add tests for AtomsBase integration

Author: jrdegreeff

src/integrations/atomsbase_integration.jl

@@ -22,6 +22,12 @@ AtomsBase.species_type(s::DynamicSystem) = species_type(s.system)
 Base.length(s::DynamicSystem) = length(s.system)
 Base.getindex(s::DynamicSystem, i::Integer) = getindex(s.system, i)
 
+AtomsBase.position(s::DynamicSystem) = position(s.system)
+AtomsBase.velocity(s::DynamicSystem) = velocity(s.system)
+AtomsBase.atomic_mass(s::DynamicSystem) = atomic_mass(s.system)
+AtomsBase.atomic_symbol(s::DynamicSystem) = AtomsBase.atomic_symbol(s.system)
+AtomsBase.atomic_number(s::DynamicSystem) = atomic_number(s.system)
+
 AtomsBase.position(s::DynamicSystem, i) = position(s.system, i)
 AtomsBase.velocity(s::DynamicSystem, i) = velocity(s.system, i)
 AtomsBase.atomic_mass(s::DynamicSystem, i) = atomic_mass(s.system, i)

test/Project.toml

@@ -1,7 +1,9 @@
 [deps]
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
+DFTK = "acf6eb54-70d9-11e9-0013-234b7a5f5337"
 InteratomicPotentials = "a9efe35a-c65d-452d-b8a8-82646cd5cb04"
 PeriodicTable = "7b2266bf-644c-5ea3-82d8-af4bbd25a884"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"

test/runtests.jl

@@ -2,8 +2,10 @@
 
 using Atomistic
 using AtomsBase
+using DFTK
 using InteratomicPotentials
 using PeriodicTable
+using StaticArrays
 using Test
 using Unitful
 using UnitfulAtomic

test/unit/api/md_result.jl

@@ -1,11 +1,11 @@
 # Unit tests for api/md_result.jl
 
-struct MockResult1 <: MolecularDynamicsResult end
-struct MockResult2 <: MolecularDynamicsResult end
-Atomistic.kinetic_energy(::MockResult2, t::Integer = 0) = t * u"bohr"
-Atomistic.potential_energy(::MockResult2, t::Integer = 0) = -2t * u"bohr"
-
 @testset "api/md_result.jl" begin
+    struct MockResult1 <: MolecularDynamicsResult end
+    struct MockResult2 <: MolecularDynamicsResult end
+    Atomistic.kinetic_energy(::MockResult2, t::Integer = 0) = t * u"bohr"
+    Atomistic.potential_energy(::MockResult2, t::Integer = 0) = -2t * u"bohr"
+
     target1 = MockResult1()
     target2 = MockResult2()
 

test/unit/api/md_simulator.jl

@@ -1,9 +1,9 @@
 # Unit tests for api/md_simulator.jl
 
-struct MockSystem <: AbstractSystem{3} end
-struct MockSimulator <: MolecularDynamicsSimulator end
-struct MockPotential <: InteratomicPotentials.ArbitraryPotential end
-
 @testset "api/md_simulator.jl" begin
+    struct MockSystem <: AbstractSystem{3} end
+    struct MockSimulator <: MolecularDynamicsSimulator end
+    struct MockPotential <: InteratomicPotentials.ArbitraryPotential end
+
     @test_throws Atomistic.UnimplementedError{MockSimulator} simulate(MockSystem(), MockSimulator(), MockPotential())
 end

test/unit/integrations/atomsbase_integration.jl

@@ -1,5 +1,41 @@
 # Unit tests for integrations/atomsbase_integration.jl
 
 @testset "integrations/atomsbase_integration.jl" begin
-    # TODO
+    struct MockSystem1D <: AbstractSystem{1} end
+    AtomsBase.bounding_box(s::MockSystem1D) = infinite_box(3)
+    AtomsBase.boundary_conditions(s::MockSystem1D) = [Periodic(), Periodic(), Periodic()]
+    Base.length(s::MockSystem1D) = 3
+    AtomsBase.species_type(s::MockSystem1D) = Symbol
+    Base.getindex(s::MockSystem1D, index::Int) = Symbol(index)
+    AtomsBase.position(s::MockSystem1D) = [11, 12, 13]u"m"
+    AtomsBase.atomic_symbol(s::MockSystem1D) = [Symbol(11), Symbol(12), Symbol(13)]
+    AtomsBase.atomic_number(s::MockSystem1D) = [10, 10, 10]
+    AtomsBase.atomic_mass(s::MockSystem1D) = [10, 10, 10]u"kg"
+    AtomsBase.velocity(s::MockSystem1D) = missing
+    AtomsBase.position(s::MockSystem1D, i) = i * u"m"
+    AtomsBase.atomic_symbol(s::MockSystem1D, i) = Symbol(i)
+    AtomsBase.atomic_number(s::MockSystem1D, i) = 0
+    AtomsBase.atomic_mass(s::MockSystem1D, i) = 0u"kg"
+    AtomsBase.velocity(s::MockSystem1D, i) = missing
+
+    target = DynamicSystem(MockSystem1D(), 3.14u"s")
+
+    @test bounding_box(target) == infinite_box(3)
+    @test boundary_conditions(target) == [Periodic(), Periodic(), Periodic()]
+    @test periodicity(target) == [true, true, true]
+    @test n_dimensions(target) == 1
+    @test length(target) == 3
+    @test size(target) == (3,)
+    @test species_type(target) == Symbol
+    @test [x for x ∈ target] == [Symbol(1), Symbol(2), Symbol(3)]
+    @test position(target) == [11, 12, 13]u"m"
+    @test ismissing(velocity(target))
+    @test AtomsBase.atomic_symbol(target) == [Symbol(11), Symbol(12), Symbol(13)]
+    @test atomic_number(target) == [10, 10, 10]
+    @test atomic_mass(target) == [10, 10, 10]u"kg"
+    @test position(target, 1) == 1u"m"
+    @test ismissing(velocity(target, 1))
+    @test AtomsBase.atomic_symbol(target, 1) == Symbol(1)
+    @test atomic_number(target, 1) == 0
+    @test atomic_mass(target, 1) == 0u"kg"
 end