The MOLDY short-range molecular dynamics package
The MOLDY short-range molecular dynamics package
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DOI：
10.1016/j.cpc.2011.07.014
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发表时间：
2011-12-01
影响因子：
6.3
通讯作者：
Stratford, K.
中科院分区：
文献类型：
--
作者：
Ackland, G. J.;D'Mellow, K.;Stratford, K.
我们描述了一个并行版本的MOLDY分子动力学程序。本Fortran代码针对的是可以用短程势描述的系统，特别是那些可以用嵌入原子方法处理的系统。这包括广泛的过渡金属和合金。MOLDY在所使用的分子动力学系综和可能应用的边界条件方面提供了一系列选择。提供了许多标准电位，并且代码的模块化结构允许轻松添加新的电位。代码是使用OpenMP并行的，因此可以在共享内存系统上运行，包括现代多核处理器。特别要注意的是在主力循环中需要的更新，在分子动力学的OpenMP实现中通常需要同步。我们详细研究了并行代码的性能，并给出了一些应用于实际问题的例子，包括铁碳合金中铜的动态压缩和碳的迁移。程序摘要程序名称：moldy目录标识符：aeju_v1_0程序摘要URL: http://cpc.cs.qub.ac.uk/summaries/AEJU_v1_0.htmlProgram可从：CPC程序库，女王大学，贝尔法斯特，N.爱尔兰许可条款：GNU通用公共许可版本2号。分布式程序的行数，包括测试数据等：382 881分布程序的字节数，包括测试数据等：6 705 242分布格式：tar。编程语言：Fortran 95/OpenMPComputer: any操作系统：any代码矢量化或并行化了吗？:是的。并行执行需要OpenMP内存：100 MB或更多分类：7.7问题性质：Moldy解决了许多原子（106阶）在微秒时间尺度上通过经典原子间势相互作用的问题。它是为必须在许多等效运行中收集统计数据的问题而设计的，例如测量热力学性质、扩散、辐射损伤、断裂。孪晶变形、相变成核和生长、溅射等。在绝大多数材料中，相互作用是非成对的，代码必须能够处理多体力。解法：分子动力学涉及牛顿运动方程的积分。MOLDY使用verlet（用于良好的节能）或预测校正（用于精确的轨迹）算法。它是使用开放MP并行化的。它还包括一个静态最小化程序来找到最低的能量结构。提供了表面、簇、晶界、恒温器（Nose）、气压调节器（Parrinello-Rahman）和外部施加应变的边界条件。初始构型可以是一个重复的单胞，也可以是所有原子都明确给出的构型。初始速度是内部生成的，但也可以指定特定原子的速度。实现了广泛的原子间力模型，包括嵌入原子，莫尔斯或伦纳德-琼斯。因此，该程序特别适合于金属的计算。限制：代码是为短程电位设计的，没有埃瓦尔德和。因此，对于所有粒子与所有其他粒子相互作用的长距离相互作用，n阶缩放将失败。不同的原子间势形式需要重新编译代码。附加说明：有一组相关的开源分析软件用于后处理和可视化。这包括局部晶体结构识别和拓扑缺陷识别。运行时间：提供了一组用于运行时间的测试模块。代码按n阶缩放，并行化显示了共享内存环境中处理器数量的近似线性缩放。在多处理器桌面上，典型的几十纳米、几纳秒的运行将在几天的时间尺度上运行。(C) 2011 Elsevier B.V.版权所有
We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method. This includes a wide range of transition metals and alloys. MOLDY provides a range of options in terms of the molecular dynamics ensemble used and the boundary conditions which may be applied. A number of standard potentials are provided, and the modular structure of the code allows new potentials to be added easily. The code is parallelisecl using OpenMP and can therefore be run on shared memory systems, including modern multicore processors. Particular attention is paid to the updates required in the main force loop, where synchronisation is often required in OpenMP implementations of molecular dynamics. We examine the performance of the parallel code in detail and give some examples of applications to realistic problems, including the dynamic compression of copper and carbon migration in an iron-carbon alloy.Program summaryProgram title: MOLDYCatalogue identifier: AEJU_v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEJU_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: GNU General Public License version 2No. of lines in distributed program, including test data, etc.: 382 881No. of bytes in distributed program, including test data, etc.: 6 705 242Distribution format: tar.gzProgramming language: Fortran 95/OpenMPComputer: AnyOperating system: AnyHas the code been vectorised or parattelized?: Yes. OpenMP is required for parallel executionRAM: 100 MB or moreClassification: 7.7Nature of problem: Moldy addresses the problem of many atoms (of order 106) interacting via a classical interatomic potential on a timescale of microseconds. It is designed for problems where statistics must be gathered over a number of equivalent runs, such as measuring thermodynamic properities, diffusion, radiation damage, fracture. twinning deformation, nucleation and growth of phase transitions, sputtering etc. In the vast majority of materials, the interactions are non-pairwise, and the code must be able to deal with many-body forces.Solution method: Molecular dynamics involves integrating Newton's equations of motion. MOLDY uses verlet (for good energy conservation) or predictor-corrector (for accurate trajectories) algorithms. It is parallelised using open MP. It also includes a static minimisation routine to find the lowest energy structure. Boundary conditions for surfaces, clusters, grain boundaries, thermostat (Nose), barostat (Parrinello-Rahman), and externally applied strain are provided. The initial configuration can be either a repeated unit cell or have all atoms given explictly. Initial velocities are generated internally, but it is also possible to specify the velocity of a particular atom. A wide range of interatomic force models are implemented, including embedded atom, Morse or Lennard-Jones. Thus the program is especially well suited to calculations of metals.Restrictions: The code is designed for short-ranged potentials, and there is no Ewald sum. Thus for long range interactions where all particles interact with all others, the order-N scaling will fail. Different interatomic potential forms require recompilation of the code.Additional comments: There is a set of associated open-source analysis software for postprocessing and visualisation. This includes local crystal structure recognition and identification of topological defects.Running time: A set of test modules for running time are provided. The code scales as order N. The parallelisation shows near-linear scaling with number of processors in a shared memory environment. A typical run of a few tens of nanometers for a few nanoseconds will run on a timescale of days on a multiprocessor desktop. (C) 2011 Elsevier B.V. All rights reserved.