fix bond/create command

Syntax

fix ID group-ID bond/create Nevery itype jtype Rmin bondtype keyword values ...
  • ID, group-ID are documented in fix command
  • bond/create = style name of this fix command
  • Nevery = attempt bond creation every this many steps
  • itype,jtype = atoms of itype can bond to atoms of jtype
  • Rmin = 2 atoms separated by less than Rmin can bond (distance units)
  • bondtype = type of created bonds
  • zero or more keyword/value pairs may be appended to args
  • keyword = iparam or jparam or prob
iparam values = maxbond, newtype
  maxbond = max # of bonds of bondtype the itype atom can have
  newtype = change the itype atom to this type when maxbonds exist
jparam values = maxbond, newtype
  maxbond = max # of bonds of bondtype the jtype atom can have
  newtype = change the jtype atom to this type when maxbonds exist
prob values = fraction seed
  fraction = create a bond with this probability if otherwise eligible
  seed = random number seed (prime number greater 10000)

Examples

fix 5 all bond/create 10 1 2 0.8 1
fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 123457 iparam 2 3

Description

Create bonds between pairs of atoms as a simulation runs according to specified criteria. This can be used to model cross-linking of polymers, the formation of a percolation network, etc. In this context, a bond means an interaction between a pair of atoms computed by the bond_style command. Once the bond is created it will be permanently in place.

A check for possible new bonds is performed every Nevery timesteps. If two atoms I,J are within a distance Rmin of each other, if I is of atom type itype, if J is of atom type jtype, if both I and J are in the specified fix group, if a bond does not already exist between I and J, and if both I and J meet their respective maxbond requirement (explained below), then I,J is labeled as a “possible” bond pair.

If several atoms are close to an atom, it may have multiple possible bond partners. Every atom checks its list of possible bond partners and labels the closest such partner as its “sole” bond partner. After this is done, if atom I has atom J as its sole partner, and atom J has atom I as its sole partner, then the I,J bond is “eligible” to be formed.

Note that these rules mean an atom will only be part of at most one created 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 form a bond on this timestep, even if it has other possible bond partners.

It is permissible to have itype = jtype. Rmin must be <= the pairwise cutoff distance between itype and jtype atoms, as defined by the pair_style command.

The iparam and jparam keywords can be used to limit the bonding functionality of the participating atoms. Each atom keeps track of how many bonds of bondtype it already has. If atom I of itype already has maxbond bonds (as set by the iparam keyword), then it will not form any more. Likewise for atom J. If maxbond is set to 0, then there is no limit on the number of bonds that can be formed with that atom.

The newtype value for iparam and jparam can be used to change the atom type of atom I or J when it reaches maxbond number of bonds of type bondtype. This means it can now interact in a pairwise fashion with other atoms in a different way by specifying different pair_coeff coefficients. If you do not wish the atom type to change, simply specify newtype as itype or jtype.

The prob keyword can also effect whether an eligible bond is actually created. 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 created if the random number < fraction.

Any bond that is created is assigned a bond type of bondtype. Data structures within LIGGGHTS(R)-PUBLIC that store bond topology are updated to reflect the new bond. This can also affect subsequent computation of pairwise interactions involving the atoms in the bond. See the Restriction section below for additional information.

Warning

To create a new bond, the internal LIGGGHTS(R)-PUBLIC data structures that store this information must have space for it. When LIGGGHTS(R)-PUBLIC is initialized from a data file, the list of bonds is scanned and the maximum number of bonds per atom is tallied. If some atom will acquire more bonds than this limit as this fix operates, then the “extra bonds per atom” parameter in the data file header must be set to allow for it. See the read_data command for more details. Note that if this parameter needs to be set, it means a data file must be used to initialize the system, even if it initially has no bonds. A data file with no atoms can be used if you wish to add unbonded atoms via the create atoms command, e.g. for a percolation simulation.

Warning

LIGGGHTS(R)-PUBLIC also maintains a data structure that stores a list of 1st, 2nd, and 3rd neighbors of each atom (in the bond topology of the system) for use in weighting pairwise interactions for bonded atoms. Adding a bond adds a single entry to this list. The “extra” keyword of the special_bonds command should be used to leave space for new bonds if the maximum number of entries for any atom will be exceeded as this fix operates. See the special_bonds command for details.

Note that even if your simulation starts with no bonds, you must define a bond_style and use the bond_coeff command to specify coefficients for the bondtype. Similarly, if new atom types are specified by the iparam or jparam keywords, they must be within the range of atom types allowed by the simulation and pairwise coefficients must be specified for the new types.

Computationally, each timestep this fix operates, it loops over neighbor lists and computes distances between pairs of atoms in the list. It also communicates between neighboring processors to coordinate which bonds are created. Thus it roughly doubles 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

Creating a bond typically alters the energy of a system. You should be careful not to choose bond creation criteria that induce a dramatic change in energy. For example, if you define a very stiff harmonic bond and create it when 2 atoms are separated by a distance far from the equilibribum bond length, then the 2 atoms will oscillate dramatically when the bond is formed. More generally, you may need to thermostat your system to compensate for energy changes resulting from created 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 created on the most recent creation timestep
    1. cummulative # of bonds created

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 created, you might wish to induce new angle and dihedral interactions that include that bond. However, LIGGGHTS(R)-PUBLIC does not create 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 will be turned off when a bond between them is created. It also means that the pairwise interaction of I with J’s other bond partners will be unaffected by the new bond.

Default

The option defaults are iparam = (0,itype), jparam = (0,jtype), and prob = 1.0.