mdFoam+: Advanced molecular dynamics in OpenFOAM
mdFoam+: Advanced molecular dynamics in OpenFOAM
复制标题
DOI：
10.1016/j.cpc.2017.09.029
复制
发表时间：
2017-09
期刊：
影响因子：
--
通讯作者：
S. Longshaw;M. Borg;S. Ramisetti;Jun Zhang;D. Lockerby;David R. Emerson;J. Reese
中科院分区：
文献类型：
--
作者：
S. Longshaw;M. Borg;S. Ramisetti;Jun Zhang;D. Lockerby;David R. Emerson;J. Reese
本文介绍了mdFoam+，这是一个MPI并行分子动力学（MD）求解器完全在OpenFOAM软件框架内实现。它是开源的，并在与OpenFOAM相同的GNU通用公共许可证（GPL）下发布。源代码作为公开开放的软件存储库发布，其中包括详细的文档和教程案例。由于mdFoam+完全在OpenFOAM C++面向对象框架内设计，因此它继承了许多关键功能。该代码的设计具有可扩展性和灵活性，因此它的首要目标是作为MD研究工具，可以快速开发和测试新模型和测试用例。在OpenFOAM中实现mdFoam+还可以更轻松地开发将MD与基于连续体的求解器耦合的混合方法。设置MD案例遵循标准OpenFOAM格式，因为mdFoam+也依赖于基于OpenFOAMdictionary的目录结构。这确保了OpenFOAM提供的有用的预处理和后处理功能仍然可用，即使MD模拟的完全拉格朗日性质在大多数OpenFOAM应用程序中并不典型。结果表明，mdFoam+比较以及另一个著名的MD代码（如LAMMPS）的基准问题，虽然它也有额外的功能，不存在于其他开源的MD代码。程序摘要程序标题：mdFoam+程序文件doi：http://dx.doi.org/10.17632/7b4xkpx43b.1Licensing规定：GNU通用公共许可证3（GPL v3）编程语言：C++问题的性质：mdFoam+已经开发，以帮助调查复杂的流体流动问题，在微米和纳米尺度上使用分子动力学（MD）。它提供了一个易于扩展、并行化的分子动力学环境。求解方法：mdFoam+使用显式时间步进机制和分子间力场类型实现经典的分子动力学求解，适用于研究纳米尺度的流体动力学问题。
This paper introduces mdFoam+, which is an MPI parallelised molecular dynamics (MD) solver implemented entirely within the OpenFOAM software framework. It is open-source and released under the same GNU General Public License (GPL) as OpenFOAM. The source code is released as a publicly open software repository that includes detailed documentation and tutorial cases. Since mdFoam+is designed entirely within the OpenFOAM C++object-oriented framework, it inherits a number of key features. The code is designed for extensibility and flexibility, so it is aimed first and foremost as an MD research tool, in which new models and test cases can be developed and tested rapidly. Implementing mdFoam+in OpenFOAM also enables easier development of hybrid methods that couple MD with continuum-based solvers. Setting up MD cases follows the standard OpenFOAM format, as mdFoam+also relies upon the OpenFOAMdictionary-based directory structure. This ensures that useful pre- and post-processing capabilities provided by OpenFOAM remain available even though the fully Lagrangian nature of an MD simulation is not typical of most OpenFOAM applications. Results show that mdFoam+compares well to another well-known MD code (e.g. LAMMPS) in terms of benchmark problems, although it also has additional functionality that does not exist in other open-source MD codes.Program summaryProgram title:mdFoam+Program Files doi:http://dx.doi.org/10.17632/7b4xkpx43b.1Licensing provisions:GNU General Public License 3 (GPLv3)Programming language:C++Nature of problem:mdFoam+has been developed to help investigate complex fluid flow problems at the micro and nano scales using molecular dynamics (MD). It provides an easily extended, parallelised, molecular dynamics environment.Solution method:mdFoam+implements a classical molecular dynamics solution using an explicit time-stepping regime and inter-molecular force-field types appropriate for studying fluid dynamics problems down to the nano-scale.References:All appropriate methodological references are contained in the section entitledReferences.