Bump version to v2.9.0 to align with main package (#211)

Author: ytdHuang

Project.toml

@@ -1,7 +1,7 @@
 name = "HierarchicalEOM"
 uuid = "a62dbcb7-80f5-4d31-9a88-8b19fd92b128"
+version = "2.9.0"
 authors = ["Yi-Te Huang"]
-version = "2.8.0"
 
 [deps]
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
@@ -12,6 +12,7 @@ LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
 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"
@@ -35,7 +36,8 @@ LinearSolve = "2.4.2 - 3"
 OrdinaryDiffEqCore = "1"
 OrdinaryDiffEqLowOrderRK = "1"
 Pkg = "1"
-QuantumToolbox = "0.37"
+ProgressMeter = "1.11.0"
+QuantumToolbox = "0.38.1"
 Reexport = "1"
 SciMLBase = "2.105"
 SciMLOperators = "1.4"

docs/src/spectrum.md

@@ -17,7 +17,7 @@ The output of the above listed functions will always be in the type of `Vector{F
 
 ## Common and optional parameters
 Furthermore, there are two common optional parameters for all the functions provided below:
-- `verbose::Bool` : To display verbose output and progress bar during the process or not. Defaults to `true`.
+- `progress_bar::Union{Val,Bool}`: Whether to show the progress bar. Defaults to `Val(true)`.
 - `filename::String` : If filename was specified, the value of spectrum for each ω will be saved into the file "filename.txt" during the solving process.
 
 If the filename is specified, the function will automatically save (update) the value (together with a comma behind it) to a new line in the file (with ".txt" behind the filename) once it obtains the solution of each specified ``\omega``. For example, if you specify `filename="test"` and `ωlist=0:1:5`, you will obtain a file `test.txt` where each line in this file (as shown below) is the result of spectrum corresponding to the given `ωlist`:

docs/src/time_evolution.md

@@ -129,7 +129,7 @@ To construct the propagator, we wrap the function in the package [`fastExpm.jl`]
 See the docstring of this method:  
 
 ```@docs
-HEOMsolve(M::AbstractHEOMLSMatrix ,ρ0::T_state, Δt::Real, steps::Int; e_ops::Union{Nothing,AbstractVector} = nothing, threshold = 1.0e-6, nonzero_tol = 1.0e-14, verbose::Bool = true) where {T_state<:Union{QuantumObject,ADOs}}
+HEOMsolve(M::AbstractHEOMLSMatrix ,ρ0::T_state, Δt::Real, steps::Int; e_ops::Union{Nothing,AbstractVector} = nothing, threshold = 1.0e-6, nonzero_tol = 1.0e-14, progress_bar::Union{Val,Bool} = Val(true)) where {T_state<:Union{QuantumObject,ADOs}}
 ```
 
 ```julia

src/HierarchicalEOM.jl

@@ -60,6 +60,7 @@ import Base.Threads: @threads, nthreads, Channel
 import FastExpm: fastExpm
 import IncompleteLU: ilu
 import Pkg
+import ProgressMeter: Progress, next!
 
 # Basic functions
 include("HeomBase.jl")

src/density_of_states.jl

@@ -1,7 +1,7 @@
 export DensityOfStates
 
 @doc raw"""
-    DensityOfStates(M, ρ, d_op, ωlist; alg, verbose, filename, kwargs...)
+    DensityOfStates(M, ρ, d_op, ωlist; alg, progress_bar, filename, kwargs...)
 Calculate density of states for the fermionic system in frequency domain.
 
 ```math
@@ -14,7 +14,7 @@ Calculate density of states for the fermionic system in frequency domain.
 - `d_op::QuantumObject` : The annihilation operator (``d`` as shown above) acting on the fermionic system.
 - `ωlist::AbstractVector` : the specific frequency points to solve.
 - `alg::SciMLLinearSolveAlgorithm` : The solving algorithm in package `LinearSolve.jl`. Default to `KrylovJL_GMRES(rtol=1e-12, atol=1e-14)`.
-- `verbose::Bool` : To display verbose output and progress bar during the process or not. Defaults to `true`.
+- `progress_bar::Union{Val,Bool}`: Whether to show the progress bar. Defaults to `Val(true)`.
 - `filename::String` : If filename was specified, the value of spectrum for each ω will be saved into the file "filename.txt" during the solving process.
 - `kwargs` : The keyword arguments for `LinearProblem`.
 
@@ -30,24 +30,22 @@ Calculate density of states for the fermionic system in frequency domain.
     d_op::QuantumObject,
     ωlist::AbstractVector;
     alg::SciMLLinearSolveAlgorithm = KrylovJL_GMRES(rtol = 1e-12, atol = 1e-14),
-    verbose::Bool = true,
+    progress_bar::Union{Val,Bool} = Val(true),
     filename::String = "",
     kwargs...,
 )
     haskey(kwargs, :solver) &&
-        error("The keyword argument `solver` for DensityOfStates has been deprecated, please use `alg` instead.")
+        error("The keyword argument `solver` for DensityOfStates is deprecated, use `alg` instead.")
+    haskey(kwargs, :verbose) &&
+        error("The keyword argument `verbose` for DensityOfStates is deprecated, use `progress_bar` instead.")
 
     # check M
-    if M.parity == EVEN
-        error("The HEOMLS matrix M must be acting on `ODD`-parity operators.")
-    end
+    (M.parity == EVEN) && error("The HEOMLS matrix M must be acting on `ODD`-parity operators.")
 
     # Handle ρ
     if typeof(ρ) == ADOs  # ρ::ADOs
         ados = ρ
-        if ados.parity != EVEN
-            error("The parity of ρ must be `EVEN`.")
-        end
+        (ados.parity != EVEN) && error("The parity of ρ must be `EVEN`.")
     else
         ados = ADOs(ρ, M.N)
     end
@@ -75,45 +73,36 @@ Calculate density of states for the fermionic system in frequency domain.
     Length = length(ωList)
     Aω = Vector{Float64}(undef, Length)
 
-    if verbose
-        print("Calculating density of states in frequency domain...\n")
-        flush(stdout)
-    end
-    prog = ProgressBar(Length; enable = verbose)
+    progr = Progress(
+        Length;
+        enabled = getVal(progress_bar),
+        desc = "[DensityOfStates] ",
+        QuantumToolbox.settings.ProgressMeterKWARGS...,
+    )
     i = convert(ElType, 1im)
     I_total = I(size(M, 1))
-    cache_m = cache_p = nothing
-    for ω in ωList
-        Iω = i * ω * I_total
-
-        if prog.counter[] == 0
-            cache_m = init(LinearProblem(M.data.A - Iω, b_m), alg, kwargs...)
-            sol_m = solve!(cache_m)
-
-            cache_p = init(LinearProblem(M.data.A + Iω, b_p), alg, kwargs...)
-            sol_p = solve!(cache_p)
-        else
+    Iω1 = i * ωList[1] * I_total
+    cache_m = init(LinearProblem(M.data.A - Iω1, b_m), alg, kwargs...)
+    cache_p = init(LinearProblem(M.data.A + Iω1, b_p), alg, kwargs...)
+    for (idx, ω) in enumerate(ωList)
+        if idx > 1
+            Iω = i * ω * I_total
             cache_m.A = M.data.A - Iω
-            sol_m = solve!(cache_m)
-
             cache_p.A = M.data.A + Iω
-            sol_p = solve!(cache_p)
         end
+        sol_m = solve!(cache_m)
+        sol_p = solve!(cache_p)
 
         # trace over the Hilbert space of system (expectation value)
         val = -1 * real(dot(_tr_d_normal, sol_p.u) + dot(_tr_d_dagger, sol_m.u))
-        Aω[prog.counter[]+1] = val
+        Aω[idx] = val
 
         if SAVE
             open(FILENAME, "a") do file
                 return write(file, "$(val),\n")
             end
         end
-        next!(prog)
+        next!(progr)
     end
-    if verbose
-        println("[DONE]")
-    end
-
     return Aω
 end

src/deprecated.jl

@@ -53,7 +53,7 @@ function C(args...)
 end
 
 _HEOMSuperOp_deprecated_method_error() = error(
-    "Specifying `mul_basis = \"L\", \"R\", or \"LR\"` to `HEOMSuperOp` has been deprecated, try to construct system SuperOperator manually by using `spre`, `spost`, or `sprepost`.",
+    "Specifying `mul_basis = \"L\", \"R\", or \"LR\"` to `HEOMSuperOp` is deprecated, try to construct system SuperOperator manually by using `spre`, `spost`, or `sprepost`.",
 )
 
 HEOMSuperOp(op, opParity::AbstractParity, dims, N::Int, mul_basis::AbstractString; Id_cache = I(N)) =

src/evolution.jl

@@ -57,8 +57,8 @@ function Base.show(io::IO, sol::TimeEvolutionHEOMSol)
 end
 
 @doc raw"""
-    HEOMsolve(M, ρ0, Δt, steps; e_ops, threshold, nonzero_tol, verbose)
-    heomsolve(M, ρ0, Δt, steps; e_ops, threshold, nonzero_tol, verbose)
+    HEOMsolve(M, ρ0, Δt, steps; e_ops, threshold, nonzero_tol, progress_bar)
+    heomsolve(M, ρ0, Δt, steps; e_ops, threshold, nonzero_tol, progress_bar)
 
 Solve the time evolution for auxiliary density operators based on propagator (generated by `FastExpm.jl`).
 
@@ -70,7 +70,7 @@ Solve the time evolution for auxiliary density operators based on propagator (ge
 - `e_ops::Union{Nothing,AbstractVector}`: List of operators for which to calculate expectation values.
 - `threshold::Real` : Determines the threshold for the Taylor series. Defaults to `1.0e-6`.
 - `nonzero_tol::Real` : Strips elements smaller than `nonzero_tol` at each computation step to preserve sparsity. Defaults to `1.0e-14`.
-- `verbose::Bool` : To display verbose output and progress bar during the process or not. Defaults to `true`.
+- `progress_bar::Union{Val,Bool}`: Whether to show the progress bar. Defaults to `Val(true)`.
 
 # Notes
 - The [`ADOs`](@ref) will be saved depend on the keyword argument `e_ops`.
@@ -91,7 +91,7 @@ function HEOMsolve(
     e_ops::Union{Nothing,AbstractVector} = nothing,
     threshold = 1.0e-6,
     nonzero_tol = 1.0e-14,
-    verbose::Bool = true,
+    progress_bar::Union{Val,Bool} = Val(true),
 ) where {T_state<:Union{QuantumObject,ADOs}}
 
     # handle initial state
@@ -122,31 +122,31 @@ function HEOMsolve(
     end
 
     # Generate propagator
-    verbose && print("Generating propagator...")
+    getVal(progress_bar) && print("Generating propagator...")
     exp_Mt = Propagator(M, Δt; threshold = threshold, nonzero_tol = nonzero_tol)
-    verbose && println("[DONE]")
+    getVal(progress_bar) && println("[DONE]")
 
     # start solving
-    if verbose
-        print("Solving time evolution for ADOs by propagator method...")
-        flush(stdout)
-    end
-    progr = ProgressBar(steps + 1, enable = verbose)
+    progr = Progress(
+        steps + 1;
+        enabled = getVal(progress_bar),
+        desc = "[HEOMsolve (propagator)] ",
+        QuantumToolbox.settings.ProgressMeterKWARGS...,
+    )
     for n in 0:steps
         # calculate expectation values
         if !is_empty_e_ops
             _expect = op -> dot(op, ρvec)
-            @. expvals[:, progr.counter[]+1] = _expect(tr_e_ops)
+            @. expvals[:, n+1] = _expect(tr_e_ops)
             n == steps ? ADOs_list[1] = ADOs(ρvec, M.dimensions, M.N, M.parity) : nothing
         else
             ADOs_list[n+1] = ADOs(ρvec, M.dimensions, M.N, M.parity)
         end
 
         ρvec = exp_Mt * ρvec
-        next!(progr)
-    end
 
-    verbose && println("[DONE]")
+        getVal(progress_bar) && next!(progr)
+    end
 
     return TimeEvolutionHEOMSol(
         _getBtier(M),
@@ -245,11 +245,10 @@ function HEOMsolve(
     inplace::Union{Val,Bool} = Val(true),
     kwargs...,
 ) where {T_state<:Union{QuantumObject,ADOs}}
-    haskey(kwargs, :solver) &&
-        error("The keyword argument `solver` for HEOMsolve has been deprecated, please use `alg` instead.")
+    haskey(kwargs, :solver) && error("The keyword argument `solver` for HEOMsolve is deprecated, use `alg` instead.")
     haskey(kwargs, :verbose) &&
-        error("The keyword argument `verbose` for HEOMsolve has been deprecated, please use `progress_bar` instead.")
-    haskey(kwargs, :filename) && error("The keyword argument `filename` for HEOMsolve has been deprecated.")
+        error("The keyword argument `verbose` for HEOMsolve is deprecated, use `progress_bar` instead.")
+    haskey(kwargs, :filename) && error("The keyword argument `filename` for HEOMsolve is deprecated.")
 
     # Move sensealg argument to solve for Enzyme.jl support.
     # TODO: Remove it when https://github.com/SciML/SciMLSensitivity.jl/issues/1225 is fixed.
@@ -314,7 +313,7 @@ function _generate_Eops(M::AbstractHEOMLSMatrix, e_ops, Id_sys, Id_HEOM)
     return tr_e_ops
 end
 
-struct SaveFuncHEOMSolve{TE,PT<:Union{Nothing,ProgressBar},IT,TEXPV<:Union{Nothing,AbstractMatrix}} <: AbstractSaveFunc
+struct SaveFuncHEOMSolve{TE,PT<:Union{Nothing,Progress},IT,TEXPV<:Union{Nothing,AbstractMatrix}} <: AbstractSaveFunc
     tr_e_ops::TE
     progr::PT
     iter::IT
@@ -341,7 +340,14 @@ function _generate_heom_kwargs(
 )
     tr_e_ops = e_ops isa Nothing ? nothing : _generate_Eops(M, e_ops, I(prod(M.dimensions)), I(M.N))
 
-    progr = getVal(progress_bar) ? ProgressBar(length(tlist), enable = getVal(progress_bar)) : nothing
+    progr =
+        getVal(progress_bar) ?
+        Progress(
+            length(tlist);
+            enabled = getVal(progress_bar),
+            desc = "[HEOMsolve (ODE)] ",
+            QuantumToolbox.settings.ProgressMeterKWARGS...,
+        ) : nothing
 
     expvals = e_ops isa Nothing ? nothing : Array{ComplexF64}(undef, length(e_ops), length(tlist))
 
@@ -451,7 +457,7 @@ HEOMsolve_map(
 # this method is for advanced usage
 # User can define their own iterator structure, prob_func and output_func
 #   - `prob_func`: Function to use for generating the ODEProblem.
-#   - `output_func`: a `Tuple` containing the `Function` to use for generating the output of a single trajectory, the (optional) `ProgressBar` object, and the (optional) `RemoteChannel` object.
+#   - `output_func`: a `Tuple` containing the `Function` to use for generating the output of a single trajectory, the (optional) `Progress` object, and the (optional) `RemoteChannel` object.
 #
 # Return: An array of TimeEvolutionSol objects with the size same as the given iter.
 function HEOMsolve_map(
@@ -468,7 +474,13 @@ function HEOMsolve_map(
     _prob_func = isnothing(prob_func) ? (prob, i, repeat) -> _se_me_map_prob_func(prob, i, repeat, iter) : prob_func
     _output_func =
         isnothing(output_func) ?
-        _ensemble_dispatch_output_func(ensemblealg, progress_bar, ntraj, _standard_output_func) : output_func
+        _ensemble_dispatch_output_func(
+            ensemblealg,
+            progress_bar,
+            ntraj,
+            _standard_output_func;
+            progr_desc = "[HEOMsolve_map] ",
+        ) : output_func
     ens_prob = TimeEvolutionProblem(
         EnsembleProblem(prob.prob, prob_func = _prob_func, output_func = _output_func[1], safetycopy = false),
         prob.times,

src/heom_matrices/M_Boson.jl

@@ -95,7 +95,7 @@ Note that the parity only need to be set as `ODD` when the system contains fermi
     if verbose
         println("Preparing block matrices for HEOM Liouvillian superoperator (using $(Nthread) threads)...")
         flush(stdout)
-        prog = ProgressBar(Nado)
+        progr = Progress(Nado; enabled = verbose, desc = "[M_Boson] ", QuantumToolbox.settings.ProgressMeterKWARGS...)
     end
     @threads for idx in 1:Nado
 
@@ -146,9 +146,7 @@ Note that the parity only need to be set as `ODD` when the system contains fermi
                 end
             end
         end
-        if verbose
-            next!(prog) # trigger a progress bar update
-        end
+        verbose && next!(progr) # trigger a progress bar update
     end
     if verbose
         print("Constructing matrix...")

src/heom_matrices/M_Boson_Fermion.jl

@@ -133,7 +133,12 @@ Note that the parity only need to be set as `ODD` when the system contains fermi
     if verbose
         println("Preparing block matrices for HEOM Liouvillian superoperator (using $(Nthread) threads)...")
         flush(stdout)
-        prog = ProgressBar(Nado)
+        progr = Progress(
+            Nado;
+            enabled = verbose,
+            desc = "[M_Boson_Fermion] ",
+            QuantumToolbox.settings.ProgressMeterKWARGS...,
+        )
     end
     @threads for idx in 1:Nado
 
@@ -221,9 +226,7 @@ Note that the parity only need to be set as `ODD` when the system contains fermi
                 end
             end
         end
-        if verbose
-            next!(prog) # trigger a progress bar update
-        end
+        verbose && next!(progr) # trigger a progress bar update
     end
     if verbose
         print("Constructing matrix...")

src/heom_matrices/M_Fermion.jl

@@ -93,7 +93,7 @@ Generate the fermion-type HEOM Liouvillian superoperator matrix
     if verbose
         println("Preparing block matrices for HEOM Liouvillian superoperator (using $(Nthread) threads)...")
         flush(stdout)
-        prog = ProgressBar(Nado)
+        progr = Progress(Nado; enabled = verbose, desc = "[M_Fermion] ", QuantumToolbox.settings.ProgressMeterKWARGS...)
     end
     @threads for idx in 1:Nado
 
@@ -143,9 +143,7 @@ Generate the fermion-type HEOM Liouvillian superoperator matrix
                 end
             end
         end
-        if verbose
-            next!(prog) # trigger a progress bar update
-        end
+        verbose && next!(progr) # trigger a progress bar update
     end
     if verbose
         print("Constructing matrix...")