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