Struct PyMdSimulation 

pub struct PyMdSimulation { /* private fields */ }

Molecular Dynamics simulation (NVE/NVT) with periodic boundary conditions.

Uses a velocity-Verlet integrator and a truncated-shifted Lennard-Jones pair potential. Supports an optional velocity-rescaling thermostat.

Implementations

impl PyMdSimulation

pub fn new(config: PyMdConfig) -> Self

Create a new empty MD simulation from the given configuration.

pub fn add_atom(&mut self, position: [f64; 3], atom_type: u32) -> usize

Add an atom at position with the given type index.

Returns the index of the newly added atom.

pub fn set_velocity(&mut self, i: usize, vel: [f64; 3])

Set the velocity of atom i. No-op if i is out of bounds.

pub fn position(&self, i: usize) -> Option<[f64; 3]>

Get the position of atom i, or None if out of bounds.

pub fn velocity(&self, i: usize) -> Option<[f64; 3]>

Get the velocity of atom i, or None if out of bounds.

pub fn atom_count(&self) -> usize

Number of atoms in the simulation.

pub fn time(&self) -> f64

Accumulated simulation time.

pub fn step_count(&self) -> u64

Number of completed steps.

pub fn set_thermostat(&mut self, active: bool)

Enable or disable the velocity-rescaling thermostat.

pub fn thermostat_active(&self) -> bool

Whether the thermostat is active.

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

Set the target temperature for the thermostat.

pub fn potential_energy(&self) -> f64

Total potential energy from the last step.

pub fn kinetic_energy(&self) -> f64

Total kinetic energy summed over all atoms.

pub fn total_energy(&self) -> f64

Total energy (kinetic + potential).

pub fn temperature(&self) -> f64

Instantaneous temperature from equipartition: T = 2KE / (3N*k_B).

In reduced units k_B = 1, so T = 2KE / (3N).

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

Advance the simulation by dt using velocity Verlet integration.

Steps:

1. Half-kick velocities: v += 0.5 * f/m * dt
2. Update positions: x += v * dt (with PBC wrap)
3. Recompute forces from LJ pair potential
4. Half-kick velocities again
5. Optionally rescale velocities to match target temperature

pub fn run(&mut self, dt: f64, steps: u64)

Advance the simulation by dt for steps steps.

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

Return all atom positions as a flat Vecf64of[x,y,z]` triples.

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

Return all atom velocities as a flat Vec<f64> of [vx,vy,vz] triples.

Trait Implementations

impl Clone for PyMdSimulation

fn clone(&self) -> PyMdSimulation

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for PyMdSimulation

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

Formats the value using the given formatter.