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 show how a differentiable, physics-based renderer suitable for photometric vision tasks can be implemented as layers in a deep neural network. The layers include geometric operations for representation transformations, reflectance evaluations with arbitrary numbers of light sources and statistical bidirectional reflectance distribution function (BRDF) models. We make an implementation of these layers available as a neural network library (PVNN) for Theano. The layers can be incorporated into any neural network architecture, allowing parts of the photometric image formation process to be explicitly modelled in a network that is trained end to end via backpropagation. As an exemplar application, we show how to train a network with encoder-decoder architecture that learns to estimate BRDF parameters from a single image in an unsupervised manner.

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PVNN: A Neural Network Library for Photometric Vision

Three-dimensional Morphable Models (3DMMs) are powerful statistical tools for representing the 3D shapes and textures of an object class. Here we present the most complete 3DMM of the human head to date that includes face, cranium, ears, eyes, teeth and tongue. To achieve this, we propose two methods for combining existing 3DMMs of different overlapping head parts: i. use a regressor to complete missing parts of one model using the other, ii. use the Gaussian Process framework to blend covariance matrices from multiple models. Thus we build a new combined face-and-head shape model that blends the variability and facial detail of an existing face model (the LSFM) with the full head modelling capability of an existing head model (the LYHM). Then we construct and fuse a highly-detailed ear model to extend the variation of the ear shape. Eye and eye region models are incorporated into the head model, along with basic models of the teeth, tongue and inner mouth cavity. The new model achieves state-of-the-art performance. We use our model to reconstruct full head representations from single, unconstrained images allowing us to parameterize craniofacial shape and texture, along with the ear shape, eye gaze and eye color.

Towards a complete 3D morphable model of the human head

One of the enduring mysteries in the history of the Renaissance is the adult appearance of the archetypical "Renaissance Man," Leonardo da Vinci. His only acknowledged self-portrait is from an advanced age, and various candidate images of younger men are difficult to assess given the absence of documentary evidence. One clue about Leonardo's appearance comes from the remark of the contemporary historian, Vasari, that the sculpture of David by Leonardo's master, Andrea del Verrocchio, was based on the appearance of Leonardo
when he was an apprentice. Taking a cue from this statement, we suggest that the more mature sculpture of St. Thomas, also by Verrocchio, might also have been a portrait of Leonardo. We tested the possibility Leonardo was the subject for Verrocchio's sculpture by a novel computational technique for the comparison of
three-dimensional facial configurations. Based on quantitative measures of similarities, we also assess whether
another pair of candidate two-dimensional images are plausibly attributable as being portraits of Leonardo as
a young adult. Our results are consistent with the claim Leonardo is indeed the subject in these works, but
we need comparisons with images in a larger corpora of candidate artworks before our results achieve statistical significance.

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In search of Leonardo: Computer-based facial image analysis of Renaissance artworks for identifying Leonardo as subject

In this paper, we describe a weighted principal geodesic analysis (WPGA) method to extract features for gender classification based on 2.5D facial surface normals (needle-maps) which can be extracted from 2D intensity images using shape-from-shading (SFS). By incorporating the weight matrix into principal geodesic analysis (PGA), we control the obtained principal axis to be in the direction of the variance on gender information. Experiments show that using WPGA, the leading eigenvectors encode more gender discriminating power than using PGA, and that gender classification based on leading WPGA parameters is more accurate and stable than based on leading PGA parameters.

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William A. P. Smith

Papers

PVNN: A Neural Network Library for Photometric Vision

Towards a complete 3D morphable model of the human head

In search of Leonardo: Computer-based facial image analysis of Renaissance artworks for identifying Leonardo as subject

Weighted principal geodesic analysis for facial gender classification

Driving 3D morphable models using shading cues