LJExp6RF: Lennard-Jones + 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 Lennard-Jones flavour; see LJExp6RF: Exp-6 + Reaction Field for the other one.

With a Lennard-Jones short-range term, the pair energy reads

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

\(E_{\mathrm{shift}}\) is the Lennard-Jones 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 Lennard-Jones 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 Lennard-Jones energy is shifted to zero (required)
`lj.epsilon`	energy	Lennard-Jones well depth \(\varepsilon\)
`lj.sigma`	distance	Lennard-Jones distance \(\sigma\)
`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.

YAML syntax¶

ljexp6rf_compute_force:
  rcut: VALUE UNITS
  parameters:
    rcut: VALUE UNITS
    lj: { epsilon: VALUE UNITS , sigma: 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 } , lj: { epsilon: 0.01 kcal/mol , sigma: 3.830864488 ang } }

# Symetric variant
ljexp6rf_compute_force_symetric:
  rcut: 12.5 ang
  parameters: { rcut: 12.5 ang , rf: { epsilon: 100. , rc: 12.5 ang } , lj: { epsilon: 0.01 kcal/mol , sigma: 3.830864488 ang } }

Systems with multiple atomic species

ljexp6rf_multi_force:
  rcut: 12.5 ang
  common_parameters: { rcut: 12.5 ang , rf: { epsilon: 100. , rc: 12.5 ang } , lj: { epsilon: 0.01 kcal/mol , sigma: 3.83 ang } }
  parameters:
    - { type_a: C , type_b: C , rcut: 12.5 ang , parameters: { rcut: 12.5 ang , rf: { epsilon: 100. , rc: 12.5 ang } , lj: { epsilon: 0.01 kcal/mol , sigma: 3.83 ang } } }
    - { type_a: C , type_b: N , rcut: 12.5 ang , parameters: { rcut: 12.5 ang , rf: { epsilon: 100. , rc: 12.5 ang } , lj: { epsilon: 0.02 kcal/mol , sigma: 3.60 ang } } }

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).