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<HTML>
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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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</CENTER>
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<HR>
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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 a simulation be "ready to run", as
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if a <A HREF = "run.html">run</A> command were about to be issued. This means, for
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example, that all <A HREF = "pair_style.html">pair_style</A> coefficients be set via
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the <A HREF = "pair_coeff.html">pair_coeff</A> command. A
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<A HREF = "bond_style.html">bond_style</A> command and all bond coefficients must
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also be set, even if no bonds exist before this command is invoked.
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This is because the building of neighbor list requires initialization
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and setup of a simulation, similar to what a <A HREF = "run.html">run</A> command
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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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</HTML>
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@ -0,0 +1,110 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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create_bonds command :h3
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[Syntax:]
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create_bonds group-ID group2-ID btype rmin rmax :pre
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group-ID = ID of first group
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group2-ID = ID of second group, bonds will be between atoms in the 2 groups
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btype = bond type of created bonds
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rmin = minimum distance between pair of atoms to bond together
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rmax = minimum distance between pair of atoms to bond together :ul
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[Examples:]
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create_bonds all all 1 1.0 1.2
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create_bonds surf solvent 3 2.0 2.4 :pre
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[Description:]
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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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"bond_style"_bond_style.html and "bond_coeff"_bond_coeff.html
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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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"read_data"_read_data.html command.
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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. "angle"_angle_style.html, "dihedral"_dihedral_style.html, or
|
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"improper"_improper_style.html interactions.
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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 {btype}, where {btype} 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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"read_data"_read_data.html command, or via the optional "bond/types"
|
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argument of the "create_box"_create_box.html command.
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For a bond to be created, an I,J pair of atoms must be a distance D
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apart such that {rmin} <= D <= {rmax}.
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The following settings must have been made in an input
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script before this command is used:
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special_bonds weight for 1-2 interactions must be 0.0
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a "pair_style"_pair_style.html must be defined
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no "kspace_style"_kspace_style.html defined
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minimum "pair_style"_pair_style.html cutoff + "neighbor"_neighbor.html skin >= {rmax} :ul
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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 {rmax} for new bonds to create.
|
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An additional requirement is that a simulation be "ready to run", as
|
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if a "run"_run.html command were about to be issued. This means, for
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example, that all "pair_style"_pair_style.html coefficients be set via
|
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the "pair_coeff"_pair_coeff.html command. A
|
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"bond_style"_bond_style.html command and all bond coefficients must
|
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also be set, even if no bonds exist before this command is invoked.
|
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This is because the building of neighbor list requires initialization
|
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and setup of a simulation, similar to what a "run"_run.html command
|
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would require.
|
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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 "kspace_style"_kspace_style.html command for your subsequent
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simulation.
|
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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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"read_data"_read_data.html 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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"create_box"_create_box.html 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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[Restrictions:]
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This command cannot be used with molecular systems defined using
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molecule template files via the "molecule"_molecule.html and
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"atom_style template"_atom_style.html commands.
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[Related commands:]
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"create_atoms"_create_atoms.html, "delete_bonds"_delete_bonds.html
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[Default:] none
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