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fix: prevent cells from appearing multiple times in their neighbors list #55

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Merged
romainljsimon merged 1 commit into from
Jan 15, 2026
Merged

fix: prevent cells from appearing multiple times in their neighbors list #55

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15 changes: 8 additions & 7 deletions src/neighbours.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -94,14 +94,16 @@ function build_neighbour_cells(ncells::NTuple{d,Int}) where {d}
neighbourcells = Vector{Vector{Int}}(undef, prod(ncells))
ranges = map(Base.OneTo, ncells) # create ranges 1:n1, 1:n2, ...
for mc in Iterators.product(ranges...)
c = cell_index(ncells, mc)
c = cell_index(ncells, mc)
neighbours = []
for mc2 in Iterators.product(map(x -> x-1:x+1, mc)...)
# Calculate the scalar cell index of the neighbour cell (with PBC)
c2 = cell_index(ncells, mc2)
push!(neighbours, c2)
end
neighbourcells[c] = neighbours
# The unique is required if there are fewer than 3 cells in one direction
# Otherwise, the same index can appear multiple times
neighbourcells[c] = unique!(neighbours)
end
return neighbourcells
end
Expand All @@ -111,16 +113,16 @@ end
Cells are chosen so that their dimensions are at least `rcut`, and neighbour cells are precomputed.
"""
function CellList(box::SVector{d,T}, rcut::T, N::Int) where {d,T<:AbstractFloat}

# Calculate cell dimensions ensuring they're >= rcut
cell_box = @. box / floor(Int, box / rcut)

# Calculate number of cells in each dimension
ncells = ntuple(i -> max(1, floor(Int, box[i] / cell_box[i])), d)

# Initialize empty cells
cells = [Int[] for _ in 1:prod(ncells)]

# Initialize cell indices for particles
cs = zeros(Int, N)
neighbour_cells = build_neighbour_cells(ncells)
Expand Down Expand Up @@ -279,4 +281,3 @@ function old_new_cell(system::Particles, i, neighbour_list::LinkedList)
c2 = cell_index(neighbour_list, mc2)
return c, c2
end