up

src/spatial_reaction_systems/lattice_jump_systems.jl

@@ -48,7 +48,7 @@ function JumpProcesses.JumpProblem(lrs::LatticeReactionSystem, dprob, aggregator
     # Creates and returns a spatial JumpProblem (masked lattices are not supported by these).
     spatial_system = has_masked_lattice(lrs) ? get_lattice_graph(lrs) : lattice(lrs)
     println(JumpProblem(non_spat_dprob, aggregator, sma_jumps;
-    hopping_constants, spatial_system, name, kwargs...).prob.u0)
+        hopping_constants, spatial_system, name, kwargs...).prob.u0)
     return JumpProblem(non_spat_dprob, aggregator, sma_jumps;
         hopping_constants, spatial_system, name, kwargs...)
 end
@@ -143,4 +143,4 @@ end
 #     p = (non_spat_dprob.p isa DiffEqBase.NullParameters || non_spat_dprob.p === nothing) ? Num[] : non_spat_dprob.p
 #     majpmapper = ModelingToolkit.JumpSysMajParamMapper(js, p; jseqs = eqs, rateconsttype = invttype)
 #     return ModelingToolkit.assemble_maj(eqs.x[1], statetoid, majpmapper)
-# end
+# end

src/spatial_reaction_systems/lattice_sim_struct_interfacing.jl

@@ -53,47 +53,54 @@ end
 
 function lat_setu!(oprob::ODEProblem, sp_idx::Int64, sp_tot::Int64, u, num_verts)
     if length(u) == 1
-        foreach(idx -> (oprob.u0[sp_idx + (idx-1)*sp_tot] = u[1]), 1:num_verts)
+        foreach(idx -> (oprob.u0[sp_idx + (idx - 1) * sp_tot] = u[1]), 1:num_verts)
     else
-        foreach(idx -> (oprob.u0[sp_idx + (idx-1)*sp_tot] = u[idx]), 1:num_verts)
+        foreach(idx -> (oprob.u0[sp_idx + (idx - 1) * sp_tot] = u[idx]), 1:num_verts)
     end
 end
 function lat_setu!(jprob::JumpProblem, sp_idx::Int64, sp_tot::Int64, u, num_verts)
     if length(u) == 1
-        foreach(idx -> (jprob.prob.u0[sp_idx,idx] = u[1]), 1:num_verts)
+        foreach(idx -> (jprob.prob.u0[sp_idx, idx] = u[1]), 1:num_verts)
     else
-        foreach(idx -> (jprob.prob.u0[sp_idx,idx] = u[idx]), 1:num_verts)
+        foreach(idx -> (jprob.prob.u0[sp_idx, idx] = u[idx]), 1:num_verts)
     end
 end
-function lat_setu!(oint::SciMLBase.AbstractODEIntegrator, sp_idx::Int64, sp_tot::Int64, u, num_verts)
+function lat_setu!(oint::SciMLBase.AbstractODEIntegrator, sp_idx::Int64, sp_tot::Int64,
+        u, num_verts)
     if length(u) == 1
-        foreach(idx -> (oint.u[sp_idx + (idx-1)*sp_tot] = u[1]), 1:num_verts)
+        foreach(idx -> (oint.u[sp_idx + (idx - 1) * sp_tot] = u[1]), 1:num_verts)
     else
-        foreach(idx -> (oint.u[sp_idx + (idx-1)*sp_tot] = u[idx]), 1:num_verts)
+        foreach(idx -> (oint.u[sp_idx + (idx - 1) * sp_tot] = u[idx]), 1:num_verts)
     end
 end
-function lat_setu!(jint::JumpProcesses.SSAIntegrator, sp_idx::Int64, sp_tot::Int64, u, num_verts)
+function lat_setu!(
+        jint::JumpProcesses.SSAIntegrator, sp_idx::Int64, sp_tot::Int64, u, num_verts)
     if length(u) == 1
-        foreach(idx -> (jint.u[sp_idx,idx] = u[1]), 1:num_verts)
+        foreach(idx -> (jint.u[sp_idx, idx] = u[1]), 1:num_verts)
     else
-        foreach(idx -> (jint.u[sp_idx,idx] = u[idx]), 1:num_verts)
+        foreach(idx -> (jint.u[sp_idx, idx] = u[idx]), 1:num_verts)
     end
 end
 
 function check_lattice_format(lattice::CartesianGridRej, u)
-    (u isa AbstractArray) || error("The input u should be an AbstractArray. It is a $(typeof(u)).")
-    (size(u) == lattice.dims) || error("The input u should have size $(lattice.dims), but has size $(size(u)).")
+    (u isa AbstractArray) ||
+        error("The input u should be an AbstractArray. It is a $(typeof(u)).")
+    (size(u) == lattice.dims) ||
+        error("The input u should have size $(lattice.dims), but has size $(size(u)).")
 end
 function check_lattice_format(lattice::AbstractSparseArray, u)
-    (u isa AbstractArray) || error("The input u should be an AbstractArray. It is a $(typeof(u)).")
-    (size(u) == size(lattice)) || error("The input u should have size $(size(lattice)), but has size $(size(u)).")
+    (u isa AbstractArray) ||
+        error("The input u should be an AbstractArray. It is a $(typeof(u)).")
+    (size(u) == size(lattice)) ||
+        error("The input u should have size $(size(lattice)), but has size $(size(u)).")
 end
 function check_lattice_format(lattice::DiGraph, u)
-    (u isa AbstractArray) || error("The input u should be an AbstractVector. It is a $(typeof(u)).")
-    (size(u) == size(lattice)) || error("The input u should have length $(nv(lattice)), but has length $(length(u)).")
+    (u isa AbstractArray) ||
+        error("The input u should be an AbstractVector. It is a $(typeof(u)).")
+    (length(u) == nv(lattice)) ||
+        error("The input u should have length $(nv(lattice)), but has length $(length(u)).")
 end
 
-
 """
     lat_getu(sim_struct, sp, lrs::LatticeReactionSystem)
 
@@ -235,7 +242,7 @@ end
 
 # Function which handles the input in the case where `t` is a range of values (i.e. return `sp`s 
 # value at all designated time points.
-function lat_getu(sol::ODESolution, lattice, t::AbstractVector{T}, sp_idx::Int64, 
+function lat_getu(sol::ODESolution, lattice, t::AbstractVector{T}, sp_idx::Int64,
         sp_tot::Int64) where {T <: Number}
     # Checks that an appropriate `t` is provided (however, DiffEq does permit out of range `t`s).
     if (minimum(t) < sol.t[1]) || (maximum(t) > sol.t[end])

test/spatial_modelling/lattice_solution_interfacing.jl

@@ -69,7 +69,8 @@ end
 
 ### Problem & Integrator `lat_getu` & `lat_setu!` Tests ###
 
-# Checks `getu` for ODE and Jump problem and integrators.
+# Checks `lat_getu` for ODE and Jump problem and integrators.
+# Checks `lat_setu!` for ODE and Jump problem and integrators.
 # Checks for all types of lattices.
 # Checks for symbol and symbolic variables input.
 let
@@ -88,7 +89,7 @@ let
     for (lattice, val0) in zip([lattice_cartesian, lattice_masked, lattice_graph],[val0_cartesian, val0_masked, val0_graph])
         # Prepares various problems and integrators. Uses `deepcopy` to ensure there is no cross-talk
         # between the different u vectors as they get updated.
-        lrs = LatticeReactionSystem(brusselator_system, brusselator_srs_1, lattice_masked)
+        lrs = LatticeReactionSystem(brusselator_system, brusselator_srs_1, lattice)
         u0 = [:X => val0, :Y => 0.5]
         ps = [:A => 1.0, :B => 2.0, :dX => 0.1]
         oprob = ODEProblem(lrs, deepcopy(u0), (0.0, 1.0), ps)