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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>
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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="jul-2015-version">
<h2>27 Jul 2015 version<a class="headerlink" href="#jul-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
<HR>
<H1></H1>
<CENTER><H3>LAMMPS Documentation
</H3></CENTER>
<CENTER><H4>27 Jul 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 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
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 class="simple">
<li>If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of LAMMPS.</li>
<li>If you browse the HTML doc pages included in your tarball, they
describe the version you have.</li>
<li>The <a class="reference external" href="Manual.pdf">PDF file</a> on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don&#8217;t want
it to be part of every patch.</li>
<li>There is also a <a class="reference external" href="Developer.pdf">Developer.pdf</a> file in the doc
the first page of the manual (this page).
</P>
<UL><LI>If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of LAMMPS.
<LI>If you browse the HTML doc pages included in your tarball, they
describe the version you have.
<LI>The <A HREF = "Manual.pdf">PDF file</A> on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don't want
it to be part of every patch.
<LI>There is also a <A HREF = "Developer.pdf">Developer.pdf</A> file in the doc
directory, which describes the internal structure and algorithms of
LAMMPS.</li>
</ul>
<p>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.</p>
<p>LAMMPS is a classical molecular dynamics simulation code designed to
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 class="reference external" href="http://www.sandia.gov/~sjplimp">Steve Plimpton</a>, Aidan
under the terms of the GNU Public License (GPL).
</P>
<P>The primary developers of LAMMPS are <A 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 class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> at
<a class="reference external" href="http://lammps.sandia.gov">http://lammps.sandia.gov</a> has more information about the code and its
uses.</p>
<hr class="docutils" />
<p>The LAMMPS documentation is organized into the following sections. If
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 class="reference internal" href="Section_commands.html#comm"><span>this page</span></a> at Section_commands.html#comm since
it gives quick access to documentation for all LAMMPS commands.</p>
<p><a class="reference external" href="Manual.pdf">PDF file</a> of the entire manual, generated by
<a class="reference external" href="http://freecode.com/projects/htmldoc">htmldoc</a></p>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#what-is-lammps">1.1. What is LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-features">1.2. LAMMPS features</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-non-features">1.3. LAMMPS non-features</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#open-source-distribution">1.4. Open source distribution</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#acknowledgments-and-citations">1.5. Acknowledgments and citations</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#what-s-in-the-lammps-distribution">2.1. What&#8217;s in the LAMMPS distribution</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps">2.2. Making LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps-with-optional-packages">2.3. Making LAMMPS with optional packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-via-the-make-py-script">2.4. Building LAMMPS via the Make.py script</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-as-a-library">2.5. Building LAMMPS as a library</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#running-lammps">2.6. Running LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#command-line-options">2.7. Command-line options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#lammps-screen-output">2.8. LAMMPS screen output</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#tips-for-users-of-previous-lammps-versions">2.9. Tips for users of previous LAMMPS versions</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#lammps-input-script">3.1. LAMMPS input script</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#parsing-rules">3.2. Parsing rules</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#input-script-structure">3.3. Input script structure</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#commands-listed-by-category">3.4. Commands listed by category</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#individual-commands">3.5. Individual commands</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#fix-styles">3.6. Fix styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#compute-styles">3.7. Compute styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#pair-style-potentials">3.8. Pair_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#bond-style-potentials">3.9. Bond_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#angle-style-potentials">3.10. Angle_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#dihedral-style-potentials">3.11. Dihedral_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#improper-style-potentials">3.12. Improper_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#kspace-solvers">3.13. Kspace solvers</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#standard-packages">4.1. Standard packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-packages">4.2. User packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-atc-package">4.3. USER-ATC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-awpmd-package">4.4. USER-AWPMD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cg-cmm-package">4.5. USER-CG-CMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-colvars-package">4.6. USER-COLVARS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cuda-package">4.7. USER-CUDA package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-diffraction-package">4.8. USER-DIFFRACTION package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-drude-package">4.9. USER-DRUDE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-eff-package">4.10. USER-EFF package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-fep-package">4.11. USER-FEP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-intel-package">4.12. USER-INTEL package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-lb-package">4.13. USER-LB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-misc-package">4.14. USER-MISC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-molfile-package">4.15. USER-MOLFILE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-omp-package">4.16. USER-OMP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-phonon-package">4.17. USER-PHONON package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qmmm-package">4.18. USER-QMMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qtb-package">4.19. USER-QTB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-reaxc-package">4.20. USER-REAXC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-sph-package">4.21. USER-SPH package</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#measuring-performance">5.1. Measuring performance</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#general-strategies">5.2. General strategies</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#packages-with-optimized-styles">5.3. Packages with optimized styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#comparison-of-various-accelerator-packages">5.4. Comparison of various accelerator packages</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#restarting-a-simulation">6.1. Restarting a simulation</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#d-simulations">6.2. 2d simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#charmm-amber-and-dreiding-force-fields">6.3. CHARMM, AMBER, and DREIDING force fields</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#running-multiple-simulations-from-one-input-script">6.4. Running multiple simulations from one input script</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#multi-replica-simulations">6.5. Multi-replica simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#granular-models">6.6. Granular models</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip3p-water-model">6.7. TIP3P water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip4p-water-model">6.8. TIP4P water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#spc-water-model">6.9. SPC water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#coupling-lammps-to-other-codes">6.10. Coupling LAMMPS to other codes</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#visualizing-lammps-snapshots">6.11. Visualizing LAMMPS snapshots</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#triclinic-non-orthogonal-simulation-boxes">6.12. Triclinic (non-orthogonal) simulation boxes</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#nemd-simulations">6.13. NEMD simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#finite-size-spherical-and-aspherical-particles">6.14. Finite-size spherical and aspherical particles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#output-from-lammps-thermo-dumps-computes-fixes-variables">6.15. Output from LAMMPS (thermo, dumps, computes, fixes, variables)</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#thermostatting-barostatting-and-computing-temperature">6.16. Thermostatting, barostatting, and computing temperature</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#walls">6.17. Walls</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#elastic-constants">6.18. Elastic constants</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#library-interface-to-lammps">6.19. Library interface to LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-thermal-conductivity">6.20. Calculating thermal conductivity</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-viscosity">6.21. Calculating viscosity</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-a-diffusion-coefficient">6.22. Calculating a diffusion coefficient</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#using-chunks-to-calculate-system-properties">6.23. Using chunks to calculate system properties</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#setting-parameters-for-the-kspace-style-pppm-disp-command">6.24. Setting parameters for the <code class="docutils literal"><span class="pre">kspace_style</span> <span class="pre">pppm/disp</span></code> command</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#polarizable-models">6.25. Polarizable models</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#adiabatic-core-shell-model">6.26. Adiabatic core/shell model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#drude-induced-dipoles">6.27. Drude induced dipoles</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#amber2lmp-tool">9.1. amber2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#binary2txt-tool">9.2. binary2txt tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ch2lmp-tool">9.3. ch2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#chain-tool">9.4. chain tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#colvars-tools">9.5. colvars tools</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#createatoms-tool">9.6. createatoms tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#data2xmovie-tool">9.7. data2xmovie tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-database-tool">9.8. eam database tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-generate-tool">9.9. eam generate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eff-tool">9.10. eff tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#emacs-tool">9.11. emacs tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#fep-tool">9.12. fep tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#i-pi-tool">9.13. i-pi tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ipp-tool">9.14. ipp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#kate-tool">9.15. kate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2arc-tool">9.16. lmp2arc tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2cfg-tool">9.17. lmp2cfg tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2vmd-tool">9.18. lmp2vmd tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#matlab-tool">9.19. matlab tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#micelle2d-tool">9.20. micelle2d tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#moltemplate-tool">9.21. moltemplate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#msi2lmp-tool">9.22. msi2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#phonon-tool">9.23. phonon tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#polymer-bonding-tool">9.24. polymer bonding tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#pymol-asphere-tool">9.25. pymol_asphere tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#python-tool">9.26. python tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#reax-tool">9.27. reax tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#restart2data-tool">9.28. restart2data tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#vim-tool">9.29. vim tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmgrace-tool">9.30. xmgrace tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmovie-tool">9.31. xmovie tool</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#atom-styles">10.1. Atom styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#bond-angle-dihedral-improper-potentials">10.2. Bond, angle, dihedral, improper potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#compute-styles">10.3. Compute styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-styles">10.4. Dump styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-custom-output-options">10.5. Dump custom output options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#fix-styles">10.6. Fix styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#input-script-commands">10.7. Input script commands</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#kspace-computations">10.8. Kspace computations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#minimization-styles">10.9. Minimization styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#pairwise-potentials">10.10. Pairwise potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#region-styles">10.11. Region styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#body-styles">10.12. Body styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#thermodynamic-output-options">10.13. Thermodynamic output options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#variable-options">10.14. Variable options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#submitting-new-features-for-inclusion-in-lammps">10.15. Submitting new features for inclusion in LAMMPS</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-running-lammps-from-python">11.1. Overview of running LAMMPS from Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-using-python-from-a-lammps-script">11.2. Overview of using Python from a LAMMPS script</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#building-lammps-as-a-shared-library">11.3. Building LAMMPS as a shared library</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#installing-the-python-wrapper-into-python">11.4. Installing the Python wrapper into Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#extending-python-with-mpi-to-run-in-parallel">11.5. Extending Python with MPI to run in parallel</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#testing-the-python-lammps-interface">11.6. Testing the Python-LAMMPS interface</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#using-lammps-from-python">11.7. Using LAMMPS from Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#example-python-scripts-that-use-lammps">11.8. Example Python scripts that use LAMMPS</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#common-problems">12.1. Common problems</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#reporting-bugs">12.2. Reporting bugs</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error-warning-messages">12.3. Error &amp; warning messages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error">12.4. Errors:</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#warnings">12.5. Warnings:</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_history.html#coming-attractions">13.1. Coming attractions</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_history.html#past-versions">13.2. Past versions</a></li>
</ul>
</li>
</ul>
</div>
</div>
</div>
<div class="section" id="indices-and-tables">
<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline"></a></h1>
<ul class="simple">
<li><a class="reference internal" href="genindex.html"><span>Index</span></a></li>
<li><a class="reference internal" href="search.html"><span>Search Page</span></a></li>
</ul>
</BODY></div>
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>
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@ -85,7 +85,7 @@ it gives quick access to documentation for all LAMMPS commands.
.. toctree::
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:numbered:
:numbered: // comment
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@ -105,8 +105,8 @@ it gives quick access to documentation for all LAMMPS commands.
Indices and tables
==================
* :ref:`genindex`
* :ref:`search`
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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 current"><a class="current reference internal" href="">5. Accelerating LAMMPS performance</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#measuring-performance">5.1. Measuring performance</a></li>
<li class="toctree-l2"><a class="reference internal" href="#general-strategies">5.2. General strategies</a></li>
<li class="toctree-l2"><a class="reference internal" href="#packages-with-optimized-styles">5.3. Packages with optimized styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#comparison-of-various-accelerator-packages">5.4. Comparison of various accelerator packages</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#examples">5.4.1. Examples</a></li>
</ul>
</li>
</ul>
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<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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<div class="section" id="accelerating-lammps-performance">
<h1>5. Accelerating LAMMPS performance<a class="headerlink" href="#accelerating-lammps-performance" title="Permalink to this headline"></a></h1>
<p>This section describes various methods for improving LAMMPS
<HR>
<H3>5. Accelerating LAMMPS performance
</H3>
<P>This section describes various methods for improving LAMMPS
performance for different classes of problems running on different
kinds of machines.</p>
<p>There are two thrusts to the discussion that follows. The
kinds of machines.
</P>
<P>There are two thrusts to the discussion that follows. The
first is using code options that implement alternate algorithms
that can speed-up a simulation. The second is to use one
of the several accelerator packages provided with LAMMPS that
contain code optimized for certain kinds of hardware, including
multi-core CPUs, GPUs, and Intel Xeon Phi coprocessors.</p>
<ul class="simple">
<li>5.1 <a class="reference internal" href="#acc-1"><span>Measuring performance</span></a></li>
<li>5.2 <a class="reference internal" href="#acc-2"><span>Algorithms and code options to boost performace</span></a></li>
<li>5.3 <a class="reference internal" href="#acc-3"><span>Accelerator packages with optimized styles</span></a></li>
<li>5.3.1 <a class="reference internal" href="accelerate_cuda.html"><em>USER-CUDA package</em></a></li>
<li>5.3.2 <a class="reference internal" href="accelerate_gpu.html"><em>GPU package</em></a></li>
<li>5.3.3 <a class="reference internal" href="accelerate_intel.html"><em>USER-INTEL package</em></a></li>
<li>5.3.4 <a class="reference internal" href="accelerate_kokkos.html"><em>KOKKOS package</em></a></li>
<li>5.3.5 <a class="reference internal" href="accelerate_omp.html"><em>USER-OMP package</em></a></li>
<li>5.3.6 <a class="reference internal" href="accelerate_opt.html"><em>OPT package</em></a></li>
<li>5.4 <a class="reference internal" href="#acc-4"><span>Comparison of various accelerator packages</span></a></li>
</ul>
<p>The <a class="reference external" href="http://lammps.sandia.gov/bench.html">Benchmark page</a> of the LAMMPS
multi-core CPUs, GPUs, and Intel Xeon Phi coprocessors.
</P>
<UL><LI>5.1 <A HREF = "#acc_1">Measuring performance</A>
<LI>5.2 <A HREF = "#acc_2">Algorithms and code options to boost performace</A>
<LI>5.3 <A HREF = "#acc_3">Accelerator packages with optimized styles</A>
<UL><LI> 5.3.1 <A HREF = "accelerate_cuda.html">USER-CUDA package</A>
<LI> 5.3.2 <A HREF = "accelerate_gpu.html">GPU package</A>
<LI> 5.3.3 <A HREF = "accelerate_intel.html">USER-INTEL package</A>
<LI> 5.3.4 <A HREF = "accelerate_kokkos.html">KOKKOS package</A>
<LI> 5.3.5 <A HREF = "accelerate_omp.html">USER-OMP package</A>
<LI> 5.3.6 <A HREF = "accelerate_opt.html">OPT package</A>
</UL>
<LI>5.4 <A HREF = "#acc_4">Comparison of various accelerator packages</A>
</UL>
<P>The <A HREF = "http://lammps.sandia.gov/bench.html">Benchmark page</A> of the LAMMPS
web site gives performance results for the various accelerator
packages discussed in Section 5.2, for several of the standard LAMMPS
benchmark problems, as a function of problem size and number of
compute nodes, on different hardware platforms.</p>
<div class="section" id="measuring-performance">
<span id="acc-1"></span><h2>5.1. Measuring performance<a class="headerlink" href="#measuring-performance" title="Permalink to this headline"></a></h2>
<p>Before trying to make your simulation run faster, you should
understand how it currently performs and where the bottlenecks are.</p>
<p>The best way to do this is run the your system (actual number of
compute nodes, on different hardware platforms.
</P>
<HR>
<HR>
<H4><A NAME = "acc_1"></A>5.1 Measuring performance
</H4>
<P>Before trying to make your simulation run faster, you should
understand how it currently performs and where the bottlenecks are.
</P>
<P>The best way to do this is run the your system (actual number of
atoms) for a modest number of timesteps (say 100 steps) on several
different processor counts, including a single processor if possible.
Do this for an equilibrium version of your system, so that the
100-step timings are representative of a much longer run. There is
typically no need to run for 1000s of timesteps to get accurate
timings; you can simply extrapolate from short runs.</p>
<p>For the set of runs, look at the timing data printed to the screen and
log file at the end of each LAMMPS run. <a class="reference internal" href="Section_start.html#start-8"><span>This section</span></a> of the manual has an overview.</p>
<p>Running on one (or a few processors) should give a good estimate of
timings; you can simply extrapolate from short runs.
</P>
<P>For the set of runs, look at the timing data printed to the screen and
log file at the end of each LAMMPS run. <A HREF = "Section_start.html#start_8">This
section</A> of the manual has an overview.
</P>
<P>Running on one (or a few processors) should give a good estimate of
the serial performance and what portions of the timestep are taking
the most time. Running the same problem on a few different processor
counts should give an estimate of parallel scalability. I.e. if the
simulation runs 16x faster on 16 processors, its 100% parallel
efficient; if it runs 8x faster on 16 processors, it&#8217;s 50% efficient.</p>
<p>The most important data to look at in the timing info is the timing
efficient; if it runs 8x faster on 16 processors, it's 50% efficient.
</P>
<P>The most important data to look at in the timing info is the timing
breakdown and relative percentages. For example, trying different
options for speeding up the long-range solvers will have little impact
if they only consume 10% of the run time. If the pairwise time is
@ -201,49 +88,50 @@ you increase the processor count gives you a sense of how different
operations within the timestep are scaling. Note that if you are
running with a Kspace solver, there is additional output on the
breakdown of the Kspace time. For PPPM, this includes the fraction
spent on FFTs, which can be communication intensive.</p>
<p>Another important detail in the timing info are the histograms of
spent on FFTs, which can be communication intensive.
</P>
<P>Another important detail in the timing info are the histograms of
atoms counts and neighbor counts. If these vary widely across
processors, you have a load-imbalance issue. This often results in
inaccurate relative timing data, because processors have to wait when
communication occurs for other processors to catch up. Thus the
reported times for &#8220;Communication&#8221; or &#8220;Other&#8221; may be higher than they
reported times for "Communication" or "Other" may be higher than they
really are, due to load-imbalance. If this is an issue, you can
uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile
LAMMPS, to obtain synchronized timings.</p>
<hr class="docutils" />
</div>
<div class="section" id="general-strategies">
<span id="acc-2"></span><h2>5.2. General strategies<a class="headerlink" href="#general-strategies" title="Permalink to this headline"></a></h2>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">this section 5.2 is still a work in progress</p>
</div>
<p>Here is a list of general ideas for improving simulation performance.
LAMMPS, to obtain synchronized timings.
</P>
<HR>
<H4><A NAME = "acc_2"></A>5.2 General strategies
</H4>
<P>NOTE: this section 5.2 is still a work in progress
</P>
<P>Here is a list of general ideas for improving simulation performance.
Most of them are only applicable to certain models and certain
bottlenecks in the current performance, so let the timing data you
generate be your guide. It is hard, if not impossible, to predict how
much difference these options will make, since it is a function of
problem size, number of processors used, and your machine. There is
no substitute for identifying performance bottlenecks, and trying out
various options.</p>
<ul class="simple">
<li>rRESPA</li>
<li>2-FFT PPPM</li>
<li>Staggered PPPM</li>
<li>single vs double PPPM</li>
<li>partial charge PPPM</li>
<li>verlet/split run style</li>
<li>processor command for proc layout and numa layout</li>
<li>load-balancing: balance and fix balance</li>
</ul>
<p>2-FFT PPPM, also called <em>analytic differentiation</em> or <em>ad</em> PPPM, uses
2 FFTs instead of the 4 FFTs used by the default <em>ik differentiation</em>
various options.
</P>
<UL><LI>rRESPA
<LI>2-FFT PPPM
<LI>Staggered PPPM
<LI>single vs double PPPM
<LI>partial charge PPPM
<LI>verlet/split run style
<LI>processor command for proc layout and numa layout
<LI>load-balancing: balance and fix balance
</UL>
<P>2-FFT PPPM, also called <I>analytic differentiation</I> or <I>ad</I> PPPM, uses
2 FFTs instead of the 4 FFTs used by the default <I>ik differentiation</I>
PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to
achieve the same accuracy as 4-FFT PPPM. For problems where the FFT
cost is the performance bottleneck (typically large problems running
on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM.</p>
<p>Staggered PPPM performs calculations using two different meshes, one
on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM.
</P>
<P>Staggered PPPM performs calculations using two different meshes, one
shifted slightly with respect to the other. This can reduce force
aliasing errors and increase the accuracy of the method, but also
doubles the amount of work required. For high relative accuracy, using
@ -255,233 +143,194 @@ time. For example, the rhodopsin benchmark was run on a single
processor, and results for kspace time vs. relative accuracy for the
different methods are shown in the figure below. For this system,
staggered PPPM (using ik differentiation) becomes useful when using a
relative accuracy of slightly greater than 1e-5 and above.</p>
<img alt="_images/rhodo_staggered.jpg" class="align-center" src="_images/rhodo_staggered.jpg" />
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Using staggered PPPM may not give the same increase in
relative accuracy of slightly greater than 1e-5 and above.
</P>
<CENTER><IMG SRC = "JPG/rhodo_staggered.jpg">
</CENTER>
<P>IMPORTANT NOTE: Using staggered PPPM may not give the same increase in
accuracy of energy and pressure as it does in forces, so some caution
must be used if energy and/or pressure are quantities of interest,
such as when using a barostat.</p>
</div>
<hr class="docutils" />
</div>
<div class="section" id="packages-with-optimized-styles">
<span id="acc-3"></span><h2>5.3. Packages with optimized styles<a class="headerlink" href="#packages-with-optimized-styles" title="Permalink to this headline"></a></h2>
<p>Accelerated versions of various <a class="reference internal" href="pair_style.html"><em>pair_style</em></a>,
<a class="reference internal" href="fix.html"><em>fixes</em></a>, <a class="reference internal" href="compute.html"><em>computes</em></a>, and other commands have
such as when using a barostat.
</P>
<HR>
<H4><A NAME = "acc_3"></A>5.3 Packages with optimized styles
</H4>
<P>Accelerated versions of various <A HREF = "pair_style.html">pair_style</A>,
<A HREF = "fix.html">fixes</A>, <A HREF = "compute.html">computes</A>, and other commands have
been added to LAMMPS, which will typically run faster than the
standard non-accelerated versions. Some require appropriate hardware
to be present on your system, e.g. GPUs or Intel Xeon Phi
coprocessors.</p>
<p>All of these commands are in packages provided with LAMMPS. An
overview of packages is give in <a class="reference internal" href="Section_packages.html"><em>Section packages</em></a>. These are the accelerator packages
currently in LAMMPS, either as standard or user packages:</p>
<table border="1" class="docutils">
<colgroup>
<col width="44%" />
<col width="56%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="accelerate_cuda.html"><em>USER-CUDA</em></a></td>
<td>for NVIDIA GPUs</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="accelerate_gpu.html"><em>GPU</em></a></td>
<td>for NVIDIA GPUs as well as OpenCL support</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="accelerate_intel.html"><em>USER-INTEL</em></a></td>
<td>for Intel CPUs and Intel Xeon Phi</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="accelerate_kokkos.html"><em>KOKKOS</em></a></td>
<td>for GPUs, Intel Xeon Phi, and OpenMP threading</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="accelerate_omp.html"><em>USER-OMP</em></a></td>
<td>for OpenMP threading</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="accelerate_opt.html"><em>OPT</em></a></td>
<td>generic CPU optimizations</td>
</tr>
</tbody>
</table>
<p>Any accelerated style has the same name as the corresponding standard
coprocessors.
</P>
<P>All of these commands are in packages provided with LAMMPS. An
overview of packages is give in <A HREF = "Section_packages.html">Section
packages</A>. These are the accelerator packages
currently in LAMMPS, either as standard or user packages:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD ><A HREF = "accelerate_cuda.html">USER-CUDA</A> </TD><TD > for NVIDIA GPUs</TD></TR>
<TR><TD ><A HREF = "accelerate_gpu.html">GPU</A> </TD><TD > for NVIDIA GPUs as well as OpenCL support</TD></TR>
<TR><TD ><A HREF = "accelerate_intel.html">USER-INTEL</A> </TD><TD > for Intel CPUs and Intel Xeon Phi</TD></TR>
<TR><TD ><A HREF = "accelerate_kokkos.html">KOKKOS</A> </TD><TD > for GPUs, Intel Xeon Phi, and OpenMP threading</TD></TR>
<TR><TD ><A HREF = "accelerate_omp.html">USER-OMP</A> </TD><TD > for OpenMP threading</TD></TR>
<TR><TD ><A HREF = "accelerate_opt.html">OPT</A> </TD><TD > generic CPU optimizations
</TD></TR></TABLE></DIV>
<P>Any accelerated style has the same name as the corresponding standard
style, except that a suffix is appended. Otherwise, the syntax for
the command that uses the style is identical, their functionality is
the same, and the numerical results it produces should also be the
same, except for precision and round-off effects.</p>
<p>For example, all of these styles are accelerated variants of the
Lennard-Jones <a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut</em></a>:</p>
<ul class="simple">
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/cuda</em></a></li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/gpu</em></a></li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/intel</em></a></li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/kk</em></a></li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/omp</em></a></li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/opt</em></a></li>
</ul>
<p>To see what accelerate styles are currently available, see
<a class="reference internal" href="Section_commands.html#cmd-5"><span>Section_commands 5</span></a> of the manual. The
doc pages for individual commands (e.g. <a class="reference internal" href="pair_lj.html"><em>pair lj/cut</em></a> or
<a class="reference internal" href="fix_nve.html"><em>fix nve</em></a>) also list any accelerated variants available
for that style.</p>
<p>To use an accelerator package in LAMMPS, and one or more of the styles
same, except for precision and round-off effects.
</P>
<P>For example, all of these styles are accelerated variants of the
Lennard-Jones <A HREF = "pair_lj.html">pair_style lj/cut</A>:
</P>
<UL><LI><A HREF = "pair_lj.html">pair_style lj/cut/cuda</A>
<LI><A HREF = "pair_lj.html">pair_style lj/cut/gpu</A>
<LI><A HREF = "pair_lj.html">pair_style lj/cut/intel</A>
<LI><A HREF = "pair_lj.html">pair_style lj/cut/kk</A>
<LI><A HREF = "pair_lj.html">pair_style lj/cut/omp</A>
<LI><A HREF = "pair_lj.html">pair_style lj/cut/opt</A>
</UL>
<P>To see what accelerate styles are currently available, see
<A HREF = "Section_commands.html#cmd_5">Section_commands 5</A> of the manual. The
doc pages for individual commands (e.g. <A HREF = "pair_lj.html">pair lj/cut</A> or
<A HREF = "fix_nve.html">fix nve</A>) also list any accelerated variants available
for that style.
</P>
<P>To use an accelerator package in LAMMPS, and one or more of the styles
it provides, follow these general steps. Details vary from package to
package and are explained in the individual accelerator doc pages,
listed above:</p>
<table border="1" class="docutils">
<colgroup>
<col width="26%" />
<col width="74%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>build the accelerator library</td>
<td>only for USER-CUDA and GPU packages</td>
</tr>
<tr class="row-even"><td>install the accelerator package</td>
<td>make yes-opt, make yes-user-intel, etc</td>
</tr>
</tbody>
</table>
<div class="line-block">
<div class="line">install the accelerator package | make yes-opt, make yes-user-intel, etc |</div>
</div>
<blockquote>
<div>only for USER-INTEL, KOKKOS, USER-OMP packages |</div></blockquote>
<table border="1" class="docutils">
<colgroup>
<col width="26%" />
<col width="74%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>re-build LAMMPS</td>
<td>make machine</td>
</tr>
<tr class="row-even"><td>run a LAMMPS simulation</td>
<td>lmp_machine &lt; in.script</td>
</tr>
</tbody>
</table>
<div class="line-block">
<div class="line">run a LAMMPS simulation | lmp_machine &lt; in.script |</div>
</div>
<blockquote>
<div>only for USER-CUDA and KOKKOS packages |</div></blockquote>
<blockquote>
<div><a class="reference internal" href="package.html"><em>package</em></a> command, &lt;br&gt;
only if defaults need to be changed |</div></blockquote>
<blockquote>
<div><a class="reference internal" href="suffix.html"><em>suffix</em></a> command |</div></blockquote>
<table border="1" class="docutils">
<colgroup>
</colgroup>
<tbody valign="top">
</tbody>
</table>
<p>The first 4 steps can be done as a single command, using the
src/Make.py tool. The Make.py tool is discussed in <a class="reference internal" href="Section_start.html#start-4"><span>Section 2.4</span></a> of the manual, and its use is
listed above:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >build the accelerator library </TD><TD > only for USER-CUDA and GPU packages </TD></TR>
<TR><TD >install the accelerator package </TD><TD > make yes-opt, make yes-user-intel, etc </TD></TR>
<TR><TD >add compile/link flags to Makefile.machine </TD><TD > in src/MAKE, <br> only for USER-INTEL, KOKKOS, USER-OMP packages </TD></TR>
<TR><TD >re-build LAMMPS </TD><TD > make machine </TD></TR>
<TR><TD >run a LAMMPS simulation </TD><TD > lmp_machine < in.script </TD></TR>
<TR><TD >enable the accelerator package </TD><TD > via "-c on" and "-k on" <A HREF = "Section_start.html#start_7">command-line switches</A>, <br> only for USER-CUDA and KOKKOS packages </TD></TR>
<TR><TD >set any needed options for the package </TD><TD > via "-pk" <A HREF = "Section_start.html#start_7">command-line switch</A> or <A HREF = "package.html">package</A> command, <br> only if defaults need to be changed </TD></TR>
<TR><TD >use accelerated styles in your input script </TD><TD > via "-sf" <A HREF = "Section_start.html#start_7">command-line switch</A> or <A HREF = "suffix.html">suffix</A> command
</TD></TR></TABLE></DIV>
<P>The first 4 steps can be done as a single command, using the
src/Make.py tool. The Make.py tool is discussed in <A HREF = "Section_start.html#start_4">Section
2.4</A> of the manual, and its use is
illustrated in the individual accelerator sections. Typically these
steps only need to be done once, to create an executable that uses one
or more accelerator packages.</p>
<p>The last 4 steps can all be done from the command-line when LAMMPS is
or more accelerator packages.
</P>
<P>The last 4 steps can all be done from the command-line when LAMMPS is
launched, without changing your input script, as illustrated in the
individual accelerator sections. Or you can add
<a class="reference internal" href="package.html"><em>package</em></a> and <a class="reference internal" href="suffix.html"><em>suffix</em></a> commands to your input
script.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">With a few exceptions, you can build a single LAMMPS
<A HREF = "package.html">package</A> and <A HREF = "suffix.html">suffix</A> commands to your input
script.
</P>
<P>IMPORTANT NOTE: With a few exceptions, you can build a single LAMMPS
executable with all its accelerator packages installed. Note that the
USER-INTEL and KOKKOS packages require you to choose one of their
options when building. I.e. CPU or Phi for USER-INTEL. OpenMP, Cuda,
or Phi for KOKKOS. Here are the exceptions; you cannot build a single
executable with:</p>
</div>
<ul class="simple">
<li>both the USER-INTEL Phi and KOKKOS Phi options</li>
<li>the USER-INTEL Phi or Kokkos Phi option, and either the USER-CUDA or GPU packages</li>
</ul>
<p>See the examples/accelerate/README and make.list files for sample
executable with:
</P>
<UL><LI>both the USER-INTEL Phi and KOKKOS Phi options
<LI>the USER-INTEL Phi or Kokkos Phi option, and either the USER-CUDA or GPU packages
</UL>
<P>See the examples/accelerate/README and make.list files for sample
Make.py commands that build LAMMPS with any or all of the accelerator
packages. As an example, here is a command that builds with all the
GPU related packages installed (USER-CUDA, GPU, KOKKOS with Cuda),
including settings to build the needed auxiliary USER-CUDA and GPU
libraries for Kepler GPUs:</p>
<pre class="literal-block">
Make.py -j 16 -p omp gpu cuda kokkos -cc nvcc wrap=mpi -cuda mode=double arch=35 -gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi
</pre>
<p>The examples/accelerate directory also has input scripts that can be
libraries for Kepler GPUs:
</P>
<PRE>Make.py -j 16 -p omp gpu cuda kokkos -cc nvcc wrap=mpi -cuda mode=double arch=35 -gpu mode=double arch=35 \ -kokkos cuda arch=35 lib-all file mpi
</PRE>
<P>The examples/accelerate directory also has input scripts that can be
used with all of the accelerator packages. See its README file for
details.</p>
<p>Likewise, the bench directory has FERMI and KEPLER and PHI
details.
</P>
<P>Likewise, the bench directory has FERMI and KEPLER and PHI
sub-directories with Make.py commands and input scripts for using all
the accelerator packages on various machines. See the README files in
those dirs.</p>
<p>As mentioned above, the <a class="reference external" href="http://lammps.sandia.gov/bench.html">Benchmark page</a> of the LAMMPS web site gives
those dirs.
</P>
<P>As mentioned above, the <A HREF = "http://lammps.sandia.gov/bench.html">Benchmark
page</A> of the LAMMPS web site gives
performance results for the various accelerator packages for several
of the standard LAMMPS benchmark problems, as a function of problem
size and number of compute nodes, on different hardware platforms.</p>
<p>Here is a brief summary of what the various packages provide. Details
are in the individual accelerator sections.</p>
<ul class="simple">
<li>Styles with a &#8220;cuda&#8221; or &#8220;gpu&#8221; suffix are part of the USER-CUDA or GPU
size and number of compute nodes, on different hardware platforms.
</P>
<P>Here is a brief summary of what the various packages provide. Details
are in the individual accelerator sections.
</P>
<UL><LI>Styles with a "cuda" or "gpu" suffix are part of the USER-CUDA or GPU
packages, and can be run on NVIDIA GPUs. The speed-up on a GPU
depends on a variety of factors, discussed in the accelerator
sections.</li>
<li>Styles with an &#8220;intel&#8221; suffix are part of the USER-INTEL
sections.
<LI>Styles with an "intel" suffix are part of the USER-INTEL
package. These styles support vectorized single and mixed precision
calculations, in addition to full double precision. In extreme cases,
this can provide speedups over 3.5x on CPUs. The package also
supports acceleration in &#8220;offload&#8221; mode to Intel(R) Xeon Phi(TM)
supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM)
coprocessors. This can result in additional speedup over 2x depending
on the hardware configuration.</li>
<li>Styles with a &#8220;kk&#8221; suffix are part of the KOKKOS package, and can be
on the hardware configuration.
<LI>Styles with a "kk" suffix are part of the KOKKOS package, and can be
run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel
Xeon Phi in &#8220;native&#8221; mode. The speed-up depends on a variety of
factors, as discussed on the KOKKOS accelerator page.</li>
<li>Styles with an &#8220;omp&#8221; suffix are part of the USER-OMP package and allow
Xeon Phi in "native" mode. The speed-up depends on a variety of
factors, as discussed on the KOKKOS accelerator page.
<LI>Styles with an "omp" suffix are part of the USER-OMP package and allow
a pair-style to be run in multi-threaded mode using OpenMP. This can
be useful on nodes with high-core counts when using less MPI processes
than cores is advantageous, e.g. when running with PPPM so that FFTs
are run on fewer MPI processors or when the many MPI tasks would
overload the available bandwidth for communication.</li>
<li>Styles with an &#8220;opt&#8221; suffix are part of the OPT package and typically
overload the available bandwidth for communication.
<LI>Styles with an "opt" suffix are part of the OPT package and typically
speed-up the pairwise calculations of your simulation by 5-25% on a
CPU.</li>
</ul>
<p>The individual accelerator package doc pages explain:</p>
<ul class="simple">
<li>what hardware and software the accelerated package requires</li>
<li>how to build LAMMPS with the accelerated package</li>
<li>how to run with the accelerated package either via command-line switches or modifying the input script</li>
<li>speed-ups to expect</li>
<li>guidelines for best performance</li>
<li>restrictions</li>
</ul>
<hr class="docutils" />
</div>
<div class="section" id="comparison-of-various-accelerator-packages">
<span id="acc-4"></span><h2>5.4. Comparison of various accelerator packages<a class="headerlink" href="#comparison-of-various-accelerator-packages" title="Permalink to this headline"></a></h2>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">this section still needs to be re-worked with additional KOKKOS
and USER-INTEL information.</p>
</div>
<p>The next section compares and contrasts the various accelerator
CPU.
</UL>
<P>The individual accelerator package doc pages explain:
</P>
<UL><LI>what hardware and software the accelerated package requires
<LI>how to build LAMMPS with the accelerated package
<LI>how to run with the accelerated package either via command-line switches or modifying the input script
<LI>speed-ups to expect
<LI>guidelines for best performance
<LI>restrictions
</UL>
<HR>
<H4><A NAME = "acc_4"></A>5.4 Comparison of various accelerator packages
</H4>
<P>NOTE: this section still needs to be re-worked with additional KOKKOS
and USER-INTEL information.
</P>
<P>The next section compares and contrasts the various accelerator
options, since there are multiple ways to perform OpenMP threading,
run on GPUs, and run on Intel Xeon Phi coprocessors.</p>
<p>All 3 of these packages accelerate a LAMMPS calculation using NVIDIA
hardware, but they do it in different ways.</p>
<p>As a consequence, for a particular simulation on specific hardware,
run on GPUs, and run on Intel Xeon Phi coprocessors.
</P>
<P>All 3 of these packages accelerate a LAMMPS calculation using NVIDIA
hardware, but they do it in different ways.
</P>
<P>As a consequence, for a particular simulation on specific hardware,
one package may be faster than the other. We give guidelines below,
but the best way to determine which package is faster for your input
script is to try both of them on your machine. See the benchmarking
section below for examples where this has been done.</p>
<p><strong>Guidelines for using each package optimally:</strong></p>
<ul class="simple">
<li>The GPU package allows you to assign multiple CPUs (cores) to a single
GPU (a common configuration for &#8220;hybrid&#8221; nodes that contain multicore
section below for examples where this has been done.
</P>
<P><B>Guidelines for using each package optimally:</B>
</P>
<UL><LI>The GPU package allows you to assign multiple CPUs (cores) to a single
GPU (a common configuration for "hybrid" nodes that contain multicore
CPU(s) and GPU(s)) and works effectively in this mode. The USER-CUDA
package does not allow this; you can only use one CPU per GPU.</li>
<li>The GPU package moves per-atom data (coordinates, forces)
package does not allow this; you can only use one CPU per GPU.
<LI>The GPU package moves per-atom data (coordinates, forces)
back-and-forth between the CPU and GPU every timestep. The USER-CUDA
package only does this on timesteps when a CPU calculation is required
(e.g. to invoke a fix or compute that is non-GPU-ized). Hence, if you
@ -489,129 +338,64 @@ can formulate your input script to only use GPU-ized fixes and
computes, and avoid doing I/O too often (thermo output, dump file
snapshots, restart files), then the data transfer cost of the
USER-CUDA package can be very low, causing it to run faster than the
GPU package.</li>
<li>The GPU package is often faster than the USER-CUDA package, if the
number of atoms per GPU is &#8220;small&#8221;. The crossover point, in terms of
GPU package.
<LI>The GPU package is often faster than the USER-CUDA package, if the
number of atoms per GPU is "small". The crossover point, in terms of
atoms/GPU at which the USER-CUDA package becomes faster depends
strongly on the pair style. For example, for a simple Lennard Jones
system the crossover (in single precision) is often about 50K-100K
atoms per GPU. When performing double precision calculations the
crossover point can be significantly smaller.</li>
<li>Both packages compute bonded interactions (bonds, angles, etc) on the
crossover point can be significantly smaller.
<LI>Both packages compute bonded interactions (bonds, angles, etc) on the
CPU. This means a model with bonds will force the USER-CUDA package
to transfer per-atom data back-and-forth between the CPU and GPU every
timestep. If the GPU package is running with several MPI processes
assigned to one GPU, the cost of computing the bonded interactions is
spread across more CPUs and hence the GPU package can run faster.</li>
<li>When using the GPU package with multiple CPUs assigned to one GPU, its
spread across more CPUs and hence the GPU package can run faster.
<LI>When using the GPU package with multiple CPUs assigned to one GPU, its
performance depends to some extent on high bandwidth between the CPUs
and the GPU. Hence its performance is affected if full 16 PCIe lanes
are not available for each GPU. In HPC environments this can be the
case if S2050/70 servers are used, where two devices generally share
one PCIe 2.0 16x slot. Also many multi-GPU mainboards do not provide
full 16 lanes to each of the PCIe 2.0 16x slots.</li>
</ul>
<p><strong>Differences between the two packages:</strong></p>
<ul class="simple">
<li>The GPU package accelerates only pair force, neighbor list, and PPPM
full 16 lanes to each of the PCIe 2.0 16x slots.
</UL>
<P><B>Differences between the two packages:</B>
</P>
<UL><LI>The GPU package accelerates only pair force, neighbor list, and PPPM
calculations. The USER-CUDA package currently supports a wider range
of pair styles and can also accelerate many fix styles and some
compute styles, as well as neighbor list and PPPM calculations.</li>
<li>The USER-CUDA package does not support acceleration for minimization.</li>
<li>The USER-CUDA package does not support hybrid pair styles.</li>
<li>The USER-CUDA package can order atoms in the neighbor list differently
from run to run resulting in a different order for force accumulation.</li>
<li>The USER-CUDA package has a limit on the number of atom types that can be
used in a simulation.</li>
<li>The GPU package requires neighbor lists to be built on the CPU when using
exclusion lists or a triclinic simulation box.</li>
<li>The GPU package uses more GPU memory than the USER-CUDA package. This
compute styles, as well as neighbor list and PPPM calculations.
<LI>The USER-CUDA package does not support acceleration for minimization.
<LI>The USER-CUDA package does not support hybrid pair styles.
<LI>The USER-CUDA package can order atoms in the neighbor list differently
from run to run resulting in a different order for force accumulation.
<LI>The USER-CUDA package has a limit on the number of atom types that can be
used in a simulation.
<LI>The GPU package requires neighbor lists to be built on the CPU when using
exclusion lists or a triclinic simulation box.
<LI>The GPU package uses more GPU memory than the USER-CUDA package. This
is generally not a problem since typical runs are computation-limited
rather than memory-limited.</li>
</ul>
<div class="section" id="examples">
<h3>5.4.1. Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h3>
<p>The LAMMPS distribution has two directories with sample input scripts
for the GPU and USER-CUDA packages.</p>
<ul class="simple">
<li>lammps/examples/gpu = GPU package files</li>
<li>lammps/examples/USER/cuda = USER-CUDA package files</li>
</ul>
<p>These contain input scripts for identical systems, so they can be used
to benchmark the performance of both packages on your system.</p>
</div>
</div>
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</UL>
<P><B>Examples:</B>
</P>
<P>The LAMMPS distribution has two directories with sample input scripts
for the GPU and USER-CUDA packages.
</P>
<UL><LI>lammps/examples/gpu = GPU package files
<LI>lammps/examples/USER/cuda = USER-CUDA package files
</UL>
<P>These contain input scripts for identical systems, so they can be used
to benchmark the performance of both packages on your system.
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<div class="section" id="example-problems">
<h1>7. Example problems<a class="headerlink" href="#example-problems" title="Permalink to this headline"></a></h1>
<p>The LAMMPS distribution includes an examples sub-directory with
<HR>
<H3>7. Example problems
</H3>
<P>The LAMMPS distribution includes an examples sub-directory with
several sample problems. Each problem is in a sub-directory of its
own. Most are 2d models so that they run quickly, requiring at most a
couple of minutes to run on a desktop machine. Each problem has an
@ -146,252 +20,107 @@ input script (in.*) and produces a log file (log.*) and dump file
coordinates as additional input. A few sample log file outputs on
different machines and different numbers of processors are included in
the directories to compare your answers to. E.g. a log file like
log.crack.foo.P means it ran on P processors of machine &#8220;foo&#8221;.</p>
<p>For examples that use input data files, many of them were produced by
<a class="reference external" href="http://pizza.sandia.gov">Pizza.py</a> or setup tools described in the
<a class="reference internal" href="Section_tools.html"><em>Additional Tools</em></a> section of the LAMMPS
documentation and provided with the LAMMPS distribution.</p>
<p>If you uncomment the <a class="reference internal" href="dump.html"><em>dump</em></a> command in the input script, a
log.crack.foo.P means it ran on P processors of machine "foo".
</P>
<P>For examples that use input data files, many of them were produced by
<A HREF = "http://pizza.sandia.gov">Pizza.py</A> or setup tools described in the
<A HREF = "Section_tools.html">Additional Tools</A> section of the LAMMPS
documentation and provided with the LAMMPS distribution.
</P>
<P>If you uncomment the <A HREF = "dump.html">dump</A> command in the input script, a
text dump file will be produced, which can be animated by various
<a class="reference external" href="http://lammps.sandia.gov/viz.html">visualization programs</a>. It can
also be animated using the xmovie tool described in the <a class="reference internal" href="Section_tools.html"><em>Additional Tools</em></a> section of the LAMMPS documentation.</p>
<p>If you uncomment the <a class="reference internal" href="dump.html"><em>dump image</em></a> command in the input
<A HREF = "http://lammps.sandia.gov/viz.html">visualization programs</A>. It can
also be animated using the xmovie tool described in the <A HREF = "Section_tools.html">Additional
Tools</A> section of the LAMMPS documentation.
</P>
<P>If you uncomment the <A HREF = "dump.html">dump image</A> command in the input
script, and assuming you have built LAMMPS with a JPG library, JPG
snapshot images will be produced when the simulation runs. They can
be quickly post-processed into a movie using commands described on the
<a class="reference internal" href="dump_image.html"><em>dump image</em></a> doc page.</p>
<p>Animations of many of these examples can be viewed on the Movies
section of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>.</p>
<p>These are the sample problems in the examples sub-directories:</p>
<table border="1" class="docutils">
<colgroup>
<col width="15%" />
<col width="85%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>balance</td>
<td>dynamic load balancing, 2d system</td>
</tr>
<tr class="row-even"><td>body</td>
<td>body particles, 2d system</td>
</tr>
<tr class="row-odd"><td>colloid</td>
<td>big colloid particles in a small particle solvent, 2d system</td>
</tr>
<tr class="row-even"><td>comb</td>
<td>models using the COMB potential</td>
</tr>
<tr class="row-odd"><td>crack</td>
<td>crack propagation in a 2d solid</td>
</tr>
<tr class="row-even"><td>cuda</td>
<td>use of the USER-CUDA package for GPU acceleration</td>
</tr>
<tr class="row-odd"><td>dipole</td>
<td>point dipolar particles, 2d system</td>
</tr>
<tr class="row-even"><td>dreiding</td>
<td>methanol via Dreiding FF</td>
</tr>
<tr class="row-odd"><td>eim</td>
<td>NaCl using the EIM potential</td>
</tr>
<tr class="row-even"><td>ellipse</td>
<td>ellipsoidal particles in spherical solvent, 2d system</td>
</tr>
<tr class="row-odd"><td>flow</td>
<td>Couette and Poiseuille flow in a 2d channel</td>
</tr>
<tr class="row-even"><td>friction</td>
<td>frictional contact of spherical asperities between 2d surfaces</td>
</tr>
<tr class="row-odd"><td>gpu</td>
<td>use of the GPU package for GPU acceleration</td>
</tr>
<tr class="row-even"><td>hugoniostat</td>
<td>Hugoniostat shock dynamics</td>
</tr>
<tr class="row-odd"><td>indent</td>
<td>spherical indenter into a 2d solid</td>
</tr>
<tr class="row-even"><td>intel</td>
<td>use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor</td>
</tr>
<tr class="row-odd"><td>kim</td>
<td>use of potentials in Knowledge Base for Interatomic Models (KIM)</td>
</tr>
<tr class="row-even"><td>line</td>
<td>line segment particles in 2d rigid bodies</td>
</tr>
<tr class="row-odd"><td>meam</td>
<td>MEAM test for SiC and shear (same as shear examples)</td>
</tr>
<tr class="row-even"><td>melt</td>
<td>rapid melt of 3d LJ system</td>
</tr>
<tr class="row-odd"><td>micelle</td>
<td>self-assembly of small lipid-like molecules into 2d bilayers</td>
</tr>
<tr class="row-even"><td>min</td>
<td>energy minimization of 2d LJ melt</td>
</tr>
<tr class="row-odd"><td>msst</td>
<td>MSST shock dynamics</td>
</tr>
<tr class="row-even"><td>nb3b</td>
<td>use of nonbonded 3-body harmonic pair style</td>
</tr>
<tr class="row-odd"><td>neb</td>
<td>nudged elastic band (NEB) calculation for barrier finding</td>
</tr>
<tr class="row-even"><td>nemd</td>
<td>non-equilibrium MD of 2d sheared system</td>
</tr>
<tr class="row-odd"><td>obstacle</td>
<td>flow around two voids in a 2d channel</td>
</tr>
<tr class="row-even"><td>peptide</td>
<td>dynamics of a small solvated peptide chain (5-mer)</td>
</tr>
<tr class="row-odd"><td>peri</td>
<td>Peridynamic model of cylinder impacted by indenter</td>
</tr>
<tr class="row-even"><td>pour</td>
<td>pouring of granular particles into a 3d box, then chute flow</td>
</tr>
<tr class="row-odd"><td>prd</td>
<td>parallel replica dynamics of vacancy diffusion in bulk Si</td>
</tr>
<tr class="row-even"><td>qeq</td>
<td>use of the QEQ pacakge for charge equilibration</td>
</tr>
<tr class="row-odd"><td>reax</td>
<td>RDX and TATB models using the ReaxFF</td>
</tr>
<tr class="row-even"><td>rigid</td>
<td>rigid bodies modeled as independent or coupled</td>
</tr>
<tr class="row-odd"><td>shear</td>
<td>sideways shear applied to 2d solid, with and without a void</td>
</tr>
<tr class="row-even"><td>snap</td>
<td>NVE dynamics for BCC tantalum crystal using SNAP potential</td>
</tr>
<tr class="row-odd"><td>srd</td>
<td>stochastic rotation dynamics (SRD) particles as solvent</td>
</tr>
<tr class="row-even"><td>tad</td>
<td>temperature-accelerated dynamics of vacancy diffusion in bulk Si</td>
</tr>
<tr class="row-odd"><td>tri</td>
<td>triangular particles in rigid bodies</td>
</tr>
</tbody>
</table>
<p>Here is how you might run and visualize one of the sample problems:</p>
<div class="highlight-python"><div class="highlight"><pre>cd indent
<A HREF = "dump_image.html">dump image</A> doc page.
</P>
<P>Animations of many of these examples can be viewed on the Movies
section of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>.
</P>
<P>These are the sample problems in the examples sub-directories:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >balance</TD><TD > dynamic load balancing, 2d system</TD></TR>
<TR><TD >body</TD><TD > body particles, 2d system</TD></TR>
<TR><TD >colloid</TD><TD > big colloid particles in a small particle solvent, 2d system</TD></TR>
<TR><TD >comb</TD><TD > models using the COMB potential</TD></TR>
<TR><TD >crack</TD><TD > crack propagation in a 2d solid</TD></TR>
<TR><TD >cuda</TD><TD > use of the USER-CUDA package for GPU acceleration</TD></TR>
<TR><TD >dipole</TD><TD > point dipolar particles, 2d system</TD></TR>
<TR><TD >dreiding</TD><TD > methanol via Dreiding FF</TD></TR>
<TR><TD >eim</TD><TD > NaCl using the EIM potential</TD></TR>
<TR><TD >ellipse</TD><TD > ellipsoidal particles in spherical solvent, 2d system</TD></TR>
<TR><TD >flow</TD><TD > Couette and Poiseuille flow in a 2d channel</TD></TR>
<TR><TD >friction</TD><TD > frictional contact of spherical asperities between 2d surfaces</TD></TR>
<TR><TD >gpu</TD><TD > use of the GPU package for GPU acceleration</TD></TR>
<TR><TD >hugoniostat</TD><TD > Hugoniostat shock dynamics</TD></TR>
<TR><TD >indent</TD><TD > spherical indenter into a 2d solid</TD></TR>
<TR><TD >intel</TD><TD > use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor</TD></TR>
<TR><TD >kim</TD><TD > use of potentials in Knowledge Base for Interatomic Models (KIM)</TD></TR>
<TR><TD >line</TD><TD > line segment particles in 2d rigid bodies</TD></TR>
<TR><TD >meam</TD><TD > MEAM test for SiC and shear (same as shear examples)</TD></TR>
<TR><TD >melt</TD><TD > rapid melt of 3d LJ system</TD></TR>
<TR><TD >micelle</TD><TD > self-assembly of small lipid-like molecules into 2d bilayers</TD></TR>
<TR><TD >min</TD><TD > energy minimization of 2d LJ melt</TD></TR>
<TR><TD >msst</TD><TD > MSST shock dynamics</TD></TR>
<TR><TD >nb3b</TD><TD > use of nonbonded 3-body harmonic pair style</TD></TR>
<TR><TD >neb</TD><TD > nudged elastic band (NEB) calculation for barrier finding</TD></TR>
<TR><TD >nemd</TD><TD > non-equilibrium MD of 2d sheared system</TD></TR>
<TR><TD >obstacle</TD><TD > flow around two voids in a 2d channel</TD></TR>
<TR><TD >peptide</TD><TD > dynamics of a small solvated peptide chain (5-mer)</TD></TR>
<TR><TD >peri</TD><TD > Peridynamic model of cylinder impacted by indenter</TD></TR>
<TR><TD >pour</TD><TD > pouring of granular particles into a 3d box, then chute flow</TD></TR>
<TR><TD >prd</TD><TD > parallel replica dynamics of vacancy diffusion in bulk Si</TD></TR>
<TR><TD >qeq</TD><TD > use of the QEQ pacakge for charge equilibration</TD></TR>
<TR><TD >reax</TD><TD > RDX and TATB models using the ReaxFF</TD></TR>
<TR><TD >rigid</TD><TD > rigid bodies modeled as independent or coupled</TD></TR>
<TR><TD >shear</TD><TD > sideways shear applied to 2d solid, with and without a void</TD></TR>
<TR><TD >snap</TD><TD > NVE dynamics for BCC tantalum crystal using SNAP potential</TD></TR>
<TR><TD >srd</TD><TD > stochastic rotation dynamics (SRD) particles as solvent</TD></TR>
<TR><TD >tad</TD><TD > temperature-accelerated dynamics of vacancy diffusion in bulk Si</TD></TR>
<TR><TD >tri</TD><TD > triangular particles in rigid bodies
</TD></TR></TABLE></DIV>
<P>Here is how you might run and visualize one of the sample problems:
</P>
<PRE>cd indent
cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
lmp_linux &lt; in.indent # run the problem
</pre></div>
</div>
<p>Running the simulation produces the files <em>dump.indent</em> and
<em>log.lammps</em>. You can visualize the dump file as follows:</p>
<div class="highlight-python"><div class="highlight"><pre>../../tools/xmovie/xmovie -scale dump.indent
</pre></div>
</div>
<p>If you uncomment the <a class="reference internal" href="dump_image.html"><em>dump image</em></a> line(s) in the input
lmp_linux < in.indent # run the problem
</PRE>
<P>Running the simulation produces the files <I>dump.indent</I> and
<I>log.lammps</I>. You can visualize the dump file as follows:
</P>
<PRE>../../tools/xmovie/xmovie -scale dump.indent
</PRE>
<P>If you uncomment the <A HREF = "dump_image.html">dump image</A> line(s) in the input
script a series of JPG images will be produced by the run. These can
be viewed individually or turned into a movie or animated by tools
like ImageMagick or QuickTime or various Windows-based tools. See the
<a class="reference internal" href="dump_image.html"><em>dump image</em></a> doc page for more details. E.g. this
<A HREF = "dump_image.html">dump image</A> doc page for more details. E.g. this
Imagemagick command would create a GIF file suitable for viewing in a
browser.</p>
<div class="highlight-python"><div class="highlight"><pre>% convert -loop 1 *.jpg foo.gif
</pre></div>
</div>
<hr class="docutils" />
<p>There is also a COUPLE directory with examples of how to use LAMMPS as
browser.
</P>
<PRE>% convert -loop 1 *.jpg foo.gif
</PRE>
<HR>
<P>There is also a COUPLE directory with examples of how to use LAMMPS as
a library, either by itself or in tandem with another code or library.
See the COUPLE/README file to get started.</p>
<p>There is also an ELASTIC directory with an example script for
See the COUPLE/README file to get started.
</P>
<P>There is also an ELASTIC directory with an example script for
computing elastic constants, using a zero temperature Si example. See
the in.elastic file for more info.</p>
<p>There is also a USER directory which contains subdirectories of
the in.elastic file for more info.
</P>
<P>There is also a USER directory which contains subdirectories of
user-provided examples for user packages. See the README files in
those directories for more info. See the
<a class="reference internal" href="Section_start.html"><em>Section_start.html</em></a> file for more info about user
packages.</p>
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<div class="section" id="future-and-history">
<h1>13. Future and history<a class="headerlink" href="#future-and-history" title="Permalink to this headline"></a></h1>
<p>This section lists features we plan to add to LAMMPS, features of
<HR>
<H3>13. Future and history
</H3>
<P>This section lists features we plan to add to LAMMPS, features of
previous versions of LAMMPS, and features of other parallel molecular
dynamics codes our group has distributed.</p>
<div class="line-block">
<div class="line">13.1 <a class="reference internal" href="#hist-1"><span>Coming attractions</span></a></div>
<div class="line">13.2 <a class="reference internal" href="#hist-2"><span>Past versions</span></a></div>
<div class="line"><br /></div>
</div>
<div class="section" id="coming-attractions">
<span id="hist-1"></span><h2>13.1. Coming attractions<a class="headerlink" href="#coming-attractions" title="Permalink to this headline"></a></h2>
<p>The <a class="reference external" href="http://lammps.sandia.gov/future.html">Wish list link</a> on the
dynamics codes our group has distributed.
</P>
13.1 <A HREF = "#hist_1">Coming attractions</A><BR>
13.2 <A HREF = "#hist_2">Past versions</A> <BR>
<HR>
<HR>
<H4><A NAME = "hist_1"></A>13.1 Coming attractions
</H4>
<P>The <A HREF = "http://lammps.sandia.gov/future.html">Wish list link</A> on the
LAMMPS WWW page gives a list of features we are hoping to add to
LAMMPS in the future, including contact names of individuals you can
email if you are interested in contributing to the developement or
would be a future user of that feature.</p>
<p>You can also send <a class="reference external" href="http://lammps.sandia.gov/authors.html">email to the developers</a> if you want to add
your wish to the list.</p>
<hr class="docutils" />
</div>
<div class="section" id="past-versions">
<span id="hist-2"></span><h2>13.2. Past versions<a class="headerlink" href="#past-versions" title="Permalink to this headline"></a></h2>
<p>LAMMPS development began in the mid 1990s under a cooperative research
&amp; development agreement (CRADA) between two DOE labs (Sandia and LLNL)
would be a future user of that feature.
</P>
<P>You can also send <A HREF = "http://lammps.sandia.gov/authors.html">email to the
developers</A> if you want to add
your wish to the list.
</P>
<HR>
<H4><A NAME = "hist_2"></A>13.2 Past versions
</H4>
<P>LAMMPS development began in the mid 1990s under a cooperative research
& development agreement (CRADA) between two DOE labs (Sandia and LLNL)
and 3 companies (Cray, Bristol Myers Squibb, and Dupont). The goal was
to develop a large-scale parallel classical MD code; the coding effort
was led by Steve Plimpton at Sandia.</p>
<p>After the CRADA ended, a final F77 version, LAMMPS 99, was
was led by Steve Plimpton at Sandia.
</P>
<P>After the CRADA ended, a final F77 version, LAMMPS 99, was
released. As development of LAMMPS continued at Sandia, its memory
management was converted to F90; a final F90 version was released as
LAMMPS 2001.</p>
<p>The current LAMMPS is a rewrite in C++ and was first publicly released
LAMMPS 2001.
</P>
<P>The current LAMMPS is a rewrite in C++ and was first publicly released
as an open source code in 2004. It includes many new features beyond
those in LAMMPS 99 or 2001. It also includes features from older
parallel MD codes written at Sandia, namely ParaDyn, Warp, and
GranFlow (see below).</p>
<p>In late 2006 we began merging new capabilities into LAMMPS that were
GranFlow (see below).
</P>
<P>In late 2006 we began merging new capabilities into LAMMPS that were
developed by Aidan Thompson at Sandia for his MD code GRASP, which has
a parallel framework similar to LAMMPS. Most notably, these have
included many-body potentials - Stillinger-Weber, Tersoff, ReaxFF -
and the associated charge-equilibration routines needed for ReaxFF.</p>
<p>The <a class="reference external" href="http://lammps.sandia.gov/history.html">History link</a> on the
and the associated charge-equilibration routines needed for ReaxFF.
</P>
<P>The <A HREF = "http://lammps.sandia.gov/history.html">History link</A> on the
LAMMPS WWW page gives a timeline of features added to the
C++ open-source version of LAMMPS over the last several years.</p>
<p>These older codes are available for download from the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW site</a>, except for Warp &amp; GranFlow which were primarily used
internally. A brief listing of their features is given here.</p>
<p>LAMMPS 2001</p>
<ul class="simple">
<li>F90 + MPI</li>
<li>dynamic memory</li>
<li>spatial-decomposition parallelism</li>
<li>NVE, NVT, NPT, NPH, rRESPA integrators</li>
<li>LJ and Coulombic pairwise force fields</li>
<li>all-atom, united-atom, bead-spring polymer force fields</li>
<li>CHARMM-compatible force fields</li>
<li>class 2 force fields</li>
<li>3d/2d Ewald &amp; PPPM</li>
<li>various force and temperature constraints</li>
<li>SHAKE</li>
<li>Hessian-free truncated-Newton minimizer</li>
<li>user-defined diagnostics</li>
</ul>
<p>LAMMPS 99</p>
<ul class="simple">
<li>F77 + MPI</li>
<li>static memory allocation</li>
<li>spatial-decomposition parallelism</li>
<li>most of the LAMMPS 2001 features with a few exceptions</li>
<li>no 2d Ewald &amp; PPPM</li>
<li>molecular force fields are missing a few CHARMM terms</li>
<li>no SHAKE</li>
</ul>
<p>Warp</p>
<ul class="simple">
<li>F90 + MPI</li>
<li>spatial-decomposition parallelism</li>
<li>embedded atom method (EAM) metal potentials + LJ</li>
<li>lattice and grain-boundary atom creation</li>
<li>NVE, NVT integrators</li>
<li>boundary conditions for applying shear stresses</li>
<li>temperature controls for actively sheared systems</li>
<li>per-atom energy and centro-symmetry computation and output</li>
</ul>
<p>ParaDyn</p>
<ul class="simple">
<li>F77 + MPI</li>
<li>atom- and force-decomposition parallelism</li>
<li>embedded atom method (EAM) metal potentials</li>
<li>lattice atom creation</li>
<li>NVE, NVT, NPT integrators</li>
<li>all serial DYNAMO features for controls and constraints</li>
</ul>
<p>GranFlow</p>
<ul class="simple">
<li>F90 + MPI</li>
<li>spatial-decomposition parallelism</li>
<li>frictional granular potentials</li>
<li>NVE integrator</li>
<li>boundary conditions for granular flow and packing and walls</li>
<li>particle insertion</li>
</ul>
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C++ open-source version of LAMMPS over the last several years.
</P>
<P>These older codes are available for download from the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW
site</A>, except for Warp & GranFlow which were primarily used
internally. A brief listing of their features is given here.
</P>
<P>LAMMPS 2001
</P>
<UL><LI> F90 + MPI
<LI> dynamic memory
<LI> spatial-decomposition parallelism
<LI> NVE, NVT, NPT, NPH, rRESPA integrators
<LI> LJ and Coulombic pairwise force fields
<LI> all-atom, united-atom, bead-spring polymer force fields
<LI> CHARMM-compatible force fields
<LI> class 2 force fields
<LI> 3d/2d Ewald & PPPM
<LI> various force and temperature constraints
<LI> SHAKE
<LI> Hessian-free truncated-Newton minimizer
<LI> user-defined diagnostics
</UL>
<P>LAMMPS 99
</P>
<UL><LI> F77 + MPI
<LI> static memory allocation
<LI> spatial-decomposition parallelism
<LI> most of the LAMMPS 2001 features with a few exceptions
<LI> no 2d Ewald & PPPM
<LI> molecular force fields are missing a few CHARMM terms
<LI> no SHAKE
</UL>
<P>Warp
</P>
<UL><LI> F90 + MPI
<LI> spatial-decomposition parallelism
<LI> embedded atom method (EAM) metal potentials + LJ
<LI> lattice and grain-boundary atom creation
<LI> NVE, NVT integrators
<LI> boundary conditions for applying shear stresses
<LI> temperature controls for actively sheared systems
<LI> per-atom energy and centro-symmetry computation and output
</UL>
<P>ParaDyn
</P>
<UL><LI> F77 + MPI
<LI> atom- and force-decomposition parallelism
<LI> embedded atom method (EAM) metal potentials
<LI> lattice atom creation
<LI> NVE, NVT, NPT integrators
<LI> all serial DYNAMO features for controls and constraints
</UL>
<P>GranFlow
</P>
<UL><LI> F90 + MPI
<LI> spatial-decomposition parallelism
<LI> frictional granular potentials
<LI> NVE integrator
<LI> boundary conditions for granular flow and packing and walls
<LI> particle insertion
</UL>
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<div class="section" id="performance-scalability">
<h1>8. Performance &amp; scalability<a class="headerlink" href="#performance-scalability" title="Permalink to this headline"></a></h1>
<p>LAMMPS performance on several prototypical benchmarks and machines is
discussed on the Benchmarks page of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> where
<HR>
<H3>8. Performance & scalability
</H3>
<P>LAMMPS performance on several prototypical benchmarks and machines is
discussed on the Benchmarks page of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> where
CPU timings and parallel efficiencies are listed. Here, the
benchmarks are described briefly and some useful rules of thumb about
their performance are highlighted.</p>
<p>These are the 5 benchmark problems:</p>
<ol class="arabic simple">
<li>LJ = atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55</li>
</ol>
<blockquote>
<div>neighbors per atom), NVE integration</div></blockquote>
<ol class="arabic simple">
<li>Chain = bead-spring polymer melt of 100-mer chains, FENE bonds and LJ
their performance are highlighted.
</P>
<P>These are the 5 benchmark problems:
</P>
<OL><LI>LJ = atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55
neighbors per atom), NVE integration
<LI>Chain = bead-spring polymer melt of 100-mer chains, FENE bonds and LJ
pairwise interactions with a 2^(1/6) sigma cutoff (5 neighbors per
atom), NVE integration</li>
<li>EAM = metallic solid, Cu EAM potential with 4.95 Angstrom cutoff (45
neighbors per atom), NVE integration</li>
<li>Chute = granular chute flow, frictional history potential with 1.1
sigma cutoff (7 neighbors per atom), NVE integration</li>
<li>Rhodo = rhodopsin protein in solvated lipid bilayer, CHARMM force
atom), NVE integration
<LI>EAM = metallic solid, Cu EAM potential with 4.95 Angstrom cutoff (45
neighbors per atom), NVE integration
<LI>Chute = granular chute flow, frictional history potential with 1.1
sigma cutoff (7 neighbors per atom), NVE integration
<LI>Rhodo = rhodopsin protein in solvated lipid bilayer, CHARMM force
field with a 10 Angstrom LJ cutoff (440 neighbors per atom),
particle-particle particle-mesh (PPPM) for long-range Coulombics, NPT
integration</li>
</ol>
<p>The input files for running the benchmarks are included in the LAMMPS
integration
</OL>
<P>The input files for running the benchmarks are included in the LAMMPS
distribution, as are sample output files. Each of the 5 problems has
32,000 atoms and runs for 100 timesteps. Each can be run as a serial
benchmarks (on one processor) or in parallel. In parallel, each
@ -170,54 +46,30 @@ fixed-size benchmarking, the same 32K atom problem is run on various
numbers of processors. For scaled-size benchmarking, the model size
is increased with the number of processors. E.g. on 8 processors, a
256K-atom problem is run; on 1024 processors, a 32-million atom
problem is run, etc.</p>
<p>A useful metric from the benchmarks is the CPU cost per atom per
problem is run, etc.
</P>
<P>A useful metric from the benchmarks is the CPU cost per atom per
timestep. Since LAMMPS performance scales roughly linearly with
problem size and timesteps, the run time of any problem using the same
model (atom style, force field, cutoff, etc) can then be estimated.
For example, on a 1.7 GHz Pentium desktop machine (Intel icc compiler
under Red Hat Linux), the CPU run-time in seconds/atom/timestep for
the 5 problems is</p>
<table border="1" class="docutils">
<colgroup>
<col width="25%" />
<col width="14%" />
<col width="14%" />
<col width="14%" />
<col width="14%" />
<col width="17%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>Problem:</td>
<td>LJ</td>
<td>Chain</td>
<td>EAM</td>
<td>Chute</td>
<td>Rhodopsin</td>
</tr>
<tr class="row-even"><td>CPU/atom/step:</td>
<td>4.55E-6</td>
<td>2.18E-6</td>
<td>9.38E-6</td>
<td>2.18E-6</td>
<td>1.11E-4</td>
</tr>
<tr class="row-odd"><td>Ratio to LJ:</td>
<td>1.0</td>
<td>0.48</td>
<td>2.06</td>
<td>0.48</td>
<td>24.5</td>
</tr>
</tbody>
</table>
<p>The ratios mean that if the atomic LJ system has a normalized cost of
the 5 problems is
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ALIGN ="right">Problem:</TD><TD > LJ</TD><TD > Chain</TD><TD > EAM</TD><TD > Chute</TD><TD > Rhodopsin</TD></TR>
<TR ALIGN="center"><TD ALIGN ="right">CPU/atom/step:</TD><TD > 4.55E-6</TD><TD > 2.18E-6</TD><TD > 9.38E-6</TD><TD > 2.18E-6</TD><TD > 1.11E-4</TD></TR>
<TR ALIGN="center"><TD ALIGN ="right">Ratio to LJ:</TD><TD > 1.0</TD><TD > 0.48</TD><TD > 2.06</TD><TD > 0.48</TD><TD > 24.5
</TD></TR></TABLE></DIV>
<P>The ratios mean that if the atomic LJ system has a normalized cost of
1.0, the bead-spring chains and granular systems run 2x faster, while
the EAM metal and solvated protein models run 2x and 25x slower
respectively. The bulk of these cost differences is due to the
expense of computing a particular pairwise force field for a given
number of neighbors per atom.</p>
<p>Performance on a parallel machine can also be predicted from the
number of neighbors per atom.
</P>
<P>Performance on a parallel machine can also be predicted from the
one-processor timings if the parallel efficiency can be estimated.
The communication bandwidth and latency of a particular parallel
machine affects the efficiency. On most machines LAMMPS will give
@ -225,80 +77,8 @@ fixed-size parallel efficiencies on these benchmarks above 50% so long
as the atoms/processor count is a few 100 or greater - i.e. on 64 to
128 processors. Likewise, scaled-size parallel efficiencies will
typically be 80% or greater up to very large processor counts. The
benchmark data on the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> gives specific examples on
benchmark data on the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> gives specific examples on
some different machines, including a run of 3/4 of a billion LJ atoms
on 1500 processors that ran at 85% parallel efficiency.</p>
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<div class="section" id="user-cuda-package">
<h1>5.USER-CUDA package<a class="headerlink" href="#user-cuda-package" title="Permalink to this headline"></a></h1>
<p>The USER-CUDA package was developed by Christian Trott (Sandia) while
<HR>
<P><A HREF = "Section_accelerate.html">Return to Section accelerate overview</A>
</P>
<H4>5.3.1 USER-CUDA package
</H4>
<P>The USER-CUDA package was developed by Christian Trott (Sandia) while
at U Technology Ilmenau in Germany. It provides NVIDIA GPU versions
of many pair styles, many fixes, a few computes, and for long-range
Coulombics via the PPPM command. It has the following general
features:</p>
<ul class="simple">
<li>The package is designed to allow an entire LAMMPS calculation, for
features:
</P>
<UL><LI>The package is designed to allow an entire LAMMPS calculation, for
many timesteps, to run entirely on the GPU (except for inter-processor
MPI communication), so that atom-based data (e.g. coordinates, forces)
do not have to move back-and-forth between the CPU and GPU.</li>
<li>The speed-up advantage of this approach is typically better when the
number of atoms per GPU is large</li>
<li>Data will stay on the GPU until a timestep where a non-USER-CUDA fix
do not have to move back-and-forth between the CPU and GPU.
<LI>The speed-up advantage of this approach is typically better when the
number of atoms per GPU is large
<LI>Data will stay on the GPU until a timestep where a non-USER-CUDA fix
or compute is invoked. Whenever a non-GPU operation occurs (fix,
compute, output), data automatically moves back to the CPU as needed.
This may incur a performance penalty, but should otherwise work
transparently.</li>
<li>Neighbor lists are constructed on the GPU.</li>
<li>The package only supports use of a single MPI task, running on a
single CPU (core), assigned to each GPU.</li>
</ul>
<p>Here is a quick overview of how to use the USER-CUDA package:</p>
<ul class="simple">
<li>build the library in lib/cuda for your GPU hardware with desired precision</li>
<li>include the USER-CUDA package and build LAMMPS</li>
<li>use the mpirun command to specify 1 MPI task per GPU (on each node)</li>
<li>enable the USER-CUDA package via the &#8220;-c on&#8221; command-line switch</li>
<li>specify the # of GPUs per node</li>
<li>use USER-CUDA styles in your input script</li>
</ul>
<p>The latter two steps can be done using the &#8220;-pk cuda&#8221; and &#8220;-sf cuda&#8221;
<a class="reference internal" href="Section_start.html#start-7"><span>command-line switches</span></a> respectively. Or
the effect of the &#8220;-pk&#8221; or &#8220;-sf&#8221; switches can be duplicated by adding
the <a class="reference internal" href="package.html"><em>package cuda</em></a> or <a class="reference internal" href="suffix.html"><em>suffix cuda</em></a> commands
respectively to your input script.</p>
<p><strong>Required hardware/software:</strong></p>
<p>To use this package, you need to have one or more NVIDIA GPUs and
install the NVIDIA Cuda software on your system:</p>
<p>Your NVIDIA GPU needs to support Compute Capability 1.3. This list may
help you to find out the Compute Capability of your card:</p>
<p><a class="reference external" href="http://en.wikipedia.org/wiki/Comparison_of_Nvidia_graphics_processing_units">http://en.wikipedia.org/wiki/Comparison_of_Nvidia_graphics_processing_units</a></p>
<p>Install the Nvidia Cuda Toolkit (version 3.2 or higher) and the
transparently.
<LI>Neighbor lists are constructed on the GPU.
<LI>The package only supports use of a single MPI task, running on a
single CPU (core), assigned to each GPU.
</UL>
<P>Here is a quick overview of how to use the USER-CUDA package:
</P>
<UL><LI>build the library in lib/cuda for your GPU hardware with desired precision
<LI>include the USER-CUDA package and build LAMMPS
<LI>use the mpirun command to specify 1 MPI task per GPU (on each node)
<LI>enable the USER-CUDA package via the "-c on" command-line switch
<LI>specify the # of GPUs per node
<LI>use USER-CUDA styles in your input script
</UL>
<P>The latter two steps can be done using the "-pk cuda" and "-sf cuda"
<A HREF = "Section_start.html#start_7">command-line switches</A> respectively. Or
the effect of the "-pk" or "-sf" switches can be duplicated by adding
the <A HREF = "package.html">package cuda</A> or <A HREF = "suffix.html">suffix cuda</A> commands
respectively to your input script.
</P>
<P><B>Required hardware/software:</B>
</P>
<P>To use this package, you need to have one or more NVIDIA GPUs and
install the NVIDIA Cuda software on your system:
</P>
<P>Your NVIDIA GPU needs to support Compute Capability 1.3. This list may
help you to find out the Compute Capability of your card:
</P>
<P>http://en.wikipedia.org/wiki/Comparison_of_Nvidia_graphics_processing_units
</P>
<P>Install the Nvidia Cuda Toolkit (version 3.2 or higher) and the
corresponding GPU drivers. The Nvidia Cuda SDK is not required, but
we recommend it also be installed. You can then make sure its sample
projects can be compiled without problems.</p>
<p><strong>Building LAMMPS with the USER-CUDA package:</strong></p>
<p>This requires two steps (a,b): build the USER-CUDA library, then build
LAMMPS with the USER-CUDA package.</p>
<p>You can do both these steps in one line, using the src/Make.py script,
described in <a class="reference internal" href="Section_start.html#start-4"><span>Section 2.4</span></a> of the manual.
Type &#8220;Make.py -h&#8221; for help. If run from the src directory, this
projects can be compiled without problems.
</P>
<P><B>Building LAMMPS with the USER-CUDA package:</B>
</P>
<P>This requires two steps (a,b): build the USER-CUDA library, then build
LAMMPS with the USER-CUDA package.
</P>
<P>You can do both these steps in one line, using the src/Make.py script,
described in <A HREF = "Section_start.html#start_4">Section 2.4</A> of the manual.
Type "Make.py -h" for help. If run from the src directory, this
command will create src/lmp_cuda using src/MAKE/Makefile.mpi as the
starting Makefile.machine:</p>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p cuda -cuda mode=single arch=20 -o cuda lib-cuda file mpi
</pre></div>
</div>
<p>Or you can follow these two (a,b) steps:</p>
<ol class="loweralpha simple">
<li>Build the USER-CUDA library</li>
</ol>
<p>The USER-CUDA library is in lammps/lib/cuda. If your <em>CUDA</em> toolkit
is not installed in the default system directoy <em>/usr/local/cuda</em> edit
the file <em>lib/cuda/Makefile.common</em> accordingly.</p>
<p>To build the library with the settings in lib/cuda/Makefile.default,
simply type:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">make</span>
</pre></div>
</div>
<p>To set options when the library is built, type &#8220;make OPTIONS&#8221;, where
<em>OPTIONS</em> are one or more of the following. The settings will be
written to the <em>lib/cuda/Makefile.defaults</em> before the build.</p>
<pre class="literal-block">
<em>precision=N</em> to set the precision level
starting Makefile.machine:
</P>
<PRE>Make.py -p cuda -cuda mode=single arch=20 -o cuda lib-cuda file mpi
</PRE>
<P>Or you can follow these two (a,b) steps:
</P>
<P>(a) Build the USER-CUDA library
</P>
<P>The USER-CUDA library is in lammps/lib/cuda. If your <I>CUDA</I> toolkit
is not installed in the default system directoy <I>/usr/local/cuda</I> edit
the file <I>lib/cuda/Makefile.common</I> accordingly.
</P>
<P>To build the library with the settings in lib/cuda/Makefile.default,
simply type:
</P>
<PRE>make
</PRE>
<P>To set options when the library is built, type "make OPTIONS", where
<I>OPTIONS</I> are one or more of the following. The settings will be
written to the <I>lib/cuda/Makefile.defaults</I> before the build.
</P>
<PRE><I>precision=N</I> to set the precision level
N = 1 for single precision (default)
N = 2 for double precision
N = 3 for positions in double precision
N = 4 for positions and velocities in double precision
<em>arch=M</em> to set GPU compute capability
<I>arch=M</I> to set GPU compute capability
M = 35 for Kepler GPUs
M = 20 for CC2.0 (GF100/110, e.g. C2050,GTX580,GTX470) (default)
M = 21 for CC2.1 (GF104/114, e.g. GTX560, GTX460, GTX450)
M = 13 for CC1.3 (GF200, e.g. C1060, GTX285)
<em>prec_timer=0/1</em> to use hi-precision timers
<I>prec_timer=0/1</I> to use hi-precision timers
0 = do not use them (default)
1 = use them
this is usually only useful for Mac machines
<em>dbg=0/1</em> to activate debug mode
this is usually only useful for Mac machines
<I>dbg=0/1</I> to activate debug mode
0 = no debug mode (default)
1 = yes debug mode
this is only useful for developers
<em>cufft=1</em> for use of the CUDA FFT library
<I>cufft=1</I> for use of the CUDA FFT library
0 = no CUFFT support (default)
in the future other CUDA-enabled FFT libraries might be supported
</pre>
<p>If the build is successful, it will produce the files liblammpscuda.a and
Makefile.lammps.</p>
<p>Note that if you change any of the options (like precision), you need
to re-build the entire library. Do a &#8220;make clean&#8221; first, followed by
&#8220;make&#8221;.</p>
<ol class="loweralpha simple" start="2">
<li>Build LAMMPS with the USER-CUDA package</li>
</ol>
<div class="highlight-python"><div class="highlight"><pre>cd lammps/src
in the future other CUDA-enabled FFT libraries might be supported
</PRE>
<P>If the build is successful, it will produce the files liblammpscuda.a and
Makefile.lammps.
</P>
<P>Note that if you change any of the options (like precision), you need
to re-build the entire library. Do a "make clean" first, followed by
"make".
</P>
<P>(b) Build LAMMPS with the USER-CUDA package
</P>
<PRE>cd lammps/src
make yes-user-cuda
make machine
</pre></div>
</div>
<p>No additional compile/link flags are needed in Makefile.machine.</p>
<p>Note that if you change the USER-CUDA library precision (discussed
make machine
</PRE>
<P>No additional compile/link flags are needed in Makefile.machine.
</P>
<P>Note that if you change the USER-CUDA library precision (discussed
above) and rebuild the USER-CUDA library, then you also need to
re-install the USER-CUDA package and re-build LAMMPS, so that all
affected files are re-compiled and linked to the new USER-CUDA
library.</p>
<p><strong>Run with the USER-CUDA package from the command line:</strong></p>
<p>The mpirun or mpiexec command sets the total number of MPI tasks used
library.
</P>
<P><B>Run with the USER-CUDA package from the command line:</B>
</P>
<P>The mpirun or mpiexec command sets the total number of MPI tasks used
by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the mpirun command in MPICH does this via
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.</p>
<p>When using the USER-CUDA package, you must use exactly one MPI task
per physical GPU.</p>
<p>You must use the &#8220;-c on&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> to enable the USER-CUDA package.
The &#8220;-c on&#8221; switch also issues a default <a class="reference internal" href="package.html"><em>package cuda 1</em></a>
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.
</P>
<P>When using the USER-CUDA package, you must use exactly one MPI task
per physical GPU.
</P>
<P>You must use the "-c on" <A HREF = "Section_start.html#start_7">command-line
switch</A> to enable the USER-CUDA package.
The "-c on" switch also issues a default <A HREF = "package.html">package cuda 1</A>
command which sets various USER-CUDA options to default values, as
discussed on the <a class="reference internal" href="package.html"><em>package</em></a> command doc page.</p>
<p>Use the &#8220;-sf cuda&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>,
which will automatically append &#8220;cuda&#8221; to styles that support it. Use
the &#8220;-pk cuda Ng&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> to
discussed on the <A HREF = "package.html">package</A> command doc page.
</P>
<P>Use the "-sf cuda" <A HREF = "Section_start.html#start_7">command-line switch</A>,
which will automatically append "cuda" to styles that support it. Use
the "-pk cuda Ng" <A HREF = "Section_start.html#start_7">command-line switch</A> to
set Ng = # of GPUs per node to a different value than the default set
by the &#8220;-c on&#8221; switch (1 GPU) or change other <a class="reference internal" href="package.html"><em>package cuda</em></a> options.</p>
<div class="highlight-python"><div class="highlight"><pre>lmp_machine -c on -sf cuda -pk cuda 1 -in in.script # 1 MPI task uses 1 GPU
by the "-c on" switch (1 GPU) or change other <A HREF = "package.html">package
cuda</A> options.
</P>
<PRE>lmp_machine -c on -sf cuda -pk cuda 1 -in in.script # 1 MPI task uses 1 GPU
mpirun -np 2 lmp_machine -c on -sf cuda -pk cuda 2 -in in.script # 2 MPI tasks use 2 GPUs on a single 16-core (or whatever) node
mpirun -np 24 -ppn 2 lmp_machine -c on -sf cuda -pk cuda 2 -in in.script # ditto on 12 16-core nodes
</pre></div>
</div>
<p>The syntax for the &#8220;-pk&#8221; switch is the same as same as the &#8220;package
cuda&#8221; command. See the <a class="reference internal" href="package.html"><em>package</em></a> command doc page for
mpirun -np 24 -ppn 2 lmp_machine -c on -sf cuda -pk cuda 2 -in in.script # ditto on 12 16-core nodes
</PRE>
<P>The syntax for the "-pk" switch is the same as same as the "package
cuda" command. See the <A HREF = "package.html">package</A> command doc page for
details, including the default values used for all its options if it
is not specified.</p>
<p>Note that the default for the <a class="reference internal" href="package.html"><em>package cuda</em></a> command is
to set the Newton flag to &#8220;off&#8221; for both pairwise and bonded
is not specified.
</P>
<P>Note that the default for the <A HREF = "package.html">package cuda</A> command is
to set the Newton flag to "off" for both pairwise and bonded
interactions. This typically gives fastest performance. If the
<a class="reference internal" href="newton.html"><em>newton</em></a> command is used in the input script, it can
override these defaults.</p>
<p><strong>Or run with the USER-CUDA package by editing an input script:</strong></p>
<p>The discussion above for the mpirun/mpiexec command and the requirement
of one MPI task per GPU is the same.</p>
<p>You must still use the &#8220;-c on&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> to enable the USER-CUDA package.</p>
<p>Use the <a class="reference internal" href="suffix.html"><em>suffix cuda</em></a> command, or you can explicitly add a
&#8220;cuda&#8221; suffix to individual styles in your input script, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/cuda 2.5
</pre></div>
</div>
<p>You only need to use the <a class="reference internal" href="package.html"><em>package cuda</em></a> command if you
<A HREF = "newton.html">newton</A> command is used in the input script, it can
override these defaults.
</P>
<P><B>Or run with the USER-CUDA package by editing an input script:</B>
</P>
<P>The discussion above for the mpirun/mpiexec command and the requirement
of one MPI task per GPU is the same.
</P>
<P>You must still use the "-c on" <A HREF = "Section_start.html#start_7">command-line
switch</A> to enable the USER-CUDA package.
</P>
<P>Use the <A HREF = "suffix.html">suffix cuda</A> command, or you can explicitly add a
"cuda" suffix to individual styles in your input script, e.g.
</P>
<PRE>pair_style lj/cut/cuda 2.5
</PRE>
<P>You only need to use the <A HREF = "package.html">package cuda</A> command if you
wish to change any of its option defaults, including the number of
GPUs/node (default = 1), as set by the &#8220;-c on&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>.</p>
<p><strong>Speed-ups to expect:</strong></p>
<p>The performance of a GPU versus a multi-core CPU is a function of your
GPUs/node (default = 1), as set by the "-c on" <A HREF = "Section_start.html#start_7">command-line
switch</A>.
</P>
<P><B>Speed-ups to expect:</B>
</P>
<P>The performance of a GPU versus a multi-core CPU is a function of your
hardware, which pair style is used, the number of atoms/GPU, and the
precision used on the GPU (double, single, mixed).</p>
<p>See the <a class="reference external" href="http://lammps.sandia.gov/bench.html">Benchmark page</a> of the
precision used on the GPU (double, single, mixed).
</P>
<P>See the <A HREF = "http://lammps.sandia.gov/bench.html">Benchmark page</A> of the
LAMMPS web site for performance of the USER-CUDA package on different
hardware.</p>
<p><strong>Guidelines for best performance:</strong></p>
<ul class="simple">
<li>The USER-CUDA package offers more speed-up relative to CPU performance
hardware.
</P>
<P><B>Guidelines for best performance:</B>
</P>
<UL><LI>The USER-CUDA package offers more speed-up relative to CPU performance
when the number of atoms per GPU is large, e.g. on the order of tens
or hundreds of 1000s.</li>
<li>As noted above, this package will continue to run a simulation
or hundreds of 1000s.
<LI>As noted above, this package will continue to run a simulation
entirely on the GPU(s) (except for inter-processor MPI communication),
for multiple timesteps, until a CPU calculation is required, either by
a fix or compute that is non-GPU-ized, or until output is performed
(thermo or dump snapshot or restart file). The less often this
occurs, the faster your simulation will run.</li>
</ul>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>None.</p>
</div>
</div>
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</P>
<P>None.
</P>
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<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>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
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<p><a class="reference internal" href="Section_accelerate.html"><em>Return to Section accelerate overview</em></a></p>
<div class="section" id="gpu-package">
<h1>5.GPU package<a class="headerlink" href="#gpu-package" title="Permalink to this headline"></a></h1>
<p>The GPU package was developed by Mike Brown at ORNL and his
<HR>
<P><A HREF = "Section_accelerate.html">Return to Section accelerate overview</A>
</P>
<H4>5.3.2 GPU package
</H4>
<P>The GPU package was developed by Mike Brown at ORNL and his
collaborators, particularly Trung Nguyen (ORNL). It provides GPU
versions of many pair styles, including the 3-body Stillinger-Weber
pair style, and for <a class="reference internal" href="kspace_style.html"><em>kspace_style pppm</em></a> for
long-range Coulombics. It has the following general features:</p>
<ul class="simple">
<li>It is designed to exploit common GPU hardware configurations where one
pair style, and for <A HREF = "kspace_style.html">kspace_style pppm</A> for
long-range Coulombics. It has the following general features:
</P>
<UL><LI>It is designed to exploit common GPU hardware configurations where one
or more GPUs are coupled to many cores of one or more multi-core CPUs,
e.g. within a node of a parallel machine.</li>
<li>Atom-based data (e.g. coordinates, forces) moves back-and-forth
between the CPU(s) and GPU every timestep.</li>
<li>Neighbor lists can be built on the CPU or on the GPU</li>
<li>The charge assignement and force interpolation portions of PPPM can be
e.g. within a node of a parallel machine.
<LI>Atom-based data (e.g. coordinates, forces) moves back-and-forth
between the CPU(s) and GPU every timestep.
<LI>Neighbor lists can be built on the CPU or on the GPU
<LI>The charge assignement and force interpolation portions of PPPM can be
run on the GPU. The FFT portion, which requires MPI communication
between processors, runs on the CPU.</li>
<li>Asynchronous force computations can be performed simultaneously on the
CPU(s) and GPU.</li>
<li>It allows for GPU computations to be performed in single or double
between processors, runs on the CPU.
<LI>Asynchronous force computations can be performed simultaneously on the
CPU(s) and GPU.
<LI>It allows for GPU computations to be performed in single or double
precision, or in mixed-mode precision, where pairwise forces are
computed in single precision, but accumulated into double-precision
force vectors.</li>
<li>LAMMPS-specific code is in the GPU package. It makes calls to a
force vectors.
<LI>LAMMPS-specific code is in the GPU package. It makes calls to a
generic GPU library in the lib/gpu directory. This library provides
NVIDIA support as well as more general OpenCL support, so that the
same functionality can eventually be supported on a variety of GPU
hardware.</li>
</ul>
<p>Here is a quick overview of how to use the GPU package:</p>
<ul class="simple">
<li>build the library in lib/gpu for your GPU hardware wity desired precision</li>
<li>include the GPU package and build LAMMPS</li>
<li>use the mpirun command to set the number of MPI tasks/node which determines the number of MPI tasks/GPU</li>
<li>specify the # of GPUs per node</li>
<li>use GPU styles in your input script</li>
</ul>
<p>The latter two steps can be done using the &#8220;-pk gpu&#8221; and &#8220;-sf gpu&#8221;
<a class="reference internal" href="Section_start.html#start-7"><span>command-line switches</span></a> respectively. Or
the effect of the &#8220;-pk&#8221; or &#8220;-sf&#8221; switches can be duplicated by adding
the <a class="reference internal" href="package.html"><em>package gpu</em></a> or <a class="reference internal" href="suffix.html"><em>suffix gpu</em></a> commands
respectively to your input script.</p>
<p><strong>Required hardware/software:</strong></p>
<p>To use this package, you currently need to have an NVIDIA GPU and
install the NVIDIA Cuda software on your system:</p>
<ul class="simple">
<li>Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/0/information</li>
<li>Go to <a class="reference external" href="http://www.nvidia.com/object/cuda_get.html">http://www.nvidia.com/object/cuda_get.html</a></li>
<li>Install a driver and toolkit appropriate for your system (SDK is not necessary)</li>
<li>Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to list supported devices and properties</li>
</ul>
<p><strong>Building LAMMPS with the GPU package:</strong></p>
<p>This requires two steps (a,b): build the GPU library, then build
LAMMPS with the GPU package.</p>
<p>You can do both these steps in one line, using the src/Make.py script,
described in <a class="reference internal" href="Section_start.html#start-4"><span>Section 2.4</span></a> of the manual.
Type &#8220;Make.py -h&#8221; for help. If run from the src directory, this
hardware.
</UL>
<P>Here is a quick overview of how to use the GPU package:
</P>
<UL><LI>build the library in lib/gpu for your GPU hardware wity desired precision
<LI>include the GPU package and build LAMMPS
<LI>use the mpirun command to set the number of MPI tasks/node which determines the number of MPI tasks/GPU
<LI>specify the # of GPUs per node
<LI>use GPU styles in your input script
</UL>
<P>The latter two steps can be done using the "-pk gpu" and "-sf gpu"
<A HREF = "Section_start.html#start_7">command-line switches</A> respectively. Or
the effect of the "-pk" or "-sf" switches can be duplicated by adding
the <A HREF = "package.html">package gpu</A> or <A HREF = "suffix.html">suffix gpu</A> commands
respectively to your input script.
</P>
<P><B>Required hardware/software:</B>
</P>
<P>To use this package, you currently need to have an NVIDIA GPU and
install the NVIDIA Cuda software on your system:
</P>
<UL><LI>Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/0/information
<LI>Go to http://www.nvidia.com/object/cuda_get.html
<LI>Install a driver and toolkit appropriate for your system (SDK is not necessary)
<LI>Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to list supported devices and properties
</UL>
<P><B>Building LAMMPS with the GPU package:</B>
</P>
<P>This requires two steps (a,b): build the GPU library, then build
LAMMPS with the GPU package.
</P>
<P>You can do both these steps in one line, using the src/Make.py script,
described in <A HREF = "Section_start.html#start_4">Section 2.4</A> of the manual.
Type "Make.py -h" for help. If run from the src directory, this
command will create src/lmp_gpu using src/MAKE/Makefile.mpi as the
starting Makefile.machine:</p>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p gpu -gpu mode=single arch=31 -o gpu lib-gpu file mpi
</pre></div>
</div>
<p>Or you can follow these two (a,b) steps:</p>
<ol class="loweralpha simple">
<li>Build the GPU library</li>
</ol>
<p>The GPU library is in lammps/lib/gpu. Select a Makefile.machine (in
starting Makefile.machine:
</P>
<PRE>Make.py -p gpu -gpu mode=single arch=31 -o gpu lib-gpu file mpi
</PRE>
<P>Or you can follow these two (a,b) steps:
</P>
<P>(a) Build the GPU library
</P>
<P>The GPU library is in lammps/lib/gpu. Select a Makefile.machine (in
lib/gpu) appropriate for your system. You should pay special
attention to 3 settings in this makefile.</p>
<ul class="simple">
<li>CUDA_HOME = needs to be where NVIDIA Cuda software is installed on your system</li>
<li>CUDA_ARCH = needs to be appropriate to your GPUs</li>
<li>CUDA_PREC = precision (double, mixed, single) you desire</li>
</ul>
<p>See lib/gpu/Makefile.linux.double for examples of the ARCH settings
attention to 3 settings in this makefile.
</P>
<UL><LI>CUDA_HOME = needs to be where NVIDIA Cuda software is installed on your system
<LI>CUDA_ARCH = needs to be appropriate to your GPUs
<LI>CUDA_PREC = precision (double, mixed, single) you desire
</UL>
<P>See lib/gpu/Makefile.linux.double for examples of the ARCH settings
for different GPU choices, e.g. Fermi vs Kepler. It also lists the
possible precision settings:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">CUDA_PREC</span> <span class="o">=</span> <span class="o">-</span><span class="n">D_SINGLE_SINGLE</span> <span class="c"># single precision for all calculations</span>
<span class="n">CUDA_PREC</span> <span class="o">=</span> <span class="o">-</span><span class="n">D_DOUBLE_DOUBLE</span> <span class="c"># double precision for all calculations</span>
<span class="n">CUDA_PREC</span> <span class="o">=</span> <span class="o">-</span><span class="n">D_SINGLE_DOUBLE</span> <span class="c"># accumulation of forces, etc, in double</span>
</pre></div>
</div>
<p>The last setting is the mixed mode referred to above. Note that your
possible precision settings:
</P>
<PRE>CUDA_PREC = -D_SINGLE_SINGLE # single precision for all calculations
CUDA_PREC = -D_DOUBLE_DOUBLE # double precision for all calculations
CUDA_PREC = -D_SINGLE_DOUBLE # accumulation of forces, etc, in double
</PRE>
<P>The last setting is the mixed mode referred to above. Note that your
GPU must support double precision to use either the 2nd or 3rd of
these settings.</p>
<p>To build the library, type:</p>
<div class="highlight-python"><div class="highlight"><pre>make -f Makefile.machine
</pre></div>
</div>
<p>If successful, it will produce the files libgpu.a and Makefile.lammps.</p>
<p>The latter file has 3 settings that need to be appropriate for the
these settings.
</P>
<P>To build the library, type:
</P>
<PRE>make -f Makefile.machine
</PRE>
<P>If successful, it will produce the files libgpu.a and Makefile.lammps.
</P>
<P>The latter file has 3 settings that need to be appropriate for the
paths and settings for the CUDA system software on your machine.
Makefile.lammps is a copy of the file specified by the EXTRAMAKE
setting in Makefile.machine. You can change EXTRAMAKE or create your
own Makefile.lammps.machine if needed.</p>
<p>Note that to change the precision of the GPU library, you need to
re-build the entire library. Do a &#8220;clean&#8221; first, e.g. &#8220;make -f
Makefile.linux clean&#8221;, followed by the make command above.</p>
<ol class="loweralpha simple" start="2">
<li>Build LAMMPS with the GPU package</li>
</ol>
<div class="highlight-python"><div class="highlight"><pre>cd lammps/src
own Makefile.lammps.machine if needed.
</P>
<P>Note that to change the precision of the GPU library, you need to
re-build the entire library. Do a "clean" first, e.g. "make -f
Makefile.linux clean", followed by the make command above.
</P>
<P>(b) Build LAMMPS with the GPU package
</P>
<PRE>cd lammps/src
make yes-gpu
make machine
</pre></div>
</div>
<p>No additional compile/link flags are needed in Makefile.machine.</p>
<p>Note that if you change the GPU library precision (discussed above)
make machine
</PRE>
<P>No additional compile/link flags are needed in Makefile.machine.
</P>
<P>Note that if you change the GPU library precision (discussed above)
and rebuild the GPU library, then you also need to re-install the GPU
package and re-build LAMMPS, so that all affected files are
re-compiled and linked to the new GPU library.</p>
<p><strong>Run with the GPU package from the command line:</strong></p>
<p>The mpirun or mpiexec command sets the total number of MPI tasks used
re-compiled and linked to the new GPU library.
</P>
<P><B>Run with the GPU package from the command line:</B>
</P>
<P>The mpirun or mpiexec command sets the total number of MPI tasks used
by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the mpirun command in MPICH does this via
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.</p>
<p>When using the GPU package, you cannot assign more than one GPU to a
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.
</P>
<P>When using the GPU package, you cannot assign more than one GPU to a
single MPI task. However multiple MPI tasks can share the same GPU,
and in many cases it will be more efficient to run this way. Likewise
it may be more efficient to use less MPI tasks/node than the available
# of CPU cores. Assignment of multiple MPI tasks to a GPU will happen
automatically if you create more MPI tasks/node than there are
GPUs/mode. E.g. with 8 MPI tasks/node and 2 GPUs, each GPU will be
shared by 4 MPI tasks.</p>
<p>Use the &#8220;-sf gpu&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>,
which will automatically append &#8220;gpu&#8221; to styles that support it. Use
the &#8220;-pk gpu Ng&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> to
set Ng = # of GPUs/node to use.</p>
<div class="highlight-python"><div class="highlight"><pre>lmp_machine -sf gpu -pk gpu 1 -in in.script # 1 MPI task uses 1 GPU
shared by 4 MPI tasks.
</P>
<P>Use the "-sf gpu" <A HREF = "Section_start.html#start_7">command-line switch</A>,
which will automatically append "gpu" to styles that support it. Use
the "-pk gpu Ng" <A HREF = "Section_start.html#start_7">command-line switch</A> to
set Ng = # of GPUs/node to use.
</P>
<PRE>lmp_machine -sf gpu -pk gpu 1 -in in.script # 1 MPI task uses 1 GPU
mpirun -np 12 lmp_machine -sf gpu -pk gpu 2 -in in.script # 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node
mpirun -np 48 -ppn 12 lmp_machine -sf gpu -pk gpu 2 -in in.script # ditto on 4 16-core nodes
</pre></div>
</div>
<p>Note that if the &#8220;-sf gpu&#8221; switch is used, it also issues a default
<a class="reference internal" href="package.html"><em>package gpu 1</em></a> command, which sets the number of
GPUs/node to 1.</p>
<p>Using the &#8220;-pk&#8221; switch explicitly allows for setting of the number of
mpirun -np 48 -ppn 12 lmp_machine -sf gpu -pk gpu 2 -in in.script # ditto on 4 16-core nodes
</PRE>
<P>Note that if the "-sf gpu" switch is used, it also issues a default
<A HREF = "package.html">package gpu 1</A> command, which sets the number of
GPUs/node to 1.
</P>
<P>Using the "-pk" switch explicitly allows for setting of the number of
GPUs/node to use and additional options. Its syntax is the same as
same as the &#8220;package gpu&#8221; command. See the <a class="reference internal" href="package.html"><em>package</em></a>
same as the "package gpu" command. See the <A HREF = "package.html">package</A>
command doc page for details, including the default values used for
all its options if it is not specified.</p>
<p>Note that the default for the <a class="reference internal" href="package.html"><em>package gpu</em></a> command is to
set the Newton flag to &#8220;off&#8221; pairwise interactions. It does not
affect the setting for bonded interactions (LAMMPS default is &#8220;on&#8221;).
The &#8220;off&#8221; setting for pairwise interaction is currently required for
GPU package pair styles.</p>
<p><strong>Or run with the GPU package by editing an input script:</strong></p>
<p>The discussion above for the mpirun/mpiexec command, MPI tasks/node,
and use of multiple MPI tasks/GPU is the same.</p>
<p>Use the <a class="reference internal" href="suffix.html"><em>suffix gpu</em></a> command, or you can explicitly add an
&#8220;gpu&#8221; suffix to individual styles in your input script, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/gpu 2.5
</pre></div>
</div>
<p>You must also use the <a class="reference internal" href="package.html"><em>package gpu</em></a> command to enable the
GPU package, unless the &#8220;-sf gpu&#8221; or &#8220;-pk gpu&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switches</span></a> were used. It specifies the
number of GPUs/node to use, as well as other options.</p>
<p><strong>Speed-ups to expect:</strong></p>
<p>The performance of a GPU versus a multi-core CPU is a function of your
all its options if it is not specified.
</P>
<P>Note that the default for the <A HREF = "package.html">package gpu</A> command is to
set the Newton flag to "off" pairwise interactions. It does not
affect the setting for bonded interactions (LAMMPS default is "on").
The "off" setting for pairwise interaction is currently required for
GPU package pair styles.
</P>
<P><B>Or run with the GPU package by editing an input script:</B>
</P>
<P>The discussion above for the mpirun/mpiexec command, MPI tasks/node,
and use of multiple MPI tasks/GPU is the same.
</P>
<P>Use the <A HREF = "suffix.html">suffix gpu</A> command, or you can explicitly add an
"gpu" suffix to individual styles in your input script, e.g.
</P>
<PRE>pair_style lj/cut/gpu 2.5
</PRE>
<P>You must also use the <A HREF = "package.html">package gpu</A> command to enable the
GPU package, unless the "-sf gpu" or "-pk gpu" <A HREF = "Section_start.html#start_7">command-line
switches</A> were used. It specifies the
number of GPUs/node to use, as well as other options.
</P>
<P><B>Speed-ups to expect:</B>
</P>
<P>The performance of a GPU versus a multi-core CPU is a function of your
hardware, which pair style is used, the number of atoms/GPU, and the
precision used on the GPU (double, single, mixed).</p>
<p>See the <a class="reference external" href="http://lammps.sandia.gov/bench.html">Benchmark page</a> of the
precision used on the GPU (double, single, mixed).
</P>
<P>See the <A HREF = "http://lammps.sandia.gov/bench.html">Benchmark page</A> of the
LAMMPS web site for performance of the GPU package on various
hardware, including the Titan HPC platform at ORNL.</p>
<p>You should also experiment with how many MPI tasks per GPU to use to
hardware, including the Titan HPC platform at ORNL.
</P>
<P>You should also experiment with how many MPI tasks per GPU to use to
give the best performance for your problem and machine. This is also
a function of the problem size and the pair style being using.
Likewise, you should experiment with the precision setting for the GPU
library to see if single or mixed precision will give accurate
results, since they will typically be faster.</p>
<p><strong>Guidelines for best performance:</strong></p>
<ul class="simple">
<li>Using multiple MPI tasks per GPU will often give the best performance,
as allowed my most multi-core CPU/GPU configurations.</li>
<li>If the number of particles per MPI task is small (e.g. 100s of
results, since they will typically be faster.
</P>
<P><B>Guidelines for best performance:</B>
</P>
<UL><LI>Using multiple MPI tasks per GPU will often give the best performance,
as allowed my most multi-core CPU/GPU configurations.
<LI>If the number of particles per MPI task is small (e.g. 100s of
particles), it can be more efficient to run with fewer MPI tasks per
GPU, even if you do not use all the cores on the compute node.</li>
<li>The <a class="reference internal" href="package.html"><em>package gpu</em></a> command has several options for tuning
GPU, even if you do not use all the cores on the compute node.
<LI>The <A HREF = "package.html">package gpu</A> command has several options for tuning
performance. Neighbor lists can be built on the GPU or CPU. Force
calculations can be dynamically balanced across the CPU cores and
GPUs. GPU-specific settings can be made which can be optimized
for different hardware. See the <a class="reference internal" href="package.html"><em>packakge</em></a> command
doc page for details.</li>
<li>As described by the <a class="reference internal" href="package.html"><em>package gpu</em></a> command, GPU
for different hardware. See the <A HREF = "package.html">packakge</A> command
doc page for details.
<LI>As described by the <A HREF = "package.html">package gpu</A> command, GPU
accelerated pair styles can perform computations asynchronously with
CPU computations. The &#8220;Pair&#8221; time reported by LAMMPS will be the
CPU computations. The "Pair" time reported by LAMMPS will be the
maximum of the time required to complete the CPU pair style
computations and the time required to complete the GPU pair style
computations. Any time spent for GPU-enabled pair styles for
computations that run simultaneously with <a class="reference internal" href="bond_style.html"><em>bond</em></a>,
<a class="reference internal" href="angle_style.html"><em>angle</em></a>, <a class="reference internal" href="dihedral_style.html"><em>dihedral</em></a>,
<a class="reference internal" href="improper_style.html"><em>improper</em></a>, and <a class="reference internal" href="kspace_style.html"><em>long-range</em></a>
calculations will not be included in the &#8220;Pair&#8221; time.</li>
<li>When the <em>mode</em> setting for the package gpu command is force/neigh,
computations that run simultaneously with <A HREF = "bond_style.html">bond</A>,
<A HREF = "angle_style.html">angle</A>, <A HREF = "dihedral_style.html">dihedral</A>,
<A HREF = "improper_style.html">improper</A>, and <A HREF = "kspace_style.html">long-range</A>
calculations will not be included in the "Pair" time.
<LI>When the <I>mode</I> setting for the package gpu command is force/neigh,
the time for neighbor list calculations on the GPU will be added into
the &#8220;Pair&#8221; time, not the &#8220;Neigh&#8221; time. An additional breakdown of the
the "Pair" time, not the "Neigh" time. An additional breakdown of the
times required for various tasks on the GPU (data copy, neighbor
calculations, force computations, etc) are output only with the LAMMPS
screen output (not in the log file) at the end of each run. These
timings represent total time spent on the GPU for each routine,
regardless of asynchronous CPU calculations.</li>
<li>The output section &#8220;GPU Time Info (average)&#8221; reports &#8220;Max Mem / Proc&#8221;.
regardless of asynchronous CPU calculations.
<LI>The output section "GPU Time Info (average)" reports "Max Mem / Proc".
This is the maximum memory used at one time on the GPU for data
storage by a single MPI process.</li>
</ul>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>None.</p>
</div>
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</P>
<P>None.
</P>
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@ -1,133 +1,20 @@
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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>
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<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>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<p><a class="reference internal" href="Section_accelerate.html"><em>Return to Section accelerate overview</em></a></p>
<div class="section" id="user-intel-package">
<h1>5.USER-INTEL package<a class="headerlink" href="#user-intel-package" title="Permalink to this headline"></a></h1>
<p>The USER-INTEL package was developed by Mike Brown at Intel
<HR>
<P><A HREF = "Section_accelerate.html">Return to Section accelerate overview</A>
</P>
<H4>5.3.3 USER-INTEL package
</H4>
<P>The USER-INTEL package was developed by Mike Brown at Intel
Corporation. It provides a capability to accelerate simulations by
offloading neighbor list and non-bonded force calculations to Intel(R)
Xeon Phi(TM) coprocessors (not native mode like the KOKKOS package).
@ -135,225 +22,264 @@ Additionally, it supports running simulations in single, mixed, or
double precision with vectorization, even if a coprocessor is not
present, i.e. on an Intel(R) CPU. The same C++ code is used for both
cases. When offloading to a coprocessor, the routine is run twice,
once with an offload flag.</p>
<p>The USER-INTEL package can be used in tandem with the USER-OMP
once with an offload flag.
</P>
<P>The USER-INTEL package can be used in tandem with the USER-OMP
package. This is useful when offloading pair style computations to
coprocessors, so that other styles not supported by the USER-INTEL
package, e.g. bond, angle, dihedral, improper, and long-range
electrostatics, can run simultaneously in threaded mode on the CPU
cores. Since less MPI tasks than CPU cores will typically be invoked
when running with coprocessors, this enables the extra CPU cores to be
used for useful computation.</p>
<p>If LAMMPS is built with both the USER-INTEL and USER-OMP packages
used for useful computation.
</P>
<P>If LAMMPS is built with both the USER-INTEL and USER-OMP packages
intsalled, this mode of operation is made easier to use, because the
&#8220;-suffix intel&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> or
the <a class="reference internal" href="suffix.html"><em>suffix intel</em></a> command will both set a second-choice
suffix to &#8220;omp&#8221; so that styles from the USER-OMP package will be used
"-suffix intel" <A HREF = "Section_start.html#start_7">command-line switch</A> or
the <A HREF = "suffix.html">suffix intel</A> command will both set a second-choice
suffix to "omp" so that styles from the USER-OMP package will be used
if available, after first testing if a style from the USER-INTEL
package is available.</p>
<p>When using the USER-INTEL package, you must choose at build time
package is available.
</P>
<P>When using the USER-INTEL package, you must choose at build time
whether you are building for CPU-only acceleration or for using the
Xeon Phi in offload mode.</p>
<p>Here is a quick overview of how to use the USER-INTEL package
for CPU-only acceleration:</p>
<ul class="simple">
<li>specify these CCFLAGS in your src/MAKE/Makefile.machine: -openmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost</li>
<li>specify -openmp with LINKFLAGS in your Makefile.machine</li>
<li>include the USER-INTEL package and (optionally) USER-OMP package and build LAMMPS</li>
<li>specify how many OpenMP threads per MPI task to use</li>
<li>use USER-INTEL and (optionally) USER-OMP styles in your input script</li>
</ul>
<p>Note that many of these settings can only be used with the Intel
compiler, as discussed below.</p>
<p>Using the USER-INTEL package to offload work to the Intel(R)
Xeon Phi in offload mode.
</P>
<P>Here is a quick overview of how to use the USER-INTEL package
for CPU-only acceleration:
</P>
<UL><LI>specify these CCFLAGS in your src/MAKE/Makefile.machine: -openmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost
<LI>specify -openmp with LINKFLAGS in your Makefile.machine
<LI>include the USER-INTEL package and (optionally) USER-OMP package and build LAMMPS
<LI>specify how many OpenMP threads per MPI task to use
<LI>use USER-INTEL and (optionally) USER-OMP styles in your input script
</UL>
<P>Note that many of these settings can only be used with the Intel
compiler, as discussed below.
</P>
<P>Using the USER-INTEL package to offload work to the Intel(R)
Xeon Phi(TM) coprocessor is the same except for these additional
steps:</p>
<ul class="simple">
<li>add the flag -DLMP_INTEL_OFFLOAD to CCFLAGS in your Makefile.machine</li>
<li>add the flag -offload to LINKFLAGS in your Makefile.machine</li>
</ul>
<p>The latter two steps in the first case and the last step in the
coprocessor case can be done using the &#8220;-pk intel&#8221; and &#8220;-sf intel&#8221;
<a class="reference internal" href="Section_start.html#start-7"><span>command-line switches</span></a> respectively. Or
the effect of the &#8220;-pk&#8221; or &#8220;-sf&#8221; switches can be duplicated by adding
the <a class="reference internal" href="package.html"><em>package intel</em></a> or <a class="reference internal" href="suffix.html"><em>suffix intel</em></a>
commands respectively to your input script.</p>
<p><strong>Required hardware/software:</strong></p>
<p>To use the offload option, you must have one or more Intel(R) Xeon
Phi(TM) coprocessors and use an Intel(R) C++ compiler.</p>
<p>Optimizations for vectorization have only been tested with the
steps:
</P>
<UL><LI>add the flag -DLMP_INTEL_OFFLOAD to CCFLAGS in your Makefile.machine
<LI>add the flag -offload to LINKFLAGS in your Makefile.machine
</UL>
<P>The latter two steps in the first case and the last step in the
coprocessor case can be done using the "-pk intel" and "-sf intel"
<A HREF = "Section_start.html#start_7">command-line switches</A> respectively. Or
the effect of the "-pk" or "-sf" switches can be duplicated by adding
the <A HREF = "package.html">package intel</A> or <A HREF = "suffix.html">suffix intel</A>
commands respectively to your input script.
</P>
<P><B>Required hardware/software:</B>
</P>
<P>To use the offload option, you must have one or more Intel(R) Xeon
Phi(TM) coprocessors and use an Intel(R) C++ compiler.
</P>
<P>Optimizations for vectorization have only been tested with the
Intel(R) compiler. Use of other compilers may not result in
vectorization or give poor performance.</p>
<p>Use of an Intel C++ compiler is recommended, but not required (though
vectorization or give poor performance.
</P>
<P>Use of an Intel C++ compiler is recommended, but not required (though
g++ will not recognize some of the settings, so they cannot be used).
The compiler must support the OpenMP interface.</p>
<p>The recommended version of the Intel(R) compiler is 14.0.1.106.
Versions 15.0.1.133 and later are also supported. If using Intel(R)
MPI, versions 15.0.2.044 and later are recommended.</p>
<p><strong>Building LAMMPS with the USER-INTEL package:</strong></p>
<p>You can choose to build with or without support for offload to a
The compiler must support the OpenMP interface.
</P>
<P>The recommended version of the Intel(R) compiler is 14.0.1.106.
Versions 15.0.1.133 and later are also supported. If using Intel(R)
MPI, versions 15.0.2.044 and later are recommended.
</P>
<P><B>Building LAMMPS with the USER-INTEL package:</B>
</P>
<P>You can choose to build with or without support for offload to a
Intel(R) Xeon Phi(TM) coprocessor. If you build with support for a
coprocessor, the same binary can be used on nodes with and without
coprocessors installed. However, if you do not have coprocessors
on your system, building without offload support will produce a
smaller binary.</p>
<p>You can do either in one line, using the src/Make.py script, described
in <a class="reference internal" href="Section_start.html#start-4"><span>Section 2.4</span></a> of the manual. Type
&#8220;Make.py -h&#8221; for help. If run from the src directory, these commands
smaller binary.
</P>
<P>You can do either in one line, using the src/Make.py script, described
in <A HREF = "Section_start.html#start_4">Section 2.4</A> of the manual. Type
"Make.py -h" for help. If run from the src directory, these commands
will create src/lmp_intel_cpu and lmp_intel_phi using
src/MAKE/Makefile.mpi as the starting Makefile.machine:</p>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p intel omp -intel cpu -o intel_cpu -cc icc file mpi
Make.py -p intel omp -intel phi -o intel_phi -cc icc file mpi
</pre></div>
</div>
<p>Note that this assumes that your MPI and its mpicxx wrapper
src/MAKE/Makefile.mpi as the starting Makefile.machine:
</P>
<PRE>Make.py -p intel omp -intel cpu -o intel_cpu -cc icc file mpi
Make.py -p intel omp -intel phi -o intel_phi -cc icc file mpi
</PRE>
<P>Note that this assumes that your MPI and its mpicxx wrapper
is using the Intel compiler. If it is not, you should
leave off the &#8220;-cc icc&#8221; switch.</p>
<p>Or you can follow these steps:</p>
<div class="highlight-python"><div class="highlight"><pre>cd lammps/src
leave off the "-cc icc" switch.
</P>
<P>Or you can follow these steps:
</P>
<PRE>cd lammps/src
make yes-user-intel
make yes-user-omp (if desired)
make machine
</pre></div>
</div>
<p>Note that if the USER-OMP package is also installed, you can use
styles from both packages, as described below.</p>
<p>The Makefile.machine needs a &#8220;-fopenmp&#8221; flag for OpenMP support in
make machine
</PRE>
<P>Note that if the USER-OMP package is also installed, you can use
styles from both packages, as described below.
</P>
<P>The Makefile.machine needs a "-fopenmp" flag for OpenMP support in
both the CCFLAGS and LINKFLAGS variables. You also need to add
-DLAMMPS_MEMALIGN=64 and -restrict to CCFLAGS.</p>
<p>If you are compiling on the same architecture that will be used for
the runs, adding the flag <em>-xHost</em> to CCFLAGS will enable
-DLAMMPS_MEMALIGN=64 and -restrict to CCFLAGS.
</P>
<P>If you are compiling on the same architecture that will be used for
the runs, adding the flag <I>-xHost</I> to CCFLAGS will enable
vectorization with the Intel(R) compiler. Otherwise, you must
provide the correct compute node architecture to the -x option
(e.g. -xAVX).</p>
<p>In order to build with support for an Intel(R) Xeon Phi(TM)
coprocessor, the flag <em>-offload</em> should be added to the LINKFLAGS line
and the flag -DLMP_INTEL_OFFLOAD should be added to the CCFLAGS line.</p>
<p>Example makefiles Makefile.intel_cpu and Makefile.intel_phi are
(e.g. -xAVX).
</P>
<P>In order to build with support for an Intel(R) Xeon Phi(TM)
coprocessor, the flag <I>-offload</I> should be added to the LINKFLAGS line
and the flag -DLMP_INTEL_OFFLOAD should be added to the CCFLAGS line.
</P>
<P>Example makefiles Makefile.intel_cpu and Makefile.intel_phi are
included in the src/MAKE/OPTIONS directory with settings that perform
well with the Intel(R) compiler. The latter file has support for
offload to coprocessors; the former does not.</p>
<p><strong>Notes on CPU and core affinity:</strong></p>
<p>Setting core affinity is often used to pin MPI tasks and OpenMP
offload to coprocessors; the former does not.
</P>
<P><B>Notes on CPU and core affinity:</B>
</P>
<P>Setting core affinity is often used to pin MPI tasks and OpenMP
threads to a core or group of cores so that memory access can be
uniform. Unless disabled at build time, affinity for MPI tasks and
OpenMP threads on the host will be set by default on the host
when using offload to a coprocessor. In this case, it is unnecessary
uniform. Unless disabled at build time, affinity for MPI tasks and
OpenMP threads on the host will be set by default on the host
when using offload to a coprocessor. In this case, it is unnecessary
to use other methods to control affinity (e.g. taskset, numactl,
I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input script
with the <em>no_affinity</em> option to the <a class="reference internal" href="package.html"><em>package intel</em></a>
with the <I>no_affinity</I> option to the <A HREF = "package.html">package intel</A>
command or by disabling the option at build time (by adding
-DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your Makefile).
Disabling this option is not recommended, especially when running
on a machine with hyperthreading disabled.</p>
<p><strong>Running with the USER-INTEL package from the command line:</strong></p>
<p>The mpirun or mpiexec command sets the total number of MPI tasks used
on a machine with hyperthreading disabled.
</P>
<P><B>Running with the USER-INTEL package from the command line:</B>
</P>
<P>The mpirun or mpiexec command sets the total number of MPI tasks used
by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the mpirun command in MPICH does this via
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.</p>
<p>If you plan to compute (any portion of) pairwise interactions using
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.
</P>
<P>If you plan to compute (any portion of) pairwise interactions using
USER-INTEL pair styles on the CPU, or use USER-OMP styles on the CPU,
you need to choose how many OpenMP threads per MPI task to use. Note
that the product of MPI tasks * OpenMP threads/task should not exceed
the physical number of cores (on a node), otherwise performance will
suffer.</p>
<p>If LAMMPS was built with coprocessor support for the USER-INTEL
suffer.
</P>
<P>If LAMMPS was built with coprocessor support for the USER-INTEL
package, you also need to specify the number of coprocessor/node and
the number of coprocessor threads per MPI task to use. Note that
coprocessor threads (which run on the coprocessor) are totally
independent from OpenMP threads (which run on the CPU). The default
values for the settings that affect coprocessor threads are typically
fine, as discussed below.</p>
<p>Use the &#8220;-sf intel&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>,
which will automatically append &#8220;intel&#8221; to styles that support it. If
a style does not support it, an &#8220;omp&#8221; suffix is tried next. OpenMP
threads per MPI task can be set via the &#8220;-pk intel Nphi omp Nt&#8221; or
&#8220;-pk omp Nt&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switches</span></a>, which
set Nt = # of OpenMP threads per MPI task to use. The &#8220;-pk omp&#8221; form
is only allowed if LAMMPS was also built with the USER-OMP package.</p>
<p>Use the &#8220;-pk intel Nphi&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> to set Nphi = # of Xeon Phi(TM)
fine, as discussed below.
</P>
<P>Use the "-sf intel" <A HREF = "Section_start.html#start_7">command-line switch</A>,
which will automatically append "intel" to styles that support it. If
a style does not support it, an "omp" suffix is tried next. OpenMP
threads per MPI task can be set via the "-pk intel Nphi omp Nt" or
"-pk omp Nt" <A HREF = "Section_start.html#start_7">command-line switches</A>, which
set Nt = # of OpenMP threads per MPI task to use. The "-pk omp" form
is only allowed if LAMMPS was also built with the USER-OMP package.
</P>
<P>Use the "-pk intel Nphi" <A HREF = "Section_start.html#start_7">command-line
switch</A> to set Nphi = # of Xeon Phi(TM)
coprocessors/node, if LAMMPS was built with coprocessor support. All
the available coprocessor threads on each Phi will be divided among
MPI tasks, unless the <em>tptask</em> option of the &#8220;-pk intel&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> is used to limit the coprocessor
threads per MPI task. See the <a class="reference internal" href="package.html"><em>package intel</em></a> command
for details.</p>
<div class="highlight-python"><div class="highlight"><pre>CPU-only without USER-OMP (but using Intel vectorization on CPU):
MPI tasks, unless the <I>tptask</I> option of the "-pk intel" <A HREF = "Section_start.html#start_7">command-line
switch</A> is used to limit the coprocessor
threads per MPI task. See the <A HREF = "package.html">package intel</A> command
for details.
</P>
<PRE>CPU-only without USER-OMP (but using Intel vectorization on CPU):
lmp_machine -sf intel -in in.script # 1 MPI task
mpirun -np 32 lmp_machine -sf intel -in in.script # 32 MPI tasks on as many nodes as needed (e.g. 2 16-core nodes)
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>CPU-only with USER-OMP (and Intel vectorization on CPU):
mpirun -np 32 lmp_machine -sf intel -in in.script # 32 MPI tasks on as many nodes as needed (e.g. 2 16-core nodes)
</PRE>
<PRE>CPU-only with USER-OMP (and Intel vectorization on CPU):
lmp_machine -sf intel -pk intel 16 0 -in in.script # 1 MPI task on a 16-core node
mpirun -np 4 lmp_machine -sf intel -pk omp 4 -in in.script # 4 MPI tasks each with 4 threads on a single 16-core node
mpirun -np 32 lmp_machine -sf intel -pk omp 4 -in in.script # ditto on 8 16-core nodes
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>CPUs + Xeon Phi(TM) coprocessors with or without USER-OMP:
mpirun -np 32 lmp_machine -sf intel -pk omp 4 -in in.script # ditto on 8 16-core nodes
</PRE>
<PRE>CPUs + Xeon Phi(TM) coprocessors with or without USER-OMP:
lmp_machine -sf intel -pk intel 1 omp 16 -in in.script # 1 MPI task, 16 OpenMP threads on CPU, 1 coprocessor, all 240 coprocessor threads
lmp_machine -sf intel -pk intel 1 omp 16 tptask 32 -in in.script # 1 MPI task, 16 OpenMP threads on CPU, 1 coprocessor, only 32 coprocessor threads
mpirun -np 4 lmp_machine -sf intel -pk intel 1 omp 4 -in in.script # 4 MPI tasks, 4 OpenMP threads/task, 1 coprocessor, 60 coprocessor threads/task
mpirun -np 32 -ppn 4 lmp_machine -sf intel -pk intel 1 omp 4 -in in.script # ditto on 8 16-core nodes
mpirun -np 8 lmp_machine -sf intel -pk intel 4 omp 2 -in in.script # 8 MPI tasks, 2 OpenMP threads/task, 4 coprocessors, 120 coprocessor threads/task
</pre></div>
</div>
<p>Note that if the &#8220;-sf intel&#8221; switch is used, it also invokes two
default commands: <a class="reference internal" href="package.html"><em>package intel 1</em></a>, followed by <a class="reference internal" href="package.html"><em>package omp 0</em></a>. These both set the number of OpenMP threads per
mpirun -np 8 lmp_machine -sf intel -pk intel 4 omp 2 -in in.script # 8 MPI tasks, 2 OpenMP threads/task, 4 coprocessors, 120 coprocessor threads/task
</PRE>
<P>Note that if the "-sf intel" switch is used, it also invokes two
default commands: <A HREF = "package.html">package intel 1</A>, followed by <A HREF = "package.html">package
omp 0</A>. These both set the number of OpenMP threads per
MPI task via the OMP_NUM_THREADS environment variable. The first
command sets the number of Xeon Phi(TM) coprocessors/node to 1 (and
the precision mode to &#8220;mixed&#8221;, as one of its option defaults). The
the precision mode to "mixed", as one of its option defaults). The
latter command is not invoked if LAMMPS was not built with the
USER-OMP package. The Nphi = 1 value for the first command is ignored
if LAMMPS was not built with coprocessor support.</p>
<p>Using the &#8220;-pk intel&#8221; or &#8220;-pk omp&#8221; switches explicitly allows for
if LAMMPS was not built with coprocessor support.
</P>
<P>Using the "-pk intel" or "-pk omp" switches explicitly allows for
direct setting of the number of OpenMP threads per MPI task, and
additional options for either of the USER-INTEL or USER-OMP packages.
In particular, the &#8220;-pk intel&#8221; switch sets the number of
In particular, the "-pk intel" switch sets the number of
coprocessors/node and can limit the number of coprocessor threads per
MPI task. The syntax for these two switches is the same as the
<a class="reference internal" href="package.html"><em>package omp</em></a> and <a class="reference internal" href="package.html"><em>package intel</em></a> commands.
See the <a class="reference internal" href="package.html"><em>package</em></a> command doc page for details, including
<A HREF = "package.html">package omp</A> and <A HREF = "package.html">package intel</A> commands.
See the <A HREF = "package.html">package</A> command doc page for details, including
the default values used for all its options if these switches are not
specified, and how to set the number of OpenMP threads via the
OMP_NUM_THREADS environment variable if desired.</p>
<p><strong>Or run with the USER-INTEL package by editing an input script:</strong></p>
<p>The discussion above for the mpirun/mpiexec command, MPI tasks/node,
OMP_NUM_THREADS environment variable if desired.
</P>
<P><B>Or run with the USER-INTEL package by editing an input script:</B>
</P>
<P>The discussion above for the mpirun/mpiexec command, MPI tasks/node,
OpenMP threads per MPI task, and coprocessor threads per MPI task is
the same.</p>
<p>Use the <a class="reference internal" href="suffix.html"><em>suffix intel</em></a> command, or you can explicitly add an
&#8220;intel&#8221; suffix to individual styles in your input script, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/intel 2.5
</pre></div>
</div>
<p>You must also use the <a class="reference internal" href="package.html"><em>package intel</em></a> command, unless the
&#8220;-sf intel&#8221; or &#8220;-pk intel&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switches</span></a> were used. It specifies how many
the same.
</P>
<P>Use the <A HREF = "suffix.html">suffix intel</A> command, or you can explicitly add an
"intel" suffix to individual styles in your input script, e.g.
</P>
<PRE>pair_style lj/cut/intel 2.5
</PRE>
<P>You must also use the <A HREF = "package.html">package intel</A> command, unless the
"-sf intel" or "-pk intel" <A HREF = "Section_start.html#start_7">command-line
switches</A> were used. It specifies how many
coprocessors/node to use, as well as other OpenMP threading and
coprocessor options. Its doc page explains how to set the number of
OpenMP threads via an environment variable if desired.</p>
<p>If LAMMPS was also built with the USER-OMP package, you must also use
the <a class="reference internal" href="package.html"><em>package omp</em></a> command to enable that package, unless
the &#8220;-sf intel&#8221; or &#8220;-pk omp&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switches</span></a> were used. It specifies how many
OpenMP threads via an environment variable if desired.
</P>
<P>If LAMMPS was also built with the USER-OMP package, you must also use
the <A HREF = "package.html">package omp</A> command to enable that package, unless
the "-sf intel" or "-pk omp" <A HREF = "Section_start.html#start_7">command-line
switches</A> were used. It specifies how many
OpenMP threads per MPI task to use, as well as other options. Its doc
page explains how to set the number of OpenMP threads via an
environment variable if desired.</p>
<p><strong>Speed-ups to expect:</strong></p>
<p>If LAMMPS was not built with coprocessor support when including the
environment variable if desired.
</P>
<P><B>Speed-ups to expect:</B>
</P>
<P>If LAMMPS was not built with coprocessor support when including the
USER-INTEL package, then acclerated styles will run on the CPU using
vectorization optimizations and the specified precision. This may
give a substantial speed-up for a pair style, particularly if mixed or
single precision is used.</p>
<p>If LAMMPS was built with coproccesor support, the pair styles will run
single precision is used.
</P>
<P>If LAMMPS was built with coproccesor support, the pair styles will run
on one or more Intel(R) Xeon Phi(TM) coprocessors (per node). The
performance of a Xeon Phi versus a multi-core CPU is a function of
your hardware, which pair style is used, the number of
atoms/coprocessor, and the precision used on the coprocessor (double,
single, mixed).</p>
<p>See the <a class="reference external" href="http://lammps.sandia.gov/bench.html">Benchmark page</a> of the
single, mixed).
</P>
<P>See the <A HREF = "http://lammps.sandia.gov/bench.html">Benchmark page</A> of the
LAMMPS web site for performance of the USER-INTEL package on different
hardware.</p>
<p><strong>Guidelines for best performance on an Intel(R) Xeon Phi(TM)
coprocessor:</strong></p>
<ul class="simple">
<li>The default for the <a class="reference internal" href="package.html"><em>package intel</em></a> command is to have
hardware.
</P>
<P><B>Guidelines for best performance on an Intel(R) Xeon Phi(TM)
coprocessor:</B>
</P>
<UL><LI>The default for the <A HREF = "package.html">package intel</A> command is to have
all the MPI tasks on a given compute node use a single Xeon Phi(TM)
coprocessor. In general, running with a large number of MPI tasks on
each node will perform best with offload. Each MPI task will
@ -364,121 +290,63 @@ with 60 cores available for offload and 4 hardware threads per core
each MPI task to use a subset of 10 threads on the coprocessor. Fine
tuning of the number of threads to use per MPI task or the number of
threads to use per core can be accomplished with keyword settings of
the <a class="reference internal" href="package.html"><em>package intel</em></a> command.</li>
<li>If desired, only a fraction of the pair style computation can be
the <A HREF = "package.html">package intel</A> command.
<LI>If desired, only a fraction of the pair style computation can be
offloaded to the coprocessors. This is accomplished by using the
<em>balance</em> keyword in the <a class="reference internal" href="package.html"><em>package intel</em></a> command. A
<I>balance</I> keyword in the <A HREF = "package.html">package intel</A> command. A
balance of 0 runs all calculations on the CPU. A balance of 1 runs
all calculations on the coprocessor. A balance of 0.5 runs half of
the calculations on the coprocessor. Setting the balance to -1 (the
default) will enable dynamic load balancing that continously adjusts
the fraction of offloaded work throughout the simulation. This option
typically produces results within 5 to 10 percent of the optimal fixed
balance.</li>
<li>When using offload with CPU hyperthreading disabled, it may help
balance.
<LI>When using offload with CPU hyperthreading disabled, it may help
performance to use fewer MPI tasks and OpenMP threads than available
cores. This is due to the fact that additional threads are generated
internally to handle the asynchronous offload tasks.</li>
<li>If running short benchmark runs with dynamic load balancing, adding a
internally to handle the asynchronous offload tasks.
<LI>If running short benchmark runs with dynamic load balancing, adding a
short warm-up run (10-20 steps) will allow the load-balancer to find a
near-optimal setting that will carry over to additional runs.</li>
<li>If pair computations are being offloaded to an Intel(R) Xeon Phi(TM)
near-optimal setting that will carry over to additional runs.
<LI>If pair computations are being offloaded to an Intel(R) Xeon Phi(TM)
coprocessor, a diagnostic line is printed to the screen (not to the
log file), during the setup phase of a run, indicating that offload
mode is being used and indicating the number of coprocessor threads
per MPI task. Additionally, an offload timing summary is printed at
the end of each run. When offloading, the frequency for <a class="reference internal" href="atom_modify.html"><em>atom sorting</em></a> is changed to 1 so that the per-atom data is
effectively sorted at every rebuild of the neighbor lists.</li>
<li>For simulations with long-range electrostatics or bond, angle,
the end of each run. When offloading, the frequency for <A HREF = "atom_modify.html">atom
sorting</A> is changed to 1 so that the per-atom data is
effectively sorted at every rebuild of the neighbor lists.
<LI>For simulations with long-range electrostatics or bond, angle,
dihedral, improper calculations, computation and data transfer to the
coprocessor will run concurrently with computations and MPI
communications for these calculations on the host CPU. The USER-INTEL
package has two modes for deciding which atoms will be handled by the
coprocessor. This choice is controlled with the <em>ghost</em> keyword of
the <a class="reference internal" href="package.html"><em>package intel</em></a> command. When set to 0, ghost atoms
coprocessor. This choice is controlled with the <I>ghost</I> keyword of
the <A HREF = "package.html">package intel</A> command. When set to 0, ghost atoms
(atoms at the borders between MPI tasks) are not offloaded to the
card. This allows for overlap of MPI communication of forces with
computation on the coprocessor when the <a class="reference internal" href="newton.html"><em>newton</em></a> setting
is &#8220;on&#8221;. The default is dependent on the style being used, however,
computation on the coprocessor when the <A HREF = "newton.html">newton</A> setting
is "on". The default is dependent on the style being used, however,
better performance may be achieved by setting this option
explictly.</li>
</ul>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>When offloading to a coprocessor, <a class="reference internal" href="pair_hybrid.html"><em>hybrid</em></a> styles
explictly.
</UL>
<P><B>Restrictions:</B>
</P>
<P>When offloading to a coprocessor, <A HREF = "pair_hybrid.html">hybrid</A> styles
that require skip lists for neighbor builds cannot be offloaded.
Using <a class="reference internal" href="pair_hybrid.html"><em>hybrid/overlay</em></a> is allowed. Only one intel
Using <A HREF = "pair_hybrid.html">hybrid/overlay</A> is allowed. Only one intel
accelerated style may be used with hybrid styles.
<a class="reference internal" href="special_bonds.html"><em>Special_bonds</em></a> exclusion lists are not currently
<A HREF = "special_bonds.html">Special_bonds</A> exclusion lists are not currently
supported with offload, however, the same effect can often be
accomplished by setting cutoffs for excluded atom types to 0. None of
the pair styles in the USER-INTEL package currently support the
&#8220;inner&#8221;, &#8220;middle&#8221;, &#8220;outer&#8221; options for rRESPA integration via the
<a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command; only the &#8220;pair&#8221; option is
supported.</p>
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<div class="section" id="kokkos-package">
<h1>5.KOKKOS package<a class="headerlink" href="#kokkos-package" title="Permalink to this headline"></a></h1>
<p>The KOKKOS package was developed primaritly by Christian Trott
<HR>
<P><A HREF = "Section_accelerate.html">Return to Section accelerate overview</A>
</P>
<H4>5.3.4 KOKKOS package
</H4>
<P>The KOKKOS package was developed primaritly by Christian Trott
(Sandia) with contributions of various styles by others, including
Sikandar Mashayak (UIUC), Stan Moore (Sandia), and Ray Shan (Sandia).
The underlying Kokkos library was written
primarily by Carter Edwards, Christian Trott, and Dan Sunderland (all
Sandia).</p>
<p>The KOKKOS package contains versions of pair, fix, and atom styles
Sandia).
</P>
<P>The KOKKOS package contains versions of pair, fix, and atom styles
that use data structures and macros provided by the Kokkos library,
which is included with LAMMPS in lib/kokkos.</p>
<p>The Kokkos library is part of
<a class="reference external" href="http://trilinos.sandia.gov/packages/kokkos">Trilinos</a> and can also
be downloaded from <a class="reference external" href="https://github.com/kokkos/kokkos">Github</a>. Kokkos is a
which is included with LAMMPS in lib/kokkos.
</P>
<P>The Kokkos library is part of
<A HREF = "http://trilinos.sandia.gov/packages/kokkos">Trilinos</A> and can also
be downloaded from <A HREF = "https://github.com/kokkos/kokkos">Github</A>. Kokkos is a
templated C++ library that provides two key abstractions for an
application like LAMMPS. First, it allows a single implementation of
an application kernel (e.g. a pair style) to run efficiently on
different kinds of hardware, such as a GPU, Intel Phi, or many-core
chip.</p>
<p>The Kokkos library also provides data abstractions to adjust (at
chip.
</P>
<P>The Kokkos library also provides data abstractions to adjust (at
compile time) the memory layout of basic data structures like 2d and
3d arrays and allow the transparent utilization of special hardware
load and store operations. Such data structures are used in LAMMPS to
store atom coordinates or forces or neighbor lists. The layout is
chosen to optimize performance on different platforms. Again this
functionality is hidden from the developer, and does not affect how
the kernel is coded.</p>
<p>These abstractions are set at build time, when LAMMPS is compiled with
the KOKKOS package installed. This is done by selecting a &#8220;host&#8221; and
&#8220;device&#8221; to build for, compatible with the compute nodes in your
machine (one on a desktop machine or 1000s on a supercomputer).</p>
<p>All Kokkos operations occur within the context of an individual MPI
the kernel is coded.
</P>
<P>These abstractions are set at build time, when LAMMPS is compiled with
the KOKKOS package installed. This is done by selecting a "host" and
"device" to build for, compatible with the compute nodes in your
machine (one on a desktop machine or 1000s on a supercomputer).
</P>
<P>All Kokkos operations occur within the context of an individual MPI
task running on a single node of the machine. The total number of MPI
tasks used by LAMMPS (one or multiple per compute node) is set in the
usual manner via the mpirun or mpiexec commands, and is independent of
Kokkos.</p>
<p>Kokkos provides support for two different modes of execution per MPI
Kokkos.
</P>
<P>Kokkos provides support for two different modes of execution per MPI
task. This means that computational tasks (pairwise interactions,
neighbor list builds, time integration, etc) can be parallelized for
one or the other of the two modes. The first mode is called the
&#8220;host&#8221; and is one or more threads running on one or more physical CPUs
"host" and is one or more threads running on one or more physical CPUs
(within the node). Currently, both multi-core CPUs and an Intel Phi
processor (running in native mode, not offload mode like the
USER-INTEL package) are supported. The second mode is called the
&#8220;device&#8221; and is an accelerator chip of some kind. Currently only an
"device" and is an accelerator chip of some kind. Currently only an
NVIDIA GPU is supported via Cuda. If your compute node does not have
a GPU, then there is only one mode of execution, i.e. the host and
device are the same.</p>
<p>When using the KOKKOS package, you must choose at build time whether
device are the same.
</P>
<P>When using the KOKKOS package, you must choose at build time whether
you are building for OpenMP, GPU, or for using the Xeon Phi in native
mode.</p>
<p>Here is a quick overview of how to use the KOKKOS package:</p>
<ul class="simple">
<li>specify variables and settings in your Makefile.machine that enable OpenMP, GPU, or Phi support</li>
<li>include the KOKKOS package and build LAMMPS</li>
<li>enable the KOKKOS package and its hardware options via the &#8220;-k on&#8221; command-line switch use KOKKOS styles in your input script</li>
</ul>
<p>The latter two steps can be done using the &#8220;-k on&#8221;, &#8220;-pk kokkos&#8221; and
&#8220;-sf kk&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switches</span></a>
respectively. Or the effect of the &#8220;-pk&#8221; or &#8220;-sf&#8221; switches can be
duplicated by adding the <a class="reference internal" href="package.html"><em>package kokkos</em></a> or <a class="reference internal" href="suffix.html"><em>suffix kk</em></a> commands respectively to your input script.</p>
<p><strong>Required hardware/software:</strong></p>
<p>The KOKKOS package can be used to build and run LAMMPS on the
following kinds of hardware:</p>
<ul class="simple">
<li>CPU-only: one MPI task per CPU core (MPI-only, but using KOKKOS styles)</li>
<li>CPU-only: one or a few MPI tasks per node with additional threading via OpenMP</li>
<li>Phi: on one or more Intel Phi coprocessors (per node)</li>
<li>GPU: on the GPUs of a node with additional OpenMP threading on the CPUs</li>
</ul>
<p>Kokkos support within LAMMPS must be built with a C++11 compatible
compiler. For example, gcc 4.7.2 or later.</p>
<p>Note that Intel Xeon Phi coprocessors are supported in &#8220;native&#8221; mode,
not &#8220;offload&#8221; mode like the USER-INTEL package supports.</p>
<p>Only NVIDIA GPUs are currently supported.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">For good performance of the KOKKOS package on GPUs,
mode.
</P>
<P>Here is a quick overview of how to use the KOKKOS package:
</P>
<UL><LI>specify variables and settings in your Makefile.machine that enable OpenMP, GPU, or Phi support
<LI>include the KOKKOS package and build LAMMPS
<LI>enable the KOKKOS package and its hardware options via the "-k on" command-line switch use KOKKOS styles in your input script
</UL>
<P>The latter two steps can be done using the "-k on", "-pk kokkos" and
"-sf kk" <A HREF = "Section_start.html#start_7">command-line switches</A>
respectively. Or the effect of the "-pk" or "-sf" switches can be
duplicated by adding the <A HREF = "package.html">package kokkos</A> or <A HREF = "suffix.html">suffix
kk</A> commands respectively to your input script.
</P>
<P><B>Required hardware/software:</B>
</P>
<P>The KOKKOS package can be used to build and run LAMMPS on the
following kinds of hardware:
</P>
<UL><LI>CPU-only: one MPI task per CPU core (MPI-only, but using KOKKOS styles)
<LI>CPU-only: one or a few MPI tasks per node with additional threading via OpenMP
<LI>Phi: on one or more Intel Phi coprocessors (per node)
<LI>GPU: on the GPUs of a node with additional OpenMP threading on the CPUs
</UL>
<P>Kokkos support within LAMMPS must be built with a C++11 compatible
compiler. For example, gcc 4.7.2 or later.
</P>
<P>Note that Intel Xeon Phi coprocessors are supported in "native" mode,
not "offload" mode like the USER-INTEL package supports.
</P>
<P>Only NVIDIA GPUs are currently supported.
</P>
<P>IMPORTANT NOTE: For good performance of the KOKKOS package on GPUs,
you must have Kepler generation GPUs (or later). The Kokkos library
exploits texture cache options not supported by Telsa generation GPUs
(or older).</p>
</div>
<p>To build the KOKKOS package for GPUs, NVIDIA Cuda software must be
(or older).
</P>
<P>To build the KOKKOS package for GPUs, NVIDIA Cuda software must be
installed on your system. See the discussion above for the USER-CUDA
and GPU packages for details of how to check and do this.</p>
<p><strong>Building LAMMPS with the KOKKOS package:</strong></p>
<p>You must choose at build time whether to build for OpenMP, Cuda, or
Phi.</p>
<p>You can do any of these in one line, using the src/Make.py script,
described in <a class="reference internal" href="Section_start.html#start-4"><span>Section 2.4</span></a> of the manual.
Type &#8220;Make.py -h&#8221; for help. If run from the src directory, these
and GPU packages for details of how to check and do this.
</P>
<P><B>Building LAMMPS with the KOKKOS package:</B>
</P>
<P>You must choose at build time whether to build for OpenMP, Cuda, or
Phi.
</P>
<P>You can do any of these in one line, using the src/Make.py script,
described in <A HREF = "Section_start.html#start_4">Section 2.4</A> of the manual.
Type "Make.py -h" for help. If run from the src directory, these
commands will create src/lmp_kokkos_omp, lmp_kokkos_cuda, and
lmp_kokkos_phi. Note that the OMP and PHI options use
src/MAKE/Makefile.mpi as the starting Makefile.machine. The CUDA
option uses src/MAKE/OPTIONS/Makefile.kokkos_cuda.</p>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p kokkos -kokkos omp -o kokkos_omp -a file mpi
option uses src/MAKE/OPTIONS/Makefile.kokkos_cuda.
</P>
<PRE>Make.py -p kokkos -kokkos omp -o kokkos_omp -a file mpi
Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda
Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi
</pre></div>
</div>
<p>Or you can follow these steps:</p>
<p>CPU-only (run all-MPI or with OpenMP threading):</p>
<div class="highlight-python"><div class="highlight"><pre>cd lammps/src
Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi
</PRE>
<P>Or you can follow these steps:
</P>
<P>CPU-only (run all-MPI or with OpenMP threading):
</P>
<PRE>cd lammps/src
make yes-kokkos
make g++ KOKKOS_DEVICES=OpenMP
</pre></div>
</div>
<p>Intel Xeon Phi:</p>
<div class="highlight-python"><div class="highlight"><pre>cd lammps/src
make g++ KOKKOS_DEVICES=OpenMP
</PRE>
<P>Intel Xeon Phi:
</P>
<PRE>cd lammps/src
make yes-kokkos
make g++ KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=KNC
</pre></div>
</div>
<p>CPUs and GPUs:</p>
<div class="highlight-python"><div class="highlight"><pre>cd lammps/src
make g++ KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=KNC
</PRE>
<P>CPUs and GPUs:
</P>
<PRE>cd lammps/src
make yes-kokkos
make cuda KOKKOS_DEVICES=Cuda
</pre></div>
</div>
<p>These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the
make cuda KOKKOS_DEVICES=Cuda
</PRE>
<P>These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the
make command line which requires a GNU-compatible make command. Try
&#8220;gmake&#8221; if your system&#8217;s standard make complains.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If you build using make line variables and re-build
LAMMPS twice with different KOKKOS options and the <em>same</em> target,
e.g. g++ in the first two examples above, then you <em>must</em> perform a
&#8220;make clean-all&#8221; or &#8220;make clean-machine&#8221; before each build. This is
"gmake" if your system's standard make complains.
</P>
<P>IMPORTANT NOTE: If you build using make line variables and re-build
LAMMPS twice with different KOKKOS options and the *same* target,
e.g. g++ in the first two examples above, then you *must* perform a
"make clean-all" or "make clean-machine" before each build. This is
to force all the KOKKOS-dependent files to be re-compiled with the new
options.</p>
</div>
<p>You can also hardwire these make variables in the specified machine
options.
</P>
<P>You can also hardwire these make variables in the specified machine
makefile, e.g. src/MAKE/Makefile.g++ in the first two examples above,
with a line like:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">KOKKOS_ARCH</span> <span class="o">=</span> <span class="n">KNC</span>
</pre></div>
</div>
<p>Note that if you build LAMMPS multiple times in this manner, using
with a line like:
</P>
<PRE>KOKKOS_ARCH = KNC
</PRE>
<P>Note that if you build LAMMPS multiple times in this manner, using
different KOKKOS options (defined in different machine makefiles), you
do not have to worry about doing a &#8220;clean&#8221; in between. This is
because the targets will be different.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The 3rd example above for a GPU, uses a different
do not have to worry about doing a "clean" in between. This is
because the targets will be different.
</P>
<P>IMPORTANT NOTE: The 3rd example above for a GPU, uses a different
machine makefile, in this case src/MAKE/Makefile.cuda, which is
included in the LAMMPS distribution. To build the KOKKOS package for
a GPU, this makefile must use the NVIDA &#8220;nvcc&#8221; compiler. And it must
a GPU, this makefile must use the NVIDA "nvcc" compiler. And it must
have a KOKKOS_ARCH setting that is appropriate for your NVIDIA
hardware and installed software. Typical values for KOKKOS_ARCH are given
below, as well
as other settings that must be included in the machine makefile, if
you create your own.</p>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Currently, there are no precision options with the
you create your own.
</P>
<P>IMPORTANT NOTE: Currently, there are no precision options with the
KOKKOS package. All compilation and computation is performed in
double precision.</p>
</div>
<p>There are other allowed options when building with the KOKKOS package.
double precision.
</P>
<P>There are other allowed options when building with the KOKKOS package.
As above, they can be set either as variables on the make command line
or in Makefile.machine. This is the full list of options, including
those discussed above, Each takes a value shown below. The
default value is listed, which is set in the
lib/kokkos/Makefile.kokkos file.</p>
<p>#Default settings specific options
#Options: force_uvm,use_ldg,rdc</p>
<ul class="simple">
<li>KOKKOS_DEVICES, values = <em>OpenMP</em>, <em>Serial</em>, <em>Pthreads</em>, <em>Cuda</em>, default = <em>OpenMP</em></li>
<li>KOKKOS_ARCH, values = <em>KNC</em>, <em>SNB</em>, <em>HSW</em>, <em>Kepler</em>, <em>Kepler30</em>, <em>Kepler32</em>, <em>Kepler35</em>, <em>Kepler37</em>, <em>Maxwell</em>, <em>Maxwell50</em>, <em>Maxwell52</em>, <em>Maxwell53</em>, <em>ARMv8</em>, <em>BGQ</em>, <em>Power7</em>, <em>Power8</em>, default = <em>none</em></li>
<li>KOKKOS_DEBUG, values = <em>yes</em>, <em>no</em>, default = <em>no</em></li>
<li>KOKKOS_USE_TPLS, values = <em>hwloc</em>, <em>librt</em>, default = <em>none</em></li>
<li>KOKKOS_CUDA_OPTIONS, values = <em>force_uvm</em>, <em>use_ldg</em>, <em>rdc</em></li>
</ul>
<p>KOKKOS_DEVICE sets the parallelization method used for Kokkos code
lib/kokkos/Makefile.kokkos file.
</P>
<P>#Default settings specific options
#Options: force_uvm,use_ldg,rdc
</P>
<UL><LI>KOKKOS_DEVICES, values = <I>OpenMP</I>, <I>Serial</I>, <I>Pthreads</I>, <I>Cuda</I>, default = <I>OpenMP</I>
<LI>KOKKOS_ARCH, values = <I>KNC</I>, <I>SNB</I>, <I>HSW</I>, <I>Kepler</I>, <I>Kepler30</I>, <I>Kepler32</I>, <I>Kepler35</I>, <I>Kepler37</I>, <I>Maxwell</I>, <I>Maxwell50</I>, <I>Maxwell52</I>, <I>Maxwell53</I>, <I>ARMv8</I>, <I>BGQ</I>, <I>Power7</I>, <I>Power8</I>, default = <I>none</I>
<LI>KOKKOS_DEBUG, values = <I>yes</I>, <I>no</I>, default = <I>no</I>
<LI>KOKKOS_USE_TPLS, values = <I>hwloc</I>, <I>librt</I>, default = <I>none</I>
<LI>KOKKOS_CUDA_OPTIONS, values = <I>force_uvm</I>, <I>use_ldg</I>, <I>rdc</I>
</UL>
<P>KOKKOS_DEVICE sets the parallelization method used for Kokkos code
(within LAMMPS). KOKKOS_DEVICES=OpenMP means that OpenMP will be
used. KOKKOS_DEVICES=Pthreads means that pthreads will be used.
KOKKOS_DEVICES=Cuda means an NVIDIA GPU running CUDA will be used.</p>
<p>If KOKKOS_DEVICES=Cuda, then the lo-level Makefile in the src/MAKE
directory must use &#8220;nvcc&#8221; as its compiler, via its CC setting. For
KOKKOS_DEVICES=Cuda means an NVIDIA GPU running CUDA will be used.
</P>
<P>If KOKKOS_DEVICES=Cuda, then the lo-level Makefile in the src/MAKE
directory must use "nvcc" as its compiler, via its CC setting. For
best performance its CCFLAGS setting should use -O3 and have a
KOKKOS_ARCH setting that matches the compute capability of your NVIDIA
hardware and software installation, e.g. KOKKOS_ARCH=Kepler30. Note
the minimal required compute capability is 2.0, but this will give
signicantly reduced performance compared to Kepler generation GPUs
with compute capability 3.x. For the LINK setting, &#8220;nvcc&#8221; should not
with compute capability 3.x. For the LINK setting, "nvcc" should not
be used; instead use g++ or another compiler suitable for linking C++
applications. Often you will want to use your MPI compiler wrapper
for this setting (i.e. mpicxx). Finally, the lo-level Makefile must
also have a &#8220;Compilation rule&#8221; for creating <a href="#id1"><span class="problematic" id="id2">*</span></a>.o files from <a href="#id3"><span class="problematic" id="id4">*</span></a>.cu files.
also have a "Compilation rule" for creating *.o files from *.cu files.
See src/Makefile.cuda for an example of a lo-level Makefile with all
of these settings.</p>
<p>KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not
of these settings.
</P>
<P>KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not
migrate during a simulation. KOKKOS_USE_TPLS=hwloc should always be
used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not
necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP
provides alternative methods via environment variables for binding
threads to hardware cores. More info on binding threads to cores is
given in <span class="xref std std-ref">this section</span>.</p>
<p>KOKKOS_ARCH=KNC enables compiler switches needed when compling for an
Intel Phi processor.</p>
<p>KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism
given in <A HREF = "Section_accelerate.html#acc_8">this section</A>.
</P>
<P>KOKKOS_ARCH=KNC enables compiler switches needed when compling for an
Intel Phi processor.
</P>
<P>KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism
on most Unix platforms. This library is not available on all
platforms.</p>
<p>KOKKOS_DEBUG is only useful when developing a Kokkos-enabled style
platforms.
</P>
<P>KOKKOS_DEBUG is only useful when developing a Kokkos-enabled style
within LAMMPS. KOKKOS_DEBUG=yes enables printing of run-time
debugging information that can be useful. It also enables runtime
bounds checking on Kokkos data structures.</p>
<p>KOKKOS_CUDA_OPTIONS are additional options for CUDA.</p>
<p>For more information on Kokkos see the Kokkos programmers&#8217; guide here:
/lib/kokkos/doc/Kokkos_PG.pdf.</p>
<p><strong>Run with the KOKKOS package from the command line:</strong></p>
<p>The mpirun or mpiexec command sets the total number of MPI tasks used
bounds checking on Kokkos data structures.
</P>
<P>KOKKOS_CUDA_OPTIONS are additional options for CUDA.
</P>
<P>For more information on Kokkos see the Kokkos programmers' guide here:
/lib/kokkos/doc/Kokkos_PG.pdf.
</P>
<P><B>Run with the KOKKOS package from the command line:</B>
</P>
<P>The mpirun or mpiexec command sets the total number of MPI tasks used
by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the mpirun command in MPICH does this via
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.</p>
<p>When using KOKKOS built with host=OMP, you need to choose how many
OpenMP threads per MPI task will be used (via the &#8220;-k&#8221; command-line
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.
</P>
<P>When using KOKKOS built with host=OMP, you need to choose how many
OpenMP threads per MPI task will be used (via the "-k" command-line
switch discussed below). Note that the product of MPI tasks * OpenMP
threads/task should not exceed the physical number of cores (on a
node), otherwise performance will suffer.</p>
<p>When using the KOKKOS package built with device=CUDA, you must use
exactly one MPI task per physical GPU.</p>
<p>When using the KOKKOS package built with host=MIC for Intel Xeon Phi
node), otherwise performance will suffer.
</P>
<P>When using the KOKKOS package built with device=CUDA, you must use
exactly one MPI task per physical GPU.
</P>
<P>When using the KOKKOS package built with host=MIC for Intel Xeon Phi
coprocessor support you need to insure there are one or more MPI tasks
per coprocessor, and choose the number of coprocessor threads to use
per MPI task (via the &#8220;-k&#8221; command-line switch discussed below). The
per MPI task (via the "-k" command-line switch discussed below). The
product of MPI tasks * coprocessor threads/task should not exceed the
maximum number of threads the coproprocessor is designed to run,
otherwise performance will suffer. This value is 240 for current
generation Xeon Phi(TM) chips, which is 60 physical cores * 4
threads/core. Note that with the KOKKOS package you do not need to
specify how many Phi coprocessors there are per node; each
coprocessors is simply treated as running some number of MPI tasks.</p>
<p>You must use the &#8220;-k on&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> to enable the KOKKOS package. It
coprocessors is simply treated as running some number of MPI tasks.
</P>
<P>You must use the "-k on" <A HREF = "Section_start.html#start_7">command-line
switch</A> to enable the KOKKOS package. It
takes additional arguments for hardware settings appropriate to your
system. Those arguments are <a class="reference internal" href="Section_start.html#start-7"><span>documented here</span></a>. The two most commonly used
options are:</p>
<div class="highlight-python"><div class="highlight"><pre>-k on t Nt g Ng
</pre></div>
</div>
<p>The &#8220;t Nt&#8221; option applies to host=OMP (even if device=CUDA) and
system. Those arguments are <A HREF = "Section_start.html#start_7">documented
here</A>. The two most commonly used
options are:
</P>
<PRE>-k on t Nt g Ng
</PRE>
<P>The "t Nt" option applies to host=OMP (even if device=CUDA) and
host=MIC. For host=OMP, it specifies how many OpenMP threads per MPI
task to use with a node. For host=MIC, it specifies how many Xeon Phi
threads per MPI task to use within a node. The default is Nt = 1.
Note that for host=OMP this is effectively MPI-only mode which may be
fine. But for host=MIC you will typically end up using far less than
all the 240 available threads, which could give very poor performance.</p>
<p>The &#8220;g Ng&#8221; option applies to device=CUDA. It specifies how many GPUs
all the 240 available threads, which could give very poor performance.
</P>
<P>The "g Ng" option applies to device=CUDA. It specifies how many GPUs
per compute node to use. The default is 1, so this only needs to be
specified is you have 2 or more GPUs per compute node.</p>
<p>The &#8220;-k on&#8221; switch also issues a &#8220;package kokkos&#8221; command (with no
specified is you have 2 or more GPUs per compute node.
</P>
<P>The "-k on" switch also issues a "package kokkos" command (with no
additional arguments) which sets various KOKKOS options to default
values, as discussed on the <a class="reference internal" href="package.html"><em>package</em></a> command doc page.</p>
<p>Use the &#8220;-sf kk&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>,
which will automatically append &#8220;kk&#8221; to styles that support it. Use
the &#8220;-pk kokkos&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> if
you wish to change any of the default <a class="reference internal" href="package.html"><em>package kokkos</em></a>
optionns set by the &#8220;-k on&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>.</p>
<div class="highlight-python"><div class="highlight"><pre>host=OMP, dual hex-core nodes (12 threads/node):
values, as discussed on the <A HREF = "package.html">package</A> command doc page.
</P>
<P>Use the "-sf kk" <A HREF = "Section_start.html#start_7">command-line switch</A>,
which will automatically append "kk" to styles that support it. Use
the "-pk kokkos" <A HREF = "Section_start.html#start_7">command-line switch</A> if
you wish to change any of the default <A HREF = "package.html">package kokkos</A>
optionns set by the "-k on" <A HREF = "Section_start.html#start_7">command-line
switch</A>.
</P>
<PRE>host=OMP, dual hex-core nodes (12 threads/node):
mpirun -np 12 lmp_g++ -in in.lj # MPI-only mode with no Kokkos
mpirun -np 12 lmp_g++ -k on -sf kk -in in.lj # MPI-only mode with Kokkos
mpirun -np 1 lmp_g++ -k on t 12 -sf kk -in in.lj # one MPI task, 12 threads
mpirun -np 2 lmp_g++ -k on t 6 -sf kk -in in.lj # two MPI tasks, 6 threads/task
mpirun -np 32 -ppn 2 lmp_g++ -k on t 6 -sf kk -in in.lj # ditto on 16 nodes
</pre></div>
</div>
<p>host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading):
mpirun -np 2 lmp_g++ -k on t 6 -sf kk -in in.lj # two MPI tasks, 6 threads/task
mpirun -np 32 -ppn 2 lmp_g++ -k on t 6 -sf kk -in in.lj # ditto on 16 nodes
</PRE>
<P>host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading):
mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj # 1 MPI task on 1 Phi, 1*240 = 240
mpirun -np 30 lmp_g++ -k on t 8 -sf kk -in in.lj # 30 MPI tasks on 1 Phi, 30*8 = 240
mpirun -np 12 lmp_g++ -k on t 20 -sf kk -in in.lj # 12 MPI tasks on 1 Phi, 12*20 = 240
mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj # ditto on 8 Phis</p>
<div class="highlight-python"><div class="highlight"><pre>host=OMP, device=CUDA, node = dual hex-core CPUs and a single GPU:
mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj # ditto on 8 Phis
</P>
<PRE>host=OMP, device=CUDA, node = dual hex-core CPUs and a single GPU:
mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj # one MPI task, 6 threads on CPU
mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj # ditto on 4 nodes
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>host=OMP, device=CUDA, node = dual 8-core CPUs and 2 GPUs:
mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj # ditto on 4 nodes
</PRE>
<PRE>host=OMP, device=CUDA, node = dual 8-core CPUs and 2 GPUs:
mpirun -np 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # two MPI tasks, 8 threads per CPU
mpirun -np 32 -ppn 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # ditto on 16 nodes
</pre></div>
</div>
<p>Note that the default for the <a class="reference internal" href="package.html"><em>package kokkos</em></a> command is
to use &#8220;full&#8221; neighbor lists and set the Newton flag to &#8220;off&#8221; for both
mpirun -np 32 -ppn 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # ditto on 16 nodes
</PRE>
<P>Note that the default for the <A HREF = "package.html">package kokkos</A> command is
to use "full" neighbor lists and set the Newton flag to "off" for both
pairwise and bonded interactions. This typically gives fastest
performance. If the <a class="reference internal" href="newton.html"><em>newton</em></a> command is used in the input
script, it can override the Newton flag defaults.</p>
<p>However, when running in MPI-only mode with 1 thread per MPI task, it
will typically be faster to use &#8220;half&#8221; neighbor lists and set the
Newton flag to &#8220;on&#8221;, just as is the case for non-accelerated pair
styles. You can do this with the &#8220;-pk&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>.</p>
<p><strong>Or run with the KOKKOS package by editing an input script:</strong></p>
<p>The discussion above for the mpirun/mpiexec command and setting
performance. If the <A HREF = "newton.html">newton</A> command is used in the input
script, it can override the Newton flag defaults.
</P>
<P>However, when running in MPI-only mode with 1 thread per MPI task, it
will typically be faster to use "half" neighbor lists and set the
Newton flag to "on", just as is the case for non-accelerated pair
styles. You can do this with the "-pk" <A HREF = "Section_start.html#start_7">command-line
switch</A>.
</P>
<P><B>Or run with the KOKKOS package by editing an input script:</B>
</P>
<P>The discussion above for the mpirun/mpiexec command and setting
appropriate thread and GPU values for host=OMP or host=MIC or
device=CUDA are the same.</p>
<p>You must still use the &#8220;-k on&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> to enable the KOKKOS package, and
device=CUDA are the same.
</P>
<P>You must still use the "-k on" <A HREF = "Section_start.html#start_7">command-line
switch</A> to enable the KOKKOS package, and
specify its additional arguments for hardware options appopriate to
your system, as documented above.</p>
<p>Use the <a class="reference internal" href="suffix.html"><em>suffix kk</em></a> command, or you can explicitly add a
&#8220;kk&#8221; suffix to individual styles in your input script, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/kk 2.5
</pre></div>
</div>
<p>You only need to use the <a class="reference internal" href="package.html"><em>package kokkos</em></a> command if you
wish to change any of its option defaults, as set by the &#8220;-k on&#8221;
<a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>.</p>
<p><strong>Speed-ups to expect:</strong></p>
<p>The performance of KOKKOS running in different modes is a function of
your system, as documented above.
</P>
<P>Use the <A HREF = "suffix.html">suffix kk</A> command, or you can explicitly add a
"kk" suffix to individual styles in your input script, e.g.
</P>
<PRE>pair_style lj/cut/kk 2.5
</PRE>
<P>You only need to use the <A HREF = "package.html">package kokkos</A> command if you
wish to change any of its option defaults, as set by the "-k on"
<A HREF = "Section_start.html#start_7">command-line switch</A>.
</P>
<P><B>Speed-ups to expect:</B>
</P>
<P>The performance of KOKKOS running in different modes is a function of
your hardware, which KOKKOS-enable styles are used, and the problem
size.</p>
<p>Generally speaking, the following rules of thumb apply:</p>
<ul class="simple">
<li>When running on CPUs only, with a single thread per MPI task,
size.
</P>
<P>Generally speaking, the following rules of thumb apply:
</P>
<UL><LI>When running on CPUs only, with a single thread per MPI task,
performance of a KOKKOS style is somewhere between the standard
(un-accelerated) styles (MPI-only mode), and those provided by the
USER-OMP package. However the difference between all 3 is small (less
than 20%).</li>
<li>When running on CPUs only, with multiple threads per MPI task,
than 20%).
<LI>When running on CPUs only, with multiple threads per MPI task,
performance of a KOKKOS style is a bit slower than the USER-OMP
package.</li>
<li>When running on GPUs, KOKKOS is typically faster than the USER-CUDA
and GPU packages.</li>
<li>When running on Intel Xeon Phi, KOKKOS is not as fast as
the USER-INTEL package, which is optimized for that hardware.</li>
</ul>
<p>See the <a class="reference external" href="http://lammps.sandia.gov/bench.html">Benchmark page</a> of the
package.
<LI>When running on GPUs, KOKKOS is typically faster than the USER-CUDA
and GPU packages.
<LI>When running on Intel Xeon Phi, KOKKOS is not as fast as
the USER-INTEL package, which is optimized for that hardware.
</UL>
<P>See the <A HREF = "http://lammps.sandia.gov/bench.html">Benchmark page</A> of the
LAMMPS web site for performance of the KOKKOS package on different
hardware.</p>
<p><strong>Guidelines for best performance:</strong></p>
<p>Here are guidline for using the KOKKOS package on the different
hardware configurations listed above.</p>
<p>Many of the guidelines use the <a class="reference internal" href="package.html"><em>package kokkos</em></a> command
hardware.
</P>
<P><B>Guidelines for best performance:</B>
</P>
<P>Here are guidline for using the KOKKOS package on the different
hardware configurations listed above.
</P>
<P>Many of the guidelines use the <A HREF = "package.html">package kokkos</A> command
See its doc page for details and default settings. Experimenting with
its options can provide a speed-up for specific calculations.</p>
<p><strong>Running on a multi-core CPU:</strong></p>
<p>If N is the number of physical cores/node, then the number of MPI
its options can provide a speed-up for specific calculations.
</P>
<P><B>Running on a multi-core CPU:</B>
</P>
<P>If N is the number of physical cores/node, then the number of MPI
tasks/node * number of threads/task should not exceed N, and should
typically equal N. Note that the default threads/task is 1, as set by
the &#8220;t&#8221; keyword of the &#8220;-k&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>. If you do not change this, no
the "t" keyword of the "-k" <A HREF = "Section_start.html#start_7">command-line
switch</A>. If you do not change this, no
additional parallelism (beyond MPI) will be invoked on the host
CPU(s).</p>
<p>You can compare the performance running in different modes:</p>
<ul class="simple">
<li>run with 1 MPI task/node and N threads/task</li>
<li>run with N MPI tasks/node and 1 thread/task</li>
<li>run with settings in between these extremes</li>
</ul>
<p>Examples of mpirun commands in these modes are shown above.</p>
<p>When using KOKKOS to perform multi-threading, it is important for
CPU(s).
</P>
<P>You can compare the performance running in different modes:
</P>
<UL><LI>run with 1 MPI task/node and N threads/task
<LI>run with N MPI tasks/node and 1 thread/task
<LI>run with settings in between these extremes
</UL>
<P>Examples of mpirun commands in these modes are shown above.
</P>
<P>When using KOKKOS to perform multi-threading, it is important for
performance to bind both MPI tasks to physical cores, and threads to
physical cores, so they do not migrate during a simulation.</p>
<p>If you are not certain MPI tasks are being bound (check the defaults
for your MPI installation), binding can be forced with these flags:</p>
<div class="highlight-python"><div class="highlight"><pre>OpenMPI 1.8: mpirun -np 2 -bind-to socket -map-by socket ./lmp_openmpi ...
Mvapich2 2.0: mpiexec -np 2 -bind-to socket -map-by socket ./lmp_mvapich ...
</pre></div>
</div>
<p>For binding threads with the KOKKOS OMP option, use thread affinity
physical cores, so they do not migrate during a simulation.
</P>
<P>If you are not certain MPI tasks are being bound (check the defaults
for your MPI installation), binding can be forced with these flags:
</P>
<PRE>OpenMPI 1.8: mpirun -np 2 -bind-to socket -map-by socket ./lmp_openmpi ...
Mvapich2 2.0: mpiexec -np 2 -bind-to socket -map-by socket ./lmp_mvapich ...
</PRE>
<P>For binding threads with the KOKKOS OMP option, use thread affinity
environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or
later, intel 12 or later) setting the environment variable
OMP_PROC_BIND=true should be sufficient. For binding threads with the
KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option, as
discussed in <a class="reference internal" href="Section_start.html#start-3-4"><span>Section 2.3.4</span></a> of the
manual.</p>
<p><strong>Running on GPUs:</strong></p>
<p>Insure the -arch setting in the machine makefile you are using,
discussed in <A HREF = "Sections_start.html#start_3_4">Section 2.3.4</A> of the
manual.
</P>
<P><B>Running on GPUs:</B>
</P>
<P>Insure the -arch setting in the machine makefile you are using,
e.g. src/MAKE/Makefile.cuda, is correct for your GPU hardware/software
(see <a class="reference internal" href="Section_start.html#start-3-4"><span>this section</span></a> of the manual for
details).</p>
<p>The -np setting of the mpirun command should set the number of MPI
tasks/node to be equal to the # of physical GPUs on the node.</p>
<p>Use the &#8220;-k&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> to
(see <A HREF = "Section_start.html#start_3_4">this section</A> of the manual for
details).
</P>
<P>The -np setting of the mpirun command should set the number of MPI
tasks/node to be equal to the # of physical GPUs on the node.
</P>
<P>Use the "-k" <A HREF = "Section_commands.html#start_7">command-line switch</A> to
specify the number of GPUs per node, and the number of threads per MPI
task. As above for multi-core CPUs (and no GPU), if N is the number
of physical cores/node, then the number of MPI tasks/node * number of
@ -504,117 +448,62 @@ threads/task should not exceed N. With one GPU (and one MPI task) it
may be faster to use less than all the available cores, by setting
threads/task to a smaller value. This is because using all the cores
on a dual-socket node will incur extra cost to copy memory from the
2nd socket to the GPU.</p>
<p>Examples of mpirun commands that follow these rules are shown above.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">When using a GPU, you will achieve the best
2nd socket to the GPU.
</P>
<P>Examples of mpirun commands that follow these rules are shown above.
</P>
<P>IMPORTANT NOTE: When using a GPU, you will achieve the best
performance if your input script does not use any fix or compute
styles which are not yet Kokkos-enabled. This allows data to stay on
the GPU for multiple timesteps, without being copied back to the host
CPU. Invoking a non-Kokkos fix or compute, or performing I/O for
<a class="reference internal" href="thermo_style.html"><em>thermo</em></a> or <a class="reference internal" href="dump.html"><em>dump</em></a> output will cause data
to be copied back to the CPU.</p>
</div>
<p>You cannot yet assign multiple MPI tasks to the same GPU with the
<A HREF = "thermo_style.html">thermo</A> or <A HREF = "dump.html">dump</A> output will cause data
to be copied back to the CPU.
</P>
<P>You cannot yet assign multiple MPI tasks to the same GPU with the
KOKKOS package. We plan to support this in the future, similar to the
GPU package in LAMMPS.</p>
<p>You cannot yet use both the host (multi-threaded) and device (GPU)
GPU package in LAMMPS.
</P>
<P>You cannot yet use both the host (multi-threaded) and device (GPU)
together to compute pairwise interactions with the KOKKOS package. We
hope to support this in the future, similar to the GPU package in
LAMMPS.</p>
<p><strong>Running on an Intel Phi:</strong></p>
<p>Kokkos only uses Intel Phi processors in their &#8220;native&#8221; mode, i.e.
not hosted by a CPU.</p>
<p>As illustrated above, build LAMMPS with OMP=yes (the default) and
LAMMPS.
</P>
<P><B>Running on an Intel Phi:</B>
</P>
<P>Kokkos only uses Intel Phi processors in their "native" mode, i.e.
not hosted by a CPU.
</P>
<P>As illustrated above, build LAMMPS with OMP=yes (the default) and
MIC=yes. The latter insures code is correctly compiled for the Intel
Phi. The OMP setting means OpenMP will be used for parallelization on
the Phi, which is currently the best option within Kokkos. In the
future, other options may be added.</p>
<p>Current-generation Intel Phi chips have either 61 or 57 cores. One
future, other options may be added.
</P>
<P>Current-generation Intel Phi chips have either 61 or 57 cores. One
core should be excluded for running the OS, leaving 60 or 56 cores.
Each core is hyperthreaded, so there are effectively N = 240 (4*60) or
N = 224 (4*56) cores to run on.</p>
<p>The -np setting of the mpirun command sets the number of MPI
tasks/node. The &#8220;-k on t Nt&#8221; command-line switch sets the number of
N = 224 (4*56) cores to run on.
</P>
<P>The -np setting of the mpirun command sets the number of MPI
tasks/node. The "-k on t Nt" command-line switch sets the number of
threads/task as Nt. The product of these 2 values should be N, i.e.
240 or 224. Also, the number of threads/task should be a multiple of
4 so that logical threads from more than one MPI task do not run on
the same physical core.</p>
<p>Examples of mpirun commands that follow these rules are shown above.</p>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>As noted above, if using GPUs, the number of MPI tasks per compute
the same physical core.
</P>
<P>Examples of mpirun commands that follow these rules are shown above.
</P>
<P><B>Restrictions:</B>
</P>
<P>As noted above, if using GPUs, the number of MPI tasks per compute
node should equal to the number of GPUs per compute node. In the
future Kokkos will support assigning multiple MPI tasks to a single
GPU.</p>
<p>Currently Kokkos does not support AMD GPUs due to limits in the
GPU.
</P>
<P>Currently Kokkos does not support AMD GPUs due to limits in the
available backend programming models. Specifically, Kokkos requires
extensive C++ support from the Kernel language. This is expected to
change in the future.</p>
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<p><a class="reference internal" href="Section_accelerate.html"><em>Return to Section accelerate overview</em></a></p>
<div class="section" id="user-omp-package">
<h1>5.USER-OMP package<a class="headerlink" href="#user-omp-package" title="Permalink to this headline"></a></h1>
<p>The USER-OMP package was developed by Axel Kohlmeyer at Temple
<HR>
<P><A HREF = "Section_accelerate.html">Return to Section accelerate overview</A>
</P>
<H4>5.3.5 USER-OMP package
</H4>
<P>The USER-OMP package was developed by Axel Kohlmeyer at Temple
University. It provides multi-threaded versions of most pair styles,
nearly all bonded styles (bond, angle, dihedral, improper), several
Kspace styles, and a few fix styles. The package currently
uses the OpenMP interface for multi-threading.</p>
<p>Here is a quick overview of how to use the USER-OMP package:</p>
<ul class="simple">
<li>use the -fopenmp flag for compiling and linking in your Makefile.machine</li>
<li>include the USER-OMP package and build LAMMPS</li>
<li>use the mpirun command to set the number of MPI tasks/node</li>
<li>specify how many threads per MPI task to use</li>
<li>use USER-OMP styles in your input script</li>
</ul>
<p>The latter two steps can be done using the &#8220;-pk omp&#8221; and &#8220;-sf omp&#8221;
<a class="reference internal" href="Section_start.html#start-7"><span>command-line switches</span></a> respectively. Or
the effect of the &#8220;-pk&#8221; or &#8220;-sf&#8221; switches can be duplicated by adding
the <a class="reference internal" href="package.html"><em>package omp</em></a> or <a class="reference internal" href="suffix.html"><em>suffix omp</em></a> commands
respectively to your input script.</p>
<p><strong>Required hardware/software:</strong></p>
<p>Your compiler must support the OpenMP interface. You should have one
uses the OpenMP interface for multi-threading.
</P>
<P>Here is a quick overview of how to use the USER-OMP package:
</P>
<UL><LI>use the -fopenmp flag for compiling and linking in your Makefile.machine
<LI>include the USER-OMP package and build LAMMPS
<LI>use the mpirun command to set the number of MPI tasks/node
<LI>specify how many threads per MPI task to use
<LI>use USER-OMP styles in your input script
</UL>
<P>The latter two steps can be done using the "-pk omp" and "-sf omp"
<A HREF = "Section_start.html#start_7">command-line switches</A> respectively. Or
the effect of the "-pk" or "-sf" switches can be duplicated by adding
the <A HREF = "package.html">package omp</A> or <A HREF = "suffix.html">suffix omp</A> commands
respectively to your input script.
</P>
<P><B>Required hardware/software:</B>
</P>
<P>Your compiler must support the OpenMP interface. You should have one
or more multi-core CPUs so that multiple threads can be launched by an
MPI task running on a CPU.</p>
<p><strong>Building LAMMPS with the USER-OMP package:</strong></p>
<p>To do this in one line, use the src/Make.py script, described in
<a class="reference internal" href="Section_start.html#start-4"><span>Section 2.4</span></a> of the manual. Type &#8220;Make.py
-h&#8221; for help. If run from the src directory, this command will create
MPI task running on a CPU.
</P>
<P><B>Building LAMMPS with the USER-OMP package:</B>
</P>
<P>To do this in one line, use the src/Make.py script, described in
<A HREF = "Section_start.html#start_4">Section 2.4</A> of the manual. Type "Make.py
-h" for help. If run from the src directory, this command will create
src/lmp_omp using src/MAKE/Makefile.mpi as the starting
Makefile.machine:</p>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p omp -o omp file mpi
</pre></div>
</div>
<p>Or you can follow these steps:</p>
<div class="highlight-python"><div class="highlight"><pre>cd lammps/src
Makefile.machine:
</P>
<PRE>Make.py -p omp -o omp file mpi
</PRE>
<P>Or you can follow these steps:
</P>
<PRE>cd lammps/src
make yes-user-omp
make machine
</pre></div>
</div>
<p>The CCFLAGS setting in Makefile.machine needs &#8220;-fopenmp&#8221; to add OpenMP
make machine
</PRE>
<P>The CCFLAGS setting in Makefile.machine needs "-fopenmp" to add OpenMP
support. This works for both the GNU and Intel compilers. Without
this flag the USER-OMP styles will still be compiled and work, but
will not support multi-threading. For the Intel compilers the CCFLAGS
setting also needs to include &#8220;-restrict&#8221;.</p>
<p><strong>Run with the USER-OMP package from the command line:</strong></p>
<p>The mpirun or mpiexec command sets the total number of MPI tasks used
setting also needs to include "-restrict".
</P>
<P><B>Run with the USER-OMP package from the command line:</B>
</P>
<P>The mpirun or mpiexec command sets the total number of MPI tasks used
by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the mpirun command in MPICH does this via
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.</p>
<p>You need to choose how many threads per MPI task will be used by the
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.
</P>
<P>You need to choose how many threads per MPI task will be used by the
USER-OMP package. Note that the product of MPI tasks * threads/task
should not exceed the physical number of cores (on a node), otherwise
performance will suffer.</p>
<p>Use the &#8220;-sf omp&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>,
which will automatically append &#8220;omp&#8221; to styles that support it. Use
the &#8220;-pk omp Nt&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>, to
set Nt = # of OpenMP threads per MPI task to use.</p>
<div class="highlight-python"><div class="highlight"><pre>lmp_machine -sf omp -pk omp 16 -in in.script # 1 MPI task on a 16-core node
performance will suffer.
</P>
<P>Use the "-sf omp" <A HREF = "Section_start.html#start_7">command-line switch</A>,
which will automatically append "omp" to styles that support it. Use
the "-pk omp Nt" <A HREF = "Section_start.html#start_7">command-line switch</A>, to
set Nt = # of OpenMP threads per MPI task to use.
</P>
<PRE>lmp_machine -sf omp -pk omp 16 -in in.script # 1 MPI task on a 16-core node
mpirun -np 4 lmp_machine -sf omp -pk omp 4 -in in.script # 4 MPI tasks each with 4 threads on a single 16-core node
mpirun -np 32 -ppn 4 lmp_machine -sf omp -pk omp 4 -in in.script # ditto on 8 16-core nodes
</pre></div>
</div>
<p>Note that if the &#8220;-sf omp&#8221; switch is used, it also issues a default
<a class="reference internal" href="package.html"><em>package omp 0</em></a> command, which sets the number of threads
per MPI task via the OMP_NUM_THREADS environment variable.</p>
<p>Using the &#8220;-pk&#8221; switch explicitly allows for direct setting of the
mpirun -np 32 -ppn 4 lmp_machine -sf omp -pk omp 4 -in in.script # ditto on 8 16-core nodes
</PRE>
<P>Note that if the "-sf omp" switch is used, it also issues a default
<A HREF = "package.html">package omp 0</A> command, which sets the number of threads
per MPI task via the OMP_NUM_THREADS environment variable.
</P>
<P>Using the "-pk" switch explicitly allows for direct setting of the
number of threads and additional options. Its syntax is the same as
the &#8220;package omp&#8221; command. See the <a class="reference internal" href="package.html"><em>package</em></a> command doc
the "package omp" command. See the <A HREF = "package.html">package</A> command doc
page for details, including the default values used for all its
options if it is not specified, and how to set the number of threads
via the OMP_NUM_THREADS environment variable if desired.</p>
<p><strong>Or run with the USER-OMP package by editing an input script:</strong></p>
<p>The discussion above for the mpirun/mpiexec command, MPI tasks/node,
and threads/MPI task is the same.</p>
<p>Use the <a class="reference internal" href="suffix.html"><em>suffix omp</em></a> command, or you can explicitly add an
&#8220;omp&#8221; suffix to individual styles in your input script, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/omp 2.5
</pre></div>
</div>
<p>You must also use the <a class="reference internal" href="package.html"><em>package omp</em></a> command to enable the
USER-OMP package, unless the &#8220;-sf omp&#8221; or &#8220;-pk omp&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switches</span></a> were used. It specifies how many
via the OMP_NUM_THREADS environment variable if desired.
</P>
<P><B>Or run with the USER-OMP package by editing an input script:</B>
</P>
<P>The discussion above for the mpirun/mpiexec command, MPI tasks/node,
and threads/MPI task is the same.
</P>
<P>Use the <A HREF = "suffix.html">suffix omp</A> command, or you can explicitly add an
"omp" suffix to individual styles in your input script, e.g.
</P>
<PRE>pair_style lj/cut/omp 2.5
</PRE>
<P>You must also use the <A HREF = "package.html">package omp</A> command to enable the
USER-OMP package, unless the "-sf omp" or "-pk omp" <A HREF = "Section_start.html#start_7">command-line
switches</A> were used. It specifies how many
threads per MPI task to use, as well as other options. Its doc page
explains how to set the number of threads via an environment variable
if desired.</p>
<p><strong>Speed-ups to expect:</strong></p>
<p>Depending on which styles are accelerated, you should look for a
reduction in the &#8220;Pair time&#8221;, &#8220;Bond time&#8221;, &#8220;KSpace time&#8221;, and &#8220;Loop
time&#8221; values printed at the end of a run.</p>
<p>You may see a small performance advantage (5 to 20%) when running a
if desired.
</P>
<P><B>Speed-ups to expect:</B>
</P>
<P>Depending on which styles are accelerated, you should look for a
reduction in the "Pair time", "Bond time", "KSpace time", and "Loop
time" values printed at the end of a run.
</P>
<P>You may see a small performance advantage (5 to 20%) when running a
USER-OMP style (in serial or parallel) with a single thread per MPI
task, versus running standard LAMMPS with its standard
(un-accelerated) styles (in serial or all-MPI parallelization with 1
task/core). This is because many of the USER-OMP styles contain
similar optimizations to those used in the OPT package, as described
above.</p>
<p>With multiple threads/task, the optimal choice of MPI tasks/node and
above.
</P>
<P>With multiple threads/task, the optimal choice of MPI tasks/node and
OpenMP threads/task can vary a lot and should always be tested via
benchmark runs for a specific simulation running on a specific
machine, paying attention to guidelines discussed in the next
sub-section.</p>
<p>A description of the multi-threading strategy used in the USER-OMP
package and some performance examples are <a class="reference external" href="http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&amp;d=1">presented here</a></p>
<p><strong>Guidelines for best performance:</strong></p>
<p>For many problems on current generation CPUs, running the USER-OMP
sub-section.
</P>
<P>A description of the multi-threading strategy used in the USER-OMP
package and some performance examples are <A HREF = "http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&d=1">presented
here</A>
</P>
<P><B>Guidelines for best performance:</B>
</P>
<P>For many problems on current generation CPUs, running the USER-OMP
package with a single thread/task is faster than running with multiple
threads/task. This is because the MPI parallelization in LAMMPS is
often more efficient than multi-threading as implemented in the
USER-OMP package. The parallel efficiency (in a threaded sense) also
varies for different USER-OMP styles.</p>
<p>Using multiple threads/task can be more effective under the following
circumstances:</p>
<ul class="simple">
<li>Individual compute nodes have a significant number of CPU cores but
varies for different USER-OMP styles.
</P>
<P>Using multiple threads/task can be more effective under the following
circumstances:
</P>
<UL><LI>Individual compute nodes have a significant number of CPU cores but
the CPU itself has limited memory bandwidth, e.g. for Intel Xeon 53xx
(Clovertown) and 54xx (Harpertown) quad core processors. Running one
MPI task per CPU core will result in significant performance
@ -245,111 +155,52 @@ degradation, so that running with 4 or even only 2 MPI tasks per node
is faster. Running in hybrid MPI+OpenMP mode will reduce the
inter-node communication bandwidth contention in the same way, but
offers an additional speedup by utilizing the otherwise idle CPU
cores.</li>
<li>The interconnect used for MPI communication does not provide
cores.
<LI>The interconnect used for MPI communication does not provide
sufficient bandwidth for a large number of MPI tasks per node. For
example, this applies to running over gigabit ethernet or on Cray XT4
or XT5 series supercomputers. As in the aforementioned case, this
effect worsens when using an increasing number of nodes.</li>
<li>The system has a spatially inhomogeneous particle density which does
not map well to the <a class="reference internal" href="processors.html"><em>domain decomposition scheme</em></a> or
<a class="reference internal" href="balance.html"><em>load-balancing</em></a> options that LAMMPS provides. This is
effect worsens when using an increasing number of nodes.
<LI>The system has a spatially inhomogeneous particle density which does
not map well to the <A HREF = "processors.html">domain decomposition scheme</A> or
<A HREF = "balance.html">load-balancing</A> options that LAMMPS provides. This is
because multi-threading achives parallelism over the number of
particles, not via their distribution in space.</li>
<li>A machine is being used in &#8220;capability mode&#8221;, i.e. near the point
particles, not via their distribution in space.
<LI>A machine is being used in "capability mode", i.e. near the point
where MPI parallelism is maxed out. For example, this can happen when
using the <a class="reference internal" href="kspace_style.html"><em>PPPM solver</em></a> for long-range
using the <A HREF = "kspace_style.html">PPPM solver</A> for long-range
electrostatics on large numbers of nodes. The scaling of the KSpace
calculation (see the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command) becomes
calculation (see the <A HREF = "kspace_style.html">kspace_style</A> command) becomes
the performance-limiting factor. Using multi-threading allows less
MPI tasks to be invoked and can speed-up the long-range solver, while
increasing overall performance by parallelizing the pairwise and
bonded calculations via OpenMP. Likewise additional speedup can be
sometimes be achived by increasing the length of the Coulombic cutoff
and thus reducing the work done by the long-range solver. Using the
<a class="reference internal" href="run_style.html"><em>run_style verlet/split</em></a> command, which is compatible
<A HREF = "run_style.html">run_style verlet/split</A> command, which is compatible
with the USER-OMP package, is an alternative way to reduce the number
of MPI tasks assigned to the KSpace calculation.</li>
</ul>
<p>Additional performance tips are as follows:</p>
<ul class="simple">
<li>The best parallel efficiency from <em>omp</em> styles is typically achieved
of MPI tasks assigned to the KSpace calculation.
</UL>
<P>Additional performance tips are as follows:
</P>
<UL><LI>The best parallel efficiency from <I>omp</I> styles is typically achieved
when there is at least one MPI task per physical processor,
i.e. socket or die.</li>
<li>It is usually most efficient to restrict threading to a single
socket, i.e. use one or more MPI task per socket.</li>
<li>Several current MPI implementation by default use a processor affinity
i.e. socket or die.
<LI>It is usually most efficient to restrict threading to a single
socket, i.e. use one or more MPI task per socket.
<LI>Several current MPI implementation by default use a processor affinity
setting that restricts each MPI task to a single CPU core. Using
multi-threading in this mode will force the threads to share that core
and thus is likely to be counterproductive. Instead, binding MPI
tasks to a (multi-core) socket, should solve this issue.</li>
</ul>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>None.</p>
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<p><a class="reference internal" href="Section_accelerate.html"><em>Return to Section accelerate overview</em></a></p>
<div class="section" id="opt-package">
<h1>5.OPT package<a class="headerlink" href="#opt-package" title="Permalink to this headline"></a></h1>
<p>The OPT package was developed by James Fischer (High Performance
<HR>
<P><A HREF = "Section_accelerate.html">Return to Section accelerate overview</A>
</P>
<H4>5.3.6 OPT package
</H4>
<P>The OPT package was developed by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
Technologies). It contains a handful of pair styles whose compute()
methods were rewritten in C++ templated form to reduce the overhead
due to if tests and other conditional code.</p>
<p>Here is a quick overview of how to use the OPT package:</p>
<ul class="simple">
<li>include the OPT package and build LAMMPS</li>
<li>use OPT pair styles in your input script</li>
</ul>
<p>The last step can be done using the &#8220;-sf opt&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>. Or the effect of the &#8220;-sf&#8221; switch
can be duplicated by adding a <a class="reference internal" href="suffix.html"><em>suffix opt</em></a> command to your
input script.</p>
<p><strong>Required hardware/software:</strong></p>
<p>None.</p>
<p><strong>Building LAMMPS with the OPT package:</strong></p>
<p>Include the package and build LAMMPS:</p>
<p>To do this in one line, use the src/Make.py script, described in
<a class="reference internal" href="Section_start.html#start-4"><span>Section 2.4</span></a> of the manual. Type &#8220;Make.py
-h&#8221; for help. If run from the src directory, this command will create
due to if tests and other conditional code.
</P>
<P>Here is a quick overview of how to use the OPT package:
</P>
<UL><LI>include the OPT package and build LAMMPS
<LI>use OPT pair styles in your input script
</UL>
<P>The last step can be done using the "-sf opt" <A HREF = "Section_start.html#start_7">command-line
switch</A>. Or the effect of the "-sf" switch
can be duplicated by adding a <A HREF = "suffix.html">suffix opt</A> command to your
input script.
</P>
<P><B>Required hardware/software:</B>
</P>
<P>None.
</P>
<P><B>Building LAMMPS with the OPT package:</B>
</P>
<P>Include the package and build LAMMPS:
</P>
<P>To do this in one line, use the src/Make.py script, described in
<A HREF = "Section_start.html#start_4">Section 2.4</A> of the manual. Type "Make.py
-h" for help. If run from the src directory, this command will create
src/lmp_opt using src/MAKE/Makefile.mpi as the starting
Makefile.machine:</p>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p opt -o opt file mpi
</pre></div>
</div>
<p>Or you can follow these steps:</p>
<div class="highlight-python"><div class="highlight"><pre>cd lammps/src
Makefile.machine:
</P>
<PRE>Make.py -p opt -o opt file mpi
</PRE>
<P>Or you can follow these steps:
</P>
<PRE>cd lammps/src
make yes-opt
make machine
</pre></div>
</div>
<p>If you are using Intel compilers, then the CCFLAGS setting in
Makefile.machine needs to include &#8220;-restrict&#8221;.</p>
<p><strong>Run with the OPT package from the command line:</strong></p>
<p>Use the &#8220;-sf opt&#8221; <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>,
which will automatically append &#8220;opt&#8221; to styles that support it.</p>
<div class="highlight-python"><div class="highlight"><pre>lmp_machine -sf opt -in in.script
mpirun -np 4 lmp_machine -sf opt -in in.script
</pre></div>
</div>
<p><strong>Or run with the OPT package by editing an input script:</strong></p>
<p>Use the <a class="reference internal" href="suffix.html"><em>suffix opt</em></a> command, or you can explicitly add an
&#8220;opt&#8221; suffix to individual styles in your input script, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/opt 2.5
</pre></div>
</div>
<p><strong>Speed-ups to expect:</strong></p>
<p>You should see a reduction in the &#8220;Pair time&#8221; value printed at the end
make machine
</PRE>
<P>If you are using Intel compilers, then the CCFLAGS setting in
Makefile.machine needs to include "-restrict".
</P>
<P><B>Run with the OPT package from the command line:</B>
</P>
<P>Use the "-sf opt" <A HREF = "Section_start.html#start_7">command-line switch</A>,
which will automatically append "opt" to styles that support it.
</P>
<PRE>lmp_machine -sf opt -in in.script
mpirun -np 4 lmp_machine -sf opt -in in.script
</PRE>
<P><B>Or run with the OPT package by editing an input script:</B>
</P>
<P>Use the <A HREF = "suffix.html">suffix opt</A> command, or you can explicitly add an
"opt" suffix to individual styles in your input script, e.g.
</P>
<PRE>pair_style lj/cut/opt 2.5
</PRE>
<P><B>Speed-ups to expect:</B>
</P>
<P>You should see a reduction in the "Pair time" value printed at the end
of a run. On most machines for reasonable problem sizes, it will be a
5 to 20% savings.</p>
<p><strong>Guidelines for best performance:</strong></p>
<p>None. Just try out an OPT pair style to see how it performs.</p>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>None.</p>
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5 to 20% savings.
</P>
<P><B>Guidelines for best performance:</B>
</P>
<P>None. Just try out an OPT pair style to see how it performs.
</P>
<P><B>Restrictions:</B>
</P>
<P>None.
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<div class="section" id="angle-style-charmm-command">
<span id="index-0"></span><h1>angle_style charmm command<a class="headerlink" href="#angle-style-charmm-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="angle-style-charmm-kk-command">
<h1>angle_style charmm/kk command<a class="headerlink" href="#angle-style-charmm-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="angle-style-charmm-omp-command">
<h1>angle_style charmm/omp command<a class="headerlink" href="#angle-style-charmm-omp-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>angle_style charmm
</pre></div>
</div>
</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>angle_style charmm
angle_coeff 1 300.0 107.0 50.0 3.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>charmm</em> angle style uses the potential</p>
<img alt="_images/angle_charmm.jpg" class="align-center" src="_images/angle_charmm.jpg" />
<p>with an additional Urey_Bradley term based on the distance <em>r</em> between
<HR>
<H3>angle_style charmm command
</H3>
<H3>angle_style charmm/kk command
</H3>
<H3>angle_style charmm/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style charmm
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style charmm
angle_coeff 1 300.0 107.0 50.0 3.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>charmm</I> angle style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/angle_charmm.jpg">
</CENTER>
<P>with an additional Urey_Bradley term based on the distance <I>r</I> between
the 1st and 3rd atoms in the angle. K, theta0, Kub, and Rub are
coefficients defined for each angle type.</p>
<p>See <a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
field.</p>
<p>The following coefficients must be defined for each angle type via the
<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li>K (energy/radian^2)</li>
<li>theta0 (degrees)</li>
<li>K_ub (energy/distance^2)</li>
<li>r_ub (distance)</li>
</ul>
<p>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
coefficients defined for each angle type.
</P>
<P>See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
field.
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy/radian^2)
<LI>theta0 (degrees)
<LI>K_ub (energy/distance^2)
<LI>r_ub (distance)
</UL>
<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info on packages.</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 class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="mackerell"><strong>(MacKerell)</strong> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).</p>
</div>
</div>
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B> none
</P>
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<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
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<div class="section" id="angle-style-class2-command">
<span id="index-0"></span><h1>angle_style class2 command<a class="headerlink" href="#angle-style-class2-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="angle-style-class2-omp-command">
<h1>angle_style class2/omp command<a class="headerlink" href="#angle-style-class2-omp-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>angle_style class2
</pre></div>
</div>
</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>angle_style class2
<HR>
<H3>angle_style class2 command
</H3>
<H3>angle_style class2/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style class2
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style class2
angle_coeff * 75.0
angle_coeff 1 bb 10.5872 1.0119 1.5228
angle_coeff * ba 3.6551 24.895 1.0119 1.5228
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>class2</em> angle style uses the potential</p>
<img alt="_images/angle_class2.jpg" class="align-center" src="_images/angle_class2.jpg" />
<p>where Ea is the angle term, Ebb is a bond-bond term, and Eba is a
angle_coeff * ba 3.6551 24.895 1.0119 1.5228
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>class2</I> angle style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/angle_class2.jpg">
</CENTER>
<P>where Ea is the angle term, Ebb is a bond-bond term, and Eba is a
bond-angle term. Theta0 is the equilibrium angle and r1 and r2 are
the equilibrium bond lengths.</p>
<p>See <a class="reference internal" href="pair_modify.html#sun"><span>(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
<p>Coefficients for the Ea, Ebb, and Eba formulas must be defined for
each angle type via the <a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in
the equilibrium bond lengths.
</P>
<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
</P>
<P>Coefficients for the Ea, Ebb, and Eba formulas must be defined for
each angle type via the <A HREF = "angle_coeff.html">angle_coeff</A> command as in
the example above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands.</p>
<p>These are the 4 coefficients for the Ea formula:</p>
<ul class="simple">
<li>theta0 (degrees)</li>
<li>K2 (energy/radian^2)</li>
<li>K3 (energy/radian^3)</li>
<li>K4 (energy/radian^4)</li>
</ul>
<p>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of the various K are in per-radian.</p>
<p>For the Ebb formula, each line in a <a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a>
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands.
</P>
<P>These are the 4 coefficients for the Ea formula:
</P>
<UL><LI>theta0 (degrees)
<LI>K2 (energy/radian^2)
<LI>K3 (energy/radian^3)
<LI>K4 (energy/radian^4)
</UL>
<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of the various K are in per-radian.
</P>
<P>For the Ebb formula, each line in a <A HREF = "angle_coeff.html">angle_coeff</A>
command in the input script lists 4 coefficients, the first of which
is &#8220;bb&#8221; to indicate they are BondBond coefficients. In a data file,
these coefficients should be listed under a &#8220;BondBond Coeffs&#8221; heading
and you must leave out the &#8220;bb&#8221;, i.e. only list 3 coefficients after
the angle type.</p>
<ul class="simple">
<li>bb</li>
<li>M (energy/distance^2)</li>
<li>r1 (distance)</li>
<li>r2 (distance)</li>
</ul>
<p>For the Eba formula, each line in a <a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a>
is "bb" to indicate they are BondBond coefficients. In a data file,
these coefficients should be listed under a "BondBond Coeffs" heading
and you must leave out the "bb", i.e. only list 3 coefficients after
the angle type.
</P>
<UL><LI>bb
<LI>M (energy/distance^2)
<LI>r1 (distance)
<LI>r2 (distance)
</UL>
<P>For the Eba formula, each line in a <A HREF = "angle_coeff.html">angle_coeff</A>
command in the input script lists 5 coefficients, the first of which
is &#8220;ba&#8221; to indicate they are BondAngle coefficients. In a data file,
these coefficients should be listed under a &#8220;BondAngle Coeffs&#8221; heading
and you must leave out the &#8220;ba&#8221;, i.e. only list 4 coefficients after
the angle type.</p>
<ul class="simple">
<li>ba</li>
<li>N1 (energy/distance^2)</li>
<li>N2 (energy/distance^2)</li>
<li>r1 (distance)</li>
<li>r2 (distance)</li>
</ul>
<p>The theta0 value in the Eba formula is not specified, since it is the
same value from the Ea formula.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
is "ba" to indicate they are BondAngle coefficients. In a data file,
these coefficients should be listed under a "BondAngle Coeffs" heading
and you must leave out the "ba", i.e. only list 4 coefficients after
the angle type.
</P>
<UL><LI>ba
<LI>N1 (energy/distance^2)
<LI>N2 (energy/distance^2)
<LI>r1 (distance)
<LI>r2 (distance)
</UL>
<P>The theta0 value in the Eba formula is not specified, since it is the
same value from the Ea formula.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This angle style can only be used if LAMMPS was built with the CLASS2
package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section
for more info on packages.</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 class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="sun"><strong>(Sun)</strong> Sun, J Phys Chem B 102, 7338-7364 (1998).</p>
</div>
</div>
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the CLASS2
package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B> none
</P>
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<P><B>(Sun)</B> Sun, J Phys Chem B 102, 7338-7364 (1998).
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<div class="section" id="angle-coeff-command">
<span id="index-0"></span><h1>angle_coeff command<a class="headerlink" href="#angle-coeff-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>angle_coeff N args
</pre></div>
</div>
<ul class="simple">
<li>N = angle type (see asterisk form below)</li>
<li>args = coefficients for one or more angle types</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>angle_coeff 1 300.0 107.0
<HR>
<H3>angle_coeff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_coeff N args
</PRE>
<UL><LI>N = angle type (see asterisk form below)
<LI>args = coefficients for one or more angle types
</UL>
<P><B>Examples:</B>
</P>
<PRE>angle_coeff 1 300.0 107.0
angle_coeff * 5.0
angle_coeff 2*10 5.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Specify the angle force field coefficients for one or more angle types.
angle_coeff 2*10 5.0
</PRE>
<P><B>Description:</B>
</P>
<P>Specify the angle force field coefficients for one or more angle types.
The number and meaning of the coefficients depends on the angle style.
Angle coefficients can also be set in the data file read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command or in a restart file.</p>
<p>N can be specified in one of two ways. An explicit numeric value can
<A HREF = "read_data.html">read_data</A> command or in a restart file.
</P>
<P>N can be specified in one of two ways. An explicit numeric value can
be used, as in the 1st example above. Or a wild-card asterisk can be
used to set the coefficients for multiple angle types. This takes the
form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;. If N = the number of angle types,
form "*" or "*n" or "n*" or "m*n". If N = the number of angle types,
then an asterisk with no numeric values means all types from 1 to N. A
leading asterisk means all types from 1 to n (inclusive). A trailing
asterisk means all types from n to N (inclusive). A middle asterisk
means all types from m to n (inclusive).</p>
<p>Note that using an angle_coeff command can override a previous setting
means all types from m to n (inclusive).
</P>
<P>Note that using an angle_coeff command can override a previous setting
for the same angle type. For example, these commands set the coeffs
for all angle types, then overwrite the coeffs for just angle type 2:</p>
<div class="highlight-python"><div class="highlight"><pre>angle_coeff * 200.0 107.0 1.2
angle_coeff 2 50.0 107.0
</pre></div>
</div>
<p>A line in a data file that specifies angle coefficients uses the exact
for all angle types, then overwrite the coeffs for just angle type 2:
</P>
<PRE>angle_coeff * 200.0 107.0 1.2
angle_coeff 2 50.0 107.0
</PRE>
<P>A line in a data file that specifies angle coefficients uses the exact
same format as the arguments of the angle_coeff command in an input
script, except that wild-card asterisks should not be used since
coefficients for all N types must be listed in the file. For example,
under the &#8220;Angle Coeffs&#8221; section of a data file, the line that
corresponds to the 1st example above would be listed as</p>
<div class="highlight-python"><div class="highlight"><pre>1 300.0 107.0
</pre></div>
</div>
<p>The <a class="reference internal" href="angle_class2.html"><em>angle_style class2</em></a> is an exception to this
under the "Angle Coeffs" section of a data file, the line that
corresponds to the 1st example above would be listed as
</P>
<PRE>1 300.0 107.0
</PRE>
<P>The <A HREF = "angle_class2.html">angle_style class2</A> is an exception to this
rule, in that an additional argument is used in the input script to
allow specification of the cross-term coefficients. See its
doc page for details.</p>
<hr class="docutils" />
<p>Here is an alphabetic list of angle styles defined in LAMMPS. Click on
doc page for details.
</P>
<HR>
<P>Here is an alphabetic list of angle styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated <a class="reference internal" href=""><em>angle_coeff</em></a> command.</p>
<p>Note that there are also additional angle styles submitted by users
specified by the associated <A HREF = "angle_coeff.html">angle_coeff</A> command.
</P>
<P>Note that there are also additional angle styles submitted by users
which are included in the LAMMPS distribution. The list of these with
links to the individual styles are given in the angle section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
<ul class="simple">
<li><a class="reference internal" href="angle_none.html"><em>angle_style none</em></a> - turn off angle interactions</li>
<li><a class="reference internal" href="angle_hybrid.html"><em>angle_style hybrid</em></a> - define multiple styles of angle interactions</li>
<li><a class="reference internal" href="angle_charmm.html"><em>angle_style charmm</em></a> - CHARMM angle</li>
<li><a class="reference internal" href="angle_class2.html"><em>angle_style class2</em></a> - COMPASS (class 2) angle</li>
<li><a class="reference internal" href="angle_cosine.html"><em>angle_style cosine</em></a> - cosine angle potential</li>
<li><a class="reference internal" href="angle_cosine_delta.html"><em>angle_style cosine/delta</em></a> - difference of cosines angle potential</li>
<li><a class="reference internal" href="angle_cosine_periodic.html"><em>angle_style cosine/periodic</em></a> - DREIDING angle</li>
<li><a class="reference internal" href="angle_cosine_squared.html"><em>angle_style cosine/squared</em></a> - cosine squared angle potential</li>
<li><a class="reference internal" href="angle_harmonic.html"><em>angle_style harmonic</em></a> - harmonic angle</li>
<li><a class="reference internal" href="angle_table.html"><em>angle_style table</em></a> - tabulated by angle</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This command must come after the simulation box is defined by a
<a class="reference internal" href="read_data.html"><em>read_data</em></a>, <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>, or
<a class="reference internal" href="create_box.html"><em>create_box</em></a> command.</p>
<p>An angle style must be defined before any angle coefficients are
set, either in the input script or in a data file.</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 class="reference internal" href="angle_style.html"><em>angle_style</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
links to the individual styles are given in the angle section of <A HREF = "Section_commands.html#cmd_5">this
page</A>.
</P>
<UL><LI><A HREF = "angle_none.html">angle_style none</A> - turn off angle interactions
<LI><A HREF = "angle_hybrid.html">angle_style hybrid</A> - define multiple styles of angle interactions
</UL>
<UL><LI><A HREF = "angle_charmm.html">angle_style charmm</A> - CHARMM angle
<LI><A HREF = "angle_class2.html">angle_style class2</A> - COMPASS (class 2) angle
<LI><A HREF = "angle_cosine.html">angle_style cosine</A> - cosine angle potential
<LI><A HREF = "angle_cosine_delta.html">angle_style cosine/delta</A> - difference of cosines angle potential
<LI><A HREF = "angle_cosine_periodic.html">angle_style cosine/periodic</A> - DREIDING angle
<LI><A HREF = "angle_cosine_squared.html">angle_style cosine/squared</A> - cosine squared angle potential
<LI><A HREF = "angle_harmonic.html">angle_style harmonic</A> - harmonic angle
<LI><A HREF = "angle_table.html">angle_style table</A> - tabulated by angle
</UL>
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<P><B>Restrictions:</B>
</P>
<P>This command must come after the simulation box is defined by a
<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>, or
<A HREF = "create_box.html">create_box</A> command.
</P>
<P>An angle style must be defined before any angle coefficients are
set, either in the input script or in a data file.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_style.html">angle_style</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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@ -1,249 +1,77 @@
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<div class="section" id="angle-style-cosine-command">
<span id="index-0"></span><h1>angle_style cosine command<a class="headerlink" href="#angle-style-cosine-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="angle-style-cosine-omp-command">
<h1>angle_style cosine/omp command<a class="headerlink" href="#angle-style-cosine-omp-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>angle_style cosine
</pre></div>
</div>
</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>angle_style cosine
angle_coeff * 75.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>cosine</em> angle style uses the potential</p>
<img alt="_images/angle_cosine.jpg" class="align-center" src="_images/angle_cosine.jpg" />
<p>where K is defined for each angle type.</p>
<p>The following coefficients must be defined for each angle type via the
<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li>K (energy)</li>
</ul>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
<HR>
<H3>angle_style cosine command
</H3>
<H3>angle_style cosine/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style cosine
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style cosine
angle_coeff * 75.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>cosine</I> angle style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/angle_cosine.jpg">
</CENTER>
<P>where K is defined for each angle type.
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy)
</UL>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info on packages.</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 class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
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<P><B>Restrictions:</B>
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<P>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B> none
</P>
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<div class="section" id="angle-style-cosine-delta-command">
<span id="index-0"></span><h1>angle_style cosine/delta command<a class="headerlink" href="#angle-style-cosine-delta-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="angle-style-cosine-delta-omp-command">
<h1>angle_style cosine/delta/omp command<a class="headerlink" href="#angle-style-cosine-delta-omp-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>angle_style cosine/delta
</pre></div>
</div>
</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>angle_style cosine/delta
angle_coeff 2*4 75.0 100.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>cosine/delta</em> angle style uses the potential</p>
<img alt="_images/angle_cosine_delta.jpg" class="align-center" src="_images/angle_cosine_delta.jpg" />
<p>where theta0 is the equilibrium value of the angle, and K is a
prefactor. Note that the usual 1/2 factor is included in K.</p>
<p>The following coefficients must be defined for each angle type via the
<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li>K (energy)</li>
<li>theta0 (degrees)</li>
</ul>
<p>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
<HR>
<H3>angle_style cosine/delta command
</H3>
<H3>angle_style cosine/delta/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style cosine/delta
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style cosine/delta
angle_coeff 2*4 75.0 100.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>cosine/delta</I> angle style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/angle_cosine_delta.jpg">
</CENTER>
<P>where theta0 is the equilibrium value of the angle, and K is a
prefactor. Note that the usual 1/2 factor is included in K.
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy)
<LI>theta0 (degrees)
</UL>
<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info on packages.</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 class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a>, <a class="reference internal" href="angle_cosine_squared.html"><em>angle_style cosine/squared</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<HR>
</div>
</div>
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<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>, <A HREF = "angle_cosine_squared.html">angle_style
cosine/squared</A>
</P>
<P><B>Default:</B> none
</P>
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<div class="section" id="angle-style-cosine-periodic-command">
<span id="index-0"></span><h1>angle_style cosine/periodic command<a class="headerlink" href="#angle-style-cosine-periodic-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="angle-style-cosine-periodic-omp-command">
<h1>angle_style cosine/periodic/omp command<a class="headerlink" href="#angle-style-cosine-periodic-omp-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>angle_style cosine/periodic
</pre></div>
</div>
</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>angle_style cosine/periodic
angle_coeff * 75.0 1 6
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>cosine/periodic</em> angle style uses the following potential, which
is commonly used in the <a class="reference internal" href="Section_howto.html#howto-4"><span>DREIDING</span></a> force
field, particularly for organometallic systems where <em>n</em> = 4 might be
used for an octahedral complex and <em>n</em> = 3 might be used for a
trigonal center:</p>
<img alt="_images/angle_cosine_periodic.jpg" class="align-center" src="_images/angle_cosine_periodic.jpg" />
<p>where C, B and n are coefficients defined for each angle type.</p>
<p>See <a class="reference internal" href="special_bonds.html#mayo"><span>(Mayo)</span></a> for a description of the DREIDING force field</p>
<p>The following coefficients must be defined for each angle type via the
<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li>C (energy)</li>
<li>B = 1 or -1</li>
<li>n = 1, 2, 3, 4, 5 or 6 for periodicity</li>
</ul>
<p>Note that the prefactor C is specified and not the overall force
<HR>
<H3>angle_style cosine/periodic command
</H3>
<H3>angle_style cosine/periodic/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style cosine/periodic
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style cosine/periodic
angle_coeff * 75.0 1 6
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>cosine/periodic</I> angle style uses the following potential, which
is commonly used in the <A HREF = "Section_howto.html#howto_4">DREIDING</A> force
field, particularly for organometallic systems where <I>n</I> = 4 might be
used for an octahedral complex and <I>n</I> = 3 might be used for a
trigonal center:
</P>
<CENTER><IMG SRC = "Eqs/angle_cosine_periodic.jpg">
</CENTER>
<P>where C, B and n are coefficients defined for each angle type.
</P>
<P>See <A HREF = "#Mayo">(Mayo)</A> for a description of the DREIDING force field
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>C (energy)
<LI>B = 1 or -1
<LI>n = 1, 2, 3, 4, 5 or 6 for periodicity
</UL>
<P>Note that the prefactor C is specified and not the overall force
constant K = C / n^2. When B = 1, it leads to a minimum for the
linear geometry. When B = -1, it leads to a maximum for the linear
geometry.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
geometry.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info on packages.</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 class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="mayo"><strong>(Mayo)</strong> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).</p>
</div>
</div>
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
</div>
</div>
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<P><B>(Mayo)</B> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).
</P>
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<div class="section" id="angle-style-cosine-shift-command">
<span id="index-0"></span><h1>angle_style cosine/shift command<a class="headerlink" href="#angle-style-cosine-shift-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="angle-style-cosine-shift-omp-command">
<h1>angle_style cosine/shift/omp command<a class="headerlink" href="#angle-style-cosine-shift-omp-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>angle_style cosine/shift
</pre></div>
</div>
</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>angle_style cosine/shift
angle_coeff * 10.0 45.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>cosine/shift</em> angle style uses the potential</p>
<img alt="_images/angle_cosine_shift.jpg" class="align-center" src="_images/angle_cosine_shift.jpg" />
<p>where theta0 is the equilibrium angle. The potential is bounded
<HR>
<H3>angle_style cosine/shift command
</H3>
<H3>angle_style cosine/shift/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style cosine/shift
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style cosine/shift
angle_coeff * 10.0 45.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>cosine/shift</I> angle style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/angle_cosine_shift.jpg">
</CENTER>
<P>where theta0 is the equilibrium angle. The potential is bounded
between -Umin and zero. In the neighborhood of the minimum E=- Umin +
Umin/4(theta-theta0)^2 hence the spring constant is umin/2.</p>
<p>The following coefficients must be defined for each angle type via the
<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li>umin (energy)</li>
<li>theta (angle)</li>
</ul>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
Umin/4(theta-theta0)^2 hence the spring constant is umin/2.
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>umin (energy)
<LI>theta (angle)
</UL>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This angle style can only be used if LAMMPS was built with the
USER-MISC package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info on packages.</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 class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a>,
<code class="xref doc docutils literal"><span class="pre">angle_cosineshiftexp</span></code></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
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<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>,
<A HREF = "angle_cosineshiftexp.html">angle_cosineshiftexp</A>
</P>
<P><B>Default:</B> none
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<div class="section" id="angle-style-cosine-shift-exp-command">
<span id="index-0"></span><h1>angle_style cosine/shift/exp command<a class="headerlink" href="#angle-style-cosine-shift-exp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="angle-style-cosine-shift-exp-omp-command">
<h1>angle_style cosine/shift/exp/omp command<a class="headerlink" href="#angle-style-cosine-shift-exp-omp-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>angle_style cosine/shift/exp
</pre></div>
</div>
</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>angle_style cosine/shift/exp
angle_coeff * 10.0 45.0 2.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>cosine/shift/exp</em> angle style uses the potential</p>
<img alt="_images/angle_cosine_shift_exp.jpg" class="align-center" src="_images/angle_cosine_shift_exp.jpg" />
<p>where Umin, theta, and a are defined for each angle type.</p>
<p>The potential is bounded between [-Umin:0] and the minimum is
<HR>
<H3>angle_style cosine/shift/exp command
</H3>
<H3>angle_style cosine/shift/exp/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style cosine/shift/exp
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style cosine/shift/exp
angle_coeff * 10.0 45.0 2.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>cosine/shift/exp</I> angle style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/angle_cosine_shift_exp.jpg">
</CENTER>
<P>where Umin, theta, and a are defined for each angle type.
</P>
<P>The potential is bounded between [-Umin:0] and the minimum is
located at the angle theta0. The a parameter can be both positive or
negative and is used to control the spring constant at the
equilibrium.</p>
<p>The spring constant is given by k = A exp(A) Umin / [2 (Exp(a)-1)].
For a &gt; 3, k/Umin = a/2 to better than 5% relative error. For negative
equilibrium.
</P>
<P>The spring constant is given by k = A exp(A) Umin / [2 (Exp(a)-1)].
For a > 3, k/Umin = a/2 to better than 5% relative error. For negative
values of the a parameter, the spring constant is essentially zero,
and anharmonic terms takes over. The potential is furthermore well
behaved in the limit a -&gt; 0, where it has been implemented to linear
order in a for a &lt; 0.001. In this limit the potential reduces to the
cosineshifted potential.</p>
<p>The following coefficients must be defined for each angle type via the
<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li>umin (energy)</li>
<li>theta (angle)</li>
<li>A (real number)</li>
</ul>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
behaved in the limit a -> 0, where it has been implemented to linear
order in a for a < 0.001. In this limit the potential reduces to the
cosineshifted potential.
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>umin (energy)
<LI>theta (angle)
<LI>A (real number)
</UL>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This angle style can only be used if LAMMPS was built with the
USER-MISC package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info on packages.</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 class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a>,
<code class="xref doc docutils literal"><span class="pre">angle_cosineshift</span></code>,
<code class="xref doc docutils literal"><span class="pre">dihedral_cosineshift</span></code></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
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<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>,
<A HREF = "angle_cosineshift.html">angle_cosineshift</A>,
<A HREF = "dihedral_cosineshift.html">dihedral_cosineshift</A>
</P>
<P><B>Default:</B> none
</P>
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<div class="section" id="angle-style-cosine-squared-command">
<span id="index-0"></span><h1>angle_style cosine/squared command<a class="headerlink" href="#angle-style-cosine-squared-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="angle-style-cosine-squared-omp-command">
<h1>angle_style cosine/squared/omp command<a class="headerlink" href="#angle-style-cosine-squared-omp-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>angle_style cosine/squared
</pre></div>
</div>
</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>angle_style cosine/squared
angle_coeff 2*4 75.0 100.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>cosine/squared</em> angle style uses the potential</p>
<img alt="_images/angle_cosine_squared.jpg" class="align-center" src="_images/angle_cosine_squared.jpg" />
<p>where theta0 is the equilibrium value of the angle, and K is a
prefactor. Note that the usual 1/2 factor is included in K.</p>
<p>The following coefficients must be defined for each angle type via the
<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li>K (energy)</li>
<li>theta0 (degrees)</li>
</ul>
<p>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
<HR>
<H3>angle_style cosine/squared command
</H3>
<H3>angle_style cosine/squared/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style cosine/squared
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style cosine/squared
angle_coeff 2*4 75.0 100.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>cosine/squared</I> angle style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/angle_cosine_squared.jpg">
</CENTER>
<P>where theta0 is the equilibrium value of the angle, and K is a
prefactor. Note that the usual 1/2 factor is included in K.
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy)
<LI>theta0 (degrees)
</UL>
<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info on packages.</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 class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
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<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B> none
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<div class="section" id="angle-style-dipole-command">
<span id="index-0"></span><h1>angle_style dipole command<a class="headerlink" href="#angle-style-dipole-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="angle-style-dipole-omp-command">
<h1>angle_style dipole/omp command<a class="headerlink" href="#angle-style-dipole-omp-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>angle_style dipole
</pre></div>
</div>
</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>angle_style dipole
angle_coeff 6 2.1 180.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>dipole</em> angle style is used to control the orientation of a dipolar
atom within a molecule <a class="reference internal" href="#orsi"><span>(Orsi)</span></a>. Specifically, the <em>dipole</em> angle
style restrains the orientation of a point dipole mu_j (embedded in atom
&#8216;j&#8217;) with respect to a reference (bond) vector r_ij = r_i - r_j, where &#8216;i&#8217;
is another atom of the same molecule (typically, &#8216;i&#8217; and &#8216;j&#8217; are also
covalently bonded).</p>
<p>It is convenient to define an angle gamma between the &#8216;free&#8217; vector mu_j
and the reference (bond) vector r_ij:</p>
<img alt="_images/angle_dipole_gamma.jpg" class="align-center" src="_images/angle_dipole_gamma.jpg" />
<p>The <em>dipole</em> angle style uses the potential:</p>
<img alt="_images/angle_dipole_potential.jpg" class="align-center" src="_images/angle_dipole_potential.jpg" />
<p>where K is a rigidity constant and gamma0 is an equilibrium (reference)
angle.</p>
<p>The torque on the dipole can be obtained by differentiating the
potential using the &#8216;chain rule&#8217; as in appendix C.3 of
<a class="reference internal" href="pair_gayberne.html#allen"><span>(Allen)</span></a>:</p>
<img alt="_images/angle_dipole_torque.jpg" class="align-center" src="_images/angle_dipole_torque.jpg" />
<p>Example: if gamma0 is set to 0 degrees, the torque generated by
the potential will tend to align the dipole along the reference
<HR>
<H3>angle_style dipole command
</H3>
<H3>angle_style dipole/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style dipole
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style dipole
angle_coeff 6 2.1 180.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>dipole</I> angle style is used to control the orientation of a dipolar
atom within a molecule <A HREF = "#Orsi">(Orsi)</A>. Specifically, the <I>dipole</I> angle
style restrains the orientation of a point dipole mu_j (embedded in atom
'j') with respect to a reference (bond) vector r_ij = r_i - r_j, where 'i'
is another atom of the same molecule (typically, 'i' and 'j' are also
covalently bonded).
</P>
<P>It is convenient to define an angle gamma between the 'free' vector mu_j
and the reference (bond) vector r_ij:
</P>
<CENTER><IMG SRC = "Eqs/angle_dipole_gamma.jpg">
</CENTER>
<P>The <I>dipole</I> angle style uses the potential:
</P>
<CENTER><IMG SRC = "Eqs/angle_dipole_potential.jpg">
</CENTER>
<P>where K is a rigidity constant and gamma0 is an equilibrium (reference)
angle.
</P>
<P>The torque on the dipole can be obtained by differentiating the
potential using the 'chain rule' as in appendix C.3 of
<A HREF = "#Allen">(Allen)</A>:
</P>
<CENTER><IMG SRC = "Eqs/angle_dipole_torque.jpg">
</CENTER>
<P>Example: if gamma0 is set to 0 degrees, the torque generated by
the potential will tend to align the dipole along the reference
direction defined by the (bond) vector r_ij (in other words, mu_j is
restrained to point towards atom &#8216;i&#8217;).</p>
<p>Note that the angle dipole potential does not give rise to any force,
because it does not depend on the distance between i and j (it only
depends on the angle between mu_j and r_ij).</p>
<p>The following coefficients must be defined for each angle type via the
<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li>K (energy)</li>
<li>gamma0 (degrees)</li>
</ul>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
restrained to point towards atom 'i').
</P>
<P>Note that the angle dipole potential does not give rise to any force,
because it does not depend on the distance between i and j (it only
depends on the angle between mu_j and r_ij).
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy)
<LI>gamma0 (degrees)
</UL>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-6"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This angle style can only be used if LAMMPS was built with the
USER-MISC package. See the <span class="xref std std-ref">Making LAMMPS</span>
section for more info on packages.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">In the &#8220;Angles&#8221; section of the data file, the atom ID
&#8216;j&#8217; corresponding to the dipole to restrain must come before the atom
ID of the reference atom &#8216;i&#8217;. A third atom ID &#8216;k&#8217; must also be
provided, although &#8216;k&#8217; is just a &#8216;dummy&#8217; atom which can be any atom;
it may be useful to choose a convention (e.g., &#8216;k&#8217;=&#8217;i&#8217;) and adhere to
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
USER-MISC package. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
section for more info on packages.
</P>
<P>IMPORTANT NOTE: In the "Angles" section of the data file, the atom ID
'j' corresponding to the dipole to restrain must come before the atom
ID of the reference atom 'i'. A third atom ID 'k' must also be
provided, although 'k' is just a 'dummy' atom which can be any atom;
it may be useful to choose a convention (e.g., 'k'='i') and adhere to
it. For example, if ID=1 for the dipolar atom to restrain, and ID=2
for the reference atom, the corresponding line in the &#8220;Angles&#8221; section
of the data file would read: X X 1 2 2</p>
</div>
<p>The &#8220;newton&#8221; command for intramolecular interactions must be &#8220;on&#8221;
(which is the default).</p>
<p>This angle style should not be used with SHAKE.</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 class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a>, <a class="reference internal" href="angle_hybrid.html"><em>angle_hybrid</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="orsi"><strong>(Orsi)</strong> Orsi &amp; Essex, The ELBA force field for coarse-grain modeling of
lipid membranes, PloS ONE 6(12): e28637, 2011.</p>
<p id="allen"><strong>(Allen)</strong> Allen &amp; Tildesley, Computer Simulation of Liquids,
Clarendon Press, Oxford, 1987.</p>
</div>
</div>
for the reference atom, the corresponding line in the "Angles" section
of the data file would read: X X 1 2 2
</P>
<P>The "newton" command for intramolecular interactions must be "on"
(which is the default).
</P>
<P>This angle style should not be used with SHAKE.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>, <A HREF = "angle_hybrid.html">angle_hybrid</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Orsi"></A>
</div>
</div>
<footer>
<P><B>(Orsi)</B> Orsi & Essex, The ELBA force field for coarse-grain modeling of
lipid membranes, PloS ONE 6(12): e28637, 2011.
</P>
<A NAME = "Allen"></A>
<hr/>
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<div class="section" id="angle-style-fourier-command">
<span id="index-0"></span><h1>angle_style fourier command<a class="headerlink" href="#angle-style-fourier-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="angle-style-fourier-omp-command">
<h1>angle_style fourier/omp command<a class="headerlink" href="#angle-style-fourier-omp-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>angle_style fourier
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<p>angle_style fourier
angle_coeff 75.0 1.0 1.0 1.0</p>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>fourier</em> angle style uses the potential</p>
<img alt="_images/angle_fourier.jpg" class="align-center" src="_images/angle_fourier.jpg" />
<p>The following coefficients must be defined for each angle type via the
<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li>K (energy)</li>
<li>C0 (real)</li>
<li>C1 (real)</li>
<li>C2 (real)</li>
</ul>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
<HR>
<H3>angle_style fourier command
</H3>
<H3>angle_style fourier/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style fourier
</PRE>
<P><B>Examples:</B>
</P>
<P>angle_style fourier
angle_coeff 75.0 1.0 1.0 1.0
</P>
<P><B>Description:</B>
</P>
<P>The <I>fourier</I> angle style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/angle_fourier.jpg">
</CENTER>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy)
<LI>C0 (real)
<LI>C1 (real)
<LI>C2 (real)
</UL>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This angle style can only be used if LAMMPS was built with the
USER_MISC package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info on packages.</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 class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
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<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
USER_MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B> none
</P>
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<div class="section" id="angle-style-fourier-simple-command">
<span id="index-0"></span><h1>angle_style fourier/simple command<a class="headerlink" href="#angle-style-fourier-simple-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="angle-style-fourier-simple-omp-command">
<h1>angle_style fourier/simple/omp command<a class="headerlink" href="#angle-style-fourier-simple-omp-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>angle_style fourier/simple
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<p>angle_style fourier/simple
angle_coeff 100.0 -1.0 1.0</p>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>fourier/simple</em> angle style uses the potential</p>
<img alt="_images/angle_fourier_simple.jpg" class="align-center" src="_images/angle_fourier_simple.jpg" />
<p>The following coefficients must be defined for each angle type via the
<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li>K (energy)</li>
<li>c (real)</li>
<li>n (real)</li>
</ul>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
<HR>
<H3>angle_style fourier/simple command
</H3>
<H3>angle_style fourier/simple/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style fourier/simple
</PRE>
<P><B>Examples:</B>
</P>
<P>angle_style fourier/simple
angle_coeff 100.0 -1.0 1.0
</P>
<P><B>Description:</B>
</P>
<P>The <I>fourier/simple</I> angle style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/angle_fourier_simple.jpg">
</CENTER>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy)
<LI>c (real)
<LI>n (real)
</UL>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This angle style can only be used if LAMMPS was built with the
USER_MISC package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info on packages.</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 class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<HR>
</div>
</div>
<footer>
<hr/>
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<p>
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<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
USER_MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

View File

@ -1,258 +1,84 @@
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<div class="section" id="angle-style-harmonic-command">
<span id="index-0"></span><h1>angle_style harmonic command<a class="headerlink" href="#angle-style-harmonic-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="angle-style-harmonic-kk-command">
<h1>angle_style harmonic/kk command<a class="headerlink" href="#angle-style-harmonic-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="angle-style-harmonic-omp-command">
<h1>angle_style harmonic/omp command<a class="headerlink" href="#angle-style-harmonic-omp-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>angle_style harmonic
</pre></div>
</div>
</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>angle_style harmonic
angle_coeff 1 300.0 107.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>harmonic</em> angle style uses the potential</p>
<img alt="_images/angle_harmonic.jpg" class="align-center" src="_images/angle_harmonic.jpg" />
<p>where theta0 is the equilibrium value of the angle, and K is a
prefactor. Note that the usual 1/2 factor is included in K.</p>
<p>The following coefficients must be defined for each angle type via the
<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li>K (energy/radian^2)</li>
<li>theta0 (degrees)</li>
</ul>
<p>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
<HR>
<H3>angle_style harmonic command
</H3>
<H3>angle_style harmonic/kk command
</H3>
<H3>angle_style harmonic/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style harmonic
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style harmonic
angle_coeff 1 300.0 107.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>harmonic</I> angle style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/angle_harmonic.jpg">
</CENTER>
<P>where theta0 is the equilibrium value of the angle, and K is a
prefactor. Note that the usual 1/2 factor is included in K.
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy/radian^2)
<LI>theta0 (degrees)
</UL>
<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<blockquote>
<div>none</div></blockquote>
<p>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info on packages.</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 class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<HR>
</div>
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<P><B>Restrictions:</B> none
</P>
<P>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

View File

@ -1,274 +1,96 @@
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<div class="section" id="angle-style-hybrid-command">
<span id="index-0"></span><h1>angle_style hybrid command<a class="headerlink" href="#angle-style-hybrid-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>angle_style hybrid style1 style2 ...
</pre></div>
</div>
<ul class="simple">
<li>style1,style2 = list of one or more angle styles</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>angle_style hybrid harmonic cosine
<HR>
<H3>angle_style hybrid command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style hybrid style1 style2 ...
</PRE>
<UL><LI>style1,style2 = list of one or more angle styles
</UL>
<P><B>Examples:</B>
</P>
<PRE>angle_style hybrid harmonic cosine
angle_coeff 1 harmonic 80.0 30.0
angle_coeff 2* cosine 50.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>hybrid</em> style enables the use of multiple angle styles in one
angle_coeff 2* cosine 50.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>hybrid</I> style enables the use of multiple angle styles in one
simulation. An angle style is assigned to each angle type. For
example, angles in a polymer flow (of angle type 1) could be computed
with a <em>harmonic</em> potential and angles in the wall boundary (of angle
type 2) could be computed with a <em>cosine</em> potential. The assignment
of angle type to style is made via the <a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a>
command or in the data file.</p>
<p>In the angle_coeff commands, the name of an angle style must be added
with a <I>harmonic</I> potential and angles in the wall boundary (of angle
type 2) could be computed with a <I>cosine</I> potential. The assignment
of angle type to style is made via the <A HREF = "angle_coeff.html">angle_coeff</A>
command or in the data file.
</P>
<P>In the angle_coeff commands, the name of an angle style must be added
after the angle type, with the remaining coefficients being those
appropriate to that style. In the example above, the 2 angle_coeff
commands set angles of angle type 1 to be computed with a <em>harmonic</em>
commands set angles of angle type 1 to be computed with a <I>harmonic</I>
potential with coefficients 80.0, 30.0 for K, theta0. All other angle
types (2-N) are computed with a <em>cosine</em> potential with coefficient
50.0 for K.</p>
<p>If angle coefficients are specified in the data file read via the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command, then the same rule applies.
E.g. &#8220;harmonic&#8221; or &#8220;cosine&#8221;, must be added after the angle type, for each
line in the &#8220;Angle Coeffs&#8221; section, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>Angle Coeffs
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>1 harmonic 80.0 30.0
types (2-N) are computed with a <I>cosine</I> potential with coefficient
50.0 for K.
</P>
<P>If angle coefficients are specified in the data file read via the
<A HREF = "read_data.html">read_data</A> command, then the same rule applies.
E.g. "harmonic" or "cosine", must be added after the angle type, for each
line in the "Angle Coeffs" section, e.g.
</P>
<PRE>Angle Coeffs
</PRE>
<PRE>1 harmonic 80.0 30.0
2 cosine 50.0
...
</pre></div>
</div>
<p>If <em>class2</em> is one of the angle hybrid styles, the same rule holds for
...
</PRE>
<P>If <I>class2</I> is one of the angle hybrid styles, the same rule holds for
specifying additional BondBond (and BondAngle) coefficients either via
the input script or in the data file. I.e. <em>class2</em> must be added to
the input script or in the data file. I.e. <I>class2</I> must be added to
each line after the angle type. For lines in the BondBond (or
BondAngle) section of the data file for angle types that are not
<em>class2</em>, you must use an angle style of <em>skip</em> as a placeholder, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>BondBond Coeffs
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>1 skip
<I>class2</I>, you must use an angle style of <I>skip</I> as a placeholder, e.g.
</P>
<PRE>BondBond Coeffs
</PRE>
<PRE>1 skip
2 class2 3.6512 1.0119 1.0119
...
</pre></div>
</div>
<p>Note that it is not necessary to use the angle style <em>skip</em> in the
...
</PRE>
<P>Note that it is not necessary to use the angle style <I>skip</I> in the
input script, since BondBond (or BondAngle) coefficients need not be
specified at all for angle types that are not <em>class2</em>.</p>
<p>An angle style of <em>none</em> with no additional coefficients can be used
specified at all for angle types that are not <I>class2</I>.
</P>
<P>An angle style of <I>none</I> with no additional coefficients can be used
in place of an angle style, either in a input script angle_coeff
command or in the data file, if you desire to turn off interactions
for specific angle types.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info on packages.</p>
<p>Unlike other angle styles, the hybrid angle style does not store angle
coefficient info for individual sub-styles in a <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. Thus when retarting a simulation from a restart
file, you need to re-specify angle_coeff commands.</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 class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
for specific angle types.
</P>
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<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P>Unlike other angle styles, the hybrid angle style does not store angle
coefficient info for individual sub-styles in a <A HREF = "restart.html">binary restart
files</A>. Thus when retarting a simulation from a restart
file, you need to re-specify angle_coeff commands.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B> none
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<span id="index-0"></span><h1>angle_style none command<a class="headerlink" href="#angle-style-none-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>angle_style none
</pre></div>
</div>
</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>angle_style none
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Using an angle style of none means angle forces are not computed, even
<HR>
<H3>angle_style none command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style none
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style none
</PRE>
<P><B>Description:</B>
</P>
<P>Using an angle style of none means angle forces are not computed, even
if triplets of angle atoms were listed in the data file read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<blockquote>
<div>none</div></blockquote>
<p><strong>Related commands:</strong> none</p>
<p><strong>Default:</strong> none</p>
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<A HREF = "read_data.html">read_data</A> command.
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<P><B>Related commands:</B> none
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<P><B>Default:</B> none
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<div class="section" id="angle-style-quartic-command">
<span id="index-0"></span><h1>angle_style quartic command<a class="headerlink" href="#angle-style-quartic-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="angle-style-quartic-omp-command">
<h1>angle_style quartic/omp command<a class="headerlink" href="#angle-style-quartic-omp-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>angle_style quartic
</pre></div>
</div>
</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>angle_style quartic
angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>quartic</em> angle style uses the potential</p>
<img alt="_images/angle_quartic.jpg" class="align-center" src="_images/angle_quartic.jpg" />
<p>where theta0 is the equilibrium value of the angle, and K is a
prefactor. Note that the usual 1/2 factor is included in K.</p>
<p>The following coefficients must be defined for each angle type via the
<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li>theta0 (degrees)</li>
<li>K2 (energy/radian^2)</li>
<li>K3 (energy/radian^3)</li>
<li>K4 (energy/radian^4)</li>
</ul>
<p>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
<HR>
<H3>angle_style quartic command
</H3>
<H3>angle_style quartic/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style quartic
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style quartic
angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>quartic</I> angle style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/angle_quartic.jpg">
</CENTER>
<P>where theta0 is the equilibrium value of the angle, and K is a
prefactor. Note that the usual 1/2 factor is included in K.
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>theta0 (degrees)
<LI>K2 (energy/radian^2)
<LI>K3 (energy/radian^3)
<LI>K4 (energy/radian^4)
</UL>
<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This angle style can only be used if LAMMPS was built with the
USER_MISC package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info on packages.</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 class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
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<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
USER_MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B> none
</P>
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<div class="section" id="angle-style-sdk-command">
<span id="index-0"></span><h1>angle_style sdk command<a class="headerlink" href="#angle-style-sdk-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>angle_style sdk
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>angle_style sdk/omp
</pre></div>
</div>
</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>angle_style sdk
angle_coeff 1 300.0 107.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>sdk</em> angle style is a combination of the harmonic angle potential,</p>
<img alt="_images/angle_harmonic.jpg" class="align-center" src="_images/angle_harmonic.jpg" />
<p>where theta0 is the equilibrium value of the angle and K a prefactor,
with the <em>repulsive</em> part of the non-bonded <em>lj/sdk</em> pair style
<HR>
<H3>angle_style sdk command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style sdk
</PRE>
<PRE>angle_style sdk/omp
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style sdk
angle_coeff 1 300.0 107.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>sdk</I> angle style is a combination of the harmonic angle potential,
</P>
<CENTER><IMG SRC = "Eqs/angle_harmonic.jpg">
</CENTER>
<P>where theta0 is the equilibrium value of the angle and K a prefactor,
with the <I>repulsive</I> part of the non-bonded <I>lj/sdk</I> pair style
between the atoms 1 and 3. This angle potential is intended for
coarse grained MD simulations with the CMM parametrization using the
<a class="reference internal" href="pair_sdk.html"><em>pair_style lj/sdk</em></a>. Relative to the pair_style
<em>lj/sdk</em>, however, the energy is shifted by <em>epsilon</em>, to avoid sudden
jumps. Note that the usual 1/2 factor is included in K.</p>
<p>The following coefficients must be defined for each angle type via the
<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in the example above:</p>
<ul class="simple">
<li>K (energy/radian^2)</li>
<li>theta0 (degrees)</li>
</ul>
<p>Theta0 is specified in degrees, but LAMMPS converts it to radians
<A HREF = "pair_sdk.html">pair_style lj/sdk</A>. Relative to the pair_style
<I>lj/sdk</I>, however, the energy is shifted by <I>epsilon</I>, to avoid sudden
jumps. Note that the usual 1/2 factor is included in K.
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above:
</P>
<UL><LI>K (energy/radian^2)
<LI>theta0 (degrees)
</UL>
<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
The also required <em>lj/sdk</em> parameters will be extracted automatically
from the pair_style.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This angle style can only be used if LAMMPS was built with the
USER-CG-CMM package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info on packages.</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 class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a>, <a class="reference internal" href="angle_harmonic.html"><em>angle_style harmonic</em></a>, <a class="reference internal" href="pair_sdk.html"><em>pair_style lj/sdk</em></a>,
<a class="reference internal" href="pair_sdk.html"><em>pair_style lj/sdk/coul/long</em></a></p>
<p><strong>Default:</strong> none</p>
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The also required <I>lj/sdk</I> parameters will be extracted automatically
from the pair_style.
</P>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
USER-CG-CMM package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>, <A HREF = "angle_harmonic.html">angle_style
harmonic</A>, <A HREF = "pair_sdk.html">pair_style lj/sdk</A>,
<A HREF = "pair_sdk.html">pair_style lj/sdk/coul/long</A>
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<P><B>Default:</B> none
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<div class="section" id="angle-style-command">
<span id="index-0"></span><h1>angle_style command<a class="headerlink" href="#angle-style-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>angle_style style
</pre></div>
</div>
<ul class="simple">
<li>style = <em>none</em> or <em>hybrid</em> or <em>charmm</em> or <em>class2</em> or <em>cosine</em> or <em>cosine/squared</em> or <em>harmonic</em></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>angle_style harmonic
<HR>
<H3>angle_style command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style style
</PRE>
<UL><LI>style = <I>none</I> or <I>hybrid</I> or <I>charmm</I> or <I>class2</I> or <I>cosine</I> or <I>cosine/squared</I> or <I>harmonic</I>
</UL>
<P><B>Examples:</B>
</P>
<PRE>angle_style harmonic
angle_style charmm
angle_style hybrid harmonic cosine
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Set the formula(s) LAMMPS uses to compute angle interactions between
angle_style hybrid harmonic cosine
</PRE>
<P><B>Description:</B>
</P>
<P>Set the formula(s) LAMMPS uses to compute angle interactions between
triplets of atoms, which remain in force for the duration of the
simulation. The list of angle triplets is read in by a
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command
from a data or restart file.</p>
<p>Hybrid models where angles are computed using different angle
potentials can be setup using the <em>hybrid</em> angle style.</p>
<p>The coefficients associated with a angle style can be specified in a
data or restart file or via the <a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command.</p>
<p>All angle potentials store their coefficient data in binary restart
files which means angle_style and <a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a>
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A> command
from a data or restart file.
</P>
<P>Hybrid models where angles are computed using different angle
potentials can be setup using the <I>hybrid</I> angle style.
</P>
<P>The coefficients associated with a angle style can be specified in a
data or restart file or via the <A HREF = "angle_coeff.html">angle_coeff</A> command.
</P>
<P>All angle potentials store their coefficient data in binary restart
files which means angle_style and <A HREF = "angle_coeff.html">angle_coeff</A>
commands do not need to be re-specified in an input script that
restarts a simulation. See the <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
restarts a simulation. See the <A HREF = "read_restart.html">read_restart</A>
command for details on how to do this. The one exception is that
angle_style <em>hybrid</em> only stores the list of sub-styles in the restart
file; angle coefficients need to be re-specified.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">When both an angle and pair style is defined, the
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command often needs to be used to
angle_style <I>hybrid</I> only stores the list of sub-styles in the restart
file; angle coefficients need to be re-specified.
</P>
<P>IMPORTANT NOTE: When both an angle and pair style is defined, the
<A HREF = "special_bonds.html">special_bonds</A> command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
exist between 3 bonded atoms.</p>
</div>
<p>In the formulas listed for each angle style, <em>theta</em> is the angle
between the 3 atoms in the angle.</p>
<hr class="docutils" />
<p>Here is an alphabetic list of angle styles defined in LAMMPS. Click on
exist between 3 bonded atoms.
</P>
<P>In the formulas listed for each angle style, <I>theta</I> is the angle
between the 3 atoms in the angle.
</P>
<HR>
<P>Here is an alphabetic list of angle styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated <a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command.</p>
<p>Note that there are also additional angle styles submitted by users
specified by the associated <A HREF = "angle_coeff.html">angle_coeff</A> command.
</P>
<P>Note that there are also additional angle styles submitted by users
which are included in the LAMMPS distribution. The list of these with
links to the individual styles are given in the angle section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
<ul class="simple">
<li><a class="reference internal" href="angle_none.html"><em>angle_style none</em></a> - turn off angle interactions</li>
<li><a class="reference internal" href="angle_hybrid.html"><em>angle_style hybrid</em></a> - define multiple styles of angle interactions</li>
<li><a class="reference internal" href="angle_charmm.html"><em>angle_style charmm</em></a> - CHARMM angle</li>
<li><a class="reference internal" href="angle_class2.html"><em>angle_style class2</em></a> - COMPASS (class 2) angle</li>
<li><a class="reference internal" href="angle_cosine.html"><em>angle_style cosine</em></a> - cosine angle potential</li>
<li><a class="reference internal" href="angle_cosine_delta.html"><em>angle_style cosine/delta</em></a> - difference of cosines angle potential</li>
<li><a class="reference internal" href="angle_cosine_periodic.html"><em>angle_style cosine/periodic</em></a> - DREIDING angle</li>
<li><a class="reference internal" href="angle_cosine_squared.html"><em>angle_style cosine/squared</em></a> - cosine squared angle potential</li>
<li><a class="reference internal" href="angle_harmonic.html"><em>angle_style harmonic</em></a> - harmonic angle</li>
<li><a class="reference internal" href="angle_table.html"><em>angle_style table</em></a> - tabulated by angle</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>Angle styles can only be set for atom_styles that allow angles to be
defined.</p>
<p>Most angle styles are part of the MOLECULE package. They are 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 on packages.
links to the individual styles are given in the angle section of <A HREF = "Section_commands.html#cmd_5">this
page</A>.
</P>
<UL><LI><A HREF = "angle_none.html">angle_style none</A> - turn off angle interactions
<LI><A HREF = "angle_hybrid.html">angle_style hybrid</A> - define multiple styles of angle interactions
</UL>
<UL><LI><A HREF = "angle_charmm.html">angle_style charmm</A> - CHARMM angle
<LI><A HREF = "angle_class2.html">angle_style class2</A> - COMPASS (class 2) angle
<LI><A HREF = "angle_cosine.html">angle_style cosine</A> - cosine angle potential
<LI><A HREF = "angle_cosine_delta.html">angle_style cosine/delta</A> - difference of cosines angle potential
<LI><A HREF = "angle_cosine_periodic.html">angle_style cosine/periodic</A> - DREIDING angle
<LI><A HREF = "angle_cosine_squared.html">angle_style cosine/squared</A> - cosine squared angle potential
<LI><A HREF = "angle_harmonic.html">angle_style harmonic</A> - harmonic angle
<LI><A HREF = "angle_table.html">angle_style table</A> - tabulated by angle
</UL>
<HR>
<P><B>Restrictions:</B>
</P>
<P>Angle styles can only be set for atom_styles that allow angles to be
defined.
</P>
<P>Most angle styles are part of the MOLECULE package. They are only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
The doc pages for individual bond potentials tell if it is part of a
package.</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 class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>angle_style none
</pre></div>
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package.
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<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B>
</P>
<PRE>angle_style none
</PRE>
</HTML>

View File

@ -1,206 +1,91 @@
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<div class="section" id="angle-style-table-command">
<span id="index-0"></span><h1>angle_style table command<a class="headerlink" href="#angle-style-table-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="angle-style-table-omp-command">
<h1>angle_style table/omp command<a class="headerlink" href="#angle-style-table-omp-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>angle_style table style N
</pre></div>
</div>
<ul class="simple">
<li>style = <em>linear</em> or <em>spline</em> = method of interpolation</li>
<li>N = use N values in table</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>angle_style table linear 1000
angle_coeff 3 file.table ENTRY1
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>table</em> creates interpolation tables of length <em>N</em> from angle
<HR>
<H3>angle_style table command
</H3>
<H3>angle_style table/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style table style N
</PRE>
<UL><LI>style = <I>linear</I> or <I>spline</I> = method of interpolation
<LI>N = use N values in table
</UL>
<P><B>Examples:</B>
</P>
<PRE>angle_style table linear 1000
angle_coeff 3 file.table ENTRY1
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>table</I> creates interpolation tables of length <I>N</I> from angle
potential and derivative values listed in a file(s) as a function of
angle The files are read by the <a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a>
command.</p>
<p>The interpolation tables are created by fitting cubic splines to the
angle The files are read by the <A HREF = "angle_coeff.html">angle_coeff</A>
command.
</P>
<P>The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy and derivative values at each of
<em>N</em> angles. During a simulation, these tables are used to interpolate
<I>N</I> angles. During a simulation, these tables are used to interpolate
energy and force values on individual atoms as needed. The
interpolation is done in one of 2 styles: <em>linear</em> or <em>spline</em>.</p>
<p>For the <em>linear</em> style, the angle is used to find 2 surrounding table
interpolation is done in one of 2 styles: <I>linear</I> or <I>spline</I>.
</P>
<P>For the <I>linear</I> style, the angle is used to find 2 surrounding table
values from which an energy or its derivative is computed by linear
interpolation.</p>
<p>For the <em>spline</em> style, a cubic spline coefficients are computed and
stored at each of the <em>N</em> values in the table. The angle is used to
interpolation.
</P>
<P>For the <I>spline</I> style, a cubic spline coefficients are computed and
stored at each of the <I>N</I> values in the table. The angle is used to
find the appropriate set of coefficients which are used to evaluate a
cubic polynomial which computes the energy or derivative.</p>
<p>The following coefficients must be defined for each angle type via the
<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in the example above.</p>
<ul class="simple">
<li>filename</li>
<li>keyword</li>
</ul>
<p>The filename specifies a file containing tabulated energy and
cubic polynomial which computes the energy or derivative.
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above.
</P>
<UL><LI>filename
<LI>keyword
</UL>
<P>The filename specifies a file containing tabulated energy and
derivative values. The keyword specifies a section of the file. The
format of this file is described below.</p>
<hr class="docutils" />
<p>The format of a tabulated file is as follows (without the
parenthesized comments):</p>
<div class="highlight-python"><div class="highlight"><pre><span class="c"># Angle potential for harmonic (one or more comment or blank lines)</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>HAM (keyword is the first text on line)
format of this file is described below.
</P>
<HR>
<P>The format of a tabulated file is as follows (without the
parenthesized comments):
</P>
<PRE># Angle potential for harmonic (one or more comment or blank lines)
</PRE>
<PRE>HAM (keyword is the first text on line)
N 181 FP 0 0 EQ 90.0 (N, FP, EQ parameters)
(blank line)
N 181 FP 0 0 (N, FP parameters)
1 0.0 200.5 2.5 (index, angle, energy, derivative)
2 1.0 198.0 2.5
...
181 180.0 0.0 0.0
</pre></div>
</div>
<p>A section begins with a non-blank line whose 1st character is not a
&#8220;#&#8221;; blank lines or lines starting with &#8220;#&#8221; can be used as comments
181 180.0 0.0 0.0
</PRE>
<P>A section begins with a non-blank line whose 1st character is not a
"#"; blank lines or lines starting with "#" can be used as comments
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
initial text must match the argument specified in the
<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command. The next line lists (in any
<A HREF = "angle_coeff.html">angle_coeff</A> command. The next line lists (in any
order) one or more parameters for the table. Each parameter is a
keyword followed by one or more numeric values.</p>
<p>The parameter &#8220;N&#8221; is required and its value is the number of table
entries that follow. Note that this may be different than the <em>N</em>
specified in the <a class="reference internal" href="angle_style.html"><em>angle_style table</em></a> command. Let
Ntable = <em>N</em> in the angle_style command, and Nfile = &#8220;N&#8221; in the
keyword followed by one or more numeric values.
</P>
<P>The parameter "N" is required and its value is the number of table
entries that follow. Note that this may be different than the <I>N</I>
specified in the <A HREF = "angle_style.html">angle_style table</A> command. Let
Ntable = <I>N</I> in the angle_style command, and Nfile = "N" in the
tabulated file. What LAMMPS does is a preliminary interpolation by
creating splines using the Nfile tabulated values as nodal points. It
uses these to interpolate as needed to generate energy and derivative
@ -209,17 +94,21 @@ Ntable are then used as described above, when computing energy and
force for individual angles and their atoms. This means that if you
want the interpolation tables of length Ntable to match exactly what
is in the tabulated file (with effectively no preliminary
interpolation), you should set Ntable = Nfile.</p>
<p>The &#8220;FP&#8221; parameter is optional. If used, it is followed by two values
interpolation), you should set Ntable = Nfile.
</P>
<P>The "FP" parameter is optional. If used, it is followed by two values
fplo and fphi, which are the 2nd derivatives at the innermost and
outermost angle settings. These values are needed by the spline
construction routines. If not specified by the &#8220;FP&#8221; parameter, they
construction routines. If not specified by the "FP" parameter, they
are estimated (less accurately) by the first two and last two
derivative values in the table.</p>
<p>The &#8220;EQ&#8221; parameter is also optional. If used, it is followed by a the
equilibrium angle value, which is used, for example, by the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command. If not used, the equilibrium angle is
set to 180.0.</p>
<p>Following a blank line, the next N lines list the tabulated values.
derivative values in the table.
</P>
<P>The "EQ" parameter is also optional. If used, it is followed by a the
equilibrium angle value, which is used, for example, by the <A HREF = "fix_shake.html">fix
shake</A> command. If not used, the equilibrium angle is
set to 180.0.
</P>
<P>Following a blank line, the next N lines list the tabulated values.
On each line, the 1st value is the index from 1 to N, the 2nd value is
the angle value (in degrees), the 3rd value is the energy (in energy
units), and the 4th is -dE/d(theta) (also in energy units). The 3rd
@ -228,100 +117,47 @@ angle. The last term is the derivative of the energy with respect to
the angle (in degrees, not radians). Thus the units of the last term
are still energy, not force. The angle values must increase from one
line to the next. The angle values must also begin with 0.0 and end
with 180.0, i.e. span the full range of possible angles.</p>
<p>Note that one file can contain many sections, each with a tabulated
with 180.0, i.e. span the full range of possible angles.
</P>
<P>Note that one file can contain many sections, each with a tabulated
potential. LAMMPS reads the file section by section until it finds
one that matches the specified keyword.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
one that matches the specified keyword.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info on packages.</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 class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
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<P><B>Restrictions:</B>
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<P>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
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<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B> none
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<div class="section" id="atom-modify-command">
<span id="index-0"></span><h1>atom_modify command<a class="headerlink" href="#atom-modify-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>atom_modify keyword values ...
</pre></div>
</div>
<ul class="simple">
<li>one or more keyword/value pairs may be appended</li>
<li>keyword = <em>id</em> or <em>map</em> or <em>first</em> or <em>sort</em></li>
</ul>
<pre class="literal-block">
<em>id</em> value = <em>yes</em> or <em>no</em>
<em>map</em> value = <em>array</em> or <em>hash</em>
<em>first</em> value = group-ID = group whose atoms will appear first in internal atom lists
<em>sort</em> values = Nfreq binsize
<HR>
<H3>atom_modify command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>atom_modify keyword values ...
</PRE>
<UL><LI>one or more keyword/value pairs may be appended
<LI>keyword = <I>id</I> or <I>map</I> or <I>first</I> or <I>sort</I>
<PRE> <I>id</I> value = <I>yes</I> or <I>no</I>
<I>map</I> value = <I>array</I> or <I>hash</I>
<I>first</I> value = group-ID = group whose atoms will appear first in internal atom lists
<I>sort</I> values = Nfreq binsize
Nfreq = sort atoms spatially every this many time steps
binsize = bin size for spatial sorting (distance units)
</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>atom_modify map hash
binsize = bin size for spatial sorting (distance units)
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>atom_modify map hash
atom_modify map array sort 10000 2.0
atom_modify first colloid
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Modify certain attributes of atoms defined and stored within LAMMPS,
in addition to what is specified by the <a class="reference internal" href="atom_style.html"><em>atom_style</em></a>
command. The <em>id</em> and <em>map</em> keywords must be specified before a
simulation box is defined; other keywords can be specified any time.</p>
<p>The <em>id</em> keyword determines whether non-zero atom IDs can be assigned
to each atom. If the value is <em>yes</em>, which is the default, IDs are
assigned, whether you use the <a class="reference internal" href="create_atoms.html"><em>create atoms</em></a> or
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands to initialize atoms. If the value is <em>no</em> the IDs for all
atoms are assumed to be 0.</p>
<p>If atom IDs are used, they must all be positive integers. They should
atom_modify first colloid
</PRE>
<P><B>Description:</B>
</P>
<P>Modify certain attributes of atoms defined and stored within LAMMPS,
in addition to what is specified by the <A HREF = "atom_style.html">atom_style</A>
command. The <I>id</I> and <I>map</I> keywords must be specified before a
simulation box is defined; other keywords can be specified any time.
</P>
<P>The <I>id</I> keyword determines whether non-zero atom IDs can be assigned
to each atom. If the value is <I>yes</I>, which is the default, IDs are
assigned, whether you use the <A HREF = "create_atoms.html">create atoms</A> or
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands to initialize atoms. If the value is <I>no</I> the IDs for all
atoms are assumed to be 0.
</P>
<P>If atom IDs are used, they must all be positive integers. They should
also be unique, though LAMMPS does not check for this. Typically they
should also be consecutively numbered (from 1 to Natoms), though this
is not required. Molecular <a class="reference internal" href="atom_style.html"><em>atom styles</em></a> are those
is not required. Molecular <A HREF = "atom_style.html">atom styles</A> are those
that store bond topology information (styles bond, angle, molecular,
full). These styles require atom IDs since the IDs are used to encode
the topology. Some other LAMMPS commands also require the use of atom
IDs. E.g. some many-body pair styles use them to avoid double
computation of the I-J interaction between two atoms.</p>
<p>The only reason not to use atom IDs is if you are running an atomic
computation of the I-J interaction between two atoms.
</P>
<P>The only reason not to use atom IDs is if you are running an atomic
simulation so large that IDs cannot be uniquely assigned. For a
default LAMMPS build this limit is 2^31 or about 2 billion atoms.
However, even in this case, you can use 64-bit atom IDs, allowing 2^63
or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG
switch. This is described in <a class="reference internal" href="Section_start.html#start-2"><span>Section 2.2</span></a>
switch. This is described in <A HREF = "Section_start.html#start_2">Section 2.2</A>
of the manual. If atom IDs are not used, they must be specified as 0
for all atoms, e.g. in a data or restart file.</p>
<p>The <em>map</em> keyword determines how atom ID lookup is done for molecular
for all atoms, e.g. in a data or restart file.
</P>
<P>The <I>map</I> keyword determines how atom ID lookup is done for molecular
atom styles. Lookups are performed by bond (angle, etc) routines in
LAMMPS to find the local atom index associated with a global atom ID.</p>
<p>When the <em>array</em> value is used, each processor stores a lookup table
LAMMPS to find the local atom index associated with a global atom ID.
</P>
<P>When the <I>array</I> value is used, each processor stores a lookup table
of length N, where N is the largest atom ID in the system. This is a
fast, simple method for many simulations, but requires too much memory
for large simulations. The <em>hash</em> value uses a hash table to perform
the lookups. This can be slightly slower than the <em>array</em> method, but
for large simulations. The <I>hash</I> value uses a hash table to perform
the lookups. This can be slightly slower than the <I>array</I> method, but
its memory cost is proportional to the number of atoms owned by a
processor, i.e. N/P when N is the total number of atoms in the system
and P is the number of processors.</p>
<p>When this setting is not specified in your input script, LAMMPS
and P is the number of processors.
</P>
<P>When this setting is not specified in your input script, LAMMPS
creates a map, if one is needed, as an array or hash. See the
discussion of default values below for how LAMMPS chooses which kind
of map to build. Note that atomic systems do not normally need to
create a map. However, even in this case some LAMMPS commands will
create a map to find atoms (and then destroy it), or require a
permanent map. An example of the former is the <a class="reference internal" href="velocity.html"><em>velocity loop all</em></a> command, which uses a map when looping over all
permanent map. An example of the former is the <A HREF = "velocity.html">velocity loop
all</A> command, which uses a map when looping over all
atoms and insuring the same velocity values are assigned to an atom
ID, no matter which processor owns it.</p>
<p>The <em>first</em> keyword allows a <a class="reference internal" href="group.html"><em>group</em></a> to be specified whose
atoms will be maintained as the first atoms in each processor&#8217;s list
ID, no matter which processor owns it.
</P>
<P>The <I>first</I> keyword allows a <A HREF = "group.html">group</A> to be specified whose
atoms will be maintained as the first atoms in each processor's list
of owned atoms. This in only useful when the specified group is a
small fraction of all the atoms, and there are other operations LAMMPS
is performing that will be sped-up significantly by being able to loop
over the smaller set of atoms. Otherwise the reordering required by
this option will be a net slow-down. The <a class="reference internal" href="neigh_modify.html"><em>neigh_modify include</em></a> and <a class="reference internal" href="comm_modify.html"><em>comm_modify group</em></a>
this option will be a net slow-down. The <A HREF = "neigh_modify.html">neigh_modify
include</A> and <A HREF = "comm_modify.html">comm_modify group</A>
commands are two examples of commands that require this setting to
work efficiently. Several <a class="reference internal" href="fix.html"><em>fixes</em></a>, most notably time
integration fixes like <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a>, also take advantage of
work efficiently. Several <A HREF = "fix.html">fixes</A>, most notably time
integration fixes like <A HREF = "fix_nve.html">fix nve</A>, also take advantage of
this setting if the group they operate on is the group specified by
this command. Note that specifying &#8220;all&#8221; as the group-ID effectively
turns off the <em>first</em> option.</p>
<p>It is OK to use the <em>first</em> keyword with a group that has not yet been
this command. Note that specifying "all" as the group-ID effectively
turns off the <I>first</I> option.
</P>
<P>It is OK to use the <I>first</I> keyword with a group that has not yet been
defined, e.g. to use the atom_modify first command at the beginning of
your input script. LAMMPS does not use the group until a simullation
is run.</p>
<p>The <em>sort</em> keyword turns on a spatial sorting or reordering of atoms
within each processor&#8217;s sub-domain every <em>Nfreq</em> timesteps. If
<em>Nfreq</em> is set to 0, then sorting is turned off. Sorting can improve
is run.
</P>
<P>The <I>sort</I> keyword turns on a spatial sorting or reordering of atoms
within each processor's sub-domain every <I>Nfreq</I> timesteps. If
<I>Nfreq</I> is set to 0, then sorting is turned off. Sorting can improve
cache performance and thus speed-up a LAMMPS simulation, as discussed
in a paper by <a class="reference internal" href="#meloni"><span>(Meloni)</span></a>. Its efficacy depends on the problem
in a paper by <A HREF = "#Meloni">(Meloni)</A>. Its efficacy depends on the problem
size (atoms/processor), how quickly the system becomes disordered, and
various other factors. As a general rule, sorting is typically more
effective at speeding up simulations of liquids as opposed to solids.
In tests we have done, the speed-up can range from zero to 3-4x.</p>
<p>Reordering is peformed every <em>Nfreq</em> timesteps during a dynamics run
In tests we have done, the speed-up can range from zero to 3-4x.
</P>
<P>Reordering is peformed every <I>Nfreq</I> timesteps during a dynamics run
or iterations during a minimization. More precisely, reordering
occurs at the first reneighboring that occurs after the target
timestep. The reordering is performed locally by each processor,
using bins of the specified <em>binsize</em>. If <em>binsize</em> is set to 0.0,
then a binsize equal to half the <a class="reference internal" href="neighbor.html"><em>neighbor</em></a> cutoff
using bins of the specified <I>binsize</I>. If <I>binsize</I> is set to 0.0,
then a binsize equal to half the <A HREF = "neighbor.html">neighbor</A> cutoff
distance (force cutoff plus skin distance) is used, which is a
reasonable value. After the atoms have been binned, they are
reordered so that atoms in the same bin are adjacent to each other in
the processor&#8217;s 1d list of atoms.</p>
<p>The goal of this procedure is for atoms to put atoms close to each
other in the processor&#8217;s one-dimensional list of atoms that are also
the processor's 1d list of atoms.
</P>
<P>The goal of this procedure is for atoms to put atoms close to each
other in the processor's one-dimensional list of atoms that are also
near to each other spatially. This can improve cache performance when
pairwise intereractions and neighbor lists are computed. Note that if
bins are too small, there will be few atoms/bin. Likewise if bins are
too large, there will be many atoms/bin. In both cases, the goal of
cache locality will be undermined.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Running a simulation with sorting on versus off should
cache locality will be undermined.
</P>
<P>IMPORTANT NOTE: Running a simulation with sorting on versus off should
not change the simulation results in a statistical sense. However, a
different ordering will induce round-off differences, which will lead
to diverging trajectories over time when comparing two simluations.
Various commands, particularly those which use random numbers
(e.g. <a class="reference internal" href="velocity.html"><em>velocity create</em></a>, and <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a>), may generate (statistically identical)
(e.g. <A HREF = "velocity.html">velocity create</A>, and <A HREF = "fix_langevin.html">fix
langevin</A>), may generate (statistically identical)
results which depend on the order in which atoms are processed. The
order of atoms in a <a class="reference internal" href="dump.html"><em>dump</em></a> file will also typically change
if sorting is enabled.</p>
</div>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>The <em>first</em> and <em>sort</em> options cannot be used together. Since sorting
is on by default, it will be turned off if the <em>first</em> keyword is
used with a group-ID that is not &#8220;all&#8221;.</p>
<p><strong>Related commands:</strong> none</p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>By default, <em>id</em> is yes. By default, atomic systems (no bond topology
info) do not use a map. For molecular systems (with bond topology
info), a map is used. The default map style is array if no atom ID is
larger than 1 million, otherwise the default is hash. By default, a
&#8220;first&#8221; group is not defined. By default, sorting is enabled with a
frequency of 1000 and a binsize of 0.0, which means the neighbor
cutoff will be used to set the bin size.</p>
<hr class="docutils" />
<p id="meloni"><strong>(Meloni)</strong> Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007).</p>
</div>
</div>
order of atoms in a <A HREF = "dump.html">dump</A> file will also typically change
if sorting is enabled.
</P>
<P><B>Restrictions:</B>
</P>
<P>The <I>first</I> and <I>sort</I> options cannot be used together. Since sorting
is on by default, it will be turned off if the <I>first</I> keyword is
used with a group-ID that is not "all".
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B>
</P>
<P>By default, <I>id</I> is yes. By default, atomic systems (no bond topology
info) do not use a map. For molecular systems (with bond topology
info), a map is used. The default map style is array if no atom ID is
larger than 1 million, otherwise the default is hash. By default, a
"first" group is not defined. By default, sorting is enabled with a
frequency of 1000 and a binsize of 0.0, which means the neighbor
cutoff will be used to set the bin size.
</P>
<HR>
<A NAME = "Meloni"></A>
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<P><B>(Meloni)</B> Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007).
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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>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<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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<div class="section" id="atom-style-command">
<span id="index-0"></span><h1>atom_style command<a class="headerlink" href="#atom-style-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>atom_style style args
</pre></div>
</div>
<ul class="simple">
<li>style = <em>angle</em> or <em>atomic</em> or <em>body</em> or <em>bond</em> or <em>charge</em> or <em>dipole</em> or <em>electron</em> or <em>ellipsoid</em> or <em>full</em> or <em>line</em> or <em>meso</em> or <em>molecular</em> or <em>peri</em> or <em>sphere</em> or <em>tri</em> or <em>template</em> or <em>hybrid</em></li>
</ul>
<pre class="literal-block">
args = none for any style except <em>body</em> and <em>hybrid</em>
<em>body</em> args = bstyle bstyle-args
<HR>
<H3>atom_style command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>atom_style style args
</PRE>
<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>body</I> or <I>bond</I> or <I>charge</I> or <I>dipole</I> or <I>electron</I> or <I>ellipsoid</I> or <I>full</I> or <I>line</I> or <I>meso</I> or <I>molecular</I> or <I>peri</I> or <I>sphere</I> or <I>tri</I> or <I>template</I> or <I>hybrid</I>
<PRE> args = none for any style except <I>body</I> and <I>hybrid</I>
<I>body</I> args = bstyle bstyle-args
bstyle = style of body particles
bstyle-args = additional arguments specific to the bstyle
see the <a class="reference internal" href="body.html"><em>body</em></a> doc page for details
<em>template</em> args = template-ID
template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><em>molecule</em></a> command
<em>hybrid</em> args = list of one or more sub-styles, each with their args
</pre>
<ul class="simple">
<li>accelerated styles (with same args) = <em>angle/cuda</em> or <em>angle/kk</em> or <em>atomic/cuda</em> or <em>atomic/kk</em> or <em>bond/kk</em> or <em>charge/cuda</em> or <em>charge/kk</em> or <em>full/cuda</em> or <em>full/kk</em> or <em>molecular/kk</em></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>atom_style atomic
see the <A HREF = "body.html">body</A> doc page for details
<I>template</I> args = template-ID
template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
<I>hybrid</I> args = list of one or more sub-styles, each with their args
</PRE>
<LI>accelerated styles (with same args) = <I>angle/cuda</I> or <I>angle/kk</I> or <I>atomic/cuda</I> or <I>atomic/kk</I> or <I>bond/kk</I> or <I>charge/cuda</I> or <I>charge/kk</I> or <I>full/cuda</I> or <I>full/kk</I> or <I>molecular/kk</I>
</UL>
<P><B>Examples:</B>
</P>
<PRE>atom_style atomic
atom_style bond
atom_style full
atom_style full/cuda
atom_style body nparticle 2 10
atom_style hybrid charge bond
atom_style hybrid charge body nparticle 2 5
atom_style template myMols
</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 what style of atoms to use in a simulation. This determines
atom_style template myMols
</PRE>
<P><B>Description:</B>
</P>
<P>Define what style of atoms to use in a simulation. This determines
what attributes are associated with the atoms. This command must be
used before a simulation is setup via a <a class="reference internal" href="read_data.html"><em>read_data</em></a>,
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a>, or <a class="reference internal" href="create_box.html"><em>create_box</em></a>
command.</p>
<p>Once a style is assigned, it cannot be changed, so use a style general
enough to encompass all attributes. E.g. with style <em>bond</em>, angular
used before a simulation is setup via a <A HREF = "read_data.html">read_data</A>,
<A HREF = "read_restart.html">read_restart</A>, or <A HREF = "create_box.html">create_box</A>
command.
</P>
<P>Once a style is assigned, it cannot be changed, so use a style general
enough to encompass all attributes. E.g. with style <I>bond</I>, angular
terms cannot be used or added later to the model. It is OK to use a
style more general than needed, though it may be slightly inefficient.</p>
<p>The choice of style affects what quantities are stored by each atom,
style more general than needed, though it may be slightly inefficient.
</P>
<P>The choice of style affects what quantities are stored by each atom,
what quantities are communicated between processors to enable forces
to be computed, and what quantities are listed in the data file read
by the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command.</p>
<p>These are the additional attributes of each style and the typical
by the <A HREF = "read_data.html">read_data</A> command.
</P>
<P>These are the additional attributes of each style and the typical
kinds of physical systems they are used to model. All styles store
coordinates, velocities, atom IDs and types. See the
<a class="reference internal" href="read_data.html"><em>read_data</em></a>, <a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a>, and
<a class="reference internal" href="set.html"><em>set</em></a> commands for info on how to set these various
quantities.</p>
<table border="1" class="docutils">
<colgroup>
<col width="13%" />
<col width="50%" />
<col width="36%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><em>angle</em></td>
<td>bonds and angles</td>
<td>bead-spring polymers with stiffness</td>
</tr>
<tr class="row-even"><td><em>atomic</em></td>
<td>only the default values</td>
<td>coarse-grain liquids, solids, metals</td>
</tr>
<tr class="row-odd"><td><em>body</em></td>
<td>mass, inertia moments, quaternion, angular momentum</td>
<td>arbitrary bodies</td>
</tr>
<tr class="row-even"><td><em>bond</em></td>
<td>bonds</td>
<td>bead-spring polymers</td>
</tr>
<tr class="row-odd"><td><em>charge</em></td>
<td>charge</td>
<td>atomic system with charges</td>
</tr>
<tr class="row-even"><td><em>dipole</em></td>
<td>charge and dipole moment</td>
<td>system with dipolar particles</td>
</tr>
<tr class="row-odd"><td><em>electron</em></td>
<td>charge and spin and eradius</td>
<td>electronic force field</td>
</tr>
<tr class="row-even"><td><em>ellipsoid</em></td>
<td>shape, quaternion, angular momentum</td>
<td>aspherical particles</td>
</tr>
<tr class="row-odd"><td><em>full</em></td>
<td>molecular + charge</td>
<td>bio-molecules</td>
</tr>
<tr class="row-even"><td><em>line</em></td>
<td>end points, angular velocity</td>
<td>rigid bodies</td>
</tr>
<tr class="row-odd"><td><em>meso</em></td>
<td>rho, e, cv</td>
<td>SPH particles</td>
</tr>
<tr class="row-even"><td><em>molecular</em></td>
<td>bonds, angles, dihedrals, impropers</td>
<td>uncharged molecules</td>
</tr>
<tr class="row-odd"><td><em>peri</em></td>
<td>mass, volume</td>
<td>mesocopic Peridynamic models</td>
</tr>
<tr class="row-even"><td><em>sphere</em></td>
<td>diameter, mass, angular velocity</td>
<td>granular models</td>
</tr>
<tr class="row-odd"><td><em>template</em></td>
<td>template index, template atom</td>
<td>small molecules with fixed topology</td>
</tr>
<tr class="row-even"><td><em>tri</em></td>
<td>corner points, angular momentum</td>
<td>rigid bodies</td>
</tr>
<tr class="row-odd"><td><em>wavepacket</em></td>
<td>charge, spin, eradius, etag, cs_re, cs_im</td>
<td>AWPMD</td>
</tr>
</tbody>
</table>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">It is possible to add some attributes, such as a
molecule ID, to atom styles that do not have them via the <a class="reference internal" href="fix_property_atom.html"><em>fix property/atom</em></a> command. This command also
<A HREF = "read_data.html">read_data</A>, <A HREF = "create_atoms.html">create_atoms</A>, and
<A HREF = "set.html">set</A> commands for info on how to set these various
quantities.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD ><I>angle</I> </TD><TD > bonds and angles </TD><TD > bead-spring polymers with stiffness </TD></TR>
<TR><TD ><I>atomic</I> </TD><TD > only the default values </TD><TD > coarse-grain liquids, solids, metals </TD></TR>
<TR><TD ><I>body</I> </TD><TD > mass, inertia moments, quaternion, angular momentum </TD><TD > arbitrary bodies </TD></TR>
<TR><TD ><I>bond</I> </TD><TD > bonds </TD><TD > bead-spring polymers </TD></TR>
<TR><TD ><I>charge</I> </TD><TD > charge </TD><TD > atomic system with charges </TD></TR>
<TR><TD ><I>dipole</I> </TD><TD > charge and dipole moment </TD><TD > system with dipolar particles </TD></TR>
<TR><TD ><I>electron</I> </TD><TD > charge and spin and eradius </TD><TD > electronic force field </TD></TR>
<TR><TD ><I>ellipsoid</I> </TD><TD > shape, quaternion, angular momentum </TD><TD > aspherical particles </TD></TR>
<TR><TD ><I>full</I> </TD><TD > molecular + charge </TD><TD > bio-molecules </TD></TR>
<TR><TD ><I>line</I> </TD><TD > end points, angular velocity </TD><TD > rigid bodies </TD></TR>
<TR><TD ><I>meso</I> </TD><TD > rho, e, cv </TD><TD > SPH particles </TD></TR>
<TR><TD ><I>molecular</I> </TD><TD > bonds, angles, dihedrals, impropers </TD><TD > uncharged molecules </TD></TR>
<TR><TD ><I>peri</I> </TD><TD > mass, volume </TD><TD > mesocopic Peridynamic models </TD></TR>
<TR><TD ><I>sphere</I> </TD><TD > diameter, mass, angular velocity </TD><TD > granular models </TD></TR>
<TR><TD ><I>template</I> </TD><TD > template index, template atom </TD><TD > small molecules with fixed topology </TD></TR>
<TR><TD ><I>tri</I> </TD><TD > corner points, angular momentum </TD><TD > rigid bodies </TD></TR>
<TR><TD ><I>wavepacket</I> </TD><TD > charge, spin, eradius, etag, cs_re, cs_im </TD><TD > AWPMD
</TD></TR></TABLE></DIV>
<P>IMPORTANT NOTE: It is possible to add some attributes, such as a
molecule ID, to atom styles that do not have them via the <A HREF = "fix_property_atom.html">fix
property/atom</A> command. This command also
allows new custom attributes consisting of extra integer or
floating-point values to be added to atoms. See the <a class="reference internal" href="fix_property_atom.html"><em>fix property/atom</em></a> doc page for examples of cases
floating-point values to be added to atoms. See the <A HREF = "fix_property_atom.html">fix
property/atom</A> doc page for examples of cases
where this is useful and details on how to initialize, access, and
output the custom values.</p>
</div>
<p>All of the above styles define point particles, except the <em>sphere</em>,
<em>ellipsoid</em>, <em>electron</em>, <em>peri</em>, <em>wavepacket</em>, <em>line</em>, <em>tri</em>, and
<em>body</em> styles, which define finite-size particles. See <a class="reference internal" href="Section_howto.html#howto-14"><span>Section_howto 14</span></a> for an overview of using finite-size
particle models with LAMMPS.</p>
<p>All of the point-particle styles assign mass to particles on a
per-type basis, using the <a class="reference internal" href="mass.html"><em>mass</em></a> command, The finite-size
output the custom values.
</P>
<P>All of the above styles define point particles, except the <I>sphere</I>,
<I>ellipsoid</I>, <I>electron</I>, <I>peri</I>, <I>wavepacket</I>, <I>line</I>, <I>tri</I>, and
<I>body</I> styles, which define finite-size particles. See <A HREF = "Section_howto.html#howto_14">Section_howto
14</A> for an overview of using finite-size
particle models with LAMMPS.
</P>
<P>All of the point-particle styles assign mass to particles on a
per-type basis, using the <A HREF = "mass.html">mass</A> command, The finite-size
particle styles assign mass to individual particles on a per-particle
basis.</p>
<p>For the <em>sphere</em> style, the particles are spheres and each stores a
per-particle diameter and mass. If the diameter &gt; 0.0, the particle
basis.
</P>
<P>For the <I>sphere</I> style, the particles are spheres and each stores a
per-particle diameter and mass. If the diameter > 0.0, the particle
is a finite-size sphere. If the diameter = 0.0, it is a point
particle.</p>
<p>For the <em>ellipsoid</em> style, the particles are ellipsoids and each
particle.
</P>
<P>For the <I>ellipsoid</I> style, the particles are ellipsoids and each
stores a flag which indicates whether it is a finite-size ellipsoid or
a point particle. If it is an ellipsoid, it also stores a shape
vector with the 3 diamters of the ellipsoid and a quaternion 4-vector
with its orientation.</p>
<p>For the <em>electron</em> style, the particles representing electrons are 3d
with its orientation.
</P>
<P>For the <I>electron</I> style, the particles representing electrons are 3d
Gaussians with a specified position and bandwidth or uncertainty in
position, which is represented by the eradius = electron size.</p>
<p>For the <em>peri</em> style, the particles are spherical and each stores a
per-particle mass and volume.</p>
<p>The <em>meso</em> style is for smoothed particle hydrodynamics (SPH)
position, which is represented by the eradius = electron size.
</P>
<P>For the <I>peri</I> style, the particles are spherical and each stores a
per-particle mass and volume.
</P>
<P>The <I>meso</I> style is for smoothed particle hydrodynamics (SPH)
particles which store a density (rho), energy (e), and heat capacity
(cv).</p>
<p>The <em>wavepacket</em> style is similar to <em>electron</em>, but the electrons may
(cv).
</P>
<P>The <I>wavepacket</I> style is similar to <I>electron</I>, but the electrons may
consist of several Gaussian wave packets, summed up with coefficients
cs= (cs_re,cs_im). Each of the wave packets is treated as a separate
particle in LAMMPS, wave packets belonging to the same electron must
have identical <em>etag</em> values.</p>
<p>For the <em>line</em> style, the particles are idealized line segments and
have identical <I>etag</I> values.
</P>
<P>For the <I>line</I> style, the particles are idealized line segments and
each stores a per-particle mass and length and orientation (i.e. the
end points of the line segment).</p>
<p>For the <em>tri</em> style, the particles are planar triangles and each
end points of the line segment).
</P>
<P>For the <I>tri</I> style, the particles are planar triangles and each
stores a per-particle mass and size and orientation (i.e. the corner
points of the triangle).</p>
<p>The <em>template</em> style allows molecular topolgy (bonds,angles,etc) to be
defined via a molecule template using the <a class="reference external" href="molecule.txt">molecule</a>
points of the triangle).
</P>
<P>The <I>template</I> style allows molecular topolgy (bonds,angles,etc) to be
defined via a molecule template using the <A HREF = "molecule.txt">molecule</A>
command. The template stores one or more molecules with a single copy
of the topology info (bonds,angles,etc) of each. Individual atoms
only store a template index and template atom to identify which
molecule and which atom-within-the-molecule they represent. Using the
<em>template</em> style instead of the <em>bond</em>, <em>angle</em>, <em>molecular</em> styles
<I>template</I> style instead of the <I>bond</I>, <I>angle</I>, <I>molecular</I> styles
can save memory for systems comprised of a large number of small
molecules, all of a single type (or small number of types). See the
paper by Grime and Voth, in <a class="reference internal" href="#grime"><span>(Grime)</span></a>, for examples of how this
can be advantageous for large-scale coarse-grained systems.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">When using the <em>template</em> style with a <a class="reference internal" href="molecule.html"><em>molecule template</em></a> that contains multiple molecules, you should
paper by Grime and Voth, in <A HREF = "#Grime">(Grime)</A>, for examples of how this
can be advantageous for large-scale coarse-grained systems.
</P>
<P>IMPORTANT NOTE: When using the <I>template</I> style with a <A HREF = "molecule.html">molecule
template</A> that contains multiple molecules, you should
insure the atom types, bond types, angle_types, etc in all the
molecules are consistent. E.g. if one molecule represents H2O and
another CO2, then you probably do not want each molecule file to
define 2 atom types and a single bond type, because they will conflict
with each other when a mixture system of H2O and CO2 molecules is
defined, e.g. by the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command. Rather the
defined, e.g. by the <A HREF = "read_data.html">read_data</A> command. Rather the
H2O molecule should define atom types 1 and 2, and bond type 1. And
the CO2 molecule should define atom types 3 and 4 (or atom types 3 and
2 if a single oxygen type is desired), and bond type 2.</p>
</div>
<p>For the <em>body</em> style, the particles are arbitrary bodies with internal
attributes defined by the &#8220;style&#8221; of the bodies, which is specified by
the <em>bstyle</em> argument. Body particles can represent complex entities,
2 if a single oxygen type is desired), and bond type 2.
</P>
<P>For the <I>body</I> style, the particles are arbitrary bodies with internal
attributes defined by the "style" of the bodies, which is specified by
the <I>bstyle</I> argument. Body particles can represent complex entities,
such as surface meshes of discrete points, collections of
sub-particles, deformable objects, etc.</p>
<p>The <a class="reference internal" href="body.html"><em>body</em></a> doc page descibes the body styles LAMMPS
sub-particles, deformable objects, etc.
</P>
<P>The <A HREF = "body.html">body</A> doc page descibes the body styles LAMMPS
currently supports, and provides more details as to the kind of body
particles they represent. For all styles, each body particle stores
moments of inertia and a quaternion 4-vector, so that its orientation
and position can be time integrated due to forces and torques.</p>
<p>Note that there may be additional arguments required along with the
<em>bstyle</em> specification, in the atom_style body command. These
arguments are described in the <a class="reference internal" href="body.html"><em>body</em></a> doc page.</p>
<hr class="docutils" />
<p>Typically, simulations require only a single (non-hybrid) atom style.
and position can be time integrated due to forces and torques.
</P>
<P>Note that there may be additional arguments required along with the
<I>bstyle</I> specification, in the atom_style body command. These
arguments are described in the <A HREF = "body.html">body</A> doc page.
</P>
<HR>
<P>Typically, simulations require only a single (non-hybrid) atom style.
If some atoms in the simulation do not have all the properties defined
by a particular style, use the simplest style that defines all the
needed properties by any atom. For example, if some atoms in a
simulation are charged, but others are not, use the <em>charge</em> style.
If some atoms have bonds, but others do not, use the <em>bond</em> style.</p>
<p>The only scenario where the <em>hybrid</em> style is needed is if there is no
simulation are charged, but others are not, use the <I>charge</I> style.
If some atoms have bonds, but others do not, use the <I>bond</I> style.
</P>
<P>The only scenario where the <I>hybrid</I> style is needed is if there is no
single style which defines all needed properties of all atoms. For
example, if you want dipolar particles which will rotate due to
torque, you would need to use &#8220;atom_style hybrid sphere dipole&#8221;. When
torque, you would need to use "atom_style hybrid sphere dipole". When
a hybrid style is used, atoms store and communicate the union of all
quantities implied by the individual styles.</p>
<p>When using the <em>hybrid</em> style, you cannot combine the <em>template</em> style
quantities implied by the individual styles.
</P>
<P>When using the <I>hybrid</I> style, you cannot combine the <I>template</I> style
with another molecular style that stores bond,angle,etc info on a
per-atom basis.</p>
<p>LAMMPS can be extended with new atom styles as well as new body
styles; see <a class="reference internal" href="Section_modify.html"><em>this section</em></a>.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</em> or <em>kk</em> suffix are functionally the same as the
per-atom basis.
</P>
<P>LAMMPS can be extended with new atom styles as well as new body
styles; see <A HREF = "Section_modify.html">this section</A>.
</P>
<HR>
<P>Styles with a <I>cuda</I> or <I>kk</I> suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
<a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual. The
<A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual. The
accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues.</p>
<p>Note that other acceleration packages in LAMMPS, specifically the GPU,
results, except for round-off and precision issues.
</P>
<P>Note that other acceleration packages in LAMMPS, specifically the GPU,
USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom
styles.</p>
<p>The accelerated styles are part of the USER-CUDA and KOKKOS packages
styles.
</P>
<P>The accelerated styles are part of the USER-CUDA and KOKKOS packages
respectively. They are only enabled if LAMMPS was built with those
packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section
for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This command cannot be used after the simulation box is defined by a
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="create_box.html"><em>create_box</em></a> command.</p>
<p>The <em>angle</em>, <em>bond</em>, <em>full</em>, <em>molecular</em>, and <em>template</em> styles are
part of the MOLECULE package. The <em>line</em> and <em>tri</em> styles are part
of the ASPHERE pacakge. The <em>body</em> style is part of the BODY package.
The <em>dipole</em> style is part of the DIPOLE package. The <em>peri</em> style is
part of the PERI package for Peridynamics. The <em>electron</em> style is
part of the USER-EFF package for <a class="reference internal" href="pair_eff.html"><em>electronic force fields</em></a>. The <em>meso</em> style is part of the USER-SPH
package for smoothed particle hydrodyanmics (SPH). See <a class="reference external" href="USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</a> to using SPH in LAMMPS. The
<em>wavepacket</em> style is part of the USER-AWPMD package for the
<a class="reference internal" href="pair_awpmd.html"><em>antisymmetrized wave packet MD method</em></a>. They are
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>
</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="read_data.html"><em>read_data</em></a>, <a class="reference internal" href="pair_style.html"><em>pair_style</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>atom_style atomic</p>
<hr class="docutils" />
<p id="grime"><strong>(Grime)</strong> Grime and Voth, to appear in J Chem Theory &amp; Computation
(2014).</p>
</div>
</div>
packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<P><B>Restrictions:</B>
</P>
<P>This command cannot be used after the simulation box is defined by a
<A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command.
</P>
<P>The <I>angle</I>, <I>bond</I>, <I>full</I>, <I>molecular</I>, and <I>template</I> styles are
part of the MOLECULE package. The <I>line</I> and <I>tri</I> styles are part
of the ASPHERE pacakge. The <I>body</I> style is part of the BODY package.
The <I>dipole</I> style is part of the DIPOLE package. The <I>peri</I> style is
part of the PERI package for Peridynamics. The <I>electron</I> style is
part of the USER-EFF package for <A HREF = "pair_eff.html">electronic force
fields</A>. The <I>meso</I> style is part of the USER-SPH
package for smoothed particle hydrodyanmics (SPH). See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF
guide</A> to using SPH in LAMMPS. The
<I>wavepacket</I> style is part of the USER-AWPMD package for the
<A HREF = "pair_awpmd.html">antisymmetrized wave packet MD method</A>. They are
only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "read_data.html">read_data</A>, <A HREF = "pair_style.html">pair_style</A>
</P>
<P><B>Default:</B>
</P>
<P>atom_style atomic
</P>
<HR>
<A NAME = "Grime"></A>
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<P><B>(Grime)</B> Grime and Voth, to appear in J Chem Theory & Computation
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<div class="section" id="balance-command">
<span id="index-0"></span><h1>balance command<a class="headerlink" href="#balance-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>balance thresh style args ... keyword value ...
</pre></div>
</div>
<ul class="simple">
<li>thresh = imbalance threshhold that must be exceeded to perform a re-balance</li>
<li>one style/arg pair can be used (or multiple for <em>x</em>,*y*,*z*)</li>
<li>style = <em>x</em> or <em>y</em> or <em>z</em> or <em>shift</em> or <em>rcb</em></li>
</ul>
<pre class="literal-block">
<em>x</em> args = <em>uniform</em> or Px-1 numbers between 0 and 1
<em>uniform</em> = evenly spaced cuts between processors in x dimension
<HR>
<H3>balance command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>balance thresh style args ... keyword value ...
</PRE>
<UL><LI>thresh = imbalance threshhold that must be exceeded to perform a re-balance
<LI>one style/arg pair can be used (or multiple for <I>x</I>,<I>y</I>,<I>z</I>)
<LI>style = <I>x</I> or <I>y</I> or <I>z</I> or <I>shift</I> or <I>rcb</I>
<PRE> <I>x</I> args = <I>uniform</I> or Px-1 numbers between 0 and 1
<I>uniform</I> = evenly spaced cuts between processors in x dimension
numbers = Px-1 ascending values between 0 and 1, Px - # of processors in x dimension
<em>x</em> can be specified together with <em>y</em> or <em>z</em>
<em>y</em> args = <em>uniform</em> or Py-1 numbers between 0 and 1
<em>uniform</em> = evenly spaced cuts between processors in y dimension
<I>x</I> can be specified together with <I>y</I> or <I>z</I>
<I>y</I> args = <I>uniform</I> or Py-1 numbers between 0 and 1
<I>uniform</I> = evenly spaced cuts between processors in y dimension
numbers = Py-1 ascending values between 0 and 1, Py - # of processors in y dimension
<em>y</em> can be specified together with <em>x</em> or <em>z</em>
<em>z</em> args = <em>uniform</em> or Pz-1 numbers between 0 and 1
<em>uniform</em> = evenly spaced cuts between processors in z dimension
<I>y</I> can be specified together with <I>x</I> or <I>z</I>
<I>z</I> args = <I>uniform</I> or Pz-1 numbers between 0 and 1
<I>uniform</I> = evenly spaced cuts between processors in z dimension
numbers = Pz-1 ascending values between 0 and 1, Pz - # of processors in z dimension
<em>z</em> can be specified together with <em>x</em> or <em>y</em>
<em>shift</em> args = dimstr Niter stopthresh
dimstr = sequence of letters containing &quot;x&quot; or &quot;y&quot; or &quot;z&quot;, each not more than once
<I>z</I> can be specified together with <I>x</I> or <I>y</I>
<I>shift</I> args = dimstr Niter stopthresh
dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
Niter = # of times to iterate within each dimension of dimstr sequence
stopthresh = stop balancing when this imbalance threshhold is reached
<em>rcb</em> args = none
</pre>
<ul class="simple">
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>out</em></li>
</ul>
<pre class="literal-block">
<em>out</em> value = filename
filename = write each processor's sub-domain to a file
</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>balance 0.9 x uniform y 0.4 0.5 0.6
<I>rcb</I> args = none
</PRE>
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>out</I>
<PRE> <I>out</I> value = filename
filename = write each processor's sub-domain to a file
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>balance 0.9 x uniform y 0.4 0.5 0.6
balance 1.2 shift xz 5 1.1
balance 1.0 shift xz 5 1.1
balance 1.1 rcb
balance 1.0 shift x 20 1.0 out tmp.balance
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>This command adjusts the size and shape of processor sub-domains
balance 1.0 shift x 20 1.0 out tmp.balance
</PRE>
<P><B>Description:</B>
</P>
<P>This command adjusts the size and shape of processor sub-domains
within the simulation box, to attempt to balance the number of
particles and thus the computational cost (load) evenly across
processors. The load balancing is &#8220;static&#8221; in the sense that this
processors. The load balancing is "static" in the sense that this
command performs the balancing once, before or between simulations.
The processor sub-domains will then remain static during the
subsequent run. To perform &#8220;dynamic&#8221; balancing, see the <a class="reference internal" href="fix_balance.html"><em>fix balance</em></a> command, which can adjust processor
sub-domain sizes and shapes on-the-fly during a <a class="reference internal" href="run.html"><em>run</em></a>.</p>
<p>Load-balancing is typically only useful if the particles in the
subsequent run. To perform "dynamic" balancing, see the <A HREF = "fix_balance.html">fix
balance</A> command, which can adjust processor
sub-domain sizes and shapes on-the-fly during a <A HREF = "run.html">run</A>.
</P>
<P>Load-balancing is typically only useful if the particles in the
simulation box have a spatially-varying density distribution. E.g. a
model of a vapor/liquid interface, or a solid with an irregular-shaped
geometry containing void regions. In this case, the LAMMPS default of
dividing the simulation box volume into a regular-spaced grid of 3d
bricks, with one equal-volume sub-domain per procesor, may assign very
different numbers of particles per processor. This can lead to poor
performance when the simulation is run in parallel.</p>
<p>Note that the <a class="reference internal" href="processors.html"><em>processors</em></a> command allows some control
performance when the simulation is run in parallel.
</P>
<P>Note that the <A HREF = "processors.html">processors</A> command allows some control
over how the box volume is split across processors. Specifically, for
a Px by Py by Pz grid of processors, it allows choice of Px, Py, and
Pz, subject to the constraint that Px * Py * Pz = P, the total number
of processors. This is sufficient to achieve good load-balance for
some problems on some processor counts. However, all the processor
sub-domains will still have the same shape and same volume.</p>
<p>The requested load-balancing operation is only performed if the
current &#8220;imbalance factor&#8221; in particles owned by each processor
exceeds the specified <em>thresh</em> parameter. The imbalance factor is
sub-domains will still have the same shape and same volume.
</P>
<P>The requested load-balancing operation is only performed if the
current "imbalance factor" in particles owned by each processor
exceeds the specified <I>thresh</I> parameter. The imbalance factor is
defined as the maximum number of particles owned by any processor,
divided by the average number of particles per processor. Thus an
imbalance factor of 1.0 is perfect balance.</p>
<p>As an example, for 10000 particles running on 10 processors, if the
imbalance factor of 1.0 is perfect balance.
</P>
<P>As an example, for 10000 particles running on 10 processors, if the
most heavily loaded processor has 1200 particles, then the factor is
1.2, meaning there is a 20% imbalance. Note that a re-balance can be
forced even if the current balance is perfect (1.0) be specifying a
<em>thresh</em> &lt; 1.0.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Balancing is performed even if the imbalance factor
does not exceed the <em>thresh</em> parameter if a &#8220;grid&#8221; style is specified
when the current partitioning is &#8220;tiled&#8221;. The meaning of &#8220;grid&#8221; vs
&#8220;tiled&#8221; is explained below. This is to allow forcing of the
partitioning to &#8220;grid&#8221; so that the <a class="reference internal" href="comm_style.html"><em>comm_style brick</em></a>
command can then be used to replace a current <a class="reference internal" href="comm_style.html"><em>comm_style tiled</em></a> setting.</p>
</div>
<p>When the balance command completes, it prints statistics about the
<I>thresh</I> < 1.0.
</P>
<P>IMPORTANT NOTE: Balancing is performed even if the imbalance factor
does not exceed the <I>thresh</I> parameter if a "grid" style is specified
when the current partitioning is "tiled". The meaning of "grid" vs
"tiled" is explained below. This is to allow forcing of the
partitioning to "grid" so that the <A HREF = "comm_style.html">comm_style brick</A>
command can then be used to replace a current <A HREF = "comm_style.html">comm_style
tiled</A> setting.
</P>
<P>When the balance command completes, it prints statistics about the
result, including the change in the imbalance factor and the change in
the maximum number of particles on any processor. For &#8220;grid&#8221; methods
the maximum number of particles on any processor. For "grid" methods
(defined below) that create a logical 3d grid of processors, the
positions of all cutting planes in each of the 3 dimensions (as
fractions of the box length) are also printed.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">This command attempts to minimize the imbalance
fractions of the box length) are also printed.
</P>
<P>IMPORTANT NOTE: This command attempts to minimize the imbalance
factor, as defined above. But depending on the method a perfect
balance (1.0) may not be achieved. For example, &#8220;grid&#8221; methods
balance (1.0) may not be achieved. For example, "grid" methods
(defined below) that create a logical 3d grid cannot achieve perfect
balance for many irregular distributions of particles. Likewise, if a
portion of the system is a perfect lattice, e.g. the intiial system is
generated by the <a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a> command, then &#8220;grid&#8221;
generated by the <A HREF = "create_atoms.html">create_atoms</A> command, then "grid"
methods may be unable to achieve exact balance. This is because
entire lattice planes will be owned or not owned by a single
processor.</p>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The imbalance factor is also an estimate of the
processor.
</P>
<P>IMPORTANT NOTE: The imbalance factor is also an estimate of the
maximum speed-up you can hope to achieve by running a perfectly
balanced simulation versus an imbalanced one. In the example above,
the 10000 particle simulation could run up to 20% faster if it were
@ -248,117 +132,105 @@ perfectly balanced, versus when imbalanced. However, computational
cost is not strictly proportional to particle count, and changing the
relative size and shape of processor sub-domains may lead to
additional computational and communication overheads, e.g. in the PPPM
solver used via the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command. Thus
solver used via the <A HREF = "kspace_style.html">kspace_style</A> command. Thus
you should benchmark the run times of a simulation before and after
balancing.</p>
</div>
<hr class="docutils" />
<p>The method used to perform a load balance is specified by one of the
listed styles (or more in the case of <em>x</em>,*y*,*z*), which are
described in detail below. There are 2 kinds of styles.</p>
<p>The <em>x</em>, <em>y</em>, <em>z</em>, and <em>shift</em> styles are &#8220;grid&#8221; methods which produce
balancing.
</P>
<HR>
<P>The method used to perform a load balance is specified by one of the
listed styles (or more in the case of <I>x</I>,<I>y</I>,<I>z</I>), which are
described in detail below. There are 2 kinds of styles.
</P>
<P>The <I>x</I>, <I>y</I>, <I>z</I>, and <I>shift</I> styles are "grid" methods which produce
a logical 3d grid of processors. They operate by changing the cutting
planes (or lines) between processors in 3d (or 2d), to adjust the
volume (area in 2d) assigned to each processor, as in the following 2d
diagram where processor sub-domains are shown and atoms are colored by
the processor that owns them. The leftmost diagram is the default
partitioning of the simulation box across processors (one sub-box for
each of 16 processors); the middle diagram is after a &#8220;grid&#8221; method
has been applied.</p>
<a data-lightbox="group-default"
href="_images/balance_uniform.jpg"
class=""
title=""
data-title=""
><img src="_images/balance_uniform.jpg"
class="align-center"
width="25%"
height="auto"
alt=""/>
</a><a data-lightbox="group-default"
href="_images/balance_nonuniform.jpg"
class=""
title=""
data-title=""
><img src="_images/balance_nonuniform.jpg"
class="align-center"
width="25%"
height="auto"
alt=""/>
</a><a data-lightbox="group-default"
href="_images/balance_rcb.jpg"
class=""
title=""
data-title=""
><img src="_images/balance_rcb.jpg"
class="align-center"
width="25%"
height="auto"
alt=""/>
</a><p>The <em>rcb</em> style is a &#8220;tiling&#8221; method which does not produce a logical
each of 16 processors); the middle diagram is after a "grid" method
has been applied.
</P>
<CENTER><A HREF = "JPG/balance_uniform.jpg"><IMG SRC = "JPG/balance_uniform_small.jpg"></A><A HREF = "JPG/balance_nonuniform.jpg"><IMG SRC = "JPG/balance_nonuniform_small.jpg"></A><A HREF = "JPG/balance_rcb.jpg"><IMG SRC = "JPG/balance_rcb_small.jpg"></A>
</CENTER>
<P>The <I>rcb</I> style is a "tiling" method which does not produce a logical
3d grid of processors. Rather it tiles the simulation domain with
rectangular sub-boxes of varying size and shape in an irregular
fashion so as to have equal numbers of particles in each sub-box, as
in the rightmost diagram above.</p>
<p>The &#8220;grid&#8221; methods can be used with either of the
<a class="reference internal" href="comm_style.html"><em>comm_style</em></a> command options, <em>brick</em> or <em>tiled</em>. The
&#8220;tiling&#8221; methods can only be used with <a class="reference internal" href="comm_style.html"><em>comm_style tiled</em></a>. Note that it can be useful to use a &#8220;grid&#8221;
method with <a class="reference internal" href="comm_style.html"><em>comm_style tiled</em></a> to return the domain
partitioning to a logical 3d grid of processors so that &#8220;comm_style
brick&#8221; can afterwords be specified for subsequent <a class="reference internal" href="run.html"><em>run</em></a>
commands.</p>
<p>When a &#8220;grid&#8221; method is specified, the current domain partitioning can
in the rightmost diagram above.
</P>
<P>The "grid" methods can be used with either of the
<A HREF = "comm_style.html">comm_style</A> command options, <I>brick</I> or <I>tiled</I>. The
"tiling" methods can only be used with <A HREF = "comm_style.html">comm_style
tiled</A>. Note that it can be useful to use a "grid"
method with <A HREF = "comm_style.html">comm_style tiled</A> to return the domain
partitioning to a logical 3d grid of processors so that "comm_style
brick" can afterwords be specified for subsequent <A HREF = "run.html">run</A>
commands.
</P>
<P>When a "grid" method is specified, the current domain partitioning can
be either a logical 3d grid or a tiled partitioning. In the former
case, the current logical 3d grid is used as a starting point and
changes are made to improve the imbalance factor. In the latter case,
the tiled partitioning is discarded and a logical 3d grid is created
with uniform spacing in all dimensions. This becomes the starting
point for the balancing operation.</p>
<p>When a &#8220;tiling&#8221; method is specified, the current domain partitioning
(&#8220;grid&#8221; or &#8220;tiled&#8221;) is ignored, and a new partitioning is computed
from scratch.</p>
<hr class="docutils" />
<p>The <em>x</em>, <em>y</em>, and <em>z</em> styles invoke a &#8220;grid&#8221; method for balancing, as
point for the balancing operation.
</P>
<P>When a "tiling" method is specified, the current domain partitioning
("grid" or "tiled") is ignored, and a new partitioning is computed
from scratch.
</P>
<HR>
<P>The <I>x</I>, <I>y</I>, and <I>z</I> styles invoke a "grid" method for balancing, as
described above. Note that any or all of these 3 styles can be
specified together, one after the other, but they cannot be used with
any other style. This style adjusts the position of cutting planes
between processor sub-domains in specific dimensions. Only the
specified dimensions are altered.</p>
<p>The <em>uniform</em> argument spaces the planes evenly, as in the left
diagrams above. The <em>numeric</em> argument requires listing Ps-1 numbers
specified dimensions are altered.
</P>
<P>The <I>uniform</I> argument spaces the planes evenly, as in the left
diagrams above. The <I>numeric</I> argument requires listing Ps-1 numbers
that specify the position of the cutting planes. This requires
knowing Ps = Px or Py or Pz = the number of processors assigned by
LAMMPS to the relevant dimension. This assignment is made (and the
Px, Py, Pz values printed out) when the simulation box is created by
the &#8220;create_box&#8221; or &#8220;read_data&#8221; or &#8220;read_restart&#8221; command and is
influenced by the settings of the <a class="reference internal" href="processors.html"><em>processors</em></a>
command.</p>
<p>Each of the numeric values must be between 0 and 1, and they must be
the "create_box" or "read_data" or "read_restart" command and is
influenced by the settings of the <A HREF = "processors.html">processors</A>
command.
</P>
<P>Each of the numeric values must be between 0 and 1, and they must be
listed in ascending order. They represent the fractional position of
the cutting place. The left (or lower) edge of the box is 0.0, and
the right (or upper) edge is 1.0. Neither of these values is
specified. Only the interior Ps-1 positions are specified. Thus is
there are 2 procesors in the x dimension, you specify a single value
such as 0.75, which would make the left processor&#8217;s sub-domain 3x
larger than the right processor&#8217;s sub-domain.</p>
<hr class="docutils" />
<p>The <em>shift</em> style invokes a &#8220;grid&#8221; method for balancing, as
such as 0.75, which would make the left processor's sub-domain 3x
larger than the right processor's sub-domain.
</P>
<HR>
<P>The <I>shift</I> style invokes a "grid" method for balancing, as
described above. It changes the positions of cutting planes between
processors in an iterative fashion, seeking to reduce the imbalance
factor, similar to how the <a class="reference internal" href="fix_balance.html"><em>fix balance shift</em></a>
command operates.</p>
<p>The <em>dimstr</em> argument is a string of characters, each of which must be
an &#8220;x&#8221; or &#8220;y&#8221; or &#8220;z&#8221;. Eacn character can appear zero or one time,
factor, similar to how the <A HREF = "fix_balance.html">fix balance shift</A>
command operates.
</P>
<P>The <I>dimstr</I> argument is a string of characters, each of which must be
an "x" or "y" or "z". Eacn character can appear zero or one time,
since there is no advantage to balancing on a dimension more than
once. You should normally only list dimensions where you expect there
to be a density variation in the particles.</p>
<p>Balancing proceeds by adjusting the cutting planes in each of the
dimensions listed in <em>dimstr</em>, one dimension at a time. For a single
to be a density variation in the particles.
</P>
<P>Balancing proceeds by adjusting the cutting planes in each of the
dimensions listed in <I>dimstr</I>, one dimension at a time. For a single
dimension, the balancing operation (described below) is iterated on up
to <em>Niter</em> times. After each dimension finishes, the imbalance factor
is re-computed, and the balancing operation halts if the <em>stopthresh</em>
criterion is met.</p>
<p>A rebalance operation in a single dimension is performed using a
to <I>Niter</I> times. After each dimension finishes, the imbalance factor
is re-computed, and the balancing operation halts if the <I>stopthresh</I>
criterion is met.
</P>
<P>A rebalance operation in a single dimension is performed using a
recursive multisectioning algorithm, where the position of each
cutting plane (line in 2d) in the dimension is adjusted independently.
This is similar to a recursive bisectioning for a single value, except
@ -370,31 +242,33 @@ the cut is adjusted to be halfway between a low and high bound. The
low and high bounds are adjusted on each iteration, using new count
information, so that they become closer together over time. Thus as
the recustion progresses, the count of particles on either side of the
plane gets closer to the target value.</p>
<p>Once the rebalancing is complete and final processor sub-domains
plane gets closer to the target value.
</P>
<P>Once the rebalancing is complete and final processor sub-domains
assigned, particles are migrated to their new owning processor, and
the balance procedure ends.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">At each rebalance operation, the bisectioning for each
the balance procedure ends.
</P>
<P>IMPORTANT NOTE: At each rebalance operation, the bisectioning for each
cutting plane (line in 2d) typcially starts with low and high bounds
separated by the extent of a processor&#8217;s sub-domain in one dimension.
separated by the extent of a processor's sub-domain in one dimension.
The size of this bracketing region shrinks by 1/2 every iteration.
Thus if <em>Niter</em> is specified as 10, the cutting plane will typically
Thus if <I>Niter</I> is specified as 10, the cutting plane will typically
be positioned to 1 part in 1000 accuracy (relative to the perfect
target position). For <em>Niter</em> = 20, it will be accurate to 1 part in
a million. Thus there is no need ot set <em>Niter</em> to a large value.
target position). For <I>Niter</I> = 20, it will be accurate to 1 part in
a million. Thus there is no need ot set <I>Niter</I> to a large value.
LAMMPS will check if the threshold accuracy is reached (in a
dimension) is less iterations than <em>Niter</em> and exit early. However,
<em>Niter</em> should also not be set too small, since it will take roughly
dimension) is less iterations than <I>Niter</I> and exit early. However,
<I>Niter</I> should also not be set too small, since it will take roughly
the same number of iterations to converge even if the cutting plane is
initially close to the target value.</p>
</div>
<hr class="docutils" />
<p>The <em>rcb</em> style invokes a &#8220;tiled&#8221; method for balancing, as described
initially close to the target value.
</P>
<HR>
<P>The <I>rcb</I> style invokes a "tiled" method for balancing, as described
above. It performs a recursive coordinate bisectioning (RCB) of the
simulation domain. The basic idea is as follows.</p>
<p>The simulation domain is cut into 2 boxes by an axis-aligned cut in
simulation domain. The basic idea is as follows.
</P>
<P>The simulation domain is cut into 2 boxes by an axis-aligned cut in
the longest dimension, leaving one new box on either side of the cut.
All the processors are also partitioned into 2 groups, half assigned
to the box on the lower side of the cut, and half to the box on the
@ -405,23 +279,27 @@ box should own for load balance to be perfect. This also makes load
balance for the upper box perfect. The positioning is done
iteratively, by a bisectioning method. Note that counting atoms on
either side of the cut requires communication between all processors
at each iteration.</p>
<p>That is the procedure for the first cut. Subsequent cuts are made
at each iteration.
</P>
<P>That is the procedure for the first cut. Subsequent cuts are made
recursively, in exactly the same manner. The subset of processors
assigned to each box make a new cut in the longest dimension of that
box, splitting the box, the subset of processsors, and the atoms in
the box in two. The recursion continues until every processor is
assigned a sub-box of the entire simulation domain, and owns the atoms
in that sub-box.</p>
<hr class="docutils" />
<p>The <em>out</em> keyword writes a text file to the specified <em>filename</em> with
in that sub-box.
</P>
<HR>
<P>The <I>out</I> keyword writes a text file to the specified <I>filename</I> with
the results of the balancing operation. The file contains the bounds
of the sub-domain for each processor after the balancing operation
completes. The format of the file is compatible with the
<a class="reference external" href="pizza">Pizza.py</a> <em>mdump</em> tool which has support for manipulating and
<A HREF = "pizza">Pizza.py</A> <I>mdump</I> tool which has support for manipulating and
visualizing mesh files. An example is shown here for a balancing by 4
processors for a 2d problem:</p>
<div class="highlight-python"><div class="highlight"><pre>ITEM: TIMESTEP
processors for a 2d problem:
</P>
<PRE>ITEM: TIMESTEP
0
ITEM: NUMBER OF NODES
16
@ -454,90 +332,29 @@ ITEM: SQUARES
1 1 1 2 3 4
2 1 5 6 7 8
3 1 9 10 11 12
4 1 13 14 15 16
</pre></div>
</div>
<p>The coordinates of all the vertices are listed in the NODES section, 5
4 1 13 14 15 16
</PRE>
<P>The coordinates of all the vertices are listed in the NODES section, 5
per processor. Note that the 4 sub-domains share vertices, so there
will be duplicate nodes in the list.</p>
<p>The &#8220;SQUARES&#8221; section lists the node IDs of the 4 vertices in a
rectangle for each processor (1 to 4).</p>
<p>For a 3d problem, the syntax is similar with 8 vertices listed for
each processor, instead of 4, and &#8220;SQUARES&#8221; replaced by &#8220;CUBES&#8221;.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>For 2d simulations, the <em>z</em> style cannot be used. Nor can a &#8220;z&#8221;
appear in <em>dimstr</em> for the <em>shift</em> style.</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 class="reference internal" href="processors.html"><em>processors</em></a>, <a class="reference internal" href="fix_balance.html"><em>fix balance</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
will be duplicate nodes in the list.
</P>
<P>The "SQUARES" section lists the node IDs of the 4 vertices in a
rectangle for each processor (1 to 4).
</P>
<P>For a 3d problem, the syntax is similar with 8 vertices listed for
each processor, instead of 4, and "SQUARES" replaced by "CUBES".
</P>
<HR>
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appear in <I>dimstr</I> for the <I>shift</I> style.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "processors.html">processors</A>, <A HREF = "fix_balance.html">fix balance</A>
</P>
<P><B>Default:</B> none
</P>
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@ -1,252 +1,138 @@
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<div class="section" id="body-particles">
<h1>Body particles<a class="headerlink" href="#body-particles" title="Permalink to this headline"></a></h1>
<p><strong>Overview:</strong></p>
<p>This doc page is not about a LAMMPS input script command, but about
<HR>
<H3>Body particles
</H3>
<P><B>Overview:</B>
</P>
<P>This doc page is not about a LAMMPS input script command, but about
body particles, which are generalized finite-size particles.
Individual body particles can represent complex entities, such as
surface meshes of discrete points, collections of sub-particles,
deformable objects, etc. Note that other kinds of finite-size
spherical and aspherical particles are also supported by LAMMPS, such
as spheres, ellipsoids, line segments, and triangles, but they are
simpler entities that body particles. See <a class="reference internal" href="Section_howto.html#howto-14"><span>Section_howto 14</span></a> for a general overview of all these
particle types.</p>
<p>Body particles are used via the <a class="reference internal" href="atom_style.html"><em>atom_style body</em></a>
simpler entities that body particles. See <A HREF = "Section_howto.html#howto_14">Section_howto
14</A> for a general overview of all these
particle types.
</P>
<P>Body particles are used via the <A HREF = "atom_style.html">atom_style body</A>
command. It takes a body style as an argument. The current body
styles supported by LAMMPS are as follows. The name in the first
column is used as the <em>bstyle</em> argument for the <a class="reference internal" href="atom_style.html"><em>atom_style body</em></a> command.</p>
<table border="1" class="docutils">
<colgroup>
<col width="28%" />
<col width="72%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><em>nparticle</em></td>
<td>rigid body with N sub-particles</td>
</tr>
</tbody>
</table>
<p>The body style determines what attributes are stored for each body and
column is used as the <I>bstyle</I> argument for the <A HREF = "atom_style.html">atom_style
body</A> command.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD ><I>nparticle</I> </TD><TD > rigid body with N sub-particles
</TD></TR></TABLE></DIV>
<P>The body style determines what attributes are stored for each body and
thus how they can be used to compute pairwise body/body or
bond/non-body (point particle) interactions. More details of each
style are described below.</p>
<p>We hope to add more styles in the future. See <a class="reference internal" href="Section_modify.html#mod-12"><span>Section_modify 12</span></a> for details on how to add a new body
style to the code.</p>
<hr class="docutils" />
<p><strong>When to use body particles:</strong></p>
<p>You should not use body particles to model a rigid body made of
style are described below.
</P>
<P>We hope to add more styles in the future. See <A HREF = "Section_modify.html#mod_12">Section_modify
12</A> for details on how to add a new body
style to the code.
</P>
<HR>
<P><B>When to use body particles:</B>
</P>
<P>You should not use body particles to model a rigid body made of
simpler particles (e.g. point, sphere, ellipsoid, line segment,
triangular particles), if the interaction between pairs of rigid
bodies is just the summation of pairwise interactions between the
simpler particles. LAMMPS already supports this kind of model via the
<a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> command. Any of the numerous pair styles
<A HREF = "fix_rigid.html">fix rigid</A> command. Any of the numerous pair styles
that compute interactions between simpler particles can be used. The
<a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> command time integrates the motion of the
<A HREF = "fix_rigid.html">fix rigid</A> command time integrates the motion of the
rigid bodies. All of the standard LAMMPS commands for thermostatting,
adding constraints, performing output, etc will operate as expected on
the simple particles.</p>
<p>By contrast, when body particles are used, LAMMPS treats an entire
the simple particles.
</P>
<P>By contrast, when body particles are used, LAMMPS treats an entire
body as a single particle for purposes of computing pairwise
interactions, building neighbor lists, migrating particles between
processors, outputting particles to a dump file, etc. This means that
interactions between pairs of bodies or between a body and non-body
(point) particle need to be encoded in an appropriate pair style. If
such a pair style were to mimic the <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> model,
such a pair style were to mimic the <A HREF = "fix_rigid.html">fix rigid</A> model,
it would need to loop over the entire collection of interactions
between pairs of simple particles within the two bodies, each time a
single body/body interaction was computed.</p>
<p>Thus it only makes sense to use body particles and develop such a pair
single body/body interaction was computed.
</P>
<P>Thus it only makes sense to use body particles and develop such a pair
style, when particle/particle interactions are more complex than what
the <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> command can already calculate. For
example, if particles have one or more of the following attributes:</p>
<ul class="simple">
<li>represented by a surface mesh</li>
<li>represented by a collection of geometric entities (e.g. planes + spheres)</li>
<li>deformable</li>
<li>internal stress that induces fragmentation</li>
</ul>
<p>then the interaction between pairs of particles is likely to be more
the <A HREF = "fix_rigid.html">fix rigid</A> command can already calculate. For
example, if particles have one or more of the following attributes:
</P>
<UL><LI>represented by a surface mesh
<LI>represented by a collection of geometric entities (e.g. planes + spheres)
<LI>deformable
<LI>internal stress that induces fragmentation
</UL>
<P>then the interaction between pairs of particles is likely to be more
complex than the summation of simple sub-particle interactions. An
example is contact or frictional forces between particles with planar
sufaces that inter-penetrate.</p>
<p>These are additional LAMMPS commands that can be used with body
particles of different styles</p>
<table border="1" class="docutils">
<colgroup>
<col width="48%" />
<col width="52%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="fix_nve_body.html"><em>fix nve/body</em></a></td>
<td>integrate motion of a body particle</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_body_local.html"><em>compute body/local</em></a></td>
<td>store sub-particle attributes of a body particle</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="dump.html"><em>dump local</em></a></td>
<td>output sub-particle attributes of a body particle</td>
</tr>
</tbody>
</table>
<p>The pair styles defined for use with specific body styles are listed
in the sections below.</p>
<hr class="docutils" />
<p><strong>Specifics of body style nparticle:</strong></p>
<p>The <em>nparticle</em> body style represents body particles as a rigid body
sufaces that inter-penetrate.
</P>
<P>These are additional LAMMPS commands that can be used with body
particles of different styles
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD ><A HREF = "fix_nve_body.html">fix nve/body</A> </TD><TD > integrate motion of a body particle</TD></TR>
<TR><TD ><A HREF = "compute_body_local.html">compute body/local</A> </TD><TD > store sub-particle attributes of a body particle</TD></TR>
<TR><TD ><A HREF = "dump.html">dump local</A> </TD><TD > output sub-particle attributes of a body particle
</TD></TR></TABLE></DIV>
<P>The pair styles defined for use with specific body styles are listed
in the sections below.
</P>
<HR>
<P><B>Specifics of body style nparticle:</B>
</P>
<P>The <I>nparticle</I> body style represents body particles as a rigid body
with a variable number N of sub-particles. It is provided as a
vanillia, prototypical example of a body particle, although as
mentioned above, the <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> command already
duplicates its functionality.</p>
<p>The atom_style body command for this body style takes two additional
arguments:</p>
<div class="highlight-python"><div class="highlight"><pre>atom_style body nparticle Nmin Nmax
mentioned above, the <A HREF = "fix_rigid.html">fix rigid</A> command already
duplicates its functionality.
</P>
<P>The atom_style body command for this body style takes two additional
arguments:
</P>
<PRE>atom_style body nparticle Nmin Nmax
Nmin = minimum # of sub-particles in any body in the system
Nmax = maximum # of sub-particles in any body in the system
</pre></div>
</div>
<p>The Nmin and Nmax arguments are used to bound the size of data
structures used internally by each particle.</p>
<p>When the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command reads a data file for this
Nmax = maximum # of sub-particles in any body in the system
</PRE>
<P>The Nmin and Nmax arguments are used to bound the size of data
structures used internally by each particle.
</P>
<P>When the <A HREF = "read_data.html">read_data</A> command reads a data file for this
body style, the following information must be provided for each entry
in the <em>Bodies</em> section of the data file:</p>
<div class="highlight-python"><div class="highlight"><pre>atom-ID 1 M
in the <I>Bodies</I> section of the data file:
</P>
<PRE>atom-ID 1 M
N
ixx iyy izz ixy ixz iyz x1 y1 z1 ...
...
... xN yN zN
</pre></div>
</div>
<p>N is the number of sub-particles in the body particle. M = 6 + 3*N.
... xN yN zN
</PRE>
<P>N is the number of sub-particles in the body particle. M = 6 + 3*N.
The integer line has a single value N. The floating point line(s)
list 6 moments of inertia followed by the coordinates of the N
sub-particles (x1 to zN) as 3N values on as many lines as required.
Note that this in not N lines, but 10 values per line; see the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command for details. The 6 moments of
<A HREF = "read_data.html">read_data</A> command for details. The 6 moments of
inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the values consistent with
the current orientation of the rigid body around its center of mass.
The values are with respect to the simulation box XYZ axes, not with
@ -254,84 +140,24 @@ respect to the prinicpal axes of the rigid body itself. LAMMPS
performs the latter calculation internally. The coordinates of each
sub-particle are specified as its x,y,z displacement from the
center-of-mass of the body particle. The center-of-mass position of
the particle is specified by the x,y,z values in the <em>Atoms</em> section
of the data file.</p>
<p>The <a class="reference internal" href="pair_body.html"><em>pair_style body</em></a> command can be used with this
body style to compute body/body and body/non-body interactions.</p>
<p>For output purposes via the <a class="reference internal" href="compute_body_local.html"><em>compute body/local</em></a> and <a class="reference internal" href="dump.html"><em>dump local</em></a>
the particle is specified by the x,y,z values in the <I>Atoms</I> section
of the data file.
</P>
<P>The <A HREF = "pair_body.html">pair_style body</A> command can be used with this
body style to compute body/body and body/non-body interactions.
</P>
<P>For output purposes via the <A HREF = "compute_body_local.html">compute
body/local</A> and <A HREF = "dump.html">dump local</A>
commands, this body style produces one datum for each of the N
sub-particles in a body particle. The datum has 3 values:</p>
<div class="highlight-python"><div class="highlight"><pre>1 = x position of sub-particle
sub-particles in a body particle. The datum has 3 values:
</P>
<PRE>1 = x position of sub-particle
2 = y position of sub-particle
3 = z position of sub-particle
</pre></div>
</div>
<p>These values are the current position of the sub-particle within the
3 = z position of sub-particle
</PRE>
<P>These values are the current position of the sub-particle within the
simulation domain, not a displacement from the center-of-mass (COM) of
the body particle itself. These values are calculated using the
current COM and orientiation of the body particle.</p>
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<div class="section" id="bond-style-class2-command">
<span id="index-0"></span><h1>bond_style class2 command<a class="headerlink" href="#bond-style-class2-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="bond-style-class2-omp-command">
<h1>bond_style class2/omp command<a class="headerlink" href="#bond-style-class2-omp-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>bond_style class2
</pre></div>
</div>
</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>bond_style class2
bond_coeff 1 1.0 100.0 80.0 80.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>class2</em> bond style uses the potential</p>
<img alt="_images/bond_class2.jpg" class="align-center" src="_images/bond_class2.jpg" />
<p>where r0 is the equilibrium bond distance.</p>
<p>See <a class="reference internal" href="pair_modify.html#sun"><span>(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
<p>The following coefficients must be defined for each bond type via the
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li>R0 (distance)</li>
<li>K2 (energy/distance^2)</li>
<li>K3 (energy/distance^3)</li>
<li>K4 (energy/distance^4)</li>
</ul>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
<HR>
<H3>bond_style class2 command
</H3>
<H3>bond_style class2/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style class2
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style class2
bond_coeff 1 1.0 100.0 80.0 80.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>class2</I> bond style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/bond_class2.jpg">
</CENTER>
<P>where r0 is the equilibrium bond distance.
</P>
<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
</P>
<P>The following coefficients must be defined for each bond type via the
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>R0 (distance)
<LI>K2 (energy/distance^2)
<LI>K3 (energy/distance^3)
<LI>K4 (energy/distance^4)
</UL>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This bond style can only be used if LAMMPS was built with the CLASS2
package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section
for more info on packages.</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 class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>, <a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="sun"><strong>(Sun)</strong> Sun, J Phys Chem B 102, 7338-7364 (1998).</p>
</div>
</div>
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the CLASS2
package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
</P>
<P><B>Default:</B> none
</P>
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<div class="section" id="bond-coeff-command">
<span id="index-0"></span><h1>bond_coeff command<a class="headerlink" href="#bond-coeff-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>bond_coeff N args
</pre></div>
</div>
<ul class="simple">
<li>N = bond type (see asterisk form below)</li>
<li>args = coefficients for one or more bond types</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>bond_coeff 5 80.0 1.2
<HR>
<H3>bond_coeff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_coeff N args
</PRE>
<UL><LI>N = bond type (see asterisk form below)
<LI>args = coefficients for one or more bond types
</UL>
<P><B>Examples:</B>
</P>
<PRE>bond_coeff 5 80.0 1.2
bond_coeff * 30.0 1.5 1.0 1.0
bond_coeff 1*4 30.0 1.5 1.0 1.0
bond_coeff 1 harmonic 200.0 1.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Specify the bond force field coefficients for one or more bond types.
bond_coeff 1 harmonic 200.0 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>Specify the bond force field coefficients for one or more bond types.
The number and meaning of the coefficients depends on the bond style.
Bond coefficients can also be set in the data file read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command or in a restart file.</p>
<p>N can be specified in one of two ways. An explicit numeric value can
<A HREF = "read_data.html">read_data</A> command or in a restart file.
</P>
<P>N can be specified in one of two ways. An explicit numeric value can
be used, as in the 1st example above. Or a wild-card asterisk can be
used to set the coefficients for multiple bond types. This takes the
form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;. If N = the number of bond types,
form "*" or "*n" or "n*" or "m*n". If N = the number of bond types,
then an asterisk with no numeric values means all types from 1 to N. A
leading asterisk means all types from 1 to n (inclusive). A trailing
asterisk means all types from n to N (inclusive). A middle asterisk
means all types from m to n (inclusive).</p>
<p>Note that using a bond_coeff command can override a previous setting
means all types from m to n (inclusive).
</P>
<P>Note that using a bond_coeff command can override a previous setting
for the same bond type. For example, these commands set the coeffs
for all bond types, then overwrite the coeffs for just bond type 2:</p>
<div class="highlight-python"><div class="highlight"><pre>bond_coeff * 100.0 1.2
bond_coeff 2 200.0 1.2
</pre></div>
</div>
<p>A line in a data file that specifies bond coefficients uses the exact
for all bond types, then overwrite the coeffs for just bond type 2:
</P>
<PRE>bond_coeff * 100.0 1.2
bond_coeff 2 200.0 1.2
</PRE>
<P>A line in a data file that specifies bond coefficients uses the exact
same format as the arguments of the bond_coeff command in an input
script, except that wild-card asterisks should not be used since
coefficients for all N types must be listed in the file. For example,
under the &#8220;Bond Coeffs&#8221; section of a data file, the line that
corresponds to the 1st example above would be listed as</p>
<div class="highlight-python"><div class="highlight"><pre>5 80.0 1.2
</pre></div>
</div>
<hr class="docutils" />
<p>Here is an alphabetic list of bond styles defined in LAMMPS. Click on
under the "Bond Coeffs" section of a data file, the line that
corresponds to the 1st example above would be listed as
</P>
<PRE>5 80.0 1.2
</PRE>
<HR>
<P>Here is an alphabetic list of bond styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated <a class="reference internal" href=""><em>bond_coeff</em></a> command.</p>
<p>Note that here are also additional bond styles submitted by users
specified by the associated <A HREF = "bond_coeff.html">bond_coeff</A> command.
</P>
<P>Note that here are also additional bond styles submitted by users
which are included in the LAMMPS distribution. The list of these with
links to the individual styles are given in the bond section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
<ul class="simple">
<li><a class="reference internal" href="bond_none.html"><em>bond_style none</em></a> - turn off bonded interactions</li>
<li><a class="reference internal" href="bond_hybrid.html"><em>bond_style hybrid</em></a> - define multiple styles of bond interactions</li>
<li><a class="reference internal" href="bond_class2.html"><em>bond_style class2</em></a> - COMPASS (class 2) bond</li>
<li><a class="reference internal" href="bond_fene.html"><em>bond_style fene</em></a> - FENE (finite-extensible non-linear elastic) bond</li>
<li><a class="reference internal" href="bond_fene_expand.html"><em>bond_style fene/expand</em></a> - FENE bonds with variable size particles</li>
<li><a class="reference internal" href="bond_harmonic.html"><em>bond_style harmonic</em></a> - harmonic bond</li>
<li><a class="reference internal" href="bond_morse.html"><em>bond_style morse</em></a> - Morse bond</li>
<li><a class="reference internal" href="bond_nonlinear.html"><em>bond_style nonlinear</em></a> - nonlinear bond</li>
<li><a class="reference internal" href="bond_quartic.html"><em>bond_style quartic</em></a> - breakable quartic bond</li>
<li><a class="reference internal" href="bond_table.html"><em>bond_style table</em></a> - tabulated by bond length</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This command must come after the simulation box is defined by a
<a class="reference internal" href="read_data.html"><em>read_data</em></a>, <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>, or
<a class="reference internal" href="create_box.html"><em>create_box</em></a> command.</p>
<p>A bond style must be defined before any bond coefficients are set,
either in the input script or in a data file.</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 class="reference internal" href="bond_style.html"><em>bond_style</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
links to the individual styles are given in the bond section of <A HREF = "Section_commands.html#cmd_5">this
page</A>.
</P>
<UL><LI><A HREF = "bond_none.html">bond_style none</A> - turn off bonded interactions
<LI><A HREF = "bond_hybrid.html">bond_style hybrid</A> - define multiple styles of bond interactions
</UL>
<UL><LI><A HREF = "bond_class2.html">bond_style class2</A> - COMPASS (class 2) bond
<LI><A HREF = "bond_fene.html">bond_style fene</A> - FENE (finite-extensible non-linear elastic) bond
<LI><A HREF = "bond_fene_expand.html">bond_style fene/expand</A> - FENE bonds with variable size particles
<LI><A HREF = "bond_harmonic.html">bond_style harmonic</A> - harmonic bond
<LI><A HREF = "bond_morse.html">bond_style morse</A> - Morse bond
<LI><A HREF = "bond_nonlinear.html">bond_style nonlinear</A> - nonlinear bond
<LI><A HREF = "bond_quartic.html">bond_style quartic</A> - breakable quartic bond
<LI><A HREF = "bond_table.html">bond_style table</A> - tabulated by bond length
</UL>
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<P><B>Restrictions:</B>
</P>
<P>This command must come after the simulation box is defined by a
<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>, or
<A HREF = "create_box.html">create_box</A> command.
</P>
<P>A bond style must be defined before any bond coefficients are set,
either in the input script or in a data file.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_style.html">bond_style</A>
</P>
<P><B>Default:</B> none
</P>
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<div class="section" id="bond-style-fene-command">
<span id="index-0"></span><h1>bond_style fene command<a class="headerlink" href="#bond-style-fene-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="bond-style-fene-kk-command">
<h1>bond_style fene/kk command<a class="headerlink" href="#bond-style-fene-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="bond-style-fene-omp-command">
<h1>bond_style fene/omp command<a class="headerlink" href="#bond-style-fene-omp-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>bond_style fene
</pre></div>
</div>
</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>bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>fene</em> bond style uses the potential</p>
<img alt="_images/bond_fene.jpg" class="align-center" src="_images/bond_fene.jpg" />
<p>to define a finite extensible nonlinear elastic (FENE) potential
<a class="reference internal" href="special_bonds.html#kremer"><span>(Kremer)</span></a>, used for bead-spring polymer models. The first
<HR>
<H3>bond_style fene command
</H3>
<H3>bond_style fene/kk command
</H3>
<H3>bond_style fene/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style fene
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>fene</I> bond style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/bond_fene.jpg">
</CENTER>
<P>to define a finite extensible nonlinear elastic (FENE) potential
<A HREF = "#Kremer">(Kremer)</A>, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive. The
first term extends to R0, the maximum extent of the bond. The 2nd
term is cutoff at 2^(1/6) sigma, the minimum of the LJ potential.</p>
<p>The following coefficients must be defined for each bond type via the
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li>K (energy/distance^2)</li>
<li>R0 (distance)</li>
<li>epsilon (energy)</li>
<li>sigma (distance)</li>
</ul>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
term is cutoff at 2^(1/6) sigma, the minimum of the LJ potential.
</P>
<P>The following coefficients must be defined for each bond type via the
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy/distance^2)
<LI>R0 (distance)
<LI>epsilon (energy)
<LI>sigma (distance)
</UL>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info on packages.</p>
<p>You typically should specify <a class="reference external" href="special_bonds.html&quot;">special_bonds fene</a>
or <a class="reference internal" href="special_bonds.html"><em>special_bonds lj/coul 0 1 1</em></a> to use this bond
style. LAMMPS will issue a warning it that&#8217;s not the case.</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 class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>, <a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="kremer"><strong>(Kremer)</strong> Kremer, Grest, J Chem Phys, 92, 5057 (1990).</p>
</div>
</div>
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P>You typically should specify <A HREF = "special_bonds.html"">special_bonds fene</A>
or <A HREF = "special_bonds.html">special_bonds lj/coul 0 1 1</A> to use this bond
style. LAMMPS will issue a warning it that's not the case.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
</P>
<P><B>Default:</B> none
</P>
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<P><B>(Kremer)</B> Kremer, Grest, J Chem Phys, 92, 5057 (1990).
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<div class="section" id="bond-style-fene-expand-command">
<span id="index-0"></span><h1>bond_style fene/expand command<a class="headerlink" href="#bond-style-fene-expand-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="bond-style-fene-expand-omp-command">
<h1>bond_style fene/expand/omp command<a class="headerlink" href="#bond-style-fene-expand-omp-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>bond_style fene/expand
</pre></div>
</div>
</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>bond_style fene/expand
bond_coeff 1 30.0 1.5 1.0 1.0 0.5
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>fene/expand</em> bond style uses the potential</p>
<img alt="_images/bond_fene_expand.jpg" class="align-center" src="_images/bond_fene_expand.jpg" />
<p>to define a finite extensible nonlinear elastic (FENE) potential
<a class="reference internal" href="special_bonds.html#kremer"><span>(Kremer)</span></a>, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive.</p>
<p>The <em>fene/expand</em> bond style is similar to <em>fene</em> except that an extra
shift factor of delta (positive or negative) is added to <em>r</em> to
<HR>
<H3>bond_style fene/expand command
</H3>
<H3>bond_style fene/expand/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style fene/expand
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style fene/expand
bond_coeff 1 30.0 1.5 1.0 1.0 0.5
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>fene/expand</I> bond style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/bond_fene_expand.jpg">
</CENTER>
<P>to define a finite extensible nonlinear elastic (FENE) potential
<A HREF = "#Kremer">(Kremer)</A>, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive.
</P>
<P>The <I>fene/expand</I> bond style is similar to <I>fene</I> except that an extra
shift factor of delta (positive or negative) is added to <I>r</I> to
effectively change the bead size of the bonded atoms. The first term
now extends to R0 + delta and the 2nd term is cutoff at 2^(1/6) sigma
+ delta.</p>
<p>The following coefficients must be defined for each bond type via the
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li>K (energy/distance^2)</li>
<li>R0 (distance)</li>
<li>epsilon (energy)</li>
<li>sigma (distance)</li>
<li>delta (distance)</li>
</ul>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
+ delta.
</P>
<P>The following coefficients must be defined for each bond type via the
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy/distance^2)
<LI>R0 (distance)
<LI>epsilon (energy)
<LI>sigma (distance)
<LI>delta (distance)
</UL>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info on packages.</p>
<p>You typically should specify <a class="reference external" href="special_bonds.html&quot;">special_bonds fene</a>
or <a class="reference internal" href="special_bonds.html"><em>special_bonds lj/coul 0 1 1</em></a> to use this bond
style. LAMMPS will issue a warning it that&#8217;s not the case.</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 class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>, <a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="kremer"><strong>(Kremer)</strong> Kremer, Grest, J Chem Phys, 92, 5057 (1990).</p>
</div>
</div>
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P>You typically should specify <A HREF = "special_bonds.html"">special_bonds fene</A>
or <A HREF = "special_bonds.html">special_bonds lj/coul 0 1 1</A> to use this bond
style. LAMMPS will issue a warning it that's not the case.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
</P>
<P><B>Default:</B> none
</P>
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<P><B>(Kremer)</B> Kremer, Grest, J Chem Phys, 92, 5057 (1990).
</P>
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<div class="section" id="bond-style-harmonic-command">
<span id="index-0"></span><h1>bond_style harmonic command<a class="headerlink" href="#bond-style-harmonic-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="bond-style-harmonic-kk-command">
<h1>bond_style harmonic/kk command<a class="headerlink" href="#bond-style-harmonic-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="bond-style-harmonic-omp-command">
<h1>bond_style harmonic/omp command<a class="headerlink" href="#bond-style-harmonic-omp-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>bond_style harmonic
</pre></div>
</div>
</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>bond_style harmonic
bond_coeff 5 80.0 1.2
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>harmonic</em> bond style uses the potential</p>
<img alt="_images/bond_harmonic.jpg" class="align-center" src="_images/bond_harmonic.jpg" />
<p>where r0 is the equilibrium bond distance. Note that the usual 1/2
factor is included in K.</p>
<p>The following coefficients must be defined for each bond type via the
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li>K (energy/distance^2)</li>
<li>r0 (distance)</li>
</ul>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
<HR>
<H3>bond_style harmonic command
</H3>
<H3>bond_style harmonic/kk command
</H3>
<H3>bond_style harmonic/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style harmonic
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style harmonic
bond_coeff 5 80.0 1.2
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>harmonic</I> bond style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/bond_harmonic.jpg">
</CENTER>
<P>where r0 is the equilibrium bond distance. Note that the usual 1/2
factor is included in K.
</P>
<P>The following coefficients must be defined for each bond type via the
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy/distance^2)
<LI>r0 (distance)
</UL>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info on packages.</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 class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>, <a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<HR>
</div>
</div>
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</p>
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<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
</P>
<P><B>Default:</B> none
</P>
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<div class="section" id="bond-style-harmonic-shift-command">
<span id="index-0"></span><h1>bond_style harmonic/shift command<a class="headerlink" href="#bond-style-harmonic-shift-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="bond-style-harmonic-shift-omp-command">
<h1>bond_style harmonic/shift/omp command<a class="headerlink" href="#bond-style-harmonic-shift-omp-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>bond_style harmonic/shift
</pre></div>
</div>
</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>bond_style harmonic/shift
bond_coeff 5 10.0 0.5 1.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>harmonic/shift</em> bond style is a shifted harmonic bond that uses
the potential</p>
<img alt="_images/bond_harmonic_shift.jpg" class="align-center" src="_images/bond_harmonic_shift.jpg" />
<p>where r0 is the equilibrium bond distance, and rc the critical distance.
<HR>
<H3>bond_style harmonic/shift command
</H3>
<H3>bond_style harmonic/shift/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style harmonic/shift
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style harmonic/shift
bond_coeff 5 10.0 0.5 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>harmonic/shift</I> bond style is a shifted harmonic bond that uses
the potential
</P>
<CENTER><IMG SRC = "Eqs/bond_harmonic_shift.jpg">
</CENTER>
<P>where r0 is the equilibrium bond distance, and rc the critical distance.
The potential is -Umin at r0 and zero at rc. The spring constant is
k = Umin / [ 2 (r0-rc)^2].</p>
<p>The following coefficients must be defined for each bond type via the
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li>Umin (energy)</li>
<li>r0 (distance)</li>
<li>rc (distance)</li>
</ul>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
k = Umin / [ 2 (r0-rc)^2].
</P>
<P>The following coefficients must be defined for each bond type via the
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>Umin (energy)
</UL>
<UL><LI>r0 (distance)
</UL>
<UL><LI>rc (distance)
</UL>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This bond style can only be used if LAMMPS was built with the
USER-MISC package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info on packages.</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 class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>, <a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a>,
<a class="reference internal" href="bond_harmonic.html"><em>bond_harmonic</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
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<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>,
<A HREF = "bond_harmonic.html">bond_harmonic</A>
</P>
<P><B>Default:</B> none
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<div class="section" id="bond-style-harmonic-shift-cut-command">
<span id="index-0"></span><h1>bond_style harmonic/shift/cut command<a class="headerlink" href="#bond-style-harmonic-shift-cut-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="bond-style-harmonic-shift-cut-omp-command">
<h1>bond_style harmonic/shift/cut/omp command<a class="headerlink" href="#bond-style-harmonic-shift-cut-omp-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>bond_style harmonic/shift/cut
</pre></div>
</div>
</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>bond_style harmonic/shift/cut
bond_coeff 5 10.0 0.5 1.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>harmonic/shift/cut</em> bond style is a shifted harmonic bond that
uses the potential</p>
<img alt="_images/bond_harmonic_shift_cut.jpg" class="align-center" src="_images/bond_harmonic_shift_cut.jpg" />
<p>where r0 is the equilibrium bond distance, and rc the critical distance.
The bond potential is zero for distances r &gt; rc. The potential is -Umin
at r0 and zero at rc. The spring constant is k = Umin / [ 2 (r0-rc)^2].</p>
<p>The following coefficients must be defined for each bond type via the
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li>Umin (energy)</li>
<li>r0 (distance)</li>
<li>rc (distance)</li>
</ul>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
<HR>
<H3>bond_style harmonic/shift/cut command
</H3>
<H3>bond_style harmonic/shift/cut/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style harmonic/shift/cut
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style harmonic/shift/cut
bond_coeff 5 10.0 0.5 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>harmonic/shift/cut</I> bond style is a shifted harmonic bond that
uses the potential
</P>
<CENTER><IMG SRC = "Eqs/bond_harmonic_shift_cut.jpg">
</CENTER>
<P>where r0 is the equilibrium bond distance, and rc the critical distance.
The bond potential is zero for distances r > rc. The potential is -Umin
at r0 and zero at rc. The spring constant is k = Umin / [ 2 (r0-rc)^2].
</P>
<P>The following coefficients must be defined for each bond type via the
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>Umin (energy)
<LI>r0 (distance)
<LI>rc (distance)
</UL>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This bond style can only be used if LAMMPS was built with the
USER-MISC package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info on packages.</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 class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>, <a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a>,
<a class="reference internal" href="bond_harmonic.html"><em>bond_harmonic</em></a>,
<code class="xref doc docutils literal"><span class="pre">bond_harmonicshift</span></code></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
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<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>,
<A HREF = "bond_harmonic.html">bond_harmonic</A>,
<A HREF = "bond_harmonicshift.html">bond_harmonicshift</A>
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<div class="section" id="bond-style-hybrid-command">
<span id="index-0"></span><h1>bond_style hybrid command<a class="headerlink" href="#bond-style-hybrid-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>bond_style hybrid style1 style2 ...
</pre></div>
</div>
<ul class="simple">
<li>style1,style2 = list of one or more bond styles</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>bond_style hybrid harmonic fene
<HR>
<H3>bond_style hybrid command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style hybrid style1 style2 ...
</PRE>
<UL><LI>style1,style2 = list of one or more bond styles
</UL>
<P><B>Examples:</B>
</P>
<PRE>bond_style hybrid harmonic fene
bond_coeff 1 harmonic 80.0 1.2
bond_coeff 2* fene 30.0 1.5 1.0 1.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>hybrid</em> style enables the use of multiple bond styles in one
bond_coeff 2* fene 30.0 1.5 1.0 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>hybrid</I> style enables the use of multiple bond styles in one
simulation. A bond style is assigned to each bond type. For example,
bonds in a polymer flow (of bond type 1) could be computed with a
<em>fene</em> potential and bonds in the wall boundary (of bond type 2) could
be computed with a <em>harmonic</em> potential. The assignment of bond type
to style is made via the <a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> command or in
the data file.</p>
<p>In the bond_coeff commands, the name of a bond style must be added
<I>fene</I> potential and bonds in the wall boundary (of bond type 2) could
be computed with a <I>harmonic</I> potential. The assignment of bond type
to style is made via the <A HREF = "bond_coeff.html">bond_coeff</A> command or in
the data file.
</P>
<P>In the bond_coeff commands, the name of a bond style must be added
after the bond type, with the remaining coefficients being those
appropriate to that style. In the example above, the 2 bond_coeff
commands set bonds of bond type 1 to be computed with a <em>harmonic</em>
commands set bonds of bond type 1 to be computed with a <I>harmonic</I>
potential with coefficients 80.0, 1.2 for K, r0. All other bond types
(2-N) are computed with a <em>fene</em> potential with coefficients 30.0,
1.5, 1.0, 1.0 for K, R0, epsilon, sigma.</p>
<p>If bond coefficients are specified in the data file read via the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command, then the same rule applies.
E.g. &#8220;harmonic&#8221; or &#8220;fene&#8221; must be added after the bond type, for each
line in the &#8220;Bond Coeffs&#8221; section, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>Bond Coeffs
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>1 harmonic 80.0 1.2
(2-N) are computed with a <I>fene</I> potential with coefficients 30.0,
1.5, 1.0, 1.0 for K, R0, epsilon, sigma.
</P>
<P>If bond coefficients are specified in the data file read via the
<A HREF = "read_data.html">read_data</A> command, then the same rule applies.
E.g. "harmonic" or "fene" must be added after the bond type, for each
line in the "Bond Coeffs" section, e.g.
</P>
<PRE>Bond Coeffs
</PRE>
<PRE>1 harmonic 80.0 1.2
2 fene 30.0 1.5 1.0 1.0
...
</pre></div>
</div>
<p>A bond style of <em>none</em> with no additional coefficients can be used in
...
</PRE>
<P>A bond style of <I>none</I> with no additional coefficients can be used in
place of a bond style, either in a input script bond_coeff command or
in the data file, if you desire to turn off interactions for specific
bond types.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info on packages.</p>
<p>Unlike other bond styles, the hybrid bond style does not store bond
coefficient info for individual sub-styles in a <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. Thus when retarting a simulation from a restart
file, you need to re-specify bond_coeff commands.</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 class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>, <a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
bond types.
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<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P>Unlike other bond styles, the hybrid bond style does not store bond
coefficient info for individual sub-styles in a <A HREF = "restart.html">binary restart
files</A>. Thus when retarting a simulation from a restart
file, you need to re-specify bond_coeff commands.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
</P>
<P><B>Default:</B> none
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<div class="section" id="bond-style-morse-command">
<span id="index-0"></span><h1>bond_style morse command<a class="headerlink" href="#bond-style-morse-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="bond-style-morse-omp-command">
<h1>bond_style morse/omp command<a class="headerlink" href="#bond-style-morse-omp-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>bond_style morse
</pre></div>
</div>
</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>bond_style morse
bond_coeff 5 1.0 2.0 1.2
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>morse</em> bond style uses the potential</p>
<img alt="_images/bond_morse.jpg" class="align-center" src="_images/bond_morse.jpg" />
<p>where r0 is the equilibrium bond distance, alpha is a stiffness
parameter, and D determines the depth of the potential well.</p>
<p>The following coefficients must be defined for each bond type via the
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li>D (energy)</li>
<li>alpha (inverse distance)</li>
<li>r0 (distance)</li>
</ul>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
<HR>
<H3>bond_style morse command
</H3>
<H3>bond_style morse/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style morse
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style morse
bond_coeff 5 1.0 2.0 1.2
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>morse</I> bond style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/bond_morse.jpg">
</CENTER>
<P>where r0 is the equilibrium bond distance, alpha is a stiffness
parameter, and D determines the depth of the potential well.
</P>
<P>The following coefficients must be defined for each bond type via the
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>D (energy)
<LI>alpha (inverse distance)
<LI>r0 (distance)
</UL>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info on packages.</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 class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>, <a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
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<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
</P>
<P><B>Default:</B> none
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<div class="section" id="bond-style-none-command">
<span id="index-0"></span><h1>bond_style none command<a class="headerlink" href="#bond-style-none-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>bond_style none
</pre></div>
</div>
</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>bond_style none
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Using a bond style of none means bond forces are not computed, even if
<HR>
<H3>bond_style none command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style none
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style none
</PRE>
<P><B>Description:</B>
</P>
<P>Using a bond style of none means bond forces are not computed, even if
pairs of bonded atoms were listed in the data file read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<blockquote>
<div>none</div></blockquote>
<p><strong>Related commands:</strong> none</p>
<p><strong>Default:</strong> none</p>
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<A HREF = "read_data.html">read_data</A> command.
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<P><B>Restrictions:</B> none
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<P><B>Related commands:</B> none
</P>
<P><B>Default:</B> none
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<div class="section" id="bond-style-nonlinear-command">
<span id="index-0"></span><h1>bond_style nonlinear command<a class="headerlink" href="#bond-style-nonlinear-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="bond-style-nonlinear-omp-command">
<h1>bond_style nonlinear/omp command<a class="headerlink" href="#bond-style-nonlinear-omp-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>bond_style nonlinear
</pre></div>
</div>
</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>bond_style nonlinear
bond_coeff 2 100.0 1.1 1.4
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>nonlinear</em> bond style uses the potential</p>
<img alt="_images/bond_nonlinear.jpg" class="align-center" src="_images/bond_nonlinear.jpg" />
<p>to define an anharmonic spring <a class="reference internal" href="#rector"><span>(Rector)</span></a> of equilibrium
length r0 and maximum extension lamda.</p>
<p>The following coefficients must be defined for each bond type via the
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li>epsilon (energy)</li>
<li>r0 (distance)</li>
<li>lamda (distance)</li>
</ul>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
<HR>
<H3>bond_style nonlinear command
</H3>
<H3>bond_style nonlinear/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style nonlinear
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style nonlinear
bond_coeff 2 100.0 1.1 1.4
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>nonlinear</I> bond style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/bond_nonlinear.jpg">
</CENTER>
<P>to define an anharmonic spring <A HREF = "#Rector">(Rector)</A> of equilibrium
length r0 and maximum extension lamda.
</P>
<P>The following coefficients must be defined for each bond type via the
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>epsilon (energy)
<LI>r0 (distance)
<LI>lamda (distance)
</UL>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info on packages.</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 class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>, <a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="rector"><strong>(Rector)</strong> Rector, Van Swol, Henderson, Molecular Physics, 82, 1009 (1994).</p>
</div>
</div>
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
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<A NAME = "Rector"></A>
<hr/>
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<P><B>(Rector)</B> Rector, Van Swol, Henderson, Molecular Physics, 82, 1009 (1994).
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<div class="section" id="bond-style-quartic-command">
<span id="index-0"></span><h1>bond_style quartic command<a class="headerlink" href="#bond-style-quartic-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="bond-style-quartic-omp-command">
<h1>bond_style quartic/omp command<a class="headerlink" href="#bond-style-quartic-omp-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>bond_style quartic
</pre></div>
</div>
</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>bond_style quartic
bond_coeff 2 1200 -0.55 0.25 1.3 34.6878
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>quartic</em> bond style uses the potential</p>
<img alt="_images/bond_quartic.jpg" class="align-center" src="_images/bond_quartic.jpg" />
<p>to define a bond that can be broken as the simulation proceeds (e.g.
<HR>
<H3>bond_style quartic command
</H3>
<H3>bond_style quartic/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style quartic
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style quartic
bond_coeff 2 1200 -0.55 0.25 1.3 34.6878
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>quartic</I> bond style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/bond_quartic.jpg">
</CENTER>
<P>to define a bond that can be broken as the simulation proceeds (e.g.
due to a polymer being stretched). The sigma and epsilon used in the
LJ portion of the formula are both set equal to 1.0 by LAMMPS.</p>
<p>The following coefficients must be defined for each bond type via the
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li>K (energy/distance^4)</li>
<li>B1 (distance)</li>
<li>B2 (distance)</li>
<li>Rc (distance)</li>
<li>U0 (energy)</li>
</ul>
<p>This potential was constructed to mimic the FENE bond potential for
LJ portion of the formula are both set equal to 1.0 by LAMMPS.
</P>
<P>The following coefficients must be defined for each bond type via the
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy/distance^4)
<LI>B1 (distance)
<LI>B2 (distance)
<LI>Rc (distance)
<LI>U0 (energy)
</UL>
<P>This potential was constructed to mimic the FENE bond potential for
coarse-grained polymer chains. When monomers with sigma = epsilon =
1.0 are used, the following choice of parameters gives a quartic
potential that looks nearly like the FENE potential: K = 1200, B1 =
-0.55, B2 = 0.25, Rc = 1.3, and U0 = 34.6878. Different parameters
can be specified using the <a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> command, but
can be specified using the <A HREF = "bond_coeff.html">bond_coeff</A> command, but
you will need to choose them carefully so they form a suitable bond
potential.</p>
<p>Rc is the cutoff length at which the bond potential goes smoothly to a
local maximum. If a bond length ever becomes &gt; Rc, LAMMPS &#8220;breaks&#8221;
potential.
</P>
<P>Rc is the cutoff length at which the bond potential goes smoothly to a
local maximum. If a bond length ever becomes > Rc, LAMMPS "breaks"
the bond, which means two things. First, the bond potential is turned
off by setting its type to 0, and is no longer computed. Second, a
pairwise interaction between the two atoms is turned on, since they
are no longer bonded.</p>
<p>LAMMPS does the second task via a computational sleight-of-hand. It
are no longer bonded.
</P>
<P>LAMMPS does the second task via a computational sleight-of-hand. It
subtracts the pairwise interaction as part of the bond computation.
When the bond breaks, the subtraction stops. For this to work, the
pairwise interaction must always be computed by the
<a class="reference internal" href="pair_style.html"><em>pair_style</em></a> command, whether the bond is broken or
not. This means that <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> must be set
to 1,1,1, as indicated as a restriction below.</p>
<p>Note that when bonds are dumped to a file via the <a class="reference internal" href="dump.html"><em>dump local</em></a> command, bonds with type 0 are not included. The
<a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a> command can also be used to query the
status of broken bonds or permanently delete them, e.g.:</p>
<div class="highlight-python"><div class="highlight"><pre>delete_bonds all stats
delete_bonds all bond 0 remove
</pre></div>
</div>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
<A HREF = "pair_style.html">pair_style</A> command, whether the bond is broken or
not. This means that <A HREF = "special_bonds.html">special_bonds</A> must be set
to 1,1,1, as indicated as a restriction below.
</P>
<P>Note that when bonds are dumped to a file via the <A HREF = "dump.html">dump
local</A> command, bonds with type 0 are not included. The
<A HREF = "delete_bonds.html">delete_bonds</A> command can also be used to query the
status of broken bonds or permanently delete them, e.g.:
</P>
<PRE>delete_bonds all stats
delete_bonds all bond 0 remove
</PRE>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info on packages.</p>
<p>The <em>quartic</em> style requires that <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a>
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P>The <I>quartic</I> style requires that <A HREF = "special_bonds.html">special_bonds</A>
parameters be set to 1,1,1. Three- and four-body interactions (angle,
dihedral, etc) cannot be used with <em>quartic</em> bonds.</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 class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>, <a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a></p>
<p><strong>Default:</strong> none</p>
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dihedral, etc) cannot be used with <I>quartic</I> bonds.
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<P><B>Related commands:</B>
</P>
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<P><B>Default:</B> none
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<div class="section" id="bond-style-command">
<span id="index-0"></span><h1>bond_style command<a class="headerlink" href="#bond-style-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>bond_style style args
</pre></div>
</div>
<ul class="simple">
<li>style = <em>none</em> or <em>hybrid</em> or <em>class2</em> or <em>fene</em> or <em>fene/expand</em> or <em>harmonic</em> or <em>morse</em> or <em>nonlinear</em> or <em>quartic</em></li>
</ul>
<pre class="literal-block">
args = none for any style except <em>hybrid</em>
<em>hybrid</em> args = list of one or more styles
</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>bond_style harmonic
<HR>
<H3>bond_style command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style style args
</PRE>
<UL><LI>style = <I>none</I> or <I>hybrid</I> or <I>class2</I> or <I>fene</I> or <I>fene/expand</I> or <I>harmonic</I> or <I>morse</I> or <I>nonlinear</I> or <I>quartic</I>
</UL>
<PRE> args = none for any style except <I>hybrid</I>
<I>hybrid</I> args = list of one or more styles
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style harmonic
bond_style fene
bond_style hybrid harmonic fene
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Set the formula(s) LAMMPS uses to compute bond interactions between
bond_style hybrid harmonic fene
</PRE>
<P><B>Description:</B>
</P>
<P>Set the formula(s) LAMMPS uses to compute bond interactions between
pairs of atoms. In LAMMPS, a bond differs from a pairwise
interaction, which are set via the <a class="reference internal" href="pair_style.html"><em>pair_style</em></a>
interaction, which are set via the <A HREF = "pair_style.html">pair_style</A>
command. Bonds are defined between specified pairs of atoms and
remain in force for the duration of the simulation (unless the bond
breaks which is possible in some bond potentials). The list of bonded
atoms is read in by a <a class="reference internal" href="read_data.html"><em>read_data</em></a> or
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command from a data or restart file.
atoms is read in by a <A HREF = "read_data.html">read_data</A> or
<A HREF = "read_restart.html">read_restart</A> command from a data or restart file.
By contrast, pair potentials are typically defined between all pairs
of atoms within a cutoff distance and the set of active interactions
changes over time.</p>
<p>Hybrid models where bonds are computed using different bond potentials
can be setup using the <em>hybrid</em> bond style.</p>
<p>The coefficients associated with a bond style can be specified in a
data or restart file or via the <a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> command.</p>
<p>All bond potentials store their coefficient data in binary restart
files which means bond_style and <a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> commands
changes over time.
</P>
<P>Hybrid models where bonds are computed using different bond potentials
can be setup using the <I>hybrid</I> bond style.
</P>
<P>The coefficients associated with a bond style can be specified in a
data or restart file or via the <A HREF = "bond_coeff.html">bond_coeff</A> command.
</P>
<P>All bond potentials store their coefficient data in binary restart
files which means bond_style and <A HREF = "bond_coeff.html">bond_coeff</A> commands
do not need to be re-specified in an input script that restarts a
simulation. See the <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command for
simulation. See the <A HREF = "read_restart.html">read_restart</A> command for
details on how to do this. The one exception is that bond_style
<em>hybrid</em> only stores the list of sub-styles in the restart file; bond
coefficients need to be re-specified.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">When both a bond and pair style is defined, the
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command often needs to be used to
<I>hybrid</I> only stores the list of sub-styles in the restart file; bond
coefficients need to be re-specified.
</P>
<P>IMPORTANT NOTE: When both a bond and pair style is defined, the
<A HREF = "special_bonds.html">special_bonds</A> command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
exist between 2 bonded atoms.</p>
</div>
<p>In the formulas listed for each bond style, <em>r</em> is the distance
between the 2 atoms in the bond.</p>
<hr class="docutils" />
<p>Here is an alphabetic list of bond styles defined in LAMMPS. Click on
exist between 2 bonded atoms.
</P>
<P>In the formulas listed for each bond style, <I>r</I> is the distance
between the 2 atoms in the bond.
</P>
<HR>
<P>Here is an alphabetic list of bond styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated <a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> command.</p>
<p>Note that there are also additional bond styles submitted by users
specified by the associated <A HREF = "bond_coeff.html">bond_coeff</A> command.
</P>
<P>Note that there are also additional bond styles submitted by users
which are included in the LAMMPS distribution. The list of these with
links to the individual styles are given in the bond section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
<ul class="simple">
<li><a class="reference internal" href="bond_none.html"><em>bond_style none</em></a> - turn off bonded interactions</li>
<li><a class="reference internal" href="bond_hybrid.html"><em>bond_style hybrid</em></a> - define multiple styles of bond interactions</li>
<li><a class="reference internal" href="bond_class2.html"><em>bond_style class2</em></a> - COMPASS (class 2) bond</li>
<li><a class="reference internal" href="bond_fene.html"><em>bond_style fene</em></a> - FENE (finite-extensible non-linear elastic) bond</li>
<li><a class="reference internal" href="bond_fene_expand.html"><em>bond_style fene/expand</em></a> - FENE bonds with variable size particles</li>
<li><a class="reference internal" href="bond_harmonic.html"><em>bond_style harmonic</em></a> - harmonic bond</li>
<li><a class="reference internal" href="bond_morse.html"><em>bond_style morse</em></a> - Morse bond</li>
<li><a class="reference internal" href="bond_nonlinear.html"><em>bond_style nonlinear</em></a> - nonlinear bond</li>
<li><a class="reference internal" href="bond_quartic.html"><em>bond_style quartic</em></a> - breakable quartic bond</li>
<li><a class="reference internal" href="bond_table.html"><em>bond_style table</em></a> - tabulated by bond length</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>Bond styles can only be set for atom styles that allow bonds to be
defined.</p>
<p>Most bond styles are part of the MOLECULE package. They are 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 on packages.
links to the individual styles are given in the bond section of <A HREF = "Section_commands.html#cmd_5">this
page</A>.
</P>
<UL><LI><A HREF = "bond_none.html">bond_style none</A> - turn off bonded interactions
<LI><A HREF = "bond_hybrid.html">bond_style hybrid</A> - define multiple styles of bond interactions
</UL>
<UL><LI><A HREF = "bond_class2.html">bond_style class2</A> - COMPASS (class 2) bond
<LI><A HREF = "bond_fene.html">bond_style fene</A> - FENE (finite-extensible non-linear elastic) bond
<LI><A HREF = "bond_fene_expand.html">bond_style fene/expand</A> - FENE bonds with variable size particles
<LI><A HREF = "bond_harmonic.html">bond_style harmonic</A> - harmonic bond
<LI><A HREF = "bond_morse.html">bond_style morse</A> - Morse bond
<LI><A HREF = "bond_nonlinear.html">bond_style nonlinear</A> - nonlinear bond
<LI><A HREF = "bond_quartic.html">bond_style quartic</A> - breakable quartic bond
<LI><A HREF = "bond_table.html">bond_style table</A> - tabulated by bond length
</UL>
<HR>
<P><B>Restrictions:</B>
</P>
<P>Bond styles can only be set for atom styles that allow bonds to be
defined.
</P>
<P>Most bond styles are part of the MOLECULE package. They are only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
The doc pages for individual bond potentials tell if it is part of a
package.</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 class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>, <a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>bond_style none</p>
</div>
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package.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
</P>
<P><B>Default:</B>
</P>
<P>bond_style none
</P>
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@ -1,205 +1,90 @@
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<div class="section" id="bond-style-table-command">
<span id="index-0"></span><h1>bond_style table command<a class="headerlink" href="#bond-style-table-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="bond-style-table-omp-command">
<h1>bond_style table/omp command<a class="headerlink" href="#bond-style-table-omp-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>bond_style table style N
</pre></div>
</div>
<ul class="simple">
<li>style = <em>linear</em> or <em>spline</em> = method of interpolation</li>
<li>N = use N values in table</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>bond_style table linear 1000
bond_coeff 1 file.table ENTRY1
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>table</em> creates interpolation tables of length <em>N</em> from bond
<HR>
<H3>bond_style table command
</H3>
<H3>bond_style table/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style table style N
</PRE>
<UL><LI>style = <I>linear</I> or <I>spline</I> = method of interpolation
<LI>N = use N values in table
</UL>
<P><B>Examples:</B>
</P>
<PRE>bond_style table linear 1000
bond_coeff 1 file.table ENTRY1
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>table</I> creates interpolation tables of length <I>N</I> from bond
potential and force values listed in a file(s) as a function of bond
length. The files are read by the <a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>
command.</p>
<p>The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy and force values at each of <em>N</em>
length. The files are read by the <A HREF = "bond_coeff.html">bond_coeff</A>
command.
</P>
<P>The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy and force values at each of <I>N</I>
distances. During a simulation, these tables are used to interpolate
energy and force values as needed. The interpolation is done in one
of 2 styles: <em>linear</em> or <em>spline</em>.</p>
<p>For the <em>linear</em> style, the bond length is used to find 2 surrounding
of 2 styles: <I>linear</I> or <I>spline</I>.
</P>
<P>For the <I>linear</I> style, the bond length is used to find 2 surrounding
table values from which an energy or force is computed by linear
interpolation.</p>
<p>For the <em>spline</em> style, a cubic spline coefficients are computed and
stored at each of the <em>N</em> values in the table. The bond length is
interpolation.
</P>
<P>For the <I>spline</I> style, a cubic spline coefficients are computed and
stored at each of the <I>N</I> values in the table. The bond length is
used to find the appropriate set of coefficients which are used to
evaluate a cubic polynomial which computes the energy or force.</p>
<p>The following coefficients must be defined for each bond type via the
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> command as in the example above.</p>
<ul class="simple">
<li>filename</li>
<li>keyword</li>
</ul>
<p>The filename specifies a file containing tabulated energy and force
evaluate a cubic polynomial which computes the energy or force.
</P>
<P>The following coefficients must be defined for each bond type via the
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above.
</P>
<UL><LI>filename
<LI>keyword
</UL>
<P>The filename specifies a file containing tabulated energy and force
values. The keyword specifies a section of the file. The format of
this file is described below.</p>
<hr class="docutils" />
<p>The format of a tabulated file is as follows (without the
parenthesized comments):</p>
<div class="highlight-python"><div class="highlight"><pre><span class="c"># Bond potential for harmonic (one or more comment or blank lines)</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>HAM (keyword is the first text on line)
this file is described below.
</P>
<HR>
<P>The format of a tabulated file is as follows (without the
parenthesized comments):
</P>
<PRE># Bond potential for harmonic (one or more comment or blank lines)
</PRE>
<PRE>HAM (keyword is the first text on line)
N 101 FP 0 0 EQ 0.5 (N, FP, EQ parameters)
(blank line)
1 0.00 338.0000 1352.0000 (index, bond-length, energy, force)
2 0.01 324.6152 1324.9600
...
101 1.00 338.0000 -1352.0000
</pre></div>
</div>
<p>A section begins with a non-blank line whose 1st character is not a
&#8220;#&#8221;; blank lines or lines starting with &#8220;#&#8221; can be used as comments
101 1.00 338.0000 -1352.0000
</PRE>
<P>A section begins with a non-blank line whose 1st character is not a
"#"; blank lines or lines starting with "#" can be used as comments
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
initial text must match the argument specified in the
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> command. The next line lists (in any
<A HREF = "bond_coeff.html">bond_coeff</A> command. The next line lists (in any
order) one or more parameters for the table. Each parameter is a
keyword followed by one or more numeric values.</p>
<p>The parameter &#8220;N&#8221; is required and its value is the number of table
entries that follow. Note that this may be different than the <em>N</em>
specified in the <a class="reference internal" href="bond_style.html"><em>bond_style table</em></a> command. Let
Ntable = <em>N</em> in the bond_style command, and Nfile = &#8220;N&#8221; in the
keyword followed by one or more numeric values.
</P>
<P>The parameter "N" is required and its value is the number of table
entries that follow. Note that this may be different than the <I>N</I>
specified in the <A HREF = "bond_style.html">bond_style table</A> command. Let
Ntable = <I>N</I> in the bond_style command, and Nfile = "N" in the
tabulated file. What LAMMPS does is a preliminary interpolation by
creating splines using the Nfile tabulated values as nodal points. It
uses these to interpolate as needed to generate energy and force
@ -208,117 +93,68 @@ Ntable are then used as described above, when computing energy and
force for individual bond lengths. This means that if you want the
interpolation tables of length Ntable to match exactly what is in the
tabulated file (with effectively no preliminary interpolation), you
should set Ntable = Nfile.</p>
<p>The &#8220;FP&#8221; parameter is optional. If used, it is followed by two values
should set Ntable = Nfile.
</P>
<P>The "FP" parameter is optional. If used, it is followed by two values
fplo and fphi, which are the derivatives of the force at the innermost
and outermost bond lengths. These values are needed by the spline
construction routines. If not specified by the &#8220;FP&#8221; parameter, they
construction routines. If not specified by the "FP" parameter, they
are estimated (less accurately) by the first two and last two force
values in the table.</p>
<p>The &#8220;EQ&#8221; parameter is also optional. If used, it is followed by a the
equilibrium bond length, which is used, for example, by the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command. If not used, the equilibrium bond
length is set to 0.0.</p>
<p>Following a blank line, the next N lines list the tabulated values.
values in the table.
</P>
<P>The "EQ" parameter is also optional. If used, it is followed by a the
equilibrium bond length, which is used, for example, by the <A HREF = "fix_shake.html">fix
shake</A> command. If not used, the equilibrium bond
length is set to 0.0.
</P>
<P>Following a blank line, the next N lines list the tabulated values.
On each line, the 1st value is the index from 1 to N, the 2nd value is
the bond length r (in distance units), the 3rd value is the energy (in
energy units), and the 4th is the force (in force units). The bond
lengths must range from a LO value to a HI value, and increase from
one line to the next. If the actual bond length is ever smaller than
the LO value or larger than the HI value, then the bond energy and
force is evaluated as if the bond were the LO or HI length.</p>
<p>Note that one file can contain many sections, each with a tabulated
force is evaluated as if the bond were the LO or HI length.
</P>
<P>Note that one file can contain many sections, each with a tabulated
potential. LAMMPS reads the file section by section until it finds
one that matches the specified keyword.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
one that matches the specified keyword.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info on packages.</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 class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>, <a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
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<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

View File

@ -1,282 +1,106 @@
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<div class="section" id="boundary-command">
<span id="index-0"></span><h1>boundary command<a class="headerlink" href="#boundary-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>boundary x y z
</pre></div>
</div>
<ul class="simple">
<li>x,y,z = <em>p</em> or <em>s</em> or <em>f</em> or <em>m</em>, one or two letters</li>
</ul>
<pre class="literal-block">
<em>p</em> is periodic
<em>f</em> is non-periodic and fixed
<em>s</em> is non-periodic and shrink-wrapped
<em>m</em> is non-periodic and shrink-wrapped with a minimum value
</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>boundary p p f
<HR>
<H3>boundary command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>boundary x y z
</PRE>
<UL><LI>x,y,z = <I>p</I> or <I>s</I> or <I>f</I> or <I>m</I>, one or two letters
<PRE> <I>p</I> is periodic
<I>f</I> is non-periodic and fixed
<I>s</I> is non-periodic and shrink-wrapped
<I>m</I> is non-periodic and shrink-wrapped with a minimum value
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>boundary p p f
boundary p fs p
boundary s f fm
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Set the style of boundaries for the global simulation box in each
boundary s f fm
</PRE>
<P><B>Description:</B>
</P>
<P>Set the style of boundaries for the global simulation box in each
dimension. A single letter assigns the same style to both the lower
and upper face of the box. Two letters assigns the first style to the
lower face and the second style to the upper face. The initial size
of the simulation box is set by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>,
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a>, or <a class="reference internal" href="create_box.html"><em>create_box</em></a>
commands.</p>
<p>The style <em>p</em> means the box is periodic, so that particles interact
of the simulation box is set by the <A HREF = "read_data.html">read_data</A>,
<A HREF = "read_restart.html">read_restart</A>, or <A HREF = "create_box.html">create_box</A>
commands.
</P>
<P>The style <I>p</I> means the box is periodic, so that particles interact
across the boundary, and they can exit one end of the box and re-enter
the other end. A periodic dimension can change in size due to
constant pressure boundary conditions or box deformation (see the <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> and <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> commands). The <em>p</em>
style must be applied to both faces of a dimension.</p>
<p>The styles <em>f</em>, <em>s</em>, and <em>m</em> mean the box is non-periodic, so that
constant pressure boundary conditions or box deformation (see the <A HREF = "fix_nh.html">fix
npt</A> and <A HREF = "fix_deform.html">fix deform</A> commands). The <I>p</I>
style must be applied to both faces of a dimension.
</P>
<P>The styles <I>f</I>, <I>s</I>, and <I>m</I> mean the box is non-periodic, so that
particles do not interact across the boundary and do not move from one
side of the box to the other.</p>
<p>For style <em>f</em>, the position of the face is fixed. If an atom moves
side of the box to the other.
</P>
<P>For style <I>f</I>, the position of the face is fixed. If an atom moves
outside the face it will be deleted on the next timestep that
reneighboring occurs. This will typically generate an error unless
you have set the <a class="reference internal" href="thermo_modify.html"><em>thermo_modify lost</em></a> option to
allow for lost atoms.</p>
<p>For style <em>s</em>, the position of the face is set so as to encompass the
you have set the <A HREF = "thermo_modify.html">thermo_modify lost</A> option to
allow for lost atoms.
</P>
<P>For style <I>s</I>, the position of the face is set so as to encompass the
atoms in that dimension (shrink-wrapping), no matter how far they
move.</p>
<p>For style <em>m</em>, shrink-wrapping occurs, but is bounded by the value
move.
</P>
<P>For style <I>m</I>, shrink-wrapping occurs, but is bounded by the value
specified in the data or restart file or set by the
<a class="reference internal" href="create_box.html"><em>create_box</em></a> command. For example, if the upper z
<A HREF = "create_box.html">create_box</A> command. For example, if the upper z
face has a value of 50.0 in the data file, the face will always be
positioned at 50.0 or above, even if the maximum z-extent of all the
atoms becomes less than 50.0. This can be useful if you start a
simulation with an empty box or if you wish to leave room on one side
of the box, e.g. for atoms to evaporate from a surface.</p>
<p>For triclinic (non-orthogonal) simulation boxes, if the 2nd dimension
of the box, e.g. for atoms to evaporate from a surface.
</P>
<P>For triclinic (non-orthogonal) simulation boxes, if the 2nd dimension
of a tilt factor (e.g. y for xy) is periodic, then the periodicity is
enforced with the tilt factor offset. If the 1st dimension is
shrink-wrapped, then the shrink wrapping is applied to the tilted box
face, to encompass the atoms. E.g. for a positive xy tilt, the xlo
and xhi faces of the box are planes tilting in the +y direction as y
increases. These tilted planes are shrink-wrapped around the atoms to
determine the x extent of the box.</p>
<p>See <a class="reference internal" href="Section_howto.html#howto-12"><span>Section_howto 12</span></a> of the doc pages
determine the x extent of the box.
</P>
<P>See <A HREF = "Section_howto.html#howto_12">Section_howto 12</A> of the doc pages
for a geometric description of triclinic boxes, as defined by LAMMPS,
and how to transform these parameters to and from other commonly used
triclinic representations.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This command cannot be used after the simulation box is defined by a
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="create_box.html"><em>create_box</em></a> command or
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command. See the
<a class="reference internal" href="change_box.html"><em>change_box</em></a> command for how to change the simulation
box boundaries after it has been defined.</p>
<p>For 2d simulations, the z dimension must be periodic.</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>See the <a class="reference internal" href="thermo_modify.html"><em>thermo_modify</em></a> command for a discussion
of lost atoms.</p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>boundary p p p
</pre></div>
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triclinic representations.
</P>
<P><B>Restrictions:</B>
</P>
<P>This command cannot be used after the simulation box is defined by a
<A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command or
<A HREF = "read_restart.html">read_restart</A> command. See the
<A HREF = "change_box.html">change_box</A> command for how to change the simulation
box boundaries after it has been defined.
</P>
<P>For 2d simulations, the z dimension must be periodic.
</P>
<P><B>Related commands:</B>
</P>
<P>See the <A HREF = "thermo_modify.html">thermo_modify</A> command for a discussion
of lost atoms.
</P>
<P><B>Default:</B>
</P>
<PRE>boundary p p p
</PRE>
</HTML>

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<div class="section" id="box-command">
<span id="index-0"></span><h1>box command<a class="headerlink" href="#box-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>box keyword value ...
</pre></div>
</div>
<ul class="simple">
<li>one or more keyword/value pairs may be appended</li>
<li>keyword = <em>tilt</em></li>
</ul>
<pre class="literal-block">
<em>tilt</em> value = <em>small</em> or <em>large</em>
</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>box tilt large
box tilt small
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Set attributes of the simulation box.</p>
<p>For triclinic (non-orthogonal) simulation boxes, the <em>tilt</em> keyword
<HR>
<H3>box command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>box keyword value ...
</PRE>
<UL><LI>one or more keyword/value pairs may be appended
<LI>keyword = <I>tilt</I>
<PRE> <I>tilt</I> value = <I>small</I> or <I>large</I>
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>box tilt large
box tilt small
</PRE>
<P><B>Description:</B>
</P>
<P>Set attributes of the simulation box.
</P>
<P>For triclinic (non-orthogonal) simulation boxes, the <I>tilt</I> keyword
allows simulation domains to be created with arbitrary tilt factors,
e.g. via the <a class="reference internal" href="create_box.html"><em>create_box</em></a> or
<a class="reference internal" href="read_data.html"><em>read_data</em></a> commands. Tilt factors determine how
skewed the triclinic box is; see <a class="reference internal" href="Section_howto.html#howto-12"><span>this section</span></a> of the manual for a discussion of
triclinic boxes in LAMMPS.</p>
<p>LAMMPS normally requires that no tilt factor can skew the box more
e.g. via the <A HREF = "create_box.html">create_box</A> or
<A HREF = "read_data.html">read_data</A> commands. Tilt factors determine how
skewed the triclinic box is; see <A HREF = "Section_howto.html#howto_12">this
section</A> of the manual for a discussion of
triclinic boxes in LAMMPS.
</P>
<P>LAMMPS normally requires that no tilt factor can skew the box more
than half the distance of the parallel box length, which is the 1st
dimension in the tilt factor (x for xz). If <em>tilt</em> is set to
<em>small</em>, which is the default, then an error will be
generated if a box is created which exceeds this limit. If <em>tilt</em>
is set to <em>large</em>, then no limit is enforced. You can create
a box with any tilt factors you wish.</p>
<p>Note that if a simulation box has a large tilt factor, LAMMPS will run
dimension in the tilt factor (x for xz). If <I>tilt</I> is set to
<I>small</I>, which is the default, then an error will be
generated if a box is created which exceeds this limit. If <I>tilt</I>
is set to <I>large</I>, then no limit is enforced. You can create
a box with any tilt factors you wish.
</P>
<P>Note that if a simulation box has a large tilt factor, LAMMPS will run
less efficiently, due to the large volume of communication needed to
acquire ghost atoms around a processor&#8217;s irregular-shaped sub-domain.
acquire ghost atoms around a processor's irregular-shaped sub-domain.
For extreme values of tilt, LAMMPS may also lose atoms and generate an
error.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This command cannot be used after the simulation box is defined by a
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="create_box.html"><em>create_box</em></a> command or
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command.</p>
<p><strong>Related commands:</strong> none</p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The default value is tilt = small.</p>
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error.
</P>
<P><B>Restrictions:</B>
</P>
<P>This command cannot be used after the simulation box is defined by a
<A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command or
<A HREF = "read_restart.html">read_restart</A> command.
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B>
</P>
<P>The default value is tilt = small.
</P>
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@ -1,188 +1,69 @@
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<li>change_box command</li>
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<div class="section" id="change-box-command">
<span id="index-0"></span><h1>change_box command<a class="headerlink" href="#change-box-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>change_box group-ID parameter args ... keyword args ...
</pre></div>
</div>
<ul class="simple">
<li>group-ID = ID of group of atoms to (optionally) displace</li>
<li>one or more parameter/arg pairs may be appended</li>
</ul>
<pre class="literal-block">
parameter = <em>x</em> or <em>y</em> or <em>z</em> or <em>xy</em> or <em>xz</em> or <em>yz</em> or <em>boundary</em> or <em>ortho</em> or <em>triclinic</em> or <em>set</em> or <em>remap</em>
<em>x</em>, <em>y</em>, <em>z</em> args = style value(s)
style = <em>final</em> or <em>delta</em> or <em>scale</em> or <em>volume</em>
<em>final</em> values = lo hi
<HR>
<H3>change_box command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>change_box group-ID parameter args ... keyword args ...
</PRE>
<UL><LI>group-ID = ID of group of atoms to (optionally) displace
<LI>one or more parameter/arg pairs may be appended
<PRE>parameter = <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>xz</I> or <I>yz</I> or <I>boundary</I> or <I>ortho</I> or <I>triclinic</I> or <I>set</I> or <I>remap</I>
<I>x</I>, <I>y</I>, <I>z</I> args = style value(s)
style = <I>final</I> or <I>delta</I> or <I>scale</I> or <I>volume</I>
<I>final</I> values = lo hi
lo hi = box boundaries after displacement (distance units)
<em>delta</em> values = dlo dhi
<I>delta</I> values = dlo dhi
dlo dhi = change in box boundaries after displacement (distance units)
<em>scale</em> values = factor
<I>scale</I> values = factor
factor = multiplicative factor for change in box length after displacement
<em>volume</em> value = none = adjust this dim to preserve volume of system
<em>xy</em>, <em>xz</em>, <em>yz</em> args = style value
style = <em>final</em> or <em>delta</em>
<em>final</em> value = tilt
<I>volume</I> value = none = adjust this dim to preserve volume of system
<I>xy</I>, <I>xz</I>, <I>yz</I> args = style value
style = <I>final</I> or <I>delta</I>
<I>final</I> value = tilt
tilt = tilt factor after displacement (distance units)
<em>delta</em> value = dtilt
<I>delta</I> value = dtilt
dtilt = change in tilt factor after displacement (distance units)
<em>boundary</em> args = x y z
x,y,z = <em>p</em> or <em>s</em> or <em>f</em> or <em>m</em>, one or two letters
<em>p</em> is periodic
<em>f</em> is non-periodic and fixed
<em>s</em> is non-periodic and shrink-wrapped
<em>m</em> is non-periodic and shrink-wrapped with a minimum value
<em>ortho</em> args = none = change box to orthogonal
<em>triclinic</em> args = none = change box to triclinic
<em>set</em> args = none = store state of current box
<em>remap</em> args = none = remap atom coords from last saved state to current box
</pre>
<ul class="simple">
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>units</em></li>
</ul>
<pre class="literal-block">
<em>units</em> value = <em>lattice</em> or <em>box</em>
<I>boundary</I> args = x y z
x,y,z = <I>p</I> or <I>s</I> or <I>f</I> or <I>m</I>, one or two letters
<I>p</I> is periodic
<I>f</I> is non-periodic and fixed
<I>s</I> is non-periodic and shrink-wrapped
<I>m</I> is non-periodic and shrink-wrapped with a minimum value
<I>ortho</I> args = none = change box to orthogonal
<I>triclinic</I> args = none = change box to triclinic
<I>set</I> args = none = store state of current box
<I>remap</I> args = none = remap atom coords from last saved state to current box
</PRE>
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>units</I>
<PRE> <I>units</I> value = <I>lattice</I> or <I>box</I>
lattice = distances are defined in lattice units
box = distances are defined in simulation box units
</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>change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box
change_box all x scale 1.1 y volume z volume remap
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Change the volume and/or shape and/or boundary conditions for the
box = distances are defined in simulation box units
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box
change_box all x scale 1.1 y volume z volume remap
</PRE>
<P><B>Description:</B>
</P>
<P>Change the volume and/or shape and/or boundary conditions for the
simulation box. Orthogonal simulation boxes have 3 adjustable size
parameters (x,y,z). Triclinic (non-orthogonal) simulation boxes have
6 adjustable size/shape parameters (x,y,z,xy,xz,yz). Any or all of
@ -190,59 +71,60 @@ them can be adjusted independently by this command. Thus it can be
used to expand or contract a box, or to apply a shear strain to a
non-orthogonal box. It can also be used to change the boundary
conditions for the simulation box, similar to the
<a class="reference internal" href="boundary.html"><em>boundary</em></a> command.</p>
<p>The size and shape of the initial simulation box are specified by the
<a class="reference internal" href="create_box.html"><em>create_box</em></a> or <a class="reference internal" href="read_data.html"><em>read_data</em></a> or
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command used to setup the simulation.
<A HREF = "boundary.html">boundary</A> command.
</P>
<P>The size and shape of the initial simulation box are specified by the
<A HREF = "create_box.html">create_box</A> or <A HREF = "read_data.html">read_data</A> or
<A HREF = "read_restart.html">read_restart</A> command used to setup the simulation.
The size and shape may be altered by subsequent runs, e.g. by use of
the <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> or <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> commands.
The <a class="reference internal" href="create_box.html"><em>create_box</em></a>, <a class="reference internal" href="read_data.html"><em>read data</em></a>, and
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands also determine whether the
the <A HREF = "fix_nh.html">fix npt</A> or <A HREF = "fix_deform.html">fix deform</A> commands.
The <A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read data</A>, and
<A HREF = "read_restart.html">read_restart</A> commands also determine whether the
simulation box is orthogonal or triclinic and their doc pages explain
the meaning of the xy,xz,yz tilt factors.</p>
<p>See <a class="reference internal" href="Section_howto.html#howto-12"><span>Section_howto 12</span></a> of the doc pages
the meaning of the xy,xz,yz tilt factors.
</P>
<P>See <A HREF = "Section_howto.html#howto_12">Section_howto 12</A> of the doc pages
for a geometric description of triclinic boxes, as defined by LAMMPS,
and how to transform these parameters to and from other commonly used
triclinic representations.</p>
<p>The keywords used in this command are applied sequentially to the
simulation box and the atoms in it, in the order specified.</p>
<p>Before the sequence of keywords are invoked, the current box
size/shape is stored, in case a <em>remap</em> keyword is used to map the
triclinic representations.
</P>
<P>The keywords used in this command are applied sequentially to the
simulation box and the atoms in it, in the order specified.
</P>
<P>Before the sequence of keywords are invoked, the current box
size/shape is stored, in case a <I>remap</I> keyword is used to map the
atom coordinates from a previously stored box size/shape to the
current one.</p>
<p>After all the keywords have been processed, any shrink-wrap boundary
conditions are invoked (see the <a class="reference internal" href="boundary.html"><em>boundary</em></a> command)
current one.
</P>
<P>After all the keywords have been processed, any shrink-wrap boundary
conditions are invoked (see the <A HREF = "boundary.html">boundary</A> command)
which may change simulation box boundaries, and atoms are migrated to
new owning processors.</p>
<p>IMPORTANT_NOTE: This means that you cannot use the change_box command
new owning processors.
</P>
<P>IMPORTANT_NOTE: This means that you cannot use the change_box command
to enlarge a shrink-wrapped box, e.g. to make room to insert more
atoms via the <a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a> command, because the
atoms via the <A HREF = "create_atoms.html">create_atoms</A> command, because the
simulation box will be re-shrink-wrapped before the change_box command
completes. Instead you could do something like this, assuming the
simulation box is non-periodic and atoms extend from 0 to 20 in all
dimensions:</p>
<div class="highlight-python"><div class="highlight"><pre>change_box all x final -10 20
create_atoms 1 single -5 5 5 # this will fail to insert an atom
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>change_box all x final -10 20 boundary f s s
dimensions:
</P>
<PRE>change_box all x final -10 20
create_atoms 1 single -5 5 5 # this will fail to insert an atom
</PRE>
<PRE>change_box all x final -10 20 boundary f s s
create_atoms 1 single -5 5 5
change_box boundary s s s # this will work
</pre></div>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Unlike the earlier &#8220;displace_box&#8221; version of this
change_box boundary s s s # this will work
</PRE>
<P>IMPORTANT NOTE: Unlike the earlier "displace_box" version of this
command, atom remapping is NOT performed by default. This command
allows remapping to be done in a more general way, exactly when you
specify it (zero or more times) in the sequence of transformations.
Thus if you do not use the <em>remap</em> keyword, atom coordinates will not
Thus if you do not use the <I>remap</I> keyword, atom coordinates will not
be changed even if the box size/shape changes. If a uniformly
strained state is desired, the <em>remap</em> keyword should be specified.</p>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">It is possible to lose atoms with this command.
strained state is desired, the <I>remap</I> keyword should be specified.
</P>
<P>IMPORTANT NOTE: It is possible to lose atoms with this command.
E.g. by changing the box without remapping the atoms, and having atoms
end up outside of non-periodic boundaries. It is also possible to
alter bonds between atoms straddling a boundary in bad ways. E.g. by
@ -250,95 +132,101 @@ converting a boundary from periodic to non-periodic. It is also
possible when remapping atoms to put them (nearly) on top of each
other. E.g. by converting a boundary from non-periodic to periodic.
All of these will typically lead to bad dynamics and/or generate error
messages.</p>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The simulation box size/shape can be changed by
messages.
</P>
<P>IMPORTANT NOTE: The simulation box size/shape can be changed by
arbitrarily large amounts by this command. This is not a problem,
except that the mapping of processors to the simulation box is not
changed from its initial 3d configuration; see the
<a class="reference internal" href="processors.html"><em>processors</em></a> command. Thus, if the box size/shape
<A HREF = "processors.html">processors</A> command. Thus, if the box size/shape
changes dramatically, the mapping of processors to the simulation box
may not end up as optimal as the initial mapping attempted to be.</p>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Because the keywords used in this command are applied
may not end up as optimal as the initial mapping attempted to be.
</P>
<P>IMPORTANT NOTE: Because the keywords used in this command are applied
one at a time to the simulation box and the atoms in it, care must be
taken with triclinic cells to avoid exceeding the limits on skew after
each transformation in the sequence. If skew is exceeded before the
final transformation this can be avoided by changing the order of the
sequence, or breaking the transformation into two or more smaller
transformations. For more information on the allowed limits for box
skew see the discussion on triclinic boxes on <a class="reference internal" href="Section_howto.html#howto-12"><span>this page</span></a>.</p>
</div>
<hr class="docutils" />
<p>For the <em>x</em>, <em>y</em>, and <em>z</em> parameters, this is the meaning of their
styles and values.</p>
<p>For style <em>final</em>, the final lo and hi box boundaries of a dimension
skew see the discussion on triclinic boxes on <A HREF = "Section_howto.html#howto_12">this
page</A>.
</P>
<HR>
<P>For the <I>x</I>, <I>y</I>, and <I>z</I> parameters, this is the meaning of their
styles and values.
</P>
<P>For style <I>final</I>, the final lo and hi box boundaries of a dimension
are specified. The values can be in lattice or box distance units.
See the discussion of the units keyword below.</p>
<p>For style <em>delta</em>, plus or minus changes in the lo/hi box boundaries
See the discussion of the units keyword below.
</P>
<P>For style <I>delta</I>, plus or minus changes in the lo/hi box boundaries
of a dimension are specified. The values can be in lattice or box
distance units. See the discussion of the units keyword below.</p>
<p>For style <em>scale</em>, a multiplicative factor to apply to the box length
distance units. See the discussion of the units keyword below.
</P>
<P>For style <I>scale</I>, a multiplicative factor to apply to the box length
of a dimension is specified. For example, if the initial box length
is 10, and the factor is 1.1, then the final box length will be 11. A
factor less than 1.0 means compression.</p>
<p>The <em>volume</em> style changes the specified dimension in such a way that
factor less than 1.0 means compression.
</P>
<P>The <I>volume</I> style changes the specified dimension in such a way that
the overall box volume remains constant with respect to the operation
performed by the preceding keyword. The <em>volume</em> style can only be
performed by the preceding keyword. The <I>volume</I> style can only be
used following a keyword that changed the volume, which is any of the
<em>x</em>, <em>y</em>, <em>z</em> keywords. If the preceding keyword &#8220;key&#8221; had a <em>volume</em>
<I>x</I>, <I>y</I>, <I>z</I> keywords. If the preceding keyword "key" had a <I>volume</I>
style, then both it and the current keyword apply to the keyword
preceding &#8220;key&#8221;. I.e. this sequence of keywords is allowed:</p>
<div class="highlight-python"><div class="highlight"><pre>change_box all x scale 1.1 y volume z volume
</pre></div>
</div>
<p>The <em>volume</em> style changes the associated dimension so that the
preceding "key". I.e. this sequence of keywords is allowed:
</P>
<PRE>change_box all x scale 1.1 y volume z volume
</PRE>
<P>The <I>volume</I> style changes the associated dimension so that the
overall box volume is unchanged relative to its value before the
preceding keyword was invoked.</p>
<p>If the following command is used, then the z box length will shrink by
the same 1.1 factor the x box length was increased by:</p>
<div class="highlight-python"><div class="highlight"><pre>change_box all x scale 1.1 z volume
</pre></div>
</div>
<p>If the following command is used, then the y,z box lengths will each
preceding keyword was invoked.
</P>
<P>If the following command is used, then the z box length will shrink by
the same 1.1 factor the x box length was increased by:
</P>
<PRE>change_box all x scale 1.1 z volume
</PRE>
<P>If the following command is used, then the y,z box lengths will each
shrink by sqrt(1.1) to keep the volume constant. In this case, the
y,z box lengths shrink so as to keep their relative aspect ratio
constant:</p>
<div class="highlight-python"><div class="highlight"><pre>change_box all&quot;x scale 1.1 y volume z volume
</pre></div>
</div>
<p>If the following command is used, then the final box will be a factor
constant:
</P>
<PRE>change_box all"x scale 1.1 y volume z volume
</PRE>
<P>If the following command is used, then the final box will be a factor
of 10% larger in x and y, and a factor of 21% smaller in z, so as to
keep the volume constant:</p>
<div class="highlight-python"><div class="highlight"><pre>change_box all x scale 1.1 z volume y scale 1.1 z volume
</pre></div>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">For solids or liquids, when one dimension of the box
keep the volume constant:
</P>
<PRE>change_box all x scale 1.1 z volume y scale 1.1 z volume
</PRE>
<P>IMPORTANT NOTE: For solids or liquids, when one dimension of the box
is expanded, it may be physically undesirable to hold the other 2 box
lengths constant since that implies a density change. For solids,
adjusting the other dimensions via the <em>volume</em> style may make
adjusting the other dimensions via the <I>volume</I> style may make
physical sense (just as for a liquid), but may not be correct for
materials and potentials whose Poisson ratio is not 0.5.</p>
</div>
<p>For the <em>scale</em> and <em>volume</em> styles, the box length is expanded or
compressed around its mid point.</p>
<hr class="docutils" />
<p>For the <em>xy</em>, <em>xz</em>, and <em>yz</em> parameters, this is the meaning of their
materials and potentials whose Poisson ratio is not 0.5.
</P>
<P>For the <I>scale</I> and <I>volume</I> styles, the box length is expanded or
compressed around its mid point.
</P>
<HR>
<P>For the <I>xy</I>, <I>xz</I>, and <I>yz</I> parameters, this is the meaning of their
styles and values. Note that changing the tilt factors of a triclinic
box does not change its volume.</p>
<p>For style <em>final</em>, the final tilt factor is specified. The value
box does not change its volume.
</P>
<P>For style <I>final</I>, the final tilt factor is specified. The value
can be in lattice or box distance units. See the discussion of the
units keyword below.</p>
<p>For style <em>delta</em>, a plus or minus change in the tilt factor is
units keyword below.
</P>
<P>For style <I>delta</I>, a plus or minus change in the tilt factor is
specified. The value can be in lattice or box distance units. See
the discussion of the units keyword below.</p>
<p>All of these styles change the xy, xz, yz tilt factors. In LAMMPS,
the discussion of the units keyword below.
</P>
<P>All of these styles change the xy, xz, yz tilt factors. In LAMMPS,
tilt factors (xy,xz,yz) for triclinic boxes are required to be no more
than half the distance of the parallel box length. For example, if
xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt
@ -347,152 +235,108 @@ between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a
limitation, since if the maximum tilt factor is 5 (as in this
example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
... are all equivalent. Any tilt factor specified by this command
must be within these limits.</p>
<hr class="docutils" />
<p>The <em>boundary</em> keyword takes arguments that have exactly the same
meaning as they do for the <a class="reference internal" href="boundary.html"><em>boundary</em></a> command. In each
must be within these limits.
</P>
<HR>
<P>The <I>boundary</I> keyword takes arguments that have exactly the same
meaning as they do for the <A HREF = "boundary.html">boundary</A> command. In each
dimension, a single letter assigns the same style to both the lower
and upper face of the box. Two letters assigns the first style to the
lower face and the second style to the upper face.</p>
<p>The style <em>p</em> means the box is periodic; the other styles mean
non-periodic. For style <em>f</em>, the position of the face is fixed. For
style <em>s</em>, the position of the face is set so as to encompass the
lower face and the second style to the upper face.
</P>
<P>The style <I>p</I> means the box is periodic; the other styles mean
non-periodic. For style <I>f</I>, the position of the face is fixed. For
style <I>s</I>, the position of the face is set so as to encompass the
atoms in that dimension (shrink-wrapping), no matter how far they
move. For style <em>m</em>, shrink-wrapping occurs, but is bounded by the
move. For style <I>m</I>, shrink-wrapping occurs, but is bounded by the
current box edge in that dimension, so that the box will become no
smaller. See the <a class="reference internal" href="boundary.html"><em>boundary</em></a> command for more
explanation of these style options.</p>
<p>Note that the &#8220;boundary&#8221; command itself can only be used before the
simulation box is defined via a <a class="reference internal" href="read_data.html"><em>read_data</em></a> or
<a class="reference internal" href="create_box.html"><em>create_box</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
smaller. See the <A HREF = "boundary.html">boundary</A> command for more
explanation of these style options.
</P>
<P>Note that the "boundary" command itself can only be used before the
simulation box is defined via a <A HREF = "read_data.html">read_data</A> or
<A HREF = "create_box.html">create_box</A> or <A HREF = "read_restart.html">read_restart</A>
command. This command allows the boundary conditions to be changed
later in your input script. Also note that the
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> will change boundary conditions to
<A HREF = "read_restart.html">read_restart</A> will change boundary conditions to
match what is stored in the restart file. So if you wish to change
them, you should use the change_box command after the read_restart
command.</p>
<hr class="docutils" />
<p>The <em>ortho</em> and <em>triclinic</em> keywords convert the simulation box to be
orthogonal or triclinic (non-orthongonal). See <a class="reference internal" href="Section_howto.html#howto-13"><span>this section</span></a> for a discussion of how non-orthongal
boxes are represented in LAMMPS.</p>
<p>The simulation box is defined as either orthogonal or triclinic when
it is created via the <a class="reference internal" href="create_box.html"><em>create_box</em></a>,
<a class="reference internal" href="read_data.html"><em>read_data</em></a>, or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands.</p>
<p>These keywords allow you to toggle the existing simulation box from
command.
</P>
<HR>
<P>The <I>ortho</I> and <I>triclinic</I> keywords convert the simulation box to be
orthogonal or triclinic (non-orthongonal). See <A HREF = "Section_howto#howto_13">this
section</A> for a discussion of how non-orthongal
boxes are represented in LAMMPS.
</P>
<P>The simulation box is defined as either orthogonal or triclinic when
it is created via the <A HREF = "create_box.html">create_box</A>,
<A HREF = "read_data.html">read_data</A>, or <A HREF = "read_restart.html">read_restart</A>
commands.
</P>
<P>These keywords allow you to toggle the existing simulation box from
orthogonal to triclinic and vice versa. For example, an initial
equilibration simulation can be run in an orthogonal box, the box can
be toggled to triclinic, and then a <a class="reference internal" href="Section_howto.html#howto-13"><span>non-equilibrium MD (NEMD) simulation</span></a> can be run with deformation
via the <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> command.</p>
<p>If the simulation box is currently triclinic and has non-zero tilt in
xy, yz, or xz, then it cannot be converted to an orthogonal box.</p>
<hr class="docutils" />
<p>The <em>set</em> keyword saves the current box size/shape. This can be
useful if you wish to use the <em>remap</em> keyword more than once or if you
be toggled to triclinic, and then a <A HREF = "Section_howto.html#howto_13">non-equilibrium MD (NEMD)
simulation</A> can be run with deformation
via the <A HREF = "fix_deform.html">fix deform</A> command.
</P>
<P>If the simulation box is currently triclinic and has non-zero tilt in
xy, yz, or xz, then it cannot be converted to an orthogonal box.
</P>
<HR>
<P>The <I>set</I> keyword saves the current box size/shape. This can be
useful if you wish to use the <I>remap</I> keyword more than once or if you
wish it to be applied to an intermediate box size/shape in a sequence
of keyword operations. Note that the box size/shape is saved before
any of the keywords are processed, i.e. the box size/shape at the time
the create_box command is encountered in the input script.</p>
<p>The <em>remap</em> keyword remaps atom coordinates from the last saved box
the create_box command is encountered in the input script.
</P>
<P>The <I>remap</I> keyword remaps atom coordinates from the last saved box
size/shape to the current box state. For example, if you stretch the
box in the x dimension or tilt it in the xy plane via the <em>x</em> and <em>xy</em>
keywords, then the <em>remap</em> commmand will dilate or tilt the atoms to
box in the x dimension or tilt it in the xy plane via the <I>x</I> and <I>xy</I>
keywords, then the <I>remap</I> commmand will dilate or tilt the atoms to
conform to the new box size/shape, as if the atoms moved with the box
as it deformed.</p>
<p>Note that this operation is performed without regard to periodic
as it deformed.
</P>
<P>Note that this operation is performed without regard to periodic
boundaries. Also, any shrink-wrapping of non-periodic boundaries (see
the <a class="reference internal" href="boundary.html"><em>boundary</em></a> command) occurs after all keywords,
including this one, have been processed.</p>
<p>Only atoms in the specified group are remapped.</p>
<hr class="docutils" />
<p>The <em>units</em> keyword determines the meaning of the distance units used
to define various arguments. A <em>box</em> value selects standard distance
units as defined by the <a class="reference internal" href="units.html"><em>units</em></a> command, e.g. Angstroms for
units = real or metal. A <em>lattice</em> value means the distance units are
in lattice spacings. The <a class="reference internal" href="lattice.html"><em>lattice</em></a> command must have
been previously used to define the lattice spacing.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>If you use the <em>ortho</em> or <em>triclinic</em> keywords, then at the point in
the input script when this command is issued, no <a class="reference internal" href="dump.html"><em>dumps</em></a> can
be active, nor can a <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a> or <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> be active. This is because these commands
the <A HREF = "boundary.html">boundary</A> command) occurs after all keywords,
including this one, have been processed.
</P>
<P>Only atoms in the specified group are remapped.
</P>
<HR>
<P>The <I>units</I> keyword determines the meaning of the distance units used
to define various arguments. A <I>box</I> value selects standard distance
units as defined by the <A HREF = "units.html">units</A> command, e.g. Angstroms for
units = real or metal. A <I>lattice</I> value means the distance units are
in lattice spacings. The <A HREF = "lattice.html">lattice</A> command must have
been previously used to define the lattice spacing.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>If you use the <I>ortho</I> or <I>triclinic</I> keywords, then at the point in
the input script when this command is issued, no <A HREF = "dump.html">dumps</A> can
be active, nor can a <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> or <A HREF = "fix_deform.html">fix
deform</A> be active. This is because these commands
test whether the simulation box is orthogonal when they are first
issued. Note that these commands can be used in your script before a
change_box command is issued, so long as an <a class="reference internal" href="undump.html"><em>undump</em></a> or
<a class="reference internal" href="unfix.html"><em>unfix</em></a> command is also used to turn them off.</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 class="reference internal" href="fix_deform.html"><em>fix deform</em></a>, <a class="reference internal" href="boundary.html"><em>boundary</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The option default is units = lattice.</p>
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<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_deform.html">fix deform</A>, <A HREF = "boundary.html">boundary</A>
</P>
<P><B>Default:</B>
</P>
<P>The option default is units = lattice.
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<div class="section" id="clear-command">
<span id="index-0"></span><h1>clear command<a class="headerlink" href="#clear-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><span class="n">clear</span>
</pre></div>
</div>
</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>(commands for 1st simulation)
<HR>
<H3>clear command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>clear
</PRE>
<P><B>Examples:</B>
</P>
<PRE>(commands for 1st simulation)
clear
(commands for 2nd simulation)
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>This command deletes all atoms, restores all settings to their default
(commands for 2nd simulation)
</PRE>
<P><B>Description:</B>
</P>
<P>This command deletes all atoms, restores all settings to their default
values, and frees all memory allocated by LAMMPS. Once a clear
command has been executed, it is almost as if LAMMPS were starting
over, with only the exceptions noted below. This command enables
multiple jobs to be run sequentially from one input script.</p>
<p>These settings are not affected by a clear command: the working
directory (<a class="reference internal" href="shell.html"><em>shell</em></a> command), log file status
(<a class="reference internal" href="log.html"><em>log</em></a> command), echo status (<a class="reference internal" href="echo.html"><em>echo</em></a> command), and
input script variables (<a class="reference internal" href="variable.html"><em>variable</em></a> command).</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<blockquote>
<div>none</div></blockquote>
<p><strong>Related commands:</strong> none</p>
<p><strong>Default:</strong> none</p>
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multiple jobs to be run sequentially from one input script.
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<P>These settings are not affected by a clear command: the working
directory (<A HREF = "shell.html">shell</A> command), log file status
(<A HREF = "log.html">log</A> command), echo status (<A HREF = "echo.html">echo</A> command), and
input script variables (<A HREF = "variable.html">variable</A> command).
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B> none
</P>
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<div class="section" id="comm-modify-command">
<span id="index-0"></span><h1>comm_modify command<a class="headerlink" href="#comm-modify-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>comm_modify keyword value ...
</pre></div>
</div>
<ul class="simple">
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>mode</em> or <em>cutoff</em> or <em>group</em> or <em>vel</em></li>
</ul>
<pre class="literal-block">
<em>mode</em> value = <em>single</em> or <em>multi</em> = communicate atoms within a single or multiple distances
<em>cutoff</em> value = Rcut (distance units) = communicate atoms from this far away
<em>group</em> value = group-ID = only communicate atoms in the group
<em>vel</em> value = <em>yes</em> or <em>no</em> = do or do not communicate velocity info with ghost atoms
</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>comm_modify mode multi
<HR>
<H3>comm_modify command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>comm_modify keyword value ...
</PRE>
<UL><LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>mode</I> or <I>cutoff</I> or <I>group</I> or <I>vel</I>
<PRE> <I>mode</I> value = <I>single</I> or <I>multi</I> = communicate atoms within a single or multiple distances
<I>cutoff</I> value = Rcut (distance units) = communicate atoms from this far away
<I>group</I> value = group-ID = only communicate atoms in the group
<I>vel</I> value = <I>yes</I> or <I>no</I> = do or do not communicate velocity info with ghost atoms
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>comm_modify mode multi
comm_modify mode multi group solvent
comm_modify vel yes
comm_modify cutoff 5.0 vel yes
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>This command sets parameters that affect the inter-processor
comm_modify cutoff 5.0 vel yes
</PRE>
<P><B>Description:</B>
</P>
<P>This command sets parameters that affect the inter-processor
communication of atom information that occurs each timestep as
coordinates and other properties are exchanged between neighboring
processors and stored as properties of ghost atoms.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">These options apply to the currently defined comm
style. When you specify a <a class="reference internal" href="comm_style.html"><em>comm_style</em></a> command, all
processors and stored as properties of ghost atoms.
</P>
<P>IMPORTANT NOTE: These options apply to the currently defined comm
style. When you specify a <A HREF = "comm_style.html">comm_style</A> command, all
communication settings are restored to their default values, including
those previously reset by a comm_modify command. Thus if your input
script specifies a comm_style command, you should use the comm_modify
command after it.</p>
</div>
<p>The <em>mode</em> keyword determines whether a single or multiple cutoff
distances are used to determine which atoms to communicate.</p>
<p>The default mode is <em>single</em> which means each processor acquires
command after it.
</P>
<P>The <I>mode</I> keyword determines whether a single or multiple cutoff
distances are used to determine which atoms to communicate.
</P>
<P>The default mode is <I>single</I> which means each processor acquires
information for ghost atoms that are within a single distance from its
sub-domain. The distance is the maximum of the neighbor cutoff for
all atom type pairs.</p>
<p>For many systems this is an efficient algorithm, but for systems with
widely varying cutoffs for different type pairs, the <em>multi</em> mode can
all atom type pairs.
</P>
<P>For many systems this is an efficient algorithm, but for systems with
widely varying cutoffs for different type pairs, the <I>multi</I> mode can
be faster. In this case, each atom type is assigned its own distance
cutoff for communication purposes, and fewer atoms will be
communicated. See the <a class="reference internal" href="neighbor.html"><em>neighbor multi</em></a> command for a
communicated. See the <A HREF = "neighbor.html">neighbor multi</A> command for a
neighbor list construction option that may also be beneficial for
simulations of this kind.</p>
<p>The <em>cutoff</em> keyword allows you to set a ghost cutoff distance, which
is the distance from the borders of a processor&#8217;s sub-domain at which
simulations of this kind.
</P>
<P>The <I>cutoff</I> keyword allows you to set a ghost cutoff distance, which
is the distance from the borders of a processor's sub-domain at which
ghost atoms are acquired from other processors. By default the ghost
cutoff = neighbor cutoff = pairwise force cutoff + neighbor skin. See
the <a class="reference internal" href="neighbor.html"><em>neighbor</em></a> command for more information about the
the <A HREF = "neighbor.html">neighbor</A> command for more information about the
skin distance. If the specified Rcut is greater than the neighbor
cutoff, then extra ghost atoms will be acquired. If it is smaller,
the ghost cutoff is set to the neighbor cutoff.</p>
<p>These are simulation scenarios in which it may be useful or even
necessary to set a ghost cutoff &gt; neighbor cutoff:</p>
<ul class="simple">
<li>a single polymer chain with bond interactions, but no pairwise interactions</li>
<li>bonded interactions (e.g. dihedrals) extend further than the pairwise cutoff</li>
<li>ghost atoms beyond the pairwise cutoff are needed for some computation</li>
</ul>
<p>In the first scenario, a pairwise potential is not defined. Thus the
the ghost cutoff is set to the neighbor cutoff.
</P>
<P>These are simulation scenarios in which it may be useful or even
necessary to set a ghost cutoff > neighbor cutoff:
</P>
<UL><LI>a single polymer chain with bond interactions, but no pairwise interactions
<LI>bonded interactions (e.g. dihedrals) extend further than the pairwise cutoff
<LI>ghost atoms beyond the pairwise cutoff are needed for some computation
</UL>
<P>In the first scenario, a pairwise potential is not defined. Thus the
pairwise neighbor cutoff will be 0.0. But ghost atoms are still
needed for computing bond, angle, etc interactions between atoms on
different processors, or when the interaction straddles a periodic
boundary.</p>
<p>The appropriate ghost cutoff depends on the <a class="reference internal" href="newton.html"><em>newton bond</em></a>
setting. For newton bond <em>off</em>, the distance needs to be the furthest
boundary.
</P>
<P>The appropriate ghost cutoff depends on the <A HREF = "newton.html">newton bond</A>
setting. For newton bond <I>off</I>, the distance needs to be the furthest
distance between any two atoms in the bond, angle, etc. E.g. the
distance between 1-4 atoms in a dihedral. For newton bond <em>on</em>, the
distance between 1-4 atoms in a dihedral. For newton bond <I>on</I>, the
distance between the central atom in the bond, angle, etc and any
other atom is sufficient. E.g. the distance between 2-4 atoms in a
dihedral.</p>
<p>In the second scenario, a pairwise potential is defined, but its
dihedral.
</P>
<P>In the second scenario, a pairwise potential is defined, but its
neighbor cutoff is not sufficiently long enough to enable bond, angle,
etc terms to be computed. As in the previous scenario, an appropriate
ghost cutoff should be set.</p>
<p>In the last scenario, a <a class="reference internal" href="fix.html"><em>fix</em></a> or <a class="reference internal" href="compute.html"><em>compute</em></a> or
<a class="reference internal" href="pair_style.html"><em>pairwise potential</em></a> needs to calculate with ghost
ghost cutoff should be set.
</P>
<P>In the last scenario, a <A HREF = "fix.html">fix</A> or <A HREF = "compute.html">compute</A> or
<A HREF = "pair_style.html">pairwise potential</A> needs to calculate with ghost
atoms beyond the normal pairwise cutoff for some computation it
performs (e.g. locate neighbors of ghost atoms in a multibody pair
potential). Setting the ghost cutoff appropriately can insure it will
find the needed atoms.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">In these scenarios, if you do not set the ghost cutoff
find the needed atoms.
</P>
<P>IMPORTANT NOTE: In these scenarios, if you do not set the ghost cutoff
long enough, and if there is only one processor in a periodic
dimension (e.g. you are running in serial), then LAMMPS may &#8220;find&#8221; the
dimension (e.g. you are running in serial), then LAMMPS may "find" the
atom it is looking for (e.g. the partner atom in a bond), that is on
the far side of the simulation box, across a periodic boundary. This
will typically lead to bad dynamics (i.e. the bond length is now the
simulation box length). To detect if this is happening, see the
<a class="reference internal" href="neigh_modify.html"><em>neigh_modify cluster</em></a> command.</p>
</div>
<p>The <em>group</em> keyword will limit communication to atoms in the specified
<A HREF = "neigh_modify.html">neigh_modify cluster</A> command.
</P>
<P>The <I>group</I> keyword will limit communication to atoms in the specified
group. This can be useful for models where no ghost atoms are needed
for some kinds of particles. All atoms (not just those in the
specified group) will still migrate to new processors as they move.
The group specified with this option must also be specified via the
<a class="reference internal" href="atom_modify.html"><em>atom_modify first</em></a> command.</p>
<p>The <em>vel</em> keyword enables velocity information to be communicated with
ghost particles. Depending on the <a class="reference internal" href="atom_style.html"><em>atom_style</em></a>,
<A HREF = "atom_modify.html">atom_modify first</A> command.
</P>
<P>The <I>vel</I> keyword enables velocity information to be communicated with
ghost particles. Depending on the <A HREF = "atom_style.html">atom_style</A>,
velocity info includes the translational velocity, angular velocity,
and angular momentum of a particle. If the <em>vel</em> option is set to
<em>yes</em>, then ghost atoms store these quantities; if <em>no</em> then they do
not. The <em>yes</em> setting is needed by some pair styles which require
and angular momentum of a particle. If the <I>vel</I> option is set to
<I>yes</I>, then ghost atoms store these quantities; if <I>no</I> then they do
not. The <I>yes</I> setting is needed by some pair styles which require
the velocity state of both the I and J particles to compute a pairwise
I,J interaction.</p>
<p>Note that if the <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> command is being used
with its &#8220;remap v&#8221; option enabled, then the velocities for ghost atoms
I,J interaction.
</P>
<P>Note that if the <A HREF = "fix_deform.html">fix deform</A> command is being used
with its "remap v" option enabled, then the velocities for ghost atoms
(in the fix deform group) mirrored across a periodic boundary will
also include components due to any velocity shift that occurs across
that boundary (e.g. due to dilation or shear).</p>
</div>
<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="comm_style.html"><em>comm_style</em></a>, <a class="reference internal" href="neighbor.html"><em>neighbor</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The option defauls are mode = single, group = all, cutoff = 0.0, vel =
that boundary (e.g. due to dilation or shear).
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "comm_style.html">comm_style</A>, <A HREF = "neighbor.html">neighbor</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defauls are mode = single, group = all, cutoff = 0.0, vel =
no. The cutoff default of 0.0 means that ghost cutoff = neighbor
cutoff = pairwise force cutoff + neighbor skin.</p>
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cutoff = pairwise force cutoff + neighbor skin.
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<div class="section" id="comm-style-command">
<span id="index-0"></span><h1>comm_style command<a class="headerlink" href="#comm-style-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>comm_style style
</pre></div>
</div>
<ul class="simple">
<li>style = <em>brick</em> or <em>tiled</em></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>comm_style brick
comm_style tiled
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>This command sets the style of inter-processor communication of atom
<HR>
<H3>comm_style command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>comm_style style
</PRE>
<UL><LI>style = <I>brick</I> or <I>tiled</I>
</UL>
<P><B>Examples:</B>
</P>
<PRE>comm_style brick
comm_style tiled
</PRE>
<P><B>Description:</B>
</P>
<P>This command sets the style of inter-processor communication of atom
information that occurs each timestep as coordinates and other
properties are exchanged between neighboring processors and stored as
properties of ghost atoms.</p>
<p>For the default <em>brick</em> style, the domain decomposition used by LAMMPS
properties of ghost atoms.
</P>
<P>For the default <I>brick</I> style, the domain decomposition used by LAMMPS
to partition the simulation box must be a regular 3d grid of bricks,
one per processor. Each processor communicates with its 6 Cartesian
neighbors in the grid to acquire information for nearby atoms.</p>
<p>For the <em>tiled</em> style, a more general domain decomposition can be
used, as triggered by the <a class="reference internal" href="balance.html"><em>balance</em></a> or <a class="reference internal" href="fix_balance.html"><em>fix balance</em></a> commands. The simulation box can be
partitioned into non-overlapping rectangular-shaped &#8220;tiles&#8221; or varying
neighbors in the grid to acquire information for nearby atoms.
</P>
<P>For the <I>tiled</I> style, a more general domain decomposition can be
used, as triggered by the <A HREF = "balance.html">balance</A> or <A HREF = "fix_balance.html">fix
balance</A> commands. The simulation box can be
partitioned into non-overlapping rectangular-shaped "tiles" or varying
sizes and shapes. Again there is one tile per processor. To acquire
information for nearby atoms, communication must now be done with a
more complex pattern of neighboring processors.</p>
<p>Note that this command does not actually define a partitoining of the
more complex pattern of neighboring processors.
</P>
<P>Note that this command does not actually define a partitoining of the
simulation box (a domain decomposition), rather it determines what
kinds of decompositions are allowed and the pattern of communication
used to enable the decomposition. A decomposition is created when the
simulation box is first created, via the <a class="reference internal" href="create_box.html"><em>create_box</em></a>
or <a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands. For both the <em>brick</em> and <em>tiled</em> styles, the initial
simulation box is first created, via the <A HREF = "create_box.html">create_box</A>
or <A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands. For both the <I>brick</I> and <I>tiled</I> styles, the initial
decomposition will be the same, as described by
<a class="reference internal" href="create_box.html"><em>create_box</em></a> and <a class="reference internal" href="processors.html"><em>processors</em></a>
<A HREF = "create_box.html">create_box</A> and <A HREF = "processors.html">processors</A>
commands. The decomposition can be changed via the
<a class="reference internal" href="balance.html"><em>balance</em></a> or <a class="reference internal" href="fix_balance.html"><em>fix_balance</em></a> commands.</p>
</div>
<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="comm_modify.html"><em>comm_modify</em></a>, <a class="reference internal" href="processors.html"><em>processors</em></a>,
<a class="reference internal" href="balance.html"><em>balance</em></a>, <a class="reference internal" href="fix_balance.html"><em>fix balance</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The default style is brick.</p>
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<A HREF = "balance.html">balance</A> or <A HREF = "fix_balance.html">fix_balance</A> commands.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
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<P><A HREF = "comm_modify.html">comm_modify</A>, <A HREF = "processors.html">processors</A>,
<A HREF = "balance.html">balance</A>, <A HREF = "fix_balance.html">fix balance</A>
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</P>
<P>The default style is brick.
</P>
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@ -1,154 +1,34 @@
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<div class="section" id="compute-command">
<span id="index-0"></span><h1>compute command<a class="headerlink" href="#compute-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 args
</pre></div>
</div>
<ul class="simple">
<li>ID = user-assigned name for the computation</li>
<li>group-ID = ID of the group of atoms to perform the computation on</li>
<li>style = one of a list of possible style names (see below)</li>
<li>args = arguments used by a particular style</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 all temp
<HR>
<H3>compute command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID style args
</PRE>
<UL><LI>ID = user-assigned name for the computation
<LI>group-ID = ID of the group of atoms to perform the computation on
<LI>style = one of a list of possible style names (see below)
<LI>args = arguments used by a particular style
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all temp
compute newtemp flow temp/partial 1 1 0
compute 3 all ke/atom
</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 will be performed on a group of atoms.
compute 3 all ke/atom
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that will be performed on a group of atoms.
Quantities calculated by a compute are instantaneous values, meaning
they are calculated from information about atoms on the current
timestep or iteration, though a compute may internally store some
@ -156,12 +36,15 @@ information about a previous state of the system. Defining a compute
does not perform a computation. Instead computes are invoked by other
LAMMPS commands as needed, e.g. to calculate a temperature needed for
a thermostat fix or to generate thermodynamic or dump file output.
See this <a class="reference internal" href="Section_howto.html#howto-15"><span>howto section</span></a> for a summary of
various LAMMPS output options, many of which involve computes.</p>
<p>The ID of a compute can only contain alphanumeric characters and
underscores.</p>
<hr class="docutils" />
<p>Computes calculate one of three styles of quantities: global,
See this <A HREF = "Section_howto.html#howto_15">howto section</A> for a summary of
various LAMMPS output options, many of which involve computes.
</P>
<P>The ID of a compute can only contain alphanumeric characters and
underscores.
</P>
<HR>
<P>Computes calculate one of three styles of quantities: global,
per-atom, or local. A global quantity is one or more system-wide
values, e.g. the temperature of the system. A per-atom quantity is
one or more values per atom, e.g. the kinetic energy of each atom.
@ -169,260 +52,215 @@ Per-atom values are set to 0.0 for atoms not in the specified compute
group. Local quantities are calculated by each processor based on the
atoms it owns, but there may be zero or more per atom, e.g. a list of
bond distances. Computes that produce per-atom quantities have the
word &#8220;atom&#8221; in their style, e.g. <em>ke/atom</em>. Computes that produce
local quantities have the word &#8220;local&#8221; in their style,
e.g. <em>bond/local</em>. Styles with neither &#8220;atom&#8221; or &#8220;local&#8221; in their
style produce global quantities.</p>
<p>Note that a single compute produces either global or per-atom or local
quantities, but never more than one of these.</p>
<p>Global, per-atom, and local quantities each come in three kinds: a
word "atom" in their style, e.g. <I>ke/atom</I>. Computes that produce
local quantities have the word "local" in their style,
e.g. <I>bond/local</I>. Styles with neither "atom" or "local" in their
style produce global quantities.
</P>
<P>Note that a single compute produces either global or per-atom or local
quantities, but never more than one of these.
</P>
<P>Global, per-atom, and local quantities each come in three kinds: a
single scalar value, a vector of values, or a 2d array of values. The
doc page for each compute describes the style and kind of values it
produces, e.g. a per-atom vector. Some computes produce more than one
kind of a single style, e.g. a global scalar and a global vector.</p>
<p>When a compute quantity is accessed, as in many of the output commands
kind of a single style, e.g. a global scalar and a global vector.
</P>
<P>When a compute quantity is accessed, as in many of the output commands
discussed below, it can be referenced via the following bracket
notation, where ID is the ID of the compute:</p>
<table border="1" class="docutils">
<colgroup>
<col width="21%" />
<col width="79%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>c_ID</td>
<td>entire scalar, vector, or array</td>
</tr>
<tr class="row-even"><td>c_ID[I]</td>
<td>one element of vector, one column of array</td>
</tr>
<tr class="row-odd"><td>c_ID[I][J]</td>
<td>one element of array</td>
</tr>
</tbody>
</table>
<p>In other words, using one bracket reduces the dimension of the
quantity once (vector -&gt; scalar, array -&gt; vector). Using two brackets
reduces the dimension twice (array -&gt; scalar). Thus a command that
notation, where ID is the ID of the compute:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >c_ID </TD><TD > entire scalar, vector, or array</TD></TR>
<TR><TD >c_ID[I] </TD><TD > one element of vector, one column of array</TD></TR>
<TR><TD >c_ID[I][J] </TD><TD > one element of array
</TD></TR></TABLE></DIV>
<P>In other words, using one bracket reduces the dimension of the
quantity once (vector -> scalar, array -> vector). Using two brackets
reduces the dimension twice (array -> scalar). Thus a command that
uses scalar compute values as input can also process elements of a
vector or array.</p>
<p>Note that commands and <a class="reference internal" href="variable.html"><em>variables</em></a> which use compute
vector or array.
</P>
<P>Note that commands and <A HREF = "variable.html">variables</A> which use compute
quantities typically do not allow for all kinds, e.g. a command may
require a vector of values, not a scalar. This means there is no
ambiguity about referring to a compute quantity as c_ID even if it
produces, for example, both a scalar and vector. The doc pages for
various commands explain the details.</p>
<hr class="docutils" />
<p>In LAMMPS, the values generated by a compute can be used in several
ways:</p>
<ul class="simple">
<li>The results of computes that calculate a global temperature or
various commands explain the details.
</P>
<HR>
<P>In LAMMPS, the values generated by a compute can be used in several
ways:
</P>
<UL><LI>The results of computes that calculate a global temperature or
pressure can be used by fixes that do thermostatting or barostatting
or when atom velocities are created.</li>
<li>Global values can be output via the <a class="reference internal" href="thermo_style.html"><em>thermo_style custom</em></a> or <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a> command.
Or the values can be referenced in a <a class="reference internal" href="variable.html"><em>variable equal</em></a> or
<a class="reference internal" href="variable.html"><em>variable atom</em></a> command.</li>
<li>Per-atom values can be output via the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command
or the <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a> command. Or they can be
time-averaged via the <a class="reference internal" href="fix_ave_atom.html"><em>fix ave/atom</em></a> command or
reduced by the <a class="reference internal" href="compute_reduce.html"><em>compute reduce</em></a> command. Or the
per-atom values can be referenced in an <a class="reference internal" href="variable.html"><em>atom-style variable</em></a>.</li>
<li>Local values can be reduced by the <a class="reference internal" href="compute_reduce.html"><em>compute reduce</em></a> command, or histogrammed by the <a class="reference internal" href="fix_ave_histo.html"><em>fix ave/histo</em></a> command, or output by the <a class="reference internal" href="dump.html"><em>dump local</em></a> command.</li>
</ul>
<p>The results of computes that calculate global quantities can be either
&#8220;intensive&#8221; or &#8220;extensive&#8221; values. Intensive means the value is
or when atom velocities are created.
<LI>Global values can be output via the <A HREF = "thermo_style.html">thermo_style
custom</A> or <A HREF = "fix_ave_time.html">fix ave/time</A> command.
Or the values can be referenced in a <A HREF = "variable.html">variable equal</A> or
<A HREF = "variable.html">variable atom</A> command.
<LI>Per-atom values can be output via the <A HREF = "dump.html">dump custom</A> command
or the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command. Or they can be
time-averaged via the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command or
reduced by the <A HREF = "compute_reduce.html">compute reduce</A> command. Or the
per-atom values can be referenced in an <A HREF = "variable.html">atom-style
variable</A>.
<LI>Local values can be reduced by the <A HREF = "compute_reduce.html">compute
reduce</A> command, or histogrammed by the <A HREF = "fix_ave_histo.html">fix
ave/histo</A> command, or output by the <A HREF = "dump.html">dump
local</A> command.
</UL>
<P>The results of computes that calculate global quantities can be either
"intensive" or "extensive" values. Intensive means the value is
independent of the number of atoms in the simulation,
e.g. temperature. Extensive means the value scales with the number of
atoms in the simulation, e.g. total rotational kinetic energy.
<a class="reference internal" href="thermo_style.html"><em>Thermodynamic output</em></a> will normalize extensive
<A HREF = "thermo_style.html">Thermodynamic output</A> will normalize extensive
values by the number of atoms in the system, depending on the
&#8220;thermo_modify norm&#8221; setting. It will not normalize intensive values.
"thermo_modify norm" setting. It will not normalize intensive values.
If a compute value is accessed in another way, e.g. by a
<a class="reference internal" href="variable.html"><em>variable</em></a>, you may want to know whether it is an
<A HREF = "variable.html">variable</A>, you may want to know whether it is an
intensive or extensive value. See the doc page for individual
computes for further info.</p>
<hr class="docutils" />
<p>LAMMPS creates its own computes internally for thermodynamic output.
Three computes are always created, named &#8220;thermo_temp&#8221;,
&#8220;thermo_press&#8221;, and &#8220;thermo_pe&#8221;, as if these commands had been invoked
in the input script:</p>
<div class="highlight-python"><div class="highlight"><pre>compute thermo_temp all temp
computes for further info.
</P>
<HR>
<P>LAMMPS creates its own computes internally for thermodynamic output.
Three computes are always created, named "thermo_temp",
"thermo_press", and "thermo_pe", as if these commands had been invoked
in the input script:
</P>
<PRE>compute thermo_temp all temp
compute thermo_press all pressure thermo_temp
compute thermo_pe all pe
</pre></div>
</div>
<p>Additional computes for other quantities are created if the thermo
compute thermo_pe all pe
</PRE>
<P>Additional computes for other quantities are created if the thermo
style requires it. See the documentation for the
<a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command.</p>
<p>Fixes that calculate temperature or pressure, i.e. for thermostatting
<A HREF = "thermo_style.html">thermo_style</A> command.
</P>
<P>Fixes that calculate temperature or pressure, i.e. for thermostatting
or barostatting, may also create computes. These are discussed in the
documentation for specific <a class="reference internal" href="fix.html"><em>fix</em></a> commands.</p>
<p>In all these cases, the default computes LAMMPS creates can be
documentation for specific <A HREF = "fix.html">fix</A> commands.
</P>
<P>In all these cases, the default computes LAMMPS creates can be
replaced by computes defined by the user in the input script, as
described by the <a class="reference internal" href="thermo_modify.html"><em>thermo_modify</em></a> and <a class="reference internal" href="fix_modify.html"><em>fix modify</em></a> commands.</p>
<p>Properties of either a default or user-defined compute can be modified
via the <a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a> command.</p>
<p>Computes can be deleted with the <a class="reference internal" href="uncompute.html"><em>uncompute</em></a> command.</p>
<p>Code for new computes can be added to LAMMPS (see <a class="reference internal" href="Section_modify.html"><em>this section</em></a> of the manual) and the results of their
calculations accessed in the various ways described above.</p>
<hr class="docutils" />
<p>Each compute style has its own doc page which describes its arguments
described by the <A HREF = "thermo_modify.html">thermo_modify</A> and <A HREF = "fix_modify.html">fix
modify</A> commands.
</P>
<P>Properties of either a default or user-defined compute can be modified
via the <A HREF = "compute_modify.html">compute_modify</A> command.
</P>
<P>Computes can be deleted with the <A HREF = "uncompute.html">uncompute</A> command.
</P>
<P>Code for new computes can be added to LAMMPS (see <A HREF = "Section_modify.html">this
section</A> of the manual) and the results of their
calculations accessed in the various ways described above.
</P>
<HR>
<P>Each compute style has its own doc page which describes its arguments
and what it does. Here is an alphabetic list of compute styles
available in LAMMPS. They are also given in more compact form in the
compute section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
<p>There are also additional compute styles (not listed here) submitted
compute section of <A HREF = "Section_commands.html#cmd_5">this page</A>.
</P>
<P>There are also additional compute styles (not listed here) submitted
by users which are included in the LAMMPS distribution. The list of
these with links to the individual styles are given in the compute
section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
<p>There are also additional accelerated compute styles (note listed
section of <A HREF = "Section_commands.html#cmd_5">this page</A>.
</P>
<P>There are also additional accelerated compute styles (note listed
here) included in the LAMMPS distribution for faster performance on
CPUs and GPUs. The list of these with links to the individual styles
are given in the compute section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
<ul class="simple">
<li><a class="reference internal" href="compute_bond_local.html"><em>angle/local</em></a> - theta and energy of each angle</li>
<li><a class="reference internal" href="compute_body_local.html"><em>body/local</em></a> - attributes of body sub-particles</li>
<li><a class="reference internal" href="compute_bond_local.html"><em>bond/local</em></a> - distance and energy of each bond</li>
<li><a class="reference internal" href="compute_centro_atom.html"><em>centro/atom</em></a> - centro-symmetry parameter for each atom</li>
<li><a class="reference internal" href="compute_cluster_atom.html"><em>cluster/atom</em></a> - cluster ID for each atom</li>
<li><a class="reference internal" href="compute_cna_atom.html"><em>cna/atom</em></a> - common neighbor analysis (CNA) for each atom</li>
<li><a class="reference internal" href="compute_com.html"><em>com</em></a> - center-of-mass of group of atoms</li>
<li><a class="reference internal" href="compute_com_chunk.html"><em>com/chunk</em></a> - center-of-mass for each chunk</li>
<li><a class="reference internal" href="compute_contact_atom.html"><em>contact/atom</em></a> - contact count for each spherical particle</li>
<li><a class="reference internal" href="compute_coord_atom.html"><em>coord/atom</em></a> - coordination number for each atom</li>
<li><a class="reference internal" href="compute_damage_atom.html"><em>damage/atom</em></a> - Peridynamic damage for each atom</li>
<li><a class="reference internal" href="compute_dihedral_local.html"><em>dihedral/local</em></a> - angle of each dihedral</li>
<li><a class="reference internal" href="compute_dilatation_atom.html"><em>dilatation/atom</em></a> - Peridynamic dilatation for each atom</li>
<li><a class="reference internal" href="compute_displace_atom.html"><em>displace/atom</em></a> - displacement of each atom</li>
<li><a class="reference internal" href="compute_erotate_asphere.html"><em>erotate/asphere</em></a> - rotational energy of aspherical particles</li>
<li><a class="reference internal" href="compute_erotate_rigid.html"><em>erotate/rigid</em></a> - rotational energy of rigid bodies</li>
<li><a class="reference internal" href="compute_erotate_sphere.html"><em>erotate/sphere</em></a> - rotational energy of spherical particles</li>
<li><a class="reference internal" href="compute_erotate_sphere.html"><em>erotate/sphere/atom</em></a> - rotational energy for each spherical particle</li>
<li><a class="reference internal" href="compute_event_displace.html"><em>event/displace</em></a> - detect event on atom displacement</li>
<li><a class="reference internal" href="compute_group_group.html"><em>group/group</em></a> - energy/force between two groups of atoms</li>
<li><a class="reference internal" href="compute_gyration.html"><em>gyration</em></a> - radius of gyration of group of atoms</li>
<li><a class="reference internal" href="compute_gyration_chunk.html"><em>gyration/chunk</em></a> - radius of gyration for each chunk</li>
<li><a class="reference internal" href="compute_heat_flux.html"><em>heat/flux</em></a> - heat flux through a group of atoms</li>
<li><a class="reference internal" href="compute_improper_local.html"><em>improper/local</em></a> - angle of each improper</li>
<li><a class="reference internal" href="compute_inertia_chunk.html"><em>inertia/chunk</em></a> - inertia tensor for each chunk</li>
<li><a class="reference internal" href="compute_ke.html"><em>ke</em></a> - translational kinetic energy</li>
<li><a class="reference internal" href="compute_ke_atom.html"><em>ke/atom</em></a> - kinetic energy for each atom</li>
<li><a class="reference internal" href="compute_ke_rigid.html"><em>ke/rigid</em></a> - translational kinetic energy of rigid bodies</li>
<li><a class="reference internal" href="compute_msd.html"><em>msd</em></a> - mean-squared displacement of group of atoms</li>
<li><a class="reference internal" href="compute_msd_chunk.html"><em>msd/chunk</em></a> - mean-squared displacement for each chunk</li>
<li><a class="reference internal" href="compute_msd_nongauss.html"><em>msd/nongauss</em></a> - MSD and non-Gaussian parameter of group of atoms</li>
<li><a class="reference internal" href="compute_pair.html"><em>pair</em></a> - values computed by a pair style</li>
<li><a class="reference internal" href="compute_pair_local.html"><em>pair/local</em></a> - distance/energy/force of each pairwise interaction</li>
<li><a class="reference internal" href="compute_pe.html"><em>pe</em></a> - potential energy</li>
<li><a class="reference internal" href="compute_pe_atom.html"><em>pe/atom</em></a> - potential energy for each atom</li>
<li><a class="reference internal" href="compute_plasticity_atom.html"><em>plasticity/atom</em></a> - Peridynamic plasticity for each atom</li>
<li><a class="reference internal" href="compute_pressure.html"><em>pressure</em></a> - total pressure and pressure tensor</li>
<li><a class="reference internal" href="compute_property_atom.html"><em>property/atom</em></a> - convert atom attributes to per-atom vectors/arrays</li>
<li><a class="reference internal" href="compute_property_local.html"><em>property/local</em></a> - convert local attributes to localvectors/arrays</li>
<li><a class="reference internal" href="compute_property_chunk.html"><em>property/chunk</em></a> - extract various per-chunk attributes</li>
<li><a class="reference internal" href="compute_rdf.html"><em>rdf</em></a> - radial distribution function g(r) histogram of group of atoms</li>
<li><a class="reference internal" href="compute_reduce.html"><em>reduce</em></a> - combine per-atom quantities into a single global value</li>
<li><a class="reference internal" href="compute_reduce.html"><em>reduce/region</em></a> - same as compute reduce, within a region</li>
<li><a class="reference internal" href="compute_slice.html"><em>slice</em></a> - extract values from global vector or array</li>
<li><code class="xref doc docutils literal"><span class="pre">sna/atom</span></code> - calculate bispectrum coefficients for each atom</li>
<li><code class="xref doc docutils literal"><span class="pre">snad/atom</span></code> - derivative of bispectrum coefficients for each atom</li>
<li><code class="xref doc docutils literal"><span class="pre">snav/atom</span></code> - virial contribution from bispectrum coefficients for each atom</li>
<li><a class="reference internal" href="compute_stress_atom.html"><em>stress/atom</em></a> - stress tensor for each atom</li>
<li><a class="reference internal" href="compute_temp.html"><em>temp</em></a> - temperature of group of atoms</li>
<li><a class="reference internal" href="compute_temp_asphere.html"><em>temp/asphere</em></a> - temperature of aspherical particles</li>
<li><a class="reference internal" href="compute_temp_chunk.html"><em>temp/chunk</em></a> - temperature of each chunk</li>
<li><a class="reference internal" href="compute_temp_com.html"><em>temp/com</em></a> - temperature after subtracting center-of-mass velocity</li>
<li><a class="reference internal" href="compute_temp_deform.html"><em>temp/deform</em></a> - temperature excluding box deformation velocity</li>
<li><a class="reference internal" href="compute_temp_partial.html"><em>temp/partial</em></a> - temperature excluding one or more dimensions of velocity</li>
<li><a class="reference internal" href="compute_temp_profile.html"><em>temp/profile</em></a> - temperature excluding a binned velocity profile</li>
<li><a class="reference internal" href="compute_temp_ramp.html"><em>temp/ramp</em></a> - temperature excluding ramped velocity component</li>
<li><a class="reference internal" href="compute_temp_region.html"><em>temp/region</em></a> - temperature of a region of atoms</li>
<li><a class="reference internal" href="compute_temp_sphere.html"><em>temp/sphere</em></a> - temperature of spherical particles</li>
<li><a class="reference internal" href="compute_ti.html"><em>ti</em></a> - thermodyanmic integration free energy values</li>
<li><a class="reference internal" href="compute_torque_chunk.html"><em>torque/chunk</em></a> - torque applied on each chunk</li>
<li><a class="reference internal" href="compute_vacf.html"><em>vacf</em></a> - velocity-autocorrelation function of group of atoms</li>
<li><a class="reference internal" href="compute_vcm_chunk.html"><em>vcm/chunk</em></a> - velocity of center-of-mass for each chunk</li>
<li><a class="reference internal" href="compute_voronoi_atom.html"><em>voronoi/atom</em></a> - Voronoi volume and neighbors for each atom</li>
</ul>
<p>There are also additional compute styles submitted by users which are
are given in the compute section of <A HREF = "Section_commands.html#cmd_5">this
page</A>.
</P>
<UL><LI><A HREF = "compute_bond_local.html">angle/local</A> - theta and energy of each angle
<LI><A HREF = "compute_body_local.html">body/local</A> - attributes of body sub-particles
<LI><A HREF = "compute_bond_local.html">bond/local</A> - distance and energy of each bond
<LI><A HREF = "compute_centro_atom.html">centro/atom</A> - centro-symmetry parameter for each atom
<LI><A HREF = "compute_cluster_atom.html">cluster/atom</A> - cluster ID for each atom
<LI><A HREF = "compute_cna_atom.html">cna/atom</A> - common neighbor analysis (CNA) for each atom
<LI><A HREF = "compute_com.html">com</A> - center-of-mass of group of atoms
<LI><A HREF = "compute_com_chunk.html">com/chunk</A> - center-of-mass for each chunk
<LI><A HREF = "compute_contact_atom.html">contact/atom</A> - contact count for each spherical particle
<LI><A HREF = "compute_coord_atom.html">coord/atom</A> - coordination number for each atom
<LI><A HREF = "compute_damage_atom.html">damage/atom</A> - Peridynamic damage for each atom
<LI><A HREF = "compute_dihedral_local.html">dihedral/local</A> - angle of each dihedral
<LI><A HREF = "compute_dilatation_atom.html">dilatation/atom</A> - Peridynamic dilatation for each atom
<LI><A HREF = "compute_displace_atom.html">displace/atom</A> - displacement of each atom
<LI><A HREF = "compute_erotate_asphere.html">erotate/asphere</A> - rotational energy of aspherical particles
<LI><A HREF = "compute_erotate_rigid.html">erotate/rigid</A> - rotational energy of rigid bodies
<LI><A HREF = "compute_erotate_sphere.html">erotate/sphere</A> - rotational energy of spherical particles
<LI><A HREF = "compute_erotate_sphere.html">erotate/sphere/atom</A> - rotational energy for each spherical particle
<LI><A HREF = "compute_event_displace.html">event/displace</A> - detect event on atom displacement
<LI><A HREF = "compute_group_group.html">group/group</A> - energy/force between two groups of atoms
<LI><A HREF = "compute_gyration.html">gyration</A> - radius of gyration of group of atoms
<LI><A HREF = "compute_gyration_chunk.html">gyration/chunk</A> - radius of gyration for each chunk
<LI><A HREF = "compute_heat_flux.html">heat/flux</A> - heat flux through a group of atoms
<LI><A HREF = "compute_improper_local.html">improper/local</A> - angle of each improper
<LI><A HREF = "compute_inertia_chunk.html">inertia/chunk</A> - inertia tensor for each chunk
<LI><A HREF = "compute_ke.html">ke</A> - translational kinetic energy
<LI><A HREF = "compute_ke_atom.html">ke/atom</A> - kinetic energy for each atom
<LI><A HREF = "compute_ke_rigid.html">ke/rigid</A> - translational kinetic energy of rigid bodies
<LI><A HREF = "compute_msd.html">msd</A> - mean-squared displacement of group of atoms
<LI><A HREF = "compute_msd_chunk.html">msd/chunk</A> - mean-squared displacement for each chunk
<LI><A HREF = "compute_msd_nongauss.html">msd/nongauss</A> - MSD and non-Gaussian parameter of group of atoms
<LI><A HREF = "compute_pair.html">pair</A> - values computed by a pair style
<LI><A HREF = "compute_pair_local.html">pair/local</A> - distance/energy/force of each pairwise interaction
<LI><A HREF = "compute_pe.html">pe</A> - potential energy
<LI><A HREF = "compute_pe_atom.html">pe/atom</A> - potential energy for each atom
<LI><A HREF = "compute_plasticity_atom.html">plasticity/atom</A> - Peridynamic plasticity for each atom
<LI><A HREF = "compute_pressure.html">pressure</A> - total pressure and pressure tensor
<LI><A HREF = "compute_property_atom.html">property/atom</A> - convert atom attributes to per-atom vectors/arrays
<LI><A HREF = "compute_property_local.html">property/local</A> - convert local attributes to localvectors/arrays
<LI><A HREF = "compute_property_chunk.html">property/chunk</A> - extract various per-chunk attributes
<LI><A HREF = "compute_rdf.html">rdf</A> - radial distribution function g(r) histogram of group of atoms
<LI><A HREF = "compute_reduce.html">reduce</A> - combine per-atom quantities into a single global value
<LI><A HREF = "compute_reduce.html">reduce/region</A> - same as compute reduce, within a region
<LI><A HREF = "compute_slice.html">slice</A> - extract values from global vector or array
<LI><A HREF = "compute_sna.html">sna/atom</A> - calculate bispectrum coefficients for each atom
<LI><A HREF = "compute_sna.html">snad/atom</A> - derivative of bispectrum coefficients for each atom
<LI><A HREF = "compute_sna.html">snav/atom</A> - virial contribution from bispectrum coefficients for each atom
<LI><A HREF = "compute_stress_atom.html">stress/atom</A> - stress tensor for each atom
<LI><A HREF = "compute_temp.html">temp</A> - temperature of group of atoms
<LI><A HREF = "compute_temp_asphere.html">temp/asphere</A> - temperature of aspherical particles
<LI><A HREF = "compute_temp_chunk.html">temp/chunk</A> - temperature of each chunk
<LI><A HREF = "compute_temp_com.html">temp/com</A> - temperature after subtracting center-of-mass velocity
<LI><A HREF = "compute_temp_deform.html">temp/deform</A> - temperature excluding box deformation velocity
<LI><A HREF = "compute_temp_partial.html">temp/partial</A> - temperature excluding one or more dimensions of velocity
<LI><A HREF = "compute_temp_profile.html">temp/profile</A> - temperature excluding a binned velocity profile
<LI><A HREF = "compute_temp_ramp.html">temp/ramp</A> - temperature excluding ramped velocity component
<LI><A HREF = "compute_temp_region.html">temp/region</A> - temperature of a region of atoms
<LI><A HREF = "compute_temp_sphere.html">temp/sphere</A> - temperature of spherical particles
<LI><A HREF = "compute_ti.html">ti</A> - thermodyanmic integration free energy values
<LI><A HREF = "compute_torque_chunk.html">torque/chunk</A> - torque applied on each chunk
<LI><A HREF = "compute_vacf.html">vacf</A> - velocity-autocorrelation function of group of atoms
<LI><A HREF = "compute_vcm_chunk.html">vcm/chunk</A> - velocity of center-of-mass for each chunk
<LI><A HREF = "compute_voronoi_atom.html">voronoi/atom</A> - Voronoi volume and neighbors for each atom
</UL>
<P>There are also additional compute styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the compute section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
<p>There are also additional accelerated compute styles included in the
the individual styles are given in the compute section of <A HREF = "Section_commands.html#cmd_5">this
page</A>.
</P>
<P>There are also additional accelerated compute styles included in the
LAMMPS distribution for faster performance on CPUs and GPUs. The list
of these with links to the individual styles are given in the pair
section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
</div>
<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="uncompute.html"><em>uncompute</em></a>, <a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a>, <a class="reference internal" href="fix_ave_atom.html"><em>fix ave/atom</em></a>, <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a>,
<a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a>, <a class="reference internal" href="fix_ave_histo.html"><em>fix ave/histo</em></a></p>
<p><strong>Default:</strong> none</p>
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section of <A HREF = "Section_commands.html#cmd_5">this page</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "uncompute.html">uncompute</A>, <A HREF = "compute_modify.html">compute_modify</A>, <A HREF = "fix_ave_atom.html">fix
ave/atom</A>, <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>,
<A HREF = "fix_ave_time.html">fix ave/time</A>, <A HREF = "fix_ave_histo.html">fix ave/histo</A>
</P>
<P><B>Default:</B> none
</P>
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<div class="section" id="compute-ackland-atom-command">
<span id="index-0"></span><h1>compute ackland/atom command<a class="headerlink" href="#compute-ackland-atom-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 ackland/atom
</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>ackland/atom = style name of this compute command</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 all ackland/atom
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Defines a computation that calculates the local lattice structure
according to the formulation given in <a class="reference internal" href="#ackland"><span>(Ackland)</span></a>.</p>
<p>In contrast to the <a class="reference internal" href="compute_centro_atom.html"><em>centro-symmetry parameter</em></a> this method is stable against
<HR>
<H3>compute ackland/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID ackland/atom
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>ackland/atom = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all ackland/atom
</PRE>
<P><B>Description:</B>
</P>
<P>Defines a computation that calculates the local lattice structure
according to the formulation given in <A HREF = "#Ackland">(Ackland)</A>.
</P>
<P>In contrast to the <A HREF = "compute_centro_atom.html">centro-symmetry
parameter</A> this method is stable against
temperature boost, because it is based not on the distance between
particles but the angles. Therefore statistical fluctuations are
averaged out a little more. A comparison with the Common Neighbor
Analysis metric is made in the paper.</p>
<p>The result is a number which is mapped to the following different
lattice structures:</p>
<ul class="simple">
<li>0 = UNKNOWN</li>
<li>1 = BCC</li>
<li>2 = FCC</li>
<li>3 = HCP</li>
<li>4 = ICO</li>
</ul>
<p>The neighbor list needed to compute this quantity is constructed each
Analysis metric is made in the paper.
</P>
<P>The result is a number which is mapped to the following different
lattice structures:
</P>
<UL><LI>0 = UNKNOWN
<LI>1 = BCC
<LI>2 = FCC
<LI>3 = HCP
<LI>4 = ICO
</UL>
<P>The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each of
which computes this quantity.-</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-atom vector, which can be accessed by
which computes this quantity.-
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of
LAMMPS output options.</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-MISC 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>The per-atom vector values will be unitless since they are the
integers defined above.</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 class="reference internal" href="compute_centro_atom.html"><em>compute centro/atom</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="ackland"><strong>(Ackland)</strong> Ackland, Jones, Phys Rev B, 73, 054104 (2006).</p>
</div>
</div>
<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>The per-atom vector values will be unitless since they are the
integers defined above.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_centro_atom.html">compute centro/atom</A>
</P>
<P><B>Default:</B> none
</P>
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<P><B>(Ackland)</B> Ackland, Jones, Phys Rev B, 73, 054104 (2006).
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<div class="section" id="compute-angle-local-command">
<span id="index-0"></span><h1>compute angle/local command<a class="headerlink" href="#compute-angle-local-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 angle/local input1 input2 ...
</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>angle/local = style name of this compute command</li>
<li>one or more keywords may be appended</li>
<li>keyword = <em>theta</em> or <em>eng</em></li>
</ul>
<pre class="literal-block">
<em>theta</em> = tabulate angles
<em>eng</em> = tabulate angle energies
</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>compute 1 all angle/local theta
compute 1 all angle/local eng theta
</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 of individual angle
<HR>
<H3>compute angle/local command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID angle/local input1 input2 ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>angle/local = style name of this compute command
<LI>one or more keywords may be appended
<LI>keyword = <I>theta</I> or <I>eng</I>
<PRE> <I>theta</I> = tabulate angles
<I>eng</I> = tabulate angle energies
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all angle/local theta
compute 1 all angle/local eng theta
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates properties of individual angle
interactions. The number of datums generated, aggregated across all
processors, equals the number of angles in the system, modified by the
group parameter as explained below.</p>
<p>The local data stored by this command is generated by looping over all
group parameter as explained below.
</P>
<P>The local data stored by this command is generated by looping over all
the atoms owned on a processor and their angles. An angle will only
be included if all 3 atoms in the angle are in the specified compute
group. Any angles that have been broken (see the
<a class="reference internal" href="angle_style.html"><em>angle_style</em></a> command) by setting their angle type to
0 are not included. Angles that have been turned off (see the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> or <a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a> commands) by
<A HREF = "angle_style.html">angle_style</A> command) by setting their angle type to
0 are not included. Angles that have been turned off (see the <A HREF = "fix_shake.html">fix
shake</A> or <A HREF = "delete_bonds.html">delete_bonds</A> commands) by
setting their angle type negative are written into the file, but their
energy will be 0.0.</p>
<p>Note that as atoms migrate from processor to processor, there will be
energy will be 0.0.
</P>
<P>Note that as atoms migrate from processor to processor, there will be
no consistent ordering of the entries within the local vector or array
from one timestep to the next. The only consistency that is
guaranteed is that the ordering on a particular timestep will be the
same for local vectors or arrays generated by other compute commands.
For example, angle output from the <a class="reference internal" href="compute_property_local.html"><em>compute property/local</em></a> command can be combined
with data from this command and output by the <a class="reference internal" href="dump.html"><em>dump local</em></a>
command in a consistent way.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a local vector or local array depending on the
For example, angle output from the <A HREF = "compute_property_local.html">compute
property/local</A> command can be combined
with data from this command and output by the <A HREF = "dump.html">dump local</A>
command in a consistent way.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a local vector or local array depending on the
number of keywords. The length of the vector or number of rows in the
array is the number of angles. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>this section</span></a> for an overview of LAMMPS output
options.</p>
<p>The output for <em>theta</em> will be in degrees. The output for <em>eng</em> will
be in energy <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<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="dump.html"><em>dump local</em></a>, <a class="reference internal" href="compute_property_local.html"><em>compute property/local</em></a></p>
<p><strong>Default:</strong> none</p>
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uses local values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The output for <I>theta</I> will be in degrees. The output for <I>eng</I> will
be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dump.html">dump local</A>, <A HREF = "compute_property_local.html">compute
property/local</A>
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<P><B>Default:</B> none
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<div class="section" id="compute-angmom-chunk-command">
<span id="index-0"></span><h1>compute angmom/chunk command<a class="headerlink" href="#compute-angmom-chunk-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 angmom/chunk chunkID
</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>angmom/chunk = style name of this compute command</li>
<li>chunkID = ID of <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command</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 fluid angmom/chunk molchunk
</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 the angular momemtum of multiple
chunks of atoms.</p>
<p>In LAMMPS, chunks are collections of atoms defined by a <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command, which assigns each atom
<HR>
<H3>compute angmom/chunk command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID angmom/chunk chunkID
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>angmom/chunk = style name of this compute command
<LI>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 fluid angmom/chunk molchunk
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the angular momemtum of multiple
chunks of atoms.
</P>
<P>In LAMMPS, chunks are collections of atoms defined by a <A HREF = "compute_chunk_atom.html">compute
chunk/atom</A> command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> doc page and &#8220;<a class="reference internal" href="Section_howto.html#howto-23"><span>Section_howto 23</span></a> for details of how chunks can be
molecule or atoms in a spatial bin. See the <A HREF = "compute_chunk_atom.html">compute
chunk/atom</A> doc page and "<A HREF = "Section_howto.html#howto_23">Section_howto
23</A> for details of how chunks can be
defined and examples of how they can be used to measure properties of
a system.</p>
<p>This compute calculates the 3 components of the angular momentum
a system.
</P>
<P>This compute calculates the 3 components of the angular momentum
vector for each chunk, due to the velocity/momentum of the individual
atoms in the chunk around the center-of-mass of the chunk. The
calculation includes all effects due to atoms passing thru periodic
boundaries.</p>
<p>Note that only atoms in the specified group contribute to the
calculation. The <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command
boundaries.
</P>
<P>Note that only atoms in the specified group contribute to the
calculation. The <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
defines its own group; atoms will have a chunk ID = 0 if they are not
in that group, signifying they are not assigned to a chunk, and will
thus also not contribute to this calculation. You can specify the
&#8220;all&#8221; group for this command if you simply want to include atoms with
non-zero chunk IDs.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The coordinates of an atom contribute to the chunk&#8217;s
angular momentum in &#8220;unwrapped&#8221; form, by using the image flags
associated with each atom. See the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command
for a discussion of &#8220;unwrapped&#8221; coordinates. See the Atoms section of
the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command for a discussion of image flags
"all" group for this command if you simply want to include atoms with
non-zero chunk IDs.
</P>
<P>IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's
angular momentum in "unwrapped" form, by using the image flags
associated with each atom. See the <A HREF = "dump.html">dump custom</A> command
for a discussion of "unwrapped" coordinates. See the Atoms section of
the <A HREF = "read_data.html">read_data</A> command for a discussion of image flags
and how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the <a class="reference internal" href="set.html"><em>set image</em></a> command.</p>
</div>
<p>The simplest way to output the results of the compute angmom/chunk
calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a>
command, for example:</p>
<div class="highlight-python"><div class="highlight"><pre>compute cc1 all chunk/atom molecule
(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
image</A> command.
</P>
<P>The simplest way to output the results of the compute angmom/chunk
calculation to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A>
command, for example:
</P>
<PRE>compute cc1 all chunk/atom molecule
compute myChunk all angmom/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</pre></div>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global array where the number of rows = the
number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command. The number of columns =
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</PRE>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global array where the number of rows = the
number of chunks <I>Nchunk</I> as calculated by the specified <A HREF = "compute_chunk_atom.html">compute
chunk/atom</A> command. The number of columns =
3 for the 3 xyz components of the angular momentum for each chunk.
These values can be accessed by any command that uses global array
values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of LAMMPS output
options.</p>
<p>The array values are &#8220;intensive&#8221;. The array values will be in
mass-velocity-distance <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<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="variable.html"><em>variable angmom() function</em></a></p>
<p><strong>Default:</strong> none</p>
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values from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
15</A> for an overview of LAMMPS output
options.
</P>
<P>The array values are "intensive". The array values will be in
mass-velocity-distance <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "variable.html">variable angmom() function</A>
</P>
<P><B>Default:</B> none
</P>
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<div class="section" id="compute-basal-atom-command">
<span id="index-0"></span><h1>compute basal/atom command<a class="headerlink" href="#compute-basal-atom-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 basal/atom
</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>basal/atom = style name of this compute command</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 all basal/atom
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Defines a computation that calculates the hexagonal close-packed &#8220;c&#8221;
<HR>
<H3>compute basal/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID basal/atom
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>basal/atom = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all basal/atom
</PRE>
<P><B>Description:</B>
</P>
<P>Defines a computation that calculates the hexagonal close-packed "c"
lattice vector for each atom in the group. It does this by
calculating the normal unit vector to the basal plane for each atom.
The results enable efficient identification and characterization of
twins and grains in hexagonal close-packed structures.</p>
<p>The output of the compute is thus the 3 components of a unit vector
twins and grains in hexagonal close-packed structures.
</P>
<P>The output of the compute is thus the 3 components of a unit vector
associdate with each atom. The components are set to 0.0 for
atoms not in the group.</p>
<p>Details of the calculation are given in <a class="reference internal" href="#barrett"><span>(Barrett)</span></a>.</p>
<p>The neighbor list needed to compute this quantity is constructed each
atoms not in the group.
</P>
<P>Details of the calculation are given in <A HREF = "#Barrett">(Barrett)</A>.
</P>
<P>The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each of
which computes this quantity.</p>
<p>An example input script that uses this compute is provided
in examples/USER/misc/basal.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-atom array with 3 columns, which can be
which computes this quantity.
</P>
<P>An example input script that uses this compute is provided
in examples/USER/misc/basal.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-atom array with 3 columns, which can be
accessed by indices 1-3 by any command that uses per-atom values from
a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of LAMMPS output
options.</p>
<p>The per-atom vector values are unitless since the 3 columns represent
components of a unit vector.</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-MISC 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>The output of this compute will be meaningless unless the atoms are on
a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
15</A> for an overview of LAMMPS output
options.
</P>
<P>The per-atom vector values are unitless since the 3 columns represent
components of a unit vector.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>The output of this compute will be meaningless unless the atoms are on
(or near) hcp lattice sites, since the calculation assumes a
well-defined basal plane.</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 class="reference internal" href="compute_centro_atom.html"><em>compute centro/atom</em></a>, <a class="reference internal" href="compute_ackland_atom.html"><em>compute ackland/atom</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="barrett"><strong>(Barrett)</strong> Barrett, Tschopp, El Kadiri, Scripta Mat. 66, p.666 (2012).</p>
</div>
</div>
well-defined basal plane.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_centro_atom.html">compute centro/atom</A>, <A HREF = "compute_ackland_atom.html">compute
ackland/atom</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Barrett"></A>
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<P><B>(Barrett)</B> Barrett, Tschopp, El Kadiri, Scripta Mat. 66, p.666 (2012).
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<div class="section" id="compute-body-local-command">
<span id="index-0"></span><h1>compute body/local command<a class="headerlink" href="#compute-body-local-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 body/local input1 input2 ...
</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>body/local = style name of this compute command</li>
<li>one or more keywords may be appended</li>
<li>keyword = <em>type</em> or <em>integer</em></li>
</ul>
<pre class="literal-block">
<em>type</em> = atom type of the body particle
<em>integer</em> = 1,2,3,etc = index of fields defined by body style
</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>compute 1 all body/local type 1 2 3
compute 1 all body/local 3 6
</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 of individual body
<HR>
<H3>compute body/local command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID body/local input1 input2 ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>body/local = style name of this compute command
<LI>one or more keywords may be appended
<LI>keyword = <I>type</I> or <I>integer</I>
<PRE> <I>type</I> = atom type of the body particle
<I>integer</I> = 1,2,3,etc = index of fields defined by body style
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all body/local type 1 2 3
compute 1 all body/local 3 6
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates properties of individual body
sub-particles. The number of datums generated, aggregated across all
processors, equals the number of body sub-particles plus the number of
non-body particles in the system, modified by the group parameter as
explained below. See <a class="reference internal" href="Section_howto.html#howto-14"><span>Section_howto 14</span></a>
of the manual and the <a class="reference internal" href="body.html"><em>body</em></a> doc page for more details on
using body particles.</p>
<p>The local data stored by this command is generated by looping over all
explained below. See <A HREF = "Section_howto.html#howto_14">Section_howto 14</A>
of the manual and the <A HREF = "body.html">body</A> doc page for more details on
using body particles.
</P>
<P>The local data stored by this command is generated by looping over all
the atoms. An atom will only be included if it is in the group. If
the atom is a body particle, then its N sub-particles will be looped
over, and it will contribute N datums to the count of datums. If it
is not a body particle, it will contribute 1 datum.</p>
<p>For both body particles and non-body particles, the <em>type</em> keyword
will store the type of the atom.</p>
<p>The <em>integer</em> keywords mean different things for body and non-body
particles. If the atom is not a body particle, only its <em>x</em>, <em>y</em>, <em>z</em>
coordinates can be referenced, using the <em>integer</em> keywords 1,2,3.
is not a body particle, it will contribute 1 datum.
</P>
<P>For both body particles and non-body particles, the <I>type</I> keyword
will store the type of the atom.
</P>
<P>The <I>integer</I> keywords mean different things for body and non-body
particles. If the atom is not a body particle, only its <I>x</I>, <I>y</I>, <I>z</I>
coordinates can be referenced, using the <I>integer</I> keywords 1,2,3.
Note that this means that if you want to access more fields than this
for body particles, then you cannot include non-body particles in the
group.</p>
<p>For a body particle, the <em>integer</em> keywords refer to fields calculated
group.
</P>
<P>For a body particle, the <I>integer</I> keywords refer to fields calculated
by the body style for each sub-particle. The body style, as specified
by the <a class="reference internal" href="atom_style.html"><em>atom_style body</em></a>, determines how many fields
exist and what they are. See the <a class="reference internal" href="body.html"><em>body</em></a> doc page for
details of the different styles.</p>
<p>Here is an example of how to output body information using the <a class="reference internal" href="dump.html"><em>dump local</em></a> command with this compute. If fields 1,2,3 for the
by the <A HREF = "atom_style.html">atom_style body</A>, determines how many fields
exist and what they are. See the <A HREF = "body.html">body</A> doc page for
details of the different styles.
</P>
<P>Here is an example of how to output body information using the <A HREF = "dump.html">dump
local</A> command with this compute. If fields 1,2,3 for the
body sub-particles are x,y,z coordinates, then the dump file will be
formatted similar to the output of a <a class="reference internal" href="dump.html"><em>dump atom or custom</em></a>
command.</p>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all body/local type 1 2 3
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4]
</pre></div>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a local vector or local array depending on the
formatted similar to the output of a <A HREF = "dump.html">dump atom or custom</A>
command.
</P>
<PRE>compute 1 all body/local type 1 2 3
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4]
</PRE>
<P><B>Output info:</B>
</P>
<P>This compute calculates a local vector or local array depending on the
number of keywords. The length of the vector or number of rows in the
array is the number of datums as described above. If a single keyword
is specified, a local vector is produced. If two or more keywords are
specified, a local array is produced where the number of columns = the
number of keywords. The vector or array can be accessed by any
command that uses local values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>this section</span></a> for an overview of LAMMPS output
options.</p>
<p>The <a class="reference internal" href="units.html"><em>units</em></a> for output values depend on the body style.</p>
</div>
<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="dump.html"><em>dump local</em></a></p>
<p><strong>Default:</strong> none</p>
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command that uses local values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The <A HREF = "units.html">units</A> for output values depend on the body style.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dump.html">dump local</A>
</P>
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<div class="section" id="compute-bond-local-command">
<span id="index-0"></span><h1>compute bond/local command<a class="headerlink" href="#compute-bond-local-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 bond/local input1 input2 ...
</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>bond/local = style name of this compute command</li>
<li>one or more keywords may be appended</li>
<li>keyword = <em>dist</em> or <em>eng</em></li>
</ul>
<pre class="literal-block">
<em>dist</em> = bond distance
<em>eng</em> = bond energy
<em>force</em> = bond force
</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>compute 1 all bond/local eng
compute 1 all bond/local dist eng force
</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 of individual bond
<HR>
<H3>compute bond/local command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID bond/local input1 input2 ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>bond/local = style name of this compute command
<LI>one or more keywords may be appended
<LI>keyword = <I>dist</I> or <I>eng</I>
<PRE> <I>dist</I> = bond distance
<I>eng</I> = bond energy
<I>force</I> = bond force
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all bond/local eng
compute 1 all bond/local dist eng force
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates properties of individual bond
interactions. The number of datums generated, aggregated across all
processors, equals the number of bonds in the system, modified
by the group parameter as explained below.</p>
<p>The local data stored by this command is generated by looping over all
by the group parameter as explained below.
</P>
<P>The local data stored by this command is generated by looping over all
the atoms owned on a processor and their bonds. A bond will only be
included if both atoms in the bond are in the specified compute group.
Any bonds that have been broken (see the <a class="reference internal" href="bond_style.html"><em>bond_style</em></a>
Any bonds that have been broken (see the <A HREF = "bond_style.html">bond_style</A>
command) by setting their bond type to 0 are not included. Bonds that
have been turned off (see the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> or
<a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a> commands) by setting their bond type
negative are written into the file, but their energy will be 0.0.</p>
<p>Note that as atoms migrate from processor to processor, there will be
have been turned off (see the <A HREF = "fix_shake.html">fix shake</A> or
<A HREF = "delete_bonds.html">delete_bonds</A> commands) by setting their bond type
negative are written into the file, but their energy will be 0.0.
</P>
<P>Note that as atoms migrate from processor to processor, there will be
no consistent ordering of the entries within the local vector or array
from one timestep to the next. The only consistency that is
guaranteed is that the ordering on a particular timestep will be the
same for local vectors or arrays generated by other compute commands.
For example, bond output from the <a class="reference internal" href="compute_property_local.html"><em>compute property/local</em></a> command can be combined
with data from this command and output by the <a class="reference internal" href="dump.html"><em>dump local</em></a>
command in a consistent way.</p>
<p>Here is an example of how to do this:</p>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all property/local batom1 batom2 btype
For example, bond output from the <A HREF = "compute_property_local.html">compute
property/local</A> command can be combined
with data from this command and output by the <A HREF = "dump.html">dump local</A>
command in a consistent way.
</P>
<P>Here is an example of how to do this:
</P>
<PRE>compute 1 all property/local batom1 batom2 btype
compute 2 all bond/local dist eng
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
</pre></div>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a local vector or local array depending on the
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
</PRE>
<P><B>Output info:</B>
</P>
<P>This compute calculates a local vector or local array depending on the
number of keywords. The length of the vector or number of rows in the
array is the number of bonds. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>this section</span></a> for an overview of LAMMPS output
options.</p>
<p>The output for <em>dist</em> will be in distance <a class="reference internal" href="units.html"><em>units</em></a>. The
output for <em>eng</em> will be in energy <a class="reference internal" href="units.html"><em>units</em></a>. The output for
<em>force</em> will be in force <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<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="dump.html"><em>dump local</em></a>, <a class="reference internal" href="compute_property_local.html"><em>compute property/local</em></a></p>
<p><strong>Default:</strong> none</p>
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uses local values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The output for <I>dist</I> will be in distance <A HREF = "units.html">units</A>. The
output for <I>eng</I> will be in energy <A HREF = "units.html">units</A>. The output for
<I>force</I> will be in force <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dump.html">dump local</A>, <A HREF = "compute_property_local.html">compute
property/local</A>
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<P><B>Default:</B> none
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<div class="section" id="compute-centro-atom-command">
<span id="index-0"></span><h1>compute centro/atom command<a class="headerlink" href="#compute-centro-atom-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 centro/atom lattice
</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>centro/atom = style name of this compute command</li>
<li>lattice = <em>fcc</em> or <em>bcc</em> or N = # of neighbors per atom to include</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 all centro/atom fcc
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all centro/atom 8
</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 the centro-symmetry parameter for
<HR>
<H3>compute centro/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID centro/atom lattice
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>centro/atom = style name of this compute command
<LI>lattice = <I>fcc</I> or <I>bcc</I> or N = # of neighbors per atom to include
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all centro/atom fcc
</PRE>
<PRE>compute 1 all centro/atom 8
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the centro-symmetry parameter for
each atom in the group. In solid-state systems the centro-symmetry
parameter is a useful measure of the local lattice disorder around an
atom and can be used to characterize whether the atom is part of a
perfect lattice, a local defect (e.g. a dislocation or stacking
fault), or at a surface.</p>
<p>The value of the centro-symmetry parameter will be 0.0 for atoms not
in the specified compute group.</p>
<p>This parameter is computed using the following formula from
<a class="reference internal" href="#kelchner"><span>(Kelchner)</span></a></p>
<img alt="_images/centro_symmetry.jpg" class="align-center" src="_images/centro_symmetry.jpg" />
<p>where the <em>N</em> nearest neighbors or each atom are identified and Ri and
fault), or at a surface.
</P>
<P>The value of the centro-symmetry parameter will be 0.0 for atoms not
in the specified compute group.
</P>
<P>This parameter is computed using the following formula from
<A HREF = "#Kelchner">(Kelchner)</A>
</P>
<CENTER><IMG SRC = "Eqs/centro_symmetry.jpg">
</CENTER>
<P>where the <I>N</I> nearest neighbors or each atom are identified and Ri and
Ri+N/2 are vectors from the central atom to a particular pair of
nearest neighbors. There are N*(N-1)/2 possible neighbor pairs that
can contribute to this formula. The quantity in the sum is computed
for each, and the N/2 smallest are used. This will typically be for
pairs of atoms in symmetrically opposite positions with respect to the
central atom; hence the i+N/2 notation.</p>
<p><em>N</em> is an input parameter, which should be set to correspond to the
central atom; hence the i+N/2 notation.
</P>
<P><I>N</I> is an input parameter, which should be set to correspond to the
number of nearest neighbors in the underlying lattice of atoms. If
the keyword <em>fcc</em> or <em>bcc</em> is used, <em>N</em> is set to 12 and 8
respectively. More generally, <em>N</em> can be set to a positive, even
integer.</p>
<p>For an atom on a lattice site, surrounded by atoms on a perfect
the keyword <I>fcc</I> or <I>bcc</I> is used, <I>N</I> is set to 12 and 8
respectively. More generally, <I>N</I> can be set to a positive, even
integer.
</P>
<P>For an atom on a lattice site, surrounded by atoms on a perfect
lattice, the centro-symmetry parameter will be 0. It will be near 0
for small thermal perturbations of a perfect lattice. If a point
defect exists, the symmetry is broken, and the parameter will be a
larger positive value. An atom at a surface will have a large
positive parameter. If the atom does not have <em>N</em> neighbors (within
positive parameter. If the atom does not have <I>N</I> neighbors (within
the potential cutoff), then its centro-symmetry parameter is set to
0.0.</p>
<p>Only atoms within the cutoff of the pairwise neighbor list are
0.0.
</P>
<P>Only atoms within the cutoff of the pairwise neighbor list are
considered as possible neighbors. Atoms not in the compute group are
included in the <em>N</em> neighbors used in this calculation.</p>
<p>The neighbor list needed to compute this quantity is constructed each
included in the <I>N</I> neighbors used in this calculation.
</P>
<P>The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (e.g. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each with a
<em>centro/atom</em> style.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-atom vector, which can be accessed by
<I>centro/atom</I> style.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of
LAMMPS output options.</p>
<p>The per-atom vector values are unitless values &gt;= 0.0. Their
<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The per-atom vector values are unitless values >= 0.0. Their
magnitude depends on the lattice style due to the number of
contibuting neighbor pairs in the summation in the formula above. And
it depends on the local defects surrounding the central atom, as
described above.</p>
<p>Here are typical centro-symmetry values, from a a nanoindentation
described above.
</P>
<P>Here are typical centro-symmetry values, from a a nanoindentation
simulation into gold (FCC). These were provided by Jon Zimmerman
(Sandia):</p>
<div class="highlight-python"><div class="highlight"><pre>Bulk lattice = 0
(Sandia):
</P>
<PRE>Bulk lattice = 0
Dislocation core ~ 1.0 (0.5 to 1.25)
Stacking faults ~ 5.0 (4.0 to 6.0)
Free surface ~ 23.0
</pre></div>
</div>
<p>These values are <em>not</em> normalized by the square of the lattice
parameter. If they were, normalized values would be:</p>
<div class="highlight-python"><div class="highlight"><pre>Bulk lattice = 0
Free surface ~ 23.0
</PRE>
<P>These values are *not* normalized by the square of the lattice
parameter. If they were, normalized values would be:
</P>
<PRE>Bulk lattice = 0
Dislocation core ~ 0.06 (0.03 to 0.075)
Stacking faults ~ 0.3 (0.24 to 0.36)
Free surface ~ 1.38
</pre></div>
</div>
<p>For BCC materials, the values for dislocation cores and free surfaces
Free surface ~ 1.38
</PRE>
<P>For BCC materials, the values for dislocation cores and free surfaces
would be somewhat different, due to their being only 8 neighbors instead
of 12.</p>
</div>
<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="compute_cna_atom.html"><em>compute cna/atom</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="kelchner"><strong>(Kelchner)</strong> Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998).</p>
</div>
</div>
of 12.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_cna_atom.html">compute cna/atom</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Kelchner"></A>
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<P><B>(Kelchner)</B> Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998).
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<div class="section" id="compute-cluster-atom-command">
<span id="index-0"></span><h1>compute cluster/atom command<a class="headerlink" href="#compute-cluster-atom-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 cluster/atom cutoff
</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>cluster/atom = style name of this compute command</li>
<li>cutoff = distance within which to label atoms as part of same cluster (distance units)</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 all cluster/atom 1.0
</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 assigns each atom a cluster ID.</p>
<p>A cluster is defined as a set of atoms, each of which is within the
<HR>
<H3>compute cluster/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID cluster/atom cutoff
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>cluster/atom = style name of this compute command
<LI>cutoff = distance within which to label atoms as part of same cluster (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all cluster/atom 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that assigns each atom a cluster ID.
</P>
<P>A cluster is defined as a set of atoms, each of which is within the
cutoff distance from one or more other atoms in the cluster. If an
atom has no neighbors within the cutoff distance, then it is a 1-atom
cluster. The ID of every atom in the cluster will be the smallest
atom ID of any atom in the cluster.</p>
<p>Only atoms in the compute group are clustered and assigned cluster
IDs. Atoms not in the compute group are assigned a cluster ID = 0.</p>
<p>The neighbor list needed to compute this quantity is constructed each
atom ID of any atom in the cluster.
</P>
<P>Only atoms in the compute group are clustered and assigned cluster
IDs. Atoms not in the compute group are assigned a cluster ID = 0.
</P>
<P>The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each of a
<em>clsuter/atom</em> style.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-atom vector, which can be accessed by
<I>clsuter/atom</I> style.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of
LAMMPS output options.</p>
<p>The per-atom vector values will be an ID &gt; 0, as explained above.</p>
</div>
<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="compute_coord_atom.html"><em>compute coord/atom</em></a></p>
<p><strong>Default:</strong> none</p>
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<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The per-atom vector values will be an ID > 0, as explained above.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_coord_atom.html">compute coord/atom</A>
</P>
<P><B>Default:</B> none
</P>
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<div class="section" id="compute-cna-atom-command">
<span id="index-0"></span><h1>compute cna/atom command<a class="headerlink" href="#compute-cna-atom-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 cna/atom cutoff
</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>cna/atom = style name of this compute command</li>
<li>cutoff = cutoff distance for nearest neighbors (distance units)</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 all cna/atom 3.08
</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 the CNA (Common Neighbor
<HR>
<H3>compute cna/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID cna/atom cutoff
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>cna/atom = style name of this compute command
<LI>cutoff = cutoff distance for nearest neighbors (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all cna/atom 3.08
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the CNA (Common Neighbor
Analysis) pattern for each atom in the group. In solid-state systems
the CNA pattern is a useful measure of the local crystal structure
around an atom. The CNA methodology is described in <a class="reference internal" href="#faken"><span>(Faken)</span></a>
and <a class="reference internal" href="#tsuzuki"><span>(Tsuzuki)</span></a>.</p>
<p>Currently, there are five kinds of CNA patterns LAMMPS recognizes:</p>
<ul class="simple">
<li>fcc = 1</li>
<li>hcp = 2</li>
<li>bcc = 3</li>
<li>icosohedral = 4</li>
<li>unknown = 5</li>
</ul>
<p>The value of the CNA pattern will be 0 for atoms not in the specified
around an atom. The CNA methodology is described in <A HREF = "#Faken">(Faken)</A>
and <A HREF = "#Tsuzuki">(Tsuzuki)</A>.
</P>
<P>Currently, there are five kinds of CNA patterns LAMMPS recognizes:
</P>
<UL><LI>fcc = 1
<LI>hcp = 2
<LI>bcc = 3
<LI>icosohedral = 4
<LI>unknown = 5
</UL>
<P>The value of the CNA pattern will be 0 for atoms not in the specified
compute group. Note that normally a CNA calculation should only be
performed on mono-component systems.</p>
<p>The CNA calculation can be sensitive to the specified cutoff value.
performed on mono-component systems.
</P>
<P>The CNA calculation can be sensitive to the specified cutoff value.
You should insure the appropriate nearest neighbors of an atom are
found within the cutoff distance for the presumed crystal strucure.
E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest
neighbors for perfect BCC crystals. These formulas can be used to
obtain a good cutoff distance:</p>
<img alt="_images/cna_cutoff1.jpg" class="align-center" src="_images/cna_cutoff1.jpg" />
<p>where a is the lattice constant for the crystal structure concerned
obtain a good cutoff distance:
</P>
<CENTER><IMG SRC = "Eqs/cna_cutoff1.jpg">
</CENTER>
<P>where a is the lattice constant for the crystal structure concerned
and in the HCP case, x = (c/a) / 1.633, where 1.633 is the ideal c/a
for HCP crystals.</p>
<p>Also note that since the CNA calculation in LAMMPS uses the neighbors
for HCP crystals.
</P>
<P>Also note that since the CNA calculation in LAMMPS uses the neighbors
of an owned atom to find the nearest neighbors of a ghost atom, the
following relation should also be satisfied:</p>
<img alt="_images/cna_cutoff2.jpg" class="align-center" src="_images/cna_cutoff2.jpg" />
<p>where Rc is the cutoff distance of the potential, Rs is the skin
distance as specified by the <a class="reference internal" href="neighbor.html"><em>neighbor</em></a> command, and
following relation should also be satisfied:
</P>
<CENTER><IMG SRC = "Eqs/cna_cutoff2.jpg">
</CENTER>
<P>where Rc is the cutoff distance of the potential, Rs is the skin
distance as specified by the <A HREF = "neighbor.html">neighbor</A> command, and
cutoff is the argument used with the compute cna/atom command. LAMMPS
will issue a warning if this is not the case.</p>
<p>The neighbor list needed to compute this quantity is constructed each
will issue a warning if this is not the case.
</P>
<P>The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (e.g. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each with a
<em>cna/atom</em> style.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-atom vector, which can be accessed by
<I>cna/atom</I> style.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of
LAMMPS output options.</p>
<p>The per-atom vector values will be a number from 0 to 5, as explained
above.</p>
</div>
<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="compute_centro_atom.html"><em>compute centro/atom</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="faken"><strong>(Faken)</strong> Faken, Jonsson, Comput Mater Sci, 2, 279 (1994).</p>
<p id="tsuzuki"><strong>(Tsuzuki)</strong> Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007).</p>
</div>
</div>
<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The per-atom vector values will be a number from 0 to 5, as explained
above.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_centro_atom.html">compute centro/atom</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
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<P><B>(Faken)</B> Faken, Jonsson, Comput Mater Sci, 2, 279 (1994).
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<div class="section" id="compute-com-command">
<span id="index-0"></span><h1>compute com command<a class="headerlink" href="#compute-com-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 com
</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>com = style name of this compute command</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 all com
</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 the center-of-mass of the group
<HR>
<H3>compute com command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID com
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>com = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all com
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the center-of-mass of the group
of atoms, including all effects due to atoms passing thru periodic
boundaries.</p>
<p>A vector of three quantites is calculated by this compute, which
are the x,y,z coordinates of the center of mass.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The coordinates of an atom contribute to the
center-of-mass in &#8220;unwrapped&#8221; form, by using the image flags
associated with each atom. See the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command
for a discussion of &#8220;unwrapped&#8221; coordinates. See the Atoms section of
the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command for a discussion of image flags
boundaries.
</P>
<P>A vector of three quantites is calculated by this compute, which
are the x,y,z coordinates of the center of mass.
</P>
<P>IMPORTANT NOTE: The coordinates of an atom contribute to the
center-of-mass in "unwrapped" form, by using the image flags
associated with each atom. See the <A HREF = "dump.html">dump custom</A> command
for a discussion of "unwrapped" coordinates. See the Atoms section of
the <A HREF = "read_data.html">read_data</A> command for a discussion of image flags
and how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the <a class="reference internal" href="set.html"><em>set image</em></a> command.</p>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global vector of length 3, which can be
(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
image</A> command.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global vector of length 3, which can be
accessed by indices 1-3 by any command that uses global vector values
from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>this section</span></a> for an overview of LAMMPS output
options.</p>
<p>The vector values are &#8220;intensive&#8221;. The vector values will be in
distance <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<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="compute_com_chunk.html"><em>compute com/chunk</em></a></p>
<p><strong>Default:</strong> none</p>
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from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The vector values are "intensive". The vector values will be in
distance <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_com_chunk.html">compute com/chunk</A>
</P>
<P><B>Default:</B> none
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<div class="section" id="compute-com-chunk-command">
<span id="index-0"></span><h1>compute com/chunk command<a class="headerlink" href="#compute-com-chunk-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 com/chunk chunkID
</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>com/chunk = style name of this compute command</li>
<li>chunkID = ID of <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command</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 fluid com/chunk molchunk
</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 the center-of-mass for multiple
chunks of atoms.</p>
<p>In LAMMPS, chunks are collections of atoms defined by a <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command, which assigns each atom
<HR>
<H3>compute com/chunk command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID com/chunk chunkID
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>com/chunk = style name of this compute command
<LI>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 fluid com/chunk molchunk
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the center-of-mass for multiple
chunks of atoms.
</P>
<P>In LAMMPS, chunks are collections of atoms defined by a <A HREF = "compute_chunk_atom.html">compute
chunk/atom</A> command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> doc page and &#8220;<a class="reference internal" href="Section_howto.html#howto-23"><span>Section_howto 23</span></a> for details of how chunks can be
molecule or atoms in a spatial bin. See the <A HREF = "compute_chunk_atom.html">compute
chunk/atom</A> doc page and "<A HREF = "Section_howto.html#howto_23">Section_howto
23</A> for details of how chunks can be
defined and examples of how they can be used to measure properties of
a system.</p>
<p>This compute calculates the x,y,z coordinates of the center-of-mass
a system.
</P>
<P>This compute calculates the x,y,z coordinates of the center-of-mass
for each chunk, which includes all effects due to atoms passing thru
periodic boundaries.</p>
<p>Note that only atoms in the specified group contribute to the
calculation. The <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command
periodic boundaries.
</P>
<P>Note that only atoms in the specified group contribute to the
calculation. The <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
defines its own group; atoms will have a chunk ID = 0 if they are not
in that group, signifying they are not assigned to a chunk, and will
thus also not contribute to this calculation. You can specify the
&#8220;all&#8221; group for this command if you simply want to include atoms with
non-zero chunk IDs.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The coordinates of an atom contribute to the chunk&#8217;s
center-of-mass in &#8220;unwrapped&#8221; form, by using the image flags
associated with each atom. See the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command
for a discussion of &#8220;unwrapped&#8221; coordinates. See the Atoms section of
the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command for a discussion of image flags
"all" group for this command if you simply want to include atoms with
non-zero chunk IDs.
</P>
<P>IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's
center-of-mass in "unwrapped" form, by using the image flags
associated with each atom. See the <A HREF = "dump.html">dump custom</A> command
for a discussion of "unwrapped" coordinates. See the Atoms section of
the <A HREF = "read_data.html">read_data</A> command for a discussion of image flags
and how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the <a class="reference internal" href="set.html"><em>set image</em></a> command.</p>
</div>
<p>The simplest way to output the results of the compute com/chunk
calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a>
command, for example:</p>
<div class="highlight-python"><div class="highlight"><pre>compute cc1 all chunk/atom molecule
(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
image</A> command.
</P>
<P>The simplest way to output the results of the compute com/chunk
calculation to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A>
command, for example:
</P>
<PRE>compute cc1 all chunk/atom molecule
compute myChunk all com/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</pre></div>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global array where the number of rows = the
number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command. The number of columns =
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</PRE>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global array where the number of rows = the
number of chunks <I>Nchunk</I> as calculated by the specified <A HREF = "compute_chunk_atom.html">compute
chunk/atom</A> command. The number of columns =
3 for the x,y,z center-of-mass coordinates of each chunk. These
values can be accessed by any command that uses global array values
from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of LAMMPS output
options.</p>
<p>The array values are &#8220;intensive&#8221;. The array values will be in
distance <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<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="compute_com.html"><em>compute com</em></a></p>
<p><strong>Default:</strong> none</p>
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from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
15</A> for an overview of LAMMPS output
options.
</P>
<P>The array values are "intensive". The array values will be in
distance <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_com.html">compute com</A>
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<P><B>Default:</B> none
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<div class="section" id="compute-contact-atom-command">
<span id="index-0"></span><h1>compute contact/atom command<a class="headerlink" href="#compute-contact-atom-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 contact/atom
</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>contact/atom = style name of this compute command</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 all contact/atom
</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 the number of contacts
for each atom in a group.</p>
<p>The contact number is defined for finite-size spherical particles as
<HR>
<H3>compute contact/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID contact/atom
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>contact/atom = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all contact/atom
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the number of contacts
for each atom in a group.
</P>
<P>The contact number is defined for finite-size spherical particles as
the number of neighbor atoms which overlap the central particle,
meaning that their distance of separation is less than or equal to the
sum of the radii of the two particles.</p>
<p>The value of the contact number will be 0.0 for atoms not in the
specified compute group.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-atom vector, whose values can be
sum of the radii of the two particles.
</P>
<P>The value of the contact number will be 0.0 for atoms not in the
specified compute group.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-atom vector, whose values can be
accessed by any command that uses per-atom values from a compute as
input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an
overview of LAMMPS output options.</p>
<p>The per-atom vector values will be a number &gt;= 0.0, as explained
above.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute requires that atoms store a radius as defined by the
<a class="reference internal" href="atom_style.html"><em>atom_style sphere</em></a> command.</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 class="reference internal" href="compute_coord_atom.html"><em>compute coord/atom</em></a></p>
<p><strong>Default:</strong> none</p>
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input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
overview of LAMMPS output options.
</P>
<P>The per-atom vector values will be a number >= 0.0, as explained
above.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute requires that atoms store a radius as defined by the
<A HREF = "atom_style.html">atom_style sphere</A> command.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_coord_atom.html">compute coord/atom</A>
</P>
<P><B>Default:</B> none
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<div class="section" id="compute-coord-atom-command">
<span id="index-0"></span><h1>compute coord/atom command<a class="headerlink" href="#compute-coord-atom-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 coord/atom cutoff type1 type2 ...
</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>coord/atom = style name of this compute command</li>
<li>cutoff = distance within which to count coordination neighbors (distance units)</li>
<li>typeN = atom type for Nth coordination count (see asterisk form below)</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 all coord/atom 2.0
<HR>
<H3>compute coord/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID coord/atom cutoff type1 type2 ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>coord/atom = style name of this compute command
<LI>cutoff = distance within which to count coordination neighbors (distance units)
<LI>typeN = atom type for Nth coordination count (see asterisk form below)
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all coord/atom 2.0
compute 1 all coord/atom 6.0 1 2
compute 1 all coord/atom 6.0 2*4 5*8 *
</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 one or more coordination numbers
for each atom in a group.</p>
<p>A coordination number is defined as the number of neighbor atoms with
compute 1 all coord/atom 6.0 2*4 5*8 *
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates one or more coordination numbers
for each atom in a group.
</P>
<P>A coordination number is defined as the number of neighbor atoms with
specified atom type(s) that are within the specified cutoff distance
from the central atom. Atoms not in the group are included in a
coordination number of atoms in the group.</p>
<p>The <em>typeN</em> keywords allow you to specify which atom types contribute
coordination number of atoms in the group.
</P>
<P>The <I>typeN</I> keywords allow you to specify which atom types contribute
to each coordination number. One coordination number is computed for
each of the <em>typeN</em> keywords listed. If no <em>typeN</em> keywords are
each of the <I>typeN</I> keywords listed. If no <I>typeN</I> keywords are
listed, a single coordination number is calculated, which includes
atoms of all types (same as the &#8220;*&#8221; format, see below).</p>
<p>The <em>typeN</em> keywords can be specified in one of two ways. An explicit
atoms of all types (same as the "*" format, see below).
</P>
<P>The <I>typeN</I> keywords can be specified in one of two ways. An explicit
numeric value can be used, as in the 2nd example above. Or a
wild-card asterisk can be used to specify a range of atom types. This
takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;. If N = the number of
takes the form "*" or "*n" or "n*" or "m*n". If N = the number of
atom types, then an asterisk with no numeric values means all types
from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive).</p>
<p>The value of all coordination numbers will be 0.0 for atoms not in the
specified compute group.</p>
<p>The neighbor list needed to compute this quantity is constructed each
(inclusive).
</P>
<P>The value of all coordination numbers will be 0.0 for atoms not in the
specified compute group.
</P>
<P>The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If you have a bonded system, then the settings of
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command can remove pairwise
too frequently.
</P>
<P>IMPORTANT NOTE: If you have a bonded system, then the settings of
<A HREF = "special_bonds.html">special_bonds</A> command can remove pairwise
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 HREF = "special_bonds.html">special_bonds</A>
command, and means those pairwise interactions do not appear in the
neighbor list. Because this fix uses the neighbor list, it also means
those pairs will not be included in the coordination count. One way
to get around this, is to write a dump file, and use the
<a class="reference internal" href="rerun.html"><em>rerun</em></a> command to compute the coordination for snapshots
<A HREF = "rerun.html">rerun</A> command to compute the coordination 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 pairs in
the neighbor list.</p>
</div>
<p><strong>Output info:</strong></p>
<p>If single <em>type1</em> keyword is specified (or if none are specified),
this compute calculates a per-atom vector. If multiple <em>typeN</em>
<A HREF = "special_bonds.html">special_bonds</A> command that includes all pairs in
the neighbor list.
</P>
<P><B>Output info:</B>
</P>
<P>If single <I>type1</I> keyword is specified (or if none are specified),
this compute calculates a per-atom vector. If multiple <I>typeN</I>
keywords are specified, this compute calculates a per-atom array, with
N columns. These values can be accessed by any command that uses
per-atom values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of LAMMPS output
options.</p>
<p>The per-atom vector or array values will be a number &gt;= 0.0, as
explained above.</p>
</div>
<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="compute_cluster_atom.html"><em>compute cluster/atom</em></a></p>
<p><strong>Default:</strong> none</p>
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per-atom values from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
15</A> for an overview of LAMMPS output
options.
</P>
<P>The per-atom vector or array values will be a number >= 0.0, as
explained above.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_cluster_atom.html">compute cluster/atom</A>
</P>
<P><B>Default:</B> none
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<div class="section" id="compute-damage-atom-command">
<span id="index-0"></span><h1>compute damage/atom command<a class="headerlink" href="#compute-damage-atom-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 damage/atom
</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>damage/atom = style name of this compute command</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 all damage/atom
</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 the per-atom damage for each atom
in a group. This is a quantity relevant for <a class="reference internal" href="pair_peri.html"><em>Peridynamics models</em></a>. See <a class="reference external" href="PDF/PDLammps_overview.pdf">this document</a>
for an overview of LAMMPS commands for Peridynamics modeling.</p>
<p>The &#8220;damage&#8221; of a Peridymaics particles is based on the bond breakage
<HR>
<H3>compute damage/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID damage/atom
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>damage/atom = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all damage/atom
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the per-atom damage for each atom
in a group. This is a quantity relevant for <A HREF = "pair_peri.html">Peridynamics
models</A>. See <A HREF = "PDF/PDLammps_overview.pdf">this document</A>
for an overview of LAMMPS commands for Peridynamics modeling.
</P>
<P>The "damage" of a Peridymaics particles is based on the bond breakage
between the particle and its neighbors. If all the bonds are broken
the particle is considered to be fully damaged.</p>
<p>See the <a class="reference external" href="http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf">PDLAMMPS user guide</a> for a formal
definition of &#8220;damage&#8221; and more details about Peridynamics as it is
implemented in LAMMPS.</p>
<p>This command can be used with all the Peridynamic pair styles.</p>
<p>The damage value will be 0.0 for atoms not in the specified compute
group.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-atom vector, which can be accessed by
the particle is considered to be fully damaged.
</P>
<P>See the <A HREF = "http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf">PDLAMMPS user
guide</A> for a formal
definition of "damage" and more details about Peridynamics as it is
implemented in LAMMPS.
</P>
<P>This command can be used with all the Peridynamic pair styles.
</P>
<P>The damage value will be 0.0 for atoms not in the specified compute
group.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of
LAMMPS output options.</p>
<p>The per-atom vector values are unitlesss numbers (damage) &gt;= 0.0.</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 PERI 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>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><code class="xref doc docutils literal"><span class="pre">compute</span> <span class="pre">dilatation</span></code>, <code class="xref doc docutils literal"><span class="pre">compute</span> <span class="pre">plasticity</span></code></p>
<p><strong>Default:</strong> none</p>
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<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The per-atom vector values are unitlesss numbers (damage) >= 0.0.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the PERI package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_dilatation.html">compute dilatation</A>, <A HREF = "compute_plasticity.html">compute
plasticity</A>
</P>
<P><B>Default:</B> none
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<div class="section" id="compute-dihedral-local-command">
<span id="index-0"></span><h1>compute dihedral/local command<a class="headerlink" href="#compute-dihedral-local-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 dihedral/local input1 input2 ...
</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>dihedral/local = style name of this compute command</li>
<li>one or more keywords may be appended</li>
<li>keyword = <em>phi</em></li>
</ul>
<pre class="literal-block">
<em>phi</em> = tabulate dihedral angles
</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>compute 1 all dihedral/local phi
</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 of individual dihedral
<HR>
<H3>compute dihedral/local command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID dihedral/local input1 input2 ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>dihedral/local = style name of this compute command
<LI>one or more keywords may be appended
<LI>keyword = <I>phi</I>
<PRE> <I>phi</I> = tabulate dihedral angles
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all dihedral/local phi
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates properties of individual dihedral
interactions. The number of datums generated, aggregated across all
processors, equals the number of angles in the system, modified by the
group parameter as explained below.</p>
<p>The local data stored by this command is generated by looping over all
group parameter as explained below.
</P>
<P>The local data stored by this command is generated by looping over all
the atoms owned on a processor and their dihedrals. A dihedral will
only be included if all 4 atoms in the dihedral are in the specified
compute group.</p>
<p>Note that as atoms migrate from processor to processor, there will be
compute group.
</P>
<P>Note that as atoms migrate from processor to processor, there will be
no consistent ordering of the entries within the local vector or array
from one timestep to the next. The only consistency that is
guaranteed is that the ordering on a particular timestep will be the
same for local vectors or arrays generated by other compute commands.
For example, dihedral output from the <a class="reference internal" href="compute_property_local.html"><em>compute property/local</em></a> command can be combined
with data from this command and output by the <a class="reference internal" href="dump.html"><em>dump local</em></a>
command in a consistent way.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a local vector or local array depending on the
For example, dihedral output from the <A HREF = "compute_property_local.html">compute
property/local</A> command can be combined
with data from this command and output by the <A HREF = "dump.html">dump local</A>
command in a consistent way.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a local vector or local array depending on the
number of keywords. The length of the vector or number of rows in the
array is the number of dihedrals. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>this section</span></a> for an overview of LAMMPS output
options.</p>
<p>The output for <em>phi</em> will be in degrees.</p>
</div>
<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="dump.html"><em>dump local</em></a>, <a class="reference internal" href="compute_property_local.html"><em>compute property/local</em></a></p>
<p><strong>Default:</strong> none</p>
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uses local values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The output for <I>phi</I> will be in degrees.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dump.html">dump local</A>, <A HREF = "compute_property_local.html">compute
property/local</A>
</P>
<P><B>Default:</B> none
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<div class="section" id="compute-dilatation-atom-command">
<span id="index-0"></span><h1>compute dilatation/atom command<a class="headerlink" href="#compute-dilatation-atom-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 dilatation/atom
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in compute command</li>
<li>dilation/atom = style name of this compute command</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 all dilatation/atom
</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 the per-atom dilatation for each
atom in a group. This is a quantity relevant for <a class="reference internal" href="pair_peri.html"><em>Peridynamics models</em></a>. See <a class="reference external" href="PDF/PDLammps_overview.pdf">this document</a>
for an overview of LAMMPS commands for Peridynamics modeling.</p>
<p>For small deformation, dilatation of is the measure of the volumetric
strain.</p>
<p>The dilatation &#8220;theta&#8221; for each peridynamic particle I is calculated
<HR>
<H3>compute dilatation/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID dilatation/atom
</PRE>
<UL><LI>ID, group-ID are documented in compute command
<LI>dilation/atom = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all dilatation/atom
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the per-atom dilatation for each
atom in a group. This is a quantity relevant for <A HREF = "pair_peri.html">Peridynamics
models</A>. See <A HREF = "PDF/PDLammps_overview.pdf">this document</A>
for an overview of LAMMPS commands for Peridynamics modeling.
</P>
<P>For small deformation, dilatation of is the measure of the volumetric
strain.
</P>
<P>The dilatation "theta" for each peridynamic particle I is calculated
as a sum over its neighbors with unbroken bonds, where the
contribution of the IJ pair is a function of the change in bond length
(versus the initial length in the reference state), the volume
fraction of the particles and an influence function. See the
<a class="reference external" href="http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf">PDLAMMPS user guide</a> for a formal
definition of dilatation.</p>
<p>This command can only be used with a subset of the Peridynamic <a class="reference internal" href="pair_peri.html"><em>pair styles</em></a>: peri/lps, peri/ves and peri/eps.</p>
<p>The dilatation value will be 0.0 for atoms not in the specified
compute group.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-atom vector, which can be accessed by
<A HREF = "http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf">PDLAMMPS user
guide</A> for a formal
definition of dilatation.
</P>
<P>This command can only be used with a subset of the Peridynamic <A HREF = "pair_peri.html">pair
styles</A>: peri/lps, peri/ves and peri/eps.
</P>
<P>The dilatation value will be 0.0 for atoms not in the specified
compute group.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
Section_howto 15 for an overview of LAMMPS output options.</p>
<p>The per-atom vector values are unitlesss numbers (theta) &gt;= 0.0.</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 PERI 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>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><code class="xref doc docutils literal"><span class="pre">compute</span> <span class="pre">damage</span></code>, <code class="xref doc docutils literal"><span class="pre">compute</span> <span class="pre">plasticity</span></code></p>
<p><strong>Default:</strong> none</p>
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Section_howto 15 for an overview of LAMMPS output options.
</P>
<P>The per-atom vector values are unitlesss numbers (theta) >= 0.0.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the PERI package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_damage.html">compute damage</A>, <A HREF = "compute_plasticity.html">compute
plasticity</A>
</P>
<P><B>Default:</B> none
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<div class="section" id="compute-displace-atom-command">
<span id="index-0"></span><h1>compute displace/atom command<a class="headerlink" href="#compute-displace-atom-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 displace/atom
</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>displace/atom = style name of this compute command</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 all displace/atom
</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 the current displacement of each
<HR>
<H3>compute displace/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID displace/atom
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>displace/atom = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all displace/atom
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the current displacement of each
atom in the group from its original coordinates, including all effects
due to atoms passing thru periodic boundaries.</p>
<p>A vector of four quantites per atom is calculated by this compute.
due to atoms passing thru periodic boundaries.
</P>
<P>A vector of four quantites per atom is calculated by this compute.
The first 3 elements of the vector are the dx,dy,dz displacements.
The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy +
dz*dz).</p>
<p>The displacement of an atom is from its original position at the time
dz*dz).
</P>
<P>The displacement of an atom is from its original position at the time
the compute command was issued. The value of the displacement will be
0.0 for atoms not in the specified compute group.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Initial coordinates are stored in &#8220;unwrapped&#8221; form, by
using the image flags associated with each atom. See the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command for a discussion of &#8220;unwrapped&#8221; coordinates.
See the Atoms section of the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command for a
0.0 for atoms not in the specified compute group.
</P>
<P>IMPORTANT NOTE: Initial coordinates are stored in "unwrapped" form, by
using the image flags associated with each atom. See the <A HREF = "dump.html">dump
custom</A> command for a discussion of "unwrapped" coordinates.
See the Atoms section of the <A HREF = "read_data.html">read_data</A> command for a
discussion of image flags and how they are set for each atom. You can
reset the image flags (e.g. to 0) before invoking this compute by
using the <a class="reference internal" href="set.html"><em>set image</em></a> command.</p>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If you want the quantities calculated by this compute
to be continuous when running from a <a class="reference internal" href="read_restart.html"><em>restart file</em></a>,
using the <A HREF = "set.html">set image</A> command.
</P>
<P>IMPORTANT NOTE: If you want the quantities calculated by this compute
to be continuous when running from a <A HREF = "read_restart.html">restart file</A>,
then you should use the same ID for this compute, as in the original
run. This is so that the fix this compute creates to store per-atom
quantities will also have the same ID, and thus be initialized
correctly with time=0 atom coordinates from the restart file.</p>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-atom array with 4 columns, which can be
correctly with time=0 atom coordinates from the restart file.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-atom array with 4 columns, which can be
accessed by indices 1-4 by any command that uses per-atom values from
a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of LAMMPS output
options.</p>
<p>The per-atom array values will be in distance <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<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="compute_msd.html"><em>compute msd</em></a>, <a class="reference internal" href="dump.html"><em>dump custom</em></a>, <a class="reference internal" href="fix_store_state.html"><em>fix store/state</em></a></p>
<p><strong>Default:</strong> none</p>
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a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
15</A> for an overview of LAMMPS output
options.
</P>
<P>The per-atom array values will be in distance <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_msd.html">compute msd</A>, <A HREF = "dump.html">dump custom</A>, <A HREF = "fix_store_state.html">fix
store/state</A>
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<P><B>Default:</B> none
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<div class="section" id="compute-erotate-asphere-command">
<span id="index-0"></span><h1>compute erotate/asphere command<a class="headerlink" href="#compute-erotate-asphere-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 erotate/asphere
</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>erotate/asphere = style name of this compute command</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 all erotate/asphere
</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 the rotational kinetic energy of
<HR>
<H3>compute erotate/asphere command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID erotate/asphere
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>erotate/asphere = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all erotate/asphere
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the rotational kinetic energy of
a group of aspherical particles. The aspherical particles can be
ellipsoids, or line segments, or triangles. See the
<a class="reference internal" href="atom_style.html"><em>atom_style</em></a> and <a class="reference internal" href="read_data.html"><em>read_data</em></a> commands
for descriptions of these options.</p>
<p>For all 3 types of particles, the rotational kinetic energy is
<A HREF = "atom_style.html">atom_style</A> and <A HREF = "read_data.html">read_data</A> commands
for descriptions of these options.
</P>
<P>For all 3 types of particles, the rotational kinetic energy is
computed as 1/2 I w^2, where I is the inertia tensor for the
aspherical particle and w is its angular velocity, which is computed
from its angular momentum if needed.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">For <a class="reference internal" href="dimension.html"><em>2d models</em></a>, ellipsoidal particles
from its angular momentum if needed.
</P>
<P>IMPORTANT NOTE: For <A HREF = "dimension.html">2d models</A>, ellipsoidal particles
are treated as ellipsoids, not ellipses, meaning their moments of
inertia will be the same as in 3d.</p>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global scalar (the KE). This value can be
inertia will be the same as in 3d.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an
overview of LAMMPS output options.</p>
<p>The scalar value calculated by this compute is &#8220;extensive&#8221;. The
scalar value will be in energy <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute requires that ellipsoidal particles atoms store a shape
input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
overview of LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "extensive". The
scalar value will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute requires that ellipsoidal particles atoms store a shape
and quaternion orientation and angular momentum as defined by the
<a class="reference internal" href="atom_style.html"><em>atom_style ellipsoid</em></a> command.</p>
<p>This compute requires that line segment particles atoms store a length
and orientation and angular velocity as defined by the <a class="reference internal" href="atom_style.html"><em>atom_style line</em></a> command.</p>
<p>This compute requires that triangular particles atoms store a size and
<A HREF = "atom_style.html">atom_style ellipsoid</A> command.
</P>
<P>This compute requires that line segment particles atoms store a length
and orientation and angular velocity as defined by the <A HREF = "atom_style.html">atom_style
line</A> command.
</P>
<P>This compute requires that triangular particles atoms store a size and
shape and quaternion orientation and angular momentum as defined by
the <a class="reference internal" href="atom_style.html"><em>atom_style tri</em></a> command.</p>
<p>All particles in the group must be finite-size. They cannot be point
particles.</p>
<p><strong>Related commands:</strong> none</p>
<p><a class="reference internal" href="compute_erotate_sphere.html"><em>compute erotate/sphere</em></a></p>
<p><strong>Default:</strong> none</p>
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<P>All particles in the group must be finite-size. They cannot be point
particles.
</P>
<P><B>Related commands:</B> none
</P>
<P><A HREF = "compute_erotate_sphere.html">compute erotate/sphere</A>
</P>
<P><B>Default:</B> none
</P>
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<div class="section" id="compute-erotate-rigid-command">
<span id="index-0"></span><h1>compute erotate/rigid command<a class="headerlink" href="#compute-erotate-rigid-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 erotate/rigid fix-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>erotate/rigid = style name of this compute command</li>
<li>fix-ID = ID of rigid body fix</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 all erotate/rigid myRigid
</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 the rotational kinetic energy of
a collection of rigid bodies, as defined by one of the <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> command variants.</p>
<p>The rotational energy of each rigid body is computed as 1/2 I Wbody^2,
<HR>
<H3>compute erotate/rigid command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID erotate/rigid fix-ID
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>erotate/rigid = style name of this compute command
<LI>fix-ID = ID of rigid body fix
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all erotate/rigid myRigid
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the rotational kinetic energy of
a collection of rigid bodies, as defined by one of the <A HREF = "fix_rigid.html">fix
rigid</A> command variants.
</P>
<P>The rotational energy of each rigid body is computed as 1/2 I Wbody^2,
where I is the inertia tensor for the rigid body, and Wbody is its
angular velocity vector. Both I and Wbody are in the frame of
reference of the rigid body, i.e. I is diagonalized.</p>
<p>The <em>fix-ID</em> should be the ID of one of the <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a>
reference of the rigid body, i.e. I is diagonalized.
</P>
<P>The <I>fix-ID</I> should be the ID of one of the <A HREF = "fix_rigid.html">fix rigid</A>
commands which defines the rigid bodies. The group specified in the
compute command is ignored. The rotational energy of all the rigid
bodies defined by the fix rigid command in included in the
calculation.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global scalar (the summed rotational energy
calculation.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the summed rotational energy
of all the rigid bodies). This value can be used by any command that
uses a global scalar value from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of
LAMMPS output options.</p>
<p>The scalar value calculated by this compute is &#8220;extensive&#8221;. The
scalar value will be in energy <a class="reference internal" href="units.html"><em>units</em></a>.</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 RIGID 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>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><code class="xref doc docutils literal"><span class="pre">compute</span> <span class="pre">ke/rigid</span></code></p>
<p><strong>Default:</strong> none</p>
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<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "extensive". The
scalar value will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the RIGID package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_erotate_ke_rigid.html">compute ke/rigid</A>
</P>
<P><B>Default:</B> none
</P>
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<div class="section" id="compute-erotate-sphere-command">
<span id="index-0"></span><h1>compute erotate/sphere command<a class="headerlink" href="#compute-erotate-sphere-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 erotate/sphere
</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>erotate/sphere = style name of this compute command</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 all erotate/sphere
</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 the rotational kinetic energy of
a group of spherical particles.</p>
<p>The rotational energy is computed as 1/2 I w^2, where I is the moment
of inertia for a sphere and w is the particle&#8217;s angular velocity.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">For <a class="reference internal" href="dimension.html"><em>2d models</em></a>, particles are treated
<HR>
<H3>compute erotate/sphere command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID erotate/sphere
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>erotate/sphere = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all erotate/sphere
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the rotational kinetic energy of
a group of spherical particles.
</P>
<P>The rotational energy is computed as 1/2 I w^2, where I is the moment
of inertia for a sphere and w is the particle's angular velocity.
</P>
<P>IMPORTANT NOTE: For <A HREF = "dimension.html">2d models</A>, particles are treated
as spheres, not disks, meaning their moment of inertia will be the
same as in 3d.</p>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global scalar (the KE). This value can be
same as in 3d.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an
overview of LAMMPS output options.</p>
<p>The scalar value calculated by this compute is &#8220;extensive&#8221;. The
scalar value will be in energy <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute requires that atoms store a radius and angular velocity
(omega) as defined by the <a class="reference internal" href="atom_style.html"><em>atom_style sphere</em></a> command.</p>
<p>All particles in the group must be finite-size spheres or point
input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
overview of LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "extensive". The
scalar value will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute requires that atoms store a radius and angular velocity
(omega) as defined by the <A HREF = "atom_style.html">atom_style sphere</A> command.
</P>
<P>All particles in the group must be finite-size spheres or point
particles. They cannot be aspherical. Point particles will not
contribute to the rotational energy.</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 class="reference internal" href="compute_erotate_asphere.html"><em>compute erotate/asphere</em></a></p>
<p><strong>Default:</strong> none</p>
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contribute to the rotational energy.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_erotate_asphere.html">compute erotate/asphere</A>
</P>
<P><B>Default:</B> none
</P>
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<div class="section" id="compute-erotate-sphere-atom-command">
<span id="index-0"></span><h1>compute erotate/sphere/atom command<a class="headerlink" href="#compute-erotate-sphere-atom-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 erotate/sphere/atom
</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>erotate/sphere/atom = style name of this compute command</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 all erotate/sphere/atom
</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 the rotational kinetic energy for
each particle in a group.</p>
<p>The rotational energy is computed as 1/2 I w^2, where I is the moment
of inertia for a sphere and w is the particle&#8217;s angular velocity.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">For <a class="reference internal" href="dimension.html"><em>2d models</em></a>, particles are treated
<HR>
<H3>compute erotate/sphere/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID erotate/sphere/atom
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>erotate/sphere/atom = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all erotate/sphere/atom
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the rotational kinetic energy for
each particle in a group.
</P>
<P>The rotational energy is computed as 1/2 I w^2, where I is the moment
of inertia for a sphere and w is the particle's angular velocity.
</P>
<P>IMPORTANT NOTE: For <A HREF = "dimension.html">2d models</A>, particles are treated
as spheres, not disks, meaning their moment of inertia will be the
same as in 3d.</p>
</div>
<p>The value of the rotational kinetic energy will be 0.0 for atoms not
same as in 3d.
</P>
<P>The value of the rotational kinetic energy will be 0.0 for atoms not
in the specified compute group or for point particles with a radius =
0.0.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-atom vector, which can be accessed by
0.0.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of
LAMMPS output options.</p>
<p>The per-atom vector values will be in energy <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<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="dump.html"><em>dump custom</em></a></p>
<p><strong>Default:</strong> none</p>
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<P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dump.html">dump custom</A>
</P>
<P><B>Default:</B> none
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<div class="section" id="compute-event-displace-command">
<span id="index-0"></span><h1>compute event/displace command<a class="headerlink" href="#compute-event-displace-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 event/displace threshold
</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>event/displace = style name of this compute command</li>
<li>threshold = minimum distance anyparticle must move to trigger an event (distance units)</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 all event/displace 0.5
</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 flags an &#8220;event&#8221; if any particle in the
<HR>
<H3>compute event/displace command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID event/displace threshold
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>event/displace = style name of this compute command
<LI>threshold = minimum distance anyparticle must move to trigger an event (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all event/displace 0.5
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that flags an "event" if any particle in the
group has moved a distance greater than the specified threshold
distance when compared to a previously stored reference state
(i.e. the previous event). This compute is typically used in
conjunction with the <a class="reference internal" href="prd.html"><em>prd</em></a> and <a class="reference internal" href="tad.html"><em>tad</em></a> commands,
conjunction with the <A HREF = "prd.html">prd</A> and <A HREF = "tad.html">tad</A> commands,
to detect if a transition
to a new minimum energy basin has occurred.</p>
<p>This value calculated by the compute is equal to 0 if no particle has
to a new minimum energy basin has occurred.
</P>
<P>This value calculated by the compute is equal to 0 if no particle has
moved far enough, and equal to 1 if one or more particles have moved
further than the threshold distance.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If the system is undergoing significant center-of-mass motion,
due to thermal motion, an external force, or an initial net momentum,
further than the threshold distance.
</P>
<P>NOTE: If the system is undergoing significant center-of-mass motion,
due to thermal motion, an external force, or an initial net momentum,
then this compute will not be able to distinguish that motion from
local atom displacements and may generate &#8220;false postives.&#8221;</p>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global scalar (the flag). This value can be
local atom displacements and may generate "false postives."
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the flag). This value can be
used by any command that uses a global scalar value from a compute as
input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an
overview of LAMMPS output options.</p>
<p>The scalar value calculated by this compute is &#8220;intensive&#8221;. The
scalar value will be a 0 or 1 as explained above.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This command can only be used if LAMMPS was built with the REPLICA
package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section
for more info on packages.</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 class="reference internal" href="prd.html"><em>prd</em></a>, <a class="reference internal" href="tad.html"><em>tad</em></a></p>
<p><strong>Default:</strong> none</p>
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input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
overview of LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "intensive". The
scalar value will be a 0 or 1 as explained above.
</P>
<P><B>Restrictions:</B>
</P>
<P>This command can only be used if LAMMPS was built with the REPLICA
package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "prd.html">prd</A>, <A HREF = "tad.html">tad</A>
</P>
<P><B>Default:</B> none
</P>
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<div class="section" id="compute-fep-command">
<span id="index-0"></span><h1>compute fep command<a class="headerlink" href="#compute-fep-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 fep temp attribute args ... keyword value ...
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in the <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>fep = name of this compute command</li>
<li>temp = external temperature (as specified for constant-temperature run)</li>
<li>one or more attributes with args may be appended</li>
<li>attribute = <em>pair</em> or <em>atom</em></li>
</ul>
<pre class="literal-block">
<em>pair</em> args = pstyle pparam I J v_delta
<HR>
<H3>compute fep command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID fep temp attribute args ... keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in the <A HREF = "compute.html">compute</A> command
<LI>fep = name of this compute command
<LI>temp = external temperature (as specified for constant-temperature run)
<LI>one or more attributes with args may be appended
<LI>attribute = <I>pair</I> or <I>atom</I>
<PRE> <I>pair</I> args = pstyle pparam I J v_delta
pstyle = pair style name, e.g. lj/cut
pparam = parameter to perturb
I,J = type pair(s) to set parameter for
v_delta = variable with perturbation to apply (in the units of the parameter)
<em>atom</em> args = aparam I v_delta
<I>atom</I> args = aparam I v_delta
aparam = parameter to perturb
I = type to set parameter for
v_delta = variable with perturbation to apply (in the units of the parameter)
</pre>
<ul class="simple">
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>tail</em> or <em>volume</em></li>
</ul>
<pre class="literal-block">
<em>tail</em> value = <em>no</em> or <em>yes</em>
<em>no</em> = ignore tail correction to pair energies (usually small in fep)
<em>yes</em> = include tail correction to pair energies
<em>volume</em> value = <em>no</em> or <em>yes</em>
<em>no</em> = ignore volume changes (e.g. in <em>NVE</em> or <em>NVT</em> trajectories)
<em>yes</em> = include volume changes (e.g. in <em>NpT</em> trajectories)
</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>compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes
compute 1 all fep 300 atom charge 2 v_delta
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Apply a perturbation to parameters of the interaction potential and
v_delta = variable with perturbation to apply (in the units of the parameter)
</PRE>
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>tail</I> or <I>volume</I>
<PRE> <I>tail</I> value = <I>no</I> or <I>yes</I>
<I>no</I> = ignore tail correction to pair energies (usually small in fep)
<I>yes</I> = include tail correction to pair energies
<I>volume</I> value = <I>no</I> or <I>yes</I>
<I>no</I> = ignore volume changes (e.g. in <I>NVE</I> or <I>NVT</I> trajectories)
<I>yes</I> = include volume changes (e.g. in <I>NpT</I> trajectories)
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes
compute 1 all fep 300 atom charge 2 v_delta
</PRE>
<P><B>Description:</B>
</P>
<P>Apply a perturbation to parameters of the interaction potential and
recalculate the pair potential energy without changing the atomic
coordinates from those of the reference, unperturbed system. This
compute can be used to calculate free energy differences using several
methods, such as free-energy perturbation (FEP), finite-difference
thermodynamic integration (FDTI) or Bennet&#8217;s acceptance ratio method
(BAR).</p>
<p>The potential energy of the system is decomposed in three terms: a
thermodynamic integration (FDTI) or Bennet's acceptance ratio method
(BAR).
</P>
<P>The potential energy of the system is decomposed in three terms: a
background term corresponding to interaction sites whose parameters
remain constant, a reference term <a href="#id1"><span class="problematic" id="id2">*</span></a>U*&lt;sub&gt;0&lt;/sub&gt; corresponding to the
remain constant, a reference term <I>U</I><sub>0</sub> corresponding to the
initial interactions of the atoms that will undergo perturbation, and
a term <a href="#id3"><span class="problematic" id="id4">*</span></a>U*&lt;sub&gt;1&lt;/sub&gt; corresponding to the final interactions of
these atoms:</p>
<img alt="_images/compute_fep_u.jpg" class="align-center" src="_images/compute_fep_u.jpg" />
<p>A coupling parameter &amp;lambda; varying from 0 to 1 connects the
reference and perturbed systems:</p>
<img alt="_images/compute_fep_lambda.jpg" class="align-center" src="_images/compute_fep_lambda.jpg" />
<p>It is possible but not necessary that the coupling parameter (or a
a term <I>U</I><sub>1</sub> corresponding to the final interactions of
these atoms:
</P>
<CENTER><IMG SRC = "Eqs/compute_fep_u.jpg">
</CENTER>
<P>A coupling parameter &lambda; varying from 0 to 1 connects the
reference and perturbed systems:
</P>
<CENTER><IMG SRC = "Eqs/compute_fep_lambda.jpg">
</CENTER>
<P>It is possible but not necessary that the coupling parameter (or a
function thereof) appears as a multiplication factor of the potential
energy. Therefore, this compute can apply perturbations to interaction
parameters that are not directly proportional to the potential energy
(e.g. &amp;sigma; in Lennard-Jones potentials).</p>
<p>This command can be combined with <a class="reference internal" href="fix_adapt.html"><em>fix adapt</em></a> to
(e.g. &sigma; in Lennard-Jones potentials).
</P>
<P>This command can be combined with <A HREF = "fix_adapt.html">fix adapt</A> to
perform multistage free-energy perturbation calculations along
stepwise alchemical transformations during a simulation run:</p>
<img alt="_images/compute_fep_fep.jpg" class="align-center" src="_images/compute_fep_fep.jpg" />
<p>This compute is suitable for the finite-difference thermodynamic
integration (FDTI) method <a class="reference internal" href="#mezei"><span>(Mezei)</span></a>, which is based on an
stepwise alchemical transformations during a simulation run:
</P>
<CENTER><IMG SRC = "Eqs/compute_fep_fep.jpg">
</CENTER>
<P>This compute is suitable for the finite-difference thermodynamic
integration (FDTI) method <A HREF = "#Mezei">(Mezei)</A>, which is based on an
evaluation of the numerical derivative of the free energy by a
perturbation method using a very small &amp;delta;:</p>
<img alt="_images/compute_fep_fdti.jpg" class="align-center" src="_images/compute_fep_fdti.jpg" />
<p>where <a href="#id5"><span class="problematic" id="id6">*</span></a>w*&lt;sub&gt;i&lt;/sub&gt; are weights of a numerical quadrature. The <a class="reference internal" href="fix_adapt.html"><em>fix adapt</em></a> command can be used to define the stages of
&amp;lambda; at which the derivative is calculated and averaged.</p>
<p>The compute fep calculates the exponential Boltzmann term and also the
potential energy difference <a href="#id7"><span class="problematic" id="id8">*</span></a>U*&lt;sub&gt;1&lt;/sub&gt;-<a href="#id9"><span class="problematic" id="id10">*</span></a>U*&lt;sub&gt;0&lt;/sub&gt;. By
choosing a very small perturbation &amp;delta; the thermodynamic
perturbation method using a very small &delta;:
</P>
<CENTER><IMG SRC = "Eqs/compute_fep_fdti.jpg">
</CENTER>
<P>where <I>w</I><sub>i</sub> are weights of a numerical quadrature. The <A HREF = "fix_adapt.html">fix
adapt</A> command can be used to define the stages of
&lambda; at which the derivative is calculated and averaged.
</P>
<P>The compute fep calculates the exponential Boltzmann term and also the
potential energy difference <I>U</I><sub>1</sub>-<I>U</I><sub>0</sub>. By
choosing a very small perturbation &delta; the thermodynamic
integration method can be implemented using a numerical evaluation of
the derivative of the potential energy with respect to &amp;lambda;:</p>
<img alt="_images/compute_fep_ti.jpg" class="align-center" src="_images/compute_fep_ti.jpg" />
<p>Another technique to calculate free energy differences is the
acceptance ratio method <a class="reference internal" href="#bennet"><span>(Bennet)</span></a>, which can be implemented
by calculating the potential energy differences with &amp;delta; = 1.0 on
both the forward and reverse routes:</p>
<img alt="_images/compute_fep_bar.jpg" class="align-center" src="_images/compute_fep_bar.jpg" />
<p>The value of the free energy difference is determined by numerical
root finding to establish the equality.</p>
<p>Concerning the choice of how the atomic parameters are perturbed in
the derivative of the potential energy with respect to &lambda;:
</P>
<CENTER><IMG SRC = "Eqs/compute_fep_ti.jpg">
</CENTER>
<P>Another technique to calculate free energy differences is the
acceptance ratio method <A HREF = "#Bennet">(Bennet)</A>, which can be implemented
by calculating the potential energy differences with &delta; = 1.0 on
both the forward and reverse routes:
</P>
<CENTER><IMG SRC = "Eqs/compute_fep_bar.jpg">
</CENTER>
<P>The value of the free energy difference is determined by numerical
root finding to establish the equality.
</P>
<P>Concerning the choice of how the atomic parameters are perturbed in
order to setup an alchemical transformation route, several strategies
are available, such as single-topology or double-topology strategies
<a class="reference internal" href="#pearlman"><span>(Pearlman)</span></a>. The latter does not require modification of
bond lengths, angles or other internal coordinates.</p>
<p>IMPORTANT NOTES: This compute command does not take kinetic energy
<A HREF = "#Pearlman">(Pearlman)</A>. The latter does not require modification of
bond lengths, angles or other internal coordinates.
</P>
<P>IMPORTANT NOTES: This compute command does not take kinetic energy
into account, therefore the masses of the particles should not be
modified between the reference and perturbed states, or along the
alchemical transformation route. This compute command does not change
bond lengths or other internal coordinates <a class="reference internal" href="#boreschkarplus"><span>(Boresch, Karplus)</span></a>.</p>
<hr class="docutils" />
<p>The <em>pair</em> attribute enables various parameters of potentials defined
by the <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> and <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>
commands to be changed, if the pair style supports it.</p>
<p>The <em>pstyle</em> argument is the name of the pair style. For example,
<em>pstyle</em> could be specified as &#8220;lj/cut&#8221;. The <em>pparam</em> argument is the
bond lengths or other internal coordinates <A HREF = "#BoreschKarplus">(Boresch,
Karplus)</A>.
</P>
<HR>
<P>The <I>pair</I> attribute enables various parameters of potentials defined
by the <A HREF = "pair_style.html">pair_style</A> and <A HREF = "pair_coeff.html">pair_coeff</A>
commands to be changed, if the pair style supports it.
</P>
<P>The <I>pstyle</I> argument is the name of the pair style. For example,
<I>pstyle</I> could be specified as "lj/cut". The <I>pparam</I> argument is the
name of the parameter to change. This is a (non-exclusive) list of
pair styles and parameters that can be used with this compute. See
the doc pages for individual pair styles and their energy formulas for
the meaning of these parameters:</p>
<table border="1" class="docutils">
<colgroup>
<col width="59%" />
<col width="27%" />
<col width="15%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="pair_lj.html"><em>lj/cut</em></a></td>
<td>epsilon,sigma</td>
<td>type pairs</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/cut</em></a></td>
<td>epsilon,sigma</td>
<td>type pairs</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/long</em></a></td>
<td>epsilon,sigma</td>
<td>type pairs</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_lj_soft.html"><em>lj/cut/soft</em></a></td>
<td>epsilon,sigma,lambda</td>
<td>type pairs</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_lj_soft.html"><em>coul/cut/soft</em></a></td>
<td>lambda</td>
<td>type pairs</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_lj_soft.html"><em>coul/long/soft</em></a></td>
<td>lambda</td>
<td>type pairs</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_lj_soft.html"><em>lj/cut/coul/cut/soft</em></a></td>
<td>epsilon,sigma,lambda</td>
<td>type pairs</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_lj_soft.html"><em>lj/cut/coul/long/soft</em></a></td>
<td>epsilon,sigma,lambda</td>
<td>type pairs</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_lj_soft.html"><em>lj/cut/tip4p/long/soft</em></a></td>
<td>epsilon,sigma,lambda</td>
<td>type pairs</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_lj_soft.html"><em>tip4p/long/soft</em></a></td>
<td>lambda</td>
<td>type pairs</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_lj_soft.html"><em>lj/charmm/coul/long/soft</em></a></td>
<td>epsilon,sigma,lambda</td>
<td>type pairs</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_born.html"><em>born</em></a></td>
<td>a,b,c</td>
<td>type pairs</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_buck.html"><em>buck</em></a></td>
<td>a,c</td>
<td>type pairs</td>
</tr>
</tbody>
</table>
<p>Note that it is easy to add new potentials and their parameters to
the meaning of these parameters:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD > epsilon,sigma</TD><TD > type pairs</TD></TR>
<TR><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD><TD > epsilon,sigma</TD><TD > type pairs</TD></TR>
<TR><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD><TD > epsilon,sigma</TD><TD > type pairs</TD></TR>
<TR><TD ><A HREF = "pair_lj_soft.html">lj/cut/soft</A></TD><TD > epsilon,sigma,lambda</TD><TD > type pairs</TD></TR>
<TR><TD ><A HREF = "pair_lj_soft.html">coul/cut/soft</A></TD><TD > lambda</TD><TD > type pairs</TD></TR>
<TR><TD ><A HREF = "pair_lj_soft.html">coul/long/soft</A></TD><TD > lambda</TD><TD > type pairs</TD></TR>
<TR><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/cut/soft</A></TD><TD > epsilon,sigma,lambda</TD><TD > type pairs</TD></TR>
<TR><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/long/soft</A></TD><TD > epsilon,sigma,lambda</TD><TD > type pairs</TD></TR>
<TR><TD ><A HREF = "pair_lj_soft.html">lj/cut/tip4p/long/soft</A></TD><TD > epsilon,sigma,lambda</TD><TD > type pairs</TD></TR>
<TR><TD ><A HREF = "pair_lj_soft.html">tip4p/long/soft</A></TD><TD > lambda</TD><TD > type pairs</TD></TR>
<TR><TD ><A HREF = "pair_lj_soft.html">lj/charmm/coul/long/soft</A></TD><TD > epsilon,sigma,lambda</TD><TD > type pairs</TD></TR>
<TR><TD ><A HREF = "pair_born.html">born</A></TD><TD > a,b,c</TD><TD > type pairs</TD></TR>
<TR><TD ><A HREF = "pair_buck.html">buck</A></TD><TD > a,c </TD><TD > type pairs
</TD></TR></TABLE></DIV>
<P>Note that it is easy to add new potentials and their parameters to
this list. All it typically takes is adding an extract() method to
the pair_*.cpp file associated with the potential.</p>
<p>Similar to the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command, I and J can be
the pair_*.cpp file associated with the potential.
</P>
<P>Similar to the <A HREF = "pair_coeff.html">pair_coeff</A> command, I and J can be
specified in one of two ways. Explicit numeric values can be used for
each, as in the 1st example above. I &lt;= J is required. LAMMPS sets
each, as in the 1st example above. I <= J is required. LAMMPS sets
the coefficients for the symmetric J,I interaction to the same
values. A wild-card asterisk can be used in place of or in conjunction
with the I,J arguments to set the coefficients for multiple pairs of
atom types. This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;. If N =
atom types. This takes the form "*" or "*n" or "n*" or "m*n". If N =
the number of atom types, then an asterisk with no numeric values
means all types from 1 to N. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive). Note that only type pairs with I &lt;= J are considered; if
asterisks imply type pairs where J &lt; I, they are ignored.</p>
<p>If <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid or hybrid/overlay</em></a> is being
used, then the <em>pstyle</em> will be a sub-style name. You must specify
(inclusive). Note that only type pairs with I <= J are considered; if
asterisks imply type pairs where J < I, they are ignored.
</P>
<P>If <A HREF = "pair_hybrid.html">pair_style hybrid or hybrid/overlay</A> is being
used, then the <I>pstyle</I> will be a sub-style name. You must specify
I,J arguments that correspond to type pair values defined (via the
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command) for that sub-style.</p>
<p>The <em>v_name</em> argument for keyword <em>pair</em> is the name of an
<a class="reference internal" href="variable.html"><em>equal-style variable</em></a> which will be evaluated each time
<A HREF = "pair_coeff.html">pair_coeff</A> command) for that sub-style.
</P>
<P>The <I>v_name</I> argument for keyword <I>pair</I> is the name of an
<A HREF = "variable.html">equal-style variable</A> which will be evaluated each time
this compute is invoked. It should be specified as v_name, where name
is the variable name.</p>
<hr class="docutils" />
<p>The <em>atom</em> attribute enables atom properties to be changed. The
<em>aparam</em> argument is the name of the parameter to change. This is the
current list of atom parameters that can be used with this compute:</p>
<ul class="simple">
<li>charge = charge on particle</li>
</ul>
<p>The <em>v_name</em> argument for keyword <em>pair</em> is the name of an
<a class="reference internal" href="variable.html"><em>equal-style variable</em></a> which will be evaluated each time
is the variable name.
</P>
<HR>
<P>The <I>atom</I> attribute enables atom properties to be changed. The
<I>aparam</I> argument is the name of the parameter to change. This is the
current list of atom parameters that can be used with this compute:
</P>
<UL><LI>charge = charge on particle
</UL>
<P>The <I>v_name</I> argument for keyword <I>pair</I> is the name of an
<A HREF = "variable.html">equal-style variable</A> which will be evaluated each time
this compute is invoked. It should be specified as v_name, where name
is the variable name.</p>
<hr class="docutils" />
<p>The <em>tail</em> keyword controls the calculation of the tail correction to
&#8220;van der Waals&#8221; pair energies beyond the cutoff, if this has been
activated via the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> command. If the
is the variable name.
</P>
<HR>
<P>The <I>tail</I> keyword controls the calculation of the tail correction to
"van der Waals" pair energies beyond the cutoff, if this has been
activated via the <A HREF = "pair_modify.html">pair_modify</A> command. If the
perturbation is small, the tail contribution to the energy difference
between the reference and perturbed systems should be negligible.</p>
<p>If the keyword <em>volume</em> = <em>yes</em>, then the Boltzmann term is multiplied
between the reference and perturbed systems should be negligible.
</P>
<P>If the keyword <I>volume</I> = <I>yes</I>, then the Boltzmann term is multiplied
by the volume so that correct ensemble averaging can be performed over
trajectories during which the volume fluctuates or changes <a class="reference internal" href="#allentildesley"><span>(Allen and Tildesley)</span></a>:</p>
<img alt="_images/compute_fep_vol.jpg" class="align-center" src="_images/compute_fep_vol.jpg" />
<hr class="docutils" />
<p><strong>Output info:</strong></p>
<p>This compute calculates a global vector of length 3 which contains the
energy difference (<em>U*&lt;sub&gt;1&lt;/sub&gt;-*U*&lt;sub&gt;0&lt;/sub&gt;) as c_ID[1], the
Boltzmann factor exp(-(*U*&lt;sub&gt;1&lt;/sub&gt;-*U*&lt;sub&gt;0&lt;/sub&gt;)/*kT</em>), or
<em>V*exp(-(*U*&lt;sub&gt;1&lt;/sub&gt;-*U*&lt;sub&gt;0&lt;/sub&gt;)/*kT</em>), as c_ID[2] and the
volume of the simulation box <em>V</em> as c_ID[3]. <a href="#id11"><span class="problematic" id="id12">*</span></a>U*&lt;sub&gt;1&lt;/sub&gt; is the
trajectories during which the volume fluctuates or changes <A HREF = "#AllenTildesley">(Allen and
Tildesley)</A>:
</P>
<CENTER><IMG SRC = "Eqs/compute_fep_vol.jpg">
</CENTER>
<HR>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global vector of length 3 which contains the
energy difference (<I>U</I><sub>1</sub>-<I>U</I><sub>0</sub>) as c_ID[1], the
Boltzmann factor exp(-(<I>U</I><sub>1</sub>-<I>U</I><sub>0</sub>)/<I>kT</I>), or
<I>V</I>exp(-(<I>U</I><sub>1</sub>-<I>U</I><sub>0</sub>)/<I>kT</I>), as c_ID[2] and the
volume of the simulation box <I>V</I> as c_ID[3]. <I>U</I><sub>1</sub> is the
pair potential energy obtained with the perturbed parameters and
<a href="#id13"><span class="problematic" id="id14">*</span></a>U*&lt;sub&gt;0&lt;/sub&gt; is the pair potential energy obtained with the
<I>U</I><sub>0</sub> is the pair potential energy obtained with the
unperturbed parameters. The energies include kspace terms if these
are used in the simulation.</p>
<p>These output results can be used by any command that uses a global
scalar or vector from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of LAMMPS output
options. For example, the computed values can be averaged using <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a>.</p>
<p>The 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 distributed as the USER-FEP 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>
</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="fix_adapt_fep.html"><em>fix adapt/fep</em></a>, <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a>,
<a class="reference external" href="pair_lj_soft_coul_soft.txt">pair_lj_soft_coul_soft</a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The option defaults are <em>tail</em> = <em>no</em>, <em>volume</em> = <em>no</em>.</p>
<hr class="docutils" />
<p id="pearlman"><strong>(Pearlman)</strong> Pearlman, J Chem Phys, 98, 1487 (1994)</p>
<p id="mezei"><strong>(Mezei)</strong> Mezei, J Chem Phys, 86, 7084 (1987)</p>
<p id="bennet"><strong>(Bennet)</strong> Bennet, J Comput Phys, 22, 245 (1976)</p>
<p id="boreschkarplus"><strong>(BoreschKarplus)</strong> Boresch and Karplus, J Phys Chem A, 103, 103 (1999)</p>
<p id="allentildesley"><strong>(AllenTildesley)</strong> Allen and Tildesley, Computer Simulation of
Liquids, Oxford University Press (1987)</p>
</div>
</div>
are used in the simulation.
</P>
<P>These output results can be used by any command that uses a global
scalar or vector from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
15</A> for an overview of LAMMPS output
options. For example, the computed values can be averaged using <A HREF = "fix_ave_time.html">fix
ave/time</A>.
</P>
<P>The values calculated by this compute are "extensive".
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is distributed as the USER-FEP package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_adapt_fep.html">fix adapt/fep</A>, <A HREF = "fix_ave_time.html">fix ave/time</A>,
<A HREF = "pair_lj_soft_coul_soft.txt">pair_lj_soft_coul_soft</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are <I>tail</I> = <I>no</I>, <I>volume</I> = <I>no</I>.
</P>
<HR>
<A NAME = "Pearlman"></A>
</div>
</div>
<footer>
<P><B>(Pearlman)</B> Pearlman, J Chem Phys, 98, 1487 (1994)
</P>
<A NAME = "Mezei"></A>
<hr/>
<P><B>(Mezei)</B> Mezei, J Chem Phys, 86, 7084 (1987)
</P>
<A NAME = "Bennet"></A>
<div role="contentinfo">
<p>
&copy; Copyright .
</p>
</div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
<P><B>(Bennet)</B> Bennet, J Comput Phys, 22, 245 (1976)
</P>
<A NAME = "BoreschKarplus"></A>
</footer>
<P><B>(BoreschKarplus)</B> Boresch and Karplus, J Phys Chem A, 103, 103 (1999)
</P>
<A NAME = "AllenTildesley"></A>
</div>
</div>
</section>
</div>
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<P><B>(AllenTildesley)</B> Allen and Tildesley, Computer Simulation of
Liquids, Oxford University Press (1987)
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<div class="section" id="compute-group-group-command">
<span id="index-0"></span><h1>compute group/group command<a class="headerlink" href="#compute-group-group-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 group/group group2-ID keyword value ...
</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>group/group = style name of this compute command</li>
<li>group2-ID = group ID of second (or same) group</li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>pair</em> or <em>kspace</em> or <em>boundary</em></li>
</ul>
<pre class="literal-block">
<em>pair</em> value = <em>yes</em> or <em>no</em>
<em>kspace</em> value = <em>yes</em> or <em>no</em>
<em>boundary</em> value = <em>yes</em> or <em>no</em>
</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>compute 1 lower group/group upper
<HR>
<H3>compute group/group command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID group/group group2-ID keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>group/group = style name of this compute command
<LI>group2-ID = group ID of second (or same) group
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>pair</I> or <I>kspace</I> or <I>boundary</I>
<PRE> <I>pair</I> value = <I>yes</I> or <I>no</I>
<I>kspace</I> value = <I>yes</I> or <I>no</I>
<I>boundary</I> value = <I>yes</I> or <I>no</I>
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 lower group/group upper
compute 1 lower group/group upper kspace yes
compute mine fluid group/group wall
</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 the total energy and force
compute mine fluid group/group wall
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the total energy and force
interaction between two groups of atoms: the compute group and the
specified group2. The two groups can be the same.</p>
<p>If the <em>pair</em> keyword is set to <em>yes</em>, which is the default, then the
specified group2. The two groups can be the same.
</P>
<P>If the <I>pair</I> keyword is set to <I>yes</I>, which is the default, then the
the interaction energy will include a pair component which is defined
as the pairwise energy between all pairs of atoms where one atom in
the pair is in the first group and the other is in the second group.
Likewise, the interaction force calculated by this compute will
include the force on the compute group atoms due to pairwise
interactions with atoms in the specified group2.</p>
<p>If the <em>kspace</em> keyword is set to <em>yes</em>, which is not the default, and
if a <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> is defined, then the interaction
interactions with atoms in the specified group2.
</P>
<P>If the <I>kspace</I> keyword is set to <I>yes</I>, which is not the default, and
if a <A HREF = "kspace_style.html">kspace_style</A> is defined, then the interaction
energy will include a Kspace component which is the long-range
Coulombic energy between all the atoms in the first group and all the
atoms in the 2nd group. Likewise, the interaction force calculated by
this compute will include the force on the compute group atoms due to
long-range Coulombic interactions with atoms in the specified group2.</p>
<p>Normally the long-range Coulombic energy converges only when the net
long-range Coulombic interactions with atoms in the specified group2.
</P>
<P>Normally the long-range Coulombic energy converges only when the net
charge of the unit cell is zero. However, one can assume the net
charge of the system is neutralized by a uniform background plasma,
and a correction to the system energy can be applied to reduce
artifacts. For more information see <a class="reference internal" href="#bogusz"><span>(Bogusz)</span></a>. If the
<em>boundary</em> keyword is set to <em>yes</em>, which is the default, and <em>kspace</em>
artifacts. For more information see <A HREF = "#Bogusz">(Bogusz)</A>. If the
<I>boundary</I> keyword is set to <I>yes</I>, which is the default, and <I>kspace</I>
contributions are included, then this energy correction term will be
added to the total group-group energy. This correction term does not
affect the force calculation and will be zero if one or both of the
groups are charge neutral. This energy correction term is the same as
that included in the regular Ewald and PPPM routines.</p>
<p>This compute does not calculate any bond or angle or dihedral or
improper interactions between atoms in the two groups.</p>
<hr class="docutils" />
<p>The pairwise contributions to the group-group interactions are
that included in the regular Ewald and PPPM routines.
</P>
<P>This compute does not calculate any bond or angle or dihedral or
improper interactions between atoms in the two groups.
</P>
<HR>
<P>The pairwise contributions to the group-group interactions are
calculated by looping over a neighbor list. The Kspace contribution
to the group-group interactions require essentially the same amount of
work (FFTs, Ewald summation) as computing long-range forces for the
entire system. Thus it can be costly to invoke this compute too
frequently.</p>
<p>If you desire a breakdown of the interactions into a pairwise and
frequently.
</P>
<P>If you desire a breakdown of the interactions into a pairwise and
Kspace component, simply invoke the compute twice with the appropriate
yes/no settings for the <em>pair</em> and <em>kspace</em> keywords. This is no more
costly than using a single compute with both keywords set to <em>yes</em>.
yes/no settings for the <I>pair</I> and <I>kspace</I> keywords. This is no more
costly than using a single compute with both keywords set to <I>yes</I>.
The individual contributions can be summed in a
<a class="reference internal" href="variable.html"><em>variable</em></a> if desired.</p>
<p>This <a class="reference external" href="PDF/kspace.pdf">document</a> describes how the long-range
group-group calculations are performed.</p>
<hr class="docutils" />
<p><strong>Output info:</strong></p>
<p>This compute calculates a global scalar (the energy) and a global
<A HREF = "variable.html">variable</A> if desired.
</P>
<P>This <A HREF = "PDF/kspace.pdf">document</A> describes how the long-range
group-group calculations are performed.
</P>
<HR>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the energy) and a global
vector of length 3 (force), which can be accessed by indices 1-3.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>this section</span></a> for an overview of LAMMPS output
options.</p>
<p>Both the scalar and vector values calculated by this compute are
&#8220;extensive&#8221;. The scalar value will be in energy <a class="reference internal" href="units.html"><em>units</em></a>.
The vector values will be in force <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>Not all pair styles can be evaluated in a pairwise mode as required by
vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>Both the scalar and vector values calculated by this compute are
"extensive". The scalar value will be in energy <A HREF = "units.html">units</A>.
The vector values will be in force <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</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>
such as <A HREF = "pair_tersoff.html">Tersoff</A> and
<A HREF = "pair_sw.html">Stillinger-Weber</A> cannot be used. <A HREF = "pair_eam.html">EAM</A>
potentials only include the pair potential portion of the EAM
interaction when used by this compute, not the embedding term.</p>
<p>Not all Kspace styles support calculation of group/group interactions.
The <em>ewald</em> and <em>pppm</em> styles do.</p>
<p><strong>Related commands:</strong> none</p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The option defaults are pair = yes, kspace = no, and boundary = yes.</p>
<hr class="docutils" />
<p id="bogusz">Bogusz et al, J Chem Phys, 108, 7070 (1998)</p>
</div>
</div>
interaction when used by this compute, not the embedding term.
</P>
<P>Not all Kspace styles support calculation of group/group interactions.
The <I>ewald</I> and <I>pppm</I> styles do.
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are pair = yes, kspace = no, and boundary = yes.
</P>
<HR>
<A NAME = "Bogusz"></A>
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<P>Bogusz et al, J Chem Phys, 108, 7070 (1998)
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<div class="section" id="compute-gyration-command">
<span id="index-0"></span><h1>compute gyration command<a class="headerlink" href="#compute-gyration-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 gyration
</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>gyration = style name of this compute command</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 molecule gyration
</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 the radius of gyration Rg of the
<HR>
<H3>compute gyration command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID gyration
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>gyration = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 molecule gyration
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the radius of gyration Rg of the
group of atoms, including all effects due to atoms passing thru
periodic boundaries.</p>
<p>Rg is a measure of the size of the group of atoms, and is computed as
the square root of the Rg^2 value in this formula</p>
<img alt="_images/compute_gyration.jpg" class="align-center" src="_images/compute_gyration.jpg" />
<p>where M is the total mass of the group, Rcm is the center-of-mass
position of the group, and the sum is over all atoms in the group.</p>
<p>A Rg^2 tensor, stored as a 6-element vector, is also calculated by
periodic boundaries.
</P>
<P>Rg is a measure of the size of the group of atoms, and is computed as
the square root of the Rg^2 value in this formula
</P>
<CENTER><IMG SRC = "Eqs/compute_gyration.jpg">
</CENTER>
<P>where M is the total mass of the group, Rcm is the center-of-mass
position of the group, and the sum is over all atoms in the group.
</P>
<P>A Rg^2 tensor, stored as a 6-element vector, is also calculated by
this compute. The formula for the components of the tensor is the
same as the above formula, except that (Ri - Rcm)^2 is replaced by
(Rix - Rcmx) * (Riy - Rcmy) for the xy component, etc. The 6
components of the vector are ordered xx, yy, zz, xy, xz, yz. Note
that unlike the scalar Rg, each of the 6 values of the tensor is
effectively a &#8220;squared&#8221; value, since the cross-terms may be negative
and taking a sqrt() would be invalid.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The coordinates of an atom contribute to Rg in
&#8220;unwrapped&#8221; form, by using the image flags associated with each atom.
See the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command for a discussion of
&#8220;unwrapped&#8221; coordinates. See the Atoms section of the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command for a discussion of image flags and
effectively a "squared" value, since the cross-terms may be negative
and taking a sqrt() would be invalid.
</P>
<P>IMPORTANT NOTE: The coordinates of an atom contribute to Rg in
"unwrapped" form, by using the image flags associated with each atom.
See the <A HREF = "dump.html">dump custom</A> command for a discussion of
"unwrapped" coordinates. See the Atoms section of the
<A HREF = "read_data.html">read_data</A> command for a discussion of image flags and
how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the <a class="reference internal" href="set.html"><em>set image</em></a> command.</p>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global scalar (Rg) and a global vector of
(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
image</A> command.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (Rg) and a global vector of
length 6 (Rg^2 tensor), which can be accessed by indices 1-6. These
values can be used by any command that uses a global scalar value or
vector values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of LAMMPS output
options.</p>
<p>The scalar and vector values calculated by this compute are
&#8220;intensive&#8221;. The scalar and vector values will be in distance and
distance^2 <a class="reference internal" href="units.html"><em>units</em></a> respectively.</p>
</div>
<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="compute_gyration_chunk.html"><em>compute gyration/chunk</em></a></p>
<p><strong>Default:</strong> none</p>
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vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
15</A> for an overview of LAMMPS output
options.
</P>
<P>The scalar and vector values calculated by this compute are
"intensive". The scalar and vector values will be in distance and
distance^2 <A HREF = "units.html">units</A> respectively.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_gyration_chunk.html">compute gyration/chunk</A>
</P>
<P><B>Default:</B> none
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<div class="section" id="compute-gyration-chunk-command">
<span id="index-0"></span><h1>compute gyration/chunk command<a class="headerlink" href="#compute-gyration-chunk-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 gyration/chunk chunkID keyword value ...
</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>gyration/chunk = style name of this compute command</li>
<li>chunkID = ID of <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command</li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>tensor</em></li>
</ul>
<pre class="literal-block">
<em>tensor</em> value = none
</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>compute 1 molecule gyration/chunk molchunk
compute 2 molecule gyration/chunk molchunk tensor
</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 the radius of gyration Rg for
multiple chunks of atoms.</p>
<p>In LAMMPS, chunks are collections of atoms defined by a <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command, which assigns each atom
<HR>
<H3>compute gyration/chunk command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID gyration/chunk chunkID keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>gyration/chunk = style name of this compute command
<LI>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>tensor</I>
<PRE> <I>tensor</I> value = none
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 molecule gyration/chunk molchunk
compute 2 molecule gyration/chunk molchunk tensor
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the radius of gyration Rg for
multiple chunks of atoms.
</P>
<P>In LAMMPS, chunks are collections of atoms defined by a <A HREF = "compute_chunk_atom.html">compute
chunk/atom</A> command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> doc page and &#8220;<a class="reference internal" href="Section_howto.html#howto-23"><span>Section_howto 23</span></a> for details of how chunks can be
molecule or atoms in a spatial bin. See the <A HREF = "compute_chunk_atom.html">compute
chunk/atom</A> doc page and "<A HREF = "Section_howto.html#howto_23">Section_howto
23</A> for details of how chunks can be
defined and examples of how they can be used to measure properties of
a system.</p>
<p>This compute calculates the radius of gyration Rg for each chunk,
a system.
</P>
<P>This compute calculates the radius of gyration Rg for each chunk,
which includes all effects due to atoms passing thru periodic
boundaries.</p>
<p>Rg is a measure of the size of a chunk, and is computed by this
formula</p>
<img alt="_images/compute_gyration.jpg" class="align-center" src="_images/compute_gyration.jpg" />
<p>where M is the total mass of the chunk, Rcm is the center-of-mass
boundaries.
</P>
<P>Rg is a measure of the size of a chunk, and is computed by this
formula
</P>
<CENTER><IMG SRC = "Eqs/compute_gyration.jpg">
</CENTER>
<P>where M is the total mass of the chunk, Rcm is the center-of-mass
position of the chunk, and the sum is over all atoms in the
chunk.</p>
<p>Note that only atoms in the specified group contribute to the
calculation. The <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command
chunk.
</P>
<P>Note that only atoms in the specified group contribute to the
calculation. The <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
defines its own group; atoms will have a chunk ID = 0 if they are not
in that group, signifying they are not assigned to a chunk, and will
thus also not contribute to this calculation. You can specify the
&#8220;all&#8221; group for this command if you simply want to include atoms with
non-zero chunk IDs.</p>
<p>If the <em>tensor</em> keyword is specified, then the scalar Rg value is not
"all" group for this command if you simply want to include atoms with
non-zero chunk IDs.
</P>
<P>If the <I>tensor</I> keyword is specified, then the scalar Rg value is not
calculated, but an Rg tensor is instead calculated for each chunk.
The formula for the components of the tensor is the same as the above
formula, except that (Ri - Rcm)^2 is replaced by (Rix - Rcmx) * (Riy -
Rcmy) for the xy component, etc. The 6 components of the tensor are
ordered xx, yy, zz, xy, xz, yz.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The coordinates of an atom contribute to Rg in
&#8220;unwrapped&#8221; form, by using the image flags associated with each atom.
See the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command for a discussion of
&#8220;unwrapped&#8221; coordinates. See the Atoms section of the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command for a discussion of image flags and
ordered xx, yy, zz, xy, xz, yz.
</P>
<P>IMPORTANT NOTE: The coordinates of an atom contribute to Rg in
"unwrapped" form, by using the image flags associated with each atom.
See the <A HREF = "dump.html">dump custom</A> command for a discussion of
"unwrapped" coordinates. See the Atoms section of the
<A HREF = "read_data.html">read_data</A> command for a discussion of image flags and
how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the <a class="reference internal" href="set.html"><em>set image</em></a> command.</p>
</div>
<p>The simplest way to output the results of the compute gyration/chunk
calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a>
command, for example:</p>
<div class="highlight-python"><div class="highlight"><pre>compute cc1 all chunk/atom molecule
(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
image</A> command.
</P>
<P>The simplest way to output the results of the compute gyration/chunk
calculation to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A>
command, for example:
</P>
<PRE>compute cc1 all chunk/atom molecule
compute myChunk all gyration/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</pre></div>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global vector if the <em>tensor</em> keyword is not
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</PRE>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global vector if the <I>tensor</I> keyword is not
specified and a global array if it is. The length of the vector or
number of rows in the array = the number of chunks <em>Nchunk</em> as
calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command. If the <em>tensor</em> keyword
number of rows in the array = the number of chunks <I>Nchunk</I> as
calculated by the specified <A HREF = "compute_chunk_atom.html">compute
chunk/atom</A> command. If the <I>tensor</I> keyword
is specified, the global array has 6 columns. The vector or array can
be accessed by any command that uses global values from a compute as
input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>this section</span></a> for an overview
of LAMMPS output options.</p>
<p>All the vector or array values calculated by this compute are
&#8220;intensive&#8221;. The vector or array values will be in distance
<a class="reference internal" href="units.html"><em>units</em></a>, since they are the square root of values
represented by the formula above.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<blockquote>
<div>none</div></blockquote>
<p><strong>Related commands:</strong> none</p>
<p><a class="reference internal" href="compute_gyration.html"><em>compute gyration</em></a></p>
<p><strong>Default:</strong> none</p>
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input. See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
of LAMMPS output options.
</P>
<P>All the vector or array values calculated by this compute are
"intensive". The vector or array values will be in distance
<A HREF = "units.html">units</A>, since they are the square root of values
represented by the formula above.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none
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<P><A HREF = "compute_gyration.html">compute gyration</A>
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<div class="section" id="compute-heat-flux-command">
<span id="index-0"></span><h1>compute heat/flux command<a class="headerlink" href="#compute-heat-flux-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 heat/flux ke-ID pe-ID stress-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>heat/flux = style name of this compute command</li>
<li>ke-ID = ID of a compute that calculates per-atom kinetic energy</li>
<li>pe-ID = ID of a compute that calculates per-atom potential energy</li>
<li>stress-ID = ID of a compute that calculates per-atom stress</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 myFlux all heat/flux myKE myPE myStress
</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 the heat flux vector based on
<HR>
<H3>compute heat/flux command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID heat/flux ke-ID pe-ID stress-ID
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>heat/flux = style name of this compute command
<LI>ke-ID = ID of a compute that calculates per-atom kinetic energy
<LI>pe-ID = ID of a compute that calculates per-atom potential energy
<LI>stress-ID = ID of a compute that calculates per-atom stress
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute myFlux all heat/flux myKE myPE myStress
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the heat flux vector based on
contributions from atoms in the specified group. This can be used by
itself to measure the heat flux into or out of a reservoir of atoms,
or to calculate a thermal conductivity using the Green-Kubo formalism.</p>
<p>See the <a class="reference internal" href="fix_thermal_conductivity.html"><em>fix thermal/conductivity</em></a>
or to calculate a thermal conductivity using the Green-Kubo formalism.
</P>
<P>See the <A HREF = "fix_thermal_conductivity.html">fix thermal/conductivity</A>
command for details on how to compute thermal conductivity in an
alternate way, via the Muller-Plathe method. See the <a class="reference internal" href="fix_heat.html"><em>fix heat</em></a> command for a way to control the heat added or
subtracted to a group of atoms.</p>
<p>The compute takes three arguments which are IDs of other
<a class="reference internal" href="compute.html"><em>computes</em></a>. One calculates per-atom kinetic energy
(<em>ke-ID</em>), one calculates per-atom potential energy (<em>pe-ID)</em>, and the
third calcualtes per-atom stress (<em>stress-ID</em>). These should be
alternate way, via the Muller-Plathe method. See the <A HREF = "fix_heat.html">fix
heat</A> command for a way to control the heat added or
subtracted to a group of atoms.
</P>
<P>The compute takes three arguments which are IDs of other
<A HREF = "compute.html">computes</A>. One calculates per-atom kinetic energy
(<I>ke-ID</I>), one calculates per-atom potential energy (<I>pe-ID)</I>, and the
third calcualtes per-atom stress (<I>stress-ID</I>). These should be
defined for the same group used by compute heat/flux, though LAMMPS
does not check for this.</p>
<p>The Green-Kubo formulas relate the ensemble average of the
auto-correlation of the heat flux J to the thermal conductivity kappa:</p>
<img alt="_images/heat_flux_J.jpg" class="align-center" src="_images/heat_flux_J.jpg" />
<img alt="_images/heat_flux_k.jpg" class="align-center" src="_images/heat_flux_k.jpg" />
<p>Ei in the first term of the equation for J is the per-atom energy
(potential and kinetic). This is calculated by the computes <em>ke-ID</em>
and <em>pe-ID</em>. Si in the second term of the equation for J is the
per-atom stress tensor calculated by the compute <em>stress-ID</em>. The
does not check for this.
</P>
<P>The Green-Kubo formulas relate the ensemble average of the
auto-correlation of the heat flux J to the thermal conductivity kappa:
</P>
<CENTER><IMG SRC = "Eqs/heat_flux_J.jpg">
</CENTER>
<CENTER><IMG SRC = "Eqs/heat_flux_k.jpg">
</CENTER>
<P>Ei in the first term of the equation for J is the per-atom energy
(potential and kinetic). This is calculated by the computes <I>ke-ID</I>
and <I>pe-ID</I>. Si in the second term of the equation for J is the
per-atom stress tensor calculated by the compute <I>stress-ID</I>. The
tensor multiplies Vi as a 3x3 matrix-vector multiply to yield a
vector. Note that as discussed below, the 1/V scaling factor in the
equation for J is NOT included in the calculation performed by this
compute; you need to add it for a volume appropriate to the atoms
included in the calculation.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The <a class="reference internal" href="compute_pe_atom.html"><em>compute pe/atom</em></a> and
<a class="reference internal" href="compute_stress_atom.html"><em>compute stress/atom</em></a> commands have options
included in the calculation.
</P>
<P>IMPORTANT NOTE: The <A HREF = "compute_pe_atom.html">compute pe/atom</A> and
<A HREF = "compute_stress_atom.html">compute stress/atom</A> commands have options
for which terms to include in their calculation (pair, bond, etc).
The heat flux calculation will thus include exactly the same terms.
Normally you should use <a class="reference internal" href="compute_stress_atom.html"><em>compute stress/atom virial</em></a> so as not to include a kinetic energy
term in the heat flux.</p>
</div>
<p>This compute calculates 6 quantities and stores them in a 6-component
Normally you should use <A HREF = "compute_stress_atom.html">compute stress/atom
virial</A> so as not to include a kinetic energy
term in the heat flux.
</P>
<P>This compute calculates 6 quantities and stores them in a 6-component
vector. The first 3 components are the x, y, z components of the full
heat flux vector, i.e. (Jx, Jy, Jz). The next 3 components are the x,
y, z components of just the convective portion of the flux, i.e. the
first term in the equation for J above.</p>
<hr class="docutils" />
<p>The heat flux can be output every so many timesteps (e.g. via the
<a class="reference internal" href="thermo_style.html"><em>thermo_style custom</em></a> command). Then as a
first term in the equation for J above.
</P>
<HR>
<P>The heat flux can be output every so many timesteps (e.g. via the
<A HREF = "thermo_style.html">thermo_style custom</A> command). Then as a
post-processing operation, an autocorrelation can be performed, its
integral estimated, and the Green-Kubo formula above evaluated.</p>
<p>The <a class="reference internal" href="fix_ave_correlate.html"><em>fix ave/correlate</em></a> command can calclate
integral estimated, and the Green-Kubo formula above evaluated.
</P>
<P>The <A HREF = "fix_ave_correlate.html">fix ave/correlate</A> command can calclate
the autocorrelation. The trap() function in the
<a class="reference internal" href="variable.html"><em>variable</em></a> command can calculate the integral.</p>
<p>An example LAMMPS input script for solid Ar is appended below. The
result should be: average conductivity ~0.29 in W/mK.</p>
<hr class="docutils" />
<p><strong>Output info:</strong></p>
<p>This compute calculates a global vector of length 6 (total heat flux
<A HREF = "variable.html">variable</A> command can calculate the integral.
</P>
<P>An example LAMMPS input script for solid Ar is appended below. The
result should be: average conductivity ~0.29 in W/mK.
</P>
<HR>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global vector of length 6 (total heat flux
vector, followed by convective heat flux vector), which can be
accessed by indices 1-6. These values can be used by any command that
uses global vector values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>this section</span></a> for an overview of LAMMPS output
options.</p>
<p>The vector values calculated by this compute are &#8220;extensive&#8221;, meaning
uses global vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The vector values calculated by this compute are "extensive", meaning
they scale with the number of atoms in the simulation. They can be
divided by the appropriate volume to get a flux, which would then be
an &#8220;intensive&#8221; value, meaning independent of the number of atoms in
the simulation. Note that if the compute is &#8220;all&#8221;, then the
an "intensive" value, meaning independent of the number of atoms in
the simulation. Note that if the compute is "all", then the
appropriate volume to divide by is the simulation box volume.
However, if a sub-group is used, it should be the volume containing
those atoms.</p>
<p>The vector values will be in energy*velocity <a class="reference internal" href="units.html"><em>units</em></a>. Once
those atoms.
</P>
<P>The vector values will be in energy*velocity <A HREF = "units.html">units</A>. Once
divided by a volume the units will be that of flux, namely
energy/area/time <a class="reference internal" href="units.html"><em>units</em></a></p>
</div>
<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="fix_thermal_conductivity.html"><em>fix thermal/conductivity</em></a>,
<a class="reference internal" href="fix_ave_correlate.html"><em>fix ave/correlate</em></a>,
<a class="reference internal" href="variable.html"><em>variable</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<div class="highlight-python"><div class="highlight"><pre><span class="c"># Sample LAMMPS input script for thermal conductivity of solid Ar</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>units real
energy/area/time <A HREF = "units.html">units</A>
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_thermal_conductivity.html">fix thermal/conductivity</A>,
<A HREF = "fix_ave_correlate.html">fix ave/correlate</A>,
<A HREF = "variable.html">variable</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<PRE># Sample LAMMPS input script for thermal conductivity of solid Ar
</PRE>
<PRE>units real
variable T equal 70
variable V equal vol
variable dt equal 4.0
variable p equal 200 # correlation length
variable s equal 10 # sample interval
variable d equal $p*$s # dump interval
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span class="c"># convert from LAMMPS real units to SI</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>variable kB equal 1.3806504e-23 # [J/K] Boltzmann
variable d equal $p*$s # dump interval
</PRE>
<PRE># convert from LAMMPS real units to SI
</PRE>
<PRE>variable kB equal 1.3806504e-23 # [J/K] Boltzmann
variable kCal2J equal 4186.0/6.02214e23
variable A2m equal 1.0e-10
variable fs2s equal 1.0e-15
variable convert equal ${kCal2J}*${kCal2J}/${fs2s}/${A2m}
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span class="c"># setup problem</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>dimension 3
variable convert equal ${kCal2J}*${kCal2J}/${fs2s}/${A2m}
</PRE>
<PRE># setup problem
</PRE>
<PRE>dimension 3
boundary p p p
lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
region box block 0 4 0 4 0 4
create_box 1 box
create_atoms 1 box
mass 1 39.948
mass 1 39.948
pair_style lj/cut 13.0
pair_coeff * * 0.2381 3.405
timestep ${dt}
thermo $d
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span class="c"># equilibration and thermalization</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>velocity all create $T 102486 mom yes rot yes dist gaussian
thermo $d
</PRE>
<PRE># equilibration and thermalization
</PRE>
<PRE>velocity all create $T 102486 mom yes rot yes dist gaussian
fix NVT all nvt temp $T $T 10 drag 0.2
run 8000
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span class="c"># thermal conductivity calculation, switch to NVE if desired</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span class="c">#unfix NVT</span>
<span class="c">#fix NVE all nve</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>reset_timestep 0
run 8000
</PRE>
<PRE># thermal conductivity calculation, switch to NVE if desired
</PRE>
<PRE>#unfix NVT
#fix NVE all nve
</PRE>
<PRE>reset_timestep 0
compute myKE all ke/atom
compute myPE all pe/atom
compute myStress all stress/atom NULL virial
@ -290,7 +177,7 @@ compute flux all heat/flux myKE myPE myStress
variable Jx equal c_flux[1]/vol
variable Jy equal c_flux[2]/vol
variable Jz equal c_flux[3]/vol
fix JJ all ave/correlate $s $p $d &amp;
fix JJ all ave/correlate $s $p $d &
c_flux[1] c_flux[2] c_flux[3] type auto file J0Jt.dat ave running
variable scale equal ${convert}/${kB}/$T/$T/$V*$s*${dt}
variable k11 equal trap(f_JJ[3])*${scale}
@ -300,72 +187,6 @@ thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
run 100000
variable k equal (v_k11+v_k22+v_k33)/3.0
variable ndens equal count(all)/vol
print &quot;average conductivity: $k[W/mK] @ $T K, ${ndens} /A^3&quot;
</pre></div>
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print "average conductivity: $k[W/mK] @ $T K, ${ndens} /A^3"
</PRE>
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<div class="section" id="compute-improper-local-command">
<span id="index-0"></span><h1>compute improper/local command<a class="headerlink" href="#compute-improper-local-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 improper/local input1 input2 ...
</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>improper/local = style name of this compute command</li>
<li>one or more keywords may be appended</li>
<li>keyword = <em>chi</em></li>
</ul>
<pre class="literal-block">
<em>chi</em> = tabulate improper angles
</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>compute 1 all improper/local chi
</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 of individual improper
<HR>
<H3>compute improper/local command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID improper/local input1 input2 ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>improper/local = style name of this compute command
<LI>one or more keywords may be appended
<LI>keyword = <I>chi</I>
<PRE> <I>chi</I> = tabulate improper angles
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all improper/local chi
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates properties of individual improper
interactions. The number of datums generated, aggregated across all
processors, equals the number of impropers in the system, modified by
the group parameter as explained below.</p>
<p>The local data stored by this command is generated by looping over all
the group parameter as explained below.
</P>
<P>The local data stored by this command is generated by looping over all
the atoms owned on a processor and their impropers. An improper will
only be included if all 4 atoms in the improper are in the specified
compute group.</p>
<p>Note that as atoms migrate from processor to processor, there will be
compute group.
</P>
<P>Note that as atoms migrate from processor to processor, there will be
no consistent ordering of the entries within the local vector or array
from one timestep to the next. The only consistency that is
guaranteed is that the ordering on a particular timestep will be the
same for local vectors or arrays generated by other compute commands.
For example, improper output from the <a class="reference internal" href="compute_property_local.html"><em>compute property/local</em></a> command can be combined
with data from this command and output by the <a class="reference internal" href="dump.html"><em>dump local</em></a>
command in a consistent way.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a local vector or local array depending on the
For example, improper output from the <A HREF = "compute_property_local.html">compute
property/local</A> command can be combined
with data from this command and output by the <A HREF = "dump.html">dump local</A>
command in a consistent way.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a local vector or local array depending on the
number of keywords. The length of the vector or number of rows in the
array is the number of impropers. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>this section</span></a> for an overview of LAMMPS output
options.</p>
<p>The output for <em>chi</em> will be in degrees.</p>
</div>
<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="dump.html"><em>dump local</em></a>, <a class="reference internal" href="compute_property_local.html"><em>compute property/local</em></a></p>
<p><strong>Default:</strong> none</p>
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uses local values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The output for <I>chi</I> will be in degrees.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dump.html">dump local</A>, <A HREF = "compute_property_local.html">compute
property/local</A>
</P>
<P><B>Default:</B> none
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<div class="section" id="compute-inertia-chunk-command">
<span id="index-0"></span><h1>compute inertia/chunk command<a class="headerlink" href="#compute-inertia-chunk-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 inertia/chunk chunkID
</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>inertia/chunk = style name of this compute command</li>
<li>chunkID = ID of <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command</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 fluid inertia/chunk molchunk
</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 the inertia tensor for multiple
chunks of atoms.</p>
<p>In LAMMPS, chunks are collections of atoms defined by a <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command, which assigns each atom
<HR>
<H3>compute inertia/chunk command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID inertia/chunk chunkID
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>inertia/chunk = style name of this compute command
<LI>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 fluid inertia/chunk molchunk
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the inertia tensor for multiple
chunks of atoms.
</P>
<P>In LAMMPS, chunks are collections of atoms defined by a <A HREF = "compute_chunk_atom.html">compute
chunk/atom</A> command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> doc page and &#8220;<a class="reference internal" href="Section_howto.html#howto-23"><span>Section_howto 23</span></a> for details of how chunks can be
molecule or atoms in a spatial bin. See the <A HREF = "compute_chunk_atom.html">compute
chunk/atom</A> doc page and "<A HREF = "Section_howto.html#howto_23">Section_howto
23</A> for details of how chunks can be
defined and examples of how they can be used to measure properties of
a system.</p>
<p>This compute calculates the 6 components of the symmetric intertia
a system.
</P>
<P>This compute calculates the 6 components of the symmetric intertia
tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz. The
calculation includes all effects due to atoms passing thru periodic
boundaries.</p>
<p>Note that only atoms in the specified group contribute to the
calculation. The <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command
boundaries.
</P>
<P>Note that only atoms in the specified group contribute to the
calculation. The <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
defines its own group; atoms will have a chunk ID = 0 if they are not
in that group, signifying they are not assigned to a chunk, and will
thus also not contribute to this calculation. You can specify the
&#8220;all&#8221; group for this command if you simply want to include atoms with
non-zero chunk IDs.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The coordinates of an atom contribute to the chunk&#8217;s
inertia tensor in &#8220;unwrapped&#8221; form, by using the image flags
associated with each atom. See the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command
for a discussion of &#8220;unwrapped&#8221; coordinates. See the Atoms section of
the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command for a discussion of image flags
"all" group for this command if you simply want to include atoms with
non-zero chunk IDs.
</P>
<P>IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's
inertia tensor in "unwrapped" form, by using the image flags
associated with each atom. See the <A HREF = "dump.html">dump custom</A> command
for a discussion of "unwrapped" coordinates. See the Atoms section of
the <A HREF = "read_data.html">read_data</A> command for a discussion of image flags
and how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the <a class="reference internal" href="set.html"><em>set image</em></a> command.</p>
</div>
<p>The simplest way to output the results of the compute inertia/chunk
calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a>
command, for example:</p>
<div class="highlight-python"><div class="highlight"><pre>compute cc1 all chunk/atom molecule
(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
image</A> command.
</P>
<P>The simplest way to output the results of the compute inertia/chunk
calculation to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A>
command, for example:
</P>
<PRE>compute cc1 all chunk/atom molecule
compute myChunk all inertia/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</pre></div>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global array where the number of rows = the
number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command. The number of columns =
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</PRE>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global array where the number of rows = the
number of chunks <I>Nchunk</I> as calculated by the specified <A HREF = "compute_chunk_atom.html">compute
chunk/atom</A> command. The number of columns =
6 for the 6 components of the inertia tensor for each chunk, ordered
as listed above. These values can be accessed by any command that
uses global array values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of LAMMPS output
options.</p>
<p>The array values are &#8220;intensive&#8221;. The array values will be in
mass*distance^2 <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<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="variable.html"><em>variable inertia() function</em></a></p>
<p><strong>Default:</strong> none</p>
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uses global array values from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
15</A> for an overview of LAMMPS output
options.
</P>
<P>The array values are "intensive". The array values will be in
mass*distance^2 <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "variable.html">variable inertia() function</A>
</P>
<P><B>Default:</B> none
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<div class="section" id="compute-ke-command">
<span id="index-0"></span><h1>compute ke command<a class="headerlink" href="#compute-ke-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 ke
</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>ke = style name of this compute command</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 all ke
</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 the translational kinetic energy
of a group of particles.</p>
<p>The kinetic energy of each particle is computed as 1/2 m v^2, where m
and v are the mass and velocity of the particle.</p>
<p>There is a subtle difference between the quantity calculated by this
compute and the kinetic energy calculated by the <em>ke</em> or <em>etotal</em>
<HR>
<H3>compute ke command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID ke
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>ke = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all ke
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the translational kinetic energy
of a group of particles.
</P>
<P>The kinetic energy of each particle is computed as 1/2 m v^2, where m
and v are the mass and velocity of the particle.
</P>
<P>There is a subtle difference between the quantity calculated by this
compute and the kinetic energy calculated by the <I>ke</I> or <I>etotal</I>
keyword used in thermodynamic output, as specified by the
<a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command. For this compute, kinetic
energy is &#8220;translational&#8221; kinetic energy, calculated by the simple
formula above. For thermodynamic output, the <em>ke</em> keyword infers
<A HREF = "thermo_style.html">thermo_style</A> command. For this compute, kinetic
energy is "translational" kinetic energy, calculated by the simple
formula above. For thermodynamic output, the <I>ke</I> keyword infers
kinetic energy from the temperature of the system with 1/2 Kb T of
energy for each degree of freedom. For the default temperature
computation via the <a class="reference internal" href="compute_temp.html"><em>compute temp</em></a> command, these
computation via the <A HREF = "compute_temp.html">compute temp</A> command, these
are the same. But different computes that calculate temperature can
subtract out different non-thermal components of velocity and/or
include different degrees of freedom (translational, rotational, etc).</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global scalar (the summed KE). This value
include different degrees of freedom (translational, rotational, etc).
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the summed KE). This value
can be used by any command that uses a global scalar value from a
compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a>
for an overview of LAMMPS output options.</p>
<p>The scalar value calculated by this compute is &#8220;extensive&#8221;. The
scalar value will be in energy <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<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="compute_erotate_sphere.html"><em>compute erotate/sphere</em></a></p>
<p><strong>Default:</strong> none</p>
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compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A>
for an overview of LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "extensive". The
scalar value will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_erotate_sphere.html">compute erotate/sphere</A>
</P>
<P><B>Default:</B> none
</P>
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<div class="section" id="compute-ke-atom-command">
<span id="index-0"></span><h1>compute ke/atom command<a class="headerlink" href="#compute-ke-atom-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 ke/atom
</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>ke/atom = style name of this compute command</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 all ke/atom
</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 the per-atom translational
kinetic energy for each atom in a group.</p>
<p>The kinetic energy is simply 1/2 m v^2, where m is the mass and v is
the velocity of each atom.</p>
<p>The value of the kinetic energy will be 0.0 for atoms not in the
specified compute group.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-atom vector, which can be accessed by
<HR>
<H3>compute ke/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID ke/atom
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>ke/atom = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all ke/atom
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the per-atom translational
kinetic energy for each atom in a group.
</P>
<P>The kinetic energy is simply 1/2 m v^2, where m is the mass and v is
the velocity of each atom.
</P>
<P>The value of the kinetic energy will be 0.0 for atoms not in the
specified compute group.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of
LAMMPS output options.</p>
<p>The per-atom vector values will be in energy <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<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="dump.html"><em>dump custom</em></a></p>
<p><strong>Default:</strong> none</p>
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<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dump.html">dump custom</A>
</P>
<P><B>Default:</B> none
</P>
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<div class="section" id="compute-ke-atom-eff-command">
<span id="index-0"></span><h1>compute ke/atom/eff command<a class="headerlink" href="#compute-ke-atom-eff-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 ke/atom/eff
</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>ke/atom/eff = style name of this compute command</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 all ke/atom/eff
</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 the per-atom translational
<HR>
<H3>compute ke/atom/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID ke/atom/eff
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>ke/atom/eff = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all ke/atom/eff
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the per-atom translational
(nuclei and electrons) and radial kinetic energy (electron only) in a
group. The particles are assumed to be nuclei and electrons modeled
with the <a class="reference internal" href="pair_eff.html"><em>electronic force field</em></a>.</p>
<p>The kinetic energy for each nucleus is computed as 1/2 m v^2, where m
with the <A HREF = "pair_eff.html">electronic force field</A>.
</P>
<P>The kinetic energy for each nucleus is computed as 1/2 m v^2, where m
corresponds to the corresponding nuclear mass, and the kinetic energy
for each electron is computed as 1/2 (me v^2 + 3/4 me s^2), where me
and v correspond to the mass and translational velocity of each
electron, and s to its radial velocity, respectively.</p>
<p>There is a subtle difference between the quantity calculated by this
compute and the kinetic energy calculated by the <em>ke</em> or <em>etotal</em>
electron, and s to its radial velocity, respectively.
</P>
<P>There is a subtle difference between the quantity calculated by this
compute and the kinetic energy calculated by the <I>ke</I> or <I>etotal</I>
keyword used in thermodynamic output, as specified by the
<a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command. For this compute, kinetic
energy is &#8220;translational&#8221; plus electronic &#8220;radial&#8221; kinetic energy,
<A HREF = "thermo_style.html">thermo_style</A> command. For this compute, kinetic
energy is "translational" plus electronic "radial" kinetic energy,
calculated by the simple formula above. For thermodynamic output, the
<em>ke</em> keyword infers kinetic energy from the temperature of the system
<I>ke</I> keyword infers kinetic energy from the temperature of the system
with 1/2 Kb T of energy for each (nuclear-only) degree of freedom in
eFF.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The temperature in eFF should be monitored via the
<a class="reference internal" href="compute_temp_eff.html"><em>compute temp/eff</em></a> command, which can be printed
eFF.
</P>
<P>IMPORTANT NOTE: The temperature in eFF should be monitored via the
<A HREF = "compute_temp_eff.html">compute temp/eff</A> command, which can be printed
with thermodynamic output by using the
<a class="reference internal" href="thermo_modify.html"><em>thermo_modify</em></a> command, as shown in the following
example:</p>
</div>
<div class="highlight-python"><div class="highlight"><pre>compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp
</pre></div>
</div>
<p>The value of the kinetic energy will be 0.0 for atoms (nuclei or
electrons) not in the specified compute group.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a scalar quantity for each atom, which can be
<A HREF = "thermo_modify.html">thermo_modify</A> command, as shown in the following
example:
</P>
<PRE>compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp
</PRE>
<P>The value of the kinetic energy will be 0.0 for atoms (nuclei or
electrons) not in the specified compute group.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom computes as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of
LAMMPS output options.</p>
<p>The per-atom vector values will be in energy <a class="reference internal" href="units.html"><em>units</em></a>.</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-EFF 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>
</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="dump.html"><em>dump custom</em></a></p>
<p><strong>Default:</strong> none</p>
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<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dump.html">dump custom</A>
</P>
<P><B>Default:</B> none
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<li>compute ke/eff command</li>
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<div class="section" id="compute-ke-eff-command">
<span id="index-0"></span><h1>compute ke/eff command<a class="headerlink" href="#compute-ke-eff-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 ke/eff
</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>ke/eff = style name of this compute command</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 all ke/eff
</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 the kinetic energy of motion of a
<HR>
<H3>compute ke/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID ke/eff
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>ke/eff = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all ke/eff
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the kinetic energy of motion of a
group of eFF particles (nuclei and electrons), as modeled with the
<a class="reference internal" href="pair_eff.html"><em>electronic force field</em></a>.</p>
<p>The kinetic energy for each nucleus is computed as 1/2 m v^2 and the
<A HREF = "pair_eff.html">electronic force field</A>.
</P>
<P>The kinetic energy for each nucleus is computed as 1/2 m v^2 and the
kinetic energy for each electron is computed as 1/2(me v^2 + 3/4 me
s^2), where m corresponds to the nuclear mass, me to the electron
mass, v to the translational velocity of each particle, and s to the
radial velocity of the electron, respectively.</p>
<p>There is a subtle difference between the quantity calculated by this
compute and the kinetic energy calculated by the <em>ke</em> or <em>etotal</em>
radial velocity of the electron, respectively.
</P>
<P>There is a subtle difference between the quantity calculated by this
compute and the kinetic energy calculated by the <I>ke</I> or <I>etotal</I>
keyword used in thermodynamic output, as specified by the
<a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command. For this compute, kinetic
energy is &#8220;translational&#8221; and &#8220;radial&#8221; (only for electrons) kinetic
<A HREF = "thermo_style.html">thermo_style</A> command. For this compute, kinetic
energy is "translational" and "radial" (only for electrons) kinetic
energy, calculated by the simple formula above. For thermodynamic
output, the <em>ke</em> keyword infers kinetic energy from the temperature of
output, the <I>ke</I> keyword infers kinetic energy from the temperature of
the system with 1/2 Kb T of energy for each degree of freedom. For
the eFF temperature computation via the <a class="reference internal" href="compute_temp_eff.html"><em>compute temp_eff</em></a> command, these are the same. But
the eFF temperature computation via the <A HREF = "compute_temp_eff.html">compute
temp_eff</A> command, these are the same. But
different computes that calculate temperature can subtract out
different non-thermal components of velocity and/or include other
degrees of freedom.</p>
<p>IMPRORTANT NOTE: The temperature in eFF models should be monitored via
the <a class="reference internal" href="compute_temp_eff.html"><em>compute temp/eff</em></a> command, which can be
degrees of freedom.
</P>
<P>IMPRORTANT NOTE: The temperature in eFF models should be monitored via
the <A HREF = "compute_temp_eff.html">compute temp/eff</A> command, which can be
printed with thermodynamic output by using the
<a class="reference internal" href="thermo_modify.html"><em>thermo_modify</em></a> command, as shown in the following
example:</p>
<div class="highlight-python"><div class="highlight"><pre>compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp
</pre></div>
</div>
<p>See <a class="reference internal" href="compute_temp_eff.html"><em>compute temp/eff</em></a>.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global scalar (the KE). This value can be
<A HREF = "thermo_modify.html">thermo_modify</A> command, as shown in the following
example:
</P>
<PRE>compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp
</PRE>
<P>See <A HREF = "compute_temp_eff.html">compute temp/eff</A>.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an
overview of LAMMPS output options.</p>
<p>The scalar value calculated by this compute is &#8220;extensive&#8221;. The
scalar value will be in energy <a class="reference internal" href="units.html"><em>units</em></a>.</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-EFF 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><strong>Related commands:</strong> none</p>
<p><strong>Default:</strong> none</p>
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input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
overview of LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "extensive". The
scalar value will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B> none
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<div class="section" id="compute-ke-rigid-command">
<span id="index-0"></span><h1>compute ke/rigid command<a class="headerlink" href="#compute-ke-rigid-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 ke/rigid fix-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>ke = style name of this compute command</li>
<li>fix-ID = ID of rigid body fix</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 all ke/rigid myRigid
</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 the translational kinetic energy
of a collection of rigid bodies, as defined by one of the <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> command variants.</p>
<p>The kinetic energy of each rigid body is computed as 1/2 M Vcm^2,
<HR>
<H3>compute ke/rigid command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID ke/rigid fix-ID
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>ke = style name of this compute command
<LI>fix-ID = ID of rigid body fix
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all ke/rigid myRigid
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the translational kinetic energy
of a collection of rigid bodies, as defined by one of the <A HREF = "fix_rigid.html">fix
rigid</A> command variants.
</P>
<P>The kinetic energy of each rigid body is computed as 1/2 M Vcm^2,
where M is the total mass of the rigid body, and Vcm is its
center-of-mass velocity.</p>
<p>The <em>fix-ID</em> should be the ID of one of the <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a>
center-of-mass velocity.
</P>
<P>The <I>fix-ID</I> should be the ID of one of the <A HREF = "fix_rigid.html">fix rigid</A>
commands which defines the rigid bodies. The group specified in the
compute command is ignored. The kinetic energy of all the rigid
bodies defined by the fix rigid command in included in the
calculation.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global scalar (the summed KE of all the
calculation.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the summed KE of all the
rigid bodies). This value can be used by any command that uses a
global scalar value from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of LAMMPS output
options.</p>
<p>The scalar value calculated by this compute is &#8220;extensive&#8221;. The
scalar value will be in energy <a class="reference internal" href="units.html"><em>units</em></a>.</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 RIGID 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>
</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="compute_erotate_rigid.html"><em>compute erotate/rigid</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
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global scalar value from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
15</A> for an overview of LAMMPS output
options.
</P>
<P>The scalar value calculated by this compute is "extensive". The
scalar value will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the RIGID package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_erotate_rigid.html">compute erotate/rigid</A>
</P>
<P><B>Default:</B> none
</P>
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