2008-05-16 05:21:50 +08:00
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<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>
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<H3>fix bond/swap command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID bond/swap fraction cutoff seed
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>bond/swap = style name of this fix command
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<LI>fraction = fraction of group atoms to consider for swapping
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<LI>cutoff = distance at which swapping will be considered (distance units)
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<LI>seed = random # seed (positive integer)
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</UL>
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<P><B>Examples:</B>
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</P>
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2008-07-30 03:56:08 +08:00
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<PRE>fix 1 all bond/swap 0.5 1.3 598934
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2008-05-16 05:21:50 +08:00
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>In a simulation of polymer chains, this command attempts to swap bonds
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between two different chains, effectively grafting the end of one
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chain onto another chain and vice versa. This is done via Monte Carlo
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rules using the Boltzmann acceptance criterion. The purpose is to
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2008-07-02 22:18:18 +08:00
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equilibrate the polymer chain conformations more rapidly than dynamics
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alone would do it, by enabling instantaneous large conformational
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changes in a dense polymer melt. The polymer chains should thus more
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rapidly converge to the proper end-to-end distances and radii of
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gyration. It is designed for use with systems of
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2009-04-02 22:09:47 +08:00
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<A HREF = "bond_fene.html">FENE</A> or <A HREF = "bond_harmonic.html">harmonic</A> bead-spring
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polymer chains where each polymer is a linear chain of monomers, but
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LAMMPS does not enforce this requirement, i.e. any
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<A HREF = "bond_style.html">bond_style</A> can be used.
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2008-05-16 05:21:50 +08:00
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</P>
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<P>A schematic of the kinds of bond swaps that can occur is shown here:
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</P>
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<CENTER><IMG SRC = "JPG/bondswap.jpg">
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</CENTER>
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<P>On the left, the red and blue chains have two monomers A1 and B1 close
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to each other, which are currently bonded to monomers A2 and B2
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respectively within their own chains. The bond swap operation will
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attempt to delete the A1-A2 and B1-B2 bonds and replace them with
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A1-B2 and B1-A2 bonds. If the swap is energetically favorable, the
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two chains on the right are the result and each polymer chain has
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undergone a dramatic conformational change. This reference provides
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more details on how the algorithm works and its application:
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<A HREF = "#Sides">(Sides)</A>.
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</P>
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<P>The bond swapping operation is invoked each time neighbor lists are
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built during a simulation, since it potentially alters the list of
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which neighbors are considered for pairwise interaction. At each
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reneighboring step, each processor considers a random specified
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<I>fraction</I> of its atoms as potential swapping monomers for this
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timestep. Choosing a small <I>fraction</I> value can reduce the likelihood
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of a reverse swap occurring soon after an initial swap.
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</P>
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<P>For each monomer A1, its neighbors are examined to find a possible B1
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monomer. Both A1 and B1 must be in the fix group, their separation
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must be less than the specified <I>cutoff</I>, and the molecule IDs of A1
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and B1 must be the same (see below). If a suitable partner is found,
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the energy change due to swapping the 2 bonds is computed. This
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includes changes in pairwise, bond, and angle energies due to the
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altered connectivity of the 2 chains. Dihedral and improper
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interactions are not allowed to be defined when this fix is used.
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</P>
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<P>If the energy decreases due to the swap operation, the bond swap is
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accepted. If the energy increases it is accepted with probability
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exp(-delta/kT) where delta is the increase in energy, k is the
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Boltzmann constant, and T is the current temperature of the system.
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Whether the swap is accepted or rejected, no other swaps are attempted
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by this processor on this timestep.
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</P>
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<P>The criterion for matching molecule IDs is how bond swaps performed by
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this fix conserve chain length. To use this features you must setup
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the molecule IDs for your polymer chains in a certain way, typically
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in the data file, read by the <A HREF = "read_data.html">read_data</A> comand.
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Consider a system of 6-mer chains. You have 3 choices. If the
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molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then
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swaps will conserve length. For a particular momoner there will be
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only one other monomer on another chain which is a potential swap
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partner. If the molecule IDs for monomers on each chain are set to
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1,2,3,3,2,1 then swaps will conserve length but swaps will be able to
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occur at either end of a chain. Thus for a particular monomer there
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will be 2 possible swap partners on another chain. In this scenario,
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swaps can also occur within a single chain, i.e. the two ends of a
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chain swap with each other. The third choice is to give all monomers
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on all chains the same molecule ID, e.g. 0. This will allow a wide
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variety of swaps to occur, but will NOT conserve chain lengths.
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</P>
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<P>IMPORTANT NOTE: If your simulation uses molecule IDs in the usual way,
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where all monomers on a single chain are assigned the same ID
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(different for each chain), then swaps will only occur within the same
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chain and will NOT conserve chain length. This is probably not what
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you want for this fix.
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</P>
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<HR>
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<P>This fix computes a temperature each time it is invoked for use by the
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Boltzmann criterion. To do this, the fix creates its own compute of
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style <I>temp</I>, as if this command had been issued:
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</P>
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<PRE>compute fix-ID_temp all temp
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</PRE>
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<P>See the <A HREF = "compute_temp.html">compute temp</A> command for details. Note
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that the ID of the new compute is the fix-ID with underscore + "temp"
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appended and the group for the new compute is "all", so that the
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temperature of the entire system is used.
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</P>
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<P>Note that this is NOT the compute used by thermodynamic output (see
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the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>.
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This means you can change the attributes of this fix's temperature
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(e.g. its degrees-of-freedom) via the
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<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
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during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
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custom</A> command using the appropriate compute-ID.
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It also means that changing attributes of <I>thermo_temp</I> will have no
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effect on this fix.
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</P>
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<HR>
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<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
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</P>
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<P>No information about this fix is written to <A HREF = "restart.html">binary restart
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files</A>. Because the state of the random number generator
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is not saved in restart files, this means you cannot do "exact"
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restarts with this fix, where the simulation continues on the same as
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if no restart had taken place. However, in a statistical sense, a
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restarted simulation should produce the same behavior. Also note that
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each processor generates possible swaps independently of other
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processors. Thus if you repeat the same simulation on a different number
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of processors, the specific swaps performed will be different.
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</P>
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<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
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fix. You can use it to assign a <A HREF = "compute.html">compute</A> you have
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defined to this fix which will be used to compute the temperature for
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the Boltzmann criterion.
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</P>
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2010-04-03 00:51:06 +08:00
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<P>This fix computes two statistical quantities as a global 2-vector of
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output, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
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2008-05-16 05:21:50 +08:00
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commands</A>. The first component of the vector
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is the cummulative number of swaps performed by all processors. The
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second component of the vector is the cummulative number of swaps
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attempted (whether accepted or rejected). Note that a swap "attempt"
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only occurs when swap partners meeting the criteria described above
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are found on a particular timestep. The vector values calculated by
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2010-03-03 05:59:33 +08:00
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this fix are "intensive".
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2008-05-16 05:21:50 +08:00
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</P>
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<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
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the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
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minimization</A>.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>The setings of the "special_bond" command must be 0,1,1 in order to
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2009-04-02 22:09:47 +08:00
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use this fix, which is typical of bead-spring chains with FENE or
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harmonic bonds. This means that pairwise interactions between bonded
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atoms are turned off, but are turned on between atoms two or three
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hops away along the chain backbone.
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2008-05-16 05:21:50 +08:00
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</P>
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<P>Currently, energy changes in dihedral and improper interactions due to
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a bond swap are not considered. Thus a simulation that uses this fix
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cannot use a dihedral or improper potential.
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</P>
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<P><B>Related commands:</B> none
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</P>
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<P><B>Default:</B> none
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</P>
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<HR>
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<A NAME = "Sides"></A>
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<P><B>(Sides)</B> Sides, Grest, Stevens, Plimpton, J Polymer Science B, 42,
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199-208 (2004).
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</P>
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</HTML>
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