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 to train an image-to-image network to predict dense correspondence between a face image and a 3D morphable model using only the model for supervision. We show that both geometric parameters (shape, pose and camera intrinsics) and photometric parameters (texture and lighting) can be inferred directly from the correspondence map using linear least squares and our novel inverse spherical harmonic lighting model. The least squares residuals provide an unsupervised training signal that allows us to avoid artefacts common in the literature such as shrinking and conservative underfitting. Our approach uses a network that is 10\(\times \) smaller than parameter regression networks, significantly reduces sensitivity to image alignment and allows known camera calibration or multi-image constraints to be incorporated during inference. We achieve results competitive with state-of-the-art but without any auxiliary supervision used by previous methods.

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“Look Ma, No Landmarks!” – Unsupervised, Model-Based Dense Face Alignment

In this paper we present a method for computing dense correspondence between a set of 3D face meshes using functional maps. The functional maps paradigm brings with it a number of advantages for face correspondence. First, it allows us to combine various notions of correspondence. We do so by proposing a number of face-specific functions, suited to either within-or between-subject correspondence. Second, we propose a groupwise variant of the method allowing us to compute cycle-consistent functional maps between all faces in a training set. Since functional maps are of much lower dimension than point-to-point correspondences, this is feasible even when the input meshes are very high resolution. Finally, we show how a functional map provides a geometric constraint that can be used to filter feature matches between non-rigidly deforming surfaces.

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Functional Faces: Groupwise Dense Correspondence Using Functional Maps

Molecular dynamics simulations were carried out to study contact behaviour of MgO pyramidal tips with atomically flat MgO surfaces in the (001) direction. Both commensurate and incommensurate contact modes over a wide range of surface interaction have been considered, from weakly interacting to highly compressed. Characteristic mechanical instability 'jump' effects were observed in the former case, and, to a much smaller extent, in the latter case as well. By making comparison between the rectangular MgO probes from our previous work and the pyramidal probe it was found that detailed contact and withdrawal behaviour depended very much upon the local geometrical structure of the contacting tips. Specifically, the strain distribution and the change in interplanar spacing were different during contacts. When a pyramidal probe is withdrawn, the first sign of hysteresis results in disrupted crystal structures near the contacting tip and is almost always followed by subsequent complex plastic dislocation and 'neck' formation. The probe with the 'sharpest tip' is found to undergo modification at the tip to give a truncated octahedron structure and subsequently shows a very different contact behaviour. For example, the modified probe can be withdrawn completely from the surface without any damage, a phenomenon not commonly encountered with other clean MgO contact systems in our work.

https://iopscience.iop.org/article/10.1088/0957-4484/14/8/301/pdf

William A. P. Smith

Papers

“Look Ma, No Landmarks!” – Unsupervised, Model-Based Dense Face Alignment

Functional Faces: Groupwise Dense Correspondence Using Functional Maps

Molecular dynamics simulations of (001) MgO surface contacts: effects of tip structures and surface matching

Gender discriminating models from facial surface normals

A shadow constrained conditional generative adversarial net for SRTM data restoration