forked from lijiext/lammps
171 lines
6.3 KiB
HTML
171 lines
6.3 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>pair_style srp command
|
|
</H3>
|
|
<P><B>Syntax:</B>
|
|
</P>
|
|
<P>pair_style srp cutoff bond_type dist keyword value ...
|
|
</P>
|
|
<UL><LI>cutoff = global cutoff for SRP interactions (distance units)
|
|
|
|
<LI>bond_type = bond type to apply SRP interactions
|
|
|
|
<LI>distance = <I>min</I> or <I>mid</I>
|
|
|
|
<LI>zero or more keyword/value pairs may be appended
|
|
|
|
<LI>keyword = <I>exclude</I>
|
|
|
|
<PRE> <I>exclude</I> value = <I>yes</I> or <I>no</I>
|
|
</PRE>
|
|
|
|
</UL>
|
|
<P><B>Examples:</B>
|
|
</P>
|
|
<PRE>pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes
|
|
pair_coeff 1 1 dpd 60.0 4.5 1.0
|
|
pair_coeff 1 2 none
|
|
pair_coeff 2 2 srp 100.0 0.8
|
|
</PRE>
|
|
<PRE>pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 min exclude yes
|
|
pair_coeff 1 1 dpd 60.0 50 1.0
|
|
pair_coeff 1 2 none
|
|
pair_coeff 2 2 srp 40.0
|
|
</PRE>
|
|
<PRE>pair_style hybrid srp 0.8 2 mid
|
|
pair_coeff 1 1 none
|
|
pair_coeff 1 2 none
|
|
pair_coeff 2 2 srp 100.0 0.8
|
|
</PRE>
|
|
<P><B>Description:</B>
|
|
</P>
|
|
<P>Style <I>srp</I> computes a soft segmental repulsive potential (SRP) that
|
|
acts between pairs of bonds. This potential is useful for preventing
|
|
bonds from passing through one another when a soft non-bonded
|
|
potential acts between beads in, for example, DPD polymer chains. An
|
|
example input script that uses this command is provided in
|
|
examples/USER/srp.
|
|
</P>
|
|
<P>Bonds of type <I>btype</I> interact with one another through a
|
|
bond-pairwise potential, such that the force on bond <I>i</I> due to bond
|
|
<I>j</I> is as follows
|
|
</P>
|
|
<CENTER><IMG SRC = "Eqs/pair_srp1.jpg">
|
|
</CENTER>
|
|
<P>where <I>r</I> and <I>rij</I> are the distance and unit vector between the two
|
|
bonds. The <I>mid</I> option computes <I>r</I> and <I>rij</I> from the midpoint
|
|
distance between bonds. The <I>min</I> option computes <I>r</I> and <I>rij</I> from
|
|
the minimum distance between bonds. The force acting on a bond is
|
|
mapped onto the two bond atoms according to the lever rule,
|
|
</P>
|
|
<CENTER><IMG SRC = "Eqs/pair_srp2.jpg">
|
|
</CENTER>
|
|
<P>where <I>L</I> is the normalized distance from the atom to the point of
|
|
closest approach of bond <I>i</I> and <I>j</I>. The <I>mid</I> option takes <I>L</I> as
|
|
0.5 for each interaction as described in <A HREF = "#Sirk">(Sirk)</A>.
|
|
</P>
|
|
<P>The following coefficients must be defined via the
|
|
<A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples above, or in
|
|
the data file or restart file read by the <A HREF = "read_data.html">read_data</A>
|
|
or <A HREF = "read_restart.html">read_restart</A> commands:
|
|
</P>
|
|
<UL><LI><I>C</I> (force units)
|
|
<LI><I>rc</I> (distance units)
|
|
</UL>
|
|
<P>The last coefficient is optional. If not specified, the global cutoff
|
|
is used.
|
|
</P>
|
|
<P>IMPORTANT NOTE: Pair style srp considers each bond of type <I>btype</I> as
|
|
a fictitious particle of type <I>bptype</I>, where <I>bptype</I> is the largest
|
|
atom type in the system. These "bond particles" are inserted at the
|
|
beginning of the run, and serve as placeholders that define the
|
|
position of the bonds. This allows neighbor lists to be constructed
|
|
and pairwise interactions to be computed in almost the same way as is
|
|
done for point particles. Because bonds interact only with other
|
|
bonds, <A HREF = "pair_hybrid.html">pair_style hybrid</A> should be used to turn off
|
|
interactions between atom type <I>bptype</I> and all other types of atoms.
|
|
An error will be flagged if <A HREF = "pair_hybrid.html">pair_style hybrid</A> is
|
|
not used. Further, only bond particles should be given an atom type
|
|
of <I>bptype</I>; a check is done at the beginning of the run to ensure
|
|
there are no regular atoms of <I>bptype</I>.
|
|
</P>
|
|
<P>The optional <I>exclude</I> keyword determines if forces are computed
|
|
between first neighbor (directly connected) bonds. For a setting of
|
|
<I>no</I>, first neighbor forces are computed; for <I>yes</I> they are not computed. A setting of <I>no</I>
|
|
cannot be used with the <I>min</I> option for distance calculation because the the minimum distance between
|
|
directly connected bonds is zero.
|
|
</P>
|
|
<P>Pair style <I>srp</I> turns off normalization of thermodynamic properties
|
|
by particle number, as if the command <A HREF = "thermo_modify.html">thermo_modify norm
|
|
no</A> had been issued.
|
|
</P>
|
|
<P>The pairwise energy associated with style <I>srp</I> is shifted to be zero
|
|
at the cutoff distance <I>rc</I>.
|
|
</P>
|
|
<HR>
|
|
|
|
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
|
|
</P>
|
|
<P>This pair styles does not support mixing.
|
|
</P>
|
|
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
|
|
shift option for the energy of the pair interaction. Note that as
|
|
discussed above, the energy term is already shifted to be 0.0 at the
|
|
cutoff distance <I>rc</I>.
|
|
</P>
|
|
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant for
|
|
this pair style.
|
|
</P>
|
|
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
|
|
tail option for adding long-range tail corrections to energy and
|
|
pressure.
|
|
</P>
|
|
<P>This pair style writes global and per-atom information to <A HREF = "restart.html">binary
|
|
restart files</A>. Pair srp should be used with <A HREF = "pair_hybrid.html">pair_style
|
|
hybrid</A>, thus the pair_coeff commands need to be
|
|
specified in the input script when reading a restart file.
|
|
</P>
|
|
<P>This pair style can only be used via the <I>pair</I> keyword of the
|
|
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
|
|
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
|
|
</P>
|
|
<HR>
|
|
|
|
<P><B>Restrictions:</B>
|
|
</P>
|
|
<P>This pair style is part of the USER-MISC package. It is only enabled
|
|
if LAMMPS was built with that package. See the Making LAMMPS section
|
|
for more info.
|
|
</P>
|
|
<P>This pair style must be used with <A HREF = "pair_hybrid.html">pair_style hybrid</A>.
|
|
</P>
|
|
<P>This pair style requires the <A HREF = "newton.html">newton</A> command to be <I>on</I>
|
|
for non-bonded interactions.
|
|
</P>
|
|
<P><B>Related commands:</B>
|
|
</P>
|
|
<P><A HREF = "pair_hybrid.html">pair_style hybrid</A>, <A HREF = "pair_coeff.html">pair_coeff</A>,
|
|
<A HREF = "pair_dpd.html">pair dpd</A>
|
|
</P>
|
|
<P><B>Default:</B>
|
|
</P>
|
|
<P>The default keyword value is exclude = yes.
|
|
</P>
|
|
<HR>
|
|
|
|
<A NAME = "Sirk"></A>
|
|
|
|
<P><B>(Sirk)</B> Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J
|
|
Chem Phys, 136 (13) 134903, 2012.
|
|
</P>
|
|
</HTML>
|