Struct UffOptimizer 

pub struct UffOptimizer {
    pub max_iterations: usize,
    pub force_threshold: f64,
    pub verbose: bool,
    pub num_threads: usize,
    pub cutoff: f64,
    pub history_size: usize,
}

Optimizer for molecular structures using the FIRE (Fast Iterative Relaxation Engine) algorithm.

Fields

max_iterations: usize

Maximum number of iterations to perform.

force_threshold: f64

Threshold for the maximum force on any atom (kcal/mol/Å).

verbose: bool

Whether to print optimization progress to stdout.

num_threads: usize

Number of threads to use. 0 means automatic based on system size.

cutoff: f64

Cutoff distance for non-bonded interactions (Å).

history_size: usize

Number of steps to average for convergence criteria.

Implementations

impl UffOptimizer

pub fn new(max_iterations: usize, force_threshold: f64) -> Self

Creates a new optimizer with default settings.

Arguments

• max_iterations - Maximum number of steps.
• force_threshold - Convergence threshold for forces.

Examples found in repository

examples/benzene.rs (line 37)

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 with_num_threads(self, num_threads: usize) -> Self

pub fn with_cutoff(self, cutoff: f64) -> Self

pub fn with_history_size(self, size: usize) -> Self

pub fn with_verbose(self, verbose: bool) -> Self

Examples found in repository

examples/benzene.rs (line 38)

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 optimize(&self, system: &mut System)

Optimized structural geometry using the FIRE algorithm.

Examples found in repository

examples/benzene.rs (line 43)

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);
}