# create_bonds command ## Syntax ``` LAMMPS create_bonds style args ... keyword value ... ``` - style = *many* or *single/bond* or *single/angle* or *single/dihedral* or *single/improper* *many* args = group-ID group2-ID btype rmin rmax group-ID = ID of first group group2-ID = ID of second group, bonds will be between atoms in the 2 groups btype = bond type of created bonds rmin = minimum distance between pair of atoms to bond together rmax = maximum distance between pair of atoms to bond together *single/bond* args = btype batom1 batom2 btype = bond type of new bond batom1,batom2 = atom IDs for two atoms in bond *single/angle* args = atype aatom1 aatom2 aatom3 atype = angle type of new angle aatom1,aatom2,aatom3 = atom IDs for three atoms in angle *single/dihedral* args = dtype datom1 datom2 datom3 datom4 dtype = dihedral type of new dihedral datom1,datom2,datom3,datom4 = atom IDs for four atoms in dihedral *single/improper* args = itype iatom1 iatom2 iatom3 iatom4 itype = improper type of new improper iatom1,iatom2,iatom3,iatom4 = atom IDs for four atoms in improper - zero or more keyword/value pairs may be appended - keyword = *special* *special* value = *yes* or *no* ## Examples ``` LAMMPS create_bonds many all all 1 1.0 1.2 create_bonds many surf solvent 3 2.0 2.4 create_bonds single/bond 1 1 2 create_bonds single/angle 5 52 98 107 special no create_bonds single/dihedral 2 4 19 27 101 create_bonds single/improper 3 23 26 31 57 ``` ## Description Create bonds between pairs of atoms that meet a specified distance criteria. Or create a single bond, angle, dihedral or improper between 2, 3, or 4 specified atoms. The new bond (angle, dihedral, improper) interactions will then be computed during a simulation by the bond (angle, dihedral, improper) potential defined by the [bond_style](bond_style), [bond_coeff](bond_coeff), [angle_style](angle_style), [angle_coeff](angle_coeff), [dihedral_style](dihedral_style), [dihedral_coeff](dihedral_coeff), [improper_style](improper_style), [improper_coeff](improper_coeff) commands. The *many* style is useful for adding bonds to a system (e.g., between nearest neighbors in a lattice of atoms) without having to enumerate all the bonds in the data file read by the [read_data](read_data) command. The *single* styles are useful for adding bonds, angles, dihedrals, and impropers to a system incrementally, then continuing a simulation. Note that this command does not auto-create any angle, dihedral, or improper interactions when a bond is added, nor does it auto-create any bonds when an angle, dihedral, or improper is added. It also will not auto-create any angles when a dihedral or improper is added. Thus, the flexibility of this command is limited. It can be used several times to create different types of bond at different distances, but it cannot typically auto-create all the bonds or angles or dihedrals or impropers that would normally be defined in a data file for a complex system of molecules. :::: note ::: title Note ::: If the system has no bonds (angles, dihedrals, impropers) to begin with, or if more bonds per atom are being added than currently exist, then you must ensure that the number of bond types and the maximum number of bonds per atom are set to large enough values, and similarly for angles, dihedrals, and impropers, otherwise an error may occur when too many bonds (angles, dihedrals, impropers) are added to an atom. If the [read_data](read_data) command is used to define the system, these parameters can be set via the \"bond types\" and \"extra bond per atom\" fields in the header section of the data file. If the [create_box](create_box) command is used to define the system, these two parameters can be set via its optional *bond/types* and *extra/bond/per/atom* arguments, and similarly for angles, dihedrals, and impropers. See the doc pages for these two commands for details. :::: ------------------------------------------------------------------------ The *many* style will create bonds between pairs of atoms $I,J$, where $I$ is in one of the two specified groups and $J$ is in the other. The two groups can be the same (e.g., group \"all\"). The created bonds will be of bond type *btype*, where *btype* must be a value between 1 and the number of bond types defined. For a bond to be created, an $I,J$ pair of atoms must be a distance $D$ apart such that $r_\text{min} \le D \le r_\text{max}$. The following settings must have been made in an input script before this style is used: - special_bonds weight for 1\--2 interactions must be 0.0 - a [pair_style](pair_style) must be defined - no [kspace_style](kspace_style) defined - minimum [pair_style](pair_style) cutoff + [neighbor](neighbor) skin $\ge r_\text{max}$ These settings are required so that a neighbor list can be created to search for nearby atoms. Pairs of atoms that are already bonded cannot appear in the neighbor list, to avoid creation of duplicate bonds. The neighbor list for all atom type pairs must also extend to a distance that encompasses the *rmax* for new bonds to create. :::: note ::: title Note ::: If you want to create bonds between pairs of 1\--3 or 1\--4 atoms in the current bond topology, then you need to use [special_bonds lj 0 1 1](special_bonds) to ensure those pairs appear in the neighbor list. They will not appear with the default special_bonds settings, which are zero for 1\--2, 1\--3, and 1\--4 atoms. 1\--3 or 1\--4 atoms are those which are two hops or three hops apart in the bond topology. :::: An additional requirement for this style is that your system must be ready to perform a simulation. This means, for example, that all [pair_style](pair_style) coefficients be set via the [pair_coeff](pair_coeff) command. A [bond_style](bond_style) command and all bond coefficients must also be set, even if no bonds exist before this command is invoked. This is because the building of neighbor list requires initialization and setup of a simulation, similar to what a [run](run) command would require. Note that you can change any of these settings after this command executes (e.g., if you wish to use long-range Coulombic interactions) via the [kspace_style](kspace_style) command for your subsequent simulation. ------------------------------------------------------------------------ The *single/bond* style creates a single bond of type *btype* between two atoms with IDs *batom1* and *batom2*. *Btype* must be a value between 1 and the number of bond types defined. The *single/angle* style creates a single angle of type *atype* between three atoms with IDs *aatom1*, *aatom2*, and *aatom3*. The ordering of the atoms is the same as in the *Angles* section of a data file read by the [read_data](read_data) command (i.e., the three atoms are ordered linearly within the angle; the central atom is *aatom2*). *Atype* must be a value between 1 and the number of angle types defined. The *single/dihedral* style creates a single dihedral of type *dtype* between four atoms with IDs *datom1*, *datom2*, *datom3*, and *datom4*. The ordering of the atoms is the same as in the *Dihedrals* section of a data file read by the [read_data](read_data) command. I.e. the 4 atoms are ordered linearly within the dihedral. *dtype* must be a value between 1 and the number of dihedral types defined. The *single/improper* style creates a single improper of type *itype* between four atoms with IDs *iatom1*, *iatom2*, *iatom3*, and *iatom4*. The ordering of the atoms is the same as in the *Impropers* section of a data file read by the [read_data](read_data) command. I.e. the 4 atoms are ordered linearly within the improper. *itype* must be a value between 1 and the number of improper types defined. ------------------------------------------------------------------------ The keyword *special* controls whether an internal list of special bonds is created after one or more bonds, or a single angle, dihedral, or improper is added to the system. The default value is *yes*. A value of *no* cannot be used with the *many* style. This is an expensive operation since the bond topology for the system must be walked to find all 1\--2, 1\--3, and 1\--4 interactions to store in an internal list, which is used when pairwise interactions are weighted; see the [special_bonds](special_bonds) command for details. Thus if you are adding a few bonds or a large list of angles all at the same time, by using this command repeatedly, it is more efficient to only trigger the internal list to be created once, after the last bond (or angle, or dihedral, or improper) is added: ``` LAMMPS create_bonds single/bond 5 52 98 special no create_bonds single/bond 5 73 74 special no ... create_bonds single/bond 5 17 386 special no create_bonds single/bond 4 112 183 special yes ``` Note that you **must** ensure the internal list is rebuilt after the last bond (angle, dihedral, improper) is added, *before* performing a simulation. Otherwise, pairwise interactions will not be properly excluded or weighted. LAMMPS does **not** check that you have done this correctly. ------------------------------------------------------------------------ ## Restrictions This command cannot be used with molecular systems defined using molecule template files via the [molecule](molecule) and [atom_style template](atom_style) commands. ## Related commands [create_atoms](create_atoms), [delete_bonds](delete_bonds) ## Default The keyword default is special = yes.