ModelingToolkit.jl is an intermediate representation (IR) of computational graphs for scientific computing problems. Its purpose is to be a common target for modeling DSLs in order to allow for a common platform for model inspection and transformation. It uses a tagged variable IR in order to allow specification of complex models and allow for transformations of models. It has ways to plug into its function registration and derivative system so that way it can interact nicely with user-defined routines. Together, this is an abstract form of a scientific model that is easy for humans to generate but also easy for programs to manipulate.

For an introductory tutorial to using ModelingToolkit.jl, please checkout ModelingToolkit.jl, An IR and Compiler for Scientific Models.

Let's build an ODE. First we define some variables. In a differential equation system, we need to differentiate between our (dependent) variables and parameters. Therefore we label them as follows:

```
using ModelingToolkit
# Define some variables
@parameters t σ ρ β
@variables x(t) y(t) z(t)
@derivatives D'~t
```

Then we build the system:

```
eqs = [D(x) ~ σ*(y-x),
D(y) ~ x*(ρ-z)-y,
D(z) ~ x*y - β*z]
```

Each operation builds an `Operation`

type, and thus `eqs`

is an array of
`Operation`

and `Variable`

s. This holds a tree of the full system that can be
analyzed by other programs. We can turn this into a `ODESystem`

via:

```
de = ODESystem(eqs, t, [x,y,z], [σ,ρ,β])
```

where we tell it the variable types and ordering in the first version, or let it automatically determine the variable types in the second version. This can then generate the function. For example, we can see the generated code via:

```
using MacroTools
myode_oop = generate_function(de)[1] # first one is the out-of-place function
MacroTools.striplines(myode_oop) # print without line numbers
#=
:((u, p, t)->begin
if u isa Array
return @inbounds(begin
let (x, y, z, σ, ρ, β) = (u[1], u[2], u[3], p[1], p[2], p[3])
[σ * (y - x), x * (ρ - z) - y, x * y - β * z]
end
end)
else
X = @inbounds(begin
let (x, y, z, σ, ρ, β) = (u[1], u[2], u[3], p[1], p[2], p[3])
(σ * (y - x), x * (ρ - z) - y, x * y - β * z)
end
end)
end
T = promote_type(map(typeof, X)...)
map(T, X)
construct = if u isa ModelingToolkit.StaticArrays.StaticArray
ModelingToolkit.StaticArrays.similar_type(typeof(u), eltype(X))
else
x->begin
convert(typeof(u), x)
end
end
construct(X)
end)
=#
myode_iip = generate_function(de)[2] # second one is the in-place function
MacroTools.striplines(myode_iip) # print without line numbers
#=
:((var"##MTIIPVar#793", u, p, t)->begin
@inbounds begin
@inbounds begin
let (x, y, z, σ, ρ, β) = (u[1], u[2], u[3], p[1], p[2], p[3])
var"##MTIIPVar#793"[1] = σ * (y - x)
var"##MTIIPVar#793"[2] = x * (ρ - z) - y
var"##MTIIPVar#793"[3] = x * y - β * z
end
end
end
nothing
end)
=#
```

or directly get the generated ODE function via:

```
f = ODEFunction(de, [x,y,z], [σ,ρ,β])
```

Here already you can see some advantages of the ModelingToolkit.jl compilation system. As an IR to target, this output can compile to multiple different forms, including ones specific to static arrays and in-place functions. Forms which automatically parallelize the calculations based on internal cost models are a work-in-progress as well. This means DSLs built on top of this as a model compiler can write domain-specific languages without having to write complex optimized Julia function compilers.

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.

```
using ModelingToolkit
@variables x y z
@parameters σ ρ β
# Define a nonlinear system
eqs = [0 ~ σ*(y-x),
0 ~ x*(ρ-z)-y,
0 ~ x*y - β*z]
ns = NonlinearSystem(eqs, [x,y,z], [σ,ρ,β])
nlsys_func = generate_function(ns)[2] # second is the inplace version
```

which generates:

```
(var"##MTIIPVar#405", u, p)->begin
@inbounds begin
@inbounds begin
let (x, y, z, σ, ρ, β) = (u[1], u[2], u[3], p[1], p[2], p[3])
var"##MTIIPVar#405"[1] = (*)(σ, (-)(y, x))
var"##MTIIPVar#405"[2] = (-)((*)(x, (-)(ρ, z)), y)
var"##MTIIPVar#405"[3] = (-)((*)(x, y), (*)(β, z))
end
end
end
nothing
end
```

We can use this to build a nonlinear function for use with NLsolve.jl:

```
f = eval(nlsys_func)
du = zeros(3); u = ones(3)
f(du,u,(10.0,26.0,2.33))
du
#=
3-element Array{Float64,1}:
0.0
24.0
-1.33
=#
```

We can similarly ask to generate the in-place Jacobian function:

```
j_func = generate_jacobian(ns)[2] # second is in-place
j! = eval(j_func)
```

which gives:

```
:((var"##MTIIPVar#582", u, p)->begin
#= C:\Users\accou\.julia\dev\ModelingToolkit\src\utils.jl:70 =#
#= C:\Users\accou\.julia\dev\ModelingToolkit\src\utils.jl:71 =#
#= C:\Users\accou\.julia\dev\ModelingToolkit\src\utils.jl:71 =# @inbounds begin
#= C:\Users\accou\.julia\dev\ModelingToolkit\src\utils.jl:72 =#
#= C:\Users\accou\.julia\dev\ModelingToolkit\src\utils.jl:53 =# @inbounds begin
#= C:\Users\accou\.julia\dev\ModelingToolkit\src\utils.jl:53 =#
let (x, y, z, σ, ρ, β) = (u[1], u[2], u[3], p[1], p[2], p[3])
var"##MTIIPVar#582"[1] = (*)(σ, -1)
var"##MTIIPVar#582"[2] = (-)(ρ, z)
var"##MTIIPVar#582"[3] = y
var"##MTIIPVar#582"[4] = σ
var"##MTIIPVar#582"[5] = -1
var"##MTIIPVar#582"[6] = x
var"##MTIIPVar#582"[7] = 0
var"##MTIIPVar#582"[8] = (*)(x, -1)
var"##MTIIPVar#582"[9] = (*)(-1, β)
end
end
end
#= C:\Users\accou\.julia\dev\ModelingToolkit\src\utils.jl:74 =#
nothing
end)
```

Now we can call `nlsolve`

by enclosing our parameters into the functions:

```
nlsolve((out, x) -> f(out, x, params), (out, x) -> j!(out, x, params), ones(3))
```

If one would like the generated function to be a Julia function instead of an expression, and allow this
function to be used from within the same world-age, one simply needs to pass `Val{false}`

to tell it to
generate the function, i.e.:

```
nlsys_func = generate_function(ns, [x,y,z], [σ,ρ,β], Val{false})[2]
```

which uses GeneralizedGenerated.jl to build a same world-age function on the fly without eval.

Sometimes it is convenient to define arrays of variables to model things like `x₁,…,x₃`

.
The `@variables`

and `@parameters`

macros support this with the following syntax:

```
julia> @variables x[1:3];
julia> x
3-element Array{Operation,1}:
x₁()
x₂()
x₃()
# support for arbitrary ranges and tensors
julia> @variables y[2:3,1:5:6];
julia> y
2×2 Array{Operation,2}:
y₂̒₁() y₂̒₆()
y₃̒₁() y₃̒₆()
# also works for dependent variables
julia> @parameters t; @variables z[1:3](t);
julia> z
3-element Array{Operation,1}:
z₁(t())
z₂(t())
z₃(t())
```

The core idea behind ModelingToolkit.jl is that mathematical equations require context, and thus any symbolic manipulations and full model specifications requires the ability to handle such context. When writing DSLs, this fact comes to light very quickly. Every DSL seems to lower to some intermediate representation from which the final result is computed, but this process means there's a lot of repeated ideas for every DSL that creates scientific computing objects like differential equations and nonlinear systems. By having a single common contexualized IR, this gives DSLs a target to write to so that way lower-level details like computation of system Jacobians can be disconnected from the DSL and its syntax, allowing for code-reuse between modeling packages and languages.

In this section we define the core pieces of the IR and what they mean.

The most fundamental part of the IR is the `Variable`

. In order to mirror the
intention of solving for variables and representing function-like parameters,
we treat each instance of `Variable`

as a function which is called on its
arguments using the natural syntax. Rather than having additional mechanisms
for handling constant variables and parameters, we simply represent them as
constant functions.

The `Variable`

is the
context-aware single variable of the IR. Its fields are described as follows:

`name`

: the name of the`Variable`

. Note that this is not necessarily the same as the name of the Julia variable. But this symbol itself is considered the core identifier of the`Variable`

in the sense of equality.`known`

: the main denotation of context, storing whether or not the value of the variable is known.

For example, the following code defines an independent variable `t`

, a parameter
`α`

, a function parameter `σ`

, a variable `x`

which depends on `t`

, a variable
`y`

with no dependents, a variable `z`

which depends on `t`

, `α`

, and `x(t)`

and a parameters `β₁`

and `β₂`

.

```
t = Variable(:t; known = true)() # independent variables are treated as known
α = Variable(:α; known = true)() # parameters are known
σ = Variable(:σ; known = true) # left uncalled, since it is used as a function
w = Variable(:w; known = false) # unknown, left uncalled
x = Variable(:x; known = false)(t) # unknown, depends on `t`
y = Variable(:y; known = false)() # unknown, no dependents
z = Variable(:z; known = false)(t, α, x) # unknown, multiple arguments
β₁ = Variable(:β, 1; known = true)() # with index 1
β₂ = Variable(:β, 2; known = true)() # with index 2
expr = β₁ * x + y^α + σ(3) * (z - t) - β₂ * w(t - 1)
```

We can rewrite this more concisely using macros. Note the difference between including and excluding empty parentheses. When in call format, variables are aliased to the given call, allowing implicit use of dependents for convenience.

```
@parameters t α σ(..) β[1:2]
@variables w(..) x(t) y() z(t, α, x)
expr = β₁* x + y^α + σ(3) * (z - t) - β₂ * w(t - 1)
```

Note that `@parameters`

and `@variables`

implicitly add `()`

to values that
are not given a call. The former specifies the values as known, while the
latter specifies it as unknown. `(..)`

signifies that the value should be
left uncalled.

`Constant`

is a simple wrapper type to store numerical Julia constants.

Operations are the basic composition of variables and puts together the pieces with a function.

Equations are stored using the `Equation`

datatype. Given expressions for the
left-hand and right-hand sides, an equation is constructed as `Equation(lhs, rhs)`

,
or equivalently `lhs ~ rhs`

.

A `Differential`

denotes the derivative with respect to a given variable. It can
be expanded via `expand_derivatives`

, which symbolically differentiates
expressions recursively and cancels out appropriate constant variables.

A system is a collection of operations with expanded context. While different systems can have different constructors and interpretations, the general structure is as follows:

`eqs`

is the first argument which is an array of`Operation`

which describe 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 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 other pieces like that.

Transformation functions send IR objects to like IR objects. These utilize the
contextual information in a given `Operation`

/`System`

to build another
`Operation`

/`System`

.

A function is registered into the operation system via:

```
@register f(x)
@register g(x,y)
```

etc. where each macro call registers the function with the given signature. This
will cause operations to stop recursing at this function, building `Operation(g,args)`

nodes into the graph instead of tracing calls of `g`

itself into `Operation`

s.

There is a large amount of derivatives pre-defined by
DiffRules.jl. Note that `Expression`

types are defined as `<:Real`

, and thus any functions which allow the use of real
numbers can automatically be traced by the derivative mechanism. Thus for example:

```
f(x,y,z) = x^2 + sin(x+y) - z
```

automatically has the derivatives defined via the tracing mechanism. It will do this by directly building the operation the internals of your function and differentiating that.

However, in many cases you may want to define your own derivatives so that way automatic Jacobian etc. calculations can utilize this information. This can allow for more succinct versions of the derivatives to be calculated in order to better scale to larger systems. You can define derivatives for your own function via the dispatch:

```
# `N` arguments are accepted by the relevant method of `my_function`
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
array of arguments, so for example if your function is `f(x,t)`

then `args = [x,t]`

.
You should return an `Operation`

for the derivative of your function.

For example, `sin(t)`

's derivative (by `t`

) is given by the following:

```
ModelingToolkit.derivative(::typeof(sin), args::NTuple{1,Any}, ::Val{1}) = cos(args[1])
```

Given the insistence on being programming friendly, all of the functionality is accessible via a function-based interface. This means that all macros are syntactic sugar in some form. For example, the variable construction:

```
@parameters t σ ρ β[1:3]
@variables x(t) y(t) z(t)
@derivatives D'~t
```

is syntactic sugar for:

```
t = Variable(:t; known = true)()
σ = Variable(:σ; known = true)()
ρ = Variable(:ρ; known = true)()
β = [Variable(:β, i; known = true)() for i in 1:3]
x = Variable(:x)(t)
y = Variable(:y)(t)
z = Variable(:z)(t)
D = Differential(t)
```

The system building functions can handle intermediate calculations. For example,

```
@variables x y z
@parameters σ ρ β
a = y - x
eqs = [0 ~ σ*a,
0 ~ x*(ρ-z)-y,
0 ~ x*y - β*z]
ns = NonlinearSystem(eqs, [x,y,z])
nlsys_func = generate_function(ns, [x,y,z], [σ,ρ,β])
```

expands to:

```
:((##365, u, p)->begin
let (x, y, z, σ, ρ, β) = (u[1], u[2], u[3], p[1], p[2], p[3])
##365[1] = σ * (y - x)
##365[2] = x * (ρ - z) - y
##365[3] = x * y - β * z
end
end)
```

In addition, the Jacobian calculations take into account intermediate variables to appropriately handle them.

02/27/2018

2 days ago

497 commits