Improve chemical formula

docs/src/apireference.md

@@ -15,6 +15,7 @@ Pages = ["apireference.md"]
 boundary_conditions
 bounding_box
 chemical_formula
+element_symbol
 isinfinite
 n_dimensions
 periodicity

src/properties.jl

@@ -1,4 +1,18 @@
-export chemical_formula
+export chemical_formula, element_symbol
+
+"""
+    element_symbol(system)
+
+Return the symbols corresponding to the elements of the atoms. Note that
+this may be different than `atomic_symbol` for cases where `atomic_symbol`
+is chosen to be more specific (i.e. designate a special atom).
+"""
+function element_symbol(system::AbstractSystem)
+    # Note that atomic_symbol cannot be used here, since this may map
+    # to something more specific than the element
+    [Symbol(element(num).symbol) for num in atomic_number(system)]
+end
+
 
 """
 Returns the chemical formula of an AbstractSystem as a string.
@@ -16,4 +30,4 @@ function chemical_formula(symbols::AbstractVector{Symbol})
     end
     join(sort(parts))
 end
-chemical_formula(system) = chemical_formula(atomic_symbol(system))
+chemical_formula(system::AbstractSystem) = chemical_formula(element_symbol(system))

test/printing.jl

@@ -9,16 +9,16 @@ using Test
 
     atoms = [:Si => [0.0, -0.125, 0.0],
              :C  => [0.125, 0.0, 0.0]]
-    box = [[10, 0.0, 0.0], [0.0, 5, 0.0], [0.0, 0.0, 7]]u"Å"
+    box = [[10, 0.0, 0.0], [0.0, 5, 0.0], [0.0, 0.0, 7]]u"bohr"
 
     flexible_system = periodic_system(atoms, box; fractional=true, data=-12)
     @test repr(flexible_system) == """
-    FlexibleSystem(CSi, periodic = TTT, bounding_box = [[10.0, 0.0, 0.0], [0.0, 5.0, 0.0], [0.0, 0.0, 7.0]]u"Å")"""
+    FlexibleSystem(CSi, periodic = TTT, bounding_box = [[10.0, 0.0, 0.0], [0.0, 5.0, 0.0], [0.0, 0.0, 7.0]]u"a₀")"""
     show(stdout, MIME("text/plain"), flexible_system)
 
     fast_system = FastSystem(flexible_system)
     @test repr(fast_system) == """
-    FastSystem(CSi, periodic = TTT, bounding_box = [[10.0, 0.0, 0.0], [0.0, 5.0, 0.0], [0.0, 0.0, 7.0]]u"Å")"""
+    FastSystem(CSi, periodic = TTT, bounding_box = [[10.0, 0.0, 0.0], [0.0, 5.0, 0.0], [0.0, 0.0, 7.0]]u"a₀")"""
     show(stdout, MIME("text/plain"), fast_system)
     show(stdout, MIME("text/plain"), fast_system[1])
 end

test/properties.jl

@@ -1,11 +1,25 @@
 using AtomsBase
 using Test
+using Unitful
+using UnitfulAtomic
 
-@testset "Chemical formula" begin
+@testset "Chemical formula with symbols" begin
     @test chemical_formula([:H])                  == "H"
     @test chemical_formula([:H, :H])              == "H₂"
     @test chemical_formula([:H, :O, :H])          == "H₂O"
     @test chemical_formula([:O, :H, :O, :H])      == "H₂O₂"
     @test chemical_formula([:Ga, :N, :O, :H, :H]) == "GaH₂NO"
 end
 
+@testset "Chemical formula with system" begin
+    lattice     = [12u"bohr" * rand(3) for _ in 1:3]
+    atoms       = [Atom(6, randn(3)u"Å"; atomic_symbol=:C1),
+                   Atom(6, randn(3)u"Å"; atomic_symbol=:C2),
+                   Atom(1, randn(3)u"Å"; atomic_symbol=:D),
+                   Atom(1, randn(3)u"Å"; atomic_symbol=:D),
+                   Atom(1, randn(3)u"Å"; atomic_symbol=:D),
+                  ]
+    system      = periodic_system(atoms, lattice)
+    @test atomic_symbol(system) == [:C1, :C2, :D, :D, :D]
+    @test chemical_formula(system) == "C₂H₃"
+end