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

A third-generation numerical wave model to compute random, short-crested waves in coastal regions with shallow water and ambient currents (Simulating Waves Nearshore (SWAN)) has been developed, implemented, and validated. The model is based on a Eulerian formulation of the discrete spectral balance of action density that accounts for refractive propagation over arbitrary bathymetry and current fields. It is driven by boundary conditions and local winds. As in other third-generation wave models, the processes of wind generation, whitecapping, quadruplet wave-wave interactions, and bottom dissipation are represented explicitly. In SWAN, triad wave-wave interactions and depth-induced wave breaking are added. In contrast to other third-generation wave models, the numerical propagation scheme is implicit, which implies that the computations are more economic in shallow water. The model results agree well with analytical solutions, laboratory observations, and (generalized) field observations.

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A third-generation wave model for coastal regions: 1. Model description and validation

to be done in this area. Face recognition is a problem that scarcely clamoured for attention before the computer age but, having surfaced, has involved a wide range of techniques and has attracted the attention of some fine minds (David Mumford was a Fields Medallist in 1974). This singular application of mathematical modelling to a messy applied problem of obvious utility and importance but with no unique solution is a pretty one to share with students: perhaps, returning to the source of our opening quotation, we may invert Duncan's earlier observation, 'There is an art to find the mind's construction in the face!'.

Linear and nonlinear waves, by G. B. Whitham. Pp.636. £50. 1999. ISBN 0 471 35942 4 (Wiley).

This book is a tutorial written by researchers and developers behind the FEniCS Project and explores an advanced, expressive approach to the development of mathematical software. The presentation spans mathematical background, software design and the use of FEniCS in applications. Theoretical aspects are complemented with computer code which is available as free/open source software. The book begins with a special introductory tutorial for beginners. Followingare chapters in Part I addressing fundamental aspects of the approach to automating the creation of finite element solvers. Chapters in Part II address the design and implementation of the FEnicS software. Chapters in Part III present the application of FEniCS to a wide range of applications, including fluid flow, solid mechanics, electromagnetics and geophysics.

Automated Solution of Differential Equations by the Finite Element Method: The FEniCS Book

IEEE Transactions on Pattern Analysis and Machine Intelligence

Fully nonlinear extensions of Boussinesq equations are derived to simulate surface wave propagation in coastal regions. By using the velocity at a certain depth as a dependent variable (Nwogu 1993), the resulting equations have significantly improved linear dispersion properties in intermediate water depths when compared to standard Boussinesq approximations. Since no assumption of small nonlinearity is made, the equations can be applied to simulate strong wave interactions prior to wave breaking. A high-order numerical model based on the equations is developed and applied to the study of two canonical problems: solitary wave shoaling on slopes and undular bore propagation over a horizontal bed. Results of the Boussinesq model with and without strong nonlinearity are compared in detail to those of a boundary element solution of the fully nonlinear potential flow problem developed by Grilli et al. (1989). The fully nonlinear variant of the Boussinesq model is found to predict wave heights, phase speeds and particle kinematics more accurately than the standard approximation.

A fully nonlinear Boussinesq model for surface waves. Part 1. Highly nonlinear unsteady waves

In this paper, we focus on the implementation and verification of an extended Boussinesq model for surf zone hydrodynamics in two horizontal dimensions The time-domain numerical model is based on the fully nonlinear Boussinesq equations As described in Part I of this two-part paper, the energy dissipation due to wave breaking is modeled by introducing an eddy viscosity term into the momentum equations, with the viscosity strongly localized on the front face of the breaking waves Wave runup on the beach is simulated using a permeable-seabed technique We apply the model to simulate two laboratory experiments in large wave basins They are wave transformation and breaking over a submerged circular shoal and solitary wave runup on a conical island Satisfactory agreement is found between the numerical results and the laboratory measurements

Boussinesq modeling of wave transformation, breaking, and runup. ii: 2d

The extended Boussinesq equations derived by Nwogu (1993) significantly improve the linear dispersive properties of long-wave models in intermediate water depths, making it suitable to simulate wave propagation from relatively deep to shallow water. In this study, a numerical code based on Nwogu's equations is developed. The model uses a fourth-order predictor-corrector method to advance in time, and discretizes first-order spatial derivatives to fourth-order accuracy, thus reducing all truncation errors to a level smaller than the dispersive terms retained by the model. The basic numerical scheme and associated boundary conditions are described. The model is applied to several examples of wave propagation in variable depth, and computed solutions are compared with experimental data. These initial results indicate that the model is capable of simulating wave transformation from relatively deep water to shallow water, giving accurate predictions of the height and shape of shoaled waves in both regular and irregular wave experiments.

Time-Dependent Numerical Code for Extended Boussinesq Equations

https://personal.egr.uri.edu/grilli/shi_etal_om_2012.pdf

A high-order adaptive time-stepping TVD solver for Boussinesq modeling of breaking waves and coastal inundation

A parabolic model for calculating the combined refraction/diffraction of monochromatic linear waves is developed, including a term which allows for the dissipation of wave energy. The coefficient of the dissipation term is related to a number of dissipative models. Wave calculations are performed for a localized area of dissipation, based on a friction model for a spatial distribution of rigid vertical cylinders. The region of localized dissipation creates a shadow region of low wave energy, which may have important implications for the response of neighboring shore lines.

James T. Kirby

Papers

A fully nonlinear Boussinesq model for surface waves. Part 1. Highly nonlinear unsteady waves

Boussinesq modeling of wave transformation, breaking, and runup. ii: 2d

Time-Dependent Numerical Code for Extended Boussinesq Equations

A high-order adaptive time-stepping TVD solver for Boussinesq modeling of breaking waves and coastal inundation

Wave diffraction due to areas of energy dissipation