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<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>&lt;no title&gt; &mdash; LAMMPS documentation</title>
<title>LAMMPS Documentation &mdash; LAMMPS documentation</title>
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<link rel="top" title="LAMMPS documentation" href="index.html"/>
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<link rel="next" title="1. Introduction" href="Section_intro.html"/>
<script src="_static/js/modernizr.min.js"></script>
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<!-- Local TOC -->
<div class="local-toc"><ul class="simple">
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
</div>
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<ul class="wy-breadcrumbs">
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<hr/>
<div class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
<a href="Section_intro.html" class="btn btn-neutral float-right" title="1. Introduction" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
</div>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<H1></H1><div class="section" id="lammps-documentation">
<h1>LAMMPS Documentation</h1>
<div class="section" id="aug-2016-version">
<h2>23 Aug 2016 version</h2>
</div>
<div class="section" id="version-info">
<h2>Version info:</h2>
<p>The LAMMPS &#8220;version&#8221; is the date when it was released, such as 1 May
2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
feature, we release it immediately, and post a notice on <a class="reference external" href="http://lammps.sandia.gov/bug.html">this page of the WWW site</a>. Each dated copy of LAMMPS contains all the
features and bug-fixes up to and including that version date. The
version date is printed to the screen and logfile every time you run
LAMMPS. It is also in the file src/version.h and in the LAMMPS
directory name created when you unpack a tarball, and at the top of
the first page of the manual (this page).</p>
<ul class="simple">
<li>If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of LAMMPS.</li>
<li>If you browse the HTML doc pages included in your tarball, they
describe the version you have.</li>
<li>The <a class="reference external" href="Manual.pdf">PDF file</a> on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don&#8217;t want
it to be part of every patch.</li>
<li>There is also a <a class="reference external" href="Developer.pdf">Developer.pdf</a> file in the doc
directory, which describes the internal structure and algorithms of
LAMMPS.</li>
</ul>
<p>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.</p>
<p>LAMMPS is a classical molecular dynamics simulation code designed to
run efficiently on parallel computers. It was developed at Sandia
National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL).</p>
<p>The primary developers of LAMMPS are <a class="reference external" href="http://www.sandia.gov/~sjplimp">Steve Plimpton</a>, Aidan
Thompson, and Paul Crozier who can be contacted at
sjplimp,athomps,pscrozi at sandia.gov. The <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> at
<a class="reference external" href="http://lammps.sandia.gov">http://lammps.sandia.gov</a> has more information about the code and its
uses.</p>
<hr class="docutils" />
<p>The LAMMPS documentation is organized into the following sections. If
you find errors or omissions in this manual or have suggestions for
useful information to add, please send an email to the developers so
we can improve the LAMMPS documentation.</p>
<p>Once you are familiar with LAMMPS, you may want to bookmark <a class="reference internal" href="Section_commands.html#comm"><span class="std std-ref">this page</span></a> at Section_commands.html#comm since
it gives quick access to documentation for all LAMMPS commands.</p>
<p><a class="reference external" href="Manual.pdf">PDF file</a> of the entire manual, generated by
<a class="reference external" href="http://freecode.com/projects/htmldoc">htmldoc</a></p>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#what-is-lammps">1.1. What is LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-features">1.2. LAMMPS features</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-non-features">1.3. LAMMPS non-features</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#open-source-distribution">1.4. Open source distribution</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#acknowledgments-and-citations">1.5. Acknowledgments and citations</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#what-s-in-the-lammps-distribution">2.1. What&#8217;s in the LAMMPS distribution</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps">2.2. Making LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps-with-optional-packages">2.3. Making LAMMPS with optional packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-via-the-make-py-tool">2.4. Building LAMMPS via the Make.py tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-as-a-library">2.5. Building LAMMPS as a library</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#running-lammps">2.6. Running LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#command-line-options">2.7. Command-line options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#lammps-screen-output">2.8. LAMMPS screen output</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#tips-for-users-of-previous-lammps-versions">2.9. Tips for users of previous LAMMPS versions</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#lammps-input-script">3.1. LAMMPS input script</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#parsing-rules">3.2. Parsing rules</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#input-script-structure">3.3. Input script structure</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#commands-listed-by-category">3.4. Commands listed by category</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#individual-commands">3.5. Individual commands</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#fix-styles">3.6. Fix styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#compute-styles">3.7. Compute styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#pair-style-potentials">3.8. Pair_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#bond-style-potentials">3.9. Bond_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#angle-style-potentials">3.10. Angle_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#dihedral-style-potentials">3.11. Dihedral_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#improper-style-potentials">3.12. Improper_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#kspace-solvers">3.13. Kspace solvers</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#standard-packages">4.1. Standard packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-packages">4.2. User packages</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><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_example.html#lowercase-directories">7.1. Lowercase directories</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_example.html#uppercase-directories">7.2. Uppercase directories</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#amber2lmp-tool">9.1. amber2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#binary2txt-tool">9.2. binary2txt tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ch2lmp-tool">9.3. ch2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#chain-tool">9.4. chain tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#colvars-tools">9.5. colvars tools</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#createatoms-tool">9.6. createatoms tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#data2xmovie-tool">9.7. data2xmovie tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-database-tool">9.8. eam database tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-generate-tool">9.9. eam generate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eff-tool">9.10. eff tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#emacs-tool">9.11. emacs tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#fep-tool">9.12. fep tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#i-pi-tool">9.13. i-pi tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ipp-tool">9.14. ipp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#kate-tool">9.15. kate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2arc-tool">9.16. lmp2arc tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2cfg-tool">9.17. lmp2cfg tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2vmd-tool">9.18. lmp2vmd tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#matlab-tool">9.19. matlab tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#micelle2d-tool">9.20. micelle2d tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#moltemplate-tool">9.21. moltemplate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#msi2lmp-tool">9.22. msi2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#phonon-tool">9.23. phonon tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#polymer-bonding-tool">9.24. polymer bonding tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#pymol-asphere-tool">9.25. pymol_asphere tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#python-tool">9.26. python tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#reax-tool">9.27. reax tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#restart2data-tool">9.28. restart2data tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#vim-tool">9.29. vim tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmgrace-tool">9.30. xmgrace tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmovie-tool">9.31. xmovie tool</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#atom-styles">10.1. Atom styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#bond-angle-dihedral-improper-potentials">10.2. Bond, angle, dihedral, improper potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#compute-styles">10.3. Compute styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-styles">10.4. Dump styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-custom-output-options">10.5. Dump custom output options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#fix-styles">10.6. Fix styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#input-script-commands">10.7. Input script commands</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#kspace-computations">10.8. Kspace computations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#minimization-styles">10.9. Minimization styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#pairwise-potentials">10.10. Pairwise potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#region-styles">10.11. Region styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#body-styles">10.12. Body styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#thermodynamic-output-options">10.13. Thermodynamic output options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#variable-options">10.14. Variable options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#submitting-new-features-for-inclusion-in-lammps">10.15. Submitting new features for inclusion in LAMMPS</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-running-lammps-from-python">11.1. Overview of running LAMMPS from Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-using-python-from-a-lammps-script">11.2. Overview of using Python from a LAMMPS script</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#building-lammps-as-a-shared-library">11.3. Building LAMMPS as a shared library</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#installing-the-python-wrapper-into-python">11.4. Installing the Python wrapper into Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#extending-python-with-mpi-to-run-in-parallel">11.5. Extending Python with MPI to run in parallel</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#testing-the-python-lammps-interface">11.6. Testing the Python-LAMMPS interface</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#using-lammps-from-python">11.7. Using LAMMPS from Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#example-python-scripts-that-use-lammps">11.8. Example Python scripts that use LAMMPS</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#common-problems">12.1. Common problems</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#reporting-bugs">12.2. Reporting bugs</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error-warning-messages">12.3. Error &amp; warning messages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error">12.4. Errors:</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#warnings">12.5. Warnings:</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_history.html#coming-attractions">13.1. Coming attractions</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_history.html#past-versions">13.2. Past versions</a></li>
</ul>
</li>
</ul>
</div>
</div>
</div>
<div class="section" id="indices-and-tables">
<h1>Indices and tables</h1>
<ul class="simple">
<li><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></li>
<li><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></li>
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@ -8,7 +8,7 @@
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<title>Accelerating LAMMPS performance &mdash; LAMMPS documentation</title>
<title>5. Accelerating LAMMPS performance &mdash; LAMMPS documentation</title>
@ -32,7 +32,9 @@
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<link rel="top" title="LAMMPS documentation" href="index.html"/>
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@ -71,17 +73,28 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Accelerating LAMMPS performance</a><ul>
<li><a class="reference internal" href="#measuring-performance">Measuring performance</a></li>
<li><a class="reference internal" href="#general-strategies">General strategies</a></li>
<li><a class="reference internal" href="#packages-with-optimized-styles">Packages with optimized styles</a></li>
<li><a class="reference internal" href="#comparison-of-various-accelerator-packages">Comparison of various accelerator packages</a></li>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">5. Accelerating LAMMPS performance</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#measuring-performance">5.1. Measuring performance</a></li>
<li class="toctree-l2"><a class="reference internal" href="#general-strategies">5.2. General strategies</a></li>
<li class="toctree-l2"><a class="reference internal" href="#packages-with-optimized-styles">5.3. Packages with optimized styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#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></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
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@ -104,7 +117,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>Accelerating LAMMPS performance</li>
<li>5. Accelerating LAMMPS performance</li>
<li class="wy-breadcrumbs-aside">
@ -115,12 +128,21 @@
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<hr/>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="accelerating-lammps-performance">
<h1>Accelerating LAMMPS performance</h1>
<h1>5. Accelerating LAMMPS performance</h1>
<p>This section describes various methods for improving LAMMPS
performance for different classes of problems running on different
kinds of machines.</p>
@ -147,7 +169,7 @@ packages discussed in Section 5.2, for several of the standard LAMMPS
benchmark problems, as a function of problem size and number of
compute nodes, on different hardware platforms.</p>
<div class="section" id="measuring-performance">
<span id="acc-1"></span><h2>Measuring performance</h2>
<span id="acc-1"></span><h2>5.1. Measuring performance</h2>
<p>Before trying to make your simulation run faster, you should
understand how it currently performs and where the bottlenecks are.</p>
<p>The best way to do this is run the your system (actual number of
@ -158,7 +180,7 @@ Do this for an equilibrium version of your system, so that the
typically no need to run for 1000s of timesteps to get accurate
timings; you can simply extrapolate from short runs.</p>
<p>For the set of runs, look at the timing data printed to the screen and
log file at the end of each LAMMPS run. <span class="xref std std-ref">This section</span> of the manual has an overview.</p>
log file at the end of each LAMMPS run. <a class="reference internal" href="Section_start.html#start-8"><span class="std std-ref">This section</span></a> of the manual has an overview.</p>
<p>Running on one (or a few processors) should give a good estimate of
the serial performance and what portions of the timestep are taking
the most time. Running the same problem on a few different processor
@ -188,7 +210,7 @@ LAMMPS, to obtain synchronized timings.</p>
<hr class="docutils" />
</div>
<div class="section" id="general-strategies">
<span id="acc-2"></span><h2>General strategies</h2>
<span id="acc-2"></span><h2>5.2. General strategies</h2>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">this section 5.2 is still a work in progress</p>
@ -241,7 +263,7 @@ when using a barostat.</p>
<hr class="docutils" />
</div>
<div class="section" id="packages-with-optimized-styles">
<span id="acc-3"></span><h2>Packages with optimized styles</h2>
<span id="acc-3"></span><h2>5.3. Packages with optimized styles</h2>
<p>Accelerated versions of various <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a>,
<a class="reference internal" href="fix.html"><span class="doc">fixes</span></a>, <a class="reference internal" href="compute.html"><span class="doc">computes</span></a>, and other commands have
been added to LAMMPS, which will typically run faster than the
@ -371,7 +393,7 @@ only if defaults need to be changed |</div></blockquote>
</tbody>
</table>
<p>Note that the first 4 steps can be done as a single command, using the
src/Make.py tool. This tool is discussed in <span class="xref std std-ref">Section 2.4</span> of the manual, and its use is
src/Make.py tool. This tool is discussed in <a class="reference internal" href="Section_start.html#start-4"><span class="std std-ref">Section 2.4</span></a> of the manual, and its use is
illustrated in the individual accelerator sections. Typically these
steps only need to be done once, to create an executable that uses one
or more accelerator packages.</p>
@ -452,7 +474,7 @@ CPU.</li>
<hr class="docutils" />
</div>
<div class="section" id="comparison-of-various-accelerator-packages">
<span id="acc-4"></span><h2>Comparison of various accelerator packages</h2>
<span id="acc-4"></span><h2>5.4. Comparison of various accelerator packages</h2>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">this section still needs to be re-worked with additional KOKKOS
@ -516,6 +538,15 @@ exclusion lists or a triclinic simulation box.</li>
</div>
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<title>Commands &mdash; LAMMPS documentation</title>
<title>3. Commands &mdash; LAMMPS documentation</title>
@ -32,7 +32,9 @@
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<link rel="next" title="4. Packages" href="Section_packages.html"/>
<link rel="prev" title="2. Getting Started" href="Section_start.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -71,26 +73,37 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Commands</a><ul>
<li><a class="reference internal" href="#lammps-input-script">LAMMPS input script</a></li>
<li><a class="reference internal" href="#parsing-rules">Parsing rules</a></li>
<li><a class="reference internal" href="#input-script-structure">Input script structure</a></li>
<li><a class="reference internal" href="#commands-listed-by-category">Commands listed by category</a></li>
<li><a class="reference internal" href="#individual-commands">Individual commands</a></li>
<li><a class="reference internal" href="#fix-styles">Fix styles</a></li>
<li><a class="reference internal" href="#compute-styles">Compute styles</a></li>
<li><a class="reference internal" href="#pair-style-potentials">Pair_style potentials</a></li>
<li><a class="reference internal" href="#bond-style-potentials">Bond_style potentials</a></li>
<li><a class="reference internal" href="#angle-style-potentials">Angle_style potentials</a></li>
<li><a class="reference internal" href="#dihedral-style-potentials">Dihedral_style potentials</a></li>
<li><a class="reference internal" href="#improper-style-potentials">Improper_style potentials</a></li>
<li><a class="reference internal" href="#kspace-solvers">Kspace solvers</a></li>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">3. Commands</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#lammps-input-script">3.1. LAMMPS input script</a></li>
<li class="toctree-l2"><a class="reference internal" href="#parsing-rules">3.2. Parsing rules</a></li>
<li class="toctree-l2"><a class="reference internal" href="#input-script-structure">3.3. Input script structure</a></li>
<li class="toctree-l2"><a class="reference internal" href="#commands-listed-by-category">3.4. Commands listed by category</a></li>
<li class="toctree-l2"><a class="reference internal" href="#individual-commands">3.5. Individual commands</a></li>
<li class="toctree-l2"><a class="reference internal" href="#fix-styles">3.6. Fix styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#compute-styles">3.7. Compute styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#pair-style-potentials">3.8. Pair_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="#bond-style-potentials">3.9. Bond_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="#angle-style-potentials">3.10. Angle_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="#dihedral-style-potentials">3.11. Dihedral_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="#improper-style-potentials">3.12. Improper_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="#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></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
</div>
@ -113,7 +126,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>Commands</li>
<li>3. Commands</li>
<li class="wy-breadcrumbs-aside">
@ -124,12 +137,21 @@
</ul>
<hr/>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="commands">
<h1>Commands</h1>
<h1>3. Commands</h1>
<p>This section describes how a LAMMPS input script is formatted and the
input script commands used to define a LAMMPS simulation.</p>
<div class="line-block">
@ -141,7 +163,7 @@ input script commands used to define a LAMMPS simulation.</p>
<div class="line"><br /></div>
</div>
<div class="section" id="lammps-input-script">
<span id="cmd-1"></span><h2>LAMMPS input script</h2>
<span id="cmd-1"></span><h2>3.1. LAMMPS input script</h2>
<p>LAMMPS executes by reading commands from a input script (text file),
one line at a time. When the input script ends, LAMMPS exits. Each
command causes LAMMPS to take some action. It may set an internal
@ -188,7 +210,7 @@ command lists restrictions on how the command can be used.</p>
<hr class="docutils" />
</div>
<div class="section" id="parsing-rules">
<span id="cmd-2"></span><h2>Parsing rules</h2>
<span id="cmd-2"></span><h2>3.2. Parsing rules</h2>
<p>Each non-blank line in the input script is treated as a command.
LAMMPS commands are case sensitive. Command names are lower-case, as
are specified command arguments. Upper case letters may be used in
@ -292,7 +314,7 @@ allowed, but that should be sufficient for most use cases.</p>
<hr class="docutils" />
</div>
<div class="section" id="input-script-structure">
<span id="cmd-3"></span><h2>Input script structure</h2>
<span id="cmd-3"></span><h2>3.3. Input script structure</h2>
<p>This section describes the structure of a typical LAMMPS input script.
The &#8220;examples&#8221; directory in the LAMMPS distribution contains many
sample input scripts; the corresponding problems are discussed in
@ -371,7 +393,7 @@ the <a class="reference internal" href="minimize.html"><span class="doc">minimiz
<hr class="docutils" />
</div>
<div class="section" id="commands-listed-by-category">
<span id="cmd-4"></span><h2>Commands listed by category</h2>
<span id="cmd-4"></span><h2>3.4. Commands listed by category</h2>
<p>This section lists all LAMMPS commands, grouped by category. The
<a class="reference internal" href="#cmd-5"><span class="std std-ref">next section</span></a> lists the same commands alphabetically. Note
that some style options for some commands are part of specific LAMMPS
@ -430,7 +452,7 @@ in the command&#8217;s documentation.</p>
<hr class="docutils" />
</div>
<div class="section" id="individual-commands">
<span id="comm"></span><span id="cmd-5"></span><h2>Individual commands</h2>
<span id="comm"></span><span id="cmd-5"></span><h2>3.5. Individual commands</h2>
<p>This section lists all LAMMPS commands alphabetically, with a separate
listing below of styles within certain commands. The <a class="reference internal" href="#cmd-4"><span class="std std-ref">previous section</span></a> lists the same commands, grouped by category. Note
that some style options for some commands are part of specific LAMMPS
@ -570,7 +592,7 @@ in the command&#8217;s documentation.</p>
</tbody>
</table>
<p>These are additional commands in USER packages, which can be used if
<span class="xref std std-ref">LAMMPS is built with the appropriate package</span>.</p>
<a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">LAMMPS is built with the appropriate package</span></a>.</p>
<table border="1" class="docutils">
<colgroup>
<col width="41%" />
@ -587,7 +609,7 @@ in the command&#8217;s documentation.</p>
</div>
<hr class="docutils" />
<div class="section" id="fix-styles">
<h2>Fix styles</h2>
<h2>3.6. Fix styles</h2>
<p>See the <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command for one-line descriptions of each style
or click on the style itself for a full description. Some of the
styles have accelerated versions, which can be used if LAMMPS is built
@ -753,7 +775,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
</tbody>
</table>
<p>These are additional fix styles in USER packages, which can be used if
<span class="xref std std-ref">LAMMPS is built with the appropriate package</span>.</p>
<a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">LAMMPS is built with the appropriate package</span></a>.</p>
<table border="1" class="docutils">
<colgroup>
<col width="23%" />
@ -832,7 +854,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
</div>
<hr class="docutils" />
<div class="section" id="compute-styles">
<h2>Compute styles</h2>
<h2>3.7. Compute styles</h2>
<p>See the <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command for one-line descriptions of
each style or click on the style itself for a full description. Some
of the styles have accelerated versions, which can be used if LAMMPS
@ -943,7 +965,7 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
</tbody>
</table>
<p>These are additional compute styles in USER packages, which can be
used if <span class="xref std std-ref">LAMMPS is built with the appropriate package</span>.</p>
used if <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">LAMMPS is built with the appropriate package</span></a>.</p>
<table border="1" class="docutils">
<colgroup>
<col width="16%" />
@ -1008,7 +1030,7 @@ used if <span class="xref std std-ref">LAMMPS is built with the appropriate pack
</div>
<hr class="docutils" />
<div class="section" id="pair-style-potentials">
<h2>Pair_style potentials</h2>
<h2>3.8. Pair_style potentials</h2>
<p>See the <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> command for an overview of pair
potentials. Click on the style itself for a full description. Many
of the styles have accelerated versions, which can be used if LAMMPS
@ -1166,7 +1188,7 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
</tbody>
</table>
<p>These are additional pair styles in USER packages, which can be used
if <span class="xref std std-ref">LAMMPS is built with the appropriate package</span>.</p>
if <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">LAMMPS is built with the appropriate package</span></a>.</p>
<table border="1" class="docutils">
<colgroup>
<col width="24%" />
@ -1245,7 +1267,7 @@ if <span class="xref std std-ref">LAMMPS is built with the appropriate package</
</div>
<hr class="docutils" />
<div class="section" id="bond-style-potentials">
<h2>Bond_style potentials</h2>
<h2>3.9. Bond_style potentials</h2>
<p>See the <a class="reference internal" href="bond_style.html"><span class="doc">bond_style</span></a> command for an overview of bond
potentials. Click on the style itself for a full description. Some
of the styles have accelerated versions, which can be used if LAMMPS
@ -1278,7 +1300,7 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
</tbody>
</table>
<p>These are additional bond styles in USER packages, which can be used
if <span class="xref std std-ref">LAMMPS is built with the appropriate package</span>.</p>
if <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">LAMMPS is built with the appropriate package</span></a>.</p>
<table border="1" class="docutils">
<colgroup>
<col width="46%" />
@ -1293,7 +1315,7 @@ if <span class="xref std std-ref">LAMMPS is built with the appropriate package</
</div>
<hr class="docutils" />
<div class="section" id="angle-style-potentials">
<h2>Angle_style potentials</h2>
<h2>3.10. Angle_style potentials</h2>
<p>See the <a class="reference internal" href="angle_style.html"><span class="doc">angle_style</span></a> command for an overview of
angle potentials. Click on the style itself for a full description.
Some of the styles have accelerated versions, which can be used if
@ -1326,7 +1348,7 @@ USER-OMP, t = OPT.</p>
</tbody>
</table>
<p>These are additional angle styles in USER packages, which can be used
if <span class="xref std std-ref">LAMMPS is built with the appropriate package</span>.</p>
if <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">LAMMPS is built with the appropriate package</span></a>.</p>
<table border="1" class="docutils">
<colgroup>
<col width="29%" />
@ -1350,7 +1372,7 @@ if <span class="xref std std-ref">LAMMPS is built with the appropriate package</
</div>
<hr class="docutils" />
<div class="section" id="dihedral-style-potentials">
<h2>Dihedral_style potentials</h2>
<h2>3.11. Dihedral_style potentials</h2>
<p>See the <a class="reference internal" href="dihedral_style.html"><span class="doc">dihedral_style</span></a> command for an overview
of dihedral potentials. Click on the style itself for a full
description. Some of the styles have accelerated versions, which can
@ -1383,7 +1405,7 @@ USER-OMP, t = OPT.</p>
</tbody>
</table>
<p>These are additional dihedral styles in USER packages, which can be
used if <span class="xref std std-ref">LAMMPS is built with the appropriate package</span>.</p>
used if <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">LAMMPS is built with the appropriate package</span></a>.</p>
<table border="1" class="docutils">
<colgroup>
<col width="31%" />
@ -1407,7 +1429,7 @@ used if <span class="xref std std-ref">LAMMPS is built with the appropriate pack
</div>
<hr class="docutils" />
<div class="section" id="improper-style-potentials">
<h2>Improper_style potentials</h2>
<h2>3.12. Improper_style potentials</h2>
<p>See the <a class="reference internal" href="improper_style.html"><span class="doc">improper_style</span></a> command for an overview
of improper potentials. Click on the style itself for a full
description. Some of the styles have accelerated versions, which can
@ -1435,7 +1457,7 @@ USER-OMP, t = OPT.</p>
</tbody>
</table>
<p>These are additional improper styles in USER packages, which can be
used if <span class="xref std std-ref">LAMMPS is built with the appropriate package</span>.</p>
used if <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">LAMMPS is built with the appropriate package</span></a>.</p>
<table border="1" class="docutils">
<colgroup>
<col width="24%" />
@ -1454,7 +1476,7 @@ used if <span class="xref std std-ref">LAMMPS is built with the appropriate pack
</div>
<hr class="docutils" />
<div class="section" id="kspace-solvers">
<h2>Kspace solvers</h2>
<h2>3.13. Kspace solvers</h2>
<p>See the <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a> command for an overview of
Kspace solvers. Click on the style itself for a full description.
Some of the styles have accelerated versions, which can be used if
@ -1494,6 +1516,15 @@ USER-OMP, t = OPT.</p>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="Section_packages.html" class="btn btn-neutral float-right" title="4. Packages" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Errors &mdash; LAMMPS documentation</title>
<title>12. Errors &mdash; LAMMPS documentation</title>
@ -32,7 +32,9 @@
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<link rel="next" title="13. Future and history" href="Section_history.html"/>
<link rel="prev" title="11. Python interface to LAMMPS" href="Section_python.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -71,18 +73,29 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Errors</a><ul>
<li><a class="reference internal" href="#common-problems">Common problems</a></li>
<li><a class="reference internal" href="#reporting-bugs">Reporting bugs</a></li>
<li><a class="reference internal" href="#error-warning-messages">Error &amp; warning messages</a></li>
<li><a class="reference internal" href="#error">Errors:</a></li>
<li><a class="reference internal" href="#warnings">Warnings:</a></li>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><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 current"><a class="current reference internal" href="#">12. Errors</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#common-problems">12.1. Common problems</a></li>
<li class="toctree-l2"><a class="reference internal" href="#reporting-bugs">12.2. Reporting bugs</a></li>
<li class="toctree-l2"><a class="reference internal" href="#error-warning-messages">12.3. Error &amp; warning messages</a></li>
<li class="toctree-l2"><a class="reference internal" href="#error">12.4. Errors:</a></li>
<li class="toctree-l2"><a class="reference internal" href="#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></li>
</ul>
</div>
</div>
@ -105,7 +118,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>Errors</li>
<li>12. Errors</li>
<li class="wy-breadcrumbs-aside">
@ -116,12 +129,21 @@
</ul>
<hr/>
<div class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
<a href="Section_history.html" class="btn btn-neutral float-right" title="13. Future and history" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="Section_python.html" class="btn btn-neutral" title="11. Python interface to LAMMPS" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="errors">
<h1>Errors</h1>
<h1>12. Errors</h1>
<p>This section describes the errors you can encounter when using LAMMPS,
either conceptually, or as printed out by the program.</p>
<div class="line-block">
@ -131,7 +153,7 @@ either conceptually, or as printed out by the program.</p>
<div class="line"><br /></div>
</div>
<div class="section" id="common-problems">
<span id="err-1"></span><h2>Common problems</h2>
<span id="err-1"></span><h2>12.1. Common problems</h2>
<p>If two LAMMPS runs do not produce the same answer on different
machines or different numbers of processors, this is typically not a
bug. In theory you should get identical answers on any number of
@ -172,8 +194,8 @@ to see it on the screen. If you get an error like &#8220;Invalid ...
style&#8221;, with ... being fix, compute, pair, etc, it means that you
mistyped the style name or that the command is part of an optional
package which was not compiled into your executable. The list of
available styles in your executable can be listed by using <span class="xref std std-ref">the -h command-line argument</span>. The installation
and compilation of optional packages is explained in the <span class="xref std std-ref">installation instructions</span>.</p>
available styles in your executable can be listed by using <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">the -h command-line argument</span></a>. The installation
and compilation of optional packages is explained in the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">installation instructions</span></a>.</p>
<p>For a given command, LAMMPS expects certain arguments in a specified
order. If you mess this up, LAMMPS will often flag the error, but it
may also simply read a bogus argument and assign a value that is
@ -220,7 +242,7 @@ buffering or boost the sizes of messages that can be buffered.</p>
<hr class="docutils" />
</div>
<div class="section" id="reporting-bugs">
<span id="err-2"></span><h2>Reporting bugs</h2>
<span id="err-2"></span><h2>12.2. Reporting bugs</h2>
<p>If you are confident that you have found a bug in LAMMPS, follow these
steps.</p>
<p>Check the <a class="reference external" href="http://lammps.sandia.gov/bug.html">New features and bug fixes</a> section of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW site</a> to see if the bug has already been reported or fixed or the
@ -242,7 +264,7 @@ causing the problem.</p>
<hr class="docutils" />
</div>
<div class="section" id="error-warning-messages">
<span id="err-3"></span><h2>Error &amp; warning messages</h2>
<span id="err-3"></span><h2>12.3. Error &amp; warning messages</h2>
<p>These are two alphabetic lists of the <a class="reference internal" href="#error"><span class="std std-ref">ERROR</span></a> and
<a class="reference internal" href="#warn"><span class="std std-ref">WARNING</span></a> messages LAMMPS prints out and the reason why. If the
explanation here is not sufficient, the documentation for the
@ -252,12 +274,12 @@ where the error was generated. For example, this message</p>
<p>ERROR: Illegal velocity command (velocity.cpp:78)</p>
<p>means that line #78 in the file src/velocity.cpp generated the error.
Looking in the source code may help you figure out what went wrong.</p>
<p>Note that error messages from <span class="xref std std-ref">user-contributed packages</span> are not listed here. If such an
<p>Note that error messages from <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">user-contributed packages</span></a> are not listed here. If such an
error occurs and is not self-explanatory, you&#8217;ll need to look in the
source code or contact the author of the package.</p>
</div>
<div class="section" id="error">
<span id="id2"></span><h2>Errors:</h2>
<span id="id2"></span><h2>12.4. Errors:</h2>
<dl class="docutils">
<dt><em>1-3 bond count is inconsistent</em></dt>
<dd>An inconsistency was detected when computing the number of 1-3
@ -6127,7 +6149,7 @@ read_restart, or create_box command.</dd>
</dl>
</div>
<div class="section" id="warnings">
<span id="warn"></span><h2>Warnings:</h2>
<span id="warn"></span><h2>12.5. Warnings:</h2>
<dl class="docutils">
<dt><em>Adjusting Coulombic cutoff for MSM, new cutoff = %g</em></dt>
<dd>The adjust/cutoff command is turned on and the Coulombic cutoff has been
@ -6674,6 +6696,15 @@ infinity.</dd>
</div>
<footer>
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Example problems &mdash; LAMMPS documentation</title>
<title>7. Example problems &mdash; LAMMPS documentation</title>
@ -32,7 +32,9 @@
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<link rel="next" title="8. Performance &amp; scalability" href="Section_perf.html"/>
<link rel="prev" title="6. How-to discussions" href="Section_howto.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -71,15 +73,26 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Example problems</a><ul>
<li><a class="reference internal" href="#lowercase-directories">Lowercase directories</a></li>
<li><a class="reference internal" href="#uppercase-directories">Uppercase directories</a></li>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">7. Example problems</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#lowercase-directories">7.1. Lowercase directories</a></li>
<li class="toctree-l2"><a class="reference internal" href="#uppercase-directories">7.2. Uppercase directories</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
</div>
@ -102,7 +115,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>Example problems</li>
<li>7. Example problems</li>
<li class="wy-breadcrumbs-aside">
@ -113,12 +126,21 @@
</ul>
<hr/>
<div class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
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<div itemprop="articleBody">
<div class="section" id="example-problems">
<h1>Example problems</h1>
<h1>7. Example problems</h1>
<p>The LAMMPS distribution includes an examples sub-directory with many
sample problems. Many are 2d models that run quickly are are
straightforward to visualize, requiring at most a couple of minutes to
@ -151,7 +173,7 @@ longer times, e.g. to measure a particular quantity.</p>
<p>Lists of both kinds of directories are given below.</p>
<hr class="docutils" />
<div class="section" id="lowercase-directories">
<h2>Lowercase directories</h2>
<h2>7.1. Lowercase directories</h2>
<table border="1" class="docutils">
<colgroup>
<col width="16%" />
@ -305,7 +327,7 @@ browser.</p>
</div>
<hr class="docutils" />
<div class="section" id="uppercase-directories">
<h2>Uppercase directories</h2>
<h2>7.2. Uppercase directories</h2>
<table border="1" class="docutils">
<colgroup>
<col width="10%" />
@ -357,6 +379,15 @@ page for more info on specific USER packages.</p>
</div>
<footer>
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Future and history &mdash; LAMMPS documentation</title>
<title>13. Future and history &mdash; LAMMPS documentation</title>
@ -32,7 +32,8 @@
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<link rel="prev" title="12. Errors" href="Section_errors.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -71,15 +72,26 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Future and history</a><ul>
<li><a class="reference internal" href="#coming-attractions">Coming attractions</a></li>
<li><a class="reference internal" href="#past-versions">Past versions</a></li>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><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 current"><a class="current reference internal" href="#">13. Future and history</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#coming-attractions">13.1. Coming attractions</a></li>
<li class="toctree-l2"><a class="reference internal" href="#past-versions">13.2. Past versions</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -102,7 +114,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>Future and history</li>
<li>13. Future and history</li>
<li class="wy-breadcrumbs-aside">
@ -113,12 +125,19 @@
</ul>
<hr/>
<div class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
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<div itemprop="articleBody">
<div class="section" id="future-and-history">
<h1>Future and history</h1>
<h1>13. Future and history</h1>
<p>This section lists features we plan to add to LAMMPS, features of
previous versions of LAMMPS, and features of other parallel molecular
dynamics codes our group has distributed.</p>
@ -128,7 +147,7 @@ dynamics codes our group has distributed.</p>
<div class="line"><br /></div>
</div>
<div class="section" id="coming-attractions">
<span id="hist-1"></span><h2>Coming attractions</h2>
<span id="hist-1"></span><h2>13.1. Coming attractions</h2>
<p>The <a class="reference external" href="http://lammps.sandia.gov/future.html">Wish list link</a> on the
LAMMPS WWW page gives a list of features we are hoping to add to
LAMMPS in the future, including contact names of individuals you can
@ -139,7 +158,7 @@ your wish to the list.</p>
<hr class="docutils" />
</div>
<div class="section" id="past-versions">
<span id="hist-2"></span><h2>Past versions</h2>
<span id="hist-2"></span><h2>13.2. Past versions</h2>
<p>LAMMPS development began in the mid 1990s under a cooperative research
&amp; development agreement (CRADA) between two DOE labs (Sandia and LLNL)
and 3 companies (Cray, Bristol Myers Squibb, and Dupont). The goal was
@ -227,6 +246,13 @@ internally. A brief listing of their features is given here.</p>
</div>
<footer>
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@ -8,7 +8,7 @@
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<title>How-to discussions &mdash; LAMMPS documentation</title>
<title>6. How-to discussions &mdash; LAMMPS documentation</title>
@ -32,7 +32,9 @@
<link rel="top" title="LAMMPS documentation" href="index.html"/>
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<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">How-to discussions</a><ul>
<li><a class="reference internal" href="#restarting-a-simulation">Restarting a simulation</a></li>
<li><a class="reference internal" href="#d-simulations">2d simulations</a></li>
<li><a class="reference internal" href="#charmm-amber-and-dreiding-force-fields">CHARMM, AMBER, and DREIDING force fields</a></li>
<li><a class="reference internal" href="#running-multiple-simulations-from-one-input-script">Running multiple simulations from one input script</a></li>
<li><a class="reference internal" href="#multi-replica-simulations">Multi-replica simulations</a></li>
<li><a class="reference internal" href="#granular-models">Granular models</a></li>
<li><a class="reference internal" href="#tip3p-water-model">TIP3P water model</a></li>
<li><a class="reference internal" href="#tip4p-water-model">TIP4P water model</a></li>
<li><a class="reference internal" href="#spc-water-model">SPC water model</a></li>
<li><a class="reference internal" href="#coupling-lammps-to-other-codes">Coupling LAMMPS to other codes</a></li>
<li><a class="reference internal" href="#visualizing-lammps-snapshots">Visualizing LAMMPS snapshots</a></li>
<li><a class="reference internal" href="#triclinic-non-orthogonal-simulation-boxes">Triclinic (non-orthogonal) simulation boxes</a></li>
<li><a class="reference internal" href="#nemd-simulations">NEMD simulations</a></li>
<li><a class="reference internal" href="#finite-size-spherical-and-aspherical-particles">Finite-size spherical and aspherical particles</a><ul>
<li><a class="reference internal" href="#atom-styles">Atom styles</a></li>
<li><a class="reference internal" href="#pair-potentials">Pair potentials</a></li>
<li><a class="reference internal" href="#time-integration">Time integration</a></li>
<li><a class="reference internal" href="#computes-thermodynamics-and-dump-output">Computes, thermodynamics, and dump output</a></li>
<li><a class="reference internal" href="#rigid-bodies-composed-of-finite-size-particles">Rigid bodies composed of finite-size particles</a></li>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">6. How-to discussions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#restarting-a-simulation">6.1. Restarting a simulation</a></li>
<li class="toctree-l2"><a class="reference internal" href="#d-simulations">6.2. 2d simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="#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="#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="#multi-replica-simulations">6.5. Multi-replica simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="#granular-models">6.6. Granular models</a></li>
<li class="toctree-l2"><a class="reference internal" href="#tip3p-water-model">6.7. TIP3P water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="#tip4p-water-model">6.8. TIP4P water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="#spc-water-model">6.9. SPC water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="#coupling-lammps-to-other-codes">6.10. Coupling LAMMPS to other codes</a></li>
<li class="toctree-l2"><a class="reference internal" href="#visualizing-lammps-snapshots">6.11. Visualizing LAMMPS snapshots</a></li>
<li class="toctree-l2"><a class="reference internal" href="#triclinic-non-orthogonal-simulation-boxes">6.12. Triclinic (non-orthogonal) simulation boxes</a></li>
<li class="toctree-l2"><a class="reference internal" href="#nemd-simulations">6.13. NEMD simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="#finite-size-spherical-and-aspherical-particles">6.14. Finite-size spherical and aspherical particles</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#atom-styles">6.14.1. Atom styles</a></li>
<li class="toctree-l3"><a class="reference internal" href="#pair-potentials">6.14.2. Pair potentials</a></li>
<li class="toctree-l3"><a class="reference internal" href="#time-integration">6.14.3. Time integration</a></li>
<li class="toctree-l3"><a class="reference internal" href="#computes-thermodynamics-and-dump-output">6.14.4. Computes, thermodynamics, and dump output</a></li>
<li class="toctree-l3"><a class="reference internal" href="#rigid-bodies-composed-of-finite-size-particles">6.14.5. Rigid bodies composed of finite-size particles</a></li>
</ul>
</li>
<li><a class="reference internal" href="#output-from-lammps-thermo-dumps-computes-fixes-variables">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</a><ul>
<li><a class="reference internal" href="#global-per-atom-local-data">Global/per-atom/local data</a></li>
<li><a class="reference internal" href="#scalar-vector-array-data">Scalar/vector/array data</a></li>
<li><a class="reference internal" href="#thermodynamic-output">Thermodynamic output</a></li>
<li><a class="reference internal" href="#dump-file-output">Dump file output</a></li>
<li><a class="reference internal" href="#fixes-that-write-output-files">Fixes that write output files</a></li>
<li><a class="reference internal" href="#computes-that-process-output-quantities">Computes that process output quantities</a></li>
<li><a class="reference internal" href="#fixes-that-process-output-quantities">Fixes that process output quantities</a></li>
<li><a class="reference internal" href="#computes-that-generate-values-to-output">Computes that generate values to output</a></li>
<li><a class="reference internal" href="#fixes-that-generate-values-to-output">Fixes that generate values to output</a></li>
<li><a class="reference internal" href="#variables-that-generate-values-to-output">Variables that generate values to output</a></li>
<li><a class="reference internal" href="#summary-table-of-output-options-and-data-flow-between-commands">Summary table of output options and data flow between commands</a></li>
<li class="toctree-l2"><a class="reference internal" href="#output-from-lammps-thermo-dumps-computes-fixes-variables">6.15. Output from LAMMPS (thermo, dumps, computes, fixes, variables)</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#global-per-atom-local-data">6.15.1. Global/per-atom/local data</a></li>
<li class="toctree-l3"><a class="reference internal" href="#scalar-vector-array-data">6.15.2. Scalar/vector/array data</a></li>
<li class="toctree-l3"><a class="reference internal" href="#thermodynamic-output">6.15.3. Thermodynamic output</a></li>
<li class="toctree-l3"><a class="reference internal" href="#dump-file-output">6.15.4. Dump file output</a></li>
<li class="toctree-l3"><a class="reference internal" href="#fixes-that-write-output-files">6.15.5. Fixes that write output files</a></li>
<li class="toctree-l3"><a class="reference internal" href="#computes-that-process-output-quantities">6.15.6. Computes that process output quantities</a></li>
<li class="toctree-l3"><a class="reference internal" href="#fixes-that-process-output-quantities">6.15.7. Fixes that process output quantities</a></li>
<li class="toctree-l3"><a class="reference internal" href="#computes-that-generate-values-to-output">6.15.8. Computes that generate values to output</a></li>
<li class="toctree-l3"><a class="reference internal" href="#fixes-that-generate-values-to-output">6.15.9. Fixes that generate values to output</a></li>
<li class="toctree-l3"><a class="reference internal" href="#variables-that-generate-values-to-output">6.15.10. Variables that generate values to output</a></li>
<li class="toctree-l3"><a class="reference internal" href="#summary-table-of-output-options-and-data-flow-between-commands">6.15.11. Summary table of output options and data flow between commands</a></li>
</ul>
</li>
<li><a class="reference internal" href="#thermostatting-barostatting-and-computing-temperature">Thermostatting, barostatting, and computing temperature</a></li>
<li><a class="reference internal" href="#walls">Walls</a></li>
<li><a class="reference internal" href="#elastic-constants">Elastic constants</a></li>
<li><a class="reference internal" href="#library-interface-to-lammps">Library interface to LAMMPS</a></li>
<li><a class="reference internal" href="#calculating-thermal-conductivity">Calculating thermal conductivity</a></li>
<li><a class="reference internal" href="#calculating-viscosity">Calculating viscosity</a></li>
<li><a class="reference internal" href="#calculating-a-diffusion-coefficient">Calculating a diffusion coefficient</a></li>
<li><a class="reference internal" href="#using-chunks-to-calculate-system-properties">Using chunks to calculate system properties</a><ul>
<li><a class="reference internal" href="#compute-chunk-atom-command">Compute chunk/atom command:</a></li>
<li><a class="reference internal" href="#fix-ave-chunk-command">Fix ave/chunk command:</a></li>
<li><a class="reference internal" href="#compute-chunk-commands">Compute */chunk commands:</a></li>
<li><a class="reference internal" href="#example-calculations-with-chunks">Example calculations with chunks</a></li>
<li class="toctree-l2"><a class="reference internal" href="#thermostatting-barostatting-and-computing-temperature">6.16. Thermostatting, barostatting, and computing temperature</a></li>
<li class="toctree-l2"><a class="reference internal" href="#walls">6.17. Walls</a></li>
<li class="toctree-l2"><a class="reference internal" href="#elastic-constants">6.18. Elastic constants</a></li>
<li class="toctree-l2"><a class="reference internal" href="#library-interface-to-lammps">6.19. Library interface to LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="#calculating-thermal-conductivity">6.20. Calculating thermal conductivity</a></li>
<li class="toctree-l2"><a class="reference internal" href="#calculating-viscosity">6.21. Calculating viscosity</a></li>
<li class="toctree-l2"><a class="reference internal" href="#calculating-a-diffusion-coefficient">6.22. Calculating a diffusion coefficient</a></li>
<li class="toctree-l2"><a class="reference internal" href="#using-chunks-to-calculate-system-properties">6.23. Using chunks to calculate system properties</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#compute-chunk-atom-command">6.23.1. Compute chunk/atom command:</a></li>
<li class="toctree-l3"><a class="reference internal" href="#fix-ave-chunk-command">6.23.2. Fix ave/chunk command:</a></li>
<li class="toctree-l3"><a class="reference internal" href="#compute-chunk-commands">6.23.3. Compute */chunk commands:</a></li>
<li class="toctree-l3"><a class="reference internal" href="#example-calculations-with-chunks">6.23.4. Example calculations with chunks</a></li>
</ul>
</li>
<li><a class="reference internal" href="#setting-parameters-for-the-kspace-style-pppm-disp-command">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><a class="reference internal" href="#polarizable-models">Polarizable models</a></li>
<li><a class="reference internal" href="#adiabatic-core-shell-model">Adiabatic core/shell model</a></li>
<li><a class="reference internal" href="#drude-induced-dipoles">Drude induced dipoles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#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="#polarizable-models">6.25. Polarizable models</a></li>
<li class="toctree-l2"><a class="reference internal" href="#adiabatic-core-shell-model">6.26. Adiabatic core/shell model</a></li>
<li class="toctree-l2"><a class="reference internal" href="#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></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
</div>
@ -153,7 +166,7 @@
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@ -164,12 +177,21 @@
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div class="section" id="how-to-discussions">
<h1>How-to discussions</h1>
<h1>6. How-to discussions</h1>
<p>This section describes how to perform common tasks using LAMMPS.</p>
<div class="line-block">
<div class="line">6.1 <a class="reference internal" href="#howto-1"><span class="std std-ref">Restarting a simulation</span></a></div>
@ -205,14 +227,14 @@
highlighted in <a class="reference internal" href="Section_example.html"><span class="doc">Section_example</span></a> also show how to
setup and run various kinds of simulations.</p>
<div class="section" id="restarting-a-simulation">
<span id="howto-1"></span><h2>Restarting a simulation</h2>
<span id="howto-1"></span><h2>6.1. Restarting a simulation</h2>
<p>There are 3 ways to continue a long LAMMPS simulation. Multiple
<a class="reference internal" href="run.html"><span class="doc">run</span></a> commands can be used in the same input script. Each
run will continue from where the previous run left off. Or binary
restart files can be saved to disk using the <a class="reference internal" href="restart.html"><span class="doc">restart</span></a>
command. At a later time, these binary files can be read via a
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command in a new script. Or they can
be converted to text data files using the <span class="xref std std-ref">-r command-line switch</span> and read by a
be converted to text data files using the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-r command-line switch</span></a> and read by a
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command in a new script.</p>
<p>Here we give examples of 2 scripts that read either a binary restart
file or a converted data file and then issue a new run command to
@ -298,7 +320,7 @@ but not in data files.</p>
<hr class="docutils" />
</div>
<div class="section" id="d-simulations">
<span id="howto-2"></span><h2>2d simulations</h2>
<span id="howto-2"></span><h2>6.2. 2d simulations</h2>
<p>Use the <a class="reference internal" href="dimension.html"><span class="doc">dimension</span></a> command to specify a 2d simulation.</p>
<p>Make the simulation box periodic in z via the <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a>
command. This is the default.</p>
@ -330,7 +352,7 @@ as in 3d.</p>
<hr class="docutils" />
</div>
<div class="section" id="charmm-amber-and-dreiding-force-fields">
<span id="howto-3"></span><h2>CHARMM, AMBER, and DREIDING force fields</h2>
<span id="howto-3"></span><h2>6.3. CHARMM, AMBER, and DREIDING force fields</h2>
<p>A force field has 2 parts: the formulas that define it and the
coefficients used for a particular system. Here we only discuss
formulas implemented in LAMMPS that correspond to formulas commonly
@ -392,7 +414,7 @@ documentation for the formula it computes.</p>
<hr class="docutils" />
</div>
<div class="section" id="running-multiple-simulations-from-one-input-script">
<span id="howto-4"></span><h2>Running multiple simulations from one input script</h2>
<span id="howto-4"></span><h2>6.4. Running multiple simulations from one input script</h2>
<p>This can be done in several ways. See the documentation for
individual commands for more details on how these examples work.</p>
<p>If &#8220;multiple simulations&#8221; means continue a previous simulation for
@ -461,7 +483,7 @@ jump in.polymer
<p>All of the above examples work whether you are running on 1 or
multiple processors, but assumed you are running LAMMPS on a single
partition of processors. LAMMPS can be run on multiple partitions via
the &#8220;-partition&#8221; command-line switch as described in <span class="xref std std-ref">this section</span> of the manual.</p>
the &#8220;-partition&#8221; command-line switch as described in <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">this section</span></a> of the manual.</p>
<p>In the last 2 examples, if LAMMPS were run on 3 partitions, the same
scripts could be used if the &#8220;index&#8221; and &#8220;loop&#8221; variables were
replaced with <em>universe</em>-style variables, as described in the
@ -475,7 +497,7 @@ the 4th simulation, and so forth, until all 8 were completed.</p>
<hr class="docutils" />
</div>
<div class="section" id="multi-replica-simulations">
<span id="howto-5"></span><h2>Multi-replica simulations</h2>
<span id="howto-5"></span><h2>6.5. Multi-replica simulations</h2>
<p>Several commands in LAMMPS run mutli-replica simulations, meaning
that multiple instances (replicas) of your simulation are run
simultaneously, with small amounts of data exchanged between replicas
@ -494,16 +516,16 @@ and perform infrequent events. Parallel tempering or replica exchange
runs different replicas at a series of temperature to facilitate
rare-event sampling.</p>
<p>These commands can only be used if LAMMPS was built with the REPLICA
package. See the <span class="xref std std-ref">Making LAMMPS</span> section
package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section
for more info on packages.</p>
<p>PIMD runs different replicas whose individual particles are coupled
together by springs to model a system or ring-polymers.</p>
<p>This commands can only be used if LAMMPS was built with the USER-MISC
package. See the <span class="xref std std-ref">Making LAMMPS</span> section
package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section
for more info on packages.</p>
<p>In all these cases, you must run with one or more processors per
replica. The processors assigned to each replica are determined at
run-time by using the <span class="xref std std-ref">-partition command-line switch</span> to launch LAMMPS on multiple
run-time by using the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-partition command-line switch</span></a> to launch LAMMPS on multiple
partitions, which in this context are the same as replicas. E.g.
these commands:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">16</span> <span class="n">lmp_linux</span> <span class="o">-</span><span class="n">partition</span> <span class="mi">8</span><span class="n">x2</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">temper</span>
@ -511,7 +533,7 @@ these commands:</p>
</pre></div>
</div>
<p>would each run 8 replicas, on either 16 or 8 processors. Note the use
of the <span class="xref std std-ref">-in command-line switch</span> to specify
of the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-in command-line switch</span></a> to specify
the input script which is required when running in multi-replica mode.</p>
<p>Also note that with MPI installed on a machine (e.g. your desktop),
you can run on more (virtual) processors than you have physical
@ -522,7 +544,7 @@ physical processors.</p>
<hr class="docutils" />
</div>
<div class="section" id="granular-models">
<span id="howto-6"></span><h2>Granular models</h2>
<span id="howto-6"></span><h2>6.6. Granular models</h2>
<p>Granular system are composed of spherical particles with a diameter,
as opposed to point particles. This means they have an angular
velocity and torque can be imparted to them to cause them to rotate.</p>
@ -563,7 +585,7 @@ computations between frozen atoms by using this command:</p>
<hr class="docutils" />
</div>
<div class="section" id="tip3p-water-model">
<span id="howto-7"></span><h2>TIP3P water model</h2>
<span id="howto-7"></span><h2>6.7. TIP3P water model</h2>
<p>The TIP3P water model as implemented in CHARMM
<a class="reference internal" href="#howto-mackerell"><span class="std std-ref">(MacKerell)</span></a> specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
@ -615,7 +637,7 @@ details:</p>
<hr class="docutils" />
</div>
<div class="section" id="tip4p-water-model">
<span id="howto-8"></span><h2>TIP4P water model</h2>
<span id="howto-8"></span><h2>6.8. TIP4P water model</h2>
<p>The four-point TIP4P rigid water model extends the traditional
three-point TIP3P model by adding an additional site, usually
massless, where the charge associated with the oxygen atom is placed.
@ -711,7 +733,7 @@ and Coulombic cutoffs are set in the <a class="reference internal" href="pair_lj
<hr class="docutils" />
</div>
<div class="section" id="spc-water-model">
<span id="howto-9"></span><h2>SPC water model</h2>
<span id="howto-9"></span><h2>6.9. SPC water model</h2>
<p>The SPC water model specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
In LAMMPS the <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> command can be used to hold
@ -750,7 +772,7 @@ the SPC and SPC/E models.</p>
<hr class="docutils" />
</div>
<div class="section" id="coupling-lammps-to-other-codes">
<span id="howto-10"></span><h2>Coupling LAMMPS to other codes</h2>
<span id="howto-10"></span><h2>6.10. Coupling LAMMPS to other codes</h2>
<p>LAMMPS is designed to allow it to be coupled to other codes. For
example, a quantum mechanics code might compute forces on a subset of
atoms and pass those forces to LAMMPS. Or a continuum finite element
@ -803,7 +825,7 @@ MD with quantum forces calculated by a density functional code</li>
a kinetic Monte Carlo model for grain growth using MD to calculate
strain induced across grain boundaries</li>
</ul>
<p><span class="xref std std-ref">This section</span> of the documentation
<p><a class="reference internal" href="Section_start.html#start-5"><span class="std std-ref">This section</span></a> of the documentation
describes how to build LAMMPS as a library. Once this is done, you
can interface with LAMMPS either via C++, C, Fortran, or Python (or
any other language that supports a vanilla C-like interface). For
@ -831,7 +853,7 @@ instances of LAMMPS to perform different calculations.</p>
<hr class="docutils" />
</div>
<div class="section" id="visualizing-lammps-snapshots">
<span id="howto-11"></span><h2>Visualizing LAMMPS snapshots</h2>
<span id="howto-11"></span><h2>6.11. Visualizing LAMMPS snapshots</h2>
<p>LAMMPS itself does not do visualization, but snapshots from LAMMPS
simulations can be visualized (and analyzed) in a variety of ways.</p>
<p>LAMMPS snapshots are created by the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> command which can
@ -874,7 +896,7 @@ See the <a class="reference internal" href="dump.html"><span class="doc">dump</s
<hr class="docutils" />
</div>
<div class="section" id="triclinic-non-orthogonal-simulation-boxes">
<span id="howto-12"></span><h2>Triclinic (non-orthogonal) simulation boxes</h2>
<span id="howto-12"></span><h2>6.12. Triclinic (non-orthogonal) simulation boxes</h2>
<p>By default, LAMMPS uses an orthogonal simulation box to encompass the
particles. The <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a> command sets the boundary
conditions of the box (periodic, non-periodic, etc). The orthogonal
@ -1052,7 +1074,7 @@ on non-equilibrium MD (NEMD) simulations.</p>
<hr class="docutils" />
</div>
<div class="section" id="nemd-simulations">
<span id="howto-13"></span><h2>NEMD simulations</h2>
<span id="howto-13"></span><h2>6.13. NEMD simulations</h2>
<p>Non-equilibrium molecular dynamics or NEMD simulations are typically
used to measure a fluid&#8217;s rheological properties such as viscosity.
In LAMMPS, such simulations can be performed by first setting up a
@ -1082,7 +1104,7 @@ profile consistent with the applied shear strain rate.</p>
<hr class="docutils" />
</div>
<div class="section" id="finite-size-spherical-and-aspherical-particles">
<span id="howto-14"></span><h2>Finite-size spherical and aspherical particles</h2>
<span id="howto-14"></span><h2>6.14. Finite-size spherical and aspherical particles</h2>
<p>Typical MD models treat atoms or particles as point masses. Sometimes
it is desirable to have a model with finite-size particles such as
spheroids or ellipsoids or generalized aspherical bodies. The
@ -1102,7 +1124,7 @@ particles. The following aspects are discussed in turn:</p>
colloid, dipole, ellipse, line, peri, pour, and tri directories of the
<a class="reference internal" href="Section_example.html"><span class="doc">examples directory</span></a> in the LAMMPS distribution.</p>
<div class="section" id="atom-styles">
<h3>Atom styles</h3>
<h3>6.14.1. Atom styles</h3>
<p>There are several <a class="reference internal" href="atom_style.html"><span class="doc">atom styles</span></a> that allow for
definition of finite-size particles: sphere, dipole, ellipsoid, line,
tri, peri, and body.</p>
@ -1172,7 +1194,7 @@ object. When temperature is computed, the correct degrees of freedom
are used for rotation in a 2d versus 3d system.</p>
</div>
<div class="section" id="pair-potentials">
<h3>Pair potentials</h3>
<h3>6.14.2. Pair potentials</h3>
<p>When a system with finite-size particles is defined, the particles
will only rotate and experience torque if the force field computes
such interactions. These are the various <a class="reference internal" href="pair_style.html"><span class="doc">pair styles</span></a> that generate torque:</p>
@ -1199,7 +1221,7 @@ The line, tri, and body potentials are used with line segment,
triangular, and body particles respectively.</p>
</div>
<div class="section" id="time-integration">
<h3>Time integration</h3>
<h3>6.14.3. Time integration</h3>
<p>There are several fixes that perform time integration on finite-size
spherical particles, meaning the integrators update the rotational
orientation and angular velocity or angular momentum of the particles:</p>
@ -1234,7 +1256,7 @@ integration fixes can only be used with <a class="reference internal" href="grou
contain finite-size particles.</p>
</div>
<div class="section" id="computes-thermodynamics-and-dump-output">
<h3>Computes, thermodynamics, and dump output</h3>
<h3>6.14.4. Computes, thermodynamics, and dump output</h3>
<p>There are several computes that calculate the temperature or
rotational energy of spherical or ellipsoidal particles:</p>
<ul class="simple">
@ -1265,7 +1287,7 @@ corner-point coordinates (for line and tri particles), and
sub-particle attributes of body particles.</p>
</div>
<div class="section" id="rigid-bodies-composed-of-finite-size-particles">
<h3>Rigid bodies composed of finite-size particles</h3>
<h3>6.14.5. Rigid bodies composed of finite-size particles</h3>
<p>The <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a> command treats a collection of
particles as a rigid body, computes its inertia tensor, sums the total
force and torque on the rigid body each timestep due to forces on its
@ -1294,7 +1316,7 @@ particles are computed via a command like <a class="reference internal" href="pa
</div>
</div>
<div class="section" id="output-from-lammps-thermo-dumps-computes-fixes-variables">
<span id="howto-15"></span><h2>Output from LAMMPS (thermo, dumps, computes, fixes, variables)</h2>
<span id="howto-15"></span><h2>6.15. Output from LAMMPS (thermo, dumps, computes, fixes, variables)</h2>
<p>There are four basic kinds of LAMMPS output:</p>
<ul class="simple">
<li><a class="reference internal" href="thermo_style.html"><span class="doc">Thermodynamic output</span></a>, which is a list
@ -1331,7 +1353,7 @@ to output and the kind of data they operate on and produce:</p>
<li><a class="reference internal" href="#table"><span class="std std-ref">Summary table of output options and data flow between commands</span></a></li>
</ul>
<div class="section" id="global-per-atom-local-data">
<span id="global"></span><h3>Global/per-atom/local data</h3>
<span id="global"></span><h3>6.15.1. Global/per-atom/local data</h3>
<p>Various output-related commands work with three different styles of
data: global, per-atom, or local. A global datum is one or more
system-wide values, e.g. the temperature of the system. A per-atom
@ -1341,7 +1363,7 @@ atoms it owns, but there may be zero or more per atom, e.g. a list of
bond distances.</p>
</div>
<div class="section" id="scalar-vector-array-data">
<span id="scalar"></span><h3>Scalar/vector/array data</h3>
<span id="scalar"></span><h3>6.15.2. Scalar/vector/array data</h3>
<p>Global, per-atom, and local datums can each come in three kinds: a
single scalar value, a vector of values, or a 2d array of values. The
doc page for a &#8220;compute&#8221; or &#8220;fix&#8221; or &#8220;variable&#8221; that generates data
@ -1375,7 +1397,7 @@ scalar values as input can typically also process elements of a vector
or array.</p>
</div>
<div class="section" id="thermodynamic-output">
<span id="thermo"></span><h3>Thermodynamic output</h3>
<span id="thermo"></span><h3>6.15.3. Thermodynamic output</h3>
<p>The frequency and format of thermodynamic output is set by the
<a class="reference internal" href="thermo.html"><span class="doc">thermo</span></a>, <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a>, and
<a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a> commands. The
@ -1399,7 +1421,7 @@ formula if desired, to make an extensive calculation produce an
intensive result.</p>
</div>
<div class="section" id="dump-file-output">
<span id="dump"></span><h3>Dump file output</h3>
<span id="dump"></span><h3>6.15.4. Dump file output</h3>
<p>Dump file output is specified by the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> and
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> commands. There are several
pre-defined formats (dump atom, dump xtc, etc).</p>
@ -1420,7 +1442,7 @@ must generate local values for input to the <a class="reference internal" href="
command.</p>
</div>
<div class="section" id="fixes-that-write-output-files">
<span id="fixoutput"></span><h3>Fixes that write output files</h3>
<span id="fixoutput"></span><h3>6.15.5. Fixes that write output files</h3>
<p>Several fixes take various quantities as input and can write output
files: <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>, <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>, <a class="reference internal" href="fix_ave_histo.html"><span class="doc">fix ave/histo</span></a>,
<a class="reference internal" href="fix_ave_correlate.html"><span class="doc">fix ave/correlate</span></a>, and <a class="reference internal" href="fix_print.html"><span class="doc">fix print</span></a>.</p>
@ -1466,7 +1488,7 @@ command is a means to output a wide variety of quantities separate
from normal thermodynamic or dump file output.</p>
</div>
<div class="section" id="computes-that-process-output-quantities">
<span id="computeoutput"></span><h3>Computes that process output quantities</h3>
<span id="computeoutput"></span><h3>6.15.6. Computes that process output quantities</h3>
<p>The <a class="reference internal" href="compute_reduce.html"><span class="doc">compute reduce</span></a> and <a class="reference internal" href="compute_reduce.html"><span class="doc">compute reduce/region</span></a> commands take one or more per-atom
or local vector quantities as inputs and &#8220;reduce&#8221; them (sum, min, max,
ave) to scalar quantities. These are produced as output values which
@ -1487,7 +1509,7 @@ are produced as output values which can be used as input to other
output commands.</p>
</div>
<div class="section" id="fixes-that-process-output-quantities">
<span id="fixprocoutput"></span><h3>Fixes that process output quantities</h3>
<span id="fixprocoutput"></span><h3>6.15.7. Fixes that process output quantities</h3>
<p>The <a class="reference internal" href="fix_vector.html"><span class="doc">fix vector</span></a> command can create global vectors as
output from global scalars as input, accumulating them one element at
a time.</p>
@ -1507,7 +1529,7 @@ by a <a class="reference internal" href="fix.html"><span class="doc">fix</span><
The output of this fix can be used as input to other output commands.</p>
</div>
<div class="section" id="computes-that-generate-values-to-output">
<span id="compute"></span><h3>Computes that generate values to output</h3>
<span id="compute"></span><h3>6.15.8. Computes that generate values to output</h3>
<p>Every <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> in LAMMPS produces either global or
per-atom or local values. The values can be scalars or vectors or
arrays of data. These values can be output using the other commands
@ -1517,7 +1539,7 @@ values have the word &#8220;atom&#8221; or &#8220;local&#8221; in their style na
without the word &#8220;atom&#8221; or &#8220;local&#8221; produce global values.</p>
</div>
<div class="section" id="fixes-that-generate-values-to-output">
<span id="fix"></span><h3>Fixes that generate values to output</h3>
<span id="fix"></span><h3>6.15.9. Fixes that generate values to output</h3>
<p>Some <a class="reference internal" href="fix.html"><span class="doc">fixes</span></a> in LAMMPS produces either global or per-atom or
local values which can be accessed by other commands. The values can
be scalars or vectors or arrays of data. These values can be output
@ -1526,7 +1548,7 @@ each fix command tells whether it produces any output quantities and
describes them.</p>
</div>
<div class="section" id="variables-that-generate-values-to-output">
<span id="variable"></span><h3>Variables that generate values to output</h3>
<span id="variable"></span><h3>6.15.10. Variables that generate values to output</h3>
<p><a class="reference internal" href="variable.html"><span class="doc">Variables</span></a> defined in an input script can store one or
more strings. But equal-style, vector-style, and atom-style or
atomfile-style variables generate a global scalar value, global vector
@ -1538,7 +1560,7 @@ variables can be used as input to and thus output by the other
commands described in this section.</p>
</div>
<div class="section" id="summary-table-of-output-options-and-data-flow-between-commands">
<span id="table"></span><h3>Summary table of output options and data flow between commands</h3>
<span id="table"></span><h3>6.15.11. Summary table of output options and data flow between commands</h3>
<p>This table summarizes the various commands that can be used for
generating output from LAMMPS. Each command produces output data of
some kind and/or writes data to a file. Most of the commands can take
@ -1644,7 +1666,7 @@ vector input could be a column of an array.</p>
</div>
</div>
<div class="section" id="thermostatting-barostatting-and-computing-temperature">
<span id="howto-16"></span><h2>Thermostatting, barostatting, and computing temperature</h2>
<span id="howto-16"></span><h2>6.16. Thermostatting, barostatting, and computing temperature</h2>
<p>Thermostatting means controlling the temperature of particles in an MD
simulation. Barostatting means controlling the pressure. Since the
pressure includes a kinetic component due to particle velocities, both
@ -1779,7 +1801,7 @@ thermodynamic output.</p>
<hr class="docutils" />
</div>
<div class="section" id="walls">
<span id="howto-17"></span><h2>Walls</h2>
<span id="howto-17"></span><h2>6.17. Walls</h2>
<p>Walls in an MD simulation are typically used to bound particle motion,
i.e. to serve as a boundary condition.</p>
<p>Walls in LAMMPS can be of rough (made of particles) or idealized
@ -1843,7 +1865,7 @@ frictional walls, as well as triangulated surfaces.</p>
<hr class="docutils" />
</div>
<div class="section" id="elastic-constants">
<span id="howto-18"></span><h2>Elastic constants</h2>
<span id="howto-18"></span><h2>6.18. Elastic constants</h2>
<p>Elastic constants characterize the stiffness of a material. The formal
definition is provided by the linear relation that holds between the
stress and strain tensors in the limit of infinitesimal deformation.
@ -1875,8 +1897,8 @@ converge and requires careful post-processing <a class="reference internal" href
<hr class="docutils" />
</div>
<div class="section" id="library-interface-to-lammps">
<span id="howto-19"></span><h2>Library interface to LAMMPS</h2>
<p>As described in <span class="xref std std-ref">Section_start 5</span>, LAMMPS
<span id="howto-19"></span><h2>6.19. Library interface to LAMMPS</h2>
<p>As described in <a class="reference internal" href="Section_start.html#start-5"><span class="std std-ref">Section_start 5</span></a>, LAMMPS
can be built as a library, so that it can be called by another code,
used in a <a class="reference internal" href="#howto-10"><span class="std std-ref">coupled manner</span></a> with other
codes, or driven through a <a class="reference internal" href="Section_python.html"><span class="doc">Python interface</span></a>.</p>
@ -1897,7 +1919,7 @@ application.</p>
</pre></div>
</div>
<p>The lammps_open() function is used to initialize LAMMPS, passing in a
list of strings as if they were <span class="xref std std-ref">command-line arguments</span> when LAMMPS is run in
list of strings as if they were <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line arguments</span></a> when LAMMPS is run in
stand-alone mode from the command line, and a MPI communicator for
LAMMPS to run under. It returns a ptr to the LAMMPS object that is
created, and which is used in subsequent library calls. The
@ -1958,7 +1980,7 @@ LAMMPS.</p>
<hr class="docutils" />
</div>
<div class="section" id="calculating-thermal-conductivity">
<span id="howto-20"></span><h2>Calculating thermal conductivity</h2>
<span id="howto-20"></span><h2>6.20. Calculating thermal conductivity</h2>
<p>The thermal conductivity kappa of a material can be measured in at
least 4 ways using various options in LAMMPS. See the examples/KAPPA
directory for scripts that implement the 4 methods discussed here for
@ -2014,7 +2036,7 @@ formalism.</p>
<hr class="docutils" />
</div>
<div class="section" id="calculating-viscosity">
<span id="howto-21"></span><h2>Calculating viscosity</h2>
<span id="howto-21"></span><h2>6.21. Calculating viscosity</h2>
<p>The shear viscosity eta of a fluid can be measured in at least 5 ways
using various options in LAMMPS. See the examples/VISCOSITY directory
for scripts that implement the 5 methods discussed here for a simple
@ -2141,7 +2163,7 @@ with time at sufficiently long times.</p>
<hr class="docutils" />
</div>
<div class="section" id="calculating-a-diffusion-coefficient">
<span id="howto-22"></span><h2>Calculating a diffusion coefficient</h2>
<span id="howto-22"></span><h2>6.22. Calculating a diffusion coefficient</h2>
<p>The diffusion coefficient D of a material can be measured in at least
2 ways using various options in LAMMPS. See the examples/DIFFUSE
directory for scripts that implement the 2 methods discussed here for
@ -2163,7 +2185,7 @@ and thus extract D.</p>
<hr class="docutils" />
</div>
<div class="section" id="using-chunks-to-calculate-system-properties">
<span id="howto-23"></span><h2>Using chunks to calculate system properties</h2>
<span id="howto-23"></span><h2>6.23. Using chunks to calculate system properties</h2>
<p>In LAMMS, &#8220;chunks&#8221; are collections of atoms, as defined by the
<a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command, which assigns
each atom to a chunk ID (or to no chunk at all). The number of chunks
@ -2180,7 +2202,7 @@ commands, to calculate various properties of a system:</p>
overviewed. Then some examples are given of how to compute different
properties with chunk commands.</p>
<div class="section" id="compute-chunk-atom-command">
<h3>Compute chunk/atom command:</h3>
<h3>6.23.1. Compute chunk/atom command:</h3>
<p>This compute can assign atoms to chunks of various styles. Only atoms
in the specified group and optional specified region are assigned to a
chunk. Here are some possible chunk definitions:</p>
@ -2238,7 +2260,7 @@ the input script that uses a formula to generate a chunk ID for each
atom.</p>
</div>
<div class="section" id="fix-ave-chunk-command">
<h3>Fix ave/chunk command:</h3>
<h3>6.23.2. Fix ave/chunk command:</h3>
<p>This fix takes the ID of a <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command as input. For each chunk,
it then sums one or more specified per-atom values over the atoms in
each chunk. The per-atom values can be any atom property, such as
@ -2252,7 +2274,7 @@ fix produces a global array as output with one row of values per
chunk.</p>
</div>
<div class="section" id="compute-chunk-commands">
<h3>Compute <a href="#id71"><span class="problematic" id="id72">*</span></a>/chunk commands:</h3>
<h3>6.23.3. Compute <a href="#id71"><span class="problematic" id="id72">*</span></a>/chunk commands:</h3>
<p>Currently the following computes operate on chunks of atoms to produce
per-chunk values.</p>
<ul class="simple">
@ -2289,7 +2311,7 @@ largest cluster or fastest diffusing molecule.</li>
</ul>
</div>
<div class="section" id="example-calculations-with-chunks">
<h3>Example calculations with chunks</h3>
<h3>6.23.4. Example calculations with chunks</h3>
<p>Here are eaxmples using chunk commands to calculate various
properties:</p>
<ol class="arabic simple">
@ -2338,7 +2360,7 @@ thermo_style custom step temp v_xave v_xmax
</div>
</div>
<div class="section" id="setting-parameters-for-the-kspace-style-pppm-disp-command">
<span id="howto-24"></span><h2>Setting parameters for the <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style pppm/disp</span></a> command</h2>
<span id="howto-24"></span><h2>6.24. Setting parameters for the <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style pppm/disp</span></a> command</h2>
<p>The PPPM method computes interactions by splitting the pair potential
into two parts, one of which is computed in a normal pairwise fashion,
the so-called real-space part, and one of which is computed using the
@ -2431,7 +2453,7 @@ to specify this command explicitly.</p>
<hr class="docutils" />
</div>
<div class="section" id="polarizable-models">
<span id="howto-25"></span><h2>Polarizable models</h2>
<span id="howto-25"></span><h2>6.25. Polarizable models</h2>
<p>In polarizable force fields the charge distributions in molecules and
materials respond to their electrostatic environements. Polarizable
systems can be simulated in LAMMPS using three methods:</p>
@ -2501,7 +2523,7 @@ well.</p>
<hr class="docutils" />
</div>
<div class="section" id="adiabatic-core-shell-model">
<span id="howto-26"></span><h2>Adiabatic core/shell model</h2>
<span id="howto-26"></span><h2>6.26. Adiabatic core/shell model</h2>
<p>The adiabatic core-shell model by <a class="reference internal" href="pair_cs.html#mitchellfinchham"><span class="std std-ref">Mitchell and Finchham</span></a> is a simple method for adding
polarizability to a system. In order to mimic the electron shell of
an ion, a satellite particle is attached to it. This way the ions are
@ -2706,7 +2728,7 @@ pairs as chunks.</p>
<hr class="docutils" />
</div>
<div class="section" id="drude-induced-dipoles">
<span id="howto-27"></span><h2>Drude induced dipoles</h2>
<span id="howto-27"></span><h2>6.27. Drude induced dipoles</h2>
<p>The thermalized Drude model, similarly to the <a class="reference internal" href="#howto-26"><span class="std std-ref">core-shell</span></a>
model, representes induced dipoles by a pair of charges (the core atom
and the Drude particle) connected by a harmonic spring. The Drude
@ -2785,6 +2807,15 @@ Phys, 79, 926 (1983).</p>
</div>
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@ -8,7 +8,7 @@
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<title>Introduction &mdash; LAMMPS documentation</title>
<title>1. Introduction &mdash; LAMMPS documentation</title>
@ -32,7 +32,9 @@
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<link rel="next" title="2. Getting Started" href="Section_start.html"/>
<link rel="prev" title="LAMMPS Documentation" href="Manual.html"/>
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@ -71,31 +73,42 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Introduction</a><ul>
<li><a class="reference internal" href="#what-is-lammps">What is LAMMPS</a></li>
<li><a class="reference internal" href="#lammps-features">LAMMPS features</a><ul>
<li><a class="reference internal" href="#general-features">General features</a></li>
<li><a class="reference internal" href="#particle-and-model-types">Particle and model types</a></li>
<li><a class="reference internal" href="#force-fields">Force fields</a></li>
<li><a class="reference internal" href="#atom-creation">Atom creation</a></li>
<li><a class="reference internal" href="#ensembles-constraints-and-boundary-conditions">Ensembles, constraints, and boundary conditions</a></li>
<li><a class="reference internal" href="#integrators">Integrators</a></li>
<li><a class="reference internal" href="#diagnostics">Diagnostics</a></li>
<li><a class="reference internal" href="#output">Output</a></li>
<li><a class="reference internal" href="#multi-replica-models">Multi-replica models</a></li>
<li><a class="reference internal" href="#pre-and-post-processing">Pre- and post-processing</a></li>
<li><a class="reference internal" href="#specialized-features">Specialized features</a></li>
<ul class="current">
<li class="toctree-l1 current"><a class="current reference internal" href="#">1. Introduction</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#what-is-lammps">1.1. What is LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="#lammps-features">1.2. LAMMPS features</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#general-features">1.2.1. General features</a></li>
<li class="toctree-l3"><a class="reference internal" href="#particle-and-model-types">1.2.2. Particle and model types</a></li>
<li class="toctree-l3"><a class="reference internal" href="#force-fields">1.2.3. Force fields</a></li>
<li class="toctree-l3"><a class="reference internal" href="#atom-creation">1.2.4. Atom creation</a></li>
<li class="toctree-l3"><a class="reference internal" href="#ensembles-constraints-and-boundary-conditions">1.2.5. Ensembles, constraints, and boundary conditions</a></li>
<li class="toctree-l3"><a class="reference internal" href="#integrators">1.2.6. Integrators</a></li>
<li class="toctree-l3"><a class="reference internal" href="#diagnostics">1.2.7. Diagnostics</a></li>
<li class="toctree-l3"><a class="reference internal" href="#output">1.2.8. Output</a></li>
<li class="toctree-l3"><a class="reference internal" href="#multi-replica-models">1.2.9. Multi-replica models</a></li>
<li class="toctree-l3"><a class="reference internal" href="#pre-and-post-processing">1.2.10. Pre- and post-processing</a></li>
<li class="toctree-l3"><a class="reference internal" href="#specialized-features">1.2.11. Specialized features</a></li>
</ul>
</li>
<li><a class="reference internal" href="#lammps-non-features">LAMMPS non-features</a></li>
<li><a class="reference internal" href="#open-source-distribution">Open source distribution</a></li>
<li><a class="reference internal" href="#acknowledgments-and-citations">Acknowledgments and citations</a></li>
<li class="toctree-l2"><a class="reference internal" href="#lammps-non-features">1.3. LAMMPS non-features</a></li>
<li class="toctree-l2"><a class="reference internal" href="#open-source-distribution">1.4. Open source distribution</a></li>
<li class="toctree-l2"><a class="reference internal" href="#acknowledgments-and-citations">1.5. Acknowledgments and citations</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
</div>
@ -118,7 +131,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>Introduction</li>
<li>1. Introduction</li>
<li class="wy-breadcrumbs-aside">
@ -129,12 +142,21 @@
</ul>
<hr/>
<div class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
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</div>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="introduction">
<h1>Introduction</h1>
<h1>1. Introduction</h1>
<p>This section provides an overview of what LAMMPS can and can&#8217;t do,
describes what it means for LAMMPS to be an open-source code, and
acknowledges the funding and people who have contributed to LAMMPS
@ -148,7 +170,7 @@ over the years.</p>
<div class="line"><br /></div>
</div>
<div class="section" id="what-is-lammps">
<span id="intro-1"></span><h2>What is LAMMPS</h2>
<span id="intro-1"></span><h2>1.1. What is LAMMPS</h2>
<p>LAMMPS is a classical molecular dynamics code that models an ensemble
of particles in a liquid, solid, or gaseous state. It can model
atomic, polymeric, biological, metallic, granular, and coarse-grained
@ -199,14 +221,14 @@ LAMMPS are listed in <a class="reference internal" href="#intro-5"><span class="
<hr class="docutils" />
</div>
<div class="section" id="lammps-features">
<span id="intro-2"></span><h2>LAMMPS features</h2>
<span id="intro-2"></span><h2>1.2. LAMMPS features</h2>
<p>This section highlights LAMMPS features, with pointers to specific
commands which give more details. If LAMMPS doesn&#8217;t have your
favorite interatomic potential, boundary condition, or atom type, see
<a class="reference internal" href="Section_modify.html"><span class="doc">Section_modify</span></a>, which describes how you can add
it to LAMMPS.</p>
<div class="section" id="general-features">
<h3>General features</h3>
<h3>1.2.1. General features</h3>
<ul class="simple">
<li>runs on a single processor or in parallel</li>
<li>distributed-memory message-passing parallelism (MPI)</li>
@ -225,7 +247,7 @@ it to LAMMPS.</p>
</ul>
</div>
<div class="section" id="particle-and-model-types">
<h3>Particle and model types</h3>
<h3>1.2.2. Particle and model types</h3>
<p>(<a class="reference internal" href="atom_style.html"><span class="doc">atom style</span></a> command)</p>
<ul class="simple">
<li>atoms</li>
@ -243,7 +265,7 @@ it to LAMMPS.</p>
</ul>
</div>
<div class="section" id="force-fields">
<h3>Force fields</h3>
<h3>1.2.3. Force fields</h3>
<p>(<a class="reference internal" href="pair_style.html"><span class="doc">pair style</span></a>, <a class="reference internal" href="bond_style.html"><span class="doc">bond style</span></a>,
<a class="reference internal" href="angle_style.html"><span class="doc">angle style</span></a>, <a class="reference internal" href="dihedral_style.html"><span class="doc">dihedral style</span></a>,
<a class="reference internal" href="improper_style.html"><span class="doc">improper style</span></a>, <a class="reference internal" href="kspace_style.html"><span class="doc">kspace style</span></a>
@ -272,7 +294,7 @@ commands)</p>
</ul>
</div>
<div class="section" id="atom-creation">
<h3>Atom creation</h3>
<h3>1.2.4. Atom creation</h3>
<p>(<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>, <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a>,
<a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a>, <a class="reference internal" href="delete_atoms.html"><span class="doc">delete_atoms</span></a>,
<a class="reference internal" href="displace_atoms.html"><span class="doc">displace_atoms</span></a>, <a class="reference internal" href="replicate.html"><span class="doc">replicate</span></a> commands)</p>
@ -285,7 +307,7 @@ commands)</p>
</ul>
</div>
<div class="section" id="ensembles-constraints-and-boundary-conditions">
<h3>Ensembles, constraints, and boundary conditions</h3>
<h3>1.2.5. Ensembles, constraints, and boundary conditions</h3>
<p>(<a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command)</p>
<ul class="simple">
<li>2d or 3d systems</li>
@ -305,7 +327,7 @@ commands)</p>
</ul>
</div>
<div class="section" id="integrators">
<h3>Integrators</h3>
<h3>1.2.6. Integrators</h3>
<p>(<a class="reference internal" href="run.html"><span class="doc">run</span></a>, <a class="reference internal" href="run_style.html"><span class="doc">run_style</span></a>, <a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a> commands)</p>
<ul class="simple">
<li>velocity-Verlet integrator</li>
@ -317,13 +339,13 @@ commands)</p>
</ul>
</div>
<div class="section" id="diagnostics">
<h3>Diagnostics</h3>
<h3>1.2.7. Diagnostics</h3>
<ul class="simple">
<li>see the various flavors of the <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> and <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> commands</li>
</ul>
</div>
<div class="section" id="output">
<h3>Output</h3>
<h3>1.2.8. Output</h3>
<p>(<a class="reference internal" href="dump.html"><span class="doc">dump</span></a>, <a class="reference internal" href="restart.html"><span class="doc">restart</span></a> commands)</p>
<ul class="simple">
<li>log file of thermodynamic info</li>
@ -338,14 +360,14 @@ commands)</p>
</ul>
</div>
<div class="section" id="multi-replica-models">
<h3>Multi-replica models</h3>
<h3>1.2.9. Multi-replica models</h3>
<p><a class="reference internal" href="neb.html"><span class="doc">nudged elastic band</span></a>
<a class="reference internal" href="prd.html"><span class="doc">parallel replica dynamics</span></a>
<a class="reference internal" href="tad.html"><span class="doc">temperature accelerated dynamics</span></a>
<a class="reference internal" href="temper.html"><span class="doc">parallel tempering</span></a></p>
</div>
<div class="section" id="pre-and-post-processing">
<h3>Pre- and post-processing</h3>
<h3>1.2.10. Pre- and post-processing</h3>
<ul class="simple">
<li>Various pre- and post-processing serial tools are packaged
with LAMMPS; see these <a class="reference internal" href="Section_tools.html"><span class="doc">doc pages</span></a>.</li>
@ -356,7 +378,7 @@ written in <a class="reference external" href="http://www.python.org">Python</a>
</ul>
</div>
<div class="section" id="specialized-features">
<h3>Specialized features</h3>
<h3>1.2.11. Specialized features</h3>
<p>These are LAMMPS capabilities which you may not think of as typical
molecular dynamics options:</p>
<ul class="simple">
@ -380,7 +402,7 @@ molecular dynamics options:</p>
</div>
</div>
<div class="section" id="lammps-non-features">
<span id="intro-3"></span><h2>LAMMPS non-features</h2>
<span id="intro-3"></span><h2>1.3. LAMMPS non-features</h2>
<p>LAMMPS is designed to efficiently compute Newton&#8217;s equations of motion
for a system of interacting particles. Many of the tools needed to
pre- and post-process the data for such simulations are not included
@ -473,7 +495,7 @@ spatial-decomposition version exist.</p>
<hr class="docutils" />
</div>
<div class="section" id="open-source-distribution">
<span id="intro-4"></span><h2>Open source distribution</h2>
<span id="intro-4"></span><h2>1.4. Open source distribution</h2>
<p>LAMMPS comes with no warranty of any kind. As each source file states
in its header, it is a copyrighted code that is distributed free-of-
charge, under the terms of the <a class="reference external" href="http://www.gnu.org/copyleft/gpl.html">GNU Public License</a> (GPL). This
@ -535,7 +557,7 @@ encouraged.</li>
<hr class="docutils" />
</div>
<div class="section" id="acknowledgments-and-citations">
<span id="intro-5"></span><h2>Acknowledgments and citations</h2>
<span id="intro-5"></span><h2>1.5. Acknowledgments and citations</h2>
<p>LAMMPS development has been funded by the <a class="reference external" href="http://www.doe.gov">US Department of Energy</a> (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life
programs and its <a class="reference external" href="http://www.sc.doe.gov/ascr/home.html">OASCR</a> and <a class="reference external" href="http://www.er.doe.gov/production/ober/ober_top.html">OBER</a> offices.</p>
<p>Specifically, work on the latest version was funded in part by the US
@ -604,6 +626,15 @@ version of LAMMPS were the following:</p>
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@ -8,7 +8,7 @@
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<title>10. Modifying &amp; extending LAMMPS &mdash; LAMMPS documentation</title>
@ -32,7 +32,9 @@
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@ -71,28 +73,39 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Modifying &amp; extending LAMMPS</a><ul>
<li><a class="reference internal" href="#atom-styles">Atom styles</a></li>
<li><a class="reference internal" href="#bond-angle-dihedral-improper-potentials">Bond, angle, dihedral, improper potentials</a></li>
<li><a class="reference internal" href="#compute-styles">Compute styles</a></li>
<li><a class="reference internal" href="#dump-styles">Dump styles</a></li>
<li><a class="reference internal" href="#dump-custom-output-options">Dump custom output options</a></li>
<li><a class="reference internal" href="#fix-styles">Fix styles</a></li>
<li><a class="reference internal" href="#input-script-commands">Input script commands</a></li>
<li><a class="reference internal" href="#kspace-computations">Kspace computations</a></li>
<li><a class="reference internal" href="#minimization-styles">Minimization styles</a></li>
<li><a class="reference internal" href="#pairwise-potentials">Pairwise potentials</a></li>
<li><a class="reference internal" href="#region-styles">Region styles</a></li>
<li><a class="reference internal" href="#body-styles">Body styles</a></li>
<li><a class="reference internal" href="#thermodynamic-output-options">Thermodynamic output options</a></li>
<li><a class="reference internal" href="#variable-options">Variable options</a></li>
<li><a class="reference internal" href="#submitting-new-features-for-inclusion-in-lammps">Submitting new features for inclusion in LAMMPS</a></li>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><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 current"><a class="current reference internal" href="#">10. Modifying &amp; extending LAMMPS</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#atom-styles">10.1. Atom styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#bond-angle-dihedral-improper-potentials">10.2. Bond, angle, dihedral, improper potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="#compute-styles">10.3. Compute styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#dump-styles">10.4. Dump styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#dump-custom-output-options">10.5. Dump custom output options</a></li>
<li class="toctree-l2"><a class="reference internal" href="#fix-styles">10.6. Fix styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#input-script-commands">10.7. Input script commands</a></li>
<li class="toctree-l2"><a class="reference internal" href="#kspace-computations">10.8. Kspace computations</a></li>
<li class="toctree-l2"><a class="reference internal" href="#minimization-styles">10.9. Minimization styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#pairwise-potentials">10.10. Pairwise potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="#region-styles">10.11. Region styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#body-styles">10.12. Body styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#thermodynamic-output-options">10.13. Thermodynamic output options</a></li>
<li class="toctree-l2"><a class="reference internal" href="#variable-options">10.14. Variable options</a></li>
<li class="toctree-l2"><a class="reference internal" href="#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></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
</div>
@ -115,7 +128,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>Modifying &amp; extending LAMMPS</li>
<li>10. Modifying &amp; extending LAMMPS</li>
<li class="wy-breadcrumbs-aside">
@ -126,12 +139,21 @@
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<div itemprop="articleBody">
<div class="section" id="modifying-extending-lammps">
<h1>Modifying &amp; extending LAMMPS</h1>
<h1>10. Modifying &amp; extending LAMMPS</h1>
<p>This section describes how to customize LAMMPS by modifying
and extending its source code.</p>
<div class="line-block">
@ -241,7 +263,7 @@ interested in adding it to the LAMMPS distribution. See further
details on this at the bottom of this page.</li>
</ul>
<div class="section" id="atom-styles">
<span id="mod-1"></span><h2>Atom styles</h2>
<span id="mod-1"></span><h2>10.1. Atom styles</h2>
<p>Classes that define an <a class="reference internal" href="atom_style.html"><span class="doc">atom style</span></a> are derived from
the AtomVec class and managed by the Atom class. The atom style
determines what attributes are associated with an atom. A new atom
@ -388,7 +410,7 @@ which store the attributes of individual atoms.</p>
<hr class="docutils" />
</div>
<div class="section" id="bond-angle-dihedral-improper-potentials">
<span id="mod-2"></span><h2>Bond, angle, dihedral, improper potentials</h2>
<span id="mod-2"></span><h2>10.2. Bond, angle, dihedral, improper potentials</h2>
<p>Classes that compute molecular interactions are derived from the Bond,
Angle, Dihedral, and Improper classes. New styles can be created to
add new potentials to LAMMPS.</p>
@ -439,7 +461,7 @@ for details and specific additional methods.</p>
<hr class="docutils" />
</div>
<div class="section" id="compute-styles">
<span id="mod-3"></span><h2>Compute styles</h2>
<span id="mod-3"></span><h2>10.3. Compute styles</h2>
<p>Classes that compute scalar and vector quantities like temperature
and the pressure tensor, as well as classes that compute per-atom
quantities like kinetic energy and the centro-symmetry parameter
@ -516,10 +538,10 @@ provides <em>examples</em>_compute_tally.html for utilizing this mechanism.</p>
<hr class="docutils" />
</div>
<div class="section" id="dump-styles">
<span id="mod-4"></span><h2>Dump styles</h2>
<span id="mod-4"></span><h2>10.4. Dump styles</h2>
</div>
<div class="section" id="dump-custom-output-options">
<span id="mod-5"></span><h2>Dump custom output options</h2>
<span id="mod-5"></span><h2>10.5. Dump custom output options</h2>
<p>Classes that dump per-atom info to files are derived from the Dump
class. To dump new quantities or in a new format, a new derived dump
class can be added, but it is typically simpler to modify the
@ -558,7 +580,7 @@ half-dozen or so locations where code will need to be added.</p>
<hr class="docutils" />
</div>
<div class="section" id="fix-styles">
<span id="mod-6"></span><h2>Fix styles</h2>
<span id="mod-6"></span><h2>10.6. Fix styles</h2>
<p>In LAMMPS, a &#8220;fix&#8221; is any operation that is computed during
timestepping that alters some property of the system. Essentially
everything that happens during a simulation besides force computation,
@ -766,7 +788,7 @@ quantities and/or to be summed to the potential energy of the system.</p>
<hr class="docutils" />
</div>
<div class="section" id="input-script-commands">
<span id="mod-7"></span><h2>Input script commands</h2>
<span id="mod-7"></span><h2>10.7. Input script commands</h2>
<p>New commands can be added to LAMMPS input scripts by adding new
classes that have a &#8220;command&#8221; method. For example, the create_atoms,
read_data, velocity, and run commands are all implemented in this
@ -792,7 +814,7 @@ needed.</p>
<hr class="docutils" />
</div>
<div class="section" id="kspace-computations">
<span id="mod-8"></span><h2>Kspace computations</h2>
<span id="mod-8"></span><h2>10.8. Kspace computations</h2>
<p>Classes that compute long-range Coulombic interactions via K-space
representations (Ewald, PPPM) are derived from the KSpace class. New
styles can be created to add new K-space options to LAMMPS.</p>
@ -822,7 +844,7 @@ class. See kspace.h for details.</p>
<hr class="docutils" />
</div>
<div class="section" id="minimization-styles">
<span id="mod-9"></span><h2>Minimization styles</h2>
<span id="mod-9"></span><h2>10.9. Minimization styles</h2>
<p>Classes that perform energy minimization derived from the Min class.
New styles can be created to add new minimization algorithms to
LAMMPS.</p>
@ -849,7 +871,7 @@ class. See min.h for details.</p>
<hr class="docutils" />
</div>
<div class="section" id="pairwise-potentials">
<span id="mod-10"></span><h2>Pairwise potentials</h2>
<span id="mod-10"></span><h2>10.10. Pairwise potentials</h2>
<p>Classes that compute pairwise interactions are derived from the Pair
class. In LAMMPS, pairwise calculation include manybody potentials
such as EAM or Tersoff where particles interact without a static bond
@ -897,7 +919,7 @@ includes some optional methods to enable its use with rRESPA.</p>
<hr class="docutils" />
</div>
<div class="section" id="region-styles">
<span id="mod-11"></span><h2>Region styles</h2>
<span id="mod-11"></span><h2>10.11. Region styles</h2>
<p>Classes that define geometric regions are derived from the Region
class. Regions are used elsewhere in LAMMPS to group atoms, delete
atoms to create a void, insert atoms in a specified region, etc. New
@ -928,7 +950,7 @@ class. See region.h for details.</p>
<hr class="docutils" />
</div>
<div class="section" id="body-styles">
<span id="mod-12"></span><h2>Body styles</h2>
<span id="mod-12"></span><h2>10.12. Body styles</h2>
<p>Classes that define body particles are derived from the Body class.
Body particles can represent complex entities, such as surface meshes
of discrete points, collections of sub-particles, deformable objects,
@ -976,7 +998,7 @@ class. See body.h for details.</p>
<hr class="docutils" />
</div>
<div class="section" id="thermodynamic-output-options">
<span id="mod-13"></span><h2>Thermodynamic output options</h2>
<span id="mod-13"></span><h2>10.13. Thermodynamic output options</h2>
<p>There is one class that computes and prints thermodynamic information
to the screen and log file; see the file thermo.cpp.</p>
<p>There are two styles defined in thermo.cpp: &#8220;one&#8221; and &#8220;multi&#8221;. There
@ -1000,7 +1022,7 @@ by adding a new keyword to the thermo command.</p>
<hr class="docutils" />
</div>
<div class="section" id="variable-options">
<span id="mod-14"></span><h2>Variable options</h2>
<span id="mod-14"></span><h2>10.14. Variable options</h2>
<p>There is one class that computes and stores <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>
information in LAMMPS; see the file variable.cpp. The value
associated with a variable can be periodically printed to the screen
@ -1034,14 +1056,14 @@ then be accessed by variables) was discussed
<a class="reference internal" href="Section_howto.html#compute"><span class="std std-ref">here</span></a> on this page.</p>
</div>
<div class="section" id="submitting-new-features-for-inclusion-in-lammps">
<span id="mod-15"></span><h2>Submitting new features for inclusion in LAMMPS</h2>
<span id="mod-15"></span><h2>10.15. Submitting new features for inclusion in LAMMPS</h2>
<p>We encourage users to submit new features to <a class="reference external" href="http://lammps.sandia.gov/authors.html">the developers</a> that they add to
LAMMPS, especially if you think they will be of interest to other
users. The preferred way to do this is via GitHub. Once you have
prepared the content described below, see <a class="reference internal" href="tutorial_github.html"><span class="doc">this tutorial</span></a> for instructions on how to submit
your changes or new files.</p>
<p>If the new features/files are broadly useful we may add them as core
files to LAMMPS or as part of a <span class="xref std std-ref">standard package</span>. Else we will add them as a
files to LAMMPS or as part of a <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">standard package</span></a>. Else we will add them as a
user-contributed file or package. Examples of user packages are in
src sub-directories that start with USER. The USER-MISC package is
simply a collection of (mostly) unrelated single files, which is the
@ -1174,6 +1196,15 @@ feature.</p>
</div>
<footer>
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@ -8,7 +8,7 @@
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<title>Packages &mdash; LAMMPS documentation</title>
<title>4. Packages &mdash; LAMMPS documentation</title>
@ -32,7 +32,9 @@
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<link rel="top" title="LAMMPS documentation" href="index.html"/>
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@ -71,76 +73,87 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Packages</a><ul>
<li><a class="reference internal" href="#standard-packages">Standard packages</a><ul>
<li><a class="reference internal" href="#asphere-package">ASPHERE package</a></li>
<li><a class="reference internal" href="#body-package">BODY package</a></li>
<li><a class="reference internal" href="#class2-package">CLASS2 package</a></li>
<li><a class="reference internal" href="#colloid-package">COLLOID package</a></li>
<li><a class="reference internal" href="#compress-package">COMPRESS package</a></li>
<li><a class="reference internal" href="#coreshell-package">CORESHELL package</a></li>
<li><a class="reference internal" href="#dipole-package">DIPOLE package</a></li>
<li><a class="reference internal" href="#gpu-package">GPU package</a></li>
<li><a class="reference internal" href="#granular-package">GRANULAR package</a></li>
<li><a class="reference internal" href="#kim-package">KIM package</a></li>
<li><a class="reference internal" href="#kokkos-package">KOKKOS package</a></li>
<li><a class="reference internal" href="#kspace-package">KSPACE package</a></li>
<li><a class="reference internal" href="#manybody-package">MANYBODY package</a></li>
<li><a class="reference internal" href="#mc-package">MC package</a></li>
<li><a class="reference internal" href="#meam-package">MEAM package</a></li>
<li><a class="reference internal" href="#misc-package">MISC package</a></li>
<li><a class="reference internal" href="#molecule-package">MOLECULE package</a></li>
<li><a class="reference internal" href="#mpiio-package">MPIIO package</a></li>
<li><a class="reference internal" href="#opt-package">OPT package</a></li>
<li><a class="reference internal" href="#peri-package">PERI package</a></li>
<li><a class="reference internal" href="#poems-package">POEMS package</a></li>
<li><a class="reference internal" href="#python-package">PYTHON package</a></li>
<li><a class="reference internal" href="#qeq-package">QEQ package</a></li>
<li><a class="reference internal" href="#reax-package">REAX package</a></li>
<li><a class="reference internal" href="#replica-package">REPLICA package</a></li>
<li><a class="reference internal" href="#rigid-package">RIGID package</a></li>
<li><a class="reference internal" href="#shock-package">SHOCK package</a></li>
<li><a class="reference internal" href="#snap-package">SNAP package</a></li>
<li><a class="reference internal" href="#srd-package">SRD package</a></li>
<li><a class="reference internal" href="#voronoi-package">VORONOI package</a></li>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">4. Packages</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#standard-packages">4.1. Standard packages</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#asphere-package">4.1.1. ASPHERE package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#body-package">4.1.2. BODY package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#class2-package">4.1.3. CLASS2 package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#colloid-package">4.1.4. COLLOID package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#compress-package">4.1.5. COMPRESS package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#coreshell-package">4.1.6. CORESHELL package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#dipole-package">4.1.7. DIPOLE package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#gpu-package">4.1.8. GPU package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#granular-package">4.1.9. GRANULAR package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#kim-package">4.1.10. KIM package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#kokkos-package">4.1.11. KOKKOS package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#kspace-package">4.1.12. KSPACE package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#manybody-package">4.1.13. MANYBODY package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#mc-package">4.1.14. MC package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#meam-package">4.1.15. MEAM package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#misc-package">4.1.16. MISC package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#molecule-package">4.1.17. MOLECULE package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#mpiio-package">4.1.18. MPIIO package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#opt-package">4.1.19. OPT package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#peri-package">4.1.20. PERI package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#poems-package">4.1.21. POEMS package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#python-package">4.1.22. PYTHON package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#qeq-package">4.1.23. QEQ package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#reax-package">4.1.24. REAX package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#replica-package">4.1.25. REPLICA package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#rigid-package">4.1.26. RIGID package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#shock-package">4.1.27. SHOCK package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#snap-package">4.1.28. SNAP package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#srd-package">4.1.29. SRD package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#voronoi-package">4.1.30. VORONOI package</a></li>
</ul>
</li>
<li><a class="reference internal" href="#user-packages">User packages</a><ul>
<li><a class="reference internal" href="#user-atc-package">USER-ATC package</a></li>
<li><a class="reference internal" href="#user-awpmd-package">USER-AWPMD package</a></li>
<li><a class="reference internal" href="#user-cg-cmm-package">USER-CG-CMM package</a></li>
<li><a class="reference internal" href="#user-colvars-package">USER-COLVARS package</a></li>
<li><a class="reference internal" href="#user-diffraction-package">USER-DIFFRACTION package</a></li>
<li><a class="reference internal" href="#user-dpd-package">USER-DPD package</a></li>
<li><a class="reference internal" href="#user-drude-package">USER-DRUDE package</a></li>
<li><a class="reference internal" href="#user-eff-package">USER-EFF package</a></li>
<li><a class="reference internal" href="#user-fep-package">USER-FEP package</a></li>
<li><a class="reference internal" href="#user-h5md-package">USER-H5MD package</a></li>
<li><a class="reference internal" href="#user-intel-package">USER-INTEL package</a></li>
<li><a class="reference internal" href="#user-lb-package">USER-LB package</a></li>
<li><a class="reference internal" href="#user-mgpt-package">USER-MGPT package</a></li>
<li><a class="reference internal" href="#user-misc-package">USER-MISC package</a></li>
<li><a class="reference internal" href="#user-manifold-package">USER-MANIFOLD package</a></li>
<li><a class="reference internal" href="#user-molfile-package">USER-MOLFILE package</a></li>
<li><a class="reference internal" href="#user-omp-package">USER-OMP package</a></li>
<li><a class="reference internal" href="#user-phonon-package">USER-PHONON package</a></li>
<li><a class="reference internal" href="#user-qmmm-package">USER-QMMM package</a></li>
<li><a class="reference internal" href="#user-qtb-package">USER-QTB package</a></li>
<li><a class="reference internal" href="#user-quip-package">USER-QUIP package</a></li>
<li><a class="reference internal" href="#user-reaxc-package">USER-REAXC package</a></li>
<li><a class="reference internal" href="#user-smd-package">USER-SMD package</a></li>
<li><a class="reference internal" href="#user-smtbq-package">USER-SMTBQ package</a></li>
<li><a class="reference internal" href="#user-sph-package">USER-SPH package</a></li>
<li><a class="reference internal" href="#user-tally-package">USER-TALLY package</a></li>
<li><a class="reference internal" href="#user-vtk-package">USER-VTK package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-packages">4.2. User packages</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#user-atc-package">4.2.1. USER-ATC package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-awpmd-package">4.2.2. USER-AWPMD package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-cg-cmm-package">4.2.3. USER-CG-CMM package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-colvars-package">4.2.4. USER-COLVARS package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-diffraction-package">4.2.5. USER-DIFFRACTION package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-dpd-package">4.2.6. USER-DPD package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-drude-package">4.2.7. USER-DRUDE package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-eff-package">4.2.8. USER-EFF package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-fep-package">4.2.9. USER-FEP package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-h5md-package">4.2.10. USER-H5MD package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-intel-package">4.2.11. USER-INTEL package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-lb-package">4.2.12. USER-LB package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-mgpt-package">4.2.13. USER-MGPT package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-misc-package">4.2.14. USER-MISC package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-manifold-package">4.2.15. USER-MANIFOLD package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-molfile-package">4.2.16. USER-MOLFILE package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-omp-package">4.2.17. USER-OMP package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-phonon-package">4.2.18. USER-PHONON package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-qmmm-package">4.2.19. USER-QMMM package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-qtb-package">4.2.20. USER-QTB package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-quip-package">4.2.21. USER-QUIP package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-reaxc-package">4.2.22. USER-REAXC package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-smd-package">4.2.23. USER-SMD package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-smtbq-package">4.2.24. USER-SMTBQ package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-sph-package">4.2.25. USER-SPH package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-tally-package">4.2.26. USER-TALLY package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-vtk-package">4.2.27. USER-VTK package</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
</div>
@ -163,7 +176,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>Packages</li>
<li>4. Packages</li>
<li class="wy-breadcrumbs-aside">
@ -174,12 +187,21 @@
</ul>
<hr/>
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<a href="Section_accelerate.html" class="btn btn-neutral float-right" title="5. Accelerating LAMMPS performance" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
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</div>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="packages">
<h1>Packages</h1>
<h1>4. Packages</h1>
<p>This section gives an overview of the add-on optional packages that
extend LAMMPS functionality. Packages are groups of files that enable
a specific set of features. For example, force fields for molecular
@ -193,7 +215,7 @@ packages.</p>
<div class="line">4.2 <a class="reference internal" href="#pkg-2"><span class="std std-ref">User packages</span></a></div>
<div class="line"><br /></div>
</div>
<p><span class="xref std std-ref">Section_start 3</span> of the manual describes
<p><a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Section_start 3</span></a> of the manual describes
the difference between standard packages and user packages. It also
has general details on how to include/exclude specific packages as
part of the LAMMPS build process, and on how to build auxiliary
@ -227,7 +249,7 @@ the USER-OMP package is already installed, both the pair
lj/cut/coul/long and lj/cut/coul/long/omp commands will be installed.</p>
<hr class="docutils" />
<div class="section" id="standard-packages">
<span id="pkg-1"></span><h2>Standard packages</h2>
<span id="pkg-1"></span><h2>4.1. Standard packages</h2>
<p>The current list of standard packages is as follows. Each package
name links to a sub-section below with more details.</p>
<table border="1" class="docutils">
@ -592,7 +614,7 @@ See details on all of this below for individual packages.
p.s.: are we ever going to get commit messages from you? ;-)</p>
<hr class="docutils" />
<div class="section" id="asphere-package">
<span id="asphere"></span><h3>ASPHERE package</h3>
<span id="asphere"></span><h3>4.1.1. ASPHERE package</h3>
<p>Contents: Several computes, time-integration fixes, and pair styles
for aspherical particle models: ellipsoids, 2d lines, 3d triangles.</p>
<p>To install via make or Make.py:</p>
@ -619,7 +641,7 @@ examples/ASPHERE, examples/ellipse</p>
<hr class="docutils" />
</div>
<div class="section" id="body-package">
<span id="body"></span><h3>BODY package</h3>
<span id="body"></span><h3>4.1.2. BODY package</h3>
<p>Contents: Support for body-style particles. Computes,
time-integration fixes, pair styles, as well as the body styles
themselves. See the <a class="reference internal" href="body.html"><span class="doc">body</span></a> doc page for an overview.</p>
@ -644,7 +666,7 @@ themselves. See the <a class="reference internal" href="body.html"><span class=
<hr class="docutils" />
</div>
<div class="section" id="class2-package">
<span id="class2"></span><h3>CLASS2 package</h3>
<span id="class2"></span><h3>4.1.3. CLASS2 package</h3>
<p>Contents: Bond, angle, dihedral, improper, and pair styles for the
COMPASS CLASS2 molecular force field.</p>
<p>To install via make or Make.py:</p>
@ -667,7 +689,7 @@ COMPASS CLASS2 molecular force field.</p>
<hr class="docutils" />
</div>
<div class="section" id="colloid-package">
<span id="colloid"></span><h3>COLLOID package</h3>
<span id="colloid"></span><h3>4.1.4. COLLOID package</h3>
<p>Contents: Support for coarse-grained colloidal particles. Wall fix
and pair styles that implement colloidal interaction models for
finite-size particles. This includes the Fast Lubrication Dynamics
@ -693,7 +715,7 @@ approximation to Stokesian dynamics.</p>
<hr class="docutils" />
</div>
<div class="section" id="compress-package">
<span id="compress"></span><h3>COMPRESS package</h3>
<span id="compress"></span><h3>4.1.5. COMPRESS package</h3>
<p>Contents: Support for compressed output of dump files via the zlib
compression library, using dump styles with a &#8220;gz&#8221; in their style
name.</p>
@ -722,7 +744,7 @@ zlib info it specifies.</p>
<hr class="docutils" />
</div>
<div class="section" id="coreshell-package">
<span id="coreshell"></span><h3>CORESHELL package</h3>
<span id="coreshell"></span><h3>4.1.6. CORESHELL package</h3>
<p>Contents: Compute and pair styles that implement the adiabatic
core/shell model for polarizability. The compute temp/cs command
measures the temperature of a system with core/shell particles. The
@ -751,7 +773,7 @@ lj/cut/coul/long/cs&#8221;_pair_lj.html, examples/coreshell</p>
<hr class="docutils" />
</div>
<div class="section" id="dipole-package">
<span id="dipole"></span><h3>DIPOLE package</h3>
<span id="dipole"></span><h3>4.1.7. DIPOLE package</h3>
<p>Contents: An atom style and several pair styles to support point
dipole models with short-range or long-range interactions.</p>
<p>To install via make or Make.py:</p>
@ -774,7 +796,7 @@ dipole models with short-range or long-range interactions.</p>
<hr class="docutils" />
</div>
<div class="section" id="gpu-package">
<span id="gpu"></span><h3>GPU package</h3>
<span id="gpu"></span><h3>4.1.8. GPU package</h3>
<p>Contents: Dozens of pair styles and a version of the PPPM long-range
Coulombic solver for NVIDIA GPUs. All of them have a &#8220;gpu&#8221; in their
style name. <a class="reference internal" href="accelerate_gpu.html"><span class="doc">Section accelerate gpu</span></a> gives
@ -828,7 +850,7 @@ examples/accelerate, bench/FERMI, bench/KEPLER</p>
<hr class="docutils" />
</div>
<div class="section" id="granular-package">
<span id="granular"></span><h3>GRANULAR package</h3>
<span id="granular"></span><h3>4.1.9. GRANULAR package</h3>
<p>Contents: Fixes and pair styles that support models of finite-size
granular particles, which interact with each other and boundaries via
frictional and dissipative potentials.</p>
@ -852,7 +874,7 @@ frictional and dissipative potentials.</p>
<hr class="docutils" />
</div>
<div class="section" id="kim-package">
<span id="kim"></span><h3>KIM package</h3>
<span id="kim"></span><h3>4.1.10. KIM package</h3>
<p>Contents: A pair style that interfaces to the Knowledge Base for
Interatomic Models (KIM) repository of interatomic potentials, so that
KIM potentials can be used in a LAMMPS simulation.</p>
@ -881,7 +903,7 @@ process. You should not need to edit this file.</p>
<hr class="docutils" />
</div>
<div class="section" id="kokkos-package">
<span id="kokkos"></span><h3>KOKKOS package</h3>
<span id="kokkos"></span><h3>4.1.11. KOKKOS package</h3>
<p>Contents: Dozens of atom, pair, bond, angle, dihedral, improper styles
which run with the Kokkos library to provide optimization for
multicore CPUs (via OpenMP), NVIDIA GPUs, or the Intel Xeon Phi (in
@ -929,7 +951,7 @@ examples/accelerate, bench/FERMI, bench/KEPLER</p>
<hr class="docutils" />
</div>
<div class="section" id="kspace-package">
<span id="kspace"></span><h3>KSPACE package</h3>
<span id="kspace"></span><h3>4.1.12. KSPACE package</h3>
<p>Contents: A variety of long-range Coulombic solvers, and pair styles
which compute the corresponding short-range portion of the pairwise
Coulombic interactions. These include Ewald, particle-particle
@ -937,7 +959,7 @@ particle-mesh (PPPM), and multilevel summation method (MSM) solvers.</p>
<p>Building with the KSPACE package requires a 1d FFT library be present
on your system for use by the PPPM solvers. This can be the KISS FFT
library provided with LAMMPS, or 3rd party libraries like FFTW or a
vendor-supplied FFT library. See step 6 of <span class="xref std std-ref">Section start 2.2.2</span> of the manual for details of how
vendor-supplied FFT library. See step 6 of <a class="reference internal" href="Section_start.html#start-2-2"><span class="std std-ref">Section start 2.2.2</span></a> of the manual for details of how
to select different FFT options in your machine Makefile. The Make.py
tool has an &#8220;-fft&#8221; option which can insert these settings into your
machine Makefile automatically. Type &#8220;python src/Make.py -h -fft&#8221; to
@ -965,7 +987,7 @@ style name, examples/peptide, bench/in.rhodo</p>
<hr class="docutils" />
</div>
<div class="section" id="manybody-package">
<span id="manybody"></span><h3>MANYBODY package</h3>
<span id="manybody"></span><h3>4.1.13. MANYBODY package</h3>
<p>Contents: A variety of many-body and bond-order potentials. These
include (AI)REBO, EAM, EIM, BOP, Stillinger-Weber, and Tersoff
potentials. Do a directory listing, &#8220;ls src/MANYBODY&#8221;, to see
@ -992,7 +1014,7 @@ examples/nb3d, examples/vashishta</p>
<hr class="docutils" />
</div>
<div class="section" id="mc-package">
<span id="mc"></span><h3>MC package</h3>
<span id="mc"></span><h3>4.1.14. MC package</h3>
<p>Contents: Several fixes and a pair style that have Monte Carlo (MC) or
MC-like attributes. These include fixes for creating, breaking, and
swapping bonds, and for performing atomic swaps and grand-canonical MC
@ -1018,7 +1040,7 @@ in conjuction with dynamics.</p>
<hr class="docutils" />
</div>
<div class="section" id="meam-package">
<span id="meam"></span><h3>MEAM package</h3>
<span id="meam"></span><h3>4.1.15. MEAM package</h3>
<p>Contents: A pair style for the modified embedded atom (MEAM)
potential.</p>
<p>Building LAMMPS with the MEAM package requires first building the MEAM
@ -1065,7 +1087,7 @@ examples/meam</p>
<hr class="docutils" />
</div>
<div class="section" id="misc-package">
<span id="misc"></span><h3>MISC package</h3>
<span id="misc"></span><h3>4.1.16. MISC package</h3>
<p>Contents: A variety of computes, fixes, and pair styles that are not
commonly used, but don&#8217;t align with other packages. Do a directory
listing, &#8220;ls src/MISC&#8221;, to see the list of commands.</p>
@ -1089,7 +1111,7 @@ listing, &#8220;ls src/MISC&#8221;, to see the list of commands.</p>
<hr class="docutils" />
</div>
<div class="section" id="molecule-package">
<span id="molecule"></span><h3>MOLECULE package</h3>
<span id="molecule"></span><h3>4.1.17. MOLECULE package</h3>
<p>Contents: A large number of atom, pair, bond, angle, dihedral,
improper styles that are used to model molecular systems with fixed
covalent bonds. The pair styles include terms for the Dreiding
@ -1118,7 +1140,7 @@ bench/in.chain, bench/in.rhodo</p>
<hr class="docutils" />
</div>
<div class="section" id="mpiio-package">
<span id="mpiio"></span><h3>MPIIO package</h3>
<span id="mpiio"></span><h3>4.1.18. MPIIO package</h3>
<p>Contents: Support for parallel output/input of dump and restart files
via the MPIIO library, which is part of the standard message-passing
interface (MPI) library. It adds <a class="reference internal" href="dump.html"><span class="doc">dump styles</span></a> with a
@ -1145,7 +1167,7 @@ are also written and read in parallel.</p>
<hr class="docutils" />
</div>
<div class="section" id="opt-package">
<span id="opt"></span><h3>OPT package</h3>
<span id="opt"></span><h3>4.1.19. OPT package</h3>
<p>Contents: A handful of pair styles with an &#8220;opt&#8221; in their style name
which are optimized for improved CPU performance on single or multiple
cores. These include EAM, LJ, CHARMM, and Morse potentials. <a class="reference internal" href="accelerate_opt.html"><span class="doc">Section accelerate opt</span></a> gives details of how to build and
@ -1178,7 +1200,7 @@ with an (o), examples/accelerate, bench/KEPLER</p>
<hr class="docutils" />
</div>
<div class="section" id="peri-package">
<span id="peri"></span><h3>PERI package</h3>
<span id="peri"></span><h3>4.1.20. PERI package</h3>
<p>Contents: Support for the Peridynamics method, a particle-based
meshless continuum model. The package includes an atom style, several
computes which calculate diagnostics, and several Peridynamic pair
@ -1207,7 +1229,7 @@ styles which implement different materials models.</p>
<hr class="docutils" />
</div>
<div class="section" id="poems-package">
<span id="poems"></span><h3>POEMS package</h3>
<span id="poems"></span><h3>4.1.21. POEMS package</h3>
<p>Contents: A fix that wraps the Parallelizable Open source Efficient
Multibody Software (POEMS) librar, which is able to simulate the
dynamics of articulated body systems. These are systems with multiple
@ -1247,7 +1269,7 @@ one step. Type &#8220;python src/Make.py -h -poems&#8221; to see the details.</
<hr class="docutils" />
</div>
<div class="section" id="python-package">
<span id="python"></span><h3>PYTHON package</h3>
<span id="python"></span><h3>4.1.22. PYTHON package</h3>
<p>Contents: A <a class="reference internal" href="python.html"><span class="doc">python</span></a> command which allow you to execute
Python code from a LAMMPS input script. The code can be in a separate
file or embedded in the input script itself. See <span class="xref std std-ref">Section python 11.2</span> for an overview of using Python from
@ -1282,7 +1304,7 @@ in one step. Type &#8220;python src/Make.py -h -python&#8221; to see the detail
<hr class="docutils" />
</div>
<div class="section" id="qeq-package">
<span id="qeq"></span><h3>QEQ package</h3>
<span id="qeq"></span><h3>4.1.23. QEQ package</h3>
<p>Contents: Several fixes for performing charge equilibration (QEq) via
severeal different algorithms. These can be used with pair styles
that use QEq as part of their formulation.</p>
@ -1306,7 +1328,7 @@ that use QEq as part of their formulation.</p>
<hr class="docutils" />
</div>
<div class="section" id="reax-package">
<span id="reax"></span><h3>REAX package</h3>
<span id="reax"></span><h3>4.1.24. REAX package</h3>
<p>Contents: A pair style for the ReaxFF potential, a universal reactive
force field, as well as a <a class="reference internal" href="fix_reax_bonds.html"><span class="doc">fix reax/bonds</span></a> command
for monitoring molecules as bonds are created and destroyed.</p>
@ -1349,7 +1371,7 @@ one step. Type &#8220;python src/Make.py -h -reax&#8221; to see the details.</p
<hr class="docutils" />
</div>
<div class="section" id="replica-package">
<span id="replica"></span><h3>REPLICA package</h3>
<span id="replica"></span><h3>4.1.25. REPLICA package</h3>
<p>Contents: A collection of multi-replica methods that are used by
invoking multiple instances (replicas) of LAMMPS
simulations. Communication between individual replicas is performed in
@ -1383,7 +1405,7 @@ examples/tad</p>
<hr class="docutils" />
</div>
<div class="section" id="rigid-package">
<span id="rigid"></span><h3>RIGID package</h3>
<span id="rigid"></span><h3>4.1.26. RIGID package</h3>
<p>Contents: A collection of computes and fixes which enforce rigid
constraints on collections of atoms or particles. This includes SHAKE
and RATTLE, as well as variants of rigid-body time integrators for a
@ -1409,7 +1431,7 @@ few large bodies or many small bodies.</p>
<hr class="docutils" />
</div>
<div class="section" id="shock-package">
<span id="shock"></span><h3>SHOCK package</h3>
<span id="shock"></span><h3>4.1.27. SHOCK package</h3>
<p>Contents: A small number of fixes useful for running impact
simulations where a shock-wave passes through a material.</p>
<p>To install via make or Make.py:</p>
@ -1432,7 +1454,7 @@ simulations where a shock-wave passes through a material.</p>
<hr class="docutils" />
</div>
<div class="section" id="snap-package">
<span id="snap"></span><h3>SNAP package</h3>
<span id="snap"></span><h3>4.1.28. SNAP package</h3>
<p>Contents: A pair style for the spectral neighbor analysis potential
(SNAP), which is an empirical potential which can be quantum accurate
when fit to an archive of DFT data. Computes useful for analyzing
@ -1458,7 +1480,7 @@ properties of the potential are also included.</p>
<hr class="docutils" />
</div>
<div class="section" id="srd-package">
<span id="srd"></span><h3>SRD package</h3>
<span id="srd"></span><h3>4.1.29. SRD package</h3>
<p>Contents: Two fixes which implement the Stochastic Rotation Dynamics
(SRD) method for coarse-graining of a solvent, typically around large
colloidal-scale particles.</p>
@ -1482,7 +1504,7 @@ colloidal-scale particles.</p>
<hr class="docutils" />
</div>
<div class="section" id="voronoi-package">
<span id="voronoi"></span><h3>VORONOI package</h3>
<span id="voronoi"></span><h3>4.1.30. VORONOI package</h3>
<p>Contents: A <a class="reference internal" href="compute_voronoi_atom.html"><span class="doc">compute voronoi/atom</span></a> command
which computes the Voronoi tesselation of a collection of atoms or
particles by wrapping the Voro++ lib</p>
@ -1528,7 +1550,7 @@ src/Make.py -h -voronoi&#8221; to see the details.</p>
</div>
</div>
<div class="section" id="user-packages">
<span id="pkg-2"></span><h2>User packages</h2>
<span id="pkg-2"></span><h2>4.2. User packages</h2>
<p>The current list of user-contributed packages is as follows:</p>
<table border="1" class="docutils">
<colgroup>
@ -1945,7 +1967,7 @@ it is a third-party library not included in the LAMMPS distribution.
See details on all of this below for individual packages.</p>
<hr class="docutils" />
<div class="section" id="user-atc-package">
<span id="user-atc"></span><h3>USER-ATC package</h3>
<span id="user-atc"></span><h3>4.2.1. USER-ATC package</h3>
<p>Contents: ATC stands for atoms-to-continuum. This package implements
a <a class="reference internal" href="fix_atc.html"><span class="doc">fix atc</span></a> command to either couple MD with continuum
finite element equations or perform on-the-fly post-processing of
@ -1976,7 +1998,7 @@ Contact them directly if you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-awpmd-package">
<span id="user-awpmd"></span><h3>USER-AWPMD package</h3>
<span id="user-awpmd"></span><h3>4.2.2. USER-AWPMD package</h3>
<p>Contents: AWPMD stands for Antisymmetrized Wave Packet Molecular
Dynamics. This package implements an atom, pair, and fix style which
allows electrons to be treated as explicit particles in an MD
@ -1988,7 +2010,7 @@ physik.hu-berlin.de). Contact him directly if you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-cg-cmm-package">
<span id="user-cg-cmm"></span><h3>USER-CG-CMM package</h3>
<span id="user-cg-cmm"></span><h3>4.2.3. USER-CG-CMM package</h3>
<p>Contents: CG-CMM stands for coarse-grained ??. This package
implements several pair styles and an angle style using the coarse
grained parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27
@ -2003,7 +2025,7 @@ him directly if you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-colvars-package">
<span id="user-colvars"></span><h3>USER-COLVARS package</h3>
<span id="user-colvars"></span><h3>4.2.4. USER-COLVARS package</h3>
<p>Contents: COLVARS stands for collective variables which can be used to
implement Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella
Sampling and Restraints. This package implements a <a class="reference internal" href="fix_colvars.html"><span class="doc">fix colvars</span></a> command which wraps a COLVARS library which
@ -2020,7 +2042,7 @@ have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-diffraction-package">
<span id="user-diffraction"></span><h3>USER-DIFFRACTION package</h3>
<span id="user-diffraction"></span><h3>4.2.5. USER-DIFFRACTION package</h3>
<p>Contents: This packages implements two computes and a fix for
calculating x-ray and electron diffraction intensities based on
kinematic diffraction theory. See src/USER-DIFFRACTION/README for
@ -2033,7 +2055,7 @@ questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-dpd-package">
<span id="user-dpd"></span><h3>USER-DPD package</h3>
<span id="user-dpd"></span><h3>4.2.6. USER-DPD package</h3>
<p>Contents: DPD stands for dissipative particle dynamics, This package
implements DPD for isothermal, isoenergetic, isobaric and isenthalpic
conditions. It also has extensions for performing reactive DPD, where
@ -2055,7 +2077,7 @@ directly if you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-drude-package">
<span id="user-drude"></span><h3>USER-DRUDE package</h3>
<span id="user-drude"></span><h3>4.2.7. USER-DRUDE package</h3>
<p>Contents: This package contains methods for simulating polarizable
systems using thermalized Drude oscillators. It has computes, fixes,
and pair styles for this purpose. See <a class="reference internal" href="Section_howto.html#howto-27"><span class="std std-ref">Section howto 6.27</span></a> for an overview of how to use the
@ -2071,7 +2093,7 @@ Agilio Padua. Contact them directly if you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-eff-package">
<span id="user-eff"></span><h3>USER-EFF package</h3>
<span id="user-eff"></span><h3>4.2.8. USER-EFF package</h3>
<p>Contents: EFF stands for electron force field. This package contains
atom, pair, fix and compute styles which implement the eFF as
described in A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III,
@ -2085,7 +2107,7 @@ wag.caltech.edu). Contact him directly if you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-fep-package">
<span id="user-fep"></span><h3>USER-FEP package</h3>
<span id="user-fep"></span><h3>4.2.9. USER-FEP package</h3>
<p>Contents: FEP stands for free energy perturbation. This package
provides methods for performing FEP simulations by using a <a class="reference internal" href="fix_adapt_fep.html"><span class="doc">fix adapt/fep</span></a> command with soft-core pair potentials,
which have a &#8220;soft&#8221; in their style name. See src/USER-FEP/README for
@ -2099,7 +2121,7 @@ questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-h5md-package">
<span id="user-h5md"></span><h3>USER-H5MD package</h3>
<span id="user-h5md"></span><h3>4.2.10. USER-H5MD package</h3>
<p>Contents: H5MD stands for HDF5 for MD. <a class="reference external" href="http://www.hdfgroup.org/HDF5/">HDF5</a> is a binary,
portable, self-describing file format, used by many scientific
simulations. H5MD is a format for molecular simulations, built on top
@ -2113,7 +2135,7 @@ directly if you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-intel-package">
<span id="user-intel"></span><h3>USER-INTEL package</h3>
<span id="user-intel"></span><h3>4.2.11. USER-INTEL package</h3>
<p>Contents: Dozens of pair, bond, angle, dihedral, and improper styles
that are optimized for Intel CPUs and the Intel Xeon Phi (in offload
mode). All of them have an &#8220;intel&#8221; in their style name. <a class="reference internal" href="accelerate_intel.html"><span class="doc">Section accelerate intel</span></a> gives details of what hardware
@ -2147,7 +2169,7 @@ your Makefile.machine for CCFLAGS and LINKFLAGS.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-lb-package">
<span id="user-lb"></span><h3>USER-LB package</h3>
<span id="user-lb"></span><h3>4.2.12. USER-LB package</h3>
<p>Supporting info:</p>
<p>This package contains a LAMMPS implementation of a background
Lattice-Boltzmann fluid, which can be used to model MD particles
@ -2161,7 +2183,7 @@ Western Ontario. Contact them directly if you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-mgpt-package">
<span id="user-mgpt"></span><h3>USER-MGPT package</h3>
<span id="user-mgpt"></span><h3>4.2.13. USER-MGPT package</h3>
<p>Supporting info:</p>
<p>This package contains a fast implementation for LAMMPS of
quantum-based MGPT multi-ion potentials. The MGPT or model GPT method
@ -2186,7 +2208,7 @@ Contact them directly if you have any questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-misc-package">
<span id="user-misc"></span><h3>USER-MISC package</h3>
<span id="user-misc"></span><h3>4.2.14. USER-MISC package</h3>
<p>Supporting info:</p>
<p>The files in this package are a potpourri of (mostly) unrelated
features contributed to LAMMPS by users. Each feature is a single
@ -2205,7 +2227,7 @@ about the feature or its coding.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-manifold-package">
<span id="user-manifold"></span><h3>USER-MANIFOLD package</h3>
<span id="user-manifold"></span><h3>4.2.15. USER-MANIFOLD package</h3>
<p>Supporting info:</p>
<p>This package contains a dump molfile command which uses molfile
plugins that are bundled with the
@ -2225,7 +2247,7 @@ Contact him directly if you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-molfile-package">
<span id="user-molfile"></span><h3>USER-MOLFILE package</h3>
<span id="user-molfile"></span><h3>4.2.16. USER-MOLFILE package</h3>
<p>Supporting info:</p>
<p>This package contains a dump molfile command which uses molfile
plugins that are bundled with the
@ -2245,7 +2267,7 @@ application itself.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-omp-package">
<span id="user-omp"></span><h3>USER-OMP package</h3>
<span id="user-omp"></span><h3>4.2.17. USER-OMP package</h3>
<p>Supporting info:</p>
<p>This package provides OpenMP multi-threading support and
other optimizations of various LAMMPS pair styles, dihedral
@ -2264,7 +2286,7 @@ settings for CCFLAGS and LINKFLAGS.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-phonon-package">
<span id="user-phonon"></span><h3>USER-PHONON package</h3>
<span id="user-phonon"></span><h3>4.2.18. USER-PHONON package</h3>
<p>This package contains a fix phonon command that calculates dynamical
matrices, which can then be used to compute phonon dispersion
relations, directly from molecular dynamics simulations.</p>
@ -2277,7 +2299,7 @@ if you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-qmmm-package">
<span id="user-qmmm"></span><h3>USER-QMMM package</h3>
<span id="user-qmmm"></span><h3>4.2.19. USER-QMMM package</h3>
<p>Supporting info:</p>
<p>This package provides a fix qmmm command which allows LAMMPS to be
used in a QM/MM simulation, currently only in combination with pw.x
@ -2295,7 +2317,7 @@ without changes to LAMMPS itself.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-qtb-package">
<span id="user-qtb"></span><h3>USER-QTB package</h3>
<span id="user-qtb"></span><h3>4.2.20. USER-QTB package</h3>
<p>Supporting info:</p>
<p>This package provides a self-consistent quantum treatment of the
vibrational modes in a classical molecular dynamics simulation. By
@ -2319,13 +2341,13 @@ have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-quip-package">
<span id="user-quip"></span><h3>USER-QUIP package</h3>
<span id="user-quip"></span><h3>4.2.21. USER-QUIP package</h3>
<p>Supporting info:</p>
<p>Examples: examples/USER/quip</p>
<hr class="docutils" />
</div>
<div class="section" id="user-reaxc-package">
<span id="user-reaxc"></span><h3>USER-REAXC package</h3>
<span id="user-reaxc"></span><h3>4.2.22. USER-REAXC package</h3>
<p>Supporting info:</p>
<p>This package contains a implementation for LAMMPS of the ReaxFF force
field. ReaxFF uses distance-dependent bond-order functions to
@ -2355,7 +2377,7 @@ questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-smd-package">
<span id="user-smd"></span><h3>USER-SMD package</h3>
<span id="user-smd"></span><h3>4.2.23. USER-SMD package</h3>
<p>Supporting info:</p>
<p>This package implements smoothed Mach dynamics (SMD) in
LAMMPS. Currently, the package has the following features:</p>
@ -2381,7 +2403,7 @@ you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-smtbq-package">
<span id="user-smtbq"></span><h3>USER-SMTBQ package</h3>
<span id="user-smtbq"></span><h3>4.2.24. USER-SMTBQ package</h3>
<p>Supporting info:</p>
<p>This package implements the Second Moment Tight Binding - QEq (SMTB-Q)
potential for the description of ionocovalent bonds in oxides.</p>
@ -2397,7 +2419,7 @@ them directly if you have any questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-sph-package">
<span id="user-sph"></span><h3>USER-SPH package</h3>
<span id="user-sph"></span><h3>4.2.25. USER-SPH package</h3>
<p>Supporting info:</p>
<p>This package implements smoothed particle hydrodynamics (SPH) in
LAMMPS. Currently, the package has the following features:</p>
@ -2421,13 +2443,13 @@ you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-tally-package">
<span id="user-tally"></span><h3>USER-TALLY package</h3>
<span id="user-tally"></span><h3>4.2.26. USER-TALLY package</h3>
<p>Supporting info:</p>
<p>Examples: examples/USER/tally</p>
<hr class="docutils" />
</div>
<div class="section" id="user-vtk-package">
<span id="user-vtk"></span><h3>USER-VTK package</h3>
<span id="user-vtk"></span><h3>4.2.27. USER-VTK package</h3>
</div>
</div>
</div>
@ -2437,6 +2459,15 @@ you have questions.</p>
</div>
<footer>
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@ -8,7 +8,7 @@
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<title>Performance &amp; scalability &mdash; LAMMPS documentation</title>
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@ -32,7 +32,9 @@
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<link rel="top" title="LAMMPS documentation" href="index.html"/>
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@ -71,11 +73,22 @@
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<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Performance &amp; scalability</a></li>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
</div>
@ -98,7 +111,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>Performance &amp; scalability</li>
<li>8. Performance &amp; scalability</li>
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@ -109,12 +122,21 @@
</ul>
<hr/>
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<div itemprop="articleBody">
<div class="section" id="performance-scalability">
<h1>Performance &amp; scalability</h1>
<h1>8. Performance &amp; scalability</h1>
<p>Current LAMMPS performance is discussed on the Benchmarks page of the
<a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> where CPU timings and parallel efficiencies are
listed. The page has several sections, which are briefly described
@ -188,6 +210,15 @@ atoms/node to achieve good scalability.</p>
</div>
<footer>
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Python interface to LAMMPS &mdash; LAMMPS documentation</title>
<title>11. Python interface to LAMMPS &mdash; LAMMPS documentation</title>
@ -32,7 +32,9 @@
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<link rel="next" title="12. Errors" href="Section_errors.html"/>
<link rel="prev" title="10. Modifying &amp; extending LAMMPS" href="Section_modify.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -71,26 +73,37 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Python interface to LAMMPS</a><ul>
<li><a class="reference internal" href="#overview-of-running-lammps-from-python">Overview of running LAMMPS from Python</a></li>
<li><a class="reference internal" href="#overview-of-using-python-from-a-lammps-script">Overview of using Python from a LAMMPS script</a></li>
<li><a class="reference internal" href="#building-lammps-as-a-shared-library">Building LAMMPS as a shared library</a></li>
<li><a class="reference internal" href="#installing-the-python-wrapper-into-python">Installing the Python wrapper into Python</a></li>
<li><a class="reference internal" href="#extending-python-with-mpi-to-run-in-parallel">Extending Python with MPI to run in parallel</a></li>
<li><a class="reference internal" href="#testing-the-python-lammps-interface">Testing the Python-LAMMPS interface</a><ul>
<li><a class="reference internal" href="#test-lammps-and-python-in-serial"><strong>Test LAMMPS and Python in serial:</strong></a></li>
<li><a class="reference internal" href="#test-lammps-and-python-in-parallel"><strong>Test LAMMPS and Python in parallel:</strong></a></li>
<li><a class="reference internal" href="#running-python-scripts"><strong>Running Python scripts:</strong></a></li>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><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 current"><a class="current reference internal" href="#">11. Python interface to LAMMPS</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#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="#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="#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="#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="#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="#testing-the-python-lammps-interface">11.6. Testing the Python-LAMMPS interface</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#test-lammps-and-python-in-serial">11.6.1. <strong>Test LAMMPS and Python in serial:</strong></a></li>
<li class="toctree-l3"><a class="reference internal" href="#test-lammps-and-python-in-parallel">11.6.2. <strong>Test LAMMPS and Python in parallel:</strong></a></li>
<li class="toctree-l3"><a class="reference internal" href="#running-python-scripts">11.6.3. <strong>Running Python scripts:</strong></a></li>
</ul>
</li>
<li><a class="reference internal" href="#using-lammps-from-python">Using LAMMPS from Python</a></li>
<li><a class="reference internal" href="#example-python-scripts-that-use-lammps">Example Python scripts that use LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="#using-lammps-from-python">11.7. Using LAMMPS from Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="#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></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
</div>
@ -113,7 +126,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>Python interface to LAMMPS</li>
<li>11. Python interface to LAMMPS</li>
<li class="wy-breadcrumbs-aside">
@ -124,12 +137,21 @@
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="python-interface-to-lammps">
<h1>Python interface to LAMMPS</h1>
<h1>11. Python interface to LAMMPS</h1>
<p>LAMMPS can work together with Python in two ways. First, Python can
wrap LAMMPS through the <a class="reference internal" href="Section_howto.html#howto-19"><span class="std std-ref">LAMMPS library interface</span></a>, so that a Python script can
create one or more instances of LAMMPS and launch one or more
@ -175,7 +197,7 @@ interesting Python functions that can be called from a LAMMPS input
script, that you think would be useful to other users, please <a class="reference external" href="http://lammps.sandia.gov/authors.html">email them to the developers</a>. We can
include them in the LAMMPS distribution.</p>
<div class="section" id="overview-of-running-lammps-from-python">
<span id="py-1"></span><h2>Overview of running LAMMPS from Python</h2>
<span id="py-1"></span><h2>11.1. Overview of running LAMMPS from Python</h2>
<p>The LAMMPS distribution includes a python directory with all you need
to run LAMMPS from Python. The python/lammps.py file wraps the LAMMPS
library interface, with one wrapper function per LAMMPS library
@ -215,7 +237,7 @@ check which version of Python you have installed, by simply typing
<hr class="docutils" />
</div>
<div class="section" id="overview-of-using-python-from-a-lammps-script">
<span id="py-2"></span><h2>Overview of using Python from a LAMMPS script</h2>
<span id="py-2"></span><h2>11.2. Overview of using Python from a LAMMPS script</h2>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">It is not currently possible to use the <a class="reference internal" href="python.html"><span class="doc">python</span></a>
@ -278,9 +300,9 @@ file and the shared library.</p>
<hr class="docutils" />
</div>
<div class="section" id="building-lammps-as-a-shared-library">
<span id="py-3"></span><h2>Building LAMMPS as a shared library</h2>
<span id="py-3"></span><h2>11.3. Building LAMMPS as a shared library</h2>
<p>Instructions on how to build LAMMPS as a shared library are given in
<span class="xref std std-ref">Section_start 5</span>. A shared library is one
<a class="reference internal" href="Section_start.html#start-5"><span class="std std-ref">Section_start 5</span></a>. A shared library is one
that is dynamically loadable, which is what Python requires to wrap
LAMMPS. On Linux this is a library file that ends in &#8221;.so&#8221;, not &#8221;.a&#8221;.</p>
<p>From the src directory, type</p>
@ -299,12 +321,12 @@ most recently built version.</p>
auxiliary libraries (used by various packages), then all of these
extra libraries must also be shared libraries. If the LAMMPS
shared-library build fails with an error complaining about this, see
<span class="xref std std-ref">Section_start 5</span> for more details.</p>
<a class="reference internal" href="Section_start.html#start-5"><span class="std std-ref">Section_start 5</span></a> for more details.</p>
</div>
<hr class="docutils" />
</div>
<div class="section" id="installing-the-python-wrapper-into-python">
<span id="py-4"></span><h2>Installing the Python wrapper into Python</h2>
<span id="py-4"></span><h2>11.4. Installing the Python wrapper into Python</h2>
<p>For Python to invoke LAMMPS, there are 2 files it needs to know about:</p>
<ul class="simple">
<li>python/lammps.py</li>
@ -366,7 +388,7 @@ environment variable as described above.</p>
<hr class="docutils" />
</div>
<div class="section" id="extending-python-with-mpi-to-run-in-parallel">
<span id="py-5"></span><h2>Extending Python with MPI to run in parallel</h2>
<span id="py-5"></span><h2>11.5. Extending Python with MPI to run in parallel</h2>
<p>If you wish to run LAMMPS in parallel from Python, you need to extend
your Python with an interface to MPI. This also allows you to
make MPI calls directly from Python in your script, if you desire.</p>
@ -504,7 +526,7 @@ the right one.</p>
<hr class="docutils" />
</div>
<div class="section" id="testing-the-python-lammps-interface">
<span id="py-6"></span><h2>Testing the Python-LAMMPS interface</h2>
<span id="py-6"></span><h2>11.6. Testing the Python-LAMMPS interface</h2>
<p>To test if LAMMPS is callable from Python, launch Python interactively
and type:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">lammps</span> <span class="k">import</span> <span class="n">lammps</span>
@ -527,11 +549,11 @@ first importing from the lammps.py file:</p>
<span class="gp">&gt;&gt;&gt; </span><span class="n">CDLL</span><span class="p">(</span><span class="s2">&quot;liblammps.so&quot;</span><span class="p">)</span>
</pre></div>
</div>
<p>If an error occurs, carefully go thru the steps in <span class="xref std std-ref">Section_start 5</span> and above about building a shared
<p>If an error occurs, carefully go thru the steps in <a class="reference internal" href="Section_start.html#start-5"><span class="std std-ref">Section_start 5</span></a> and above about building a shared
library and about insuring Python can find the necessary two files
it needs.</p>
<div class="section" id="test-lammps-and-python-in-serial">
<h3><strong>Test LAMMPS and Python in serial:</strong></h3>
<h3>11.6.1. <strong>Test LAMMPS and Python in serial:</strong></h3>
<p>To run a LAMMPS test in serial, type these lines into Python
interactively from the bench directory:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">lammps</span> <span class="k">import</span> <span class="n">lammps</span>
@ -551,7 +573,7 @@ typed something like:</p>
</div>
</div>
<div class="section" id="test-lammps-and-python-in-parallel">
<h3><strong>Test LAMMPS and Python in parallel:</strong></h3>
<h3>11.6.2. <strong>Test LAMMPS and Python in parallel:</strong></h3>
<p>To run LAMMPS in parallel, assuming you have installed the
<a class="reference external" href="Pypar">Pypar</a> package as discussed above, create a test.py file
containing these lines:</p>
@ -598,7 +620,7 @@ script should be pypar.finalize(), to insure MPI is shut down
correctly.</p>
</div>
<div class="section" id="running-python-scripts">
<h3><strong>Running Python scripts:</strong></h3>
<h3>11.6.3. <strong>Running Python scripts:</strong></h3>
<p>Note that any Python script (not just for LAMMPS) can be invoked in
one of several ways:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">python</span> <span class="n">foo</span><span class="o">.</span><span class="n">script</span>
@ -625,7 +647,7 @@ Python on a single processor, not in parallel.</p>
</div>
</div>
<div class="section" id="using-lammps-from-python">
<span id="py-7"></span><h2>Using LAMMPS from Python</h2>
<span id="py-7"></span><h2>11.7. Using LAMMPS from Python</h2>
<p>As described above, the Python interface to LAMMPS consists of a
Python &#8220;lammps&#8221; module, the source code for which is in
python/lammps.py, which creates a &#8220;lammps&#8221; object, with a set of
@ -833,7 +855,7 @@ Python script. Isn&#8217;t ctypes amazing?</li>
</ul>
</div>
<div class="section" id="example-python-scripts-that-use-lammps">
<span id="py-8"></span><h2>Example Python scripts that use LAMMPS</h2>
<span id="py-8"></span><h2>11.8. Example Python scripts that use LAMMPS</h2>
<p>These are the Python scripts included as demos in the python/examples
directory of the LAMMPS distribution, to illustrate the kinds of
things that are possible when Python wraps LAMMPS. If you create your
@ -954,6 +976,15 @@ different visualization package options. Click to see larger images:</p>
</div>
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Additional tools &mdash; LAMMPS documentation</title>
<title>9. Additional tools &mdash; LAMMPS documentation</title>
@ -32,7 +32,9 @@
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<link rel="next" title="10. Modifying &amp; extending LAMMPS" href="Section_modify.html"/>
<link rel="prev" title="8. Performance &amp; scalability" href="Section_perf.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -71,44 +73,55 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Additional tools</a><ul>
<li><a class="reference internal" href="#amber2lmp-tool">amber2lmp tool</a></li>
<li><a class="reference internal" href="#binary2txt-tool">binary2txt tool</a></li>
<li><a class="reference internal" href="#ch2lmp-tool">ch2lmp tool</a></li>
<li><a class="reference internal" href="#chain-tool">chain tool</a></li>
<li><a class="reference internal" href="#colvars-tools">colvars tools</a></li>
<li><a class="reference internal" href="#createatoms-tool">createatoms tool</a></li>
<li><a class="reference internal" href="#data2xmovie-tool">data2xmovie tool</a></li>
<li><a class="reference internal" href="#eam-database-tool">eam database tool</a></li>
<li><a class="reference internal" href="#eam-generate-tool">eam generate tool</a></li>
<li><a class="reference internal" href="#eff-tool">eff tool</a></li>
<li><a class="reference internal" href="#emacs-tool">emacs tool</a></li>
<li><a class="reference internal" href="#fep-tool">fep tool</a></li>
<li><a class="reference internal" href="#i-pi-tool">i-pi tool</a></li>
<li><a class="reference internal" href="#ipp-tool">ipp tool</a></li>
<li><a class="reference internal" href="#kate-tool">kate tool</a></li>
<li><a class="reference internal" href="#lmp2arc-tool">lmp2arc tool</a></li>
<li><a class="reference internal" href="#lmp2cfg-tool">lmp2cfg tool</a></li>
<li><a class="reference internal" href="#lmp2vmd-tool">lmp2vmd tool</a></li>
<li><a class="reference internal" href="#matlab-tool">matlab tool</a></li>
<li><a class="reference internal" href="#micelle2d-tool">micelle2d tool</a></li>
<li><a class="reference internal" href="#moltemplate-tool">moltemplate tool</a></li>
<li><a class="reference internal" href="#msi2lmp-tool">msi2lmp tool</a></li>
<li><a class="reference internal" href="#phonon-tool">phonon tool</a></li>
<li><a class="reference internal" href="#polymer-bonding-tool">polymer bonding tool</a></li>
<li><a class="reference internal" href="#pymol-asphere-tool">pymol_asphere tool</a></li>
<li><a class="reference internal" href="#python-tool">python tool</a></li>
<li><a class="reference internal" href="#reax-tool">reax tool</a></li>
<li><a class="reference internal" href="#restart2data-tool">restart2data tool</a></li>
<li><a class="reference internal" href="#vim-tool">vim tool</a></li>
<li><a class="reference internal" href="#xmgrace-tool">xmgrace tool</a></li>
<li><a class="reference internal" href="#xmovie-tool">xmovie tool</a></li>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><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 current"><a class="current reference internal" href="#">9. Additional tools</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#amber2lmp-tool">9.1. amber2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#binary2txt-tool">9.2. binary2txt tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#ch2lmp-tool">9.3. ch2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#chain-tool">9.4. chain tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#colvars-tools">9.5. colvars tools</a></li>
<li class="toctree-l2"><a class="reference internal" href="#createatoms-tool">9.6. createatoms tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#data2xmovie-tool">9.7. data2xmovie tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#eam-database-tool">9.8. eam database tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#eam-generate-tool">9.9. eam generate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#eff-tool">9.10. eff tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#emacs-tool">9.11. emacs tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#fep-tool">9.12. fep tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#i-pi-tool">9.13. i-pi tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#ipp-tool">9.14. ipp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#kate-tool">9.15. kate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#lmp2arc-tool">9.16. lmp2arc tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#lmp2cfg-tool">9.17. lmp2cfg tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#lmp2vmd-tool">9.18. lmp2vmd tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#matlab-tool">9.19. matlab tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#micelle2d-tool">9.20. micelle2d tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#moltemplate-tool">9.21. moltemplate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#msi2lmp-tool">9.22. msi2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#phonon-tool">9.23. phonon tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#polymer-bonding-tool">9.24. polymer bonding tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#pymol-asphere-tool">9.25. pymol_asphere tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#python-tool">9.26. python tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#reax-tool">9.27. reax tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#restart2data-tool">9.28. restart2data tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#vim-tool">9.29. vim tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#xmgrace-tool">9.30. xmgrace tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#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></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
</div>
@ -131,7 +144,7 @@
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<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>Additional tools</li>
<li>9. Additional tools</li>
<li class="wy-breadcrumbs-aside">
@ -142,12 +155,21 @@
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div class="section" id="additional-tools">
<h1>Additional tools</h1>
<h1>9. Additional tools</h1>
<p>LAMMPS is designed to be a computational kernel for performing
molecular dynamics computations. Additional pre- and post-processing
steps are often necessary to setup and analyze a simulation. A few
@ -204,7 +226,7 @@ own sub-directories with their own Makefiles.</p>
</ul>
<hr class="docutils" />
<div class="section" id="amber2lmp-tool">
<span id="amber"></span><h2>amber2lmp tool</h2>
<span id="amber"></span><h2>9.1. amber2lmp tool</h2>
<p>The amber2lmp sub-directory contains two Python scripts for converting
files back-and-forth between the AMBER MD code and LAMMPS. See the
README file in amber2lmp for more information.</p>
@ -217,7 +239,7 @@ necessary modifications yourself.</p>
<hr class="docutils" />
</div>
<div class="section" id="binary2txt-tool">
<span id="binary"></span><h2>binary2txt tool</h2>
<span id="binary"></span><h2>9.2. binary2txt tool</h2>
<p>The file binary2txt.cpp converts one or more binary LAMMPS dump file
into ASCII text files. The syntax for running the tool is</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">binary2txt</span> <span class="n">file1</span> <span class="n">file2</span> <span class="o">...</span>
@ -229,7 +251,7 @@ since binary files are not compatible across all platforms.</p>
<hr class="docutils" />
</div>
<div class="section" id="ch2lmp-tool">
<span id="charmm"></span><h2>ch2lmp tool</h2>
<span id="charmm"></span><h2>9.3. ch2lmp tool</h2>
<p>The ch2lmp sub-directory contains tools for converting files
back-and-forth between the CHARMM MD code and LAMMPS.</p>
<p>They are intended to make it easy to use CHARMM as a builder and as a
@ -242,7 +264,7 @@ and Paul Crozier (pscrozi at sandia.gov) at Sandia.</p>
<hr class="docutils" />
</div>
<div class="section" id="chain-tool">
<span id="chain"></span><h2>chain tool</h2>
<span id="chain"></span><h2>9.4. chain tool</h2>
<p>The file chain.f creates a LAMMPS data file containing bead-spring
polymer chains and/or monomer solvent atoms. It uses a text file
containing chain definition parameters as an input. The created
@ -258,7 +280,7 @@ system for the <a class="reference internal" href="Section_perf.html"><span clas
<hr class="docutils" />
</div>
<div class="section" id="colvars-tools">
<span id="colvars"></span><h2>colvars tools</h2>
<span id="colvars"></span><h2>9.5. colvars tools</h2>
<p>The colvars directory contains a collection of tools for postprocessing
data produced by the colvars collective variable library.
To compile the tools, edit the makefile for your system and run &#8220;make&#8221;.</p>
@ -276,7 +298,7 @@ gmail.com) at ICTP, Italy.</p>
<hr class="docutils" />
</div>
<div class="section" id="createatoms-tool">
<span id="create"></span><h2>createatoms tool</h2>
<span id="create"></span><h2>9.6. createatoms tool</h2>
<p>The tools/createatoms directory contains a Fortran program called
createAtoms.f which can generate a variety of interesting crystal
structures and geometries and output the resulting list of atom
@ -286,7 +308,7 @@ coordinates in LAMMPS or other formats.</p>
<hr class="docutils" />
</div>
<div class="section" id="data2xmovie-tool">
<span id="data"></span><h2>data2xmovie tool</h2>
<span id="data"></span><h2>9.7. data2xmovie tool</h2>
<p>The file data2xmovie.c converts a LAMMPS data file into a snapshot
suitable for visualizing with the <a class="reference internal" href="#xmovie"><span class="std std-ref">xmovie</span></a> tool, as if it had
been output with a dump command from LAMMPS itself. The syntax for
@ -298,7 +320,7 @@ running the tool is</p>
<hr class="docutils" />
</div>
<div class="section" id="eam-database-tool">
<span id="eamdb"></span><h2>eam database tool</h2>
<span id="eamdb"></span><h2>9.8. eam database tool</h2>
<p>The tools/eam_database directory contains a Fortran program that will
generate EAM alloy setfl potential files for any combination of 16
elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti,
@ -310,7 +332,7 @@ and is based on his paper:</p>
<hr class="docutils" />
</div>
<div class="section" id="eam-generate-tool">
<span id="eamgn"></span><h2>eam generate tool</h2>
<span id="eamgn"></span><h2>9.9. eam generate tool</h2>
<p>The tools/eam_generate directory contains several one-file C programs
that convert an analytic formula into a tabulated <a class="reference internal" href="pair_eam.html"><span class="doc">embedded atom method (EAM)</span></a> setfl potential file. The potentials they
produce are in the potentials directory, and can be used with the
@ -320,7 +342,7 @@ produce are in the potentials directory, and can be used with the
<hr class="docutils" />
</div>
<div class="section" id="eff-tool">
<span id="eff"></span><h2>eff tool</h2>
<span id="eff"></span><h2>9.10. eff tool</h2>
<p>The tools/eff directory contains various scripts for generating
structures and post-processing output for simulations using the
electron force field (eFF).</p>
@ -329,7 +351,7 @@ electron force field (eFF).</p>
<hr class="docutils" />
</div>
<div class="section" id="emacs-tool">
<span id="emacs"></span><h2>emacs tool</h2>
<span id="emacs"></span><h2>9.11. emacs tool</h2>
<p>The tools/emacs directory contains a Lips add-on file for Emacs that
enables a lammps-mode for editing of input scripts when using Emacs,
with various highlighting options setup.</p>
@ -338,7 +360,7 @@ with various highlighting options setup.</p>
<hr class="docutils" />
</div>
<div class="section" id="fep-tool">
<span id="fep"></span><h2>fep tool</h2>
<span id="fep"></span><h2>9.12. fep tool</h2>
<p>The tools/fep directory contains Python scripts useful for
post-processing results from performing free-energy perturbation
simulations using the USER-FEP package.</p>
@ -348,7 +370,7 @@ Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr.</p>
<hr class="docutils" />
</div>
<div class="section" id="i-pi-tool">
<span id="ipi"></span><h2>i-pi tool</h2>
<span id="ipi"></span><h2>9.13. i-pi tool</h2>
<p>The tools/i-pi directory contains a version of the i-PI package, with
all the LAMMPS-unrelated files removed. It is provided so that it can
be used with the <a class="reference internal" href="fix_ipi.html"><span class="doc">fix ipi</span></a> command to perform
@ -362,7 +384,7 @@ calculations with LAMMPS.</p>
<hr class="docutils" />
</div>
<div class="section" id="ipp-tool">
<span id="ipp"></span><h2>ipp tool</h2>
<span id="ipp"></span><h2>9.14. ipp tool</h2>
<p>The tools/ipp directory contains a Perl script ipp which can be used
to facilitate the creation of a complicated file (say, a lammps input
script or tools/createatoms input file) using a template file.</p>
@ -373,7 +395,7 @@ tools/createatoms tool&#8217;s input file.</p>
<hr class="docutils" />
</div>
<div class="section" id="kate-tool">
<span id="kate"></span><h2>kate tool</h2>
<span id="kate"></span><h2>9.15. kate tool</h2>
<p>The file in the tools/kate directory is an add-on to the Kate editor
in the KDE suite that allow syntax highlighting of LAMMPS input
scripts. See the README.txt file for details.</p>
@ -382,7 +404,7 @@ scripts. See the README.txt file for details.</p>
<hr class="docutils" />
</div>
<div class="section" id="lmp2arc-tool">
<span id="arc"></span><h2>lmp2arc tool</h2>
<span id="arc"></span><h2>9.16. lmp2arc tool</h2>
<p>The lmp2arc sub-directory contains a tool for converting LAMMPS output
files to the format for Accelrys&#8217; Insight MD code (formerly
MSI/Biosym and its Discover MD code). See the README file for more
@ -395,7 +417,7 @@ Greathouse at Sandia (jagreat at sandia.gov).</p>
<hr class="docutils" />
</div>
<div class="section" id="lmp2cfg-tool">
<span id="cfg"></span><h2>lmp2cfg tool</h2>
<span id="cfg"></span><h2>9.17. lmp2cfg tool</h2>
<p>The lmp2cfg sub-directory contains a tool for converting LAMMPS output
files into a series of <a href="#id1"><span class="problematic" id="id2">*</span></a>.cfg files which can be read into the
<a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a> visualizer. See
@ -404,7 +426,7 @@ the README file for more information.</p>
<hr class="docutils" />
</div>
<div class="section" id="lmp2vmd-tool">
<span id="vmd"></span><h2>lmp2vmd tool</h2>
<span id="vmd"></span><h2>9.18. lmp2vmd tool</h2>
<p>The lmp2vmd sub-directory contains a README.txt file that describes
details of scripts and plugin support within the <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD package</a> for visualizing LAMMPS
dump files.</p>
@ -413,7 +435,7 @@ Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.</p>
<hr class="docutils" />
</div>
<div class="section" id="matlab-tool">
<span id="matlab"></span><h2>matlab tool</h2>
<span id="matlab"></span><h2>9.19. matlab tool</h2>
<p>The matlab sub-directory contains several <span class="xref std std-ref">MATLAB</span> scripts for
post-processing LAMMPS output. The scripts include readers for log
and dump files, a reader for EAM potential files, and a converter that
@ -426,7 +448,7 @@ visualizer.</p>
<hr class="docutils" />
</div>
<div class="section" id="micelle2d-tool">
<span id="micelle"></span><h2>micelle2d tool</h2>
<span id="micelle"></span><h2>9.20. micelle2d tool</h2>
<p>The file micelle2d.f creates a LAMMPS data file containing short lipid
chains in a monomer solution. It uses a text file containing lipid
definition parameters as an input. The created molecules and solvent
@ -442,7 +464,7 @@ definition file. This tool was used to create the system for the
<hr class="docutils" />
</div>
<div class="section" id="moltemplate-tool">
<span id="moltemplate"></span><h2>moltemplate tool</h2>
<span id="moltemplate"></span><h2>9.21. moltemplate tool</h2>
<p>The moltemplate sub-directory contains a Python-based tool for
building molecular systems based on a text-file description, and
creating LAMMPS data files that encode their molecular topology as
@ -454,7 +476,7 @@ supports it. It has its own WWW page at
<hr class="docutils" />
</div>
<div class="section" id="msi2lmp-tool">
<span id="msi"></span><h2>msi2lmp tool</h2>
<span id="msi"></span><h2>9.22. msi2lmp tool</h2>
<p>The msi2lmp sub-directory contains a tool for creating LAMMPS input
data files from Accelrys&#8217; Insight MD code (formerly MSI/Biosym and
its Discover MD code). See the README file for more information.</p>
@ -467,7 +489,7 @@ experiment with it yourself.</p>
<hr class="docutils" />
</div>
<div class="section" id="phonon-tool">
<span id="phonon"></span><h2>phonon tool</h2>
<span id="phonon"></span><h2>9.23. phonon tool</h2>
<p>The phonon sub-directory contains a post-processing tool useful for
analyzing the output of the <a class="reference internal" href="fix_phonon.html"><span class="doc">fix phonon</span></a> command in
the USER-PHONON package.</p>
@ -479,7 +501,7 @@ University.</p>
<hr class="docutils" />
</div>
<div class="section" id="polymer-bonding-tool">
<span id="polybond"></span><h2>polymer bonding tool</h2>
<span id="polybond"></span><h2>9.24. polymer bonding tool</h2>
<p>The polybond sub-directory contains a Python-based tool useful for
performing &#8220;programmable polymer bonding&#8221;. The Python file
lmpsdata.py provides a &#8220;Lmpsdata&#8221; class with various methods which can
@ -490,7 +512,7 @@ complex bonding topologies.</p>
<hr class="docutils" />
</div>
<div class="section" id="pymol-asphere-tool">
<span id="pymol"></span><h2>pymol_asphere tool</h2>
<span id="pymol"></span><h2>9.25. pymol_asphere tool</h2>
<p>The pymol_asphere sub-directory contains a tool for converting a
LAMMPS dump file that contains orientation info for ellipsoidal
particles into an input file for the <span class="xref std std-ref">PyMol visualization package</span>.</p>
@ -501,7 +523,7 @@ examples directory within pymol_asphere for more information.</p>
<hr class="docutils" />
</div>
<div class="section" id="python-tool">
<span id="pythontools"></span><h2>python tool</h2>
<span id="pythontools"></span><h2>9.26. python tool</h2>
<p>The python sub-directory contains several Python scripts
that perform common LAMMPS post-processing tasks, such as:</p>
<ul class="simple">
@ -516,7 +538,7 @@ README for more info on Pizza.py and how to use these scripts.</p>
<hr class="docutils" />
</div>
<div class="section" id="reax-tool">
<span id="reax"></span><h2>reax tool</h2>
<span id="reax"></span><h2>9.27. reax tool</h2>
<p>The reax sub-directory contains stand-alond codes that can
post-process the output of the <a class="reference internal" href="fix_reax_bonds.html"><span class="doc">fix reax/bonds</span></a>
command from a LAMMPS simulation using <a class="reference internal" href="pair_reax.html"><span class="doc">ReaxFF</span></a>. See
@ -525,14 +547,14 @@ the README.txt file for more info.</p>
<hr class="docutils" />
</div>
<div class="section" id="restart2data-tool">
<span id="restart"></span><h2>restart2data tool</h2>
<span id="restart"></span><h2>9.28. restart2data tool</h2>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">This tool is now obsolete and is not included in the current
LAMMPS distribution. This is becaues there is now a
<a class="reference internal" href="write_data.html"><span class="doc">write_data</span></a> command, which can create a data file
from within an input script. Running LAMMPS with the &#8220;-r&#8221;
<span class="xref std std-ref">command-line switch</span> as follows:</p>
<a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> as follows:</p>
</div>
<p>lmp_g++ -r restartfile datafile</p>
<p>is the same as running a 2-line input script:</p>
@ -564,7 +586,7 @@ of files are written by LAMMPS, and how the files are named.</p>
<hr class="docutils" />
</div>
<div class="section" id="vim-tool">
<span id="vim"></span><h2>vim tool</h2>
<span id="vim"></span><h2>9.29. vim tool</h2>
<p>The files in the tools/vim directory are add-ons to the VIM editor
that allow easier editing of LAMMPS input scripts. See the README.txt
file for details.</p>
@ -573,7 +595,7 @@ ziegenhain.com)</p>
<hr class="docutils" />
</div>
<div class="section" id="xmgrace-tool">
<span id="xmgrace"></span><h2>xmgrace tool</h2>
<span id="xmgrace"></span><h2>9.30. xmgrace tool</h2>
<p>The files in the tools/xmgrace directory can be used to plot the
thermodynamic data in LAMMPS log files via the xmgrace plotting
package. There are several tools in the directory that can be used in
@ -585,7 +607,7 @@ simulation.</p>
<hr class="docutils" />
</div>
<div class="section" id="xmovie-tool">
<span id="xmovie"></span><h2>xmovie tool</h2>
<span id="xmovie"></span><h2>9.31. xmovie tool</h2>
<p>The xmovie tool is an X-based visualization package that can read
LAMMPS dump files and animate them. It is in its own sub-directory
with the tools directory. You may need to modify its Makefile so that
@ -616,6 +638,15 @@ distributing his great tool!</p>
</div>
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.. raw:: html
<H1></H1>
LAMMPS Documentation
====================
23 Aug 2016 version
-------------------
Version info:
-------------
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 `this page of the WWW site <bug_>`_. 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).
* If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of LAMMPS.
* If you browse the HTML doc pages included in your tarball, they
describe the version you have.
* The `PDF file <Manual.pdf>`_ 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.
* There is also a `Developer.pdf <Developer.pdf>`_ file in the doc
directory, which describes the internal structure and algorithms of
LAMMPS.
LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.
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).
The primary developers of LAMMPS are `Steve Plimpton <sjp_>`_, Aidan
Thompson, and Paul Crozier who can be contacted at
sjplimp,athomps,pscrozi at sandia.gov. The `LAMMPS WWW Site <lws_>`_ at
http://lammps.sandia.gov has more information about the code and its
uses.
.. _bug: http://lammps.sandia.gov/bug.html
.. _sjp: http://www.sandia.gov/~sjplimp
----------
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.
Once you are familiar with LAMMPS, you may want to bookmark :ref:`this page <comm>` at Section_commands.html#comm since
it gives quick access to documentation for all LAMMPS commands.
`PDF file <Manual.pdf>`_ of the entire manual, generated by
`htmldoc <http://freecode.com/projects/htmldoc>`_
.. toctree::
:maxdepth: 2
:numbered:
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
Indices and tables
==================
* :ref:`genindex`
* :ref:`search`
.. raw:: html
</BODY>
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm

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.. index:: compute sna/atom
compute sna/atom command
========================
compute snad/atom command
=========================
compute snav/atom command
=========================
Syntax
""""""
.. parsed-literal::
compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
* ID, group-ID are documented in :doc:`compute <compute>` command
* sna/atom = style name of this compute command
* rcutfac = scale factor applied to all cutoff radii (positive real)
* rfac0 = parameter in distance to angle conversion (0 < rcutfac < 1)
* twojmax = band limit for bispectrum components (non-negative integer)
* R_1, R_2,... = list of cutoff radii, one for each type (distance units)
* w_1, w_2,... = list of neighbor weights, one for each type
* zero or more keyword/value pairs may be appended
* keyword = *diagonal* or *rmin0* or *switchflag*
.. parsed-literal::
*diagonal* value = *0* or *1* or *2* or *3*
*0* = all j1, j2, j <= twojmax, j2 <= j1
*1* = subset satisfying j1 == j2
*2* = subset satisfying j1 == j2 == j3
*3* = subset satisfying j2 <= j1 <= j
*rmin0* value = parameter in distance to angle conversion (distance units)
*switchflag* value = *0* or *1*
*0* = do not use switching function
*1* = use switching function
Examples
""""""""
.. parsed-literal::
compute b all sna/atom 1.4 0.99363 6 2.0 2.4 0.75 1.0 diagonal 3 rmin0 0.0
compute db all sna/atom 1.4 0.95 6 2.0 1.0
compute vb all sna/atom 1.4 0.95 6 2.0 1.0
Description
"""""""""""
Define a computation that calculates a set of bispectrum components
for each atom in a group.
Bispectrum components of an atom are order parameters characterizing
the radial and angular distribution of neighbor atoms. The detailed
mathematical definition is given in the paper by Thompson et
al. :ref:`(Thompson) <Thompson2014>`
The position of a neighbor atom *i'* relative to a central atom *i* is
a point within the 3D ball of radius *R_ii' = rcutfac*(R_i + R_i')*
Bartok et al. :ref:`(Bartok) <Bartok2010>`, proposed mapping this 3D ball
onto the 3-sphere, the surface of the unit ball in a four-dimensional
space. The radial distance *r* within *R_ii'* is mapped on to a third
polar angle *theta0* defined by,
.. image:: Eqs/compute_sna_atom1.jpg
:align: center
In this way, all possible neighbor positions are mapped on to a subset
of the 3-sphere. Points south of the latitude *theta0max=rfac0*Pi*
are excluded.
The natural basis for functions on the 3-sphere is formed by the 4D
hyperspherical harmonics *U^j_m,m'(theta, phi, theta0).* These
functions are better known as *D^j_m,m',* the elements of the Wigner
*D*\ -matrices :ref:`(Meremianin <Meremianin2006>`,
:ref:`Varshalovich) <Varshalovich1987>`.
The density of neighbors on the 3-sphere can be written as a sum of
Dirac-delta functions, one for each neighbor, weighted by species and
radial distance. Expanding this density function as a generalized
Fourier series in the basis functions, we can write each Fourier
coefficient as
.. image:: Eqs/compute_sna_atom2.jpg
:align: center
The *w_i'* neighbor weights are dimensionless numbers that are chosen
to distinguish atoms of different types, while the central atom is
arbitrarily assigned a unit weight. The function *fc(r)* ensures that
the contribution of each neighbor atom goes smoothly to zero at
*R_ii'*\ :
.. image:: Eqs/compute_sna_atom4.jpg
:align: center
The expansion coefficients *u^j_m,m'* are complex-valued and they are
not directly useful as descriptors, because they are not invariant
under rotation of the polar coordinate frame. However, the following
scalar triple products of expansion coefficients can be shown to be
real-valued and invariant under rotation :ref:`(Bartok) <Bartok2010>`.
.. image:: Eqs/compute_sna_atom3.jpg
:align: center
The constants *H^jmm'_j1m1m1'_j2m2m2'* are coupling coefficients,
analogous to Clebsch-Gordan coefficients for rotations on the
2-sphere. These invariants are the components of the bispectrum and
these are the quantities calculated by the compute *sna/atom*\ . They
characterize the strength of density correlations at three points on
the 3-sphere. The j2=0 subset form the power spectrum, which
characterizes the correlations of two points. The lowest-order
components describe the coarsest features of the density function,
while higher-order components reflect finer detail. Note that the
central atom is included in the expansion, so three point-correlations
can be either due to three neighbors, or two neighbors and the central
atom.
Compute *snad/atom* calculates the derivative of the bispectrum components
summed separately for each atom type:
.. image:: Eqs/compute_sna_atom5.jpg
:align: center
The sum is over all atoms *i'* of atom type *I*\ . For each atom *i*\ ,
this compute evaluates the above expression for each direction, each
atom type, and each bispectrum component. See section below on output
for a detailed explanation.
Compute *snav/atom* calculates the virial contribution due to the
derivatives:
.. image:: Eqs/compute_sna_atom6.jpg
:align: center
Again, the sum is over all atoms *i'* of atom type *I*\ . For each atom
*i*\ , this compute evaluates the above expression for each of the six
virial components, each atom type, and each bispectrum component. See
section below on output for a detailed explanation.
The value of all bispectrum components will be zero for atoms not in
the group. Neighbor atoms not in the group do not contribute to the
bispectrum of atoms in the group.
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.
The argument *rcutfac* is a scale factor that controls the ratio of
atomic radius to radial cutoff distance.
The argument *rfac0* and the optional keyword *rmin0* define the
linear mapping from radial distance to polar angle *theta0* on the
3-sphere.
The argument *twojmax* and the keyword *diagonal* define which
bispectrum components are generated. See section below on output for a
detailed explanation of the number of bispectrum components and the
ordered in which they are listed
The keyword *switchflag* can be used to turn off the switching
function.
.. note::
If you have a bonded system, then the settings of
:doc:`special_bonds <special_bonds>` command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the :doc:`special_bonds <special_bonds>`
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 calculation. One way to get
around this, is to write a dump file, and use the :doc:`rerun <rerun>`
command to compute the bispectrum components for snapshots in the dump
file. The rerun script can use a :doc:`special_bonds <special_bonds>`
command that includes all pairs in the neighbor list.
;line
**Output info:**
Compute *sna/atom* calculates a per-atom array, each column
corresponding to a particular bispectrum component. The total number
of columns and the identities of the bispectrum component contained in
each column depend on the values of *twojmax* and *diagonal*\ , as
described by the following piece of python code:
.. parsed-literal::
for j1 in range(0,twojmax+1):
if(diagonal==2):
print j1/2.,j1/2.,j1/2.
elif(diagonal==1):
for j in range(0,min(twojmax,2*j1)+1,2):
print j1/2.,j1/2.,j/2.
elif(diagonal==0):
for j2 in range(0,j1+1):
for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
print j1/2.,j2/2.,j/2.
elif(diagonal==3):
for j2 in range(0,j1+1):
for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
if (j>=j1): print j1/2.,j2/2.,j/2.
Compute *snad/atom* evaluates a per-atom array. The columns are
arranged into *ntypes* blocks, listed in order of atom type *I*\ . Each
block contains three sub-blocks corresponding to the *x*\ , *y*\ , and *z*
components of the atom position. Each of these sub-blocks contains
one column for each bispectrum component, the same as for compute
*sna/atom*
Compute *snav/atom* evaluates a per-atom array. The columns are
arranged into *ntypes* blocks, listed in order of atom type *I*\ . Each
block contains six sub-blocks corresponding to the *xx*\ , *yy*\ , *zz*\ ,
*yz*\ , *xz*\ , and *xy* components of the virial tensor in Voigt
notation. Each of these sub-blocks contains one column for each
bispectrum component, the same as for compute *sna/atom*
These values can be accessed by any command that uses per-atom values
from a compute as input. See :ref:`Section_howto 15 <howto_15>` for an overview of LAMMPS output
options.
Restrictions
""""""""""""
These computes are part of the SNAP package. They are only enabled if
LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
Related commands
""""""""""""""""
:doc:`pair_style snap <pair_snap>`
Default
"""""""
The optional keyword defaults are *diagonal* = 0, *rmin0* = 0,
*switchflag* = 1.
----------
.. _Thompson2014:
**(Thompson)** Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint
available at `arXiv:1409.3880 <http://arxiv.org/abs/1409.3880>`_
.. _Bartok2010:
**(Bartok)** Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
.. _Meremianin2006:
**(Meremianin)** Meremianin, J. Phys. A, 39, 3099 (2006).
.. _Varshalovich1987:
**(Varshalovich)** Varshalovich, Moskalev, Khersonskii, Quantum Theory
of Angular Momentum, World Scientific, Singapore (1987).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm

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<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">5.GPU package</a><ul>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -155,7 +163,7 @@ hardware.</li>
<li>use GPU styles in your input script</li>
</ul>
<p>The latter two steps can be done using the &#8220;-pk gpu&#8221; and &#8220;-sf gpu&#8221;
<span class="xref std std-ref">command-line switches</span> respectively. Or
<a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switches</span></a> respectively. Or
the effect of the &#8220;-pk&#8221; or &#8220;-sf&#8221; switches can be duplicated by adding
the <a class="reference internal" href="package.html"><span class="doc">package gpu</span></a> or <a class="reference internal" href="suffix.html"><span class="doc">suffix gpu</span></a> commands
respectively to your input script.</p>
@ -172,7 +180,7 @@ install the NVIDIA Cuda software on your system:</p>
<p>This requires two steps (a,b): build the GPU library, then build
LAMMPS with the GPU package.</p>
<p>You can do both these steps in one line, using the src/Make.py script,
described in <span class="xref std std-ref">Section 2.4</span> of the manual.
described in <a class="reference internal" href="Section_start.html#start-4"><span class="std std-ref">Section 2.4</span></a> of the manual.
Type &#8220;Make.py -h&#8221; for help. If run from the src directory, this
command will create src/lmp_gpu using src/MAKE/Makefile.mpi as the
starting Makefile.machine:</p>
@ -241,9 +249,9 @@ it may be more efficient to use less MPI tasks/node than the available
automatically if you create more MPI tasks/node than there are
GPUs/mode. E.g. with 8 MPI tasks/node and 2 GPUs, each GPU will be
shared by 4 MPI tasks.</p>
<p>Use the &#8220;-sf gpu&#8221; <span class="xref std std-ref">command-line switch</span>,
<p>Use the &#8220;-sf gpu&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a>,
which will automatically append &#8220;gpu&#8221; to styles that support it. Use
the &#8220;-pk gpu Ng&#8221; <span class="xref std std-ref">command-line switch</span> to
the &#8220;-pk gpu Ng&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> to
set Ng = # of GPUs/node to use.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">gpu</span> <span class="o">-</span><span class="n">pk</span> <span class="n">gpu</span> <span class="mi">1</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 1 MPI task uses 1 GPU</span>
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">12</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">gpu</span> <span class="o">-</span><span class="n">pk</span> <span class="n">gpu</span> <span class="mi">2</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node</span>
@ -272,7 +280,7 @@ and use of multiple MPI tasks/GPU is the same.</p>
</pre></div>
</div>
<p>You must also use the <a class="reference internal" href="package.html"><span class="doc">package gpu</span></a> command to enable the
GPU package, unless the &#8220;-sf gpu&#8221; or &#8220;-pk gpu&#8221; <span class="xref std std-ref">command-line switches</span> were used. It specifies the
GPU package, unless the &#8220;-sf gpu&#8221; or &#8220;-pk gpu&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switches</span></a> were used. It specifies the
number of GPUs/node to use, as well as other options.</p>
<p><strong>Speed-ups to expect:</strong></p>
<p>The performance of a GPU versus a multi-core CPU is a function of your

32
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@ -71,14 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">5.USER-INTEL package</a><ul>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -279,7 +287,7 @@ process can be as simple as:</p>
</pre></div>
</div>
<p>Alternatively, the build can be accomplished with the src/Make.py
script, described in <span class="xref std std-ref">Section 2.4</span> of the
script, described in <a class="reference internal" href="Section_start.html#start-4"><span class="std std-ref">Section 2.4</span></a> of the
manual. Type &#8220;Make.py -h&#8221; for help. For an example:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">v</span> <span class="o">-</span><span class="n">p</span> <span class="n">intel</span> <span class="n">omp</span> <span class="o">-</span><span class="n">intel</span> <span class="n">cpu</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">intel_cpu_intelmpi</span>
</pre></div>
@ -352,7 +360,7 @@ Hyper-Threading technology disabled.</p>
<p><strong>Run with the USER-INTEL package from the command line:</strong></p>
<p>To enable USER-INTEL optimizations for all available styles used in
the input script, the &#8220;-sf intel&#8221;
<span class="xref std std-ref">command-line switch</span> can be used without
<a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> can be used without
any requirement for editing the input script. This switch will
automatically append &#8220;intel&#8221; to styles that support it. It also
invokes a default command: <a class="reference internal" href="package.html"><span class="doc">package intel 1</span></a>. This
@ -364,7 +372,7 @@ if coprocessors are present and the binary was built with offload
support, that 1 coprocessor per node will be used with automatic
balancing of work between the CPU and the coprocessor.</p>
<p>You can specify different options for the USER-INTEL package by using
the &#8220;-pk intel Nphi&#8221; <span class="xref std std-ref">command-line switch</span>
the &#8220;-pk intel Nphi&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a>
with keyword/value pairs as specified in the documentation. Here,
Nphi = # of Xeon Phi coprocessors/node (ignored without offload
support). Common options to the USER-INTEL package include <em>omp</em> to
@ -427,7 +435,7 @@ can performed automatically by using &#8220;-sf hybrid intel opt&#8221; or
&#8220;-sf hybrid intel omp&#8221; command-line options. Alternatively, the &#8220;opt&#8221;
and &#8220;omp&#8221; suffixes can be appended manually in the input script. For
the latter, the <a class="reference internal" href="package.html"><span class="doc">package omp</span></a> command must be in the
input script or the &#8220;-pk omp Nt&#8221; <span class="xref std std-ref">command-line switch</span> must be used where Nt is the
input script or the &#8220;-pk omp Nt&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> must be used where Nt is the
number of OpenMP threads. The number of OpenMP threads should not be
set differently for the different packages. Note that the <a class="reference internal" href="suffix.html"><span class="doc">suffix hybrid intel omp</span></a> command can also be used within the
input script to automatically append the &#8220;omp&#8221; suffix to styles when
@ -507,7 +515,7 @@ per MPI task. Additionally, an offload timing summary is printed at
the end of each run. When offloading, the frequency for <a class="reference internal" href="atom_modify.html"><span class="doc">atom sorting</span></a> is changed to 1 so that the per-atom data is
effectively sorted at every rebuild of the neighbor lists. All the
available coprocessor threads on each Phi will be divided among MPI
tasks, unless the <em>tptask</em> option of the &#8220;-pk intel&#8221; <span class="xref std std-ref">command-line switch</span> is used to limit the coprocessor
tasks, unless the <em>tptask</em> option of the &#8220;-pk intel&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> is used to limit the coprocessor
threads per MPI task.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>

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@ -71,14 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">5.KOKKOS package</a><ul>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -237,14 +245,14 @@ mode like the USER-INTEL package supports.</p>
<p>You must choose at build time whether to build for CPUs (OpenMP),
GPUs, or Phi.</p>
<p>You can do any of these in one line, using the src/Make.py script,
described in <span class="xref std std-ref">Section 2.4</span> of the manual.
described in <a class="reference internal" href="Section_start.html#start-4"><span class="std std-ref">Section 2.4</span></a> of the manual.
Type &#8220;Make.py -h&#8221; for help. If run from the src directory, these
commands will create src/lmp_kokkos_omp, lmp_kokkos_cuda, and
lmp_kokkos_phi. Note that the OMP and PHI options use
src/MAKE/Makefile.mpi as the starting Makefile.machine. The CUDA
option uses src/MAKE/OPTIONS/Makefile.kokkos_cuda.</p>
<p>The latter two steps can be done using the &#8220;-k on&#8221;, &#8220;-pk kokkos&#8221; and
&#8220;-sf kk&#8221; <span class="xref std std-ref">command-line switches</span>
&#8220;-sf kk&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switches</span></a>
respectively. Or the effect of the &#8220;-pk&#8221; or &#8220;-sf&#8221; switches can be
duplicated by adding the <a class="reference internal" href="package.html"><span class="doc">package kokkos</span></a> or <a class="reference internal" href="suffix.html"><span class="doc">suffix kk</span></a> commands respectively to your input script.</p>
<p>Or you can follow these steps:</p>
@ -379,9 +387,9 @@ generation Xeon Phi(TM) chips, which is 60 physical cores * 4
threads/core. Note that with the KOKKOS package you do not need to
specify how many Phi coprocessors there are per node; each
coprocessors is simply treated as running some number of MPI tasks.</p>
<p>You must use the &#8220;-k on&#8221; <span class="xref std std-ref">command-line switch</span> to enable the KOKKOS package. It
<p>You must use the &#8220;-k on&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> to enable the KOKKOS package. It
takes additional arguments for hardware settings appropriate to your
system. Those arguments are <span class="xref std std-ref">documented here</span>. The two most commonly used
system. Those arguments are <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">documented here</span></a>. The two most commonly used
options are:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="n">Nt</span> <span class="n">g</span> <span class="n">Ng</span>
</pre></div>
@ -399,11 +407,11 @@ specified is you have 2 or more GPUs per compute node.</p>
<p>The &#8220;-k on&#8221; switch also issues a &#8220;package kokkos&#8221; command (with no
additional arguments) which sets various KOKKOS options to default
values, as discussed on the <a class="reference internal" href="package.html"><span class="doc">package</span></a> command doc page.</p>
<p>Use the &#8220;-sf kk&#8221; <span class="xref std std-ref">command-line switch</span>,
<p>Use the &#8220;-sf kk&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a>,
which will automatically append &#8220;kk&#8221; to styles that support it. Use
the &#8220;-pk kokkos&#8221; <span class="xref std std-ref">command-line switch</span> if
the &#8220;-pk kokkos&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> if
you wish to change any of the default <a class="reference internal" href="package.html"><span class="doc">package kokkos</span></a>
optionns set by the &#8220;-k on&#8221; <span class="xref std std-ref">command-line switch</span>.</p>
optionns set by the &#8220;-k on&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a>.</p>
<p>Note that the default for the <a class="reference internal" href="package.html"><span class="doc">package kokkos</span></a> command is
to use &#8220;full&#8221; neighbor lists and set the Newton flag to &#8220;off&#8221; for both
pairwise and bonded interactions. This typically gives fastest
@ -412,12 +420,12 @@ script, it can override the Newton flag defaults.</p>
<p>However, when running in MPI-only mode with 1 thread per MPI task, it
will typically be faster to use &#8220;half&#8221; neighbor lists and set the
Newton flag to &#8220;on&#8221;, just as is the case for non-accelerated pair
styles. You can do this with the &#8220;-pk&#8221; <span class="xref std std-ref">command-line switch</span>.</p>
styles. You can do this with the &#8220;-pk&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a>.</p>
<p><strong>Or run with the KOKKOS package by editing an input script:</strong></p>
<p>The discussion above for the mpirun/mpiexec command and setting
appropriate thread and GPU values for host=OMP or host=MIC or
device=CUDA are the same.</p>
<p>You must still use the &#8220;-k on&#8221; <span class="xref std std-ref">command-line switch</span> to enable the KOKKOS package, and
<p>You must still use the &#8220;-k on&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> to enable the KOKKOS package, and
specify its additional arguments for hardware options appopriate to
your system, as documented above.</p>
<p>Use the <a class="reference internal" href="suffix.html"><span class="doc">suffix kk</span></a> command, or you can explicitly add a
@ -427,7 +435,7 @@ your system, as documented above.</p>
</div>
<p>You only need to use the <a class="reference internal" href="package.html"><span class="doc">package kokkos</span></a> command if you
wish to change any of its option defaults, as set by the &#8220;-k on&#8221;
<span class="xref std std-ref">command-line switch</span>.</p>
<a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a>.</p>
<p><strong>Speed-ups to expect:</strong></p>
<p>The performance of KOKKOS running in different modes is a function of
your hardware, which KOKKOS-enable styles are used, and the problem
@ -460,7 +468,7 @@ its options can provide a speed-up for specific calculations.</p>
<p>If N is the number of physical cores/node, then the number of MPI
tasks/node * number of threads/task should not exceed N, and should
typically equal N. Note that the default threads/task is 1, as set by
the &#8220;t&#8221; keyword of the &#8220;-k&#8221; <span class="xref std std-ref">command-line switch</span>. If you do not change this, no
the &#8220;t&#8221; keyword of the &#8220;-k&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a>. If you do not change this, no
additional parallelism (beyond MPI) will be invoked on the host
CPU(s).</p>
<p>You can compare the performance running in different modes:</p>
@ -484,16 +492,16 @@ environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or
later, intel 12 or later) setting the environment variable
OMP_PROC_BIND=true should be sufficient. For binding threads with the
KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option, as
discussed in <span class="xref std std-ref">Section 2.3.4</span> of the
discussed in <a class="reference internal" href="Section_start.html#start-3-4"><span class="std std-ref">Section 2.3.4</span></a> of the
manual.</p>
<p><strong>Running on GPUs:</strong></p>
<p>Insure the -arch setting in the machine makefile you are using,
e.g. src/MAKE/Makefile.cuda, is correct for your GPU hardware/software
(see <span class="xref std std-ref">this section</span> of the manual for
(see <a class="reference internal" href="Section_start.html#start-3-4"><span class="std std-ref">this section</span></a> of the manual for
details).</p>
<p>The -np setting of the mpirun command should set the number of MPI
tasks/node to be equal to the # of physical GPUs on the node.</p>
<p>Use the &#8220;-k&#8221; <span class="xref std std-ref">command-line switch</span> to
<p>Use the &#8220;-k&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> to
specify the number of GPUs per node, and the number of threads per MPI
task. As above for multi-core CPUs (and no GPU), if N is the number
of physical cores/node, then the number of MPI tasks/node * number of

28
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@ -71,14 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">5.USER-OMP package</a><ul>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -145,7 +153,7 @@ each MPI task running on a CPU.</p>
<p><strong>Building LAMMPS with the USER-OMP package:</strong></p>
<p>The lines above illustrate how to include/build with the USER-OMP
package in two steps, using the &#8220;make&#8221; command. Or how to do it with
one command via the src/Make.py script, described in <span class="xref std std-ref">Section 2.4</span> of the manual. Type &#8220;Make.py -h&#8221; for
one command via the src/Make.py script, described in <a class="reference internal" href="Section_start.html#start-4"><span class="std std-ref">Section 2.4</span></a> of the manual. Type &#8220;Make.py -h&#8221; for
help.</p>
<p>Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must
include &#8220;-fopenmp&#8221;. Likewise, if you use an Intel compiler, the
@ -160,12 +168,12 @@ its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.</p>
by the USER-OMP package. Note that the product of MPI tasks *
threads/task should not exceed the physical number of cores (on a
node), otherwise performance will suffer.</p>
<p>As in the lines above, use the &#8220;-sf omp&#8221; <span class="xref std std-ref">command-line switch</span>, which will automatically append
<p>As in the lines above, use the &#8220;-sf omp&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a>, which will automatically append
&#8220;omp&#8221; to styles that support it. The &#8220;-sf omp&#8221; switch also issues a
default <a class="reference internal" href="package.html"><span class="doc">package omp 0</span></a> command, which will set the
number of threads per MPI task via the OMP_NUM_THREADS environment
variable.</p>
<p>You can also use the &#8220;-pk omp Nt&#8221; <span class="xref std std-ref">command-line switch</span>, to explicitly set Nt = # of OpenMP
<p>You can also use the &#8220;-pk omp Nt&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a>, to explicitly set Nt = # of OpenMP
threads per MPI task to use, as well as additional options. Its
syntax is the same as the <a class="reference internal" href="package.html"><span class="doc">package omp</span></a> command whose doc
page gives details, including the default values used if it is not

26
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@ -71,14 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">5.OPT package</a><ul>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -140,13 +148,13 @@ follow.</p>
<p><strong>Building LAMMPS with the OPT package:</strong></p>
<p>The lines above illustrate how to build LAMMPS with the OPT package in
two steps, using the &#8220;make&#8221; command. Or how to do it with one command
via the src/Make.py script, described in <span class="xref std std-ref">Section 2.4</span> of the manual. Type &#8220;Make.py -h&#8221; for
via the src/Make.py script, described in <a class="reference internal" href="Section_start.html#start-4"><span class="std std-ref">Section 2.4</span></a> of the manual. Type &#8220;Make.py -h&#8221; for
help.</p>
<p>Note that if you use an Intel compiler to build with the OPT package,
the CCFLAGS setting in your Makefile.machine must include &#8220;-restrict&#8221;.
The Make.py command will add this automatically.</p>
<p><strong>Run with the OPT package from the command line:</strong></p>
<p>As in the lines above, use the &#8220;-sf opt&#8221; <span class="xref std std-ref">command-line switch</span>, which will automatically append
<p>As in the lines above, use the &#8220;-sf opt&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a>, which will automatically append
&#8220;opt&#8221; to styles that support it.</p>
<p><strong>Or run with the OPT package by editing an input script:</strong></p>
<p>Use the <a class="reference internal" href="suffix.html"><span class="doc">suffix opt</span></a> command, or you can explicitly add an

35
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@ -71,21 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">angle_style charmm command</a></li>
<li><a class="reference internal" href="#angle-style-charmm-intel-command">angle_style charmm/intel command</a></li>
<li><a class="reference internal" href="#angle-style-charmm-kk-command">angle_style charmm/kk command</a></li>
<li><a class="reference internal" href="#angle-style-charmm-omp-command">angle_style charmm/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -178,9 +179,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -189,7 +190,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <span class="xref std std-ref">Making LAMMPS</span> section for more info on packages.</p>
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

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@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">angle_style class2 command</a></li>
<li><a class="reference internal" href="#angle-style-class2-omp-command">angle_style class2/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -200,9 +203,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -211,7 +214,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This angle style can only be used if LAMMPS was built with the CLASS2
package. See the <span class="xref std std-ref">Making LAMMPS</span> section
package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section
for more info on packages.</p>
</div>
<div class="section" id="related-commands">

26
doc/html/angle_coeff.html
View File

@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">angle_coeff command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

33
doc/html/angle_cosine.html
View File

@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">angle_style cosine command</a></li>
<li><a class="reference internal" href="#angle-style-cosine-omp-command">angle_style cosine/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -161,9 +164,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -172,7 +175,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <span class="xref std std-ref">Making LAMMPS</span> section for more info on packages.</p>
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

33
doc/html/angle_cosine_delta.html
View File

@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">angle_style cosine/delta command</a></li>
<li><a class="reference internal" href="#angle-style-cosine-delta-omp-command">angle_style cosine/delta/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -165,9 +168,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -176,7 +179,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <span class="xref std std-ref">Making LAMMPS</span> section for more info on packages.</p>
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

33
doc/html/angle_cosine_periodic.html
View File

@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">angle_style cosine/periodic command</a></li>
<li><a class="reference internal" href="#angle-style-cosine-periodic-omp-command">angle_style cosine/periodic/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -172,9 +175,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -183,7 +186,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <span class="xref std std-ref">Making LAMMPS</span> section for more info on packages.</p>
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

33
doc/html/angle_cosine_shift.html
View File

@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">angle_style cosine/shift command</a></li>
<li><a class="reference internal" href="#angle-style-cosine-shift-omp-command">angle_style cosine/shift/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -164,9 +167,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -175,7 +178,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This angle style can only be used if LAMMPS was built with the
USER-MISC package. See the <span class="xref std std-ref">Making LAMMPS</span>
USER-MISC package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a>
section for more info on packages.</p>
</div>
<div class="section" id="related-commands">

33
doc/html/angle_cosine_shift_exp.html
View File

@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">angle_style cosine/shift/exp command</a></li>
<li><a class="reference internal" href="#angle-style-cosine-shift-exp-omp-command">angle_style cosine/shift/exp/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -174,9 +177,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -185,7 +188,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This angle style can only be used if LAMMPS was built with the
USER-MISC package. See the <span class="xref std std-ref">Making LAMMPS</span>
USER-MISC package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a>
section for more info on packages.</p>
</div>
<div class="section" id="related-commands">

33
doc/html/angle_cosine_squared.html
View File

@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">angle_style cosine/squared command</a></li>
<li><a class="reference internal" href="#angle-style-cosine-squared-omp-command">angle_style cosine/squared/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -165,9 +168,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -176,7 +179,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <span class="xref std std-ref">Making LAMMPS</span> section for more info on packages.</p>
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

33
doc/html/angle_dipole.html
View File

@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">angle_style dipole command</a></li>
<li><a class="reference internal" href="#angle-style-dipole-omp-command">angle_style dipole/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -185,9 +188,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-6"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -195,7 +198,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This angle style can only be used if LAMMPS was built with the
USER-MISC package. See the <span class="xref std std-ref">Making LAMMPS</span>
USER-MISC package. See the <a class="reference internal" href="Section_start.html#start-2-3"><span class="std std-ref">Making LAMMPS</span></a>
section for more info on packages.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>

33
doc/html/angle_fourier.html
View File

@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">angle_style fourier command</a></li>
<li><a class="reference internal" href="#angle-style-fourier-omp-command">angle_style fourier/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -161,9 +164,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -172,7 +175,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This angle style can only be used if LAMMPS was built with the
USER_MISC package. See the <span class="xref std std-ref">Making LAMMPS</span>
USER_MISC package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a>
section for more info on packages.</p>
</div>
<div class="section" id="related-commands">

33
doc/html/angle_fourier_simple.html
View File

@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">angle_style fourier/simple command</a></li>
<li><a class="reference internal" href="#angle-style-fourier-simple-omp-command">angle_style fourier/simple/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -160,9 +163,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -171,7 +174,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This angle style can only be used if LAMMPS was built with the
USER_MISC package. See the <span class="xref std std-ref">Making LAMMPS</span>
USER_MISC package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a>
section for more info on packages.</p>
</div>
<div class="section" id="related-commands">

35
doc/html/angle_harmonic.html
View File

@ -71,21 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">angle_style harmonic command</a></li>
<li><a class="reference internal" href="#angle-style-harmonic-intel-command">angle_style harmonic/intel command</a></li>
<li><a class="reference internal" href="#angle-style-harmonic-kk-command">angle_style harmonic/kk command</a></li>
<li><a class="reference internal" href="#angle-style-harmonic-omp-command">angle_style harmonic/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -173,9 +174,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -186,7 +187,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<blockquote>
<div>none</div></blockquote>
<p>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <span class="xref std std-ref">Making LAMMPS</span> section for more info on packages.</p>
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

28
doc/html/angle_hybrid.html
View File

@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">angle_style hybrid command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -193,7 +197,7 @@ for specific angle types.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <span class="xref std std-ref">Making LAMMPS</span> section for more info on packages.</p>
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
<p>Unlike other angle styles, the hybrid angle style does not store angle
coefficient info for individual sub-styles in a <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. Thus when retarting a simulation from a restart
file, you need to re-specify angle_coeff commands.</p>

26
doc/html/angle_none.html
View File

@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">angle_style none command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

33
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@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">angle_style quartic command</a></li>
<li><a class="reference internal" href="#angle-style-quartic-omp-command">angle_style quartic/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -167,9 +170,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -178,7 +181,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This angle style can only be used if LAMMPS was built with the
USER_MISC package. See the <span class="xref std std-ref">Making LAMMPS</span>
USER_MISC package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a>
section for more info on packages.</p>
</div>
<div class="section" id="related-commands">

28
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">angle_style sdk command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -163,7 +167,7 @@ from the pair_style.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This angle style can only be used if LAMMPS was built with the
USER-CG-CMM package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info on packages.</p>
USER-CG-CMM package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

29
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@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">angle_style command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<li><a class="reference internal" href="#default">Default</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -194,7 +197,7 @@ links to the individual styles are given in the angle section of <a class="refer
<p>Angle styles can only be set for atom_styles that allow angles to be
defined.</p>
<p>Most angle styles are part of the MOLECULE package. They are only
enabled if LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info on packages.
enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info on packages.
The doc pages for individual bond potentials tell if it is part of a
package.</p>
</div>

33
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@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">angle_style table command</a></li>
<li><a class="reference internal" href="#angle-style-table-omp-command">angle_style table/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -239,9 +242,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -250,7 +253,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <span class="xref std std-ref">Making LAMMPS</span> section for more info on packages.</p>
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

26
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View File

@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">angle_style zero command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

28
doc/html/atom_modify.html
View File

@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">atom_modify command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#default">Default</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -174,7 +178,7 @@ simulation so large that IDs cannot be uniquely assigned. For a
default LAMMPS build this limit is 2^31 or about 2 billion atoms.
However, even in this case, you can use 64-bit atom IDs, allowing 2^63
or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG
switch. This is described in <span class="xref std std-ref">Section 2.2</span>
switch. This is described in <a class="reference internal" href="Section_start.html#start-2"><span class="std std-ref">Section 2.2</span></a>
of the manual. If atom IDs are not used, they must be specified as 0
for all atoms, e.g. in a data or restart file.</p>
<p>The <em>map</em> keyword determines how atom ID lookup is done for molecular

33
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@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">atom_style command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<li><a class="reference internal" href="#default">Default</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -399,9 +402,9 @@ results, except for round-off and precision issues.</p>
USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom
styles.</p>
<p>The accelerated styles are part of the KOKKOS package. They are only
enabled if LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -411,7 +414,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<p>This command cannot be used after the simulation box is defined by a
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command.</p>
<p>Many of the styles listed above are only enabled if LAMMPS was built
with a specific package, as listed below. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
with a specific package, as listed below. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>The <em>angle</em>, <em>bond</em>, <em>full</em>, <em>molecular</em>, and <em>template</em> styles are
part of the MOLECULE package.</p>
<p>The <em>line</em> and <em>tri</em> styles are part of the ASPHERE package.</p>

26
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">balance command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

19
doc/html/body.html
View File

@ -71,11 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Body particles</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
</div>

33
doc/html/bond_class2.html
View File

@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">bond_style class2 command</a></li>
<li><a class="reference internal" href="#bond-style-class2-omp-command">bond_style class2/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -165,9 +168,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -176,7 +179,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This bond style can only be used if LAMMPS was built with the CLASS2
package. See the <span class="xref std std-ref">Making LAMMPS</span> section
package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section
for more info on packages.</p>
</div>
<div class="section" id="related-commands">

26
doc/html/bond_coeff.html
View File

@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">bond_coeff command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

35
doc/html/bond_fene.html
View File

@ -71,21 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">bond_style fene command</a></li>
<li><a class="reference internal" href="#bond-style-fene-intel-command">bond_style fene/intel command</a></li>
<li><a class="reference internal" href="#bond-style-fene-kk-command">bond_style fene/kk command</a></li>
<li><a class="reference internal" href="#bond-style-fene-omp-command">bond_style fene/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -176,9 +177,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -187,7 +188,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <span class="xref std std-ref">Making LAMMPS</span> section for more info on packages.</p>
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
<p>You typically should specify <a class="reference external" href="special_bonds.html&quot;">special_bonds fene</a>
or <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds lj/coul 0 1 1</span></a> to use this bond
style. LAMMPS will issue a warning it that&#8217;s not the case.</p>

33
doc/html/bond_fene_expand.html
View File

@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">bond_style fene/expand command</a></li>
<li><a class="reference internal" href="#bond-style-fene-expand-omp-command">bond_style fene/expand/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -172,9 +175,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -183,7 +186,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <span class="xref std std-ref">Making LAMMPS</span> section for more info on packages.</p>
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
<p>You typically should specify <a class="reference external" href="special_bonds.html&quot;">special_bonds fene</a>
or <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds lj/coul 0 1 1</span></a> to use this bond
style. LAMMPS will issue a warning it that&#8217;s not the case.</p>

35
doc/html/bond_harmonic.html
View File

@ -71,21 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">bond_style harmonic command</a></li>
<li><a class="reference internal" href="#bond-style-harmonic-intel-command">bond_style harmonic/intel command</a></li>
<li><a class="reference internal" href="#bond-style-harmonic-kk-command">bond_style harmonic/kk command</a></li>
<li><a class="reference internal" href="#bond-style-harmonic-omp-command">bond_style harmonic/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -171,9 +172,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -182,7 +183,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <span class="xref std std-ref">Making LAMMPS</span> section for more info on packages.</p>
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

33
doc/html/bond_harmonic_shift.html
View File

@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">bond_style harmonic/shift command</a></li>
<li><a class="reference internal" href="#bond-style-harmonic-shift-omp-command">bond_style harmonic/shift/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -166,9 +169,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -177,7 +180,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This bond style can only be used if LAMMPS was built with the
USER-MISC package. See the <span class="xref std std-ref">Making LAMMPS</span>
USER-MISC package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a>
section for more info on packages.</p>
</div>
<div class="section" id="related-commands">

33
doc/html/bond_harmonic_shift_cut.html
View File

@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">bond_style harmonic/shift/cut command</a></li>
<li><a class="reference internal" href="#bond-style-harmonic-shift-cut-omp-command">bond_style harmonic/shift/cut/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -166,9 +169,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -177,7 +180,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This bond style can only be used if LAMMPS was built with the
USER-MISC package. See the <span class="xref std std-ref">Making LAMMPS</span>
USER-MISC package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a>
section for more info on packages.</p>
</div>
<div class="section" id="related-commands">

28
doc/html/bond_hybrid.html
View File

@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">bond_style hybrid command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -176,7 +180,7 @@ bond types.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <span class="xref std std-ref">Making LAMMPS</span> section for more info on packages.</p>
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
<p>Unlike other bond styles, the hybrid bond style does not store bond
coefficient info for individual sub-styles in a <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. Thus when retarting a simulation from a restart
file, you need to re-specify bond_coeff commands.</p>

33
doc/html/bond_morse.html
View File

@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">bond_style morse command</a></li>
<li><a class="reference internal" href="#bond-style-morse-omp-command">bond_style morse/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -164,9 +167,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -175,7 +178,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <span class="xref std std-ref">Making LAMMPS</span> section for more info on packages.</p>
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

25
doc/html/bond_none.html
View File

@ -71,17 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">bond_style none command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

33
doc/html/bond_nonlinear.html
View File

@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">bond_style nonlinear command</a></li>
<li><a class="reference internal" href="#bond-style-nonlinear-omp-command">bond_style nonlinear/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -164,9 +167,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -175,7 +178,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <span class="xref std std-ref">Making LAMMPS</span> section for more info on packages.</p>
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

33
doc/html/bond_quartic.html
View File

@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">bond_style quartic command</a></li>
<li><a class="reference internal" href="#bond-style-quartic-omp-command">bond_style quartic/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -195,9 +198,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -206,7 +209,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <span class="xref std std-ref">Making LAMMPS</span> section for more info on packages.</p>
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
<p>The <em>quartic</em> style requires that <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a>
parameters be set to 1,1,1. Three- and four-body interactions (angle,
dihedral, etc) cannot be used with <em>quartic</em> bonds.</p>

29
doc/html/bond_style.html
View File

@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">bond_style command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<li><a class="reference internal" href="#default">Default</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -204,7 +207,7 @@ links to the individual styles are given in the bond section of <a class="refere
<p>Bond styles can only be set for atom styles that allow bonds to be
defined.</p>
<p>Most bond styles are part of the MOLECULE package. They are only
enabled if LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info on packages.
enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info on packages.
The doc pages for individual bond potentials tell if it is part of a
package.</p>
</div>

33
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@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">bond_style table command</a></li>
<li><a class="reference internal" href="#bond-style-table-omp-command">bond_style table/omp command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -236,9 +239,9 @@ should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <span class="xref std std-ref">-suffix command-line switch</span> when you invoke LAMMPS, or you can
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
@ -247,7 +250,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <span class="xref std std-ref">Making LAMMPS</span> section for more info on packages.</p>
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">bond_write command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

26
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">bond_style zero command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

27
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@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">boundary command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<li><a class="reference internal" href="#default">Default</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

26
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">box command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#default">Default</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

27
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@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">change_box command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<li><a class="reference internal" href="#default">Default</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

25
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@ -71,17 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">clear command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

27
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@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">comm_modify command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<li><a class="reference internal" href="#default">Default</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

27
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@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">comm_style command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<li><a class="reference internal" href="#default">Default</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

28
doc/html/compute_ackland_atom.html
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute ackland/atom command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -170,7 +174,7 @@ LAMMPS output options.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This compute is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>The per-atom vector values will be unitless since they are the
integers defined above.</p>
</div>

26
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute angle command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

26
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute angle/local command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

26
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute angmom/chunk command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

28
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute basal/atom command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -167,7 +171,7 @@ components of a unit vector.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This compute is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>The output of this compute will be meaningless unless the atoms are on
(or near) hcp lattice sites, since the calculation assumes a
well-defined basal plane.</p>

26
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute body/local command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

26
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute bond command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

26
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute bond/local command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

27
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@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute centro/atom command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<li><a class="reference internal" href="#default">Default</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

27
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@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute chunk/atom command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<li><a class="reference internal" href="#default">Default</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

26
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute cluster/atom command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

26
doc/html/compute_cna_atom.html
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute cna/atom command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

26
doc/html/compute_com.html
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute com command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

26
doc/html/compute_com_chunk.html
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute com/chunk command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

26
doc/html/compute_contact_atom.html
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute contact/atom command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

26
doc/html/compute_coord_atom.html
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute coord/atom command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

28
doc/html/compute_damage_atom.html
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute damage/atom command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -162,7 +166,7 @@ LAMMPS output options.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This compute is part of the PERI package. It is only enabled if
LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

26
doc/html/compute_dihedral.html
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute dihedral command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

26
doc/html/compute_dihedral_local.html
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute dihedral/local command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

28
doc/html/compute_dilatation_atom.html
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute dilatation/atom command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -164,7 +168,7 @@ Section_howto 15 for an overview of LAMMPS output options.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This compute is part of the PERI package. It is only enabled if
LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

26
doc/html/compute_dipole_chunk.html
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute dipole/chunk command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

26
doc/html/compute_displace_atom.html
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute displace/atom command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

28
doc/html/compute_dpd.html
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@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute dpd command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -161,7 +165,7 @@ output options.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This command is part of the USER-DPD package. It is only enabled if
LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>This command also requires use of the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dpd</span></a>
command.</p>
</div>

28
doc/html/compute_dpd_atom.html
View File

@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute dpd/atom command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -159,7 +163,7 @@ and temperature (dpdTheta) <a class="reference internal" href="units.html"><span
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This command is part of the USER-DPD package. It is only enabled if
LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>This command also requires use of the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dpd</span></a>
command.</p>
</div>

25
doc/html/compute_erotate_asphere.html
View File

@ -71,17 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute erotate/asphere command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

28
doc/html/compute_erotate_rigid.html
View File

@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute erotate/rigid command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -164,7 +168,7 @@ scalar value will be in energy <a class="reference internal" href="units.html"><
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This compute is part of the RIGID package. It is only enabled if
LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

26
doc/html/compute_erotate_sphere.html
View File

@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute erotate/sphere command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

26
doc/html/compute_erotate_sphere_atom.html
View File

@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute erotate/sphere/atom command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

28
doc/html/compute_event_displace.html
View File

@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute event/displace command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -169,7 +173,7 @@ scalar value will be a 0 or 1 as explained above.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This command can only be used if LAMMPS was built with the REPLICA
package. See the <span class="xref std std-ref">Making LAMMPS</span> section
package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section
for more info on packages.</p>
</div>
<div class="section" id="related-commands">

29
doc/html/compute_fep.html
View File

@ -71,19 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute fep command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<li><a class="reference internal" href="#default">Default</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>
@ -359,7 +362,7 @@ options. For example, the computed values can be averaged using <a class="refere
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This compute is distributed as the USER-FEP package. It is only
enabled if LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

26
doc/html/compute_group_group.html
View File

@ -71,18 +71,22 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">compute group/group command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#default">Default</a></li>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</li>
</ul>
</div>
</div>

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