git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9996 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
151
doc/pair_list.html
Normal file
151
doc/pair_list.html
Normal file
@ -0,0 +1,151 @@
|
|||||||
|
<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 for the rest
|
||||||
|
of LAMMPS, minimum image conventions apply.
|
||||||
|
</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>
|
||||||
142
doc/pair_list.txt
Normal file
142
doc/pair_list.txt
Normal file
@ -0,0 +1,142 @@
|
|||||||
|
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||||
|
|
||||||
|
:link(lws,http://lammps.sandia.gov)
|
||||||
|
:link(ld,Manual.html)
|
||||||
|
:link(lc,Section_commands.html#comm)
|
||||||
|
|
||||||
|
:line
|
||||||
|
|
||||||
|
pair_style list command :h3
|
||||||
|
|
||||||
|
[Syntax:]
|
||||||
|
|
||||||
|
pair_style list listfile cutoff keyword :pre
|
||||||
|
|
||||||
|
listfile = name of file with list of pairwise interactions
|
||||||
|
cutoff = global cutoff (distance units)
|
||||||
|
keyword = optional flag {nocheck} or {check} (default is {check}) :ul
|
||||||
|
|
||||||
|
[Examples:]
|
||||||
|
|
||||||
|
pair_style list restraints.txt 200.0
|
||||||
|
pair_coeff * * :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
|
||||||
|
|
||||||
|
[Description:]
|
||||||
|
|
||||||
|
Style {list} 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 {check} and {nocheck} keywords enable/disable a test
|
||||||
|
that checks whether all listed bonds were present and computed.
|
||||||
|
|
||||||
|
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 {hybrid/overlay} pair style. It
|
||||||
|
currently supports three interaction styles: a 12-6 Lennard-Jones, a
|
||||||
|
Morse and a harmonic potential.
|
||||||
|
|
||||||
|
The format of the list file is as follows:
|
||||||
|
|
||||||
|
one line per pair of atoms :ulb,l
|
||||||
|
empty lines will be ignored :l
|
||||||
|
comment text starts with a '#' character
|
||||||
|
line syntax: ID1 ID2 style coeffs cutoff :l
|
||||||
|
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
|
||||||
|
:ule
|
||||||
|
|
||||||
|
The cutoff parameter is optional. If not specified, the global cutoff
|
||||||
|
is used.
|
||||||
|
|
||||||
|
Here is an example file:
|
||||||
|
|
||||||
|
# this is a comment :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
|
||||||
|
|
||||||
|
The style {lj126} computes pairwise interactions with the formula
|
||||||
|
|
||||||
|
:c,image(Eqs/pair_lj.jpg)
|
||||||
|
|
||||||
|
and the coefficients:
|
||||||
|
|
||||||
|
epsilon (energy units)
|
||||||
|
sigma (distance units) :ul
|
||||||
|
|
||||||
|
The style {morse} computes pairwise interactions with the formula
|
||||||
|
|
||||||
|
:c,image(Eqs/pair_morse.jpg)
|
||||||
|
|
||||||
|
and the coefficients:
|
||||||
|
|
||||||
|
D0 (energy units)
|
||||||
|
alpha (1/distance units)
|
||||||
|
r0 (distance units) :ul
|
||||||
|
|
||||||
|
The style {harmonic} computes pairwise interactions with the formula
|
||||||
|
|
||||||
|
:c,image(Eqs/bond_harmonic.jpg)
|
||||||
|
|
||||||
|
and the coefficients:
|
||||||
|
|
||||||
|
K (energy units)
|
||||||
|
r0 (distance units) :ul
|
||||||
|
|
||||||
|
Note that the usual 1/2 factor is included in K.
|
||||||
|
|
||||||
|
:line
|
||||||
|
|
||||||
|
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||||
|
|
||||||
|
This pair style does not support mixing since all parameters are
|
||||||
|
explicit for each pair.
|
||||||
|
|
||||||
|
The "pair_modify"_pair_modify.html shift option is supported by this
|
||||||
|
pair style.
|
||||||
|
|
||||||
|
The "pair_modify"_pair_modify.html table and tail options are not
|
||||||
|
relevant for this pair style.
|
||||||
|
|
||||||
|
This pair style does not write its information to "binary restart
|
||||||
|
files"_restart.html, so pair_style and pair_coeff commands need
|
||||||
|
to be specified in an input script that reads a restart file.
|
||||||
|
|
||||||
|
This pair style can only be used via the {pair} keyword of the
|
||||||
|
"run_style respa"_run_style.html command. It does not support the
|
||||||
|
{inner}, {middle}, {outer} keywords.
|
||||||
|
|
||||||
|
:line
|
||||||
|
|
||||||
|
[Restrictions:]
|
||||||
|
|
||||||
|
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 {check}
|
||||||
|
option to detect, if interactions are missing. 2) Unlike for the rest
|
||||||
|
of LAMMPS, minimum image conventions apply.
|
||||||
|
|
||||||
|
This style is part of the USER-MISC package. It is only enabled if
|
||||||
|
LAMMPS is build with that package. See the "Making of
|
||||||
|
LAMMPS"_Section_start.html#3 section for more info.
|
||||||
|
|
||||||
|
[Related commands:]
|
||||||
|
|
||||||
|
"pair_coeff"_pair_coeff.html,
|
||||||
|
"pair_style hybrid/overlay"_pair_hybrid.html,
|
||||||
|
"pair_style lj/cut"_pair_lj.html,
|
||||||
|
"pair_style morse"_pair_morse.html,
|
||||||
|
"bond_style harmonic"_bond_harmonic.html
|
||||||
|
|
||||||
|
[Default:] none
|
||||||
Reference in New Issue
Block a user