API

An AbstractPortion object to be used in the SciMLStructures.jl interfaces, i.e. canonicalize(::AbstractPortion, p::T1) or replace!(::AbstractPortion, p::T1).

The caches portion of the SciMLStructure, i.e. the caches which are meant to allow for writing the model function without allocations.

Rules for caches:

• Caches should be a mutable object.
• Caches should not assume any previous value in them. All values within the cache should be written into in the f cal that it is used from.

For making caches compatible with automatic differentiation, see PreallocationTools.jl.

The constant portion of the SciMLStructure, i.e. the parameters which are meant to be constant with respect to optimization.

The discrete portion of the SciMLStructure.

The portion of the SciMLStructure used for parameters solely involved in initialization. These should be floating point numbers supporting automatic differentiation.

The inputs portion of the SciMLStructure.

The tunable portion of the SciMLStructure, i.e. the parameters which are meant to be optimized.

canonicalize(::AbstractPortion, p::T1) -> values::T2, repack, aliases::Bool

The core function of the interface is the canonicalize function. canonicalize allows the user to define to the solver how to represent the given "portion" in a standard AbstractVector type which allows for interfacing with standard tools like linear algebra in an efficient manner. The type of portions which are defined are:

• Tunable: the tunable values/parameters, i.e. the values of the structure which are supposed to be considered non-constant when used in the context of an inverse problem solve. For example, this is the set of parameters to be optimized during a parameter estimation of an ODE.

  • Tunable parameters are expected to return an AbstractVector of unitless values.
  • Tunable parameters are expected to be constant during the solution of the ODE.

• Constants: the values which are to be considered constant by the solver, i.e. values which are not estimated in an inverse problem and which are unchanged in any operation by the user as part of the solver's usage.

• Caches: the stored cache values of the struct, i.e. the values of the structure which are used as intermediates within other computations in order to avoid extra allocations.

• Discrete: the discrete portions of the state captured inside of the structure. For example, discrete values stored outside of the u in the parameters to be modified in the callbacks of an ODE.

  • Any parameter that is modified inside of callbacks should be considered Discrete.

Definitions for Base Objects

• Vector: returns an aliased version of itself as Tunable, and an empty vector matching type for Constants, Caches, and Discrete.
• Array: returns the vec(p) aliased version of itself as Tunable, and an empty vector matching type for Constants, Caches, and Discrete.

hasportion(::AbstractPortion, p)::Bool

Denotes whether a portion is used in a given definition of a SciMLStructure. If false, then it's expected that the canonical values are nothing.

Returns whether the SciMLStructure object is mutable and thus compatible with the interface functions that require mutation. Note that this is not mutable in the sense of the Julia type, rather mutable in the sense of AbstractPortion replacement, i.e. replace!

Returns whether the object satisfies the SciMLStructure interface. Defaults to false and types are required to opt-into the interface.

replace(::AbstractPortion, p::T1, new_values) -> p::T1

Equivalent to canonicalize(::AbstractPortion, p::T1)[2](new_values), though allowed to optimize and not construct intermediates. For more information on the arguments, see canonicalize.

replace!(::AbstractPortion, p::T1, new_values)::Nothing

Equivalent to canonicalize(::AbstractPortion, p::T1)[2](new_values), though done in a mutating fashion and is allowed to optimize and not construct intermediates. Requires a mutable SciMLStructure. For more information on the arguments, see canonicalize.