The MOLDY short-range molecular dynamics package

Ackland G.J.; DMellow K.; Daraszewicz S.L.; Hepburn D.J.; Uhrin M.; Stratford K.

摘要

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 parallelised 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 summary: Program title: MOLDY Catalogue identifier: AEJU-v1-0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEJU-v1-0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 2 No. of lines in distributed program, including test data, etc.: 382 881 No. of bytes in distributed program, including test data, etc.: 6 705 242 Distribution format: tar.gz Programming language: Fortran 95/OpenMP Computer: Any Operating system: Any Has the code been vectorised or parallelized?: Yes. OpenMP is required for parallel execution RAM: 100 MB or more Classification: 7.7 Nature of problem: Moldy addresses the problem of many atoms (of order 10~6) 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.

机译：我们描述了MOLDY分子动力学程序的并行版本。此Fortran代码针对的是可以用短距离电势描述的系统，尤其是可以用嵌入式原子方法解决的系统。这包括各种过渡金属和合金。根据所使用的分子动力学系综和可能适用的边界条件，MOLDY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电位。该代码使用OpenMP并行化，因此可以在共享内存系统上运行，包括现代多核处理器。特别要注意主力循环中所需的更新，在分子动力学的OpenMP实现中通常需要同步。我们详细检查了并行代码的性能，并给出了一些实际问题的应用示例，包括铜的动态压缩和铁碳合金中的碳迁移。程序摘要：程序标题：MOLDY目录标识：AEJU-v1-0程序摘要URL：http://cpc.cs.qub.ac.uk/summaries/AEJU-v1-0.html程序可从以下网站获得：CPC程序库，爱尔兰北爱尔兰贝尔法斯特女王大学许可条款：GNU通用公共许可证版本2分布式程序中的行数，包括测试数据等：382881分布式程序中的字节数，包括测试数据等：6 705 242分发格式：tar.gz编程语言：Fortran 95 / OpenMP计算机：任何操作系统：任何代码是否已向量化或并行化？：是。并行执行RAM需要OpenMP：100 MB或更多分类：7.7问题的性质：Moldy解决了许多原子（10〜6阶）通过经典原子间势在微秒级上相互作用的问题。它设计用于必须在多个等效运行中收集统计信息的问题，例如测量热力学性质，扩散，辐射损伤，断裂，孪生变形，相变的成核和生长，溅射等。在绝大多数材料中，相互作用是非成对的，并且代码必须能够应对多体作用力。解决方法：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）或预测器-校正器（用于精确的轨迹）算法。使用开放式MP将其并行化。它还包括一个静态最小化例程，以找到最低的能量结构。提供了表面，团簇，晶界，恒温器（Nose），恒压器（Parrinello-Rahman）和外部施加应变的边界条件。初始构型可以是重复的晶胞，也可以是所有原子都明确给出。初始速度是在内部生成的，但是也可以指定特定原子的速度。实现了广泛的原子间力模型，包括嵌入的原子，Morse或Lennard-Jones。因此，该程序特别适合于金属的计算。限制：该代码是为短距离电势设计的，没有Ewald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。不同的原子间电势形式需要重新编译代码。附加说明：有一组用于后处理和可视化的关联开源分析软件。这包括局部晶体结构识别和拓扑缺陷识别。运行时间：提供了一组运行时间测试模块。代码按N阶缩放。并行化显示在共享内存环境中，随着处理器数量的增加，接近线性缩放。在多处理器桌面上，几十纳米到几纳秒的典型运行时间为几天。

The MOLDY short-range molecular dynamics package

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