Merge branch 'master' into as/optional-inbounds

Author: ChrisRackauckas

ext/MTKHomotopyContinuationExt.jl

@@ -101,15 +101,16 @@ function MTK.HomotopyContinuationProblem(
     return prob
 end
 
-function MTK._safe_HomotopyContinuationProblem(sys, u0map, parammap = nothing; kwargs...)
+function MTK._safe_HomotopyContinuationProblem(sys, u0map, parammap = nothing;
+        fraction_cancel_fn = SymbolicUtils.simplify_fractions, kwargs...)
     if !iscomplete(sys)
         error("A completed `NonlinearSystem` is required. Call `complete` or `structural_simplify` on the system before creating a `HomotopyContinuationProblem`")
     end
     transformation = MTK.PolynomialTransformation(sys)
     if transformation isa MTK.NotPolynomialError
         return transformation
     end
-    result = MTK.transform_system(sys, transformation)
+    result = MTK.transform_system(sys, transformation; fraction_cancel_fn)
     if result isa MTK.NotPolynomialError
         return result
     end

src/systems/model_parsing.jl

@@ -497,7 +497,7 @@ function generate_var!(dict, a, b, varclass, mod;
     vd isa Vector && (vd = first(vd))
     vd[a] = Dict{Symbol, Any}()
     var = if indices === nothing
-        Symbolics.variable(a, T = SymbolicUtils.FnType{Tuple{Any}, type})(iv)
+        first(@variables $a(iv)::type)
     else
         vd[a][:size] = Tuple(lastindex.(indices))
         first(@variables $a(iv)[indices...]::type)

src/systems/nonlinear/homotopy_continuation.jl

@@ -442,7 +442,8 @@ Transform the system `sys` with `transformation` and return a
 `PolynomialTransformationResult`, or a `NotPolynomialError` if the system cannot
 be transformed.
 """
-function transform_system(sys::NonlinearSystem, transformation::PolynomialTransformation)
+function transform_system(sys::NonlinearSystem, transformation::PolynomialTransformation;
+        fraction_cancel_fn = simplify_fractions)
     subrules = transformation.substitution_rules
     dvs = unknowns(sys)
     eqs = full_equations(sys)
@@ -463,7 +464,7 @@ function transform_system(sys::NonlinearSystem, transformation::PolynomialTransf
             return NotPolynomialError(
                 VariablesAsPolyAndNonPoly(dvs[poly_and_nonpoly]), eqs, polydata)
         end
-        num, den = handle_rational_polynomials(t, new_dvs)
+        num, den = handle_rational_polynomials(t, new_dvs; fraction_cancel_fn)
         # make factors different elements, otherwise the nonzero factors artificially
         # inflate the error of the zero factor.
         if iscall(den) && operation(den) == *
@@ -492,43 +493,67 @@ $(TYPEDSIGNATURES)
 Given a `x`, a polynomial in variables in `wrt` which may contain rational functions,
 express `x` as a single rational function with polynomial `num` and denominator `den`.
 Return `(num, den)`.
+
+Keyword arguments:
+- `fraction_cancel_fn`: A function which takes a fraction (`operation(expr) == /`) and returns
+  a simplified symbolic quantity with common factors in the numerator and denominator are
+  cancelled. Defaults to `SymbolicUtils.simplify_fractions`, but can be changed to
+  `nothing` to improve performance on large polynomials at the cost of avoiding non-trivial
+  cancellation.
 """
-function handle_rational_polynomials(x, wrt)
+function handle_rational_polynomials(x, wrt; fraction_cancel_fn = simplify_fractions)
     x = unwrap(x)
     symbolic_type(x) == NotSymbolic() && return x, 1
     iscall(x) || return x, 1
     contains_variable(x, wrt) || return x, 1
     any(isequal(x), wrt) && return x, 1
 
-    # simplify_fractions cancels out some common factors
-    # and expands (a / b)^c to a^c / b^c, so we only need
-    # to handle these cases
-    x = simplify_fractions(x)
     op = operation(x)
     args = arguments(x)
 
     if op == /
         # numerator and denominator are trivial
         num, den = args
-        # but also search for rational functions in numerator
-        n, d = handle_rational_polynomials(num, wrt)
-        num, den = n, den * d
-    elseif op == +
+        n1, d1 = handle_rational_polynomials(num, wrt; fraction_cancel_fn)
+        n2, d2 = handle_rational_polynomials(den, wrt; fraction_cancel_fn)
+        num, den = n1 * d2, d1 * n2
+    elseif (op == +) || (op == -)
         num = 0
         den = 1
-
-        # we don't need to do common denominator
-        # because we don't care about cases where denominator
-        # is zero. The expression is zero when all the numerators
-        # are zero.
+        if op == -
+            args[2] = -args[2]
+        end
+        for arg in args
+            n, d = handle_rational_polynomials(arg, wrt; fraction_cancel_fn)
+            num = num * d + n * den
+            den *= d
+        end
+    elseif op == ^
+        base, pow = args
+        num, den = handle_rational_polynomials(base, wrt; fraction_cancel_fn)
+        num ^= pow
+        den ^= pow
+    elseif op == *
+        num = 1
+        den = 1
         for arg in args
-            n, d = handle_rational_polynomials(arg, wrt)
-            num += n
+            n, d = handle_rational_polynomials(arg, wrt; fraction_cancel_fn)
+            num *= n
             den *= d
         end
     else
-        return x, 1
+        error("Unhandled operation in `handle_rational_polynomials`. This should never happen. Please open an issue in ModelingToolkit.jl with an MWE.")
+    end
+
+    if fraction_cancel_fn !== nothing
+        expr = fraction_cancel_fn(num / den)
+        if iscall(expr) && operation(expr) == /
+            num, den = arguments(expr)
+        else
+            num, den = expr, 1
+        end
     end
+
     # if the denominator isn't a polynomial in `wrt`, better to not include it
     # to reduce the size of the gcd polynomial
     if !contains_variable(den, wrt)

src/systems/nonlinear/nonlinearsystem.jl

@@ -527,13 +527,16 @@ end
 
 function DiffEqBase.NonlinearProblem{iip}(sys::NonlinearSystem, u0map,
         parammap = DiffEqBase.NullParameters();
-        check_length = true, use_homotopy_continuation = true, kwargs...) where {iip}
+        check_length = true, use_homotopy_continuation = false, kwargs...) where {iip}
     if !iscomplete(sys)
         error("A completed `NonlinearSystem` is required. Call `complete` or `structural_simplify` on the system before creating a `NonlinearProblem`")
     end
-    prob = safe_HomotopyContinuationProblem(sys, u0map, parammap; check_length, kwargs...)
-    if prob isa HomotopyContinuationProblem
-        return prob
+    if use_homotopy_continuation
+        prob = safe_HomotopyContinuationProblem(
+            sys, u0map, parammap; check_length, kwargs...)
+        if prob isa HomotopyContinuationProblem
+            return prob
+        end
     end
     f, u0, p = process_SciMLProblem(NonlinearFunction{iip}, sys, u0map, parammap;
         check_length, kwargs...)

test/extensions/homotopy_continuation.jl

@@ -1,4 +1,5 @@
 using ModelingToolkit, NonlinearSolve, SymbolicIndexingInterface
+using SymbolicUtils
 import ModelingToolkit as MTK
 using LinearAlgebra
 using Test
@@ -29,11 +30,13 @@ import HomotopyContinuation
     @test SciMLBase.successful_retcode(sol)
     @test norm(sol.resid)≈0.0 atol=1e-10
 
-    prob2 = NonlinearProblem(sys, u0)
+    prob2 = NonlinearProblem(sys, u0; use_homotopy_continuation = true)
     @test prob2 isa HomotopyContinuationProblem
     sol = solve(prob2; threading = false)
     @test SciMLBase.successful_retcode(sol)
     @test norm(sol.resid)≈0.0 atol=1e-10
+
+    @test NonlinearProblem(sys, u0; use_homotopy_continuation = false) isa NonlinearProblem
 end
 
 struct Wrapper
@@ -217,7 +220,17 @@ end
         @mtkbuild sys = NonlinearSystem([x^2 + y^2 - 2x - 2 ~ 0, y ~ (x - 1) / (x - 2)])
         prob = HomotopyContinuationProblem(sys, [])
         @test any(prob.denominator([2.0], parameter_values(prob)) .≈ 0.0)
-        @test_nowarn solve(prob; threading = false)
+        @test SciMLBase.successful_retcode(solve(prob; threading = false))
+    end
+
+    @testset "Rational function forced to common denominators" begin
+        @variables x = 1
+        @mtkbuild sys = NonlinearSystem([0 ~ 1 / (1 + x) - x])
+        prob = HomotopyContinuationProblem(sys, [])
+        @test any(prob.denominator([-1.0], parameter_values(prob)) .≈ 0.0)
+        sol = solve(prob; threading = false)
+        @test SciMLBase.successful_retcode(sol)
+        @test 1 / (1 + sol.u[1]) - sol.u[1]≈0.0 atol=1e-10
     end
 end
 
@@ -229,3 +242,19 @@ end
     @test sol[x] ≈ √2.0
     @test sol[y] ≈ sin(√2.0)
 end
+
+@testset "`fraction_cancel_fn`" begin
+    @variables x = 1
+    @named sys = NonlinearSystem([0 ~ ((x^2 - 5x + 6) / (x - 2) - 1) * (x^2 - 7x + 12) /
+                                      (x - 4)^3])
+    sys = complete(sys)
+
+    @testset "`simplify_fractions`" begin
+        prob = HomotopyContinuationProblem(sys, [])
+        @test prob.denominator([0.0], parameter_values(prob)) ≈ [4.0]
+    end
+    @testset "`nothing`" begin
+        prob = HomotopyContinuationProblem(sys, []; fraction_cancel_fn = nothing)
+        @test sort(prob.denominator([0.0], parameter_values(prob))) ≈ [2.0, 4.0^3]
+    end
+end

test/model_parsing.jl

@@ -1,4 +1,4 @@
-using ModelingToolkit, Test
+using ModelingToolkit, Symbolics, Test
 using ModelingToolkit: get_connector_type, get_defaults, get_gui_metadata,
                        get_systems, get_ps, getdefault, getname, readable_code,
                        scalarize, symtype, VariableDescription, RegularConnector,
@@ -990,3 +990,22 @@ struct CustomStruct end
     @named sys = MyModel(p = CustomStruct())
     @test ModelingToolkit.defaults(sys)[@nonamespace sys.p] == CustomStruct()
 end
+
+@testset "Variables are not callable symbolics" begin
+    @mtkmodel Example begin
+        @variables begin
+            x(t)
+            y(t)
+        end
+        @equations begin
+            x ~ y
+        end
+    end
+    @named ex = Example()
+    vars = Symbolics.get_variables(only(equations(ex)))
+    @test length(vars) == 2
+    for u in Symbolics.unwrap.(unknowns(ex))
+        @test !Symbolics.hasmetadata(u, Symbolics.CallWithParent)
+        @test any(isequal(u), vars)
+    end
+end