effectiveness of a haptic augmented simulation in learning physics. The results indicate that haptic augmented simulations, both the force and kinesthetic and the purely kinesthetic simulations, were more effective than the equivalent non-haptic simulation in providing perceptual experiences and helping elementary students create multimodal representations of the movements of gears. However, in most cases, force feedback was needed to construct a fully loaded multimodal representation that helps students to comprehend later instruction with less sensory modalities. In addition, the force and kinesthetic simulation was effective in helping to transfer knowledge to new learning situations. These findings suggest that it is important to help elementary students make a solid cognitive grounding with the use of a perceptual anchor.     

A computational scheme for H∞ model reduction

In this paper, a computational scheme for the H∞ model reduction problem is introduced. The scheme is illustrated by three examples. The algorithm is based on the recent characterization of the solution to the H∞ model reduction problem. A suboptimal computational procedure for the general multivariable continuous-time rth order optimal H_∞ model reduction problem is developed     

Low power consumption physics package for chip-scale atomic clock through gold-tin eutectic bonding

Microsystem Technologies - Reducing power consumption of chip-scale atomic clocks (CSACs) is a common goal for researchers. An effective but challenging issue for this goal is the reduction of...     

Editorial: Java for computational science and engineering – simulation and modeling

We are pleased to present a set of papers discussing the role of Java in Science and Engineering Simulation. These were presented at a small workshop with 45 participants at Syracuse on 16-17 December 1996. This was very successful, and a follow-up event will be sponsored by ACM in Las Vegas on 21 June 1997. The growing interest in this field is also supported by an email discussion list and other materials collected at the web site http://www.npac.syr.edu/projects/javaforcse. Java and Web technology can be used in many areas of science and engineering computation. These include sophisticated user interfaces and coarse-grain integration of different modules in complex meta-applications. However, also interesting (and controversial) is perhaps the use of Java as the language used for the computationally intense parts of a scientific code. All these areas were discussed at the workshop, with promising initial results and studies reported in each case. Again applications were described both for large-scale event-driven and time-stepped simulations and also for smaller client-side applets aimed at education. The appeal of Java as a simulation language includes its object-oriented characteristics, elegant applet software distribution model and natural support of graphical user interfaces. There are also non-technical reasons to think Java will be very important. In particular, one expects children to learn Java naturally as part of their Web experiences. On entering University, I find it hard to believe that many will be willing to switch from Java to Fortran77 or Fortran90. The papers in this issue fall into five areas. The first paper (‘Java for parallel computing and as a general language for scientific and engineering simulation and modeling’ by Geoffrey C. Fox and Wojtek Furmanski) is a general overview and the next three (‘Optimizing Java bytecodes’ by Michał Cierniak an Wei Li; ‘Optimizing Java: theory and practice’ by Zoran Budimlic and Ken Kennedy; ‘Technologies for ubiquitous supercomputing: a Java interface to the Nexus communication system’ by Ian Foster, George K. Thiruvathukal and Steven Tuecke) describe base Java technology from optimized compilation to linkage with communication infrastructure. The next two papers (‘Java simulations for physics education’ by Simeon Warner, Simon Catterall and Edward Lipson; ‘Using Java and JavaScript in the Virtual Programming Laboratory: a Web-based parallel programming environment’ by Kivanc Dincer and Geoffrey C. Fox) describe uses of Java in both science and computer science education. Then we have two papers (‘Java's role in distributed collaboration by Marina Chen and James Cowie’; ‘Java enabling collaborative education, health care, and computing’ by Lukasz Beca, Gang Cheng, Geoffrey C. Fox, Tomasz Jurga, Konrad Olszewski, Marek Podgorny, Piotr Sokolowski and Krzysztof Walczak) centred on the fascinating field of collaboration. The last six papers study the critical area of parallel and distributed computing in Java. These discuss world-wide computing (‘SuperWeb: research issues in Java-based global computing’ by Albert D. Alexandrov, Maximilian Ibel, Klaus E. Schauser and Chris J. Scheiman), large-scale software integration with Java servers (‘WebFlow – a visual programming paradigm for Web/Java based coarse grain distributed computing’ by Dimple Bhatia, Vanco Burzevski, Maja Camuseva, Geoffrey Fox, Wojtek Furmanski and Girish Premchandran) and mobility (‘Resource-aware metacomputing’ by Anurag Acharya, M. Ranganathan and Joel Saltz). These three distributed computing studies are contrasted with three on parallel computing: ‘Automatically exploiting implicit parallelism in Java’ by Aart J. C. Bik and Dennis B. Gannon on shared memory; ‘SPMD programming in Java’ by Susan Flynn Hummel, Ton Ngo and Harini Srinivasan on the SPMD style, and ‘Experiments with “HP Java”’ by Bryan Carpenter, Yuh-Jye Chang, Geoffrey Fox, Donald Leskiw and Xiaoming Li on classic distributed memory data parallelism. Currently, it appears that Java promises the computational scientist programming environments which have both attractive user interfaces and high-performance execution. An important purpose of the first workshop and the follow-up events is to get a broad input and study of the issues in this field so that we can guide the rapidly moving Java juggernaut to be maximally effective for scientific and engineering computation. © 1997 John Wiley & Sons, Ltd.     

Muon simulation codes MUSIC and MUSUN for underground physics

The paper describes two Monte Carlo codes dedicated to muon simulations: MUSIC (MUon SImulation Code) and MUSUN (MUon Simulations UNderground). MUSIC is a package for muon transport through matter. It is particularly useful for propagating muons through large thickness of rock or water, for instance from the surface down to underground/underwater laboratory. MUSUN is designed to use the results of muon transport through rock/water to generate muons in or around underground laboratory taking into account their energy spectrum and angular distribution.     

QPlus: computer package for coding theory research and education

A shared computer tool QPlus for studying coding theory studying is presented. The system offers computations over Z _q ={0, 1, …, q?1} (q<256) and includes modular arithmetic, elementary number theory, vectors and matrices arithmetic and an environment for research on q-ary codes – linear, constant-weight and equidistant codes. QPlus includes a DLL library package that implements coding theory algorithms. We explore the problem of finding bounds on the size of q-ary codes by computer methods. Some examples for optimal equidistant codes and constant-weight equidistant codes that have been constructed by computer methods developed in QPlus are described. We also research some optimal linear codes.