LJExp6RF: Exp-6 + Reaction Field¶

Description¶

ljexp6rf is a combined potential designed for molecular systems: each pair of species uses either a Lennard-Jones or an exponential-6 short-range term, plus a reaction-field electrostatic term. This page describes the exponential-6 flavour; see LJExp6RF: Lennard-Jones + Reaction Field for the other one.

With an exponential-6 short-range term, the pair energy reads

\[ E(r) = A\,e^{-Br} - \frac{C}{r^{6}} + D\left(\frac{12}{B\,r}\right)^{12} - E_{\mathrm{shift}} + \frac{q_i q_j}{4\pi\varepsilon_0}\left[\frac{1}{r} + k_{\mathrm{rf}} r^2 - C_{\mathrm{rf}}\right] \quad \text{for} \quad r<r_{\mathrm{cut}} \]

\(E_{\mathrm{shift}}\) is the exponential-6 energy at the distance given by parameters.rcut, so that the short-range term is zero there. \(k_{\mathrm{rf}}\) and \(C_{\mathrm{rf}}\) are computed from rf.epsilon and rf.rc as described on the reaction field page. Each term only contributes below its own cutoff: the exponential-6 term below parameters.rcut and the reaction field below rf.rc. The operator cutoff rcut must be at least the larger of the two. The charges \(q_i\), \(q_j\) are the species charges.

Parameter	Units	Description
`parameters.rcut`	distance	Distance where the exponential-6 energy is shifted to zero (required)
`exp6.A`	energy	Amplitude of the exponential repulsion
`exp6.B`	1/distance	Inverse range of the exponential
`exp6.C`	energy·distance\(^6\)	Dispersion coefficient
`exp6.D`	energy	Amplitude of the short-range wall
`rf.epsilon`	—	Dielectric constant of the surrounding continuum
`rf.rc`	distance	Reaction field cutoff \(r_c\) used in \(k_{\mathrm{rf}}\) and \(C_{\mathrm{rf}}\)
`rcut`	distance	Cutoff radius of the pair potential

Warning

Give lj or exp6 for a given pair, not both: the simulation aborts if both are present. Unlike exp6rf, ljexp6rf has no exp6_rcut key: the shift distance is parameters.rcut.

YAML syntax¶

ljexp6rf_compute_force:
  rcut: VALUE UNITS
  parameters:
    rcut: VALUE UNITS
    exp6: { A: VALUE UNITS , B: VALUE UNITS , C: VALUE UNITS , D: VALUE UNITS }
    rf: { epsilon: VALUE , rc: VALUE UNITS }

VALUE = Physical value of the intended parameter.
UNITS = Units of the provided value that will be passed to the conversion helper for internal units conversion.

Usage examples¶

Systems with a single atomic specy

# Default variant
ljexp6rf_compute_force:
  rcut: 12.5 ang
  parameters: { rcut: 12.5 ang , rf: { epsilon: 100. , rc: 12.5 ang } , exp6: { A: 107023.9 Da*kcal/g , B: 3.6405 1/ang , C: 554.01 Da*kcal*ang^6/g , D: 5.0e-5 Da*kcal/g } }

# Symetric variant
ljexp6rf_compute_force_symetric:
  rcut: 12.5 ang
  parameters: { rcut: 12.5 ang , rf: { epsilon: 100. , rc: 12.5 ang } , exp6: { A: 107023.9 Da*kcal/g , B: 3.6405 1/ang , C: 554.01 Da*kcal*ang^6/g , D: 5.0e-5 Da*kcal/g } }

Systems with multiple atomic species

compute_force_pair_multimat:
  potentials:
    - { type_a: C , type_b: C , potential: ljexp6rf , rcut: 12.5 ang , parameters: { rcut: 12.5 ang , rf: { epsilon: 100. , rc: 12.5 ang } , exp6: { A: 107023.9 Da*kcal/g , B: 3.6405 1/ang ,     C: 554.01 Da*kcal*ang^6/g ,      D: 5.0e-5 Da*kcal/g } } }
    - { type_a: C , type_b: N , potential: ljexp6rf , rcut: 12.5 ang , parameters: { rcut: 12.5 ang , rf: { epsilon: 100. , rc: 12.5 ang } , exp6: { A: 37111.29 Da*kcal/g , B: 3.46350030 1/ang , C: 484.2991571 Da*kcal*ang^6/g , D: 5.0e-5 Da*kcal/g } } }

Molecular systems

A rigid molecule variant, ljexp6rf_rigidmol_force, is available. For flexible molecules, the dedicated ljexp6rf_pc operator handles per-atom charges and intramolecular pair weights; it is set up by data/config/config_molecule.msp (see Bonding potentials).