fix bond/break command — LAMMPS documentation

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# 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

- keyword = prob

      prob values = fraction seed
        fraction = break a bond with this probability if otherwise eligible
        seed = random number seed (positive integer)

## Examples

    fix 5 all bond/break 10 2 1.2
    fix 5 polymer bond/break 1 1 2.0 prob 0.5 49829

## 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, as will all angle, dihedral, and improper interactions that bond is part of.

This is different than a pair-wise 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 and higher-order many-body interactions from timestep to timestep as atoms move.

A check for possible bond breakage is performed every Nevery timesteps. If two bonded atoms \(i\) and \(j\) are farther than the distance Rmax from each other, the bond is of type bondtype, and both \(i\) and \(j\) are in the specified fix group, then the bond between \(i\) and \(j\) 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 \(j\) in its sole bond, then the bond between \(i\) and \(j\) 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 time step. It also means that if atom \(i\) chooses atom \(j\) as its sole partner, but atom \(j\) chooses atom \(k\) as its sole partner (because \(R_{jk} > R_{ij}\)), then this means atom \(i\) will not be part of a broken bond on this time step, 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 is less than fraction.

When a bond is broken, data structures within LAMMPS that store bond topologies are updated to reflect the breakage. Likewise, if the bond is part of a 3-body (angle) or 4-body (dihedral, improper) interaction, that interaction is removed as well. These changes typically affect pair-wise interactions between atoms that used to be part of bonds, angles, etc.

Note

One data structure that is not updated when a bond breaks are the molecule IDs stored by each atom. Even though one molecule becomes two molecules due to the broken bond, all atoms in both new molecules retain their original molecule IDs.

Computationally, each time step this fix is invoked, it loops over all the bonds in the system and computes distances between pairs of bonded atoms. It also communicates between neighboring processors to coordinate which bonds are broken. Moreover, if any bonds are broken, neighbor lists must be immediately updated on the same time step. This is to ensure that any pair-wise interactions that should be turned “on” due to a bond breaking, because they are no longer excluded by the presence of the bond and the settings of the special_bonds command, will be immediately recognized. All of these operations increase the cost of a time step. 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.

Note

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 two atoms are separated by a distance far from the equilibrium bond length, then the two 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 (as well as angles, dihedrals, and impropers).

See the Howto page on broken bonds for more information on related features in LAMMPS.

## 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. This vector can be accessed by various output commands. The vector values calculated by this fix are “intensive”.

The two quantities in the global vector are

> 1. number of bonds broken on the most recent breakage time step

> 2. cumulative number 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 LAMMPS was built with that package. See the Build package doc page for more info.

## Related commands

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

## Default

The option defaults are prob = 1.0.