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

We use molecular-dynamics simulations to study processes related to resistance to amorphization by radiation damage. We simulate high-energy radiation events in ${\mathrm{SiO}}_{2}$, ${\mathrm{GeO}}_{2}$, ${\mathrm{TiO}}_{2}$, ${\mathrm{Al}}_{2}{\mathrm{O}}_{3}$, and $\mathrm{MgO}$, and find that simulation results match the experiments. We discuss the difference between the damage that the structures along this series can support. We find that for the same material, activation barriers for damage recovery can strongly depend on the degree of structural damage. We observe that the effect of resistance to amorphization is primarily governed by the relaxation processes at the time scales of several picoseconds. On this time scale, we observe two distinct relaxation processes, reversible elastic deformation around the radiation cascade and recovery of the in-cascade damage of high topological disorder. Finally, we discuss how resistance to amorphization is related to interatomic interactions and to the nature of the chemical bond.

/pdf/atomistic-simulations-of-resistance-to-amorphization-by-2y9wcpbgep.pdf

Atomistic simulations of resistance to amorphization by radiation damage

Constrained reaction coordinate (Bluemoon) dynamics have
been used to characterise the free energy profile of benzene
in silicalite-1 at 300 K along the mean reaction path for
diffusion The reaction path was found empirically by
fitting a parametric curve through the mean positions of the
benzene centre of mass Both rigid and flexible zeolite
lattices have been investigated In both cases the primary
adsorption site was located at the intersection of the
straight and sinusoidal channels Two other distinct
adsorption sites exist in the straight channel and four in
the sinusoidal channel Lattice flexibility was found to
have a very strong influence on the relative free energies
of the adsorption sites and on the free energies of the
transition states connecting them The free energies,
combined with estimates of the transmission coefficient,
κ, were used to obtain rate constants for diffusion
between the main adsorption sites in the flexible lattice
Subsequent diffusive Monte Carlo simulations, using these
parameters, provided the self-diffusion coefficient,
D, and its components, at 300 K We obtained
D=336×10
 -14
 m2
s
 -1
, in excellent accord with the best
experimental value of 22×10
 -14

m2 s
 -1
 Diffusion was fastest in
the Y direction with the
D
 yy
/D
 xx

=149 and
D
 yy
/D
 zz

= 565 being observed

Bluemoon simulations of benzene in silicalite-1 : prediction of free energies and diffusion coefficients

We present a method for estimating surface height directly from a single polarisation image simply by solving a large, sparse system of linear equations. To do so, we show how to express polarisation constraints as equations that are linear in the unknown depth. The ambiguity in the surface normal azimuth angle is resolved globally when the optimal surface height is reconstructed. Our method is applicable to objects with uniform albedo exhibiting diffuse and specular reflectance. We extend it to an uncalibrated scenario by demonstrating that the illumination (point source or first/second order spherical harmonics) can be estimated from the polarisation image, up to a binary convex/concave ambiguity. We believe that our method is the first monocular, passive shape-from-x technique that enables well-posed depth estimation with only a single, uncalibrated illumination condition. We present results on glossy objects, including in uncontrolled, outdoor illumination.

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Linear Depth Estimation from an Uncalibrated, Monocular Polarisation Image

We present an iterative constraint algorithm, QSHAKE, for use with semirigid molecules in molecular dynamics simulations. The algorithm is based on ''SHAKE-ing'' bond constraints between rigid bodies, whose equations of motion are solved in the quaternion framework. The algorithm is derived and its performance compared with SHAKE for liquid octane. QSHAKE is . significantly more efficient whenever SHAKE requires triangles or tetrahedra of constraints to maintain molecular shape. Efficiencies are gained because QSHAKE reduces the number of holonomic constraints that must be solved iteratively and requires fewer iterations to obtain convergence. The gains in efficiency are most noticeable when a high degree of precision is imposed on the constraint criteria. QSHAKE is also stable at larger time steps than SHAKE, thus allowing for even more efficient exploration of phase space for semirigid molecules. Q 1998 John Wiley & Sons, Inc. J Comput Chem 19: 102)111, 1998

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SHAKE, Rattle, and Roll: Efficient Constraint Algorithms for Linked Rigid Bodies

The aim in this paper is to use principal geodesic analysis to model the statistical variations for sets of facial needle maps. We commence by showing how to represent the distribution of surface normals using the exponential map. Shape deformations are described using principal geodesic analysis on the exponential map. Using ideas from robust statistics we show how this deformable model may be fitted to facial images in which there is significant self-shadowing. Moreover, we demonstrate that the resulting shape-from-shading algorithm can be used to recover accurate facial shape and albedo from real world images. In particular, the algorithm can effectively fill-in the facial surface when more than 30% of its area is subject to self-shadowing. To investigate the utility of the shape parameters delivered by the method, we conduct experiments with illumination insensitive face recognition. We present a novel recognition strategy in which similarity is measured in the space of the principal geodesic parameters. We also use the recovered shape information to generate illumination normalized prototype images on which recognition can be performed. Finally we show that, from a single input image, we are able to generate the basis images employed by a number of well known illumination-insensitive recognition algorithms. We also demonstrate that the principal geodesics provide an efficient parameterization of the space of harmonic basis images.

William A. P. Smith

Papers

Atomistic simulations of resistance to amorphization by radiation damage

Bluemoon simulations of benzene in silicalite-1 : prediction of free energies and diffusion coefficients

Linear Depth Estimation from an Uncalibrated, Monocular Polarisation Image

SHAKE, Rattle, and Roll: Efficient Constraint Algorithms for Linked Rigid Bodies

Facial Shape-from-shading and Recognition Using Principal Geodesic Analysis and Robust Statistics