ReactionMechanismSimulator.jl
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ReactionMechanismGenerator
ParametrizedTConstantVDomain must take "T" as a function or if an array of times for "ts" is supplied as an array of volumes
I'm running a liquid simulation using an RMG-generated .rms file.
When given initial conditions such as
initialconds = Dict(["T"=>300.0, "V"=>1.0e-6*1e6, "water" => 0.055332, "mol1" => 1.30E-5]);
domain, y0 = ParametrizedTConstantVDomain(phase=liq, initialconds=initial_conds);
RMS says:
ParametrizedTConstantVDomain must take "T" as a function or if an array of times for "ts" is supplied as an array of volumes
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:35
[2] ParametrizedTConstantVDomain(; phase::IdealDiluteSolution{Tuple{Arrheniusvec{Vector{Float64}, Vector{Float64}, Vector{Float64}}}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}}, initialconds::Dict{String, Float64}, constantspecies::Vector{String}, sparse::Bool, sensitivity::Bool)
@ ReactionMechanismSimulator ~/mambaforge/envs/rmg_env/share/julia/site/packages/ReactionMechanismSimulator/ztchp/src/Domain.jl:613
[3] top-level scope
@ In[56]:1
The structure of the above input also appears in the docs. I can run if I give a list of ts and a list of Ts though
@mjohnson541, could you please take a look?
For the code above you want ConstantTVDomain, ParametrizedTConstantVDomain is for cases when the temperature is variable...these are distinct because in the former the rate coefficients are constant and don't need recomputed.
Thanks! I should have payed more attention.
I'm still getting errors, let me know if you'd like me to open new issues or move the conversation offline
I'm now doing the following:
phaseDict = readinput(rms_file);
spcs = phaseDict["phase"]["Species"];
rxns = phaseDict["phase"]["Reactions"];
solv = Solvent("water", RiedelViscosity(-52.843, 3703.6, 5.866, -5.88e-29, 10.0));
liq = IdealDiluteSolution(spcs, rxns, solv, name="phase", diffusionlimited=true);
# BTW, concentration units below are mol/cm3 like in RMG, do I need to multiply by 1e6 to convert?
initialconds = Dict(["T" => 300.0, "V" => V, "water" => 0.055332, "mol1" => 1.30E-5]);
domain, y0 = ConstantTVDomain(phase=liq, initialconds=initialconds, constantspecies=[]);
reactor = Reactor(domain, y0, (0.0, max_time * 1.05));
But I get:
MethodError: calcthermo(::ConstantTVDomain{IdealDiluteSolution{Tuple{Arrheniusvec{Vector{Float64}, Vector{Float64}, Vector{Float64}}}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}}, Int64, Float64, Float64, Integer, Vector{Int64}}, ::Vector{ForwardDiff.Dual{ForwardDiff.Tag{ReactionMechanismSimulator.var"#f#612"{SciMLBase.NullParameters, Float64, ConstantTVDomain{IdealDiluteSolution{Tuple{Arrheniusvec{Vector{Float64}, Vector{Float64}, Vector{Float64}}}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}}, Int64, Float64, Float64, Integer, Vector{Int64}}, Vector{Any}}, Float64}, Float64, 9}}, ::Float64, ::SciMLBase.NullParameters) is ambiguous. Candidates:
calcthermo(d::ConstantTVDomain{W, Y}, y::J, t::Q, p::Q2) where {Q2<:SciMLBase.NullParameters, W<:IdealDiluteSolution, Y<:Integer, J<:AbstractArray, Q} in ReactionMechanismSimulator at /home/alon/mambaforge/envs/rmg_env/share/julia/site/packages/ReactionMechanismSimulator/ztchp/src/Domain.jl:1421
calcthermo(d::ConstantTVDomain{W, Y}, y::Vector{W2}, t::Q, p::Q2) where {W2<:ForwardDiff.Dual, Q2, W<:IdealDiluteSolution, Y<:Integer, J<:AbstractArray, Q} in ReactionMechanismSimulator at /home/alon/mambaforge/envs/rmg_env/share/julia/site/packages/ReactionMechanismSimulator/ztchp/src/Domain.jl:1470
Possible fix, define
calcthermo(::ConstantTVDomain{W, Y}, ::J, ::Q, ::SciMLBase.NullParameters) where {W2<:ForwardDiff.Dual, W<:IdealDiluteSolution, Y<:Integer, Q, J<:Vector{W2}}
Stacktrace:
[1] #dydtreactor!#608
@ ~/mambaforge/envs/rmg_env/share/julia/site/packages/ReactionMechanismSimulator/ztchp/src/Reactor.jl:638 [inlined]
[2] (::ReactionMechanismSimulator.var"#f#612"{SciMLBase.NullParameters, Float64, ConstantTVDomain{IdealDiluteSolution{Tuple{Arrheniusvec{Vector{Float64}, Vector{Float64}, Vector{Float64}}}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}}, Int64, Float64, Float64, Integer, Vector{Int64}}, Vector{Any}})(dy::Vector{ForwardDiff.Dual{ForwardDiff.Tag{ReactionMechanismSimulator.var"#f#612"{SciMLBase.NullParameters, Float64, ConstantTVDomain{IdealDiluteSolution{Tuple{Arrheniusvec{Vector{Float64}, Vector{Float64}, Vector{Float64}}}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}}, Int64, Float64, Float64, Integer, Vector{Int64}}, Vector{Any}}, Float64}, Float64, 9}}, y::Vector{ForwardDiff.Dual{ForwardDiff.Tag{ReactionMechanismSimulator.var"#f#612"{SciMLBase.NullParameters, Float64, ConstantTVDomain{IdealDiluteSolution{Tuple{Arrheniusvec{Vector{Float64}, Vector{Float64}, Vector{Float64}}}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}}, Int64, Float64, Float64, Integer, Vector{Int64}}, Vector{Any}}, Float64}, Float64, 9}})
@ ReactionMechanismSimulator ~/mambaforge/envs/rmg_env/share/julia/site/packages/ReactionMechanismSimulator/ztchp/src/Reactor.jl:765
[3] vector_mode_dual_eval!(f!::ReactionMechanismSimulator.var"#f#612"{SciMLBase.NullParameters, Float64, ConstantTVDomain{IdealDiluteSolution{Tuple{Arrheniusvec{Vector{Float64}, Vector{Float64}, Vector{Float64}}}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}}, Int64, Float64, Float64, Integer, Vector{Int64}}, Vector{Any}}, cfg::ForwardDiff.JacobianConfig{ForwardDiff.Tag{ReactionMechanismSimulator.var"#f#612"{SciMLBase.NullParameters, Float64, ConstantTVDomain{IdealDiluteSolution{Tuple{Arrheniusvec{Vector{Float64}, Vector{Float64}, Vector{Float64}}}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}}, Int64, Float64, Float64, Integer, Vector{Int64}}, Vector{Any}}, Float64}, Float64, 9, Tuple{Vector{ForwardDiff.Dual{ForwardDiff.Tag{ReactionMechanismSimulator.var"#f#612"{SciMLBase.NullParameters, Float64, ConstantTVDomain{IdealDiluteSolution{Tuple{Arrheniusvec{Vector{Float64}, Vector{Float64}, Vector{Float64}}}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}}, Int64, Float64, Float64, Integer, Vector{Int64}}, Vector{Any}}, Float64}, Float64, 9}}, Vector{ForwardDiff.Dual{ForwardDiff.Tag{ReactionMechanismSimulator.var"#f#612"{SciMLBase.NullParameters, Float64, ConstantTVDomain{IdealDiluteSolution{Tuple{Arrheniusvec{Vector{Float64}, Vector{Float64}, Vector{Float64}}}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}}, Int64, Float64, Float64, Integer, Vector{Int64}}, Vector{Any}}, Float64}, Float64, 9}}}}, y::Vector{Float64}, x::Vector{Float64})
@ ForwardDiff ~/mambaforge/envs/rmg_env/share/julia/site/packages/ForwardDiff/vXysl/src/apiutils.jl:31
[4] vector_mode_jacobian!(result::SparseArrays.SparseMatrixCSC{Float64, Int64}, f!::ReactionMechanismSimulator.var"#f#612"{SciMLBase.NullParameters, Float64, ConstantTVDomain{IdealDiluteSolution{Tuple{Arrheniusvec{Vector{Float64}, Vector{Float64}, Vector{Float64}}}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}}, Int64, Float64, Float64, Integer, Vector{Int64}}, Vector{Any}}, y::Vector{Float64}, x::Vector{Float64}, cfg::ForwardDiff.JacobianConfig{ForwardDiff.Tag{ReactionMechanismSimulator.var"#f#612"{SciMLBase.NullParameters, Float64, ConstantTVDomain{IdealDiluteSolution{Tuple{Arrheniusvec{Vector{Float64}, Vector{Float64}, Vector{Float64}}}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}}, Int64, Float64, Float64, Integer, Vector{Int64}}, Vector{Any}}, Float64}, Float64, 9, Tuple{Vector{ForwardDiff.Dual{ForwardDiff.Tag{ReactionMechanismSimulator.var"#f#612"{SciMLBase.NullParameters, Float64, ConstantTVDomain{IdealDiluteSolution{Tuple{Arrheniusvec{Vector{Float64}, Vector{Float64}, Vector{Float64}}}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}}, Int64, Float64, Float64, Integer, Vector{Int64}}, Vector{Any}}, Float64}, Float64, 9}}, Vector{ForwardDiff.Dual{ForwardDiff.Tag{ReactionMechanismSimulator.var"#f#612"{SciMLBase.NullParameters, Float64, ConstantTVDomain{IdealDiluteSolution{Tuple{Arrheniusvec{Vector{Float64}, Vector{Float64}, Vector{Float64}}}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}}, Int64, Float64, Float64, Integer, Vector{Int64}}, Vector{Any}}, Float64}, Float64, 9}}}})
@ ForwardDiff ~/mambaforge/envs/rmg_env/share/julia/site/packages/ForwardDiff/vXysl/src/jacobian.jl:153
[5] jacobian!(result::SparseArrays.SparseMatrixCSC{Float64, Int64}, f!::Function, y::Vector{Float64}, x::Vector{Float64}, cfg::ForwardDiff.JacobianConfig{ForwardDiff.Tag{ReactionMechanismSimulator.var"#f#612"{SciMLBase.NullParameters, Float64, ConstantTVDomain{IdealDiluteSolution{Tuple{Arrheniusvec{Vector{Float64}, Vector{Float64}, Vector{Float64}}}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}}, Int64, Float64, Float64, Integer, Vector{Int64}}, Vector{Any}}, Float64}, Float64, 9, Tuple{Vector{ForwardDiff.Dual{ForwardDiff.Tag{ReactionMechanismSimulator.var"#f#612"{SciMLBase.NullParameters, Float64, ConstantTVDomain{IdealDiluteSolution{Tuple{Arrheniusvec{Vector{Float64}, Vector{Float64}, Vector{Float64}}}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}}, Int64, Float64, Float64, Integer, Vector{Int64}}, Vector{Any}}, Float64}, Float64, 9}}, Vector{ForwardDiff.Dual{ForwardDiff.Tag{ReactionMechanismSimulator.var"#f#612"{SciMLBase.NullParameters, Float64, ConstantTVDomain{IdealDiluteSolution{Tuple{Arrheniusvec{Vector{Float64}, Vector{Float64}, Vector{Float64}}}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}}, Int64, Float64, Float64, Integer, Vector{Int64}}, Vector{Any}}, Float64}, Float64, 9}}}}, ::Val{true})
@ ForwardDiff ~/mambaforge/envs/rmg_env/share/julia/site/packages/ForwardDiff/vXysl/src/jacobian.jl:78
[6] jacobian!(result::SparseArrays.SparseMatrixCSC{Float64, Int64}, f!::Function, y::Vector{Float64}, x::Vector{Float64}, cfg::ForwardDiff.JacobianConfig{ForwardDiff.Tag{ReactionMechanismSimulator.var"#f#612"{SciMLBase.NullParameters, Float64, ConstantTVDomain{IdealDiluteSolution{Tuple{Arrheniusvec{Vector{Float64}, Vector{Float64}, Vector{Float64}}}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}}, Int64, Float64, Float64, Integer, Vector{Int64}}, Vector{Any}}, Float64}, Float64, 9, Tuple{Vector{ForwardDiff.Dual{ForwardDiff.Tag{ReactionMechanismSimulator.var"#f#612"{SciMLBase.NullParameters, Float64, ConstantTVDomain{IdealDiluteSolution{Tuple{Arrheniusvec{Vector{Float64}, Vector{Float64}, Vector{Float64}}}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}}, Int64, Float64, Float64, Integer, Vector{Int64}}, Vector{Any}}, Float64}, Float64, 9}}, Vector{ForwardDiff.Dual{ForwardDiff.Tag{ReactionMechanismSimulator.var"#f#612"{SciMLBase.NullParameters, Float64, ConstantTVDomain{IdealDiluteSolution{Tuple{Arrheniusvec{Vector{Float64}, Vector{Float64}, Vector{Float64}}}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}}, Int64, Float64, Float64, Integer, Vector{Int64}}, Vector{Any}}, Float64}, Float64, 9}}}}) (repeats 2 times)
@ ForwardDiff ~/mambaforge/envs/rmg_env/share/julia/site/packages/ForwardDiff/vXysl/src/jacobian.jl:76
[7] jacobianyforwarddiff!
@ ~/mambaforge/envs/rmg_env/share/julia/site/packages/ReactionMechanismSimulator/ztchp/src/Reactor.jl:766 [inlined]
[8] jacyforwarddiff!
@ ~/mambaforge/envs/rmg_env/share/julia/site/packages/ReactionMechanismSimulator/ztchp/src/Reactor.jl:33 [inlined]
[9] Reactor(domain::ConstantTVDomain{IdealDiluteSolution{Tuple{Arrheniusvec{Vector{Float64}, Vector{Float64}, Vector{Float64}}}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}}, Int64, Float64, Float64, Integer, Vector{Int64}}, y0::Vector{Float64}, tspan::Tuple{Float64, Int64}, interfaces::Vector{Any}; p::SciMLBase.NullParameters, forwardsensitivities::Bool, forwarddiff::Bool, modelingtoolkit::Bool, tau::Float64)
@ ReactionMechanismSimulator ~/mambaforge/envs/rmg_env/share/julia/site/packages/ReactionMechanismSimulator/ztchp/src/Reactor.jl:44
[10] Reactor (repeats 2 times)
@ ~/mambaforge/envs/rmg_env/share/julia/site/packages/ReactionMechanismSimulator/ztchp/src/Reactor.jl:30 [inlined]
[11] top-level scope
@ In[11]:1
Since I'm not calling calcthermo directly, I'm not sure what I need to change.
My code follows this RMS example.
Update: solved by modifying
domain, y0 = ConstantTVDomain(phase=liq, initialconds=initialconds, constantspecies=[]);
reactor = Reactor(domain, y0, (0.0, max_time * 1.05));
into
domain, y0, p = ConstantTVDomain(phase=liq, initialconds=initialconds, constantspecies=[]);
reactor = Reactor(domain, y0, (0.0, max_time * 1.05), p=p);
Perhaps the examples should be updated if this is change is correct?
Yes, that is the correct format now...it looks like that never got changed in the docs...
Also you may want to switch to commit: https://github.com/ReactionMechanismGenerator/ReactionMechanismSimulator.jl/commit/baba92ae5b85bdb53e919ca9b22c44380803f561. There's some bugs on main right now related to plotting (https://github.com/ReactionMechanismGenerator/ReactionMechanismSimulator.jl/issues/219).
The first bit I understand, but I'm a little confused why the p=p is necessary. We may need to tweak the method typings. I'm particularly unsure why it was calling forwarddiff when it should be able to use analytic jacobians.
@mjohnson541 I think p=p is necessary because otherwise the default SciMLBase.NullParameters() is getting passed in, rather than the actual p. Why did we make this optional in the first place? I don't see why p can be optional. forwarddiff is called once in the beginning for all domains to determine their Jacobian sparsity pattern here.
