forked from lijiext/lammps
254 lines
12 KiB
HTML
254 lines
12 KiB
HTML
<HTML>
|
|
<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>
|
|
</CENTER>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<HR>
|
|
|
|
<H3>fix bond/create command
|
|
</H3>
|
|
<P><B>Syntax:</B>
|
|
</P>
|
|
<PRE>fix ID group-ID bond/create Nevery itype jtype Rmin bondtype keyword values ...
|
|
</PRE>
|
|
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
|
|
|
<LI>bond/create = style name of this fix command
|
|
|
|
<LI>Nevery = attempt bond creation every this many steps
|
|
|
|
<LI>itype,jtype = atoms of itype can bond to atoms of jtype
|
|
|
|
<LI>Rmin = 2 atoms separated by less than Rmin can bond (distance units)
|
|
|
|
<LI>bondtype = type of created bonds
|
|
|
|
<LI>zero or more keyword/value pairs may be appended to args
|
|
|
|
<LI>keyword = <I>iparam</I> or <I>jparam</I> or <I>prob</I> or <I>atype</I> or <I>dtype</I> or <I>itype</I>
|
|
|
|
<PRE> <I>iparam</I> values = maxbond, newtype
|
|
maxbond = max # of bonds of bondtype the itype atom can have
|
|
newtype = change the itype atom to this type when maxbonds exist
|
|
<I>jparam</I> values = maxbond, newtype
|
|
maxbond = max # of bonds of bondtype the jtype atom can have
|
|
newtype = change the jtype atom to this type when maxbonds exist
|
|
<I>prob</I> values = fraction seed
|
|
fraction = create a bond with this probability if otherwise eligible
|
|
seed = random number seed (positive integer)
|
|
<I>atype</I> value = angletype
|
|
angletype = type of created angles
|
|
<I>dtype</I> value = dihedraltype
|
|
dihedraltype = type of created dihedrals
|
|
<I>itype</I> value = impropertype
|
|
impropertype = type of created impropers
|
|
</PRE>
|
|
|
|
</UL>
|
|
<P><B>Examples:</B>
|
|
</P>
|
|
<PRE>fix 5 all bond/create 10 1 2 0.8 1
|
|
fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3
|
|
fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3 atype 1 dtype 2
|
|
</PRE>
|
|
<P><B>Description:</B>
|
|
</P>
|
|
<P>Create bonds between pairs of atoms as a simulation runs according to
|
|
specified criteria. This can be used to model cross-linking of
|
|
polymers, the formation of a percolation network, etc. In this
|
|
context, a bond means an interaction between a pair of atoms computed
|
|
by the <A HREF = "bond_style.html">bond_style</A> command. Once the bond is created
|
|
it will be permanently in place. Optionally, the creation of a bond
|
|
can also create angle, dihedral, and improper interactions that bond
|
|
is part of. See the discussion of the <I>atype</I>, <I>dtype</I>, and <I>itype</I>
|
|
keywords below.
|
|
</P>
|
|
<P>This is different than a <A HREF = "pair_style.html">pairwise</A> 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 and higher-order many-body
|
|
interactions from timestep to timestep as atoms move.
|
|
</P>
|
|
<P>A check for possible new bonds is performed every <I>Nevery</I> timesteps.
|
|
If two atoms I,J are within a distance <I>Rmin</I> of each other, if I is
|
|
of atom type <I>itype</I>, if J is of atom type <I>jtype</I>, if both I and J
|
|
are in the specified fix group, if a bond does not already exist
|
|
between I and J, and if both I and J meet their respective <I>maxbond</I>
|
|
requirement (explained below), then I,J is labeled as a "possible"
|
|
bond pair.
|
|
</P>
|
|
<P>If several atoms are close to an atom, it may have multiple possible
|
|
bond partners. Every atom checks its list of possible bond partners
|
|
and labels the closest such partner as its "sole" bond partner. After
|
|
this is done, if atom I has atom J as its sole partner, and atom J has
|
|
atom I as its sole partner, then the I,J bond is "eligible" to be
|
|
formed.
|
|
</P>
|
|
<P>Note that these rules mean an atom will only be part of at most one
|
|
created 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 form
|
|
a bond on this timestep, even if it has other possible bond partners.
|
|
</P>
|
|
<P>It is permissible to have <I>itype</I> = <I>jtype</I>. <I>Rmin</I> must be <= the
|
|
pairwise cutoff distance between <I>itype</I> and <I>jtype</I> atoms, as defined
|
|
by the <A HREF = "pair_style.html">pair_style</A> command.
|
|
</P>
|
|
<P>The <I>iparam</I> and <I>jparam</I> keywords can be used to limit the bonding
|
|
functionality of the participating atoms. Each atom keeps track of
|
|
how many bonds of <I>bondtype</I> it already has. If atom I of
|
|
itype already has <I>maxbond</I> bonds (as set by the <I>iparam</I>
|
|
keyword), then it will not form any more. Likewise for atom J. If
|
|
<I>maxbond</I> is set to 0, then there is no limit on the number of bonds
|
|
that can be formed with that atom.
|
|
</P>
|
|
<P>The <I>newtype</I> value for <I>iparam</I> and <I>jparam</I> can be used to change
|
|
the atom type of atom I or J when it reaches <I>maxbond</I> number of bonds
|
|
of type <I>bondtype</I>. This means it can now interact in a pairwise
|
|
fashion with other atoms in a different way by specifying different
|
|
<A HREF = "pair_coeff.html">pair_coeff</A> coefficients. If you do not wish the
|
|
atom type to change, simply specify <I>newtype</I> as <I>itype</I> or <I>jtype</I>.
|
|
</P>
|
|
<P>The <I>prob</I> keyword can also effect whether an eligible bond is
|
|
actually created. The <I>fraction</I> 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 created if the random number < fraction.
|
|
</P>
|
|
<P>Any bond that is created is assigned a bond type of <I>bondtype</I>
|
|
</P>
|
|
<P>When a bond is created, data structures within LAMMPS that store bond
|
|
topology are updated to reflect the creation. If the bond is part of
|
|
new 3-body (angle) or 4-body (dihedral, improper) interactions, you
|
|
can choose to create new angles, dihedrals, impropers as well, using
|
|
the <I>atype</I>, <I>dtype</I>, and <I>itype</I> keywords. All of these changes
|
|
typically affect pairwise interactions between atoms that are now part
|
|
of new bonds, angles, etc.
|
|
</P>
|
|
<P>IMPORTANT NOTE: One data structure that is not updated when a bond
|
|
breaks are the molecule IDs stored by each atom. Even though two
|
|
molecules become one moleclue due to the created bond, all atoms in
|
|
the new moleclue retain their original molecule IDs.
|
|
</P>
|
|
<P>If the <I>atype</I> keyword is used and if an angle potential is defined
|
|
via the <A HREF = "angle.html">angle_style</A> command, then any new 3-body
|
|
interactions inferred by the creation of a bond will create new angles
|
|
of type <I>angletype</I>, with parameters assigned by the corresponding
|
|
<A HREF = "angle_coeff.html">angle_coeff</A> command. Likewise, the <I>dtype</I> and
|
|
<I>itype</I> keywords will create new dihedrals and impropers of type
|
|
<I>dihedraltype</I> and <I>impropertype</I>.
|
|
</P>
|
|
<P>IMPORTANT NOTE: To create a new bond, the internal LAMMPS data
|
|
structures that store this information must have space for it. When
|
|
LAMMPS is initialized from a data file, the list of bonds is scanned
|
|
and the maximum number of bonds per atom is tallied. If some atom
|
|
will acquire more bonds than this limit as this fix operates, then the
|
|
"extra bond per atom" parameter must be set to allow for it. Ditto
|
|
for "extra angle per atom", "extra dihedral per atom", and "extra
|
|
improper per atom" if angles, dihedrals, or impropers are being added
|
|
when bonds are created. See the <A HREF = "read_data.html">read_data</A> or
|
|
<A HREF = "create_box.html">create_box</A> command for more details. Note that a
|
|
data file with no atoms can be used if you wish to add unbonded atoms
|
|
via the <A HREF = "create_atoms.html">create atoms</A> command, e.g. for a
|
|
percolation simulation.
|
|
</P>
|
|
<P>IMPORTANT NOTE: LAMMPS also maintains a data structure that stores a
|
|
list of 1st, 2nd, and 3rd neighbors of each atom (within the bond
|
|
topology of the system) for use in weighting pairwise interactions for
|
|
bonded atoms. Adding a bond adds a single entry to this list. The
|
|
"extra special per atom" parameter must typically be set to allow for
|
|
it. There are 3 ways to do this. See the <A HREF = "read_data.html">read_data</A>
|
|
or <A HREF = "create_box.html">create_box</A> or "special_bonds extra" commands for
|
|
details.
|
|
</P>
|
|
<P>IMPORTANT NOTE: Even if you do not use the <I>atype</I>, <I>dtype</I>, or
|
|
<I>itype</I> keywords, the list of topological neighbors is updated for
|
|
atoms affected by the new bond. This in turn affects which neighbors
|
|
are considered for pairwise interactions, using the weighting rules
|
|
set by the <A HREF = "special_bonds.html">special_bonds</A> command. Consider a new
|
|
bond created between atoms I,J. If J has a bonded neighbor K, then K
|
|
becomes a 2nd neighbor of I. Even if the <I>atype</I> keyword is not used
|
|
to create angle I-J-K, the pairwise interaction between I and K will
|
|
be potentially turned off or weighted by the 1-3 weighting specified
|
|
by the <A HREF = "special_bonds.html">special_bonds</A> command. This is the case
|
|
even if the "angle yes" option was used with that command. The same
|
|
is true for 3rd neighbors (1-4 interactions), the <I>dtype</I> keyword, and
|
|
the "dihedral yes" option used with the
|
|
<A HREF = "special_bonds.html">special_bonds</A> command.
|
|
</P>
|
|
<P>Note that even if your simulation starts with no bonds, you must
|
|
define a <A HREF = "bond_style.html">bond_style</A> and use the
|
|
<A HREF = "bond_coeff.html">bond_coeff</A> command to specify coefficients for the
|
|
<I>bondtype</I>. Similarly, if new atom types are specified by the
|
|
<I>iparam</I> or <I>jparam</I> keywords, they must be within the range of atom
|
|
types allowed by the simulation and pairwise coefficients must be
|
|
specified for the new types.
|
|
</P>
|
|
<P>Computationally, each timestep this fix operates, it loops over
|
|
neighbor lists and computes distances between pairs of atoms in the
|
|
list. It also communicates between neighboring processors to
|
|
coordinate which bonds are created. Moreover, if any bonds are
|
|
created, neighbor lists must be immediately updated on the same
|
|
timestep. This is to insure that any pairwise interactions that
|
|
should be turned "off" due to a bond creation, because they are now
|
|
excluded by the presence of the bond and the settings of the
|
|
<A HREF = "special_bonds.html">special_bonds</A> command, will be immediately
|
|
recognized. All of these operations increase the cost of a timestep.
|
|
Thus you should be cautious about invoking this fix too frequently.
|
|
</P>
|
|
<P>You can dump out snapshots of the current bond topology via the <A HREF = "dump.html">dump
|
|
local</A> command.
|
|
</P>
|
|
<P>IMPORTANT NOTE: Creating a bond typically alters the energy of a
|
|
system. You should be careful not to choose bond creation criteria
|
|
that induce a dramatic change in energy. For example, if you define a
|
|
very stiff harmonic bond and create it when 2 atoms are separated by a
|
|
distance far from the equilibribum bond length, then the 2 atoms will
|
|
oscillate dramatically when the bond is formed. More generally, you
|
|
may need to thermostat your system to compensate for energy changes
|
|
resulting from created bonds (and angles, dihedrals, impropers).
|
|
</P>
|
|
<HR>
|
|
|
|
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
|
</P>
|
|
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
|
|
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
|
|
are relevant to this fix.
|
|
</P>
|
|
<P>This fix computes two statistics which it stores in a global vector of
|
|
length 2, which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
|
|
commands</A>. The vector values calculated
|
|
by this fix are "intensive".
|
|
</P>
|
|
<P>These are the 2 quantities:
|
|
</P>
|
|
<UL><LI>(1) # of bonds created on the most recent creation timestep
|
|
<LI>(2) cummulative # of bonds created
|
|
</UL>
|
|
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
|
|
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
|
|
minimization</A>.
|
|
</P>
|
|
<P><B>Restrictions:</B>
|
|
</P>
|
|
<P>This fix is part of the MC package. It is only enabled if LAMMPS was
|
|
built with that package. See the <A HREF = "Section_start.html#start_3">Making
|
|
LAMMPS</A> section for more info.
|
|
</P>
|
|
<P><B>Related commands:</B>
|
|
</P>
|
|
<P><A HREF = "fix_bond_break.html">fix bond/break</A>, <A HREF = "fix_bond_swap.html">fix
|
|
bond/swap</A>, <A HREF = "dump.html">dump local</A>,
|
|
<A HREF = "special_bonds.html">special_bonds</A>
|
|
</P>
|
|
<P><B>Default:</B>
|
|
</P>
|
|
<P>The option defaults are iparam = (0,itype), jparam = (0,jtype), and
|
|
prob = 1.0.
|
|
</P>
|
|
</HTML>
|