jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13965 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2015-08-29 00:19:08 +00:00
parent d95acaced0
commit c20049b583
2 changed files with 458 additions and 423 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

871
doc/Manual.html
View File

@ -1,443 +1,478 @@
<HTML>
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="29 Aug 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
<BODY>
<!-- END_HTML_ONLY -->
<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>
<!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">
<title>LAMMPS Documentation &mdash; LAMMPS 15 May 2015 version documentation</title>
<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" />
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<link rel="next" title="1. Introduction" href="Section_intro.html"/>
<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="#" 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 &amp; 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 &amp; 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>
&nbsp;
</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="#">LAMMPS</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content"> <HR>
<div role="navigation" aria-label="breadcrumbs navigation">
<ul class="wy-breadcrumbs"> <H1></H1>
<li><a href="#">Docs</a> &raquo;</li>
<CENTER><H3>LAMMPS Documentation
<li>LAMMPS Documentation</li> </H3></CENTER>
<li class="wy-breadcrumbs-aside"> <CENTER><H4>29 Aug 2015 version
</H4></CENTER>
<H4>Version info:
<a href="http://lammps.sandia.gov">Website</a> </H4>
<a href="Section_commands.html#comm">Commands</a> <P>The LAMMPS "version" is the date when it was released, such as 1 May
</li>
</ul>
<hr/>
<div class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
<a href="Section_intro.html" class="btn btn-neutral float-right" title="1. Introduction" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
</div>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<H1></H1><div class="section" id="lammps-documentation">
<h1>LAMMPS Documentation<a class="headerlink" href="#lammps-documentation" title="Permalink to this headline"></a></h1>
<div class="section" id="aug-2015-version">
<h2>10 Aug 2015 version<a class="headerlink" href="#aug-2015-version" title="Permalink to this headline"></a></h2>
</div>
<div class="section" id="version-info">
<h2>Version info:<a class="headerlink" href="#version-info" title="Permalink to this headline"></a></h2>
<p>The LAMMPS &#8220;version&#8221; is the date when it was released, such as 1 May
2010. LAMMPS is updated continuously. Whenever we fix a bug or add a 2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
feature, we release it immediately, and post a notice on <a class="reference external" href="http://lammps.sandia.gov/bug.html">this page of the WWW site</a>. Each dated copy of LAMMPS contains all the feature, we release it immediately, and post a notice on <A HREF = "http://lammps.sandia.gov/bug.html">this page of
the WWW site</A>. Each dated copy of LAMMPS contains all the
features and bug-fixes up to and including that version date. The features and bug-fixes up to and including that version date. The
version date is printed to the screen and logfile every time you run version date is printed to the screen and logfile every time you run
LAMMPS. It is also in the file src/version.h and in the LAMMPS LAMMPS. It is also in the file src/version.h and in the LAMMPS
directory name created when you unpack a tarball, and at the top of directory name created when you unpack a tarball, and at the top of
the first page of the manual (this page).</p> the first page of the manual (this page).
<ul class="simple"> </P>
<li>If you browse the HTML doc pages on the LAMMPS WWW site, they always <UL><LI>If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of LAMMPS.</li> describe the most current version of LAMMPS.
<li>If you browse the HTML doc pages included in your tarball, they
describe the version you have.</li> <LI>If you browse the HTML doc pages included in your tarball, they
<li>The <a class="reference external" href="Manual.pdf">PDF file</a> on the WWW site or in the tarball is updated describe the version you have.
about once per month. This is because it is large, and we don&#8217;t want
it to be part of every patch.</li> <LI>The <A HREF = "Manual.pdf">PDF file</A> on the WWW site or in the tarball is updated
<li>There is also a <a class="reference external" href="Developer.pdf">Developer.pdf</a> file in the doc about once per month. This is because it is large, and we don't want
it to be part of every patch.
<LI>There is also a <A HREF = "Developer.pdf">Developer.pdf</A> file in the doc
directory, which describes the internal structure and algorithms of directory, which describes the internal structure and algorithms of
LAMMPS.</li> LAMMPS.
</ul> </UL>
<p>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel <P>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.</p> Simulator.
<p>LAMMPS is a classical molecular dynamics simulation code designed to </P>
<P>LAMMPS is a classical molecular dynamics simulation code designed to
run efficiently on parallel computers. It was developed at Sandia run efficiently on parallel computers. It was developed at Sandia
National Laboratories, a US Department of Energy facility, with National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL).</p> under the terms of the GNU Public License (GPL).
<p>The primary developers of LAMMPS are <a class="reference external" href="http://www.sandia.gov/~sjplimp">Steve Plimpton</a>, Aidan </P>
<P>The primary developers of LAMMPS are <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Aidan
Thompson, and Paul Crozier who can be contacted at Thompson, and Paul Crozier who can be contacted at
sjplimp,athomps,pscrozi at sandia.gov. The <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> at sjplimp,athomps,pscrozi at sandia.gov. The <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> at
<a class="reference external" href="http://lammps.sandia.gov">http://lammps.sandia.gov</a> has more information about the code and its http://lammps.sandia.gov has more information about the code and its
uses.</p> uses.
<hr class="docutils" /> </P>
<p>The LAMMPS documentation is organized into the following sections. If
<HR>
<P>The LAMMPS documentation is organized into the following sections. If
you find errors or omissions in this manual or have suggestions for you find errors or omissions in this manual or have suggestions for
useful information to add, please send an email to the developers so useful information to add, please send an email to the developers so
we can improve the LAMMPS documentation.</p> we can improve the LAMMPS documentation.
<p>Once you are familiar with LAMMPS, you may want to bookmark <a class="reference internal" href="Section_commands.html#comm"><span>this page</span></a> at Section_commands.html#comm since </P>
it gives quick access to documentation for all LAMMPS commands.</p> <P>Once you are familiar with LAMMPS, you may want to bookmark <A HREF = "Section_commands.html#comm">this
<p><a class="reference external" href="Manual.pdf">PDF file</a> of the entire manual, generated by page</A> at Section_commands.html#comm since
<a class="reference external" href="http://freecode.com/projects/htmldoc">htmldoc</a></p> it gives quick access to documentation for all LAMMPS commands.
<div class="toctree-wrapper compound"> </P>
<ul> <P><A HREF = "Manual.pdf">PDF file</A> of the entire manual, generated by
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a><ul> <A HREF = "http://freecode.com/projects/htmldoc">htmldoc</A>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#what-is-lammps">1.1. What is LAMMPS</a></li> </P>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-features">1.2. LAMMPS features</a></li> <P><!-- RST
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-non-features">1.3. LAMMPS non-features</a></li> </P>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#open-source-distribution">1.4. Open source distribution</a></li> <P>.. toctree::
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#acknowledgments-and-citations">1.5. Acknowledgments and citations</a></li> :maxdepth: 2
</ul> :numbered: // comment
</li> </P>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a><ul> <P> Section_intro
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#what-s-in-the-lammps-distribution">2.1. What&#8217;s in the LAMMPS distribution</a></li> Section_start
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps">2.2. Making LAMMPS</a></li> Section_commands
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps-with-optional-packages">2.3. Making LAMMPS with optional packages</a></li> Section_packages
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-via-the-make-py-script">2.4. Building LAMMPS via the Make.py script</a></li> Section_accelerate
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-as-a-library">2.5. Building LAMMPS as a library</a></li> Section_howto
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#running-lammps">2.6. Running LAMMPS</a></li> Section_example
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#command-line-options">2.7. Command-line options</a></li> Section_perf
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#lammps-screen-output">2.8. LAMMPS screen output</a></li> Section_tools
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#tips-for-users-of-previous-lammps-versions">2.9. Tips for users of previous LAMMPS versions</a></li> Section_modify
</ul> Section_python
</li> Section_errors
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a><ul> Section_history
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#lammps-input-script">3.1. LAMMPS input script</a></li> </P>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#parsing-rules">3.2. Parsing rules</a></li> <P>Indices and tables
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#input-script-structure">3.3. Input script structure</a></li> ==================
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#commands-listed-by-category">3.4. Commands listed by category</a></li> </P>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#individual-commands">3.5. Individual commands</a></li> <P>* :ref:`genindex` // comment
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#fix-styles">3.6. Fix styles</a></li> * :ref:`search` // comment
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#compute-styles">3.7. Compute styles</a></li> </P>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#pair-style-potentials">3.8. Pair_style potentials</a></li> <P>END_RST -->
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#bond-style-potentials">3.9. Bond_style potentials</a></li> </P>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#angle-style-potentials">3.10. Angle_style potentials</a></li> <OL><LI><!-- HTML_ONLY -->
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#dihedral-style-potentials">3.11. Dihedral_style potentials</a></li> <A HREF = "Section_intro.html">Introduction</A>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#improper-style-potentials">3.12. Improper_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#kspace-solvers">3.13. Kspace solvers</a></li> <UL> 1.1 <A HREF = "Section_intro.html#intro_1">What is LAMMPS</A>
</ul> <BR>
</li> 1.2 <A HREF = "Section_intro.html#intro_2">LAMMPS features</A>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a><ul> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#standard-packages">4.1. Standard packages</a></li> 1.3 <A HREF = "Section_intro.html#intro_3">LAMMPS non-features</A>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-packages">4.2. User packages</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-atc-package">4.3. USER-ATC package</a></li> 1.4 <A HREF = "Section_intro.html#intro_4">Open source distribution</A>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-awpmd-package">4.4. USER-AWPMD package</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cg-cmm-package">4.5. USER-CG-CMM package</a></li> 1.5 <A HREF = "Section_intro.html#intro_5">Acknowledgments and citations</A>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-colvars-package">4.6. USER-COLVARS package</a></li> <BR></UL>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cuda-package">4.7. USER-CUDA package</a></li> <LI><A HREF = "Section_start.html">Getting started</A>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-diffraction-package">4.8. USER-DIFFRACTION package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-drude-package">4.9. USER-DRUDE package</a></li> <UL> 2.1 <A HREF = "Section_start.html#start_1">What's in the LAMMPS distribution</A>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-eff-package">4.10. USER-EFF package</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-fep-package">4.11. USER-FEP package</a></li> 2.2 <A HREF = "Section_start.html#start_2">Making LAMMPS</A>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-h5md-package">4.12. USER-H5MD package</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-intel-package">4.13. USER-INTEL package</a></li> 2.3 <A HREF = "Section_start.html#start_3">Making LAMMPS with optional packages</A>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-lb-package">4.14. USER-LB package</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-misc-package">4.15. USER-MISC package</a></li> 2.4 <A HREF = "Section_start.html#start_4">Building LAMMPS via the Make.py script</A>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-molfile-package">4.16. USER-MOLFILE package</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-omp-package">4.17. USER-OMP package</a></li> 2.5 <A HREF = "Section_start.html#start_5">Building LAMMPS as a library</A>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-phonon-package">4.18. USER-PHONON package</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qmmm-package">4.19. USER-QMMM package</a></li> 2.6 <A HREF = "Section_start.html#start_6">Running LAMMPS</A>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qtb-package">4.20. USER-QTB package</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-reaxc-package">4.21. USER-REAXC package</a></li> 2.7 <A HREF = "Section_start.html#start_7">Command-line options</A>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smd-package">4.22. USER-SMD package</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-sph-package">4.23. USER-SPH package</a></li> 2.8 <A HREF = "Section_start.html#start_8">Screen output</A>
</ul> <BR>
</li> 2.9 <A HREF = "Section_start.html#start_9">Tips for users of previous versions</A>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a><ul> <BR></UL>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#measuring-performance">5.1. Measuring performance</a></li> <LI><A HREF = "Section_commands.html">Commands</A>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#general-strategies">5.2. General strategies</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#packages-with-optimized-styles">5.3. Packages with optimized styles</a></li> <UL> 3.1 <A HREF = "Section_commands.html#cmd_1">LAMMPS input script</A>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#comparison-of-various-accelerator-packages">5.4. Comparison of various accelerator packages</a></li> <BR>
</ul> 3.2 <A HREF = "Section_commands.html#cmd_2">Parsing rules</A>
</li> <BR>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a><ul> 3.3 <A HREF = "Section_commands.html#cmd_3">Input script structure</A>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#restarting-a-simulation">6.1. Restarting a simulation</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#d-simulations">6.2. 2d simulations</a></li> 3.4 <A HREF = "Section_commands.html#cmd_4">Commands listed by category</A>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#charmm-amber-and-dreiding-force-fields">6.3. CHARMM, AMBER, and DREIDING force fields</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#running-multiple-simulations-from-one-input-script">6.4. Running multiple simulations from one input script</a></li> 3.5 <A HREF = "Section_commands.html#cmd_5">Commands listed alphabetically</A>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#multi-replica-simulations">6.5. Multi-replica simulations</a></li> <BR></UL>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#granular-models">6.6. Granular models</a></li> <LI><A HREF = "Section_packages.html">Packages</A>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip3p-water-model">6.7. TIP3P water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip4p-water-model">6.8. TIP4P water model</a></li> <UL> 4.1 <A HREF = "Section_packages.html#pkg_1">Standard packages</A>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#spc-water-model">6.9. SPC water model</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#coupling-lammps-to-other-codes">6.10. Coupling LAMMPS to other codes</a></li> 4.2 <A HREF = "Section_packages.html#pkg_2">User packages</A>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#visualizing-lammps-snapshots">6.11. Visualizing LAMMPS snapshots</a></li> <BR></UL>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#triclinic-non-orthogonal-simulation-boxes">6.12. Triclinic (non-orthogonal) simulation boxes</a></li> <LI><A HREF = "Section_accelerate.html">Accelerating LAMMPS performance</A>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#nemd-simulations">6.13. NEMD simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#finite-size-spherical-and-aspherical-particles">6.14. Finite-size spherical and aspherical particles</a></li> <UL> 5.1 <A HREF = "Section_accelerate.html#acc_1">Measuring performance</A>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#output-from-lammps-thermo-dumps-computes-fixes-variables">6.15. Output from LAMMPS (thermo, dumps, computes, fixes, variables)</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#thermostatting-barostatting-and-computing-temperature">6.16. Thermostatting, barostatting, and computing temperature</a></li> 5.2 <A HREF = "Section_accelerate.html#acc_2">Algorithms and code options to boost performace</A>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#walls">6.17. Walls</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#elastic-constants">6.18. Elastic constants</a></li> 5.3 <A HREF = "Section_accelerate.html#acc_3">Accelerator packages with optimized styles</A>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#library-interface-to-lammps">6.19. Library interface to LAMMPS</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-thermal-conductivity">6.20. Calculating thermal conductivity</a></li> <UL> 5.3.1 <A HREF = "accelerate_cuda.html">USER-CUDA package</A>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-viscosity">6.21. Calculating viscosity</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-a-diffusion-coefficient">6.22. Calculating a diffusion coefficient</a></li> 5.3.2 <A HREF = "accelerate_gpu.html">GPU package</A>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#using-chunks-to-calculate-system-properties">6.23. Using chunks to calculate system properties</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#setting-parameters-for-the-kspace-style-pppm-disp-command">6.24. Setting parameters for the <code class="docutils literal"><span class="pre">kspace_style</span> <span class="pre">pppm/disp</span></code> command</a></li> 5.3.3 <A HREF = "accelerate_intel.html">USER-INTEL package</A>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#polarizable-models">6.25. Polarizable models</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#adiabatic-core-shell-model">6.26. Adiabatic core/shell model</a></li> 5.3.4 <A HREF = "accelerate_kokkos.html">KOKKOS package</A>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#drude-induced-dipoles">6.27. Drude induced dipoles</a></li> <BR>
</ul> 5.3.5 <A HREF = "accelerate_omp.html">USER-OMP package</A>
</li> <BR>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li> 5.3.6 <A HREF = "accelerate_opt.html">OPT package</A>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li> <BR></UL>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a><ul> 5.4 <A HREF = "Section_accelerate.html#acc_4">Comparison of various accelerator packages</A>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#amber2lmp-tool">9.1. amber2lmp tool</a></li> <BR></UL>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#binary2txt-tool">9.2. binary2txt tool</a></li> <LI><A HREF = "Section_howto.html">How-to discussions</A>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ch2lmp-tool">9.3. ch2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#chain-tool">9.4. chain tool</a></li> <UL> 6.1 <A HREF = "Section_howto.html#howto_1">Restarting a simulation</A>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#colvars-tools">9.5. colvars tools</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#createatoms-tool">9.6. createatoms tool</a></li> 6.2 <A HREF = "Section_howto.html#howto_2">2d simulations</A>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#data2xmovie-tool">9.7. data2xmovie tool</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-database-tool">9.8. eam database tool</a></li> 6.3 <A HREF = "Section_howto.html#howto_3">CHARMM and AMBER force fields</A>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-generate-tool">9.9. eam generate tool</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eff-tool">9.10. eff tool</a></li> 6.4 <A HREF = "Section_howto.html#howto_4">Running multiple simulations from one input script</A>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#emacs-tool">9.11. emacs tool</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#fep-tool">9.12. fep tool</a></li> 6.5 <A HREF = "Section_howto.html#howto_5">Multi-replica simulations</A>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#i-pi-tool">9.13. i-pi tool</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ipp-tool">9.14. ipp tool</a></li> 6.6 <A HREF = "Section_howto.html#howto_6">Granular models</A>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#kate-tool">9.15. kate tool</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2arc-tool">9.16. lmp2arc tool</a></li> 6.7 <A HREF = "Section_howto.html#howto_7">TIP3P water model</A>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2cfg-tool">9.17. lmp2cfg tool</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2vmd-tool">9.18. lmp2vmd tool</a></li> 6.8 <A HREF = "Section_howto.html#howto_8">TIP4P water model</A>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#matlab-tool">9.19. matlab tool</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#micelle2d-tool">9.20. micelle2d tool</a></li> 6.9 <A HREF = "Section_howto.html#howto_9">SPC water model</A>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#moltemplate-tool">9.21. moltemplate tool</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#msi2lmp-tool">9.22. msi2lmp tool</a></li> 6.10 <A HREF = "Section_howto.html#howto_10">Coupling LAMMPS to other codes</A>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#phonon-tool">9.23. phonon tool</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#polymer-bonding-tool">9.24. polymer bonding tool</a></li> 6.11 <A HREF = "Section_howto.html#howto_11">Visualizing LAMMPS snapshots</A>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#pymol-asphere-tool">9.25. pymol_asphere tool</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#python-tool">9.26. python tool</a></li> 6.12 <A HREF = "Section_howto.html#howto_12">Triclinic (non-orthogonal) simulation boxes</A>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#reax-tool">9.27. reax tool</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#restart2data-tool">9.28. restart2data tool</a></li> 6.13 <A HREF = "Section_howto.html#howto_13">NEMD simulations</A>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#vim-tool">9.29. vim tool</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmgrace-tool">9.30. xmgrace tool</a></li> 6.14 <A HREF = "Section_howto.html#howto_14">Finite-size spherical and aspherical particles</A>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmovie-tool">9.31. xmovie tool</a></li> <BR>
</ul> 6.15 <A HREF = "Section_howto.html#howto_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A>
</li> <BR>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a><ul> 6.16 <A HREF = "Section_howto.html#howto_16">Thermostatting, barostatting, and compute temperature</A>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#atom-styles">10.1. Atom styles</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#bond-angle-dihedral-improper-potentials">10.2. Bond, angle, dihedral, improper potentials</a></li> 6.17 <A HREF = "Section_howto.html#howto_17">Walls</A>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#compute-styles">10.3. Compute styles</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-styles">10.4. Dump styles</a></li> 6.18 <A HREF = "Section_howto.html#howto_18">Elastic constants</A>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-custom-output-options">10.5. Dump custom output options</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#fix-styles">10.6. Fix styles</a></li> 6.19 <A HREF = "Section_howto.html#howto_19">Library interface to LAMMPS</A>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#input-script-commands">10.7. Input script commands</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#kspace-computations">10.8. Kspace computations</a></li> 6.20 <A HREF = "Section_howto.html#howto_20">Calculating thermal conductivity</A>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#minimization-styles">10.9. Minimization styles</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#pairwise-potentials">10.10. Pairwise potentials</a></li> 6.21 <A HREF = "Section_howto.html#howto_21">Calculating viscosity</A>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#region-styles">10.11. Region styles</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#body-styles">10.12. Body styles</a></li> 6.22 <A HREF = "Section_howto.html#howto_22">Calculating a diffusion coefficient</A>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#thermodynamic-output-options">10.13. Thermodynamic output options</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#variable-options">10.14. Variable options</a></li> 6.23 <A HREF = "Section_howto.html#howto_23">Using chunks to calculate system properties</A>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#submitting-new-features-for-inclusion-in-lammps">10.15. Submitting new features for inclusion in LAMMPS</a></li> <BR>
</ul> 6.24 <A HREF = "Section_howto.html#howto_24">Setting parameters for pppm/disp</A>
</li> <BR>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a><ul> 6.25 <A HREF = "Section_howto.html#howto_25">Polarizable models</A>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-running-lammps-from-python">11.1. Overview of running LAMMPS from Python</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-using-python-from-a-lammps-script">11.2. Overview of using Python from a LAMMPS script</a></li> 6.26 <A HREF = "Section_howto.html#howto_26">Adiabatic core/shell model</A>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#building-lammps-as-a-shared-library">11.3. Building LAMMPS as a shared library</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#installing-the-python-wrapper-into-python">11.4. Installing the Python wrapper into Python</a></li> 6.27 <A HREF = "Section_howto.html#howto_27">Drude induced dipoles</A>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#extending-python-with-mpi-to-run-in-parallel">11.5. Extending Python with MPI to run in parallel</a></li> <BR></UL>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#testing-the-python-lammps-interface">11.6. Testing the Python-LAMMPS interface</a></li> <LI><A HREF = "Section_example.html">Example problems</A>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#using-lammps-from-python">11.7. Using LAMMPS from Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#example-python-scripts-that-use-lammps">11.8. Example Python scripts that use LAMMPS</a></li> <LI><A HREF = "Section_perf.html">Performance & scalability</A>
</ul>
</li> <LI><A HREF = "Section_tools.html">Additional tools</A>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#common-problems">12.1. Common problems</a></li> <LI><A HREF = "Section_modify.html">Modifying & extending LAMMPS</A>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#reporting-bugs">12.2. Reporting bugs</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error-warning-messages">12.3. Error &amp; warning messages</a></li> <UL> 10.1 <A HREF = "Section_modify.html#mod_1">Atom styles</A>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error">12.4. Errors:</a></li> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#warnings">12.5. Warnings:</a></li> 10.2 <A HREF = "Section_modify.html#mod_2">Bond, angle, dihedral, improper potentials</A>
</ul> <BR>
</li> 10.3 <A HREF = "Section_modify.html#mod_3">Compute styles</A>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a><ul> <BR>
<li class="toctree-l2"><a class="reference internal" href="Section_history.html#coming-attractions">13.1. Coming attractions</a></li> 10.4 <A HREF = "Section_modify.html#mod_4">Dump styles</A>
<li class="toctree-l2"><a class="reference internal" href="Section_history.html#past-versions">13.2. Past versions</a></li> <BR>
</ul> 10.5 <A HREF = "Section_modify.html#mod_5">Dump custom output options</A>
</li> <BR>
</ul> 10.6 <A HREF = "Section_modify.html#mod_6">Fix styles</A>
</div> <BR>
</div> 10.7 <A HREF = "Section_modify.html#mod_7">Input script commands</A>
</div> <BR>
<div class="section" id="indices-and-tables"> 10.8 <A HREF = "Section_modify.html#mod_8">Kspace computations</A>
<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline"></a></h1> <BR>
<ul class="simple"> 10.9 <A HREF = "Section_modify.html#mod_9">Minimization styles</A>
<li><a class="reference internal" href="genindex.html"><span>Index</span></a></li> <BR>
<li><a class="reference internal" href="search.html"><span>Search Page</span></a></li> 10.10 <A HREF = "Section_modify.html#mod_10">Pairwise potentials</A>
</ul> <BR>
</BODY></div> 10.11 <A HREF = "Section_modify.html#mod_11">Region styles</A>
<BR>
10.12 <A HREF = "Section_modify.html#mod_12">Body styles</A>
<BR>
10.13 <A HREF = "Section_modify.html#mod_13">Thermodynamic output options</A>
<BR>
10.14 <A HREF = "Section_modify.html#mod_14">Variable options</A>
<BR>
10.15 <A HREF = "Section_modify.html#mod_15">Submitting new features for inclusion in LAMMPS</A>
<BR></UL>
<LI><A HREF = "Section_python.html">Python interface</A>
<UL> 11.1 <A HREF = "Section_python.html#py_1">Overview of running LAMMPS from Python</A>
<BR>
11.2 <A HREF = "Section_python.html#py_2">Overview of using Python from a LAMMPS script</A>
<BR>
11.3 <A HREF = "Section_python.html#py_3">Building LAMMPS as a shared library</A>
<BR>
11.4 <A HREF = "Section_python.html#py_4">Installing the Python wrapper into Python</A>
<BR>
11.5 <A HREF = "Section_python.html#py_5">Extending Python with MPI to run in parallel</A>
<BR>
11.6 <A HREF = "Section_python.html#py_6">Testing the Python-LAMMPS interface</A>
<BR>
11.7 <A HREF = "py_7">Using LAMMPS from Python</A>
<BR>
11.8 <A HREF = "py_8">Example Python scripts that use LAMMPS</A>
<BR></UL>
<LI><A HREF = "Section_errors.html">Errors</A>
<UL> 12.1 <A HREF = "Section_errors.html#err_1">Common problems</A>
<BR>
12.2 <A HREF = "Section_errors.html#err_2">Reporting bugs</A>
<BR>
12.3 <A HREF = "Section_errors.html#err_3">Error & warning messages</A>
<BR></UL>
<LI><A HREF = "Section_history.html">Future and history</A>
<UL> 13.1 <A HREF = "Section_history.html#hist_1">Coming attractions</A>
<BR>
13.2 <A HREF = "Section_history.html#hist_2">Past versions</A>
<BR></UL>
</OL>
</div>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="Section_intro.html" class="btn btn-neutral float-right" title="1. Introduction" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
</div>
<hr/>
<div role="contentinfo">
<p>
&copy; Copyright .
</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:'./',
VERSION:'15 May 2015 version',
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>
<!-- END_HTML_ONLY -->
</BODY>
</HTML>

10
doc/Manual.txt
View File

@ -1,7 +1,7 @@
<!-- HTML_ONLY --> <!-- HTML_ONLY -->
<HEAD> <HEAD>
<TITLE>LAMMPS Users Manual</TITLE> <TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="10 Aug 2015 version"> <META NAME="docnumber" CONTENT="29 Aug 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD> </HEAD>
@ -21,7 +21,7 @@
<H1></H1> <H1></H1>
LAMMPS Documentation :c,h3 LAMMPS Documentation :c,h3
10 Aug 2015 version :c,h4 29 Aug 2015 version :c,h4
Version info: :h4 Version info: :h4
@ -85,7 +85,7 @@ it gives quick access to documentation for all LAMMPS commands.
.. toctree:: .. toctree::
:maxdepth: 2 :maxdepth: 2
:numbered: :numbered: // comment
Section_intro Section_intro
Section_start Section_start
@ -105,8 +105,8 @@ it gives quick access to documentation for all LAMMPS commands.
Indices and tables Indices and tables
================== ==================
* :ref:`genindex` * :ref:`genindex` // comment
* :ref:`search` * :ref:`search` // comment
END_RST --> END_RST -->