Data Structure

A Network contains a list of vertex and edge models along with a graph. However, in tight numerical loops, it will never access these lists of models directly. Instead, the network maintains an internal representation that tracks all symbolic indices, defining the precise ordering of states and parameters in a flat array representation. To optimize performance, especially for heterogeneous networks, the network employs specialized data structures that batch identical models together.

This disconnect between the explicit lists and the internal data structures can be confusing.

Flat Parameter and State Arrays

The vertex and edge models may contain metadata, such as initial values for states and parameters. Crucially, this metadata is only for building and initialization of the simulation. During actual simulation, the state and parameters are handled as flat arrays, i.e., plain Vector{Float64} objects.

NWState and NWParameter serve as wrappers around flat arrays and the Network objects, allowing you to inspect and modify those flat arrays by addressing vertices and edges directly.

A typical workflow is:

1. Set default values in the models using the metadata (see Metadata).
2. Create a network (see Network Construction).
3. Generate a state s = NWState(nw) which will be prefilled with the default values from the component metadata (see Symbolic Indexing).
4. Change the values of s, i.e., s.v[1,:x] = 1.0: This changes the underlying flat array but not the metadata of the models.
5. Build a problem with the updated flat arrays using uflat(s) and pflat(s).

Accessing Components

Per default, the models are not copied on Network construction:

v1 = VertexModel(f=kuramoto_first, sym=[:θ], psym=[:ω], g=1)
v2 = VertexModel(f=kuramoto_secnd, sym=[:δ, :ω], psym=[:M, :D, :Pm], g=1)
e = EdgeModel(;g=AntiSymmetric(kuramoto_edge), outsym=[:P], psym=[:K])
nw = Network(complete_graph(2), [v1, v2], e)

Network with 3 states and 5 parameters
 ├─ 2 vertices (2 unique types)
 └─ 1 edges (1 unique type)
Edge-Aggregation using SequentialAggregator(+)

You can access the models using getindex/[] with VIndex or EIndex:

v1 === nw[VIndex(1)]

true

This can be important when changing metadata of components. i.e., both lines below are equivalent:

set_position!(v1, (1,0))
set_position!(nw[VIndex(1)], (1,0))

nw = Network(complete_graph(3), [v1,v2,v1], e)
v1 === nw[VIndex(1)] === nw[VIndex(3)]

true

nw = Network(complete_graph(3), [v1,v2,v1], e; dealias=true)
nw[VIndex(1)] === nw[VIndex(3)] # neither of them === v1

false

Extracting Network-object from Containers

NetworkDynamics.jl provides a extract_nw function, to get a reference to the wrapped Network object from different containers, such as solution objects or integrator objects.