Lennard-Jones potential

This module implements the Lennard-Jones potential,

U_\text{LJ}\left(r_{ij}\right) = 4\epsilon_{ij} \left(
    \left(\frac{\sigma_{ij}}{r_{ij}}\right)^{12}
  - \left(\frac{\sigma_{ij}}{r_{ij}}\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.cutoff (table) – matrix with elements r_{\text{c}, ij}
  • 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.

Note

The cutoff is only relevant with halmd.mdsim.forces.pair_trunc.

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.