2006-09-22 00:22:34 +08:00
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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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<HR>
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<H3>delete_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>delete_bonds group-ID style args keyword ...
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</PRE>
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<UL><LI>group-ID = group ID
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<LI>style = <I>multi</I> or <I>atom</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or
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<I>improper</I> or <I>stats</I>
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<PRE> <I>multi</I> args = none
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<I>atom</I> args = an atom type
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<I>bond</I> args = a bond type
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<I>angle</I> args = an angle type
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<I>dihedral</I> args = a dihedral type
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<I>improper</I> args = an improper type
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<I>stats</I> args = none
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</PRE>
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2007-07-03 04:04:44 +08:00
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<LI>zero or more keywords may be appended
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2012-02-29 01:46:36 +08:00
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<LI>keyword = <I>any</I> or <I>undo</I> or <I>remove</I> or <I>special</I>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>delete_bonds frozen multi remove
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delete_bonds all atom 4 special
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delete_bonds all stats
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Turn off (or on) molecular topology interactions, i.e. bonds, angles,
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dihedrals, impropers. This command is useful for deleting
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interactions that have been previously turned off by bond-breaking
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potentials. It is also useful for turning off topology interactions
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between frozen or rigid atoms. Pairwise interactions can be turned
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off via the <A HREF = "neigh_modify.html">neigh_modify exclude</A> command. The
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<A HREF = "fix_shake.html">fix shake</A> command also effectively turns off certain
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bond and angle interactions.
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</P>
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<P>For all styles, an interaction is only turned off (or on) if all the
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atoms involved are in the specified group. For style <I>multi</I> this is
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the only criterion applied - all types of bonds, angles, dihedrals,
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impropers in the group turned off.
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</P>
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<P>For style <I>atom</I>, one or more of the atoms involved must also be of
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the specified type.
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</P>
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<P>For style <I>bond</I>, only bonds are candidates for turn-off, and the bond
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must also be of the specified type. Styles <I>angle</I>, <I>dihedral</I>, and
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<I>improper</I> are treated similarly.
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2006-09-22 00:22:34 +08:00
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</P>
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<P>For style <I>bond</I>, you can set the type to 0 to delete bonds that have
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been previously broken by a bond-breaking potential (which sets the
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bond type to 0 when a bond is broken); e.g. see the <A HREF = "bond_style.html">bond_style
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quartic</A> command.
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</P>
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<P>For style <I>stats</I> no interactions are turned off (or on); the status
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of all interactions in the specified group is simply reported. This
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is useful for diagnostic purposes if bonds have been turned off by a
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bond-breaking potential during a previous run.
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</P>
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<P>The default behavior of the delete_bonds command is to turn off
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interactions by toggling their type to a negative value, but not to
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permanently remove the interaction. E.g. a bond_type of 2 is set to
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-2. The neighbor list creation routines will not include such an
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interaction in their interaction lists. The default is also to not
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alter the list of 1-2, 1-3, 1-4 neighbors computed by the
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<A HREF = "special_bonds.html">special_bonds</A> command and used to weight pairwise
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force and energy calculations. This means that pairwise computations
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will proceed as if the bond (or angle, etc) were still turned on.
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</P>
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<P>Several keywords can be appended to the argument list to alter the
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default behavior.
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</P>
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<P>The <I>any</I> keyword changes the requirement that all atoms in the bond
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(angle, etc) must be in the specified group in order to turn-off the
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interaction. If any of the atoms in the interaction are in the
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specified group, it will be turned off (or on if the <I>undo</I> keyword is
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used).
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</P>
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<P>The <I>undo</I> keyword inverts the delete_bonds command so that the
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specified bonds, angles, etc are turned on if they are currently
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turned off. This means a negative value is toggled to positive.
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2006-09-22 00:22:34 +08:00
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Note that the <A HREF = "fix_shake.html">fix shake</A> command also sets bond and
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angle types negative, so this option should not be used on those
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interactions.
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</P>
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<P>The <I>remove</I> keyword is invoked at the end of the delete_bonds
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operation. It causes turned-off bonds (angles, etc) to be removed
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from each atom's data structure and then adjusts the global bond
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(angle, etc) counts accordingly. Removal is a permanent change;
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removed bonds cannot be turned back on via the <I>undo</I> keyword.
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Removal does not alter the pairwise 1-2, 1-3, 1-4 weighting list.
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</P>
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<P>The <I>special</I> keyword is invoked at the end of the delete_bonds
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operation, after (optional) removal. It re-computes the pairwise 1-2,
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1-3, 1-4 weighting list. The weighting list computation treats
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turned-off bonds the same as turned-on. Thus, turned-off bonds must
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be removed if you wish to change the weighting list.
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</P>
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<P>Note that the choice of <I>remove</I> and <I>special</I> options affects how
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1-2, 1-3, 1-4 pairwise interactions will be computed across bonds that
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have been modified by the delete_bonds command.
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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 requires inter-processor communication to coordinate the
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deleting of bonds. This means that your system must be ready to
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perform a simulation before using this command (force fields setup,
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atom masses set, etc).
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</P>
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<P>If deleted bonds (angles, etc) are removed but the 1-2, 1-3, 1-4
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weighting list is not recomputed, this can cause a later <A HREF = "fix_shake.html">fix
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shake</A> command to fail due to an atom's bonds being
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inconsistent with the weighting list. This should only happen if the
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group used in the fix command includes both atoms in the bond, in
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which case you probably should be recomputing the weighting list.
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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 = "neigh_modify.html">neigh_modify</A> exclude,
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<A HREF = "special_bonds.html">special_bonds</A>, <A HREF = "fix_shake.html">fix shake</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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