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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>
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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="3 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
3 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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@ -5963,7 +5963,7 @@ feature is disabled by using &#8216;pair_modify table 0&#8217;.</dd>
<dd>The fix_modify command is specifying a temperature computation that <dd>The fix_modify command is specifying a temperature computation that
computes a temperature on a different group of atoms than the fix computes a temperature on a different group of atoms than the fix
itself operates on. This is probably not what you want to do.</dd> itself operates on. This is probably not what you want to do.</dd>
<dt><em>H matrix size has been exceeded: m_fill=%d H.m=%dn</em></dt> <dt><em>H matrix size has been exceeded: m_fill=%d H.m=%d\n</em></dt>
<dd>This is the size of the matrix.</dd> <dd>This is the size of the matrix.</dd>
<dt><em>Improper atoms missing at step %ld</em></dt> <dt><em>Improper atoms missing at step %ld</em></dt>
<dd>One or more of 4 atoms needed to compute a particular improper are <dd>One or more of 4 atoms needed to compute a particular improper are

2
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@ -10600,7 +10600,7 @@ The fix_modify command is specifying a temperature computation that
computes a temperature on a different group of atoms than the fix computes a temperature on a different group of atoms than the fix
itself operates on. This is probably not what you want to do. :dd itself operates on. This is probably not what you want to do. :dd
{H matrix size has been exceeded: m_fill=%d H.m=%d\n} :dt {H matrix size has been exceeded: m_fill=%d H.m=%d\\n} :dt
This is the size of the matrix. :dd This is the size of the matrix. :dd

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@ -166,8 +166,11 @@ interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> is the default setting for the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a>
command, and means those pairwise interactions do not appear in the command, and means those pairwise interactions do not appear in the
neighbor list. Because this fix uses the neighbor list, it also means neighbor list. Because this fix uses the neighbor list, it also means
those pairs will not be included in the RDF. One way to get around those pairs will not be included in the RDF. This does not apply when
this, is to write a dump file, and use the <a class="reference internal" href="rerun.html"><em>rerun</em></a> command using long-range coulomb (<em>coul/long</em>, <em>coul/msm</em>, <em>coul/wolf</em> or similar.
One way to get around this would be to set special_bond scaling factors
to very tiny numbers that are not exactly zero (e.g. 1.0e-50). Another
workaround is to write a dump file, and use the <a class="reference internal" href="rerun.html"><em>rerun</em></a> command
to compute the RDF for snapshots in the dump file. The rerun script to compute the RDF for snapshots in the dump file. The rerun script
can use a <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command that includes all can use a <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command that includes all
pairs in the neighbor list.</p> pairs in the neighbor list.</p>
@ -209,10 +212,13 @@ one individual histogram, due to the way the <em>itypeN</em> and <em>jtypeN</em>
arguments are specified.</p> arguments are specified.</p>
<p>The g(r) value for a bin is calculated from the histogram count by <p>The g(r) value for a bin is calculated from the histogram count by
scaling it by the idealized number of how many counts there would be scaling it by the idealized number of how many counts there would be
if atoms of type <em>jtypeN</em> were uniformly distributed. Thus it if atoms of type <em>jtypeN</em> were uniformly distributed. Thus it involves
involves the count of <em>itypeN</em> atoms, the count of <em>jtypeN</em> atoms, the the count of <em>itypeN</em> atoms, the count of <em>jtypeN</em> atoms, the volume
volume of the entire simulation box, and the volume of the bin&#8217;s thin of the entire simulation box, and the volume of the bin&#8217;s thin shell
shell in 3d (or the area of the bin&#8217;s thin ring in 2d).</p> in 3d (or the area of the bin&#8217;s thin ring in 2d). The normalization
is corrected for finite size effects so that the large <em>r</em> limit for
a homogeneous liquid system of a single atom type becomes exactly 1.0
(without the correction it would be (natoms-1)/natoms).</p>
<p>A coordination number coord(r) is also calculated, which is the number <p>A coordination number coord(r) is also calculated, which is the number
of atoms of type <em>jtypeN</em> within the current bin or closer, averaged of atoms of type <em>jtypeN</em> within the current bin or closer, averaged
over atoms of type <em>itypeN</em>. This is calculated as the area- or over atoms of type <em>itypeN</em>. This is calculated as the area- or

18
doc/compute_rdf.txt
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@ -42,8 +42,11 @@ interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the "special_bonds"_special_bonds.html is the default setting for the "special_bonds"_special_bonds.html
command, and means those pairwise interactions do not appear in the command, and means those pairwise interactions do not appear in the
neighbor list. Because this fix uses the neighbor list, it also means neighbor list. Because this fix uses the neighbor list, it also means
those pairs will not be included in the RDF. One way to get around those pairs will not be included in the RDF. This does not apply when
this, is to write a dump file, and use the "rerun"_rerun.html command using long-range coulomb ({coul/long}, {coul/msm}, {coul/wolf} or similar.
One way to get around this would be to set special_bond scaling factors
to very tiny numbers that are not exactly zero (e.g. 1.0e-50). Another
workaround is to write a dump file, and use the "rerun"_rerun.html command
to compute the RDF for snapshots in the dump file. The rerun script to compute the RDF for snapshots in the dump file. The rerun script
can use a "special_bonds"_special_bonds.html command that includes all can use a "special_bonds"_special_bonds.html command that includes all
pairs in the neighbor list. pairs in the neighbor list.
@ -89,10 +92,13 @@ arguments are specified.
The g(r) value for a bin is calculated from the histogram count by The g(r) value for a bin is calculated from the histogram count by
scaling it by the idealized number of how many counts there would be scaling it by the idealized number of how many counts there would be
if atoms of type {jtypeN} were uniformly distributed. Thus it if atoms of type {jtypeN} were uniformly distributed. Thus it involves
involves the count of {itypeN} atoms, the count of {jtypeN} atoms, the the count of {itypeN} atoms, the count of {jtypeN} atoms, the volume
volume of the entire simulation box, and the volume of the bin's thin of the entire simulation box, and the volume of the bin's thin shell
shell in 3d (or the area of the bin's thin ring in 2d). in 3d (or the area of the bin's thin ring in 2d). The normalization
is corrected for finite size effects so that the large {r} limit for
a homogeneous liquid system of a single atom type becomes exactly 1.0
(without the correction it would be (natoms-1)/natoms).
A coordination number coord(r) is also calculated, which is the number A coordination number coord(r) is also calculated, which is the number
of atoms of type {jtypeN} within the current bin or closer, averaged of atoms of type {jtypeN} within the current bin or closer, averaged

2
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<div class="section" id="timestep-command">
<span id="index-0"></span><h1>timestep command<a class="headerlink" href="#timestep-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>timers args
</pre></div>
</div>
<ul class="simple">
<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>
<pre class="literal-block">
<em>off</em> = do not collect and print timing information
<em>loop</em> = collect only the total time for the simulation loop
<em>normal</em> = collect timer information broken down in sections (default)
<em>full</em> = like <em>normal</em> but also include CPU and thread utilzation
<em>sync</em> = explicitly synchronize MPI tasks between sections
<em>nosync</em> = do not synchronize MPI tasks when collecting timer info (default)
</pre>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>timers full sync
timers loop
</pre></div>
</div>
</div>
<div class="section" id="description">
<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>During regular runs LAMMPS will collect information about how much time is
spent in different sections of the code and thus can provide valuable
information for determining performance and load imbalance problems. This
can be done at different levels of detail and accuracy. For more
information about the timing output, please have a look at the <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> setting
will only measure the total time of run loop and not collect any detailed
per section information. With the <em>normal</em> setting, timing information for
individual sections of the code are collected and also information about
load imbalances inside those sections presented. 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 call
and thus allowing to study load imbalance more accuractly, but this usually
has some performance impact. Using the <em>nosync</em> setting this can be turned
off (which is the default).</p>
<p>Multiple keywords can be provided and for keywords that are mutually
exclusive, the last one in that group is taking effect.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<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 significant
negative performance impact due to the overhead of the many required system
calls. It is thus recommended to use these settings only when making tests
to identify the performance. For calculations with few atoms or a very
large number of performance, even using the <em>normal</em> setting can have
a measurable performance impact. It is recommended in those cases to use
the <em>loop</em> or <em>off</em> setting.</p>
</div>
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<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="run.html"><em>run post no</em></a>, <a class="reference internal" href="kspace_modify.html"><em>kspace_modify fftbench</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>timers normal nosync</p>
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