From 16c52c174c0d9409739a61178917946cd9d6b938 Mon Sep 17 00:00:00 2001
From: Christoph Ortner <christophortner0@gmail.com>
Date: Mon, 9 Sep 2024 11:45:29 -0700
Subject: [PATCH] Several Minor Bugfixes (#114)

* bugfixes for #113, 112, 109

* some io checks for ChemicalSpecies

* fixing default neutron number

* add atomic_number(::Symbol)

* bump v0.4.1

---------

Co-authored-by: Christoph Ortner <christohortner@gmail.com>
---
 Project.toml             |  2 +-
 src/AtomsBase.jl         |  2 +-
 src/utils/chemspecies.jl | 11 +++++++++--
 test/runtests.jl         |  1 +
 test/species.jl          | 33 +++++++++++++++++++++++++++++++++
 5 files changed, 45 insertions(+), 4 deletions(-)
 create mode 100644 test/species.jl

diff --git a/Project.toml b/Project.toml
index a89f6ac..79b0167 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
 name = "AtomsBase"
 uuid = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
 authors = ["JuliaMolSim community"]
-version = "0.4"
+version = "0.4.1"
 
 [deps]
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
diff --git a/src/AtomsBase.jl b/src/AtomsBase.jl
index 6785b5d..243cab1 100644
--- a/src/AtomsBase.jl
+++ b/src/AtomsBase.jl
@@ -5,7 +5,7 @@ using UnitfulAtomic
 using StaticArrays
 using Requires
 
-export Atom, FlexibleSystem, FastSystem
+export Atom, FlexibleSystem, FastSystem, AbstractSystem 
 
 # Main Interface specification and inline docs 
 include("interface.jl")
diff --git a/src/utils/chemspecies.jl b/src/utils/chemspecies.jl
index e9d1331..73c873e 100644
--- a/src/utils/chemspecies.jl
+++ b/src/utils/chemspecies.jl
@@ -51,7 +51,10 @@ end
 
 Base.Broadcast.broadcastable(s::ChemicalSpecies) = Ref(s)
 
-ChemicalSpecies(z::Integer) = ChemicalSpecies(z, 0, 0)
+# better to convert z -> symbol to catch special cases such as D; e.g. 
+# Should ChemicalSpecies(z) == ChemicalSpecies(z,z,0)? For H this is false.
+ChemicalSpecies(z::Integer) = ChemicalSpecies(_chem_el_info[z].symbol)
+
 ChemicalSpecies(sym::ChemicalSpecies) = sym
 
 ==(a::ChemicalSpecies, sym::Symbol) = 
@@ -79,7 +82,7 @@ for z in 1:length(_chem_el_info)
 end
 
 function _nneut_default(z::Integer) 
-    nplusp = floor(Int, ustrip(u"u", _chem_el_info[z].atomic_mass))
+    nplusp = round(Int, ustrip(u"u", _chem_el_info[z].atomic_mass))
     return nplusp - z
 end
 
@@ -135,6 +138,10 @@ end
 # UInt* is not readable
 atomic_number(element::ChemicalSpecies) = element.atomic_number
 
+atomic_number(z::Integer) = z 
+
+atomic_number(s::Symbol) = _sym2z[s]
+
 atomic_symbol(element::ChemicalSpecies) = element 
 
 Base.convert(::Type{Symbol}, element::ChemicalSpecies) = Symbol(element) 
diff --git a/test/runtests.jl b/test/runtests.jl
index 1a5f0f4..bd0585e 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -7,6 +7,7 @@ const GROUP_COVERAGE = !isempty(get(ENV, "GROUP_COVERAGE", ""))
 if GROUP == "Core"
     @testset "AtomsBase.jl" begin
         include("interface.jl")
+        include("species.jl")
         include("atom.jl")
         include("fast_system.jl")
         include("properties.jl")
diff --git a/test/species.jl b/test/species.jl
new file mode 100644
index 0000000..b97b9f9
--- /dev/null
+++ b/test/species.jl
@@ -0,0 +1,33 @@
+
+using AtomsBase
+using Unitful
+using UnitfulAtomic
+using Test
+
+##
+
+@testset "ChemicalSpecies" begin 
+
+symbols = [:H, :He, :Li, :Be, :B, :C, :N, :O, :F, :Ne, 
+          :Na, :Mg, :Al, :Si, :P, :S, :Cl, :Ar, :K, :Ca]
+
+# https://thechemicalelements.com/protons-neutrons-electrons-of-elements/
+n_neut =  [0, 2, 4, 5, 6, 6, 7, 8, 10, 10, 
+           12, 12, 14, 14, 16, 16, 18, 22, 20, 20] 
+
+for z = 1:10
+   @test ChemicalSpecies(symbols[z]) == ChemicalSpecies(z) == ChemicalSpecies(z, n_neut[z], 0)
+end
+
+@test ChemicalSpecies(:D) == ChemicalSpecies(1, 1, 0)
+@test ChemicalSpecies(:C13) == ChemicalSpecies(6, 7, 0)
+
+@test atomic_number( UInt(8) ) == 8
+@test atomic_number( Int16(12) ) == 12
+
+@test "$(ChemicalSpecies(:O))" == "$(ChemicalSpecies(8))" == "O"
+@test "$(ChemicalSpecies(8, 8, 0))" == "O"
+@test "$(ChemicalSpecies(:C; n_neutrons=6))" == "C"
+@test "$(ChemicalSpecies(:C; n_neutrons=7))" == "C13"
+
+end