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<HTML>
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<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="6 Nov 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
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<HR>
<H1></H1>
<CENTER><H3>LAMMPS Documentation
</H3></CENTER>
<CENTER><H4>6 Nov 2015 version
</H4></CENTER>
<H4>Version info:
</H4>
<P>The LAMMPS "version" is the date when it was released, such as 1 May
<div class="wy-nav-content">
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<div class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
<a href="Section_intro.html" class="btn btn-neutral float-right" title="1. Introduction" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
</div>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<H1></H1><div class="section" id="lammps-documentation">
<h1>LAMMPS Documentation<a class="headerlink" href="#lammps-documentation" title="Permalink to this headline"></a></h1>
<div class="section" id="aug-2015-version">
<h2>10 Aug 2015 version<a class="headerlink" href="#aug-2015-version" title="Permalink to this headline"></a></h2>
</div>
<div class="section" id="version-info">
<h2>Version info:<a class="headerlink" href="#version-info" title="Permalink to this headline"></a></h2>
<p>The LAMMPS &#8220;version&#8221; is the date when it was released, such as 1 May
2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
feature, we release it immediately, and post a notice on <A HREF = "http://lammps.sandia.gov/bug.html">this page of
the WWW site</A>. Each dated copy of LAMMPS contains all the
feature, we release it immediately, and post a notice on <a class="reference external" href="http://lammps.sandia.gov/bug.html">this page of the WWW site</a>. Each dated copy of LAMMPS contains all the
features and bug-fixes up to and including that version date. The
version date is printed to the screen and logfile every time you run
LAMMPS. It is also in the file src/version.h and in the LAMMPS
directory name created when you unpack a tarball, and at the top of
the first page of the manual (this page).
</P>
<UL><LI>If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of LAMMPS.
<LI>If you browse the HTML doc pages included in your tarball, they
describe the version you have.
<LI>The <A HREF = "Manual.pdf">PDF file</A> on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don't want
it to be part of every patch.
<LI>There is also a <A HREF = "Developer.pdf">Developer.pdf</A> file in the doc
the first page of the manual (this page).</p>
<ul class="simple">
<li>If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of LAMMPS.</li>
<li>If you browse the HTML doc pages included in your tarball, they
describe the version you have.</li>
<li>The <a class="reference external" href="Manual.pdf">PDF file</a> on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don&#8217;t want
it to be part of every patch.</li>
<li>There is also a <a class="reference external" href="Developer.pdf">Developer.pdf</a> file in the doc
directory, which describes the internal structure and algorithms of
LAMMPS.
</UL>
<P>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.
</P>
<P>LAMMPS is a classical molecular dynamics simulation code designed to
LAMMPS.</li>
</ul>
<p>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.</p>
<p>LAMMPS is a classical molecular dynamics simulation code designed to
run efficiently on parallel computers. It was developed at Sandia
National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL).
</P>
<P>The primary developers of LAMMPS are <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Aidan
under the terms of the GNU Public License (GPL).</p>
<p>The primary developers of LAMMPS are <a class="reference external" href="http://www.sandia.gov/~sjplimp">Steve Plimpton</a>, Aidan
Thompson, and Paul Crozier who can be contacted at
sjplimp,athomps,pscrozi at sandia.gov. The <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> at
http://lammps.sandia.gov has more information about the code and its
uses.
</P>
<HR>
<P>The LAMMPS documentation is organized into the following sections. If
sjplimp,athomps,pscrozi at sandia.gov. The <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> at
<a class="reference external" href="http://lammps.sandia.gov">http://lammps.sandia.gov</a> has more information about the code and its
uses.</p>
<hr class="docutils" />
<p>The LAMMPS documentation is organized into the following sections. If
you find errors or omissions in this manual or have suggestions for
useful information to add, please send an email to the developers so
we can improve the LAMMPS documentation.
</P>
<P>Once you are familiar with LAMMPS, you may want to bookmark <A HREF = "Section_commands.html#comm">this
page</A> at Section_commands.html#comm since
it gives quick access to documentation for all LAMMPS commands.
</P>
<P><A HREF = "Manual.pdf">PDF file</A> of the entire manual, generated by
<A HREF = "http://freecode.com/projects/htmldoc">htmldoc</A>
</P>
<P><!-- RST
</P>
<P>.. toctree::
:maxdepth: 2
:numbered: // comment
</P>
<P> Section_intro
Section_start
Section_commands
Section_packages
Section_accelerate
Section_howto
Section_example
Section_perf
Section_tools
Section_modify
Section_python
Section_errors
Section_history
</P>
<P>Indices and tables
==================
</P>
<P>* :ref:`genindex` // comment
* :ref:`search` // comment
</P>
<P>END_RST -->
</P>
<OL><LI><!-- HTML_ONLY -->
<A HREF = "Section_intro.html">Introduction</A>
<UL> 1.1 <A HREF = "Section_intro.html#intro_1">What is LAMMPS</A>
<BR>
1.2 <A HREF = "Section_intro.html#intro_2">LAMMPS features</A>
<BR>
1.3 <A HREF = "Section_intro.html#intro_3">LAMMPS non-features</A>
<BR>
1.4 <A HREF = "Section_intro.html#intro_4">Open source distribution</A>
<BR>
1.5 <A HREF = "Section_intro.html#intro_5">Acknowledgments and citations</A>
<BR></UL>
<LI><A HREF = "Section_start.html">Getting started</A>
<UL> 2.1 <A HREF = "Section_start.html#start_1">What's in the LAMMPS distribution</A>
<BR>
2.2 <A HREF = "Section_start.html#start_2">Making LAMMPS</A>
<BR>
2.3 <A HREF = "Section_start.html#start_3">Making LAMMPS with optional packages</A>
<BR>
2.4 <A HREF = "Section_start.html#start_4">Building LAMMPS via the Make.py script</A>
<BR>
2.5 <A HREF = "Section_start.html#start_5">Building LAMMPS as a library</A>
<BR>
2.6 <A HREF = "Section_start.html#start_6">Running LAMMPS</A>
<BR>
2.7 <A HREF = "Section_start.html#start_7">Command-line options</A>
<BR>
2.8 <A HREF = "Section_start.html#start_8">Screen output</A>
<BR>
2.9 <A HREF = "Section_start.html#start_9">Tips for users of previous versions</A>
<BR></UL>
<LI><A HREF = "Section_commands.html">Commands</A>
<UL> 3.1 <A HREF = "Section_commands.html#cmd_1">LAMMPS input script</A>
<BR>
3.2 <A HREF = "Section_commands.html#cmd_2">Parsing rules</A>
<BR>
3.3 <A HREF = "Section_commands.html#cmd_3">Input script structure</A>
<BR>
3.4 <A HREF = "Section_commands.html#cmd_4">Commands listed by category</A>
<BR>
3.5 <A HREF = "Section_commands.html#cmd_5">Commands listed alphabetically</A>
<BR></UL>
<LI><A HREF = "Section_packages.html">Packages</A>
<UL> 4.1 <A HREF = "Section_packages.html#pkg_1">Standard packages</A>
<BR>
4.2 <A HREF = "Section_packages.html#pkg_2">User packages</A>
<BR></UL>
<LI><A HREF = "Section_accelerate.html">Accelerating LAMMPS performance</A>
<UL> 5.1 <A HREF = "Section_accelerate.html#acc_1">Measuring performance</A>
<BR>
5.2 <A HREF = "Section_accelerate.html#acc_2">Algorithms and code options to boost performace</A>
<BR>
5.3 <A HREF = "Section_accelerate.html#acc_3">Accelerator packages with optimized styles</A>
<BR>
<UL> 5.3.1 <A HREF = "accelerate_cuda.html">USER-CUDA package</A>
<BR>
5.3.2 <A HREF = "accelerate_gpu.html">GPU package</A>
<BR>
5.3.3 <A HREF = "accelerate_intel.html">USER-INTEL package</A>
<BR>
5.3.4 <A HREF = "accelerate_kokkos.html">KOKKOS package</A>
<BR>
5.3.5 <A HREF = "accelerate_omp.html">USER-OMP package</A>
<BR>
5.3.6 <A HREF = "accelerate_opt.html">OPT package</A>
<BR></UL>
5.4 <A HREF = "Section_accelerate.html#acc_4">Comparison of various accelerator packages</A>
<BR></UL>
<LI><A HREF = "Section_howto.html">How-to discussions</A>
<UL> 6.1 <A HREF = "Section_howto.html#howto_1">Restarting a simulation</A>
<BR>
6.2 <A HREF = "Section_howto.html#howto_2">2d simulations</A>
<BR>
6.3 <A HREF = "Section_howto.html#howto_3">CHARMM and AMBER force fields</A>
<BR>
6.4 <A HREF = "Section_howto.html#howto_4">Running multiple simulations from one input script</A>
<BR>
6.5 <A HREF = "Section_howto.html#howto_5">Multi-replica simulations</A>
<BR>
6.6 <A HREF = "Section_howto.html#howto_6">Granular models</A>
<BR>
6.7 <A HREF = "Section_howto.html#howto_7">TIP3P water model</A>
<BR>
6.8 <A HREF = "Section_howto.html#howto_8">TIP4P water model</A>
<BR>
6.9 <A HREF = "Section_howto.html#howto_9">SPC water model</A>
<BR>
6.10 <A HREF = "Section_howto.html#howto_10">Coupling LAMMPS to other codes</A>
<BR>
6.11 <A HREF = "Section_howto.html#howto_11">Visualizing LAMMPS snapshots</A>
<BR>
6.12 <A HREF = "Section_howto.html#howto_12">Triclinic (non-orthogonal) simulation boxes</A>
<BR>
6.13 <A HREF = "Section_howto.html#howto_13">NEMD simulations</A>
<BR>
6.14 <A HREF = "Section_howto.html#howto_14">Finite-size spherical and aspherical particles</A>
<BR>
6.15 <A HREF = "Section_howto.html#howto_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A>
<BR>
6.16 <A HREF = "Section_howto.html#howto_16">Thermostatting, barostatting, and compute temperature</A>
<BR>
6.17 <A HREF = "Section_howto.html#howto_17">Walls</A>
<BR>
6.18 <A HREF = "Section_howto.html#howto_18">Elastic constants</A>
<BR>
6.19 <A HREF = "Section_howto.html#howto_19">Library interface to LAMMPS</A>
<BR>
6.20 <A HREF = "Section_howto.html#howto_20">Calculating thermal conductivity</A>
<BR>
6.21 <A HREF = "Section_howto.html#howto_21">Calculating viscosity</A>
<BR>
6.22 <A HREF = "Section_howto.html#howto_22">Calculating a diffusion coefficient</A>
<BR>
6.23 <A HREF = "Section_howto.html#howto_23">Using chunks to calculate system properties</A>
<BR>
6.24 <A HREF = "Section_howto.html#howto_24">Setting parameters for pppm/disp</A>
<BR>
6.25 <A HREF = "Section_howto.html#howto_25">Polarizable models</A>
<BR>
6.26 <A HREF = "Section_howto.html#howto_26">Adiabatic core/shell model</A>
<BR>
6.27 <A HREF = "Section_howto.html#howto_27">Drude induced dipoles</A>
<BR></UL>
<LI><A HREF = "Section_example.html">Example problems</A>
<LI><A HREF = "Section_perf.html">Performance & scalability</A>
<LI><A HREF = "Section_tools.html">Additional tools</A>
<LI><A HREF = "Section_modify.html">Modifying & extending LAMMPS</A>
<UL> 10.1 <A HREF = "Section_modify.html#mod_1">Atom styles</A>
<BR>
10.2 <A HREF = "Section_modify.html#mod_2">Bond, angle, dihedral, improper potentials</A>
<BR>
10.3 <A HREF = "Section_modify.html#mod_3">Compute styles</A>
<BR>
10.4 <A HREF = "Section_modify.html#mod_4">Dump styles</A>
<BR>
10.5 <A HREF = "Section_modify.html#mod_5">Dump custom output options</A>
<BR>
10.6 <A HREF = "Section_modify.html#mod_6">Fix styles</A>
<BR>
10.7 <A HREF = "Section_modify.html#mod_7">Input script commands</A>
<BR>
10.8 <A HREF = "Section_modify.html#mod_8">Kspace computations</A>
<BR>
10.9 <A HREF = "Section_modify.html#mod_9">Minimization styles</A>
<BR>
10.10 <A HREF = "Section_modify.html#mod_10">Pairwise potentials</A>
<BR>
10.11 <A HREF = "Section_modify.html#mod_11">Region styles</A>
<BR>
10.12 <A HREF = "Section_modify.html#mod_12">Body styles</A>
<BR>
10.13 <A HREF = "Section_modify.html#mod_13">Thermodynamic output options</A>
<BR>
10.14 <A HREF = "Section_modify.html#mod_14">Variable options</A>
<BR>
10.15 <A HREF = "Section_modify.html#mod_15">Submitting new features for inclusion in LAMMPS</A>
<BR></UL>
<LI><A HREF = "Section_python.html">Python interface</A>
<UL> 11.1 <A HREF = "Section_python.html#py_1">Overview of running LAMMPS from Python</A>
<BR>
11.2 <A HREF = "Section_python.html#py_2">Overview of using Python from a LAMMPS script</A>
<BR>
11.3 <A HREF = "Section_python.html#py_3">Building LAMMPS as a shared library</A>
<BR>
11.4 <A HREF = "Section_python.html#py_4">Installing the Python wrapper into Python</A>
<BR>
11.5 <A HREF = "Section_python.html#py_5">Extending Python with MPI to run in parallel</A>
<BR>
11.6 <A HREF = "Section_python.html#py_6">Testing the Python-LAMMPS interface</A>
<BR>
11.7 <A HREF = "py_7">Using LAMMPS from Python</A>
<BR>
11.8 <A HREF = "py_8">Example Python scripts that use LAMMPS</A>
<BR></UL>
<LI><A HREF = "Section_errors.html">Errors</A>
<UL> 12.1 <A HREF = "Section_errors.html#err_1">Common problems</A>
<BR>
12.2 <A HREF = "Section_errors.html#err_2">Reporting bugs</A>
<BR>
12.3 <A HREF = "Section_errors.html#err_3">Error & warning messages</A>
<BR></UL>
<LI><A HREF = "Section_history.html">Future and history</A>
<UL> 13.1 <A HREF = "Section_history.html#hist_1">Coming attractions</A>
<BR>
13.2 <A HREF = "Section_history.html#hist_2">Past versions</A>
<BR></UL>
</OL>
<!-- END_HTML_ONLY -->
</BODY>
</HTML>
we can improve the LAMMPS documentation.</p>
<p>Once you are familiar with LAMMPS, you may want to bookmark <a class="reference internal" href="Section_commands.html#comm"><span>this page</span></a> at Section_commands.html#comm since
it gives quick access to documentation for all LAMMPS commands.</p>
<p><a class="reference external" href="Manual.pdf">PDF file</a> of the entire manual, generated by
<a class="reference external" href="http://freecode.com/projects/htmldoc">htmldoc</a></p>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#what-is-lammps">1.1. What is LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-features">1.2. LAMMPS features</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-non-features">1.3. LAMMPS non-features</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#open-source-distribution">1.4. Open source distribution</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#acknowledgments-and-citations">1.5. Acknowledgments and citations</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#what-s-in-the-lammps-distribution">2.1. What&#8217;s in the LAMMPS distribution</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps">2.2. Making LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps-with-optional-packages">2.3. Making LAMMPS with optional packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-via-the-make-py-tool">2.4. Building LAMMPS via the Make.py tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-as-a-library">2.5. Building LAMMPS as a library</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#running-lammps">2.6. Running LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#command-line-options">2.7. Command-line options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#lammps-screen-output">2.8. LAMMPS screen output</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#tips-for-users-of-previous-lammps-versions">2.9. Tips for users of previous LAMMPS versions</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#lammps-input-script">3.1. LAMMPS input script</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#parsing-rules">3.2. Parsing rules</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#input-script-structure">3.3. Input script structure</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#commands-listed-by-category">3.4. Commands listed by category</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#individual-commands">3.5. Individual commands</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#fix-styles">3.6. Fix styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#compute-styles">3.7. Compute styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#pair-style-potentials">3.8. Pair_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#bond-style-potentials">3.9. Bond_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#angle-style-potentials">3.10. Angle_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#dihedral-style-potentials">3.11. Dihedral_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#improper-style-potentials">3.12. Improper_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#kspace-solvers">3.13. Kspace solvers</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#standard-packages">4.1. Standard packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-compress-package">4.2. Build instructions for COMPRESS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-gpu-package">4.3. Build instructions for GPU package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-kim-package">4.4. Build instructions for KIM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-kokkos-package">4.5. Build instructions for KOKKOS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-kspace-package">4.6. Build instructions for KSPACE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-meam-package">4.7. Build instructions for MEAM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-poems-package">4.8. Build instructions for POEMS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-python-package">4.9. Build instructions for PYTHON package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-reax-package">4.10. Build instructions for REAX package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-voronoi-package">4.11. Build instructions for VORONOI package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-xtc-package">4.12. Build instructions for XTC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-packages">4.13. User packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-atc-package">4.14. USER-ATC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-awpmd-package">4.15. USER-AWPMD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cg-cmm-package">4.16. USER-CG-CMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-colvars-package">4.17. USER-COLVARS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cuda-package">4.18. USER-CUDA package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-diffraction-package">4.19. USER-DIFFRACTION package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-drude-package">4.20. USER-DRUDE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-eff-package">4.21. USER-EFF package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-fep-package">4.22. USER-FEP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-h5md-package">4.23. USER-H5MD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-intel-package">4.24. USER-INTEL package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-lb-package">4.25. USER-LB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-mgpt-package">4.26. USER-MGPT package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-misc-package">4.27. USER-MISC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-molfile-package">4.28. USER-MOLFILE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-omp-package">4.29. USER-OMP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-phonon-package">4.30. USER-PHONON package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qmmm-package">4.31. USER-QMMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qtb-package">4.32. USER-QTB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-reaxc-package">4.33. USER-REAXC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smd-package">4.34. USER-SMD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smtbq-package">4.35. USER-SMTBQ package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-sph-package">4.36. USER-SPH package</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#measuring-performance">5.1. Measuring performance</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#general-strategies">5.2. General strategies</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#packages-with-optimized-styles">5.3. Packages with optimized styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#comparison-of-various-accelerator-packages">5.4. Comparison of various accelerator packages</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#restarting-a-simulation">6.1. Restarting a simulation</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#d-simulations">6.2. 2d simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#charmm-amber-and-dreiding-force-fields">6.3. CHARMM, AMBER, and DREIDING force fields</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#running-multiple-simulations-from-one-input-script">6.4. Running multiple simulations from one input script</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#multi-replica-simulations">6.5. Multi-replica simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#granular-models">6.6. Granular models</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip3p-water-model">6.7. TIP3P water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip4p-water-model">6.8. TIP4P water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#spc-water-model">6.9. SPC water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#coupling-lammps-to-other-codes">6.10. Coupling LAMMPS to other codes</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#visualizing-lammps-snapshots">6.11. Visualizing LAMMPS snapshots</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#triclinic-non-orthogonal-simulation-boxes">6.12. Triclinic (non-orthogonal) simulation boxes</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#nemd-simulations">6.13. NEMD simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#finite-size-spherical-and-aspherical-particles">6.14. Finite-size spherical and aspherical particles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#output-from-lammps-thermo-dumps-computes-fixes-variables">6.15. Output from LAMMPS (thermo, dumps, computes, fixes, variables)</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#thermostatting-barostatting-and-computing-temperature">6.16. Thermostatting, barostatting, and computing temperature</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#walls">6.17. Walls</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#elastic-constants">6.18. Elastic constants</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#library-interface-to-lammps">6.19. Library interface to LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-thermal-conductivity">6.20. Calculating thermal conductivity</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-viscosity">6.21. Calculating viscosity</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-a-diffusion-coefficient">6.22. Calculating a diffusion coefficient</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#using-chunks-to-calculate-system-properties">6.23. Using chunks to calculate system properties</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#setting-parameters-for-the-kspace-style-pppm-disp-command">6.24. Setting parameters for the <code class="docutils literal"><span class="pre">kspace_style</span> <span class="pre">pppm/disp</span></code> command</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#polarizable-models">6.25. Polarizable models</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#adiabatic-core-shell-model">6.26. Adiabatic core/shell model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#drude-induced-dipoles">6.27. Drude induced dipoles</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#amber2lmp-tool">9.1. amber2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#binary2txt-tool">9.2. binary2txt tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ch2lmp-tool">9.3. ch2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#chain-tool">9.4. chain tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#colvars-tools">9.5. colvars tools</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#createatoms-tool">9.6. createatoms tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#data2xmovie-tool">9.7. data2xmovie tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-database-tool">9.8. eam database tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-generate-tool">9.9. eam generate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eff-tool">9.10. eff tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#emacs-tool">9.11. emacs tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#fep-tool">9.12. fep tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#i-pi-tool">9.13. i-pi tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ipp-tool">9.14. ipp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#kate-tool">9.15. kate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2arc-tool">9.16. lmp2arc tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2cfg-tool">9.17. lmp2cfg tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2vmd-tool">9.18. lmp2vmd tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#matlab-tool">9.19. matlab tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#micelle2d-tool">9.20. micelle2d tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#moltemplate-tool">9.21. moltemplate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#msi2lmp-tool">9.22. msi2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#phonon-tool">9.23. phonon tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#polymer-bonding-tool">9.24. polymer bonding tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#pymol-asphere-tool">9.25. pymol_asphere tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#python-tool">9.26. python tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#reax-tool">9.27. reax tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#restart2data-tool">9.28. restart2data tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#vim-tool">9.29. vim tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmgrace-tool">9.30. xmgrace tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmovie-tool">9.31. xmovie tool</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#atom-styles">10.1. Atom styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#bond-angle-dihedral-improper-potentials">10.2. Bond, angle, dihedral, improper potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#compute-styles">10.3. Compute styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-styles">10.4. Dump styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-custom-output-options">10.5. Dump custom output options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#fix-styles">10.6. Fix styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#input-script-commands">10.7. Input script commands</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#kspace-computations">10.8. Kspace computations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#minimization-styles">10.9. Minimization styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#pairwise-potentials">10.10. Pairwise potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#region-styles">10.11. Region styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#body-styles">10.12. Body styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#thermodynamic-output-options">10.13. Thermodynamic output options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#variable-options">10.14. Variable options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#submitting-new-features-for-inclusion-in-lammps">10.15. Submitting new features for inclusion in LAMMPS</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-running-lammps-from-python">11.1. Overview of running LAMMPS from Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-using-python-from-a-lammps-script">11.2. Overview of using Python from a LAMMPS script</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#building-lammps-as-a-shared-library">11.3. Building LAMMPS as a shared library</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#installing-the-python-wrapper-into-python">11.4. Installing the Python wrapper into Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#extending-python-with-mpi-to-run-in-parallel">11.5. Extending Python with MPI to run in parallel</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#testing-the-python-lammps-interface">11.6. Testing the Python-LAMMPS interface</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#using-lammps-from-python">11.7. Using LAMMPS from Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#example-python-scripts-that-use-lammps">11.8. Example Python scripts that use LAMMPS</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#common-problems">12.1. Common problems</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#reporting-bugs">12.2. Reporting bugs</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error-warning-messages">12.3. Error &amp; warning messages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error">12.4. Errors:</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#warnings">12.5. Warnings:</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_history.html#coming-attractions">13.1. Coming attractions</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_history.html#past-versions">13.2. Past versions</a></li>
</ul>
</li>
</ul>
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doc/Manual.html.html
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@ -3,7 +3,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="31 Oct 2015 version">
<META NAME="docnumber" CONTENT="6 Nov 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
<P><CENTER><H3>LAMMPS Documentation
</H3></CENTER>
<CENTER><H4>31 Oct 2015 version
<CENTER><H4>6 Nov 2015 version
</H4></CENTER>
<H4>Version info:
</H4>

10
doc/Manual.txt
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@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="6 Nov 2015 version">
<META NAME="docnumber" CONTENT="10 Aug 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
<H1></H1>
LAMMPS Documentation :c,h3
6 Nov 2015 version :c,h4
10 Aug 2015 version :c,h4
Version info: :h4
@ -85,7 +85,7 @@ it gives quick access to documentation for all LAMMPS commands.
.. toctree::
:maxdepth: 2
:numbered: // comment
:numbered:
Section_intro
Section_start
@ -105,8 +105,8 @@ it gives quick access to documentation for all LAMMPS commands.
Indices and tables
==================
* :ref:`genindex` // comment
* :ref:`search` // comment
* :ref:`genindex`
* :ref:`search`
END_RST -->

30
doc/Section_commands.html
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@ -839,9 +839,9 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
<col width="16%" />
<col width="19%" />
<col width="16%" />
<col width="15%" />
<col width="16%" />
<col width="16%" />
<col width="16%" />
<col width="17%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="compute_angle_local.html"><em>angle/local</em></a></td>
@ -884,45 +884,45 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
<td><a class="reference internal" href="compute_msd_chunk.html"><em>msd/chunk</em></a></td>
<td><a class="reference internal" href="compute_msd_nongauss.html"><em>msd/nongauss</em></a></td>
<td><a class="reference internal" href="compute_omega_chunk.html"><em>omega/chunk</em></a></td>
<td><a class="reference internal" href="compute_pair.html"><em>pair</em></a></td>
<td><a class="reference internal" href="compute_orientorder_atom.html"><em>orientorder/atom</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_pair_local.html"><em>pair/local</em></a></td>
<tr class="row-odd"><td><a class="reference internal" href="compute_pair.html"><em>pair</em></a></td>
<td><a class="reference internal" href="compute_pair_local.html"><em>pair/local</em></a></td>
<td><a class="reference internal" href="compute_pe.html"><em>pe (c)</em></a></td>
<td><a class="reference internal" href="compute_pe_atom.html"><em>pe/atom</em></a></td>
<td><a class="reference internal" href="compute_plasticity_atom.html"><em>plasticity/atom</em></a></td>
<td><a class="reference internal" href="compute_pressure.html"><em>pressure (c)</em></a></td>
<td><a class="reference internal" href="compute_property_atom.html"><em>property/atom</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_property_local.html"><em>property/local</em></a></td>
<tr class="row-even"><td><a class="reference internal" href="compute_property_atom.html"><em>property/atom</em></a></td>
<td><a class="reference internal" href="compute_property_local.html"><em>property/local</em></a></td>
<td><a class="reference internal" href="compute_property_chunk.html"><em>property/chunk</em></a></td>
<td><a class="reference internal" href="compute_rdf.html"><em>rdf</em></a></td>
<td><a class="reference internal" href="compute_reduce.html"><em>reduce</em></a></td>
<td><a class="reference internal" href="compute_reduce.html"><em>reduce/region</em></a></td>
<td><a class="reference internal" href="compute_slice.html"><em>slice</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_sna_atom.html"><em>sna/atom</em></a></td>
<tr class="row-odd"><td><a class="reference internal" href="compute_slice.html"><em>slice</em></a></td>
<td><a class="reference internal" href="compute_sna_atom.html"><em>sna/atom</em></a></td>
<td><a class="reference internal" href="compute_sna_atom.html"><em>snad/atom</em></a></td>
<td><a class="reference internal" href="compute_sna_atom.html"><em>snav/atom</em></a></td>
<td><a class="reference internal" href="compute_stress_atom.html"><em>stress/atom</em></a></td>
<td><a class="reference internal" href="compute_temp.html"><em>temp (ck)</em></a></td>
<td><a class="reference internal" href="compute_temp_asphere.html"><em>temp/asphere</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_temp_com.html"><em>temp/com</em></a></td>
<tr class="row-even"><td><a class="reference internal" href="compute_temp_asphere.html"><em>temp/asphere</em></a></td>
<td><a class="reference internal" href="compute_temp_com.html"><em>temp/com</em></a></td>
<td><a class="reference internal" href="compute_temp_chunk.html"><em>temp/chunk</em></a></td>
<td><a class="reference internal" href="compute_temp_deform.html"><em>temp/deform</em></a></td>
<td><a class="reference internal" href="compute_temp_partial.html"><em>temp/partial (c)</em></a></td>
<td><a class="reference internal" href="compute_temp_profile.html"><em>temp/profile</em></a></td>
<td><a class="reference internal" href="compute_temp_ramp.html"><em>temp/ramp</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_temp_region.html"><em>temp/region</em></a></td>
<tr class="row-odd"><td><a class="reference internal" href="compute_temp_ramp.html"><em>temp/ramp</em></a></td>
<td><a class="reference internal" href="compute_temp_region.html"><em>temp/region</em></a></td>
<td><a class="reference internal" href="compute_temp_sphere.html"><em>temp/sphere</em></a></td>
<td><a class="reference internal" href="compute_ti.html"><em>ti</em></a></td>
<td><a class="reference internal" href="compute_torque_chunk.html"><em>torque/chunk</em></a></td>
<td><a class="reference internal" href="compute_vacf.html"><em>vacf</em></a></td>
<td><a class="reference internal" href="compute_vcm_chunk.html"><em>vcm/chunk</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_voronoi_atom.html"><em>voronoi/atom</em></a></td>
<td>&nbsp;</td>
<tr class="row-even"><td><a class="reference internal" href="compute_vcm_chunk.html"><em>vcm/chunk</em></a></td>
<td><a class="reference internal" href="compute_voronoi_atom.html"><em>voronoi/atom</em></a></td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>

1
doc/Section_commands.txt
View File

@ -694,6 +694,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"msd/chunk"_compute_msd_chunk.html,
"msd/nongauss"_compute_msd_nongauss.html,
"omega/chunk"_compute_omega_chunk.html,
"orientorder/atom"_compute_orientorder_atom.html,
"pair"_compute_pair.html,
"pair/local"_compute_pair_local.html,
"pe (c)"_compute_pe.html,

10
doc/compute.html
View File

@ -268,20 +268,18 @@ calculations accessed in the various ways described above.</p>
<p>Each compute style has its own doc page which describes its arguments
and what it does. Here is an alphabetic list of compute styles
available in LAMMPS. They are also given in more compact form in the
compute section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
Compute section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
<p>There are also additional compute styles (not listed here) submitted
by users which are included in the LAMMPS distribution. The list of
these with links to the individual styles are given in the compute
section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
<p>There are also additional accelerated compute styles (note listed
here) included in the LAMMPS distribution for faster performance on
CPUs and GPUs. The list of these with links to the individual styles
are given in the compute section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
<ul class="simple">
<li><a class="reference internal" href="compute_bond_local.html"><em>angle/local</em></a> - theta and energy of each angle</li>
<li><a class="reference internal" href="compute_angmom_chunk.html"><em>angmom/chunk</em></a> - angular momentum for each chunk</li>
<li><a class="reference internal" href="compute_body_local.html"><em>body/local</em></a> - attributes of body sub-particles</li>
<li><a class="reference internal" href="compute_bond_local.html"><em>bond/local</em></a> - distance and energy of each bond</li>
<li><a class="reference internal" href="compute_centro_atom.html"><em>centro/atom</em></a> - centro-symmetry parameter for each atom</li>
<li><a class="reference internal" href="compute_chunk_atom.html"><em>chunk/atom</em></a> - assign chunk IDs to each atom</li>
<li><a class="reference internal" href="compute_cluster_atom.html"><em>cluster/atom</em></a> - cluster ID for each atom</li>
<li><a class="reference internal" href="compute_cna_atom.html"><em>cna/atom</em></a> - common neighbor analysis (CNA) for each atom</li>
<li><a class="reference internal" href="compute_com.html"><em>com</em></a> - center-of-mass of group of atoms</li>
@ -310,6 +308,8 @@ are given in the compute section of <a class="reference internal" href="Section_
<li><a class="reference internal" href="compute_msd.html"><em>msd</em></a> - mean-squared displacement of group of atoms</li>
<li><a class="reference internal" href="compute_msd_chunk.html"><em>msd/chunk</em></a> - mean-squared displacement for each chunk</li>
<li><a class="reference internal" href="compute_msd_nongauss.html"><em>msd/nongauss</em></a> - MSD and non-Gaussian parameter of group of atoms</li>
<li><a class="reference internal" href="compute_omega_chunk.html"><em>omega/chunk</em></a> - angular velocity for each chunk</li>
<li><a class="reference internal" href="compute_orientorder_atom.html"><em>orientorder/atom</em></a> - Steinhardt bond orientational order parameters Ql</li>
<li><a class="reference internal" href="compute_pair.html"><em>pair</em></a> - values computed by a pair style</li>
<li><a class="reference internal" href="compute_pair_local.html"><em>pair/local</em></a> - distance/energy/force of each pairwise interaction</li>
<li><a class="reference internal" href="compute_pe.html"><em>pe</em></a> - potential energy</li>

12
doc/compute.txt
View File

@ -161,23 +161,19 @@ calculations accessed in the various ways described above.
Each compute style has its own doc page which describes its arguments
and what it does. Here is an alphabetic list of compute styles
available in LAMMPS. They are also given in more compact form in the
compute section of "this page"_Section_commands.html#cmd_5.
Compute section of "this page"_Section_commands.html#cmd_5.
There are also additional compute styles (not listed here) submitted
by users which are included in the LAMMPS distribution. The list of
these with links to the individual styles are given in the compute
section of "this page"_Section_commands.html#cmd_5.
There are also additional accelerated compute styles (note listed
here) included in the LAMMPS distribution for faster performance on
CPUs and GPUs. The list of these with links to the individual styles
are given in the compute section of "this
page"_Section_commands.html#cmd_5.
"angle/local"_compute_bond_local.html - theta and energy of each angle
"angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk
"body/local"_compute_body_local.html - attributes of body sub-particles
"bond/local"_compute_bond_local.html - distance and energy of each bond
"centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom
"chunk/atom"_compute_chunk_atom.html - assign chunk IDs to each atom
"cluster/atom"_compute_cluster_atom.html - cluster ID for each atom
"cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom
"com"_compute_com.html - center-of-mass of group of atoms
@ -206,6 +202,8 @@ page"_Section_commands.html#cmd_5.
"msd"_compute_msd.html - mean-squared displacement of group of atoms
"msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk
"msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms
"omega/chunk"_compute_omega_chunk.html - angular velocity for each chunk
"orientorder/atom"_compute_orientorder_atom.html - Steinhardt bond orientational order parameters Ql
"pair"_compute_pair.html - values computed by a pair style
"pair/local"_compute_pair_local.html - distance/energy/force of each pairwise interaction
"pe"_compute_pe.html - potential energy

18
doc/compute_cluster_atom.html
View File

@ -158,6 +158,24 @@ 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 or to have multiple compute/dump commands, each of a
<em>clsuter/atom</em> style.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If you have a bonded system, then the settings of
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a>
command, and means those pairwise interactions do not appear in the
neighbor list. Because this fix uses the neighbor list, it also means
those pairs will not be included when computing the clusters. This
does not apply when using long-range coulomb (<em>coul/long</em>, <em>coul/msm</em>,
<em>coul/wolf</em> or similar. One way to get around this would be to set
special_bond scaling factors to very tiny numbers that are not exactly
zero (e.g. 1.0e-50). Another workaround is to write a dump file, and
use the <a class="reference internal" href="rerun.html"><em>rerun</em></a> command to compute the clusters for
snapshots in the dump file. The rerun script can use a
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command that includes all pairs in
the neighbor list.</p>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See

16
doc/compute_cluster_atom.txt
View File

@ -39,6 +39,22 @@ is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each of a
{clsuter/atom} style.
IMPORTANT NOTE: If you have a bonded system, then the settings of
"special_bonds"_special_bonds.html command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the "special_bonds"_special_bonds.html
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 when computing the clusters. This
does not apply when using long-range coulomb ({coul/long}, {coul/msm},
{coul/wolf} or similar. One way to get around this would be to set
special_bond scaling factors to very tiny numbers that are not exactly
zero (e.g. 1.0e-50). Another workaround is to write a dump file, and
use the "rerun"_rerun.html command to compute the clusters for
snapshots in the dump file. The rerun script can use a
"special_bonds"_special_bonds.html command that includes all pairs in
the neighbor list.
[Output info:]
This compute calculates a per-atom vector, which can be accessed by

383
doc/compute_hexorder_atom.html
View File

@ -1,125 +1,296 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<H3>compute hexorder/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID hexorder/atom keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>hexorder/atom = style name of this compute command
<LI>one or more keyword/value pairs may be appended
<PRE>keyword = <I>degree</I> or <I>nnn</I> or <I>cutoff</I>
<I>cutoff</I> value = distance cutoff
<I>nnn</I> value = number of nearest neighbors
<I>degree</I> value = degree <I>n</I> of order parameter
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all hexorder/atom
compute 1 all hexorder/atom degree 4 nnn 4 cutoff 1.2
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates <I>qn</I> the bond-orientational
order parameter for each atom in a group. The hexatic (<I>n</I> = 6) order
parameter was introduced by <A HREF = "#Nelson">Nelson and Halperin</A> as a way to detect
hexagonal symmetry in two-dimensional systems. For each atom, <I>qn</I>
is a complex number (stored as two real numbers) defined as follows:
</P>
<CENTER><IMG SRC = "Eqs/hexorder.jpg">
</CENTER>
<P>where the sum is over the <I>nnn</I> nearest neighbors
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<div class="section" id="compute-hexorder-atom-command">
<span id="index-0"></span><h1>compute hexorder/atom command<a class="headerlink" href="#compute-hexorder-atom-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID hexorder/atom keyword values ...
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>hexorder/atom = style name of this compute command</li>
<li>one or more keyword/value pairs may be appended</li>
</ul>
<pre class="literal-block">
keyword = <em>degree</em> or <em>nnn</em> or <em>cutoff</em>
<em>cutoff</em> value = distance cutoff
<em>nnn</em> value = number of nearest neighbors
<em>degree</em> value = degree <em>n</em> of order parameter
</pre>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all hexorder/atom
compute 1 all hexorder/atom degree 4 nnn 4 cutoff 1.2
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that calculates <em>qn</em> the bond-orientational
order parameter for each atom in a group. The hexatic (<em>n</em> = 6) order
parameter was introduced by <a class="reference internal" href="#nelson"><span>Nelson and Halperin</span></a> as a way to detect
hexagonal symmetry in two-dimensional systems. For each atom, <em>qn</em>
is a complex number (stored as two real numbers) defined as follows:</p>
<img alt="_images/hexorder.jpg" class="align-center" src="_images/hexorder.jpg" />
<p>where the sum is over the <em>nnn</em> nearest neighbors
of the central atom. The angle theta
is formed by the bond vector rij and the <I>x</I> axis. theta is calculated
only using the <I>x</I> and <I>y</I> components, whereas the distance from the
central atom is calculated using all three
<I>x</I>, <I>y</I>, and <I>z</I> components of the bond vector.
Neighbor atoms not in the group
are included in the order parameter of atoms in the group.
</P>
<P>The optional keyword <I>cutoff</I> defines the distance cutoff
is formed by the bond vector rij and the <em>x</em> axis. theta is calculated
only using the <em>x</em> and <em>y</em> components, whereas the distance from the
central atom is calculated using all three
<em>x</em>, <em>y</em>, and <em>z</em> components of the bond vector.
Neighbor atoms not in the group
are included in the order parameter of atoms in the group.</p>
<p>The optional keyword <em>cutoff</em> defines the distance cutoff
used when searching for neighbors. The default value, also
the maximum allowable value, is the cutoff specified
by the pair style.
</P>
<P>The optional keyword <I>nnn</I> defines the number of nearest
neighbors used to calculate <I>qn</I>. The default value is 6.
If the value is NULL, then all neighbors up to the
distance cutoff are used.
</P>
<P>The optional keyword <I>degree</I> sets the degree <I>n</I> of the order parameter.
The default value is 6. For a perfect hexagonal lattice with
<I>nnn</I> = 6,
<I>q</I>6 = exp(6 i phi) for all atoms, where the constant 0 < phi < pi/3
depends only on the orientation of the lattice relative to the <I>x</I> axis.
In an isotropic liquid, local neighborhoods may still exhibit
by the pair style.</p>
<p>The optional keyword <em>nnn</em> defines the number of nearest
neighbors used to calculate <em>qn</em>. The default value is 6.
If the value is NULL, then all neighbors up to the
distance cutoff are used.</p>
<p>The optional keyword <em>degree</em> sets the degree <em>n</em> of the order parameter.
The default value is 6. For a perfect hexagonal lattice with
<em>nnn</em> = 6,
<em>q*6 = exp(6 i phi) for all atoms, where the constant 0 &lt; phi &lt; pi/3
depends only on the orientation of the lattice relative to the *x</em> axis.
In an isotropic liquid, local neighborhoods may still exhibit
weak hexagonal symmetry, but because the orientational correlation
decays quickly with distance, the value of phi will be different for
different atoms, and so when <I>q</I>6 is averaged over all the atoms
in the system, |<<I>q</I>6>| << 1.
</P>
<P>The value of <I>qn</I> is set to zero for atoms not in the
specified compute group, as well as for atoms that have less than
<I>nnn</I> neighbors within the distance cutoff.
</P>
<P>The neighbor list needed to compute this quantity is constructed each
different atoms, and so when <a href="#id1"><span class="problematic" id="id2">*</span></a>q*6 is averaged over all the atoms
in the system, <a href="#id3"><span class="problematic" id="id4">|&lt;*q*6&gt;|</span></a> &lt;&lt; 1.</p>
<p>The value of <em>qn</em> is set to zero for atoms not in the
specified compute group, as well as for atoms that have less than
<em>nnn</em> neighbors within the distance cutoff.</p>
<p>The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently.
</P>
<P>IMPORTANT NOTE: If you have a bonded system, then the settings of
<A HREF = "special_bonds.html">special_bonds</A> command can remove pairwise
too frequently.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If you have a bonded system, then the settings of
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the <A HREF = "special_bonds.html">special_bonds</A>
is the default setting for the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a>
command, and means those pairwise interactions do not appear in the
neighbor list. Because this fix uses the neighbor list, it also means
those pairs will not be included in the order parameter. This difficulty
can be circumvented by writing a dump file, and using the
<A HREF = "rerun.html">rerun</A> command to compute the order parameter for snapshots
<a class="reference internal" href="rerun.html"><em>rerun</em></a> command to compute the order parameter for snapshots
in the dump file. The rerun script can use a
<A HREF = "special_bonds.html">special_bonds</A> command that includes all pairs in
the neighbor list.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-atom array with 2 columns, giving the
real and imaginary parts <I>qn</I>, a complex number restricted to the
unit disk of the complex plane i.e. Re(<I>qn</I>)^2 + Im(<I>qn</I>)^2 <= 1 .
</P>
<P>These values can be accessed by any command that uses
per-atom values from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
15</A> for an overview of LAMMPS output
options.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_orientorder_atom.html">compute orientorder/atom</A>, <A HREF = "compute_coord_atom.html">compute coord/atom</A>, <A HREF = "compute_centro_atom.html">compute centro/atom</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are <I>cutoff</I> = pair style cutoff, <I>nnn</I> = 6, <I>degree</I> = 6
</P>
<HR>
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command that includes all pairs in
the neighbor list.</p>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-atom array with 2 columns, giving the
real and imaginary parts <em>qn</em>, a complex number restricted to the
unit disk of the complex plane i.e. Re(<em>qn</em>)^2 + Im(<em>qn</em>)^2 &lt;= 1 .</p>
<p>These values can be accessed by any command that uses
per-atom values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of LAMMPS output
options.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="compute_orientorder_atom.html"><em>compute orientorder/atom</em></a>, <a class="reference internal" href="compute_coord_atom.html"><em>compute coord/atom</em></a>, <a class="reference internal" href="compute_centro_atom.html"><em>compute centro/atom</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The option defaults are <em>cutoff</em> = pair style cutoff, <em>nnn</em> = 6, <em>degree</em> = 6</p>
<hr class="docutils" />
<p id="nelson"><strong>(Nelson)</strong> Nelson, Halperin, Phys Rev B, 19, 2457 (1979).</p>
</div>
</div>
<A NAME = "Nelson"></A>
<P><B>(Nelson)</B> Nelson, Halperin, Phys Rev B, 19, 2457 (1979).
</P>
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<div class="section" id="compute-orientorder-atom-command">
<span id="index-0"></span><h1>compute orientorder/atom command<a class="headerlink" href="#compute-orientorder-atom-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID orientorder/atom keyword values ...
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>orientorder/atom = style name of this compute command</li>
<li>one or more keyword/value pairs may be appended</li>
</ul>
<pre class="literal-block">
keyword = <em>cutoff</em> or <em>nnn</em> or <em>ql</em>
<em>cutoff</em> value = distance cutoff
<em>nnn</em> value = number of nearest neighbors
<em>degrees</em> values = nlvalues, l1, l2,...
</pre>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all orientorder/atom
compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that calculates a set of bond-orientational
order parameters <em>Ql</em> for each atom in a group. These order parameters
were introduced by <a class="reference internal" href="#steinhardt"><span>Steinhardt et al.</span></a> as a way to
characterize the local orientational order in atomic structures.
For each atom, <em>Ql</em> is a real number defined as follows:</p>
<img alt="_images/orientorder.jpg" class="align-center" src="_images/orientorder.jpg" />
<p>The first equation defines the spherical harmonic order parameters.
These are complex number components of the 3D analog of the 2D order
parameter <em>qn</em>, which is implemented as LAMMPS compute
<a class="reference internal" href="compute_hexorder_atom.html"><em>hexorder/atom</em></a>.
The summation is over the <em>nnn</em> nearest
neighbors of the central atom.
The angles theta and phi are the standard spherical polar angles
defining the direction of the bond vector <em>rij</em>.
The second equation defines <em>Ql</em>, which is a
rotationally invariant scalar quantity obtained by summing
over all the components of degree <em>l</em>.</p>
<p>The optional keyword <em>cutoff</em> defines the distance cutoff
used when searching for neighbors. The default value, also
the maximum allowable value, is the cutoff specified
by the pair style.</p>
<p>The optional keyword <em>nnn</em> defines the number of nearest
neighbors used to calculate <em>Ql</em>. The default value is 12.
If the value is NULL, then all neighbors up to the
specified distance cutoff are used.</p>
<p>The optional keyword <em>degrees</em> defines the list of order parameters to
be computed. The first argument <em>nlvalues</em> is the number of order
parameters. This is followed by that number of integers giving the
degree of each order parameter. Because <a href="#id1"><span class="problematic" id="id2">*</span></a>Q*2 and all odd-degree
order parameters are zero for atoms in cubic crystals
(see <a class="reference internal" href="#steinhardt"><span>Steinhardt</span></a>), the default order parameters
are <a href="#id3"><span class="problematic" id="id4">*</span></a>Q*4, <a href="#id5"><span class="problematic" id="id6">*</span></a>Q*6, <a href="#id7"><span class="problematic" id="id8">*</span></a>Q*8, <a href="#id9"><span class="problematic" id="id10">*</span></a>Q*10, and <a href="#id11"><span class="problematic" id="id12">*</span></a>Q*12. The correct
numerical values for commonly encountered high-symmetry
structures are given by <a class="reference internal" href="#mickel"><span>Mickel et al.</span></a></p>
<p>The value of <em>Ql</em> is set to zero for atoms not in the
specified compute group, as well as for atoms that have less than
<em>nnn</em> neighbors within the distance cutoff.</p>
<p>The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If you have a bonded system, then the settings of
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a>
command, and means those pairwise interactions do not appear in the
neighbor list. Because this fix uses the neighbor list, it also means
those pairs will not be included in the order parameter. This difficulty
can be circumvented by writing a dump file, and using the
<a class="reference internal" href="rerun.html"><em>rerun</em></a> command to compute the order parameter for snapshots
in the dump file. The rerun script can use a
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command that includes all pairs in
the neighbor list.</p>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-atom array with <em>nlvalues</em> columns, giving the
<em>Ql</em> values for each atom, which are real numbers on the range 0 &lt;= <em>Ql</em> &lt;= 1.</p>
<p>These values can be accessed by any command that uses
per-atom values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of LAMMPS output
options.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="compute_coord_atom.html"><em>compute coord/atom</em></a>, <a class="reference internal" href="compute_centro_atom.html"><em>compute centro/atom</em></a>, <a class="reference internal" href="compute_hexorder_atom.html"><em>compute hexorder/atom</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The option defaults are <em>cutoff</em> = pair style cutoff, <em>nnn</em> = 12, <em>degrees</em> = 5 4 6 8 9 10 12 i.e. <a href="#id13"><span class="problematic" id="id14">*</span></a>Q*4, <a href="#id15"><span class="problematic" id="id16">*</span></a>Q*6, <a href="#id17"><span class="problematic" id="id18">*</span></a>Q*8, <a href="#id19"><span class="problematic" id="id20">*</span></a>Q*10, and <a href="#id21"><span class="problematic" id="id22">*</span></a>Q*12.</p>
<hr class="docutils" />
<p id="mickel"><span id="steinhardt"></span><strong>(Steinhardt)</strong> P. Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983).</p>
<p><strong>(Mickel)</strong> W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, J. Chem. Phys. 138, 044501 (2013).</p>
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6
doc/fix.html
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@ -267,15 +267,11 @@ for further info.</p>
<p>Each fix style has its own documentation page which describes its
arguments and what it does, as listed below. Here is an alphabetic
list of fix styles available in LAMMPS. They are also given in more
compact form in the fix section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
compact form in the Fix section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
<p>There are also additional fix styles (not listed here) submitted by
users which are included in the LAMMPS distribution. The list of
these with links to the individual styles are given in the fix section
of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
<p>There are also additional accelerated fix styles (not listed here)
included in the LAMMPS distribution for faster performance on CPUs and
GPUs. The list of these with links to the individual styles are given
in the fix section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
<ul class="simple">
<li><a class="reference internal" href="fix_adapt.html"><em>adapt</em></a> - change a simulation parameter over time</li>
<li><a class="reference internal" href="fix_addforce.html"><em>addforce</em></a> - add a force to each atom</li>

7
doc/fix.txt
View File

@ -154,7 +154,7 @@ for further info.
Each fix style has its own documentation page which describes its
arguments and what it does, as listed below. Here is an alphabetic
list of fix styles available in LAMMPS. They are also given in more
compact form in the fix section of "this
compact form in the Fix section of "this
page"_Section_commands.html#cmd_5.
There are also additional fix styles (not listed here) submitted by
@ -162,11 +162,6 @@ users which are included in the LAMMPS distribution. The list of
these with links to the individual styles are given in the fix section
of "this page"_Section_commands.html#cmd_5.
There are also additional accelerated fix styles (not listed here)
included in the LAMMPS distribution for faster performance on CPUs and
GPUs. The list of these with links to the individual styles are given
in the fix section of "this page"_Section_commands.html#cmd_5.
"adapt"_fix_adapt.html - change a simulation parameter over time
"addforce"_fix_addforce.html - add a force to each atom
"append/atoms"_fix_append_atoms.html - append atoms to a running simulation

8
doc/genindex.html
View File

@ -520,6 +520,10 @@
</dt>
<dt><a href="compute_orientorder_atom.html#index-0">compute orientorder/atom</a>
</dt>
<dt><a href="compute_pair.html#index-0">compute pair</a>
</dt>
@ -539,12 +543,12 @@
<dt><a href="compute_plasticity_atom.html#index-0">compute plasticity/atom</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="compute_pressure.html#index-0">compute pressure</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="compute_property_atom.html#index-0">compute property/atom</a>
</dt>

2
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