moved profile codes and started updating them

profile/profile_pairlist.jl

@@ -0,0 +1,83 @@
+using NeighbourLists
+using JuLIP
+using BenchmarkTools
+
+##
+
+
+# using PyCall
+# using ASE
+# using ProfileView
+
+# include("../test/test_aux.jl")
+
+# @pyimport matscipy.neighbours as matscipy_neighbours
+# matscipy_neighbours = pyimport("matscipy.neighbours")
+
+# function matscipy_nlist(at, cutoff)
+#    pycall(matscipy_neighbours["neighbour_list"],
+#           NTuple{5, PyArray}, "ijdDS", at.po, cutoff)
+# end
+
+println("# Threads = ", Base.Threads.nthreads())
+
+##
+
+println("Neighbourlist assembly benchmark")
+for L in [2, 4, 10, 30]
+   print("L = $L")
+   # si, non-cubic cell, mixed bc
+   at = bulk(:Si, cubic=true) * L
+   println(", N = $(length(at))")
+   set_pbc!(at, (true, true, true))
+   C = JMat(cell(at))
+   X = positions(at)
+   perbc = JVec(pbc(at))
+   cutoff = 3.5 * rnn(:Si)
+
+   # println("Julia Nlist")
+   @btime PairList($X, $cutoff, $C, $perbc)
+   # println("Matscipy Nlist")
+   # @btime matscipy_nlist($(ASEAtoms(at)), $cutoff)
+   println("------------------------------------------")
+end
+
+##
+
+# at = bulk(:Si, cubic=true, pbc = true ) * 10
+# rcut = 2.5 * rnn(:Si)
+# C = JMat(cell(at))
+# X = positions(at)
+# perbc = JVec(pbc(at))
+
+# # NeighbourLists._pairlist_(X, C, perbc, rcut, Int, false)
+# clist = NeighbourLists._celllist_(X, C, perbc, rcut, Int)
+
+# @btime NeighbourLists._celllist_($X, $C, $perbc, $rcut, Int)
+# @btime NeighbourLists._pairlist_($clist)
+
+# # @btime NeighbourLists._pairlist_($X, $C, $perbc, $rcut, Int, false)
+# #    clist = _celllist_(X, cell, pbc, cutoff, TI)
+# #    i, j, S = _pairlist_(clist)
+
+# @code_warntype NeighbourLists._pairlist_(clist)
+
+##
+
+# @profview let clist = clist 
+#    for _ = 1:100 
+#       NeighbourLists._pairlist_(clist)
+#    end
+# end
+
+##
+
+# at = bulk(:Si, cubic=true, pbc = true ) * 10
+# rcut = 2.5 * rnn(:Si)
+
+# @profview let C = JMat(cell(at)), X = positions(at), perbc = JVec(pbc(at)), 
+#               rcut = rcut 
+#    for _ = 1:30 
+#       PairList(X, rcut, C, perbc)
+#    end
+# end