In the vectorfield function
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""" vectorfield(pn::AbstractPetriNet) |
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Generates a Julia function which calculates the vectorfield of the Petri net |
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being simulated under the law of mass action. |
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The resulting function has a signature of the form `f!(du, u, p, t)` and can be |
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passed to the DifferentialEquations.jl solver package. |
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""" |
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vectorfield(pn::AbstractPetriNet) = begin |
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tm = TransitionMatrices(pn) |
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dt = tm.output - tm.input |
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(du, u, p, t) -> begin |
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rates = zeros(valtype(du), nt(pn)) |
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u_m = [u[sname(pn, i)] for i in 1:ns(pn)] |
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p_m = [p[tname(pn, i)] for i in 1:nt(pn)] |
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for i in 1:nt(pn) |
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rates[i] = valueat(p_m[i], u, t) * prod(u_m[j]^tm.input[i, j] for j in 1:ns(pn)) |
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end |
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for j in 1:ns(pn) |
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du[sname(pn, j)] = sum(rates[i] * dt[i, j] for i in 1:nt(pn); init=0.0) |
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end |
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du |
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end |
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end |
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it is assumed that the state and parameter arrays u, p etc can be indexed by the species name. This is fine when the species name is a symbol, but its also possible to have species names that are tuples of symbols e.g. from using typed_product.
Is there a recommended way to define arrays that can be indexed by Tuples of symbols?
