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lammps/doc/delete_bonds.txt
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
delete_bonds command :h3
[Syntax:]
delete_bonds group-ID style args keyword ... :pre
group-ID = group ID :ulb,l
style = {multi} or {atom} or {bond} or {angle} or {dihedral} or
{improper} or {stats} :l
{multi} args = none
{atom} args = an atom type
{bond} args = a bond type
{angle} args = an angle type
{dihedral} args = a dihedral type
{improper} args = an improper type
{stats} args = none :pre
zero or more keywords may be appended :l
keyword = {any} or {undo} or {remove} or {special} :l
:ule
[Examples:]
delete_bonds frozen multi remove
delete_bonds all atom 4 special
delete_bonds all stats :pre
[Description:]
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 "neigh_modify exclude"_neigh_modify.html command. The
"fix shake"_fix_shake.html command also effectively turns off certain
bond and angle interactions.
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 {any}
keyword to change the behavior.
For style {multi} all bond, angle, dihedral, and improper interactions
of any type, involving atoms in the group, are turned off.
Style {atom} is the same as style {multi} 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.
For style {bond}, only bonds are candidates for turn-off, and the bond
must also be of the specified type. Styles {angle}, {dihedral}, and
{improper} are treated similarly.
For style {bond}, 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 "bond_style
quartic"_bond_style.html command.
For style {stats} 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.
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
"special_bonds"_special_bonds.html 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.
Several keywords can be appended to the argument list to alter the
default behaviors.
The {any} 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 {undo}
keyword is used).
The {undo} 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 "fix shake"_fix_shake.html command also sets bond and
angle types negative, so this option should not be used on those
interactions.
The {remove} 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 {undo} keyword.
Removal does not alter the pairwise 1-2, 1-3, 1-4 weighting list.
The {special} 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.
Note that the choice of {remove} and {special} 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.
[Restrictions:]
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).
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 "fix
shake"_fix_shake.html 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.
[Related commands:]
"neigh_modify"_neigh_modify.html exclude,
"special_bonds"_special_bonds.html, "fix shake"_fix_shake.html
[Default:] none
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