Linearly truncated Lennard-Jones potential

This module implements the Lennard-Jones potential with a linear truncation scheme (which is equivalent to a shifted force),

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
  + (r_{ij} - r_c)\cdot F_c
\right)

for the interaction between two particles of species i and j. Here, r_c denotes the cutoff distance and F_c = -
U_\text{LJ}\prime(r_c) the force at the cutoff for the untruncated potential.

This linear truncation scheme modifies the potential drastically and at all distances by adding a constant force, and we do not recommend it for future work. It is mainly provided for historical reasons to connect to existing data and publications. Please refer to the local r⁴ truncation scheme for an alternative.

References

  1. S. K. Das, J. Horbach, K. Binder, M. E. Fisher, and J. V. Sengers, J. Chem. Phys. 125, 024506 (2006)
  2. S. Toxvaerd and J. C. Dyre, J. Chem. Phys. 134, 081102 (2011)
  3. S. Toxvaerd, O. J. Heilmann, and J. C. Dyre, J. Chem. Phys. 136, 224106 (2012)
class halmd.mdsim.potentials.pair.lennard_jones_linear(args)

Construct linearly truncated 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.