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).

Examples found in repository

examples/benzene.rs (line 33)

fn main() {
    // 1. Create atoms for Benzene (6 Carbons, 6 Hydrogens)
    let mut atoms = Vec::new();
    
    // Carbon ring (approximate positions)
    for i in 0..6 {
        let angle = (i as f64) * 60.0f64.to_radians();
        let pos = DVec3::new(angle.cos() * 1.4, angle.sin() * 1.4, 0.0);
        atoms.push(Atom::new(6, pos)); // 6 is Atomic Number for Carbon
    }
    
    // Hydrogen atoms (approximate positions)
    for i in 0..6 {
        let angle = (i as f64) * 60.0f64.to_radians();
        let pos = DVec3::new(angle.cos() * 2.4, angle.sin() * 2.4, 0.0);
        atoms.push(Atom::new(1, pos)); // 1 is Atomic Number for Hydrogen
    }

    // 2. Define bonds
    let mut bonds = Vec::new();
    for i in 0..6 {
        // C-C aromatic bonds (order 1.5)
        bonds.push(Bond { atom_indices: (i, (i + 1) % 6), order: 1.5 });
        // C-H single bonds (order 1.0)
        bonds.push(Bond { atom_indices: (i, i + 6), order: 1.0 });
    }

    // 3. Setup the system (No periodic boundary conditions)
    let cell = UnitCell::new_none();
    let mut system = System::new(atoms, bonds, cell);

    // 4. Configure the optimizer
    // Max 1000 iterations, force threshold 1e-3 kcal/mol/A
    let optimizer = UffOptimizer::new(1000, 1e-3)
        .with_verbose(true); // Print progress to console

    println!("Starting optimization of Benzene...");
    
    // 5. Run the optimization
    optimizer.optimize(&mut system);

    println!("Optimization complete!");
    
    // Check final C-C bond length
    let d01 = (system.atoms[0].position - system.atoms[1].position).length();
    println!("Final C-C bond length: {:.4} Å", d01);
}

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