save prog

Author: TorkelE

src/spatial_reaction_systems/spatial_ODE_systems.jl

@@ -68,7 +68,7 @@ struct LatticeTransportODEf{S,T}
     """An iterator over all the edges of the lattice."""
     edge_iterator::Vector{Pair{Int64, Int64}}
 
-    function LatticeTransportODEf(ofunc::S, vert_ps::Vector{Pair{BasicSymbolic{Real},Vector{T}}}, 
+    function LatticeTransportODEf(ofunc::S, vert_ps, 
                                   transport_rates::Vector{Pair{Int64, SparseMatrixCSC{T, Int64}}}, 
                                   lrs::LatticeReactionSystem) where {S,T}        
         # Records which parameters and rates are uniform and which are not.
@@ -82,7 +82,8 @@ struct LatticeTransportODEf{S,T}
 
         # WIP.
         nonspatial_osys = complete(convert(ODESystem, reactionsystem(lrs)))
-        mtk_ps = MT.MTKParameters(nonspatial_osys, [e[1] => e[2][1] for e in vert_ps])
+        p_init = [p => Dict(vert_ps)[p][1] for p in parameters(nonspatial_osys)]
+        mtk_ps = MT.MTKParameters(nonspatial_osys, p_init)
         p_setters = [MT.setp(nonspatial_osys, p) for p in parameters(nonspatial_osys)]
 
         # Computes the indexes of the vertex parameters in the vector of parameters.
@@ -157,7 +158,7 @@ struct LatticeTransportODEjac{R,S,T}
     """The transport rates. This is a dense or sparse matrix (depending on what type of Jacobian is used)."""
     jac_transport::T
 
-    function LatticeTransportODEjac(ofunc::R, vert_ps::Vector{Pair{BasicSymbolic{Real},Vector{S}}}, 
+    function LatticeTransportODEjac(ofunc::R, vert_ps, 
                                     jac_transport::Union{Nothing, SparseMatrixCSC{Float64, Int64}}, 
                                     lrs::LatticeReactionSystem, sparse::Bool) where {R,S}
 
@@ -250,23 +251,23 @@ function build_odefunction(lrs::LatticeReactionSystem, vert_ps::Vector{Pair{Basi
         ofunc_sparse = ODEFunction(osys; jac = true, sparse = true)
         jac_transport = build_jac_prototype(ofunc_sparse.jac_prototype, transport_rates, lrs; set_nonzero = true)
         if sparse
-            f = LatticeTransportODEf(ofunc_sparse, vert_ps, transport_rates, lrs)
+            f = LatticeTransportODEf(ofunc_sparse, [vert_ps; edge_ps], transport_rates, lrs)
             jac_transport = build_jac_prototype(ofunc_sparse.jac_prototype, transport_rates, lrs; set_nonzero = true)
-            J = LatticeTransportODEjac(ofunc_dense, vert_ps, jac_transport, lrs, true)
+            J = LatticeTransportODEjac(ofunc_dense, [vert_ps; edge_ps], jac_transport, lrs, true)
             jac_prototype = jac_transport
         else
-            f = LatticeTransportODEf(ofunc_dense, vert_ps, transport_rates, lrs)
-            J = LatticeTransportODEjac(ofunc_dense, vert_ps, jac_transport, lrs, false)
+            f = LatticeTransportODEf(ofunc_dense, [vert_ps; edge_ps], transport_rates, lrs)
+            J = LatticeTransportODEjac(ofunc_dense, [vert_ps; edge_ps], jac_transport, lrs, false)
             jac_prototype = nothing
         end
     else
         if sparse
             ofunc_sparse = ODEFunction(osys; jac = false, sparse = true)
-            f = LatticeTransportODEf(ofunc_sparse, vert_ps, transport_rates, lrs)
+            f = LatticeTransportODEf(ofunc_sparse, [vert_ps; edge_ps], transport_rates, lrs)
             jac_prototype = build_jac_prototype(ofunc_sparse.jac_prototype, transport_rates, lrs; set_nonzero = false)
         else
             ofunc_dense = ODEFunction(osys; jac = false, sparse = false)
-            f = LatticeTransportODEf(ofunc_dense, vert_ps, transport_rates, lrs)
+            f = LatticeTransportODEf(ofunc_dense, [vert_ps; edge_ps], transport_rates, lrs)
             jac_prototype = nothing
         end
         J = nothing