2 - Outline of Methodology of Simulations

Abstract

An overview of the general methodology is necessary in order to develop a simulation program. It should include the assignment of the initial configuration and velocities, the treatment of boundary conditions, and techniques for reducing computation time. This chapter describes the methods frequently employed in simulations. An appropriate initial configuration has to be set with careful consideration given to the physical property of interest, so that the essential phenomena can be grasped. The periodic boundary condition is a representative model to manage the boundary of a simulation region. It is almost always used for systems in thermodynamic equilibrium. On the other hand, for investigating the dynamic properties of a system, the simple shear flow is frequently treated. In generating a simple shear flow in actual molecular simulations, the upper and lower replicated simulation boxes are made to slide in different directions with a certain constant speed. This sliding periodic boundary condition is called the Lees-Edwards boundary condition. Techniques for reducing computation time have become very important in large-scale three-dimensional simulations, and methods of tracking particle neighbors, such as the cell index method, are indispensable.