2006-09-22 00:22:34 +08:00
|
|
|
<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 fene/expand command
|
|
|
|
|
</H3>
|
2011-12-01 23:35:32 +08:00
|
|
|
<H3>bond_style fene/expand/omp command
|
|
|
|
|
</H3>
|
2006-09-22 00:22:34 +08:00
|
|
|
<P><B>Syntax:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>bond_style fene/expand
|
|
|
|
|
</PRE>
|
|
|
|
|
<P><B>Examples:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>bond_style fene/expand
|
|
|
|
|
bond_coeff 1 30.0 1.5 1.0 1.0 0.5
|
|
|
|
|
</PRE>
|
|
|
|
|
<P><B>Description:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P>The <I>fene/expand</I> bond style uses the potential
|
|
|
|
|
</P>
|
|
|
|
|
<CENTER><IMG SRC = "Eqs/bond_fene_expand.jpg">
|
|
|
|
|
</CENTER>
|
|
|
|
|
<P>to define a finite extensible nonlinear elastic (FENE) potential
|
|
|
|
|
<A HREF = "#Kremer">(Kremer)</A>, used for bead-spring polymer models. The first
|
|
|
|
|
term is attractive, the 2nd Lennard-Jones term is repulsive.
|
|
|
|
|
</P>
|
|
|
|
|
<P>The <I>fene/expand</I> bond style is similar to <I>fene</I> except that an extra
|
|
|
|
|
shift factor of delta (positive or negative) is added to <I>r</I> to
|
|
|
|
|
effectively change the bead size of the bonded atoms. The first term
|
|
|
|
|
now extends to R0 + delta and the 2nd term is cutoff at 2^(1/6) sigma
|
|
|
|
|
+ delta.
|
|
|
|
|
</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>R0 (distance)
|
|
|
|
|
<LI>epsilon (energy)
|
|
|
|
|
<LI>sigma (distance)
|
|
|
|
|
<LI>delta (distance)
|
|
|
|
|
</UL>
|
2011-12-01 23:35:32 +08:00
|
|
|
<HR>
|
|
|
|
|
|
2014-08-15 00:30:25 +08:00
|
|
|
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
|
|
|
|
|
functionally the same as the corresponding style without the suffix.
|
|
|
|
|
They have been optimized to run faster, depending on your available
|
|
|
|
|
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
|
|
|
|
|
of the manual. The accelerated styles take the same arguments and
|
|
|
|
|
should produce the same results, except for round-off and precision
|
|
|
|
|
issues.
|
2011-12-01 23:35:32 +08:00
|
|
|
</P>
|
2014-08-15 00:30:25 +08:00
|
|
|
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
|
|
|
|
|
KOKKOS, USER-OMP and OPT packages, respectively. They are only
|
|
|
|
|
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
|
|
|
|
|
LAMMPS</A> section for more info.
|
2011-12-01 23:35:32 +08:00
|
|
|
</P>
|
|
|
|
|
<P>You can specify the accelerated styles explicitly in your input script
|
2012-01-28 07:39:14 +08:00
|
|
|
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
|
2011-12-01 23:35:32 +08:00
|
|
|
switch</A> when you invoke LAMMPS, or you can
|
|
|
|
|
use the <A HREF = "suffix.html">suffix</A> command in your input script.
|
|
|
|
|
</P>
|
2011-12-14 04:35:35 +08:00
|
|
|
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
|
|
|
|
|
more instructions on how to use the accelerated styles effectively.
|
2011-12-01 23:35:32 +08:00
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
2007-06-25 22:36:36 +08:00
|
|
|
<P><B>Restrictions:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P>This bond style can only be used if LAMMPS was built with the
|
2011-08-27 02:53:00 +08:00
|
|
|
MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
|
2007-06-25 22:36:36 +08:00
|
|
|
LAMMPS</A> section for more info on packages.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2009-01-14 22:29:55 +08:00
|
|
|
<P>You typically should specify <A HREF = "special_bonds.html"">special_bonds fene</A>
|
|
|
|
|
or <A HREF = "special_bonds.html">special_bonds lj/coul 0 1 1</A> to use this bond
|
|
|
|
|
style. LAMMPS will issue a warning it that's not the case.
|
2008-07-30 03:56:08 +08:00
|
|
|
</P>
|
2006-09-22 00:22:34 +08:00
|
|
|
<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>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<A NAME = "Kremer"></A>
|
|
|
|
|
|
|
|
|
|
<P><B>(Kremer)</B> Kremer, Grest, J Chem Phys, 92, 5057 (1990).
|
|
|
|
|
</P>
|
|
|
|
|
</HTML>
|
