Hi all. I currently have a large ODE system that I’ve defined as a reaction network using Catalyst. I was wondering if it would be possible to essentially put this reaction network into DynamicalSystems to find the attractors for the ODE system. If so, what would be the best possible way to achieve this? Thank you!
Hi, cast the ode into a dynamical system using CoupledODEs(prob::ODEProblem, diffeq) (see DynamicalSystemsBase.jl · DynamicalSystemsBase.jl ) . Then use one of the main two methods of Attractors.jl: Finding Attractors · Attractors.jl
Thank you so much! I tried this and seem to have run into an error I’m not sure how to resolve. Here is my code:
shuttle = @reaction_network begin
(k₁,k₂), Yₐ + X <--> C_YX
k₃, C_YX --> Yₐ + ∅
(k₄,k₅), ∅ <--> X
(k₆,k₇), Yₐ + Dₐ <--> C_YD
k₈, C_YD --> Yᵢ + Dₐ
(k₉,k₁₀), Yᵢ + P <--> C_YP
k₁₁, C_YP --> Yₐ + P
(k₁₂,k₁₃), Yₐₙ + Xₙ <--> C_YXn
k₁₄, C_YXn --> Yₐₙ + ∅
k₁₅, Xₙ --> ∅
(k₁₆,k₁₇), Yₐₙ + Dₐₙ <--> C_YDn
k₁₈, C_YDn --> Yᵢₙ + Dₐₙ
(k₁₉,k₂₀), Yᵢₙ + Pₙ <--> C_YPn
k₂₁, C_YPn --> Yₐₙ + Pₙ
(k₂₂,k₂₃), Yᵢ <--> Yᵢₙ
(k₂₄,k₂₅), Xₙ <--> X
(k₂₆,k₂₇), Dₐ <--> Dₐₙ
(k₂₈,k₂₉), Dᵢ <--> Dₐ
(k₃₀,k₃₁), Xₙ + T <--> C_XT
end
p0=[92.331732,0.86466471,79.9512906,97.932525,1,3.4134082,0.61409879,0.61409879,3.4134082,0.98168436,0.98168436,4.7267833,0.17182818,0.68292191,1,3.2654672,0.61699064,0.61699064,37.913879,0.86466471,0.86466471,0.99326205,0.99326205,1,5.9744464,1.7182818,1.7182818,1.7182818,1.7182818,0.55950727,1.0117639]
u0 = new_u0(rand(19))
tspan = (0,250)
op = ODEProblem(shuttle, u0, tspan, p0)
diffeq = (alg = Vern9(), abstol = 1e-9, reltol = 1e-9)
ds = CoupledODEs(op; diffeq)
Here is the error that I’m getting on the last line of code:
MethodError: no method matching nextfloat(::Int64)
Closest candidates are:
nextfloat(!Matched::Union{Float16, Float32, Float64}, !Matched::Integer) at float.jl:685
nextfloat(!Matched::ForwardDiff.Dual{T, V, N}) where {T, V, N} at C:\Users\Dragolonth\.julia\packages\ForwardDiff\vXysl\src\dual.jl:309
nextfloat(!Matched::Measurements.Measurement) at C:\Users\Dragolonth\.julia\packages\Measurements\AA3YK\src\math.jl:725
...
ode_determine_initdt(::Vector{Float64}, ::Int64, ::Int64, ::Int64, ::Float64, ::Float64, ::typeof(DiffEqBase.ODE_DEFAULT_NORM), ::SciMLBase.ODEProblem{Vector{Float64}, Tuple{Int64, Int64}, true, Vector{Float64}, SciMLBase.ODEFunction{true, SciMLBase.AutoSpecialize, ModelingToolkit.var"#f#520"{RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋arg1, :ˍ₋arg2, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xa7f7f560, 0xe2cee825, 0x50271c96, 0x3685869a, 0xb2f4f4be)}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :ˍ₋arg1, :ˍ₋arg2, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xe5d05ca7, 0x122181de, 0xacaabfa6, 0xcbe3a63d, 0xce945a89)}}, LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Vector{Symbol}, Symbol, Vector{Symbol}, ModelingToolkit.var"#545#generated_observed#528"{Bool, ModelingToolkit.ODESystem, Dict{Any, Any}}, Nothing, ModelingToolkit.ODESystem}, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}, SciMLBase.StandardODEProblem}, ::OrdinaryDiffEq.ODEIntegrator{OrdinaryDiffEq.Tsit5{typeof(OrdinaryDiffEq.trivial_limiter!), typeof(OrdinaryDiffEq.trivial_limiter!), Static.False}, true, Vector{Float64}, Nothing, Int64, Vector{Float64}, Float64, Rational{Int64}, Rational{Int64}, Int64, Vector{Vector{Float64}}, SciMLBase.ODESolution{Float64, 2, Vector{Vector{Float64}}, Nothing, Nothing, Vector{Int64}, Vector{Vector{Vector{Float64}}}, SciMLBase.ODEProblem{Vector{Float64}, Tuple{Int64, Int64}, true, Vector{Float64}, SciMLBase.ODEFunction{true, SciMLBase.AutoSpecialize, ModelingToolkit.var"#f#520"{RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋arg1, :ˍ₋arg2, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xa7f7f560, 0xe2cee825, 0x50271c96, 0x3685869a, 0xb2f4f4be)}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :ˍ₋arg1, :ˍ₋arg2, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xe5d05ca7, 0x122181de, 0xacaabfa6, 0xcbe3a63d, 0xce945a89)}}, LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Vector{Symbol}, Symbol, Vector{Symbol}, ModelingToolkit.var"#545#generated_observed#528"{Bool, ModelingToolkit.ODESystem, Dict{Any, Any}}, Nothing, ModelingToolkit.ODESystem}, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}, SciMLBase.StandardODEProblem}, OrdinaryDiffEq.Tsit5{typeof(OrdinaryDiffEq.trivial_limiter!), typeof(OrdinaryDiffEq.trivial_limiter!), Static.False}, OrdinaryDiffEq.InterpolationData{SciMLBase.ODEFunction{true, SciMLBase.AutoSpecialize, ModelingToolkit.var"#f#520"{RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋arg1, :ˍ₋arg2, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xa7f7f560, 0xe2cee825, 0x50271c96, 0x3685869a, 0xb2f4f4be)}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :ˍ₋arg1, :ˍ₋arg2, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xe5d05ca7, 0x122181de, 0xacaabfa6, 0xcbe3a63d, 0xce945a89)}}, LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Vector{Symbol}, Symbol, Vector{Symbol}, ModelingToolkit.var"#545#generated_observed#528"{Bool, ModelingToolkit.ODESystem, Dict{Any, Any}}, Nothing, ModelingToolkit.ODESystem}, Vector{Vector{Float64}}, Vector{Int64}, Vector{Vector{Vector{Float64}}}, OrdinaryDiffEq.Tsit5Cache{Vector{Float64}, Vector{Float64}, Vector{Float64}, typeof(OrdinaryDiffEq.trivial_limiter!), typeof(OrdinaryDiffEq.trivial_limiter!), Static.False}}, DiffEqBase.Stats, Nothing}, SciMLBase.ODEFunction{true, SciMLBase.AutoSpecialize, ModelingToolkit.var"#f#520"{RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋arg1, :ˍ₋arg2, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xa7f7f560, 0xe2cee825, 0x50271c96, 0x3685869a, 0xb2f4f4be)}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :ˍ₋arg1, :ˍ₋arg2, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xe5d05ca7, 0x122181de, 0xacaabfa6, 0xcbe3a63d, 0xce945a89)}}, LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Vector{Symbol}, Symbol, Vector{Symbol}, ModelingToolkit.var"#545#generated_observed#528"{Bool, ModelingToolkit.ODESystem, Dict{Any, Any}}, Nothing, ModelingToolkit.ODESystem}, OrdinaryDiffEq.Tsit5Cache{Vector{Float64}, Vector{Float64}, Vector{Float64}, typeof(OrdinaryDiffEq.trivial_limiter!), typeof(OrdinaryDiffEq.trivial_limiter!), Static.False}, OrdinaryDiffEq.DEOptions{Float64, Float64, Rational{Int64}, Int64, OrdinaryDiffEq.PIController{Rational{Int64}}, typeof(DiffEqBase.ODE_DEFAULT_NORM), typeof(LinearAlgebra.opnorm), Bool, SciMLBase.CallbackSet{Tuple{}, Tuple{}}, typeof(DiffEqBase.ODE_DEFAULT_ISOUTOFDOMAIN), typeof(DiffEqBase.ODE_DEFAULT_PROG_MESSAGE), typeof(DiffEqBase.ODE_DEFAULT_UNSTABLE_CHECK), DataStructures.BinaryHeap{Int64, DataStructures.FasterForward}, DataStructures.BinaryHeap{Int64, DataStructures.FasterForward}, Nothing, Nothing, Float64, Tuple{}, Tuple{}, Tuple{}}, Vector{Float64}, Float64, Nothing, OrdinaryDiffEq.DefaultInit})@initdt.jl:11
auto_dt_reset!(::OrdinaryDiffEq.ODEIntegrator{OrdinaryDiffEq.Tsit5{typeof(OrdinaryDiffEq.trivial_limiter!), typeof(OrdinaryDiffEq.trivial_limiter!), Static.False}, true, Vector{Float64}, Nothing, Int64, Vector{Float64}, Float64, Rational{Int64}, Rational{Int64}, Int64, Vector{Vector{Float64}}, SciMLBase.ODESolution{Float64, 2, Vector{Vector{Float64}}, Nothing, Nothing, Vector{Int64}, Vector{Vector{Vector{Float64}}}, SciMLBase.ODEProblem{Vector{Float64}, Tuple{Int64, Int64}, true, Vector{Float64}, SciMLBase.ODEFunction{true, SciMLBase.AutoSpecialize, ModelingToolkit.var"#f#520"{RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋arg1, :ˍ₋arg2, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xa7f7f560, 0xe2cee825, 0x50271c96, 0x3685869a, 0xb2f4f4be)}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :ˍ₋arg1, :ˍ₋arg2, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xe5d05ca7, 0x122181de, 0xacaabfa6, 0xcbe3a63d, 0xce945a89)}}, LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Vector{Symbol}, Symbol, Vector{Symbol}, ModelingToolkit.var"#545#generated_observed#528"{Bool, ModelingToolkit.ODESystem, Dict{Any, Any}}, Nothing, ModelingToolkit.ODESystem}, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}, SciMLBase.StandardODEProblem}, OrdinaryDiffEq.Tsit5{typeof(OrdinaryDiffEq.trivial_limiter!), typeof(OrdinaryDiffEq.trivial_limiter!), Static.False}, OrdinaryDiffEq.InterpolationData{SciMLBase.ODEFunction{true, SciMLBase.AutoSpecialize, ModelingToolkit.var"#f#520"{RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋arg1, :ˍ₋arg2, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xa7f7f560, 0xe2cee825, 0x50271c96, 0x3685869a, 0xb2f4f4be)}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :ˍ₋arg1, :ˍ₋arg2, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xe5d05ca7, 0x122181de, 0xacaabfa6, 0xcbe3a63d, 0xce945a89)}}, LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Vector{Symbol}, Symbol, Vector{Symbol}, ModelingToolkit.var"#545#generated_observed#528"{Bool, ModelingToolkit.ODESystem, Dict{Any, Any}}, Nothing, ModelingToolkit.ODESystem}, Vector{Vector{Float64}}, Vector{Int64}, Vector{Vector{Vector{Float64}}}, OrdinaryDiffEq.Tsit5Cache{Vector{Float64}, Vector{Float64}, Vector{Float64}, typeof(OrdinaryDiffEq.trivial_limiter!), typeof(OrdinaryDiffEq.trivial_limiter!), Static.False}}, DiffEqBase.Stats, Nothing}, SciMLBase.ODEFunction{true, SciMLBase.AutoSpecialize, ModelingToolkit.var"#f#520"{RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋arg1, :ˍ₋arg2, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xa7f7f560, 0xe2cee825, 0x50271c96, 0x3685869a, 0xb2f4f4be)}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :ˍ₋arg1, :ˍ₋arg2, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xe5d05ca7, 0x122181de, 0xacaabfa6, 0xcbe3a63d, 0xce945a89)}}, LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Vector{Symbol}, Symbol, Vector{Symbol}, ModelingToolkit.var"#545#generated_observed#528"{Bool, ModelingToolkit.ODESystem, Dict{Any, Any}}, Nothing, ModelingToolkit.ODESystem}, OrdinaryDiffEq.Tsit5Cache{Vector{Float64}, Vector{Float64}, Vector{Float64}, typeof(OrdinaryDiffEq.trivial_limiter!), typeof(OrdinaryDiffEq.trivial_limiter!), Static.False}, OrdinaryDiffEq.DEOptions{Float64, Float64, Rational{Int64}, Int64, OrdinaryDiffEq.PIController{Rational{Int64}}, typeof(DiffEqBase.ODE_DEFAULT_NORM), typeof(LinearAlgebra.opnorm), Bool, SciMLBase.CallbackSet{Tuple{}, Tuple{}}, typeof(DiffEqBase.ODE_DEFAULT_ISOUTOFDOMAIN), typeof(DiffEqBase.ODE_DEFAULT_PROG_MESSAGE), typeof(DiffEqBase.ODE_DEFAULT_UNSTABLE_CHECK), DataStructures.BinaryHeap{Int64, DataStructures.FasterForward}, DataStructures.BinaryHeap{Int64, DataStructures.FasterForward}, Nothing, Nothing, Float64, Tuple{}, Tuple{}, Tuple{}}, Vector{Float64}, Float64, Nothing, OrdinaryDiffEq.DefaultInit})@integrator_interface.jl:442
handle_dt!@solve.jl:547[inlined]
var"#__init#632"(::Tuple{}, ::Tuple{}, ::Tuple{}, ::Nothing, ::Bool, ::Bool, ::Bool, ::Bool, ::Nothing, ::Bool, ::Bool, ::Int64, ::Nothing, ::Int64, ::Bool, ::Bool, ::Rational{Int64}, ::Float64, ::Float64, ::Rational{Int64}, ::Int64, ::Int64, ::Int64, ::Nothing, ::Nothing, ::Rational{Int64}, ::Nothing, ::Bool, ::Int64, ::Float64, ::typeof(DiffEqBase.ODE_DEFAULT_NORM), ::typeof(LinearAlgebra.opnorm), ::typeof(DiffEqBase.ODE_DEFAULT_ISOUTOFDOMAIN), ::typeof(DiffEqBase.ODE_DEFAULT_UNSTABLE_CHECK), ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Int64, ::String, ::typeof(DiffEqBase.ODE_DEFAULT_PROG_MESSAGE), ::Nothing, ::Bool, ::Bool, ::Bool, ::Bool, ::OrdinaryDiffEq.DefaultInit, ::Base.Pairs{Symbol, NamedTuple{(:alg, :abstol, :reltol), Tuple{OrdinaryDiffEq.Vern9{typeof(OrdinaryDiffEq.trivial_limiter!), typeof(OrdinaryDiffEq.trivial_limiter!), Static.False}, Float64, Float64}}, Tuple{Symbol}, NamedTuple{(:diffeq,), Tuple{NamedTuple{(:alg, :abstol, :reltol), Tuple{OrdinaryDiffEq.Vern9{typeof(OrdinaryDiffEq.trivial_limiter!), typeof(OrdinaryDiffEq.trivial_limiter!), Static.False}, Float64, Float64}}}}}, ::typeof(SciMLBase.__init), ::SciMLBase.ODEProblem{Vector{Float64}, Tuple{Int64, Int64}, true, Vector{Float64}, SciMLBase.ODEFunction{true, SciMLBase.AutoSpecialize, ModelingToolkit.var"#f#520"{RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋arg1, :ˍ₋arg2, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xa7f7f560, 0xe2cee825, 0x50271c96, 0x3685869a, 0xb2f4f4be)}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :ˍ₋arg1, :ˍ₋arg2, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xe5d05ca7, 0x122181de, 0xacaabfa6, 0xcbe3a63d, 0xce945a89)}}, LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Vector{Symbol}, Symbol, Vector{Symbol}, ModelingToolkit.var"#545#generated_observed#528"{Bool, ModelingToolkit.ODESystem, Dict{Any, Any}}, Nothing, ModelingToolkit.ODESystem}, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}, SciMLBase.StandardODEProblem}, ::OrdinaryDiffEq.Tsit5{typeof(OrdinaryDiffEq.trivial_limiter!), typeof(OrdinaryDiffEq.trivial_limiter!), Static.False}, ::Tuple{}, ::Tuple{}, ::Tuple{}, ::Type{Val{true}})@solve.jl:509
var"#CoupledODEs#14"(::Base.Pairs{Symbol, NamedTuple{(:alg, :abstol, :reltol), Tuple{OrdinaryDiffEq.Vern9{typeof(OrdinaryDiffEq.trivial_limiter!), typeof(OrdinaryDiffEq.trivial_limiter!), Static.False}, Float64, Float64}}, Tuple{Symbol}, NamedTuple{(:diffeq,), Tuple{NamedTuple{(:alg, :abstol, :reltol), Tuple{OrdinaryDiffEq.Vern9{typeof(OrdinaryDiffEq.trivial_limiter!), typeof(OrdinaryDiffEq.trivial_limiter!), Static.False}, Float64, Float64}}}}}, ::Type{DynamicalSystemsBase.CoupledODEs}, ::SciMLBase.ODEProblem{Vector{Float64}, Tuple{Int64, Int64}, true, Vector{Float64}, SciMLBase.ODEFunction{true, SciMLBase.AutoSpecialize, ModelingToolkit.var"#f#520"{RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋arg1, :ˍ₋arg2, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xa7f7f560, 0xe2cee825, 0x50271c96, 0x3685869a, 0xb2f4f4be)}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :ˍ₋arg1, :ˍ₋arg2, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xe5d05ca7, 0x122181de, 0xacaabfa6, 0xcbe3a63d, 0xce945a89)}}, LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Vector{Symbol}, Symbol, Vector{Symbol}, ModelingToolkit.var"#545#generated_observed#528"{Bool, ModelingToolkit.ODESystem, Dict{Any, Any}}, Nothing, ModelingToolkit.ODESystem}, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}, SciMLBase.StandardODEProblem}, ::NamedTuple{(:alg, :abstol, :reltol), Tuple{OrdinaryDiffEq.Tsit5{typeof(OrdinaryDiffEq.trivial_limiter!), typeof(OrdinaryDiffEq.trivial_limiter!), Static.False}, Float64, Float64}})@continuous_time_ode.jl:93
top-level scope@Local: 1[inlined]
tspan = (0.0,250.0), though I’m surprised because that should have an automatic promotion. DynamicalSystems.jl must somehow be skipping that.
Don’t specify tspan as integers. Time is float.
CU!
George