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Merge pull request #113 from ytdHuang/dev/structure
Re-structure the code fore entire package
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,164 +1,55 @@ | ||
| module HierarchicalEOM | ||
|
|
||
| # Re-export QuantumToolbox | ||
| import Reexport: @reexport | ||
| @reexport using QuantumToolbox | ||
|
|
||
| # sub-module HeomBase for HierarchicalEOM | ||
| module HeomBase | ||
| import Pkg | ||
| import LinearAlgebra: BLAS, kron, I | ||
| import SparseArrays: sparse, SparseVector, SparseMatrixCSC, AbstractSparseMatrix | ||
| import StaticArraysCore: SVector | ||
| import QuantumToolbox: _FType, _CType, QuantumObject, QuantumObjectType, Operator, SuperOperator | ||
|
|
||
| export _Tr, | ||
| AbstractHEOMLSMatrix, | ||
| _check_sys_dim_and_ADOs_num, | ||
| _check_parity, | ||
| HandleMatrixType, | ||
| _HandleVectorType, | ||
| _HandleSteadyStateMatrix | ||
|
|
||
| include("HeomBase.jl") | ||
| end | ||
| import .HeomBase.versioninfo as versioninfo | ||
| import .HeomBase.print_logo as print_logo | ||
| @reexport import .HeomBase: AbstractHEOMLSMatrix | ||
|
|
||
| # sub-module Bath for HierarchicalEOM | ||
| module Bath | ||
| using ..HeomBase | ||
| import Base: show, length, getindex, lastindex, iterate, checkbounds | ||
| import LinearAlgebra: ishermitian, eigvals, I | ||
| import SparseArrays: SparseMatrixCSC | ||
| import StaticArraysCore: SVector | ||
| import QuantumToolbox: QuantumObject, _spre, _spost | ||
|
|
||
| export AbstractBath, | ||
| BosonBath, | ||
| BosonBathRWA, | ||
| FermionBath, | ||
| Exponent, | ||
| C, | ||
| AbstractBosonBath, | ||
| bosonReal, | ||
| bosonImag, | ||
| bosonRealImag, | ||
| bosonAbsorb, | ||
| bosonEmit, | ||
| AbstractFermionBath, | ||
| fermionAbsorb, | ||
| fermionEmit, | ||
| Boson_DrudeLorentz_Matsubara, | ||
| Boson_DrudeLorentz_Pade, | ||
| Fermion_Lorentz_Matsubara, | ||
| Fermion_Lorentz_Pade | ||
|
|
||
| include("Bath.jl") | ||
| include("bath_correlation_functions/bath_correlation_func.jl") | ||
| end | ||
| @reexport using .Bath | ||
|
|
||
| # sub-module HeomAPI for HierarchicalEOM | ||
| module HeomAPI | ||
| import Reexport: @reexport | ||
| using ..HeomBase | ||
| using ..Bath | ||
| import Base: | ||
| ==, | ||
| !, | ||
| +, | ||
| -, | ||
| *, | ||
| show, | ||
| length, | ||
| size, | ||
| getindex, | ||
| keys, | ||
| setindex!, | ||
| lastindex, | ||
| iterate, | ||
| checkbounds, | ||
| hash, | ||
| copy, | ||
| eltype | ||
| import Base.Threads: @threads, threadid, nthreads, lock, unlock, SpinLock | ||
| import LinearAlgebra: I, kron, tr, norm, dot, mul! | ||
| import SparseArrays: sparse, sparsevec, spzeros, SparseVector, SparseMatrixCSC, AbstractSparseMatrix | ||
| import StaticArraysCore: SVector | ||
| import QuantumToolbox: | ||
| _FType, | ||
| QuantumObject, | ||
| Operator, | ||
| SuperOperator, | ||
| _spre, | ||
| _spost, | ||
| spre, | ||
| spost, | ||
| sprepost, | ||
| expect, | ||
| ket2dm, | ||
| liouvillian, | ||
| lindblad_dissipator, | ||
| steadystate, | ||
| ProgressBar, | ||
| next! | ||
|
|
||
| import FastExpm: fastExpm | ||
| import SciMLBase: init, solve, solve!, u_modified!, ODEProblem, FullSpecialize, CallbackSet | ||
| import SciMLOperators: MatrixOperator | ||
| import OrdinaryDiffEqCore: OrdinaryDiffEqAlgorithm | ||
| import OrdinaryDiffEqLowOrderRK: DP5 | ||
| import DiffEqCallbacks: PresetTimeCallback, TerminateSteadyState | ||
| import LinearSolve: LinearProblem, SciMLLinearSolveAlgorithm, UMFPACKFactorization | ||
| import JLD2: jldopen | ||
|
|
||
| export AbstractParity, | ||
| OddParity, | ||
| EvenParity, | ||
| value, | ||
| ODD, | ||
| EVEN, | ||
| ADOs, | ||
| getRho, | ||
| getADO, | ||
| Nvec, | ||
| AbstractHierarchyDict, | ||
| HierarchyDict, | ||
| MixHierarchyDict, | ||
| getIndexEnsemble, | ||
| HEOMSuperOp, | ||
| M_S, | ||
| M_Boson, | ||
| M_Fermion, | ||
| M_Boson_Fermion, | ||
| Propagator, | ||
| addBosonDissipator, | ||
| addFermionDissipator, | ||
| addTerminator, | ||
| TimeEvolutionHEOMSol, | ||
| HEOMsolve, | ||
| PowerSpectrum, | ||
| DensityOfStates | ||
|
|
||
| include("Parity.jl") | ||
| include("ADOs.jl") | ||
|
|
||
| include("heom_matrices/heom_matrix_base.jl") | ||
| include("heom_matrices/Nvec.jl") | ||
| include("heom_matrices/HierarchyDict.jl") | ||
| include("heom_matrices/M_S.jl") | ||
| include("heom_matrices/M_Boson.jl") | ||
| include("heom_matrices/M_Fermion.jl") | ||
| include("heom_matrices/M_Boson_Fermion.jl") | ||
|
|
||
| include("evolution.jl") | ||
| include("steadystate.jl") | ||
| include("power_spectrum.jl") | ||
| include("density_of_states.jl") | ||
| end | ||
| @reexport using .HeomAPI | ||
|
|
||
| # intrinsic QuantumToolbox functions | ||
| import QuantumToolbox: _FType, _CType, _spre, _spost | ||
|
|
||
| # SciML packages (for OrdinaryDiffEq and LinearSolve) | ||
| import SciMLBase: init, solve, solve!, u_modified!, ODEProblem, FullSpecialize, CallbackSet | ||
| import SciMLOperators: MatrixOperator | ||
| import OrdinaryDiffEqCore: OrdinaryDiffEqAlgorithm | ||
| import OrdinaryDiffEqLowOrderRK: DP5 | ||
| import DiffEqCallbacks: PresetTimeCallback, TerminateSteadyState | ||
| import LinearSolve: LinearProblem, SciMLLinearSolveAlgorithm, UMFPACKFactorization | ||
|
|
||
| # other dependencies (in alphabetical order) | ||
| import Base.Threads: @threads, threadid, nthreads, lock, unlock, SpinLock | ||
| import FastExpm: fastExpm | ||
| import JLD2: jldopen | ||
| import Pkg | ||
|
|
||
| # Basic functions | ||
| include("HeomBase.jl") | ||
|
|
||
| # Bath | ||
| include("bath/BathBase.jl") | ||
| include("bath/BosonBath.jl") | ||
| include("bath/FermionBath.jl") | ||
| include("bath_correlation_functions/bath_correlation_func.jl") | ||
|
|
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| # Parity and ADOs | ||
| include("Parity.jl") | ||
| include("ADOs.jl") | ||
|
|
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| # HEOM Liouvillian superoperator (HEOMLS) matrices | ||
| include("heom_matrices/heom_matrix_base.jl") | ||
| include("heom_matrices/Nvec.jl") | ||
| include("heom_matrices/HierarchyDict.jl") | ||
| include("heom_matrices/M_S.jl") | ||
| include("heom_matrices/M_Boson.jl") | ||
| include("heom_matrices/M_Fermion.jl") | ||
| include("heom_matrices/M_Boson_Fermion.jl") | ||
|
|
||
| # Solvers | ||
| include("evolution.jl") | ||
| include("steadystate.jl") | ||
| include("power_spectrum.jl") | ||
| include("density_of_states.jl") | ||
|
|
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| # deprecated functions | ||
| include("deprecated.jl") | ||
|
|
||
| end |
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