Homec4science
Diffusion lammps (HEAD -> master) Browse

lammps/doc/delete_bonds.txt
0cc1d090f44eHEAD -> master

Last Change
Raw File

delete_bonds.txt
View Options

"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 = {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, an interaction is only turned off (or on) if all the
atoms involved are in the specified group. For style {multi} this is
the only criterion applied - all types of bonds, angles, dihedrals,
impropers in the group turned off.
For style {atom}, one or more of the atoms involved must also be of
the specified type. For style {bond}, only bonds are candidates for
turn-off, and the bond must 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; 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. 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.
The keywords listed above can be appended to the argument list to
alter the default behavior.
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 any 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
c4science · Help