Added a bit more documentation for the monitoring operator, and added runtests.jl to run all the tests

Author: Ste1nb0cK

docs/src/monitoring_metrology.md

@@ -17,7 +17,7 @@ BackAction.expheff_derivative(Heff_par::Function, tau::Float64, theta::Vector{Fl
 ```
 
 ```@docs
-BackAction.jumpoperators_derivatives(Ls_par, theta, dtheta)
+BackAction.jumpoperators_derivatives(Ls_par, theta::Vector{Float64}, dtheta::Vector{Float64})
 ```
 
 ```@docs

src/monitoring.jl

@@ -4,7 +4,14 @@
 getheff_parametrized(H_par::Function, Ls_par)
 ```
 
-TODO: write this documentation
+From the function `H_par`, which is assumed to be the parametrization of the hamiltonian, and
+an array of functions `Ls` which are assumed to parametrize the jump operators, return a function
+that's the  parametrization of the effective Hamiltonian.
+
+!!! note "About the Arguments"
+    The calculation of monitoring operator assumes that the arguments of `H_par` and the functions in
+    `Ls` are the same and in the same order.
+
 """
 function getheff_parametrized(H_par::Function, Ls_par)::Function
     # here theta is expected to be a vector
@@ -22,7 +29,21 @@ end
 expheff_derivative(Heff_par::Function, tau::Float64, theta::Vector{Float64}, dtheta::Vector{Float64})
 ```
 
-TODO: write this documentation
+Calculate the derivative  ``\\partial_{i}e^{-i\\tau H_e(\\theta)}``, where ``i`` is the ``i-th`` component
+of the vector ``\\theta``.
+
+# Arguments
+- `Heff_par::Function`: the parametrization of the effective hamiltonian
+- `tau::Float64`: the time in the exponential
+- `theta::Vector{Float64}`: vector with the values of the parameters at which the derivative is calculated
+- `dtheta::Vector{Float64}`: the displacement vector used to calculate the derivative, if you want the derivative
+                             respect to the ``i-th`` parameter `dtheta` must have zero entries except for `dtheta[i]`.
+
+!!! note "Derivative order "
+    The derivative is calculate using the five-point stencil rule.
+
+!!! todo "TODO: add an example"
+    Preferably one in which  ``\\partial_i H_e`` commutes with ``H_e``, those are easier.
 """
 function expheff_derivative(Heff_par::Function, tau::Float64, theta::Vector{Float64}, dtheta::Vector{Float64})
     f1 =  exp(-1im*tau*Heff_par((theta + 2*dtheta)...))
@@ -36,12 +57,14 @@ end
 """
 
 ```
-jumpoperators_derivatives(Ls_par, theta, dtheta)
+jumpoperators_derivatives(Ls_par, theta::Vector{Float64}, dtheta::Vector{Float64})
 ```
 
-TODO: write this documentation
+Calculate the derivatives of the list of jump operators, the logic is the same as
+for `expheff_derivative`.
+
 """
-function jumpoperators_derivatives(Ls_par, theta, dtheta)
+function jumpoperators_derivatives(Ls_par, theta::Vector{Float64}, dtheta::Vector{Float64})
     nchannels = size(Ls_par)[1]
     nlevels = size(Ls_par[1](theta...))[1]
     dLs = zeros(ComplexF64, nlevels, nlevels, nchannels)
@@ -55,6 +78,7 @@ function jumpoperators_derivatives(Ls_par, theta, dtheta)
     return dLs
 end
 
+
 """
 
 ```
@@ -64,7 +88,13 @@ writederivative!(dpsi::SubArray{ComplexF64, 1}, L::Matrix{ComplexF64},
                           psi0::Vector{ComplexF64})
 ```
 
-TODO: write this documentation
+Writes the derivative of ``|\\psi\\rangle = L(\\theta)V(\\theta)|\\psi_0\\rangle ``
+at ``\\theta`` in the subarray `dpsi` respect to the ``i-th`` component of ``theta``,
+following the same logic as `expheff_derivative`. The derivatives of ``V`` and ``L`` at
+must be provided via `dL` and `dV`.
+
+!!! note "Initial State dependency"
+    This is intended to be used when ``|\\psi_0\\rangle`` doesn't have dependeny on ``\\theta``.
 """
 function writederivative!(dpsi::SubArray{ComplexF64, 1},
                           L::Matrix{ComplexF64},
@@ -85,7 +115,12 @@ writederivative!(dpsi::SubArray{ComplexF64, 1},
                  dpsi0::SubArray{ComplexF64, 1})
 ```
 
-TODO: write this documentation
+Writes the derivative of ``|\\psi\\rangle = L(\\theta)V(\\theta)|\\psi_0\\rangle ``
+at ``\\theta`` in the subarray `dpsi` respect to the ``i-th`` component of ``theta``,
+following the same logic as `expheff_derivative`. The derivatives of ``V`` and ``L`` at
+must be provided via `dL` and `dV`, and also that of ``|\\psi0\\rangle`` as `dpsi0`.
+
+
 """
 function writederivative!(dpsi::SubArray{ComplexF64, 1},
                           L::Matrix{ComplexF64},

test/Project.toml

@@ -1,9 +1,11 @@
 [deps]
-BackAction = "32f8aca8-888b-4d2f-bb84-700bec69f41d"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 HypothesisTests = "09f84164-cd44-5f33-b23f-e6b0d136a0d5"
 LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
-QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

test/runtests.jl

@@ -0,0 +1,28 @@
+using BackAction
+using Test
+
+@testset "Radiative Damping" begin
+    include("test_radiative_damping.jl")
+end
+
+@testset "states_atjumps" begin
+    include("test_states_atjumps.jl")
+end
+
+@testset "states_att" begin
+    include("test_states_att.jl")
+end
+
+
+@testset "Resonance Fluorescene" begin
+    include("test_drive_qubit.jl")
+end
+
+@testset "Driven Qubit" begin
+    include("test_drive_qubit.jl")
+end
+
+@testset "Monitoring Operator" begin
+    include("test_monitoring.jl")
+end
+

test/test_drive_qubit.jl

@@ -1,6 +1,6 @@
 # This visual test is intended to test the evolution of mixed states
 # # Import all the necessary libraries
-libraries = ["BackAction", "LinearAlgebra", "Statistics", "Plots", "LaTeXStrings", "OrdinaryDiffEq", "Test"]
+libraries = ["LinearAlgebra", "Statistics", "Plots", "LaTeXStrings", "OrdinaryDiffEq", "Test"]
 
 function ensure_imports(packages::Vector{String})
     for pkg in packages

test/test_monitoring.jl

@@ -1,6 +1,6 @@
 # This test evaluates if the trace of the monitoring operator is working
 using Test
-using BackAction
+# using BackAction
 using LinearAlgebra
 using LaTeXStrings
 using ProgressMeter
@@ -153,7 +153,8 @@ fi_t_gammelmark = [0.115, 0.221, 0.338, 0.425, 0.507, 0.557, 0.573, 0.566, 0.532
     end
 end
 
-scatter(delta_gammelmark, fi_t_gammelmark, label="Gammelmark-Molmer") # dashlengths=dashlengths)
-plot!(delta_gammelmark, fi_t_gammelmark,  label=false, linestyle=:dash, xlabel=L"\Delta", ylabel=L"I_{\Delta\Delta}/T")
-scatter!(delta_gammelmark, my_fi_t , label="Produced")
-plot!(delta_gammelmark, my_fi_t, label=false, linestyle=:dash)
+# Activate plots in case you want to see them
+# scatter(delta_gammelmark, fi_t_gammelmark, label="Gammelmark-Molmer") # dashlengths=dashlengths)
+# plot!(delta_gammelmark, fi_t_gammelmark,  label=false, linestyle=:dash, xlabel=L"\Delta", ylabel=L"I_{\Delta\Delta}/T")
+# scatter!(delta_gammelmark, my_fi_t , label="Produced")
+# plot!(delta_gammelmark, my_fi_t, label=false, linestyle=:dash)

test/test_radiative_damping.jl

@@ -1,6 +1,6 @@
 import Distributions, HypothesisTests
 using Test
-using BackAction
+# using BackAction
 using Statistics
 using LinearAlgebra
 using Plots

test/test_resonance_fluorescene.jl

@@ -1,5 +1,5 @@
 import HypothesisTests, Distributions
-using BackAction, LinearAlgebra, Statistics, Random, QuadGK, Test, Plots,
+using  LinearAlgebra, Statistics, Random, QuadGK, Test, Plots,
     OrdinaryDiffEq
 ########## Setup
 sys = BackAction.rf_sys

test/test_states_atjumps.jl

@@ -1,4 +1,4 @@
-using BackAction, LinearAlgebra, Test
+using  LinearAlgebra, Test
 
 function identifystate(s::Matrix{ComplexF64})
     excited = [[0, 0] [0, 1.0+0im]]

test/test_states_att.jl

@@ -1,4 +1,4 @@
-using BackAction, LinearAlgebra, Test
+using  LinearAlgebra, Test
 function identifystate(s::Vector{ComplexF64})
     s1 = [1.0+0im, 0]
     s2 = [0, 1.0+0im]