Merge pull request #25 from MineralsCloud:AtomsBaseExt

Implement `AtomsBaseExt`

Project.toml

@@ -9,10 +9,12 @@ StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 StructEquality = "6ec83bb0-ed9f-11e9-3b4c-2b04cb4e219c"
 
 [weakdeps]
+AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 UnitfulLinearAlgebra = "c14bd059-d406-4571-8f61-9bd20e53c30b"
 
 [extensions]
+AtomsBaseExt = "AtomsBase"
 UnitfulExt = "Unitful"
 UnitfulLinearAlgebraExt = ["Unitful", "UnitfulLinearAlgebra"]
 
@@ -22,9 +24,11 @@ StructEquality = "1, 2"
 julia = "1"
 
 [extras]
+AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"
+UnitfulLinearAlgebra = "c14bd059-d406-4571-8f61-9bd20e53c30b"
 
 [targets]
-test = ["Test", "Unitful", "UnitfulAtomic"]
+test = ["Test", "AtomsBase", "Unitful", "UnitfulAtomic", "UnitfulLinearAlgebra"]

ext/AtomsBaseExt.jl

@@ -0,0 +1,38 @@
+module AtomsBaseExt
+
+using AtomsBase:
+    AbstractSystem,
+    Atom,
+    bounding_box,
+    periodicity,
+    isinfinite,
+    element_symbol,
+    periodic_system
+using CrystallographyCore: basisvectors, eachatom
+
+import AtomsBase: FlexibleSystem
+import CrystallographyCore: Lattice, Cell
+
+Lattice(system::AbstractSystem) = Lattice(bounding_box(system))
+
+function Cell(system::AbstractSystem)
+    if !all(periodicity(system)) || isinfinite(system)
+        error("the system is not periodic!")
+    end
+    lattice = Lattice(system)
+    atoms = element_symbol(system)
+    positions = position(system)
+    reduced = inv(lattice).(positions)
+    return Cell(lattice, reduced, atoms)
+end
+
+function FlexibleSystem(cell::Cell)
+    lattice = Lattice(cell)
+    box = collect(basisvectors(lattice))
+    atomicpositions = map(eachatom(cell)) do (atom, position)
+        Atom(atom, lattice(position))
+    end
+    return periodic_system(atomicpositions, box; fractional=true)
+end
+
+end

test/AtomsBase.jl

@@ -0,0 +1,20 @@
+using AtomsBase
+using Unitful: ustrip, @u_str
+using UnitfulLinearAlgebra
+
+# See https://juliamolsim.github.io/AtomsBase.jl/stable/tutorial/#System-interface-and-conventions v0.3.5
+@testset "Test example from AtomsBase.jl documentation" begin
+    box = [[10.0, 0.0, 0.0], [0.0, 10.0, 0.0], [0.0, 0.0, 10.0]]u"Å"  # Note the unit!
+    bc = [Periodic(), Periodic(), Periodic()]
+    hydrogen = FlexibleSystem(
+        [Atom(:H, [0, 0, 1.0]u"bohr"), Atom(:H, [0, 0, 3.0]u"bohr")], box, bc
+    )
+    cell = Cell(
+        box, [[0, 0, ustrip(u"Å", 0.1u"bohr")], [0, 0, ustrip(u"Å", 0.3u"bohr")]], [:H, :H]
+    )
+    @test Cell(hydrogen) == cell
+    @test all(
+        position(FlexibleSystem(cell)) .≈
+        [uconvert.(u"Å", [0, 0, 1.0]u"bohr"), uconvert.(u"Å", [0, 0, 3.0]u"bohr")],
+    )
+end

test/runtests.jl

@@ -5,4 +5,5 @@ using Test
     # Write your tests here.
     include("lattice.jl")
     include("eachatom.jl")
+    include("AtomsBase.jl")
 end