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

The DL_POLY package provides a set of classical molecular dynamics programs that have application over a wide range of atomic and molecular systems. Written for parallel computers they offer capabilities stretching from small systems consisting of a few hundred atoms running on a single processor, up to systems of several million atoms running on massively parallel computers with thousands of processors. In this article we describe the structure of the programs and some applications.

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The DL_POLY molecular dynamics package

A face image contains geometric cues in the form of configurational information and contours that can be used to estimate 3D face shape. While it is clear that 3D reconstruction from 2D points is highly ambiguous if no further constraints are enforced, one might expect that the face-space constraint solves this problem. We show that this is not the case and that geometric information is an ambiguous cue. There are two sources for this ambiguity. The first is that, within the space of 3D face shapes, there are flexibility modes that remain when some parts of the face are fixed. The second occurs only under perspective projection and is a result of perspective transformation as camera distance varies. Two different faces, when viewed at different distances, can give rise to the same 2D geometry. To demonstrate these ambiguities, we develop new algorithms for fitting a 3D morphable model to 2D landmarks or contours under either orthographic or perspective projection and show how to compute flexibility modes for both cases. We show that both fitting problems can be posed as a separable nonlinear least squares problem and solved efficiently. We demonstrate both quantitatively and qualitatively that the ambiguity is present in reconstructions from geometric information alone but also in reconstructions from a state-of-the-art CNN-based method.

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What Does 2D Geometric Information Really Tell Us About 3D Face Shape

Morphable models are useful shape priors for biometric recognition tasks. Here we present an iterative process of refinement for a 3D Morphable Model (3DMM) of the human ear that employs data augmentation. The process employs the following stages 1) landmark-based 3DMM fitting; 2) 3D template deformation to overcome noisy over-fitting; 3) 3D mesh editing, to improve the fit to manual 2D landmarks. These processes are wrapped in an iterative procedure that is able to bootstrap a weak, approximate model into a significantly better model. Evaluations using several performance metrics verify the improvement of our model using the proposed algorithm. We use this new 3DMM model-booting algorithm to generate a refined 3D morphable model of the human ear, and we make this new model and our augmented training dataset public.

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A Data-Augmented 3D Morphable Model of the Ear

In this paper we present a differential approach to photo-polarimetric shape estimation. We propose several alternative differential constraints based on polarisation and photometric shading information and show how to express them in a unified partial differential system. Our method uses the image ratios technique to combine shading and polarisation information in order to directly reconstruct surface height, without first computing surface normal vectors. Moreover, we are able to remove the non-linearities so that the problem reduces to solving a linear differential problem. We also introduce a new method for estimating a polarisation image from multichannel data and, finally, we show it is possible to estimate the illumination directions in a two source setup, extending the method into an uncalibrated scenario. From a numerical point of view, we use a least-squares formulation of the discrete version of the problem. To the best of our knowledge, this is the first work to consider a unified differential approach to solve photo-polarimetric shape estimation directly for height. Numerical results on synthetic and real-world data confirm the effectiveness of our proposed method.

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Linear Differential Constraints for Photo-Polarimetric Height Estimation

Important sources of shape variability, such as articulated motion of body models or soft tissue dynamics, are highly nonlinear and are usually superposed on top of rigid body motion which must be factored out. We propose a novel, nonlinear, rigid body motion invariant Principal Geodesic Analysis (PGA) that allows us to analyse this variability, compress large variations based on statistical shape analysis and fit a model to measurements. For given input shape data sets we show how to compute a low dimensional approximating submanifold on the space of discrete shells, making our approach a hybrid between a physical and statistical model. General discrete shells can be projected onto the submanifold and sparsely represented by a small set of coefficients. We demonstrate two specific applications: model‐constrained mesh editing and reconstruction of a dense animated mesh from sparse motion capture markers using the statistical knowledge as a prior.

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William A. P. Smith

Papers

The DL_POLY molecular dynamics package

What Does 2D Geometric Information Really Tell Us About 3D Face Shape

A Data-Augmented 3D Morphable Model of the Ear

Linear Differential Constraints for Photo-Polarimetric Height Estimation

Principal Geodesic Analysis in the Space of Discrete Shells