Use contiguous memory layout for neighbor lists

Author: efaulhaber

Project.toml

@@ -4,12 +4,14 @@ authors = ["Erik Faulhaber <[email protected]>"]
 version = "0.2.2-dev"
 
 [deps]
+ArraysOfArrays = "65a8f2f4-9b39-5baf-92e2-a9cc46fdf018"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Polyester = "f517fe37-dbe3-4b94-8317-1923a5111588"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 
 [compat]
+ArraysOfArrays = "0.6
 LinearAlgebra = "1"
 Polyester = "0.7.5"
 Reexport = "1"

src/PointNeighbors.jl

@@ -2,6 +2,7 @@ module PointNeighbors
 
 using Reexport: @reexport
 
+using ArraysOfArrays: VectorOfVectors
 using LinearAlgebra: dot
 using Polyester: @batch
 @reexport using StaticArrays: SVector

src/neighbor_lists_nhs.jl

@@ -5,14 +5,15 @@ struct NeighborListsNeighborhoodSearch{NDIMS, NHS, NL, PB}
 
     function NeighborListsNeighborhoodSearch{NDIMS}(search_radius, n_particles;
                                                     periodic_box_min_corner = nothing,
-                                                    periodic_box_max_corner = nothing) where {
-                                                                                              NDIMS
-                                                                                              }
+                                                    periodic_box_max_corner = nothing
+                                                    backend = VectorOfVectors{Int}) where {
+                                                                                           NDIMS
+                                                                                           }
         backend = GridNeighborhoodSearch{NDIMS}(search_radius, n_particles,
                                                 periodic_box_min_corner = periodic_box_min_corner,
                                                 periodic_box_max_corner = periodic_box_max_corner)
 
-        neighbor_lists = Vector{Vector{Int}}()
+        neighbor_lists = backend()
 
         new{NDIMS, typeof(backend),
             typeof(neighbor_lists),
@@ -59,6 +60,17 @@ function initialize_neighbor_lists!(neighbor_lists, neighborhood_search, x, y)
     end
 end
 
+function initialize_neighbor_lists!(neighbor_lists::VectorOfVectors, neighborhood_search, x,
+                                    y)
+    neighbor_lists_ = Vector{Vector{Int}}()
+    initialize_neighbor_lists!(neighbor_lists_, neighborhood_search, x, y)
+
+    empty!(neighbor_lists)
+    for i in eachindex(neighbor_lists_)
+        push!(neighbor_lists, neighbor_lists_[i])
+    end
+end
+
 @inline function for_particle_neighbor_inner(f, system_coords, neighbor_system_coords,
                                              neighborhood_search::NeighborListsNeighborhoodSearch,
                                              particle)