Near-neighbor calculations using a modified cell-linked list method

We have modified the conventional cell-linked list method to reduce the number of unnecessary internuclear distance calculations in molecular simulations of systems containing many particles. In the conventional method, the simulation space is partitioned into cells with edge lengths no less than the cutoff distance of the interaction potential (rcut). The atoms are assigned to cells according to their spatial positions, and all internuclear distances for atoms within a cell and atoms in the same and nearest neighbor cells are evaluated. While this method ensures that the internuclear separations between all atom pairs within rcut are calculated, it allows for unnecessary internuclear distance calculations between pairs that are within the volume encompassing the neighbor cells, but that are separated by more than rcut. The modified method presented here allows for reductions in the cell sizes and the number of atoms within the volume encompassing the neighbor cells. These reductions decrease the number of atoms that are outside of the interaction range and the number of unnecessary internuclear distance calculations while ensuring that all internuclear distances within the cutoff range are evaluated. We present algorithms to determine the volume with the minimum number of neighbor cells as a function of cell size and the identities of the neighboring cells. We also evaluate the serial performance using the modified form as functions of cell size and particle density for comparison with the performance using the conventional cell-linked list method. Published by Elsevier Science B.V. PACS: 31.15.Qg; 33.15.Dj