Basic printing for atomic structures (#39)

Project.toml

@@ -1,7 +1,7 @@
 name = "AtomsBase"
 uuid = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
 authors = ["JuliaMolSim community"]
-version = "0.2.1"
+version = "0.2.2"
 
 [deps]
 PeriodicTable = "7b2266bf-644c-5ea3-82d8-af4bbd25a884"

docs/src/apireference.md

@@ -18,6 +18,7 @@ AbstractSystem{D}
 atomic_mass
 atomic_number
 atomic_symbol
+chemical_formula
 boundary_conditions
 bounding_box
 element

src/AtomsBase.jl

@@ -5,6 +5,7 @@ import PeriodicTable: elements
 using StaticArrays
 
 include("interface.jl")
+include("properties.jl")
 include("flexible_system.jl")
 include("atom.jl")
 include("atomview.jl")

src/atom.jl

@@ -58,6 +58,11 @@ function Base.convert(::Type{Atom}, id_pos::Pair{<:AtomId,<:AbstractVector{<:Uni
     Atom(id_pos...)
 end
 
+function Base.show(io::IO, at::Atom{D, L}) where {D, L}
+    pos  = ustrip.(at.position)
+    print(io, "Atom($(at.atomic_symbol), [", join(pos, ", "), "]u\"$(unit(L))\")")
+end
+
 #
 # Special high-level functions to construct atomic systems
 #

src/flexible_system.jl

@@ -30,6 +30,11 @@ function FlexibleSystem(system::AbstractSystem;
     FlexibleSystem(particles, box, boundary_conditions)
 end
 
+function Base.show(io::IO, system::FlexibleSystem)
+    print(io, "FlexibleSystem")
+    show_system(io, system)
+end
+
 bounding_box(sys::FlexibleSystem)        = sys.box
 boundary_conditions(sys::FlexibleSystem) = sys.boundary_conditions
 species_type(sys::FlexibleSystem{D, S, L}) where {D, S, L} = S

src/properties.jl

@@ -0,0 +1,37 @@
+export chemical_formula
+
+
+"""
+Returns the chemical formula of an AbstractSystem as a string.
+"""
+function chemical_formula(symbols::AbstractVector{Symbol})
+    parts = map(collect(Set(symbols))) do sym
+        sym_count = count(isequal(sym), symbols)
+        sym_count < 2 && return string(sym)
+
+        str_count = string(sym_count)
+        for i in 0:9
+            str_count = replace(str_count, ('0' + i) => ('₀' + i))  # Make subscripts
+        end
+        string(sym) * str_count
+    end
+    join(sort(parts))
+end
+chemical_formula(system) = chemical_formula(atomic_symbol(system))
+
+
+function show_system(io::IO, system::AbstractSystem{D}) where {D}
+    print(io, "($(chemical_formula(system)), ")
+    bc = boundary_conditions(system)
+    if all(isequal(bc[1]), bc)
+        print(io, typeof(bc[1]), ", ")
+    end
+    box = bounding_box(system)
+    if box != infinite_box(D)
+        box_str = ["[" * join(ustrip.(bvector), ", ") * "]" for bvector in box]
+        print(io, "box=[", join(box_str, ", "), "]u\"$(unit(box[1][1]))\"")
+    else
+        print(io, "box=infinite")
+    end
+    print(io, ")")
+end

test/printing.jl

@@ -0,0 +1,14 @@
+using AtomsBase
+using Unitful
+using Test
+
+@testset "Printing atomic systems" begin
+    at = Atom(:Si, zeros(3) * u"m", extradata=42)
+    println(at)
+
+    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"
+    system = periodic_system(atoms, box; fractional=true)
+    println(system)
+end

test/properties.jl

@@ -0,0 +1,11 @@
+using AtomsBase
+using Test
+
+@testset "Chemical formula" 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
+

test/runtests.jl

@@ -4,4 +4,6 @@ using Test
     include("interface.jl")
     include("fast_system.jl")
     include("atom.jl")
+    include("properties.jl")
+    include("printing.jl")
 end