cvode_wrap

A wrapper around the cvode(S) ODE solver from sundials. Mirror of https://gitlab.inria.fr/InBio/Public/cvode-rust-wrap

https://github.com/krtab/cvode_wrap

Science Score: 44.0%

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Low similarity (4.5%) to scientific vocabulary

Keywords

ode ode-solver sensitivity-analysis

Last synced: 6 months ago · JSON representation ·

Repository

A wrapper around the cvode(S) ODE solver from sundials. Mirror of https://gitlab.inria.fr/InBio/Public/cvode-rust-wrap

Basic Info

Host: GitHub
Owner: krtab
Language: Rust
Default Branch: master
Homepage:
Size: 59.6 KB

Statistics

Stars: 0
Watchers: 1
Forks: 0
Open Issues: 0
Releases: 2

Topics

ode ode-solver sensitivity-analysis

Created over 4 years ago · Last pushed over 4 years ago

Metadata Files

Readme Citation

Readme.md

A wrapper around the cvode(S) ODE solver from sundials.

[ documentation ] [ lib.rs ] [ git repository ]

Building sundials

To build sundials, activate the sundials-sys/build_libraries feature.

Examples

Oscillator

An oscillatory system defined by x'' = -k * x.

Without sensitivities

rust let y0 = [0., 1.]; //define the right-hand-side fn f(_t: Realtype, y: &[Realtype; 2], ydot: &mut [Realtype; 2], k: &Realtype) -> RhsResult { *ydot = [y[1], -y[0] * k]; RhsResult::Ok } //initialize the solver let mut solver = SolverNoSensi::new( LinearMultistepMethod::Adams, f, 0., &y0, 1e-4, AbsTolerance::scalar(1e-4), 1e-2, ) .unwrap(); //and solve let ts: Vec<_> = (1..100).collect(); println!("0,{},{}", y0[0], y0[1]); for &t in &ts { let (_tret, &[x, xdot]) = solver.step(t as _, StepKind::Normal).unwrap(); println!("{},{},{}", t, x, xdot); }

With sensitivities

The sensitivities are computed with respect to x(0), x'(0) and k.

```rust let y0 = [0., 1.]; //define the right-hand-side fn f(t: Realtype, y: &[Realtype; 2], ydot: &mut [Realtype; 2], k: &Realtype) -> RhsResult { *ydot = [y[1], -y[0] * k]; RhsResult::Ok } //define the sensitivity function for the right hand side fn fs( _t: Realtype, y: &[Realtype; 2], _ydot: &[Realtype; 2], ys: [&[Realtype; 2]; NSENSI], ysdot: [&mut [Realtype; 2]; N_SENSI], k: &Realtype, ) -> RhsResult { // Mind that when indexing sensitivities, the first index // is the parameter index, and the second the state variable // index *ysdot[0] = [ys[0][1], -ys[0][0] * k]; *ysdot[1] = [ys[1][1], -ys[1][0] * k]; *ysdot[2] = [ys[2][1], -ys[2][0] * k - y[0]]; RhsResult::Ok }

const N_SENSI: usize = 3;

// the sensitivities in order are d/dy0[0], d/dy0[1] and d/dk let ys0 = [[1., 0.], [0., 1.], [0., 0.]];

//initialize the solver let mut solver = SolverSensi::new( LinearMultistepMethod::Adams, f, fs, 0., &y0, &ys0, 1e-4, AbsTolerance::scalar(1e-4), SensiAbsTolerance::scalar([1e-4; NSENSI]), 1e-2, ) .unwrap(); //and solve let ts: Vec<> = (1..100).collect(); println!("0,{},{}", y0[0], y0[1]); for &t in &ts { let (tret, &[x, xdot], [&[dy0dy00, dy1dy00], &[dy0dy01, dy1dy01], &[dy0dk, dy1dk]]) = solver.step(t as _, StepKind::Normal).unwrap(); println!( "{},{},{},{},{},{},{},{},{}", t, x, xdot, dy0dy00, dy1dy00, dy0dy01, dy1dy01, dy0dk, dy1_dk ); } ```

Owner

Name: Arthur Carcano
Login: krtab
Kind: user
Location: Paris, France
Company: @OCamlPro

Website: ngr.yt
Repositories: 14
Profile: https://github.com/krtab

Flazingly bast

Citation (CITATION.cff)

authors: 
  -
    affiliation: "Inria, Institut Pasteur, Université de Paris"
    family-names: Carcano
    given-names: Arthur
    orcid: "https://orcid.org/0000-0002-9946-1645"
cff-version: "1.1.0"
message: "If you use this software, please cite it using these metadata."
title: "cvode-wrap"
version: 0.1.3
doi: 10.5281/zenodo.5337060

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