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thevolatilebitthevolatilebit
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agentize state, observables
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‎LICENSE‎

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The MIT License
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Copyright © 2022 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved.
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Copyright © 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved.
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Jan Bima (MSD), Otto Ritter (MSD), Sean L. Wu (Merck)
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‎LICENSES_THIRD_PARTY‎

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ReactiveDynamics.jl depends on third-party Julia packages which may be distributed under different licenses. We have listed all of these third party packages and their licenses below. For the most up-to-date information, see `Project.toml`.
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ReactiveDynamics.jl depends on third-party Julia packages, which may be distributed under various licenses. For the most recent list of these packages, refer to `Project.toml` and consult the license terms of the individual packages.
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You must agree to the terms of these licenses, in addition to the ReactiveDynamics source code license, in order to use this software.
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You must agree to the terms of these licenses, in addition to the ReactiveDynamics.jl source code license, in order to use this software.
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--------------------------------------------------
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Third party software listed by License type
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--------------------------------------------------
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MIT License (or adaptations) (https://www.opensource.org/licenses/MIT)
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* The Julia Language - https://github.com/JuliaLang/julia/blob/master/LICENSE.md
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* BenchmarkTools.jl - https://github.com/JuliaCI/BenchmarkTools.jl
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* CSV - https://github.com/JuliaData/CSV.jl
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* Catlab - https://github.com/AlgebraicJulia/Catlab.jl
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* ComponentArrays.jl - https://github.com/jonniedie/ComponentArrays.jl
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* Crayons - https://github.com/KristofferC/Crayons.jl
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* DataFrames.jl - https://github.com/JuliaData/DataFrames.jl
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* DiffEqBase.jl - https://github.com/SciML/DiffEqBase.jl
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* DifferentialEquations.jl - https://github.com/SciML/DifferentialEquations.jl
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* Distributions.jl - https://github.com/JuliaStats/Distributions.jl
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* Documenter - https://github.com/JuliaDocs/Documenter.jl
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* DocumenterMarkdown - https://github.com/JuliaDocs/DocumenterMarkdown.jl
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* GeneratedExpressions.jl - https://github.com/Merck/GeneratedExpressions.jl
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* IJulia - https://github.com/JuliaLang/IJulia.jl
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* JLD2 - https://github.com/JuliaIO/JLD2.jl
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* JSON.jl - https://github.com/JuliaIO/JSON.jl
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* MacroTools.jl - https://github.com/FluxML/MacroTools.jl
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* NLopt - https://github.com/JuliaOpt/NLopt.jl
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* OrdinaryDiffEq - https://github.com/SciML/OrdinaryDiffEq.jl
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* Plots - https://github.com/JuliaPlots/Plots.jl
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* Pluto.jl - https://github.com/fonsp/Pluto.jl
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* Reexport - https://github.com/simonster/Reexport.jl
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* SafeTestsets - https://github.com/YingboMa/SafeTestsets.jl
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* Statistics.jl - https://github.com/JuliaStats/Statistics.jl
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* StatsFuns.jl - https://github.com/JuliaStats/StatsFuns.jl
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* Symbolics.jl - https://github.com/JuliaSymbolics/Symbolics.jl
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* TOML.jl - https://github.com/JuliaLang/TOML.jl
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* Tables.jl - https://github.com/JuliaData/Tables.jl
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The Unlicense (https://opensource.org/licenses/unlicense)
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* PlutoUI.jl - https://github.com/JuliaPluto/PlutoUI.jl
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* The Julia Language - https://github.com/JuliaLang/julia/blob/master/LICENSE.md

‎Project.toml‎

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version = "0.2.7"
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[deps]
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AlgebraicAgents = "f6eb0ae3-10fa-40e6-88dd-9006ba45093a"
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CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
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Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
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ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
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Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
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Pluto = "c3e4b0f8-55cb-11ea-2926-15256bba5781"
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PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8"
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Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
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Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
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SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
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Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
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Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
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[compat]
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julia = "1.9"
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DifferentialEquations = "7.9"
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StatsFuns = "1.3"
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CSV = "0.10"
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Catlab = "0.14"
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ComponentArrays = "0.14"
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Crayons = "4.1"
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DataFrames = "1.6"
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PlutoUI = "0.7"
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Statistics = "1.9"
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DiffEqBase = "6.128"
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DifferentialEquations = "7.9"
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Distributions = "0.25"
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Documenter = "0.27"
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DocumenterMarkdown = "0.2"
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ComponentArrays = "0.14"
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JLD2 = "0.4"
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GeneratedExpressions = "0.1"
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DiffEqBase = "6.128"
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IJulia = "1.24"
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JLD2 = "0.4"
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JSON = "0.21"
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MacroTools = "0.5"
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NLopt = "1.0"
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OrdinaryDiffEq = "6.55"
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Symbolics = "5.5"
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IJulia = "1.24"
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SafeTestsets = "0.1"
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CSV = "0.10"
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Plots = "1.39"
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Pluto = "0.19"
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PlutoUI = "0.7"
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Reexport = "1.2"
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SafeTestsets = "0.1"
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Statistics = "1.9"
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StatsFuns = "1.3"
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Symbolics = "5.5"
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TOML = "1.0"
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MacroTools = "0.5"
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Crayons = "4.1"
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Documenter = "0.27"
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Tables = "1.10"
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Distributions = "0.25"
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Pluto = "0.19"
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julia = "1.9"

‎src/ReactiveDynamics.jl‎

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include.(readdir(joinpath(@__DIR__, "utils"); join = true))
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include.(readdir(joinpath(@__DIR__, "operators"); join = true))
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include("solvers.jl")
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include("optim.jl")
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#include("optim.jl")
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include("loadsave.jl")
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end

‎src/compilers.jl‎

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)
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push!(letex.args[2].args, fex)
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# the function shall be a function of the dynamic ReactiveDynamicsState structure: letex -> :(state -> $letex)
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# the function shall be a function of the dynamic ReactiveNetwork structure: letex -> :(state -> $letex)
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# eval the expression to a Julia function, save that function into the "compiled" acset
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return eval(:(state -> $letex))
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end

‎src/interface/reaction_parser.jl‎

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end
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end
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function extract_reactants(r_line, state::ReactiveDynamicsState)
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function extract_reactants(r_line, state::ReactiveNetwork)
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r_line = recursively_choose(r_line, state)
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return recursive_find_reactants!(

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