Ground states for condensed amorphous systems: Optimizing annealing schemes

Using optimized Simulated Annealing allows finding distinctly lower minima for the potential energy of amorphous systems. A new scheme resulting in an optimal annealing schedule has been found that can be readily applied to the simulation of molecules, clusters and condensed systems with any atomic composition. The scheme remains applicable if, due to the complexity of the system and its interatomic potentials, the configuration space cannot be explored in more detail.     

Global optimization and finite temperature simulations of atomic clusters: Use of XenArm clusters as test systems

The large potential energy barriers separating local minima on the potential energy surface of cluster systems pose serious problems for optimization and simulation methods. This article discusses algorithms for dealing with these problems. Lennard-Jones clusters are used to illustrate the important issues. In addition, the complexities in going from one-component to binary Lennard-Jones clusters are explored.     

Hybrid quantum mechanical/molecular dynamics simulation on parallel computers: density functional theory on real-space multigrids

A hybrid quantum mechanical/molecular dynamics simulation scheme is developed, in which a quantum mechanical system described by the density functional theory on real-space multigrids is embedded in a classical system of atoms interacting via an empirical interatomic potential. Handshake atoms coupling the quantum and the classical systems are treated by a novel scaled position method. The scheme is implemented on parallel computers using both task and spatial decompositions. An application to oxidation of Si (100) surface demonstrates seamless coupling of the quantum and the classical systems.     

Line-by-line spectroscopic simulations on graphics processing units

We report here on software that performs line-by-line spectroscopic simulations on gases. Elaborate models (such as narrow band and correlated-K) are accurate and efficient for bands where various components are not simultaneously and significantly active. Line-by-line is probably the most accurate model in the infrared for blends of gases that contain high proportions of H₂O and CO₂ as this was the case for our prototype simulation. Our implementation on graphics processing units sustains a speedup close to 330 on computation-intensive tasks and 12 on memory intensive tasks compared to implementations on one core of high-end processors. This speedup is due to data parallelism, efficient memory access for specific patterns and some dedicated hardware operators only available in graphics processing units. It is obtained leaving most of processor resources available and it would scale linearly with the number of graphics processing units in parallel machines. Line-by-line simulation coupled with simulation of fluid dynamics was long believed to be economically intractable but our work shows that it could be done with some affordable additional resources compared to what is necessary to perform simulations on fluid dynamics alone.

Program summary

Program title: GPU4RECatalogue identifier: ADZY_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZY_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.: 62 776No. of bytes in distributed program, including test data, etc.: 1 513 247Distribution format: tar.gzProgramming language: C++Computer: x86 PCOperating system: Linux, Microsoft Windows. Compilation requires either gcc/g++ under Linux or Visual C++ 2003/2005 and Cygwin under Windows. It has been tested using gcc 4.1.2 under Ubuntu Linux 7.04 and using Visual C++ 2005 with Cygwin 1.5.24 under Windows XP.RAM: 1 gigabyteClassification: 21.2External routines: OpenGL (http://www.opengl.org)Nature of problem: Simulating radiative transfer on high-temperature high-pressure gases.Solution method: Line-by-line Monte-Carlo ray-tracing.Unusual features: Parallel computations are moved to the GPU.Additional comments: nVidia GeForce 7000 or ATI Radeon X1000 series graphics processing unit is required.Running time: A few minutes.     

Optimizing lattice Boltzmann simulations for unsteady flows

We present detailed analysis of a lattice Boltzmann approach to model time-dependent Newtonian flows. The aim of this study is to find optimized simulation parameters for a desired accuracy with minimal computational time. Simulation parameters for fixed Reynolds and Womersley numbers are studied. We investigate influences from the Mach number and different boundary conditions on the accuracy and performance of the method and suggest ways to enhance the convergence behavior.     

Two algorithms for approximate construction of the set of positional absorption in the game problem of pursuit

Consideration is given to the differential game on the finite period of time in which the first player has to guarantee that the phase point will entry the terminal set and the second one must ensure the evasion of the terminal set on this interval. Is proposed a method for approximate construction of the set of positional absorption, i.e, the set of all initial points for which the problem of pursuit posed for the first player is solvable. The method is based on unification constructions and structures close to them. Relations defining the system of sets that approximates the set of positional absorption are written out. The convergence of the approximating system to the set of positional absorption is proved.     

Large eddy simulation and ALE mesh motion in Rayleigh-Taylor instability simulation

Many large eddy simulation (LES) techniques have been developed for stationary computational meshes. This study applies a single equation LES to Arbitrary Lagrangian-Eulerian (ALE) simulations of Rayleigh-Taylor instability and investigates its effects. Behavior of LES is similar for Eulerian and ALE simulations for the test problem studied. However, the motion of the mesh can be tied to the subgrid scale model in the form of a relaxation weight based on subgrid scale energy. This increases mesh resolution in areas of high subgrid scale energy.     

Cellular automaton modeling of computer network

The dramatically increasing growth of computer network has brought us more and more complex systems that reveals plenty of nonlinear complex phenomena. On the other hand, cellular automaton model used to be in the study of a variety of nonlinear and spatially extended systems. This paper proposes a simplified cellular model for computer network, namely the NaSch network model, which is originated at the NaSch model of road traffic. Typically, the NaSch network model is a one-dimension cellular automaton and consists of two kinds of cells, i.e. node cell and link cell. In this paper, the node cell stands for switch nodes in computer network, such as routers and switchers, while the link cell is the abstract of the lines of communication among these switch nodes. The simulation results show that this model indeed captures some of properties of flux of computer networks. The space-time plots illustrate that the randomization in this modeling plays an important role in the emerging of self-organization of congestion. It also demonstrates that the density of packet is another key factor to having influence on congestion. On the contrary, the boundary condition has few contribution to our model.     

Numerical simulation of the flow field in a model of the nasal cavity

Results of a numerical simulation of the flow in a model of the human nasal cavity using an AUSM-based method of second-order accuracy on a multi-block structured grid are presented and compared with experimental data. Computations are performed for inspiration and expiration at rest with Reynolds numbers Re=1560 and Re=1230 at the nostril, respectively. The comparison shows good agreement with experimental findings.     

A novel numerical approach to heterojunction bipolar transistors circuit simulation

In this paper we present a novel computational method for calculating the heterojunction bipolar transistor (HBT) physical characteristics in the time domain. To calculate the HBT high frequency properties, the Gummel-Poon equivalent circuit model is applied to replace the HBT in the circuit and a set of governing ordinary differential equations (ODEs) is formulated. We directly decouple the system ODEs and solve each decoupled ODE with the monotone iterative method in the time domain. This solution methodology proposed here has been applied to semiconductor device simulation by us earlier, and we find this method for the HBT simulation has good accuracy and converges globally. Compared with the HSPICE circuit simulator results, our results present the accuracy, efficiency, and robustness of the method.     

Recognition and analysis of local structure in polycrystalline configurations

A method is described for obtaining information about the local order existing in monoatomic model solids or real materials based on their atomistic configurations. An efficient algorithmic implementation is provided. The shape of the polyhedra formed by ‘relevant’ neighbors of each atom enter a pattern recognition method to resolve the type of the (usually non-ideal) crystal structure to which atoms surrounded by their relevant neighbors belong: hexagonal close-packed, face-centered cubic or body-centered cubic. Further, this approach allows for the analysis of icosahedral structure which preferably occurs in amorphous solids. Results of a molecular dynamics computer simulation illustrate how this method can be applied to contribute to an understanding of the mechanical and structural properties of solids (i) undergoing a steady shear stress and (ii) upon increasing temperature.     

Multicanonical simulations step by step

The purpose of this article is to provide a starter kit for multicanonical simulations in statistical physics. Fortran code for the q-state Potts model in d=2,3,… dimensions can be downloaded from the Web and this paper describes simulation results, which are in all details reproducible by running prepared programs. To allow for comparison with exact results, the internal energy, the specific heat, the free energy and the entropy are calculated for the d=2 Ising (q=2) and the q=10 Potts model. Analysis programs, relying on an all-log jackknife technique, which is suitable for handling sums of very large numbers, are introduced to calculate our final estimators.     

A parallel implementation of the Wang-Landau algorithm

The Wang-Landau algorithm is a flat-histogram Monte Carlo method that performs random walks in the configuration space of a system to obtain a close estimation of the density of states iteratively. It has been applied successfully to many research fields. In this paper, we propose a parallel implementation of the Wang-Landau algorithm on computers of shared memory architectures by utilizing the OpenMP API for distributed computing. This implementation is applied to Ising model systems with promising speedups. We also examine the effects on the running speed when using different strategies in accessing the shared memory space during the updating procedure. The allowance of data race is recommended in consideration of the simulation efficiency. Such treatment does not affect the accuracy of the final density of states obtained.     

Smoothed particle hydrodynamics: Applications to heat conduction

In this paper, we modify the numerical steps involved in a smoothed particle hydrodynamics (SPH) simulation. Specifically, the second order partial differential equation (PDE) is decomposed into two first order PDEs. Using the ghost particle method, consistent estimation of near-boundary corrections for system variables is also accomplished. Here, we focus on SPH equations for heat conduction to verify our numerical scheme. Each particle carries a physical entity (here, this entity is temperature) and transfers it to neighboring particles, thus exhibiting the mesh-less nature of the SPH framework, which is potentially applicable to complex geometries and nanoscale heat transfer. We demonstrate here only 1D and 2D simulations because 3D codes are as simple to generate as 1D codes in the SPH framework. Our methodology can be extended to systems where the governing equations are described by PDEs.     

JetWeb: A WWW interface and database for Monte Carlo tuning and validation

A World Wide Web interface to a Monte Carlo tuning facility is described. The aim of the package is to allow rapid and reproducible comparisons to be made between detailed measurements at high-energy physics colliders and general physics simulation packages. The package includes a relational database, a Java servlet query and display facility, and clean interfaces to simulation packages and their parameters.     

Recursive controllability and observability tests for large dynamic systems

Controllability and observability criteria for a linear stationary system are used to design recursive tests for slackening the computing system requirements for verification of the controllability and observability of large systems. Practical examples are given.     

Mathematical modeling of blood circulation system and its practical application

The human blood circulation system is represented by a nonlinear oscillation system for computer-aided digital modeling in real time scale. A parametric identification problem is formulated and its numerical solution algorithm is designed. A computer-aided blood circulation modeling and identification system is designed. The new approaches to construct real control systems for artificial and auxiliary blood circulation elements are based on neurocomputer technologies.     

One-Dimensional Turbulence: A new approach to high-fidelity subgrid closure of turbulent flow simulations

Consideration of the requirements for robust, high-fidelity subgrid closure of large-eddy simulations of multiphysics turbulent flows indicates the need for a spatially and temporally resolved representation of fine-scale physical and chemical processes that are coupled to fluid motion. One-Dimensional Turbulence (ODT), a potentially cost-effective approach for this purpose, captures these couplings by means of a stochastic simulation implemented on a one-dimensional domain. A subgrid implementation of ODT is formulated and its potential advantages and limitations are assessed.     

Estimation of attraction domains in wheeled robot control

Considered is the control design problem for planar motion of a wheeled robot. The mathematical model of the robot accounts for kinematic relationships between the velocity of a given point of chassis referred to as the reference point, orientation of the chassis, and control. Among the kinematic relations is the requirement that each of the four wheels perform a slip-free motion. The rear wheels are assumed to be driving while the front wheels are responsible for the rotation of the chassis. The control objective is to place the reference point in the prespecified trajectory and to stabilize the motion of the reference point along the prespecified trajectory. The trajectory consists of line segments and circular arcs. In the mathematical model under consideration, the current curvature of the trajectory of the reference point is taken as control; it is related to the steering angle of the front wheels by a simple algebraic expression. The control is subject to two-sided constraints due to limitations on the steering angle of the front wheels. For the control law proposed, the attraction domain in the space “distance to the trajectory—orientation” is analyzed. For the initial conditions from this domain, the system is guaranteed to hit a trajectory with given index of exponential stability.     

A special-purpose computer for exploring similar protein sequences by the dynamic programming method

We built a special-purpose computer for exploring similar protein sequences by the dynamic programming method, BIOLER-1 (BIOLogical sequence explorER). It can compute a complete similarity between two protein sequences which have less than 1024 amino acids. We integrated the system on a PLD (Programmable Logic Device) chip, APEX EP20K300EQC240-1 (300,000 gates) by Altera corporation. It is mounted on the 32 bit PCI (Peripheral Component Interconnect) bus board which is connected to a personal computer. The performance is 3564 MIPS (Million Instructions Per Second) which is three times faster than a personal computer with Pentium4 at 1.8 GHz. BIOLER-1 showed us the effectiveness in the field of biological sequence analysis.