New style

src/IonSim.jl

@@ -35,17 +35,17 @@ export IonSimBasis
 
 include("constants.jl")
 include("ions.jl")
-include("vibrational_modes.jl")
+include("vibrationalmodes.jl")
 include("lasers.jl")
-include("ion_configurations.jl")
-include("traps.jl")
+include("iontraps.jl")
+include("chambers.jl")
 include("operators.jl")
 include("hamiltonians.jl")
-include("time_evolution.jl")
+include("timeevolution.jl")
 include("species/_include_species.jl")
 
 module analytical
-include("analytic_functions.jl")
+include("analyticfunctions.jl")
 end
 
 end  # main module

src/analytic_functions.jl → src/analyticfunctions.jl

@@ -1,14 +1,14 @@
 using IonSim: _alaguerre
-export two_ion_ms, rabi_flop
+export molmersorensen2ion, rabiflop
 
 """
-    two_ion_ms(tspan, Ω::Real, ν::Real, δ::Real, η::Real, n̄::Real)
+    molmersorensen2ion(tspan, Ω::Real, ν::Real, δ::Real, η::Real, n̄::Real)
 [ref](https://doi.org/10.1103/PhysRevA.62.022311) <br>
 Assumes vibrational mode starts in a thermal state with: ``\\langle a^\\dagger a\\rangle = n̄`` 
 and ions start in doubly ground state. Returns `(ρgg, ρee)`, the population in the doubly 
 ground and doubly excited state, respectively. ``[Ω], [ν], [δ] = Hz``
 """
-function two_ion_ms(tspan, Ω::Real, ν::Real, δ::Real, η::Real, n̄::Real)
+function molmersorensen2ion(tspan, Ω::Real, ν::Real, δ::Real, η::Real, n̄::Real)
     ρgg = Float64[]
     ρee = Float64[]
     n̄ *= 1.0
@@ -38,15 +38,15 @@ function two_ion_ms(tspan, Ω::Real, ν::Real, δ::Real, η::Real, n̄::Real)
 end
 
 """
-    rabi_flop(tspan, Ω::Real, η::Real, n̄::Real; s::Int=0) <br>
+    rabiflop(tspan, Ω::Real, η::Real, n̄::Real; s::Int=0) <br>
 Single ion rabi flop. Returns:
 ``\\sum_{n=0}^∞ p_n sin^2(\\Omega_n t)`` <br> with
 ``\\Omega_n = Ωe^{-η^2/2}η^s\\sqrt{\\frac{n!}{(n+s)!}}L_{n}^{s}(η^2)`` <br>
 where ``s`` is the order of the (blue) sideband that we are driving and ``L_{n}^{s}`` is the
 associated Laguerre polynomial. [ref](https://doi.org/10.1103/RevModPhys.75.281)
 
 """
-function rabi_flop(tspan, Ω::Real, η::Real, n̄::Real; s::Int = 0)
+function rabiflop(tspan, Ω::Real, η::Real, n̄::Real; s::Int = 0)
     n̄ *= 1.0
     Ω *= 2π
     p = Vector{Float64}(undef, 0)