Module bonded 

Bonded (intramolecular) interaction potentials.

Bonded interactions define the covalent structure and local flexibility of molecules.

Components

1. Bond Stretch (2-body)

Interactions between two directly bonded atoms.

• Harmonic: Standard harmonic spring potential.
• Morse: Anharmonic potential allowing bond dissociation.

2. Angle Bend (3-body)

Interactions defined by the angle between two bonds sharing a common atom.

• CosineHarmonic: Harmonic in cosine of the angle.
• ThetaHarmonic: Harmonic in the angle itself.

3. Torsion (4-body)

Interactions associated with rotation about a bond axis (dihedral angle).

• Torsion: Standard periodic cosine series expansion.

4. Inversion / Improper (4-body)

Interactions maintaining planarity or chiral centers.

• PlanarInversion: Harmonic potential on the out-of-plane distance.
• UmbrellaInversion: Harmonic potential on the Wilson angle.

Structs

CosineHarmonic

Cosine Harmonic potential for bond angles.

Harmonic

Harmonic potential implementation for 1-2 bond stretching.

Morse

Morse potential implementation for 1-2 bond stretching.

PlanarInversion

Planar inversion potential for sp² centers.

ThetaHarmonic

Theta Harmonic potential for bond angles.

Torsion

Periodic torsion potential for dihedral angles.

UmbrellaInversion

Umbrella inversion potential for sp³ centers.