Molecular dynamics in arbitrary geometries: parallel evaluation of pair forces

Graham B. Macpherson, Jason M. Reese

Research output: Contribution to journalArticle

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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.
Original languageEnglish
Pages (from-to)97-115
Number of pages18
JournalMolecular Simulation
Volume34
Issue number1
DOIs
Publication statusPublished - Jan 2008

Fingerprint

Molecular Dynamics
Molecular dynamics
molecular dynamics
Geometry
evaluation
mesh
Cell
Evaluation
Arbitrary
geometry
cells
Mesh
simulation
Fluid mechanics
parallel computers
Simulation
intermolecular forces
Performance Test
fluid mechanics
performance tests

Keywords

  • molecular dynamics
  • pair forces
  • fluid mechanics

Cite this

Macpherson, Graham B. ; Reese, Jason M. / Molecular dynamics in arbitrary geometries : parallel evaluation of pair forces. In: Molecular Simulation. 2008 ; Vol. 34, No. 1. pp. 97-115.
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Molecular dynamics in arbitrary geometries : parallel evaluation of pair forces. / Macpherson, Graham B.; Reese, Jason M.

In: Molecular Simulation, Vol. 34, No. 1, 01.2008, p. 97-115.

Research output: Contribution to journalArticle

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