Molecular dynamics in arbitrary geometries : parallel evaluation of pair forces

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Macpherson, Graham B. and Reese, Jason M. (2008) Molecular dynamics in arbitrary geometries : parallel evaluation of pair forces. Molecular Simulation, 34 (1). pp. 97-115. ISSN 1029-0435 (https://doi.org/10.1080/08927020801930554)

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Abstract

A new algorithm for calculating intermolecular pair forces in molecular dynamics (MD) simulations on a distributed parallel computer is presented. The arbitrary interacting cells algorithm (AICA) is designed to operate on geometrical domains defined by an unstructured, arbitrary polyhedral mesh that has been spatially decomposed into irregular portions for parallelisation. It is intended for nano scale fluid mechanics simulation by MD in complex geometries, and to provide the MD component of a hybrid MD/continuum simulation. The spatial relationship of the cells of the mesh is calculated at the start of the simulation and only the molecules contained in cells that have part of their surface closer than the cut-off radius of the intermolecular pair potential are required to interact. AICA has been implemented in the open source C++ code OpenFOAM, and its accuracy has been indirectly verified against a published MD code. The same system simulated in serial and in parallel on 12 and 32 processors gives the same results. Performance tests show that there is an optimal number of cells in a mesh for maximum speed of calculating intermolecular forces, and that having a large number of empty cells in the mesh does not add a significant computational overhead.

ORCID iDs

Macpherson, Graham B. and Reese, Jason M. ORCID logoORCID: https://orcid.org/0000-0001-5188-1627;
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