Merge pull request #83 from ytdHuang/compat/QT

Compat with `QuantumToolbox v0.13`
qutip · Sep 8, 2024 · aef03cf · aef03cf
2 parents 322f8f0 + bdf9f90
commit aef03cf
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diff --git a/.github/workflows/Runtests.yml b/.github/workflows/Runtests.yml
@@ -38,8 +38,8 @@ jobs:
       matrix:
         # for core tests (latest and oldest supported versions)
         julia-version:
-          - '1.9'  # oldest
-          - '1'    # latest
+          - '1.10'  # oldest
+        #  - '1'    # latest
         os:
           - ubuntu-latest
           - windows-latest
@@ -50,14 +50,14 @@ jobs:
 
         include:
           # for core tests on macOS
-          - julia-version: '1.9' # oldest
-            os: 'macOS-latest'
-            arch: 'arm64'
-            group: 'Core'
-          - julia-version: '1'   # latest
+          - julia-version: '1.10' # oldest
             os: 'macOS-latest'
             arch: 'arm64'
             group: 'Core'
+          # - julia-version: '1'    # latest
+          #   os: 'macOS-latest'
+          #   arch: 'arm64'
+          #   group: 'Core'
 
           # for core tests (intermediate versions)
           #- julia-version: '1.x'

diff --git a/Project.toml b/Project.toml
@@ -1,21 +1,24 @@
 name = "HierarchicalEOM"
 uuid = "a62dbcb7-80f5-4d31-9a88-8b19fd92b128"
 authors = ["Yi-Te Huang <[email protected]>"]
-version = "2.0.0"
+version = "2.0.1"
 
 [deps]
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 FastExpm = "7868e603-8603-432e-a1a1-694bd70b01f2"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
-OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
+OrdinaryDiffEqCore = "bbf590c4-e513-4bbe-9b18-05decba2e5d8"
+OrdinaryDiffEqLowOrderRK = "1344f307-1e59-4825-a18e-ace9aa3fa4c6"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 QuantumToolbox = "6c2fb7c5-b903-41d2-bc5e-5a7c320b9fab"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
+SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 SciMLOperators = "c0aeaf25-5076-4817-a8d5-81caf7dfa961"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
 
 [weakdeps]
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
@@ -30,15 +33,18 @@ FastExpm = "1.1"
 JLD2 = "0.4.31 - 0.4"
 LinearAlgebra = "<0.0.1, 1"
 LinearSolve = "2.4.2 - 2"
-OrdinaryDiffEq = "6.53.4 - 6"
+OrdinaryDiffEqCore = "1"
+OrdinaryDiffEqLowOrderRK = "1"
 Pkg = "<0.0.1, 1"
 ProgressMeter = "1.7"
-QuantumToolbox = "0.12"
+QuantumToolbox = "0.13"
 Reexport = "1"
-SciMLOperators = "0.3.5"
+SciMLBase = "2"
+SciMLOperators = "0.3"
 SparseArrays = "<0.0.1, 1"
+StaticArraysCore = "1"
 Test = "<0.0.1, 1"
-julia = "1.9"
+julia = "1.10"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

diff --git a/README.md b/README.md
@@ -39,17 +39,19 @@
 ![](./docs/src/assets/heom_ecosystem.jpeg)
 
 ## Installation
+
+> **_NOTE:_**  `QuantumToolbox.jl` requires `Julia 1.10+`.
+
 To install `HierarchicalEOM.jl`, run the following commands inside Julia's interactive session (also known as REPL):
 ```julia
 using Pkg
 Pkg.add("HierarchicalEOM")
 ```
 Alternatively, this can also be done in Julia's [Pkg REPL](https://julialang.github.io/Pkg.jl/v1/getting-started/) by pressing the key `]` in the REPL to use the package mode, and then type the following command:
 ```julia-REPL
-(1.9) pkg> add HierarchicalEOM
+(1.10) pkg> add HierarchicalEOM
 ```
 More information about `Julia`'s package manager can be found at [`Pkg.jl`](https://julialang.github.io/Pkg.jl/v1/).  
-`HierarchicalEOM.jl` now requires Julia 1.9 or higher. Installing it on an older version of Julia will result in many errors.
 
 To load the package and check the version information, use the command:
 ```julia

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -20,4 +20,4 @@ Literate = "2"
 OrdinaryDiffEq = "6"
 Pardiso = "0.5"
 Plots = "1"
-QuantumToolbox = "0"
+QuantumToolbox = "0.13"
diff --git a/docs/make.jl b/docs/make.jl
@@ -19,101 +19,89 @@ const MathEngine = MathJax3(
             "tags" => "ams",
             "packages" => ["base", "ams", "autoload", "physics"],
         ),
-    )
+    ),
 )
 
 # clean and rebuild the output markdown directory for examples
 doc_output_path = abspath(joinpath(@__DIR__, "src", "examples"))
 if isdir(doc_output_path)
-    rm(doc_output_path, recursive=true)
+    rm(doc_output_path, recursive = true)
 end
 mkdir(doc_output_path)
 
 # Generate page: Quick Start
-QS_source_file = abspath(joinpath(@__DIR__, "..",  "examples", "quick_start.jl"))
+QS_source_file = abspath(joinpath(@__DIR__, "..", "examples", "quick_start.jl"))
 Literate.markdown(QS_source_file, doc_output_path)
 
 # Generate example pages
-EXAMPLES = [
-    "cavityQED",
-    "dynamical_decoupling",
-    "SIAM",
-    "electronic_current"
-]
-EX_source_files = [abspath(joinpath(@__DIR__, "..",  "examples", "$(ex_name).jl")) for ex_name in EXAMPLES]
+EXAMPLES = ["cavityQED", "dynamical_decoupling", "SIAM", "electronic_current"]
+EX_source_files = [abspath(joinpath(@__DIR__, "..", "examples", "$(ex_name).jl")) for ex_name in EXAMPLES]
 EX_output_files = ["examples/$(ex_name).md" for ex_name in EXAMPLES]
 for file in EX_source_files
     Literate.markdown(file, doc_output_path)
 end
 
 # Generate benchmark pages
-BENCHMARKS = [
-    "benchmark_ODE_solvers",
-    "benchmark_LS_solvers"
-]
-BM_source_files = [abspath(joinpath(@__DIR__, "..",  "examples", "$(bm_name).jl")) for bm_name in BENCHMARKS]
+BENCHMARKS = ["benchmark_ODE_solvers", "benchmark_LS_solvers"]
+BM_source_files = [abspath(joinpath(@__DIR__, "..", "examples", "$(bm_name).jl")) for bm_name in BENCHMARKS]
 BM_output_files = ["examples/$(bm_name).md" for bm_name in BENCHMARKS]
 for file in BM_source_files
     Literate.markdown(file, doc_output_path)
 end
 
 const PAGES = Any[
-    "Home" => Any[
-        "Introduction" => "index.md",
-        "Installation" => "install.md",
-        "Quick Start"  => "examples/quick_start.md",
-        "Cite HierarchicalEOM.jl" => "cite.md"
+    "Home"=>Any[
+        "Introduction"=>"index.md",
+        "Installation"=>"install.md",
+        "Quick Start"=>"examples/quick_start.md",
+        "Cite HierarchicalEOM.jl"=>"cite.md",
     ],
-    "Manual" => Any[
-        "Bosonic Bath" => Any[
-            "Introduction" => "bath_boson/bosonic_bath_intro.md",
-            "Drude-Lorentz Spectral Density" => "bath_boson/Boson_Drude_Lorentz.md"
-        ],
-        "Bosonic Bath (RWA)" => Any[
-            "Introduction" => "bath_boson_RWA/bosonic_bath_RWA_intro.md"
+    "Manual"=>Any[
+        "Bosonic Bath"=>Any[
+            "Introduction"=>"bath_boson/bosonic_bath_intro.md",
+            "Drude-Lorentz Spectral Density"=>"bath_boson/Boson_Drude_Lorentz.md",
         ],
-        "Fermionic Bath" => Any[
-            "Introduction" => "bath_fermion/fermionic_bath_intro.md",
-            "Lorentz Spectral Density" => "bath_fermion/Fermion_Lorentz.md"
+        "Bosonic Bath (RWA)"=>Any["Introduction"=>"bath_boson_RWA/bosonic_bath_RWA_intro.md"],
+        "Fermionic Bath"=>Any[
+            "Introduction"=>"bath_fermion/fermionic_bath_intro.md",
+            "Lorentz Spectral Density"=>"bath_fermion/Fermion_Lorentz.md",
         ],
-        "Auxiliary Density Operators" => "ADOs.md",
-        "HEOMLS Matrices" => Any[
-            "Introduction" => "heom_matrix/HEOMLS_intro.md",
-            "HEOMLS for Schrödinger Equation" => "heom_matrix/schrodinger_eq.md",
-            "HEOMLS for Bosonic Bath" => "heom_matrix/M_Boson.md",
-            "HEOMLS for Fermionic Bath" => "heom_matrix/M_Fermion.md",
-            "HEOMLS for Bosonic and Fermionic Bath" => "heom_matrix/M_Boson_Fermion.md",
-            "HEOMLS for Master Equation" => "heom_matrix/master_eq.md",
+        "Auxiliary Density Operators"=>"ADOs.md",
+        "HEOMLS Matrices"=>Any[
+            "Introduction"=>"heom_matrix/HEOMLS_intro.md",
+            "HEOMLS for Schrödinger Equation"=>"heom_matrix/schrodinger_eq.md",
+            "HEOMLS for Bosonic Bath"=>"heom_matrix/M_Boson.md",
+            "HEOMLS for Fermionic Bath"=>"heom_matrix/M_Fermion.md",
+            "HEOMLS for Bosonic and Fermionic Bath"=>"heom_matrix/M_Boson_Fermion.md",
+            "HEOMLS for Master Equation"=>"heom_matrix/master_eq.md",
         ],
-        "Parity Support" => "Parity.md",
-        "Hierarchy Dictionary" => "hierarchy_dictionary.md",
-        "Time Evolution" => "time_evolution.md",
-        "Stationary State" => "stationary_state.md",
-        "Spectrum" => "spectrum.md",
-        "Examples" => EX_output_files,
-        "Benchmark Solvers" => BM_output_files,
-        "Extensions" => Any[
-            "CUDA.jl" => "extensions/CUDA.md"
-        ]
+        "Parity Support"=>"Parity.md",
+        "Hierarchy Dictionary"=>"hierarchy_dictionary.md",
+        "Time Evolution"=>"time_evolution.md",
+        "Stationary State"=>"stationary_state.md",
+        "Spectrum"=>"spectrum.md",
+        "Examples"=>EX_output_files,
+        "Benchmark Solvers"=>BM_output_files,
+        "Extensions"=>Any["CUDA.jl"=>"extensions/CUDA.md"],
     ],
-    "Library API" => "libraryAPI.md"
+    "Library API"=>"libraryAPI.md",
 ]
 
 makedocs(;
     modules = [HierarchicalEOM],
     authors = "Yi-Te Huang",
     repo = Remotes.GitHub("qutip", "HierarchicalEOM.jl"),
     sitename = "Documentation | HierarchicalEOM.jl",
-    pages  = PAGES,
+    pages = PAGES,
     format = Documenter.HTML(;
         prettyurls = get(ENV, "CI", "false") == "true",
         canonical = "https://qutip.github.io/HierarchicalEOM.jl",
         edit_link = "main",
         mathengine = MathEngine,
-        ansicolor  = true,
+        ansicolor = true,
         size_threshold_ignore = ["libraryAPI.md"],
     ),
-    draft  = DRAFT
+    draft = DRAFT,
 )
 
-deploydocs(; repo="github.com/qutip/HierarchicalEOM.jl", devbranch = "main")
+deploydocs(; repo = "github.com/qutip/HierarchicalEOM.jl", devbranch = "main")
diff --git a/docs/src/install.md b/docs/src/install.md
@@ -8,11 +8,11 @@ Pkg.add("HierarchicalEOM")
 ```
 Alternatively, this can also be done in Julia's [Pkg REPL](https://julialang.github.io/Pkg.jl/v1/getting-started/) by pressing the key `]` in the REPL to use the package mode, and then type the following command:
 ```julia-REPL
-(1.9) pkg> add HierarchicalEOM
+(1.10) pkg> add HierarchicalEOM
 ```
 More information about `Julia`'s package manager can be found at [`Pkg.jl`](https://julialang.github.io/Pkg.jl/v1/).  
-!!! note "Julia 1.9"
-    `HierarchicalEOM.jl` requires Julia 1.9 or higher (we dropped Julia 1.8 since ver.1.12.1)
+!!! note "Julia 1.10"
+    `HierarchicalEOM.jl` requires Julia 1.10 or higher (we dropped Julia 1.9 since ver.2.0.1)
 
 To load the package and check the version information, use the command:
 ```julia

diff --git a/docs/src/libraryAPI.md b/docs/src/libraryAPI.md
@@ -62,7 +62,7 @@ ODD
 HEOMSuperOp
 HEOMSuperOp(op, opParity::AbstractParity, refHEOMLS::AbstractHEOMLSMatrix, mul_basis::AbstractString="L")
 HEOMSuperOp(op, opParity::AbstractParity, refADOs::ADOs, mul_basis::AbstractString="L")
-HEOMSuperOp(op, opParity::AbstractParity, dims::Vector{Int}, N::Int, mul_basis::AbstractString)
+HEOMSuperOp(op, opParity::AbstractParity, dims::SVector, N::Int, mul_basis::AbstractString)
 M_S
 M_S(Hsys::QuantumObject, parity::AbstractParity=EVEN; verbose::Bool=true)
 M_Boson

diff --git a/src/ADOs.jl b/src/ADOs.jl
@@ -23,7 +23,7 @@ end
 """
 struct ADOs
     data::SparseVector{ComplexF64,Int64}
-    dims::Vector{Int}
+    dims::SVector
     N::Int
     parity::AbstractParity
 end
@@ -42,7 +42,7 @@ function ADOs(V::AbstractVector, N::Int, parity::AbstractParity = EVEN)
     d = size(V, 1)
     dim = √(d / N)
     if isinteger(dim)
-        return ADOs(sparsevec(V), [Int(dim)], N, parity)
+        return ADOs(sparsevec(V), SVector{1,Int}(Int(dim)), N, parity)
     else
         error("The dimension of vector is not consistent with the ADOs number \"N\".")
     end

diff --git a/src/Bath.jl b/src/Bath.jl
@@ -218,7 +218,7 @@ end
 struct BosonBath <: AbstractBath
     bath::Vector{AbstractBosonBath}
     op::QuantumObject
-    dims::Vector{Int}
+    dims::SVector
     Nterm::Int
     δ::Number
 end
@@ -364,7 +364,7 @@ A bosonic bath for the real part of bath correlation function ``C^{u=\textrm{R}}
 """
 struct bosonReal <: AbstractBosonBath
     Comm::SparseMatrixCSC{ComplexF64,Int64}
-    dims::Vector{Int}
+    dims::SVector
     η::AbstractVector
     γ::AbstractVector
     Nterm::Int
@@ -406,7 +406,7 @@ A bosonic bath for the imaginary part of bath correlation function ``C^{u=\textr
 struct bosonImag <: AbstractBosonBath
     Comm::SparseMatrixCSC{ComplexF64,Int64}
     anComm::SparseMatrixCSC{ComplexF64,Int64}
-    dims::Vector{Int}
+    dims::SVector
     η::AbstractVector
     γ::AbstractVector
     Nterm::Int
@@ -451,7 +451,7 @@ A bosonic bath which the real part and imaginary part of the bath correlation fu
 struct bosonRealImag <: AbstractBosonBath
     Comm::SparseMatrixCSC{ComplexF64,Int64}
     anComm::SparseMatrixCSC{ComplexF64,Int64}
-    dims::Vector{Int}
+    dims::SVector
     η_real::AbstractVector
     η_imag::AbstractVector
     γ::AbstractVector
@@ -545,7 +545,7 @@ struct bosonAbsorb <: AbstractBosonBath
     spre::SparseMatrixCSC{ComplexF64,Int64}
     spost::SparseMatrixCSC{ComplexF64,Int64}
     CommD::SparseMatrixCSC{ComplexF64,Int64}
-    dims::Vector{Int}
+    dims::SVector
     η::AbstractVector
     γ::AbstractVector
     η_emit::AbstractVector
@@ -606,7 +606,7 @@ struct bosonEmit <: AbstractBosonBath
     spre::SparseMatrixCSC{ComplexF64,Int64}
     spost::SparseMatrixCSC{ComplexF64,Int64}
     CommD::SparseMatrixCSC{ComplexF64,Int64}
-    dims::Vector{Int}
+    dims::SVector
     η::AbstractVector
     γ::AbstractVector
     η_absorb::AbstractVector
@@ -675,7 +675,7 @@ end
 struct FermionBath <: AbstractBath
     bath::Vector{AbstractFermionBath}
     op::QuantumObject
-    dims::Vector{Int}
+    dims::SVector
     Nterm::Int
     δ::Number
 end
@@ -740,7 +740,7 @@ struct fermionAbsorb <: AbstractFermionBath
     spost::SparseMatrixCSC{ComplexF64,Int64}
     spreD::SparseMatrixCSC{ComplexF64,Int64}
     spostD::SparseMatrixCSC{ComplexF64,Int64}
-    dims::Vector{Int}
+    dims::SVector
     η::AbstractVector
     γ::AbstractVector
     η_emit::AbstractVector
@@ -804,7 +804,7 @@ struct fermionEmit <: AbstractFermionBath
     spost::SparseMatrixCSC{ComplexF64,Int64}
     spreD::SparseMatrixCSC{ComplexF64,Int64}
     spostD::SparseMatrixCSC{ComplexF64,Int64}
-    dims::Vector{Int}
+    dims::SVector
     η::AbstractVector
     γ::AbstractVector
     η_absorb::AbstractVector