Atom Structure

New atom structure SimpleAtom is a bits type structure that aims to be a simple small structure.

You can create SimpleAtom in one of the following ways

julia> SimpleAtom(:H, [0.0, 0.0, 0.0]u"Å")SimpleAtom(H, Z = 1, m = 1.008 u):
    position          : [0,0,0]u"Å"
    species           : H
julia> SimpleAtom( 1, [0.0, 0.0, 0.0]u"Å") # same as aboveSimpleAtom(H, Z = 1, m = 1.008 u):
    position          : [0,0,0]u"Å"
    species           : H
julia> SimpleAtom(:O, [1.0, 0.0, 0.0]u"Å", [0.1, 0.0, 0.0]u"Å/s"; mass = 16.0u"u", charge = -1.0u"q")SimpleAtom(O, Z = 8, m = 16.0 u):
    position          : [1,0,0]u"Å"
    velocity          : [0.1,0,0]u"Å s^-1"
    species           : O
    charge            : -1.602176634e-19 C
julia> SimpleAtom(ChemicalSpecies(:H), [0.0, 0.0, 0.0]u"Å")SimpleAtom(H, Z = 1, m = 1.008 u):
    position          : [0,0,0]u"Å"
    species           : H
julia> SimpleAtom( :O => [1.0, 0.0, 0.0]u"Å" )SimpleAtom(O, Z = 8, m = 15.999 u):
    position          : [1,0,0]u"Å"
    species           : O

You can add extra atomkeys to an existing atom, by creating a new SimpleAtom and adding a keyword argument

sa = SimpleAtom(:H, [0.0, 0.0, 0.0]u"Å")
SimpleAtom(sa; charge = 1.0u"q" ) # same as sa but with added charge

SimpleAtom(H, Z = 1, m = 1.008 u):
    position          : [0,0,0]u"Å"
    species           : H
    charge            : 1.602176634e-19 C

Compared to AtomsBase Atom SimpleAtom is smaller in size and is also bitstype

julia> ab_atom = AtomsBase.Atom( :O, [1.0, 0.0, 0.0]u"Å" )Atom(O, Z = 8, m = 15.999 u):
    position          : [1,0,0]u"Å"
    species           : O
julia> sa = SimpleAtom( :O, [1.0, 0.0, 0.0]u"Å" )SimpleAtom(O, Z = 8, m = 15.999 u):
    position          : [1,0,0]u"Å"
    species           : O
julia> Base.summarysize(ab_atom)456
julia> Base.summarysize(sa)32
julia> isbits(ab_atom)false
julia> isbits(sa)true

Vector of SimpleAtoms

Vector os SimpleAtoms has basic AtomsBase interface implemented

julia> va = [ SimpleAtom(i, i * ones(3)u"Å") for i in 1:5 ]5-element Vector{SimpleAtom{3, @NamedTuple{species::ChemicalSpecies, position::StaticArraysCore.SVector{3, Quantity{Float64, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}}}, Quantity{Float64, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}}}:
 SimpleAtom(H,  [       1,        1,        1]u"Å")
 SimpleAtom(He, [       2,        2,        2]u"Å")
 SimpleAtom(Li, [       3,        3,        3]u"Å")
 SimpleAtom(Be, [       4,        4,        4]u"Å")
 SimpleAtom(B,  [       5,        5,        5]u"Å")
julia> species(va, 3)Li
julia> position(va, 4)3-element StaticArraysCore.SVector{3, Quantity{Float64, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}} with indices SOneTo(3):
 4.0 Å
 4.0 Å
 4.0 Å
julia> mass(va, :)5-element Vector{Quantity{Float64, 𝐌, Unitful.FreeUnits{(u,), 𝐌, nothing}}}:
  1.008 u
  4.002602 u
  6.94 u
  9.0121831 u
 10.81 u
julia> hasatomkey(va, :velocity)false
julia> cell(va)IsolatedCell{3, Quantity{Float64, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}}()