The Simulation Model

Initialize from a State Point

The file src/model.rs implements the simulation model similarly to all the previous tutorials (see Applying Interactions for a full explanation). One slight difference is in the initialization. Instead of hard-coding simulation parameters, the simulation in the workflow template initializes using parameters from the state point:

pub fn new(state_point: StatePoint) -> anyhow::Result<Self> {
    let macrostate = Isothermal {
        temperature: state_point.temperature,
    };

    let hamiltonian = PairwiseCutoff(Isotropic {
        interaction: LennardJones {
            epsilon: state_point.epsilon,
            sigma: state_point.sigma,
        },
        r_cut: 2.5 * state_point.sigma,
    });

    let initial_box_volume = state_point.n as f64 / INITIAL_NUMBER_DENSITY;
    let initial_box_edge_length = initial_box_volume.cbrt();
    let cuboid = Cuboid::with_equal_edges(initial_box_edge_length.try_into()?);
    let periodic_cuboid = Periodic::new(hamiltonian.maximum_interaction_range(), cuboid)?;

    let vec_cell = VecCell::builder()
        .nominal_search_radius(hamiltonian.maximum_interaction_range().try_into()?)
        .build();
    let microstate = Microstate::builder()
        .seed(state_point.replicate)
        .boundary(periodic_cuboid)
        .spatial_data(vec_cell)
        .try_build()?;

    // ...

Tip

Use a replicate state point field as the random number seed (as shown here) to execute many different realizations of the same state point parameters.

Constant Parameters

In the row/signac workflow model, it is important that every simulation can be constructed only as a function of the state point. At the same time, there are usually some parameters that are a fixed part of the simulation protocol. Define those as constants:

const INITIAL_NUMBER_DENSITY: f64 = 0.2;
const INITIAL_MAXIMUM_DISTANCE: f64 = 0.1;
const RELAX_STEPS: u64 = 10_000;

Serialization

As with the state point, notice that all types in model.rs also include #[derive(Serialize, Deserialize)]. On the next page, the simulate_one method will make use of these traits.

Tip

To implement your own simulation model, replace the struct fields and method implementations.