Merge pull request #10 from kestrelquantum/feat_piccolo_options

Adding piccolo options to quantum collocation

Manifest.toml

@@ -1,6 +1,6 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.10.3"
+julia_version = "1.10.0"
 manifest_format = "2.0"
 project_hash = "0af13b9126caf21a7349df842fd536f87be35b2f"
 
@@ -338,7 +338,7 @@ weakdeps = ["Dates", "LinearAlgebra"]
 [[deps.CompilerSupportLibraries_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
-version = "1.1.1+0"
+version = "1.0.5+1"
 
 [[deps.CompositeTypes]]
 git-tree-sha1 = "bce26c3dab336582805503bed209faab1c279768"
@@ -1542,7 +1542,7 @@ version = "0.3.24+0"
 [[deps.OpenBLAS_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
 uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
-version = "0.3.23+4"
+version = "0.3.23+2"
 
 [[deps.OpenEXR]]
 deps = ["Colors", "FileIO", "OpenEXR_jll"]

README.md

@@ -48,3 +48,43 @@ See the example script [examples/scripts/single_qubit_gate.jl](examples/scripts/
 
 ![Single Qubit X-Gate](images/T_100_Q_1000_iter_1000_00004_fidelity_0.9999999999994745.png)
 
+## Quickstart developers guide
+
+__Install Julia__ [Juliaup](https://github.com/JuliaLang/juliaup) is an installer and version manager. This is one useful way to manage Julia versions and keep up with the latest changes. After installing, run `julia` to obtain the Julia _REPL_.
+
+__Julia environments__
+[(Documentation)](https://pkgdocs.julialang.org/v1/environments/#Using-someone-else's-project) Your project's environment is stored in _Project.toml_. You can interactively add packages to an environment by using the Julia command line _REPL_ and _package manager_.  Start Julia in the project folder. Type `]` to enter the package manager. Type `activate .` to activate or create an environment specified by _Project.toml_ located in the current folder. Separately, you generate a manifest (solving the versions to create a valid environment) by running `instantiate`; instantiate will check that the environment is correct after you add all the packages you want.
+
+__Adding packages__
+[(Documentation)](https://pkgdocs.julialang.org/v1/managing-packages/#Adding-packages) The initial cell for a Piccolo notebook might look something like the following:
+```Julia
+# Standard packages
+using LinearAlgebra
+using CairoMakie
+
+# Piccolo packages
+using QuantumCollocation
+using NamedTrajectories
+using TrajectoryIndexingUtils
+```
+
+First, let's install some standard packages (these are like Numpy and Matplotlib). Open the package manager in the current environment (type `julia`, `]`, and `activate .`), type `add LinearAlgebra` to install and precompile _LinearAlgebra_. Same with `CairoMakie`. 
+
+Second, let's install _Piccolo_. There are three packages (_QuantumCollocation_, _NamedTrajetories_, _TrajectoryIndexingUtils_) inside [Piccolo](https://docs.juliahub.com/General/Piccolo/stable/). We could do `add Piccolo` to get the three as a bundle from the Julia repository. Instead of individually calling `using ...` for each, this approach only requires `using Piccolo` at the start of a file or notebook.
+
+As a developer, we want to use the git repositories directly from [the Kestrel Quantum Github page](https://github.com/kestrelquantum). Clone, then add the local packages to the Project file with e.g. `dev ../relative/path/to/repo/QuantumCollocation`. This command installs the development version of _QuantumCollocation_ pointing to the local Github code instead of the package repository. You can repeat this for the others, also.
+
+__Developing__
+[Revise.jl](https://timholy.github.io/Revise.jl/stable/) will let you edit source code, update packages, and reload the changes in a notebook---automatically! This is a great tool for development. `add Revise` from the REPL and then include it before any packages you intend to edit:
+```Julia
+using Revise
+using QuantumCollocation
+```
+
+### Tips for Visual Studio Code
+__Julia extension__ You can run Julia notebooks and much more with [the Julia extension](https://code.visualstudio.com/docs/languages/julia). Upon opening your project folder in VS code and attempting to run an `.ipynb`, you will see that VS Code finds the interpreters managed by juliaup and defaults to using the environment based on the _Project.toml_ in the project directory.
+
+__Fonts__ VS Code will not display all characters allowed by Julia. You can change the editor font family in the settings to `'JuliaMono'` to get full support. If you don't want to mix and mash, you can create a new VS Code settings profile for working in Julia at _File>Preferences>Profile_.
+
+__Tests__ Tests should automatically populate in VS Code when working with a Piccolo package. For example, just by adding the `QuantumCollocation.jl` folder to your workspace, you should see tests appear if you click on the _Testing_ sidebar icon. If you run one of these tests, a new Julia kernel is spawned for the test. You can find the kernel if you click on the _Julia_ sidebar icon (after installing the Julia extensions). Sometimes, for the tests to recognize new changes, you may need to manually kill this kernel to see your changes reflected.
+

docs/src/contribution_guide.md

@@ -63,7 +63,7 @@ Tests are implemented using the [`TestItemRunner.jl`](https://github.com/julia-v
 
     prob = UnitarySmoothPulseProblem(
         H_drift, H_drives, U_goal, T, Δt,
-        ipopt_options=Options(print_level=1)
+        ipopt_options=IpoptOptions(print_level=1)
     )
 
     solve!(prob, max_iter=100)

src/QuantumCollocation.jl

@@ -38,8 +38,8 @@ include("dynamics.jl")
 include("evaluators.jl")
 @reexport using .Evaluators
 
-include("ipopt_options.jl")
-@reexport using .IpoptOptions
+include("options.jl")
+@reexport using .Options
 
 include("problems.jl")
 @reexport using .Problems

src/constraints.jl

@@ -130,7 +130,7 @@ function FinalFidelityConstraint(;
     zdim::Union{Int,Nothing}=nothing,
     T::Union{Int,Nothing}=nothing,
     subspace::Union{AbstractVector{<:Integer}, Nothing}=nothing,
-    hessian::Bool=true
+    eval_hessian::Bool=true
 )
     @assert !isnothing(fidelity_function) "must provide a fidelity function"
     @assert !isnothing(value) "must provide a fidelity value"
@@ -194,7 +194,7 @@ function FinalFidelityConstraint(;
         end
     end
 
-    if hessian
+    if eval_hessian
         ∂²ℱ(x) = ForwardDiff.hessian(fid, x)
 
         ∂²ℱ_structure = hessian_of_lagrangian_structure(∂²ℱ, statedim, 1)
@@ -242,7 +242,7 @@ function FinalUnitaryFidelityConstraint(
     val::Float64,
     traj::NamedTrajectory;
     subspace::Union{AbstractVector{<:Integer}, Nothing}=nothing,
-    hessian::Bool=true
+    eval_hessian::Bool=true
 )
     @assert statesymb ∈ traj.names
     return FinalFidelityConstraint(;
@@ -254,7 +254,7 @@ function FinalUnitaryFidelityConstraint(
         zdim=traj.dim,
         T=traj.T,
         subspace=subspace,
-        hessian=hessian
+        eval_hessian=eval_hessian
     )
 end
 
@@ -268,7 +268,8 @@ is the NamedTrajectory symbol representing the unitary.
 function FinalQuantumStateFidelityConstraint(
     statesymb::Symbol,
     val::Float64,
-    traj::NamedTrajectory,
+    traj::NamedTrajectory;
+    kwargs...
 )
     @assert statesymb ∈ traj.names
     return FinalFidelityConstraint(;
@@ -278,26 +279,12 @@ function FinalQuantumStateFidelityConstraint(
         goal=traj.goal[statesymb],
         statedim=traj.dims[statesymb],
         zdim=traj.dim,
-        T=traj.T
+        T=traj.T,
+        kwargs...
     )
 end
 
 
-
-# function FinalStateFidelityConstraint(
-#     val::Float64,
-#     statesymb::Symbol,
-#     statedim::Int;
-#     fidelity_function::Function=fidelity
-# )
-#     return FinalFidelityConstraint(;
-#         fidelity_function=fidelity_function,
-#         value=val,
-#         statesymb=statesymb,
-#         statedim=statedim
-#     )
-# end
-
 """
     ComplexModulusContraint(<keyword arguments>)
 

src/dynamics.jl

@@ -199,7 +199,7 @@ end
 function QuantumDynamics(
     integrators::Vector{<:AbstractIntegrator},
     traj::NamedTrajectory;
-    hessian_approximation=false,
+    eval_hessian=true,
     jacobian_structure=true,
     verbose=false
 )
@@ -235,10 +235,10 @@ function QuantumDynamics(
 
     ∂f = dynamics_jacobian(integrators, traj)
 
-    if hessian_approximation
-        μ∂²f = nothing
-    else
+    if eval_hessian
         μ∂²f = dynamics_hessian_of_lagrangian(integrators, traj)
+    else
+        μ∂²f = nothing
     end
 
     if verbose
@@ -247,13 +247,7 @@ function QuantumDynamics(
 
     dynamics_dim = dim(integrators)
 
-    if hessian_approximation
-        ∂f_structure, ∂F_structure = dynamics_structure(∂f, traj, dynamics_dim;
-            verbose=verbose,
-            jacobian=jacobian_structure,
-        )
-        μ∂²F_structure = nothing
-    else
+    if eval_hessian
         ∂f_structure, ∂F_structure, μ∂²f_structure, μ∂²F_structure =
             dynamics_structure(∂f, μ∂²f, traj, dynamics_dim;
                 verbose=verbose,
@@ -263,6 +257,12 @@ function QuantumDynamics(
                 )
             )
         μ∂²f_nnz = length(μ∂²f_structure)
+    else
+        ∂f_structure, ∂F_structure = dynamics_structure(∂f, traj, dynamics_dim;
+            verbose=verbose,
+            jacobian=jacobian_structure,
+        )
+        μ∂²F_structure = nothing
     end
 
     ∂f_nnz = length(∂f_structure)
@@ -294,9 +294,7 @@ function QuantumDynamics(
         return ∂s
     end
 
-    if hessian_approximation
-        μ∂²F = nothing
-    else
+    if eval_hessian
         @views μ∂²F = (Z⃗::AbstractVector{<:Real}, μ⃗::AbstractVector{<:Real}) -> begin
             μ∂²s = Vector{eltype(Z⃗)}(undef, length(μ∂²F_structure))
             Threads.@threads for t = 1:traj.T-1
@@ -310,7 +308,10 @@ function QuantumDynamics(
             end
             return μ∂²s
         end
+    else
+        μ∂²F = nothing
     end
+
     return QuantumDynamics(
         integrators,
         F,

src/embedded_operators.jl

@@ -54,10 +54,18 @@ end
 EmbeddedOperator(op::Matrix{<:Number}, subspace_indices::AbstractVector{Int}, levels::Int) =
     EmbeddedOperator(op, subspace_indices, [levels])
 
+function embed(matrix::Matrix{ComplexF64}, op::EmbeddedOperator)
+    return embed(matrix, op.subspace_indices, prod(op.subsystem_levels))
+end  
+
 function unembed(op::EmbeddedOperator)::Matrix{ComplexF64}
     return op.operator[op.subspace_indices, op.subspace_indices]
 end
 
+function unembed(matrix::AbstractMatrix, op::EmbeddedOperator)
+    return matrix[op.subspace_indices, op.subspace_indices]
+end
+
 Base.size(op::EmbeddedOperator) = size(op.operator)
 Base.size(op::EmbeddedOperator, dim::Union{Int, Nothing}) = size(op.operator, dim)
 

src/evaluators.jl

@@ -26,8 +26,8 @@ mutable struct PicoEvaluator <: MOI.AbstractNLPEvaluator
         trajectory::NamedTrajectory,
         objective::Objective,
         dynamics::QuantumDynamics,
-        nonlinear_constraints::Vector{<:NonlinearConstraint},
-        eval_hessian::Bool
+        nonlinear_constraints::Vector{<:NonlinearConstraint};
+        eval_hessian::Bool=true
     )
         n_dynamics_constraints = dynamics.dim * (trajectory.T - 1)
         n_nonlinear_constraints = sum(con.dim for con ∈ nonlinear_constraints; init=0)

src/integrators/_integrator_utils.jl

@@ -1,5 +1,5 @@
-# G(a) helper function
-function G(
+# G_bilinear(a) helper function
+function G_bilinear(
     a::AbstractVector,
     G_drift::AbstractMatrix,
     G_drives::AbstractVector{<:AbstractMatrix}

src/integrators/_integrators.jl

@@ -35,6 +35,7 @@ using TrajectoryIndexingUtils
 using LinearAlgebra
 using SparseArrays
 using ForwardDiff
+using TestItemRunner
 
 abstract type AbstractIntegrator end