Merge pull request #477 from sivasathyaseeelan/removing-exrendedjumparray

feat: Introducing vr_aggregator with VRDirectCB and VRFRMODE

Author: ChrisRackauckas

Project.toml

@@ -7,6 +7,7 @@ version = "9.14.3"
 ArrayInterface = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
+DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 FunctionWrappers = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
@@ -30,6 +31,7 @@ FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898"
 ArrayInterface = "7.9"
 DataStructures = "0.18"
 DiffEqBase = "6.154"
+DiffEqCallbacks = "4.3.0"
 DocStringExtensions = "0.9"
 FastBroadcast = "0.3"
 FunctionWrappers = "1.1"
@@ -46,7 +48,6 @@ UnPack = "1.0.2"
 julia = "1.10"
 
 [extras]
-DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
@@ -58,5 +59,4 @@ StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["DiffEqCallbacks", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEq", 
-    "SafeTestsets", "StableRNGs", "Statistics", "StochasticDiffEq", "Test", "FastBroadcast"]
+test = ["LinearAlgebra", "LinearSolve", "OrdinaryDiffEq", "SafeTestsets", "StableRNGs", "Statistics", "StochasticDiffEq", "Test", "FastBroadcast"]

src/JumpProcesses.jl

@@ -11,6 +11,7 @@ using SciMLBase: SciMLBase, isdenseplot
 using Base.FastMath: add_fast
 using Setfield: @set, @set!
 
+import DiffEqCallbacks: gauss_points, gauss_weights
 import DiffEqBase: DiscreteCallback, init, solve, solve!, plot_indices, initialize!,
                    get_tstops, get_tstops_array, get_tstops_max
 import Base: size, getindex, setindex!, length, similar, show, merge!, merge
@@ -21,6 +22,8 @@ import RecursiveArrayTools: recursivecopy!
 using StaticArrays, Base.Threads
 import SymbolicIndexingInterface as SII
 
+import Random: AbstractRNG
+
 abstract type AbstractJump end
 abstract type AbstractMassActionJump <: AbstractJump end
 abstract type AbstractAggregatorAlgorithm end
@@ -70,6 +73,7 @@ include("spatial/directcrdirect.jl")
 include("aggregators/aggregated_api.jl")
 
 include("extended_jump_array.jl")
+include("variable_rate.jl")
 include("problem.jl")
 include("solve.jl")
 include("coupled_array.jl")
@@ -98,6 +102,9 @@ export reset_aggregated_jumps!
 
 export ExtendedJumpArray
 
+# Export VariableRateAggregator types
+export VariableRateAggregator, VR_FRM, VR_Direct
+
 # spatial structs and functions
 export CartesianGrid, CartesianGridRej
 export SpatialMassActionJump

src/problem.jl

@@ -13,8 +13,10 @@ $(TYPEDEF)
 
 Defines a collection of jump processes to associate with another problem type.
 - [Documentation Page](https://docs.sciml.ai/JumpProcesses/stable/jump_types/)
-- [Tutorial Page](https://docs.sciml.ai/JumpProcesses/stable/tutorials/discrete_stochastic_example/)
-- [FAQ Page](https://docs.sciml.ai/JumpProcesses/stable/tutorials/discrete_stochastic_example/#FAQ)
+- [Tutorial
+  Page](https://docs.sciml.ai/JumpProcesses/stable/tutorials/discrete_stochastic_example/)
+- [FAQ
+  Page](https://docs.sciml.ai/JumpProcesses/stable/tutorials/discrete_stochastic_example/#FAQ)
 
 ### Constructors
 
@@ -44,20 +46,21 @@ then be passed within a single [`JumpSet`](@ref) or as subsequent sequential arg
 $(FIELDS)
 
 ## Keyword Arguments
-- `rng`, the random number generator to use. Defaults to Julia's built-in
-  generator.
-- `save_positions=(true,true)`, specifies whether to save the system's state (before, after)
-  the jump occurs.
+- `rng`, the random number generator to use. Defaults to Julia's built-in generator.
+- `save_positions=(true,true)` when including variable rates and `(false,true)` for constant
+  rates, specifies whether to save the system's state (before, after) the jump occurs.
 - `spatial_system`, for spatial problems the underlying spatial structure.
 - `hopping_constants`, for spatial problems the spatial transition rate coefficients.
-- `use_vrj_bounds = true`, set to false to disable handling bounded `VariableRateJump`s
-  with a supporting aggregator (such as `Coevolve`). They will then be handled via the
-  continuous integration interface, and treated like general `VariableRateJump`s.
+- `use_vrj_bounds = true`, set to false to disable handling bounded `VariableRateJump`s with
+  a supporting aggregator (such as `Coevolve`). They will then be handled via the continuous
+  integration interface, and treated like general `VariableRateJump`s.
+- `vr_aggregator`, indicates the aggregator to use for sampling variable rate jumps. Current
+  default is `VR_FRM`.
 
 Please see the [tutorial
-page](https://docs.sciml.ai/JumpProcesses/stable/tutorials/discrete_stochastic_example/) in the
-DifferentialEquations.jl [docs](https://docs.sciml.ai/JumpProcesses/stable/) for usage examples and
-commonly asked questions.
+page](https://docs.sciml.ai/JumpProcesses/stable/tutorials/discrete_stochastic_example/) in
+the DifferentialEquations.jl [docs](https://docs.sciml.ai/JumpProcesses/stable/) for usage
+examples and commonly asked questions.
 """
 mutable struct JumpProblem{iip, P, A, C, J <: Union{Nothing, AbstractJumpAggregator}, J2,
     J3, J4, R, K} <: DiffEqBase.AbstractJumpProblem{P, J}
@@ -213,6 +216,7 @@ end
 make_kwarg(; kwargs...) = kwargs
 
 function JumpProblem(prob, aggregator::AbstractAggregatorAlgorithm, jumps::JumpSet;
+        vr_aggregator::VariableRateAggregator = VR_FRM(),
         save_positions = prob isa DiffEqBase.AbstractDiscreteProblem ?
                          (false, true) : (true, true),
         rng = DEFAULT_RNG, scale_rates = true, useiszero = true,
@@ -270,9 +274,9 @@ function JumpProblem(prob, aggregator::AbstractAggregatorAlgorithm, jumps::JumpS
 
     # handle any remaining vrjs
     if length(cvrjs) > 0
-        new_prob = extend_problem(prob, cvrjs; rng)
-        variable_jump_callback = build_variable_callback(CallbackSet(), 0, cvrjs...; rng)
-        cont_agg = cvrjs
+        # Handle variable rate jumps based on vr_aggregator
+        new_prob, variable_jump_callback, cont_agg = configure_jump_problem(prob, 
+            vr_aggregator, jumps, cvrjs; rng)  
     else
         new_prob = prob
         variable_jump_callback = CallbackSet()
@@ -293,163 +297,6 @@ function JumpProblem(prob, aggregator::AbstractAggregatorAlgorithm, jumps::JumpS
         solkwargs)
 end
 
-# extends prob.u0 to an ExtendedJumpArray with Njumps integrated intensity values,
-# of type prob.tspan
-function extend_u0(prob, Njumps, rng)
-    ttype = eltype(prob.tspan)
-    u0 = ExtendedJumpArray(prob.u0, [-randexp(rng, ttype) for i in 1:Njumps])
-    return u0
-end
-
-function extend_problem(prob::DiffEqBase.AbstractDiscreteProblem, jumps; rng = DEFAULT_RNG)
-    error("General `VariableRateJump`s require a continuous problem, like an ODE/SDE/DDE/DAE problem. To use a `DiscreteProblem` bounded `VariableRateJump`s must be used. See the JumpProcesses docs.")
-end
-
-function extend_problem(prob::DiffEqBase.AbstractODEProblem, jumps; rng = DEFAULT_RNG)
-    _f = SciMLBase.unwrapped_f(prob.f)
-
-    if isinplace(prob)
-        jump_f = let _f = _f
-            function (du::ExtendedJumpArray, u::ExtendedJumpArray, p, t)
-                _f(du.u, u.u, p, t)
-                update_jumps!(du, u, p, t, length(u.u), jumps...)
-            end
-        end
-    else
-        jump_f = let _f = _f
-            function (u::ExtendedJumpArray, p, t)
-                du = ExtendedJumpArray(_f(u.u, p, t), u.jump_u)
-                update_jumps!(du, u, p, t, length(u.u), jumps...)
-                return du
-            end
-        end
-    end
-
-    u0 = extend_u0(prob, length(jumps), rng)
-    f = ODEFunction{isinplace(prob)}(jump_f; sys = prob.f.sys,
-        observed = prob.f.observed)
-    remake(prob; f, u0)
-end
-
-function extend_problem(prob::DiffEqBase.AbstractSDEProblem, jumps; rng = DEFAULT_RNG)
-    _f = SciMLBase.unwrapped_f(prob.f)
-
-    if isinplace(prob)
-        jump_f = let _f = _f
-            function (du::ExtendedJumpArray, u::ExtendedJumpArray, p, t)
-                _f(du.u, u.u, p, t)
-                update_jumps!(du, u, p, t, length(u.u), jumps...)
-            end
-        end
-    else
-        jump_f = let _f = _f
-            function (u::ExtendedJumpArray, p, t)
-                du = ExtendedJumpArray(_f(u.u, p, t), u.jump_u)
-                update_jumps!(du, u, p, t, length(u.u), jumps...)
-                return du
-            end
-        end
-    end
-
-    if prob.noise_rate_prototype === nothing
-        jump_g = function (du, u, p, t)
-            prob.g(du.u, u.u, p, t)
-        end
-    else
-        jump_g = function (du, u, p, t)
-            prob.g(du, u.u, p, t)
-        end
-    end
-
-    u0 = extend_u0(prob, length(jumps), rng)
-    f = SDEFunction{isinplace(prob)}(jump_f, jump_g; sys = prob.f.sys,
-        observed = prob.f.observed)
-    remake(prob; f, g = jump_g, u0)
-end
-
-function extend_problem(prob::DiffEqBase.AbstractDDEProblem, jumps; rng = DEFAULT_RNG)
-    _f = SciMLBase.unwrapped_f(prob.f)
-
-    if isinplace(prob)
-        jump_f = let _f = _f
-            function (du::ExtendedJumpArray, u::ExtendedJumpArray, h, p, t)
-                _f(du.u, u.u, h, p, t)
-                update_jumps!(du, u, p, t, length(u.u), jumps...)
-            end
-        end
-    else
-        jump_f = let _f = _f
-            function (u::ExtendedJumpArray, h, p, t)
-                du = ExtendedJumpArray(_f(u.u, h, p, t), u.jump_u)
-                update_jumps!(du, u, p, t, length(u.u), jumps...)
-                return du
-            end
-        end
-    end
-
-    u0 = extend_u0(prob, length(jumps), rng)
-    f = DDEFunction{isinplace(prob)}(jump_f; sys = prob.f.sys,
-        observed = prob.f.observed)
-    remake(prob; f, u0)
-end
-
-# Not sure if the DAE one is correct: Should be a residual of sorts
-function extend_problem(prob::DiffEqBase.AbstractDAEProblem, jumps; rng = DEFAULT_RNG)
-    _f = SciMLBase.unwrapped_f(prob.f)
-
-    if isinplace(prob)
-        jump_f = let _f = _f
-            function (out, du::ExtendedJumpArray, u::ExtendedJumpArray, h, p, t)
-                _f(out, du.u, u.u, h, p, t)
-                update_jumps!(out, u, p, t, length(u.u), jumps...)
-            end
-        end
-    else
-        jump_f = let _f = _f
-            function (du, u::ExtendedJumpArray, h, p, t)
-                out = ExtendedJumpArray(_f(du.u, u.u, h, p, t), u.jump_u)
-                update_jumps!(du, u, p, t, length(u.u), jumps...)
-                return du
-            end
-        end
-    end
-
-    u0 = extend_u0(prob, length(jumps), rng)
-    f = DAEFunction{isinplace(prob)}(jump_f, sys = prob.f.sys,
-        observed = prob.f.observed)
-    remake(prob; f, u0)
-end
-
-function wrap_jump_in_callback(idx, jump; rng = DEFAULT_RNG)
-    condition = function(u, t, integrator)
-        u.jump_u[idx]
-    end
-    affect! = function(integrator)
-        jump.affect!(integrator)
-        integrator.u.jump_u[idx] = -randexp(rng, typeof(integrator.t))
-        nothing
-    end
-    new_cb = ContinuousCallback(condition, affect!;
-        idxs = jump.idxs,
-        rootfind = jump.rootfind,
-        interp_points = jump.interp_points,
-        save_positions = jump.save_positions,
-        abstol = jump.abstol,
-        reltol = jump.reltol)
-    return new_cb
-end
-
-function build_variable_callback(cb, idx, jump, jumps...; rng = DEFAULT_RNG)
-    idx += 1
-    new_cb = wrap_jump_in_callback(idx, jump; rng)
-    build_variable_callback(CallbackSet(cb, new_cb), idx, jumps...; rng = DEFAULT_RNG)
-end
-
-function build_variable_callback(cb, idx, jump; rng = DEFAULT_RNG)
-    idx += 1
-    CallbackSet(cb, wrap_jump_in_callback(idx, jump; rng))
-end
-
 aggregator(jp::JumpProblem{iip, P, A, C, J}) where {iip, P, A, C, J} = A
 
 @inline function extend_tstops!(tstops,
@@ -458,17 +305,6 @@ aggregator(jp::JumpProblem{iip, P, A, C, J}) where {iip, P, A, C, J} = A
         push!(tstops, jp.jump_callback.discrete_callbacks[1].condition.next_jump_time)
 end
 
-@inline function update_jumps!(du, u, p, t, idx, jump)
-    idx += 1
-    du[idx] = jump.rate(u.u, p, t)
-end
-
-@inline function update_jumps!(du, u, p, t, idx, jump, jumps...)
-    idx += 1
-    du[idx] = jump.rate(u.u, p, t)
-    update_jumps!(du, u, p, t, idx, jumps...)
-end
-
 ### Displays
 num_constant_rate_jumps(aggregator::AbstractSSAJumpAggregator) = length(aggregator.rates)
 

src/solve.jl

@@ -56,8 +56,7 @@ function resetted_jump_problem(_jump_prob, seed)
         end
     end
 
-    if !isempty(jump_prob.variable_jumps)
-        @assert jump_prob.prob.u0 isa ExtendedJumpArray
+    if !isempty(jump_prob.variable_jumps) && jump_prob.prob.u0 isa ExtendedJumpArray
         randexp!(_jump_prob.rng, jump_prob.prob.u0.jump_u)
         jump_prob.prob.u0.jump_u .*= -1
     end
@@ -69,9 +68,8 @@ function reset_jump_problem!(jump_prob, seed)
         Random.seed!(jump_prob.jump_callback.discrete_callbacks[1].condition.rng, seed)
     end
 
-    if !isempty(jump_prob.variable_jumps)
-        @assert jump_prob.prob.u0 isa ExtendedJumpArray
+    if !isempty(jump_prob.variable_jumps) && jump_prob.prob.u0 isa ExtendedJumpArray
         randexp!(jump_prob.rng, jump_prob.prob.u0.jump_u)
         jump_prob.prob.u0.jump_u .*= -1
     end
-end
+end