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lammps/doc/fix_bond_break.txt
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fix_bond_break.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
fix bond/break command :h3
[Syntax:]
fix ID group-ID bond/break Nevery bondtype Rmax keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
bond/break = style name of this fix command :l
Nevery = attempt bond breaking every this many steps :l
bondtype = type of bonds to break :l
Rmax = bond longer than Rmax can break (distance units) :l
zero or more keyword/value pairs may be appended to args :l
keyword = {prob} :l
{prob} values = fraction seed
fraction = break a bond with this probability if otherwise eligible
seed = random number seed (positive integer) :pre
:ule
[Examples:]
fix 5 all bond/break 10 2 1.2
fix 5 polymer bond/break 1 1 2.0 prob 0.5 49829 :pre
[Description:]
Break bonds between pairs of atoms as a simulation runs according to
specified criteria. This can be used to model the dissolution of a
polymer network due to stretching of the simulation box or other
deformations. In this context, a bond means an interaction between a
pair of atoms computed by the "bond_style"_bond_style.html command.
Once the bond is broken it will be permanently deleted. This is
different than a "pairwise"_pair_style.html bond-order potential such
as Tersoff or AIREBO which infers bonds and many-body interactions
based on the current geometry of a small cluster of atoms and
effectively creates and destroys bonds from timestep to timestep as
atoms move.
A check for possible bond breakage is performed every {Nevery}
timesteps. If two bonded atoms I,J are further than a distance {Rmax}
of each other, if the bond is of type {bondtype}, and if both I and J
are in the specified fix group, then I,J is labeled as a "possible"
bond to break.
If several bonds involving an atom are stretched, it may have multiple
possible bonds to break. Every atom checks its list of possible bonds
to break and labels the longest such bond as its "sole" bond to break.
After this is done, if atom I is bonded to atom J in its sole bond,
and atom J is bonded to atom I in its sole bond, then the I,J bond is
"eligible" to be broken.
Note that these rules mean an atom will only be part of at most one
broken bond on a given timestep. It also means that if atom I chooses
atom J as its sole partner, but atom J chooses atom K is its sole
partner (due to Rjk > Rij), then this means atom I will not be part of
a broken bond on this timestep, even if it has other possible bond
partners.
The {prob} keyword can effect whether an eligible bond is actually
broken. The {fraction} setting must be a value between 0.0 and 1.0.
A uniform random number between 0.0 and 1.0 is generated and the
eligible bond is only broken if the random number < fraction.
When a bond is broken, data structures within LAMMPS that store bond
topology are updated to reflect the breakage. This can also affect
subsequent computation of pairwise interactions involving the atoms in
the bond. See the Restriction section below for additional
information.
Computationally, each timestep this fix operates, it loops over bond
lists and computes distances between pairs of bonded atoms in the
list. It also communicates between neighboring processors to
coordinate which bonds are broken. Thus it will increase the cost of
a timestep. Thus you should be cautious about invoking this fix too
frequently.
You can dump out snapshots of the current bond topology via the "dump
local"_dump.html command.
IMPORTANT NOTE: Breaking a bond typically alters the energy of a
system. You should be careful not to choose bond breaking criteria
that induce a dramatic change in energy. For example, if you define a
very stiff harmonic bond and break it when 2 atoms are separated by a
distance far from the equilibribum bond length, then the 2 atoms will
be dramatically released when the bond is broken. More generally, you
may need to thermostat your system to compensate for energy changes
resulting from broken bonds.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes two statistics which it stores in a global vector of
length 2, which can be accessed by various "output
commands"_Section_howto.html#howto_15. The vector values calculated
by this fix are "intensive".
These are the 2 quantities:
(1) # of bonds broken on the most recent breakage timestep
(2) cummulative # of bonds broken :ul
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
This fix is part of the MC package. It is only enabled if LAMMPS was
built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
Currently, there are 2 restrictions for using this fix. We may relax
these in the future if there are new models that would be enabled by
it.
When a bond is broken, you might wish to turn off angle and dihedral
interactions that include that bond. However, LAMMPS does not check
for these angles and dihedrals, even if your simulation defines an
"angle_style"_angle_style.html or
"dihedral_style"_dihedral_style.html.
This fix requires that the pairwise weightings defined by the
"special_bonds"_special_bonds.html command be 0,1,1 for 1-2, 1-3, and
1-4 neighbors within the bond topology. This effectively means that
the pairwise interaction between atoms I and J is turned off when a
bond between them exists and will be turned on when the bond is
broken. It also means that the pairwise interaction of I with J's
other bond partners is unaffected by the existence of the bond.
[Related commands:]
"fix bond/create"_fix_bond_create.html, "fix
bond/swap"_fix_bond_swap.html, "dump local"_dump.html,
"special_bonds"_special_bonds.html
[Default:]
The option defaults are prob = 1.0.
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