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

다중혈관 관상동맥 환자에서 y-문합을 이용하여 양쪽 내흉동맥만을 사용한 우회술의 조기 성적

Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions Not only does this combination of a

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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation

From the Publisher: 
The accessible presentation of this book gives both a general view of the entire computer vision enterprise and also offers sufficient detail to be able to build useful applications. Users learn techniques that have proven to be useful by first-hand experience and a wide range of mathematical methods. A CD-ROM with every copy of the text contains source code for programming practice, color images, and illustrative movies. Comprehensive and up-to-date, this book includes essential topics that either reflect practical significance or are of theoretical importance. Topics are discussed in substantial and increasing depth. Application surveys describe numerous important application areas such as image based rendering and digital libraries. Many important algorithms broken down and illustrated in pseudo code. Appropriate for use by engineers as a comprehensive reference to the computer vision enterprise.

Computer vision : a modern approach = 计算机视觉 : 一种现代的方法

IEEE Transactions on Pattern Analysis and Machine Intelligence

In this paper we present a new framework for shape-from-shading which relies on a novel regularisation term which preserves surface structure. The resulting algorithm is both robust and accurate. We show that it can recover stable surface estimates from both synthetic and real world images of complex objects, even under extreme illumination.

Structure-Preserving Regularisation Constraints for Shape-from-Shading

In this paper we derive formal constraints relating terrain elevation and observed cast shadows. We show how an optimisation framework can be used to refine surface estimates using shadowing constraints from one or more images. The method is particularly applicable to the digital elevation models produced by the Shuttle Radar Topography Mission (SRTM), which have an abundance of voids in mountainous areas where elevation data is missing. Cast shadow maps are detected automatically from multi-spectral satellite imagery using a simple heuristic which is reliable over varying types of surface cover. We show that the combination of our shadow segmentation and terrain correction methods can restore the structure of mountain ridges in interpolated SRTM voids using five satellite images, decreasing the RMS error by over 25%.

Refinement of digital elevation models from shadowing cues

This paper describes how a facial albedo map can be recovered from a single image using a statistical model that captures variations in surface normal direction. We fit the model to intensity data using constraints on the surface normal direction provided by Lambert's law and then use the differences between observed and reconstructed image brightness to estimate the albedo map. We show that this process is stable under varying illumination and use the process to render images under novel illumination.

Single image estimation of facial albedo maps

In this paper we show how to estimate facial surface reflectance properties (a slice of the BRDF and the albedo) in conjunction with the facial shape from a single image. The key idea underpinning our approach is to iteratively interleave the two processes of estimating reflectance properties based on the current shape estimate and updating the shape estimate based on the current estimate of the reflectance function. For frontally illuminated faces, the reflectance properties can be described by a function of one variable which we estimate by fitting a curve to the scattered and noisy reflectance samples provided by the input image and estimated shape. For non-frontal illumination, we fit a smooth surface to the scattered 2D reflectance samples. We make use of a novel statistical face shape constraint which we term `model-based integrability' which we use to regularise the shape estimation. We show that the method is capable of recovering accurate shape and reflectance information from single grayscale or colour images using both synthetic and real world imagery. We use the estimated reflectance measurements to render synthetic images of the face in varying poses. To synthesise images under novel illumination, we show how to fit a parametric model of reflectance to the estimated reflectance function.

William A. P. Smith

Papers

Structure-Preserving Regularisation Constraints for Shape-from-Shading

Refinement of digital elevation models from shadowing cues

Single image estimation of facial albedo maps

Estimating Facial Reflectance Properties Using Shape-from-Shading

Molecular dynamics simulations of valinomycin and its potassium complex in homogeneous solvents