init

Author: TorkelE

test/miscellaneous_tests/nonlinear_solve.jl

@@ -0,0 +1,98 @@
+### Fetch Packages ###
+
+# Fetch packages.
+using Catalyst, NonlinearSolve, OrdinaryDiffEq, SteadyStateDiffEq
+using Random, Test
+
+# Sets rnd number.
+using StableRNGs
+rng = StableRNG(12345)
+
+### Run Tests ###
+
+# Creates a simple problem and find steady states just different approaches. Compares to analytic solution.
+let 
+    # Model with easily computable steady states.
+    steady_state_network_1 = @reaction_network begin
+        (k1, k2), ∅ ↔ X1
+        (k3, k4), ∅ ↔ 3X2
+        (k5, k6), ∅ ↔ X3 + X4
+    end
+    
+    # Creates NonlinearProblem.
+    u0 = rand(rng, length(states(steady_state_network_1)))
+    p = rand(rng, length(parameters(steady_state_network_1)))
+    nl_prob = NonlinearProblem(steady_state_network_1, u0, p)
+    
+    # Solves it using standard algorithm and simulation based algorithm.
+    sol1 = solve(nl_prob; abstol=1e-15, reltol=1e-15).u
+    sol2 = solve(nl_prob, DynamicSS(Tsit5(); abstol=1e-15, reltol=1e-15); abstol=1e-15, reltol=1e-15).u
+    
+    # Tests solutions are correct.
+    @test abs.(sol1[1] - p[1] / p[2]) < 1e-8
+    @test abs.(sol1[2]^3 / factorial(3) - p[3] / p[4]) < 1e-8
+    @test abs.(sol1[3] * sol1[4] - p[5] / p[6]) < 1e-8
+    @test sol1 ≈ sol2
+end
+
+# Creates a system with multiple steady states.
+# Checks that corresponding ODEFunction return 0.0 in both cases. Checks for manually computed function as well.
+# Checks with SYmbol `u0` and Symbolic `p`.
+let 
+    # Creates steady state network, unpack the parameter values.
+    steady_state_network_2 = @reaction_network begin
+        v / 10 + hill(X, v, K, n), ∅ → X
+        d, X → ∅
+    end
+    @unpack v, K, n, d = steady_state_network_2
+
+    # Creates NonlinearProblem.
+    u0 = [:X => 1.0]
+    p = [v => 1.0 + rand(rng), K => 0.8, n => 3, d => 1.0]
+    nl_prob = NonlinearProblem(steady_state_network_2, u0, p)
+    
+    # Solves it using standard algorithm and simulation based algorithm.
+    sol1 = solve(nl_prob; abstol=1e-18, reltol=1e-18).u
+    sol2 = solve(nl_prob, DynamicSS(Tsit5(); abstol=1e-18, reltol=1e-18); abstol=1e-18, reltol=1e-18).u
+    
+    # Computes NonlinearFunction (manually and automatically).
+    nfunc = NonlinearFunction(convert(NonlinearSystem, steady_state_network_2))    
+    function nf_manual(u,p)
+        X = u[1]
+        v, K, n, d = p
+        return v/10 + v * X^n/(X^n + K^n) - d*X
+    end
+
+    # Tests solutions are correct.
+    @test nfunc(sol1, last.(p))[1] ≈ 0.0
+    @test nfunc(sol2, last.(p))[1] ≈ 0.0
+    @test nf_manual(sol1, last.(p)) ≈ 0.0
+    @test nf_manual(sol2, last.(p)) ≈ 0.0
+end
+
+# Checks for system with conservation laws.
+# Checks using interfacing with output solution.
+let 
+    # Creates steady state network, unpack the parameter values.
+    steady_state_network_3 = complete(@reaction_network begin
+        (p,d), 0 <--> X
+        (k1, k2), 2Y <--> Y2
+        (k3, k4), X + Y2 <--> XY2
+    end)
+    @unpack X, Y, Y2, XY2 = steady_state_network_3
+
+    # Creates NonlinearProblem.
+    u0 = [steady_state_network_3.X => rand(), steady_state_network_3.Y => rand() + 1.0, steady_state_network_3.Y2 => rand() + 3.0, steady_state_network_3.XY2 => 0.0]
+    p = [:p => rand()+1.0, :d => 0.5, :k1 => 1.0, :k2 => 2.0, :k3 => 3.0, :k4 => 4.0]
+    nl_prob_1 = NonlinearProblem(steady_state_network_3, u0, p; remove_conserved = true)
+    nl_prob_2 = NonlinearProblem(steady_state_network_3, u0, p)
+
+    # Solves it using standard algorithm and simulation based algorithm.
+    sol1 = solve(nl_prob_1; abstol=1e-18, reltol=1e-18)
+    sol2 = solve(nl_prob_2, DynamicSS(Tsit5(); abstol=1e-18, reltol=1e-18); abstol=1e-18, reltol=1e-18)
+
+    # Checks output using NonlinearFunction.
+    nfunc = NonlinearFunction(convert(NonlinearSystem, steady_state_network_3))   
+    @test all(nfunc([sol1[X], sol1[Y], sol1[Y2], sol1[XY2]], last.(p)) .≈ 0.0)
+    @test all(nfunc([sol2[X], sol2[Y], sol2[Y2], sol2[XY2]], last.(p)) .≈ 0.0)
+end

test/runtests.jl

@@ -14,13 +14,14 @@ using SafeTestsets
     @time @safetestset "Custom CRN Functions" begin include("dsl/custom_functions.jl") end
     @time @safetestset "DSL Options" begin include("dsl/dsl_options.jl") end
 
-    ### Non-DSL model cration and modication. ###
+    ### Non-DSL model creation and modification. ###
     @time @safetestset "ReactionSystem Components Based Creation" begin include("programmatic_model_creation/component_based_model_creation.jl") end
     @time @safetestset "Programmatic Model Expansion" begin include("programmatic_model_creation/programmatic_model_expansion.jl") end
 
     # Runs various miscellaneous tests.
     @time @safetestset "API" begin include("miscellaneous_tests/api.jl") end
     @time @safetestset "Symbolic Stoichiometry" begin include("miscellaneous_tests/symbolic_stoichiometry.jl") end
+    @time @safetestset "NonlinearProblems and Steady State Solving" begin include("miscellaneous_tests/nonlinear_solve.jl") end
     @time @safetestset "Events" begin include("miscellaneous_tests/events.jl") end
     @time @safetestset "Compound species" begin include("miscellaneous_tests/compound_macro.jl") end
     @time @safetestset "Reaction balancing" begin include("miscellaneous_tests/reaction_balancing.jl") end