feat: support symbolic indexing of a subset of the system

src/SciMLBase.jl

@@ -724,6 +724,7 @@ include("problems/problem_interface.jl")
 include("problems/optimization_problems.jl")
 
 include("clock.jl")
+include("solutions/save_idxs.jl")
 include("solutions/basic_solutions.jl")
 include("solutions/nonlinear_solutions.jl")
 include("solutions/ode_solutions.jl")

src/integrator_interface.jl

@@ -331,19 +331,22 @@ Otherwise the integrator is allowed to skip recalculating the interpolation.
 
 # Arguments
 
-- `continuous_modification`: determines whether the modification is due to a continuous change (continuous callback)
-  or a discrete callback. For a continuous change, this can include a change to time which requires a re-evaluation
-  of the interpolations.
-- `callback_initializealg`: the initialization algorithm provided by the callback. For DAEs, this is the choice for the
-  initialization that is done post callback. The default value of `nothing` means that the initialization choice
-  used for the DAE should be performed post-callback.
+  - `continuous_modification`: determines whether the modification is due to a continuous change (continuous callback)
+    or a discrete callback. For a continuous change, this can include a change to time which requires a re-evaluation
+    of the interpolations.
+  - `callback_initializealg`: the initialization algorithm provided by the callback. For DAEs, this is the choice for the
+    initialization that is done post callback. The default value of `nothing` means that the initialization choice
+    used for the DAE should be performed post-callback.
 """
 function reeval_internals_due_to_modification!(
         integrator::DEIntegrator, continuous_modification;
         callback_initializealg = nothing)
     reeval_internals_due_to_modification!(integrator::DEIntegrator)
 end
-reeval_internals_due_to_modification!(integrator::DEIntegrator; callback_initializealg = nothing) = nothing
+function reeval_internals_due_to_modification!(
+        integrator::DEIntegrator; callback_initializealg = nothing)
+    nothing
+end
 
 """
     set_t!(integrator::DEIntegrator, t)

src/scimlfunctions.jl

@@ -2693,8 +2693,8 @@ function SplitFunction{iip, specialize}(f1, f2;
                         f1.jac_prototype :
                         nothing,
         W_prototype = __has_W_prototype(f1) ?
-                        f1.W_prototype :
-                        nothing,
+                      f1.W_prototype :
+                      nothing,
         sparsity = __has_sparsity(f1) ? f1.sparsity :
                    jac_prototype,
         Wfact = __has_Wfact(f1) ? f1.Wfact : nothing,

src/solutions/dae_solutions.jl

@@ -27,7 +27,7 @@ https://docs.sciml.ai/DiffEqDocs/stable/basics/solution/
   exited due to an error. For more details, see
   [the return code documentation](https://docs.sciml.ai/SciMLBase/stable/interfaces/Solutions/#retcodes).
 """
-struct DAESolution{T, N, uType, duType, uType2, DType, tType, P, A, ID, S, rateType} <:
+struct DAESolution{T, N, uType, duType, uType2, DType, tType, P, A, ID, S, rateType, V} <:
        AbstractDAESolution{T, N, uType}
     u::uType
     du::duType
@@ -42,6 +42,31 @@ struct DAESolution{T, N, uType, duType, uType2, DType, tType, P, A, ID, S, rateT
     tslocation::Int
     stats::S
     retcode::ReturnCode.T
+    saved_subsystem::V
+end
+
+function DAESolution{T, N}(u, du, u_analytic, errors, t, k, prob, alg, interp, dense,
+        tslocation, stats, retcode, saved_subsystem) where {T, N}
+    return DAESolution{T, N, typeof(u), typeof(du), typeof(u_analytic), typeof(errors),
+        typeof(t), typeof(prob), typeof(alg), typeof(interp), typeof(stats), typeof(k),
+        typeof(saved_subsystem)}(
+        u, du, u_analytic, errors, t, k, prob, alg, interp, dense, tslocation, stats,
+        retcode, saved_subsystem
+    )
+end
+
+function ConstructionBase.constructorof(::Type{O}) where {T, N, O <: DAESolution{T, N}}
+    DAESolution{T, N}
+end
+
+function ConstructionBase.setproperties(sol::DAESolution, patch::NamedTuple)
+    u = get(patch, :u, sol.u)
+    N = u === nothing ? 2 : ndims(eltype(u)) + 1
+    T = eltype(eltype(u))
+    patch = merge(getproperties(sol), patch)
+    return DAESolution{T, N}(patch.u, patch.du, patch.u_analytic, patch.errors, patch.t,
+        patch.k, patch.prob, patch.alg, patch.interp, patch.dense, patch.tslocation,
+        patch.stats, patch.retcode, patch.saved_subsystem)
 end
 
 Base.@propagate_inbounds function Base.getproperty(x::AbstractDAESolution, s::Symbol)
@@ -65,13 +90,14 @@ function build_solution(prob::AbstractDAEProblem, alg, t, u, du = nothing;
         retcode = ReturnCode.Default,
         destats = missing,
         stats = nothing,
+        saved_subsystem = nothing,
         kwargs...)
     T = eltype(eltype(u))
 
     if prob.u0 === nothing
         N = 2
     else
-        N = length((size(prob.u0)..., length(u)))
+        N = ndims(eltype(u)) + 1
     end
 
     if !ismissing(destats)
@@ -88,7 +114,8 @@ function build_solution(prob::AbstractDAEProblem, alg, t, u, du = nothing;
         errors = Dict{Symbol, real(eltype(prob.u0))}()
 
         sol = DAESolution{T, N, typeof(u), typeof(du), typeof(u_analytic), typeof(errors),
-            typeof(t), typeof(prob), typeof(alg), typeof(interp), typeof(stats), typeof(k)}(
+            typeof(t), typeof(prob), typeof(alg), typeof(interp), typeof(stats), typeof(k),
+            typeof(saved_subsystem)}(
             u,
             du,
             u_analytic,
@@ -101,7 +128,8 @@ function build_solution(prob::AbstractDAEProblem, alg, t, u, du = nothing;
             dense,
             0,
             stats,
-            retcode)
+            retcode,
+            saved_subsystem)
 
         if calculate_error
             calculate_solution_errors!(sol; timeseries_errors = timeseries_errors,
@@ -110,15 +138,17 @@ function build_solution(prob::AbstractDAEProblem, alg, t, u, du = nothing;
         sol
     else
         DAESolution{T, N, typeof(u), typeof(du), Nothing, Nothing, typeof(t),
-            typeof(prob), typeof(alg), typeof(interp), typeof(stats), typeof(k)}(
+            typeof(prob), typeof(alg), typeof(interp), typeof(stats), typeof(k),
+            typeof(saved_subsystem)}(
             u, du,
             nothing,
             nothing, t, k,
             prob, alg,
             interp,
             dense, 0,
             stats,
-            retcode)
+            retcode,
+            saved_subsystem)
     end
 end
 
@@ -161,76 +191,23 @@ function calculate_solution_errors!(sol::AbstractDAESolution;
 end
 
 function build_solution(sol::AbstractDAESolution{T, N}, u_analytic, errors) where {T, N}
-    DAESolution{T, N, typeof(sol.u), typeof(sol.du), typeof(u_analytic), typeof(errors),
-        typeof(sol.t), typeof(sol.prob), typeof(sol.alg), typeof(sol.interp),
-        typeof(sol.stats), typeof(sol.k)}(sol.u,
-        sol.du,
-        u_analytic,
-        errors,
-        sol.t,
-        sol.k,
-        sol.prob,
-        sol.alg,
-        sol.interp,
-        sol.dense,
-        sol.tslocation,
-        sol.stats,
-        sol.retcode)
+    @reset sol.u_analytic = u_analytic
+    return @set sol.errors = errors
 end
 
 function solution_new_retcode(sol::AbstractDAESolution{T, N}, retcode) where {T, N}
-    DAESolution{T, N, typeof(sol.u), typeof(sol.du), typeof(sol.u_analytic),
-        typeof(sol.errors), typeof(sol.t), typeof(sol.prob), typeof(sol.alg),
-        typeof(sol.interp), typeof(sol.stats), typeof(sol.k)}(sol.u,
-        sol.du,
-        sol.u_analytic,
-        sol.errors,
-        sol.t,
-        sol.k,
-        sol.prob,
-        sol.alg,
-        sol.interp,
-        sol.dense,
-        sol.tslocation,
-        sol.stats,
-        retcode)
+    return @set sol.retcode = retcode
 end
 
 function solution_new_tslocation(sol::AbstractDAESolution{T, N}, tslocation) where {T, N}
-    DAESolution{T, N, typeof(sol.u), typeof(sol.du), typeof(sol.u_analytic),
-        typeof(sol.errors), typeof(sol.t), typeof(sol.prob), typeof(sol.alg),
-        typeof(sol.interp), typeof(sol.stats), typeof(k)}(sol.u,
-        sol.du,
-        sol.u_analytic,
-        sol.errors,
-        sol.t,
-        sol.k,
-        sol.prob,
-        sol.alg,
-        sol.interp,
-        sol.dense,
-        tslocation,
-        sol.stats,
-        sol.retcode)
+    return @set sol.tslocation = tslocation
 end
 
 function solution_slice(sol::AbstractDAESolution{T, N}, I) where {T, N}
-    DAESolution{T, N, typeof(sol.u), typeof(sol.du), typeof(sol.u_analytic),
-        typeof(sol.errors), typeof(sol.t), typeof(sol.prob), typeof(sol.alg),
-        typeof(sol.interp), typeof(sol.stats), typeof(sol.k)}(sol.u[I],
-        sol.du[I],
-        sol.u_analytic ===
-        nothing ?
-        nothing :
-        sol.u_analytic[I],
-        sol.errors,
-        sol.t[I],
-        sol.k[I],
-        sol.prob,
-        sol.alg,
-        sol.interp,
-        false,
-        sol.tslocation,
-        sol.stats,
-        sol.retcode)
+    @reset sol.u = sol.u[I]
+    @reset sol.du = sol.du[I]
+    @reset sol.u_analytic = sol.u_analytic === nothing ? nothing : sol.u_analytic[I]
+    @reset sol.t = sol.t[I]
+    @reset sol.k = sol.dense ? sol.k[I] : sol.k
+    return @set sol.dense = false
 end

src/solutions/ode_solutions.jl

@@ -104,9 +104,12 @@ https://docs.sciml.ai/DiffEqDocs/stable/basics/solution/
   successfully, whether it terminated early due to a user-defined callback, or whether it
   exited due to an error. For more details, see
   [the return code documentation](https://docs.sciml.ai/SciMLBase/stable/interfaces/Solutions/#retcodes).
+- `saved_subsystem`: a [`SavedSubsystem`](@ref) representing the subset of variables saved
+  in this solution, or `nothing` if all variables are saved. Here "variables" refers to
+  both continuous-time state variables and timeseries parameters.
 """
 struct ODESolution{T, N, uType, uType2, DType, tType, rateType, discType, P, A, IType, S,
-    AC <: Union{Nothing, Vector{Int}}, R, O} <:
+    AC <: Union{Nothing, Vector{Int}}, R, O, V} <:
        AbstractODESolution{T, N, uType}
     u::uType
     u_analytic::uType2
@@ -124,6 +127,7 @@ struct ODESolution{T, N, uType, uType2, DType, tType, rateType, discType, P, A,
     retcode::ReturnCode.T
     resid::R
     original::O
+    saved_subsystem::V
 end
 
 function ConstructionBase.constructorof(::Type{O}) where {T, N, O <: ODESolution{T, N}}
@@ -137,7 +141,7 @@ function ConstructionBase.setproperties(sol::ODESolution, patch::NamedTuple)
     patch = merge(getproperties(sol), patch)
     return ODESolution{T, N}(patch.u, patch.u_analytic, patch.errors, patch.t, patch.k,
         patch.discretes, patch.prob, patch.alg, patch.interp, patch.dense, patch.tslocation, patch.stats,
-        patch.alg_choice, patch.retcode, patch.resid, patch.original)
+        patch.alg_choice, patch.retcode, patch.resid, patch.original, patch.saved_subsystem)
 end
 
 Base.@propagate_inbounds function Base.getproperty(x::AbstractODESolution, s::Symbol)
@@ -154,12 +158,12 @@ end
 function ODESolution{T, N}(
         u, u_analytic, errors, t, k, discretes, prob, alg, interp, dense,
         tslocation, stats, alg_choice, retcode, resid = nothing,
-        original = nothing) where {T, N}
+        original = nothing, saved_subsystem = nothing) where {T, N}
     return ODESolution{T, N, typeof(u), typeof(u_analytic), typeof(errors), typeof(t),
         typeof(k), typeof(discretes), typeof(prob), typeof(alg), typeof(interp),
-        typeof(stats), typeof(alg_choice), typeof(resid),
-        typeof(original)}(u, u_analytic, errors, t, k, discretes, prob, alg, interp,
-        dense, tslocation, stats, alg_choice, retcode, resid, original)
+        typeof(stats), typeof(alg_choice), typeof(resid), typeof(original),
+        typeof(saved_subsystem)}(u, u_analytic, errors, t, k, discretes, prob, alg, interp,
+        dense, tslocation, stats, alg_choice, retcode, resid, original, saved_subsystem)
 end
 
 error_if_observed_derivative(_, _, ::Type{Val{0}}) = nothing
@@ -409,15 +413,25 @@ const PeriodicDiffEqArray = DiffEqArray{T, N, A, B} where {T, N, A, B <: Abstrac
 # public API, used by MTK
 """
     get_saveable_values(sys, ps, timeseries_idx)
+
+Return the values to be saved in parameter object `ps` for timeseries index `timeseries_idx`. Called by
+`save_discretes!`. If this returns `nothing`, `save_discretes!` will not save anything.
 """
 function get_saveable_values(sys, ps, timeseries_idx)
     return get_saveable_values(symbolic_container(sys), ps, timeseries_idx)
 end
 
+"""
+    save_discretes!(integ::DEIntegrator, timeseries_idx)
+
+Save the parameter timeseries with index `timeseries_idx`. Calls `get_saveable_values` to
+get the values to save. If it returns `nothing`, then the save does not happen.
+"""
 function save_discretes!(integ::DEIntegrator, timeseries_idx)
-    save_discretes!(integ.sol, current_time(integ),
-        get_saveable_values(integ, parameter_values(integ), timeseries_idx),
-        timeseries_idx)
+    inner_sol = get_sol(integ)
+    vals = get_saveable_values(inner_sol, parameter_values(integ), timeseries_idx)
+    vals === nothing && return
+    save_discretes!(integ.sol, current_time(integ), vals, timeseries_idx)
 end
 
 save_discretes!(args...) = nothing
@@ -451,6 +465,7 @@ function build_solution(prob::Union{AbstractODEProblem, AbstractDDEProblem},
         interp = LinearInterpolation(t, u),
         retcode = ReturnCode.Default, destats = missing, stats = nothing,
         resid = nothing, original = nothing,
+        saved_subsystem = nothing,
         kwargs...)
     T = eltype(eltype(u))
 
@@ -482,7 +497,12 @@ function build_solution(prob::Union{AbstractODEProblem, AbstractDDEProblem},
 
     ps = parameter_values(prob)
     if has_sys(prob.f)
-        discretes = create_parameter_timeseries_collection(prob.f.sys, ps, prob.tspan)
+        sswf = if saved_subsystem === nothing
+            prob.f.sys
+        else
+            SavedSubsystemWithFallback(saved_subsystem, prob.f.sys)
+        end
+        discretes = create_parameter_timeseries_collection(sswf, ps, prob.tspan)
     else
         discretes = nothing
     end
@@ -503,7 +523,8 @@ function build_solution(prob::Union{AbstractODEProblem, AbstractDDEProblem},
             alg_choice,
             retcode,
             resid,
-            original)
+            original,
+            saved_subsystem)
         if calculate_error
             calculate_solution_errors!(sol; timeseries_errors = timeseries_errors,
                 dense_errors = dense_errors)
@@ -524,7 +545,8 @@ function build_solution(prob::Union{AbstractODEProblem, AbstractDDEProblem},
             alg_choice,
             retcode,
             resid,
-            original)
+            original,
+            saved_subsystem)
     end
 end
 
@@ -593,7 +615,7 @@ function solution_slice(sol::ODESolution{T, N}, I) where {T, N}
     @reset sol.u_analytic = sol.u_analytic === nothing ? nothing : sol.u_analytic[I]
     @reset sol.t = sol.t[I]
     @reset sol.k = sol.dense ? sol.k[I] : sol.k
-    return @set sol.alg = false
+    return @set sol.dense = false
 end
 
 mask_discretes(::Nothing, _, _...) = nothing