Merge branch 'iss141'

Author: fchen121

src/ModelingToolkit.jl

@@ -297,7 +297,7 @@ export isinput, isoutput, getbounds, hasbounds, getguess, hasguess, isdisturbanc
        hasunit, getunit, hasconnect, getconnect,
        hasmisc, getmisc, state_priority
 export liouville_transform, change_independent_variable, substitute_component,
-       add_accumulations, noise_to_brownians, Girsanov_transform
+       add_accumulations, noise_to_brownians, Girsanov_transform, changeofvariables, change_of_variable_SDE
 export PDESystem
 export Differential, expand_derivatives, @derivatives
 export Equation, ConstrainedEquation

src/systems/diffeqs/basic_transformations.jl

@@ -53,6 +53,120 @@ function liouville_transform(sys::System; kwargs...)
     )
 end
 
+"""
+$(TYPEDSIGNATURES)
+
+Generates the set of ODEs after change of variables.
+
+
+Example:
+
+```julia
+using ModelingToolkit, OrdinaryDiffEq, Test
+
+# Change of variables: z = log(x)
+# (this implies that x = exp(z) is automatically non-negative)
+
+@parameters t α
+@variables x(t)
+D = Differential(t)
+eqs = [D(x) ~ α*x]
+
+tspan = (0., 1.)
+u0 = [x => 1.0]
+p = [α => -0.5]
+
+@named sys = ODESystem(eqs; defaults=u0)
+prob = ODEProblem(sys, [], tspan, p)
+sol = solve(prob, Tsit5())
+
+@variables z(t)
+forward_subs  = [log(x) => z]
+backward_subs = [x => exp(z)]
+
+@named new_sys = changeofvariables(sys, forward_subs, backward_subs)
+@test equations(new_sys)[1] == (D(z) ~ α)
+
+new_prob = ODEProblem(new_sys, [], tspan, p)
+new_sol = solve(new_prob, Tsit5())
+
+@test isapprox(new_sol[x][end], sol[x][end], atol=1e-4)
+```
+
+"""
+function changeofvariables(sys::System, forward_subs, backward_subs; simplify=false, t0=missing)
+    t = independent_variable(sys)
+
+    old_vars = first.(backward_subs)
+    new_vars = last.(forward_subs)
+    kept_vars = setdiff(states(sys), old_vars)
+    rhs = [eq.rhs for eq in equations(sys)]
+
+    # use: dz/dt = ∂z/∂x dx/dt + ∂z/∂t
+    dzdt = Symbolics.derivative( first.(forward_subs), t )
+    new_eqs = Equation[]
+    for (new_var, ex) in zip(new_vars, dzdt)
+        for ode_eq in equations(sys)
+            ex = substitute(ex, ode_eq.lhs => ode_eq.rhs)
+        end
+        ex = substitute(ex, Dict(forward_subs))
+        ex = substitute(ex, Dict(backward_subs))
+        if simplify
+            ex = Symbolics.simplify(ex, expand=true)
+        end
+        push!(new_eqs, Differential(t)(new_var) ~ ex)
+    end
+
+    defs = get_defaults(sys)
+    new_defs = Dict()
+    for f_sub in forward_subs
+        #TODO call value(...)?
+        ex = substitute(first(f_sub), defs)
+        if !ismissing(t0)
+            ex = substitute(ex, t => t0)
+        end
+        new_defs[last(f_sub)] = ex
+    end
+    return ODESystem(new_eqs;
+                        defaults=new_defs,
+                        observed=vcat(observed(sys),first.(backward_subs) .~ last.(backward_subs))
+                        )
+end
+
+function change_of_variable_SDE(sys::System, forward_subs, backward_subs, iv; simplify=false, t0=missing)
+    t = independent_variable(sys)
+
+    old_vars = first.(backward_subs)
+    new_vars = last.(forward_subs)
+    
+    # use: f = Y(t, X)
+    # use: dY = (∂f/∂t + μ∂f/∂x + (1/2)*σ^2*∂2f/∂x2)dt + σ∂f/∂xdW
+    old_eqs = equations(sys)
+    old_noise = get_noiseeqs(sys)
+    ∂f∂t = Symbolics.derivative( first.(forward_subs), t )
+    ∂f∂x = Symbolics.derivative( first.(forward_subs), old_vars )
+    ∂2f∂x2 = Symbolics.derivative( ∂f∂x, old_vars )
+    new_eqs = Equation[]
+
+    for (new_var, eq, noise, first, second, third) in zip(new_vars, old_eqs, old_noise, ∂f∂t, ∂f∂x, ∂2f∂x2)
+        ex = first + eq.rhs * second + 1/2 * noise^2 * third
+        for eqs in old_eqs
+            ex = substitute(ex, eqs.lhs => eqs.rhs)
+        end
+        ex = substitute(ex, Dict(forward_subs))
+        ex = substitute(ex, Dict(backward_subs))
+        if simplify
+            ex = Symbolics.simplify(ex, expand=true)
+        end
+        push!(new_eqs, Differential(t)(new_var) ~ ex)
+    end
+    new_noise = [noise * div for (noise, div) in zip(old_noise, ∂f∂x)]
+
+    return SDESystem(new_eqs, new_noise;
+            observed=vcat(observed(sys),first.(backward_subs) .~ last.(backward_subs))
+            )
+end
+
 """
     change_independent_variable(
         sys::System, iv, eqs = [];

test/changeofvariables.jl

@@ -0,0 +1,96 @@
+using ModelingToolkit, OrdinaryDiffEq
+using Test, LinearAlgebra
+
+
+# Change of variables: z = log(x)
+# (this implies that x = exp(z) is automatically non-negative)
+
+@parameters t α
+@variables x(t)
+D = Differential(t)
+eqs = [D(x) ~ α*x]
+
+tspan = (0., 1.)
+u0 = [x => 1.0]
+p = [α => -0.5]
+
+sys = ODESystem(eqs; defaults=u0)
+prob = ODEProblem(sys, [], tspan, p)
+sol = solve(prob, Tsit5())
+
+@variables z(t)
+forward_subs  = [log(x) => z]
+backward_subs = [x => exp(z)]
+new_sys = changeofvariables(sys, forward_subs, backward_subs)
+@test equations(new_sys)[1] == (D(z) ~ α)
+
+new_prob = ODEProblem(new_sys, [], tspan, p)
+new_sol = solve(new_prob, Tsit5())
+
+@test isapprox(new_sol[x][end], sol[x][end], atol=1e-4)
+
+
+
+# Riccati equation
+@parameters t α
+@variables x(t)
+D = Differential(t)
+eqs = [D(x) ~ t^2 + α - x^2]
+sys = ODESystem(eqs, defaults=[x=>1.])
+
+@variables z(t)
+forward_subs  = [t + α/(x+t) =>    z       ]
+backward_subs = [       x    => α/(z-t) - t]
+
+new_sys = changeofvariables(sys, forward_subs, backward_subs; simplify=true, t0=0.)
+# output should be equivalent to
+# t^2 + α - z^2 + 2   (but this simplification is not found automatically)
+
+tspan = (0., 1.)
+p = [α => 1.]
+prob = ODEProblem(sys,[],tspan,p)
+new_prob = ODEProblem(new_sys,[],tspan,p)
+
+sol = solve(prob, Tsit5())
+new_sol = solve(new_prob, Tsit5())
+
+@test isapprox(sol[x][end], new_sol[x][end], rtol=1e-4)
+
+
+# Linear transformation to diagonal system
+@parameters t
+@variables x[1:3](t)
+D = Differential(t)
+A = [0. -1. 0.; -0.5 0.5 0.; 0. 0. -1.]
+eqs = D.(x) .~ A*x
+
+tspan = (0., 10.)
+u0 = x .=> [1.0, 2.0, -1.0]
+
+sys = ODESystem(eqs; defaults=u0)
+prob = ODEProblem(sys,[],tspan)
+sol = solve(prob, Tsit5())
+
+T = eigen(A).vectors
+
+@variables z[1:3](t)
+forward_subs  = T \ x .=> z
+backward_subs = x     .=> T*z
+
+new_sys = changeofvariables(sys, forward_subs, backward_subs; simplify=true)
+
+new_prob = ODEProblem(new_sys, [], tspan, p)
+new_sol = solve(new_prob, Tsit5())
+
+# test RHS
+new_rhs = [eq.rhs for eq in equations(new_sys)]
+new_A = Symbolics.value.(Symbolics.jacobian(new_rhs, z))
+@test isapprox(diagm(eigen(A).values), new_A, rtol = 1e-10)
+@test isapprox( new_sol[x[1],end], sol[x[1],end], rtol=1e-4)
+
+# Change of variables for sde
+@Browian B
+@parameters μ σ
+@variables x(t) y(t)
+
+