JumpSystem

struct JumpSystem{U<:RecursiveArrayTools.ArrayPartition} <: AbstractTimeDependentSystem

A system of jump processes.

Fields

• tag: tag: a tag for the system. If two systems have the same tag, then they are structurally identical.

• eqs: The jumps of the system. Allowable types are ConstantRateJump, VariableRateJump, MassActionJump.

• iv: The independent variable, usually time.

• states: The dependent variables, representing the state of the system. Must not contain the independent variable.

• ps: The parameters of the system. Must not contain the independent variable.

• var_to_name: Array variables.

• observed

• name: The name of the system. . These are required to have unique names.

• systems: The internal systems.

• defaults: defaults: The default values to use when initial conditions and/or parameters are not supplied in ODEProblem.

• connector_type: type: type of the system

• discrete_events: discreteevents: A Vector{SymbolicDiscreteCallback} that models events. Symbolic analog to SciMLBase.DiscreteCallback that executes an affect when a given condition is true at the end of an integration step. *Note, one must make sure to call `resetaggregated_jumps!(integrator)` if using a custom affect function that changes any state value or parameter.*

• metadata: metadata: metadata for the system, to be used by downstream packages.

• gui_metadata: gui_metadata: metadata for MTK GUI.

• complete: complete: if a model sys is complete, then sys.x no longer performs namespacing.

Example

using ModelingToolkit, JumpProcesses

@parameters β γ
@variables t S(t) I(t) R(t)
rate₁   = β*S*I
affect₁ = [S ~ S - 1, I ~ I + 1]
rate₂   = γ*I
affect₂ = [I ~ I - 1, R ~ R + 1]
j₁      = ConstantRateJump(rate₁,affect₁)
j₂      = ConstantRateJump(rate₂,affect₂)
j₃      = MassActionJump(2*β+γ, [R => 1], [S => 1, R => -1])
@named js      = JumpSystem([j₁,j₂,j₃], t, [S,I,R], [β,γ])

structural_simplify(sys)
structural_simplify(sys, io; simplify, kwargs...)

Structurally simplify algebraic equations in a system and compute the topological sort of the observed equations. When simplify=true, the simplify function will be applied during the tearing process. It also takes kwargs allow_symbolic=false and allow_parameter=true which limits the coefficient types during tearing.

The optional argument io may take a tuple (inputs, outputs). This will convert all inputs to parameters and allow them to be unconnected, i.e., simplification will allow models where n_states = n_equations - n_inputs.