2013-05-31 23:48:00 +08:00
2015-07-30 22:53:28 +08:00
<!DOCTYPE html>
<!-- [if IE 8]><html class="no - js lt - ie9" lang="en" > <![endif] -->
<!-- [if gt IE 8]><! --> < html class = "no-js" lang = "en" > <!-- <![endif] -->
< head >
< meta charset = "utf-8" >
< meta name = "viewport" content = "width=device-width, initial-scale=1.0" >
2015-12-21 23:20:41 +08:00
< title > pair_style list command — LAMMPS documentation< / title >
2015-07-30 22:53:28 +08:00
2013-05-31 23:48:00 +08:00
2015-07-30 22:53:28 +08:00
2013-05-31 23:48:00 +08:00
2015-07-30 22:53:28 +08:00
2013-05-31 23:48:00 +08:00
2015-07-30 22:53:28 +08:00
2013-05-31 23:48:00 +08:00
2015-07-30 22:53:28 +08:00
2013-05-31 23:48:00 +08:00
2015-07-30 22:53:28 +08:00
< link rel = "stylesheet" href = "_static/css/theme.css" type = "text/css" / >
< link rel = "stylesheet" href = "_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type = "text/css" / >
2015-12-21 23:20:41 +08:00
< link rel = "top" title = "LAMMPS documentation" href = "index.html" / >
2015-07-30 22:53:28 +08:00
< script src = "_static/js/modernizr.min.js" > < / script >
< / head >
< body class = "wy-body-for-nav" role = "document" >
< div class = "wy-grid-for-nav" >
< nav data-toggle = "wy-nav-shift" class = "wy-nav-side" >
< div class = "wy-side-nav-search" >
< a href = "Manual.html" class = "icon icon-home" > LAMMPS
< / a >
< div role = "search" >
< form id = "rtd-search-form" class = "wy-form" action = "search.html" method = "get" >
< input type = "text" name = "q" placeholder = "Search docs" / >
< input type = "hidden" name = "check_keywords" value = "yes" / >
< input type = "hidden" name = "area" value = "default" / >
< / form >
< / div >
< / div >
< div class = "wy-menu wy-menu-vertical" data-spy = "affix" role = "navigation" aria-label = "main navigation" >
< ul >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_intro.html" > 1. Introduction< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_start.html" > 2. Getting Started< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_commands.html" > 3. Commands< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_packages.html" > 4. Packages< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_accelerate.html" > 5. Accelerating LAMMPS performance< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_howto.html" > 6. How-to discussions< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_example.html" > 7. Example problems< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_perf.html" > 8. Performance & scalability< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_tools.html" > 9. Additional tools< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_modify.html" > 10. Modifying & extending LAMMPS< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_python.html" > 11. Python interface to LAMMPS< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_errors.html" > 12. Errors< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_history.html" > 13. Future and history< / a > < / li >
< / ul >
< / div >
< / nav >
< section data-toggle = "wy-nav-shift" class = "wy-nav-content-wrap" >
< nav class = "wy-nav-top" role = "navigation" aria-label = "top navigation" >
< i data-toggle = "wy-nav-top" class = "fa fa-bars" > < / i >
< a href = "Manual.html" > LAMMPS< / a >
< / nav >
< div class = "wy-nav-content" >
< div class = "rst-content" >
< div role = "navigation" aria-label = "breadcrumbs navigation" >
< ul class = "wy-breadcrumbs" >
< li > < a href = "Manual.html" > Docs< / a > » < / li >
< li > pair_style list command< / li >
< li class = "wy-breadcrumbs-aside" >
< a href = "http://lammps.sandia.gov" > Website< / a >
< a href = "Section_commands.html#comm" > Commands< / a >
< / li >
< / ul >
< hr / >
< / div >
< div role = "main" class = "document" itemscope = "itemscope" itemtype = "http://schema.org/Article" >
< div itemprop = "articleBody" >
< div class = "section" id = "pair-style-list-command" >
< span id = "index-0" > < / span > < h1 > pair_style list command< a class = "headerlink" href = "#pair-style-list-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< a class = "headerlink" href = "#syntax" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > pair_style list listfile cutoff keyword
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > listfile = name of file with list of pairwise interactions< / li >
< li > cutoff = global cutoff (distance units)< / li >
< li > keyword = optional flag < em > nocheck< / em > or < em > check< / em > (default is < em > check< / em > )< / li >
< / ul >
< / div >
< div class = "section" id = "examples" >
< h2 > Examples< a class = "headerlink" href = "#examples" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > pair_style list restraints.txt 200.0
pair_coeff * *
< / pre > < / div >
< / div >
< div class = "highlight-python" > < div class = "highlight" > < pre > pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0
2013-05-31 23:48:00 +08:00
pair_coeff * * lj/cut 1.0 1.0
2015-07-30 22:53:28 +08:00
pair_coeff 3* 3* list
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > Style < em > list< / em > computes interactions between explicitly listed pairs of
2013-05-31 23:48:00 +08:00
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
2015-07-30 22:53:28 +08:00
provided). The < em > check< / em > and < em > nocheck< / em > 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,
2013-05-31 23:48:00 +08:00
non-bonded, and restraint interactions. It will typically be used as
2015-07-30 22:53:28 +08:00
an additional interaction within the < em > hybrid/overlay< / em > pair style. It
2013-05-31 23:48:00 +08:00
currently supports three interaction styles: a 12-6 Lennard-Jones, a
2015-07-30 22:53:28 +08:00
Morse and a harmonic potential.< / p >
< p > The format of the list file is as follows:< / p >
< ul class = "simple" >
< li > one line per pair of atoms< / li >
< li > empty lines will be ignored< / li >
< li > comment text starts with a ‘ #’ character< / li >
< li > line syntax: < em > ID1 ID2 style coeffs cutoff< / em > < / li >
< / ul >
< div class = "highlight-python" > < div class = "highlight" > < pre > ID1 = atom ID of first atom
2015-07-31 00:49:30 +08:00
ID2 = atom ID of second atom
style = style of interaction
coeffs = list of coeffs
cutoff = cutoff for interaction (optional)
2015-07-30 22:53:28 +08:00
< / pre > < / div >
< / div >
< p > The cutoff parameter is optional. If not specified, the global cutoff
is used.< / p >
< p > Here is an example file:< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > < span class = "c" > # this is a comment< / span >
< / pre > < / div >
< / div >
< div class = "highlight-python" > < div class = "highlight" > < 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 > < / div >
< / div >
< p > The style < em > lj126< / em > computes pairwise interactions with the formula< / p >
< img alt = "_images/pair_lj.jpg" class = "align-center" src = "_images/pair_lj.jpg" / >
< p > and the coefficients:< / p >
< ul class = "simple" >
< li > epsilon (energy units)< / li >
< li > sigma (distance units)< / li >
< / ul >
< p > The style < em > morse< / em > computes pairwise interactions with the formula< / p >
< img alt = "_images/pair_morse.jpg" class = "align-center" src = "_images/pair_morse.jpg" / >
< p > and the coefficients:< / p >
< ul class = "simple" >
< li > D0 (energy units)< / li >
< li > alpha (1/distance units)< / li >
< li > r0 (distance units)< / li >
< / ul >
< p > The style < em > harmonic< / em > computes pairwise interactions with the formula< / p >
< img alt = "_images/bond_harmonic.jpg" class = "align-center" src = "_images/bond_harmonic.jpg" / >
< p > and the coefficients:< / p >
< ul class = "simple" >
< li > K (energy units)< / li >
< li > r0 (distance units)< / li >
< / ul >
< p > Note that the usual 1/2 factor is included in K.< / p >
< hr class = "docutils" / >
< p > < strong > Mixing, shift, table, tail correction, restart, rRESPA info< / strong > :< / p >
< p > This pair style does not support mixing since all parameters are
explicit for each pair.< / p >
< p > The < a class = "reference internal" href = "pair_modify.html" > < em > pair_modify< / em > < / a > shift option is supported by this
pair style.< / p >
< p > The < a class = "reference internal" href = "pair_modify.html" > < em > pair_modify< / em > < / a > table and tail options are not
relevant for this pair style.< / p >
< p > This pair style does not write its information to < a class = "reference internal" href = "restart.html" > < em > binary restart files< / em > < / 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 < em > pair< / em > keyword of the
< a class = "reference internal" href = "run_style.html" > < em > run_style respa< / em > < / a > command. It does not support the
< em > inner< / em > , < em > middle< / em > , < em > outer< / em > keywords.< / p >
< / div >
< hr class = "docutils" / >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > This pair style does not use a neighbor list and instead identifies
2013-05-31 23:48:00 +08:00
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;
2015-07-30 22:53:28 +08:00
otherwise the interaction will be skipped. You can use the < em > check< / em >
2013-06-01 02:20:26 +08:00
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
2015-07-30 22:53:28 +08:00
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 < span class = "xref std std-ref" > Making of LAMMPS< / span > section for more info.< / p >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< a class = "headerlink" href = "#related-commands" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > < a class = "reference internal" href = "pair_coeff.html" > < em > pair_coeff< / em > < / a > ,
< a class = "reference internal" href = "pair_hybrid.html" > < em > pair_style hybrid/overlay< / em > < / a > ,
< a class = "reference internal" href = "pair_lj.html" > < em > pair_style lj/cut< / em > < / a > ,
< a class = "reference internal" href = "pair_morse.html" > < em > pair_style morse< / em > < / a > ,
< a class = "reference internal" href = "bond_harmonic.html" > < em > bond_style harmonic< / em > < / a > < / p >
< p > < strong > Default:< / strong > none< / p >
< / div >
< / div >
< / div >
< / div >
< footer >
< hr / >
< div role = "contentinfo" >
< p >
2015-12-11 01:23:56 +08:00
© Copyright 2013 Sandia Corporation.
2015-07-30 22:53:28 +08:00
< / p >
< / div >
Built with < a href = "http://sphinx-doc.org/" > Sphinx< / a > using a < a href = "https://github.com/snide/sphinx_rtd_theme" > theme< / a > provided by < a href = "https://readthedocs.org" > Read the Docs< / a > .
< / footer >
< / div >
< / div >
< / section >
< / div >
< script type = "text/javascript" >
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
2015-12-21 23:20:41 +08:00
VERSION:'',
2015-07-30 22:53:28 +08:00
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true
};
< / script >
< script type = "text/javascript" src = "_static/jquery.js" > < / script >
< script type = "text/javascript" src = "_static/underscore.js" > < / script >
< script type = "text/javascript" src = "_static/doctools.js" > < / script >
< script type = "text/javascript" src = "https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" > < / script >
< script type = "text/javascript" src = "_static/sphinxcontrib-images/LightBox2/lightbox2/js/jquery-1.11.0.min.js" > < / script >
< script type = "text/javascript" src = "_static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.js" > < / script >
< script type = "text/javascript" src = "_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js" > < / script >
< script type = "text/javascript" src = "_static/js/theme.js" > < / script >
< script type = "text/javascript" >
jQuery(function () {
SphinxRtdTheme.StickyNav.enable();
});
< / script >
< / body >
< / html >
