use pair for neigh list entry

src/LAMMPS.jl

@@ -957,21 +957,19 @@ end
 
 _check_valid_category(category::String) = category in ("compute", "dump", "fix", "group", "molecule", "region", "variable") || error("$category is not a valid category name!")
 
-struct NeighListElement <: AbstractVector{Int32}
-    iatom::Int32
+struct NeighListVec <: AbstractVector{Int32}
     numneigh::Int
     neighbors::Ptr{Int32}
 end
 
-function Base.getindex(nle::NeighListElement, i::Integer)
-    1 <= i <= nle.numneigh+1 || throw(BoundsError(nle, i))
-    # add one to account for 1-based indexing in julia.
-    return i == 1 ? nle.iatom+1 : unsafe_load(nle.neighbors, i-1)+1
+function Base.getindex(nle::NeighListVec, i::Integer)
+    1 <= i <= nle.numneigh || throw(BoundsError(nle, i))
+    return unsafe_load(nle.neighbors, i)+1
 end
 
-Base.size(nle::NeighListElement) = (nle.numneigh+1,)
+Base.size(nle::NeighListVec) = (nle.numneigh,)
 
-struct NeighList <: AbstractVector{NeighListElement}
+struct NeighList <: AbstractVector{Pair{Int32, NeighListVec}}
     lmp::LMP
     idx::Int
 end
@@ -982,7 +980,7 @@ function Base.getindex(nl::NeighList, element::Integer)
     neighbors = Ref{Ptr{Int32}}()
     API.lammps_neighlist_element_neighbors(nl.lmp, nl.idx, element-1 #= 0-based indexing =#, iatom, numneigh, neighbors)
     iatom[] == -1 && throw(BoundsError(nl, element))
-    return NeighListElement(iatom[], numneigh[], neighbors[])
+    return iatom[]+1 => NeighListVec(numneigh[], neighbors[])
 end
 
 Base.size(nl::NeighList) = (API.lammps_neighlist_num_elements(nl.lmp, nl.idx),)

test/runtests.jl

@@ -371,7 +371,9 @@ end
 
         neighlist = find_pair_neighlist(lmp, "zero")
         @test length(neighlist) == 27
-        @test length(neighlist[1]) == 4
+        iatom, neihgs = neighlist[1]
+        @test iatom == 1 # account for 1-based indexing
+        @test length(neihgs) == 3
         @test_throws KeyError find_pair_neighlist(lmp, "nonesense")
     end
 end