Syntax: +
+create_bonds group-ID group2-ID btype rmin rmax ++
Examples: +
+create_bonds all all 1 1.0 1.2 +create_bonds surf solvent 3 2.0 2.4 ++
Description: +
+Create bonds between pairs of atoms that meet specified distance +criteria. The bond interactions can then be computed during a +simulation by the bond potential defined by the +bond_style and bond_coeff +commands. This command 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 command. +
+Note that 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 create all the bonds that would +normally be defined in a complex system of molecules. Also note that +this command does not add any 3-body or 4-body interactions which, +depending on your model, may be induced by added bonds, +e.g. angle, dihedral, or +improper interactions. +
+All created bonds will be 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. This maximum value is set by the "bond types" +field in the header of the data file read by the +read_data command, or via the optional "bond/types" +argument of the create_box command. +
+For a bond to be created, an I,J pair of atoms must be a distance D +apart such that rmin <= D <= rmax. +
+The following settings must have been made in an input +script before this command is used: +
+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. +
+An additional requirement is that a simulation be "ready to run", as +if a run command were about to be issued. This means, for +example, that all pair_style coefficients be set via +the pair_coeff command. A +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 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 command for your subsequent +simulation. +
+IMPORTANT NOTE: If the system has no bonds to begin with, or if more +bonds per atom are being added than currently exist, then you must +insure that the number of bond types and the maximum number of bonds +per atom are set to large enough values. Otherwise an error may occur +when too many bonds are added to an atom. If the +read_data command is used to define the system, these +2 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 command is used to define the system, +these 2 parameters can be set via its optional "bond/types" and +"extra/bond/per/atom" arguments. See the doc pages for the 2 commands +for details. +
+Restrictions: +
+This command cannot be used with molecular systems defined using +molecule template files via the molecule and +atom_style template commands. +
+Related commands: +
+ +Default: none +
+ diff --git a/doc/create_bonds.txt b/doc/create_bonds.txt new file mode 100644 index 0000000000..f5b3dcc337 --- /dev/null +++ b/doc/create_bonds.txt @@ -0,0 +1,110 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +create_bonds command :h3 + +[Syntax:] + +create_bonds group-ID group2-ID btype rmin rmax :pre + +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 = minimum distance between pair of atoms to bond together :ul + +[Examples:] + +create_bonds all all 1 1.0 1.2 +create_bonds surf solvent 3 2.0 2.4 :pre + +[Description:] + +Create bonds between pairs of atoms that meet specified distance +criteria. The bond interactions can then be computed during a +simulation by the bond potential defined by the +"bond_style"_bond_style.html and "bond_coeff"_bond_coeff.html +commands. This command 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.html command. + +Note that 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 create all the bonds that would +normally be defined in a complex system of molecules. Also note that +this command does not add any 3-body or 4-body interactions which, +depending on your model, may be induced by added bonds, +e.g. "angle"_angle_style.html, "dihedral"_dihedral_style.html, or +"improper"_improper_style.html interactions. + +All created bonds will be 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. This maximum value is set by the "bond types" +field in the header of the data file read by the +"read_data"_read_data.html command, or via the optional "bond/types" +argument of the "create_box"_create_box.html command. + +For a bond to be created, an I,J pair of atoms must be a distance D +apart such that {rmin} <= D <= {rmax}. + +The following settings must have been made in an input +script before this command is used: + +special_bonds weight for 1-2 interactions must be 0.0 +a "pair_style"_pair_style.html must be defined +no "kspace_style"_kspace_style.html defined +minimum "pair_style"_pair_style.html cutoff + "neighbor"_neighbor.html skin >= {rmax} :ul + +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. + +An additional requirement is that a simulation be "ready to run", as +if a "run"_run.html command were about to be issued. This means, for +example, that all "pair_style"_pair_style.html coefficients be set via +the "pair_coeff"_pair_coeff.html command. A +"bond_style"_bond_style.html 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.html 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.html command for your subsequent +simulation. + +IMPORTANT NOTE: If the system has no bonds to begin with, or if more +bonds per atom are being added than currently exist, then you must +insure that the number of bond types and the maximum number of bonds +per atom are set to large enough values. Otherwise an error may occur +when too many bonds are added to an atom. If the +"read_data"_read_data.html command is used to define the system, these +2 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.html command is used to define the system, +these 2 parameters can be set via its optional "bond/types" and +"extra/bond/per/atom" arguments. See the doc pages for the 2 commands +for details. + +[Restrictions:] + +This command cannot be used with molecular systems defined using +molecule template files via the "molecule"_molecule.html and +"atom_style template"_atom_style.html commands. + +[Related commands:] + +"create_atoms"_create_atoms.html, "delete_bonds"_delete_bonds.html + +[Default:] none