move atomic stuff to another file, fix some broken functions

Signed-off-by: Rachel Kurchin <[email protected]>

src/AtomsBase.jl

@@ -1,6 +1,7 @@
 module AtomsBase
 
 include("interface.jl")
+include("atoms.jl")
 include("implementation_soa.jl")
 include("implementation_aos.jl")
 

src/atoms.jl

@@ -0,0 +1,38 @@
+#
+# Extra stuff only for Systems composed of atoms
+#
+
+export StaticAtom, AbstractAtomicSystem
+export atomic_mass,
+    atomic_number,
+    atomic_symbol
+export atomic_property, has_atomic_property, atomic_propertynames
+
+struct StaticAtom{D,L<:Unitful.Length}
+    position::SVector{D,L}
+    element::Element
+end
+StaticAtom(position, element) = StaticAtom{length(position)}(position, element)
+position(atom::StaticAtom) = atom.position
+species(atom::StaticAtom) = atom.element
+
+function StaticAtom(position, symbol::Union{Integer,AbstractString,Symbol,AbstractVector})
+    StaticAtom(position, elements[symbol])
+end
+
+function Base.show(io::IO, a::StaticAtom)
+    print(io, "StaticAtom: $(a.element.symbol)")
+end
+
+const AbstractAtomicSystem{D} = AbstractSystem{D,Element}
+
+atomic_symbol(e::Element) = e.symbol
+atomic_mass(e::Element) = e.atomic_mass
+atomic_number(e::Element) = e.number
+atomic_property(e::Element, property::Symbol) = getproperty(e, property)
+
+atomic_symbol(sys::AbstractAtomicSystem) = atomic_symbol.(species(sys))
+atomic_number(sys::AbstractAtomicSystem) = atomic_number.(species(sys))
+atomic_mass(sys::AbstractAtomicSystem) = atomic_mass.(species(sys))
+atomic_property(sys::AbstractAtomicSystem, property::Symbol)::Vector{Any} =
+    atomic_property.(species(sys), property)

src/interface.jl

@@ -4,19 +4,14 @@ using PeriodicTable
 using StaticArrays
 import Base.position
 
-export AbstractSystem, AbstractAtomicSystem
-export StaticAtom
+export AbstractSystem
 export BoundaryCondition, DirichletZero, Periodic
-export atomic_mass,
-    atomic_number,
-    atomic_symbol,
-    bounding_box,
+export bounding_box,
     species,
     position,
     velocity,
     boundary_conditions,
-    periodic_dims
-export atomic_property, has_atomic_property, atomic_propertynames
+    get_periodic
 export n_dimensions
 
 velocity(p)::Union{Unitful.Velocity,Missing} = missing
@@ -48,7 +43,6 @@ get_periodic(sys::AbstractSystem) =
 # Note: Can't use ndims, because that is ndims(sys) == 1 (because of indexing interface)
 n_dimensions(::AbstractSystem{D}) where {D} = D
 
-
 # indexing and iteration interface
 Base.getindex(::AbstractSystem, ::Int) = error("Implement me")
 Base.length(::AbstractSystem) = error("Implement me")
@@ -68,33 +62,6 @@ position(sys::AbstractSystem) = position.(sys)    # in Cartesian coordinates!
 velocity(sys::AbstractSystem) = velocity.(sys)    # in Cartesian coordinates!
 species(sys::AbstractSystem) = species.(sys)
 
-#
-# Extra stuff only for Systems composed of atoms
-#
-const AbstractAtomicSystem{D} = AbstractSystem{D,Element}
-atomic_symbol(sys::AbstractAtomicSystem) = atomic_symbol.(sys)
-atomic_number(sys::AbstractAtomicSystem) = atomic_number.(sys)
-atomic_mass(sys::AbstractAtomicSystem) = atomic_mass.(sys)
-atomic_property(sys::AbstractAtomicSystem, property::Symbol)::Vector{Any} =
-    atomic_property.(sys, property)
-atomic_propertiesnames(sys::AbstractAtomicSystem) = unique(sort(atomic_propertynames.(sys)))
-
-struct StaticAtom{D,L<:Unitful.Length}
-    position::SVector{D,L}
-    element::Element
-end
-StaticAtom(position, element) = StaticAtom{length(position),eltype(position)}(position, element)
-position(atom::StaticAtom) = atom.position
-species(atom::StaticAtom) = atom.element
-
-function StaticAtom(position, symbol::Union{Integer,AbstractString,Symbol,AbstractVector})
-    StaticAtom(position, elements[symbol])
-end
-
-function Base.show(io::IO, a::StaticAtom)
-    print(io, "StaticAtom: $(a.element.symbol)")
-end
-
 # Just to make testing a little easier for now
 function Base.show(io::IO, mime::MIME"text/plain", sys::AbstractSystem)
     println(io, "$(string(nameof(typeof(sys)))):")