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/create 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/create Nevery itype jtype Rmin bondtype 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/create = style name of this fix command
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<LI>Nevery = attempt bond creation every this many steps
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<LI>itype,jtype = atoms of itype can bond to atoms of jtype
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<LI>Rmin = 2 atoms separated by less than Rmin can bond (distance units)
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<LI>bondtype = type of created bonds
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<LI>zero or more keyword/value pairs may be appended to args
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<LI>keyword = <I>iparam</I> or <I>jparam</I> or <I>prob</I>
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<PRE> <I>iparam</I> values = maxbond, newtype
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maxbond = max # of bonds of bondtype the itype atom can have
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newtype = change the itype atom to this type when maxbonds exist
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<I>jparam</I> values = maxbond, newtype
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maxbond = max # of bonds of bondtype the jtype atom can have
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newtype = change the jtype atom to this type when maxbonds exist
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<I>prob</I> values = fraction seed
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fraction = create 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/create 10 1 2 0.8 1
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fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Create bonds between pairs of atoms as a simulation runs according to
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specified criteria. This can be used to model cross-linking of
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polymers, the formation of a percolation network, etc. In this
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context, a bond means an interaction between a pair of atoms computed
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by the <A HREF = "bond_style.html">bond_style</A> command. Once the bond is created
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it will be permanently in place. This is different than a
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<A HREF = "pair_style.html">pairwise</A> bond-order potential such as Tersoff or
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AIREBO which infers bonds and many-body interactions based on the
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current geometry of a small cluster of atoms and effectively creates
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and destroys bonds from timestep to timestep as atoms move.
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</P>
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<P>A check for possible new bonds is performed every <I>Nevery</I> timesteps.
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If two atoms I,J are within a distance <I>Rmin</I> of each other, if I is
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of atom type <I>itype</I>, if J is of atom type <I>jtype</I>, if both I and J
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are in the specified fix group, if a bond does not already exist
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between I and J, and if both I and J meet their respective <I>maxbond</I>
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requirement (explained below), then I,J is labeled as a "possible"
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bond pair.
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</P>
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<P>If several atoms are close to an atom, it may have multiple possible
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bond partners. Every atom checks its list of possible bond partners
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and labels the closest such partner as its "sole" bond partner. After
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this is done, if atom I has atom J as its sole partner, and atom J has
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atom I as its sole partner, then the I,J bond is "eligible" to be
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formed.
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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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created bond on a given timestep. It also means that if atom I
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chooses atom J as its sole partner, but atom J chooses atom K is its
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sole partner (due to Rjk < Rij), then this means atom I will not form
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a bond on this timestep, even if it has other possible bond partners.
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</P>
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<P>It is permissible to have <I>itype</I> = <I>jtype</I>. <I>Rmin</I> must be <= the
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pairwise cutoff distance between <I>itype</I> and <I>jtype</I> atoms, as defined
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by the <A HREF = "pair_style.html">pair_style</A> command.
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</P>
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<P>The <I>iparam</I> and <I>jparam</I> keywords can be used to limit the bonding
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functionality of the participating atoms. Each atom keeps track of
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how many bonds of <I>bondtype</I> it already has. If atom I of
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itype already has <I>maxbond</I> bonds (as set by the <I>iparam</I>
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keyword), then it will not form any more. Likewise for atom J. If
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<I>maxbond</I> is set to 0, then there is no limit on the number of bonds
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that can be formed with that atom.
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</P>
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<P>The <I>newtype</I> value for <I>iparam</I> and <I>jparam</I> can be used to change
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the atom type of atom I or J when it reaches <I>maxbond</I> number of bonds
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of type <I>bondtype</I>. This means it can now interact in a pairwise
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fashion with other atoms in a different way by specifying different
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<A HREF = "pair_coeff.html">pair_coeff</A> coefficients. If you do not wish the
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atom type to change, simply specify <I>newtype</I> as <I>itype</I> or <I>jtype</I>.
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</P>
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<P>The <I>prob</I> keyword can also effect whether an eligible bond is
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actually created. The <I>fraction</I> setting must be a value between 0.0
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and 1.0. A uniform random number between 0.0 and 1.0 is generated and
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the eligible bond is only created if the random number < fraction.
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</P>
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<P>Any bond that is created is assigned a bond type of <I>bondtype</I>. Data
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structures within LAMMPS that store bond topology are updated to
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reflect the new bond. This can also affect subsequent computation of
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pairwise interactions involving the atoms in the bond. See the
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Restriction section below for additional information.
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</P>
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<P>IMPORTANT NOTE: To create a new bond, the internal LAMMPS data
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structures that store this information must have space for it. When
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LAMMPS is initialized from a data file, the list of bonds is scanned
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and the maximum number of bonds per atom is tallied. If some atom
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will acquire more bonds than this limit as this fix operates, then the
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"extra bonds per atom" parameter in the data file header must be set
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to allow for it. See the <A HREF = "read_data.html">read_data</A> command for more
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details. Note that if this parameter needs to be set, it means a data
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file must be used to initialize the system, even if it initially has
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no bonds. A data file with no atoms can be used if you wish to add
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unbonded atoms via the <A HREF = "create_atoms.html">create atoms</A> command,
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e.g. for a percolation simulation.
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</P>
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<P>IMPORTANT NOTE: LAMMPS also maintains a data structure that stores a
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list of 1st, 2nd, and 3rd neighbors of each atom (in the bond topology
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of the system) for use in weighting pairwise interactions for bonded
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atoms. Adding a bond adds a single entry to this list. The "extra"
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keyword of the <A HREF = "special_bonds.html">special_bonds</A> command should be
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used to leave space for new bonds if the maximum number of entries for
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any atom will be exceeded as this fix operates. See the
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<A HREF = "special_bonds.html">special_bonds</A> command for details.
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</P>
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<P>Note that even if your simulation starts with no bonds, you must
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define a <A HREF = "bond_style.html">bond_style</A> and use the
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<A HREF = "bond_coeff.html">bond_coeff</A> command to specify coefficients for the
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<I>bondtype</I>. Similarly, if new atom types are specified by the
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<I>iparam</I> or <I>jparam</I> keywords, they must be within the range of atom
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types allowed by the simulation and pairwise coefficients must be
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specified for the new types.
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</P>
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<P>Computationally, each timestep this fix operates, it loops over
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neighbor lists and computes distances between pairs of atoms in the
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list. It also communicates between neighboring processors to
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coordinate which bonds are created. Thus it roughly doubles the cost
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of a timestep. Thus you should be cautious about invoking this fix
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too 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: Creating a bond typically alters the energy of a
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system. You should be careful not to choose bond creation 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 create 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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oscillate dramatically when the bond is formed. More generally, you
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may need to thermostat your system to compensate for energy changes
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resulting from created 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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2011-08-26 01:01:01 +08:00
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length 2, which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
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commands</A>. The vector values calculated
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by 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 created on the most recent creation timestep
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<LI>(2) cummulative # of bonds created
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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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2011-08-27 02:53:00 +08:00
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<P>This fix is part of the MC package. It is only enabled if LAMMPS was
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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 created, you might wish to induce new angle and
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dihedral interactions that include that bond. However, LAMMPS does
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not create these angles and dihedrals, even if your simulation defines
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an <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 will be turned off when
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a bond between them is created. It also means that the pairwise
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interaction of I with J's other bond partners will be unaffected by
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the new 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_break.html">fix bond/break</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 iparam = (0,itype), jparam = (0,jtype), and
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prob = 1.0.
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</P>
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</HTML>
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