Clean up generate_initializesystem()

src/systems/nonlinear/initializesystem.jl

@@ -5,109 +5,92 @@ Generate `NonlinearSystem` which initializes an ODE problem from specified initi
 """
 function generate_initializesystem(sys::ODESystem;
         u0map = Dict(),
-        name = nameof(sys),
-        guesses = Dict(), check_defguess = false,
-        default_dd_value = 0.0,
-        algebraic_only = false,
         initialization_eqs = [],
-        check_units = true,
-        kwargs...)
-    sts, eqs = unknowns(sys), equations(sys)
+        guesses = Dict(),
+        default_dd_guess = 0.0,
+        algebraic_only = false,
+        check_units = true, check_defguess = false,
+        name = nameof(sys), kwargs...)
+    vars = unique([unknowns(sys); getfield.((observed(sys)), :lhs)])
+    vars_set = Set(vars) # for efficient in-lookup
+
+    eqs = equations(sys)
     idxs_diff = isdiffeq.(eqs)
     idxs_alge = .!idxs_diff
-    num_alge = sum(idxs_alge)
-
-    # Start the equations list with algebraic equations
-    eqs_ics = eqs[idxs_alge]
-    u0 = Vector{Pair}(undef, 0)
 
+    # prepare map for dummy derivative substitution
     eqs_diff = eqs[idxs_diff]
-    diffmap = Dict(getfield.(eqs_diff, :lhs) .=> getfield.(eqs_diff, :rhs))
-    observed_diffmap = Dict(Differential(get_iv(sys)).(getfield.((observed(sys)), :lhs)) .=>
-        Differential(get_iv(sys)).(getfield.((observed(sys)), :rhs)))
-    full_diffmap = merge(diffmap, observed_diffmap)
+    D = Differential(get_iv(sys))
+    diffmap = merge(
+        Dict(eq.lhs => eq.rhs for eq in eqs_diff),
+        Dict(D(eq.lhs) => D(eq.rhs) for eq in observed(sys))
+    )
 
-    full_states = unique([sts; getfield.((observed(sys)), :lhs)])
-    set_full_states = Set(full_states)
+    # 1) process dummy derivatives and u0map into initialization system
+    eqs_ics = eqs[idxs_alge] # start equation list with algebraic equations
+    defs = copy(defaults(sys)) # copy so we don't modify sys.defaults
     guesses = merge(get_guesses(sys), todict(guesses))
     schedule = getfield(sys, :schedule)
-
-    if schedule !== nothing
-        guessmap = [x[1] => get(guesses, x[1], default_dd_value)
-                    for x in schedule.dummy_sub]
-        dd_guess = Dict(filter(x -> !isnothing(x[1]), guessmap))
-        if u0map === nothing || isempty(u0map)
-            filtered_u0 = u0map
-        else
-            filtered_u0 = Pair[]
-            for x in u0map
-                y = get(schedule.dummy_sub, x[1], x[1])
-                y = ModelingToolkit.fixpoint_sub(y, full_diffmap)
-
-                if y ∈ set_full_states
-                    # defer initialization until defaults are merged below
-                    push!(filtered_u0, y => x[2])
+    if !isnothing(schedule)
+        for x in filter(x -> !isnothing(x[1]), schedule.dummy_sub)
+            # set dummy derivatives to default_dd_guess unless specified
+            push!(defs, x[1] => get(guesses, x[1], default_dd_guess))
+        end
+        if !isnothing(u0map)
+            for (y, x) in u0map
+                y = get(schedule.dummy_sub, y, y)
+                y = fixpoint_sub(y, diffmap)
+                if y ∈ vars_set
+                    # variables specified in u0 overrides defaults
+                    push!(defs, y => x)
                 elseif y isa Symbolics.Arr
-                    # scalarize array # TODO: don't scalarize arrays
-                    _y = collect(y)
-                    for i in eachindex(_y)
-                        push!(filtered_u0, _y[i] => x[2][i])
-                    end
+                    # TODO: don't scalarize arrays
+                    push!(defs, collect(y) .=> x)
                 elseif y isa Symbolics.BasicSymbolic
-                    # y is a derivative expression expanded
-                    # add to the initialization equations
-                    push!(eqs_ics, y ~ x[2])
+                    # y is a derivative expression expanded; add it to the initialization equations
+                    push!(eqs_ics, y ~ x)
                 else
                     error("Initialization expression $y is currently not supported. If its a higher order derivative expression, then only the dummy derivative expressions are supported.")
                 end
             end
-            filtered_u0 = todict(filtered_u0)
         end
-    else
-        dd_guess = Dict()
-        filtered_u0 = todict(u0map)
     end
 
-    defs = merge(defaults(sys), filtered_u0)
-
-    for st in full_states
-        if st ∈ keys(defs)
-            def = defs[st]
-
+    # 2) process other variables
+    for var in vars
+        if var ∈ keys(defs)
+            def = defs[var]
             if def isa Equation
-                st ∉ keys(guesses) && check_defguess &&
-                    error("Invalid setup: unknown $(st) has an initial condition equation with no guess.")
+                # TODO: this behavior is not tested!
+                var ∉ keys(guesses) && check_defguess &&
+                    error("Invalid setup: variable $(var) has an initial condition equation with no guess.")
                 push!(eqs_ics, def)
-                push!(u0, st => guesses[st])
+                push!(defs, var => guesses[var])
             else
-                push!(eqs_ics, st ~ def)
-                push!(u0, st => def)
+                push!(eqs_ics, var ~ def)
             end
-        elseif st ∈ keys(guesses)
-            push!(u0, st => guesses[st])
+        elseif var ∈ keys(guesses)
+            push!(defs, var => guesses[var])
         elseif check_defguess
-            error("Invalid setup: unknown $(st) has no default value or initial guess")
+            error("Invalid setup: variable $(var) has no default value or initial guess")
         end
     end
 
+    # 3) process explicitly provided initialization equations
     if !algebraic_only
-        for eq in [get_initialization_eqs(sys); initialization_eqs]
-            _eq = ModelingToolkit.fixpoint_sub(eq, full_diffmap)
-            push!(eqs_ics, _eq)
+        initialization_eqs = [get_initialization_eqs(sys); initialization_eqs]
+        for eq in initialization_eqs
+            eq = fixpoint_sub(eq, diffmap) # expand dummy derivatives
+            push!(eqs_ics, eq)
         end
     end
 
-    pars = [parameters(sys); get_iv(sys)]
-    nleqs = [eqs_ics; observed(sys)]
-
-    sys_nl = NonlinearSystem(nleqs,
-        full_states,
-        pars;
-        defaults = merge(ModelingToolkit.defaults(sys), todict(u0), dd_guess),
-        parameter_dependencies = parameter_dependencies(sys),
+    pars = [parameters(sys); get_iv(sys)] # include independent variable as pseudo-parameter
+    eqs_ics = [eqs_ics; observed(sys)]
+    return NonlinearSystem(
+        eqs_ics, vars, pars;
+        defaults = defs, parameter_dependencies = parameter_dependencies(sys),
         checks = check_units,
-        name,
-        kwargs...)
-
-    return sys_nl
+        name, kwargs...
+    )
 end