Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Data Mining Practical Machine Learning Tools and Techniques

We present a new method for solving stochastic differential equations based on Galerkin projections and extensions of Wiener's polynomial chaos Specifically, we represent the stochastic processes with an optimum trial basis from the Askey family of orthogonal polynomials that reduces the dimensionality of the system and leads to exponential convergence of the error Several continuous and discrete processes are treated, and numerical examples show substantial speed-up compared to Monte Carlo simulations for low dimensional stochastic inputs

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The Wiener--Askey Polynomial Chaos for Stochastic Differential Equations

In this book, Andrew Harvey sets out to provide a unified and comprehensive theory of structural time series models. Unlike the traditional ARIMA models, structural time series models consist explicitly of unobserved components, such as trends and seasonals, which have a direct interpretation. As a result the model selection methodology associated with structural models is much closer to econometric methodology. The link with econometrics is made even closer by the natural way in which the models can be extended to include explanatory variables and to cope with multivariate time series. From the technical point of view, state space models and the Kalman filter play a key role in the statistical treatment of structural time series models. The book includes a detailed treatment of the Kalman filter. This technique was originally developed in control engineering, but is becoming increasingly important in fields such as economics and operations research. This book is concerned primarily with modelling economic and social time series, and with addressing the special problems which the treatment of such series poses. The properties of the models and the methodological techniques used to select them are illustrated with various applications. These range from the modellling of trends and cycles in US macroeconomic time series to to an evaluation of the effects of seat belt legislation in the UK.

Forecasting, Structural Time Series Models and the Kalman Filter

The author's preface gives an outline: "This book is about weakconvergence methods in metric spaces, with applications sufficient to show their power and utility. The Introduction motivates the definitions and indicates how the theory will yield solutions to problems arising outside it. Chapter 1 sets out the basic general theorems, which are then specialized in Chapter 2 to the space C[0, l ] of continuous functions on the unit interval and in Chapter 3 to the space D [0, 1 ] of functions with discontinuities of the first kind. The results of the first three chapters are used in Chapter 4 to derive a variety of limit theorems for dependent sequences of random variables. " The book develops and expands on Donsker's 1951 and 1952 papers on the invariance principle and empirical distributions. The basic random variables remain real-valued although, of course, measures on C[0, l ] and D[0, l ] are vitally used. Within this framework, there are various possibilities for a different and apparently better treatment of the material. More of the general theory of weak convergence of probabilities on separable metric spaces would be useful. Metrizability of the convergence is not brought up until late in the Appendix. The close relation of the Prokhorov metric and a metric for convergence in probability is (hence) not mentioned (see V. Strassen, Ann. Math. Statist. 36 (1965), 423-439; the reviewer, ibid. 39 (1968), 1563-1572). This relation would illuminate and organize such results as Theorems 4.1, 4.2 and 4.4 which give isolated, ad hoc connections between weak convergence of measures and nearness in probability. In the middle of p. 16, it should be noted that C*(S) consists of signed measures which need only be finitely additive if 5 is not compact. On p. 239, where the author twice speaks of separable subsets having nonmeasurable cardinal, he means "discrete" rather than "separable." Theorem 1.4 is Ulam's theorem that a Borel probability on a complete separable metric space is tight. Theorem 1 of Appendix 3 weakens completeness to topological completeness. After mentioning that probabilities on the rationals are tight, the author says it is an

Convergence of probability measures

Representation of stochastic processes stochastic finite element method - response representation stochastic finite element method - response statistics numerical examples.

Stochastic Finite Elements: A Spectral Approach

The basic random variables on which random uncertainties can in a given model depend can be viewed as defining a measure space with respect to which the solution to the mathematical problem can be defined. This measure space is defined on a product measure associated with the collection of basic random variables. This paper clarifies the mathematical structure of this space and its relationship to the underlying spaces associated with each of the random variables. Cases of both dependent and independent basic random variables are addressed. Bases on the product space are developed that can be viewed as generalizations of the standard polynomial chaos approximation. Moreover, two numerical constructions of approximations in this space are presented along with the associated convergence analysis.

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Physical Systems with Random Uncertainties: Chaos Representations with Arbitrary Probability Measure

A new method for the solution of problems involving material variability is proposed. The material property is modeled as a stochastic process. The method makes use of the Karhunen‐Loeve expansion to represent the random material property. The expansion is a representation of the process in terms of a finite set of uncorrelated random variables. The resulting formulation is compatible with the finite element method. A Neumann expansion scheme is subsequently employed to obtain a convergent expansion of the response process. The response is thus obtained as a homogeneous multivariate polynomial in the uncorrelated random variables. From this representation various statistical quantities may be derived. The usefulness of the proposed method, in terms of accuracy and efficiency, is exemplified by considering a cantilever beam with random rigidity. The derived results pertaining to the second‐order statistics of the response are found in good agreement with those obtained by a Monte Carlo simulation solution ...

Stochastic Finite Element Expansion for Random Media

Uncertainty propagation using Wiener-Haar expansions

This paper gives an overview of the use of polynomial chaos (PC) expansions to represent stochastic processes in numerical simulations. Several methods are presented for performing arithmetic on, as well as for evaluating polynomial and nonpolynomial functions of variables represented by PC expansions. These methods include {Taylor} series, a newly developed integration method, as well as a sampling-based spectral projection method for nonpolynomial function evaluations. A detailed analysis of the accuracy of the PC representations, and of the different methods for nonpolynomial function evaluations, is performed. It is found that the integration method offers a robust and accurate approach for evaluating nonpolynomial functions, even when very high-order information is present in the PC expansions.

Roger Ghanem

Papers

Stochastic Finite Elements: A Spectral Approach

Physical Systems with Random Uncertainties: Chaos Representations with Arbitrary Probability Measure

Stochastic Finite Element Expansion for Random Media

Uncertainty propagation using Wiener-Haar expansions

Numerical Challenges in the Use of Polynomial Chaos Representations for Stochastic Processes