Parallel evaluation of pair forces for molecular dynamics in arbitrary geometries

We develop a new molecular dynamics algorithm for pair force evaluation of molecules occupying arbitrary polyhedral, unstructured mesh geometries. This is designed for hybrid MD/continuum simulation of nanofluidic systems. We show that the conventional MD pair force evaluation method of neighbour lists cannot be used in parallel computation simulations of complex geometries. Our new algorithm is shown to be of comparable speed to neighbour lists. This algorithm is implemented in parallel to create an MD code built into the open source CFD software OpenFOAM. This allows easy hybridisation and tight integration with an existing, well developed and widely used continuum solver. We show computational performance characteristics for the new algorithm and initial simulation results in a complex geometry.