# The AbstractSystem Interface

## Overview

The `AbstractSystem`

interface is the core of the system level of ModelingToolkit.jl. It establishes a common set of functionality that is used between systems from ODEs and chemical reactions, allowing users to have a common framework for model manipulation and compilation.

## Constructors and Naming

The `AbstractSystem`

interface has a consistent method for constructing systems. Generally it follows the order of:

- Equations
- Independent Variables
- Dependent Variables (or States)
- Parameters

All other pieces are handled via keyword arguments. `AbstractSystem`

s share the same keyword arguments, which are:

`system`

: This is used for specifying subsystems for hierarchical modeling with reusable components. For more information, see the components page- Defaults: Keyword arguments like
`defaults`

are used for specifying default values which are used. If a value is not given at the`SciMLProblem`

construction time, its numerical value will be the default.

## Composition and Accessor Functions

Each `AbstractSystem`

has lists of variables in context, such as distinguishing parameters vs states. In addition, an `AbstractSystem`

also can hold other `AbstractSystem`

types. Direct accessing of the values, such as `sys.states`

, gives the immediate list, while the accessor functions `states(sys)`

gives the total set, which includes that of all systems held inside.

The values which are common to all `AbstractSystem`

s are:

`equations(sys)`

: All equations that define the system and its subsystems.`states(sys)`

: All the states in the system and its subsystems.`parameters(sys)`

: All parameters of the system and its subsystems.`nameof(sys)`

: The name of the current-level system.`get_eqs(sys)`

: Equations that define the current-level system.`get_states(sys)`

: States that are in the current-level system.`get_ps(sys)`

: Parameters that are in the current-level system.`get_systems(sys)`

: Subsystems of the current-level system.

Optionally, a system could have:

`observed(sys)`

: All observed equations of the system and its subsystems.`get_observed(sys)`

: Observed equations of the current-level system.`get_defaults(sys)`

: A`Dict`

that maps variables into their default values.`independent_variable(sys)`

: The independent variable of a system.`get_noiseeqs(sys)`

: Noise equations of the current-level system.

Note that there's `get_iv(sys)`

, but it is not advised to use, since it errors when the system has no field `iv`

. `independent_variable(sys)`

returns `nothing`

for `NonlinearSystem`

s.

A system could also have caches:

`get_jac(sys)`

: The Jacobian of a system.`get_tgrad(sys)`

: The gradient with respect to time of a system.

## Transformations

Transformations are functions which send a valid `AbstractSystem`

definition to another `AbstractSystem`

. These are passes, like optimizations (e.g., Block-Lower Triangle transformations), or changes to the representation, which allow for alternative numerical methods to be utilized on the model (e.g., DAE index reduction).

## Analyses

Analyses are functions on a system which return information about the corresponding properties, like whether its parameters are structurally identifiable, or whether it's linear.

## Function Calculation and Generation

The calculation and generation functions allow for calculating additional quantities to enhance the numerical methods applied to the resulting system. The calculations, like `calculate_jacobian`

, generate ModelingToolkit IR for the Jacobian of the system, while the generations, like `generate_jacobian`

, generate compiled output for the numerical solvers by applying `build_function`

to the generated code. Additionally, many systems have function-type outputs, which cobble together the generation functionality for a system, for example, `ODEFunction`

can be used to generate a DifferentialEquations-based `ODEFunction`

with compiled version of the ODE itself, the Jacobian, the mass matrix, etc.

Below are the possible calculation and generation functions:

`ModelingToolkit.calculate_tgrad`

— Function`calculate_tgrad(sys::AbstractSystem)`

Calculate the time gradient of a system.

Returns a vector of `Num`

instances. The result from the first call will be cached in the system object.

`ModelingToolkit.calculate_gradient`

— Function`calculate_gradient(sys::AbstractSystem)`

Calculate the gradient of a scalar system.

Returns a vector of `Num`

instances. The result from the first call will be cached in the system object.

`ModelingToolkit.calculate_jacobian`

— Function`calculate_jacobian(sys::AbstractSystem)`

Calculate the jacobian matrix of a system.

Returns a matrix of `Num`

instances. The result from the first call will be cached in the system object.

`ModelingToolkit.calculate_factorized_W`

— Function`calculate_factorized_W(sys::AbstractSystem)`

Calculate the factorized W-matrix of a system.

Returns a matrix of `Num`

instances. The result from the first call will be cached in the system object.

`ModelingToolkit.calculate_hessian`

— Function`calculate_hessian(sys::AbstractSystem)`

Calculate the hessian matrix of a scalar system.

Returns a matrix of `Num`

instances. The result from the first call will be cached in the system object.

`ModelingToolkit.generate_tgrad`

— Function`generate_tgrad(sys::AbstractSystem, dvs = states(sys), ps = parameters(sys), expression = Val{true}; kwargs...)`

Generates a function for the time gradient of a system. Extra arguments control the arguments to the internal `build_function`

call.

`ModelingToolkit.generate_gradient`

— Function`generate_gradient(sys::AbstractSystem, dvs = states(sys), ps = parameters(sys), expression = Val{true}; kwargs...)`

Generates a function for the gradient of a system. Extra arguments control the arguments to the internal `build_function`

call.

`ModelingToolkit.generate_jacobian`

— Function`generate_jacobian(sys::AbstractSystem, dvs = states(sys), ps = parameters(sys), expression = Val{true}; sparse = false, kwargs...)`

Generates a function for the jacobian matrix matrix of a system. Extra arguments control the arguments to the internal `build_function`

call.

`ModelingToolkit.generate_factorized_W`

— Function`generate_factorized_W(sys::AbstractSystem, dvs = states(sys), ps = parameters(sys), expression = Val{true}; sparse = false, kwargs...)`

Generates a function for the factorized W-matrix matrix of a system. Extra arguments control the arguments to the internal `build_function`

call.

`ModelingToolkit.generate_hessian`

— Function`generate_hessian(sys::AbstractSystem, dvs = states(sys), ps = parameters(sys), expression = Val{true}; sparse = false, kwargs...)`

Generates a function for the hessian matrix matrix of a system. Extra arguments control the arguments to the internal `build_function`

call.

Additionally, `jacobian_sparsity(sys)`

and `hessian_sparsity(sys)`

exist on the appropriate systems for fast generation of the sparsity patterns via an abstract interpretation without requiring differentiation.

## Problem Constructors

At the end, the system types have `DEProblem`

constructors, like `ODEProblem`

, which allow for directly generating the problem types required for numerical methods. The first argument is always the `AbstractSystem`

, and the proceeding arguments match the argument order of their original constructors. Whenever an array would normally be provided, such as `u0`

the initial condition of an `ODEProblem`

, it is instead replaced with a variable map, i.e., an array of pairs `var=>value`

, which allows the user to designate the values without having to know the order that ModelingToolkit is internally using.

For the value maps, the parameters are allowed to be functions of each other, and value maps of states can be functions of the parameters, i.e. you can do:

```
u0 = [
lorenz1.x => 2.0
lorenz2.x => lorenz1.x * lorenz1.p
]
```

## Default Value Handling

The `AbstractSystem`

types allow for specifying default values, for example `defaults`

inside of them. At problem construction time, these values are merged into the value maps, where for any repeats the value maps override the default. In addition, defaults of a higher level in the system override the defaults of a lower level in the system.