\(\renewcommand{\AA}{\text{Å}}\)

bond_style fene command

Accelerator Variants: fene/intel, fene/kk, fene/omp

bond_style fene/nm command

Syntax

bond_style fene
bond_style fene/nm

Examples

bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0

bond_style fene/nm
bond_coeff 1 2.25344 1.5 1.0 1.12246 2 6

Description

The fene bond style uses the potential

\[E = -0.5 K R_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] + 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon\]

to define a finite extensible nonlinear elastic (FENE) potential (Kremer), used for bead-spring polymer models. The first term is attractive, the second Lennard-Jones term is repulsive. The first term extends to \(R_0\), the maximum extent of the bond. The second term is cutoff at \(2^\frac{1}{6} \sigma\), the minimum of the LJ potential.

The fene/nm bond style substitutes the standard LJ potential with the generalized LJ potential in the same form as in pair style nm/cut. The bond energy is then given by

\[E = -0.5 K R_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] + \frac{E_0}{(n-m)} \left[ m \left(\frac{r_0}{r}\right)^n - n \left(\frac{r_0}{r}\right)^m \right]\]

Similar to the fene style, the generalized Lennard-Jones is cut off at the potential minimum, \(r_0\), to be repulsive only. The following coefficients must be defined for each bond type via the bond_coeff command as in the example above, or in the data file or restart files read by the read_data or read_restart commands:

  • \(K\) (energy/distance^2)

  • \(R_0\) (distance)

  • \(\epsilon\) (energy)

  • \(\sigma\) (distance)

For the fene/nm style, the following coefficients are used. Please note, that the standard LJ potential and thus the regular FENE potential is recovered for (n=12 m=6) and \(r_0 = 2^\frac{1}{6} \sigma\).

  • \(K\) (energy/distance^2)

  • \(R_0\) (distance)

  • \(E_0\) (energy)

  • \(r_0\) (distance)

  • \(n\) (unitless)

  • \(m\) (unitless)

Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the Accelerator packages page. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

These accelerated styles are part of the GPU, INTEL, KOKKOS, OPENMP, and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the Build package page for more info.

You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

See the Accelerator packages page for more instructions on how to use the accelerated styles effectively.

Restrictions

The fene bond style can only be used if LAMMPS was built with the MOLECULE package; the fene/nm bond style can only be used if LAMMPS was built with the EXTRA-MOLECULE package. See the Build package page for more info.

You typically should specify special_bonds fene or special_bonds lj/coul 0 1 1 to use this bond style. LAMMPS will issue a warning it that’s not the case.

Default

none

(Kremer) Kremer, Grest, J Chem Phys, 92, 5057 (1990).