基于LAMMPS系统的集群运算系统架构

为解决分子动力学计算系统LAMMPS（Large-scale Atomic/Molecular Massively Parallel Simulator）运算数据量大、不易控制的问题,应用云计算方法,设计了智能化、高效化的集群LAMMPS运算系统架构。该架构将FTP（File Transfer Protocol）存储技术、UDP（User Datagram Protocol）快速网络传输、LAMMPS分子动力学计算技术相结合,降低了运算过程中的人工干预,提高了分子模型处理效率,并为分子级别物理、化学的计算机仿真研究提供了新的集群化解决方案。     

The Flexible Rare Event Sampling Harness System (FRESHS)

We present the software package FRESHS (http://www.freshs.org) for parallel simulation of rare events using sampling techniques from the ‘splitting’ family of methods. Initially, Forward Flux Sampling (FFS) and Stochastic Process Rare Event Sampling (SPRES) have been implemented. These two methods together make rare event sampling available for both quasi-static and full non-equilibrium regimes. Our framework provides a plugin system for software implementing the underlying physics of the system of interest. At present, example plugins exist for our framework to steer the popular MD packages GROMACS, LAMMPS and ESPResSo, but due to the simple interface of our plugin system, it is also easy to attach other simulation software or self-written code. Use of our framework does not require recompilation of the simulation program. The modular structure allows the flexible implementation of further sampling methods or physics engines and creates a basis for objective comparison of different sampling algorithms.     

基于KNL平台的LAMMPS优化

Intel 新一代处理器 KNL 作为一种具有极强运算能力的多核处理器,拥有 16GB 高速片上内存(MCDRAM),物理核心数量高达 72 个,单 CPU 的双精度浮点峰值为 3TFlops,为高并行负载应用提供强大的性能支持。各种主流的并行软件也纷纷使用 KNL 众核、高速内存技术,由于 LAMMPS (large-scale atomic/molecular massively parallel simulator) 在材料科学和计算化学中的广泛应用,因此在 KNL 节点上优化 LAMMPS 成为相关领域近些年的研究热点。本文以郑州超算中心的 KNL 集群为平台,采用 MCDRAM 和第三方扩展包两种方法对 LAMMPS 进行优化。MCDRAM 可以加快 CPU 读取数据的速度,第三方扩展包从源码的角度对程序中的条件判断进行优化。试验结果表明,优化后的 LAMMPS 执行时间明显减少,加速比可达 49x,是 CPU 平台加速比的 5.5x。     

高温对含氢DLC涂层的微观结构及力学性能的影响

目的 针对含氢DLC涂层热稳定性很差的问题,探究高温下含氢DLC涂层的微观组织变化特征,以及高温对其力学性能的影响。方法 采用等离子体强化化学气相沉积(PlasmaEnhancedChemicalVapor Deposition, PECVD)在S136模具不锈钢表面沉积以Si为过渡层的含氢DLC复合涂层,利用光学显微镜、扫描电镜、拉曼光谱、X射线电子衍射仪、三维轮廓仪研究DLC涂层的微观结构,采用划痕测试仪、往复式摩擦磨损试验机、纳米压痕仪研究DLC涂层的力学性能,并通过LAMMPS软件,利用液相淬火法建立含氢DLC模型,模拟分析经高温处理后涂层的组织变化特征和纳米压痕行为。结果 在400℃、2 h的退火条件下,拉曼谱峰强度ID/IG由未退火的0.7增至1.5,涂层发生了石墨化转变,同时基线斜率下降,H元素析出;XPS结果表明,在此条件下涂层中sp²杂化组织相对增加,氧元素增多,涂层粗糙度增大;在600℃、2 h退火条件下,DLC发生了严重氧化,LAMMPS模拟结果表明,在400℃高温下涂层的分子键长变短,表明sp³杂化组织在高温下吸收能量...     

Dopant effect on Li+ ion transport in NASICON-type solid electrolyte: Insights from molecular dynamics simulations and experiments

The performance of sodium superionic conductor (NASICON)-type LiZr₂(PO₄)₃ (LZP) solid electrolytes for Li-ion batteries is dependent on their ion transportation properties. Therefore, to achieve high stability, ionic conductivity, and good compatibility with Li, the LZP solid electrolyte has chosen and doped with Al to improve aforesaid properties. Also, the effect of the dopant on various parameters has been investigated via MD simulations and experimentally. In this study, molecular dynamics (MD) simulations were used to investigate the effect of Al doping on the ion transport properties of Li_1+xAl_xZr_2?x(PO₄)₃ (LAZP, x = 0.0–1.0) solid electrolytes. A facile solid-state reaction was used to synthesize both pristine and Al-doped solid electrolytes and to estimate the effect of doping on the ionic conductivity and ion diffusion in LZP. Computational and experimental results provided strong evidence of improved ion conductivity and diffusion in LZP owing to the presence of the Al dopant. Furthermore, the computational results agreed well with the experimental results, thereby validating the computational model. A maximum ionic conductivity of σ_Li = 2.77 × 10^?5 S cm ^?1 (for x = 0.2) was obtained. Enhanced ionic conductivity was observed with Al dopants owing to the creation of interstitial Li ions through a reduction in grain boundary resistance. However, a further increase in the amount of dopant reduced the ionic conductivity of LZP owing to Li-ion trapping at the most stable and metastable sites around the Al insertions. Doped LZP solid electrolytes are suitable for use in energy storage devices because of their enhanced ionic conductivity compared to that of pristine LZP.     

混合模型下LAMMPS并行探究

面对分子动力学模拟在串行计算上的速度瓶颈问题,设计一种并行计算模型来加快计算速度,在分子动力学模拟软件LAMMPS下引入MPI+OpenMP并行模型,这个模型可以在LAMMPS下提供两级并行处理,充分利用集群优势,提高模拟计算速度.实验结果表明,在十节点下,采用并行模型加速比至少提高8倍以上.     

Accelerating dissipative particle dynamics simulations on GPUs: Algorithms,numerics and applications

We present a scalable dissipative particle dynamics simulation code, fully implemented on the Graphics Processing Units (GPUs) using a hybrid CUDA/MPI programming model, which achieves 10–30 times speedup on a single GPU over 16 CPU cores and almost linear weak scaling across a thousand nodes. A unified framework is developed within which the efficient generation of the neighbor list and maintaining particle data locality are addressed. Our algorithm generates strictly ordered neighbor lists in parallel, while the construction is deterministic and makes no use of atomic operations or sorting. Such neighbor list leads to optimal data loading efficiency when combined with a two-level particle reordering scheme. A faster in situ generation scheme for Gaussian random numbers is proposed using precomputed binary signatures. We designed custom transcendental functions that are fast and accurate for evaluating the pairwise interaction. The correctness and accuracy of the code is verified through a set of test cases simulating Poiseuille flow and spontaneous vesicle formation. Computer benchmarks demonstrate the speedup of our implementation over the CPU implementation as well as strong and weak scalability. A large-scale simulation of spontaneous vesicle formation consisting of 128 million particles was conducted to further illustrate the practicality of our code in real-world applications.