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

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@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="4 Sep 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
4 Sep 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 -->

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@ -1001,7 +1001,7 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
<col width="24%" />
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<col width="24%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="pair_none.html"><em>none</em></a></td>
@ -1081,63 +1081,68 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/dsf (gko)</em></a></td>
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/long (cgikot)</em></a></td>
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/long/cs</em></a></td>
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/msm (go)</em></a></td>
<td><a class="reference internal" href="pair_dipole.html"><em>lj/cut/dipole/cut (go)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_dipole.html"><em>lj/cut/dipole/long</em></a></td>
<tr class="row-odd"><td><a class="reference internal" href="pair_dipole.html"><em>lj/cut/dipole/cut (go)</em></a></td>
<td><a class="reference internal" href="pair_dipole.html"><em>lj/cut/dipole/long</em></a></td>
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/tip4p/cut (o)</em></a></td>
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/tip4p/long (ot)</em></a></td>
<td><a class="reference internal" href="pair_lj_expand.html"><em>lj/expand (cgko)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_gromacs.html"><em>lj/gromacs (cgko)</em></a></td>
<tr class="row-even"><td><a class="reference internal" href="pair_lj_expand.html"><em>lj/expand (cgko)</em></a></td>
<td><a class="reference internal" href="pair_gromacs.html"><em>lj/gromacs (cgko)</em></a></td>
<td><a class="reference internal" href="pair_gromacs.html"><em>lj/gromacs/coul/gromacs (cko)</em></a></td>
<td><a class="reference internal" href="pair_lj_long.html"><em>lj/long/coul/long (o)</em></a></td>
<td><a class="reference internal" href="pair_dipole.html"><em>lj/long/dipole/long</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_lj_long.html"><em>lj/long/tip4p/long</em></a></td>
<tr class="row-odd"><td><a class="reference internal" href="pair_dipole.html"><em>lj/long/dipole/long</em></a></td>
<td><a class="reference internal" href="pair_lj_long.html"><em>lj/long/tip4p/long</em></a></td>
<td><a class="reference internal" href="pair_lj_smooth.html"><em>lj/smooth (co)</em></a></td>
<td><a class="reference internal" href="pair_lj_smooth_linear.html"><em>lj/smooth/linear (o)</em></a></td>
<td><a class="reference internal" href="pair_lj96.html"><em>lj96/cut (cgo)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_lubricate.html"><em>lubricate (o)</em></a></td>
<tr class="row-even"><td><a class="reference internal" href="pair_lj96.html"><em>lj96/cut (cgo)</em></a></td>
<td><a class="reference internal" href="pair_lubricate.html"><em>lubricate (o)</em></a></td>
<td><a class="reference internal" href="pair_lubricate.html"><em>lubricate/poly (o)</em></a></td>
<td><a class="reference internal" href="pair_lubricateU.html"><em>lubricateU</em></a></td>
<td><a class="reference internal" href="pair_lubricateU.html"><em>lubricateU/poly</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_meam.html"><em>meam (o)</em></a></td>
<tr class="row-odd"><td><a class="reference internal" href="pair_lubricateU.html"><em>lubricateU/poly</em></a></td>
<td><a class="reference internal" href="pair_meam.html"><em>meam (o)</em></a></td>
<td><a class="reference internal" href="pair_mie.html"><em>mie/cut (o)</em></a></td>
<td><a class="reference internal" href="pair_morse.html"><em>morse (cgot)</em></a></td>
<td><a class="reference internal" href="pair_nb3b_harmonic.html"><em>nb3b/harmonic (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_nm.html"><em>nm/cut (o)</em></a></td>
<tr class="row-even"><td><a class="reference internal" href="pair_nb3b_harmonic.html"><em>nb3b/harmonic (o)</em></a></td>
<td><a class="reference internal" href="pair_nm.html"><em>nm/cut (o)</em></a></td>
<td><a class="reference internal" href="pair_nm.html"><em>nm/cut/coul/cut (o)</em></a></td>
<td><a class="reference internal" href="pair_nm.html"><em>nm/cut/coul/long (o)</em></a></td>
<td><a class="reference internal" href="pair_peri.html"><em>peri/eps</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_peri.html"><em>peri/lps (o)</em></a></td>
<tr class="row-odd"><td><a class="reference internal" href="pair_peri.html"><em>peri/eps</em></a></td>
<td><a class="reference internal" href="pair_peri.html"><em>peri/lps (o)</em></a></td>
<td><a class="reference internal" href="pair_peri.html"><em>peri/pmb (o)</em></a></td>
<td><a class="reference internal" href="pair_peri.html"><em>peri/ves</em></a></td>
<td><a class="reference internal" href="pair_polymorphic.html"><em>polymorphic</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_reax.html"><em>reax</em></a></td>
<tr class="row-even"><td><a class="reference internal" href="pair_polymorphic.html"><em>polymorphic</em></a></td>
<td><a class="reference internal" href="pair_reax.html"><em>reax</em></a></td>
<td><a class="reference internal" href="pair_airebo.html"><em>rebo (o)</em></a></td>
<td><a class="reference internal" href="pair_resquared.html"><em>resquared (go)</em></a></td>
<td><a class="reference internal" href="pair_snap.html"><em>snap</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_soft.html"><em>soft (go)</em></a></td>
<tr class="row-odd"><td><a class="reference internal" href="pair_snap.html"><em>snap</em></a></td>
<td><a class="reference internal" href="pair_soft.html"><em>soft (go)</em></a></td>
<td><a class="reference internal" href="pair_sw.html"><em>sw (cgkio)</em></a></td>
<td><a class="reference internal" href="pair_table.html"><em>table (gko)</em></a></td>
<td><a class="reference internal" href="pair_tersoff.html"><em>tersoff (cgko)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_tersoff_mod.html"><em>tersoff/mod (ko)</em></a></td>
<tr class="row-even"><td><a class="reference internal" href="pair_tersoff.html"><em>tersoff (cgko)</em></a></td>
<td><a class="reference internal" href="pair_tersoff_mod.html"><em>tersoff/mod (ko)</em></a></td>
<td><a class="reference internal" href="pair_tersoff_zbl.html"><em>tersoff/zbl (ko)</em></a></td>
<td><a class="reference internal" href="pair_coul.html"><em>tip4p/cut (o)</em></a></td>
<td><a class="reference internal" href="pair_coul.html"><em>tip4p/long (o)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_tri_lj.html"><em>tri/lj (o)</em></a></td>
<tr class="row-odd"><td><a class="reference internal" href="pair_coul.html"><em>tip4p/long (o)</em></a></td>
<td><a class="reference internal" href="pair_tri_lj.html"><em>tri/lj (o)</em></a></td>
<td><a class="reference internal" href="pair_yukawa.html"><em>yukawa (go)</em></a></td>
<td><a class="reference internal" href="pair_yukawa_colloid.html"><em>yukawa/colloid (go)</em></a></td>
<td><a class="reference internal" href="pair_zbl.html"><em>zbl (go)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_zbl.html"><em>zbl (go)</em></a></td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
</tr>
</tbody>
</table>

1
doc/Section_commands.txt
View File

@ -843,6 +843,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"lj/cut/coul/debye (cgko)"_pair_lj.html,
"lj/cut/coul/dsf (gko)"_pair_lj.html,
"lj/cut/coul/long (cgikot)"_pair_lj.html,
"lj/cut/coul/long/cs"_pair_lj.html,
"lj/cut/coul/msm (go)"_pair_lj.html,
"lj/cut/dipole/cut (go)"_pair_dipole.html,
"lj/cut/dipole/long"_pair_dipole.html,

60
doc/Section_howto.html
View File

@ -598,7 +598,7 @@ atoms and the water molecule to run a rigid TIP3P-CHARMM model with a
cutoff. The K values can be used if a flexible TIP3P model (without
fix shake) is desired. If the LJ epsilon and sigma for HH and OH are
set to 0.0, it corresponds to the original 1983 TIP3P model
<a class="reference internal" href="#jorgensen"><span>(Jorgensen)</span></a>.</p>
<a class="reference internal" href="pair_lj.html#jorgensen"><span>(Jorgensen)</span></a>.</p>
<div class="line-block">
<div class="line">O mass = 15.9994</div>
<div class="line">H mass = 1.008</div>
@ -656,7 +656,7 @@ for a cutoff model:</p>
using the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command.</p>
<p>These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid TIP4P model with a cutoff
<a class="reference internal" href="#jorgensen"><span>(Jorgensen)</span></a>. Note that the OM distance is specified in
<a class="reference internal" href="pair_lj.html#jorgensen"><span>(Jorgensen)</span></a>. Note that the OM distance is specified in
the <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> command, not as part of the pair
coefficients.</p>
<div class="line-block">
@ -1963,10 +1963,10 @@ and free all its memory.</p>
<p>The lammps_version() function can be used to determined the specific
version of the underlying LAMMPS code. This is particularly useful
when loading LAMMPS as a shared library via dlopen(). The code using
the library interface can than use this information to adapt to changes
to the LAMMPS command syntax between versions. The returned LAMMPS
version code is an integer (e.g. 2 Sep 2015 results in 20150902) that
is growing with every new LAMMPS version.</p>
the library interface can than use this information to adapt to
changes to the LAMMPS command syntax between versions. The returned
LAMMPS version code is an integer (e.g. 2 Sep 2015 results in
20150902) that grows with every new LAMMPS version.</p>
<p>The lammps_file() and lammps_command() functions are used to pass a
file or string to LAMMPS as if it were an input script or single
command in an input script. Thus the calling code can read or
@ -2541,7 +2541,7 @@ well.</p>
</div>
<div class="section" id="adiabatic-core-shell-model">
<span id="howto-26"></span><h2>6.26. Adiabatic core/shell model<a class="headerlink" href="#adiabatic-core-shell-model" title="Permalink to this headline"></a></h2>
<p>The adiabatic core-shell model by <a class="reference internal" href="#mitchellfinchham"><span>Mitchell and Finchham</span></a> is a simple method for adding
<p>The adiabatic core-shell model by <a class="reference internal" href="compute_temp_cs.html#mitchellfinchham"><span>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
split into a core and a shell where the latter is meant to react to
@ -2606,10 +2606,16 @@ specified between cores.</p>
turn-off the Coulombic interaction within core/shell pairs, since that
interaction is set by the bond spring. This is done using the
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command with a 1-2 weight = 0.0,
which is the default value.</p>
which is the default value. It needs to be considered whether one has
to adjust the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> weighting according
to the molecular topology since the interactions of the shells are
bypassed over an extra bond.</p>
<p>Note that this core/shell implementation does not require all ions to
be polarized. One can mix core/shell pairs and ions without a
satellite particle if desired.</p>
<p>Since the core/shell model permits distances of r = 0.0 between the
core and shell, a pair style with a &#8220;cs&#8221; suffix needs to be used to
implement a valid long-range Coulombic correction. Several such pair
implement a valid long-rangeCoulombic correction. Several such pair
styles are provided in the CORESHELL package. See <a class="reference internal" href="pair_cs.html"><em>this doc page</em></a> for details. All of the core/shell enabled pair
styles require the use of a long-range Coulombic solver, as specified
by the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command. Either the PPPM or
@ -2638,14 +2644,20 @@ core/shell pair, which is an imaginary degree of freedom, from the
real physical system. To do that, the <a class="reference internal" href="compute_temp_cs.html"><em>compute temp/cs</em></a> command can be used, in conjunction with
any of the thermostat fixes, such as <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a> or <a class="reference external" href="fix_langevin">fix langevin</a>. This compute uses the center-of-mass velocity
of the core/shell pairs to calculate a temperature, and insures that
velocity is what is rescaled for thermostatting purposes. The
velocity is what is rescaled for thermostatting purposes. This
compute also works for a system with both core/shell pairs and
non-polarized ions (ions without an attached satellite particle). The
<a class="reference internal" href="compute_temp_cs.html"><em>compute temp/cs</em></a> command requires input of two
groups, one for the core atoms, another for the shell atoms. These
can be defined using the <a class="reference internal" href="group.html"><em>group *type*</em></a> command. Note that
to perform thermostatting using this definition of temperature, the
<a class="reference internal" href="fix_modify.html"><em>fix modify temp</em></a> command should be used to assign the
comptue to the thermostat fix. Likewise the <a class="reference internal" href="thermo_modify.html"><em>thermo_modify temp</em></a> command can be used to make this temperature
be output for the overall system.</p>
groups, one for the core atoms, another for the shell atoms.
Non-polarized ions which might also be included in the treated system
should not be included into either of these groups, they are taken
into account by the <em>group-ID</em> (2nd argument) of the compute. The
groups can be defined using the <a class="reference internal" href="group.html"><em>group *type*</em></a> command.
Note that to perform thermostatting using this definition of
temperature, the <a class="reference internal" href="fix_modify.html"><em>fix modify temp</em></a> command should be
used to assign the comptue to the thermostat fix. Likewise the
<a class="reference internal" href="thermo_modify.html"><em>thermo_modify temp</em></a> command can be used to make
this temperature be output for the overall system.</p>
<p>For the NaCl example, this can be done as follows:</p>
<div class="highlight-python"><div class="highlight"><pre>group cores type 1 2
group shells type 3 4
@ -2679,18 +2691,18 @@ imaginary degrees of freedom. However, this transfer will typically
lead to a a small drift in total energy over time. This internal
energy can be monitored using the <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> and <a class="reference internal" href="compute_temp_chunk.html"><em>compute temp/chunk</em></a> commands. The internal kinetic
energies of each core/shell pair can then be summed using the sum()
special functino of the <a class="reference internal" href="variable.html"><em>variable</em></a> command. Or they can
special function of the <a class="reference internal" href="variable.html"><em>variable</em></a> command. Or they can
be time/averaged and output using the <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a>
command. To use these commands, each core/shell pair must be defined
as a &#8220;chunk&#8221;. If each core/shell pair is defined as its own molecule,
the molecule ID can be used to define the chunks. If cores are bonded
to each other to form larger molecules, then another way to define the
chunks is to use the <a class="reference internal" href="fix_property_atom.html"><em>fix property/atom</em></a> to
assign a core/shell ID to each atom via a special field in the data
file read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command. This field can
then be accessed by the <a class="reference internal" href="compute_property_atom.html"><em>compute property/atom</em></a> command, to use as input to
the <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command to define the
core/shell pairs as chunks.</p>
to each other to form larger molecules, the chunks can be identified
by the <a class="reference internal" href="fix_property_atom.html"><em>fix property/atom</em></a> via assigning a
core/shell ID to each atom using a special field in the data file read
by the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command. This field can then be
accessed by the <a class="reference internal" href="compute_property_atom.html"><em>compute property/atom</em></a>
command, to use as input to the <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command to define the core/shell
pairs as chunks.</p>
<p>For example,</p>
<div class="highlight-python"><div class="highlight"><pre>fix csinfo all property/atom i_CSID # property/atom command
read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file

58
doc/Section_howto.txt
View File

@ -1884,10 +1884,10 @@ and free all its memory.
The lammps_version() function can be used to determined the specific
version of the underlying LAMMPS code. This is particularly useful
when loading LAMMPS as a shared library via dlopen(). The code using
the library interface can than use this information to adapt to changes
to the LAMMPS command syntax between versions. The returned LAMMPS
version code is an integer (e.g. 2 Sep 2015 results in 20150902) that
is growing with every new LAMMPS version.
the library interface can than use this information to adapt to
changes to the LAMMPS command syntax between versions. The returned
LAMMPS version code is an integer (e.g. 2 Sep 2015 results in
20150902) that grows with every new LAMMPS version.
The lammps_file() and lammps_command() functions are used to pass a
file or string to LAMMPS as if it were an input script or single
@ -2549,11 +2549,18 @@ The "special_bonds"_special_bonds.html command should be used to
turn-off the Coulombic interaction within core/shell pairs, since that
interaction is set by the bond spring. This is done using the
"special_bonds"_special_bonds.html command with a 1-2 weight = 0.0,
which is the default value.
which is the default value. It needs to be considered whether one has
to adjust the "special_bonds"_special_bonds.html weighting according
to the molecular topology since the interactions of the shells are
bypassed over an extra bond.
Note that this core/shell implementation does not require all ions to
be polarized. One can mix core/shell pairs and ions without a
satellite particle if desired.
Since the core/shell model permits distances of r = 0.0 between the
core and shell, a pair style with a "cs" suffix needs to be used to
implement a valid long-range Coulombic correction. Several such pair
implement a valid long-rangeCoulombic correction. Several such pair
styles are provided in the CORESHELL package. See "this doc
page"_pair_cs.html for details. All of the core/shell enabled pair
styles require the use of a long-range Coulombic solver, as specified
@ -2585,15 +2592,20 @@ temp/cs"_compute_temp_cs.html command can be used, in conjunction with
any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix
langevin"_fix_langevin. This compute uses the center-of-mass velocity
of the core/shell pairs to calculate a temperature, and insures that
velocity is what is rescaled for thermostatting purposes. The
velocity is what is rescaled for thermostatting purposes. This
compute also works for a system with both core/shell pairs and
non-polarized ions (ions without an attached satellite particle). The
"compute temp/cs"_compute_temp_cs.html command requires input of two
groups, one for the core atoms, another for the shell atoms. These
can be defined using the "group {type}"_group.html command. Note that
to perform thermostatting using this definition of temperature, the
"fix modify temp"_fix_modify.html command should be used to assign the
comptue to the thermostat fix. Likewise the "thermo_modify
temp"_thermo_modify.html command can be used to make this temperature
be output for the overall system.
groups, one for the core atoms, another for the shell atoms.
Non-polarized ions which might also be included in the treated system
should not be included into either of these groups, they are taken
into account by the {group-ID} (2nd argument) of the compute. The
groups can be defined using the "group {type}"_group.html command.
Note that to perform thermostatting using this definition of
temperature, the "fix modify temp"_fix_modify.html command should be
used to assign the comptue to the thermostat fix. Likewise the
"thermo_modify temp"_thermo_modify.html command can be used to make
this temperature be output for the overall system.
For the NaCl example, this can be done as follows:
@ -2632,19 +2644,19 @@ energy can be monitored using the "compute
chunk/atom"_compute_chunk_atom.html and "compute
temp/chunk"_compute_temp_chunk.html commands. The internal kinetic
energies of each core/shell pair can then be summed using the sum()
special functino of the "variable"_variable.html command. Or they can
special function of the "variable"_variable.html command. Or they can
be time/averaged and output using the "fix ave/time"_fix_ave_time.html
command. To use these commands, each core/shell pair must be defined
as a "chunk". If each core/shell pair is defined as its own molecule,
the molecule ID can be used to define the chunks. If cores are bonded
to each other to form larger molecules, then another way to define the
chunks is to use the "fix property/atom"_fix_property_atom.html to
assign a core/shell ID to each atom via a special field in the data
file read by the "read_data"_read_data.html command. This field can
then be accessed by the "compute
property/atom"_compute_property_atom.html command, to use as input to
the "compute chunk/atom"_compute_chunk_atom.html command to define the
core/shell pairs as chunks.
to each other to form larger molecules, the chunks can be identified
by the "fix property/atom"_fix_property_atom.html via assigning a
core/shell ID to each atom using a special field in the data file read
by the "read_data"_read_data.html command. This field can then be
accessed by the "compute property/atom"_compute_property_atom.html
command, to use as input to the "compute
chunk/atom"_compute_chunk_atom.html command to define the core/shell
pairs as chunks.
For example,

20
doc/compute_temp_cs.html
View File

@ -128,7 +128,9 @@
<span id="index-0"></span><h1>compute temp/cs command<a class="headerlink" href="#compute-temp-cs-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>
<p>compute ID group-ID temp/cs group1 group2 pre</p>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID temp/cs group1 group2
</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>temp/cs = style name of this compute command</li>
@ -148,7 +150,7 @@ compute core_shells all temp/cs cores shells
<p>Define a computation that calculates the temperature of a system based
on the center-of-mass velocity of atom pairs that are bonded to each
other. This compute is designed to be used with the adiabatic
core/shell model of <a class="reference internal" href="pair_cs.html#mitchellfinchham"><span>(Mitchell and Finchham)</span></a>. See
core/shell model of <a class="reference internal" href="#mitchellfinchham"><span>(Mitchell and Finchham)</span></a>. See
<a class="reference internal" href="Section_howto.html#howto-25"><span>Section_howto 25</span></a> of the manual for an
overview of the model as implemented in LAMMPS. Specifically, this
compute enables correct temperature calculation and thermostatting of
@ -156,21 +158,25 @@ core/shell pairs where it is desirable for the internal degrees of
freedom of the core/shell pairs to not be influenced by a thermostat.
A compute of this style can be used by any command that computes a
temperature via <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> e.g. <a class="reference internal" href="fix_temp_rescale.html"><em>fix temp/rescale</em></a>, <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a>, etc.</p>
<p>Note that this compute does not require all ions to be polarized,
hence defined as core/shell pairs. One can mix core/shell pairs and
ions without a satellite particle if desired. The compute will
consider the non-polarized ions according to the physical system.</p>
<p>For this compute, core and shell particles are specified by two
respective group IDs, which can be defined using the
<a class="reference internal" href="group.html"><em>group</em></a> command. The number of atoms in the two groups
must be the same and there should be one bond defined between a pair
of atoms in the two groups.</p>
of atoms in the two groups. Non-polarized ions which might also be
included in the treated system should not be included into either of
these groups, they are taken into account by the <em>group-ID</em> (2nd
argument) of the compute.</p>
<p>The temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
in the group, k = Boltzmann constant, and T = temperature. Note that
the velocity of each core or shell atom used in the KE calculation is
the velocity of the center-of-mass (COM) of the core/shell pair the
atom is part of. Note that atoms that are not core or shell particles
are also included in the temperature calculation (if they are in the
specified group-ID); they contribute to the total kinetic energy in
the usual way.</p>
atom is part of.</p>
<p>A kinetic energy tensor, stored as a 6-element vector, is also
calculated by this compute for use in the computation of a pressure
tensor. The formula for the components of the tensor is the same as

17
doc/compute_temp_cs.txt
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@ -10,7 +10,7 @@ compute temp/cs command :h3
[Syntax:]
compute ID group-ID temp/cs group1 group2 pre
compute ID group-ID temp/cs group1 group2 :pre
ID, group-ID are documented in "compute"_compute.html command
temp/cs = style name of this compute command
@ -37,11 +37,19 @@ A compute of this style can be used by any command that computes a
temperature via "fix_modify"_fix_modify.html e.g. "fix
temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_nh.html, etc.
Note that this compute does not require all ions to be polarized,
hence defined as core/shell pairs. One can mix core/shell pairs and
ions without a satellite particle if desired. The compute will
consider the non-polarized ions according to the physical system.
For this compute, core and shell particles are specified by two
respective group IDs, which can be defined using the
"group"_group.html command. The number of atoms in the two groups
must be the same and there should be one bond defined between a pair
of atoms in the two groups.
of atoms in the two groups. Non-polarized ions which might also be
included in the treated system should not be included into either of
these groups, they are taken into account by the {group-ID} (2nd
argument) of the compute.
The temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
@ -49,10 +57,7 @@ dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
in the group, k = Boltzmann constant, and T = temperature. Note that
the velocity of each core or shell atom used in the KE calculation is
the velocity of the center-of-mass (COM) of the core/shell pair the
atom is part of. Note that atoms that are not core or shell particles
are also included in the temperature calculation (if they are in the
specified group-ID); they contribute to the total kinetic energy in
the usual way.
atom is part of.
A kinetic energy tensor, stored as a 6-element vector, is also
calculated by this compute for use in the computation of a pressure

10
doc/pair_lj.html
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@ -187,6 +187,9 @@
<div class="section" id="pair-style-lj-cut-coul-long-command">
<h1>pair_style lj/cut/coul/long command<a class="headerlink" href="#pair-style-lj-cut-coul-long-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-long-cs-command">
<h1>pair_style lj/cut/coul/long/cs command<a class="headerlink" href="#pair-style-lj-cut-coul-long-cs-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-long-cuda-command">
<h1>pair_style lj/cut/coul/long/cuda command<a class="headerlink" href="#pair-style-lj-cut-coul-long-cuda-command" title="Permalink to this headline"></a></h1>
</div>
@ -231,7 +234,7 @@
</pre></div>
</div>
<ul class="simple">
<li>style = <em>lj/cut</em> or <em>lj/cut/coul/cut</em> or <em>lj/cut/coul/debye</em> or <em>lj/cut/coul/dsf</em> or <em>lj/cut/coul/long</em> or <em>lj/cut/coul/msm</em> or <em>lj/cut/tip4p/long</em></li>
<li>style = <em>lj/cut</em> or <em>lj/cut/coul/cut</em> or <em>lj/cut/coul/debye</em> or <em>lj/cut/coul/dsf</em> or <em>lj/cut/coul/long</em> or <em>lj/cut/coul/long/cs</em> or <em>lj/cut/coul/msm</em> or <em>lj/cut/tip4p/long</em></li>
<li>args = list of arguments for a particular style</li>
</ul>
<pre class="literal-block">
@ -295,7 +298,9 @@ pair_coeff 1 1 1.0 1.0 2.5
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/coul/long 10.0
pair_style lj/cut/coul/long/cs 10.0
pair_style lj/cut/coul/long 10.0 8.0
pair_style lj/cut/coul/long/cs 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
</pre></div>
@ -360,6 +365,9 @@ command and its <em>ewald</em> or <em>pppm</em> option. The Coulombic cutoff
specified for this style means that pairwise interactions within this
distance are computed directly; interactions outside that distance are
computed in reciprocal space.</p>
<p>Style <em>lj/cut/coul/long/cs</em> is identical to <em>lj/cut/coul/long</em> except
that a term is added for the <a class="reference internal" href="Section_howto.html#howto-25"><span>core/shell model</span></a> to allow charges on core and shell
particles to be separated by r = 0.0.</p>
<p>Styles <em>lj/cut/tip4p/cut</em> and <em>lj/cut/tip4p/long</em> implement the TIP4P
water model of <a class="reference internal" href="#jorgensen"><span>(Jorgensen)</span></a>, which introduces a massless
site located a short distance away from the oxygen atom along the

10
doc/pair_lj.txt
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@ -27,6 +27,7 @@ pair_style lj/cut/coul/dsf/gpu command :h3
pair_style lj/cut/coul/dsf/kk command :h3
pair_style lj/cut/coul/dsf/omp command :h3
pair_style lj/cut/coul/long command :h3
pair_style lj/cut/coul/long/cs command :h3
pair_style lj/cut/coul/long/cuda command :h3
pair_style lj/cut/coul/long/gpu command :h3
pair_style lj/cut/coul/long/intel command :h3
@ -45,7 +46,7 @@ pair_style lj/cut/tip4p/long/opt command :h3
pair_style style args :pre
style = {lj/cut} or {lj/cut/coul/cut} or {lj/cut/coul/debye} or {lj/cut/coul/dsf} or {lj/cut/coul/long} or {lj/cut/coul/msm} or {lj/cut/tip4p/long}
style = {lj/cut} or {lj/cut/coul/cut} or {lj/cut/coul/debye} or {lj/cut/coul/dsf} or {lj/cut/coul/long} or {lj/cut/coul/long/cs} or {lj/cut/coul/msm} or {lj/cut/tip4p/long}
args = list of arguments for a particular style :ul
{lj/cut} args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
@ -102,7 +103,9 @@ pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.0 2.5 :pre
pair_style lj/cut/coul/long 10.0
pair_style lj/cut/coul/long/cs 10.0
pair_style lj/cut/coul/long 10.0 8.0
pair_style lj/cut/coul/long/cs 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0 :pre
@ -175,6 +178,11 @@ specified for this style means that pairwise interactions within this
distance are computed directly; interactions outside that distance are
computed in reciprocal space.
Style {lj/cut/coul/long/cs} is identical to {lj/cut/coul/long} except
that a term is added for the "core/shell
model"_Section_howto.html#howto_25 to allow charges on core and shell
particles to be separated by r = 0.0.
Styles {lj/cut/tip4p/cut} and {lj/cut/tip4p/long} implement the TIP4P
water model of "(Jorgensen)"_#Jorgensen, which introduces a massless
site located a short distance away from the oxygen atom along the

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