catlog/stdlib/analyses/ode/
mod.rs

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1//! ODE analyses of models.
2
3use std::{collections::HashMap, hash::Hash};
4
5use derivative::Derivative;
6use ode_solvers::dop_shared::IntegrationError;
7
8#[cfg(feature = "serde")]
9use serde::{Deserialize, Serialize};
10#[cfg(feature = "serde-wasm")]
11use tsify_next::Tsify;
12
13use crate::simulate::ode::{ODEProblem, ODESystem};
14
15/// Solution to an ODE problem.
16#[derive(Clone, Derivative)]
17#[derivative(Default(bound = ""))]
18#[cfg_attr(feature = "serde", derive(Serialize, Deserialize))]
19#[cfg_attr(feature = "serde-wasm", derive(Tsify))]
20#[cfg_attr(feature = "serde-wasm", tsify(into_wasm_abi, from_wasm_abi))]
21pub struct ODESolution<Id>
22where
23    Id: Eq + Hash,
24{
25    /// Values of time variable for the duration of the simulation.
26    time: Vec<f32>,
27
28    /// Values of state variables for the duration of the simulation.
29    states: HashMap<Id, Vec<f32>>,
30}
31
32/// Data needed to simulate and interpret an ODE analysis of a model.
33pub struct ODEAnalysis<Id, Sys> {
34    /// ODE problem for the analysis.
35    pub problem: ODEProblem<Sys>,
36
37    /// Mapping from IDs in model (usually object IDs) to variable indices.
38    pub variable_index: HashMap<Id, usize>,
39}
40
41impl<Id, Sys> ODEAnalysis<Id, Sys> {
42    /// Constructs a new ODE analysis.
43    pub fn new(problem: ODEProblem<Sys>, variable_index: HashMap<Id, usize>) -> Self {
44        Self {
45            problem,
46            variable_index,
47        }
48    }
49
50    /// Solves the ODE with reasonable default settings and collects results.
51    pub fn solve_with_defaults(self) -> Result<ODESolution<Id>, IntegrationError>
52    where
53        Id: Eq + Hash,
54        Sys: ODESystem,
55    {
56        // ODE solver will fail in the degenerate case of an empty system.
57        if self.variable_index.is_empty() {
58            return Ok(Default::default());
59        }
60
61        let duration = self.problem.end_time - self.problem.start_time;
62        let output_step_size = (duration / 100.0).min(0.01f32);
63        let result = self.problem.solve_dopri5(output_step_size)?;
64
65        let (t_out, x_out) = result.get();
66        Ok(ODESolution {
67            time: t_out.clone(),
68            states: self
69                .variable_index
70                .into_iter()
71                .map(|(ob, i)| (ob, x_out.iter().map(|x| x[i]).collect()))
72                .collect(),
73        })
74    }
75}
76
77#[allow(non_snake_case)]
78pub mod lotka_volterra;
79#[allow(clippy::type_complexity)]
80pub mod mass_action;
81
82pub use lotka_volterra::*;
83pub use mass_action::*;
catlog/stdlib/analyses/ode/mod.rs

catlog/stdlib/analyses/ode/
mod.rs
