lammps/doc/fix_bond_swap.txt

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fix bond/swap command :h3

[Syntax:]

fix ID group-ID bond/swap fraction cutoff seed :pre

ID, group-ID are documented in "fix"_fix.html command
bond/swap = style name of this fix command
fraction = fraction of group atoms to consider for swapping
cutoff = distance at which swapping will be considered (distance units)
seed = random # seed (positive integer) :ul

[Examples:]

fix 1 all bond/swap 0.5 1.3 598934 :pre

[Description:]

In a simulation of polymer chains, this command attempts to swap bonds
between two different chains, effectively grafting the end of one
chain onto another chain and vice versa.  This is done via Monte Carlo
rules using the Boltzmann acceptance criterion.  The purpose is to
equilibrate the polymer chain conformations more rapidly than dynamics
alone would do it, by enabling instantaneous large conformational
changes in a dense polymer melt.  The polymer chains should thus more
rapidly converge to the proper end-to-end distances and radii of
gyration.  It is designed for use with systems of
"FENE"_bond_fene.html bead-spring polymer chains where each polymer is
a linear chain of monomers, but LAMMPS does not enforce this
requirement.

A schematic of the kinds of bond swaps that can occur is shown here:

:c,image(JPG/bondswap.jpg)

On the left, the red and blue chains have two monomers A1 and B1 close
to each other, which are currently bonded to monomers A2 and B2
respectively within their own chains.  The bond swap operation will
attempt to delete the A1-A2 and B1-B2 bonds and replace them with
A1-B2 and B1-A2 bonds.  If the swap is energetically favorable, the
two chains on the right are the result and each polymer chain has
undergone a dramatic conformational change.  This reference provides
more details on how the algorithm works and its application:
"(Sides)"_#Sides.

The bond swapping operation is invoked each time neighbor lists are
built during a simulation, since it potentially alters the list of
which neighbors are considered for pairwise interaction.  At each
reneighboring step, each processor considers a random specified
{fraction} of its atoms as potential swapping monomers for this
timestep.  Choosing a small {fraction} value can reduce the likelihood
of a reverse swap occurring soon after an initial swap.

For each monomer A1, its neighbors are examined to find a possible B1
monomer.  Both A1 and B1 must be in the fix group, their separation
must be less than the specified {cutoff}, and the molecule IDs of A1
and B1 must be the same (see below).  If a suitable partner is found,
the energy change due to swapping the 2 bonds is computed.  This
includes changes in pairwise, bond, and angle energies due to the
altered connectivity of the 2 chains.  Dihedral and improper
interactions are not allowed to be defined when this fix is used.

If the energy decreases due to the swap operation, the bond swap is
accepted.  If the energy increases it is accepted with probability
exp(-delta/kT) where delta is the increase in energy, k is the
Boltzmann constant, and T is the current temperature of the system.
Whether the swap is accepted or rejected, no other swaps are attempted
by this processor on this timestep.

The criterion for matching molecule IDs is how bond swaps performed by
this fix conserve chain length.  To use this features you must setup
the molecule IDs for your polymer chains in a certain way, typically
in the data file, read by the "read_data"_read_data.html comand.
Consider a system of 6-mer chains.  You have 3 choices.  If the
molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then
swaps will conserve length.  For a particular momoner there will be
only one other monomer on another chain which is a potential swap
partner.  If the molecule IDs for monomers on each chain are set to
1,2,3,3,2,1 then swaps will conserve length but swaps will be able to
occur at either end of a chain.  Thus for a particular monomer there
will be 2 possible swap partners on another chain.  In this scenario,
swaps can also occur within a single chain, i.e. the two ends of a
chain swap with each other.  The third choice is to give all monomers
on all chains the same molecule ID, e.g. 0.  This will allow a wide
variety of swaps to occur, but will NOT conserve chain lengths.

IMPORTANT NOTE: If your simulation uses molecule IDs in the usual way,
where all monomers on a single chain are assigned the same ID
(different for each chain), then swaps will only occur within the same
chain and will NOT conserve chain length.  This is probably not what
you want for this fix.

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This fix computes a temperature each time it is invoked for use by the
Boltzmann criterion.  To do this, the fix creates its own compute of
style {temp}, as if this command had been issued:

compute fix-ID_temp all temp :pre

See the "compute temp"_compute_temp.html command for details.  Note
that the ID of the new compute is the fix-ID with underscore + "temp"
appended and the group for the new compute is "all", so that the
temperature of the entire system is used.

Note that this is NOT the compute used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
"compute_modify"_compute_modify.html command or print this temperature
during thermodyanmic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} will have no
effect on this fix.

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[Restart, fix_modify, thermo output, run start/stop, minimize info:]

No information about this fix is written to "binary restart
files"_restart.html.  Because the state of the random number generator
is not saved in restart files, this means you cannot do "exact"
restarts with this fix, where the simulation continues on the same as
if no restart had taken place.  However, in a statistical sense, a
restarted simulation should produce the same behavior.  Also note that
each processor generates possible swaps independently of other
processors.  Thus if you repeat the same simulation on a different number
of processors, the specific swaps performed will be different.

The "fix_modify"_fix_modify.html {temp} option is supported by this
fix.  You can use it to assign a "compute"_compute.html you have
defined to this fix which will be used to compute the temperature for
the Boltzmann criterion.

This fix computes two statistical quantities as a 2-vector of output,
which can be accessed by various "output
commands"_Section_howto.html#4_15.  The first component of the vector
is the cummulative number of swaps performed by all processors.  The
second component of the vector is the cummulative number of swaps
attempted (whether accepted or rejected).  Note that a swap "attempt"
only occurs when swap partners meeting the criteria described above
are found on a particular timestep.  The vector values calculated by
this fix are "extensive", meaning they scale with the number of atoms
in the simulation.

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:]

The setings of the "special_bond" command must be 0,1,1 in order to
use this fix, which is typical of FENE bead-spring chains.
I.e. pairwise interactions between bonded atoms are turned off, but
are turned on between atoms two or three hops away along the chain
backbone.

Currently, energy changes in dihedral and improper interactions due to
a bond swap are not considered.  Thus a simulation that uses this fix
cannot use a dihedral or improper potential.

[Related commands:] none

[Default:] none

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:link(Sides)
[(Sides)] Sides, Grest, Stevens, Plimpton, J Polymer Science B, 42,
199-208 (2004).