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 demonstrate how to recover surface shape from single images of faces using shape-from-shading when shadows are present. We make use of a statistical representation of the distribution of surface normal directions based on the equidistant azimuthal projection. This is allows us to develop a statistical model of the variations in facial shape in the surface normal domain. We show how ideas from robust statistics can be used to fit the model to facial images in which there is significant self-shadowing. The method is evaluated on both synthetic and real-world images. It is demonstrated to effectively fill-in the facial surface when more than 30% of the area is subject to self-shadowing.

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Facial shadow removal

We have carried out a comprehensive computational study of the structures and
properties of a series of iron-bearing minerals under various conditions using grid
technologies developed within the eMinerals project. The work has enabled by a close
collaboration between computational scientists from different institutions across the UK,
as well as the involvement of computer and grid scientists in a true team effort. We show
here that our new approach for scientific research is only feasible with the use of the
eMinerals minigrid. Prior to the eMinerals project, such an approach would have been
almost impossible within the timescale available. The new approach allows us to achieve
our goals in a much quicker, more comprehensive and detailed way. Preliminary
scientific results of an investigation of the transport and immobilization of arsenic
species in the environment are presented in the paper.

A virtual research organization enabled by eMinerals minigrid: An integrated study of the transport and immobilisation of arsenic species in the environment

In this paper we describe a model-based method for recovering the 3D shape of faces using shape-from-shading. Using range-data, we learn a statistical model of the variation in surface normal direction for faces. This model uses the azimuthal equidistant projection to represent the distribution of surface normal directions. We fit the model to intensity data using constraints on the surface normal direction provided by Lambert's law. We illustrate the effectiveness of the method on real-world image data.

A model-based method for face shape recovery

Lego is one of the most successful toys in the world. Being able to scan, analyse and reconstruct Lego models has many applications, for example studying creativity. In this paper, from a set of 2D input images, we create a monolithic mesh, representing a physical 3D Lego model as input, and split it in to its known components such that the output of the program can be used to completely reconstruct the input model, brick for brick. We present a novel, fully automatic pipeline to reconstruct Lego models in 3D from 2D images; A-DBSCAN, an angular variant of DBSCAN, useful for grouping both parallel and anti-parallel vectors; and a method for reducing the problem of non-Manhattan reconstruction to that of Manhattan reconstruction. We evaluate the presented approach both qualitatively and quantitatively on a set of Lego duck models from a public data set, and show that the algorithm is able to identify and reconstruct the Lego models successfully.

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Reconstructing Creative Lego Models

Outdoor scene relighting is a challenging problem that requires good understanding of the scene geometry, illumination and albedo. Current techniques are completely supervised, requiring high quality synthetic renderings to train a solution. Such renderings are synthesized using priors learned from limited data. In contrast, we propose a self-supervised approach for relighting. Our approach is trained only on corpora of images collected from the internet without any user-supervision. This virtually endless source of training data allows training a general relighting solution. Our approach first decomposes an image into its albedo, geometry and illumination. A novel relighting is then produced by modifying the illumination parameters. Our solution capture shadow using a dedicated shadow prediction map, and does not rely on accurate geometry estimation. We evaluate our technique subjectively and objectively using a new dataset with ground-truth relighting. Results show the ability of our technique to produce photo-realistic and physically plausible results, that generalizes to unseen scenes.

William A. P. Smith

Papers

Facial shadow removal

A virtual research organization enabled by eMinerals minigrid: An integrated study of the transport and immobilisation of arsenic species in the environment

A model-based method for face shape recovery

Reconstructing Creative Lego Models

Self-supervised Outdoor Scene Relighting