Study On Modification Of Diffusion Computation By Periodic Boundary Conditions In Molecular Simulation

With the rapid development of computer technology and computing equipment,there is more room for numerical simulation of the mode of motion and microstructures of materials by using computer and molecular dynamics.In molecular dynamics simulation,periodic boundary conditions are usually used to eliminate boundary effects,and for convenience,cubic simulation boxes are usually used to simulate.However,it is found that the existence of periodic boundary conditions will lead to a smaller diffusion coefficient than that of infinite system when simulating with cubic simulation boxes,so the results of simulation calculation need to be revised before comparing with experiments,and different correction coefficients are needed for different shapes of simulation boxes.In this paper,based on the theory of fluid mechanics,the corresponding modified formula is deduced,and the diffusion of argon atom under different conditions is simulated by molecular dynamics method,and the rationality of the modified formula is verified.Through theoretical calculation,it is found that the diffusion correction coefficients of the three principal symmetric axes of the cubic simulation box are equal to 2.873.But for the cuboid simulation box,the diffusion coefficient along the short side is always greater than that along the long side,and sometimes the diffusion coefficient in the cuboid simulation box is larger than that in the infinite system,which shows that the correction coefficient is a negative value at this time.In order to explain this special phenomenon,we analyzed the flow model of the fluid around the diffused particles,and found that the positive and negative diffusion correction coefficients are related to whether the fluid vortices present an overallcircumferential situation except through the whole system.In addition,in molecular dynamics simulation,in addition to the common cubes and cubes,there are two special shapes of simulation boxes available: truncated octahedron and rhombic dodecahedron.Because they can also cover the whole space without space and are closer to spherical properties than cubic boxes,they are often used to simulate liquid structures associated with biological molecules.In this paper,the diffusion of truncated octahedron and rhombic dodecahedron simulation boxes is corrected for the first time and the corresponding correction coefficients are obtained.The correctness of the corrected formulas and correction coefficients are verified by simulating and calculating three different densities of argon atoms.