Merge pull request #103 from JuliaDiffEq/hg/fix/cleanup

Minor cleanup

Author: ChrisRackauckas

README.md

@@ -21,16 +21,16 @@ to manipulate.
 ### Example: ODE
 
 Let's build an ODE. First we define some variables. In a differential equation
-system, we need to differentiate between our unknown (dependent) variables
+system, we need to differentiate between our (dependent) variables
 and parameters. Therefore we label them as follows:
 
 ```julia
 using ModelingToolkit
 
 # Define some variables
-@Param t σ ρ β
-@Unknown x(t) y(t) z(t)
-@Deriv D'~t
+@parameters t σ ρ β
+@variables x(t) y(t) z(t)
+@derivatives D'~t
 ```
 
 Then we build the system:
@@ -78,11 +78,11 @@ f = ODEFunction(de)
 
 We can also build nonlinear systems. Let's say we wanted to solve for the steady
 state of the previous ODE. This is the nonlinear system defined by where the
-derivatives are zero. We use unknown variables for our nonlinear system.
+derivatives are zero. We use (unknown) variables for our nonlinear system.
 
 ```julia
-@Unknown x y z
-@Param σ ρ β
+@variables x y z
+@parameters σ ρ β
 
 # Define a nonlinear system
 eqs = [0 ~ σ*(y-x),
@@ -173,7 +173,7 @@ structure is as follows:
   the system of equations.
 - Name to subtype mappings: these describe how variable `subtype`s are mapped
   to the contexts of the system. For example, for a differential equation,
-  the unknown variable corresponds to given subtypes and then the `eqs` can
+  the variable corresponds to given subtypes and then the `eqs` can
   be analyzed knowing what the state variables are.
 - Variable names which do not fall into one of the system's core subtypes are
   treated as intermediates which can be used for holding subcalculations and
@@ -223,7 +223,7 @@ function via the dispatch:
 
 ```julia
 # `N` arguments are accepted by the relevant method of `my_function`
-ModelingToolkit.Derivative(::typeof(my_function), args::NTuple{N,Any}, ::Val{i})
+ModelingToolkit.derivative(::typeof(my_function), args::NTuple{N,Any}, ::Val{i})
 ```
 
 where `i` means that it's the derivative of the `i`th argument. `args` is the
@@ -233,7 +233,7 @@ You should return an `Operation` for the derivative of your function.
 For example, `sin(t)`'s derivative (by `t`) is given by the following:
 
 ```julia
-ModelingToolkit.Derivative(::typeof(sin), args::NTuple{1,Any}, ::Val{1}) = cos(args[1])
+ModelingToolkit.derivative(::typeof(sin), args::NTuple{1,Any}, ::Val{1}) = cos(args[1])
 ```
 
 ### Macro-free Usage
@@ -243,31 +243,31 @@ is accessible via a function-based interface. This means that all macros are
 syntactic sugar in some form. For example, the variable construction:
 
 ```julia
-@Param t σ ρ β
-@Unknown x(t) y(t) z(t)
-@Deriv D'~t
+@parameters t σ ρ β
+@variables x(t) y(t) z(t)
+@derivatives D'~t
 ```
 
 is syntactic sugar for:
 
 ```julia
-t = Parameter(:t)
-x = Unknown(:x, [t])
-y = Unknown(:y, [t])
-z = Unknown(:z, [t])
+t = Variable(:t; known = true)
+x = Variable(:x, [t])
+y = Variable(:y, [t])
+z = Variable(:z, [t])
 D = Differential(t)
-σ = Parameter(:σ)
-ρ = Parameter(:ρ)
-β = Parameter(:β)
+σ = Variable(:σ; known = true)
+ρ = Variable(:ρ; known = true)
+β = Variable(:β; known = true)
 ```
 
 ### Intermediate Calculations
 
 The system building functions can handle intermediate calculations. For example,
 
 ```julia
-@Unknown x y z
-@Param σ ρ β
+@variables x y z
+@parameters σ ρ β
 a = y - x
 eqs = [0 ~ σ*a,
        0 ~ x*(ρ-z)-y,

src/ModelingToolkit.jl

@@ -1,5 +1,10 @@
 module ModelingToolkit
 
+export Operation, Expression
+export calculate_jacobian, generate_jacobian, generate_function
+export @register
+
+
 using DiffEqBase
 using StaticArrays, LinearAlgebra
 
@@ -30,9 +35,4 @@ include("function_registration.jl")
 include("simplify.jl")
 include("utils.jl")
 
-export Operation, Expression, AbstractComponent
-export calculate_jacobian, generate_jacobian, generate_function
-export ArrayFunction, SArrayFunction
-export @register
-
 end # module

src/differentials.jl

@@ -1,3 +1,6 @@
+export Differential, expand_derivatives, @derivatives
+
+
 struct Differential <: Function
     x::Expression
 end
@@ -12,7 +15,7 @@ function (D::Differential)(x::Variable)
     return Operation(D, Expression[x])
 end
 (::Differential)(::Any) = Constant(0)
-Base.:(==)(D1::Differential, D2::Differential) = D1.x == D2.x
+Base.:(==)(D1::Differential, D2::Differential) = isequal(D1.x, D2.x)
 
 function expand_derivatives(O::Operation)
     @. O.args = expand_derivatives(O.args)
@@ -21,21 +24,21 @@ function expand_derivatives(O::Operation)
         D = O.op
         o = O.args[1]
         isa(o, Operation) || return O
-        return simplify_constants(sum(i->Derivative(o,i)*expand_derivatives(D(o.args[i])),1:length(o.args)))
+        return simplify_constants(sum(i->derivative(o,i)*expand_derivatives(D(o.args[i])),1:length(o.args)))
     end
 
     return O
 end
 expand_derivatives(x) = x
 
 # Don't specialize on the function here
-Derivative(O::Operation, idx) = Derivative(O.op, (O.args...,), Val(idx))
+derivative(O::Operation, idx) = derivative(O.op, (O.args...,), Val(idx))
 
 # Pre-defined derivatives
 import DiffRules, SpecialFunctions, NaNMath
 for (modu, fun, arity) ∈ DiffRules.diffrules()
     for i ∈ 1:arity
-        @eval function Derivative(::typeof($modu.$fun), args::NTuple{$arity,Any}, ::Val{$i})
+        @eval function derivative(::typeof($modu.$fun), args::NTuple{$arity,Any}, ::Val{$i})
             M, f = $(modu, fun)
             partials = DiffRules.diffrule(M, f, args...)
             dx = @static $arity == 1 ? partials : partials[$i]
@@ -60,7 +63,7 @@ function _differential_macro(x)
     lhss = Symbol[]
     x = flatten_expr!(x)
     for di in x
-        @assert di isa Expr && di.args[1] == :~ "@Deriv expects a form that looks like `@Deriv D''~t E'~t`"
+        @assert di isa Expr && di.args[1] == :~ "@derivatives expects a form that looks like `@derivatives D''~t E'~t`"
         lhs = di.args[2]
         rhs = di.args[3]
         order, lhs = count_order(lhs)
@@ -72,12 +75,10 @@ function _differential_macro(x)
     ex
 end
 
-macro Deriv(x...)
+macro derivatives(x...)
     esc(_differential_macro(x))
 end
 
 function calculate_jacobian(eqs,vars)
     Expression[Differential(vars[j])(eqs[i]) for i in 1:length(eqs), j in 1:length(vars)]
 end
-
-export Differential, expand_derivatives, @Deriv, calculate_jacobian

src/equations.jl

@@ -5,15 +5,15 @@ struct Equation
     lhs::Expression
     rhs::Expression
 end
-Base.:(==)(a::Equation, b::Equation) = (a.lhs, a.rhs) == (b.lhs, b.rhs)
+Base.:(==)(a::Equation, b::Equation) = isequal((a.lhs, a.rhs), (b.lhs, b.rhs))
 
 Base.:~(lhs::Expression, rhs::Expression) = Equation(lhs, rhs)
 Base.:~(lhs::Expression, rhs::Number    ) = Equation(lhs, rhs)
 Base.:~(lhs::Number    , rhs::Expression) = Equation(lhs, rhs)
 
 
 _is_dependent(x::Variable) = !x.known && !isempty(x.dependents)
-_is_parameter(iv) = x -> x.known && x ≠ iv
+_is_parameter(iv) = x -> x.known && !isequal(x, iv)
 _is_known(x::Variable) = x.known
 _is_unknown(x::Variable) = !x.known
 

src/function_registration.jl

@@ -32,7 +32,13 @@ for (M, f, arity) in DiffRules.diffrules()
     @eval @register $sig
 end
 
-for fun = (:<, :>, :(==), :!, :&, :|, :div)
+for fun ∈ [:!]
+    basefun = Expr(:., Base, QuoteNode(fun))
+    sig = :($basefun(x))
+    @eval @register $sig
+end
+
+for fun ∈ [:<, :>, :(==), :&, :|, :div]
     basefun = Expr(:., Base, QuoteNode(fun))
     sig = :($basefun(x,y))
     @eval @register $sig

src/operations.jl

@@ -4,15 +4,15 @@ struct Operation <: Expression
 end
 
 # Recursive ==
-function Base.:(==)(x::Operation,y::Operation)
+function Base.isequal(x::Operation,y::Operation)
     x.op == y.op && length(x.args) == length(y.args) && all(isequal.(x.args,y.args))
 end
-Base.:(==)(::Operation, ::Number   ) = false
-Base.:(==)(::Number   , ::Operation) = false
-Base.:(==)(::Operation, ::Variable ) = false
-Base.:(==)(::Variable , ::Operation) = false
-Base.:(==)(::Operation, ::Constant ) = false
-Base.:(==)(::Constant , ::Operation) = false
+Base.isequal(::Operation, ::Number   ) = false
+Base.isequal(::Number   , ::Operation) = false
+Base.isequal(::Operation, ::Variable ) = false
+Base.isequal(::Variable , ::Operation) = false
+Base.isequal(::Operation, ::Constant ) = false
+Base.isequal(::Constant , ::Operation) = false
 
 Base.convert(::Type{Expr}, O::Operation) =
     build_expr(:call, Any[Symbol(O.op); convert.(Expr, O.args)])

src/simplify.jl

@@ -1,10 +1,13 @@
+export simplify_constants
+
+
 function simplify_constants(O::Operation, shorten_tree)
     while true
         O′ = _simplify_constants(O, shorten_tree)
         if is_operation(O′)
             O′ = Operation(O′.op, simplify_constants.(O′.args, shorten_tree))
         end
-        O == O′ && return O
+        isequal(O, O′) && return O
         O = O′
     end
 end
@@ -72,5 +75,3 @@ function _simplify_constants(O::Operation, shorten_tree)
 end
 _simplify_constants(x, shorten_tree) = x
 _simplify_constants(x) = _simplify_constants(x, true)
-
-export simplify_constants

src/systems/diffeqs/diffeqsystem.jl

@@ -10,7 +10,7 @@ function flatten_differential(O::Operation)
     @assert is_derivative(O) "invalid differential: $O"
     is_derivative(O.args[1]) || return (O.args[1], O.op.x, 1)
     (x, t, order) = flatten_differential(O.args[1])
-    t == O.op.x || throw(ArgumentError("non-matching differentials on lhs: $t, $(O.op.x)"))
+    isequal(t, O.op.x) || throw(ArgumentError("non-matching differentials on lhs: $t, $(O.op.x)"))
     return (x, t, order + 1)
 end
 
@@ -26,7 +26,7 @@ function Base.convert(::Type{DiffEq}, eq::Equation)
     (x, t, n) = flatten_differential(eq.lhs)
     return DiffEq(x, t, n, eq.rhs)
 end
-Base.:(==)(a::DiffEq, b::DiffEq) = (a.x, a.t, a.n, a.rhs) == (b.x, b.t, b.n, b.rhs)
+Base.:(==)(a::DiffEq, b::DiffEq) = isequal((a.x, a.t, a.n, a.rhs), (b.x, b.t, b.n, b.rhs))
 get_args(eq::DiffEq) = Expression[eq.x, eq.t, eq.rhs]
 
 struct DiffEqSystem <: AbstractSystem
@@ -79,7 +79,7 @@ end
 function generate_ode_iW(sys::DiffEqSystem, simplify=true; version::FunctionVersion = ArrayFunction)
     jac = calculate_jacobian(sys)
 
-    gam = Parameter(:gam)
+    gam = Variable(:gam; known = true)
 
     W = LinearAlgebra.I - gam*jac
     W = SMatrix{size(W,1),size(W,2)}(W)

src/systems/diffeqs/first_order_transform.jl

@@ -1,7 +1,10 @@
+export ode_order_lowering
+
+
 function lower_varname(var::Variable, idv, order)
     order == 0 && return var
     name = Symbol(var.name, :_, string(idv.name)^order)
-    return Variable(name, var.known, var.dependents)
+    return Variable(name, var.dependents; known = var.known)
 end
 
 function ode_order_lowering(sys::DiffEqSystem)
@@ -17,7 +20,7 @@ function ode_order_lowering(eqs, iv)
         var, maxorder = eq.x, eq.n
         if maxorder > get(var_order, var, 0)
             var_order[var] = maxorder
-            var ∈ vars || push!(vars, var)
+            any(isequal(var), vars) || push!(vars, var)
         end
         var′ = lower_varname(eq.x, eq.t, eq.n - 1)
         rhs′ = rename(eq.rhs)
@@ -45,5 +48,3 @@ function rename(O::Expression)
     end
     return Operation(O.op, rename.(O.args))
 end
-
-export ode_order_lowering

src/utils.jl

@@ -65,4 +65,4 @@ is_derivative(::Any) = false
 
 has_dependent(t::Variable) = Base.Fix2(has_dependent, t)
 has_dependent(x::Variable, t::Variable) =
-    t ∈ x.dependents || any(has_dependent(t), x.dependents)
+    any(isequal(t), x.dependents) || any(has_dependent(t), x.dependents)