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

The shapes of noble metal nanocrystals (NCs) are usually defined by polyhedra that are enclosed by {111} and {100} facets, such as cubes, tetrahedra, and octahedra. Platinum NCs of unusual tetrahexahedral (THH) shape were prepared at high yield by an electrochemical treatment of Pt nanospheres supported on glassy carbon by a square-wave potential. The single-crystal THH NC is enclosed by 24 high-index facets such as {730}, {210}, and/or {520} surfaces that have a large density of atomic steps and dangling bonds. These high-energy surfaces are stable thermally (to 800°C) and chemically and exhibit much enhanced (up to 400%) catalytic activity for equivalent Pt surface areas for electro-oxidation of small organic fuels such as formic acid and ethanol.

Synthesis of Tetrahexahedral Platinum Nanocrystals with High-Index Facets and High Electro-Oxidation Activity

Overview of constitutive laws, kinematics, homogenization and multiscale methods in crystal plasticity finite-element modeling: Theory, experiments, applications

Numerical Initial Value Problems in Ordinary Differential Equations

We employ a molecular statics approach based on embedded-atom-method interatomic potentials to study the elasticity of copper nanowires along [001], [110], and [111] crystallographic directions. Self-consistent comparison with the bulk response clearly shows that the overall nanowire elasticity is primarily due to nonlinear response of the nanowire core. While the surface-stress-induced surface elasticity modifies the behavior for ultrathin nanowires, their contribution is always considerably smaller than that due to nonlinear elasticity of the nanowire core. More importantly, for all three orientations, the surface is softer than an equivalently strained bulk, and the overall nanowire softening or stiffening is determined by orientation-dependent core elasticity.

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Size-dependent elasticity of nanowires: Nonlinear effects

This letter addresses the issue of surface softening versus stiffening during elastic deformation. Using a combination of molecular statics and ab initio calculations, we show that a solid surface can be either softer or stiffer elastically than the corresponding bulk. Whether a particular surface is softer or stiffer depends on the competition between atomic coordination and electron redistribution (which sometimes is referred as bond saturation) on the surface. Taking Cu as an example, we demonstrate that the Young’s modulus along 〈110〉 direction on {100} surface is larger than its bulk counterpart; meanwhile, it is smaller along 〈100〉 direction on {100} surface.

Are surfaces elastically softer or stiffer

We describe an atomistic simulator for thin film deposition in three dimensions (ADEPT). The simulator is designed to bridge the atomic and mesoscopic length scales by using efficient algorithms, including an option to speed up surface diffusion using events with multiple diffusion hops. Sputtered particles are inserted and assigned ballistic trajectories with angular distributions appropriate for magnetron sputtering. Atoms on the surface of the film execute surface diffusion hops with rates that depend on the local configuration, and are consistent with microscopic reversibility. The potential energies are chosen to match information obtained from a database of first principles and molecular dynamics (MD) calculations. Efficient computation is accomplished by selecting atoms with probabilities that are proportional to their hop rates. A first implementation of grain boundary effects is accomplished by including an orientation variable with each occupied site. Energies and mobilities are assigned to atom...

An atomistic simulator for thin film deposition in three dimensions

Models and rules for short-range interactions, cross slip and long-range interactions of dislocation segments for implementation in a 3D dislocation dynamics (3DD) model are developed. Dislocation curves of arbitrary shapes are discretized into sets of straight segments of mixed dislocations. Long-range interactions are evaluated explicitly based on results from the theory of dislocations. Models for short-range interactions, including, annihilation, formation of jogs, junctions, and dipoles, are developed on the basis of a `critical-force' criterion that captures the effect of the local fields from surrounding dislocations. In addition, a model for the cross-slip mechanism is developed and coupled with a Monte Carlo type analysis to simulate the development of double cross slip and composite slip. The model is then used to simulate stage I (easy glide) stress-strain behaviour in BCC single crystals, illustrating the feasibility of the 3DD model in predicting macroscopic properties such as flow stress and hardening, and their dependence on microscopic parameters such as dislocation mobility, dislocation structure, and pinning points.

https://iopscience.iop.org/article/10.1088/0965-0393/6/4/012/pdf

Models for long-/short-range interactions and cross slip in 3D dislocation simulation of BCC single crystals

Nanowires are among the most exciting one-dimensional nanomaterials because of their unique properties, which result primarily from their chemical composition and large surface area to volume ratio These properties make them ideal building blocks for the development of next generation electronics, opto-electronics, and sensor systems In this article, we focus on the unique mechanical properties of nanowires, which emerge from surface atoms having different electron densities and fewer bonding neighbors than atoms lying within the nanowire bulk In this respect, atomistic simulations have revealed a plethora of novel surface-driven mechanical behavior and properties, including both increases and decreases in elastic stiffness, phase transformations, shape memory, and pseudoelastic effects This article reviews such atomistic simulations, as well as experimental data of these phenomena, while assessing future challenges and directions

Hanchen Huang

Papers

Size-dependent elasticity of nanowires: Nonlinear effects

Are surfaces elastically softer or stiffer

An atomistic simulator for thin film deposition in three dimensions

Models for long-/short-range interactions and cross slip in 3D dislocation simulation of BCC single crystals

Mechanics of Crystalline Nanowires