copy and simplify JuLIP.Chemistry

src/chemistry.jl

@@ -0,0 +1,47 @@
+module Chemistry
+
+using JSON 
+
+# --------------------------------------------------------------------
+# Load data and prepare it a bit ... 
+
+const ase_data_path = joinpath(@__DIR__(), "..", "data", "asedata.json")
+
+const ase_data = JSON.parsefile(ase_data_path)
+
+const _rnn = [Float64(d) for d in ase_data["rnn"]]
+const _masses = [Float64(m) for m in ase_data["masses"]]
+const _refstates = Dict{String, Any}[ d == nothing ? Dict{String, Any}() : d
+                                      for d in ase_data["refstates"]]
+
+const _symbols = Dict{Int, Symbol}()
+const _numbers = Dict{Symbol, Int}()
+for (n, sym) in enumerate(Symbol.(ase_data["symbols"]))
+   _numbers[sym] = Int(n - 1)
+   _symbols[n-1] = sym
+end
+
+# --------------------------------------------------------------------
+#  some convenient accessor and conversion functions 
+
+
+atomic_number(sym::Symbol) = _numbers[sym]
+
+chemical_symbol(z::Integer) = _symbols[z]
+
+atomic_mass(z::Integer) = _masses[z+1]
+atomic_mass(sym::Symbol) = atomic_mass(atomic_number(sym))
+
+rnn(z::Integer) = _rnn[z+1]
+rnn(sym::Symbol) = rnn(atomic_number(sym))
+
+symmetry(z::Integer) = Symbol(_refstates[z+1]["symmetry"])
+symmetry(sym::Symbol) = symmetry(atomic_number(sym))
+
+lattice_constant(z::Integer) = Float64( _refstates[z+1]["a"] )
+lattice_constant(sym::Symbol) = lattice_constant(atomic_number(sym))
+
+refstate(z::Integer) = _refstates[z+1]
+refstate(sym::Symbol) = refstate(atomic_number(sym))
+
+end