fix bond/break command — LIGGGHTS v3.X documentation

# fix bond/break command

## Syntax

    fix ID group-ID bond/break Nevery bondtype Rmax keyword values ...

- ID, group-ID are documented in fix command
- bond/break = style name of this fix command
- Nevery = attempt bond breaking every this many steps
- bondtype = type of bonds to break
- Rmax = bond longer than Rmax can break (distance units)
- zero or more keyword/value pairs may be appended to args
- keyword = prob

    prob values = fraction seed
      fraction = break a bond with this probability if otherwise eligible
      seed = random number seed (prime number greater 10000)

## Examples

    fix 5 all bond/break 10 2 1.2
    fix 5 polymer bond/break 1 1 2.0 prob 0.5 123457

## Description

Break bonds between pairs of atoms as a simulation runs according to specified criteria. This can be used to model the dissolution of a polymer network due to stretching of the simulation box or other deformations. In this context, a bond means an interaction between a pair of atoms computed by the bond_style command. Once the bond is broken it will be permanently deleted. This is different than a pairwise bond-order potential such as Tersoff or AIREBO which infers bonds and many-body interactions based on the current geometry of a small cluster of atoms and effectively creates and destroys bonds from timestep to timestep as atoms move.

A check for possible bond breakage is performed every Nevery timesteps. If two bonded atoms I,J are further than a distance Rmax of each other, if the bond is of type bondtype, and if both I and J are in the specified fix group, then I,J is labeled as a “possible” bond to break.

If several bonds involving an atom are stretched, it may have multiple possible bonds to break. Every atom checks its list of possible bonds to break and labels the longest such bond as its “sole” bond to break. After this is done, if atom I is bonded to atom J in its sole bond, and atom J is bonded to atom I in its sole bond, then the I,J bond is “eligible” to be broken.

Note that these rules mean an atom will only be part of at most one broken bond on a given timestep. It also means that if atom I chooses atom J as its sole partner, but atom J chooses atom K is its sole partner (due to Rjk > Rij), then this means atom I will not be part of a broken bond on this timestep, even if it has other possible bond partners.

The prob keyword can effect whether an eligible bond is actually broken. The fraction setting must be a value between 0.0 and 1.0. A uniform random number between 0.0 and 1.0 is generated and the eligible bond is only broken if the random number < fraction.

When a bond is broken, data structures within LIGGGHTS(R)-PUBLIC that store bond topology are updated to reflect the breakage. This can also affect subsequent computation of pairwise interactions involving the atoms in the bond. See the Restriction section below for additional information.

Computationally, each timestep this fix operates, it loops over bond lists and computes distances between pairs of bonded atoms in the list. It also communicates between neighboring processors to coordinate which bonds are broken. Thus it will increase the cost of a timestep. Thus you should be cautious about invoking this fix too frequently.

You can dump out snapshots of the current bond topology via the dump local command.

Warning

Breaking a bond typically alters the energy of a system. You should be careful not to choose bond breaking criteria that induce a dramatic change in energy. For example, if you define a very stiff harmonic bond and break it when 2 atoms are separated by a distance far from the equilibribum bond length, then the 2 atoms will be dramatically released when the bond is broken. More generally, you may need to thermostat your system to compensate for energy changes resulting from broken bonds.

## Restart, fix_modify, output, run start/stop, minimize info

No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix.

This fix computes two statistics which it stores in a global vector of length 2, which can be accessed by various output commands. The vector values calculated by this fix are “intensive”.

These are the 2 quantities:

- 1. # of bonds broken on the most recent breakage timestep
- 2. cummulative # of bonds broken

No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during `energy minimization`.

## Restrictions

This fix is part of the MC package. It is only enabled if LIGGGHTS(R)-PUBLIC was built with that package. See the Making LIGGGHTS(R)-PUBLIC section for more info.

Currently, there are 2 restrictions for using this fix. We may relax these in the future if there are new models that would be enabled by it.

When a bond is broken, you might wish to turn off angle and dihedral interactions that include that bond. However, LIGGGHTS(R)-PUBLIC does not check for these angles and dihedrals, even if your simulation defines an `angle_style` or `dihedral_style`.

This fix requires that the pairwise weightings defined by the `special_bonds` command be 0,1,1 for 1-2, 1-3, and 1-4 neighbors within the bond topology. This effectively means that the pairwise interaction between atoms I and J is turned off when a bond between them exists and will be turned on when the bond is broken. It also means that the pairwise interaction of I with J’s other bond partners is unaffected by the existence of the bond.

## Related commands

fix bond/create, `fix bond/swap`, dump local, `special_bonds`

## Default

The option defaults are prob = 1.0.