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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 .
11.5 <A HREF = "Section_python.html#py_5">Extending Python with MPI to run in parallel</A> </p>
<BR> </div>
11.6 <A HREF = "Section_python.html#py_6">Testing the Python-LAMMPS interface</A> Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
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<UL> 12.1 <A HREF = "Section_errors.html#err_1">Common problems</A>
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12.2 <A HREF = "Section_errors.html#err_2">Reporting bugs</A>
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@ -3,7 +3,7 @@
<!-- HTML_ONLY --> <!-- HTML_ONLY -->
<HEAD> <HEAD>
<TITLE>LAMMPS Users Manual</TITLE> <TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="29 Aug 2015 version"> <META NAME="docnumber" CONTENT="2 Sep 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD> </HEAD>
@ -21,7 +21,7 @@
<P><CENTER><H3>LAMMPS Documentation <P><CENTER><H3>LAMMPS Documentation
</H3></CENTER> </H3></CENTER>
<CENTER><H4>29 Aug 2015 version <CENTER><H4>2 Sep 2015 version
</H4></CENTER> </H4></CENTER>
<H4>Version info: <H4>Version info:
</H4> </H4>

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@ -1,7 +1,7 @@
<!-- HTML_ONLY --> <!-- HTML_ONLY -->
<HEAD> <HEAD>
<TITLE>LAMMPS Users Manual</TITLE> <TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="2 Sep 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
2 Sep 2015 version :c,h4 10 Aug 2015 version :c,h4
Version info: :h4 Version info: :h4
@ -85,7 +85,7 @@ it gives quick access to documentation for all LAMMPS commands.
.. toctree:: .. toctree::
:maxdepth: 2 :maxdepth: 2
:numbered: // comment :numbered:
Section_intro Section_intro
Section_start Section_start
@ -105,8 +105,8 @@ it gives quick access to documentation for all LAMMPS commands.
Indices and tables Indices and tables
================== ==================
* :ref:`genindex` // comment * :ref:`genindex`
* :ref:`search` // comment * :ref:`search`
END_RST --> END_RST -->

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@ -363,8 +363,8 @@ commands like <a class="reference internal" href="pair_coeff.html"><em>pair_coef
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>. See <a class="reference internal" href="Section_tools.html"><em>Section_tools</em></a> <a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>. See <a class="reference internal" href="Section_tools.html"><em>Section_tools</em></a>
for additional tools that can use CHARMM or AMBER to assign force for additional tools that can use CHARMM or AMBER to assign force
field coefficients and convert their output into LAMMPS input.</p> field coefficients and convert their output into LAMMPS input.</p>
<p>See <a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force <p>See <a class="reference internal" href="#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
field. See <a class="reference internal" href="special_bonds.html#cornell"><span>(Cornell)</span></a> for a description of the AMBER force field. See <a class="reference internal" href="#cornell"><span>(Cornell)</span></a> for a description of the AMBER force
field.</p> field.</p>
<p>These style choices compute force field formulas that are consistent <p>These style choices compute force field formulas that are consistent
with common options in CHARMM or AMBER. See each command&#8217;s with common options in CHARMM or AMBER. See each command&#8217;s
@ -389,7 +389,7 @@ atoms involved in the bond, angle, or torsion terms. DREIDING has an
<a class="reference internal" href="pair_hbond_dreiding.html"><em>explicit hydrogen bond term</em></a> to describe <a class="reference internal" href="pair_hbond_dreiding.html"><em>explicit hydrogen bond term</em></a> to describe
interactions involving a hydrogen atom on very electronegative atoms interactions involving a hydrogen atom on very electronegative atoms
(N, O, F).</p> (N, O, F).</p>
<p>See <a class="reference internal" href="special_bonds.html#mayo"><span>(Mayo)</span></a> for a description of the DREIDING force field</p> <p>See <a class="reference internal" href="#mayo"><span>(Mayo)</span></a> for a description of the DREIDING force field</p>
<p>These style choices compute force field formulas that are consistent <p>These style choices compute force field formulas that are consistent
with the DREIDING force field. See each command&#8217;s with the DREIDING force field. See each command&#8217;s
documentation for the formula it computes.</p> documentation for the formula it computes.</p>
@ -587,7 +587,7 @@ computations between frozen atoms by using this command:</p>
<div class="section" id="tip3p-water-model"> <div class="section" id="tip3p-water-model">
<span id="howto-7"></span><h2>6.7. TIP3P water model<a class="headerlink" href="#tip3p-water-model" title="Permalink to this headline"></a></h2> <span id="howto-7"></span><h2>6.7. TIP3P water model<a class="headerlink" href="#tip3p-water-model" title="Permalink to this headline"></a></h2>
<p>The TIP3P water model as implemented in CHARMM <p>The TIP3P water model as implemented in CHARMM
<a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> specifies a 3-site rigid water molecule with <a class="reference internal" href="#mackerell"><span>(MacKerell)</span></a> specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms. charges and Lennard-Jones parameters assigned to each of the 3 atoms.
In LAMMPS the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command can be used to hold In LAMMPS the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of the two O-H bonds and the H-O-H angle rigid. A bond style of
@ -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 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 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 set to 0.0, it corresponds to the original 1983 TIP3P model
<a class="reference internal" href="pair_lj.html#jorgensen"><span>(Jorgensen)</span></a>.</p> <a class="reference internal" href="#jorgensen"><span>(Jorgensen)</span></a>.</p>
<div class="line-block"> <div class="line-block">
<div class="line">O mass = 15.9994</div> <div class="line">O mass = 15.9994</div>
<div class="line">H mass = 1.008</div> <div class="line">H mass = 1.008</div>
@ -617,7 +617,7 @@ set to 0.0, it corresponds to the original 1983 TIP3P model
<div class="line"><br /></div> <div class="line"><br /></div>
</div> </div>
<p>These are the parameters to use for TIP3P with a long-range Coulombic <p>These are the parameters to use for TIP3P with a long-range Coulombic
solver (e.g. Ewald or PPPM in LAMMPS), see <a class="reference internal" href="pair_dipole.html#price"><span>(Price)</span></a> for solver (e.g. Ewald or PPPM in LAMMPS), see <a class="reference internal" href="#price"><span>(Price)</span></a> for
details:</p> details:</p>
<div class="line-block"> <div class="line-block">
<div class="line">O mass = 15.9994</div> <div class="line">O mass = 15.9994</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> 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 <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 atoms and the water molecule to run a rigid TIP4P model with a cutoff
<a class="reference internal" href="pair_lj.html#jorgensen"><span>(Jorgensen)</span></a>. Note that the OM distance is specified in <a class="reference internal" href="#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 the <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> command, not as part of the pair
coefficients.</p> coefficients.</p>
<div class="line-block"> <div class="line-block">
@ -766,7 +766,7 @@ the partial charge assignemnts change:</p>
<div class="line">H charge = 0.4238</div> <div class="line">H charge = 0.4238</div>
<div class="line"><br /></div> <div class="line"><br /></div>
</div> </div>
<p>See the <a class="reference internal" href="fix_temp_berendsen.html#berendsen"><span>(Berendsen)</span></a> reference for more details on both <p>See the <a class="reference internal" href="#berendsen"><span>(Berendsen)</span></a> reference for more details on both
the SPC and SPC/E models.</p> the SPC and SPC/E models.</p>
<p>Wikipedia also has a nice article on <a class="reference external" href="http://en.wikipedia.org/wiki/Water_model">water models</a>.</p> <p>Wikipedia also has a nice article on <a class="reference external" href="http://en.wikipedia.org/wiki/Water_model">water models</a>.</p>
<hr class="docutils" /> <hr class="docutils" />
@ -933,7 +933,7 @@ vectors of a general parallelepiped, where there is no restriction on
<strong>A</strong> x <strong>B</strong> . <strong>C</strong> &gt; 0. The equivalent LAMMPS <strong>a</strong>,**b**,**c** are a linear <strong>A</strong> x <strong>B</strong> . <strong>C</strong> &gt; 0. The equivalent LAMMPS <strong>a</strong>,**b**,**c** are a linear
rotation of <strong>A</strong>, <strong>B</strong>, and <strong>C</strong> and can be computed as follows:</p> rotation of <strong>A</strong>, <strong>B</strong>, and <strong>C</strong> and can be computed as follows:</p>
<img alt="_images/transform.jpg" class="align-center" src="_images/transform.jpg" /> <img alt="_images/transform.jpg" class="align-center" src="_images/transform.jpg" />
<p>where A = <a href="#id71"><span class="problematic" id="id72">|**A**|</span></a> indicates the scalar length of <strong>A</strong>. The ^ hat symbol <p>where A = <a href="#id73"><span class="problematic" id="id74">|**A**|</span></a> indicates the scalar length of <strong>A</strong>. The ^ hat symbol
indicates the corresponding unit vector. <em>beta</em> and <em>gamma</em> are angles indicates the corresponding unit vector. <em>beta</em> and <em>gamma</em> are angles
between the vectors described below. Note that by construction, between the vectors described below. Note that by construction,
<strong>a</strong>, <strong>b</strong>, and <strong>c</strong> have strictly positive x, y, and z components, respectively. <strong>a</strong>, <strong>b</strong>, and <strong>c</strong> have strictly positive x, y, and z components, respectively.
@ -1372,7 +1372,7 @@ per-atom vector.</p>
<p>When a quantity is accessed, as in many of the output commands <p>When a quantity is accessed, as in many of the output commands
discussed below, it can be referenced via the following bracket discussed below, it can be referenced via the following bracket
notation, where ID in this case is the ID of a compute. The leading notation, where ID in this case is the ID of a compute. The leading
&#8220;<a href="#id73"><span class="problematic" id="id74">c_</span></a>&#8221; would be replaced by &#8220;<a href="#id75"><span class="problematic" id="id76">f_</span></a>&#8221; for a fix, or &#8220;<a href="#id77"><span class="problematic" id="id78">v_</span></a>&#8221; for a variable:</p> &#8220;<a href="#id75"><span class="problematic" id="id76">c_</span></a>&#8221; would be replaced by &#8220;<a href="#id77"><span class="problematic" id="id78">f_</span></a>&#8221; for a fix, or &#8220;<a href="#id79"><span class="problematic" id="id80">v_</span></a>&#8221; for a variable:</p>
<table border="1" class="docutils"> <table border="1" class="docutils">
<colgroup> <colgroup>
<col width="21%" /> <col width="21%" />
@ -1918,7 +1918,7 @@ the deformation must be chosen judiciously, and care must be taken to
fully equilibrate the deformed cell before sampling the stress fully equilibrate the deformed cell before sampling the stress
tensor. Another approach is to sample the triclinic cell fluctuations tensor. Another approach is to sample the triclinic cell fluctuations
that occur in an NPT simulation. This method can also be slow to that occur in an NPT simulation. This method can also be slow to
converge and requires careful post-processing <a class="reference internal" href="pair_sdk.html#shinoda"><span>(Shinoda)</span></a></p> converge and requires careful post-processing <a class="reference internal" href="#shinoda"><span>(Shinoda)</span></a></p>
<hr class="docutils" /> <hr class="docutils" />
</div> </div>
<div class="section" id="library-interface-to-lammps"> <div class="section" id="library-interface-to-lammps">
@ -1935,9 +1935,10 @@ directly. The C++ code in the functions illustrates how to invoke
internal LAMMPS operations. Note that LAMMPS classes are defined internal LAMMPS operations. Note that LAMMPS classes are defined
within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++ within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++
application.</p> application.</p>
<p>Library.cpp contains these 4 functions:</p> <p>Library.cpp contains these 5 basic functions:</p>
<div class="highlight-python"><div class="highlight"><pre>void lammps_open(int, char **, MPI_Comm, void **) <div class="highlight-python"><div class="highlight"><pre>void lammps_open(int, char **, MPI_Comm, void **)
void lammps_close(void *) void lammps_close(void *)
int lammps_version(void *)
void lammps_file(void *, char *) void lammps_file(void *, char *)
char *lammps_command(void *, char *) char *lammps_command(void *, char *)
</pre></div> </pre></div>
@ -1959,6 +1960,13 @@ syncing them up periodically. Or it might instantiate multiple
instances of LAMMPS to perform different calculations.</p> instances of LAMMPS to perform different calculations.</p>
<p>The lammps_close() function is used to shut down an instance of LAMMPS <p>The lammps_close() function is used to shut down an instance of LAMMPS
and free all its memory.</p> 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>
<p>The lammps_file() and lammps_command() functions are used to pass a <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 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 command in an input script. Thus the calling code can read or
@ -2283,7 +2291,7 @@ fix produces a global array as output with one row of values per
chunk.</p> chunk.</p>
</div> </div>
<div class="section" id="compute-chunk-commands"> <div class="section" id="compute-chunk-commands">
<h3>6.23.3. Compute <a href="#id68"><span class="problematic" id="id69">*</span></a>/chunk commands:<a class="headerlink" href="#compute-chunk-commands" title="Permalink to this headline"></a></h3> <h3>6.23.3. Compute <a href="#id70"><span class="problematic" id="id71">*</span></a>/chunk commands:<a class="headerlink" href="#compute-chunk-commands" title="Permalink to this headline"></a></h3>
<p>Currently the following computes operate on chunks of atoms to produce <p>Currently the following computes operate on chunks of atoms to produce
per-chunk values.</p> per-chunk values.</p>
<ul class="simple"> <ul class="simple">
@ -2533,7 +2541,7 @@ well.</p>
</div> </div>
<div class="section" id="adiabatic-core-shell-model"> <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> <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="pair_cs.html#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="#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 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 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 split into a core and a shell where the latter is meant to react to
@ -2715,7 +2723,7 @@ fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector
model, representes induced dipoles by a pair of charges (the core atom model, representes induced dipoles by a pair of charges (the core atom
and the Drude particle) connected by a harmonic spring. The Drude and the Drude particle) connected by a harmonic spring. The Drude
model has a number of features aimed at its use in molecular systems model has a number of features aimed at its use in molecular systems
(<a class="reference internal" href="tutorial_drude.html#lamoureux"><span>Lamoureux and Roux</span></a>):</p> (<a class="reference internal" href="#lamoureux"><span>Lamoureux and Roux</span></a>):</p>
<ul class="simple"> <ul class="simple">
<li>Thermostating of the additional degrees of freedom associated with the <li>Thermostating of the additional degrees of freedom associated with the
induced dipoles at very low temperature, in terms of the reduced induced dipoles at very low temperature, in terms of the reduced

11
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@ -1852,10 +1852,11 @@ internal LAMMPS operations. Note that LAMMPS classes are defined
within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++ within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++
application. application.
Library.cpp contains these 4 functions: Library.cpp contains these 5 basic functions:
void lammps_open(int, char **, MPI_Comm, void **) void lammps_open(int, char **, MPI_Comm, void **)
void lammps_close(void *) void lammps_close(void *)
int lammps_version(void *)
void lammps_file(void *, char *) void lammps_file(void *, char *)
char *lammps_command(void *, char *) :pre char *lammps_command(void *, char *) :pre
@ -1880,6 +1881,14 @@ instances of LAMMPS to perform different calculations.
The lammps_close() function is used to shut down an instance of LAMMPS The lammps_close() function is used to shut down an instance of LAMMPS
and free all its memory. 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 lammps_file() and lammps_command() functions are used to pass a 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 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 command in an input script. Thus the calling code can read or

1
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@ -600,6 +600,7 @@ from a C++ or C or Fortran program.</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">lmp</span><span class="o">.</span><span class="n">close</span><span class="p">()</span> <span class="c"># destroy a LAMMPS object</span> <div class="highlight-python"><div class="highlight"><pre><span class="n">lmp</span><span class="o">.</span><span class="n">close</span><span class="p">()</span> <span class="c"># destroy a LAMMPS object</span>
</pre></div> </pre></div>
</div> </div>
<p>version = lmp.version() # return the numerical version id, e.g. LAMMPS 2 Sep 2015 -&gt; 20150902</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">lmp</span><span class="o">.</span><span class="n">file</span><span class="p">(</span><span class="nb">file</span><span class="p">)</span> <span class="c"># run an entire input script, file = &quot;in.lj&quot;</span> <div class="highlight-python"><div class="highlight"><pre><span class="n">lmp</span><span class="o">.</span><span class="n">file</span><span class="p">(</span><span class="nb">file</span><span class="p">)</span> <span class="c"># run an entire input script, file = &quot;in.lj&quot;</span>
<span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="n">cmd</span><span class="p">)</span> <span class="c"># invoke a single LAMMPS command, cmd = &quot;run 100&quot;</span> <span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="n">cmd</span><span class="p">)</span> <span class="c"># invoke a single LAMMPS command, cmd = &quot;run 100&quot;</span>
</pre></div> </pre></div>

2
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@ -498,6 +498,8 @@ lmp = lammps("g++",list) :pre
lmp.close() # destroy a LAMMPS object :pre lmp.close() # destroy a LAMMPS object :pre
version = lmp.version() # return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902
lmp.file(file) # run an entire input script, file = "in.lj" lmp.file(file) # run an entire input script, file = "in.lj"
lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100" :pre lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100" :pre

35
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@ -347,6 +347,41 @@ non-orthogonal or rotated lattices.</p>
<p>Note that whenever the lattice command is used, the values of the <p>Note that whenever the lattice command is used, the values of the
lattice spacings LAMMPS calculates are printed out. Thus their effect lattice spacings LAMMPS calculates are printed out. Thus their effect
in commands that use the spacings should be decipherable.</p> in commands that use the spacings should be decipherable.</p>
<hr class="docutils" />
<p>Example commands for generating a Wurtzite crystal (courtesy
of Aidan Thompson), with its 8 atom unit cell.</p>
<div class="highlight-python"><div class="highlight"><pre>variable a equal 4.340330
variable b equal $a*sqrt(3.0)
variable c equal $a*sqrt(8.0/3.0)
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>variable 1_3 equal 1.0/3.0
variable 2_3 equal 2.0/3.0
variable 1_6 equal 1.0/6.0
variable 5_6 equal 5.0/6.0
variable 1_12 equal 1.0/12.0
variable 5_12 equal 5.0/12/0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>lattice custom 1.0 &amp;
a1 $a 0.0 0.0 &amp;
a2 0.0 $b 0.0 &amp;
a3 0.0 0.0 $c &amp;
basis 0.0 0.0 0.0 &amp;
basis 0.5 0.5 0.0 &amp;
basis ${1_3} 0.0 0.5 &amp;
basis ${5_6} 0.5 0.5 &amp;
basis 0.0 0.0 0.625 &amp;
basis 0.5 0.5 0.625 &amp;
basis ${1_3} 0.0 0.125 &amp;
basis ${5_6} 0.5 0.125
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>region myreg block 0 1 0 1 0 1
create_box 2 myreg
create_atoms 1 box
</pre></div>
</div>
</div> </div>
<hr class="docutils" /> <hr class="docutils" />
<div class="section" id="restrictions"> <div class="section" id="restrictions">

33
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@ -239,6 +239,39 @@ in commands that use the spacings should be decipherable.
:line :line
Example commands for generating a Wurtzite crystal (courtesy
of Aidan Thompson), with its 8 atom unit cell.
variable a equal 4.340330
variable b equal $a*sqrt(3.0)
variable c equal $a*sqrt(8.0/3.0) :pre
variable 1_3 equal 1.0/3.0
variable 2_3 equal 2.0/3.0
variable 1_6 equal 1.0/6.0
variable 5_6 equal 5.0/6.0
variable 1_12 equal 1.0/12.0
variable 5_12 equal 5.0/12/0 :pre
lattice custom 1.0 &
a1 $a 0.0 0.0 &
a2 0.0 $b 0.0 &
a3 0.0 0.0 $c &
basis 0.0 0.0 0.0 &
basis 0.5 0.5 0.0 &
basis $\{1_3\} 0.0 0.5 &
basis $\{5_6\} 0.5 0.5 &
basis 0.0 0.0 0.625 &
basis 0.5 0.5 0.625 &
basis $\{1_3\} 0.0 0.125 &
basis $\{5_6\} 0.5 0.125 :pre
region myreg block 0 1 0 1 0 1
create_box 2 myreg
create_atoms 1 box :pre
:line
[Restrictions:] [Restrictions:]
The {a1,a2,a3,basis} keywords can only be used with style {custom}. The {a1,a2,a3,basis} keywords can only be used with style {custom}.

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@ -166,7 +166,7 @@
<em>python</em> arg = function <em>python</em> arg = function
<em>equal</em> or <em>atom</em> args = one formula containing numbers, thermo keywords, math operations, group functions, atom values and vectors, compute/fix/variable references <em>equal</em> or <em>atom</em> args = one formula containing numbers, thermo keywords, math operations, group functions, atom values and vectors, compute/fix/variable references
numbers = 0.0, 100, -5.4, 2.8e-4, etc numbers = 0.0, 100, -5.4, 2.8e-4, etc
constants = PI constants = PI, version
thermo keywords = vol, ke, press, etc from <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> thermo keywords = vol, ke, press, etc from <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a>
math operators = (), -x, x+y, x-y, x*y, x/y, x^y, x%y, math operators = (), -x, x+y, x-y, x*y, x/y, x^y, x%y,
x == y, x != y, x &amp;lt y, x &amp;lt= y, x &amp;gt y, x &amp;gt= y, x &amp;&amp; y, x || y, !x x == y, x != y, x &amp;lt y, x &amp;lt= y, x &amp;gt y, x &amp;gt= y, x &amp;&amp; y, x || y, !x
@ -525,6 +525,16 @@ that define a <a class="reference internal" href="group.html"><em>group</em></a>
When they invoke the atom-style variable, only atoms in the group are When they invoke the atom-style variable, only atoms in the group are
inlcuded in the formula evaluation. The variable evaluates to 0.0 for inlcuded in the formula evaluation. The variable evaluates to 0.0 for
atoms not in the group.</p> atoms not in the group.</p>
<p>Constants are set at compile time and cannot be changed. <em>PI</em> will
return the number 3.14159265358979323846, <em>version</em> will return a
numeric version code of the current LAMMPS version (e.g. version
2 Sep 2015 will return the number 20150902). The corresponding value
for newer versions of LAMMPS will be larger, for older versions of
LAMMPS will be smaller. This can be used to make input scripts adapt
automatically to LAMMPS versions, for example:</p>
<div class="highlight-python"><div class="highlight"><pre>if $(version&lt;20140513) then &quot;communicate vel yes&quot; else &quot;comm_modify vel yes&quot;
</pre></div>
</div>
<p>The thermo keywords allowed in a formula are those defined by the <p>The thermo keywords allowed in a formula are those defined by the
<a class="reference internal" href="thermo_style.html"><em>thermo_style custom</em></a> command. Thermo keywords that <a class="reference internal" href="thermo_style.html"><em>thermo_style custom</em></a> command. Thermo keywords that
require a <a class="reference internal" href="compute.html"><em>compute</em></a> to calculate their values such as require a <a class="reference internal" href="compute.html"><em>compute</em></a> to calculate their values such as

14
doc/variable.txt
View File

@ -44,7 +44,7 @@ style = {delete} or {index} or {loop} or {world} or {universe} or
{python} arg = function {python} arg = function
{equal} or {atom} args = one formula containing numbers, thermo keywords, math operations, group functions, atom values and vectors, compute/fix/variable references {equal} or {atom} args = one formula containing numbers, thermo keywords, math operations, group functions, atom values and vectors, compute/fix/variable references
numbers = 0.0, 100, -5.4, 2.8e-4, etc numbers = 0.0, 100, -5.4, 2.8e-4, etc
constants = PI constants = PI, version
thermo keywords = vol, ke, press, etc from "thermo_style"_thermo_style.html thermo keywords = vol, ke, press, etc from "thermo_style"_thermo_style.html
math operators = (), -x, x+y, x-y, x*y, x/y, x^y, x%y, math operators = (), -x, x+y, x-y, x*y, x/y, x^y, x%y,
x == y, x != y, x &lt y, x &lt= y, x &gt y, x &gt= y, x && y, x || y, !x x == y, x != y, x &lt y, x &lt= y, x &gt y, x &gt= y, x && y, x || y, !x
@ -415,7 +415,7 @@ values, atom vectors, compute references, fix references, and
references to other variables. references to other variables.
Number: 0.2, 100, 1.0e20, -15.4, etc Number: 0.2, 100, 1.0e20, -15.4, etc
Constant: PI Constant: PI, version
Thermo keywords: vol, pe, ebond, etc Thermo keywords: vol, pe, ebond, etc
Math operators: (), -x, x+y, x-y, x*y, x/y, x^y, x%y, Math operators: (), -x, x+y, x-y, x*y, x/y, x^y, x%y,
Math operators: (), -x, x+y, x-y, x*y, x/y, x^y, x%y, x == y, x != y, x &lt y, x &lt= y, x &gt y, x &gt= y, x && y, x || y, !x Math operators: (), -x, x+y, x-y, x*y, x/y, x^y, x%y, x == y, x != y, x &lt y, x &lt= y, x &gt y, x &gt= y, x && y, x || y, !x
@ -457,6 +457,16 @@ When they invoke the atom-style variable, only atoms in the group are
inlcuded in the formula evaluation. The variable evaluates to 0.0 for inlcuded in the formula evaluation. The variable evaluates to 0.0 for
atoms not in the group. atoms not in the group.
Constants are set at compile time and cannot be changed. {PI} will
return the number 3.14159265358979323846, {version} will return a
numeric version code of the current LAMMPS version (e.g. version
2 Sep 2015 will return the number 20150902). The corresponding value
for newer versions of LAMMPS will be larger, for older versions of
LAMMPS will be smaller. This can be used to make input scripts adapt
automatically to LAMMPS versions, for example:
if $(version<20140513) then "communicate vel yes" else "comm_modify vel yes" :pre
The thermo keywords allowed in a formula are those defined by the The thermo keywords allowed in a formula are those defined by the
"thermo_style custom"_thermo_style.html command. Thermo keywords that "thermo_style custom"_thermo_style.html command. Thermo keywords that
require a "compute"_compute.html to calculate their values such as require a "compute"_compute.html to calculate their values such as