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bond_style_quartic.html
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rLAMMPS lammps
bond_style_quartic.html
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<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>
bond_style quartic command
</H3>
<P><B>
Syntax:
</B>
</P>
<PRE>
bond_style quartic
</PRE>
<P><B>
Examples:
</B>
</P>
<PRE>
bond_style quartic
bond_coeff 2 1200 -0.55 0.25 1.3 34.6878
</PRE>
<P><B>
Description:
</B>
</P>
<P>
The
<I>
quartic
</I>
bond style uses the potential
</P>
<CENTER><IMG
SRC =
"Eqs/bond_quartic.jpg"
>
</CENTER>
<P>
to define a bond that can be broken as the simulation proceeds (e.g.
due to a polymer being stretched). The sigma and epsilon used in the
LJ portion of the formula are both set equal to 1.0 by LAMMPS.
</P>
<P>
The following coefficients must be defined for each bond type via the
<A
HREF =
"bond_coeff.html"
>
bond_coeff
</A>
command as in the example above, or in
the data file or restart files read by the
<A
HREF =
"read_data.html"
>
read_data
</A>
or
<A
HREF =
"read_restart.html"
>
read_restart
</A>
commands:
</P>
<UL><LI>
K (energy/distance^2)
<LI>
B1 (distance)
<LI>
B2 (distance)
<LI>
Rc (distance)
<LI>
U0 (energy)
</UL>
<P>
This potential was constructed to mimic the FENE bond potential for
coarse-grained polymer chains. When monomers with sigma = epsilon =
1.0 are used, the following choice of parameters gives a quartic
potential that looks nearly like the FENE potential: K = 1200, B1 =
-0.55, B2 = 0.25, Rc = 1.3, and U0 = 34.6878. Different parameters
can be specified using the
<A
HREF =
"bond_coeff.html"
>
bond_coeff
</A>
command, but
you will need to choose them carefully so they form a suitable bond
potential.
</P>
<P>
Rc is the cutoff length at which the bond potential goes smoothly to a
local maximium. If a bond length ever becomes > Rc, LAMMPS "breaks"
the bond, which means two things. First, the bond potential is turned
off by setting its type to 0, and is no longer computed. Second, a
pairwise interaction between the two atoms is turned on, since they
are no longer bonded.
</P>
<P>
LAMMPS does the second task via a computational sleight-of-hand. It
subtracts the pairwise interaction as part of the bond computation.
When the bond breaks, the subtraction stops. For this to work, the
pairwise interaction must always be computed by the
<A
HREF =
"pair_style.html"
>
pair_style
</A>
command, whether the bond is broken or
not. This means that
<A
HREF =
"special_bonds.html"
>
special_bonds
</A>
must be set
to 1,1,1, as indicated as a restriction below.
</P>
<P>
Note that when bonds are dumped to a file via
<A
HREF =
"dump.html"
>
dump bond
</A>
,
bonds with type 0 are not included. The
<A
HREF =
"delete_bonds.html"
>
delete_bonds
</A>
command can also be used to query the
status of broken bonds or permanently delete them, e.g.:
</P>
<PRE>
delete_bonds all stats
delete_bonds all bond 0 remove
</PRE>
<P><B>
Restrictions:
</B>
</P>
<P>
The
<I>
quartic
</I>
style requires that
<A
HREF =
"special_bonds.html"
>
special_bonds
</A>
parameters be set to 1,1,1. Three- and four-body interactions (angle,
dihedral, etc) cannot be used with
<I>
quartic
</I>
bonds.
</P>
<P><B>
Related commands:
</B>
</P>
<P><A
HREF =
"bond_coeff.html"
>
bond_coeff
</A>
,
<A
HREF =
"delete_bonds.html"
>
delete_bonds
</A>
</P>
<P><B>
Default:
</B>
none
</P>
</HTML>
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