fix cell_vectors

Author: ejmeitz

Project.toml

@@ -1,7 +1,7 @@
 name = "SimpleCrystals"
 uuid = "64031d72-e220-11ed-1a7e-43a2532b2fa8"
 authors = ["Ethan Meitz <emeitz@andrew.cmu.edu>"]
-version = "0.4.2"
+version = "0.4.3"
 
 [deps]
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"

src/Crystal.jl

@@ -82,9 +82,13 @@ Base.length(sys::Crystal) = length(sys.atoms)
 Base.iterate(sys::Crystal, state = 1) = state > length(sys) ? nothing : (sys.atoms[state], state + 1)
 Base.eachindex(sys::Crystal) = Base.OneTo(length(sys))
 
-AtomsBase.cell_vectors(sys::Crystal) = tuple(eachrow(sys.lattice.primitive_vectors .* sys.N_unit_cells)...)
-AtomsBase.periodicity(sys::Crystal{3}) = (true, true, true)
-AtomsBase.periodicity(sys::Crystal{2}) = (true, true)
+function AtomsBase.cell_vectors(sys::Crystal)
+    t = tuple(eachrow(sys.lattice.primitive_vectors .* sys.N_unit_cells)...)
+    return AtomsBase._auto_cell_vectors(t)
+end
+
+AtomsBase.periodicity(::Crystal{3}) = (true, true, true)
+AtomsBase.periodicity(::Crystal{2}) = (true, true)
 AtomsBase.cell(sys::Crystal) = AtomsBase.PeriodicCell(cell_vectors(sys), periodicity(sys))
 AtomsBase.n_dimensions(sys::Crystal) = length(sys.N_unit_cells)
 

src/atom.jl

@@ -1,8 +1,7 @@
-export
-    Atom
+export Atom
 
 #Load periodic table data
-periodic_table = PeriodicTable.elements
+const periodic_table = PeriodicTable.elements
 
 struct Atom{D,T,C,M}
     atomic_symbol::Symbol
@@ -11,12 +10,12 @@ struct Atom{D,T,C,M}
     atomic_mass::M
 end
 
-function Atom(sym::Symbol, position; charge =0.0u"q", mass = periodic_table[sym].atomic_mass)
+function Atom(sym::Symbol, position; charge = 0.0u"q", mass = periodic_table[sym].atomic_mass)
     return Atom{length(position),eltype(position),typeof(charge),typeof(mass)}(sym, position, charge, mass)
 end
 
-function Atom(position, mass::Number; charge = 0.0u"q")
-    return Atom{length(position),eltype(position),typeof(charge), typeof(mass)}(:unknown, position, charge, mass)
+function Atom(position, mass::Number; charge = 0.0u"q", symbol = :unknown)
+    return Atom{length(position),eltype(position),typeof(charge), typeof(mass)}(symbol, position, charge, mass)
 end
 
 

test/runtests.jl

@@ -29,10 +29,18 @@ end
 @testset "AtomsBase" begin
 
     fcc_crystal = FCC(0.54u"nm", :C, SVector(4,4,4))
+    c = cell(fcc_crystal)
 
     @test n_dimensions(fcc_crystal) == 3
     @test mass(fcc_crystal, 1) == mass(fcc_crystal[1])
     @test atomic_symbol(fcc_crystal,1) == :C
+
+    @test cell_vectors(fcc_crystal) isa NTuple{3, SVector{3}}
+    @test periodicity(fcc_crystal) isa NTuple{3, Bool}
+    @test cell(fcc_crystal) isa AtomsBase.PeriodicCell
+    @test typeof(mass(fcc_crystal, 1)) <: Unitful.Mass
+    @test ismissing(velocity(fcc_crystal))
+
 end
 
 @testset "Alternate Atom Constructor" begin