Struct System 

pub struct System {
    pub atoms: Vec<Atom>,
    pub bonds: Vec<Bond>,
    pub cell: UnitCell,
}

Represents a molecular system consisting of atoms, bonds, and an optional unit cell.

Fields

atoms: Vec<Atom>

List of atoms in the system.

bonds: Vec<Bond>

List of chemical bonds.

cell: UnitCell

Unit cell for periodic boundary conditions.

Implementations

impl System

pub fn new(atoms: Vec<Atom>, bonds: Vec<Bond>, cell: UnitCell) -> Self

Creates a new molecular system and automatically assigns UFF atom types.

Arguments

• atoms - Initial atom positions and elements.
• bonds - Connectivity and bond orders.
• cell - Boundary conditions (use UnitCell::new_none() for gas phase).

pub fn auto_assign_uff_types(&mut self)

Automatically infers UFF atom types based on element, connectivity, and bond orders.

pub fn compute_forces(&mut self) -> EnergyTerms

Computes forces and total energy breakdown.

pub fn compute_forces_with_threads( &mut self, num_threads: usize, cutoff: f64, ) -> EnergyTerms