Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/doc2/pair_list.html
8b6f939ef9aeefficient_neuronet

Last Change
Raw File

pair_list.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>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
<LI>line syntax: <I>ID1 ID2 style coeffs cutoff</I>
<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>
c4science · Help