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 or atype or dtype or itype
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 (positive integer) atype value = angletype angletype = type of created angles dtype value = dihedraltype dihedraltype = type of created dihedrals itype value = impropertype impropertype = type of created impropers
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 85784 iparam 2 3
fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3 atype 1 dtype 2
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. Optionally, the creation of a bond can also create angle, dihedral, and improper interactions that bond is part of. See the discussion of the atype, dtype, and itype keywords below.
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 and higher-order many-body interactions from timestep to timestep as atoms move.
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
When a bond is created, data structures within LAMMPS that store bond topology are updated to reflect the creation. If the bond is part of new 3-body (angle) or 4-body (dihedral, improper) interactions, you can choose to create new angles, dihedrals, impropers as well, using the atype, dtype, and itype keywords. All of these changes typically affect pairwise interactions between atoms that are now part of new 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 two molecules become one moleclue due to the created bond, all atoms in the new moleclue retain their original molecule IDs.
If the atype keyword is used and if an angle potential is defined via the angle_style command, then any new 3-body interactions inferred by the creation of a bond will create new angles of type angletype, with parameters assigned by the corresponding angle_coeff command. Likewise, the dtype and itype keywords will create new dihedrals and impropers of type dihedraltype and impropertype.
Note
To create a new bond, the internal LAMMPS data structures that store this information must have space for it. When LAMMPS 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 bond per atom” parameter must be set to allow for it. Ditto for “extra angle per atom”, “extra dihedral per atom”, and “extra improper per atom” if angles, dihedrals, or impropers are being added when bonds are created. See the read_data or create_box command for more details. Note that 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.
Note
LAMMPS stores and maintains a data structure with a list of the 1st, 2nd, and 3rd neighbors of each atom (within the bond topology of the system) for use in weighting pairwise interactions for bonded atoms. Note that adding a single bond always adds a new 1st neighbor but may also induce *many* new 2nd and 3rd neighbors, depending on the molecular topology of your system. The “extra special per atom” parameter must typically be set to allow for the new maximum total size (1st + 2nd + 3rd neighbors) of this per-atom list. There are 3 ways to do this. See the read_data or create_box or “special_bonds extra” commands for details.
Note
Even if you do not use the atype, dtype, or itype keywords, the list of topological neighbors is updated for atoms affected by the new bond. This in turn affects which neighbors are considered for pairwise interactions, using the weighting rules set by the special_bonds command. Consider a new bond created between atoms I,J. If J has a bonded neighbor K, then K becomes a 2nd neighbor of I. Even if the atype keyword is not used to create angle I-J-K, the pairwise interaction between I and K will be potentially turned off or weighted by the 1-3 weighting specified by the special_bonds command. This is the case even if the “angle yes” option was used with that command. The same is true for 3rd neighbors (1-4 interactions), the dtype keyword, and the “dihedral yes” option used with the special_bonds command.
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. Moreover, if any bonds are created, neighbor lists must be immediately updated on the same timestep. This is to insure that any pairwise interactions that should be turned “off” due to a bond creation, because they are now 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 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.
Note
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 (and angles, dihedrals, impropers).
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:
- # of bonds created on the most recent creation timestep
- 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 LAMMPS was built with that package. See the Making LAMMPS section for more info.
Default
The option defaults are iparam = (0,itype), jparam = (0,jtype), and prob = 1.0.