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

From the Publisher:
Evolutionary algorithms are relatively new, but very powerful techniques used to find solutions to many real-world search and optimization problems. Many of these problems have multiple objectives, which leads to the need to obtain a set of optimal solutions, known as effective solutions. It has been found that using evolutionary algorithms is a highly effective way of finding multiple effective solutions in a single simulation run. · Comprehensive coverage of this growing area of research · Carefully introduces each algorithm with examples and in-depth discussion · Includes many applications to real-world problems, including engineering design and scheduling · Includes discussion of advanced topics and future research · Features exercises and solutions, enabling use as a course text or for self-study · Accessible to those with limited knowledge of classical multi-objective optimization and evolutionary algorithms The integrated presentation of theory, algorithms and examples will benefit those working and researching in the areas of optimization, optimal design and evolutionary computing. This text provides an excellent introduction to the use of evolutionary algorithms in multi-objective optimization, allowing use as a graduate course text or for self-study.

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Multi-Objective Optimization Using Evolutionary Algorithms

Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.

Pattern Recognition and Machine Learning

We explore in this chapter questions of existence and uniqueness for solutions to stochastic differential equations and offer a study of their properties. This endeavor is really a study of diffusion processes. Loosely speaking, the term diffusion is attributed to a Markov process which has continuous sample paths and can be characterized in terms of its infinitesimal generator.

Stochastic Differential Equations

The particle swarm optimizer (PSO) is a stochastic, population-based optimization technique that can be applied to a wide range of problems, including neural network training. This paper presents a variation on the traditional PSO algorithm, called the cooperative particle swarm optimizer, or CPSO, employing cooperative behavior to significantly improve the performance of the original algorithm. This is achieved by using multiple swarms to optimize different components of the solution vector cooperatively. Application of the new PSO algorithm on several benchmark optimization problems shows a marked improvement in performance over the traditional PSO.

A Cooperative approach to particle swarm optimization

We present a parallel evolutionary optimization algorithm that leverages surrogate models for solving computationally expensive design problems with general constraints, on a limited computational budget. The essential backbone of our framework is an evolutionary algorithm coupled with a feasible sequential quadratic programming solver in the spirit of Lamarckian learning. We employ a trust-region approach for interleaving use of exact modelsfortheobjectiveandconstraintfunctionswithcomputationallycheapsurrogatemodelsduringlocalsearch. In contrastto earlier work, we construct local surrogatemodels using radial basis functionsmotivated by theprinciple of transductive inference. Further, the present approach retains the intrinsic parallelism of evolutionary algorithms and can hence be readily implemented on grid computing infrastructures. Experimental results are presented for some benchmark test functions and an aerodynamic wing design problem to demonstrate that our algorithm converges to good designs on a limited computational budget.

Evolutionary Optimization of Computationally Expensive Problems via Surrogate Modeling

In this paper, we present a novel surrogate-assisted evolutionary optimization framework for solving computationally expensive problems. The proposed framework uses computationally cheap hierarchical surrogate models constructed through online learning to replace the exact computationally expensive objective functions during evolutionary search. At the first level, the framework employs a data-parallel Gaussian process based global surrogate model to filter the evolutionary algorithm (EA) population of promising individuals. Subsequently, these potential individuals undergo a memetic search in the form of Lamarckian learning at the second level. The Lamarckian evolution involves a trust-region enabled gradient-based search strategy that employs radial basis function local surrogate models to accelerate convergence. Numerical results are presented on a series of benchmark test functions and on an aerodynamic shape design problem. The results obtained suggest that the proposed optimization framework converges to good designs on a limited computational budget. Furthermore, it is shown that the new algorithm gives significant savings in computational cost when compared to the traditional evolutionary algorithm and other surrogate assisted optimization frameworks

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Combining Global and Local Surrogate Models to Accelerate Evolutionary Optimization

Over the last fifty years, the ability to carry out analysis as a precursor to decision making in engineering design has increased dramatically. In particular, the advent of modern computing systems and the development of advanced numerical methods have made computational modelling a vital tool for producing optimized designs.
This text explores how computer-aided analysis has revolutionized aerospace engineering, providing a comprehensive coverage of the latest technologies underpinning advanced computational design. Worked case studies and over 500 references to the primary research literature allow the reader to gain a full understanding of the technology, giving a valuable insight into the world’s most complex engineering systems.

Computational Approaches for Aerospace Design: The Pursuit of Excellence

Solving design optimization problems using evolutionary algorithms has always been perceived as finding the optimal solution over the entire search space. However, the global optima may not always be the most desirable solution in many real-world engineering design problems. In practice, if the global optimal solution is very sensitive to uncertainties, for example, small changes in design variables or operating conditions, then it may not be appropriate to use this highly sensitive solution. In this paper, we focus on combining evolutionary algorithms with function approximation techniques for robust design. In particular, we investigate the application of robust genetic algorithms to problems with high dimensions. Subsequently, we present a novel evolutionary algorithm based on the combination of a max-min optimization strategy with a Baldwinian trust-region framework employing local surrogate models for reducing the computational cost associated with robust design problems. Empirical results are presented for synthetic test functions and aerodynamic shape design problems to demonstrate that the proposed algorithm converges to robust optimum designs on a limited computational budget

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Max-min surrogate-assisted evolutionary algorithm for robust design

Over the last decade, Evolutionary Algorithms (EAs) have emerged as a powerful paradigm for global optimization of multimodal functions. More recently, there has been significant interest in applying EAs to engineering design problems. However, in many complex engineering design problems where high-fidelity analysis models are used, each function evaluation may require a Computational Structural Mechanics (CSM), Computational Fluid Dynamics (CFD) or Computational Electro-Magnetics (CEM) simulation costing minutes to hours of supercomputer time. Since EAs typically require thousands of function evaluations to locate a near optimal solution, the use of EAs often becomes computationally prohibitive for this class of problems. In this chapter, we present frameworks that employ surrogate models for solving computationally expensive optimization problems on a limited computational budget. In particular, the key factors responsible for the success of these frameworks are discussed. Experimental results obtained on benchmark test functions and real-world complex design problems are presented.

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Prasanth B. Nair

Papers

Evolutionary Optimization of Computationally Expensive Problems via Surrogate Modeling

Combining Global and Local Surrogate Models to Accelerate Evolutionary Optimization

Computational Approaches for Aerospace Design: The Pursuit of Excellence

Max-min surrogate-assisted evolutionary algorithm for robust design

Surrogate-Assisted Evolutionary Optimization Frameworks for High-Fidelity Engineering Design Problems