Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F79324370
bond_quartic.html
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Sun, Aug 25, 20:22
Size
4 KB
Mime Type
text/html
Expires
Tue, Aug 27, 20:22 (2 d)
Engine
blob
Format
Raw Data
Handle
20175361
Attached To
rLAMMPS lammps
bond_quartic.html
View Options
<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>
<H3>bond_style quartic/omp 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 maximum. 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 the <A HREF = "dump.html">dump
local</A> command, 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>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</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">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, 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.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</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>
Event Timeline
Log In to Comment