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@14133 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp 2015-10-21 18:53:15 +00:00
parent 2ea1457e5c
commit 45e18fe128
5 changed files with 1125 additions and 552 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
doc/Manual.txt
View File

@ -85,7 +85,7 @@ it gives quick access to documentation for all LAMMPS commands.
.. toctree::
:maxdepth: 2
:numbered: // comment
:numbered:
Section_intro
Section_start
@ -105,8 +105,8 @@ it gives quick access to documentation for all LAMMPS commands.
Indices and tables
==================
* :ref:`genindex` // comment
* :ref:`search` // comment
* :ref:`genindex`
* :ref:`search`
END_RST -->

479
doc/Section_example.html
View File

@ -1,17 +1,143 @@
<HTML>
<CENTER><A HREF = "Section_howto.html">Previous Section</A> - <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> - <A HREF = "Section_perf.html">Next Section</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>7. Example problems &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="8. Performance &amp; scalability" href="Section_perf.html"/>
<link rel="prev" title="6. How-to discussions" href="Section_howto.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="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 class="current">
<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 current"><a class="current reference internal" href="">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="Manual.html">LAMMPS</a>
</nav>
<HR>
<H3>7. Example problems
</H3>
<P>The LAMMPS distribution includes an examples sub-directory with
<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> &raquo;</li>
<li>7. Example problems</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 class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
<a href="Section_perf.html" class="btn btn-neutral float-right" title="8. Performance &amp; scalability" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="Section_howto.html" class="btn btn-neutral" title="6. How-to discussions" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="example-problems">
<h1>7. Example problems<a class="headerlink" href="#example-problems" title="Permalink to this headline"></a></h1>
<p>The LAMMPS distribution includes an examples sub-directory with
several sample problems. Each problem is in a sub-directory of its
own. Most are 2d models so that they run quickly, requiring at most a
couple of minutes to run on a desktop machine. Each problem has an
@ -20,111 +146,256 @@ input script (in.*) and produces a log file (log.*) and dump file
coordinates as additional input. A few sample log file outputs on
different machines and different numbers of processors are included in
the directories to compare your answers to. E.g. a log file like
log.crack.foo.P means it ran on P processors of machine "foo".
</P>
<P>For examples that use input data files, many of them were produced by
<A HREF = "http://pizza.sandia.gov">Pizza.py</A> or setup tools described in the
<A HREF = "Section_tools.html">Additional Tools</A> section of the LAMMPS
documentation and provided with the LAMMPS distribution.
</P>
<P>If you uncomment the <A HREF = "dump.html">dump</A> command in the input script, a
log.crack.foo.P means it ran on P processors of machine &#8220;foo&#8221;.</p>
<p>For examples that use input data files, many of them were produced by
<a class="reference external" href="http://pizza.sandia.gov">Pizza.py</a> or setup tools described in the
<a class="reference internal" href="Section_tools.html"><em>Additional Tools</em></a> section of the LAMMPS
documentation and provided with the LAMMPS distribution.</p>
<p>If you uncomment the <a class="reference internal" href="dump.html"><em>dump</em></a> command in the input script, a
text dump file will be produced, which can be animated by various
<A HREF = "http://lammps.sandia.gov/viz.html">visualization programs</A>. It can
also be animated using the xmovie tool described in the <A HREF = "Section_tools.html">Additional
Tools</A> section of the LAMMPS documentation.
</P>
<P>If you uncomment the <A HREF = "dump.html">dump image</A> command in the input
<a class="reference external" href="http://lammps.sandia.gov/viz.html">visualization programs</a>. It can
also be animated using the xmovie tool described in the <a class="reference internal" href="Section_tools.html"><em>Additional Tools</em></a> section of the LAMMPS documentation.</p>
<p>If you uncomment the <a class="reference internal" href="dump.html"><em>dump image</em></a> command in the input
script, and assuming you have built LAMMPS with a JPG library, JPG
snapshot images will be produced when the simulation runs. They can
be quickly post-processed into a movie using commands described on the
<A HREF = "dump_image.html">dump image</A> doc page.
</P>
<P>Animations of many of these examples can be viewed on the Movies
section of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>.
</P>
<P>These are the sample problems in the examples sub-directories:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >balance</TD><TD > dynamic load balancing, 2d system</TD></TR>
<TR><TD >body</TD><TD > body particles, 2d system</TD></TR>
<TR><TD >colloid</TD><TD > big colloid particles in a small particle solvent, 2d system</TD></TR>
<TR><TD >comb</TD><TD > models using the COMB potential</TD></TR>
<TR><TD >crack</TD><TD > crack propagation in a 2d solid</TD></TR>
<TR><TD >cuda</TD><TD > use of the USER-CUDA package for GPU acceleration</TD></TR>
<TR><TD >dipole</TD><TD > point dipolar particles, 2d system</TD></TR>
<TR><TD >dreiding</TD><TD > methanol via Dreiding FF</TD></TR>
<TR><TD >eim</TD><TD > NaCl using the EIM potential</TD></TR>
<TR><TD >ellipse</TD><TD > ellipsoidal particles in spherical solvent, 2d system</TD></TR>
<TR><TD >flow</TD><TD > Couette and Poiseuille flow in a 2d channel</TD></TR>
<TR><TD >friction</TD><TD > frictional contact of spherical asperities between 2d surfaces</TD></TR>
<TR><TD >gpu</TD><TD > use of the GPU package for GPU acceleration</TD></TR>
<TR><TD >hugoniostat</TD><TD > Hugoniostat shock dynamics</TD></TR>
<TR><TD >indent</TD><TD > spherical indenter into a 2d solid</TD></TR>
<TR><TD >intel</TD><TD > use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor</TD></TR>
<TR><TD >kim</TD><TD > use of potentials in Knowledge Base for Interatomic Models (KIM)</TD></TR>
<TR><TD >line</TD><TD > line segment particles in 2d rigid bodies</TD></TR>
<TR><TD >meam</TD><TD > MEAM test for SiC and shear (same as shear examples)</TD></TR>
<TR><TD >melt</TD><TD > rapid melt of 3d LJ system</TD></TR>
<TR><TD >micelle</TD><TD > self-assembly of small lipid-like molecules into 2d bilayers</TD></TR>
<TR><TD >min</TD><TD > energy minimization of 2d LJ melt</TD></TR>
<TR><TD >msst</TD><TD > MSST shock dynamics</TD></TR>
<TR><TD >nb3b</TD><TD > use of nonbonded 3-body harmonic pair style</TD></TR>
<TR><TD >neb</TD><TD > nudged elastic band (NEB) calculation for barrier finding</TD></TR>
<TR><TD >nemd</TD><TD > non-equilibrium MD of 2d sheared system</TD></TR>
<TR><TD >obstacle</TD><TD > flow around two voids in a 2d channel</TD></TR>
<TR><TD >peptide</TD><TD > dynamics of a small solvated peptide chain (5-mer)</TD></TR>
<TR><TD >peri</TD><TD > Peridynamic model of cylinder impacted by indenter</TD></TR>
<TR><TD >pour</TD><TD > pouring of granular particles into a 3d box, then chute flow</TD></TR>
<TR><TD >prd</TD><TD > parallel replica dynamics of vacancy diffusion in bulk Si</TD></TR>
<TR><TD >qeq</TD><TD > use of the QEQ pacakge for charge equilibration</TD></TR>
<TR><TD >reax</TD><TD > RDX and TATB models using the ReaxFF</TD></TR>
<TR><TD >rigid</TD><TD > rigid bodies modeled as independent or coupled</TD></TR>
<TR><TD >shear</TD><TD > sideways shear applied to 2d solid, with and without a void</TD></TR>
<TR><TD >snap</TD><TD > NVE dynamics for BCC tantalum crystal using SNAP potential</TD></TR>
<TR><TD >srd</TD><TD > stochastic rotation dynamics (SRD) particles as solvent</TD></TR>
<TR><TD >tad</TD><TD > temperature-accelerated dynamics of vacancy diffusion in bulk Si</TD></TR>
<TR><TD >tri</TD><TD > triangular particles in rigid bodies
</TD></TR></TABLE></DIV>
<P>Here is how you might run and visualize one of the sample problems:
</P>
<PRE>cd indent
<a class="reference internal" href="dump_image.html"><em>dump image</em></a> doc page.</p>
<p>Animations of many of these examples can be viewed on the Movies
section of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>.</p>
<p>These are the sample problems in the examples sub-directories:</p>
<table border="1" class="docutils">
<colgroup>
<col width="15%" />
<col width="85%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>balance</td>
<td>dynamic load balancing, 2d system</td>
</tr>
<tr class="row-even"><td>body</td>
<td>body particles, 2d system</td>
</tr>
<tr class="row-odd"><td>colloid</td>
<td>big colloid particles in a small particle solvent, 2d system</td>
</tr>
<tr class="row-even"><td>comb</td>
<td>models using the COMB potential</td>
</tr>
<tr class="row-odd"><td>crack</td>
<td>crack propagation in a 2d solid</td>
</tr>
<tr class="row-even"><td>cuda</td>
<td>use of the USER-CUDA package for GPU acceleration</td>
</tr>
<tr class="row-odd"><td>dipole</td>
<td>point dipolar particles, 2d system</td>
</tr>
<tr class="row-even"><td>dreiding</td>
<td>methanol via Dreiding FF</td>
</tr>
<tr class="row-odd"><td>eim</td>
<td>NaCl using the EIM potential</td>
</tr>
<tr class="row-even"><td>ellipse</td>
<td>ellipsoidal particles in spherical solvent, 2d system</td>
</tr>
<tr class="row-odd"><td>flow</td>
<td>Couette and Poiseuille flow in a 2d channel</td>
</tr>
<tr class="row-even"><td>friction</td>
<td>frictional contact of spherical asperities between 2d surfaces</td>
</tr>
<tr class="row-odd"><td>gpu</td>
<td>use of the GPU package for GPU acceleration</td>
</tr>
<tr class="row-even"><td>hugoniostat</td>
<td>Hugoniostat shock dynamics</td>
</tr>
<tr class="row-odd"><td>indent</td>
<td>spherical indenter into a 2d solid</td>
</tr>
<tr class="row-even"><td>intel</td>
<td>use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor</td>
</tr>
<tr class="row-odd"><td>kim</td>
<td>use of potentials in Knowledge Base for Interatomic Models (KIM)</td>
</tr>
<tr class="row-even"><td>line</td>
<td>line segment particles in 2d rigid bodies</td>
</tr>
<tr class="row-odd"><td>meam</td>
<td>MEAM test for SiC and shear (same as shear examples)</td>
</tr>
<tr class="row-even"><td>melt</td>
<td>rapid melt of 3d LJ system</td>
</tr>
<tr class="row-odd"><td>micelle</td>
<td>self-assembly of small lipid-like molecules into 2d bilayers</td>
</tr>
<tr class="row-even"><td>min</td>
<td>energy minimization of 2d LJ melt</td>
</tr>
<tr class="row-odd"><td>msst</td>
<td>MSST shock dynamics</td>
</tr>
<tr class="row-even"><td>nb3b</td>
<td>use of nonbonded 3-body harmonic pair style</td>
</tr>
<tr class="row-odd"><td>neb</td>
<td>nudged elastic band (NEB) calculation for barrier finding</td>
</tr>
<tr class="row-even"><td>nemd</td>
<td>non-equilibrium MD of 2d sheared system</td>
</tr>
<tr class="row-odd"><td>obstacle</td>
<td>flow around two voids in a 2d channel</td>
</tr>
<tr class="row-even"><td>peptide</td>
<td>dynamics of a small solvated peptide chain (5-mer)</td>
</tr>
<tr class="row-odd"><td>peri</td>
<td>Peridynamic model of cylinder impacted by indenter</td>
</tr>
<tr class="row-even"><td>pour</td>
<td>pouring of granular particles into a 3d box, then chute flow</td>
</tr>
<tr class="row-odd"><td>prd</td>
<td>parallel replica dynamics of vacancy diffusion in bulk Si</td>
</tr>
<tr class="row-even"><td>qeq</td>
<td>use of the QEQ pacakge for charge equilibration</td>
</tr>
<tr class="row-odd"><td>reax</td>
<td>RDX and TATB models using the ReaxFF</td>
</tr>
<tr class="row-even"><td>rigid</td>
<td>rigid bodies modeled as independent or coupled</td>
</tr>
<tr class="row-odd"><td>shear</td>
<td>sideways shear applied to 2d solid, with and without a void</td>
</tr>
<tr class="row-even"><td>snap</td>
<td>NVE dynamics for BCC tantalum crystal using SNAP potential</td>
</tr>
<tr class="row-odd"><td>srd</td>
<td>stochastic rotation dynamics (SRD) particles as solvent</td>
</tr>
<tr class="row-even"><td>tad</td>
<td>temperature-accelerated dynamics of vacancy diffusion in bulk Si</td>
</tr>
<tr class="row-odd"><td>tri</td>
<td>triangular particles in rigid bodies</td>
</tr>
</tbody>
</table>
<p>vashishta: models using the Vashishta potential</p>
<p>Here is how you might run and visualize one of the sample problems:</p>
<div class="highlight-python"><div class="highlight"><pre>cd indent
cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
lmp_linux -in in.indent # run the problem
</PRE>
<P>Running the simulation produces the files <I>dump.indent</I> and
<I>log.lammps</I>. You can visualize the dump file as follows:
</P>
<PRE>../../tools/xmovie/xmovie -scale dump.indent
</PRE>
<P>If you uncomment the <A HREF = "dump_image.html">dump image</A> line(s) in the input
lmp_linux -in in.indent # run the problem
</pre></div>
</div>
<p>Running the simulation produces the files <em>dump.indent</em> and
<em>log.lammps</em>. You can visualize the dump file as follows:</p>
<div class="highlight-python"><div class="highlight"><pre>../../tools/xmovie/xmovie -scale dump.indent
</pre></div>
</div>
<p>If you uncomment the <a class="reference internal" href="dump_image.html"><em>dump image</em></a> line(s) in the input
script a series of JPG images will be produced by the run. These can
be viewed individually or turned into a movie or animated by tools
like ImageMagick or QuickTime or various Windows-based tools. See the
<A HREF = "dump_image.html">dump image</A> doc page for more details. E.g. this
<a class="reference internal" href="dump_image.html"><em>dump image</em></a> doc page for more details. E.g. this
Imagemagick command would create a GIF file suitable for viewing in a
browser.
</P>
<PRE>% convert -loop 1 *.jpg foo.gif
</PRE>
<HR>
<P>There is also a COUPLE directory with examples of how to use LAMMPS as
browser.</p>
<div class="highlight-python"><div class="highlight"><pre>% convert -loop 1 *.jpg foo.gif
</pre></div>
</div>
<hr class="docutils" />
<p>There is also a COUPLE directory with examples of how to use LAMMPS as
a library, either by itself or in tandem with another code or library.
See the COUPLE/README file to get started.
</P>
<P>There is also an ELASTIC directory with an example script for
See the COUPLE/README file to get started.</p>
<p>There is also an ELASTIC directory with an example script for
computing elastic constants at zero temperature, using an Si example. See
the ELASTIC/in.elastic file for more info.
</P>
<P>There is also an ELASTIC_T directory with an example script for
the ELASTIC/in.elastic file for more info.</p>
<p>There is also an ELASTIC_T directory with an example script for
computing elastic constants at finite temperature, using an Si example. See
the ELASTIC_T/in.elastic file for more info.
</P>
<P>There is also a USER directory which contains subdirectories of
the ELASTIC_T/in.elastic file for more info.</p>
<p>There is also a USER directory which contains subdirectories of
user-provided examples for user packages. See the README files in
those directories for more info. See the
<A HREF = "Section_start.html">Section_start.html</A> file for more info about user
packages.
</P>
</HTML>
<a class="reference internal" href="Section_start.html"><em>Section_start.html</em></a> file for more info about user
packages.</p>
</div>
</div>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="Section_perf.html" class="btn btn-neutral float-right" title="8. Performance &amp; scalability" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="Section_howto.html" class="btn btn-neutral" title="6. How-to discussions" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</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>

692
doc/fix_gcmc.html
View File

@ -1,369 +1,505 @@
<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>
<!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>fix gcmc command &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"/>
<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 &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="Manual.html">LAMMPS</a>
</nav>
<HR>
<H3>fix gcmc command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID gcmc N X M type seed T mu displace keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>gcmc = style name of this fix command
<LI>N = invoke this fix every N steps
<LI>X = average number of GCMC exchanges to attempt every N steps
<LI>M = average number of MC moves to attempt every N steps
<LI>type = atom type for inserted atoms (must be 0 if mol keyword used)
<LI>seed = random # seed (positive integer)
<LI>T = temperature of the ideal gas reservoir (temperature units)
<LI>mu = chemical potential of the ideal gas reservoir (energy units)
<LI>translate = maximum Monte Carlo translation distance (length units)
<LI>zero or more keyword/value pairs may be appended to args
<PRE>keyword = <I>mol</I>, <I>region</I>, <I>maxangle</I>, <I>pressure</I>, <I>fugacity_coeff</I>, <I>full_energy</I>, <I>charge</I>, <I>group</I>, <I>grouptype</I>, <I>intra_energy</I>, or <I>tfac_insert</I>
<I>mol</I> value = template-ID
template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
<I>shake</I> value = fix-ID
fix-ID = ID of <A HREF = "fix_shake.html">fix shake</A> command
<I>region</I> value = region-ID
region-ID = ID of region where MC moves are allowed
<I>maxangle</I> value = maximum molecular rotation angle (degrees)
<I>pressure</I> value = pressure of the gas reservoir (pressure units)
<I>fugacity_coeff</I> value = fugacity coefficient of the gas reservoir (unitless)
<I>full_energy</I> = compute the entire system energy when performing MC moves
<I>charge</I> value = charge of inserted atoms (charge units)
<I>group</I> value = group-ID
<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> &raquo;</li>
<li>fix gcmc 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="fix-gcmc-command">
<span id="index-0"></span><h1>fix gcmc command<a class="headerlink" href="#fix-gcmc-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>fix ID group-ID gcmc N X M type seed T mu displace keyword values ...
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
<li>gcmc = style name of this fix command</li>
<li>N = invoke this fix every N steps</li>
<li>X = average number of GCMC exchanges to attempt every N steps</li>
<li>M = average number of MC moves to attempt every N steps</li>
<li>type = atom type for inserted atoms (must be 0 if mol keyword used)</li>
<li>seed = random # seed (positive integer)</li>
<li>T = temperature of the ideal gas reservoir (temperature units)</li>
<li>mu = chemical potential of the ideal gas reservoir (energy units)</li>
<li>translate = maximum Monte Carlo translation distance (length units)</li>
<li>zero or more keyword/value pairs may be appended to args</li>
</ul>
<pre class="literal-block">
keyword = <em>mol</em>, <em>region</em>, <em>maxangle</em>, <em>pressure</em>, <em>fugacity_coeff</em>, <em>full_energy</em>, <em>charge</em>, <em>group</em>, <em>grouptype</em>, <em>intra_energy</em>, or <em>tfac_insert</em>
<em>mol</em> value = template-ID
template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><em>molecule</em></a> command
<em>shake</em> value = fix-ID
fix-ID = ID of <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command
<em>region</em> value = region-ID
region-ID = ID of region where MC moves are allowed
<em>maxangle</em> value = maximum molecular rotation angle (degrees)
<em>pressure</em> value = pressure of the gas reservoir (pressure units)
<em>fugacity_coeff</em> value = fugacity coefficient of the gas reservoir (unitless)
<em>full_energy</em> = compute the entire system energy when performing MC moves
<em>charge</em> value = charge of inserted atoms (charge units)
<em>group</em> value = group-ID
group-ID = group-ID for inserted atoms (string)
<I>grouptype</I> values = type group-ID
<em>grouptype</em> values = type group-ID
type = atom type (int)
group-ID = group-ID for inserted atoms (string)
<I>intra_energy</I> value = intramolecular energy (energy units)
<I>tfac_insert</I> value = scale up/down temperature of inserted atoms (unitless)
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
<em>intra_energy</em> value = intramolecular energy (energy units)
<em>tfac_insert</em> value = scale up/down temperature of inserted atoms (unitless)
</pre>
</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>fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy
fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
</PRE>
<P><B>Description:</B>
</P>
<P>This fix performs grand canonical Monte Carlo (GCMC) exchanges of
fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>This fix performs grand canonical Monte Carlo (GCMC) exchanges of
atoms or molecules of the given type with an imaginary ideal gas reservoir at
the specified T and chemical potential (mu) as discussed in
<A HREF = "#Frenkel">(Frenkel)</A>. If used with the <A HREF = "fix_nh.html">fix nvt</A> command,
<a class="reference internal" href="#frenkel"><span>(Frenkel)</span></a>. If used with the <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a> command,
simulations in the grand canonical ensemble (muVT, constant chemical
potential, constant volume, and constant temperature) can be
performed. Specific uses include computing isotherms in microporous
materials, or computing vapor-liquid coexistence curves.
</P>
<P>Every N timesteps the fix attempts a number of GCMC exchanges (insertions
materials, or computing vapor-liquid coexistence curves.</p>
<p>Every N timesteps the fix attempts a number of GCMC exchanges (insertions
or deletions) of gas atoms or molecules of
the given type between the simulation cell and the imaginary
reservoir. It also attempts a number of Monte Carlo
moves (translations and molecule rotations) of gas of the given type
within the simulation cell or region. The average number of
within the simulation cell or region. The average number of
attempted GCMC exchanges is X. The average number of attempted MC moves is M.
M should typically be chosen to be
approximately equal to the expected number of gas atoms or molecules
of the given type within the simulation cell or region,
of the given type within the simulation cell or region,
which will result in roughly one
MC translation per atom or molecule per MC cycle.
</P>
<P>For MC moves of molecular gasses, rotations and translations are each
MC translation per atom or molecule per MC cycle.</p>
<p>For MC moves of molecular gasses, rotations and translations are each
attempted with 50% probability. For MC moves of atomic gasses,
translations are attempted 100% of the time. For MC exchanges of
either molecular or atomic gasses, deletions and insertions are each
attempted with 50% probability.
</P>
<P>All inserted particles are always assigned to two groups: the default group
"all" and the group specified in the fix gcmc command (which can also
be "all"). In addition, particles are also added to any groups specified
by the <I>group</I> and <I>grouptype</I> keywords.
attempted with 50% probability.</p>
<p>All inserted particles are always assigned to two groups: the default group
&#8220;all&#8221; and the group specified in the fix gcmc command (which can also
be &#8220;all&#8221;). In addition, particles are also added to any groups specified
by the <em>group</em> and <em>grouptype</em> keywords.
If inserted particles are individual atoms, they are
assigned the atom type given by the type argument. If they are molecules,
the type argument has no effect and must be set to zero. Instead,
the type of each atom in the inserted molecule is specified
in the file read by the <A HREF = "molecule.html">molecule</A> command.
</P>
<P>This fix cannot be used to perform MC insertions of gas atoms or
assigned the atom type given by the type argument. If they are molecules,
the type argument has no effect and must be set to zero. Instead,
the type of each atom in the inserted molecule is specified
in the file read by the <a class="reference internal" href="molecule.html"><em>molecule</em></a> command.</p>
<p>This fix cannot be used to perform MC insertions of gas atoms or
molecules other than the exchanged type, but MC deletions,
translations, and rotations can be performed on any atom/molecule in
the fix group. All atoms in the simulation cell can be moved using
regular time integration translations, e.g. via
<A HREF = "fix_nvt.html">fix_nvt</A>, resulting in a hybrid GCMC+MD simulation. A
<code class="xref doc docutils literal"><span class="pre">fix_nvt</span></code>, resulting in a hybrid GCMC+MD simulation. A
smaller-than-usual timestep size may be needed when running such a
hybrid simulation, especially if the inserted molecules are not well
equilibrated.
</P>
<P>This command may optionally use the <I>region</I> keyword to define an
exchange and move volume. The specified region must have been
previously defined with a <A HREF = "region.html">region</A> command. It must be
defined with side = <I>in</I>. Insertion attempts occur only within the
specified region. For non-rectangular regions, random trial
equilibrated.</p>
<p>This command may optionally use the <em>region</em> keyword to define an
exchange and move volume. The specified region must have been
previously defined with a <a class="reference internal" href="region.html"><em>region</em></a> command. It must be
defined with side = <em>in</em>. Insertion attempts occur only within the
specified region. For non-rectangular regions, random trial
points are generated within the rectangular bounding box until a point is found
that lies inside the region. If no valid point is generated after 1000 trials,
no insertion is performed, but it is counted as an attempted insertion.
Move and deletion attempt candidates are selected
Move and deletion attempt candidates are selected
from gas atoms or molecules within the region. If there are no candidates,
no move or deletion is performed, but it is counted as an attempt move
or deletion. If an attempted move places the atom or molecule center-of-mass outside
the specified region, a new attempted move is generated. This process is repeated
until the atom or molecule center-of-mass is inside the specified region.
</P>
<P>If used with <A HREF = "fix_nvt.html">fix_nvt</A>, the temperature of the imaginary
or deletion. If an attempted move places the atom or molecule center-of-mass outside
the specified region, a new attempted move is generated. This process is repeated
until the atom or molecule center-of-mass is inside the specified region.</p>
<p>If used with <code class="xref doc docutils literal"><span class="pre">fix_nvt</span></code>, the temperature of the imaginary
reservoir, T, should be set to be equivalent to the target temperature
used in <A HREF = "fix_nvt.html">fix_nvt</A>. Otherwise, the imaginary reservoir
used in <code class="xref doc docutils literal"><span class="pre">fix_nvt</span></code>. Otherwise, the imaginary reservoir
will not be in thermal equilibrium with the simulation cell. Also,
it is important that the temperature used by fix nvt be dynamic,
which can be achieved as follows:
</P>
<PRE>compute mdtemp mdatoms temp
which can be achieved as follows:</p>
<div class="highlight-python"><div class="highlight"><pre>compute mdtemp mdatoms temp
compute_modify mdtemp dynamic yes
fix mdnvt mdatoms nvt temp 300.0 300.0 10.0
fix_modify mdnvt temp mdtemp
</PRE>
<P>Note that neighbor lists are re-built every timestep that this fix is
fix_modify mdnvt temp mdtemp
</pre></div>
</div>
<p>Note that neighbor lists are re-built every timestep that this fix is
invoked, so you should not set N to be too small. However, periodic
rebuilds are necessary in order to avoid dangerous rebuilds and missed
interactions. Specifically, avoid performing so many MC translations
per timestep that atoms can move beyond the neighbor list skin
distance. See the <A HREF = "neighbor.html">neighbor</A> command for details.
</P>
<P>When an atom or molecule is to be inserted, its
distance. See the <a class="reference internal" href="neighbor.html"><em>neighbor</em></a> command for details.</p>
<p>When an atom or molecule is to be inserted, its
coordinates are chosen at a random position within the current
simulation cell or region, and new atom velocities are randomly chosen from
the specified temperature distribution given by T. The effective
temperature for new atom velocities can be increased or decreased
using the optional keyword <I>tfac_insert</I> (see below). Relative
using the optional keyword <em>tfac_insert</em> (see below). Relative
coordinates for atoms in a molecule are taken from the template
molecule provided by the user. The center of mass of the molecule
is placed at the insertion point. The orientation of the molecule
is chosen at random by rotating about this point.
</P>
<P>Individual atoms are inserted, unless the <I>mol</I> keyword is used. It
specifies a <I>template-ID</I> previously defined using the
<A HREF = "molecule.html">molecule</A> command, which reads a file that defines the
is chosen at random by rotating about this point.</p>
<p>Individual atoms are inserted, unless the <em>mol</em> keyword is used. It
specifies a <em>template-ID</em> previously defined using the
<a class="reference internal" href="molecule.html"><em>molecule</em></a> command, which reads a file that defines the
molecule. The coordinates, atom types, charges, etc, as well as any
bond/angle/etc and special neighbor information for the molecule can
be specified in the molecule file. See the <A HREF = "molecule.html">molecule</A>
be specified in the molecule file. See the <a class="reference internal" href="molecule.html"><em>molecule</em></a>
command for details. The only settings required to be in this file
are the coordinates and types of atoms in the molecule.
</P>
<P>When not using the <I>mol</I> keyword, you should ensure you do not delete
are the coordinates and types of atoms in the molecule.</p>
<p>When not using the <em>mol</em> keyword, you should ensure you do not delete
atoms that are bonded to other atoms, or LAMMPS will
soon generate an error when it tries to find bonded neighbors. LAMMPS will
warn you if any of the atoms eligible for deletion have a non-zero
molecule ID, but does not check for this at the time of deletion.
</P>
<P>If you wish to insert molecules via the <I>mol</I> keyword, that will have
their bonds or angles constrained via SHAKE, use the <I>shake</I> keyword,
specifying as its value the ID of a separate <A HREF = "fix_shake.html">fix
shake</A> command which also appears in your input script.
</P>
<P>Optionally, users may specify the maximum rotation angle for
molecular rotations using the <I>maxangle</I> keyword and specifying
molecule ID, but does not check for this at the time of deletion.</p>
<p>If you wish to insert molecules via the <em>mol</em> keyword, that will have
their bonds or angles constrained via SHAKE, use the <em>shake</em> keyword,
specifying as its value the ID of a separate <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command which also appears in your input script.</p>
<p>Optionally, users may specify the maximum rotation angle for
molecular rotations using the <em>maxangle</em> keyword and specifying
the angle in degrees. Rotations are performed by generating a random
point on the unit sphere and a random rotation angle on the
range [0,maxangle). The molecule is then rotated by that angle about an
axis passing through the molecule center of mass. The axis is parallel
to the unit vector defined by the point on the unit sphere.
axis passing through the molecule center of mass. The axis is parallel
to the unit vector defined by the point on the unit sphere.
The same procedure is used for randomly rotating molecules when they
are inserted, except that the maximum angle is 360 degrees.
</P>
<P>Note that fix GCMC does not use configurational bias
MC or any other kind of sampling of intramolecular degrees of freedom.
Inserted molecules can have different orientations, but they will all
have the same intramolecular configuration,
which was specified in the molecule command input.
</P>
<P>For atomic gasses, inserted atoms have the specified atom type, but
deleted atoms are any atoms that have been inserted or that belong
to the user-specified fix group. For molecular gasses, exchanged
molecules use the same atom types as in the template molecule
are inserted, except that the maximum angle is 360 degrees.</p>
<p>Note that fix GCMC does not use configurational bias
MC or any other kind of sampling of intramolecular degrees of freedom.
Inserted molecules can have different orientations, but they will all
have the same intramolecular configuration,
which was specified in the molecule command input.</p>
<p>For atomic gasses, inserted atoms have the specified atom type, but
deleted atoms are any atoms that have been inserted or that belong
to the user-specified fix group. For molecular gasses, exchanged
molecules use the same atom types as in the template molecule
supplied by the user. In both cases, exchanged
atoms/molecules are assigned to two groups: the default group "all"
and the group specified in the fix gcmc command (which can also be
"all").
</P>
<P>The gas reservoir pressure can be specified using the <I>pressure</I>
keyword, in which case the user-specified chemical potential is
ignored. For non-ideal gas reservoirs, the user may also specify the
fugacity coefficient using the <I>fugacity_coeff</I> keyword.
</P>
<P>The <I>full_energy</I> option means that fix GCMC will compute the total
atoms/molecules are assigned to two groups: the default group &#8220;all&#8221;
and the group specified in the fix gcmc command (which can also be
&#8220;all&#8221;).</p>
<p>The gas reservoir pressure can be specified using the <em>pressure</em>
keyword, in which case the user-specified chemical potential is
ignored. For non-ideal gas reservoirs, the user may also specify the
fugacity coefficient using the <em>fugacity_coeff</em> keyword.</p>
<p>The <em>full_energy</em> option means that fix GCMC will compute the total
potential energy of the entire simulated system. The total system
energy before and after the proposed GCMC move is then used in the
Metropolis criterion to determine whether or not to accept the
Metropolis criterion to determine whether or not to accept the
proposed GCMC move. By default, this option is off, in which case
only partial energies are computed to determine the difference in
energy that would be caused by the proposed GCMC move.
</P>
<P>The <I>full_energy</I> option is needed for systems with complicated
potential energy calculations, including the following:
</P>
<UL><LI> long-range electrostatics (kspace)
<LI> many-body pair styles
<LI> hybrid pair styles
<LI> eam pair styles
<LI> triclinic systems
<LI> need to include potential energy contributions from other fixes
</UL>
<P>In these cases, LAMMPS will automatically apply the <I>full_energy</I>
keyword and issue a warning message.
</P>
<P>When the <I>mol</I> keyword is used, the <I>full_energy</I> option also includes
the intramolecular energy of inserted and deleted molecules. If this
is not desired, the <I>intra_energy</I> keyword can be used to define an
energy that would be caused by the proposed GCMC move.</p>
<p>The <em>full_energy</em> option is needed for systems with complicated
potential energy calculations, including the following:</p>
<ul class="simple">
<li>long-range electrostatics (kspace)</li>
<li>many-body pair styles</li>
<li>hybrid pair styles</li>
<li>eam pair styles</li>
<li>triclinic systems</li>
<li>need to include potential energy contributions from other fixes</li>
</ul>
<p>In these cases, LAMMPS will automatically apply the <em>full_energy</em>
keyword and issue a warning message.</p>
<p>When the <em>mol</em> keyword is used, the <em>full_energy</em> option also includes
the intramolecular energy of inserted and deleted molecules. If this
is not desired, the <em>intra_energy</em> keyword can be used to define an
amount of energy that is subtracted from the final energy when a molecule
is inserted, and added to the initial energy when a molecule is
deleted. For molecules that have a non-zero intramolecular energy, this
will ensure roughly the same behavior whether or not the <I>full_energy</I>
option is used.
</P>
<P>Inserted atoms and molecules are assigned random velocities based on the
will ensure roughly the same behavior whether or not the <em>full_energy</em>
option is used.</p>
<p>Inserted atoms and molecules are assigned random velocities based on the
specified temperature T. Because the relative velocity of
all atoms in the molecule is zero, this may result in inserted molecules
that are systematically too cold. In addition, the intramolecular potential
energy of the inserted molecule may cause the kinetic energy
of the molecule to quickly increase or decrease after insertion.
The <I>tfac_insert</I> keyword allows the user to counteract these effects
by changing the temperature used to assign velocities to
of the molecule to quickly increase or decrease after insertion.
The <em>tfac_insert</em> keyword allows the user to counteract these effects
by changing the temperature used to assign velocities to
inserted atoms and molecules by a constant factor. For a
particular application, some experimentation may be required
to find a value of <I>tfac_insert</I> that results in inserted molecules that
equilibrate quickly to the correct temperature.
</P>
<P>Some fixes have an associated potential energy. Examples of such fixes
include: <A HREF = "fix_efield.html">efield</A>, <A HREF = "fix_gravity.html">gravity</A>,
<A HREF = "fix_addforce.html">addforce</A>, <A HREF = "fix_langevin.html">langevin</A>,
<A HREF = "fix_restrain.html">restrain</A>, <A HREF = "fix_temp_berendsen.html">temp/berendsen</A>,
<A HREF = "fix_temp_rescale.html">temp/rescale</A>, and <A HREF = "fix_wall.html">wall fixes</A>.
For that energy to be included in the total potential energy of the
to find a value of <em>tfac_insert</em> that results in inserted molecules that
equilibrate quickly to the correct temperature.</p>
<p>Some fixes have an associated potential energy. Examples of such fixes
include: <a class="reference internal" href="fix_efield.html"><em>efield</em></a>, <a class="reference internal" href="fix_gravity.html"><em>gravity</em></a>,
<a class="reference internal" href="fix_addforce.html"><em>addforce</em></a>, <a class="reference internal" href="fix_langevin.html"><em>langevin</em></a>,
<a class="reference internal" href="fix_restrain.html"><em>restrain</em></a>, <a class="reference internal" href="fix_temp_berendsen.html"><em>temp/berendsen</em></a>,
<a class="reference internal" href="fix_temp_rescale.html"><em>temp/rescale</em></a>, and <a class="reference internal" href="fix_wall.html"><em>wall fixes</em></a>.
For that energy to be included in the total potential energy of the
system (the quantity used when performing GCMC moves),
you MUST enable the <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for
that fix. The doc pages for individual <A HREF = "fix.html">fix</A> commands
specify if this should be done.
</P>
<P>Use the <I>charge</I> option to insert atoms with a user-specified point
charge. Note that doing so will cause the system to become non-neutral.
LAMMPS issues a warning when using long-range electrostatics (kspace)
with non-neutral systems. See the
<A HREF = "compute_group_group.html">compute_group_group</A> documentation for more
details about simulating non-neutral systems with kspace on.
</P>
<P>Use of this fix typically will cause the number of atoms to fluctuate,
you MUST enable the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>energy</em> option for
that fix. The doc pages for individual <a class="reference internal" href="fix.html"><em>fix</em></a> commands
specify if this should be done.</p>
<p>Use the <em>charge</em> option to insert atoms with a user-specified point
charge. Note that doing so will cause the system to become non-neutral.
LAMMPS issues a warning when using long-range electrostatics (kspace)
with non-neutral systems. See the
<a class="reference internal" href="compute_group_group.html"><em>compute_group_group</em></a> documentation for more
details about simulating non-neutral systems with kspace on.</p>
<p>Use of this fix typically will cause the number of atoms to fluctuate,
therefore, you will want to use the
<A HREF = "compute_modify.html">compute_modify</A> command to insure that the
<a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a> command to insure that the
current number of atoms is used as a normalizing factor each time
temperature is computed. Here is the necessary command:
</P>
<PRE>compute_modify thermo_temp dynamic yes
</PRE>
<P>If LJ units are used, note that a value of 0.18292026 is used by this
fix as the reduced value for Planck's constant. This value was
temperature is computed. Here is the necessary command:</p>
<div class="highlight-python"><div class="highlight"><pre>compute_modify thermo_temp dynamic yes
</pre></div>
</div>
<p>If LJ units are used, note that a value of 0.18292026 is used by this
fix as the reduced value for Planck&#8217;s constant. This value was
derived from LJ parameters for argon, where h* = h/sqrt(sigma^2 *
epsilon * mass), sigma = 3.429 angstroms, epsilon/k = 121.85 K, and
mass = 39.948 amu.
</P>
<P>The <I>group</I> keyword assigns all inserted atoms to the <A HREF = "group.html">group</A>
of the group-ID value. The <I>grouptype</I> keyword assigns all
inserted atoms of the specified type to the <A HREF = "group.html">group</A>
of the group-ID value.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of the fix to <A HREF = "restart.html">binary restart
files</A>. This includes information about the random
mass = 39.948 amu.</p>
<p>The <em>group</em> keyword assigns all inserted atoms to the <a class="reference internal" href="group.html"><em>group</em></a>
of the group-ID value. The <em>grouptype</em> keyword assigns all
inserted atoms of the specified type to the <a class="reference internal" href="group.html"><em>group</em></a>
of the group-ID value.</p>
</div>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline"></a></h2>
<p>This fix writes the state of the fix to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. This includes information about the random
number generator seed, the next timestep for MC exchanges, etc. See
the <A HREF = "read_restart.html">read_restart</A> command for info on how to
the <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command for info on how to
re-specify a fix in an input script that reads a restart file, so that
the operation of the fix continues in an uninterrupted fashion.
</P>
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
fix.
</P>
<P>This fix computes a global vector of length 8, which can be accessed
by various <A HREF = "Section_howto.html#howto_15">output commands</A>. The vector
values are the following global cumulative quantities:
</P>
<UL><LI>1 = translation attempts
<LI>2 = translation successes
<LI>3 = insertion attempts
<LI>4 = insertion successes
<LI>5 = deletion attempts
<LI>6 = deletion successes
<LI>7 = rotation attempts
<LI>8 = rotation successes
</UL>
<P>The vector values calculated by this fix are "extensive".
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the MC package. It is only enabled if LAMMPS was
built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>Do not set "neigh_modify once yes" or else this fix will never be
called. Reneighboring is required.
</P>
<P>Can be run in parallel, but aspects of the GCMC part will not scale
well in parallel. Only usable for 3D simulations.
</P>
<P>Note that very lengthy simulations involving insertions/deletions of
the operation of the fix continues in an uninterrupted fashion.</p>
<p>None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options are relevant to this
fix.</p>
<p>This fix computes a global vector of length 8, which can be accessed
by various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The vector
values are the following global cumulative quantities:</p>
<ul class="simple">
<li>1 = translation attempts</li>
<li>2 = translation successes</li>
<li>3 = insertion attempts</li>
<li>4 = insertion successes</li>
<li>5 = deletion attempts</li>
<li>6 = deletion successes</li>
<li>7 = rotation attempts</li>
<li>8 = rotation successes</li>
</ul>
<p>The vector values calculated by this fix are &#8220;extensive&#8221;.</p>
<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
the <a class="reference internal" href="run.html"><em>run</em></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This fix is part of the MC package. It is only enabled if LAMMPS was
built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>Do not set &#8220;neigh_modify once yes&#8221; or else this fix will never be
called. Reneighboring is required.</p>
<p>Can be run in parallel, but aspects of the GCMC part will not scale
well in parallel. Only usable for 3D simulations.</p>
<p>Note that very lengthy simulations involving insertions/deletions of
billions of gas molecules may run out of atom or molecule IDs and
trigger an error, so it is better to run multiple shorter-duration
trigger an error, so it is better to run multiple shorter-duration
simulations. Likewise, very large molecules have not been tested
and may turn out to be problematic.
</P>
<P>Use of multiple fix gcmc commands in the same input script can be
problematic if using a template molecule. The issue is that the
and may turn out to be problematic.</p>
<p>Use of multiple fix gcmc commands in the same input script can be
problematic if using a template molecule. The issue is that the
user-referenced template molecule in the second fix gcmc command
may no longer exist since it might have been deleted by the first
fix gcmc command. An existing template molecule will need to be
referenced by the user for each subsequent fix gcmc command.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_atom_swap.html">fix atom/swap</A>,
<A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "neighbor.html">neighbor</A>,
<A HREF = "fix_deposit.html">fix deposit</A>, <A HREF = "fix_evaporate.html">fix evaporate</A>,
<A HREF = "delete_atoms.html">delete_atoms</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are mol = no, maxangle = 10, full_energy = no,
referenced by the user for each subsequent fix gcmc command.</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="fix_atom_swap.html"><em>fix atom/swap</em></a>,
<code class="xref doc docutils literal"><span class="pre">fix</span> <span class="pre">nvt</span></code>, <a class="reference internal" href="neighbor.html"><em>neighbor</em></a>,
<a class="reference internal" href="fix_deposit.html"><em>fix deposit</em></a>, <a class="reference internal" href="fix_evaporate.html"><em>fix evaporate</em></a>,
<a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The option defaults are mol = no, maxangle = 10, full_energy = no,
except for the situations where full_energy is required, as
listed above.
</P>
<HR>
listed above.</p>
<hr class="docutils" />
<p id="frenkel"><strong>(Frenkel)</strong> Frenkel and Smit, Understanding Molecular Simulation,
Academic Press, London, 2002.</p>
</div>
</div>
<A NAME = "Frenkel"></A>
<P><B>(Frenkel)</B> Frenkel and Smit, Understanding Molecular Simulation,
Academic Press, London, 2002.
</P>
</HTML>
</div>
</div>
<footer>
<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>

498
doc/pair_reax.html
View File

@ -1,218 +1,384 @@
<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>
<!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>pair_style reax command &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"/>
<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 &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="Manual.html">LAMMPS</a>
</nav>
<HR>
<H3>pair_style reax command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style reax hbcut hbnewflag tripflag precision
</PRE>
<UL><LI>hbcut = hydrogen-bond cutoff (optional) (distance units)
<LI>hbnewflag = use old or new hbond function style (0 or 1) (optional)
<LI>tripflag = apply stabilization to all triple bonds (0 or 1) (optional)
<LI>precision = precision for charge equilibration (optional)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style reax
<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> &raquo;</li>
<li>pair_style reax 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-reax-command">
<span id="index-0"></span><h1>pair_style reax command<a class="headerlink" href="#pair-style-reax-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 reax hbcut hbnewflag tripflag precision
</pre></div>
</div>
<ul class="simple">
<li>hbcut = hydrogen-bond cutoff (optional) (distance units)</li>
<li>hbnewflag = use old or new hbond function style (0 or 1) (optional)</li>
<li>tripflag = apply stabilization to all triple bonds (0 or 1) (optional)</li>
<li>precision = precision for charge equilibration (optional)</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 reax
pair_style reax 10.0 0 1 1.0e-5
pair_coeff * * ffield.reax 3 1 2 2
pair_coeff * * ffield.reax 3 NULL NULL 3
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>reax</I> computes the ReaxFF potential of van Duin, Goddard and
pair_coeff * * ffield.reax 3 NULL NULL 3
</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>reax</em> computes the ReaxFF potential of van Duin, Goddard and
co-workers. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
energy. There is more than one version of ReaxFF. The version
implemented in LAMMPS uses the functional forms documented in the
supplemental information of the following paper:
<A HREF = "#Chenoweth_2008">(Chenoweth)</A>. The version integrated into LAMMPS matches
the most up-to-date version of ReaxFF as of summer 2010.
</P>
<P>WARNING: pair style reax is now deprecated and will soon be retired. Users
should switch to <A HREF = "pair_reax_c.html">pair_style reax/c</A>. The <I>reax</I> style
differs from the <I>reax/c</I> style in the lo-level implementation details.
The <I>reax</I> style is a
Fortran library, linked to LAMMPS. The <I>reax/c</I> style was initially
<a class="reference internal" href="#chenoweth-2008"><span>(Chenoweth)</span></a>. The version integrated into LAMMPS matches
the most up-to-date version of ReaxFF as of summer 2010.</p>
<p>WARNING: pair style reax is now deprecated and will soon be retired. Users
should switch to <a class="reference internal" href="pair_reax_c.html"><em>pair_style reax/c</em></a>. The <em>reax</em> style
differs from the <em>reax/c</em> style in the lo-level implementation details.
The <em>reax</em> style is a
Fortran library, linked to LAMMPS. The <em>reax/c</em> style was initially
implemented as stand-alone C code and is now integrated into LAMMPS as
a package.
</P>
<P>LAMMPS requires that a file called ffield.reax be provided, containing
a package.</p>
<p>LAMMPS requires that a file called ffield.reax be provided, containing
the ReaxFF parameters for each atom type, bond type, etc. The format
is identical to the ffield file used by van Duin and co-workers. The
filename is required as an argument in the pair_coeff command. Any
value other than "ffield.reax" will be rejected (see below).
</P>
<P>LAMMPS provides several different versions of ffield.reax in its
value other than &#8220;ffield.reax&#8221; will be rejected (see below).</p>
<p>LAMMPS provides several different versions of ffield.reax in its
potentials dir, each called potentials/ffield.reax.label. These are
documented in potentials/README.reax. The default ffield.reax
contains parameterizations for the following elements: C, H, O, N, S.
</P>
<P>IMPORTANT NOTE: We do not distribute a wide variety of ReaxFF force
field files with LAMMPS. Adri van Duin's group at PSU is the central
contains parameterizations for the following elements: C, H, O, N, S.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">We do not distribute a wide variety of ReaxFF force
field files with LAMMPS. Adri van Duin&#8217;s group at PSU is the central
repository for this kind of data as they are continuously deriving and
updating parameterizations for different classes of materials. You
can visit their WWW site at
<A HREF = "http://www.engr.psu.edu/adri">http://www.engr.psu.edu/adri</A>, register
as a "new user", and then submit a request to their group describing
<a class="reference external" href="http://www.engr.psu.edu/adri">http://www.engr.psu.edu/adri</a>, register
as a &#8220;new user&#8221;, and then submit a request to their group describing
material(s) you are interested in modeling with ReaxFF. They can tell
you what is currently available or what it would take to create a
suitable ReaxFF parameterization.
</P>
<P>The format of these files is identical to that used originally by van
Duin. We have tested the accuracy of <I>pair_style reax</I> potential
suitable ReaxFF parameterization.</p>
</div>
<p>The format of these files is identical to that used originally by van
Duin. We have tested the accuracy of <em>pair_style reax</em> potential
against the original ReaxFF code for the systems mentioned above. You
can use other ffield files for specific chemical systems that may be
available elsewhere (but note that their accuracy may not have been
tested).
</P>
<P>The <I>hbcut</I>, <I>hbnewflag</I>, <I>tripflag</I>, and <I>precision</I> settings are
tested).</p>
<p>The <em>hbcut</em>, <em>hbnewflag</em>, <em>tripflag</em>, and <em>precision</em> settings are
optional arguments. If none are provided, default settings are used:
<I>hbcut</I> = 6 (which is Angstroms in real units), <I>hbnewflag</I> = 1 (use
new hbond function style), <I>tripflag</I> = 1 (apply stabilization to all
triple bonds), and <I>precision</I> = 1.0e-6 (one part in 10^6). If you
<em>hbcut</em> = 6 (which is Angstroms in real units), <em>hbnewflag</em> = 1 (use
new hbond function style), <em>tripflag</em> = 1 (apply stabilization to all
triple bonds), and <em>precision</em> = 1.0e-6 (one part in 10^6). If you
wish to override any of these defaults, then all of the settings must
be specified.
</P>
<P>Two examples using <I>pair_style reax</I> are provided in the examples/reax
sub-directory, along with corresponding examples for
<A HREF = "pair_reax_c.html">pair_style reax/c</A>.
</P>
<P>Use of this pair style requires that a charge be defined for every
atom since the <I>reax</I> pair style performs a charge equilibration (QEq)
calculation. See the <A HREF = "atom_style.html">atom_style</A> and
<A HREF = "read_data.html">read_data</A> commands for details on how to specify
charges.
</P>
<P>The thermo variable <I>evdwl</I> stores the sum of all the ReaxFF potential
be specified.</p>
<p>Two examples using <em>pair_style reax</em> are provided in the examples/reax
sub-directory, along with corresponding examples for
<a class="reference internal" href="pair_reax_c.html"><em>pair_style reax/c</em></a>.</p>
<p>Use of this pair style requires that a charge be defined for every
atom since the <em>reax</em> pair style performs a charge equilibration (QEq)
calculation. See the <a class="reference internal" href="atom_style.html"><em>atom_style</em></a> and
<a class="reference internal" href="read_data.html"><em>read_data</em></a> commands for details on how to specify
charges.</p>
<p>The thermo variable <em>evdwl</em> stores the sum of all the ReaxFF potential
energy contributions, with the exception of the Coulombic and charge
equilibration contributions which are stored in the thermo variable
<I>ecoul</I>. The output of these quantities is controlled by the
<A HREF = "thermo.html">thermo</A> command.
</P>
<P>This pair style tallies a breakdown of the total ReaxFF potential
energy into sub-categories, which can be accessed via the <A HREF = "compute_pair.html">compute
pair</A> command as a vector of values of length 14.
<em>ecoul</em>. The output of these quantities is controlled by the
<a class="reference internal" href="thermo.html"><em>thermo</em></a> command.</p>
<p>This pair style tallies a breakdown of the total ReaxFF potential
energy into sub-categories, which can be accessed via the <a class="reference internal" href="compute_pair.html"><em>compute pair</em></a> command as a vector of values of length 14.
The 14 values correspond to the following sub-categories (the variable
names in italics match those used in the ReaxFF FORTRAN library):
</P>
<OL><LI><I>eb</I> = bond energy
<LI><I>ea</I> = atom energy
<LI><I>elp</I> = lone-pair energy
<LI><I>emol</I> = molecule energy (always 0.0)
<LI><I>ev</I> = valence angle energy
<LI><I>epen</I> = double-bond valence angle penalty
<LI><I>ecoa</I> = valence angle conjugation energy
<LI><I>ehb</I> = hydrogen bond energy
<LI><I>et</I> = torsion energy
<LI><I>eco</I> = conjugation energy
<LI><I>ew</I> = van der Waals energy
<LI><I>ep</I> = Coulomb energy
<LI><I>efi</I> = electric field energy (always 0.0)
<LI><I>eqeq</I> = charge equilibration energy
</OL>
<P>To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:
</P>
<PRE>compute reax all pair reax
variable eb equal c_reax[1]
variable ea equal c_reax[2]
names in italics match those used in the ReaxFF FORTRAN library):</p>
<ol class="arabic simple">
<li><em>eb</em> = bond energy</li>
<li><em>ea</em> = atom energy</li>
<li><em>elp</em> = lone-pair energy</li>
<li><em>emol</em> = molecule energy (always 0.0)</li>
<li><em>ev</em> = valence angle energy</li>
<li><em>epen</em> = double-bond valence angle penalty</li>
<li><em>ecoa</em> = valence angle conjugation energy</li>
<li><em>ehb</em> = hydrogen bond energy</li>
<li><em>et</em> = torsion energy</li>
<li><em>eco</em> = conjugation energy</li>
<li><em>ew</em> = van der Waals energy</li>
<li><em>ep</em> = Coulomb energy</li>
<li><em>efi</em> = electric field energy (always 0.0)</li>
<li><em>eqeq</em> = charge equilibration energy</li>
</ol>
<p>To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:</p>
<div class="highlight-python"><div class="highlight"><pre>compute reax all pair reax
variable eb equal c_reax[1]
variable ea equal c_reax[2]
...
variable eqeq equal c_reax[14]
thermo_style custom step temp epair v_eb v_ea ... v_eqeq
</PRE>
<P>Only a single pair_coeff command is used with the <I>reax</I> style which
variable eqeq equal c_reax[14]
thermo_style custom step temp epair v_eb v_ea ... v_eqeq
</pre></div>
</div>
<p>Only a single pair_coeff command is used with the <em>reax</em> style which
specifies a ReaxFF potential file with parameters for all needed
elements. These are mapped to LAMMPS atom types by specifying N
additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
</P>
<UL><LI>filename
<LI>N indices = mapping of ReaxFF elements to atom types
</UL>
<P>The specification of the filename and the mapping of LAMMPS atom types
where N is the number of LAMMPS atom types:</p>
<ul class="simple">
<li>filename</li>
<li>N indices = mapping of ReaxFF elements to atom types</li>
</ul>
<p>The specification of the filename and the mapping of LAMMPS atom types
recognized by the ReaxFF is done differently than for other LAMMPS
potentials, due to the non-portable difficulty of passing character
strings (e.g. filename, element names) between C++ and Fortran.
</P>
<P>The filename has to be "ffield.reax" and it has to exist in the
strings (e.g. filename, element names) between C++ and Fortran.</p>
<p>The filename has to be &#8220;ffield.reax&#8221; and it has to exist in the
directory you are running LAMMPS in. This means you cannot prepend a
path to the file in the potentials dir. Rather, you should copy that
file into the directory you are running from. If you wish to use
another ReaxFF potential file, then name it "ffield.reax" and put it
in the directory you run from.
</P>
<P>In the ReaxFF potential file, near the top, after the general
another ReaxFF potential file, then name it &#8220;ffield.reax&#8221; and put it
in the directory you run from.</p>
<p>In the ReaxFF potential file, near the top, after the general
parameters, is the atomic parameters section that contains element
names, each with a couple dozen numeric parameters. If there are M
elements specified in the <I>ffield</I> file, think of these as numbered 1
elements specified in the <em>ffield</em> file, think of these as numbered 1
to M. Each of the N indices you specify for the N atom types of LAMMPS
atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will
be mapped to whatever element you specify as the first index value,
etc. If a mapping value is specified as NULL, the mapping is not
performed. This can be used when a ReaxFF potential is used as part
of the <I>hybrid</I> pair style. The NULL values are placeholders for atom
types that will be used with other potentials.
</P>
<P>IMPORTANT NOTE: Currently the reax pair style cannot be used as part
of the <I>hybrid</I> pair style. Some additional changes still need to be
made to enable this.
</P>
<P>As an example, say your LAMMPS simulation has 4 atom types and the
elements are ordered as C, H, O, N in the <I>ffield</I> file. If you want
of the <em>hybrid</em> pair style. The NULL values are placeholders for atom
types that will be used with other potentials.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Currently the reax pair style cannot be used as part
of the <em>hybrid</em> pair style. Some additional changes still need to be
made to enable this.</p>
</div>
<p>As an example, say your LAMMPS simulation has 4 atom types and the
elements are ordered as C, H, O, N in the <em>ffield</em> file. If you want
the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
H, you would use the following pair_coeff command:
</P>
<PRE>pair_coeff * * ffield.reax 1 1 4 2
</PRE>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
mix, shift, table, and tail options.
</P>
<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
files</A>, since it is stored in potential files. Thus, you
H, you would use the following pair_coeff command:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * ffield.reax 1 1 4 2
</pre></div>
</div>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
mix, shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands 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>
<P><B>Restrictions:</B>
</P>
<P>The ReaxFF potential files provided with LAMMPS in the potentials
directory are parameterized for real <A HREF = "units.html">units</A>. You can use
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>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>The ReaxFF potential files provided with LAMMPS in the potentials
directory are parameterized for real <a class="reference internal" href="units.html"><em>units</em></a>. You can use
the ReaxFF potential with any LAMMPS units, but you would need to
create your own potential file with coefficients listed in the
appropriate units if your simulation doesn't use "real" units.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_reax_c.html">pair_style reax/c</A>,
<A HREF = "fix_reax_bonds.html">fix_reax_bonds</A>
</P>
<P><B>Default:</B>
</P>
<P>The keyword defaults are <I>hbcut</I> = 6, <I>hbnewflag</I> = 1, <I>tripflag</I> = 1,
<I>precision</I> = 1.0e-6.
</P>
<HR>
appropriate units if your simulation doesn&#8217;t use &#8220;real&#8221; units.</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_reax_c.html"><em>pair_style reax/c</em></a>,
<a class="reference internal" href="fix_reax_bonds.html"><em>fix_reax_bonds</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The keyword defaults are <em>hbcut</em> = 6, <em>hbnewflag</em> = 1, <em>tripflag</em> = 1,
<em>precision</em> = 1.0e-6.</p>
<hr class="docutils" />
<p id="chenoweth-2008"><strong>(Chenoweth_2008)</strong> Chenoweth, van Duin and Goddard,
Journal of Physical Chemistry A, 112, 1040-1053 (2008).</p>
</div>
</div>
<A NAME = "Chenoweth_2008"></A>
<P><B>(Chenoweth_2008)</B> Chenoweth, van Duin and Goddard,
Journal of Physical Chemistry A, 112, 1040-1053 (2008).
</P>
</HTML>
</div>
</div>
<footer>
<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>

2
doc/searchindex.js
View File

File diff suppressed because one or more lines are too long