add connection_type for other systems, too

Co-authored-by: "Shashi Gowda" <gowda@mit.edu>

Author: YingboMa

examples/electrical_components.jl

@@ -8,7 +8,6 @@ using ModelingToolkit, OrdinaryDiffEq
     ODESystem(Equation[], t, [v, i], [], name=name, defaults=[v=>1.0, i=>1.0])
 end
 
-# level-1
 function ModelingToolkit.connect(::Type{Pin}, ps...)
     eqs = [
            0 ~ sum(p->p.i, ps) # KCL

src/systems/diffeqs/sdesystem.jl

@@ -71,6 +71,10 @@ struct SDESystem <: AbstractODESystem
     parameters are not supplied in `ODEProblem`.
     """
     defaults::Dict
+    """
+    type: type of the system
+    """
+    connection_type::Any
 end
 
 function SDESystem(deqs::AbstractVector{<:Equation}, neqs, iv, dvs, ps;
@@ -79,7 +83,9 @@ function SDESystem(deqs::AbstractVector{<:Equation}, neqs, iv, dvs, ps;
                    default_u0=Dict(),
                    default_p=Dict(),
                    defaults=_merge(Dict(default_u0), Dict(default_p)),
-                   name = gensym(:SDESystem))
+                   name = gensym(:SDESystem)
+                   connection_type=nothing,
+                   )
     iv′ = value(iv)
     dvs′ = value.(dvs)
     ps′ = value.(ps)
@@ -94,7 +100,7 @@ function SDESystem(deqs::AbstractVector{<:Equation}, neqs, iv, dvs, ps;
     jac = RefValue{Any}(Matrix{Num}(undef, 0, 0))
     Wfact   = RefValue(Matrix{Num}(undef, 0, 0))
     Wfact_t = RefValue(Matrix{Num}(undef, 0, 0))
-    SDESystem(deqs, neqs, iv′, dvs′, ps′, observed, tgrad, jac, Wfact, Wfact_t, name, systems, defaults)
+    SDESystem(deqs, neqs, iv′, dvs′, ps′, observed, tgrad, jac, Wfact, Wfact_t, name, systems, defaults, connection_type)
 end
 
 function generate_diffusion_function(sys::SDESystem, dvs = states(sys), ps = parameters(sys); kwargs...)

src/systems/jumps/jumpsystem.jl

@@ -47,6 +47,10 @@ struct JumpSystem{U <: ArrayPartition} <: AbstractSystem
     parameters are not supplied in `ODEProblem`.
     """
     defaults::Dict
+    """
+    type: type of the system
+    """
+    connection_type::Any
 end
 
 function JumpSystem(eqs, iv, states, ps;
@@ -55,7 +59,9 @@ function JumpSystem(eqs, iv, states, ps;
                     default_u0=Dict(),
                     default_p=Dict(),
                     defaults=_merge(Dict(default_u0), Dict(default_p)),
-                    name = gensym(:JumpSystem))
+                    name = gensym(:JumpSystem)
+                    connection_type=nothing,
+                    )
 
     ap = ArrayPartition(MassActionJump[], ConstantRateJump[], VariableRateJump[])
     for eq in eqs
@@ -75,7 +81,7 @@ function JumpSystem(eqs, iv, states, ps;
     defaults = todict(defaults)
     defaults = Dict(value(k) => value(v) for (k, v) in pairs(defaults))
 
-    JumpSystem{typeof(ap)}(ap, value(iv), value.(states), value.(ps), observed, name, systems, defaults)
+    JumpSystem{typeof(ap)}(ap, value(iv), value.(states), value.(ps), observed, name, systems, defaults, connection_type)
 end
 
 function generate_rate_function(js, rate)

src/systems/nonlinear/nonlinearsystem.jl

@@ -43,21 +43,27 @@ struct NonlinearSystem <: AbstractSystem
     structure: structural information of the system
     """
     structure::Any
+    """
+    type: type of the system
+    """
+    connection_type::Any
 end
 
 function NonlinearSystem(eqs, states, ps;
-                         observed = [],
-                         name = gensym(:NonlinearSystem),
+                         observed=[],
+                         name=gensym(:NonlinearSystem),
                          default_u0=Dict(),
                          default_p=Dict(),
                          defaults=_merge(Dict(default_u0), Dict(default_p)),
-                         systems = NonlinearSystem[])
+                         systems=NonlinearSystem[],
+                         connection_type=nothing,
+                         )
     if !(isempty(default_u0) && isempty(default_p))
         Base.depwarn("`default_u0` and `default_p` are deprecated. Use `defaults` instead.", :NonlinearSystem, force=true)
     end
     defaults = todict(defaults)
     defaults = Dict(value(k) => value(v) for (k, v) in pairs(defaults))
-    NonlinearSystem(eqs, value.(states), value.(ps), observed, name, systems, defaults, nothing)
+    NonlinearSystem(eqs, value.(states), value.(ps), observed, name, systems, defaults, nothing, connection_type)
 end
 
 function calculate_jacobian(sys::NonlinearSystem;sparse=false,simplify=false)

src/systems/pde/pdesystem.jl

@@ -52,8 +52,16 @@ struct PDESystem <: ModelingToolkit.AbstractSystem
     parameters are not supplied in `ODEProblem`.
     """
     defaults::Dict
-    @add_kwonly function PDESystem(eqs, bcs, domain, indvars, depvars, ps = SciMLBase.NullParameters(), defaults = Dict())
-        new(eqs, bcs, domain, indvars, depvars, ps, defaults)
+    """
+    type: type of the system
+    """
+    connection_type::Any
+    @add_kwonly function PDESystem(eqs, bcs, domain, indvars, depvars,
+                                   ps=SciMLBase.NullParameters();
+                                   defaults=Dict(),
+                                   connection_type=nothing,
+                                  )
+        new(eqs, bcs, domain, indvars, depvars, ps, defaults, connection_type)
     end
 end
 

src/systems/reaction/reactionsystem.jl

@@ -60,10 +60,16 @@ struct Reaction{S, T <: Number}
     `true` if `rate` represents the full reaction rate law.
     """
     only_use_rate::Bool
+    """
+    type: type of the system
+    """
+    connection_type::Any
 end
 
 function Reaction(rate, subs, prods, substoich, prodstoich;
-                  netstoich=nothing, only_use_rate=false, kwargs...)
+                  netstoich=nothing, only_use_rate=false,
+                  connection_type=nothing,
+                  kwargs...)
 
     (isnothing(prods)&&isnothing(subs)) && error("A reaction requires a non-nothing substrate or product vector.")
     (isnothing(prodstoich)&&isnothing(substoich)) && error("Both substrate and product stochiometry inputs cannot be nothing.")
@@ -80,7 +86,7 @@ function Reaction(rate, subs, prods, substoich, prodstoich;
     subs = value.(subs)
     prods = value.(prods)
     ns = isnothing(netstoich) ? get_netstoich(subs, prods, substoich, prodstoich) : netstoich
-    Reaction(value(rate), subs, prods, substoich, prodstoich, ns, only_use_rate)
+    Reaction(value(rate), subs, prods, substoich, prodstoich, ns, only_use_rate, connection_type)
 end