update

src/spatial_reaction_systems/spatial_Jump_systems.jl

@@ -1,5 +1,3 @@
-
-
 ### JumpProblem ###
 
 # Builds a spatial DiscreteProblem from a Lattice Reaction System.
@@ -23,12 +21,14 @@ end
 # Builds a spatial JumpProblem from a DiscreteProblem containg a Lattice Reaction System.
 function JumpProcesses.JumpProblem(lrs::LatticeReactionSystem, dprob, aggregator, args...; name = nameof(lrs.rs), combinatoric_ratelaws = get_combinatoric_ratelaws(lrs.rs),checks = false, kwargs...)
     # Error checks.
+    println()
+    println(dprob.p)
+    println(dprob.u0)
     dprob.p isa Tuple{Vector{Vector{Float64}}, Vector{Vector{Float64}}} || error("Parameters in input DiscreteProblem is of an unexpected type: $(typeof(dprob.p)). Was a LatticeReactionProblem passed into the DiscreteProblem when it was created?")
     any(length.(dprob.p[1]) .> 1) && error("Spatial reaction rates are currently not supported in lattice jump simulations.")
 
     # Creates JumpProblem.
     hopping_constants = make_hopping_constants(dprob, lrs)
-    println(typeof(hopping_constants))
     ___dprob = DiscreteProblem(reshape(dprob.u0, lrs.nS, lrs.nV), dprob.tspan, first.(dprob.p[1]))
     majumps_ = make_majumps(___dprob, lrs.rs)
     return JumpProblem(___dprob, aggregator, majumps_, hopping_constants = hopping_constants, spatial_system = lrs.lattice, save_positions = (true, false))
@@ -38,18 +38,15 @@ end
 function make_hopping_constants(dprob::DiscreteProblem, lrs::LatticeReactionSystem)
     spatial_rates_dict = Dict(compute_all_spatial_rates(dprob.p[1], dprob.p[2], lrs))
     all_diff_rates = [haskey(spatial_rates_dict, s) ? spatial_rates_dict[s] : [0.0] for s in species(lrs)]
-    if false #all(length.(all_diff_rates) .== 1)        
-        return matrix_expand_component_values(all_diff_rates, length(vertices(lrs.lattice)))
-    else
-        hopping_constants = [Vector{Float64}() for i in 1:(lrs.nS), j in 1:(lrs.nV)]
-        for (e_idx, e) in enumerate(edges(lrs.lattice))
-            for s_idx in 1:(lrs.nS)
-                push!(hopping_constants[s_idx, e.src],
-                get_component_value(all_diff_rates[s_idx], e_idx))
+    hopping_constants = [Vector{Float64}(undef, length(lrs.lattice.fadjlist[j])) for i in 1:(lrs.nS), j in 1:(lrs.nV)]
+    for (e_idx, e) in enumerate(edges(lrs.lattice)), s_idx in 1:(lrs.nS)
+        for dst_idx in 1:length(hopping_constants[s_idx, e.src])
+            if (hopping_constants[s_idx, e.src][dst_idx] == undef)
+                hopping_constants[s_idx, e.src][dst_idx] = get_component_value(all_diff_rates[s_idx], e_idx)
             end
         end
-        return hopping_constants
     end
+    return hopping_constants
 end
 
 # Creates the mass action jumps from a discrete problem and a reaction system.