forked from lijiext/lammps
154 lines
4.8 KiB
HTML
154 lines
4.8 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 list command
|
|
</H3>
|
|
<P><B>Syntax:</B>
|
|
</P>
|
|
<PRE>pair_style list listfile cutoff keyword
|
|
</PRE>
|
|
<UL><LI>listfile = name of file with list of pairwise interactions
|
|
<LI>cutoff = global cutoff (distance units)
|
|
<LI>keyword = optional flag <I>nocheck</I> or <I>check</I> (default is <I>check</I>)
|
|
</UL>
|
|
<P><B>Examples:</B>
|
|
</P>
|
|
<PRE>pair_style list restraints.txt 200.0
|
|
pair_coeff * *
|
|
</PRE>
|
|
<PRE>pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0
|
|
pair_coeff * * lj/cut 1.0 1.0
|
|
pair_coeff 3* 3* list
|
|
</PRE>
|
|
<P><B>Description:</B>
|
|
</P>
|
|
<P>Style <I>list</I> computes interactions between explicitly listed pairs of
|
|
atoms with the option to select functional form and parameters for
|
|
each individual pair. Because the parameters are set in the list
|
|
file, the pair_coeff command has no parameters (but still needs to be
|
|
provided). The <I>check</I> and <I>nocheck</I> keywords enable/disable a test
|
|
that checks whether all listed bonds were present and computed.
|
|
</P>
|
|
<P>This pair style can be thought of as a hybrid between bonded,
|
|
non-bonded, and restraint interactions. It will typically be used as
|
|
an additional interaction within the <I>hybrid/overlay</I> pair style. It
|
|
currently supports three interaction styles: a 12-6 Lennard-Jones, a
|
|
Morse and a harmonic potential.
|
|
</P>
|
|
<P>The format of the list file is as follows:
|
|
</P>
|
|
<UL><LI>one line per pair of atoms
|
|
|
|
<LI>empty lines will be ignored
|
|
|
|
<LI>comment text starts with a '#' character
|
|
line syntax: ID1 ID2 style coeffs cutoff
|
|
|
|
<PRE> ID1 = atom ID of first atom
|
|
ID2 = atom ID of second atom
|
|
style = style of interaction
|
|
coeffs = list of coeffs
|
|
cutoff = cutoff for interaction (optional)
|
|
</PRE>
|
|
|
|
</UL>
|
|
<P>The cutoff parameter is optional. If not specified, the global cutoff
|
|
is used.
|
|
</P>
|
|
<P>Here is an example file:
|
|
</P>
|
|
<PRE># this is a comment
|
|
</PRE>
|
|
<PRE>15 259 lj126 1.0 1.0 50.0
|
|
15 603 morse 10.0 1.2 2.0 10.0 # and another comment
|
|
18 470 harmonic 50.0 1.2 5.0
|
|
</PRE>
|
|
<P>The style <I>lj126</I> computes pairwise interactions with the formula
|
|
</P>
|
|
<CENTER><IMG SRC = "Eqs/pair_lj.jpg">
|
|
</CENTER>
|
|
<P>and the coefficients:
|
|
</P>
|
|
<UL><LI>epsilon (energy units)
|
|
<LI>sigma (distance units)
|
|
</UL>
|
|
<P>The style <I>morse</I> computes pairwise interactions with the formula
|
|
</P>
|
|
<CENTER><IMG SRC = "Eqs/pair_morse.jpg">
|
|
</CENTER>
|
|
<P>and the coefficients:
|
|
</P>
|
|
<UL><LI>D0 (energy units)
|
|
<LI>alpha (1/distance units)
|
|
<LI>r0 (distance units)
|
|
</UL>
|
|
<P>The style <I>harmonic</I> computes pairwise interactions with the formula
|
|
</P>
|
|
<CENTER><IMG SRC = "Eqs/bond_harmonic.jpg">
|
|
</CENTER>
|
|
<P>and the coefficients:
|
|
</P>
|
|
<UL><LI>K (energy units)
|
|
<LI>r0 (distance units)
|
|
</UL>
|
|
<P>Note that the usual 1/2 factor is included in K.
|
|
</P>
|
|
<HR>
|
|
|
|
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
|
|
</P>
|
|
<P>This pair style does not support mixing since all parameters are
|
|
explicit for each pair.
|
|
</P>
|
|
<P>The <A HREF = "pair_modify.html">pair_modify</A> shift option is supported by this
|
|
pair style.
|
|
</P>
|
|
<P>The <A HREF = "pair_modify.html">pair_modify</A> table and tail options are not
|
|
relevant for this pair style.
|
|
</P>
|
|
<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
|
|
files</A>, so pair_style and pair_coeff commands need
|
|
to be specified in an input script that reads 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 does not use a neighbor list and instead identifies
|
|
atoms by their IDs. This has two consequences: 1) The cutoff has to be
|
|
chosen sufficiently large, so that the second atom of a pair has to be
|
|
a ghost atom on the same node on which the first atom is local;
|
|
otherwise the interaction will be skipped. You can use the <I>check</I>
|
|
option to detect, if interactions are missing. 2) Unlike other pair
|
|
styles in LAMMPS, an atom I will not interact with multiple images of
|
|
atom J (assuming the images are within the cutoff distance), but only
|
|
with the nearest image.
|
|
</P>
|
|
<P>This style is part of the USER-MISC package. It is only enabled if
|
|
LAMMPS is build with that package. See the <A HREF = "Section_start.html#3">Making of
|
|
LAMMPS</A> section for more info.
|
|
</P>
|
|
<P><B>Related commands:</B>
|
|
</P>
|
|
<P><A HREF = "pair_coeff.html">pair_coeff</A>,
|
|
<A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A>,
|
|
<A HREF = "pair_lj.html">pair_style lj/cut</A>,
|
|
<A HREF = "pair_morse.html">pair_style morse</A>,
|
|
<A HREF = "bond_harmonic.html">bond_style harmonic</A>
|
|
</P>
|
|
<P><B>Default:</B> none
|
|
</P>
|
|
</HTML>
|