forked from lijiext/lammps
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5.1 KiB
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115 lines
5.1 KiB
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<H3>create_bonds command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>create_bonds group-ID group2-ID btype rmin rmax
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</PRE>
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<UL><LI>group-ID = ID of first group
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<LI>group2-ID = ID of second group, bonds will be between atoms in the 2 groups
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<LI>btype = bond type of created bonds
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<LI>rmin = minimum distance between pair of atoms to bond together
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<LI>rmax = minimum distance between pair of atoms to bond together
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>create_bonds all all 1 1.0 1.2
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create_bonds surf solvent 3 2.0 2.4
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Create bonds between pairs of atoms that meet specified distance
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criteria. The bond interactions can then be computed during a
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simulation by the bond potential defined by the
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<A HREF = "bond_style.html">bond_style</A> and <A HREF = "bond_coeff.html">bond_coeff</A>
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commands. This command is useful for adding bonds to a system,
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e.g. between nearest neighbors in a lattice of atoms, without having
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to enumerate all the bonds in the data file read by the
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<A HREF = "read_data.html">read_data</A> command.
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</P>
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<P>Note that the flexibility of this command is limited. It can be used
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several times to create different types of bond at different
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distances. But it cannot typically create all the bonds that would
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normally be defined in a complex system of molecules. Also note that
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this command does not add any 3-body or 4-body interactions which,
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depending on your model, may be induced by added bonds,
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e.g. <A HREF = "angle_style.html">angle</A>, <A HREF = "dihedral_style.html">dihedral</A>, or
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<A HREF = "improper_style.html">improper</A> interactions.
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</P>
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<P>All created bonds will be between pairs of atoms I,J where I is in one
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of the two specified groups, and J is in the other. The two groups
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can be the same, e.g. group "all". The created bonds will be of bond
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type <I>btype</I>, where <I>btype</I> must be a value between 1 and the number
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of bond types defined. This maximum value is set by the "bond types"
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field in the header of the data file read by the
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<A HREF = "read_data.html">read_data</A> command, or via the optional "bond/types"
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argument of the <A HREF = "create_box.html">create_box</A> command.
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</P>
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<P>For a bond to be created, an I,J pair of atoms must be a distance D
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apart such that <I>rmin</I> <= D <= <I>rmax</I>.
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</P>
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<P>The following settings must have been made in an input
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script before this command is used:
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</P>
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<UL><LI>special_bonds weight for 1-2 interactions must be 0.0
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<LI>a <A HREF = "pair_style.html">pair_style</A> must be defined
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<LI>no <A HREF = "kspace_style.html">kspace_style</A> defined
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<LI>minimum <A HREF = "pair_style.html">pair_style</A> cutoff + <A HREF = "neighbor.html">neighbor</A> skin >= <I>rmax</I>
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</UL>
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<P>These settings are required so that a neighbor list can be created to
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search for nearby atoms. Pairs of atoms that are already bonded
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cannot appear in the neighbor list, to avoid creation of duplicate
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bonds. The neighbor list for all atom type pairs must also extend to
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a distance that encompasses the <I>rmax</I> for new bonds to create.
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</P>
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<P>An additional requirement is that your system must be ready to perform
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a simulation. This means, for example, that all
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<A HREF = "pair_style.html">pair_style</A> coefficients be set via the
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<A HREF = "pair_coeff.html">pair_coeff</A> command. A <A HREF = "bond_style.html">bond_style</A>
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command and all bond coefficients must also be set, even if no bonds
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exist before this command is invoked. This is because the building of
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neighbor list requires initialization and setup of a simulation,
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similar to what a <A HREF = "run.html">run</A> command would require.
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</P>
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<P>Note that you can change any of these settings after this command
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executes, e.g. if you wish to use long-range Coulombic interactions
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via the <A HREF = "kspace_style.html">kspace_style</A> command for your subsequent
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simulation.
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</P>
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<P>IMPORTANT NOTE: If the system has no bonds to begin with, or if more
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bonds per atom are being added than currently exist, then you must
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insure that the number of bond types and the maximum number of bonds
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per atom are set to large enough values. Otherwise an error may occur
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when too many bonds are added to an atom. If the
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<A HREF = "read_data.html">read_data</A> command is used to define the system, these
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2 parameters can be set via the "bond types" and "extra bond per atom"
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fields in the header section of the data file. If the
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<A HREF = "create_box.html">create_box</A> command is used to define the system,
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these 2 parameters can be set via its optional "bond/types" and
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"extra/bond/per/atom" arguments. See the doc pages for the 2 commands
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for details.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>This command cannot be used with molecular systems defined using
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molecule template files via the <A HREF = "molecule.html">molecule</A> and
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<A HREF = "atom_style.html">atom_style template</A> commands.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
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</P>
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<P><B>Default:</B> none
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</P>
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