Simulation neighbor lists

Figure 2 A particle i interacts mainly with particles that are within the cutoff radius The neighbor list contains only those particles that are within a sphere of radius rj > Particles outside this sphere will not contribute to the force or energy affecting particleThe use of a neighbor list that is periodically updated during the simulation reduces the computer time required in calculating pairwise interactions.

Let us comment on the developed schematic Monte Carlo (MC) code. Of course there are many clever ways to improve the execution speed. There is the important concept of neighbor lists, of clever implementation of numerical instructions, and so on. In developing a computer simulation one usually plugs in these enhancing concepts bit by bit. 

A11 simulations involved 256 copper atoms, had timesteps of 10 fs, and were 200 ps in duration. Tt and Tp are the temperature and pressure time coupling constants. The system was treated as a cubic box, initially with side = 14.46 A. The neighbor lists were updated every 20 timesteps. 

The first apparent MD implementation to use CUDA was by Liu et al. [22]. Like Yang et al., they too chose to implement just a simplistic van der Waals potential allowing them to avoid all of the complexities inherent in production MD simulations of condensed-phase systems. Unlike Yang, Liu et al. recomputed their neighbor list periodically providing the first example of a neighbor list update for MD on GPUs. 

Donev, A., Torquato, S., StiUinger, R Neighbor list coUision-driven molecular dynamics simulation for nonspherical hard particles. 1. Algorithmic details. J. Comput. Phys. 202,737-764 (2005). doi 10.1016/j.jcp.2004.08.014... 

For conducting numerous penetrant diffusion simulations, it isn t reasonable to inspect Fig. 2 by eye to choose when to stop adding degrees of freedom an automated procedure is required instead. One approach [88] is to continue until all degrees of freedom defined by atoms within the penetrant neighbor list have been added. The remaining atoms are affected only indirectly the penetrant interacts with atom i, which then... 

Particle neighbor lists are a device widely used in MD and MC simulations of complex fluids to speed up the calculation of interactions (Allen and Tildesley 1987). They contain, for each particle in a simulation, a list of those other particles that fall within a cutoff distance from the particle under consideration (possibly under periodic continuation conditions) and which have to be taken into account in the computation of interactions. Since the number of neighbors depends exclusively on the value of the cutoff and not on the total number of particles, the complexity of the calculation of pairwise interactions is reduced from 0 N ) to 0 Npr). 

For the purpose of calculation of force interactions, the computational algorithm keeps the list of connected pairs of neighboring micro-elements and the list of connected triplets of micro-elements. These lists are updated, i.e., new connections are created or existing connections are removed at each step of dynamic simulation. Let us describe the rules for the creation and deletion of bonds of micro-elements. 

Using a weak definition of the bond, a greater number of hydrogen bonds than the natural is obtained, and the quantity tends to the number of nearest neighbors of a molecule. This is only sli tly dependent on temperature." Statistical data have been reported recently" for the H-bond network obtained at 2S°C using various different potentials and a weak definition of the bond = —2.25 kcal/mol). The values obtained from computer simulation data with different potentials are listed in Table I. 

V. Yip and R. Fiber,/. Comput. Chem., 10, 921 (1989). Calculations of a List of Neighbors in Molecular Dynamics Simulations. 

---