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 perform scene-level inverse rendering to recover shape, reflectance and lighting from a single, uncontrolled image using a fully convolutional neural network. The network takes an RGB image as input, regresses albedo, shadow and normal maps from which we infer least squares optimal spherical harmonic lighting coefficients. Our network is trained using large uncontrolled multiview and timelapse image collections without ground truth. By incorporating a differentiable renderer, our network can learn from self-supervision. Since the problem is ill-posed we introduce additional supervision. Our key insight is to perform offline multiview stereo (MVS) on images containing rich illumination variation. From the MVS pose and depth maps, we can cross project between overlapping views such that Siamese training can be used to ensure consistent estimation of photometric invariants. MVS depth also provides direct coarse supervision for normal map estimation. We believe this is the first attempt to use MVS supervision for learning inverse rendering. In addition, we learn a statistical natural illumination prior. We evaluate performance on inverse rendering, normal map estimation and intrinsic image decomposition benchmarks.

Outdoor inverse rendering from a single image using multiview self-supervision

3D Morphable Models and Beyond (Dagstuhl Seminar 22121)

3D Morphable Models are models separating shape from appearance variation. Typically, they are used as a statistical prior in computer graphics and vision. Recent success with neural representations have caused a resurgence of interest in visual computing problems, leading to more accurate, higher fidelity, more expressive, and memory-efficient solutions. This report documents the program and the outcomes of Dagstuhl Seminar 22121, “3D Morphable Models and Beyond”. This meeting of 39 researchers covered various topics, including 3D morphable models, implicit neural representations, physics-inspired approaches, and more. We summarise the discussions, presentations and results of this workshop. Seminar March 20–25, 2022 – http://www.dagstuhl.de/22121 2012 ACM Subject Classification Computing methodologies → Computer graphics; Computing methodologies → Image-based rendering; Computing methodologies → Shape modeling; Computing methodologies → Animation; Computing methodologies → Computer vision; Computing methodologies → 3D imaging

3D Morphable Models and Beyond

We present a progressive 3D registration framework that is a highly-efficient variant of classical non-rigid Iterative Closest Points (N-ICP). Since it uses the Laplace-Beltrami operator for deformation regularisation, we view the overall process as Laplacian ICP (L-ICP). This exploits a ‘small deformation per iteration’ assumption and is progressively coarse-to-fine, employing an increasingly flexible deformation model, an increasing number of correspondence sets, and increasingly sophisticated correspondence estimation. Correspondence matching is only permitted within predefined vertex subsets derived from domain-specific feature extractors. Additionally, we present a new benchmark and a pair of evaluation metrics for 3D non-rigid registration, based on annotation transfer. We use this to evaluate our framework on a publicly-available dataset of 3D human head scans (Headspace). The method is robust and only requires a small fraction of the computation time compared to the most popular classical approach, yet has comparable registration performance.

Laplacian ICP for Progressive Registration of 3D Human Head Meshes

We describe an algorithm for rotational motion in molecular dynamics simulations. The algorithm requires neither quaternions nor Euler angles and works by updating the local Cartesian axes of the r...

William A. P. Smith

Papers

Outdoor inverse rendering from a single image using multiview self-supervision

3D Morphable Models and Beyond (Dagstuhl Seminar 22121)

3D Morphable Models and Beyond

Laplacian ICP for Progressive Registration of 3D Human Head Meshes

Rotational motion in the laboratory frame