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<TITLE>LAMMPS Users Manual</TITLE>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<P>The LAMMPS "version" is the date when it was released, such as 1 May <a href="Section_commands.html#comm">Commands</a>
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<H1></H1><div class="section" id="lammps-documentation">
<h1>LAMMPS Documentation<a class="headerlink" href="#lammps-documentation" title="Permalink to this headline"></a></h1>
<div class="section" id="aug-2015-version">
<h2>10 Aug 2015 version<a class="headerlink" href="#aug-2015-version" title="Permalink to this headline"></a></h2>
</div>
<div class="section" id="version-info">
<h2>Version info:<a class="headerlink" href="#version-info" title="Permalink to this headline"></a></h2>
<p>The LAMMPS &#8220;version&#8221; is the date when it was released, such as 1 May
2010. LAMMPS is updated continuously. Whenever we fix a bug or add a 2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
feature, we release it immediately, and post a notice on <A HREF = "http://lammps.sandia.gov/bug.html">this page of feature, we release it immediately, and post a notice on <a class="reference external" href="http://lammps.sandia.gov/bug.html">this page of the WWW site</a>. Each dated copy of LAMMPS contains all the
the WWW site</A>. Each dated copy of LAMMPS contains all the
features and bug-fixes up to and including that version date. The features and bug-fixes up to and including that version date. The
version date is printed to the screen and logfile every time you run version date is printed to the screen and logfile every time you run
LAMMPS. It is also in the file src/version.h and in the LAMMPS LAMMPS. It is also in the file src/version.h and in the LAMMPS
directory name created when you unpack a tarball, and at the top of directory name created when you unpack a tarball, and at the top of
the first page of the manual (this page). the first page of the manual (this page).</p>
</P> <ul class="simple">
<UL><LI>If you browse the HTML doc pages on the LAMMPS WWW site, they always <li>If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of LAMMPS. describe the most current version of LAMMPS.</li>
<li>If you browse the HTML doc pages included in your tarball, they
<LI>If you browse the HTML doc pages included in your tarball, they describe the version you have.</li>
describe the version you have. <li>The <a class="reference external" href="Manual.pdf">PDF file</a> on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don&#8217;t want
<LI>The <A HREF = "Manual.pdf">PDF file</A> on the WWW site or in the tarball is updated it to be part of every patch.</li>
about once per month. This is because it is large, and we don't want <li>There is also a <a class="reference external" href="Developer.pdf">Developer.pdf</a> file in the doc
it to be part of every patch.
<LI>There is also a <A HREF = "Developer.pdf">Developer.pdf</A> file in the doc
directory, which describes the internal structure and algorithms of directory, which describes the internal structure and algorithms of
LAMMPS. LAMMPS.</li>
</UL> </ul>
<P>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel <p>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator. Simulator.</p>
</P> <p>LAMMPS is a classical molecular dynamics simulation code designed to
<P>LAMMPS is a classical molecular dynamics simulation code designed to
run efficiently on parallel computers. It was developed at Sandia run efficiently on parallel computers. It was developed at Sandia
National Laboratories, a US Department of Energy facility, with National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL). under the terms of the GNU Public License (GPL).</p>
</P> <p>The primary developers of LAMMPS are <a class="reference external" href="http://www.sandia.gov/~sjplimp">Steve Plimpton</a>, Aidan
<P>The primary developers of LAMMPS are <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Aidan
Thompson, and Paul Crozier who can be contacted at Thompson, and Paul Crozier who can be contacted at
sjplimp,athomps,pscrozi at sandia.gov. The <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> at sjplimp,athomps,pscrozi at sandia.gov. The <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> at
http://lammps.sandia.gov has more information about the code and its <a class="reference external" href="http://lammps.sandia.gov">http://lammps.sandia.gov</a> has more information about the code and its
uses. uses.</p>
</P> <hr class="docutils" />
<p>The LAMMPS documentation is organized into the following sections. If
<HR>
<P>The LAMMPS documentation is organized into the following sections. If
you find errors or omissions in this manual or have suggestions for you find errors or omissions in this manual or have suggestions for
useful information to add, please send an email to the developers so useful information to add, please send an email to the developers so
we can improve the LAMMPS documentation. we can improve the LAMMPS documentation.</p>
</P> <p>Once you are familiar with LAMMPS, you may want to bookmark <a class="reference internal" href="Section_commands.html#comm"><span>this page</span></a> at Section_commands.html#comm since
<P>Once you are familiar with LAMMPS, you may want to bookmark <A HREF = "Section_commands.html#comm">this it gives quick access to documentation for all LAMMPS commands.</p>
page</A> at Section_commands.html#comm since <p><a class="reference external" href="Manual.pdf">PDF file</a> of the entire manual, generated by
it gives quick access to documentation for all LAMMPS commands. <a class="reference external" href="http://freecode.com/projects/htmldoc">htmldoc</a></p>
</P> <div class="toctree-wrapper compound">
<P><A HREF = "Manual.pdf">PDF file</A> of the entire manual, generated by <ul>
<A HREF = "http://freecode.com/projects/htmldoc">htmldoc</A> <li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a><ul>
</P> <li class="toctree-l2"><a class="reference internal" href="Section_intro.html#what-is-lammps">1.1. What is LAMMPS</a></li>
<P><!-- RST <li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-features">1.2. LAMMPS features</a></li>
</P> <li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-non-features">1.3. LAMMPS non-features</a></li>
<P>.. toctree:: <li class="toctree-l2"><a class="reference internal" href="Section_intro.html#open-source-distribution">1.4. Open source distribution</a></li>
:maxdepth: 2 <li class="toctree-l2"><a class="reference internal" href="Section_intro.html#acknowledgments-and-citations">1.5. Acknowledgments and citations</a></li>
:numbered: // comment </ul>
</P> </li>
<P> Section_intro <li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a><ul>
Section_start <li class="toctree-l2"><a class="reference internal" href="Section_start.html#what-s-in-the-lammps-distribution">2.1. What&#8217;s in the LAMMPS distribution</a></li>
Section_commands <li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps">2.2. Making LAMMPS</a></li>
Section_packages <li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps-with-optional-packages">2.3. Making LAMMPS with optional packages</a></li>
Section_accelerate <li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-via-the-make-py-script">2.4. Building LAMMPS via the Make.py script</a></li>
Section_howto <li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-as-a-library">2.5. Building LAMMPS as a library</a></li>
Section_example <li class="toctree-l2"><a class="reference internal" href="Section_start.html#running-lammps">2.6. Running LAMMPS</a></li>
Section_perf <li class="toctree-l2"><a class="reference internal" href="Section_start.html#command-line-options">2.7. Command-line options</a></li>
Section_tools <li class="toctree-l2"><a class="reference internal" href="Section_start.html#lammps-screen-output">2.8. LAMMPS screen output</a></li>
Section_modify <li class="toctree-l2"><a class="reference internal" href="Section_start.html#tips-for-users-of-previous-lammps-versions">2.9. Tips for users of previous LAMMPS versions</a></li>
Section_python </ul>
Section_errors </li>
Section_history <li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a><ul>
</P> <li class="toctree-l2"><a class="reference internal" href="Section_commands.html#lammps-input-script">3.1. LAMMPS input script</a></li>
<P>Indices and tables <li class="toctree-l2"><a class="reference internal" href="Section_commands.html#parsing-rules">3.2. Parsing rules</a></li>
================== <li class="toctree-l2"><a class="reference internal" href="Section_commands.html#input-script-structure">3.3. Input script structure</a></li>
</P> <li class="toctree-l2"><a class="reference internal" href="Section_commands.html#commands-listed-by-category">3.4. Commands listed by category</a></li>
<P>* :ref:`genindex` // comment <li class="toctree-l2"><a class="reference internal" href="Section_commands.html#individual-commands">3.5. Individual commands</a></li>
* :ref:`search` // comment <li class="toctree-l2"><a class="reference internal" href="Section_commands.html#fix-styles">3.6. Fix styles</a></li>
</P> <li class="toctree-l2"><a class="reference internal" href="Section_commands.html#compute-styles">3.7. Compute styles</a></li>
<P>END_RST --> <li class="toctree-l2"><a class="reference internal" href="Section_commands.html#pair-style-potentials">3.8. Pair_style potentials</a></li>
</P> <li class="toctree-l2"><a class="reference internal" href="Section_commands.html#bond-style-potentials">3.9. Bond_style potentials</a></li>
<OL><LI><!-- HTML_ONLY --> <li class="toctree-l2"><a class="reference internal" href="Section_commands.html#angle-style-potentials">3.10. Angle_style potentials</a></li>
<A HREF = "Section_intro.html">Introduction</A> <li class="toctree-l2"><a class="reference internal" href="Section_commands.html#dihedral-style-potentials">3.11. Dihedral_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#improper-style-potentials">3.12. Improper_style potentials</a></li>
<UL> 1.1 <A HREF = "Section_intro.html#intro_1">What is LAMMPS</A> <li class="toctree-l2"><a class="reference internal" href="Section_commands.html#kspace-solvers">3.13. Kspace solvers</a></li>
<BR> </ul>
1.2 <A HREF = "Section_intro.html#intro_2">LAMMPS features</A> </li>
<BR> <li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a><ul>
1.3 <A HREF = "Section_intro.html#intro_3">LAMMPS non-features</A> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#standard-packages">4.1. Standard packages</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-packages">4.2. User packages</a></li>
1.4 <A HREF = "Section_intro.html#intro_4">Open source distribution</A> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-atc-package">4.3. USER-ATC package</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-awpmd-package">4.4. USER-AWPMD package</a></li>
1.5 <A HREF = "Section_intro.html#intro_5">Acknowledgments and citations</A> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cg-cmm-package">4.5. USER-CG-CMM package</a></li>
<BR></UL> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-colvars-package">4.6. USER-COLVARS package</a></li>
<LI><A HREF = "Section_start.html">Getting started</A> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cuda-package">4.7. USER-CUDA package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-diffraction-package">4.8. USER-DIFFRACTION package</a></li>
<UL> 2.1 <A HREF = "Section_start.html#start_1">What's in the LAMMPS distribution</A> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-drude-package">4.9. USER-DRUDE package</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-eff-package">4.10. USER-EFF package</a></li>
2.2 <A HREF = "Section_start.html#start_2">Making LAMMPS</A> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-fep-package">4.11. USER-FEP package</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-h5md-package">4.12. USER-H5MD package</a></li>
2.3 <A HREF = "Section_start.html#start_3">Making LAMMPS with optional packages</A> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-intel-package">4.13. USER-INTEL package</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-lb-package">4.14. USER-LB package</a></li>
2.4 <A HREF = "Section_start.html#start_4">Building LAMMPS via the Make.py script</A> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-misc-package">4.15. USER-MISC package</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-molfile-package">4.16. USER-MOLFILE package</a></li>
2.5 <A HREF = "Section_start.html#start_5">Building LAMMPS as a library</A> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-omp-package">4.17. USER-OMP package</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-phonon-package">4.18. USER-PHONON package</a></li>
2.6 <A HREF = "Section_start.html#start_6">Running LAMMPS</A> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qmmm-package">4.19. USER-QMMM package</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qtb-package">4.20. USER-QTB package</a></li>
2.7 <A HREF = "Section_start.html#start_7">Command-line options</A> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-reaxc-package">4.21. USER-REAXC package</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smd-package">4.22. USER-SMD package</a></li>
2.8 <A HREF = "Section_start.html#start_8">Screen output</A> <li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-sph-package">4.23. USER-SPH package</a></li>
<BR> </ul>
2.9 <A HREF = "Section_start.html#start_9">Tips for users of previous versions</A> </li>
<BR></UL> <li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a><ul>
<LI><A HREF = "Section_commands.html">Commands</A> <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>
<UL> 3.1 <A HREF = "Section_commands.html#cmd_1">LAMMPS input script</A> <li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#packages-with-optimized-styles">5.3. Packages with optimized styles</a></li>
<BR> <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>
3.2 <A HREF = "Section_commands.html#cmd_2">Parsing rules</A> </ul>
<BR> </li>
3.3 <A HREF = "Section_commands.html#cmd_3">Input script structure</A> <li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a><ul>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#restarting-a-simulation">6.1. Restarting a simulation</a></li>
3.4 <A HREF = "Section_commands.html#cmd_4">Commands listed by category</A> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#d-simulations">6.2. 2d simulations</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#charmm-amber-and-dreiding-force-fields">6.3. CHARMM, AMBER, and DREIDING force fields</a></li>
3.5 <A HREF = "Section_commands.html#cmd_5">Commands listed alphabetically</A> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#running-multiple-simulations-from-one-input-script">6.4. Running multiple simulations from one input script</a></li>
<BR></UL> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#multi-replica-simulations">6.5. Multi-replica simulations</a></li>
<LI><A HREF = "Section_packages.html">Packages</A> <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>
<UL> 4.1 <A HREF = "Section_packages.html#pkg_1">Standard packages</A> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip4p-water-model">6.8. TIP4P water model</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#spc-water-model">6.9. SPC water model</a></li>
4.2 <A HREF = "Section_packages.html#pkg_2">User packages</A> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#coupling-lammps-to-other-codes">6.10. Coupling LAMMPS to other codes</a></li>
<BR></UL> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#visualizing-lammps-snapshots">6.11. Visualizing LAMMPS snapshots</a></li>
<LI><A HREF = "Section_accelerate.html">Accelerating LAMMPS performance</A> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#triclinic-non-orthogonal-simulation-boxes">6.12. Triclinic (non-orthogonal) simulation boxes</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#nemd-simulations">6.13. NEMD simulations</a></li>
<UL> 5.1 <A HREF = "Section_accelerate.html#acc_1">Measuring performance</A> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#finite-size-spherical-and-aspherical-particles">6.14. Finite-size spherical and aspherical particles</a></li>
<BR> <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>
5.2 <A HREF = "Section_accelerate.html#acc_2">Algorithms and code options to boost performace</A> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#thermostatting-barostatting-and-computing-temperature">6.16. Thermostatting, barostatting, and computing temperature</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#walls">6.17. Walls</a></li>
5.3 <A HREF = "Section_accelerate.html#acc_3">Accelerator packages with optimized styles</A> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#elastic-constants">6.18. Elastic constants</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#library-interface-to-lammps">6.19. Library interface to LAMMPS</a></li>
<UL> 5.3.1 <A HREF = "accelerate_cuda.html">USER-CUDA package</A> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-thermal-conductivity">6.20. Calculating thermal conductivity</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-viscosity">6.21. Calculating viscosity</a></li>
5.3.2 <A HREF = "accelerate_gpu.html">GPU package</A> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-a-diffusion-coefficient">6.22. Calculating a diffusion coefficient</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#using-chunks-to-calculate-system-properties">6.23. Using chunks to calculate system properties</a></li>
5.3.3 <A HREF = "accelerate_intel.html">USER-INTEL package</A> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#setting-parameters-for-the-kspace-style-pppm-disp-command">6.24. Setting parameters for the <code class="docutils literal"><span class="pre">kspace_style</span> <span class="pre">pppm/disp</span></code> command</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#polarizable-models">6.25. Polarizable models</a></li>
5.3.4 <A HREF = "accelerate_kokkos.html">KOKKOS package</A> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#adiabatic-core-shell-model">6.26. Adiabatic core/shell model</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_howto.html#drude-induced-dipoles">6.27. Drude induced dipoles</a></li>
5.3.5 <A HREF = "accelerate_omp.html">USER-OMP package</A> </ul>
<BR> </li>
5.3.6 <A HREF = "accelerate_opt.html">OPT package</A> <li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<BR></UL> <li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
5.4 <A HREF = "Section_accelerate.html#acc_4">Comparison of various accelerator packages</A> <li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a><ul>
<BR></UL> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#amber2lmp-tool">9.1. amber2lmp tool</a></li>
<LI><A HREF = "Section_howto.html">How-to discussions</A> <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>
<UL> 6.1 <A HREF = "Section_howto.html#howto_1">Restarting a simulation</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#chain-tool">9.4. chain tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#colvars-tools">9.5. colvars tools</a></li>
6.2 <A HREF = "Section_howto.html#howto_2">2d simulations</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#createatoms-tool">9.6. createatoms tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#data2xmovie-tool">9.7. data2xmovie tool</a></li>
6.3 <A HREF = "Section_howto.html#howto_3">CHARMM and AMBER force fields</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-database-tool">9.8. eam database tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-generate-tool">9.9. eam generate tool</a></li>
6.4 <A HREF = "Section_howto.html#howto_4">Running multiple simulations from one input script</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eff-tool">9.10. eff tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#emacs-tool">9.11. emacs tool</a></li>
6.5 <A HREF = "Section_howto.html#howto_5">Multi-replica simulations</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#fep-tool">9.12. fep tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#i-pi-tool">9.13. i-pi tool</a></li>
6.6 <A HREF = "Section_howto.html#howto_6">Granular models</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ipp-tool">9.14. ipp tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#kate-tool">9.15. kate tool</a></li>
6.7 <A HREF = "Section_howto.html#howto_7">TIP3P water model</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2arc-tool">9.16. lmp2arc tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2cfg-tool">9.17. lmp2cfg tool</a></li>
6.8 <A HREF = "Section_howto.html#howto_8">TIP4P water model</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2vmd-tool">9.18. lmp2vmd tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#matlab-tool">9.19. matlab tool</a></li>
6.9 <A HREF = "Section_howto.html#howto_9">SPC water model</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#micelle2d-tool">9.20. micelle2d tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#moltemplate-tool">9.21. moltemplate tool</a></li>
6.10 <A HREF = "Section_howto.html#howto_10">Coupling LAMMPS to other codes</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#msi2lmp-tool">9.22. msi2lmp tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#phonon-tool">9.23. phonon tool</a></li>
6.11 <A HREF = "Section_howto.html#howto_11">Visualizing LAMMPS snapshots</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#polymer-bonding-tool">9.24. polymer bonding tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#pymol-asphere-tool">9.25. pymol_asphere tool</a></li>
6.12 <A HREF = "Section_howto.html#howto_12">Triclinic (non-orthogonal) simulation boxes</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#python-tool">9.26. python tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#reax-tool">9.27. reax tool</a></li>
6.13 <A HREF = "Section_howto.html#howto_13">NEMD simulations</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#restart2data-tool">9.28. restart2data tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#vim-tool">9.29. vim tool</a></li>
6.14 <A HREF = "Section_howto.html#howto_14">Finite-size spherical and aspherical particles</A> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmgrace-tool">9.30. xmgrace tool</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmovie-tool">9.31. xmovie tool</a></li>
6.15 <A HREF = "Section_howto.html#howto_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A> </ul>
<BR> </li>
6.16 <A HREF = "Section_howto.html#howto_16">Thermostatting, barostatting, and compute temperature</A> <li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a><ul>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#atom-styles">10.1. Atom styles</a></li>
6.17 <A HREF = "Section_howto.html#howto_17">Walls</A> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#bond-angle-dihedral-improper-potentials">10.2. Bond, angle, dihedral, improper potentials</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#compute-styles">10.3. Compute styles</a></li>
6.18 <A HREF = "Section_howto.html#howto_18">Elastic constants</A> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-styles">10.4. Dump styles</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-custom-output-options">10.5. Dump custom output options</a></li>
6.19 <A HREF = "Section_howto.html#howto_19">Library interface to LAMMPS</A> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#fix-styles">10.6. Fix styles</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#input-script-commands">10.7. Input script commands</a></li>
6.20 <A HREF = "Section_howto.html#howto_20">Calculating thermal conductivity</A> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#kspace-computations">10.8. Kspace computations</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#minimization-styles">10.9. Minimization styles</a></li>
6.21 <A HREF = "Section_howto.html#howto_21">Calculating viscosity</A> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#pairwise-potentials">10.10. Pairwise potentials</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#region-styles">10.11. Region styles</a></li>
6.22 <A HREF = "Section_howto.html#howto_22">Calculating a diffusion coefficient</A> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#body-styles">10.12. Body styles</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#thermodynamic-output-options">10.13. Thermodynamic output options</a></li>
6.23 <A HREF = "Section_howto.html#howto_23">Using chunks to calculate system properties</A> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#variable-options">10.14. Variable options</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_modify.html#submitting-new-features-for-inclusion-in-lammps">10.15. Submitting new features for inclusion in LAMMPS</a></li>
6.24 <A HREF = "Section_howto.html#howto_24">Setting parameters for pppm/disp</A> </ul>
<BR> </li>
6.25 <A HREF = "Section_howto.html#howto_25">Polarizable models</A> <li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a><ul>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-running-lammps-from-python">11.1. Overview of running LAMMPS from Python</a></li>
6.26 <A HREF = "Section_howto.html#howto_26">Adiabatic core/shell model</A> <li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-using-python-from-a-lammps-script">11.2. Overview of using Python from a LAMMPS script</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_python.html#building-lammps-as-a-shared-library">11.3. Building LAMMPS as a shared library</a></li>
6.27 <A HREF = "Section_howto.html#howto_27">Drude induced dipoles</A> <li class="toctree-l2"><a class="reference internal" href="Section_python.html#installing-the-python-wrapper-into-python">11.4. Installing the Python wrapper into Python</a></li>
<BR></UL> <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><A HREF = "Section_example.html">Example problems</A> <li class="toctree-l2"><a class="reference internal" href="Section_python.html#testing-the-python-lammps-interface">11.6. Testing the Python-LAMMPS interface</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#using-lammps-from-python">11.7. Using LAMMPS from Python</a></li>
<LI><A HREF = "Section_perf.html">Performance & scalability</A> <li class="toctree-l2"><a class="reference internal" href="Section_python.html#example-python-scripts-that-use-lammps">11.8. Example Python scripts that use LAMMPS</a></li>
</ul>
<LI><A HREF = "Section_tools.html">Additional tools</A> </li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a><ul>
<LI><A HREF = "Section_modify.html">Modifying & extending LAMMPS</A> <li class="toctree-l2"><a class="reference internal" href="Section_errors.html#common-problems">12.1. Common problems</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#reporting-bugs">12.2. Reporting bugs</a></li>
<UL> 10.1 <A HREF = "Section_modify.html#mod_1">Atom styles</A> <li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error-warning-messages">12.3. Error &amp; warning messages</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error">12.4. Errors:</a></li>
10.2 <A HREF = "Section_modify.html#mod_2">Bond, angle, dihedral, improper potentials</A> <li class="toctree-l2"><a class="reference internal" href="Section_errors.html#warnings">12.5. Warnings:</a></li>
<BR> </ul>
10.3 <A HREF = "Section_modify.html#mod_3">Compute styles</A> </li>
<BR> <li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a><ul>
10.4 <A HREF = "Section_modify.html#mod_4">Dump styles</A> <li class="toctree-l2"><a class="reference internal" href="Section_history.html#coming-attractions">13.1. Coming attractions</a></li>
<BR> <li class="toctree-l2"><a class="reference internal" href="Section_history.html#past-versions">13.2. Past versions</a></li>
10.5 <A HREF = "Section_modify.html#mod_5">Dump custom output options</A> </ul>
<BR> </li>
10.6 <A HREF = "Section_modify.html#mod_6">Fix styles</A> </ul>
<BR> </div>
10.7 <A HREF = "Section_modify.html#mod_7">Input script commands</A> </div>
<BR> </div>
10.8 <A HREF = "Section_modify.html#mod_8">Kspace computations</A> <div class="section" id="indices-and-tables">
<BR> <h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline"></a></h1>
10.9 <A HREF = "Section_modify.html#mod_9">Minimization styles</A> <ul class="simple">
<BR> <li><a class="reference internal" href="genindex.html"><span>Index</span></a></li>
10.10 <A HREF = "Section_modify.html#mod_10">Pairwise potentials</A> <li><a class="reference internal" href="search.html"><span>Search Page</span></a></li>
<BR> </ul>
10.11 <A HREF = "Section_modify.html#mod_11">Region styles</A> </BODY></div>
<BR>
10.12 <A HREF = "Section_modify.html#mod_12">Body styles</A>
<BR> </div>
10.13 <A HREF = "Section_modify.html#mod_13">Thermodynamic output options</A> </div>
<BR> <footer>
10.14 <A HREF = "Section_modify.html#mod_14">Variable options</A>
<BR> <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
10.15 <A HREF = "Section_modify.html#mod_15">Submitting new features for inclusion in LAMMPS</A>
<BR></UL> <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>
<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> </div>
<BR>
11.2 <A HREF = "Section_python.html#py_2">Overview of using Python from a LAMMPS script</A>
<BR> <hr/>
11.3 <A HREF = "Section_python.html#py_3">Building LAMMPS as a shared library</A>
<BR> <div role="contentinfo">
11.4 <A HREF = "Section_python.html#py_4">Installing the Python wrapper into Python</A> <p>
<BR> &copy; Copyright .
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11.8 <A HREF = "py_8">Example Python scripts that use LAMMPS</A> </div>
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<BR> </div>
12.2 <A HREF = "Section_errors.html#err_2">Reporting bugs</A>
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<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="19 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>
<BODY>
<!-- END_HTML_ONLY -->
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H1></H1>
<P><CENTER><H3>LAMMPS Documentation
</H3></CENTER>
<CENTER><H4>19 Aug 2015 version
</H4></CENTER>
<H4>Version info:
</H4>
<P>The LAMMPS "version" is the date when it was released, such as 1 May
2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
feature, we release it immediately, and post a notice on <A HREF = "http://lammps.sandia.gov/bug.html">this page of
the WWW site</A>. Each dated copy of LAMMPS contains all the
features and bug-fixes up to and including that version date. The
version date is printed to the screen and logfile every time you run
LAMMPS. It is also in the file src/version.h and in the LAMMPS
directory name created when you unpack a tarball, and at the top of
the first page of the manual (this page).
</P>
<UL><LI>If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of LAMMPS.
</P>
<P><LI>If you browse the HTML doc pages included in your tarball, they
describe the version you have.
</P>
<P><LI>The <A HREF = "Manual.pdf">PDF file</A> on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don't want
it to be part of every patch.
</P>
<LI>There is also a <A HREF = "Developer.pdf">Developer.pdf</A> file in the doc
directory, which describes the internal structure and algorithms of
LAMMPS.
</UL>
<P>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.
</P>
<P>LAMMPS is a classical molecular dynamics simulation code designed to
run efficiently on parallel computers. It was developed at Sandia
National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL).
</P>
<P>The primary developers of LAMMPS are <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Aidan
Thompson, and Paul Crozier who can be contacted at
sjplimp,athomps,pscrozi at sandia.gov. The <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> at
http://lammps.sandia.gov has more information about the code and its
uses.
</P>
<HR>
<P>The LAMMPS documentation is organized into the following sections. If
you find errors or omissions in this manual or have suggestions for
useful information to add, please send an email to the developers so
we can improve the LAMMPS documentation.
</P>
<P>Once you are familiar with LAMMPS, you may want to bookmark <A HREF = "Section_commands.html#comm">this
page</A> at Section_commands.html#comm since
it gives quick access to documentation for all LAMMPS commands.
</P>
<P><A HREF = "Manual.pdf">PDF file</A> of the entire manual, generated by
<A HREF = "http://freecode.com/projects/htmldoc">htmldoc</A>
</P>
<P><!-- RST
</P>
<P>.. toctree::
:maxdepth: 2
:numbered: // comment
</P>
<P> Section_intro
Section_start
Section_commands
Section_packages
Section_accelerate
Section_howto
Section_example
Section_perf
Section_tools
Section_modify
Section_python
Section_errors
Section_history
</P>
<P>Indices and tables
==================
</P>
<P>* :ref:`genindex` // comment
* :ref:`search` // comment
</P>
<P>END_RST -->
</P>
<OL><LI><!-- HTML_ONLY -->
<A HREF = "Section_intro.html">Introduction</A>
<UL> 1.1 <A HREF = "Section_intro.html#intro_1">What is LAMMPS</A>
<BR>
1.2 <A HREF = "Section_intro.html#intro_2">LAMMPS features</A>
<BR>
1.3 <A HREF = "Section_intro.html#intro_3">LAMMPS non-features</A>
<BR>
1.4 <A HREF = "Section_intro.html#intro_4">Open source distribution</A>
<BR>
1.5 <A HREF = "Section_intro.html#intro_5">Acknowledgments and citations</A>
<BR></UL>
<LI><A HREF = "Section_start.html">Getting started</A>
<UL> 2.1 <A HREF = "Section_start.html#start_1">What's in the LAMMPS distribution</A>
<BR>
2.2 <A HREF = "Section_start.html#start_2">Making LAMMPS</A>
<BR>
2.3 <A HREF = "Section_start.html#start_3">Making LAMMPS with optional packages</A>
<BR>
2.4 <A HREF = "Section_start.html#start_4">Building LAMMPS via the Make.py script</A>
<BR>
2.5 <A HREF = "Section_start.html#start_5">Building LAMMPS as a library</A>
<BR>
2.6 <A HREF = "Section_start.html#start_6">Running LAMMPS</A>
<BR>
2.7 <A HREF = "Section_start.html#start_7">Command-line options</A>
<BR>
2.8 <A HREF = "Section_start.html#start_8">Screen output</A>
<BR>
2.9 <A HREF = "Section_start.html#start_9">Tips for users of previous versions</A>
<BR></UL>
<LI><A HREF = "Section_commands.html">Commands</A>
<UL> 3.1 <A HREF = "Section_commands.html#cmd_1">LAMMPS input script</A>
<BR>
3.2 <A HREF = "Section_commands.html#cmd_2">Parsing rules</A>
<BR>
3.3 <A HREF = "Section_commands.html#cmd_3">Input script structure</A>
<BR>
3.4 <A HREF = "Section_commands.html#cmd_4">Commands listed by category</A>
<BR>
3.5 <A HREF = "Section_commands.html#cmd_5">Commands listed alphabetically</A>
<BR></UL>
<LI><A HREF = "Section_packages.html">Packages</A>
<UL> 4.1 <A HREF = "Section_packages.html#pkg_1">Standard packages</A>
<BR>
4.2 <A HREF = "Section_packages.html#pkg_2">User packages</A>
<BR></UL>
<LI><A HREF = "Section_accelerate.html">Accelerating LAMMPS performance</A>
<UL> 5.1 <A HREF = "Section_accelerate.html#acc_1">Measuring performance</A>
<BR>
5.2 <A HREF = "Section_accelerate.html#acc_2">Algorithms and code options to boost performace</A>
<BR>
5.3 <A HREF = "Section_accelerate.html#acc_3">Accelerator packages with optimized styles</A>
<BR>
<UL> 5.3.1 <A HREF = "accelerate_cuda.html">USER-CUDA package</A>
<BR>
5.3.2 <A HREF = "accelerate_gpu.html">GPU package</A>
<BR>
5.3.3 <A HREF = "accelerate_intel.html">USER-INTEL package</A>
<BR>
5.3.4 <A HREF = "accelerate_kokkos.html">KOKKOS package</A>
<BR>
5.3.5 <A HREF = "accelerate_omp.html">USER-OMP package</A>
<BR>
5.3.6 <A HREF = "accelerate_opt.html">OPT package</A>
<BR></UL>
5.4 <A HREF = "Section_accelerate.html#acc_4">Comparison of various accelerator packages</A>
<BR></UL>
<LI><A HREF = "Section_howto.html">How-to discussions</A>
<UL> 6.1 <A HREF = "Section_howto.html#howto_1">Restarting a simulation</A>
<BR>
6.2 <A HREF = "Section_howto.html#howto_2">2d simulations</A>
<BR>
6.3 <A HREF = "Section_howto.html#howto_3">CHARMM and AMBER force fields</A>
<BR>
6.4 <A HREF = "Section_howto.html#howto_4">Running multiple simulations from one input script</A>
<BR>
6.5 <A HREF = "Section_howto.html#howto_5">Multi-replica simulations</A>
<BR>
6.6 <A HREF = "Section_howto.html#howto_6">Granular models</A>
<BR>
6.7 <A HREF = "Section_howto.html#howto_7">TIP3P water model</A>
<BR>
6.8 <A HREF = "Section_howto.html#howto_8">TIP4P water model</A>
<BR>
6.9 <A HREF = "Section_howto.html#howto_9">SPC water model</A>
<BR>
6.10 <A HREF = "Section_howto.html#howto_10">Coupling LAMMPS to other codes</A>
<BR>
6.11 <A HREF = "Section_howto.html#howto_11">Visualizing LAMMPS snapshots</A>
<BR>
6.12 <A HREF = "Section_howto.html#howto_12">Triclinic (non-orthogonal) simulation boxes</A>
<BR>
6.13 <A HREF = "Section_howto.html#howto_13">NEMD simulations</A>
<BR>
6.14 <A HREF = "Section_howto.html#howto_14">Finite-size spherical and aspherical particles</A>
<BR>
6.15 <A HREF = "Section_howto.html#howto_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A>
<BR>
6.16 <A HREF = "Section_howto.html#howto_16">Thermostatting, barostatting, and compute temperature</A>
<BR>
6.17 <A HREF = "Section_howto.html#howto_17">Walls</A>
<BR>
6.18 <A HREF = "Section_howto.html#howto_18">Elastic constants</A>
<BR>
6.19 <A HREF = "Section_howto.html#howto_19">Library interface to LAMMPS</A>
<BR>
6.20 <A HREF = "Section_howto.html#howto_20">Calculating thermal conductivity</A>
<BR>
6.21 <A HREF = "Section_howto.html#howto_21">Calculating viscosity</A>
<BR>
6.22 <A HREF = "Section_howto.html#howto_22">Calculating a diffusion coefficient</A>
<BR>
6.23 <A HREF = "Section_howto.html#howto_23">Using chunks to calculate system properties</A>
<BR>
6.24 <A HREF = "Section_howto.html#howto_24">Setting parameters for pppm/disp</A>
<BR>
6.25 <A HREF = "Section_howto.html#howto_25">Polarizable models</A>
<BR>
6.26 <A HREF = "Section_howto.html#howto_26">Adiabatic core/shell model</A>
<BR>
6.27 <A HREF = "Section_howto.html#howto_27">Drude induced dipoles</A>
<BR></UL>
<LI><A HREF = "Section_example.html">Example problems</A>
<LI><A HREF = "Section_perf.html">Performance & scalability</A>
<LI><A HREF = "Section_tools.html">Additional tools</A>
<LI><A HREF = "Section_modify.html">Modifying & extending LAMMPS</A>
<UL> 10.1 <A HREF = "Section_modify.html#mod_1">Atom styles</A>
<BR>
10.2 <A HREF = "Section_modify.html#mod_2">Bond, angle, dihedral, improper potentials</A>
<BR>
10.3 <A HREF = "Section_modify.html#mod_3">Compute styles</A>
<BR>
10.4 <A HREF = "Section_modify.html#mod_4">Dump styles</A>
<BR>
10.5 <A HREF = "Section_modify.html#mod_5">Dump custom output options</A>
<BR>
10.6 <A HREF = "Section_modify.html#mod_6">Fix styles</A>
<BR>
10.7 <A HREF = "Section_modify.html#mod_7">Input script commands</A>
<BR>
10.8 <A HREF = "Section_modify.html#mod_8">Kspace computations</A>
<BR>
10.9 <A HREF = "Section_modify.html#mod_9">Minimization styles</A>
<BR>
10.10 <A HREF = "Section_modify.html#mod_10">Pairwise potentials</A>
<BR>
10.11 <A HREF = "Section_modify.html#mod_11">Region styles</A>
<BR>
10.12 <A HREF = "Section_modify.html#mod_12">Body styles</A>
<BR>
10.13 <A HREF = "Section_modify.html#mod_13">Thermodynamic output options</A>
<BR>
10.14 <A HREF = "Section_modify.html#mod_14">Variable options</A>
<BR>
10.15 <A HREF = "Section_modify.html#mod_15">Submitting new features for inclusion in LAMMPS</A>
<BR></UL>
<LI><A HREF = "Section_python.html">Python interface</A>
<UL> 11.1 <A HREF = "Section_python.html#py_1">Overview of running LAMMPS from Python</A>
<BR>
11.2 <A HREF = "Section_python.html#py_2">Overview of using Python from a LAMMPS script</A>
<BR>
11.3 <A HREF = "Section_python.html#py_3">Building LAMMPS as a shared library</A>
<BR>
11.4 <A HREF = "Section_python.html#py_4">Installing the Python wrapper into Python</A>
<BR>
11.5 <A HREF = "Section_python.html#py_5">Extending Python with MPI to run in parallel</A>
<BR>
11.6 <A HREF = "Section_python.html#py_6">Testing the Python-LAMMPS interface</A>
<BR>
11.7 <A HREF = "py_7">Using LAMMPS from Python</A>
<BR>
11.8 <A HREF = "py_8">Example Python scripts that use LAMMPS</A>
<BR></UL>
<LI><A HREF = "Section_errors.html">Errors</A>
<UL> 12.1 <A HREF = "Section_errors.html#err_1">Common problems</A>
<BR>
12.2 <A HREF = "Section_errors.html#err_2">Reporting bugs</A>
<BR>
12.3 <A HREF = "Section_errors.html#err_3">Error & warning messages</A>
<BR></UL>
<LI><A HREF = "Section_history.html">Future and history</A>
<UL> 13.1 <A HREF = "Section_history.html#hist_1">Coming attractions</A>
<BR>
13.2 <A HREF = "Section_history.html#hist_2">Past versions</A>
<BR></UL>
</OL>
<!-- END_HTML_ONLY -->
</BODY>
</HTML>
</HTML>

10
doc/Manual.txt
View File

@ -1,7 +1,7 @@
<!-- HTML_ONLY --> <!-- HTML_ONLY -->
<HEAD> <HEAD>
<TITLE>LAMMPS Users Manual</TITLE> <TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="19 Aug 2015 version"> <META NAME="docnumber" CONTENT="10 Aug 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD> </HEAD>
@ -21,7 +21,7 @@
<H1></H1> <H1></H1>
LAMMPS Documentation :c,h3 LAMMPS Documentation :c,h3
19 Aug 2015 version :c,h4 10 Aug 2015 version :c,h4
Version info: :h4 Version info: :h4
@ -85,7 +85,7 @@ it gives quick access to documentation for all LAMMPS commands.
.. toctree:: .. toctree::
:maxdepth: 2 :maxdepth: 2
:numbered: // comment :numbered:
Section_intro Section_intro
Section_start Section_start
@ -105,8 +105,8 @@ it gives quick access to documentation for all LAMMPS commands.
Indices and tables Indices and tables
================== ==================
* :ref:`genindex` // comment * :ref:`genindex`
* :ref:`search` // comment * :ref:`search`
END_RST --> END_RST -->

4
doc/Section_commands.html
View File

@ -965,8 +965,8 @@ used if <a class="reference internal" href="Section_start.html#start-3"><span>LA
</tr> </tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_smd_ulsph_num_neighs.html"><em>smd/ulsph/num/neighs</em></a></td> <tr class="row-odd"><td><a class="reference internal" href="compute_smd_ulsph_num_neighs.html"><em>smd/ulsph/num/neighs</em></a></td>
<td><a class="reference internal" href="compute_smd_ulsph_strain.html"><em>smd/ulsph/strain</em></a></td> <td><a class="reference internal" href="compute_smd_ulsph_strain.html"><em>smd/ulsph/strain</em></a></td>
<td><code class="xref doc docutils literal"><span class="pre">smd/ulsph/strain/rate</span></code></td> <td><a class="reference internal" href="compute_smd_ulsph_strain_rate.html"><em>smd/ulsph/strain/rate</em></a></td>
<td><code class="xref doc docutils literal"><span class="pre">smd/ulpsh/stress</span></code></td> <td><a class="reference internal" href="compute_smd_ulsph_stress.html"><em>smd/ulsph/stress</em></a></td>
<td><a class="reference internal" href="compute_smd_vol.html"><em>smd/vol</em></a></td> <td><a class="reference internal" href="compute_smd_vol.html"><em>smd/vol</em></a></td>
<td><a class="reference internal" href="compute_temp_drude.html"><em>temp/drude</em></a></td> <td><a class="reference internal" href="compute_temp_drude.html"><em>temp/drude</em></a></td>
</tr> </tr>

4
doc/Section_commands.txt
View File

@ -754,8 +754,8 @@ package"_Section_start.html#start_3.
"smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html, "smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html,
"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html, "smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html,
"smd/ulsph/strain"_compute_smd_ulsph_strain.html, "smd/ulsph/strain"_compute_smd_ulsph_strain.html,
"smd/ulsph/strain/rate"_compute_smd_ulsph_strain/rate.html, "smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
"smd/ulpsh/stress"_compute_smd_ulpsh_stress.html, "smd/ulsph/stress"_compute_smd_ulsph_stress.html,
"smd/vol"_compute_smd_vol.html, "smd/vol"_compute_smd_vol.html,
"temp/drude"_compute_temp_drude.html, "temp/drude"_compute_temp_drude.html,
"temp/eff"_compute_temp_eff.html, "temp/eff"_compute_temp_eff.html,

2
doc/Section_example.html
View File

@ -291,7 +291,7 @@ section of the <a class="reference external" href="http://lammps.sandia.gov">LAM
<p>Here is how you might run and visualize one of the sample problems:</p> <p>Here is how you might run and visualize one of the sample problems:</p>
<div class="highlight-python"><div class="highlight"><pre>cd indent <div class="highlight-python"><div class="highlight"><pre>cd indent
cp ../../src/lmp_linux . # copy LAMMPS executable to this dir cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
lmp_linux &lt; in.indent # run the problem lmp_linux -in in.indent # run the problem
</pre></div> </pre></div>
</div> </div>
<p>Running the simulation produces the files <em>dump.indent</em> and <p>Running the simulation produces the files <em>dump.indent</em> and

2
doc/Section_example.txt
View File

@ -85,7 +85,7 @@ Here is how you might run and visualize one of the sample problems:
cd indent cd indent
cp ../../src/lmp_linux . # copy LAMMPS executable to this dir cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
lmp_linux < in.indent # run the problem :pre lmp_linux -in in.indent # run the problem :pre
Running the simulation produces the files {dump.indent} and Running the simulation produces the files {dump.indent} and
{log.lammps}. You can visualize the dump file as follows: {log.lammps}. You can visualize the dump file as follows:

4
doc/Section_python.html
View File

@ -510,7 +510,7 @@ interactively from the bench directory:</p>
<p>Either way, you should see the results of running the in.lj benchmark <p>Either way, you should see the results of running the in.lj benchmark
on a single processor appear on the screen, the same as if you had on a single processor appear on the screen, the same as if you had
typed something like:</p> typed something like:</p>
<div class="highlight-python"><div class="highlight"><pre>lmp_g++ &lt; in.lj <div class="highlight-python"><div class="highlight"><pre>lmp_g++ -in in.lj
</pre></div> </pre></div>
</div> </div>
</div> </div>
@ -532,7 +532,7 @@ pypar.finalize()
</pre></div> </pre></div>
</div> </div>
<p>and you should see the same output as if you had typed</p> <p>and you should see the same output as if you had typed</p>
<div class="highlight-python"><div class="highlight"><pre>% mpirun -np 4 lmp_g++ &lt; in.lj <div class="highlight-python"><div class="highlight"><pre>% mpirun -np 4 lmp_g++ -in in.lj
</pre></div> </pre></div>
</div> </div>
<p>Note that if you leave out the 3 lines from test.py that specify Pypar <p>Note that if you leave out the 3 lines from test.py that specify Pypar

4
doc/Section_python.txt
View File

@ -408,7 +408,7 @@ Either way, you should see the results of running the in.lj benchmark
on a single processor appear on the screen, the same as if you had on a single processor appear on the screen, the same as if you had
typed something like: typed something like:
lmp_g++ < in.lj :pre lmp_g++ -in in.lj :pre
[Test LAMMPS and Python in parallel:] :h5 [Test LAMMPS and Python in parallel:] :h5
@ -429,7 +429,7 @@ You can then run it in parallel as:
and you should see the same output as if you had typed and you should see the same output as if you had typed
% mpirun -np 4 lmp_g++ < in.lj :pre % mpirun -np 4 lmp_g++ -in in.lj :pre
Note that if you leave out the 3 lines from test.py that specify Pypar Note that if you leave out the 3 lines from test.py that specify Pypar
commands you will instantiate and run LAMMPS independently on each of commands you will instantiate and run LAMMPS independently on each of

6
doc/Section_start.html
View File

@ -1242,7 +1242,7 @@ Linux box, using mpirun to launch a parallel job:</p>
make linux make linux
cp lmp_linux ../bench cp lmp_linux ../bench
cd ../bench cd ../bench
mpirun -np 4 lmp_linux &lt; in.lj mpirun -np 4 lmp_linux -in in.lj
</pre></div> </pre></div>
</div> </div>
<p>See <a class="reference external" href="http://lammps.sandia.gov/bench.html">this page</a> for timings for this and the other benchmarks on <p>See <a class="reference external" href="http://lammps.sandia.gov/bench.html">this page</a> for timings for this and the other benchmarks on
@ -1338,8 +1338,8 @@ letter abbreviation can be used:</p>
<li>-v or -var</li> <li>-v or -var</li>
</ul> </ul>
<p>For example, lmp_ibm might be launched as follows:</p> <p>For example, lmp_ibm might be launched as follows:</p>
<div class="highlight-python"><div class="highlight"><pre>mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none &lt; in.alloy <div class="highlight-python"><div class="highlight"><pre>mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none -in in.alloy
mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none &lt; in.alloy mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none -in in.alloy
</pre></div> </pre></div>
</div> </div>
<p>Here are the details on the options:</p> <p>Here are the details on the options:</p>

6
doc/Section_start.txt
View File

@ -1205,7 +1205,7 @@ cd src
make linux make linux
cp lmp_linux ../bench cp lmp_linux ../bench
cd ../bench cd ../bench
mpirun -np 4 lmp_linux < in.lj :pre mpirun -np 4 lmp_linux -in in.lj :pre
See "this page"_bench for timings for this and the other benchmarks on See "this page"_bench for timings for this and the other benchmarks on
various platforms. Note that some of the example scripts require various platforms. Note that some of the example scripts require
@ -1321,8 +1321,8 @@ letter abbreviation can be used:
For example, lmp_ibm might be launched as follows: For example, lmp_ibm might be launched as follows:
mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none < in.alloy mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none -in in.alloy
mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none < in.alloy :pre mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none -in in.alloy :pre
Here are the details on the options: Here are the details on the options:

2
doc/delete_atoms.html
View File

@ -251,7 +251,7 @@ appear in the neighbor list, and thus will not be considered for
deletion by the <em>overlap</em> styles. You probably don&#8217;t want to be deletion by the <em>overlap</em> styles. You probably don&#8217;t want to be
deleting one atom in a bonded pair anyway.</p> deleting one atom in a bonded pair anyway.</p>
<p>The <em>bond yes</em> option cannot be used with molecular systems defined <p>The <em>bond yes</em> option cannot be used with molecular systems defined
using molecule template files via the <code class="xref doc docutils literal"><span class="pre">molecule</span></code> and using molecule template files via the <a class="reference internal" href="molecule.html"><em>molecule</em></a> and
<a class="reference internal" href="atom_style.html"><em>atom_style template</em></a> commands.</p> <a class="reference internal" href="atom_style.html"><em>atom_style template</em></a> commands.</p>
</div> </div>
<div class="section" id="related-commands"> <div class="section" id="related-commands">

2
doc/delete_atoms.txt
View File

@ -132,7 +132,7 @@ deletion by the {overlap} styles. You probably don't want to be
deleting one atom in a bonded pair anyway. deleting one atom in a bonded pair anyway.
The {bond yes} option cannot be used with molecular systems defined The {bond yes} option cannot be used with molecular systems defined
using molecule template files via the "molecule"_molecular.html and using molecule template files via the "molecule"_molecule.html and
"atom_style template"_atom_style.html commands. "atom_style template"_atom_style.html commands.
[Related commands:] [Related commands:]

6
doc/package.html
View File

@ -410,6 +410,12 @@ be set explicitly with this keyword to fine-tune performance. For
large cutoffs or with a small number of particles per GPU, increasing large cutoffs or with a small number of particles per GPU, increasing
the value can improve performance. The number of threads per atom must the value can improve performance. The number of threads per atom must
be a power of 2 and currently cannot be greater than 32.</p> be a power of 2 and currently cannot be greater than 32.</p>
<p>The <em>blocksize</em> keyword allows to tweak the number of threads used
per thread block. This number should be a multiple of 32 (for GPUs)
and its maximum depends on the specific GPU hardware. Typical choices
are 64, 128, or 256. A larger blocksize increases occupancy of individual
GPU cores, but reduces the total number of thread blocks, thus may lead
to load imbalance.</p>
<p>The <em>device</em> keyword can be used to tune parameters optimized for a <p>The <em>device</em> keyword can be used to tune parameters optimized for a
specific accelerator, when using OpenCL. For CUDA, the <em>device</em> specific accelerator, when using OpenCL. For CUDA, the <em>device</em>
keyword is ignored. Currently, the device type is limited to NVIDIA keyword is ignored. Currently, the device type is limited to NVIDIA

7
doc/package.txt
View File

@ -314,6 +314,13 @@ large cutoffs or with a small number of particles per GPU, increasing
the value can improve performance. The number of threads per atom must the value can improve performance. The number of threads per atom must
be a power of 2 and currently cannot be greater than 32. be a power of 2 and currently cannot be greater than 32.
The {blocksize} keyword allows to tweak the number of threads used
per thread block. This number should be a multiple of 32 (for GPUs)
and its maximum depends on the specific GPU hardware. Typical choices
are 64, 128, or 256. A larger blocksize increases occupancy of individual
GPU cores, but reduces the total number of thread blocks, thus may lead
to load imbalance.
The {device} keyword can be used to tune parameters optimized for a The {device} keyword can be used to tune parameters optimized for a
specific accelerator, when using OpenCL. For CUDA, the {device} specific accelerator, when using OpenCL. For CUDA, the {device}
keyword is ignored. Currently, the device type is limited to NVIDIA keyword is ignored. Currently, the device type is limited to NVIDIA

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@ -147,16 +147,15 @@ pair_coeff * * 1.0 0.8908987
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2> <h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>lj/cubic</em> style computes a truncated LJ interaction potential whose <p>The <em>lj/cubic</em> style computes a truncated LJ interaction potential
energy and force are continuous everywhere. whose energy and force are continuous everywhere. Inside the
Inside the inflection point the interaction is identical to the inflection point the interaction is identical to the standard 12/6
standard 12/6 <a class="reference internal" href="pair_lj.html"><em>Lennard-Jones</em></a> potential. <a class="reference internal" href="pair_lj.html"><em>Lennard-Jones</em></a> potential. The LJ function outside the
The LJ function outside the inflection point is replaced inflection point is replaced with a cubic function of distance. The
with a cubic function of distance. The energy, force, and second energy, force, and second derivative are continuous at the inflection
derivative are continuous at the inflection point. point. The cubic coefficient A3 is chosen so that both energy and
The cubic coefficient A3 is chosen so force go to zero at the cutoff distance. Outside the cutoff distance
that both energy and force go to zero at the cutoff distance. the energy and force are zero.</p>
Outside the cutoff distance the energy and force are zero.</p>
<img alt="_images/pair_lj_cubic.jpg" class="align-center" src="_images/pair_lj_cubic.jpg" /> <img alt="_images/pair_lj_cubic.jpg" class="align-center" src="_images/pair_lj_cubic.jpg" />
<p>The location of the inflection point rs is defined <p>The location of the inflection point rs is defined
by the LJ diameter, rs/sigma = (26/7)^1/6. The cutoff distance by the LJ diameter, rs/sigma = (26/7)^1/6. The cutoff distance
@ -165,11 +164,11 @@ The analytic expression for the
the cubic coefficient the cubic coefficient
A3*rmin^3/epsilon = 27.93... is given in the paper by A3*rmin^3/epsilon = 27.93... is given in the paper by
Holian and Ravelo <a class="reference internal" href="#holian"><span>(Holian)</span></a>.</p> Holian and Ravelo <a class="reference internal" href="#holian"><span>(Holian)</span></a>.</p>
<p>This potential is commonly used to study the shock mechanics <p>This potential is commonly used to study the shock mechanics of FCC
of FCC solids, as in Ravelo et al. <a class="reference internal" href="#ravelo"><span>(Ravelo)</span></a>.</p> solids, as in Ravelo et al. <a class="reference internal" href="#ravelo"><span>(Ravelo)</span></a>.</p>
<p>The following coefficients must be defined for each pair of atom <p>The following coefficients must be defined for each pair of atom types
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the example via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the example above,
above, or in the data file or restart files read by the or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> <a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p> commands, or by mixing as described below:</p>
<ul class="simple"> <ul class="simple">
@ -177,9 +176,9 @@ commands, or by mixing as described below:</p>
<li>sigma (distance units)</li> <li>sigma (distance units)</li>
</ul> </ul>
<p>Note that sigma is defined in the LJ formula as the zero-crossing <p>Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum, which distance for the potential, not as the energy minimum, which is
is located at rmin = 2^(1/6)*sigma. In the above example, sigma = 0.8908987, located at rmin = 2^(1/6)*sigma. In the above example, sigma =
so rmin = 1.</p> 0.8908987, so rmin = 1.</p>
<hr class="docutils" /> <hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are <p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
functionally the same as the corresponding style without the suffix. functionally the same as the corresponding style without the suffix.

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@ -21,16 +21,15 @@ pair_coeff * * 1.0 0.8908987 :pre
[Description:] [Description:]
The {lj/cubic} style computes a truncated LJ interaction potential whose The {lj/cubic} style computes a truncated LJ interaction potential
energy and force are continuous everywhere. whose energy and force are continuous everywhere. Inside the
Inside the inflection point the interaction is identical to the inflection point the interaction is identical to the standard 12/6
standard 12/6 "Lennard-Jones"_pair_lj.html potential. "Lennard-Jones"_pair_lj.html potential. The LJ function outside the
The LJ function outside the inflection point is replaced inflection point is replaced with a cubic function of distance. The
with a cubic function of distance. The energy, force, and second energy, force, and second derivative are continuous at the inflection
derivative are continuous at the inflection point. point. The cubic coefficient A3 is chosen so that both energy and
The cubic coefficient A3 is chosen so force go to zero at the cutoff distance. Outside the cutoff distance
that both energy and force go to zero at the cutoff distance. the energy and force are zero.
Outside the cutoff distance the energy and force are zero.
:c,image(Eqs/pair_lj_cubic.jpg) :c,image(Eqs/pair_lj_cubic.jpg)
@ -42,12 +41,12 @@ the cubic coefficient
A3*rmin^3/epsilon = 27.93... is given in the paper by A3*rmin^3/epsilon = 27.93... is given in the paper by
Holian and Ravelo "(Holian)"_#Holian. Holian and Ravelo "(Holian)"_#Holian.
This potential is commonly used to study the shock mechanics This potential is commonly used to study the shock mechanics of FCC
of FCC solids, as in Ravelo et al. "(Ravelo)"_#Ravelo. solids, as in Ravelo et al. "(Ravelo)"_#Ravelo.
The following coefficients must be defined for each pair of atom The following coefficients must be defined for each pair of atom types
types via the "pair_coeff"_pair_coeff.html command as in the example via the "pair_coeff"_pair_coeff.html command as in the example above,
above, or in the data file or restart files read by the or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html "read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below: commands, or by mixing as described below:
@ -55,9 +54,9 @@ epsilon (energy units)
sigma (distance units) :ul sigma (distance units) :ul
Note that sigma is defined in the LJ formula as the zero-crossing Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum, which distance for the potential, not as the energy minimum, which is
is located at rmin = 2^(1/6)*sigma. In the above example, sigma = 0.8908987, located at rmin = 2^(1/6)*sigma. In the above example, sigma =
so rmin = 1. 0.8908987, so rmin = 1.
:line :line

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