Creation of a ReactionSystem from a reaction involving compounds and only_use_rate=true #1151
Comments
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So I have been able to reproduce this in some cases. However, with only Status `~/Desktop/Julia Playground/Environment - Temporary/Project.toml`
[479239e8] Catalyst v14.4.1 `~/.julia/dev/Catalyst`
[961ee093] ModelingToolkit v9.59.0on the latest julia version (1.11.2) this works. Could you try |
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Thanks indeed it works by simply changing the release version of Catalyst by the dev one. However I have now another issue with events. Is this a temporary problem due to the dev version? using ModelingToolkit: t_nounits as t, D_nounits as D
using Catalyst
@species C(t) O(t) H(t)
@compounds begin
O₂ ~ 2O
H₂O ~ 2H + O
CO₂ ~ C + 2O
CH₄ ~ C + 4H
end
@parameters k
rx = Reaction(k*CH₄*O₂, [CH₄, O₂], [CO₂, H₂O], [1, 2], [1, 2]; only_use_rate=true)
event_CO₂ = [CO₂ ~ 1.] => [CO₂ ~ 0.5]
@named RS = ReactionSystem([rx], t; combinatoric_ratelaws=false, continuous_events = [event_CO₂])which outputs ERROR: ArgumentError: Variable CO₂ is not a function of independent variable t.
Stacktrace:
[1] check_variables(dvs::Vector{SymbolicUtils.BasicSymbolic}, iv::SymbolicUtils.BasicSymbolic{Real})
@ ModelingToolkit C:\Users\jf.barthelemy\.julia\packages\ModelingToolkit\klLLV\src\utils.jl:151
[2] ReactionSystem(eqs::Vector{…}, rxs::Vector{…}, iv::SymbolicUtils.BasicSymbolic{…}, sivs::Vector{…}, unknowns::Vector{…}, spcs::Vector{…}, ps::Vector{…}, var_to_name::Dict{…}, observed::Vector{…}, name::Symbol, systems::Vector{…}, defaults::Dict{…}, connection_type::Nothing, nps::Catalyst.NetworkProperties{…}, cls::Bool, cevs::Vector{…}, devs::Vector{…}, metadata::Nothing, complete::Bool, parent::Nothing; checks::Bool)
@ Catalyst C:\Users\jf.barthelemy\.julia\dev\Catalyst\src\reactionsystem.jl:348
[3] ReactionSystem
@ C:\Users\jf.barthelemy\.julia\dev\Catalyst\src\reactionsystem.jl:335 [inlined]
[4] ReactionSystem(eqs::Vector{…}, iv::SymbolicUtils.BasicSymbolic{…}, unknowns::Vector{…}, ps::Vector{…}; observed::Vector{…}, systems::Vector{…}, name::Symbol, default_u0::Dict{…}, default_p::Dict{…}, defaults::Dict{…}, connection_type::Nothing, checks::Bool, networkproperties::Nothing, combinatoric_ratelaws::Bool, balanced_bc_check::Bool, spatial_ivs::Nothing, continuous_events::Vector{…}, discrete_events::Vector{…}, metadata::Nothing)
@ Catalyst C:\Users\jf.barthelemy\.julia\dev\Catalyst\src\reactionsystem.jl:466
[5] make_ReactionSystem_internal(rxs_and_eqs::Vector{…}, iv::Num, us_in::Vector{…}, ps_in::Vector{…}; spatial_ivs::Nothing, continuous_events::Vector{…}, discrete_events::Vector{…}, observed::Vector{…}, kwargs::@Kwargs{…})
@ Catalyst C:\Users\jf.barthelemy\.julia\dev\Catalyst\src\reactionsystem.jl:564
[6] make_ReactionSystem_internal
@ C:\Users\jf.barthelemy\.julia\dev\Catalyst\src\reactionsystem.jl:489 [inlined]
[7] #ReactionSystem#66
@ C:\Users\jf.barthelemy\.julia\dev\Catalyst\src\reactionsystem.jl:475 [inlined]
[8] top-level scope
@ C:\Users\jf.barthelemy\.julia\packages\ModelingToolkit\klLLV\src\systems\abstractsystem.jl:2060
Some type information was truncated. Use `show(err)` to see complete types. |
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Can confirm this second one is a bug. Have gotten partially though where it is, think it should be straightforward to fix. |
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I will continue looking tomorrow, but in summary for anyone who is interested, this is the core problem: using Catalyst
t = default_t()
@species C(t) O(t)
@compounds begin
CO ~ C + O
end
vars = []
ModelingToolkit.get_variables!(vars, C + 1)
vars # [C(t)]
vars = []
ModelingToolkit.get_variables!(vars, CO + 1)
vars # [CO, t]I.e. MTK's Another thing I found, which I thought was the problem (but isn't) is that compounds are not wrapped: CO |> typeof # SymbolicUtils.BasicSymbolic{Real}
C |> typeof # NumFixing this doesn't;t actually solve the original problem (but should be fixed though). |
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Does the |
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That seems like a good guess, will have a look at it |
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Fix is up here: #1154 Should be available in the next release (unclear when that drops though) |
Hi,
After an update the following MRE doesn't work anymore whereas it worked in a set of previous versions of libraries (unfortunately I haven't kept the version numbers). Thank you very much for your help.
Minimal Reproducible Example 👇
Error & Stacktrace⚠️
Not Working Environment:
using Pkg; Pkg.status()using Pkg; Pkg.status(; mode = PKGMODE_MANIFEST)Click to open
versioninfo()The text was updated successfully, but these errors were encountered: