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<HTML>
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<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="31 Oct 2015 version">
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<CENTER><H3>LAMMPS Documentation
</H3></CENTER>
<CENTER><H4>31 Oct 2015 version
</H4></CENTER>
<H4>Version info:
</H4>
<P>The LAMMPS "version" is the date when it was released, such as 1 May
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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="aug-2015-version">
<h2>10 Aug 2015 version<a class="headerlink" href="#aug-2015-version" title="Permalink to this headline"></a></h2>
</div>
<div class="section" id="version-info">
<h2>Version info:<a class="headerlink" href="#version-info" title="Permalink to this headline"></a></h2>
<p>The LAMMPS &#8220;version&#8221; is the date when it was released, such as 1 May
2010. LAMMPS is updated continuously. Whenever we fix a bug or add a 2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
feature, we release it immediately, and post a notice on <A 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-tool">2.4. Building LAMMPS via the Make.py tool</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>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#kspace-solvers">3.13. Kspace solvers</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#standard-packages">4.1. Standard packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-compress-package">4.2. Build instructions for COMPRESS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-gpu-package">4.3. Build instructions for GPU package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-kim-package">4.4. Build instructions for KIM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-kokkos-package">4.5. Build instructions for KOKKOS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-kspace-package">4.6. Build instructions for KSPACE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-meam-package">4.7. Build instructions for MEAM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-poems-package">4.8. Build instructions for POEMS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-python-package">4.9. Build instructions for PYTHON package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-reax-package">4.10. Build instructions for REAX package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-voronoi-package">4.11. Build instructions for VORONOI package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-xtc-package">4.12. Build instructions for XTC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-packages">4.13. User packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-atc-package">4.14. USER-ATC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-awpmd-package">4.15. USER-AWPMD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cg-cmm-package">4.16. USER-CG-CMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-colvars-package">4.17. USER-COLVARS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cuda-package">4.18. USER-CUDA package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-diffraction-package">4.19. USER-DIFFRACTION package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-drude-package">4.20. USER-DRUDE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-eff-package">4.21. USER-EFF package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-fep-package">4.22. USER-FEP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-h5md-package">4.23. USER-H5MD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-intel-package">4.24. USER-INTEL package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-lb-package">4.25. USER-LB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-mgpt-package">4.26. USER-MGPT package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-misc-package">4.27. USER-MISC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-molfile-package">4.28. USER-MOLFILE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-omp-package">4.29. USER-OMP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-phonon-package">4.30. USER-PHONON package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qmmm-package">4.31. USER-QMMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qtb-package">4.32. USER-QTB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-reaxc-package">4.33. USER-REAXC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smd-package">4.34. USER-SMD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smtbq-package">4.35. USER-SMTBQ package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-sph-package">4.36. USER-SPH package</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#measuring-performance">5.1. Measuring performance</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#general-strategies">5.2. General strategies</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#packages-with-optimized-styles">5.3. Packages with optimized styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#comparison-of-various-accelerator-packages">5.4. Comparison of various accelerator packages</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#restarting-a-simulation">6.1. Restarting a simulation</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#d-simulations">6.2. 2d simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#charmm-amber-and-dreiding-force-fields">6.3. CHARMM, AMBER, and DREIDING force fields</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#running-multiple-simulations-from-one-input-script">6.4. Running multiple simulations from one input script</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#multi-replica-simulations">6.5. Multi-replica simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#granular-models">6.6. Granular models</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip3p-water-model">6.7. TIP3P water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip4p-water-model">6.8. TIP4P water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#spc-water-model">6.9. SPC water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#coupling-lammps-to-other-codes">6.10. Coupling LAMMPS to other codes</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#visualizing-lammps-snapshots">6.11. Visualizing LAMMPS snapshots</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#triclinic-non-orthogonal-simulation-boxes">6.12. Triclinic (non-orthogonal) simulation boxes</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#nemd-simulations">6.13. NEMD simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#finite-size-spherical-and-aspherical-particles">6.14. Finite-size spherical and aspherical particles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#output-from-lammps-thermo-dumps-computes-fixes-variables">6.15. Output from LAMMPS (thermo, dumps, computes, fixes, variables)</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#thermostatting-barostatting-and-computing-temperature">6.16. Thermostatting, barostatting, and computing temperature</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#walls">6.17. Walls</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#elastic-constants">6.18. Elastic constants</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#library-interface-to-lammps">6.19. Library interface to LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-thermal-conductivity">6.20. Calculating thermal conductivity</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-viscosity">6.21. Calculating viscosity</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-a-diffusion-coefficient">6.22. Calculating a diffusion coefficient</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#using-chunks-to-calculate-system-properties">6.23. Using chunks to calculate system properties</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#setting-parameters-for-the-kspace-style-pppm-disp-command">6.24. Setting parameters for the <code class="docutils literal"><span class="pre">kspace_style</span> <span class="pre">pppm/disp</span></code> command</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#polarizable-models">6.25. Polarizable models</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#adiabatic-core-shell-model">6.26. Adiabatic core/shell model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#drude-induced-dipoles">6.27. Drude induced dipoles</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#amber2lmp-tool">9.1. amber2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#binary2txt-tool">9.2. binary2txt tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ch2lmp-tool">9.3. ch2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#chain-tool">9.4. chain tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#colvars-tools">9.5. colvars tools</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#createatoms-tool">9.6. createatoms tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#data2xmovie-tool">9.7. data2xmovie tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-database-tool">9.8. eam database tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-generate-tool">9.9. eam generate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eff-tool">9.10. eff tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#emacs-tool">9.11. emacs tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#fep-tool">9.12. fep tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#i-pi-tool">9.13. i-pi tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ipp-tool">9.14. ipp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#kate-tool">9.15. kate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2arc-tool">9.16. lmp2arc tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2cfg-tool">9.17. lmp2cfg tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2vmd-tool">9.18. lmp2vmd tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#matlab-tool">9.19. matlab tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#micelle2d-tool">9.20. micelle2d tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#moltemplate-tool">9.21. moltemplate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#msi2lmp-tool">9.22. msi2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#phonon-tool">9.23. phonon tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#polymer-bonding-tool">9.24. polymer bonding tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#pymol-asphere-tool">9.25. pymol_asphere tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#python-tool">9.26. python tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#reax-tool">9.27. reax tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#restart2data-tool">9.28. restart2data tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#vim-tool">9.29. vim tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmgrace-tool">9.30. xmgrace tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmovie-tool">9.31. xmovie tool</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#atom-styles">10.1. Atom styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#bond-angle-dihedral-improper-potentials">10.2. Bond, angle, dihedral, improper potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#compute-styles">10.3. Compute styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-styles">10.4. Dump styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-custom-output-options">10.5. Dump custom output options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#fix-styles">10.6. Fix styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#input-script-commands">10.7. Input script commands</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#kspace-computations">10.8. Kspace computations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#minimization-styles">10.9. Minimization styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#pairwise-potentials">10.10. Pairwise potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#region-styles">10.11. Region styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#body-styles">10.12. Body styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#thermodynamic-output-options">10.13. Thermodynamic output options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#variable-options">10.14. Variable options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#submitting-new-features-for-inclusion-in-lammps">10.15. Submitting new features for inclusion in LAMMPS</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-running-lammps-from-python">11.1. Overview of running LAMMPS from Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-using-python-from-a-lammps-script">11.2. Overview of using Python from a LAMMPS script</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#building-lammps-as-a-shared-library">11.3. Building LAMMPS as a shared library</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#installing-the-python-wrapper-into-python">11.4. Installing the Python wrapper into Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#extending-python-with-mpi-to-run-in-parallel">11.5. Extending Python with MPI to run in parallel</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#testing-the-python-lammps-interface">11.6. Testing the Python-LAMMPS interface</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#using-lammps-from-python">11.7. Using LAMMPS from Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#example-python-scripts-that-use-lammps">11.8. Example Python scripts that use LAMMPS</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#common-problems">12.1. Common problems</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#reporting-bugs">12.2. Reporting bugs</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error-warning-messages">12.3. Error &amp; warning messages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error">12.4. Errors:</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#warnings">12.5. Warnings:</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_history.html#coming-attractions">13.1. Coming attractions</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_history.html#past-versions">13.2. Past versions</a></li>
</ul>
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</ul>
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<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>
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<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> <script type="text/javascript" src="_static/js/theme.js"></script>
<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>
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<UL> 10.1 <A HREF = "Section_modify.html#mod_1">Atom styles</A>
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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>
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<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> </body>
<BR> </html>
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>
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13.2 <A HREF = "Section_history.html#hist_2">Past versions</A>
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4
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@ -3,7 +3,7 @@
<!-- HTML_ONLY --> <!-- HTML_ONLY -->
<HEAD> <HEAD>
<TITLE>LAMMPS Users Manual</TITLE> <TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="26 Oct 2015 version"> <META NAME="docnumber" CONTENT="31 Oct 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 @@
<P><CENTER><H3>LAMMPS Documentation <P><CENTER><H3>LAMMPS Documentation
</H3></CENTER> </H3></CENTER>
<CENTER><H4>26 Oct 2015 version <CENTER><H4>31 Oct 2015 version
</H4></CENTER> </H4></CENTER>
<H4>Version info: <H4>Version info:
</H4> </H4>

10
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@ -1,7 +1,7 @@
<!-- HTML_ONLY --> <!-- HTML_ONLY -->
<HEAD> <HEAD>
<TITLE>LAMMPS Users Manual</TITLE> <TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="31 Oct 2015 version"> <META NAME="docnumber" CONTENT="10 Aug 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD> </HEAD>
@ -21,7 +21,7 @@
<H1></H1> <H1></H1>
LAMMPS Documentation :c,h3 LAMMPS Documentation :c,h3
31 Oct 2015 version :c,h4 10 Aug 2015 version :c,h4
Version info: :h4 Version info: :h4
@ -85,7 +85,7 @@ it gives quick access to documentation for all LAMMPS commands.
.. toctree:: .. toctree::
:maxdepth: 2 :maxdepth: 2
:numbered: // 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 -->

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@ -838,9 +838,9 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
<colgroup> <colgroup>
<col width="16%" /> <col width="16%" />
<col width="19%" /> <col width="19%" />
<col width="17%" /> <col width="16%" />
<col width="15%" /> <col width="16%" />
<col width="17%" /> <col width="16%" />
<col width="16%" /> <col width="16%" />
</colgroup> </colgroup>
<tbody valign="top"> <tbody valign="top">
@ -873,53 +873,60 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
<td><a class="reference internal" href="compute_gyration_chunk.html"><em>gyration/chunk</em></a></td> <td><a class="reference internal" href="compute_gyration_chunk.html"><em>gyration/chunk</em></a></td>
</tr> </tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_heat_flux.html"><em>heat/flux</em></a></td> <tr class="row-odd"><td><a class="reference internal" href="compute_heat_flux.html"><em>heat/flux</em></a></td>
<td><a class="reference internal" href="compute_hexorder_atom.html"><em>hexorder/atom</em></a></td>
<td><a class="reference internal" href="compute_improper_local.html"><em>improper/local</em></a></td> <td><a class="reference internal" href="compute_improper_local.html"><em>improper/local</em></a></td>
<td><a class="reference internal" href="compute_inertia_chunk.html"><em>inertia/chunk</em></a></td> <td><a class="reference internal" href="compute_inertia_chunk.html"><em>inertia/chunk</em></a></td>
<td><a class="reference internal" href="compute_ke.html"><em>ke</em></a></td> <td><a class="reference internal" href="compute_ke.html"><em>ke</em></a></td>
<td><a class="reference internal" href="compute_ke_atom.html"><em>ke/atom</em></a></td> <td><a class="reference internal" href="compute_ke_atom.html"><em>ke/atom</em></a></td>
<td><a class="reference internal" href="compute_ke_rigid.html"><em>ke/rigid</em></a></td>
</tr> </tr>
<tr class="row-even"><td><a class="reference internal" href="compute_msd.html"><em>msd</em></a></td> <tr class="row-even"><td><a class="reference internal" href="compute_ke_rigid.html"><em>ke/rigid</em></a></td>
<td><a class="reference internal" href="compute_msd.html"><em>msd</em></a></td>
<td><a class="reference internal" href="compute_msd_chunk.html"><em>msd/chunk</em></a></td> <td><a class="reference internal" href="compute_msd_chunk.html"><em>msd/chunk</em></a></td>
<td><a class="reference internal" href="compute_msd_nongauss.html"><em>msd/nongauss</em></a></td> <td><a class="reference internal" href="compute_msd_nongauss.html"><em>msd/nongauss</em></a></td>
<td><a class="reference internal" href="compute_omega_chunk.html"><em>omega/chunk</em></a></td> <td><a class="reference internal" href="compute_omega_chunk.html"><em>omega/chunk</em></a></td>
<td><a class="reference internal" href="compute_pair.html"><em>pair</em></a></td> <td><a class="reference internal" href="compute_pair.html"><em>pair</em></a></td>
<td><a class="reference internal" href="compute_pair_local.html"><em>pair/local</em></a></td>
</tr> </tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_pe.html"><em>pe (c)</em></a></td> <tr class="row-odd"><td><a class="reference internal" href="compute_pair_local.html"><em>pair/local</em></a></td>
<td><a class="reference internal" href="compute_pe.html"><em>pe (c)</em></a></td>
<td><a class="reference internal" href="compute_pe_atom.html"><em>pe/atom</em></a></td> <td><a class="reference internal" href="compute_pe_atom.html"><em>pe/atom</em></a></td>
<td><a class="reference internal" href="compute_plasticity_atom.html"><em>plasticity/atom</em></a></td> <td><a class="reference internal" href="compute_plasticity_atom.html"><em>plasticity/atom</em></a></td>
<td><a class="reference internal" href="compute_pressure.html"><em>pressure (c)</em></a></td> <td><a class="reference internal" href="compute_pressure.html"><em>pressure (c)</em></a></td>
<td><a class="reference internal" href="compute_property_atom.html"><em>property/atom</em></a></td> <td><a class="reference internal" href="compute_property_atom.html"><em>property/atom</em></a></td>
<td><a class="reference internal" href="compute_property_local.html"><em>property/local</em></a></td>
</tr> </tr>
<tr class="row-even"><td><a class="reference internal" href="compute_property_chunk.html"><em>property/chunk</em></a></td> <tr class="row-even"><td><a class="reference internal" href="compute_property_local.html"><em>property/local</em></a></td>
<td><a class="reference internal" href="compute_property_chunk.html"><em>property/chunk</em></a></td>
<td><a class="reference internal" href="compute_rdf.html"><em>rdf</em></a></td> <td><a class="reference internal" href="compute_rdf.html"><em>rdf</em></a></td>
<td><a class="reference internal" href="compute_reduce.html"><em>reduce</em></a></td> <td><a class="reference internal" href="compute_reduce.html"><em>reduce</em></a></td>
<td><a class="reference internal" href="compute_reduce.html"><em>reduce/region</em></a></td> <td><a class="reference internal" href="compute_reduce.html"><em>reduce/region</em></a></td>
<td><a class="reference internal" href="compute_slice.html"><em>slice</em></a></td> <td><a class="reference internal" href="compute_slice.html"><em>slice</em></a></td>
<td><a class="reference internal" href="compute_sna_atom.html"><em>sna/atom</em></a></td>
</tr> </tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_sna_atom.html"><em>snad/atom</em></a></td> <tr class="row-odd"><td><a class="reference internal" href="compute_sna_atom.html"><em>sna/atom</em></a></td>
<td><a class="reference internal" href="compute_sna_atom.html"><em>snad/atom</em></a></td>
<td><a class="reference internal" href="compute_sna_atom.html"><em>snav/atom</em></a></td> <td><a class="reference internal" href="compute_sna_atom.html"><em>snav/atom</em></a></td>
<td><a class="reference internal" href="compute_stress_atom.html"><em>stress/atom</em></a></td> <td><a class="reference internal" href="compute_stress_atom.html"><em>stress/atom</em></a></td>
<td><a class="reference internal" href="compute_temp.html"><em>temp (ck)</em></a></td> <td><a class="reference internal" href="compute_temp.html"><em>temp (ck)</em></a></td>
<td><a class="reference internal" href="compute_temp_asphere.html"><em>temp/asphere</em></a></td> <td><a class="reference internal" href="compute_temp_asphere.html"><em>temp/asphere</em></a></td>
<td><a class="reference internal" href="compute_temp_com.html"><em>temp/com</em></a></td>
</tr> </tr>
<tr class="row-even"><td><a class="reference internal" href="compute_temp_chunk.html"><em>temp/chunk</em></a></td> <tr class="row-even"><td><a class="reference internal" href="compute_temp_com.html"><em>temp/com</em></a></td>
<td><a class="reference internal" href="compute_temp_chunk.html"><em>temp/chunk</em></a></td>
<td><a class="reference internal" href="compute_temp_deform.html"><em>temp/deform</em></a></td> <td><a class="reference internal" href="compute_temp_deform.html"><em>temp/deform</em></a></td>
<td><a class="reference internal" href="compute_temp_partial.html"><em>temp/partial (c)</em></a></td> <td><a class="reference internal" href="compute_temp_partial.html"><em>temp/partial (c)</em></a></td>
<td><a class="reference internal" href="compute_temp_profile.html"><em>temp/profile</em></a></td> <td><a class="reference internal" href="compute_temp_profile.html"><em>temp/profile</em></a></td>
<td><a class="reference internal" href="compute_temp_ramp.html"><em>temp/ramp</em></a></td> <td><a class="reference internal" href="compute_temp_ramp.html"><em>temp/ramp</em></a></td>
<td><a class="reference internal" href="compute_temp_region.html"><em>temp/region</em></a></td>
</tr> </tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_temp_sphere.html"><em>temp/sphere</em></a></td> <tr class="row-odd"><td><a class="reference internal" href="compute_temp_region.html"><em>temp/region</em></a></td>
<td><a class="reference internal" href="compute_temp_sphere.html"><em>temp/sphere</em></a></td>
<td><a class="reference internal" href="compute_ti.html"><em>ti</em></a></td> <td><a class="reference internal" href="compute_ti.html"><em>ti</em></a></td>
<td><a class="reference internal" href="compute_torque_chunk.html"><em>torque/chunk</em></a></td> <td><a class="reference internal" href="compute_torque_chunk.html"><em>torque/chunk</em></a></td>
<td><a class="reference internal" href="compute_vacf.html"><em>vacf</em></a></td> <td><a class="reference internal" href="compute_vacf.html"><em>vacf</em></a></td>
<td><a class="reference internal" href="compute_vcm_chunk.html"><em>vcm/chunk</em></a></td> <td><a class="reference internal" href="compute_vcm_chunk.html"><em>vcm/chunk</em></a></td>
<td><a class="reference internal" href="compute_voronoi_atom.html"><em>voronoi/atom</em></a></td> </tr>
<tr class="row-even"><td><a class="reference internal" href="compute_voronoi_atom.html"><em>voronoi/atom</em></a></td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>

1
doc/Section_commands.txt
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@ -684,6 +684,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"gyration"_compute_gyration.html, "gyration"_compute_gyration.html,
"gyration/chunk"_compute_gyration_chunk.html, "gyration/chunk"_compute_gyration_chunk.html,
"heat/flux"_compute_heat_flux.html, "heat/flux"_compute_heat_flux.html,
"hexorder/atom"_compute_hexorder_atom.html,
"improper/local"_compute_improper_local.html, "improper/local"_compute_improper_local.html,
"inertia/chunk"_compute_inertia_chunk.html, "inertia/chunk"_compute_inertia_chunk.html,
"ke"_compute_ke.html, "ke"_compute_ke.html,

1
doc/compute.html
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@ -301,6 +301,7 @@ are given in the compute section of <a class="reference internal" href="Section_
<li><a class="reference internal" href="compute_gyration.html"><em>gyration</em></a> - radius of gyration of group of atoms</li> <li><a class="reference internal" href="compute_gyration.html"><em>gyration</em></a> - radius of gyration of group of atoms</li>
<li><a class="reference internal" href="compute_gyration_chunk.html"><em>gyration/chunk</em></a> - radius of gyration for each chunk</li> <li><a class="reference internal" href="compute_gyration_chunk.html"><em>gyration/chunk</em></a> - radius of gyration for each chunk</li>
<li><a class="reference internal" href="compute_heat_flux.html"><em>heat/flux</em></a> - heat flux through a group of atoms</li> <li><a class="reference internal" href="compute_heat_flux.html"><em>heat/flux</em></a> - heat flux through a group of atoms</li>
<li><a class="reference internal" href="compute_hexorder_atom.html"><em>hexorder/atom</em></a> - bond orientational order parameter q6</li>
<li><a class="reference internal" href="compute_improper_local.html"><em>improper/local</em></a> - angle of each improper</li> <li><a class="reference internal" href="compute_improper_local.html"><em>improper/local</em></a> - angle of each improper</li>
<li><a class="reference internal" href="compute_inertia_chunk.html"><em>inertia/chunk</em></a> - inertia tensor for each chunk</li> <li><a class="reference internal" href="compute_inertia_chunk.html"><em>inertia/chunk</em></a> - inertia tensor for each chunk</li>
<li><a class="reference internal" href="compute_ke.html"><em>ke</em></a> - translational kinetic energy</li> <li><a class="reference internal" href="compute_ke.html"><em>ke</em></a> - translational kinetic energy</li>

1
doc/compute.txt
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@ -197,6 +197,7 @@ page"_Section_commands.html#cmd_5.
"gyration"_compute_gyration.html - radius of gyration of group of atoms "gyration"_compute_gyration.html - radius of gyration of group of atoms
"gyration/chunk"_compute_gyration_chunk.html - radius of gyration for each chunk "gyration/chunk"_compute_gyration_chunk.html - radius of gyration for each chunk
"heat/flux"_compute_heat_flux.html - heat flux through a group of atoms "heat/flux"_compute_heat_flux.html - heat flux through a group of atoms
"hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6
"improper/local"_compute_improper_local.html - angle of each improper "improper/local"_compute_improper_local.html - angle of each improper
"inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk "inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk
"ke"_compute_ke.html - translational kinetic energy "ke"_compute_ke.html - translational kinetic energy

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@ -0,0 +1,286 @@
<!DOCTYPE html>
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<div class="section" id="compute-hexorder-atom-command">
<span id="index-0"></span><h1>compute hexorder/atom command<a class="headerlink" href="#compute-hexorder-atom-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID hexorder/atom keyword values ...
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>hexorder/atom = style name of this compute command</li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>degree</em></li>
</ul>
<pre class="literal-block">
<em>n</em> value = degree of order parameter
</pre>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all hexorder/atom
compute 1 all hexorder/atom n 4
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that calculates <em>qn</em> the bond-orientational
order parameter for each atom in a group. The hexatic (<em>n</em> = 6) order
parameter was introduced by <a class="reference internal" href="#nelson"><span>Nelson and Halperin</span></a> as a way to detect
hexagonal symmetry in two-dimensional systems. For each atom, <em>qn</em>
is a complex number (stored as two real numbers) defined as follows:</p>
<img alt="_images/hexorder.jpg" class="align-center" src="_images/hexorder.jpg" />
<p>where the sum is over the <em>n</em> nearest neighbors
of the central atom. The angle theta
is formed by the bond vector rij and the <em>x</em> axis. theta is calculated
only using the <em>x</em> and <em>y</em> components, whereas the distance from the
central atom is calculated using all three
<em>x</em>, <em>y</em>, and <em>z</em> components of the bond vector.
Neighbor atoms not in the group
are included in the order parameter of atoms in the group.</p>
<p>The optional keyword <em>n</em> sets the degree of the order parameter.
The default value is 6. For a perfect hexagonal lattice,
<a href="#id1"><span class="problematic" id="id2">*</span></a>q*6 = exp(6 i phi) for all atoms, where the constant 0 &lt; phi &lt; pi/3
depends only on the orientation of the lattice relative to the x axis.
In an isotropic liquid, local neighborhoods may still exhibit
weak hexagonal symmetry, but because the orientational correlation
decays quickly with distance, the value of phi will be different for
different atoms, and <a href="#id3"><span class="problematic" id="id4">|&lt;*q*6&gt;|</span></a> &lt;&lt; 1.</p>
<p>The value of <em>qn</em> will be zero for atoms not in the
specified compute group. If the atom has less than <em>n</em> neighbors (within
the potential cutoff), then <em>qn</em> is set to zero.</p>
<p>The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If you have a bonded system, then the settings of
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a>
command, and means those pairwise interactions do not appear in the
neighbor list. Because this fix uses the neighbor list, it also means
those pairs will not be included in the order parameter. One way
to get around this, is to write a dump file, and use the
<a class="reference internal" href="rerun.html"><em>rerun</em></a> command to compute the order parameter for snapshots
in the dump file. The rerun script can use a
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command that includes all pairs in
the neighbor list.</p>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-atom array with 2 columns, giving the
real and imaginary parts of <em>qn</em>, respectively.</p>
<p>These values can be accessed by any command that uses
per-atom values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of LAMMPS output
options.</p>
<p>The per-atom array contain pairs of numbers representing the
real and imaginary parts of <em>qn</em>, a complex number subject to the
constraint <a href="#id5"><span class="problematic" id="id6">|*qn*|</span></a> &lt;= 1.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="compute_coord_atom.html"><em>compute coord/atom</em></a>, <a class="reference internal" href="compute_centro_atom.html"><em>compute centro/atom</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The option default is <em>n</em> = 6.</p>
<hr class="docutils" />
<p id="nelson"><strong>(Nelson)</strong> Nelson, Halperin, Phys Rev B, 19, 2457 (1979).</p>
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7
doc/compute_rdf.html
View File

@ -251,13 +251,16 @@ also numbers &gt;= 0.0.</p>
since processors (in parallel) don&#8217;t know about atom coordinates for since processors (in parallel) don&#8217;t know about atom coordinates for
atoms further away than that distance. If you want an RDF for larger atoms further away than that distance. If you want an RDF for larger
distances, you can use the <a class="reference internal" href="rerun.html"><em>rerun</em></a> command to post-process distances, you can use the <a class="reference internal" href="rerun.html"><em>rerun</em></a> command to post-process
a dump file. The definition of g(r) used by LAMMPS is only appropriate a dump file and set the cutoff for the potential to be longer in the
rerun script. Note that in the rerun context, the force cutoff is
arbitrary, since you aren&#8217;t running dynamics and thus are not changing
your model. The definition of g(r) used by LAMMPS is only appropriate
for characterizing atoms that are uniformly distributed throughout the for characterizing atoms that are uniformly distributed throughout the
simulation cell. In such cases, the coordination number is still simulation cell. In such cases, the coordination number is still
correct and meaningful. As an example, if a large simulation cell correct and meaningful. As an example, if a large simulation cell
contains only one atom of type <em>itypeN</em> and one of <em>jtypeN</em>, then g(r) contains only one atom of type <em>itypeN</em> and one of <em>jtypeN</em>, then g(r)
will register an arbitrarily large spike at whatever distance they will register an arbitrarily large spike at whatever distance they
happen to be at, and zero everywhere else. coord(r) will show a step happen to be at, and zero everywhere else. Coord(r) will show a step
change from zero to one at the location of the spike in g(r).</p> change from zero to one at the location of the spike in g(r).</p>
</div> </div>
<div class="section" id="related-commands"> <div class="section" id="related-commands">

7
doc/compute_rdf.txt
View File

@ -136,13 +136,16 @@ The RDF is not computed for distances longer than the force cutoff,
since processors (in parallel) don't know about atom coordinates for since processors (in parallel) don't know about atom coordinates for
atoms further away than that distance. If you want an RDF for larger atoms further away than that distance. If you want an RDF for larger
distances, you can use the "rerun"_rerun.html command to post-process distances, you can use the "rerun"_rerun.html command to post-process
a dump file. The definition of g(r) used by LAMMPS is only appropriate a dump file and set the cutoff for the potential to be longer in the
rerun script. Note that in the rerun context, the force cutoff is
arbitrary, since you aren't running dynamics and thus are not changing
your model. The definition of g(r) used by LAMMPS is only appropriate
for characterizing atoms that are uniformly distributed throughout the for characterizing atoms that are uniformly distributed throughout the
simulation cell. In such cases, the coordination number is still simulation cell. In such cases, the coordination number is still
correct and meaningful. As an example, if a large simulation cell correct and meaningful. As an example, if a large simulation cell
contains only one atom of type {itypeN} and one of {jtypeN}, then g(r) contains only one atom of type {itypeN} and one of {jtypeN}, then g(r)
will register an arbitrarily large spike at whatever distance they will register an arbitrarily large spike at whatever distance they
happen to be at, and zero everywhere else. coord(r) will show a step happen to be at, and zero everywhere else. Coord(r) will show a step
change from zero to one at the location of the spike in g(r). change from zero to one at the location of the spike in g(r).
[Related commands:] [Related commands:]

4
doc/genindex.html
View File

@ -460,6 +460,10 @@
</dt> </dt>
<dt><a href="compute_hexorder_atom.html#index-0">compute hexorder/atom</a>
</dt>
<dt><a href="compute_improper_local.html#index-0">compute improper/local</a> <dt><a href="compute_improper_local.html#index-0">compute improper/local</a>
</dt> </dt>

2
doc/searchindex.js
View File

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