# Error with user-defined rates in Catalyst.jl

**URL:** <https://discourse.julialang.org/t/error-with-user-defined-rates-in-catalyst-jl/79229>\
**Category:** New to Julia\
**Created:** [April 8, 2022, 2:43pm UTC](https://discourse.julialang.org/t/error-with-user-defined-rates-in-catalyst-jl/79229 "2022-04-08T14:43:58Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![SiddhantDeshmukh](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/siddhantdeshmukh/32/35324_2.png) [@SiddhantDeshmukh](https://discourse.julialang.org/u/SiddhantDeshmukh)\
**Post date:** [April 8, 2022, 2:43pm UTC](https://discourse.julialang.org/t/error-with-user-defined-rates-in-catalyst-jl/79229/1 "2022-04-08T14:43:58Z")

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Hello everyone,  
I’m fairly new to Julia and would like to use Catalyst.jl to solve ODE systems across a large simulation grid. To that end, I’ve been trying out some test problems, and have encountered an issue with declaring a user-defined rate function and subsequently creating an ODEProblem. The following code works fine:

```julia
using Catalyst, DifferentialEquations, ModelingToolkit

test_rate(a, c, T) = a * exp(-c / T)

rn1 = @reaction_network begin
  k1, X --> Y
  k2, Y --> X
end k1 k2

@parameters k1 k2
@variables t X(t) Y(t)
pmap = (k1 => test_rate(1., 2., 300.), k2 => test_rate(2., 3., 300.))
u0map = [X => 1., Y => 1.]
odesys1 = convert(ODESystem, rn1)
prob = ODEProblem(odesys1, u0map, (1e-8, 10), pmap)
sol = solve(prob)

```

Redefining the network as follows:

```julia
rn2 = @reaction_network begin
  test_rate(1., 2., T), X --> Y
  test_rate(2., 3., T), Y --> X
end T

@parameters T
@variables t X(t) Y(t)
pmap = (T => 300.)
u0map = [X => 1., Y => 1.]
odesys2 = convert(ODESystem, rn2)
prob = ODEProblem(odesys2, u0map, (1e-8, 10), pmap)
sol = solve(prob)

```

throws the error:

“ERROR: LoadError: MethodError: no method matching create\_array(::Type{Pair{Num, Float64}}, ::Type{Union{Float64, Num}}, ::Val{1}, ::Val{2}, ::Num, ::Float64)  
Closest candidates are:  
create\_array(::Type{var”#s180"} where var"#s180"\<:LabelledArrays.LArray, ::Any, ::Val, ::Val{dims}, ::Any…) where dims at /home/sdeshmukh/.julia/packages/SymbolicUtils/v2ZkM/src/code.jl:555  
create\_array(::Type{var"#s180"} where var"#s180"\<:LabelledArrays.SLArray, ::Any, ::Val, ::Val{dims}, ::Any…) where dims at /home/sdeshmukh/.julia/packages/SymbolicUtils/v2ZkM/src/code.jl:546  
create\_array(::Type{var"#s180"} where var"#s180"\<:LinearAlgebra.Transpose{T, P}, ::Any, ::Val, ::Val, ::Any…) where {T, P} at /home/sdeshmukh/.julia/packages/SymbolicUtils/v2ZkM/src/code.jl:519  
…  
Stacktrace:  
[1] varmap\_to\_vars(varmap::Pair{Num, Float64}, varlist::Vector{Sym{Real, Base.ImmutableDict{DataType, Any}}}; defaults::Dict{Any, Any}, check::Bool, toterm::Function, promotetoconcrete::Bool)  
@ ModelingToolkit ~/.julia/packages/ModelingToolkit/a7NhS/src/variables.jl:71  
[2] process\_DEProblem(constructor::Type, sys::ODESystem, u0map::Vector{Pair{Num, Float64}}, parammap::Pair{Num, Float64}; implicit\_dae::Bool, du0map::Nothing, version::Nothing, tgrad::Bool, jac::Bool, checkbounds::Bool, sparse::Bool, simplify::Bool, linenumbers::Bool, parallel::Symbolics.SerialForm, eval\_expression::Bool, kwargs::Base.Iterators.Pairs{Symbol, Bool, Tuple{Symbol}, NamedTuple{(:has\_difference,), Tuple{Bool}}})  
@ ModelingToolkit ~/.julia/packages/ModelingToolkit/a7NhS/src/systems/diffeqs/abstractodesystem.jl:567  
[3] (ODEProblem{true, tType, isinplace, P, F, K, PT} where {tType, isinplace, P, F, K, PT})(sys::ODESystem, u0map::Vector{Pair{Num, Float64}}, tspan::Tuple{Float64, Int64}, parammap::Pair{Num, Float64}; callback::Nothing, kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})  
@ ModelingToolkit ~/.julia/packages/ModelingToolkit/a7NhS/src/systems/diffeqs/abstractodesystem.jl:657  
[4] (ODEProblem{true, tType, isinplace, P, F, K, PT} where {tType, isinplace, P, F, K, PT})(sys::ODESystem, u0map::Vector{Pair{Num, Float64}}, tspan::Tuple{Float64, Int64}, parammap::Pair{Num, Float64})  
@ ModelingToolkit ~/.julia/packages/ModelingToolkit/a7NhS/src/systems/diffeqs/abstractodesystem.jl:656  
[5] ODEProblem(::ODESystem, ::Vector{Pair{Num, Float64}}, ::Vararg{Any, N} where N; kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})  
@ ModelingToolkit ~/.julia/packages/ModelingToolkit/a7NhS/src/systems/diffeqs/abstractodesystem.jl:635  
[6] ODEProblem(::ODESystem, ::Vector{Pair{Num, Float64}}, ::Vararg{Any, N} where N)  
@ ModelingToolkit ~/.julia/packages/ModelingToolkit/a7NhS/src/systems/diffeqs/abstractodesystem.jl:635  
[7] top-level scope  
@ ~/Documents/graphCRNs/julia/user\_defined\_mwe.jl:30"

when creating the ODEProblem. Maybe I’m misunderstanding the syntax for the reaction network here; I’d like to use the function I define as the reaction rate, parametrised by the temperature T. Looking at the repressilator example ([Using Catalyst · Catalyst.jl](https://catalyst.sciml.ai/dev/tutorials/using_catalyst/)) I can see that there is a pre-defined function there that works, but all of the arguments passed in are either variables or parameters. In my case, each reaction would have a different set of (a, c) constants and the temperature is changed at each grid point in the simulation.

Any help would be greatly appreciated!

EDIT: Added full stacktrace in error.

---

<div class="post-metadata">

**Author:** ![isaacsas](https://avatars.discourse-cdn.com/v4/letter/i/f6c823/32.png) [@isaacsas](https://discourse.julialang.org/u/isaacsas)\
**Post date:** [April 8, 2022, 10:18pm UTC](https://discourse.julialang.org/t/error-with-user-defined-rates-in-catalyst-jl/79229/2 "2022-04-08T22:18:21Z")

</div>

It seems ModelingToolkit doesn’t accept a scalar for `pmap`, so you need to define `pmap` with a comma at the end to make it a tuple containing one `Pair` and not a scalar `Pair`:

```julia
pmap = (T => 300.0,) 

```

Note also that sometimes you may need to register your custom function with Symbolics.jl (though not in this case). You can read about that in the link given in the [Catalyst FAQ](https://catalyst.sciml.ai/dev/faqs/#user_functions).

---

<div class="post-metadata">

**Author:** ![isaacsas](https://avatars.discourse-cdn.com/v4/letter/i/f6c823/32.png) [@isaacsas](https://discourse.julialang.org/u/isaacsas)\
**Post date:** [April 8, 2022, 10:22pm UTC](https://discourse.julialang.org/t/error-with-user-defined-rates-in-catalyst-jl/79229/3 "2022-04-08T22:22:39Z")

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Also note you could have just made `pmap` a vector like

```julia
pmap = [T => 300.0]

```

and that would work fine. The only time you have to use tuples over vectors is if you want to mix the types of parameters (for example, having some be integers and others be floats).

---

<div class="post-metadata">

**Author:** ![ChrisRackauckas](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/chrisrackauckas/32/77_2.png) [@ChrisRackauckas](https://discourse.julialang.org/u/ChrisRackauckas)\
**Post date:** [April 8, 2022, 11:47pm UTC](https://discourse.julialang.org/t/error-with-user-defined-rates-in-catalyst-jl/79229/4 "2022-04-08T23:47:37Z")

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> [@isaacsas](#):
>
> It seems ModelingToolkit doesn’t accept a scalar for `pmap` , so you need to define `pmap` with a comma at the end to make it a tuple containing one `Pair` and not a scalar `Pair` :
> 
> ```julia
> 
> ```

In theory we can support this. It wouldn’t be hard. Worth an issue.

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<div class="post-metadata">

**Author:** ![SiddhantDeshmukh](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/siddhantdeshmukh/32/35324_2.png) [@SiddhantDeshmukh](https://discourse.julialang.org/u/SiddhantDeshmukh)\
**Post date:** [April 11, 2022, 10:19am UTC](https://discourse.julialang.org/t/error-with-user-defined-rates-in-catalyst-jl/79229/5 "2022-04-11T10:19:06Z")

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Works like a charm, thanks! When using just a single parameter, is there any significant performance hit to defining a tuple over a vector vs just using a vector?