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<TITLE>LAMMPS Users Manual</TITLE>
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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>
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<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="jul-2015-version">
<h2>27 Jul 2015 version<a class="headerlink" href="#jul-2015-version" title="Permalink to this headline"></a></h2>
</div>
<div class="section" id="version-info">
<h2>Version info:<a class="headerlink" href="#version-info" title="Permalink to this headline"></a></h2>
<p>The LAMMPS &#8220;version&#8221; is the date when it was released, such as 1 May
2010. LAMMPS is updated continuously. Whenever we fix a bug or add a 2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
feature, we release it immediately, and post a notice on <A HREF = "http://lammps.sandia.gov/bug.html">this page of 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
the WWW site</A>. Each dated copy of LAMMPS contains all the
features and bug-fixes up to and including that version date. The features and bug-fixes up to and including that version date. The
version date is printed to the screen and logfile every time you run version date is printed to the screen and logfile every time you run
LAMMPS. It is also in the file src/version.h and in the LAMMPS LAMMPS. It is also in the file src/version.h and in the LAMMPS
directory name created when you unpack a tarball, and at the top of directory name created when you unpack a tarball, and at the top of
the first page of the manual (this page). the first page of the manual (this page).</p>
</P> <ul class="simple">
<UL><LI>If you browse the HTML doc pages on the LAMMPS WWW site, they always <li>If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of LAMMPS. describe the most current version of LAMMPS.</li>
<li>If you browse the HTML doc pages included in your tarball, they
<LI>If you browse the HTML doc pages included in your tarball, they describe the version you have.</li>
describe the version you have. <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
<LI>The <A HREF = "Manual.pdf">PDF file</A> on the WWW site or in the tarball is updated it to be part of every patch.</li>
about once per month. This is because it is large, and we don't want <li>There is also a <a class="reference external" href="Developer.pdf">Developer.pdf</a> file in the doc
it to be part of every patch.
<LI>There is also a <A HREF = "Developer.pdf">Developer.pdf</A> file in the doc
directory, which describes the internal structure and algorithms of directory, which describes the internal structure and algorithms of
LAMMPS. LAMMPS.</li>
</UL> </ul>
<P>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel <p>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator. Simulator.</p>
</P> <p>LAMMPS is a classical molecular dynamics simulation code designed to
<P>LAMMPS is a classical molecular dynamics simulation code designed to
run efficiently on parallel computers. It was developed at Sandia run efficiently on parallel computers. It was developed at Sandia
National Laboratories, a US Department of Energy facility, with National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL). under the terms of the GNU Public License (GPL).</p>
</P> <p>The primary developers of LAMMPS are <a class="reference external" href="http://www.sandia.gov/~sjplimp">Steve Plimpton</a>, Aidan
<P>The primary developers of LAMMPS are <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Aidan
Thompson, and Paul Crozier who can be contacted at Thompson, and Paul Crozier who can be contacted at
sjplimp,athomps,pscrozi at sandia.gov. The <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> at sjplimp,athomps,pscrozi at sandia.gov. The <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> at
http://lammps.sandia.gov has more information about the code and its <a class="reference external" href="http://lammps.sandia.gov">http://lammps.sandia.gov</a> has more information about the code and its
uses. uses.</p>
</P> <hr class="docutils" />
<p>The LAMMPS documentation is organized into the following sections. If
<HR>
<P>The LAMMPS documentation is organized into the following sections. If
you find errors or omissions in this manual or have suggestions for you find errors or omissions in this manual or have suggestions for
useful information to add, please send an email to the developers so useful information to add, please send an email to the developers so
we can improve the LAMMPS documentation. we can improve the LAMMPS documentation.</p>
</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
<P>Once you are familiar with LAMMPS, you may want to bookmark <A HREF = "Section_commands.html#comm">this it gives quick access to documentation for all LAMMPS commands.</p>
page</A> at Section_commands.html#comm since <p><a class="reference external" href="Manual.pdf">PDF file</a> of the entire manual, generated by
it gives quick access to documentation for all LAMMPS commands. <a class="reference external" href="http://freecode.com/projects/htmldoc">htmldoc</a></p>
</P> <div class="toctree-wrapper compound">
<P><A HREF = "Manual.pdf">PDF file</A> of the entire manual, generated by <ul>
<A HREF = "http://freecode.com/projects/htmldoc">htmldoc</A> <li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a><ul>
</P> <li class="toctree-l2"><a class="reference internal" href="Section_intro.html#what-is-lammps">1.1. What is LAMMPS</a></li>
<P><!-- RST <li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-features">1.2. LAMMPS features</a></li>
</P> <li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-non-features">1.3. LAMMPS non-features</a></li>
<P>.. toctree:: <li class="toctree-l2"><a class="reference internal" href="Section_intro.html#open-source-distribution">1.4. Open source distribution</a></li>
:maxdepth: 2 <li class="toctree-l2"><a class="reference internal" href="Section_intro.html#acknowledgments-and-citations">1.5. Acknowledgments and citations</a></li>
:numbered: // comment </ul>
</P> </li>
<P> Section_intro <li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a><ul>
Section_start <li class="toctree-l2"><a class="reference internal" href="Section_start.html#what-s-in-the-lammps-distribution">2.1. What&#8217;s in the LAMMPS distribution</a></li>
Section_commands <li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps">2.2. Making LAMMPS</a></li>
Section_packages <li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps-with-optional-packages">2.3. Making LAMMPS with optional packages</a></li>
Section_accelerate <li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-via-the-make-py-script">2.4. Building LAMMPS via the Make.py script</a></li>
Section_howto <li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-as-a-library">2.5. Building LAMMPS as a library</a></li>
Section_example <li class="toctree-l2"><a class="reference internal" href="Section_start.html#running-lammps">2.6. Running LAMMPS</a></li>
Section_perf <li class="toctree-l2"><a class="reference internal" href="Section_start.html#command-line-options">2.7. Command-line options</a></li>
Section_tools <li class="toctree-l2"><a class="reference internal" href="Section_start.html#lammps-screen-output">2.8. LAMMPS screen output</a></li>
Section_modify <li class="toctree-l2"><a class="reference internal" href="Section_start.html#tips-for-users-of-previous-lammps-versions">2.9. Tips for users of previous LAMMPS versions</a></li>
Section_python </ul>
Section_errors </li>
Section_history <li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a><ul>
</P> <li class="toctree-l2"><a class="reference internal" href="Section_commands.html#lammps-input-script">3.1. LAMMPS input script</a></li>
<P>Indices and tables <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>
</P> <li class="toctree-l2"><a class="reference internal" href="Section_commands.html#commands-listed-by-category">3.4. Commands listed by category</a></li>
<P>* :ref:`genindex` // comment <li class="toctree-l2"><a class="reference internal" href="Section_commands.html#individual-commands">3.5. Individual commands</a></li>
* :ref:`search` // comment <li class="toctree-l2"><a class="reference internal" href="Section_commands.html#fix-styles">3.6. Fix styles</a></li>
</P> <li class="toctree-l2"><a class="reference internal" href="Section_commands.html#compute-styles">3.7. Compute styles</a></li>
<P>END_RST --> <li class="toctree-l2"><a class="reference internal" href="Section_commands.html#pair-style-potentials">3.8. Pair_style potentials</a></li>
</P> <li class="toctree-l2"><a class="reference internal" href="Section_commands.html#bond-style-potentials">3.9. Bond_style potentials</a></li>
<OL><LI><!-- HTML_ONLY --> <li class="toctree-l2"><a class="reference internal" href="Section_commands.html#angle-style-potentials">3.10. Angle_style potentials</a></li>
<A HREF = "Section_intro.html">Introduction</A> <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>
<UL> 1.1 <A HREF = "Section_intro.html#intro_1">What is LAMMPS</A> <li class="toctree-l2"><a class="reference internal" href="Section_commands.html#kspace-solvers">3.13. Kspace solvers</a></li>
<BR> </ul>
1.2 <A HREF = "Section_intro.html#intro_2">LAMMPS features</A> </li>
<BR> <li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a><ul>
1.3 <A HREF = "Section_intro.html#intro_3">LAMMPS non-features</A> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#standard-packages">4.1. Standard packages</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-packages">4.2. User packages</a></li>
1.4 <A HREF = "Section_intro.html#intro_4">Open source distribution</A> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-atc-package">4.3. USER-ATC package</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-awpmd-package">4.4. USER-AWPMD package</a></li>
1.5 <A HREF = "Section_intro.html#intro_5">Acknowledgments and citations</A> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cg-cmm-package">4.5. USER-CG-CMM package</a></li>
<BR></UL> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-colvars-package">4.6. USER-COLVARS package</a></li>
<LI><A HREF = "Section_start.html">Getting started</A> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cuda-package">4.7. USER-CUDA package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-diffraction-package">4.8. USER-DIFFRACTION package</a></li>
<UL> 2.1 <A HREF = "Section_start.html#start_1">What's in the LAMMPS distribution</A> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-drude-package">4.9. USER-DRUDE package</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-eff-package">4.10. USER-EFF package</a></li>
2.2 <A HREF = "Section_start.html#start_2">Making LAMMPS</A> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-fep-package">4.11. USER-FEP package</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-intel-package">4.12. USER-INTEL package</a></li>
2.3 <A HREF = "Section_start.html#start_3">Making LAMMPS with optional packages</A> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-lb-package">4.13. USER-LB package</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-misc-package">4.14. USER-MISC package</a></li>
2.4 <A HREF = "Section_start.html#start_4">Building LAMMPS via the Make.py script</A> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-molfile-package">4.15. USER-MOLFILE package</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-omp-package">4.16. USER-OMP package</a></li>
2.5 <A HREF = "Section_start.html#start_5">Building LAMMPS as a library</A> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-phonon-package">4.17. USER-PHONON package</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qmmm-package">4.18. USER-QMMM package</a></li>
2.6 <A HREF = "Section_start.html#start_6">Running LAMMPS</A> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qtb-package">4.19. USER-QTB package</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-reaxc-package">4.20. USER-REAXC package</a></li>
2.7 <A HREF = "Section_start.html#start_7">Command-line options</A> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-sph-package">4.21. USER-SPH package</a></li>
<BR> </ul>
2.8 <A HREF = "Section_start.html#start_8">Screen output</A> </li>
<BR> <li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a><ul>
2.9 <A HREF = "Section_start.html#start_9">Tips for users of previous versions</A> <li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#measuring-performance">5.1. Measuring performance</a></li>
<BR></UL> <li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#general-strategies">5.2. General strategies</a></li>
<LI><A HREF = "Section_commands.html">Commands</A> <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> 3.1 <A HREF = "Section_commands.html#cmd_1">LAMMPS input script</A> </ul>
<BR> </li>
3.2 <A HREF = "Section_commands.html#cmd_2">Parsing rules</A> <li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a><ul>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#restarting-a-simulation">6.1. Restarting a simulation</a></li>
3.3 <A HREF = "Section_commands.html#cmd_3">Input script structure</A> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#d-simulations">6.2. 2d simulations</a></li>
<BR> <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>
3.4 <A HREF = "Section_commands.html#cmd_4">Commands listed by category</A> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#running-multiple-simulations-from-one-input-script">6.4. Running multiple simulations from one input script</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#multi-replica-simulations">6.5. Multi-replica simulations</a></li>
3.5 <A HREF = "Section_commands.html#cmd_5">Commands listed alphabetically</A> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#granular-models">6.6. Granular models</a></li>
<BR></UL> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip3p-water-model">6.7. TIP3P water model</a></li>
<LI><A HREF = "Section_packages.html">Packages</A> <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>
<UL> 4.1 <A HREF = "Section_packages.html#pkg_1">Standard packages</A> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#coupling-lammps-to-other-codes">6.10. Coupling LAMMPS to other codes</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#visualizing-lammps-snapshots">6.11. Visualizing LAMMPS snapshots</a></li>
4.2 <A HREF = "Section_packages.html#pkg_2">User packages</A> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#triclinic-non-orthogonal-simulation-boxes">6.12. Triclinic (non-orthogonal) simulation boxes</a></li>
<BR></UL> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#nemd-simulations">6.13. NEMD simulations</a></li>
<LI><A HREF = "Section_accelerate.html">Accelerating LAMMPS performance</A> <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>
<UL> 5.1 <A HREF = "Section_accelerate.html#acc_1">Measuring performance</A> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#thermostatting-barostatting-and-computing-temperature">6.16. Thermostatting, barostatting, and computing temperature</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#walls">6.17. Walls</a></li>
5.2 <A HREF = "Section_accelerate.html#acc_2">Algorithms and code options to boost performace</A> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#elastic-constants">6.18. Elastic constants</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#library-interface-to-lammps">6.19. Library interface to LAMMPS</a></li>
5.3 <A HREF = "Section_accelerate.html#acc_3">Accelerator packages with optimized styles</A> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-thermal-conductivity">6.20. Calculating thermal conductivity</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-viscosity">6.21. Calculating viscosity</a></li>
<UL> 5.3.1 <A HREF = "accelerate_cuda.html">USER-CUDA package</A> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-a-diffusion-coefficient">6.22. Calculating a diffusion coefficient</a></li>
<BR> <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>
5.3.2 <A HREF = "accelerate_gpu.html">GPU package</A> <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>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#polarizable-models">6.25. Polarizable models</a></li>
5.3.3 <A HREF = "accelerate_intel.html">USER-INTEL package</A> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#adiabatic-core-shell-model">6.26. Adiabatic core/shell model</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#drude-induced-dipoles">6.27. Drude induced dipoles</a></li>
5.3.4 <A HREF = "accelerate_kokkos.html">KOKKOS package</A> </ul>
<BR> </li>
5.3.5 <A HREF = "accelerate_omp.html">USER-OMP package</A> <li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<BR> <li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
5.3.6 <A HREF = "accelerate_opt.html">OPT package</A> <li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a><ul>
<BR></UL> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#amber2lmp-tool">9.1. amber2lmp tool</a></li>
5.4 <A HREF = "Section_accelerate.html#acc_4">Comparison of various accelerator packages</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#binary2txt-tool">9.2. binary2txt tool</a></li>
<BR></UL> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ch2lmp-tool">9.3. ch2lmp tool</a></li>
<LI><A HREF = "Section_howto.html">How-to discussions</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#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>
<UL> 6.1 <A HREF = "Section_howto.html#howto_1">Restarting a simulation</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#createatoms-tool">9.6. createatoms tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#data2xmovie-tool">9.7. data2xmovie tool</a></li>
6.2 <A HREF = "Section_howto.html#howto_2">2d simulations</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-database-tool">9.8. eam database tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-generate-tool">9.9. eam generate tool</a></li>
6.3 <A HREF = "Section_howto.html#howto_3">CHARMM and AMBER force fields</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eff-tool">9.10. eff tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#emacs-tool">9.11. emacs tool</a></li>
6.4 <A HREF = "Section_howto.html#howto_4">Running multiple simulations from one input script</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#fep-tool">9.12. fep tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#i-pi-tool">9.13. i-pi tool</a></li>
6.5 <A HREF = "Section_howto.html#howto_5">Multi-replica simulations</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ipp-tool">9.14. ipp tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#kate-tool">9.15. kate tool</a></li>
6.6 <A HREF = "Section_howto.html#howto_6">Granular models</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2arc-tool">9.16. lmp2arc tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2cfg-tool">9.17. lmp2cfg tool</a></li>
6.7 <A HREF = "Section_howto.html#howto_7">TIP3P water model</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2vmd-tool">9.18. lmp2vmd tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#matlab-tool">9.19. matlab tool</a></li>
6.8 <A HREF = "Section_howto.html#howto_8">TIP4P water model</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#micelle2d-tool">9.20. micelle2d tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#moltemplate-tool">9.21. moltemplate tool</a></li>
6.9 <A HREF = "Section_howto.html#howto_9">SPC water model</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#msi2lmp-tool">9.22. msi2lmp tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#phonon-tool">9.23. phonon tool</a></li>
6.10 <A HREF = "Section_howto.html#howto_10">Coupling LAMMPS to other codes</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#polymer-bonding-tool">9.24. polymer bonding tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#pymol-asphere-tool">9.25. pymol_asphere tool</a></li>
6.11 <A HREF = "Section_howto.html#howto_11">Visualizing LAMMPS snapshots</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#python-tool">9.26. python tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#reax-tool">9.27. reax tool</a></li>
6.12 <A HREF = "Section_howto.html#howto_12">Triclinic (non-orthogonal) simulation boxes</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#restart2data-tool">9.28. restart2data tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#vim-tool">9.29. vim tool</a></li>
6.13 <A HREF = "Section_howto.html#howto_13">NEMD simulations</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmgrace-tool">9.30. xmgrace tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmovie-tool">9.31. xmovie tool</a></li>
6.14 <A HREF = "Section_howto.html#howto_14">Finite-size spherical and aspherical particles</A> </ul>
<BR> </li>
6.15 <A HREF = "Section_howto.html#howto_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A> <li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a><ul>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#atom-styles">10.1. Atom styles</a></li>
6.16 <A HREF = "Section_howto.html#howto_16">Thermostatting, barostatting, and compute temperature</A> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#bond-angle-dihedral-improper-potentials">10.2. Bond, angle, dihedral, improper potentials</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#compute-styles">10.3. Compute styles</a></li>
6.17 <A HREF = "Section_howto.html#howto_17">Walls</A> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-styles">10.4. Dump styles</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-custom-output-options">10.5. Dump custom output options</a></li>
6.18 <A HREF = "Section_howto.html#howto_18">Elastic constants</A> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#fix-styles">10.6. Fix styles</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#input-script-commands">10.7. Input script commands</a></li>
6.19 <A HREF = "Section_howto.html#howto_19">Library interface to LAMMPS</A> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#kspace-computations">10.8. Kspace computations</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#minimization-styles">10.9. Minimization styles</a></li>
6.20 <A HREF = "Section_howto.html#howto_20">Calculating thermal conductivity</A> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#pairwise-potentials">10.10. Pairwise potentials</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#region-styles">10.11. Region styles</a></li>
6.21 <A HREF = "Section_howto.html#howto_21">Calculating viscosity</A> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#body-styles">10.12. Body styles</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#thermodynamic-output-options">10.13. Thermodynamic output options</a></li>
6.22 <A HREF = "Section_howto.html#howto_22">Calculating a diffusion coefficient</A> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#variable-options">10.14. Variable options</a></li>
<BR> <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>
6.23 <A HREF = "Section_howto.html#howto_23">Using chunks to calculate system properties</A> </ul>
<BR> </li>
6.24 <A HREF = "Section_howto.html#howto_24">Setting parameters for pppm/disp</A> <li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a><ul>
<BR> <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>
6.25 <A HREF = "Section_howto.html#howto_25">Polarizable models</A> <li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-using-python-from-a-lammps-script">11.2. Overview of using Python from a LAMMPS script</a></li>
<BR> <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>
6.26 <A HREF = "Section_howto.html#howto_26">Adiabatic core/shell model</A> <li class="toctree-l2"><a class="reference internal" href="Section_python.html#installing-the-python-wrapper-into-python">11.4. Installing the Python wrapper into Python</a></li>
<BR> <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>
6.27 <A HREF = "Section_howto.html#howto_27">Drude induced dipoles</A> <li class="toctree-l2"><a class="reference internal" href="Section_python.html#testing-the-python-lammps-interface">11.6. Testing the Python-LAMMPS interface</a></li>
<BR></UL> <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><A HREF = "Section_example.html">Example problems</A> <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><A HREF = "Section_perf.html">Performance & scalability</A> </li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a><ul>
<LI><A HREF = "Section_tools.html">Additional tools</A> <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><A HREF = "Section_modify.html">Modifying & extending LAMMPS</A> <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>
<UL> 10.1 <A HREF = "Section_modify.html#mod_1">Atom styles</A> <li class="toctree-l2"><a class="reference internal" href="Section_errors.html#warnings">12.5. Warnings:</a></li>
<BR> </ul>
10.2 <A HREF = "Section_modify.html#mod_2">Bond, angle, dihedral, improper potentials</A> </li>
<BR> <li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a><ul>
10.3 <A HREF = "Section_modify.html#mod_3">Compute styles</A> <li class="toctree-l2"><a class="reference internal" href="Section_history.html#coming-attractions">13.1. Coming attractions</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_history.html#past-versions">13.2. Past versions</a></li>
10.4 <A HREF = "Section_modify.html#mod_4">Dump styles</A> </ul>
<BR> </li>
10.5 <A HREF = "Section_modify.html#mod_5">Dump custom output options</A> </ul>
<BR> </div>
10.6 <A HREF = "Section_modify.html#mod_6">Fix styles</A> </div>
<BR> </div>
10.7 <A HREF = "Section_modify.html#mod_7">Input script commands</A> <div class="section" id="indices-and-tables">
<BR> <h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline"></a></h1>
10.8 <A HREF = "Section_modify.html#mod_8">Kspace computations</A> <ul class="simple">
<BR> <li><a class="reference internal" href="genindex.html"><span>Index</span></a></li>
10.9 <A HREF = "Section_modify.html#mod_9">Minimization styles</A> <li><a class="reference internal" href="search.html"><span>Search Page</span></a></li>
<BR> </ul>
10.10 <A HREF = "Section_modify.html#mod_10">Pairwise potentials</A> </BODY></div>
<BR>
10.11 <A HREF = "Section_modify.html#mod_11">Region styles</A>
<BR> </div>
10.12 <A HREF = "Section_modify.html#mod_12">Body styles</A> </div>
<BR> <footer>
10.13 <A HREF = "Section_modify.html#mod_13">Thermodynamic output options</A>
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10.14 <A HREF = "Section_modify.html#mod_14">Variable options</A>
<BR> <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>
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> </div>
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<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="28 Jul 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>28 Jul 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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10
doc/Manual.txt
View File

@ -1,7 +1,7 @@
<!-- HTML_ONLY --> <!-- HTML_ONLY -->
<HEAD> <HEAD>
<TITLE>LAMMPS Users Manual</TITLE> <TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="28 Jul 2015 version"> <META NAME="docnumber" CONTENT="27 Jul 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD> </HEAD>
@ -21,7 +21,7 @@
<H1></H1> <H1></H1>
LAMMPS Documentation :c,h3 LAMMPS Documentation :c,h3
28 Jul 2015 version :c,h4 27 Jul 2015 version :c,h4
Version info: :h4 Version info: :h4
@ -85,7 +85,7 @@ it gives quick access to documentation for all LAMMPS commands.
.. toctree:: .. toctree::
:maxdepth: 2 :maxdepth: 2
:numbered: // comment :numbered:
Section_intro Section_intro
Section_start Section_start
@ -105,8 +105,8 @@ it gives quick access to documentation for all LAMMPS commands.
Indices and tables Indices and tables
================== ==================
* :ref:`genindex` // comment * :ref:`genindex`
* :ref:`search` // comment * :ref:`search`
END_RST --> END_RST -->