mdFoam+: Advanced molecular dynamics in OpenFOAM

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Abstract

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 OpenFOAM dictionary-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 summary: Program title: mdFoam+ Program Files doi: http://dx.doi.org/10.17632/7b4xkpx43b.1 Licensing 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 entitled References.

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APA

Longshaw, S. M., Borg, M. K., Ramisetti, S. B., Zhang, J., Lockerby, D. A., Emerson, D. R., & Reese, J. M. (2018). mdFoam+: Advanced molecular dynamics in OpenFOAM. Computer Physics Communications, 224, 1–21. https://doi.org/10.1016/j.cpc.2017.09.029

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