DRAFT — ICNMM2008-62277 MOLECULAR DYNAMICS FOR FLUID MECHANICS IN ARBITRARY GEOMETRIES

Simulations of nanoscale systems where fluid mechanics plays an important role are required to help design and under-stand nano-devices and biological systems. A simulation method which hybridises molecular dynamics (MD) and continuum com-putational fluid dynamics (CFD) models is able to accurately represent the relevant physical phenomena and be computation-ally tractable. An MD code has been written to perform MD simulations in systems where the geometry is described by a mesh of unstruc-tured arbitrary polyhedral cells that have been spatially decom-posed into irregular portions for parallel processing. The MD code that has been developed may be used for simulations on its own, or may serve as the MD component of a hybrid method. The code has been implemented using OpenFOAM, an open source C++ CFD toolbox (www.openfoam.org). The requirements for two key enabling components are described. 1) Parallel generation of initial configurations of molecules in arbitrary geometries. 2) Calculation of intermolec-ular pair forces, including between molecules that lie on mesh portions assigned to different, and possibly non-neighbouring processors. A case study of flow in a realistic nanoscale mixing channel, where the geometry is drawn and meshed in engineering CAD tools is simulated to demonstrate the capabilities of the code