When working with molecular dynamics simulations, one common task is to compute the pairwise Lennard-Jones force between particles. This force calculation can be computationally expensive, especially when dealing with a large number of particles. In this article, we will explore three different ways to accelerate the pairwise Lennard-Jones force computation in Julia.
Option 1: Naive implementation
The naive implementation of the pairwise Lennard-Jones force computation involves a double loop over all pairs of particles. For each pair, the force is calculated using the Lennard-Jones potential formula. This approach has a time complexity of O(n^2), where n is the number of particles.
function pairwise_lennard_jones_naive(positions, epsilon, sigma)
num_particles = size(positions, 1)
forces = zeros(num_particles, 3)
for i in 1:num_particles
for j in (i+1):num_particles
r = positions[j, :] - positions[i, :]
r_norm = norm(r)
force = 24 * epsilon * (2 * (sigma / r_norm)^12 - (sigma / r_norm)^6) / r_norm^2
forces[i, :] += force * r / r_norm
forces[j, :] -= force * r / r_norm
end
end
return forces
end
Option 2: Cell lists
Cell lists are a spatial partitioning technique that can be used to accelerate the pairwise Lennard-Jones force computation. The idea is to divide the simulation box into cells and only consider interactions between particles in neighboring cells. This reduces the number of pairwise interactions that need to be computed. The time complexity of this approach is O(n), where n is the number of particles.
function pairwise_lennard_jones_cell_lists(positions, epsilon, sigma, cell_size)
num_particles = size(positions, 1)
forces = zeros(num_particles, 3)
# Create cell lists
cell_lists = create_cell_lists(positions, cell_size)
for i in 1:num_particles
cell_index = get_cell_index(positions[i, :], cell_size)
# Loop over neighboring cells
for neighbor_cell_index in get_neighbor_cell_indices(cell_index)
# Loop over particles in neighboring cell
for j in cell_lists[neighbor_cell_index]
r = positions[j, :] - positions[i, :]
r_norm = norm(r)
force = 24 * epsilon * (2 * (sigma / r_norm)^12 - (sigma / r_norm)^6) / r_norm^2
forces[i, :] += force * r / r_norm
forces[j, :] -= force * r / r_norm
end
end
end
return forces
end
Option 3: Neighbor lists
Neighbor lists are another spatial partitioning technique that can be used to accelerate the pairwise Lennard-Jones force computation. The idea is to precompute a list of neighboring particles for each particle and only consider interactions between particles in these lists. This further reduces the number of pairwise interactions that need to be computed. The time complexity of this approach is also O(n), where n is the number of particles.
function pairwise_lennard_jones_neighbor_lists(positions, epsilon, sigma, cutoff_radius)
num_particles = size(positions, 1)
forces = zeros(num_particles, 3)
# Create neighbor lists
neighbor_lists = create_neighbor_lists(positions, cutoff_radius)
for i in 1:num_particles
# Loop over particles in neighbor list
for j in neighbor_lists[i]
r = positions[j, :] - positions[i, :]
r_norm = norm(r)
force = 24 * epsilon * (2 * (sigma / r_norm)^12 - (sigma / r_norm)^6) / r_norm^2
forces[i, :] += force * r / r_norm
forces[j, :] -= force * r / r_norm
end
end
return forces
end
After comparing the three options, it is clear that the neighbor lists approach is the most efficient for accelerating the pairwise Lennard-Jones force computation. It reduces the number of pairwise interactions to consider and has a time complexity of O(n), making it the best choice for large-scale simulations.
