General bonding potential¶

In exaStamp, the intramolecular bonding interactions are associated to bonds, bending angles, torsion angle and improper torsion angles. The bonding energy \(E^{\text{bonding}}\) is simply:

where \(E^{\text{bond}}\), \(E^{\text{bend}}\), \(E^{\text{torsion}}\) and \(E^{\text{improper}}\) are the energies associated to all bonds, bending angles, torsion angles and improper torsion angles, respectively. To each type of intramolecular degree of freedom corresponds an operator as illustrated by the examples below:

# Bond potential
compute_force_bond:
  potentials_for_bonds:
    - type_1
    - type_2

# Bending potential
compute_force_bend:
  potentials_for_angles:
     - type_1
     - type_2

# Torsion potential
compute_force_torsion:
  potentials_for_torsions:
    - type_1
    - type_2

# Improper torsion potential
compute_force_improper:
  potentials_for_impropers:
    - type_1
    - type_2

where type_1and type_2 can be any specific type of bonding potentials as defined in the following items, also accessible in the left panel:

• [Bond] (Bond/index.md)
• [Bend] (Bend/index.md)
• [Torsion] (Torsion/index.md)
• [Improper] (Improper/index.md)