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<HTML>
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<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="10 Dec 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 Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<title>LAMMPS Documentation &mdash; LAMMPS 15 May 2015 version documentation</title>
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<H1></H1>
<CENTER><H3>LAMMPS Documentation
</H3></CENTER>
<CENTER><H4>10 Dec 2015 version
</H4></CENTER>
<H4>Version info:
</H4>
<P>The LAMMPS "version" is the date when it was released, such as 1 May
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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<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>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<H1></H1><div class="section" id="lammps-documentation">
<h1>LAMMPS Documentation<a class="headerlink" href="#lammps-documentation" title="Permalink to this headline"></a></h1>
<div class="section" id="dec-2015-version">
<h2>10 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>
<UL><LI>If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of LAMMPS.
<LI>If you browse the HTML doc pages included in your tarball, they
describe the version you have.
<LI>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
the first page of the manual (this page).</p>
<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.</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>
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>
</li>
</ul>
</div>
</div>
</div>
<div class="section" id="indices-and-tables">
<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline"></a></h1>
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@ -411,9 +411,16 @@ downloaded and looked at a few of them, their documentation was
incomplete and I had trouble with their installation. It&#8217;s not clear
if some of the packages are still being actively developed and
supported.</p>
<p>The one I recommend, since I have successfully used it with LAMMPS, is
Pypar. Pypar requires the ubiquitous <a class="reference external" href="http://numpy.scipy.org">Numpy package</a> be installed in your Python. After
launching python, type</p>
<p>The packages Pypar and mpi4py have both been successfully tested with
LAMMPS. Pypar is simpler and easy to set up and use, but supports
only a subset of MPI. Mpi4py is more MPI-feature complete, but also a
bit more complex to use. As of version 2.0.0, mpi4py is the only
python MPI wrapper that allows passing a custom MPI communicator to
the LAMMPS constructor, which means one can easily run one or more
LAMMPS instances on subsets of the total MPI ranks.</p>
<hr class="docutils" />
<p>Pypar requires the ubiquitous <a class="reference external" href="http://numpy.scipy.org">Numpy package</a>
be installed in your Python. After launching Python, type</p>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">numpy</span>
</pre></div>
</div>
@ -466,6 +473,51 @@ address, e.g. by moving other MPI installations so that Pypar finds
the right one.</p>
</div>
<hr class="docutils" />
<p>To install mpi4py (version mpi4py-2.0.0 as of Oct 2015), unpack it
and from its main directory, type</p>
<div class="highlight-python"><div class="highlight"><pre>python setup.py build
sudo python setup.py install
</pre></div>
</div>
<p>Again, the &#8220;sudo&#8221; is only needed if required to copy mpi4py files into
your Python distribution&#8217;s site-packages directory. To install with
user privilege into the user local directory type</p>
<div class="highlight-python"><div class="highlight"><pre>python setup.py install --user
</pre></div>
</div>
<p>If you have successully installed mpi4py, you should be able to run
Python and type</p>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">mpi4py</span> <span class="kn">import</span> <span class="n">MPI</span>
</pre></div>
</div>
<p>without error. You should also be able to run python in parallel
on a simple test script</p>
<div class="highlight-python"><div class="highlight"><pre>% mpirun -np 4 python test.py
</pre></div>
</div>
<p>where test.py contains the lines</p>
<div class="highlight-python"><div class="highlight"><pre>from mpi4py import MPI
comm = MPI.COMM_WORLD
print &quot;Proc %d out of %d procs&quot; % (comm.Get_rank(),comm.Get_size())
</pre></div>
</div>
<p>and see one line of output for each processor you run on.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">To use mpi4py and LAMMPS in parallel from Python, you
must insure both are using the same version of MPI. If you only have
one MPI installed on your system, this is not an issue, but it can be
if you have multiple MPIs. Your LAMMPS build is explicit about which
MPI it is using, since you specify the details in your lo-level
src/MAKE/Makefile.foo file. Mpi4py uses the &#8220;mpicc&#8221; command to find
information about the MPI it uses to build against. And it tries to
load &#8220;libmpi.so&#8221; from the LD_LIBRARY_PATH. This may or may not find
the MPI library that LAMMPS is using. If you have problems running
both mpi4py and LAMMPS together, this is an issue you may need to
address, e.g. by moving other MPI installations so that mpi4py finds
the right one.</p>
</div>
<hr class="docutils" />
</div>
<div class="section" id="testing-the-python-lammps-interface">
<span id="py-6"></span><h2>11.6. Testing the Python-LAMMPS interface<a class="headerlink" href="#testing-the-python-lammps-interface" title="Permalink to this headline"></a></h2>
@ -517,8 +569,8 @@ typed something like:</p>
<div class="section" id="test-lammps-and-python-in-parallel">
<h3>11.6.2. <strong>Test LAMMPS and Python in parallel:</strong><a class="headerlink" href="#test-lammps-and-python-in-parallel" title="Permalink to this headline"></a></h3>
<p>To run LAMMPS in parallel, assuming you have installed the
<a class="reference external" href="http://datamining.anu.edu.au/~ole/pypar">Pypar</a> package as discussed
above, create a test.py file containing these lines:</p>
<a class="reference external" href="Pypar">Pypar</a> package as discussed above, create a test.py file
containing these lines:</p>
<div class="highlight-python"><div class="highlight"><pre>import pypar
from lammps import lammps
lmp = lammps()
@ -527,7 +579,20 @@ print &quot;Proc %d out of %d procs has&quot; % (pypar.rank(),pypar.size()),lmp
pypar.finalize()
</pre></div>
</div>
<p>You can then run it in parallel as:</p>
<p>To run LAMMPS in parallel, assuming you have installed the
<a class="reference external" href="mpi4py">mpi4py</a> package as discussed above, create a test.py file
containing these lines:</p>
<div class="highlight-python"><div class="highlight"><pre>from mpi4py import MPI
from lammps import lammps
lmp = lammps()
lmp.file(&quot;in.lj&quot;)
me = MPI.COMM_WORLD.Get_rank()
nprocs = MPI.COMM_WORLD.Get_size()
print &quot;Proc %d out of %d procs has&quot; % (me,nprocs),lmp
MPI.Finalize()
</pre></div>
</div>
<p>You can either script in parallel as:</p>
<div class="highlight-python"><div class="highlight"><pre>% mpirun -np 4 python test.py
</pre></div>
</div>
@ -590,11 +655,12 @@ Python script, as follows:</p>
the files src/library.cpp and src/library.h you will see that they
correspond one-to-one with calls you can make to the LAMMPS library
from a C++ or C or Fortran program.</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">()</span> <span class="c"># create a LAMMPS object using the default liblammps.so library</span>
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="n">ptr</span><span class="o">=</span><span class="n">lmpptr</span><span class="p">)</span> <span class="c"># ditto, but use lmpptr as previously created LAMMPS object</span>
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="s">&quot;g++&quot;</span><span class="p">)</span> <span class="c"># create a LAMMPS object using the liblammps_g++.so library</span>
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="s">&quot;&quot;</span><span class="p">,</span><span class="nb">list</span><span class="p">)</span> <span class="c"># ditto, with command-line args, e.g. list = [&quot;-echo&quot;,&quot;screen&quot;]</span>
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="s">&quot;g++&quot;</span><span class="p">,</span><span class="nb">list</span><span class="p">)</span>
<div class="highlight-python"><div class="highlight"><pre>lmp = lammps() # create a LAMMPS object using the default liblammps.so library
4 optional args are allowed: name, cmdargs, ptr, comm
lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object
lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later
lmp = lammps(name=&quot;g++&quot;) # create a LAMMPS object using the liblammps_g++.so library
lmp = lammps(name=&quot;g++&quot;,cmdargs=list) # add LAMMPS command-line args, e.g. list = [&quot;-echo&quot;,&quot;screen&quot;]
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span class="n">lmp</span><span class="o">.</span><span class="n">close</span><span class="p">()</span> <span class="c"># destroy a LAMMPS object</span>
@ -706,8 +772,8 @@ argument.</p>
returned, which you can use via normal Python subscripting. See the
extract() method in the src/atom.cpp file for a list of valid names.
Again, new names could easily be added. A pointer to a vector of
doubles or integers, or a pointer to an array of doubles (double <a href="#id2"><span class="problematic" id="id3">**</span></a>)
or integers (int <a href="#id4"><span class="problematic" id="id5">**</span></a>) is returned. You need to specify the appropriate
doubles or integers, or a pointer to an array of doubles (double <a href="#id3"><span class="problematic" id="id4">**</span></a>)
or integers (int <a href="#id5"><span class="problematic" id="id6">**</span></a>) is returned. You need to specify the appropriate
data type via the type argument.</p>
<p>For extract_compute() and extract_fix(), the global, per-atom, or
local data calulated by the compute or fix can be accessed. What is
@ -802,8 +868,8 @@ own scripts, send them to us and we can include them in the LAMMPS
distribution.</p>
<table border="1" class="docutils">
<colgroup>
<col width="27%" />
<col width="73%" />
<col width="56%" />
<col width="44%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>trivial.py</td>
@ -813,19 +879,25 @@ distribution.</p>
<td>invoke various LAMMPS library interface routines</td>
</tr>
<tr class="row-odd"><td>simple.py</td>
<td>mimic operation of couple/simple/simple.cpp in Python</td>
<td>run in parallel</td>
</tr>
<tr class="row-even"><td>gui.py</td>
<td>GUI go/stop/temperature-slider to control LAMMPS</td>
<tr class="row-even"><td>similar to examples/COUPLE/simple/simple.cpp</td>
<td>split.py</td>
</tr>
<tr class="row-odd"><td>plot.py</td>
<td>real-time temeperature plot with GnuPlot via Pizza.py</td>
<tr class="row-odd"><td>same as simple.py but running in parallel on a subset of procs</td>
<td>gui.py</td>
</tr>
<tr class="row-even"><td>viz_tool.py</td>
<td>real-time viz via some viz package</td>
<tr class="row-even"><td>GUI go/stop/temperature-slider to control LAMMPS</td>
<td>plot.py</td>
</tr>
<tr class="row-odd"><td>vizplotgui_tool.py</td>
<td>combination of viz_tool.py and plot.py and gui.py</td>
<tr class="row-odd"><td>real-time temeperature plot with GnuPlot via Pizza.py</td>
<td>viz_tool.py</td>
</tr>
<tr class="row-even"><td>real-time viz via some viz package</td>
<td>vizplotgui_tool.py</td>
</tr>
<tr class="row-odd"><td>combination of viz_tool.py and plot.py and gui.py</td>
<td>&nbsp;</td>
</tr>
</tbody>
</table>

39
doc/Section_python.txt
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@ -304,13 +304,12 @@ if some of the packages are still being actively developed and
supported.
The packages Pypar and mpi4py have both been successfully tested with
LAMMPS. Both are widely used. Pypar is simpler and easy to set up
and use, but supports only a subset of MPI. Mpi4py is more
MPI-feature complete, but also a bit more complex to use. As of
version 2.0.0, mpi4py is the only python MPI wrapper that allows
passing a custom MPI communicator to the LAMMPS constructor, which
means one can easily run one or more LAMMPS instances on subsets of
the total MPI ranks.
LAMMPS. Pypar is simpler and easy to set up and use, but supports
only a subset of MPI. Mpi4py is more MPI-feature complete, but also a
bit more complex to use. As of version 2.0.0, mpi4py is the only
python MPI wrapper that allows passing a custom MPI communicator to
the LAMMPS constructor, which means one can easily run one or more
LAMMPS instances on subsets of the total MPI ranks.
:line
@ -380,7 +379,7 @@ Again, the "sudo" is only needed if required to copy mpi4py files into
your Python distribution's site-packages directory. To install with
user privilege into the user local directory type
python setup.py install --user
python setup.py install --user :pre
If you have successully installed mpi4py, you should be able to run
Python and type
@ -467,8 +466,8 @@ lmp_g++ -in in.lj :pre
[Test LAMMPS and Python in parallel:] :h5
To run LAMMPS in parallel, assuming you have installed the
"Pypar"_http://datamining.anu.edu.au/~ole/pypar package as discussed
above, create a test.py file containing these lines:
"Pypar"_Pypar package as discussed above, create a test.py file
containing these lines:
import pypar
from lammps import lammps
@ -477,7 +476,20 @@ lmp.file("in.lj")
print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()),lmp
pypar.finalize() :pre
You can then run it in parallel as:
To run LAMMPS in parallel, assuming you have installed the
"mpi4py"_mpi4py package as discussed above, create a test.py file
containing these lines:
from mpi4py import MPI
from lammps import lammps
lmp = lammps()
lmp.file("in.lj")
me = MPI.COMM_WORLD.Get_rank()
nprocs = MPI.COMM_WORLD.Get_size()
print "Proc %d out of %d procs has" % (me,nprocs),lmp
MPI.Finalize() :pre
You can either script in parallel as:
% mpirun -np 4 python test.py :pre
@ -547,7 +559,7 @@ from a C++ or C or Fortran program.
lmp = lammps() # create a LAMMPS object using the default liblammps.so library
4 optional args are allowed: name, cmdargs, ptr, comm
lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object
lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator. Requires mpi4py 2.0.0 or later
lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later
lmp = lammps(name="g++") # create a LAMMPS object using the liblammps_g++.so library
lmp = lammps(name="g++",cmdargs=list) # add LAMMPS command-line args, e.g. list = \["-echo","screen"\] :pre
@ -772,7 +784,8 @@ distribution.
trivial.py, read/run a LAMMPS input script thru Python,
demo.py, invoke various LAMMPS library interface routines,
simple.py, mimic operation of couple/simple/simple.cpp in Python,
simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp,
split.py, same as simple.py but running in parallel on a subset of procs,
gui.py, GUI go/stop/temperature-slider to control LAMMPS,
plot.py, real-time temeperature plot with GnuPlot via Pizza.py,
viz_tool.py, real-time viz via some viz package,

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