Neighbor lists

Neighbor lists can be computed, returning all pairs of particles that are found within the cutoff, and the corresponding distances.

Non-periodic systems

Without periodic boundary conditions, just provide the coordinates and the cutoff:

julia> using CellListMap

julia> x = [ rand(2) for _ in 1:10_000 ];

julia> neighborlist(x,0.05)
376457-element Vector{Tuple{Int64, Int64, Float64}}:
 (1, 363, 0.04855594810064624)
 (1, 513, 0.03356381123125866)
 (1, 1209, 0.005159666709130686)
 ⋮
 (6575, 7378, 0.03791567990447959)
 (7378, 3450, 0.01748757015908321)

If the neighbor lists between two sets of points are required, use the following notation:

julia> x = rand(SVector{3,Float64},10^4);

julia> y = rand(SVector{3,Float64},10^3);

julia> list = neighborlist(x,y,0.1)
37309-element Vector{Tuple{Int64, Int64, Float64}}:
 (1, 971, 0.09867846773727411)
 (1, 567, 0.06630101425431004)
 (1, 3, 0.04103170149300593)
 ⋮
 (10000, 156, 0.08549899843141298)
 (10000, 444, 0.0737386384422871)

where, similarly, the third parameter is the cutoff. The returning array contains tuples with the index of the particle in the first vector, the index of the particle in the second vector, and their distance.

Periodic systems

If periodic boundary conditions are used, the unitcell can be provided explicitly as keyword parameters:

julia> x = [ rand(2) for _ in 1:10_000 ]; 

julia> neighborlist(x, 0.05; unitcell=[1,1])
392100-element Vector{Tuple{Int64, Int64, Float64}}:
 (1, 5, 0.03445098850037766)
 (1, 393, 0.039448810592487206)
 (1, 1632, 0.02276457565643465)
 ⋮
 (9501, 9781, 0.03351665194098955)
 (9501, 5429, 0.04199258248973222)

In the example above, an Orthorhombic cell was assumed, and thus a vector of sides was provided. For general periodic boundary conditions, a unit cell matrix can be provided, for example:

julia> neighborlist(x, 0.05; unitcell=[1.0 0.5; 0.5 1.0])
580693-element Vector{Tuple{Int64, Int64, Float64}}:
 (1, 457, 0.03935441952786555)
 (1, 1467, 0.033407692174569875)
 (1, 1767, 0.04490555313598093)
 ⋮
 (3652, 8475, 0.04721628783510375)
 (6260, 8475, 0.04946130971686825)
Note

Positions and unit cells can be 2 or 3-dimensional.

In-place computation of neighbor lists

If neighbor lists are computed within a interative scenario, it is interesting preallocate all the necessary data and just update the lists at every iteration. This can be achieved by constructing the InPlaceNeighborList object in advance. The performance gain of performing the operations in place might vary and may not be important for single runs, as the allocations do not dominate the computing time.

We will first illustrate the interface for a non-parallel run:

julia> using CellListMap, StaticArrays

julia> x = rand(SVector{3,Float64}, 10^4);

julia> system = InPlaceNeighborList(x=x, cutoff=0.1, unitcell=[1,1,1], parallel=false)
InPlaceNeighborList with types: 
CellList{3, Float64}
Box{OrthorhombicCell, 3, Float64, Float64, 9}
Current list buffer size: 0

Note that the buffer size has size 0. The first time the neighbor lists are computed, the list will be allocated. We will use the neighborlist! (with the bang) function, because it will effectivelly mutate the system, by allocating all necessary data:

julia> @time list = neighborlist!(system)
  0.017765 seconds (12 allocations: 7.445 MiB)
209190-element Vector{Tuple{Int64, Int64, Float64}}:
 (1, 1375, 0.09425551992016712)
 (1, 3076, 0.045320021406080775)
 (1, 3666, 0.07780146666634076)
 ⋮
 (9962, 6983, 0.07355578793348823)
 (9962, 7457, 0.07597724209140656)

Now, if we modify the coordinates, we can update the system and recompute the neighbor lists:

julia> @time update!(system, x_new)
  0.003562 seconds
InPlaceNeighborList with types: 
CellList{3, Float64}
Box{OrthorhombicCell, 3, Float64, Float64, 9}
Current list buffer size: 209190

julia> @time list = neighborlist!(system);
  0.012338 seconds
Note
  • Here we illustrate the behavior of the functions in their second calls, to remove the effects of compilation on the allocation results.
  • The cutoff and unitcell can be modified by providing additional keyword parameters to the update! function (for example update!(system, x; cutoff=0.1)).
  • Allocations can occur if the cutoff, unit cell, or number of particles change such that greater buffers are required. The number of allocations tend to disminish as the buffers become large enough to accomodate the possible variations of the computation.

For parallel runs, the allocations are minimal, but some small auxiliary data is required for the launching of multiple threads. We illustrate here the convergence of the allocations to the minimum required for multi-threaded calculations:

julia> system = InPlaceNeighborList(x=x, cutoff=0.1, unitcell=[1,1,1], parallel=true);

julia> @time list = neighborlist!(system);
  0.007762 seconds (230 allocations: 18.142 MiB)

julia> x_new = rand(SVector{3,Float64},10^4);

julia> @time update!(system, x_new)
  0.005283 seconds (20.30 k allocations: 6.200 MiB)
InPlaceNeighborList with types: 
CellList{3, Float64}
Box{OrthorhombicCell, 3, Float64, Float64, 9}
Current list buffer size: 209190

julia> @time neighborlist!(system);
  0.008190 seconds (166 allocations: 6.461 MiB)

julia> x_new = rand(SVector{3,Float64},10^4);

julia> @time update!(system, x_new);
  0.002723 seconds (221 allocations: 208.922 KiB)

julia> @time neighborlist!(system);
  0.006227 seconds (165 allocations: 2.863 MiB)

julia> x_new = rand(SVector{3,Float64},10^4);

julia> @time update!(system, x_new);
  0.002396 seconds (275 allocations: 144.078 KiB)

julia> @time neighborlist!(system);
  0.004996 seconds (161 allocations: 15.141 KiB)

Options

Additional optional parameters can be used in a neighborlist call:

KeywordValues typesDefaultAbout
parallelBooltrueturns on and off parallelization
show_progressBoolfalseturns on and off progress bar
nbatchesTuple{Int,Int}(0,0)Number of batches used in parallelization (see here)
autoswapBooltrue(advanced) automatically choose set to construct the cell lists