bond_style harmonic/restrain command

Syntax

bond_style harmonic/restrain

Examples

bond_style harmonic
bond_coeff 5 80.0

Description

New in version 28Mar2023.

The harmonic/restrain bond style uses the potential

E = K (r - r_{t = 0})^{2}

where $r_{t = 0}$ is the distance between the bonded atoms at the beginning of the first run or minimize command after the bond style has been defined (t=0). Note that the usual 1/2 factor is included in $K$ . This will effectively restrain bonds to their initial length, whatever that is. This is where this bond style differs from bond style harmonic where the bond length is set through the per bond type coefficients.

The following coefficient 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)

This bond style differs from other options to add harmonic restraints like fix restrain or pair style list or fix colvars in that it requires a bond topology, and thus the defined bonds will trigger exclusion of special neighbors from the neighbor list according to the special_bonds settings.

Restart info

This bond style supports the write_restart and read_restart commands. The state of the initial bond lengths is stored with restart files and read back.

Restrictions

This bond style can only be used if LAMMPS was built with the EXTRA-MOLECULE package. See the Build package page for more info.

This bond style maintains internal data to determine the original bond lengths $r_{t = 0}$ . This information will be written to binary restart files but not to data files. Thus, continuing a simulation is only possible with read_restart. When using the read_data command, the reference bond lengths $r_{t = 0}$ will be re-initialized from the current geometry.

This bond style cannot be used with fix shake or fix rattle, with fix filter/corotate, or any tip4p pair style since there is no specific equilibrium distance for a given bond type.

Default

none