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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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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="28 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>28 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="28 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
28 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 -->

6
doc/Section_commands.html
View File

@ -968,14 +968,14 @@ used if <a class="reference internal" href="Section_start.html#start-3"><span>LA
<td><a class="reference internal" href="compute_smd_ulsph_strain_rate.html"><em>smd/ulsph/strain/rate</em></a></td> <td><a class="reference internal" href="compute_smd_ulsph_strain_rate.html"><em>smd/ulsph/strain/rate</em></a></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_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_tally.html"><em>tally</em></a></td>
</tr> </tr>
<tr class="row-even"><td><a class="reference internal" href="compute_temp_eff.html"><em>temp/eff</em></a></td> <tr class="row-even"><td><a class="reference internal" href="compute_temp_drude.html"><em>temp/drude</em></a></td>
<td><a class="reference internal" href="compute_temp_eff.html"><em>temp/eff</em></a></td>
<td><a class="reference internal" href="compute_temp_deform_eff.html"><em>temp/deform/eff</em></a></td> <td><a class="reference internal" href="compute_temp_deform_eff.html"><em>temp/deform/eff</em></a></td>
<td><a class="reference internal" href="compute_temp_region_eff.html"><em>temp/region/eff</em></a></td> <td><a class="reference internal" href="compute_temp_region_eff.html"><em>temp/region/eff</em></a></td>
<td><a class="reference internal" href="compute_temp_rotate.html"><em>temp/rotate</em></a></td> <td><a class="reference internal" href="compute_temp_rotate.html"><em>temp/rotate</em></a></td>
<td><a class="reference internal" href="compute_xrd.html"><em>xrd</em></a></td> <td><a class="reference internal" href="compute_xrd.html"><em>xrd</em></a></td>
<td>&nbsp;</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>

1
doc/Section_commands.txt
View File

@ -758,6 +758,7 @@ package"_Section_start.html#start_3.
"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html, "smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
"smd/ulsph/stress"_compute_smd_ulsph_stress.html, "smd/ulsph/stress"_compute_smd_ulsph_stress.html,
"smd/vol"_compute_smd_vol.html, "smd/vol"_compute_smd_vol.html,
"tally"_compute_tally.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,
"temp/deform/eff"_compute_temp_deform_eff.html, "temp/deform/eff"_compute_temp_deform_eff.html,

20
doc/Section_modify.html
View File

@ -474,8 +474,8 @@ per-atom kinetic energy.</p>
class. See compute.h for details.</p> class. See compute.h for details.</p>
<table border="1" class="docutils"> <table border="1" class="docutils">
<colgroup> <colgroup>
<col width="22%" /> <col width="24%" />
<col width="78%" /> <col width="76%" />
</colgroup> </colgroup>
<tbody valign="top"> <tbody valign="top">
<tr class="row-odd"><td>init</td> <tr class="row-odd"><td>init</td>
@ -520,11 +520,21 @@ class. See compute.h for details.</p>
<tr class="row-even"><td>restore_bias_all</td> <tr class="row-even"><td>restore_bias_all</td>
<td>same as before, but for all atoms in group (optional)</td> <td>same as before, but for all atoms in group (optional)</td>
</tr> </tr>
<tr class="row-odd"><td>memory_usage</td> <tr class="row-odd"><td>pair_tally_callback</td>
<td>callback function for <em>tally</em>-style computes (optional).</td>
</tr>
<tr class="row-even"><td>memory_usage</td>
<td>tally memory usage (optional)</td> <td>tally memory usage (optional)</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
<p>Tally-style computes are a special case, as their computation is done
in two stages: the callback function is registered with the pair style
and then called from the Pair::ev_tally() function, which is called for
each pair after force and energy has been computed for this pair. Then
the tallied values are retrieved with the standard compute_scalar or
compute_vector or compute_peratom methods. The USER-TALLY package
provides <a href="#id7"><span class="problematic" id="id8">*</span></a>examples*_compute_tally.html for utilizing this mechanism.</p>
<hr class="docutils" /> <hr class="docutils" />
</div> </div>
<div class="section" id="dump-styles"> <div class="section" id="dump-styles">
@ -1098,7 +1108,7 @@ the code accesses data structures, performs its operations, and is
formatted similar to other LAMMPS source files, including the use of formatted similar to other LAMMPS source files, including the use of
the error class for error and warning messages.</li> the error class for error and warning messages.</li>
<li>If you want your contribution to be added as a user-contributed <li>If you want your contribution to be added as a user-contributed
feature, and it&#8217;s a single file (actually a <a href="#id8"><span class="problematic" id="id9">*</span></a>.cpp and <a href="#id10"><span class="problematic" id="id11">*</span></a>.h file) it can feature, and it&#8217;s a single file (actually a <a href="#id10"><span class="problematic" id="id11">*</span></a>.cpp and <a href="#id12"><span class="problematic" id="id13">*</span></a>.h file) it can
rapidly be added to the USER-MISC directory. Send us the one-line rapidly be added to the USER-MISC directory. Send us the one-line
entry to add to the USER-MISC/README file in that dir, along with the entry to add to the USER-MISC/README file in that dir, along with the
2 source files. You can do this multiple times if you wish to 2 source files. You can do this multiple times if you wish to
@ -1148,7 +1158,7 @@ directories under examples/USER for examples of input scripts other
users provided for their packages.</li> users provided for their packages.</li>
<li>If there is a paper of yours describing your feature (either the <li>If there is a paper of yours describing your feature (either the
algorithm/science behind the feature itself, or its initial usage, or algorithm/science behind the feature itself, or its initial usage, or
its implementation in LAMMPS), you can add the citation to the <a href="#id12"><span class="problematic" id="id13">*</span></a>.cpp its implementation in LAMMPS), you can add the citation to the <a href="#id14"><span class="problematic" id="id15">*</span></a>.cpp
source file. See src/USER-EFF/atom_vec_electron.cpp for an example. source file. See src/USER-EFF/atom_vec_electron.cpp for an example.
A LaTeX citation is stored in a variable at the top of the file and a A LaTeX citation is stored in a variable at the top of the file and a
single line of code that references the variable is added to the single line of code that references the variable is added to the

9
doc/Section_modify.txt
View File

@ -275,8 +275,17 @@ remove_bias: remove velocity bias from one atom (optional)
remove_bias_all: remove velocity bias from all atoms in group (optional) remove_bias_all: remove velocity bias from all atoms in group (optional)
restore_bias: restore velocity bias for one atom after remove_bias (optional) restore_bias: restore velocity bias for one atom after remove_bias (optional)
restore_bias_all: same as before, but for all atoms in group (optional) restore_bias_all: same as before, but for all atoms in group (optional)
pair_tally_callback: callback function for {tally}-style computes (optional).
memory_usage: tally memory usage (optional) :tb(s=:) memory_usage: tally memory usage (optional) :tb(s=:)
Tally-style computes are a special case, as their computation is done
in two stages: the callback function is registered with the pair style
and then called from the Pair::ev_tally() function, which is called for
each pair after force and energy has been computed for this pair. Then
the tallied values are retrieved with the standard compute_scalar or
compute_vector or compute_peratom methods. The USER-TALLY package
provides {examples}_compute_tally.html for utilizing this mechanism.
:line :line
10.4 Dump styles :link(mod_4),h4 10.4 Dump styles :link(mod_4),h4

18
doc/Section_packages.html
View File

@ -712,7 +712,7 @@ on how to build LAMMPS with both kinds of auxiliary libraries.</p>
<li></li> <li></li>
</ul> </ul>
</td> </td>
<td>h5md</td> <td>lib/h5md</td>
</tr> </tr>
<tr class="row-even"><td>USER-INTEL</td> <tr class="row-even"><td>USER-INTEL</td>
<td>Vectorized CPU and Intel(R) coprocessor styles</td> <td>Vectorized CPU and Intel(R) coprocessor styles</td>
@ -882,7 +882,21 @@ on how to build LAMMPS with both kinds of auxiliary libraries.</p>
</ul> </ul>
</td> </td>
</tr> </tr>
<tr class="row-even"><td>&nbsp;</td> <tr class="row-even"><td>USER-TALLY</td>
<td>Pairwise tallied computes</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><code class="xref doc docutils literal"><span class="pre">compute</span></code></td>
<td>USER/tally</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>&nbsp;</td>
<td>&nbsp;</td> <td>&nbsp;</td>
<td>&nbsp;</td> <td>&nbsp;</td>
<td>&nbsp;</td> <td>&nbsp;</td>

3
doc/Section_packages.txt
View File

@ -123,7 +123,7 @@ USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"c
USER-DRUDE, Drude oscillators, Dequidt & Devemy & Padua (3), "tutorial"_tutorial_drude.html, USER/drude, -, - USER-DRUDE, Drude oscillators, Dequidt & Devemy & Padua (3), "tutorial"_tutorial_drude.html, USER/drude, -, -
USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, - USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, - USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, -
USER-H5MD, dump output via HDF5, Pierre de Buyl (KU Leuven), "dump h5md"_dump_h5md.html, -, -, h5md USER-H5MD, dump output via HDF5, Pierre de Buyl (KU Leuven), "dump h5md"_dump_h5md.html, -, -, lib/h5md
USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, - USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, -
USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, - USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, -
USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, - USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
@ -136,6 +136,7 @@ USER-QUIP, QUIP/libatoms interface, Albert Bartok-Partay (U Cambridge), "pair_st
USER-REAXC, C version of ReaxFF, Metin Aktulga (LBNL), "pair_style reaxc"_pair_reax_c.html, reax, -, - USER-REAXC, C version of ReaxFF, Metin Aktulga (LBNL), "pair_style reaxc"_pair_reax_c.html, reax, -, -
USER-SMD, smoothed Mach dynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, -, - USER-SMD, smoothed Mach dynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, -, -
USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, - USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, -
USER-TALLY, Pairwise tallied computes, Axel Kohlmeyer (Temple U), "compute <...>/tally"_compute_tally.html, USER/tally, -, -
:tb(ea=c) :tb(ea=c)
:link(atc,http://lammps.sandia.gov/pictures.html#atc) :link(atc,http://lammps.sandia.gov/pictures.html#atc)

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@ -0,0 +1,266 @@
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<div class="section" id="compute-force-tally-command">
<span id="index-0"></span><h1>compute force/tally command<a class="headerlink" href="#compute-force-tally-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="compute-pe-tally-command">
<h1>compute pe/tally command<a class="headerlink" href="#compute-pe-tally-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="compute-stress-tally-command">
<h1>compute stress/tally command<a class="headerlink" href="#compute-stress-tally-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID style group2-ID
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>style = <em>force/tally</em> or <em>pe/tally</em> or <em>stress/tally</em></li>
<li>group2-ID = group ID of second (or same) group</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 lower force/tally upper
compute 1 left pe/tally right
compute 1 lower stress/tally lower
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that calculates properties between two groups of
atoms by accumulating them from pairwise non-bonded computations. The
two groups can be the same. This is similar to <a class="reference internal" href="compute_group_group.html"><em>compute group/group</em></a> only that the data is
accumulated directly during the non-bonded force computation. The
computes <em>force/tally</em>, <em>pe/tally</em>, <em>stress/tally</em>, and
<em>heat/flux/tally</em> are primarily provided as example how to program
additional, more sophisticated computes using the tally mechanism.</p>
<hr class="docutils" />
<p>The pairwise contributions are computing via a callback that the
compute registers with the non-bonded pairwise force computation.
This limits the use to systems that have no bonds, no Kspace, and no
manybody interactions. On the other hand, the computation does not
have to compute forces or energies a second time and thus can be much
more efficient. The callback mechanism allows to write more complex
pairwise property computations.</p>
<hr class="docutils" />
<p><strong>Output info:</strong></p>
<p>Compute <em>pe/tally</em> calculates a global scalar (the energy) and a per
atom scalar (the contributions of the single atom to the global
scalar). Compute <em>force/tally</em> calculates a global scalar (the force
magnitude) and a per atom 3-element vector (force contribution from
each atom). Compute <em>stress/tally</em> calculates a global scalar
(average of the diagonal elements of the stress tensor) and a per atom
vector (the 6 elements of stress tensor contributions from the
individual atom).</p>
<p>Both the scalar and vector values calculated by this compute are
&#8220;extensive&#8221;.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the USER-TALLY package. It is only enabled
if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>Not all pair styles can be evaluated in a pairwise mode as required by
this compute. For example, 3-body and other many-body potentials,
such as <a class="reference internal" href="pair_tersoff.html"><em>Tersoff</em></a> and
<a class="reference internal" href="pair_sw.html"><em>Stillinger-Weber</em></a> cannot be used. <a class="reference internal" href="pair_eam.html"><em>EAM</em></a>
potentials only include the pair potential portion of the EAM
interaction when used by this compute, not the embedding term. Also
bonded or Kspace interactions do not contribute to this compute.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a href="#id1"><span class="problematic" id="id2">*</span></a>compute group/group*_compute_group_group.html, <a href="#id3"><span class="problematic" id="id4">*</span></a>compute
heat/flux*_compute_heat_flux.html</p>
<p><strong>Default:</strong> none</p>
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84
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@ -0,0 +1,84 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute force/tally command :h3
compute pe/tally command :h3
compute stress/tally command :h3
[Syntax:]
compute ID group-ID style group2-ID :pre
ID, group-ID are documented in "compute"_compute.html command
style = {force/tally} or {pe/tally} or {stress/tally}
group2-ID = group ID of second (or same) group :ul
[Examples:]
compute 1 lower force/tally upper
compute 1 left pe/tally right
compute 1 lower stress/tally lower :pre
[Description:]
Define a computation that calculates properties between two groups of
atoms by accumulating them from pairwise non-bonded computations. The
two groups can be the same. This is similar to "compute
group/group"_compute_group_group.html only that the data is
accumulated directly during the non-bonded force computation. The
computes {force/tally}, {pe/tally}, {stress/tally}, and
{heat/flux/tally} are primarily provided as example how to program
additional, more sophisticated computes using the tally mechanism.
:line
The pairwise contributions are computing via a callback that the
compute registers with the non-bonded pairwise force computation.
This limits the use to systems that have no bonds, no Kspace, and no
manybody interactions. On the other hand, the computation does not
have to compute forces or energies a second time and thus can be much
more efficient. The callback mechanism allows to write more complex
pairwise property computations.
:line
[Output info:]
Compute {pe/tally} calculates a global scalar (the energy) and a per
atom scalar (the contributions of the single atom to the global
scalar). Compute {force/tally} calculates a global scalar (the force
magnitude) and a per atom 3-element vector (force contribution from
each atom). Compute {stress/tally} calculates a global scalar
(average of the diagonal elements of the stress tensor) and a per atom
vector (the 6 elements of stress tensor contributions from the
individual atom).
Both the scalar and vector values calculated by this compute are
"extensive".
[Restrictions:]
This compute is part of the USER-TALLY package. It is only enabled
if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
Not all pair styles can be evaluated in a pairwise mode as required by
this compute. For example, 3-body and other many-body potentials,
such as "Tersoff"_pair_tersoff.html and
"Stillinger-Weber"_pair_sw.html cannot be used. "EAM"_pair_eam.html
potentials only include the pair potential portion of the EAM
interaction when used by this compute, not the embedding term. Also
bonded or Kspace interactions do not contribute to this compute.
[Related commands:]
{compute group/group}_compute_group_group.html, {compute
heat/flux}_compute_heat_flux.html
[Default:] none

8
doc/genindex.html
View File

@ -440,6 +440,10 @@
</dt> </dt>
<dt><a href="compute_tally.html#index-0">compute force/tally</a>
</dt>
<dt><a href="compute_group_group.html#index-0">compute group/group</a> <dt><a href="compute_group_group.html#index-0">compute group/group</a>
</dt> </dt>
@ -535,12 +539,12 @@
<dt><a href="compute_pressure.html#index-0">compute pressure</a> <dt><a href="compute_pressure.html#index-0">compute pressure</a>
</dt> </dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="compute_property_atom.html#index-0">compute property/atom</a> <dt><a href="compute_property_atom.html#index-0">compute property/atom</a>
</dt> </dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="compute_property_chunk.html#index-0">compute property/chunk</a> <dt><a href="compute_property_chunk.html#index-0">compute property/chunk</a>
</dt> </dt>

2
doc/searchindex.js
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51
doc/timer.html
View File

@ -135,12 +135,12 @@
<li><em>args</em> = one or more of <em>off</em> or <em>loop</em> or <em>normal</em> or <em>full</em> or <em>sync</em> or <em>nosync</em></li> <li><em>args</em> = one or more of <em>off</em> or <em>loop</em> or <em>normal</em> or <em>full</em> or <em>sync</em> or <em>nosync</em></li>
</ul> </ul>
<pre class="literal-block"> <pre class="literal-block">
<em>off</em> = do not collect and print timing information <em>off</em> = do not collect or print any timing information
<em>loop</em> = collect only the total time for the simulation loop <em>loop</em> = collect only the total time for the simulation loop
<em>normal</em> = collect timer information broken down in sections (default) <em>normal</em> = collect timer information broken down by sections (default)
<em>full</em> = like <em>normal</em> but also include CPU and thread utilzation <em>full</em> = like <em>normal</em> but also include CPU and thread utilzation
<em>sync</em> = explicitly synchronize MPI tasks between sections <em>sync</em> = explicitly synchronize MPI tasks between sections
<em>nosync</em> = do not synchronize MPI tasks when collecting timer info (default) <em>nosync</em> = do not synchronize MPI tasks between sections (default)
</pre> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
@ -152,36 +152,37 @@ timer loop
</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>Select to which level of detail LAMMPS is performing internal profiling.</p> <p>Select the level of detail LAMMPS performs its CPU timings.</p>
<p>During regular runs LAMMPS will collect information about how much <p>During a simulation run LAMMPS collects information about how much
time is spent in different sections of the code and thus can provide time is spent in different sections of the code and thus can provide
valuable information for determining performance and load imbalance valuable information for determining performance and load imbalance
problems. This can be done at different levels of detail and problems. This can be done at different levels of detail and
accuracy. For more information about the timing output, please have a accuracy. For more information about the timing output, see this
look at the <a class="reference internal" href="Section_start.html#start-8"><span>discussion of screen output</span></a>.</p> <a class="reference internal" href="Section_start.html#start-8"><span>discussion of screen output</span></a>.</p>
<p>The <em>off</em> setting will turn all time measurements off. The <em>loop</em> <p>The <em>off</em> setting will turn all time measurements off. The <em>loop</em>
setting will only measure the total time of run loop and not collect setting will only measure the total time for a run and not collect any
any detailed per section information. With the <em>normal</em> setting, detailed per section information. With the <em>normal</em> setting, timing
timing information for individual sections of the code are collected information for portions of the timestep (pairwise calculations,
and also information about load imbalances inside those sections neighbor list construction, output, etc) are collected as well as
presented. The <em>full</em> setting adds information about CPU utilization information about load imbalances for those sections across
and thread utilization, when multi-threading is enabled.</p> procsessors. The <em>full</em> setting adds information about CPU
utilization and thread utilization, when multi-threading is enabled.</p>
<p>With the <em>sync</em> setting, all MPI tasks are synchronized at each timer <p>With the <em>sync</em> setting, all MPI tasks are synchronized at each timer
call and thus allowing to study load imbalance more accuractly, but call which meaures load imbalance more accuractly, though it can also
this usually has some performance impact. Using the <em>nosync</em> setting slow down the simulation. Using the <em>nosync</em> setting (which is the
this can be turned off (which is the default).</p> default) turns off this synchronization.</p>
<p>Multiple keywords can be provided and for keywords that are mutually <p>Multiple keywords can be specified. For keywords that are mutually
exclusive, the last one in that group is taking effect.</p> exclusive, the last one specified takes effect.</p>
<div class="admonition warning"> <div class="admonition warning">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Warning</p>
<p class="last">Using the <em>full</em> and <em>sync</em> options provides the most <p class="last">Using the <em>full</em> and <em>sync</em> options provides the most
detailed and accurate timing information, but also can have a detailed and accurate timing information, but can also have a negative
significant negative performance impact due to the overhead of the performance impact due to the overhead of the many required system
many required system calls. It is thus recommended to use these calls. It is thus recommended to use these settings only when testing
settings only when making tests to identify the performance. For tests to identify performance bottlenecks. For calculations with few
calculations with few atoms or a very large number of performance, atoms or a very large number of processors, even the <em>normal</em> setting
even using the <em>normal</em> setting can have a measurable performance can have a measurable negative performance impact. In those cases you
impact. In those cases just use the <em>loop</em> or <em>off</em> setting.</p> can just use the <em>loop</em> or <em>off</em> setting.</p>
</div> </div>
</div> </div>
<div class="section" id="restrictions"> <div class="section" id="restrictions">

52
doc/timer.txt
View File

@ -13,12 +13,12 @@ timer command :h3
timer args :pre timer args :pre
{args} = one or more of {off} or {loop} or {normal} or {full} or {sync} or {nosync} :l {args} = one or more of {off} or {loop} or {normal} or {full} or {sync} or {nosync} :l
{off} = do not collect and print timing information {off} = do not collect or print any timing information
{loop} = collect only the total time for the simulation loop {loop} = collect only the total time for the simulation loop
{normal} = collect timer information broken down in sections (default) {normal} = collect timer information broken down by sections (default)
{full} = like {normal} but also include CPU and thread utilzation {full} = like {normal} but also include CPU and thread utilzation
{sync} = explicitly synchronize MPI tasks between sections {sync} = explicitly synchronize MPI tasks between sections
{nosync} = do not synchronize MPI tasks when collecting timer info (default) :pre {nosync} = do not synchronize MPI tasks between sections (default) :pre
[Examples:] [Examples:]
@ -27,43 +27,45 @@ timer loop :pre
[Description:] [Description:]
Select to which level of detail LAMMPS is performing internal profiling. Select the level of detail LAMMPS performs its CPU timings.
During regular runs LAMMPS will collect information about how much During a simulation run LAMMPS collects information about how much
time is spent in different sections of the code and thus can provide time is spent in different sections of the code and thus can provide
valuable information for determining performance and load imbalance valuable information for determining performance and load imbalance
problems. This can be done at different levels of detail and problems. This can be done at different levels of detail and
accuracy. For more information about the timing output, please have a accuracy. For more information about the timing output, see this
look at the "discussion of screen output"_Section_start.html#start_8. "discussion of screen output"_Section_start.html#start_8.
The {off} setting will turn all time measurements off. The {loop} The {off} setting will turn all time measurements off. The {loop}
setting will only measure the total time of run loop and not collect setting will only measure the total time for a run and not collect any
any detailed per section information. With the {normal} setting, detailed per section information. With the {normal} setting, timing
timing information for individual sections of the code are collected information for portions of the timestep (pairwise calculations,
and also information about load imbalances inside those sections neighbor list construction, output, etc) are collected as well as
presented. The {full} setting adds information about CPU utilization information about load imbalances for those sections across
and thread utilization, when multi-threading is enabled. procsessors. The {full} setting adds information about CPU
utilization and thread utilization, when multi-threading is enabled.
With the {sync} setting, all MPI tasks are synchronized at each timer With the {sync} setting, all MPI tasks are synchronized at each timer
call and thus allowing to study load imbalance more accuractly, but call which meaures load imbalance more accuractly, though it can also
this usually has some performance impact. Using the {nosync} setting slow down the simulation. Using the {nosync} setting (which is the
this can be turned off (which is the default). default) turns off this synchronization.
Multiple keywords can be provided and for keywords that are mutually Multiple keywords can be specified. For keywords that are mutually
exclusive, the last one in that group is taking effect. exclusive, the last one specified takes effect.
IMPORTANT NOTE: Using the {full} and {sync} options provides the most IMPORTANT NOTE: Using the {full} and {sync} options provides the most
detailed and accurate timing information, but also can have a detailed and accurate timing information, but can also have a negative
significant negative performance impact due to the overhead of the performance impact due to the overhead of the many required system
many required system calls. It is thus recommended to use these calls. It is thus recommended to use these settings only when testing
settings only when making tests to identify the performance. For tests to identify performance bottlenecks. For calculations with few
calculations with few atoms or a very large number of performance, atoms or a very large number of processors, even the {normal} setting
even using the {normal} setting can have a measurable performance can have a measurable negative performance impact. In those cases you
impact. In those cases just use the {loop} or {off} setting. can just use the {loop} or {off} setting.
[Restrictions:] none [Restrictions:] none
[Related commands:] [Related commands:]
"run post no"_run.html, "kspace_modify fftbench"_kspace_modify.html "run post no"_run.html, "kspace_modify fftbench"_kspace_modify.html
[Default:] [Default:]