Merge pull request #26 from tjjarvinen/atoms_base

Add option to create PairList from AtomsBase structure

Project.toml

@@ -3,12 +3,16 @@ uuid = "2fcf5ba9-9ed4-57cf-b73f-ff513e316b9c"
 version = "0.5.5"
 
 [deps]
+AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [compat]
 julia = "1"
 StaticArrays = "1"
+AtomsBase = "0.3"
+Unitful = "1"
 
 [extras]
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"

src/NeighbourLists.jl

@@ -17,5 +17,8 @@ include("iterators.jl")
 # alternative assembly protocol more akin to mapreduce
 include("mapreduce.jl")
 
+# AtomsBase interface
+include("atoms_base.jl")
+
 
 end # module

src/atoms_base.jl

@@ -0,0 +1,18 @@
+using AtomsBase
+using StaticArrays: SVector
+using Unitful
+
+
+function PairList(ab::AtomsBase.AbstractSystem, cutoff::Unitful.Length; length_unit=unit(cutoff))
+    cell = ustrip.(length_unit, hcat( bounding_box(ab)... )' )
+    pbc = map( boundary_conditions(ab) ) do x
+        x == Periodic()
+    end
+    r = map( 1:length(ab)) do i
+        # Need to have SVector here for PairList to work
+        # if position does not give SVector
+        SVector( ustrip.(length_unit, position(ab,i))...)
+    end
+    nlist = PairList(r, ustrip(length_unit, cutoff), cell, pbc; int_type=Int)
+    return nlist
+end

test/Project.toml

@@ -0,0 +1,10 @@
+[deps]
+ASEconvert = "3da9722f-58c2-4165-81be-b4d7253e8fd2"
+Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
+ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
+Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"

test/runtests.jl

@@ -26,6 +26,7 @@ println("# threads = $(Base.Threads.nthreads())")
 @testset "NeighbourLists" begin
    @testset "Aux" begin include("test_aux.jl") end
    @testset "CellList" begin include("test_celllist.jl") end
+   include("test_atoms_base.jl")
 
    # pointless until we switch to comparing against ASE / matscipy
    # if hasjulip

test/test_atoms_base.jl

@@ -0,0 +1,19 @@
+using ASEconvert
+using NeighbourLists
+using Test
+using Unitful
+
+@testset "AtomsBase PairList" begin
+    cu = ase.build.bulk("Cu") * pytuple((4, 2, 3))
+    sys = pyconvert(AbstractSystem, cu)
+
+    nlist = PairList(sys, 3.5u"Å")
+
+    id, r = neigs(nlist,1)
+
+    @test length(id) == 12
+end
+
+
+
+