Struct PyMdBinding 

pub struct PyMdBinding { /* private fields */ }

PyO3-style binding handle for an MD simulation.

Wraps PyMdSimulation and exposes flat-array query helpers that mirror the #[pymethods] surface that would be used with the real PyO3 macro expansion. All methods take and return primitive Rust types so that future #[pyfunction] / #[pymethods] annotations require no changes.

Implementations

impl PyMdBinding

pub fn new_default() -> Self

Create a new MD binding with the default (argon-reduced) configuration.

pub fn new(config: PyMdConfig) -> Self

Create from explicit configuration.

pub fn add_atom( &mut self, x: f64, y: f64, z: f64, vx: f64, vy: f64, vz: f64, atom_type: u32, ) -> usize

Add an atom at [x, y, z] with optional velocity [vx, vy, vz].

Returns the index of the newly added atom.

pub fn atom_count(&self) -> usize

Return the number of atoms.

pub fn step(&mut self, dt: f64)

Advance the simulation by dt (reduced units or SI, consistent with config).

pub fn run_steps(&mut self, n_steps: u32, dt: f64)

Advance the simulation by n_steps steps, each of size dt.

pub fn get_positions_flat(&self) -> Vec<f64>

Return positions as a flat [x0,y0,z0, x1,y1,z1, …] array.

pub fn get_velocities_flat(&self) -> Vec<f64>

Return velocities as a flat array.

pub fn get_energies(&self) -> [f64; 3]

Return [kinetic, potential, total] energy.

pub fn get_temperature(&self) -> f64

Instantaneous temperature in reduced units (from equipartition theorem).

pub fn elapsed_time(&self) -> f64

Total simulation time elapsed.

pub fn step_count(&self) -> u64

Number of completed time steps.

pub fn set_thermostat_enabled(&mut self, enabled: bool)

Enable or disable the velocity-rescaling thermostat at runtime.

pub fn set_target_temperature(&mut self, temp: f64)

Set the target temperature (reduced units).

Trait Implementations

impl Clone for PyMdBinding

fn clone(&self) -> PyMdBinding

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for PyMdBinding

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.