2009-01-24 02:49:48 +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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<HR>
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<H3>fix bond/break 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/break Nevery bondtype Rmax keyword values ...
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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/break = style name of this fix command
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<LI>Nevery = attempt bond breaking every this many steps
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<LI>bondtype = type of bonds to break
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<LI>Rmax = bond longer than Rmax can break (distance units)
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<LI>zero or more keyword/value pairs may be appended to args
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<LI>keyword = <I>prob</I>
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<PRE> <I>prob</I> values = fraction seed
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fraction = break a bond with this probability if otherwise eligible
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seed = random number seed (positive integer)
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix 5 all bond/break 10 2 1.2
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fix 5 polymer bond/break 1 1 2.0 prob 0.5 49829
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Break bonds between pairs of atoms as a simulation runs according to
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specified criteria. This can be used to model the dissolution of a
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polymer network due to stretching of the simulation box or other
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deformations. In this context, a bond means an interaction between a
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pair of atoms computed by the <A HREF = "bond_style.html">bond_style</A> command.
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Once the bond is broken it will be permanently deleted. This is
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different than a <A HREF = "pair_style.html">pairwise</A> bond-order potential such
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as Tersoff or AIREBO which infers bonds and many-body interactions
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based on the current geometry of a small cluster of atoms and
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effectively creates and destroys bonds from timestep to timestep as
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atoms move.
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</P>
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<P>A check for possible bond breakage is performed every <I>Nevery</I>
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timesteps. If two bonded atoms I,J are further than a distance <I>Rmax</I>
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of each other, if the bond is of type <I>bondtype</I>, and if both I and J
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are in the specified fix group, then I,J is labeled as a "possible"
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bond to break.
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</P>
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<P>If several bonds involving an atom are stretched, it may have multiple
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possible bonds to break. Every atom checks its list of possible bonds
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to break and labels the longest such bond as its "sole" bond to break.
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After this is done, if atom I is bonded to atom J in its sole bond,
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and atom J is bonded to atom I in its sole bond, then the I,J bond is
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"eligible" to be broken.
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</P>
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<P>Note that these rules mean an atom will only be part of at most one
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broken bond on a given timestep. It also means that if atom I chooses
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atom J as its sole partner, but atom J chooses atom K is its sole
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partner (due to Rjk > Rij), then this means atom I will not be part of
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a broken bond on this timestep, even if it has other possible bond
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partners.
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</P>
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<P>The <I>prob</I> keyword can effect whether an eligible bond is actually
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broken. The <I>fraction</I> setting must be a value between 0.0 and 1.0.
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A uniform random number between 0.0 and 1.0 is generated and the
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eligible bond is only broken if the random number < fraction.
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</P>
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<P>When a bond is broken, data structures within LAMMPS that store bond
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topology are updated to reflect the breakage. This can also affect
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subsequent computation of pairwise interactions involving the atoms in
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the bond. See the Restriction section below for additional
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information.
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</P>
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<P>Computationally, each timestep this fix operates, it loops over bond
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lists and computes distances between pairs of bonded atoms in the
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list. It also communicates between neighboring processors to
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coordinate which bonds are broken. Thus it will increase the cost of
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a timestep. Thus you should be cautious about invoking this fix too
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frequently.
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</P>
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<P>You can dump out snapshots of the current bond topology via the <A HREF = "dump.html">dump
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2010-09-20 22:48:44 +08:00
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local</A> command.
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2009-01-24 02:49:48 +08:00
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</P>
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<P>IMPORTANT NOTE: Breaking a bond typically alters the energy of a
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system. You should be careful not to choose bond breaking criteria
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that induce a dramatic change in energy. For example, if you define a
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very stiff harmonic bond and break it when 2 atoms are separated by a
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distance far from the equilibribum bond length, then the 2 atoms will
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be dramatically released when the bond is broken. More generally, you
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may need to thermostat your system to compensate for energy changes
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resulting from broken bonds.
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</P>
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<HR>
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<P><B>Restart, fix_modify, 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>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
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are relevant to this fix.
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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 statistics which it stores in a global vector of
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length 2, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
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2010-03-03 05:51:16 +08:00
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commands</A>. The vector values calculated by
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this fix are "intensive".
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2009-01-24 02:49:48 +08:00
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</P>
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<P>These are the 2 quantities:
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</P>
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<UL><LI>(1) # of bonds broken on the most recent breakage timestep
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<LI>(2) cummulative # of bonds broken
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</UL>
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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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2011-08-25 23:34:45 +08:00
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<P>This fix is part of the "mc" package. It is only enabled if LAMMPS
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2011-08-26 00:46:23 +08:00
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was built with that package. See the <A HREF = "Section_start.html#start_3">Making
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2011-08-25 23:34:45 +08:00
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LAMMPS</A> section for more info.
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</P>
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2009-01-24 02:49:48 +08:00
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<P>Currently, there are 2 restrictions for using this fix. We may relax
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these in the future if there are new models that would be enabled by
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it.
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</P>
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<P>When a bond is broken, you might wish to turn off angle and dihedral
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interactions that include that bond. However, LAMMPS does not check
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for these angles and dihedrals, even if your simulation defines an
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<A HREF = "angle_style.html">angle_style</A> or
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<A HREF = "dihedral_style.html">dihedral_style</A>.
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</P>
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<P>This fix requires that the pairwise weightings defined by the
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<A HREF = "special_bonds.html">special_bonds</A> command be 0,1,1 for 1-2, 1-3, and
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1-4 neighbors within the bond topology. This effectively means that
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the pairwise interaction between atoms I and J is turned off when a
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bond between them exists and will be turned on when the bond is
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broken. It also means that the pairwise interaction of I with J's
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other bond partners is unaffected by the existence of the bond.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "fix_bond_create.html">fix bond/create</A>, <A HREF = "fix_bond_swap.html">fix
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2010-09-13 23:02:07 +08:00
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bond/swap</A>, <A HREF = "dump.html">dump local</A>,
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2009-01-24 02:49:48 +08:00
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<A HREF = "special_bonds.html">special_bonds</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>The option defaults are prob = 1.0.
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</P>
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</HTML>
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