Skip to main content
← OpenMECP Documentation

adjust_bond_length

omecp::reaction_path

Function adjust_bond_length 

Source 
fn adjust_bond_length(
    geometry: &mut Geometry,
    atom1: usize,
    atom2: usize,
    target_length: f64,
)
Expand description

Adjusts the bond length between two atoms to a target value.

This function modifies the molecular geometry by moving one atom to achieve a specific bond length. It’s a simplified constraint satisfaction method used in path optimization when geometric constraints must be maintained.

§Algorithm Description

The method uses a scaling approach:

  1. Current distance: Calculate existing bond length
  2. Scaling factor: Compute ratio of target to current length
  3. Position adjustment: Move atom2 along the bond vector
  4. Coordinate update: Apply the new position to the geometry

§Mathematical Implementation

The new position of atom2 is calculated as:

r₂_new = r₁ + (target_length / current_length) × (r₂ - r₁)

where:

  • r₁, r₂ are the current positions of atoms 1 and 2
  • target_length is the desired bond length
  • current_length is the existing bond length

§Arguments

  • geometry - Mutable reference to the molecular geometry
  • atom1 - Index of the first atom (remains fixed)
  • atom2 - Index of the second atom (will be moved)
  • target_length - Desired bond length in same units as coordinates

§Behavior Details

§Fixed Atom Choice

  • Atom1: Remains at its original position (anchor point)
  • Atom2: Moved along the bond vector to achieve target distance

§Direction Preservation

  • The bond direction (unit vector) remains unchanged
  • Only the magnitude (bond length) is modified
  • No rotation or angular changes occur

§Edge Cases

  • Zero distance: Function returns early to avoid division by zero
  • Negative target: Would invert bond direction (not physically meaningful)

§Applications

  • Constraint enforcement: Maintain specific bond lengths during optimization
  • Geometry correction: Fix unreasonable bond distances
  • Path optimization: Apply bond constraints in NEB calculations
  • Structure preparation: Set up initial geometries with desired bond lengths

§Limitations

§Simplified Approach

  • Single bond focus: Only considers the specified bond
  • No connectivity: Ignores effects on other bonds and angles
  • No energy consideration: Purely geometric adjustment
  • Fixed anchor: Always keeps atom1 stationary

§Potential Issues

  • Steric clashes: May create unrealistic atomic overlaps
  • Angle distortion: Can distort bond angles involving these atoms
  • Chain effects: Changes may propagate through molecular structure

§Future Improvements

  • Mass-weighted adjustment: Move both atoms based on their masses
  • Connectivity awareness: Consider effects on neighboring bonds
  • Energy minimization: Combine with local energy optimization
  • Multiple constraint handling: Simultaneously satisfy several constraints