Non-periodic boundary model with soft transition in molecular dynamics simulation

The imposition of non-periodic boundary conditions is a challenging issue in molecular dynamics (MD) simulation because of the difficulty in reconstructing the detailed particle dynamics from the few state variables. In this paper, a general scheme for the imposition of this kind of boundary conditions is presented. The complete model includes the imposition of Dirichlet boundary conditions and applying the boundary force to ensure the continuity of flow properties. Both the flux and the boundary force are introduced in a consistent way with the microscopic dynamics of the molecular system. Moreover, a soft constraint mechanism is included to correct the instantaneous deviation of the local state. A uniform flow and a Poiseuille flow of Lennard-Jones fluid is simulated using the boundary model. The results demonstrate that the fluctuation of flow properties near the boundary is kept at a low level, and the model is stable even subject to internal disturbance.