Lennard-Jones potential

This module implements the Lennard-Jones potential,

\[U^{(ij)}_\text{LJ}(r) = 4\epsilon_{ij} \left( \left(\frac{\sigma_{ij}}{r}\right)^{12} - \left(\frac{\sigma_{ij}}{r}\right)^6 \right)\]

for the interaction between two particles of species \(i\) and \(j\).

class halmd.mdsim.potentials.pair.lennard_jones(args)

Construct Lennard-Jones potential.

Parameters:

  • args (table) – keyword arguments

  • args.epsilon (table) – matrix with elements \(\epsilon_{ij}\) (default: 1)

  • args.sigma (table) – matrix with elements \(\sigma_{ij}\) (default: 1)

  • args.species (number) – number of particle species (optional)

  • args.memory (string) – select memory location (optional)

  • args.label (string) – instance label (optional)

If the argument species is omitted, it is inferred from the first dimension of the parameter matrices.

If all elements of a matrix are equal, a scalar value may be passed instead which is promoted to a square matrix of size given by the number of particle species.

The supported values for memory are “host” and “gpu”. If memory is not specified, the memory location is selected according to the compute device.

epsilon

Matrix with elements \(\epsilon_{ij}\).

sigma

Matrix with elements \(\sigma_{ij}\).

r_cut

Matrix with elements \(r_{\text{c}, ij}\) in reduced units.

r_cut_sigma

Matrix with elements \(r_{\text{c}, ij}\) in units of \(\sigma_{ij}\).

description

Name of potential for profiler.

memory

Device where the particle memory resides.

truncate(args)

Truncate potential. See Potential truncations for available truncations.

Parameters:

  • args (table) – keyword argument

  • args[1] (string) – name of truncation type

  • cutoff (table) – matrix with elements \(r_{\text{c}, ij}\)

  • args.* (any) – additional arguments depend on the truncation type

Returns:

truncated potential

Example:

potential = potential:truncate({"smooth_r4", cutoff = 5, h = 0.05})
modify(args)

Apply potential modification. See Potential modifications for available modifications.

Parameters:

  • args (table) – keyword argument

  • args[1] (string) – name of modification type

  • args.* (any) – additional arguments depend on the modification type

Returns:

modified potential

Example:

potential = potential:modify({"hard_core", radius = 0.5})