Generation of initial molecular dynamics configurations in arbitrary geometries and in parallel

Abstract

A computational pre-processing tool for generating initial configurations of molecules for molecular dynamics simulations in geometries described by a mesh of unstructured arbitrary polyhedra is described. The mesh is divided into separate zones and each can be filled with a single crystal lattice of atoms. Each zone is filled by creating an expanding cube of crystal unit cells, initiated from an anchor point for the lattice. Each unit cell places the appropriate atoms for the user-specified crystal structure and orientation. The cube expands until the entire zone is filled with the lattice; zones with concave and disconnected volumes may be filled. When the mesh is spatially decomposed into portions for distributed parallel processing, each portion may be filled independently, meaning that the entire molecular system never needs to fit onto a single processor, allowing very large systems to be created. The computational time required to fill a zone with molecules scales linearly with the number of cells in the zone for a fixed number of molecules, and better than linearly with the number of molecules for a fixed number of mesh cells. Our tool, molConfig, has been implemented in the open source C++ code OpenFOAM.

Keywords:

• Molecular dynamics
• Nano fluidics
• Molecular geometry definition
• Parallel computing
• OpenFOAM

Keywords:

• 31.15.Qg
• 47.11.Mn

Acknowledgements

The authors would like to thank Chris Greenshields of Strathclyde University, and Henry Weller and Mattijs Janssens of OpenCFD Ltd for useful discussions. This work is funded in the UK by Strathclyde University, the Miller Foundation and the James Weir Foundation, and through a Philip Leverhulme Prize for JMR from the Leverhulme Trust.

Notes

^† Finding which cell a position corresponds to is an existing function in the mesh description in OpenFOAM.

^‡ The number of molecules varies because the geometry for a particular aspect ratio does not exactly match the geometry of the lattice that it is being filled with. However, the maximum deviation from, in this case, 64,000 molecules is only 496, or 0.775%.