Move cell list management to a new struct (#12)

* Move cell list management to a new struct

* Move cell list to separate directory

* Add missing file

---------

Co-authored-by: Niklas Neher <[email protected]>

Author: efaulhaber

src/PointNeighbors.jl

@@ -10,6 +10,7 @@ include("util.jl")
 include("neighborhood_search.jl")
 include("nhs_trivial.jl")
 include("nhs_grid.jl")
+include("cell_lists/cell_lists.jl")
 
 export for_particle_neighbor, foreach_neighbor
 export TrivialNeighborhoodSearch, GridNeighborhoodSearch

src/cell_lists/cell_lists.jl

@@ -0,0 +1 @@
+include("dictionary.jl")

src/cell_lists/dictionary.jl

@@ -0,0 +1,54 @@
+struct DictionaryCellList{NDIMS}
+    hashtable    :: Dict{NTuple{NDIMS, Int}, Vector{Int}}
+    empty_vector :: Vector{Int} # Just an empty vector (used in `eachneighbor`)
+
+    function DictionaryCellList{NDIMS}() where {NDIMS}
+        hashtable = Dict{NTuple{NDIMS, Int}, Vector{Int}}()
+        empty_vector = Int[]
+
+        new{NDIMS}(hashtable, empty_vector)
+    end
+end
+
+function Base.empty!(cell_list::DictionaryCellList)
+    Base.empty!(cell_list.hashtable)
+
+    return cell_list
+end
+
+function push_cell!(cell_list::DictionaryCellList, cell, particle)
+    (; hashtable) = cell_list
+
+    if haskey(hashtable, cell)
+        append!(hashtable[cell], particle)
+    else
+        hashtable[cell] = [particle]
+    end
+
+    return cell_list
+end
+
+function deleteat_cell!(cell_list::DictionaryCellList, cell, i)
+    (; hashtable) = cell_list
+
+    # This works for `i::Integer`, `i::AbstractVector`, and even `i::Base.Generator`
+    if length(hashtable[cell]) <= count(_ -> true, i)
+        delete_cell!(cell_list, cell)
+    else
+        deleteat!(hashtable[cell], i)
+    end
+end
+
+function delete_cell!(cell_list, cell)
+    delete!(cell_list.hashtable, cell)
+end
+
+@inline eachcell(cell_list::DictionaryCellList) = keys(cell_list.hashtable)
+
+@inline function Base.getindex(cell_list::DictionaryCellList, cell)
+    (; hashtable, empty_vector) = cell_list
+
+    # Return an empty vector when `cell_index` is not a key of `hashtable` and
+    # reuse the empty vector to avoid allocations.
+    return get(hashtable, cell, empty_vector)
+end

src/nhs_grid.jl

@@ -48,25 +48,23 @@ since not sorting makes our implementation a lot faster (although less paralleli
   In: Computer Graphics Forum 30.1 (2011), pages 99–112.
   [doi: 10.1111/J.1467-8659.2010.01832.X](https://doi.org/10.1111/J.1467-8659.2010.01832.X)
 """
-struct GridNeighborhoodSearch{NDIMS, ELTYPE, PB} <: AbstractNeighborhoodSearch
-    hashtable           :: Dict{NTuple{NDIMS, Int}, Vector{Int}}
+struct GridNeighborhoodSearch{NDIMS, ELTYPE, CL, PB} <: AbstractNeighborhoodSearch
+    cell_list           :: CL
     search_radius       :: ELTYPE
-    empty_vector        :: Vector{Int} # Just an empty vector (used in `eachneighbor`)
+    periodic_box        :: PB
+    n_cells             :: NTuple{NDIMS, Int}    # Required to calculate periodic cell index
+    cell_size           :: NTuple{NDIMS, ELTYPE} # Required to calculate cell index
     cell_buffer         :: Array{NTuple{NDIMS, Int}, 2} # Multithreaded buffer for `update!`
     cell_buffer_indices :: Vector{Int} # Store which entries of `cell_buffer` are initialized
-    periodic_box        :: PB
-    n_cells             :: NTuple{NDIMS, Int}
-    cell_size           :: NTuple{NDIMS, ELTYPE}
     threaded_nhs_update :: Bool
 
     function GridNeighborhoodSearch{NDIMS}(search_radius, n_particles;
                                            periodic_box_min_corner = nothing,
                                            periodic_box_max_corner = nothing,
                                            threaded_nhs_update = true) where {NDIMS}
         ELTYPE = typeof(search_radius)
+        cell_list = DictionaryCellList{NDIMS}()
 
-        hashtable = Dict{NTuple{NDIMS, Int}, Vector{Int}}()
-        empty_vector = Int[]
         cell_buffer = Array{NTuple{NDIMS, Int}, 2}(undef, n_particles, Threads.nthreads())
         cell_buffer_indices = zeros(Int, Threads.nthreads())
 
@@ -98,10 +96,10 @@ struct GridNeighborhoodSearch{NDIMS, ELTYPE, PB} <: AbstractNeighborhoodSearch
                                 "must either be both `nothing` or both an array or tuple"))
         end
 
-        new{NDIMS, ELTYPE,
-            typeof(periodic_box)}(hashtable, search_radius, empty_vector,
-                                  cell_buffer, cell_buffer_indices,
-                                  periodic_box, n_cells, cell_size, threaded_nhs_update)
+        new{NDIMS, ELTYPE, typeof(cell_list),
+            typeof(periodic_box)}(cell_list, search_radius, periodic_box, n_cells,
+                                  cell_size, cell_buffer, cell_buffer_indices,
+                                  threaded_nhs_update)
     end
 end
 
@@ -122,20 +120,16 @@ function initialize_grid!(neighborhood_search::GridNeighborhoodSearch{NDIMS},
 end
 
 function initialize_grid!(neighborhood_search::GridNeighborhoodSearch, coords_fun)
-    (; hashtable) = neighborhood_search
+    (; cell_list) = neighborhood_search
 
-    empty!(hashtable)
+    empty!(cell_list)
 
     for particle in 1:nparticles(neighborhood_search)
         # Get cell index of the particle's cell
         cell = cell_coords(coords_fun(particle), neighborhood_search)
 
-        # Add particle to corresponding cell or create cell if it does not exist
-        if haskey(hashtable, cell)
-            append!(hashtable[cell], particle)
-        else
-            hashtable[cell] = [particle]
-        end
+        # Add particle to corresponding cell
+        push_cell!(cell_list, cell, particle)
     end
 
     return neighborhood_search
@@ -159,22 +153,21 @@ end
 
 # Modify the existing hash table by moving particles into their new cells
 function update_grid!(neighborhood_search::GridNeighborhoodSearch, coords_fun)
-    (; hashtable, cell_buffer, cell_buffer_indices, threaded_nhs_update) = neighborhood_search
+    (; cell_list, cell_buffer, cell_buffer_indices, threaded_nhs_update) = neighborhood_search
 
-    # Reset `cell_buffer` by moving all pointers to the beginning.
+    # Reset `cell_buffer` by moving all pointers to the beginning
     cell_buffer_indices .= 0
 
-    # Find all cells containing particles that now belong to another cell.
-    # `collect` the keyset to be able to loop over it with `@threaded`.
-    mark_changed_cell!(neighborhood_search, hashtable, coords_fun,
+    # Find all cells containing particles that now belong to another cell
+    mark_changed_cell!(neighborhood_search, cell_list, coords_fun,
                        Val(threaded_nhs_update))
 
     # Iterate over all marked cells and move the particles into their new cells.
     for thread in 1:Threads.nthreads()
         # Only the entries `1:cell_buffer_indices[thread]` are initialized for `thread`.
         for i in 1:cell_buffer_indices[thread]
             cell = cell_buffer[i, thread]
-            particles = hashtable[cell]
+            particles = cell_list[cell]
 
             # Find all particles whose coordinates do not match this cell
             moved_particle_indices = (i for i in eachindex(particles)
@@ -187,35 +180,28 @@ function update_grid!(neighborhood_search::GridNeighborhoodSearch, coords_fun)
                 new_cell_coords = cell_coords(coords_fun(particle), neighborhood_search)
 
                 # Add particle to corresponding cell or create cell if it does not exist
-                if haskey(hashtable, new_cell_coords)
-                    append!(hashtable[new_cell_coords], particle)
-                else
-                    hashtable[new_cell_coords] = [particle]
-                end
+                push_cell!(cell_list, new_cell_coords, particle)
             end
 
-            # Remove moved particles from this cell or delete the cell if it is now empty
-            if count(_ -> true, moved_particle_indices) == length(particles)
-                delete!(hashtable, cell)
-            else
-                deleteat!(particles, moved_particle_indices)
-            end
+            # Remove moved particles from this cell
+            deleteat_cell!(cell_list, cell, moved_particle_indices)
         end
     end
 
     return neighborhood_search
 end
 
-@inline function mark_changed_cell!(neighborhood_search, hashtable, coords_fun,
+@inline function mark_changed_cell!(neighborhood_search, cell_list, coords_fun,
                                     threaded_nhs_update::Val{true})
-    @threaded for cell in collect(keys(hashtable))
+    # `collect` the keyset to be able to loop over it with `@threaded`
+    @threaded for cell in collect(eachcell(cell_list))
         mark_changed_cell!(neighborhood_search, cell, coords_fun)
     end
 end
 
-@inline function mark_changed_cell!(neighborhood_search, hashtable, coords_fun,
+@inline function mark_changed_cell!(neighborhood_search, cell_list, coords_fun,
                                     threaded_nhs_update::Val{false})
-    for cell in collect(keys(hashtable))
+    for cell in eachcell(cell_list)
         mark_changed_cell!(neighborhood_search, cell, coords_fun)
     end
 end
@@ -225,9 +211,9 @@ end
 # Otherwise, `@threaded` does not work here with Julia ARM on macOS.
 # See https://github.com/JuliaSIMD/Polyester.jl/issues/88.
 @inline function mark_changed_cell!(neighborhood_search, cell, coords_fun)
-    (; hashtable, cell_buffer, cell_buffer_indices) = neighborhood_search
+    (; cell_list, cell_buffer, cell_buffer_indices) = neighborhood_search
 
-    for particle in hashtable[cell]
+    for particle in cell_list[cell]
         if cell_coords(coords_fun(particle), neighborhood_search) != cell
             # Mark this cell and continue with the next one.
             #
@@ -277,12 +263,9 @@ end
 end
 
 @inline function particles_in_cell(cell_index, neighborhood_search)
-    (; hashtable, empty_vector) = neighborhood_search
+    (; cell_list) = neighborhood_search
 
-    # Return an empty vector when `cell_index` is not a key of `hashtable` and
-    # reuse the empty vector to avoid allocations
-    return get(hashtable, periodic_cell_index(cell_index, neighborhood_search),
-               empty_vector)
+    return cell_list[periodic_cell_index(cell_index, neighborhood_search)]
 end
 
 @inline function periodic_cell_index(cell_index, neighborhood_search)
@@ -351,8 +334,3 @@ function copy_neighborhood_search(nhs::GridNeighborhoodSearch, search_radius, x,
 
     return search
 end
-
-# Create a copy of a neighborhood search but with a different search radius
-function copy_neighborhood_search(nhs::TrivialNeighborhoodSearch, search_radius, x, y)
-    return nhs
-end

src/nhs_trivial.jl

@@ -61,3 +61,8 @@ end
 end
 
 @inline eachneighbor(coords, search::TrivialNeighborhoodSearch) = search.eachparticle
+
+# Create a copy of a neighborhood search but with a different search radius
+function copy_neighborhood_search(nhs::TrivialNeighborhoodSearch, search_radius, x, y)
+    return nhs
+end