xiaomingfu2013 / delayssatoolkit.jl Goto Github PK

Is there any way to access problem parameters from the integrator interface? Currently delay_trigger functions have to be of the form (integrator, rng) -> ... and integrator.p does not seem to store these parameters. This would be useful if the waiting time (or the waiting time distribution) is treated as another parameter of the model.

@JuliaRegistrator register

At the moment this package does not work with StaticArrays:

using Catalyst
using StaticArrays
using DelaySSAToolkit
using DifferentialEquations

rn = @reaction_network begin
    1, 0 --> A
end

delay_trigger_affect! = function (integrator, rng)
    append!(integrator.de_chan[1], 10)
end

u0 = @SVector [ 0 ]
tspan = (0., 100.)

delay_trigger = Dict(1=>delay_trigger_affect!)
delay_complete = Dict(1=>[1=>-1])
delay_interrupt = Dict() 
delayjumpset = DelayJumpSet(delay_trigger, delay_complete, delay_interrupt)

dprob = DiscreteProblem(rn, u0, tspan)
jsys = convert(JumpSystem, rn)
djprob = DelayJumpProblem(jsys, dprob, DelayRejection(), delayjumpset, [[]])

solve(djprob, SSAStepper())

gives the following error:

setindex!(::SVector{1, Int64}, value, ::Int) is not defined.

Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:33
  [2] setindex!(a::SVector{1, Int64}, value::Int64, i::Int64)
    @ StaticArrays ~/.julia/packages/StaticArrays/tBRNS/src/indexing.jl:3
  [3] execute_delay_complete!
    @ ~/.julia/packages/DelaySSAToolkit/d6UCB/src/delayaggregator/delayssajump.jl:248 [inlined]
(...)

Changing @SVector to @MVector or dropping it fixes the issue. In contrast, DiffEqJump works with no issues:

rn = @reaction_network begin
    1, 0 --> A
    0.1, A --> 0
end

u0 = @SVector [ 0 ]
tspan = (0., 100.)

dprob = DiscreteProblem(rn, u0, tspan)
jsys = convert(JumpSystem, rn)
jprob = JumpProblem(jsys, dprob, Direct())

solve(jprob, SSAStepper())

Running long SSA simulations with dynamic arrays uses a lot of allocations, hence being able to use StaticArrays would be great here!

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DiffEqJump.jl was changed to JumpProcesses.jl with a new major so you should update this but will not get a CompatHelper PR.