and now AbstractSystem is gone too

Signed-off-by: Rachel Kurchin <rkurchin@cmu.edu>

src/implementation_aos.jl

@@ -5,7 +5,7 @@ using StaticArrays
 export FlexibleSystem
 
 # TODO Switch order of type arguments?
-struct FlexibleSystem{D,ET,L,AT} <: AbstractSystem{D,ET}
+struct FlexibleSystem{D,ET,L,AT}
     box::SVector{D,<:SVector{D,L}}
     boundary_conditions::SVector{D,<:BoundaryCondition}
     particles::Vector{AT}
@@ -34,3 +34,6 @@ end
 Base.size(sys::FlexibleSystem) = size(sys.particles)
 Base.length(sys::FlexibleSystem) = length(sys.particles)
 Base.getindex(sys::FlexibleSystem, i::Int) = getindex(sys.particles, i)
+Base.firstindex(::FlexibleSystem) = 1
+Base.lastindex(s::FlexibleSystem) = length(s.elements)
+Base.iterate(s::FlexibleSystem, i=1) = (1 <= i <= length(s)) ? (@inbounds s[i], i+1) : nothing

src/implementation_soa.jl

@@ -4,8 +4,7 @@ using StaticArrays
 
 export FastSystem
 
-struct FastSystem{D,ET,L<:Unitful.Length} <:
-       AbstractSystem{D,ET}
+struct FastSystem{D,ET,L<:Unitful.Length}
     box::SVector{D,SVector{D,L}}
     boundary_conditions::SVector{D,BoundaryCondition}
     positions::Vector{SVector{D,L}}
@@ -53,9 +52,9 @@ end
 bounding_box(sys::FastSystem) = sys.box
 boundary_conditions(sys::FastSystem) = sys.boundary_conditions
 
-# Base.size(sys::FastSystem) = size(sys.particles)
-Base.length(sys::FastSystem{D,ET}) where {D,ET} = length(sys.elements)
-
-# first piece of trickiness: can't do a totally abstract dispatch here because we need to know the signature of the constructor for AT
 Base.getindex(sys::FastSystem{D,ET}, i::Int) where {D,ET} =
     SimpleAtom{D}(sys.positions[i], sys.elements[i])
+Base.length(sys::FastSystem{D,ET}) where {D,ET} = length(sys.elements)
+Base.firstindex(::FastSystem) = 1
+Base.lastindex(s::FastSystem) = length(s.elements)
+Base.iterate(s::FastSystem, i=1) = (1 <= i <= length(s)) ? (@inbounds s[i], i+1) : nothing

src/interface.jl

@@ -4,8 +4,7 @@ using PeriodicTable
 using StaticArrays
 import Base.position
 
-export AbstractSystem, AbstractAtomicSystem
-export ChemicalElement, SimpleAtom
+export SimpleAtom
 export BoundaryCondition, DirichletZero, Periodic
 export atomic_mass,
     atomic_number,
@@ -19,8 +18,6 @@ export atomic_mass,
 export atomic_property, has_atomic_property, atomic_propertynames
 export n_dimensions
 
-velocity(p)::AbstractVector{<:Unitful.Velocity} = missing
-position(p)::AbstractVector{<:Unitful.Length} = error("Implement me")
 
 #
 # Identifier for boundary conditions per dimension
@@ -30,57 +27,22 @@ struct DirichletZero <: BoundaryCondition end  # Dirichlet zero boundary (i.e. m
 struct Periodic <: BoundaryCondition end  # Periodic BCs
 
 
-#
-# The system type
-#     Again readonly.
-#
-
-abstract type AbstractSystem{D,ET} end
-(bounding_box(::AbstractSystem{D})::SVector{D,SVector{D,<:Unitful.Length}}) where {D} =
+# now the interface is just functions!
+(bounding_box(sys)::SVector{D,SVector{D,<:Unitful.Length}}) where {D<:Signed} =
     error("Implement me")
-(boundary_conditions(::AbstractSystem{D})::SVector{D,BoundaryCondition}) where {D} =
+(boundary_conditions(sys)::SVector{D,BoundaryCondition}) where {D<:Signed} =
     error("Implement me")
-
-get_periodic(sys::AbstractSystem) =
+get_periodic(sys) =
     [isa(bc, Periodic) for bc in get_boundary_conditions(sys)]
 
-# Note: Can't use ndims, because that is ndims(sys) == 1 (because of AbstractVector interface)
-n_dimensions(::AbstractSystem{D}) where {D} = D
-
-
-# indexing interface
-Base.getindex(::AbstractSystem, ::Int) = error("Implement me")
-Base.size(::AbstractSystem) = error("Implement me")
-Base.length(::AbstractSystem) = error("Implement me")
-Base.setindex!(::AbstractSystem, ::Int) = error("AbstractSystem objects are not mutable.")
-Base.firstindex(::AbstractSystem) = 1
-Base.lastindex(s::AbstractSystem) = length(s)
-Base.iterate(S::AbstractSystem, i::Int=1) = (1 <= i <= length(S)) ? (@inbounds S[i], i+1) : nothing
-
-# iteration interface, needed for default broadcast dispatches below to work
-Base.iterate(sys::AbstractSystem{D,ET}, state = firstindex(sys)) where {D,ET} =
-    state > length(sys) ? nothing : (sys[state], state + 1)
 
-# TODO Support similar, push, ...
-
-# Some implementations might prefer to store data in the System as a flat list and
-# expose Atoms as a view. Therefore these functions are needed. Of course this code
-# should be autogenerated later on ...
-position(sys::AbstractSystem) = position.(sys)    # in Cartesian coordinates!
-velocity(sys::AbstractSystem) = velocity.(sys)    # in Cartesian coordinates!
-element(sys::AbstractSystem) = element.(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)))
+# indexing and iteration interface: need to dispatch getindex, size, length, firstindex, lastindex, iterate in order for these dispatches to work
+# may be a good idea also to dispatch ndims?
+position(sys) = position.(sys)    # in Cartesian coordinates!
+velocity(sys) = velocity.(sys)    # in Cartesian coordinates!
+element(sys) = element.(sys)
 
+# this is a concrete type, assuming we keep it should probably get moved to another file
 struct SimpleAtom{D}
     position::SVector{D,<:Unitful.Length}
     element::Element
@@ -92,15 +54,3 @@ element(atom::SimpleAtom) = atom.element
 function SimpleAtom(position, symbol::Union{Integer,AbstractString,Symbol,AbstractVector})
     SimpleAtom(position, elements[symbol])
 end
-
-# Just to make testing a little easier for now
-function Base.show(io::IO, mime::MIME"text/plain", sys::AbstractSystem)
-    println(io, "System:")
-    println(io, "    BCs:        ", boundary_conditions(sys))
-    println(io, "    Box:        ", bounding_box(sys))
-    println(io, "    Particles:  ")
-    for particle in sys
-        Base.show(io, mime, particle)
-        println(io)
-    end
-end