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. Each kind of term is computed by its own operator (compute_force_bond, compute_force_bend, compute_force_torsion, compute_force_improper), and intramolecular pairs (atoms of the same molecule close in the bond graph) by intramolecular_pair_force. These operators take their parameters from the force field of the system, which comes from one of three sources:

• an FAtomes file read with read_fatomes_mol, which holds the force field;
• a molecule dump read with read_dump_molecule, which stores it in its header;
• the input file, with molecule_force_field in setup_system, for systems read without their force field (e.g. read_xyz_molecules).

Force field in the input file: molecule_force_field¶

species:
  - CA: { mass: 12.011 g/mol, charge: -0.115 e-, molecule: MOL }
  - HA: { mass: 1.008 g/mol, charge: 0.115 e-, molecule: MOL }

molecule_force_field:
  rf_self_pairs: true            # reaction field between an atom and itself (default true)
  long_range_correction: true    # long range correction of the pair energy and virial (default true)
  potentials_for_bonds:
    - type_1
    - type_2
  potentials_for_angles:
    - type_1
  potentials_for_torsions:
    - type_1
  potentials_for_impropers:
    - type_1
  mol_pair_weights:
    CA_CA: { bond: 0.0, bend: 0.0, torsion: 0.5, bond_rf: 0.0, bend_rf: 0.0, torsion_rf: 0.5 }
    CA_HA: { bond: 0.0, bend: 0.0, torsion: 0.5, bond_rf: 0.0, bend_rf: 0.0, torsion_rf: 0.5 }
    HA_HA: { bond: 0.0, bend: 0.0, torsion: 0.5, bond_rf: 0.0, bend_rf: 0.0, torsion_rf: 0.5 }
  potentials_for_pairs:
    - { type_a: CA, type_b: CA, potential: { rcut: 10. ang, lj: { epsilon: 0.29 kJ/mol, sigma: 3.55 ang }, rf: { epsilon: 2.0, rc: 12. ang } } }
    - { type_a: CA, type_b: HA, potential: { rcut: 10. ang, lj: { epsilon: 0.15 kJ/mol, sigma: 2.98 ang }, rf: { epsilon: 2.0, rc: 12. ang } } }
    - { type_a: HA, type_b: HA, potential: { rcut: 10. ang, lj: { epsilon: 0.13 kJ/mol, sigma: 2.42 ang }, rf: { epsilon: 2.0, rc: 12. ang } } }

setup_system:
  - domain: { cell_size: 8. ang, periodic: [ true, true, true ], expandable: false }
  - read_xyz_molecules: { filename: "system.xyz" }
  - molecule_force_field

• potentials_for_bonds, potentials_for_angles, potentials_for_torsions, potentials_for_impropers: lists of bonded potentials. Their types are force field types: the ff key of species, the species name by default.
• mol_pair_weights: weights of intramolecular pairs, for each species pair A_B. bond, bend and torsion scale the pair potential of atoms 1-2, 1-3 and 1-4 apart in the bond graph; bond_rf, bend_rf and torsion_rf scale the reaction field. Pairs further apart are computed as intermolecular pairs.
• potentials_for_pairs: pair potentials (Lennard-Jones or Exp-6, plus reaction field) for every species pair, as in ljexp6rf_lj and ljexp6rf_exp6. Cross pairs are not built from a mixing rule: list them all.

scripts/python/fatomes_to_yaml.py writes this block, and the system in read_xyz_molecules format, from an FAtomes file and its DONNEES file (mixing rules applied). Both ways of reading the system then give the same forces and energies.

Potential types¶

where type_1 and type_2 stand for bonded potentials of the types described in the following pages, also accessible in the left panel:

• Bond
• Bend
• Torsion
• Improper