bugfixes for #113, 112, 109

src/AtomsBase.jl

@@ -5,7 +5,7 @@ using UnitfulAtomic
 using StaticArrays
 using Requires
 
-export Atom, FlexibleSystem, FastSystem
+export Atom, FlexibleSystem, FastSystem, AbstractSystem 
 
 # Main Interface specification and inline docs 
 include("interface.jl")

src/utils/chemspecies.jl

@@ -51,7 +51,10 @@ end
 
 Base.Broadcast.broadcastable(s::ChemicalSpecies) = Ref(s)
 
-ChemicalSpecies(z::Integer) = ChemicalSpecies(z, 0, 0)
+# better to convert z -> symbol to catch special cases such as D; e.g. 
+# Should ChemicalSpecies(z) == ChemicalSpecies(z,z,0)? For H this is false.
+ChemicalSpecies(z::Integer) = ChemicalSpecies(_chem_el_info[z].symbol)
+
 ChemicalSpecies(sym::ChemicalSpecies) = sym
 
 ==(a::ChemicalSpecies, sym::Symbol) = 
@@ -135,6 +138,8 @@ end
 # UInt* is not readable
 atomic_number(element::ChemicalSpecies) = element.atomic_number
 
+atomic_number(z::Integer) = z 
+
 atomic_symbol(element::ChemicalSpecies) = element 
 
 Base.convert(::Type{Symbol}, element::ChemicalSpecies) = Symbol(element) 

test/runtests.jl

@@ -7,6 +7,7 @@ const GROUP_COVERAGE = !isempty(get(ENV, "GROUP_COVERAGE", ""))
 if GROUP == "Core"
     @testset "AtomsBase.jl" begin
         include("interface.jl")
+        include("species.jl")
         include("atom.jl")
         include("fast_system.jl")
         include("properties.jl")

test/species.jl

@@ -0,0 +1,23 @@
+
+using AtomsBase
+using Unitful
+using UnitfulAtomic
+using Test
+
+##
+
+@testset "ChemicalSpecies" begin 
+
+symbols = [:H, :He, :Li, :Be, :B, :C, :N, :O, :F, :Ne]
+nneut = collect(1:10); nneut[1] = 0; nneut[4] = 5; nneut[8] = 7; 
+for z = 1:10
+   @test ChemicalSpecies(symbols[z]) == ChemicalSpecies(z) == ChemicalSpecies(z, nneut[z], 0)
+end
+
+@test ChemicalSpecies(:D) == ChemicalSpecies(1, 1, 0)
+@test ChemicalSpecies(:C13) == ChemicalSpecies(6, 7, 0)
+
+@test atomic_number( UInt(8) ) == 8
+@test atomic_number( Int16(12) ) == 12
+
+end