Merge remote-tracking branch 'origin/master' into MTK

Author: vyudu

.github/workflows/Tests.yml

@@ -32,6 +32,7 @@ jobs:
         group:
           - InterfaceI
           - InterfaceII
+          - Initialization
           - SymbolicIndexingInterface
           - Extended
           - Extensions

Project.toml

@@ -1,7 +1,7 @@
 name = "ModelingToolkit"
 uuid = "961ee093-0014-501f-94e3-6117800e7a78"
 authors = ["Yingbo Ma <[email protected]>", "Chris Rackauckas <[email protected]> and contributors"]
-version = "9.53.0"
+version = "9.54.0"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
@@ -64,6 +64,7 @@ BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
 ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
 DeepDiffs = "ab62b9b5-e342-54a8-a765-a90f495de1a6"
 HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
+InfiniteOpt = "20393b10-9daf-11e9-18c9-8db751c92c57"
 LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 
 [extensions]
@@ -72,6 +73,7 @@ MTKChainRulesCoreExt = "ChainRulesCore"
 MTKDeepDiffsExt = "DeepDiffs"
 MTKHomotopyContinuationExt = "HomotopyContinuation"
 MTKLabelledArraysExt = "LabelledArrays"
+MTKInfiniteOptExt = "InfiniteOpt"
 
 [compat]
 AbstractTrees = "0.3, 0.4"
@@ -104,6 +106,7 @@ FunctionWrappers = "1.1"
 FunctionWrappersWrappers = "0.1"
 Graphs = "1.5.2"
 HomotopyContinuation = "2.11"
+InfiniteOpt = "0.5"
 InteractiveUtils = "1"
 JuliaFormatter = "1.0.47"
 JumpProcesses = "9.13.1"

docs/src/tutorials/initialization.md

@@ -113,7 +113,7 @@ the `initialization_eqs` keyword argument, for example:
 
 ```@example init
 prob = ODEProblem(pend, [x => 1], (0.0, 1.5), [g => 1], guesses = [λ => 0, y => 1],
-    initialization_eqs = [y ~ 1])
+    initialization_eqs = [y ~ 0])
 sol = solve(prob, Rodas5P())
 plot(sol, idxs = (x, y))
 ```

ext/MTKInfiniteOptExt.jl

@@ -0,0 +1,26 @@
+module MTKInfiniteOptExt
+import ModelingToolkit
+import SymbolicUtils
+import NaNMath
+import InfiniteOpt
+import InfiniteOpt: JuMP, GeneralVariableRef
+
+# This file contains method definitions to make it possible to trace through functions generated by MTK using JuMP variables
+
+for ff in [acos, log1p, acosh, log2, asin, tan, atanh, cos, log, sin, log10, sqrt]
+    f = nameof(ff)
+    # These need to be defined so that JuMP can trace through functions built by Symbolics
+    @eval NaNMath.$f(x::GeneralVariableRef) = Base.$f(x)
+end
+
+# JuMP variables and Symbolics variables never compare equal. When tracing through dynamics, a function argument can be either a JuMP variable or A Symbolics variable, it can never be both.
+function Base.isequal(::SymbolicUtils.Symbolic,
+        ::Union{JuMP.GenericAffExpr, JuMP.GenericQuadExpr, InfiniteOpt.AbstractInfOptExpr})
+    false
+end
+function Base.isequal(
+        ::Union{JuMP.GenericAffExpr, JuMP.GenericQuadExpr, InfiniteOpt.AbstractInfOptExpr},
+        ::SymbolicUtils.Symbolic)
+    false
+end
+end

src/structural_transformation/symbolics_tearing.jl

@@ -88,6 +88,14 @@ function tearing_sub(expr, dict, s)
     s ? simplify(expr) : expr
 end
 
+function tearing_substitute_expr(sys::AbstractSystem, expr; simplify = false)
+    empty_substitutions(sys) && return expr
+    substitutions = get_substitutions(sys)
+    @unpack subs = substitutions
+    solved = Dict(eq.lhs => eq.rhs for eq in subs)
+    return tearing_sub(expr, solved, simplify)
+end
+
 """
 $(TYPEDSIGNATURES)
 

src/structural_transformation/utils.jl

@@ -58,7 +58,41 @@ end
 ###
 ### Structural check
 ###
-function check_consistency(state::TransformationState, orig_inputs)
+
+"""
+    $(TYPEDSIGNATURES)
+
+Check if the `state` represents a singular system, and return the unmatched variables.
+"""
+function singular_check(state::TransformationState)
+    @unpack graph, var_to_diff = state.structure
+    fullvars = get_fullvars(state)
+    # This is defined to check if Pantelides algorithm terminates. For more
+    # details, check the equation (15) of the original paper.
+    extended_graph = (@set graph.fadjlist = Vector{Int}[graph.fadjlist;
+                                                        map(collect, edges(var_to_diff))])
+    extended_var_eq_matching = maximal_matching(extended_graph)
+
+    nvars = ndsts(graph)
+    unassigned_var = []
+    for (vj, eq) in enumerate(extended_var_eq_matching)
+        vj > nvars && break
+        if eq === unassigned && !isempty(𝑑neighbors(graph, vj))
+            push!(unassigned_var, fullvars[vj])
+        end
+    end
+    return unassigned_var
+end
+
+"""
+    $(TYPEDSIGNATURES)
+
+Check the consistency of `state`, given the inputs `orig_inputs`. If `nothrow == false`,
+throws an error if the system is under-/over-determined or singular. In this case, if the
+function returns it will return `true`. If `nothrow == true`, it will return `false`
+instead of throwing an error. The singular case will print a warning.
+"""
+function check_consistency(state::TransformationState, orig_inputs; nothrow = false)
     fullvars = get_fullvars(state)
     neqs = n_concrete_eqs(state)
     @unpack graph, var_to_diff = state.structure
@@ -72,6 +106,7 @@ function check_consistency(state::TransformationState, orig_inputs)
     is_balanced = n_highest_vars == neqs
 
     if neqs > 0 && !is_balanced
+        nothrow && return false
         varwhitelist = var_to_diff .== nothing
         var_eq_matching = maximal_matching(graph, eq -> true, v -> varwhitelist[v]) # not assigned
         # Just use `error_reporting` to do conditional
@@ -85,22 +120,12 @@ function check_consistency(state::TransformationState, orig_inputs)
         error_reporting(state, bad_idxs, n_highest_vars, iseqs, orig_inputs)
     end
 
-    # This is defined to check if Pantelides algorithm terminates. For more
-    # details, check the equation (15) of the original paper.
-    extended_graph = (@set graph.fadjlist = Vector{Int}[graph.fadjlist;
-                                                        map(collect, edges(var_to_diff))])
-    extended_var_eq_matching = maximal_matching(extended_graph)
-
-    nvars = ndsts(graph)
-    unassigned_var = []
-    for (vj, eq) in enumerate(extended_var_eq_matching)
-        vj > nvars && break
-        if eq === unassigned && !isempty(𝑑neighbors(graph, vj))
-            push!(unassigned_var, fullvars[vj])
-        end
-    end
+    unassigned_var = singular_check(state)
 
     if !isempty(unassigned_var) || !is_balanced
+        if nothrow
+            return false
+        end
         io = IOBuffer()
         Base.print_array(io, unassigned_var)
         unassigned_var_str = String(take!(io))
@@ -110,7 +135,7 @@ function check_consistency(state::TransformationState, orig_inputs)
         throw(InvalidSystemException(errmsg))
     end
 
-    return nothing
+    return true
 end
 
 ###

src/systems/abstractsystem.jl

@@ -3335,7 +3335,8 @@ function parse_variable(sys::AbstractSystem, str::AbstractString)
     # I'd write a regex to validate `str`, but https://xkcd.com/1171/
     str = strip(str)
     derivative_level = 0
-    while ((cond1 = startswith(str, "D(")) || startswith(str, "Differential(")) && endswith(str, ")")
+    while ((cond1 = startswith(str, "D(")) || startswith(str, "Differential(")) &&
+        endswith(str, ")")
         if cond1
             derivative_level += 1
             str = _string_view_inner(str, 2, 1)

src/systems/diffeqs/abstractodesystem.jl

@@ -590,6 +590,8 @@ function DiffEqBase.DAEFunction{iip}(sys::AbstractODESystem, dvs = unknowns(sys)
         checkbounds = false,
         initializeprob = nothing,
         initializeprobmap = nothing,
+        initializeprobpmap = nothing,
+        update_initializeprob! = nothing,
         kwargs...) where {iip}
     if !iscomplete(sys)
         error("A completed system is required. Call `complete` or `structural_simplify` on the system before creating a `DAEFunction`")
@@ -643,7 +645,9 @@ function DiffEqBase.DAEFunction{iip}(sys::AbstractODESystem, dvs = unknowns(sys)
         jac_prototype = jac_prototype,
         observed = observedfun,
         initializeprob = initializeprob,
-        initializeprobmap = initializeprobmap)
+        initializeprobmap = initializeprobmap,
+        initializeprobpmap = initializeprobpmap,
+        update_initializeprob! = update_initializeprob!)
 end
 
 function DiffEqBase.DDEFunction(sys::AbstractODESystem, args...; kwargs...)
@@ -1387,7 +1391,7 @@ function InitializationProblem{iip, specialize}(sys::AbstractODESystem,
         check_length = true,
         warn_initialize_determined = true,
         initialization_eqs = [],
-        fully_determined = false,
+        fully_determined = nothing,
         check_units = true,
         kwargs...) where {iip, specialize}
     if !iscomplete(sys)
@@ -1405,6 +1409,19 @@ function InitializationProblem{iip, specialize}(sys::AbstractODESystem,
                 sys; u0map, initialization_eqs, check_units, pmap = parammap); fully_determined)
     end
 
+    ts = get_tearing_state(isys)
+    if warn_initialize_determined &&
+       (unassigned_vars = StructuralTransformations.singular_check(ts); !isempty(unassigned_vars))
+        errmsg = """
+        The initialization system is structurally singular. Guess values may \
+        significantly affect the initial values of the ODE. The problematic variables \
+        are $unassigned_vars.
+
+        Note that the identification of problematic variables is a best-effort heuristic.
+        """
+        @warn errmsg
+    end
+
     uninit = setdiff(unknowns(sys), [unknowns(isys); getfield.(observed(isys), :lhs)])
 
     # TODO: throw on uninitialized arrays
@@ -1448,6 +1465,7 @@ function InitializationProblem{iip, specialize}(sys::AbstractODESystem,
         u0T = promote_type(u0T, typeof(fullmap[eq.lhs]))
     end
     if u0T != Union{}
+        u0T = eltype(u0T)
         u0map = Dict(k => if symbolic_type(v) == NotSymbolic() && !is_array_of_symbolics(v)
                          v isa AbstractArray ? u0T.(v) : u0T(v)
                      else

src/systems/index_cache.jl

@@ -40,10 +40,12 @@ const TunableIndexMap = Dict{BasicSymbolic,
     Union{Int, UnitRange{Int}, Base.ReshapedArray{Int, N, UnitRange{Int}} where {N}}}
 const TimeseriesSetType = Set{Union{ContinuousTimeseries, Int}}
 
+const SymbolicParam = Union{BasicSymbolic, CallWithMetadata}
+
 struct IndexCache
     unknown_idx::UnknownIndexMap
     # sym => (bufferidx, idx_in_buffer)
-    discrete_idx::Dict{BasicSymbolic, DiscreteIndex}
+    discrete_idx::Dict{SymbolicParam, DiscreteIndex}
     # sym => (clockidx, idx_in_clockbuffer)
     callback_to_clocks::Dict{Any, Vector{Int}}
     tunable_idx::TunableIndexMap
@@ -56,13 +58,13 @@ struct IndexCache
     tunable_buffer_size::BufferTemplate
     constant_buffer_sizes::Vector{BufferTemplate}
     nonnumeric_buffer_sizes::Vector{BufferTemplate}
-    symbol_to_variable::Dict{Symbol, Union{BasicSymbolic, CallWithMetadata}}
+    symbol_to_variable::Dict{Symbol, SymbolicParam}
 end
 
 function IndexCache(sys::AbstractSystem)
     unks = solved_unknowns(sys)
     unk_idxs = UnknownIndexMap()
-    symbol_to_variable = Dict{Symbol, Union{BasicSymbolic, CallWithMetadata}}()
+    symbol_to_variable = Dict{Symbol, SymbolicParam}()
 
     let idx = 1
         for sym in unks
@@ -95,18 +97,18 @@ function IndexCache(sys::AbstractSystem)
 
     tunable_buffers = Dict{Any, Set{BasicSymbolic}}()
     constant_buffers = Dict{Any, Set{BasicSymbolic}}()
-    nonnumeric_buffers = Dict{Any, Set{Union{BasicSymbolic, CallWithMetadata}}}()
+    nonnumeric_buffers = Dict{Any, Set{SymbolicParam}}()
 
     function insert_by_type!(buffers::Dict{Any, S}, sym, ctype) where {S}
         sym = unwrap(sym)
         buf = get!(buffers, ctype, S())
         push!(buf, sym)
     end
 
-    disc_param_callbacks = Dict{BasicSymbolic, Set{Int}}()
+    disc_param_callbacks = Dict{SymbolicParam, Set{Int}}()
     events = vcat(continuous_events(sys), discrete_events(sys))
     for (i, event) in enumerate(events)
-        discs = Set{BasicSymbolic}()
+        discs = Set{SymbolicParam}()
         affs = affects(event)
         if !(affs isa AbstractArray)
             affs = [affs]
@@ -130,26 +132,32 @@ function IndexCache(sys::AbstractSystem)
                isequal(only(arguments(sym)), get_iv(sys))
                 clocks = get!(() -> Set{Int}(), disc_param_callbacks, sym)
                 push!(clocks, i)
-            else
+            elseif is_variable_floatingpoint(sym)
                 insert_by_type!(constant_buffers, sym, symtype(sym))
+            else
+                stype = symtype(sym)
+                if stype <: FnType
+                    stype = fntype_to_function_type(stype)
+                end
+                insert_by_type!(nonnumeric_buffers, sym, stype)
             end
         end
     end
     clock_partitions = unique(collect(values(disc_param_callbacks)))
     disc_symtypes = unique(symtype.(keys(disc_param_callbacks)))
     disc_symtype_idx = Dict(disc_symtypes .=> eachindex(disc_symtypes))
-    disc_syms_by_symtype = [BasicSymbolic[] for _ in disc_symtypes]
+    disc_syms_by_symtype = [SymbolicParam[] for _ in disc_symtypes]
     for sym in keys(disc_param_callbacks)
         push!(disc_syms_by_symtype[disc_symtype_idx[symtype(sym)]], sym)
     end
-    disc_syms_by_symtype_by_partition = [Vector{BasicSymbolic}[] for _ in disc_symtypes]
+    disc_syms_by_symtype_by_partition = [Vector{SymbolicParam}[] for _ in disc_symtypes]
     for (i, buffer) in enumerate(disc_syms_by_symtype)
         for partition in clock_partitions
             push!(disc_syms_by_symtype_by_partition[i],
                 [sym for sym in buffer if disc_param_callbacks[sym] == partition])
         end
     end
-    disc_idxs = Dict{BasicSymbolic, DiscreteIndex}()
+    disc_idxs = Dict{SymbolicParam, DiscreteIndex}()
     callback_to_clocks = Dict{
         Union{SymbolicContinuousCallback, SymbolicDiscreteCallback}, Set{Int}}()
     for (typei, disc_syms_by_partition) in enumerate(disc_syms_by_symtype_by_partition)
@@ -191,6 +199,7 @@ function IndexCache(sys::AbstractSystem)
         end
         haskey(disc_idxs, p) && continue
         haskey(constant_buffers, ctype) && p in constant_buffers[ctype] && continue
+        haskey(nonnumeric_buffers, ctype) && p in nonnumeric_buffers[ctype] && continue
         insert_by_type!(
             if ctype <: Real || ctype <: AbstractArray{<:Real}
                 if istunable(p, true) && Symbolics.shape(p) != Symbolics.Unknown() &&

src/systems/model_parsing.jl

@@ -923,7 +923,7 @@ function parse_variable_arg(dict, mod, arg, varclass, kwargs, where_types)
         end
 
         push!(varexpr.args, metadata_expr)
-        return vv isa Num ? name : :($name...), varexpr
+        return symbolic_type(vv) == ScalarSymbolic() ? name : :($name...), varexpr
     else
         return vv
     end