Support for QuantumOptics.jl

.github/workflows/Runtests.yml

@@ -10,21 +10,30 @@ on:
 
 jobs:
   test:
-    runs-on: ${{ matrix.os }}
+    runs-on: ubuntu-latest
     strategy:
       matrix:
-        julia-version: ['1.8']
-        julia-arch: [x64]
-        os: [ubuntu-latest] # [ubuntu-latest, windows-latest, macOS-latest]
+        group:
+          - Core
+        julia-version:
+          - '1'
+          - '1.8'
+        include:
+          - julia-version: '1'
+            group: 'HierarchicalEOM_QOExt'
     steps:
       - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@latest
+      - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.julia-version }}
       - uses: julia-actions/cache@v1
-      - uses: julia-actions/julia-buildpkg@latest
-      - uses: julia-actions/julia-runtest@latest
-      - uses: julia-actions/julia-processcoverage@latest
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+        env:
+          GROUP: ${{ matrix.group }}
+      - uses: julia-actions/julia-processcoverage@v1
+        with:
+          directories: src,ext
       - uses: codecov/codecov-action@v3
         with:
           file: lcov.info

.github/workflows/documentation.yml

@@ -17,9 +17,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@latest
+      - uses: julia-actions/setup-julia@v1
         with:
-          version: '1.9'
+          version: '1'
       - uses: julia-actions/cache@v1
       - name: Install X Server dependencies
         run: sudo apt-get update && sudo apt-get install -y xorg-dev mesa-utils xvfb libgl1 freeglut3-dev libxrandr-dev libxinerama-dev libxcursor-dev libxi-dev libxext-dev
@@ -29,4 +29,11 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
-        run: DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24' julia --project=docs/ docs/make.jl
+        run: DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24' julia --project=docs/ --code-coverage=user docs/make.jl
+      - uses: julia-actions/julia-processcoverage@v1
+        with:
+          directories: src
+      - uses: codecov/codecov-action@v3
+        with:
+          file: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}

Project.toml

@@ -13,11 +13,18 @@ OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
+QuantumOptics = "6e0679c1-51ea-5a7c-ac74-d61b76210b0c"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SciMLOperators = "c0aeaf25-5076-4817-a8d5-81caf7dfa961"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 SteadyStateDiffEq = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
 
+[weakdeps]
+QuantumOptics = "6e0679c1-51ea-5a7c-ac74-d61b76210b0c"
+
+[extensions]
+HierarchicalEOM_QOExt = "QuantumOptics"
+
 [compat]
 Crayons = "4.1"
 FastExpm = "1.1.0"

docs/make.jl

@@ -50,11 +50,17 @@ const PAGES = Any[
         "Cite HierarchicalEOM" => "cite.md"
     ],
     "Manual" => Any[
-        "Bosonic Bath" => "bosonic_bath.md",
-        "Fermionic Bath" => "fermionic_bath.md",
+        "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"
+        ],
         "Auxiliary Density Operators" => "ADOs.md",
         "HEOMLS Matrices" => Any[
-            "Introduction" => "heom_matrix/intro.md",
+            "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",
@@ -66,7 +72,10 @@ const PAGES = Any[
         "Stationary State" => "stationary_state.md",
         "Spectrum" => "spectrum.md",
         "Examples" => EX_output_files,
-        "Benchmark Solvers" => BM_output_files
+        "Benchmark Solvers" => BM_output_files,
+        "Extensions" => Any[
+            "QuantumOptics.jl" => "extensions/QuantumOptics.md"
+        ]
     ],
     "Library API" => "libraryAPI.md"
 ]

docs/src/bath_boson/Boson_Drude_Lorentz.md

@@ -0,0 +1,53 @@
+# [Drude-Lorentz Spectral Density](@id Boson-Drude-Lorentz)
+```math
+J(\omega)=\frac{4\Delta W\omega}{\omega^2+W^2}
+```
+Here, ``\Delta`` represents the coupling strength between system and the bosonic environment with band-width ``W``.
+
+## Matsubara Expansion
+With Matsubara Expansion, the correlation function can be analytically solved and expressed as follows:
+```math
+C(t_1, t_2)=\sum_{l=1}^{\infty} \eta_l \exp(-\gamma_l (t_1-t_2))
+```
+with
+```math
+\begin{aligned}
+\gamma_{1} &= W,\\
+\eta_{1} &= \Delta W\left[-i+\cot\left(\frac{W}{2 k_B T}\right)\right],\\
+\gamma_{l\neq 1} &= 2\pi l k_B T,\\
+\eta_{l\neq 1} &= -2 k_B T \cdot \frac{2\Delta W \cdot \gamma_l}{-\gamma_l^2 + W^2}.
+\end{aligned}
+```
+This can be constructed by the built-in function [`Boson_DrudeLorentz_Matsubara`](@ref):
+```julia
+Vs # coupling operator
+Δ  # coupling strength
+W  # band-width  of the environment
+kT # the product of the Boltzmann constant k and the absolute temperature T
+N  # Number of exponential terms
+bath = Boson_DrudeLorentz_Matsubara(Vs, Δ, W, kT, N - 1)
+```
+
+## Padé Expansion
+With Padé Expansion, the correlation function can be analytically solved and expressed as the following exponential terms:
+```math
+C(t_1, t_2)=\sum_{l=1}^{\infty} \eta_l \exp(-\gamma_l (t_1-t_2))
+```
+with
+```math
+\begin{aligned}
+\gamma_{1} &= W,\\
+\eta_{1} &= \Delta W\left[-i+\cot\left(\frac{W}{2 k_B T}\right)\right],\\
+\gamma_{l\neq 1} &= \zeta_l k_B T,\\
+\eta_{l\neq 1} &= -2 \kappa_l k_B T \cdot \frac{2\Delta W \cdot \zeta_l k_B T}{-(\zeta_l k_B T)^2 + W^2},
+\end{aligned}
+```
+where the parameters ``\kappa_l`` and ``\zeta_l`` are described in [J. Chem. Phys. 134, 244106 (2011)](https://doi.org/10.1063/1.3602466). This can be constructed by the built-in function [`Boson_DrudeLorentz_Pade`](@ref):
+```julia
+Vs # coupling operator
+Δ  # coupling strength
+W  # band-width  of the environment
+kT # the product of the Boltzmann constant k and the absolute temperature T
+N  # Number of exponential terms
+bath = Boson_DrudeLorentz_Pade(Vs, Δ, W, kT, N - 1)
+```

docs/src/bosonic_bath.md → docs/src/bath_boson/bosonic_bath_intro.md

@@ -1,5 +1,5 @@
 # [Bosonic Bath](@id doc-Bosonic-Bath)
-## [Introduction](@id Bosonic-Bath-Introduction)
+## [Overview](@id Bosonic-Bath-Overview)
 The [`BosonBath`](@ref) object describes the interaction between the system (``s``) and a exterior bosonic environment (``b``), which can be modeled by
 ```math
 H_{sb}=V_{s}\sum_k g_k (b_k + b_k^\dagger),
@@ -19,17 +19,15 @@ C(t_1, t_2)=\sum_i \eta_i e^{-\gamma_i (t_1-t_2)}.
 ```
 This allows us to define an iterative procedure which leads to the hierarchical equations of motion (HEOM).
 
-## Methods
-
-### Construct BosonBath (with real and imaginary parts are combined)
+## Construct BosonBath (with real and imaginary parts are combined)
 One can construct the [`BosonBath`](@ref) object with the coupling operator `Vs::AbstractMatrix` and the two lists `η::AbstractVector` and `γ::AbstractVector` which corresponds to the exponential terms ``\{\eta_i\}_i`` and ``\{\gamma_i\}_i``, respectively.
 ```julia
 bath = BosonBath(Vs, η, γ)
 ```
 !!! warning "Warning"
     Here, the length of `η` and `γ` should be the same.
 
-### Construct BosonBath (with real and imaginary parts are separated)
+## Construct BosonBath (with real and imaginary parts are separated)
 When ``\gamma_i \neq \gamma_i^*``, a closed form for the HEOM can be obtained by further decomposing ``C(t_1, t_2)`` into its real (R) and imaginary (I) parts as
 ```math
 C(t_1, t_2)=\sum_{u=\textrm{R},\textrm{I}}(\delta_{u, \textrm{R}} + i\delta_{u, \textrm{I}})C^{u}(t_1, t_2)
@@ -48,7 +46,7 @@ Here, `η_real::AbstractVector`, `γ_real::AbstractVector`, `η_imag::AbstractVe
 !!! note "Note"
     Instead of analytically solving the correlation function ``C(t_1, t_2)`` to obtain a sum of exponential terms, one can also use the built-in functions (for different spectral densities ``J(\omega)`` and spectral decomposition methods, which have been analytically solved by the developers already) listed in the end of this page. 
 
-### Print Bosonic Bath
+## Print Bosonic Bath
 One can check the information of the [`BosonBath`](@ref) by the `print` function, for example:
 ```julia
 print(bath)
@@ -57,14 +55,14 @@ print(bath)
 BosonBath object with (system) dim = 2 and 4 exponential-expansion terms
 ```
 
-### Calculate the correlation function
+## Calculate the correlation function
 To check whether the exponential terms in the [`BosonBath`](@ref) is correct or not, one can call [`C(bath::BosonBath, tlist::AbstractVector)`](@ref) to calculate the correlation function ``C(t)``, where ``t=t_1-t_2``:
 ```julia
 c_list = C(bath, tlist)
 ```
 Here, `c_list` is a list which contains the value of ``C(t)`` corresponds to the given time series `tlist`.
 
-### Methods for Exponent
+## Exponent
 `HierarchicalEOM.jl` also supports users to access the specific exponential term with brakets `[]`. This returns an [`Exponent`](@ref) object, which contains the corresponding value of ``\eta_i`` and ``\gamma_i``:
 ```julia
 e = bath[2] # the 2nd-term
@@ -74,6 +72,11 @@ print(e)
 Bath Exponent with types = "bRI", operator size = (2, 2), η = 1.5922874021206546e-6 + 0.0im, γ = 0.3141645167860635 + 0.0im.
 ```
 
+The different types of the (bosonic-bath) [`Exponent`](@ref):
+ - `"bR"` : from real part of bosonic correlation function ``C^{u=\textrm{R}}(t_1, t_2)``
+ - `"bI"` : from imaginary part of bosonic correlation function ``C^{u=\textrm{I}}(t_1, t_2)``
+ - `"bRI"` : from combined (real and imaginary part) bosonic bath correlation function ``C(t_1, t_2)``
+
 One can even obtain the [`Exponent`](@ref) with iterative method:
 ```julia
 for e in bath
@@ -88,64 +91,4 @@ Bath Exponent with types = "bRI", operator size = (2, 2), η = 1.592287402120654
 Bath Exponent with types = "bRI", operator size = (2, 2), η = 1.0039844180003819e-6 + 0.0im, γ = 0.6479143347831898 + 0.0im.
 
 Bath Exponent with types = "bRI", operator size = (2, 2), η = 3.1005439801387293e-6 + 0.0im, γ = 1.8059644711829272 + 0.0im.
-```
-
-### Types of Exponent
-The different types of the (bosonic-bath) [`Exponent`](@ref):
- - `"bR"` : from real part of bosonic correlation function ``C^{u=\textrm{R}}(t_1, t_2)``
- - `"bI"` : from imaginary part of bosonic correlation function ``C^{u=\textrm{I}}(t_1, t_2)``
- - `"bRI"` : from combined (real and imaginary part) bosonic bath correlation function ``C(t_1, t_2)``
-
-## [Drude-Lorentz Spectral Density](@id Boson-Drude-Lorentz)
-```math
-J(\omega)=\frac{4\Delta W\omega}{\omega^2+W^2}
-```
-Here, ``\Delta`` represents the coupling strength between system and the bosonic environment with band-width ``W``.
-
-### Matsubara Expansion
-With Matsubara Expansion, the correlation function can be analytically solved and expressed as follows:
-```math
-C(t_1, t_2)=\sum_{l=1}^{\infty} \eta_l \exp(-\gamma_l (t_1-t_2))
-```
-with
-```math
-\begin{aligned}
-\gamma_{1} &= W,\\
-\eta_{1} &= \Delta W\left[-i+\cot\left(\frac{W}{2 k_B T}\right)\right],\\
-\gamma_{l\neq 1} &= 2\pi l k_B T,\\
-\eta_{l\neq 1} &= -2 k_B T \cdot \frac{2\Delta W \cdot \gamma_l}{-\gamma_l^2 + W^2}.
-\end{aligned}
-```
-This can be constructed by the built-in function [`Boson_DrudeLorentz_Matsubara`](@ref):
-```julia
-Vs # coupling operator
-Δ  # coupling strength
-W  # band-width  of the environment
-kT # the product of the Boltzmann constant k and the absolute temperature T
-N  # Number of exponential terms
-bath = Boson_DrudeLorentz_Matsubara(Vs, Δ, W, kT, N - 1)
-```
-
-### Padé Expansion
-With Padé Expansion, the correlation function can be analytically solved and expressed as the following exponential terms:
-```math
-C(t_1, t_2)=\sum_{l=1}^{\infty} \eta_l \exp(-\gamma_l (t_1-t_2))
-```
-with
-```math
-\begin{aligned}
-\gamma_{1} &= W,\\
-\eta_{1} &= \Delta W\left[-i+\cot\left(\frac{W}{2 k_B T}\right)\right],\\
-\gamma_{l\neq 1} &= \zeta_l k_B T,\\
-\eta_{l\neq 1} &= -2 \kappa_l k_B T \cdot \frac{2\Delta W \cdot \zeta_l k_B T}{-(\zeta_l k_B T)^2 + W^2},
-\end{aligned}
-```
-where the parameters ``\kappa_l`` and ``\zeta_l`` are described in [J. Chem. Phys. 134, 244106 (2011)](https://doi.org/10.1063/1.3602466). This can be constructed by the built-in function [`Boson_DrudeLorentz_Pade`](@ref):
-```julia
-Vs # coupling operator
-Δ  # coupling strength
-W  # band-width  of the environment
-kT # the product of the Boltzmann constant k and the absolute temperature T
-N  # Number of exponential terms
-bath = Boson_DrudeLorentz_Pade(Vs, Δ, W, kT, N - 1)
 ```

docs/src/bath_fermion/Fermion_Lorentz.md

@@ -0,0 +1,57 @@
+# [Lorentz Spectral Density](@id doc-Fermion-Lorentz)
+```math
+J(\omega)=\frac{\Gamma W^2}{(\omega-\mu)^2+W^2}
+```
+Here, ``\Gamma`` represents the coupling strength between system and the fermionic environment with chemical potential ``\mu`` and band-width ``W``.
+
+## Matsubara Expansion
+With Matsubara Expansion, the correlation function can be analytically solved and expressed as follows:
+```math
+C^{\nu}(t_1, t_2)=\sum_{l=1}^{\infty} \eta_l^\nu \exp(-\gamma_l^\nu (t_1-t_2))
+```
+with
+```math
+\begin{aligned}
+\gamma_{1}^{\nu} &= W-\nu i \mu,\\
+\eta_{1}^{\nu} &= \frac{\Gamma W}{2} f\left(\frac{iW}{k_B T}\right),\\
+\gamma_{l\neq 1}^{\nu} &= \zeta_l k_B T - \nu i \mu,\\
+\eta_{l\neq 1}^{\nu} &= -i k_B T \cdot \frac{\Gamma W^2}{-(\zeta_l k_B T)^2+W^2},\\
+f(x) &= \{\exp(x) + 1\}^{-1},
+\end{aligned}
+```
+where ``\zeta_l=(2 l - 1)\pi``. This can be constructed by the built-in function [`Fermion_Lorentz_Matsubara`](@ref):
+```julia
+ds # coupling operator
+Γ  # coupling strength
+μ  # chemical potential of the environment
+W  # band-width  of the environment
+kT # the product of the Boltzmann constant k and the absolute temperature T
+N  # Number of exponential terms for each correlation functions (C^{+} and C^{-})
+bath = Fermion_Lorentz_Matsubara(ds, Γ, μ, W, kT, N - 1)
+```
+
+## Padé Expansion
+With Padé Expansion, the correlation function can be analytically solved and expressed as the following exponential terms:
+```math
+C^\nu(t_1, t_2)=\sum_{l=1}^{\infty} \eta_l^\nu \exp(-\gamma_l^\nu (t_1-t_2))
+```
+with
+```math
+\begin{aligned}
+\gamma_{1}^{\nu} &= W-\nu i \mu,\\
+\eta_{1}^{\nu} &= \frac{\Gamma W}{2} f\left(\frac{iW}{k_B T}\right),\\
+\gamma_{l\neq 1}^{\nu} &= \zeta_l k_B T - \nu i \mu,\\
+\eta_{l\neq 1}^{\nu} &= -i \kappa_l k_B T \cdot \frac{\Gamma W^2}{-(\zeta_l k_B T)^2+W^2},\\
+f(x) &= \frac{1}{2}-\sum_{l=2}^{N} \frac{2\kappa_l x}{x^2+\zeta_l^2},
+\end{aligned}
+```
+where the parameters ``\kappa_l`` and ``\zeta_l`` are described in [J. Chem. Phys. 134, 244106 (2011)](https://doi.org/10.1063/1.3602466) and ``N`` represents the number of exponential terms for ``C^{\nu=\pm}``. This can be constructed by the built-in function [`Fermion_Lorentz_Pade`](@ref):
+```julia
+ds # coupling operator
+Γ  # coupling strength
+μ  # chemical potential of the environment
+W  # band-width  of the environment
+kT # the product of the Boltzmann constant k and the absolute temperature T
+N  # Number of exponential terms for each correlation functions (C^{+} and C^{-})
+bath = Fermion_Lorentz_Pade(ds, Γ, μ, W, kT, N - 1)
+```