MPiSIM: Massively parallel simulation tool for metallic system

We report a domain decomposition molecular dynamics (MD) for simulation on metallic systems based on distributed parallel computers. The method is a development of a spatial decomposition in 3-D space with the combination of link-cell and neighbor list techniques for enhanced efficiency. The algorithm has been successfully implemented on the Origin2000, Wolf, HP Examplar etc. various platforms. The scaling performance on these platforms will be discussed and several applications in metallic systems will also be given in the paper. This revised version was published online in June 2006 with corrections to the Cover Date.     

Flow simulation and high performance computing

Flow simulation is a computational tool for exploring science and technology involving flow applications. It can provide cost-effective alternatives or complements to laboratory experiments, field tests and prototyping. Flow simulation relies heavily on high performance computing (HPC). We view HPC as having two major components. One is advanced algorithms capable of accurately simulating complex, real-world problems. The other is advanced computer hardware and networking with sufficient power, memory and bandwidth to execute those simulations. While HPC enables flow simulation, flow simulation motivates development of novel HPC techniques. This paper focuses on demonstrating that flow simulation has come a long way and is being applied to many complex, real-world problems in different fields of engineering and applied sciences, particularly in aerospace engineering and applied fluid mechanics. Flow simulation has come a long way because HPC has come a long way. This paper also provides a brief review of some of the recently-developed HPC methods and tools that has played a major role in bringing flow simulation where it is today. A number of 3D flow simulations are presented in this paper as examples of the level of computational capability reached with recent HPC methods and hardware. These examples are, flow around a fighter aircraft, flow around two trains passing in a tunnel, large ram-air parachutes, flow over hydraulic structures, contaminant dispersion in a model subway station, airflow past an automobile, multiple spheres falling in a liquid-filled tube, and dynamics of a paratrooper jumping from a cargo aircraft. Sponsored by ARO, ARPA, NASA-JSC, and by the Army High Performance Computing Research Center under the auspices of the Department of the Army, Army Research Laboratory cooperative agreement number DAAH04-95-2-0003/ contract number DAAH04-95-C-0008. The content does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred. CRAY C90 time and support for the second author was provided in part by the Minnesota Supercomputer Institute. Dedicated to the 10th anniversary of Computational Mechanics     

Developing community codes for materials modeling

For this article, we call scientific software a community code if it is freely available, written by a team of developers who welcome user input, and has attracted users beyond the developers. There are obviously many such materials modeling codes. The authors have been part of such efforts for many years in the field of atomistic simulation, specifically for two community codes, the LAMMPS and GULP packages for molecular dynamics and lattice dynamics respectively. Here we highlight lessons we have learned about how to create such codes and the pros and cons of being part of a community effort. Many of our experiences are similar, but we also have some differences of opinion (like modeling vs modelling). Our hope is that readers will find these lessons useful as they design, implement, and distribute their own materials modelling software for others to use.     

噻二唑型缓蚀剂缓蚀性能的研究

利用电化学测试和表面分析技术,研究了2,5-二巯基-1,3,4噻二唑(DMTD)在硫-乙醇溶液中对金属银、铜的缓蚀性能,结合量子化学计算和分子动力学模拟对DMTD在金属表面的吸附行为和缓蚀作用机理进行了分析讨论。结果表明,DMTD在50mg/L的硫-乙醇溶液中,对金属银、铜均起到较好的缓蚀作用。极化曲线结果表明,当缓蚀剂DMTD浓度达到50mg/L时,缓蚀效率可以达到92.3%。表面分析技术表明,缓蚀剂的加入在金属表面形成吸附膜,明显抑制了腐蚀速率。量化计算和分子动力学模拟得到了缓蚀剂分子的活性位点和缓蚀剂在金属表面的吸附形态。     

A fast ab initio approach to the simulation of spin dynamics

A spin dynamics simulation approach is proposed which is very much faster than a conventional ab initio spin dynamics code but which—nevertheless—exhibits ab initio or near-ab initio accuracy. In this approach the anewed ab initio calculation of the effective fields acting on the various spins in each time step of the spin dynamics algorithm which is required in the conventional ab initio codes and which makes them very costly is avoided. Instead, before starting the simulation, an analytical parametrization of the adiabatic energy hypersurface E for arbitrary spin orientations is obtained via the recently developed spin cluster expansion, and then the effective fields can be determined by simple derivatives. The new approach makes it possible to investigate the spin dynamics of technologically interesting spin nanostructures with strong atomic scale spin inhomogeneities like spin vortices.     

材料摩擦磨损分子动力学模拟的研究进展

随着新技术的发展以及材料服役环境的日益复杂化,传统的试验研究已经不能满足人们对摩擦磨损的认识需求,因此必须借助数值模拟方法来研究材料的摩擦磨损行为.特别是随着近年来原子尺度理论模型的不断完善和计算机运算能力的不断提高,分子动力学模拟已经成为研究材料摩擦磨损行为和机制的重要方法.本文详细综述了材料摩擦磨损分子动力学模拟的国内外研究现状.首先阐述了分子动力学模拟中势能函数的建立;其次介绍了材料摩擦磨损分子动力学模拟常用的接触模型;然后概述了采用分子动力学模拟方法研究接触面积、载荷、温度、速度和晶体取向等因素对材料摩擦磨损的影响;最后指出了目前材料摩擦磨损分子动力学模拟中存在的一些问题,并对未来发展方向进行了展望.     

On the effect of linear algebra implementations in real-time multibody system dynamics

This paper compares the efficiency of multibody system (MBS) dynamic simulation codes that rely on different implementations of linear algebra operations. The dynamics of an N-loop four-bar mechanism has been solved with an index-3 augmented Lagrangian formulation combined with the trapezoidal rule as numerical integrator. Different implementations for this method, both dense and sparse, have been developed, using a number of linear algebra software libraries (including sparse linear equation solvers) and optimized sparse matrix computation strategies. Numerical experiments have been performed in order to measure their performance, as a function of problem size and matrix filling. Results show that optimal implementations can increase the simulation efficiency in a factor of 2–3, compared with our starting classical implementations, and in some topics they disagree with widespread beliefs in MBS dynamics. Finally, advices are provided to select the implementation which delivers the best performance for a certain MBS dynamic simulation.     

多体组合式无人机飞行力学稳定性分析及增稳控制研究

多体组合式无人机是一种新概念飞行器,由多个小型无人机以翼尖铰接连接组成,该概念飞行器能够融合小型无人机与高空长航时无人机两类飞行平台的性能和任务优势,发展潜力巨大。基于Newton-Euler方程及升力线方法建立多体组合式无人机飞行力学模型,针对允许相对滚转运动自由度的双机组合式无人机系统进行配平及稳定性分析。结果表明,不同于传统构型飞行器,多体组合式无人机系统具有不稳定复合运动飞行模态,该复合模态由相对滚转运动主导,在无控状态下该构型飞行器无法稳定飞行。在完成动力学建模的基础上,基于PID控制方法,为每个单体飞行器单独设计增稳控制回路以达到增稳控制目的,仿真结果表明该控制思路有效,可以快速镇定发散的飞行力学系统。     

Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS

Molecular modelling played a central role in the discovery of the structure of DNA by Watson and Crick. Today, such modelling is done on computers: the more powerful these computers are, the more detailed and extensive can be the study of the dynamics of such biological macromolecules. To fully harness the power of modern massively parallel computers, however, we need to develop and deploy algorithms which can exploit the structure of such hardware. The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a scalable molecular dynamics code including long-range Coulomb interactions, which has been specifically designed to function efficiently on parallel platforms. Here we describe the implementation of the AMBER98 force field in LAMMPS and its validation for molecular dynamics investigations of DNA structure and flexibility against the benchmark of results obtained with the long-established code AMBER6 (Assisted Model Building with Energy Refinement, version 6). Extended molecular dynamics simulations on the hydrated DNA dodecamer d(CTTTTGCAAAAG)(2), which has previously been the subject of extensive dynamical analysis using AMBER6, show that it is possible to obtain excellent agreement in terms of static, dynamic and thermodynamic parameters between AMBER6 and LAMMPS. In comparison with AMBER6, LAMMPS shows greatly improved scalability in massively parallel environments, opening up the possibility of efficient simulations of order-of-magnitude larger systems and/or for order-of-magnitude greater simulation times.     

包装材料中化学物质迁移分子动力学模拟研究进展

概述了分子动力学模拟的基本原理及其应用方法,在此基础上,综述了分子动力学模拟在高阻隔包装材料、缓释包装材料、高性能聚合包装材料中化学物质迁移的研究现状,并提出分子动力学技术在包装材料化学物质迁移方面未来的应用方向:深入研究模型处于缺陷状态、复杂环境下的建模方法,不断完善迁移模型库,采用更高性能的计算机来构建更大分子量的模型,以验证和改进模型并提供更多的物性数据,得到一些极限条件或实验无法实现情况下的信息。     

Verification of cardiac tissue electrophysiology simulators using an N-version benchmark

Ongoing developments in cardiac modelling have resulted, in particular, in the development of advanced and increasingly complex computational frameworks for simulating cardiac tissue electrophysiology. The goal of these simulations is often to represent the detailed physiology and pathologies of the heart using codes that exploit the computational potential of high-performance computing architectures. These developments have rapidly progressed the simulation capacity of cardiac virtual physiological human style models; however, they have also made it increasingly challenging to verify that a given code provides a faithful representation of the purported governing equations and corresponding solution techniques. This study provides the first cardiac tissue electrophysiology simulation benchmark to allow these codes to be verified. The benchmark was successfully evaluated on 11 simulation platforms to generate a consensus gold-standard converged solution. The benchmark definition in combination with the gold-standard solution can now be used to verify new simulation codes and numerical methods in the future.     

Application of lightweight threading techniques to computational chemistry

The recent advent of inexpensive commodity multiprocessor computers with standardized operating system support for lightweight threads provides computational chemists and other scientists with an exciting opportunity to develop sophisticated new approaches to materials simulation. We contrast the flexible performance characteristics of lightweight threading with the restrictions of traditional scientific supercomputing, based on our experiences with multithreaded molecular dynamics simulation. Motivated by the results of our molecular dynamics experiments, we propose an approach to multi-scale materials simulation using highly dynamic thread creation and synchronization within and between concurrent simulations at many different scales. This approach will enable extremely realistic simulations, with computing resources dynamically directed to areas where they are needed. Multi-scale simulations of this kind require large amounts of processing power, but are too sophisticated to be expressed using traditional supercomputing programming models. As a result, we have developed a high-level programming system called Sthreads that allows highly dynamic, nested multithreaded algorithms to be expressed. Program development is simplified through the use of innovative synchronization operations that allow multithreaded programs to be tested and debugged using standard sequential methods and tools. For this reason, Sthreads is very well suited to the complex multi-scale simulation applications that we are developing. This revised version was published online in June 2006 with corrections to the Cover Date.     

High-performance computing in computational fluid dynamics: progress and challenges

Computational fluid dynamics (CFD) is by far the largest user of high-performance computing (HPC) in engineering. The main scientific challenge is the need to gain a greater understanding of turbulence and its consequences for the transfer of momentum, heat and mass in engineering applications, including aerodynamics, industrial flows and combustion systems. Availability of HPC has led to significant advances in direct numerical simulation (DNS) of turbulence and turbulent combustion, and has encouraged the development of large-eddy simulation (LES) for engineering flows. The statistical data generated by DNS have provided valuable insight into the physics of many turbulent flows and have led to rapid improvements in turbulence and combustion modelling for industry. Nevertheless, major challenges remain and the computational requirements for turbulence research, driven by well-established physical scaling laws, are likely to remain at the limit of the available HPC provision for some time to come.     

A method of seamlessly combining a crack tip molecular dynamics enclave with a linear elastic outer domain in simulating elastic–plastic crack advance

Molecular dynamics is applicable only to an extremely small region of simulation. In order to simulate a large region, it is necessary to combine molecular dynamics with continuum mechanics. Therefore, we propose a new model where molecular dynamics is combined with micromechanics. In this model, we apply molecular dynamics to the crack tip region and apply micromechanics to the surrounding region. Serious problems exist at the boundary between the two regions. In this study, we manage to solve these problems, and make possible the simulation of the process of crack propagation at the atomic level. In order to examine the validity of this model, we use α-iron for simulation. If the present model is valid, stress and displacement should vary continuously across the boundary between the molecular dynamics region and the micromechanics region. Our model exhibits just such behavior. This revised version was published online in August 2006 with corrections to the Cover Date.     

Low-density parity-check codes for volume holographic memory systems

We investigate the application of low-density parity-check (LDPC) codes in volume holographic memory (VHM) systems. We show that a carefully designed irregular LDPC code has a very good performance in VHM systems. We optimize high-rate LDPC codes for the nonuniform error pattern in holographic memories to reduce the bit error rate extensively. The prior knowledge of noise distribution is used for designing as well as decoding the LDPC codes. We show that these codes have a superior performance to that of Reed-Solomon (RS) codes and regular LDPC counterparts. Our simulation shows that we can increase the maximum storage capacity of holographic memories by more than 50 percent if we use irregular LDPC codes with soft-decision decoding instead of conventionally employed RS codes with hard-decision decoding. The performance of these LDPC codes is close to the information theoretic capacity.     

Systematic Evaluation of Extraction Methods for Multiplatform-Based Metabotyping: Application to the Fasciola hepatica Metabolome

Combining data from multiple analytical platforms is essential for comprehensive study of the molecular phenotype (metabotype) of a given biological sample. The metabolite profiles generated are intrinsically dependent on the analytical platforms, each requiring optimization of instrumental parameters, separation conditions, and sample extraction to deliver maximal biological information. An in-depth evaluation of extraction protocols for characterizing the metabolome of the hepatobiliary fluke Fasciola hepatica , using ultra performance liquid chromatography and capillary electrophoresis coupled with mass spectroscopy is presented. The spectrometric methods were characterized by performance, and metrics of merit were established, including precision, mass accuracy, selectivity, sensitivity, and platform stability. Although a core group of molecules was common to all methods, each platform contributed a unique set, whereby 142 metabolites out of 14,724 features were identified. A mixture design revealed that the chloroform:methanol:water proportion of 15:59:26 was globally the best composition for metabolite extraction across UPLC-MS and CE-MS platforms accommodating different columns and ionization modes. Despite the general assumption of the necessity of platform-adapted protocols for achieving effective metabotype characterization, we show that an appropriately designed single extraction procedure is able to fit the requirements of all technologies. This may constitute a paradigm shift in developing efficient protocols for high-throughput metabolite profiling with more-general analytical applicability.     

大规模柴油机动力学抗冲击并行仿真计算

针对柴油机动力冲击仿真问题,采用显式动力算法对柴油机复杂结构进行详细建模与精细仿真,并对处于不同工作状态柴油机开展机构运动、动力冲击的单独及综合模拟。为满足计算调试及多组工况所需大规模计算需求,借助高性能计算资源;通过不同计算平台多核并行计算及性能数据比较,分析独特并行加速现象、探求合理并行加速策略。计算表明,动态仿真方法有利于柴油机运动及动力问题一体化研究。该结论可为柴油机类似复杂冲击问题研究提供参考。     

Tight-binding molecular dynamics for materials simulations

Summary Tight-binding molecular dynamics has recently emerged as a useful method for atomistic simulation of the structural, dynamical and electronic properties of realistic materials. The method incorporates quantum-mechanical calculations into molecular dynamics through an empirical tight-binding Hamiltonian and bridges the gap between ab initio molecular dynamics and simulations using empirical classical potentials. In this paper, we review the accuracy, efficiency, and predictive power of the method and discuss some opportunities and challenges for future development.     

The benefits of parallel multibody simulation

To exploit the benefits of parallel computer architectures for multibody system simulation, an interdisciplinary approach has been pursued, combining knowledge of the three disciplines of dynamics, numerical mathematics and computer science. An analysis of the options available for the formulation and numerical solution of the dynamical system equations yielded a surprising result. A method initially proposed to solve the inverse problem of dynamics is the best choice to generate the system equations required for solving the simulation problem, when relying on implicit integration routines. Such routines have the particular advantage of handling stiff systems, too. The new O(N)-residual formalism, generating the system equations in a form required for implicit numerical integration, has a high potential to benefit from parallel computer architectures. Two strategies of medium and coarse grain parallelization have been implemented on a Transputer network to obtain a package for parallel multibody simulation. An analysis of the performance of this package demonstrates for typical multibody simulation problems that the new code is five times faster than existing codes when implemented on a serial computer. An additional speed-up by the same order of magnitude is obtained when the code is implemented on a Transputer network.     

Feature Activated Molecular Dynamics: Parallelization and Application to Systems with Globally Varying Mechanical Fields

A recently developed hybrid molecular dynamics method (Feature Activated Molecular Dynamics, or FAMD), which was originally designed to extend the scope of certain types of molecular dynamics simulations, is extended here in two ways. First, the method is modified to execute on parallel computer architectures using the MPI communication interface. The parallel FAMD algorithm is demonstrated to be computationally efficient and to substantially increase the length scales accessible with molecular dynamics. The performance of the parallel algorithm is demonstrated using a crystalline system containing 1× 10⁶ atoms, in which 1000 supersaturated self-interstitials are introduced and allowed to aggregate for about 4 ns. In the second part of this paper, the FAMD method is applied to problems in which spatio-temporally varying stress fields are present throughout the simulation cell. In particular, we consider the evolution of a spherical void in a hydrostatically stressed silicon crystal and show that the method can capture the extremely rapid void cavitation dynamics following material failure. Once again, the FAMD approach is demonstrated to provide substantial computational advantages over standard molecular dynamics.