git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14950 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/html/_sources/create_bonds.txt

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+.. index:: create_bonds
+
+create_bonds command
+====================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   create_bonds 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 = minimum distance between pair of atoms to bond together
+
+Examples
+""""""""
+
+.. parsed-literal::
+
+   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
+:doc:`bond_style <bond_style>` and :doc:`bond_coeff <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
+:doc:`read_data <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. :doc:`angle <angle_style>`, :doc:`dihedral <dihedral_style>`, or
+:doc:`improper <improper_style>` 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
+:doc:`read_data <read_data>` command, or via the optional "bond/types"
+argument of the :doc:`create_box <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:
+
+* special_bonds weight for 1-2 interactions must be 0.0
+* a :doc:`pair_style <pair_style>` must be defined
+* no :doc:`kspace_style <kspace_style>` defined
+* minimum :doc:`pair_style <pair_style>` cutoff + :doc:`neighbor <neighbor>` skin >= *rmax*
+
+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 your system must be ready to perform
+a simulation.  This means, for example, that all
+:doc:`pair_style <pair_style>` coefficients be set via the
+:doc:`pair_coeff <pair_coeff>` command.  A :doc:`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 :doc:`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 :doc:`kspace_style <kspace_style>` command for your subsequent
+simulation.
+
+.. 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 :doc:`read_data <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 :doc:`create_box <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 :doc:`molecule <molecule>` and
+:doc:`atom_style template <atom_style>` commands.
+
+Related commands
+""""""""""""""""
+
+:doc:`create_atoms <create_atoms>`, :doc:`delete_bonds <delete_bonds>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Section_commands.html#comm