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<HTML>
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<TITLE>LAMMPS-ICMS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="20 Nov 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS-ICMS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<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>
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<HR>
<H1></H1>
<CENTER><H3>LAMMPS-ICMS Documentation
</H3></CENTER>
<CENTER><H4>20 Nov 2015 version
</H4></CENTER>
<H4>Version info:
</H4>
<P>The LAMMPS "version" is the date when it was released, such as 1 May
<div class="wy-nav-content">
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<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-ICMS Documentation<a class="headerlink" href="#lammps-documentation" title="Permalink to this headline"></a></h1>
<div class="section" id="dec-2015-version">
<h2>7 Dec 2015 version<a class="headerlink" href="#dec-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
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
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
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
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
the first page of the manual (this page).
</P>
<P>LAMMPS-ICMS is an experimental variant of LAMMPS with additional
the first page of the manual (this page).</p>
<p>LAMMPS-ICMS is an experimental variant of LAMMPS with additional
features made available for testing before they will be submitted
for inclusion into the official LAMMPS tree. The source code is
based on the official LAMMPS svn repository mirror at the Institute
@ -50,443 +159,313 @@ LAMMPS-ICMS it can take longer until synchronization; and occasionally,
e.g. in case of the rewrite of the multi-threading support, the
development will be halted except for important bugfixes until
all features of LAMMPS-ICMS fully compatible with the upstream
version or replaced by alternate implementations.</P>
<UL><LI>If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of upstream LAMMPS, but may be
missing some new features in LAMMPS-ICMS.
version or replaced by alternate implementations.</p>
<LI>If you browse the HTML doc pages included in your tarball, they
<ul class="simple">
<li>If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of LAMMPS.</li>
<li>If you browse the HTML doc pages included in your tarball, they
describe the version you have, however, not all new features in
LAMMPS-ICMS are documented immediately.
<LI>The <A HREF = "Manual.pdf">PDF file</A> on the WWW site or in the tarball is updated
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
LAMMPS-ICMS are documented immediately.</li>
<li>The <a class="reference external" href="Manual.pdf">PDF file</a> on the WWW site or in the tarball is updated
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>There is also a <a class="reference external" href="Developer.pdf">Developer.pdf</a> file in the doc
directory, which describes the internal structure and algorithms of
LAMMPS.
</UL>
<P>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.
</P>
<P>LAMMPS is a classical molecular dynamics simulation code designed to
LAMMPS.</li>
</ul>
<p>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.</p>
<p>LAMMPS is a classical molecular dynamics simulation code designed to
run efficiently on parallel computers. It was developed at Sandia
National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL).
</P>
<P>The primary developers of LAMMPS are <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Aidan
under the terms of the GNU Public License (GPL).</p>
<p>The primary developers of LAMMPS are <a class="reference external" href="http://www.sandia.gov/~sjplimp">Steve Plimpton</a>, Aidan
Thompson, and Paul Crozier who can be contacted at
sjplimp,athomps,pscrozi at sandia.gov. The <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> at
http://lammps.sandia.gov has more information about the code and its
uses.
</P>
<HR>
<P>The LAMMPS documentation is organized into the following sections. If
sjplimp,athomps,pscrozi at sandia.gov. The <a class="reference external" 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
uses.</p>
<hr class="docutils" />
<p>The LAMMPS documentation is organized into the following sections. If
you find errors or omissions in this manual or have suggestions for
useful information to add, please send an email to the developers so
we can improve the LAMMPS documentation.
</P>
<P>Once you are familiar with LAMMPS, you may want to bookmark <A HREF = "Section_commands.html#comm">this
page</A> at Section_commands.html#comm since
it gives quick access to documentation for all LAMMPS commands.
</P>
<P><A HREF = "Manual.pdf">PDF file</A> of the entire manual, generated by
<A HREF = "http://freecode.com/projects/htmldoc">htmldoc</A>
</P>
<P><!-- RST
</P>
<P>.. toctree::
:maxdepth: 2
:numbered: // comment
</P>
<P> Section_intro
Section_start
Section_commands
Section_packages
Section_accelerate
Section_howto
Section_example
Section_perf
Section_tools
Section_modify
Section_python
Section_errors
Section_history
</P>
<P>Indices and tables
==================
</P>
<P>* :ref:`genindex` // comment
* :ref:`search` // comment
</P>
<P>END_RST -->
</P>
<OL><LI><!-- HTML_ONLY -->
<A HREF = "Section_intro.html">Introduction</A>
<UL> 1.1 <A HREF = "Section_intro.html#intro_1">What is LAMMPS</A>
<BR>
1.2 <A HREF = "Section_intro.html#intro_2">LAMMPS features</A>
<BR>
1.3 <A HREF = "Section_intro.html#intro_3">LAMMPS non-features</A>
<BR>
1.4 <A HREF = "Section_intro.html#intro_4">Open source distribution</A>
<BR>
1.5 <A HREF = "Section_intro.html#intro_5">Acknowledgments and citations</A>
<BR></UL>
<LI><A HREF = "Section_start.html">Getting started</A>
<UL> 2.1 <A HREF = "Section_start.html#start_1">What's in the LAMMPS distribution</A>
<BR>
2.2 <A HREF = "Section_start.html#start_2">Making LAMMPS</A>
<BR>
2.3 <A HREF = "Section_start.html#start_3">Making LAMMPS with optional packages</A>
<BR>
2.4 <A HREF = "Section_start.html#start_4">Building LAMMPS via the Make.py script</A>
<BR>
2.5 <A HREF = "Section_start.html#start_5">Building LAMMPS as a library</A>
<BR>
2.6 <A HREF = "Section_start.html#start_6">Running LAMMPS</A>
<BR>
2.7 <A HREF = "Section_start.html#start_7">Command-line options</A>
<BR>
2.8 <A HREF = "Section_start.html#start_8">Screen output</A>
<BR>
2.9 <A HREF = "Section_start.html#start_9">Tips for users of previous versions</A>
<BR></UL>
<LI><A HREF = "Section_commands.html">Commands</A>
<UL> 3.1 <A HREF = "Section_commands.html#cmd_1">LAMMPS input script</A>
<BR>
3.2 <A HREF = "Section_commands.html#cmd_2">Parsing rules</A>
<BR>
3.3 <A HREF = "Section_commands.html#cmd_3">Input script structure</A>
<BR>
3.4 <A HREF = "Section_commands.html#cmd_4">Commands listed by category</A>
<BR>
3.5 <A HREF = "Section_commands.html#cmd_5">Commands listed alphabetically</A>
<BR></UL>
<LI><A HREF = "Section_packages.html">Packages</A>
<UL> 4.1 <A HREF = "Section_packages.html#pkg_1">Standard packages</A>
<BR>
4.2 <A HREF = "Section_packages.html#pkg_2">User packages</A>
<BR></UL>
<LI><A HREF = "Section_accelerate.html">Accelerating LAMMPS performance</A>
<UL> 5.1 <A HREF = "Section_accelerate.html#acc_1">Measuring performance</A>
<BR>
5.2 <A HREF = "Section_accelerate.html#acc_2">Algorithms and code options to boost performace</A>
<BR>
5.3 <A HREF = "Section_accelerate.html#acc_3">Accelerator packages with optimized styles</A>
<BR>
<UL> 5.3.1 <A HREF = "accelerate_cuda.html">USER-CUDA package</A>
<BR>
5.3.2 <A HREF = "accelerate_gpu.html">GPU package</A>
<BR>
5.3.3 <A HREF = "accelerate_intel.html">USER-INTEL package</A>
<BR>
5.3.4 <A HREF = "accelerate_kokkos.html">KOKKOS package</A>
<BR>
5.3.5 <A HREF = "accelerate_omp.html">USER-OMP package</A>
<BR>
5.3.6 <A HREF = "accelerate_opt.html">OPT package</A>
<BR></UL>
5.4 <A HREF = "Section_accelerate.html#acc_4">Comparison of various accelerator packages</A>
<BR></UL>
<LI><A HREF = "Section_howto.html">How-to discussions</A>
<UL> 6.1 <A HREF = "Section_howto.html#howto_1">Restarting a simulation</A>
<BR>
6.2 <A HREF = "Section_howto.html#howto_2">2d simulations</A>
<BR>
6.3 <A HREF = "Section_howto.html#howto_3">CHARMM and AMBER force fields</A>
<BR>
6.4 <A HREF = "Section_howto.html#howto_4">Running multiple simulations from one input script</A>
<BR>
6.5 <A HREF = "Section_howto.html#howto_5">Multi-replica simulations</A>
<BR>
6.6 <A HREF = "Section_howto.html#howto_6">Granular models</A>
<BR>
6.7 <A HREF = "Section_howto.html#howto_7">TIP3P water model</A>
<BR>
6.8 <A HREF = "Section_howto.html#howto_8">TIP4P water model</A>
<BR>
6.9 <A HREF = "Section_howto.html#howto_9">SPC water model</A>
<BR>
6.10 <A HREF = "Section_howto.html#howto_10">Coupling LAMMPS to other codes</A>
<BR>
6.11 <A HREF = "Section_howto.html#howto_11">Visualizing LAMMPS snapshots</A>
<BR>
6.12 <A HREF = "Section_howto.html#howto_12">Triclinic (non-orthogonal) simulation boxes</A>
<BR>
6.13 <A HREF = "Section_howto.html#howto_13">NEMD simulations</A>
<BR>
6.14 <A HREF = "Section_howto.html#howto_14">Finite-size spherical and aspherical particles</A>
<BR>
6.15 <A HREF = "Section_howto.html#howto_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A>
<BR>
6.16 <A HREF = "Section_howto.html#howto_16">Thermostatting, barostatting, and compute temperature</A>
<BR>
6.17 <A HREF = "Section_howto.html#howto_17">Walls</A>
<BR>
6.18 <A HREF = "Section_howto.html#howto_18">Elastic constants</A>
<BR>
6.19 <A HREF = "Section_howto.html#howto_19">Library interface to LAMMPS</A>
<BR>
6.20 <A HREF = "Section_howto.html#howto_20">Calculating thermal conductivity</A>
<BR>
6.21 <A HREF = "Section_howto.html#howto_21">Calculating viscosity</A>
<BR>
6.22 <A HREF = "Section_howto.html#howto_22">Calculating a diffusion coefficient</A>
<BR>
6.23 <A HREF = "Section_howto.html#howto_23">Using chunks to calculate system properties</A>
<BR>
6.24 <A HREF = "Section_howto.html#howto_24">Setting parameters for pppm/disp</A>
<BR>
6.25 <A HREF = "Section_howto.html#howto_25">Polarizable models</A>
<BR>
6.26 <A HREF = "Section_howto.html#howto_26">Adiabatic core/shell model</A>
<BR>
6.27 <A HREF = "Section_howto.html#howto_27">Drude induced dipoles</A>
<BR></UL>
<LI><A HREF = "Section_example.html">Example problems</A>
<LI><A HREF = "Section_perf.html">Performance & scalability</A>
<LI><A HREF = "Section_tools.html">Additional tools</A>
<LI><A HREF = "Section_modify.html">Modifying & extending LAMMPS</A>
<UL> 10.1 <A HREF = "Section_modify.html#mod_1">Atom styles</A>
<BR>
10.2 <A HREF = "Section_modify.html#mod_2">Bond, angle, dihedral, improper potentials</A>
<BR>
10.3 <A HREF = "Section_modify.html#mod_3">Compute styles</A>
<BR>
10.4 <A HREF = "Section_modify.html#mod_4">Dump styles</A>
<BR>
10.5 <A HREF = "Section_modify.html#mod_5">Dump custom output options</A>
<BR>
10.6 <A HREF = "Section_modify.html#mod_6">Fix styles</A>
<BR>
10.7 <A HREF = "Section_modify.html#mod_7">Input script commands</A>
<BR>
10.8 <A HREF = "Section_modify.html#mod_8">Kspace computations</A>
<BR>
10.9 <A HREF = "Section_modify.html#mod_9">Minimization styles</A>
<BR>
10.10 <A HREF = "Section_modify.html#mod_10">Pairwise potentials</A>
<BR>
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>
<!-- END_HTML_ONLY -->
</BODY>
</HTML>
we can improve the LAMMPS documentation.</p>
<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
it gives quick access to documentation for all LAMMPS commands.</p>
<p><a class="reference external" href="Manual.pdf">PDF file</a> of the entire manual, generated by
<a class="reference external" href="http://freecode.com/projects/htmldoc">htmldoc</a></p>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#what-is-lammps">1.1. What is LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-features">1.2. LAMMPS features</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-non-features">1.3. LAMMPS non-features</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#open-source-distribution">1.4. Open source distribution</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#acknowledgments-and-citations">1.5. Acknowledgments and citations</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a><ul>
<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>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps">2.2. Making LAMMPS</a></li>
<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>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-via-the-make-py-tool">2.4. Building LAMMPS via the Make.py tool</a></li>
<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>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#running-lammps">2.6. Running LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#command-line-options">2.7. Command-line options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#lammps-screen-output">2.8. LAMMPS screen output</a></li>
<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>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#lammps-input-script">3.1. LAMMPS input script</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#parsing-rules">3.2. Parsing rules</a></li>
<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>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#individual-commands">3.5. Individual commands</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#fix-styles">3.6. Fix styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#compute-styles">3.7. Compute styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#pair-style-potentials">3.8. Pair_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#bond-style-potentials">3.9. Bond_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#angle-style-potentials">3.10. Angle_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#dihedral-style-potentials">3.11. Dihedral_style potentials</a></li>
<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>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#standard-packages">4.1. Standard packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-compress-package">4.2. Build instructions for COMPRESS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-gpu-package">4.3. Build instructions for GPU package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-kim-package">4.4. Build instructions for KIM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-kokkos-package">4.5. Build instructions for KOKKOS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-kspace-package">4.6. Build instructions for KSPACE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-meam-package">4.7. Build instructions for MEAM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-poems-package">4.8. Build instructions for POEMS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-python-package">4.9. Build instructions for PYTHON package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-reax-package">4.10. Build instructions for REAX package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-voronoi-package">4.11. Build instructions for VORONOI package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-xtc-package">4.12. Build instructions for XTC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-packages">4.13. User packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-atc-package">4.14. USER-ATC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-awpmd-package">4.15. USER-AWPMD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cg-cmm-package">4.16. USER-CG-CMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-colvars-package">4.17. USER-COLVARS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cuda-package">4.18. USER-CUDA package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-diffraction-package">4.19. USER-DIFFRACTION package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-drude-package">4.20. USER-DRUDE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-eff-package">4.21. USER-EFF package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-fep-package">4.22. USER-FEP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-h5md-package">4.23. USER-H5MD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-intel-package">4.24. USER-INTEL package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-lb-package">4.25. USER-LB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-mgpt-package">4.26. USER-MGPT package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-misc-package">4.27. USER-MISC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-molfile-package">4.28. USER-MOLFILE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-omp-package">4.29. USER-OMP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-phonon-package">4.30. USER-PHONON package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qmmm-package">4.31. USER-QMMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qtb-package">4.32. USER-QTB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-reaxc-package">4.33. USER-REAXC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smd-package">4.34. USER-SMD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smtbq-package">4.35. USER-SMTBQ package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-sph-package">4.36. USER-SPH package</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#measuring-performance">5.1. Measuring performance</a></li>
<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>
<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>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#restarting-a-simulation">6.1. Restarting a simulation</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#d-simulations">6.2. 2d simulations</a></li>
<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>
<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>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#multi-replica-simulations">6.5. Multi-replica simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#granular-models">6.6. Granular models</a></li>
<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>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#spc-water-model">6.9. SPC water model</a></li>
<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>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#visualizing-lammps-snapshots">6.11. Visualizing LAMMPS snapshots</a></li>
<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 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>
<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>
<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>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#walls">6.17. Walls</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#elastic-constants">6.18. Elastic constants</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#library-interface-to-lammps">6.19. Library interface to LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-thermal-conductivity">6.20. Calculating thermal conductivity</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-viscosity">6.21. Calculating viscosity</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-a-diffusion-coefficient">6.22. Calculating a diffusion coefficient</a></li>
<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>
<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>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#polarizable-models">6.25. Polarizable models</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#adiabatic-core-shell-model">6.26. Adiabatic core/shell model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#drude-induced-dipoles">6.27. Drude induced dipoles</a></li>
</ul>
</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><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#amber2lmp-tool">9.1. amber2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#binary2txt-tool">9.2. binary2txt tool</a></li>
<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>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#colvars-tools">9.5. colvars tools</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#createatoms-tool">9.6. createatoms tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#data2xmovie-tool">9.7. data2xmovie tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-database-tool">9.8. eam database tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-generate-tool">9.9. eam generate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eff-tool">9.10. eff tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#emacs-tool">9.11. emacs tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#fep-tool">9.12. fep tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#i-pi-tool">9.13. i-pi tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ipp-tool">9.14. ipp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#kate-tool">9.15. kate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2arc-tool">9.16. lmp2arc tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2cfg-tool">9.17. lmp2cfg tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2vmd-tool">9.18. lmp2vmd tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#matlab-tool">9.19. matlab tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#micelle2d-tool">9.20. micelle2d tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#moltemplate-tool">9.21. moltemplate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#msi2lmp-tool">9.22. msi2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#phonon-tool">9.23. phonon tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#polymer-bonding-tool">9.24. polymer bonding tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#pymol-asphere-tool">9.25. pymol_asphere tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#python-tool">9.26. python tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#reax-tool">9.27. reax tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#restart2data-tool">9.28. restart2data tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#vim-tool">9.29. vim tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmgrace-tool">9.30. xmgrace tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmovie-tool">9.31. xmovie tool</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#atom-styles">10.1. Atom styles</a></li>
<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>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#compute-styles">10.3. Compute styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-styles">10.4. Dump styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-custom-output-options">10.5. Dump custom output options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#fix-styles">10.6. Fix styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#input-script-commands">10.7. Input script commands</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#kspace-computations">10.8. Kspace computations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#minimization-styles">10.9. Minimization styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#pairwise-potentials">10.10. Pairwise potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#region-styles">10.11. Region styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#body-styles">10.12. Body styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#thermodynamic-output-options">10.13. Thermodynamic output options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#variable-options">10.14. Variable options</a></li>
<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>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a><ul>
<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>
<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>
<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>
<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>
<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>
<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 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>
</ul>
</li>
<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 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>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error">12.4. Errors:</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#warnings">12.5. Warnings:</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_history.html#coming-attractions">13.1. Coming attractions</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_history.html#past-versions">13.2. Past versions</a></li>
</ul>
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<HTML>
<HTML>
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="17 Nov 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>
<HR>
<H1></H1>
<P><CENTER><H3>LAMMPS Documentation
</H3></CENTER>
<CENTER><H4>17 Nov 2015 version
</H4></CENTER>
<H4>Version info:
</H4>
<P>The LAMMPS "version" is the date when it was released, such as 1 May
2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
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
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
directory name created when you unpack a tarball, and at the top of
the first page of the manual (this page).
</P>
<UL><LI>If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of LAMMPS.
</P>
<P><LI>If you browse the HTML doc pages included in your tarball, they
describe the version you have.
</P>
<P><LI>The <A HREF = "Manual.pdf">PDF file</A> on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don't want
it to be part of every patch.
</P>
<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
LAMMPS.
</UL>
<P>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.
</P>
<P>LAMMPS is a classical molecular dynamics simulation code designed to
run efficiently on parallel computers. It was developed at Sandia
National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL).
</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
sjplimp,athomps,pscrozi at sandia.gov. The <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> at
http://lammps.sandia.gov has more information about the code and its
uses.
</P>
<HR>
<P>The LAMMPS documentation is organized into the following sections. If
you find errors or omissions in this manual or have suggestions for
useful information to add, please send an email to the developers so
we can improve the LAMMPS documentation.
</P>
<P>Once you are familiar with LAMMPS, you may want to bookmark <A HREF = "Section_commands.html#comm">this
page</A> at Section_commands.html#comm since
it gives quick access to documentation for all LAMMPS commands.
</P>
<P><A HREF = "Manual.pdf">PDF file</A> of the entire manual, generated by
<A HREF = "http://freecode.com/projects/htmldoc">htmldoc</A>
</P>
<P><!-- RST
</P>
<P>.. toctree::
:maxdepth: 2
:numbered: // comment
</P>
<P> Section_intro
Section_start
Section_commands
Section_packages
Section_accelerate
Section_howto
Section_example
Section_perf
Section_tools
Section_modify
Section_python
Section_errors
Section_history
</P>
<P>Indices and tables
==================
</P>
<P>* :ref:`genindex` // comment
* :ref:`search` // comment
</P>
<P>END_RST -->
</P>
<OL><LI><!-- HTML_ONLY -->
<A HREF = "Section_intro.html">Introduction</A>
<UL> 1.1 <A HREF = "Section_intro.html#intro_1">What is LAMMPS</A>
<BR>
1.2 <A HREF = "Section_intro.html#intro_2">LAMMPS features</A>
<BR>
1.3 <A HREF = "Section_intro.html#intro_3">LAMMPS non-features</A>
<BR>
1.4 <A HREF = "Section_intro.html#intro_4">Open source distribution</A>
<BR>
1.5 <A HREF = "Section_intro.html#intro_5">Acknowledgments and citations</A>
<BR></UL>
<LI><A HREF = "Section_start.html">Getting started</A>
<UL> 2.1 <A HREF = "Section_start.html#start_1">What's in the LAMMPS distribution</A>
<BR>
2.2 <A HREF = "Section_start.html#start_2">Making LAMMPS</A>
<BR>
2.3 <A HREF = "Section_start.html#start_3">Making LAMMPS with optional packages</A>
<BR>
2.4 <A HREF = "Section_start.html#start_4">Building LAMMPS via the Make.py script</A>
<BR>
2.5 <A HREF = "Section_start.html#start_5">Building LAMMPS as a library</A>
<BR>
2.6 <A HREF = "Section_start.html#start_6">Running LAMMPS</A>
<BR>
2.7 <A HREF = "Section_start.html#start_7">Command-line options</A>
<BR>
2.8 <A HREF = "Section_start.html#start_8">Screen output</A>
<BR>
2.9 <A HREF = "Section_start.html#start_9">Tips for users of previous versions</A>
<BR></UL>
<LI><A HREF = "Section_commands.html">Commands</A>
<UL> 3.1 <A HREF = "Section_commands.html#cmd_1">LAMMPS input script</A>
<BR>
3.2 <A HREF = "Section_commands.html#cmd_2">Parsing rules</A>
<BR>
3.3 <A HREF = "Section_commands.html#cmd_3">Input script structure</A>
<BR>
3.4 <A HREF = "Section_commands.html#cmd_4">Commands listed by category</A>
<BR>
3.5 <A HREF = "Section_commands.html#cmd_5">Commands listed alphabetically</A>
<BR></UL>
<LI><A HREF = "Section_packages.html">Packages</A>
<UL> 4.1 <A HREF = "Section_packages.html#pkg_1">Standard packages</A>
<BR>
4.2 <A HREF = "Section_packages.html#pkg_2">User packages</A>
<BR></UL>
<LI><A HREF = "Section_accelerate.html">Accelerating LAMMPS performance</A>
<UL> 5.1 <A HREF = "Section_accelerate.html#acc_1">Measuring performance</A>
<BR>
5.2 <A HREF = "Section_accelerate.html#acc_2">Algorithms and code options to boost performace</A>
<BR>
5.3 <A HREF = "Section_accelerate.html#acc_3">Accelerator packages with optimized styles</A>
<BR>
<UL> 5.3.1 <A HREF = "accelerate_cuda.html">USER-CUDA package</A>
<BR>
5.3.2 <A HREF = "accelerate_gpu.html">GPU package</A>
<BR>
5.3.3 <A HREF = "accelerate_intel.html">USER-INTEL package</A>
<BR>
5.3.4 <A HREF = "accelerate_kokkos.html">KOKKOS package</A>
<BR>
5.3.5 <A HREF = "accelerate_omp.html">USER-OMP package</A>
<BR>
5.3.6 <A HREF = "accelerate_opt.html">OPT package</A>
<BR></UL>
5.4 <A HREF = "Section_accelerate.html#acc_4">Comparison of various accelerator packages</A>
<BR></UL>
<LI><A HREF = "Section_howto.html">How-to discussions</A>
<UL> 6.1 <A HREF = "Section_howto.html#howto_1">Restarting a simulation</A>
<BR>
6.2 <A HREF = "Section_howto.html#howto_2">2d simulations</A>
<BR>
6.3 <A HREF = "Section_howto.html#howto_3">CHARMM and AMBER force fields</A>
<BR>
6.4 <A HREF = "Section_howto.html#howto_4">Running multiple simulations from one input script</A>
<BR>
6.5 <A HREF = "Section_howto.html#howto_5">Multi-replica simulations</A>
<BR>
6.6 <A HREF = "Section_howto.html#howto_6">Granular models</A>
<BR>
6.7 <A HREF = "Section_howto.html#howto_7">TIP3P water model</A>
<BR>
6.8 <A HREF = "Section_howto.html#howto_8">TIP4P water model</A>
<BR>
6.9 <A HREF = "Section_howto.html#howto_9">SPC water model</A>
<BR>
6.10 <A HREF = "Section_howto.html#howto_10">Coupling LAMMPS to other codes</A>
<BR>
6.11 <A HREF = "Section_howto.html#howto_11">Visualizing LAMMPS snapshots</A>
<BR>
6.12 <A HREF = "Section_howto.html#howto_12">Triclinic (non-orthogonal) simulation boxes</A>
<BR>
6.13 <A HREF = "Section_howto.html#howto_13">NEMD simulations</A>
<BR>
6.14 <A HREF = "Section_howto.html#howto_14">Finite-size spherical and aspherical particles</A>
<BR>
6.15 <A HREF = "Section_howto.html#howto_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A>
<BR>
6.16 <A HREF = "Section_howto.html#howto_16">Thermostatting, barostatting, and compute temperature</A>
<BR>
6.17 <A HREF = "Section_howto.html#howto_17">Walls</A>
<BR>
6.18 <A HREF = "Section_howto.html#howto_18">Elastic constants</A>
<BR>
6.19 <A HREF = "Section_howto.html#howto_19">Library interface to LAMMPS</A>
<BR>
6.20 <A HREF = "Section_howto.html#howto_20">Calculating thermal conductivity</A>
<BR>
6.21 <A HREF = "Section_howto.html#howto_21">Calculating viscosity</A>
<BR>
6.22 <A HREF = "Section_howto.html#howto_22">Calculating a diffusion coefficient</A>
<BR>
6.23 <A HREF = "Section_howto.html#howto_23">Using chunks to calculate system properties</A>
<BR>
6.24 <A HREF = "Section_howto.html#howto_24">Setting parameters for pppm/disp</A>
<BR>
6.25 <A HREF = "Section_howto.html#howto_25">Polarizable models</A>
<BR>
6.26 <A HREF = "Section_howto.html#howto_26">Adiabatic core/shell model</A>
<BR>
6.27 <A HREF = "Section_howto.html#howto_27">Drude induced dipoles</A>
<BR></UL>
<LI><A HREF = "Section_example.html">Example problems</A>
<LI><A HREF = "Section_perf.html">Performance & scalability</A>
<LI><A HREF = "Section_tools.html">Additional tools</A>
<LI><A HREF = "Section_modify.html">Modifying & extending LAMMPS</A>
<UL> 10.1 <A HREF = "Section_modify.html#mod_1">Atom styles</A>
<BR>
10.2 <A HREF = "Section_modify.html#mod_2">Bond, angle, dihedral, improper potentials</A>
<BR>
10.3 <A HREF = "Section_modify.html#mod_3">Compute styles</A>
<BR>
10.4 <A HREF = "Section_modify.html#mod_4">Dump styles</A>
<BR>
10.5 <A HREF = "Section_modify.html#mod_5">Dump custom output options</A>
<BR>
10.6 <A HREF = "Section_modify.html#mod_6">Fix styles</A>
<BR>
10.7 <A HREF = "Section_modify.html#mod_7">Input script commands</A>
<BR>
10.8 <A HREF = "Section_modify.html#mod_8">Kspace computations</A>
<BR>
10.9 <A HREF = "Section_modify.html#mod_9">Minimization styles</A>
<BR>
10.10 <A HREF = "Section_modify.html#mod_10">Pairwise potentials</A>
<BR>
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>
<!-- END_HTML_ONLY -->
</BODY>
</HTML>
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@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="20 Nov 2015 version">
<META NAME="docnumber" CONTENT="7 Dec 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>
@ -21,7 +21,7 @@
<H1></H1>
LAMMPS-ICMS Documentation :c,h3
20 Nov 2015 version :c,h4
7 Dec 2015 version :c,h4
Version info: :h4
@ -100,7 +100,7 @@ it gives quick access to documentation for all LAMMPS commands.
.. toctree::
:maxdepth: 2
:numbered: // comment
:numbered:
Section_intro
Section_start
@ -120,8 +120,8 @@ 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 -->

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@ -135,16 +135,17 @@
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>msd = style name of this compute command</li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>com</em></li>
<li>keyword = <em>com</em> or <em>average</em></li>
</ul>
<pre class="literal-block">
<em>com</em> value = <em>yes</em> or <em>no</em>
<em>average</em> value = <em>yes</em> or <em>no</em>
</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>compute 1 all msd
compute 1 upper msd com yes
compute 1 upper msd com yes average yes
</pre></div>
</div>
</div>
@ -161,12 +162,32 @@ squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and
averaged over atoms in the group.</p>
<p>The slope of the mean-squared displacement (MSD) versus time is
proportional to the diffusion coefficient of the diffusing atoms.</p>
<p>The displacement of an atom is from its original position at the time
the compute command was issued. The value of the displacement will be
<p>The displacement of an atom is from its reference position. This is
normally the original position at the time
the compute command was issued, unless the <em>average</em> keyword is set to <em>yes</em>.
The value of the displacement will be
0.0 for atoms not in the specified compute group.</p>
<p>If the <em>com</em> option is set to <em>yes</em> then the effect of any drift in
the center-of-mass of the group of atoms is subtracted out before xhe
displacment of each atom is calcluated.</p>
the center-of-mass of the group of atoms is subtracted out before the
displacment of each atom is calculated.</p>
<p>If the <em>average</em> option is set to <em>yes</em> then the reference position of
an atom is based on the average position of that atom,
corrected for center-of-mass motion if requested.
The average position
is a running average over all previous calls to the compute, including the
current call. So on the first call
it is current position, on the second call it is the arithmetic average of the
current position and the position on the first call, and so on.
Note that when using this option, the precise value of the mean square
displacement will depend on the number of times the compute is
called. So, for example, changing the frequency of thermo output may
change the computed displacement. Also, the precise values will be
changed if a single simulation is broken up into two parts, using
either multiple run commands or a restart file. It only makes
sense to use this option if the atoms are not diffusing, so that
their average positions relative to the center of mass of the system
are stationary. The most common case is crystalline solids undergoing
thermal motion.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Initial coordinates are stored in &#8220;unwrapped&#8221; form, by
@ -183,7 +204,13 @@ to be continuous when running from a <a class="reference internal" href="read_re
then you should use the same ID for this compute, as in the original
run. This is so that the fix this compute creates to store per-atom
quantities will also have the same ID, and thus be initialized
correctly with time=0 atom coordinates from the restart file.</p>
correctly with atom reference positions from the restart file.
When <em>average</em> is set to yes, then the atom reference positions
are restored correctly, but not the number of samples used
obtain them. As a result, the reference positions from the restart
file are combined with subsequent positions as if they were from a
single sample, instead of many, which will change the values of msd
somewhat.</p>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global vector of length 4, which can be
@ -204,7 +231,7 @@ distance^2 <a class="reference internal" href="units.html"><em>units</em></a>.</
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The option default is com = no.</p>
<p>The option default are com = no, average = no.</p>
</div>
</div>

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@ -183,9 +183,11 @@ parameters. This is followed by that number of integers giving the
degree of each order parameter. Because <a href="#id1"><span class="problematic" id="id2">*</span></a>Q*2 and all odd-degree
order parameters are zero for atoms in cubic crystals
(see <a class="reference internal" href="#steinhardt"><span>Steinhardt</span></a>), the default order parameters
are <a href="#id3"><span class="problematic" id="id4">*</span></a>Q*4, <a href="#id5"><span class="problematic" id="id6">*</span></a>Q*6, <a href="#id7"><span class="problematic" id="id8">*</span></a>Q*8, <a href="#id9"><span class="problematic" id="id10">*</span></a>Q*10, and <a href="#id11"><span class="problematic" id="id12">*</span></a>Q*12. The correct
numerical values for commonly encountered high-symmetry
structures are given by <a class="reference internal" href="#mickel"><span>Mickel et al.</span></a></p>
are <a href="#id3"><span class="problematic" id="id4">*</span></a>Q*4, <a href="#id5"><span class="problematic" id="id6">*</span></a>Q*6, <a href="#id7"><span class="problematic" id="id8">*</span></a>Q*8, <a href="#id9"><span class="problematic" id="id10">*</span></a>Q*10, and <a href="#id11"><span class="problematic" id="id12">*</span></a>Q*12. For the
FCC crystal with <a href="#id13"><span class="problematic" id="id14">*</span></a>nnn*=12, <a href="#id15"><span class="problematic" id="id16">*</span></a>Q*4 = sqrt(7/3)/8 = 0.19094....
The numerical values of all order parameters up to <a href="#id17"><span class="problematic" id="id18">*</span></a>Q*12
for a range of commonly encountered high-symmetry structures are given
in Table I of <a class="reference internal" href="#mickel"><span>Mickel et al.</span></a>.</p>
<p>The value of <em>Ql</em> is set to zero for atoms not in the
specified compute group, as well as for atoms that have less than
<em>nnn</em> neighbors within the distance cutoff.</p>
@ -226,7 +228,7 @@ options.</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 <em>cutoff</em> = pair style cutoff, <em>nnn</em> = 12, <em>degrees</em> = 5 4 6 8 9 10 12 i.e. <a href="#id13"><span class="problematic" id="id14">*</span></a>Q*4, <a href="#id15"><span class="problematic" id="id16">*</span></a>Q*6, <a href="#id17"><span class="problematic" id="id18">*</span></a>Q*8, <a href="#id19"><span class="problematic" id="id20">*</span></a>Q*10, and <a href="#id21"><span class="problematic" id="id22">*</span></a>Q*12.</p>
<p>The option defaults are <em>cutoff</em> = pair style cutoff, <em>nnn</em> = 12, <em>degrees</em> = 5 4 6 8 9 10 12 i.e. <a href="#id19"><span class="problematic" id="id20">*</span></a>Q*4, <a href="#id21"><span class="problematic" id="id22">*</span></a>Q*6, <a href="#id23"><span class="problematic" id="id24">*</span></a>Q*8, <a href="#id25"><span class="problematic" id="id26">*</span></a>Q*10, and <a href="#id27"><span class="problematic" id="id28">*</span></a>Q*12.</p>
<hr class="docutils" />
<p id="mickel"><span id="steinhardt"></span><strong>(Steinhardt)</strong> P. Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983).</p>
<p><strong>(Mickel)</strong> W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, J. Chem. Phys. 138, 044501 (2013).</p>

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<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="17 Nov 2015 version">
<META NAME="docnumber" CONTENT="20 Nov 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>
@ -21,7 +21,7 @@
<P><CENTER><H3>LAMMPS Documentation
</H3></CENTER>
<CENTER><H4>17 Nov 2015 version
<CENTER><H4>20 Nov 2015 version
</H4></CENTER>
<H4>Version info:
</H4>

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<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>com</I>
<LI>keyword = <I>com</I> or <I>average</I>
<PRE> <I>com</I> value = <I>yes</I> or <I>no</I>
<PRE> <I>com</I> value = <I>yes</I> or <I>no</I>
<I>average</I> value = <I>yes</I> or <I>no</I>
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all msd
compute 1 upper msd com yes
compute 1 upper msd com yes average yes
</PRE>
<P><B>Description:</B>
</P>
@ -49,13 +50,34 @@ averaged over atoms in the group.
<P>The slope of the mean-squared displacement (MSD) versus time is
proportional to the diffusion coefficient of the diffusing atoms.
</P>
<P>The displacement of an atom is from its original position at the time
the compute command was issued. The value of the displacement will be
<P>The displacement of an atom is from its reference position. This is
normally the original position at the time
the compute command was issued, unless the <I>average</I> keyword is set to <I>yes</I>.
The value of the displacement will be
0.0 for atoms not in the specified compute group.
</P>
<P>If the <I>com</I> option is set to <I>yes</I> then the effect of any drift in
the center-of-mass of the group of atoms is subtracted out before xhe
displacment of each atom is calcluated.
the center-of-mass of the group of atoms is subtracted out before the
displacment of each atom is calculated.
</P>
<P>If the <I>average</I> option is set to <I>yes</I> then the reference position of
an atom is based on the average position of that atom,
corrected for center-of-mass motion if requested.
The average position
is a running average over all previous calls to the compute, including the
current call. So on the first call
it is current position, on the second call it is the arithmetic average of the
current position and the position on the first call, and so on.
Note that when using this option, the precise value of the mean square
displacement will depend on the number of times the compute is
called. So, for example, changing the frequency of thermo output may
change the computed displacement. Also, the precise values will be
changed if a single simulation is broken up into two parts, using
either multiple run commands or a restart file. It only makes
sense to use this option if the atoms are not diffusing, so that
their average positions relative to the center of mass of the system
are stationary. The most common case is crystalline solids undergoing
thermal motion.
</P>
<P>IMPORTANT NOTE: Initial coordinates are stored in "unwrapped" form, by
using the image flags associated with each atom. See the <A HREF = "dump.html">dump
@ -70,7 +92,13 @@ to be continuous when running from a <A HREF = "read_restart.html">restart file<
then you should use the same ID for this compute, as in the original
run. This is so that the fix this compute creates to store per-atom
quantities will also have the same ID, and thus be initialized
correctly with time=0 atom coordinates from the restart file.
correctly with atom reference positions from the restart file.
When <I>average</I> is set to yes, then the atom reference positions
are restored correctly, but not the number of samples used
obtain them. As a result, the reference positions from the restart
file are combined with subsequent positions as if they were from a
single sample, instead of many, which will change the values of msd
somewhat.
</P>
<P><B>Output info:</B>
</P>
@ -94,6 +122,6 @@ msd/chunk</A>
</P>
<P><B>Default:</B>
</P>
<P>The option default is com = no.
<P>The option default are com = no, average = no.
</P>
</HTML>

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@ -71,9 +71,11 @@ parameters. This is followed by that number of integers giving the
degree of each order parameter. Because <I>Q</I>2 and all odd-degree
order parameters are zero for atoms in cubic crystals
(see <A HREF = "#Steinhardt">Steinhardt</A>), the default order parameters
are <I>Q</I>4, <I>Q</I>6, <I>Q</I>8, <I>Q</I>10, and <I>Q</I>12. The correct
numerical values for commonly encountered high-symmetry
structures are given by <A HREF = "#Mickel">Mickel et al.</A>
are <I>Q</I>4, <I>Q</I>6, <I>Q</I>8, <I>Q</I>10, and <I>Q</I>12. For the
FCC crystal with <I>nnn</I>=12, <I>Q</I>4 = sqrt(7/3)/8 = 0.19094....
The numerical values of all order parameters up to <I>Q</I>12
for a range of commonly encountered high-symmetry structures are given
in Table I of <A HREF = "#Mickel">Mickel et al.</A>.
</P>
<P>The value of <I>Ql</I> is set to zero for atoms not in the
specified compute group, as well as for atoms that have less than

2
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@ -48,7 +48,7 @@
</P>
<PRE>fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 4.3 -5.0
fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 0.0 4.3 -5.0
</PRE>
<P><B>Description:</B>
</P>

4
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@ -81,8 +81,8 @@ that are a multiple of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
quantities, computed in the preceding portion of the simulation every
<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nfreq >
(Nrepeat-1)*Nevery is required.
contributing to the average value cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.
</P>
<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average

4
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@ -161,8 +161,8 @@ that are a multiples of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
quantities, computed in the preceding portion of the simulation every
<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nfreq >
(Nrepeat-1)*Nevery is required.
contributing to the average value cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.
</P>
<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average

6
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@ -143,9 +143,9 @@ histogram. The final histogram is generated on timesteps that are
multiple of <I>Nfreq</I>. It is averaged over <I>Nrepeat</I> histograms,
computed in the preceding portion of the simulation every <I>Nevery</I>
timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and <I>Nevery</I> must
be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps contributing
to the histogram cannot overlap, i.e. Nfreq > (Nrepeat-1)*Nevery is
required.
be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
contributing to the histogram value cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.
</P>
<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then input values
on timesteps 90,92,94,96,98,100 will be used to compute the final

4
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@ -157,8 +157,8 @@ that are a multiples of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
quantities, computed in the preceding portion of the simulation every
<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nfreq >
(Nrepeat-1)*Nevery is required.
contributing to the average value cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.
</P>
<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average

7
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@ -127,9 +127,10 @@ the average. The final averaged quantities are generated on timesteps
that are a multiples of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
quantities, computed in the preceding portion of the simulation every
<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nfreq >
(Nrepeat-1)*Nevery is required.
<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1.
Also, the timesteps
contributing to the average value cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.
</P>
<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average

4
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@ -131,8 +131,8 @@ that are a mlutiple of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
quantities, computed in the preceding portion of the simulation every
<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nfreq >
(Nrepeat-1)*Nevery is required.
contributing to the average value cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.
</P>
<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average

7
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@ -57,9 +57,10 @@ fix 2 flow indent 10.0 cylinder z 0.0 0.0 10.0 units box
<P><B>Description:</B>
</P>
<P>Insert an indenter within a simulation box. The indenter repels all
atoms that touch it, so it can be used to push into a material or as
an obstacle in a flow. Or it can be used as a constraining wall
around a simulation; see the discussion of the <I>side</I> keyword below.
atoms in the group that touch it, so it can be used to push into a
material or as an obstacle in a flow. Or it can be used as a
constraining wall around a simulation; see the discussion of the
<I>side</I> keyword below.
</P>
<P>The indenter can either be spherical or cylindrical or planar. You
must set one of those 3 keywords.

7
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@ -102,9 +102,10 @@ order. The species analysis is performed using the average bond-order
on timesteps that are a multiple of <I>Nfreq</I>. The average is over
<I>Nrepeat</I> bond-order samples, computed in the preceding portion of the
simulation every <I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of
<I>Nevery</I> and <I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also,
the timesteps contributing to the average bond-order cannot overlap,
i.e. Nfreq > (Nrepeat-1)*Nevery is required.
<I>Nevery</I> and <I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1.
Also, the timesteps
contributing to the average bond-order cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.
</P>
<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then bond-order
values on timesteps 90,92,94,96,98,100 will be used to compute the

7
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@ -82,9 +82,10 @@ average. The final averaged quantities are generated on timesteps
that are a multiple of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
quantities, computed in the preceding portion of the simulation every
<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nfreq >
(Nrepeat-1)*Nevery is required.
<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1.
Also, the timesteps
contributing to the average value cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.
</P>
<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average

2
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@ -158,7 +158,7 @@
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 4.3 -5.0
fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 0.0 4.3 -5.0
</pre></div>
</div>
</div>

2
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@ -36,7 +36,7 @@ keyword = {types} or {mu} or {ke} or {semi-grand} or {region} :l
fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 4.3 -5.0 :pre
fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 0.0 4.3 -5.0 :pre
[Description:]

4
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@ -186,8 +186,8 @@ that are a multiple of <em>Nfreq</em>. The average is over <em>Nrepeat</em>
quantities, computed in the preceding portion of the simulation every
<em>Nevery</em> timesteps. <em>Nfreq</em> must be a multiple of <em>Nevery</em> and
<em>Nevery</em> must be non-zero even if <em>Nrepeat</em> is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nfreq &gt;
(Nrepeat-1)*Nevery is required.</p>
contributing to the average value cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.</p>
<p>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on

4
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@ -260,8 +260,8 @@ that are a multiples of <em>Nfreq</em>. The average is over <em>Nrepeat</em>
quantities, computed in the preceding portion of the simulation every
<em>Nevery</em> timesteps. <em>Nfreq</em> must be a multiple of <em>Nevery</em> and
<em>Nevery</em> must be non-zero even if <em>Nrepeat</em> is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nfreq &gt;
(Nrepeat-1)*Nevery is required.</p>
contributing to the average value cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.</p>
<p>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on

6
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@ -246,9 +246,9 @@ histogram. The final histogram is generated on timesteps that are
multiple of <em>Nfreq</em>. It is averaged over <em>Nrepeat</em> histograms,
computed in the preceding portion of the simulation every <em>Nevery</em>
timesteps. <em>Nfreq</em> must be a multiple of <em>Nevery</em> and <em>Nevery</em> must
be non-zero even if <em>Nrepeat</em> is 1. Also, the timesteps contributing
to the histogram cannot overlap, i.e. Nfreq &gt; (Nrepeat-1)*Nevery is
required.</p>
be non-zero even if <em>Nrepeat</em> is 1. Also, the timesteps
contributing to the histogram value cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.</p>
<p>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then input values
on timesteps 90,92,94,96,98,100 will be used to compute the final
histogram on timestep 100. Similarly for timesteps

4
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@ -262,8 +262,8 @@ that are a multiples of <em>Nfreq</em>. The average is over <em>Nrepeat</em>
quantities, computed in the preceding portion of the simulation every
<em>Nevery</em> timesteps. <em>Nfreq</em> must be a multiple of <em>Nevery</em> and
<em>Nevery</em> must be non-zero even if <em>Nrepeat</em> is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nfreq &gt;
(Nrepeat-1)*Nevery is required.</p>
contributing to the average value cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.</p>
<p>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on

7
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@ -229,9 +229,10 @@ the average. The final averaged quantities are generated on timesteps
that are a multiples of <em>Nfreq</em>. The average is over <em>Nrepeat</em>
quantities, computed in the preceding portion of the simulation every
<em>Nevery</em> timesteps. <em>Nfreq</em> must be a multiple of <em>Nevery</em> and
<em>Nevery</em> must be non-zero even if <em>Nrepeat</em> is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nfreq &gt;
(Nrepeat-1)*Nevery is required.</p>
<em>Nevery</em> must be non-zero even if <em>Nrepeat</em> is 1.
Also, the timesteps
contributing to the average value cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.</p>
<p>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on

4
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@ -237,8 +237,8 @@ that are a mlutiple of <em>Nfreq</em>. The average is over <em>Nrepeat</em>
quantities, computed in the preceding portion of the simulation every
<em>Nevery</em> timesteps. <em>Nfreq</em> must be a multiple of <em>Nevery</em> and
<em>Nevery</em> must be non-zero even if <em>Nrepeat</em> is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nfreq &gt;
(Nrepeat-1)*Nevery is required.</p>
contributing to the average value cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.</p>
<p>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on

7
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@ -172,9 +172,10 @@ fix 2 flow indent 10.0 cylinder z 0.0 0.0 10.0 units box
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Insert an indenter within a simulation box. The indenter repels all
atoms that touch it, so it can be used to push into a material or as
an obstacle in a flow. Or it can be used as a constraining wall
around a simulation; see the discussion of the <em>side</em> keyword below.</p>
atoms in the group that touch it, so it can be used to push into a
material or as an obstacle in a flow. Or it can be used as a
constraining wall around a simulation; see the discussion of the
<em>side</em> keyword below.</p>
<p>The indenter can either be spherical or cylindrical or planar. You
must set one of those 3 keywords.</p>
<p>A spherical indenter exerts a force of magnitude</p>

7
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@ -48,9 +48,10 @@ fix 2 flow indent 10.0 cylinder z 0.0 0.0 10.0 units box :pre
[Description:]
Insert an indenter within a simulation box. The indenter repels all
atoms that touch it, so it can be used to push into a material or as
an obstacle in a flow. Or it can be used as a constraining wall
around a simulation; see the discussion of the {side} keyword below.
atoms in the group that touch it, so it can be used to push into a
material or as an obstacle in a flow. Or it can be used as a
constraining wall around a simulation; see the discussion of the
{side} keyword below.
The indenter can either be spherical or cylindrical or planar. You
must set one of those 3 keywords.

26
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@ -237,7 +237,7 @@ Martyna, Tobias and Klein in <a class="reference internal" href="#martyna"><span
energy proposed by Parrinello and Rahman in
<a class="reference internal" href="#parrinello"><span>(Parrinello)</span></a>. The time integration schemes closely
follow the time-reversible measure-preserving Verlet and rRESPA
integrators derived by Tuckerman et al. in <a class="reference internal" href="#tuckerman"><span>(Tuckerman)</span></a>.</p>
integrators derived by Tuckerman et al in <a class="reference internal" href="#tuckerman"><span>(Tuckerman)</span></a>.</p>
<hr class="docutils" />
<p>The thermostat parameters for fix styles <em>nvt</em> and <em>npt</em> is specified
using the <em>temp</em> keyword. Other thermostat-related keywords are
@ -403,8 +403,8 @@ negligible.</p>
scheme at little extra cost. The initial and final updates of the
thermostat variables are broken up into <em>tloop</em> substeps, each of
length <em>dt</em>/<em>tloop</em>. This corresponds to using a first-order
Suzuki-Yoshida scheme <span class="xref std std-ref">(Tuckerman2006)</span>. The keyword
<em>ploop</em> does the same thing for the barostat thermostat.</p>
Suzuki-Yoshida scheme <a class="reference internal" href="#tuckerman"><span>(Tuckerman)</span></a>. The keyword <em>ploop</em>
does the same thing for the barostat thermostat.</p>
<p>The keyword <em>nreset</em> controls how often the reference dimensions used
to define the strain energy are reset. If this keyword is not used,
or is given a value of zero, then the reference dimensions are set to
@ -535,16 +535,16 @@ with <em>respa</em>, LAMMPS uses an integrator constructed
according to the following factorization of the Liouville propagator
(for two rRESPA levels):</p>
<img alt="_images/fix_nh1.jpg" class="align-center" src="_images/fix_nh1.jpg" />
<p>This factorization differs somewhat from that of Tuckerman et al., in that
the barostat is only updated at the outermost rRESPA level, whereas
Tuckerman&#8217;s factorization requires splitting the pressure into pieces
corresponding to the forces computed at each rRESPA level. In theory, the
latter method will exhibit better numerical stability. In practice,
because Pdamp is normally chosen to be a large multiple of the
outermost rRESPA timestep, the barostat dynamics are not the
limiting factor for numerical stability. Both
factorizations are time-reversible and can be shown to preserve the phase
space measure of the underlying non-Hamiltonian equations of motion.</p>
<p>This factorization differs somewhat from that of Tuckerman et al, in
that the barostat is only updated at the outermost rRESPA level,
whereas Tuckerman&#8217;s factorization requires splitting the pressure into
pieces corresponding to the forces computed at each rRESPA level. In
theory, the latter method will exhibit better numerical stability. In
practice, because Pdamp is normally chosen to be a large multiple of
the outermost rRESPA timestep, the barostat dynamics are not the
limiting factor for numerical stability. Both factorizations are
time-reversible and can be shown to preserve the phase space measure
of the underlying non-Hamiltonian equations of motion.</p>
<hr class="docutils" />
<p>The fix npt and fix nph commands can be used with rigid bodies or
mixtures of rigid bodies and non-rigid particles (e.g. solvent). But

26
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@ -96,7 +96,7 @@ Martyna, Tobias and Klein in "(Martyna)"_#Martyna with the strain
energy proposed by Parrinello and Rahman in
"(Parrinello)"_#Parrinello. The time integration schemes closely
follow the time-reversible measure-preserving Verlet and rRESPA
integrators derived by Tuckerman et al. in "(Tuckerman)"_#Tuckerman.
integrators derived by Tuckerman et al in "(Tuckerman)"_#Tuckerman.
:line
@ -280,8 +280,8 @@ The keyword {tloop} can be used to improve the accuracy of integration
scheme at little extra cost. The initial and final updates of the
thermostat variables are broken up into {tloop} substeps, each of
length {dt}/{tloop}. This corresponds to using a first-order
Suzuki-Yoshida scheme "(Tuckerman2006)"_#Tuckerman2006. The keyword
{ploop} does the same thing for the barostat thermostat.
Suzuki-Yoshida scheme "(Tuckerman)"_#Tuckerman. The keyword {ploop}
does the same thing for the barostat thermostat.
The keyword {nreset} controls how often the reference dimensions used
to define the strain energy are reset. If this keyword is not used,
@ -428,16 +428,16 @@ according to the following factorization of the Liouville propagator
:c,image(Eqs/fix_nh1.jpg)
This factorization differs somewhat from that of Tuckerman et al., in that
the barostat is only updated at the outermost rRESPA level, whereas
Tuckerman's factorization requires splitting the pressure into pieces
corresponding to the forces computed at each rRESPA level. In theory, the
latter method will exhibit better numerical stability. In practice,
because Pdamp is normally chosen to be a large multiple of the
outermost rRESPA timestep, the barostat dynamics are not the
limiting factor for numerical stability. Both
factorizations are time-reversible and can be shown to preserve the phase
space measure of the underlying non-Hamiltonian equations of motion.
This factorization differs somewhat from that of Tuckerman et al, in
that the barostat is only updated at the outermost rRESPA level,
whereas Tuckerman's factorization requires splitting the pressure into
pieces corresponding to the forces computed at each rRESPA level. In
theory, the latter method will exhibit better numerical stability. In
practice, because Pdamp is normally chosen to be a large multiple of
the outermost rRESPA timestep, the barostat dynamics are not the
limiting factor for numerical stability. Both factorizations are
time-reversible and can be shown to preserve the phase space measure
of the underlying non-Hamiltonian equations of motion.
:line

7
doc/fix_reaxc_species.html
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@ -208,9 +208,10 @@ order. The species analysis is performed using the average bond-order
on timesteps that are a multiple of <em>Nfreq</em>. The average is over
<em>Nrepeat</em> bond-order samples, computed in the preceding portion of the
simulation every <em>Nevery</em> timesteps. <em>Nfreq</em> must be a multiple of
<em>Nevery</em> and <em>Nevery</em> must be non-zero even if <em>Nrepeat</em> is 1. Also,
the timesteps contributing to the average bond-order cannot overlap,
i.e. Nfreq &gt; (Nrepeat-1)*Nevery is required.</p>
<em>Nevery</em> and <em>Nevery</em> must be non-zero even if <em>Nrepeat</em> is 1.
Also, the timesteps
contributing to the average bond-order cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.</p>
<p>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then bond-order
values on timesteps 90,92,94,96,98,100 will be used to compute the
average bond-order for the species analysis output on timestep 100.</p>

7
doc/fix_saed_vtk.html
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@ -193,9 +193,10 @@ average. The final averaged quantities are generated on timesteps
that are a multiple of <em>Nfreq</em>. The average is over <em>Nrepeat</em>
quantities, computed in the preceding portion of the simulation every
<em>Nevery</em> timesteps. <em>Nfreq</em> must be a multiple of <em>Nevery</em> and
<em>Nevery</em> must be non-zero even if <em>Nrepeat</em> is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nfreq &gt;
(Nrepeat-1)*Nevery is required.</p>
<em>Nevery</em> must be non-zero even if <em>Nrepeat</em> is 1.
Also, the timesteps
contributing to the average value cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.</p>
<p>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on

2
doc/searchindex.js
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2
src/STUBS/Makefile
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@ -22,7 +22,7 @@ OBJ = $(SRC:.c=.o)
# System-specific settings
CC = g++
CCFLAGS = -O -fPIC -I.
CCFLAGS = -O -fPIC -I. # add -I to insure mpi.h from this dir is included
ARCHIVE = ar
ARCHFLAG = rs

1
src/STUBS/mpi.c
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@ -12,6 +12,7 @@
------------------------------------------------------------------------ */
/* Single-processor "stub" versions of MPI routines */
/* -I. in Makefile insures dummy mpi.h in this dir is included */
#include <stdlib.h>
#include <string.h>

2
src/version.h
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@ -1 +1 @@
#define LAMMPS_VERSION "20 Nov 2015"
#define LAMMPS_VERSION "7 Dec 2015"