Adding config-style definitions for ion species properties

.github/workflows/test.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        julia-version: ['1']
+        julia-version: ['1', 'nightly']
         julia-arch: [x64]
         os: [ubuntu-latest, windows-latest, macOS-latest]
         exclude:

Project.toml

@@ -7,14 +7,11 @@ version = "0.5.0"
 FunctionWrappers = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
-Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
-Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 PolynomialRoots = "3a141323-8675-5d76-9d11-e1df1406c778"
 QuantumOptics = "6e0679c1-51ea-5a7c-ac74-d61b76210b0c"
 QuantumOpticsBase = "4f57444f-1401-5e15-980d-4471b28d5678"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
-Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 WignerSymbols = "9f57e263-0b3d-5e2e-b1be-24f2bb48858b"
 YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 

README.md

@@ -38,8 +38,7 @@ julia> using Pkg
 julia> Pkg.add("IonSim")
 julia> Pkg.add("IJulia")
 ```
-The last line adds Jupyter compatibility, so you'll have the option to start a Julia kernel from Jupyter notebook. This is the suggested way
-to interact with IonSim.
+The last line adds Jupyter compatibility, so you'll have the option to start a Julia kernel from Jupyter notebook.
 
 ### Updating IonSim
 

configs/ions/be9.yaml

@@ -0,0 +1,36 @@
+name: "Be9"
+shortname: "⁹Be"
+mass: 1.496508080073e-26
+charge: 1
+nuclearspin: 0.5
+full_level_structure:
+  S1/2f=1: {n: 2, l: 0, j: 0.5, f: 1, E: 0.78126104631e+9}
+  S1/2f=2: {n: 2, l: 0, j: 0.5, f: 2, E: -0.468756627786e+9}
+  P1/2f=1: {n: 2, l: 1, j: 0.5, f: 1, E: 957.2010729076436e+12}
+  P1/2f=2: {n: 2, l: 1, j: 0.5, f: 2, E: 957.2008357076436e+12}
+  P3/2f=0: {n: 2, l: 1, j: 1.5, f: 0, E: 957.3965669467407e+12}
+  P3/2f=1: {n: 2, l: 1, j: 1.5, f: 1, E: 957.3965659267407e+12}
+  P3/2f=2: {n: 2, l: 1, j: 1.5, f: 2, E: 957.3965638867406e+12}
+  P3/2f=3: {n: 2, l: 1, j: 1.5, f: 3, E: 957.3965608267406e+12}
+full_transitions: 
+  - {from: S1/2f=1, to: P1/2f=1, multipole: E1, einsteinA: 19.4000000e+9}
+  - {from: S1/2f=1, to: P1/2f=2, multipole: E1, einsteinA: 19.4000000e+9}
+  - {from: S1/2f=2, to: P1/2f=1, multipole: E1, einsteinA: 19.4000000e+9}
+  - {from: S1/2f=2, to: P1/2f=2, multipole: E1, einsteinA: 19.4000000e+9}
+  - {from: S1/2f=1, to: P3/2f=0, multipole: E1, einsteinA: 19.4000000e+9}
+  - {from: S1/2f=1, to: P3/2f=1, multipole: E1, einsteinA: 19.4000000e+9}
+  - {from: S1/2f=1, to: P3/2f=2, multipole: E1, einsteinA: 19.4000000e+9}
+  - {from: S1/2f=2, to: P1/2f=1, multipole: E1, einsteinA: 19.4000000e+9}
+  - {from: S1/2f=2, to: P1/2f=2, multipole: E1, einsteinA: 19.4000000e+9}
+  - {from: S1/2f=2, to: P1/2f=3, multipole: E1, einsteinA: 19.4000000e+9}
+
+# Optional fields
+default_sublevel_selection:
+- ["S1/2f=1", "all"]
+- ["S1/2f=2", "all"]
+- ["P1/2f=1", "all"]
+- ["P1/2f=2", "all"]
+- ["P3/2f=0", "all"]
+- ["P3/2f=1", "all"]
+- ["P3/2f=2", "all"]
+- ["P3/2f=3", "all"]

configs/ions/ca40.yaml

@@ -0,0 +1,28 @@
+name: "Ca40"
+shortname: "⁴⁰Ca"
+mass: 6.635943757345042e-26
+charge: 1
+nuclearspin: 0
+full_level_structure:
+  S1/2: {n: 4, l: 0, j: 0.5, f: 0.5 , E: 0.0}
+  D3/2: {n: 3, l: 2, j: 1.5, f: 1.5 , E: 4.09335071228e+14}
+  D5/2: {n: 3, l: 2, j: 2.5, f: 2.5 , E: 4.1115503183857306e+14}
+  P1/2: {n: 4, l: 1, j: 0.5, f: 0.5 , E: 7.554e+14}
+  P3/2: {n: 4, l: 1, j: 1.5, f: 1.5 , E: 7.621e+14}
+full_transitions:
+  - {from: "S1/2", to: "D5/2", multipole: "E2", einsteinA: 8.562e-1}
+  - {from: "S1/2", to: "P1/2", multipole: "E1", einsteinA: 1.299e+8}
+  - {from: "D3/2", to: "P1/2", multipole: "E1", einsteinA: 1.060e+7}
+  - {from: "S1/2", to: "D3/2", multipole: "E2", einsteinA: 9.259e-1}
+  - {from: "S1/2", to: "P3/2", multipole: "E1", einsteinA: 1.351e+8}
+  - {from: "D3/2", to: "P3/2", multipole: "E1", einsteinA: 1.110e+6}
+  - {from: "D5/2", to: "P3/2", multipole: "E1", einsteinA: 9.901e+6}
+
+# Optional fields
+default_sublevel_selection:
+- ["S1/2", "all"]
+- ["D5/2", "all"]
+
+gfactors:
+  S1/2: 2.00225664
+  D5/2: 1.2003340

configs/ions/mg25.yaml

@@ -0,0 +1,37 @@
+name: "Mg25"
+shortname: "²⁵Mg"
+mass: 4.1489954812e-26
+charge: 1
+nuclearspin: 2.5
+full_level_structure:
+  S1/2f=2: {n: 3, l: 0, j: 0.5, f: 2, E: 1.043445158e+9}
+  S1/2f=3: {n: 3, l: 0, j: 0.5, f: 3, E: -0.745317970e+9}
+  P1/2f=2: {n: 3, l: 1, j: 0.5, f: 2, E: 1069.3408690519877e+12}
+  P1/2f=3: {n: 3, l: 1, j: 0.5, f: 3, E: 1069.3405639519879e+12}
+  P3/2f=1: {n: 3, l: 1, j: 1.5, f: 1, E: 1072.0853411194748e+12}
+  P3/2f=2: {n: 3, l: 1, j: 1.5, f: 2, E: 1072.0853033394746e+12}
+  P3/2f=3: {n: 3, l: 1, j: 1.5, f: 3, E: 1072.0852466694748e+12}
+  P3/2f=4: {n: 3, l: 1, j: 1.5, f: 4, E: 1072.0851711094747e+12}
+
+full_transitions: 
+  - {from: "S1/2f=2", to: "P1/2f=2", multipole: "E1", einsteinA: 41.3e+6}
+  - {from: "S1/2f=2", to: "P1/2f=3", multipole: "E1", einsteinA: 41.3e+6}
+  - {from: "S1/2f=3", to: "P1/2f=2", multipole: "E1", einsteinA: 41.3e+6}
+  - {from: "S1/2f=3", to: "P1/2f=3", multipole: "E1", einsteinA: 41.3e+6}
+  - {from: "S1/2f=2", to: "P3/2f=1", multipole: "E1", einsteinA: 41.3e+6}
+  - {from: "S1/2f=2", to: "P3/2f=2", multipole: "E1", einsteinA: 41.3e+6}
+  - {from: "S1/2f=2", to: "P3/2f=3", multipole: "E1", einsteinA: 41.3e+6}
+  - {from: "S1/2f=3", to: "P1/2f=2", multipole: "E1", einsteinA: 41.3e+6}
+  - {from: "S1/2f=3", to: "P1/2f=3", multipole: "E1", einsteinA: 41.3e+6}
+  - {from: "S1/2f=3", to: "P1/2f=4", multipole: "E1", einsteinA: 41.3e+6}
+
+# Optional fields
+default_sublevel_selection:
+  - ["S1/2f=2", "all"]
+  - ["S1/2f=3", "all"]
+  - ["P1/2f=2", "all"]
+  - ["P1/2f=3", "all"]
+  - ["P3/2f=1", "all"]
+  - ["P3/2f=2", "all"]
+  - ["P3/2f=3", "all"]
+  - ["P3/2f=4", "all"]

configs/ions/yb171.yaml

@@ -0,0 +1,80 @@
+name: "Yb171"
+shortname: "¹⁷¹Yb"
+mass: 28.8384644689030595108e-26
+charge: 1
+nuclearspin: 0.5
+full_level_structure:
+  "S1/2f=0": {n: 6, l: 0, j: 0.5, f: 0, E: -9.48210909315e+9}
+  "S1/2f=1": {n: 6, l: 0, j: 0.5, f: 1, E: 3.16070303105e+9}
+  "D3/2f=0": {n: 5, l: 2, j: 1.5, f: 1, E: 6.88342460964640e+14}
+  "D3/2f=1": {n: 5, l: 2, j: 1.5, f: 2, E: 6.88350470564640e+14}
+  "D5/2f=2": {n: 5, l: 2, j: 2.5, f: 2, E: 7.29477895985202e+14}
+  "D5/2f=3": {n: 5, l: 2, j: 2.5, f: 3, E: 7.29474121985202e+14}
+  "P1/2f=0": {n: 6, l: 1, j: 0.5, f: 0, E: 8.112913749003559e+14}
+  "P1/2f=1": {n: 6, l: 1, j: 0.5, f: 1, E: 8.112934798003559e+14}
+  "[3/2]1/2f=0": {n: 6, l: null, j: 0.5, f: 0, E: 1.008917341058788e+15}
+  "[3/2]1/2f=1": {n: 6, l: null, j: 0.5, f: 1, E: 1.008917341058788e+15}
+  "[3/2]3/2f=1": {n: 6, l: null, j: 1.5, f: 1, E: 8.621425511314839e+14}
+  "[3/2]3/2f=2": {n: 6, l: null, j: 1.5, f: 2, E: 8.621425511314839e+14}
+  "[5/2]5/2f=2": {n: 6, l: null, j: 2.5, f: 2, E: 9.70461163716380e+14}
+  "[5/2]5/2f=3": {n: 6, l: null, j: 2.5, f: 3, E: 9.70461163716380e+14}
+  "F7/2f=3": {n: 6, l: 3, j: 3.5, f: 3, E: 6.42115934728750e+14}
+  "F7/2f=4": {n: 6, l: 3, j: 3.5, f: 4, E: 6.42119554728750e+14}
+
+full_transitions:
+  # Laser lines
+  # 411nm
+  - {from: "S1/2f=0", to: "D5/2f=2", multipole: "E2", einsteinA: 22}
+  - {from: "S1/2f=1", to: "D5/2f=2", multipole: "E2", einsteinA: 22}
+  - {from: "S1/2f=1", to: "D5/2f=3", multipole: "E2", einsteinA: 22}
+  # 369nm
+  - {from: "S1/2f=0", to: "P1/2f=1", multipole: "E1", einsteinA: 1.155e+8}
+  - {from: "S1/2f=1", to: "P1/2f=0", multipole: "E1", einsteinA: 1.155e+8}
+  - {from: "S1/2f=1", to: "P1/2f=1", multipole: "E1", einsteinA: 1.155e+8}
+  # 935nm
+  - {from: "D3/2f=1", to: "[3/2]1/2f=0", multipole: "E1", einsteinA: 1.2e+5}
+  - {from: "D3/2f=1", to: "[3/2]1/2f=1", multipole: "E1", einsteinA: 1.2e+5}
+  - {from: "D3/2f=2", to: "[3/2]1/2f=1", multipole: "E1", einsteinA: 1.2e+5}
+  # 760nm
+  - {from: "F7/2f=3", to: "[3/2]3/2f=1", multipole: "E2", einsteinA: 5.0e+4}
+  - {from: "F7/2f=3", to: "[3/2]3/2f=2", multipole: "E2", einsteinA: 5.0e+4}
+  - {from: "F7/2f=4", to: "[3/2]3/2f=2", multipole: "E2", einsteinA: 5.0e+4}
+  # 638nm
+  # 976nm
+  # 861nm
+  # Decay lines
+  # P1/2 -> D3/2
+  - {from: "P1/2f=0", to: "D3/2f=1", multipole: "E1", einsteinA: 5.7e+5}
+  - {from: "P1/2f=1", to: "D3/2f=2", multipole: "E1", einsteinA: 5.7e+5}
+  - {from: "P1/2f=1", to: "D3/2f=2", multipole: "E1", einsteinA: 5.7e+5}
+  # [3/2]1/2 -> S1/2
+  - {from: "[3/2]1/2f=0", to: "S1/2f=1", multipole: "E1", einsteinA: 8.05e+7}
+  - {from: "[3/2]1/2f=1", to: "S1/2f=0", multipole: "E1", einsteinA: 8.05e+7}
+  - {from: "[3/2]1/2f=1", to: "S1/2f=1", multipole: "E1", einsteinA: 8.05e+7}
+  # [3/2]3/2 -> S1/2
+  - {from: "[3/2]1/2f=0", to: "S1/2f=1", multipole: "E1", einsteinA: 5.125e+7}
+  - {from: "[3/2]1/2f=1", to: "S1/2f=0", multipole: "E1", einsteinA: 5.125e+7}
+  - {from: "[3/2]1/2f=1", to: "S1/2f=1", multipole: "E1", einsteinA: 5.125e+7}
+
+# Optional fields
+default_sublevel_selection:
+  - ["S1/2f=0", "all"]
+  - ["S1/2f=1", "all"]
+  - ["P1/2f=0", "all"]
+  - ["P1/2f=1", "all"]
+
+gfactors:
+  "S1/2f=0": 1.998
+  "S1/2f=1": 1.998
+  "D5/2f=2": 1.202
+  "D5/2f=3": 1.202
+  "F7/2f=3": 1.145
+  "F7/2f=4": 1.145
+  "[3/2]1/2f=0": 1.32
+  "[3/2]1/2f=1": 1.32
+  "[3/2]3/2f=1": 1.44
+  "[3/2]3/2f=2": 1.44
+
+nonlinear_zeeman:
+- {level: "S1/2f=0", sublevel: 0, coeffs: [0.0, 0.0, -155.305]}
+- {level: "S1/2f=1", sublevel: 0, coeffs: [0.0, 0.0, 155.305]}

src/IonSim.jl

@@ -34,6 +34,7 @@ abstract type IonSimBasis <: Basis end
 export IonSimBasis
 
 include("constants.jl")
+include("ionproperties.jl")
 include("ions.jl")
 include("vibrationalmodes.jl")
 include("lasers.jl")
@@ -42,7 +43,6 @@ include("chambers.jl")
 include("operators.jl")
 include("hamiltonians.jl")
 include("timeevolution.jl")
-include("species/_include_species.jl")
 
 module analytical
 include("analyticfunctions.jl")

src/hamiltonians.jl

@@ -14,7 +14,7 @@ Constructs the Hamiltonian for `chamber` as a function of time. Return type is a
 `h(t::Real, ψ)` that, itself, returns a `QuantumOptics.SparseOperator`.
 
 **args**
-* `timescale`: e.g. a value of 1e-6 will take time to be in μs
+* `timescale`: e.g. a value of 1e-6 will take time to be in ``\\mu s``
 * `lamb_dicke_order`: Only consider terms that change the phonon number by up to this value.
     If this is an `Int`, then the cutoff is applied to all modes. If this is a `Vector{Int}`,
     then `lamb_dicke_order[i]` is applied to the iᵗʰ mode, according to the order in