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<HTML>
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<TITLE>LAMMPS Users Manual</TITLE>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<title>LAMMPS Documentation — LAMMPS 15 May 2015 version documentation</title>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<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_packages.html">4. Packages</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_howto.html">6. How-to discussions</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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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to 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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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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</li>
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</ul>
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<a href="Section_intro.html" class="btn btn-neutral float-right" title="1. Introduction" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div itemprop="articleBody">
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<H1></H1><div class="section" id="lammps-documentation">
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<h1>LAMMPS Documentation<a class="headerlink" href="#lammps-documentation" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="jul-2015-version">
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<h2>27 Jul 2015 version<a class="headerlink" href="#jul-2015-version" title="Permalink to this headline">¶</a></h2>
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</div>
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<div class="section" id="version-info">
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<h2>Version info:<a class="headerlink" href="#version-info" title="Permalink to this headline">¶</a></h2>
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<p>The LAMMPS “version” is the date when it was released, such as 1 May
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<CENTER><H3>LAMMPS Documentation
|
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</H3></CENTER>
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<CENTER><H4>27 Jul 2015 version
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</H4></CENTER>
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<H4>Version info:
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</H4>
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<P>The LAMMPS "version" is the date when it was released, such as 1 May
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2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
|
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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
|
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feature, we release it immediately, and post a notice on <A HREF = "http://lammps.sandia.gov/bug.html">this page of
|
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the WWW site</A>. Each dated copy of LAMMPS contains all the
|
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features and bug-fixes up to and including that version date. The
|
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version date is printed to the screen and logfile every time you run
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LAMMPS. It is also in the file src/version.h and in the LAMMPS
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directory name created when you unpack a tarball, and at the top of
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the first page of the manual (this page).</p>
|
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<ul class="simple">
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<li>If you browse the HTML doc pages on the LAMMPS WWW site, they always
|
||||
describe the most current version of LAMMPS.</li>
|
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<li>If you browse the HTML doc pages included in your tarball, they
|
||||
describe the version you have.</li>
|
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<li>The <a class="reference external" href="Manual.pdf">PDF file</a> on the WWW site or in the tarball is updated
|
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about once per month. This is because it is large, and we don’t want
|
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it to be part of every patch.</li>
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<li>There is also a <a class="reference external" href="Developer.pdf">Developer.pdf</a> file in the doc
|
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the first page of the manual (this page).
|
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</P>
|
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<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.
|
||||
|
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<LI>There is also a <A HREF = "Developer.pdf">Developer.pdf</A> file in the doc
|
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directory, which describes the internal structure and algorithms of
|
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LAMMPS.</li>
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</ul>
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<p>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
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Simulator.</p>
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<p>LAMMPS is a classical molecular dynamics simulation code designed to
|
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LAMMPS.
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</UL>
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<P>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
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Simulator.
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</P>
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<P>LAMMPS is a classical molecular dynamics simulation code designed to
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run efficiently on parallel computers. It was developed at Sandia
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National Laboratories, a US Department of Energy facility, with
|
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funding from the DOE. It is an open-source code, distributed freely
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under the terms of the GNU Public License (GPL).</p>
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<p>The primary developers of LAMMPS are <a class="reference external" href="http://www.sandia.gov/~sjplimp">Steve Plimpton</a>, Aidan
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under the terms of the GNU Public License (GPL).
|
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</P>
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<P>The primary developers of LAMMPS are <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Aidan
|
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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
|
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uses.</p>
|
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<hr class="docutils" />
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<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
|
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uses.
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</P>
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<HR>
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<P>The LAMMPS documentation is organized into the following sections. If
|
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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>
|
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<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>
|
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<div class="toctree-wrapper compound">
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#what-is-lammps">1.1. What is LAMMPS</a></li>
|
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<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>
|
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<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#open-source-distribution">1.4. Open source distribution</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#acknowledgments-and-citations">1.5. Acknowledgments and citations</a></li>
|
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</ul>
|
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</li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a><ul>
|
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<li class="toctree-l2"><a class="reference internal" href="Section_start.html#what-s-in-the-lammps-distribution">2.1. What’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>
|
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<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>
|
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<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>
|
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<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 & 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 & 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 & 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>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
<footer>
|
||||
<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>
|
||||
|
||||
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
|
||||
<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>
|
||||
|
||||
<a href="Section_intro.html" class="btn btn-neutral float-right" title="1. Introduction" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
|
||||
<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>
|
||||
|
||||
</div>
|
||||
<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>
|
||||
|
||||
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|
||||
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|
||||
|
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|
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© Copyright .
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|
||||
<LI><A HREF = "Section_modify.html">Modifying & extending LAMMPS</A>
|
||||
|
||||
</footer>
|
||||
<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>
|
||||
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|
||||
10.4 <A HREF = "Section_modify.html#mod_4">Dump styles</A>
|
||||
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|
||||
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|
||||
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|
||||
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>
|
||||
|
||||
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|
||||
</div>
|
||||
<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>
|
||||
|
||||
</section>
|
||||
<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>
|
||||
|
||||
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|
||||
<UL> 13.1 <A HREF = "Section_history.html#hist_1">Coming attractions</A>
|
||||
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|
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13.2 <A HREF = "Section_history.html#hist_2">Past versions</A>
|
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Section_intro
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Section_start
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Indices and tables
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==================
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</div>
|
||||
|
||||
</div>
|
||||
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
|
||||
<div itemprop="articleBody">
|
||||
|
||||
<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
|
||||
<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’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 “Communication” or “Other” 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 < in.script</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<div class="line-block">
|
||||
<div class="line">run a LAMMPS simulation | lmp_machine < 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, <br>
|
||||
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 “cuda” or “gpu” 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 “intel” 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 “offload” 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 “kk” 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 “native” mode. The speed-up depends on a variety of
|
||||
factors, as discussed on the KOKKOS accelerator page.</li>
|
||||
<li>Styles with an “omp” 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 “opt” 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 “hybrid” 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 “small”. 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>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
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|
||||
<footer>
|
||||
|
||||
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
|
||||
|
||||
<a href="Section_howto.html" class="btn btn-neutral float-right" title="6. How-to discussions" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
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||||
|
||||
|
||||
<a href="Section_packages.html" class="btn btn-neutral" title="4. Packages" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
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||||
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||||
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||||
|
||||
|
||||
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|
||||
|
||||
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||||
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rather than memory-limited.
|
||||
</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.
|
||||
</P>
|
||||
</HTML>
|
||||
|
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<CENTER><A HREF = "Section_howto.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_perf.html">Next Section</A>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<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_packages.html">4. Packages</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_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1 current"><a class="current reference internal" href="">7. Example problems</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to 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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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<div itemprop="articleBody">
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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
|
||||
<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 “foo”.</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 < 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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|
||||
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|
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|
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|
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<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_errors.html">12. Errors</a></li>
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<li class="toctree-l1 current"><a class="current reference internal" href="">13. Future and history</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="#coming-attractions">13.1. Coming attractions</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="#past-versions">13.2. Past versions</a></li>
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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
|
||||
<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
|
||||
& 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 & 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 & 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 & 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>
|
||||
</div>
|
||||
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|
||||
|
||||
|
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C++ open-source version of LAMMPS over the last several years.
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</P>
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<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>
|
||||
</HTML>
|
||||
|
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File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
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@ -1,167 +1,43 @@
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
|
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<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_packages.html">4. Packages</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_howto.html">6. How-to discussions</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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<li class="toctree-l1 current"><a class="current reference internal" href="">8. Performance & scalability</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to 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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<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="performance-scalability">
|
||||
<h1>8. Performance & 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
|
||||
<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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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
|
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<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_packages.html">4. Packages</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_howto.html">6. How-to discussions</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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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to 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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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</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-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
|
||||
<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 “-c on” 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 “-pk cuda” and “-sf cuda”
|
||||
<a class="reference internal" href="Section_start.html#start-7"><span>command-line switches</span></a> respectively. Or
|
||||
the effect of the “-pk” or “-sf” 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 “Make.py -h” 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 “make OPTIONS”, 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
|
||||
<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 “make clean” first, followed by
|
||||
“make”.</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
|
||||
</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
|
||||
</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 “-c on” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> to enable the USER-CUDA package.
|
||||
The “-c on” 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 “-sf cuda” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>,
|
||||
which will automatically append “cuda” to styles that support it. Use
|
||||
the “-pk cuda Ng” <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 “-c on” 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 “-pk” switch is the same as same as the “package
|
||||
cuda” command. See the <a class="reference internal" href="package.html"><em>package</em></a> command doc page for
|
||||
</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 “off” 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 “-c on” <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
|
||||
“cuda” 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 “-c on” <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>
|
||||
|
||||
|
||||
</div>
|
||||
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||||
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<script type="text/javascript">
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var DOCUMENTATION_OPTIONS = {
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||||
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|
||||
occurs, the faster your simulation will run.
|
||||
</UL>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>None.
|
||||
</P>
|
||||
</HTML>
|
||||
|
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@ -1,401 +1,257 @@
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||||
|
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<CENTER><A HREF = "Section_packages.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
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||||
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<ul>
|
||||
<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 & 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 & 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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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<li><a href="Manual.html">Docs</a> »</li>
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<li>5.GPU package</li>
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<li class="wy-breadcrumbs-aside">
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||||
|
||||
|
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<a href="http://lammps.sandia.gov">Website</a>
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<a href="Section_commands.html#comm">Commands</a>
|
||||
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</li>
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<hr/>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
|
||||
<div itemprop="articleBody">
|
||||
|
||||
<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
|
||||
<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 “-pk gpu” and “-sf gpu”
|
||||
<a class="reference internal" href="Section_start.html#start-7"><span>command-line switches</span></a> respectively. Or
|
||||
the effect of the “-pk” or “-sf” 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 “Make.py -h” 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 “clean” first, e.g. “make -f
|
||||
Makefile.linux clean”, 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)
|
||||
</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 “-sf gpu” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>,
|
||||
which will automatically append “gpu” to styles that support it. Use
|
||||
the “-pk gpu Ng” <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 “-sf gpu” 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 “-pk” switch explicitly allows for setting of the number of
|
||||
</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 “package gpu” 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 “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><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
|
||||
“gpu” 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 “-sf gpu” or “-pk gpu” <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 “Pair” 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 “Pair” 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 “Pair” time, not the “Neigh” 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 “GPU Time Info (average)” reports “Max Mem / Proc”.
|
||||
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>
|
||||
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|
||||
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storage by a single MPI process.
|
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</UL>
|
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<P><B>Restrictions:</B>
|
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</P>
|
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<P>None.
|
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</P>
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</HTML>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
|
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<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_packages.html">4. Packages</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_howto.html">6. How-to discussions</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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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to 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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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<li><a href="Manual.html">Docs</a> »</li>
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<li>5.USER-INTEL package</li>
|
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<li class="wy-breadcrumbs-aside">
|
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|
||||
|
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<a href="http://lammps.sandia.gov">Website</a>
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<a href="Section_commands.html#comm">Commands</a>
|
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|
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div itemprop="articleBody">
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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
|
||||
<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
|
||||
“-suffix intel” <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 “omp” 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 “-pk intel” and “-sf intel”
|
||||
<a class="reference internal" href="Section_start.html#start-7"><span>command-line switches</span></a> respectively. Or
|
||||
the effect of the “-pk” or “-sf” 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.
|
||||
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
|
||||
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
|
||||
“Make.py -h” 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
|
||||
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></div>
|
||||
</div>
|
||||
<p>Note that this assumes that your MPI and its mpicxx wrapper
|
||||
</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 “-cc icc” 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 “-fopenmp” flag for OpenMP support in
|
||||
</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
|
||||
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 “-sf intel” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></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 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 “-pk omp” form
|
||||
is only allowed if LAMMPS was also built with the USER-OMP package.</p>
|
||||
<p>Use the “-pk intel Nphi” <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 “-pk intel” <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):
|
||||
</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:
|
||||
</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 “-sf intel” 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
|
||||
</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 “mixed”, 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 “-pk intel” or “-pk omp” 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 “-pk intel” 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
|
||||
“intel” 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
|
||||
“-sf intel” or “-pk intel” <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 “-sf intel” or “-pk omp” <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 “on”. 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
|
||||
“inner”, “middle”, “outer” options for rRESPA integration via the
|
||||
<a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command; only the “pair” option is
|
||||
supported.</p>
|
||||
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|
||||
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|
||||
|
||||
|
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
|
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<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_packages.html">4. Packages</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_howto.html">6. How-to discussions</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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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to 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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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<li><a href="Manual.html">Docs</a> »</li>
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<li>5.KOKKOS package</li>
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<li class="wy-breadcrumbs-aside">
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<a href="http://lammps.sandia.gov">Website</a>
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<a href="Section_commands.html#comm">Commands</a>
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<hr/>
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</div>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div itemprop="articleBody">
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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="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
|
||||
<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 “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
|
||||
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
|
||||
“host” 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
|
||||
“device” 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 “-k on” command-line switch use KOKKOS styles in your input script</li>
|
||||
</ul>
|
||||
<p>The latter two steps can be done using the “-k on”, “-pk kokkos” and
|
||||
“-sf kk” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switches</span></a>
|
||||
respectively. Or the effect of the “-pk” or “-sf” 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 “native” mode,
|
||||
not “offload” 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 “Make.py -h” 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
|
||||
</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
|
||||
</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
|
||||
</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
|
||||
</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
|
||||
“gmake” if your system’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
|
||||
“make clean-all” or “make clean-machine” 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 “clean” 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 “nvcc” 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 “nvcc” 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, “nvcc” 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 “Compilation rule” 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’ 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 “-k” 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 “-k” 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 “-k on” <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 “t Nt” 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 “g Ng” 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 “-k on” switch also issues a “package kokkos” 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 “-sf kk” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>,
|
||||
which will automatically append “kk” to styles that support it. Use
|
||||
the “-pk kokkos” <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 “-k on” <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):
|
||||
</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:
|
||||
</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 “full” neighbor lists and set the Newton flag to “off” for both
|
||||
</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 “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 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 “-k on” <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
|
||||
“kk” 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 “-k on”
|
||||
<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 “t” keyword of the “-k” <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 ...
|
||||
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></div>
|
||||
</div>
|
||||
<p>For binding threads with the KOKKOS OMP option, use thread affinity
|
||||
</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 “-k” <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 “native” 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 “-k on t Nt” 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>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
</div>
|
||||
<footer>
|
||||
|
||||
|
||||
<hr/>
|
||||
|
||||
<div role="contentinfo">
|
||||
<p>
|
||||
© 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>.
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|
||||
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<script type="text/javascript">
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<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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<p><a class="reference internal" href="Section_accelerate.html"><em>Return to Section accelerate overview</em></a></p>
|
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<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
|
||||
<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 “-pk omp” and “-sf omp”
|
||||
<a class="reference internal" href="Section_start.html#start-7"><span>command-line switches</span></a> respectively. Or
|
||||
the effect of the “-pk” or “-sf” 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 “Make.py
|
||||
-h” 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 “-fopenmp” to add OpenMP
|
||||
</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 “-restrict”.</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 “-sf omp” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>,
|
||||
which will automatically append “omp” to styles that support it. Use
|
||||
the “-pk omp Nt” <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 “-sf omp” 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 “-pk” switch explicitly allows for direct setting of the
|
||||
</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 “package omp” 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
|
||||
“omp” 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 “-sf omp” or “-pk omp” <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 “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
|
||||
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&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 “capability mode”, 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>
|
||||
</div>
|
||||
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|
||||
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|
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</div>
|
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|
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|
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|
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
|
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<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_packages.html">4. Packages</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_howto.html">6. How-to discussions</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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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to 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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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<li>5.OPT package</li>
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<li class="wy-breadcrumbs-aside">
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<a href="http://lammps.sandia.gov">Website</a>
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<a href="Section_commands.html#comm">Commands</a>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div itemprop="articleBody">
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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
|
||||
<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 “-sf opt” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>. Or the effect of the “-sf” 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 “Make.py
|
||||
-h” 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 “-restrict”.</p>
|
||||
<p><strong>Run with the OPT package from the command line:</strong></p>
|
||||
<p>Use the “-sf opt” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>,
|
||||
which will automatically append “opt” to styles that support it.</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre>lmp_machine -sf opt -in in.script
|
||||
</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></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
|
||||
“opt” 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 “Pair time” value printed at the end
|
||||
</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>
|
||||
</div>
|
||||
</div>
|
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|
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|
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|
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|
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|
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</p>
|
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|
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|
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<div class="section" id="angle-style-charmm-command">
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<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
|
||||
<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></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
|
||||
</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
|
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<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
|
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<li>angle_style class2 command</li>
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<div class="section" id="angle-style-class2-command">
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<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>
|
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</div>
|
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<div class="section" id="angle-style-class2-omp-command">
|
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<h1>angle_style class2/omp command<a class="headerlink" href="#angle-style-class2-omp-command" title="Permalink to this headline">¶</a></h1>
|
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<div class="section" id="syntax">
|
||||
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
|
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<div class="highlight-python"><div class="highlight"><pre>angle_style class2
|
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</pre></div>
|
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</div>
|
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</div>
|
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<div class="section" id="examples">
|
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
|
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<div class="highlight-python"><div class="highlight"><pre>angle_style class2
|
||||
<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
|
||||
</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 “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 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 “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 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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<div class="section" id="angle-coeff-command">
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<span id="index-0"></span><h1>angle_coeff command<a class="headerlink" href="#angle-coeff-command" title="Permalink to this headline">¶</a></h1>
|
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<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
|
||||
<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.
|
||||
</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 “*” or “<em>n” or “n</em>” or “m*n”. 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
|
||||
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></div>
|
||||
</div>
|
||||
<p>A line in a data file that specifies angle coefficients uses the exact
|
||||
</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 “Angle Coeffs” 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
|
||||
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<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>, or
|
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</P>
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<P>An angle style must be defined before any angle coefficients are
|
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set, either in the input script or in a data file.
|
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<P><A HREF = "angle_style.html">angle_style</A>
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<div class="section" id="angle-style-cosine-command">
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<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
|
||||
<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></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
|
||||
</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.
|
||||
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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
|
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MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
|
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LAMMPS</A> section for more info on packages.
|
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</P>
|
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<P><B>Related commands:</B>
|
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</P>
|
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<P><A HREF = "angle_coeff.html">angle_coeff</A>
|
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</P>
|
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<P><B>Default:</B> none
|
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<div class="section" id="angle-style-cosine-delta-command">
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<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
|
||||
<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></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
|
||||
</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>
|
||||
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|
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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>, <A HREF = "angle_cosine_squared.html">angle_style
|
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cosine/squared</A>
|
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</P>
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|
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<div class="section" id="angle-style-cosine-periodic-command">
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<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
|
||||
<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></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
|
||||
</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
|
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<div class="section" id="angle-style-cosine-shift-command">
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<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
|
||||
<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></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
|
||||
</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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|
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|
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|
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|
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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">
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<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>
|
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</div>
|
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<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>
|
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</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
|
||||
<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></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
|
||||
</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 > 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 -> 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 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.
|
||||
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<P><B>Restrictions:</B>
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</P>
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<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>
|
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section for more info on packages.
|
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</P>
|
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<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>
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<P><B>Default:</B> none
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<div class="section" id="angle-style-cosine-squared-command">
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<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
|
||||
<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></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
|
||||
</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.
|
||||
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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
|
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MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
|
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LAMMPS</A> section for more info on packages.
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</P>
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<P><B>Related commands:</B>
|
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<P><A HREF = "angle_coeff.html">angle_coeff</A>
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<div class="section" id="angle-style-dipole-command">
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<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
|
||||
<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></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
|
||||
</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>
|
||||
<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 ‘chain rule’ 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
|
||||
'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 ‘i’).</p>
|
||||
<p>Note that the angle dipole potential does not give rise to any force,
|
||||
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 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
|
||||
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 “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
|
||||
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 “Angles” section
|
||||
of the data file would read: X X 1 2 2</p>
|
||||
</div>
|
||||
<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>
|
||||
</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 & 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 & 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/>
|
||||
|
||||
<div role="contentinfo">
|
||||
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|
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<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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|
||||
<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>
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|
||||
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|
||||
<div itemprop="articleBody">
|
||||
|
||||
<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
|
||||
<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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|
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|
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|
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<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>
|
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section for more info on packages.
|
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</P>
|
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<P><B>Related commands:</B>
|
||||
</P>
|
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<P><A HREF = "angle_coeff.html">angle_coeff</A>
|
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</P>
|
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<P><B>Default:</B> none
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<H3>angle_style fourier/simple command
|
||||
</H3>
|
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<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>
|
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<UL><LI>K (energy)
|
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<LI>c (real)
|
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<LI>n (real)
|
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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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||||
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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
|
||||
<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>
|
||||
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|
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LAMMPS</A> section for more info.
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</P>
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<P>You can specify the accelerated styles explicitly in your input script
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|
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<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
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<P><A HREF = "angle_coeff.html">angle_coeff</A>
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<div class="section" id="angle-style-harmonic-command">
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||||
<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
|
||||
<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></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
|
||||
</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>
|
||||
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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>
|
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</HTML>
|
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@ -1,274 +1,96 @@
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<div class="section" id="angle-style-hybrid-command">
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<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>
|
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<div class="section" id="syntax">
|
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<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
|
||||
<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
|
||||
</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. “harmonic” or “cosine”, must be added after the angle type, for each
|
||||
line in the “Angle Coeffs” 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.
|
||||
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<P><B>Restrictions:</B>
|
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</P>
|
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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>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>
|
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</P>
|
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<P><B>Default:</B> none
|
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<div class="section" id="angle-style-none-command">
|
||||
<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
|
||||
<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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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<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_packages.html">4. Packages</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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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to 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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<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="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
|
||||
<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></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
|
||||
</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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|
||||
|
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|
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<P><A HREF = "angle_coeff.html">angle_coeff</A>
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<div class="section" id="angle-style-sdk-command">
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||||
<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
|
||||
<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></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
|
||||
</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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|
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|
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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>
|
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<P><B>Default:</B> none
|
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</HTML>
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@ -1,277 +1,100 @@
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<div class="section" id="angle-style-command">
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<span id="index-0"></span><h1>angle_style command<a class="headerlink" href="#angle-style-command" title="Permalink to this headline">¶</a></h1>
|
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<div class="section" id="syntax">
|
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
|
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<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>
|
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<div class="section" id="examples">
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||||
<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
|
||||
<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
|
||||
</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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<P><A HREF = "angle_coeff.html">angle_coeff</A>
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<P><B>Default:</B>
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<PRE>angle_style none
|
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<ul class="wy-breadcrumbs">
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<li><a href="Manual.html">Docs</a> »</li>
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<li>angle_style table command</li>
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<div itemprop="articleBody">
|
||||
|
||||
<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
|
||||
<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></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
|
||||
</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)
|
||||
@ -187,20 +72,20 @@ N 181 FP 0 0 (N, FP parameters)
|
||||
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
|
||||
“#”; blank lines or lines starting with “#” can be used as comments
|
||||
</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 “N” 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 = “N” 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 “FP” 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 “FP” 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 “EQ” 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>
|
||||
<HR>
|
||||
|
||||
|
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|
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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
|
||||
</P>
|
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</HTML>
|
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|
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@ -1,343 +1,179 @@
|
||||
|
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|
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<!DOCTYPE html>
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<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
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<title>atom_modify command — LAMMPS 15 May 2015 version documentation</title>
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<HTML>
|
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS
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|
||||
|
||||
|
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|
||||
|
||||
<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>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<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_packages.html">4. Packages</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_howto.html">6. How-to discussions</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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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to 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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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<li>atom_modify command</li>
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<a href="http://lammps.sandia.gov">Website</a>
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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
|
||||
<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
|
||||
</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
|
||||
</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’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 “all” 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’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’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
|
||||
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 “all”.</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
|
||||
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
|
||||
"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 class="docutils" />
|
||||
<p id="meloni"><strong>(Meloni)</strong> Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007).</p>
|
||||
</div>
|
||||
</div>
|
||||
cutoff will be used to set the bin size.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "Meloni"></A>
|
||||
|
||||
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|
||||
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|
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<P><B>(Meloni)</B> Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007).
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<title>atom_style command — LAMMPS 15 May 2015 version documentation</title>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<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>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</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_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to 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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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<div itemprop="articleBody">
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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
|
||||
<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
|
||||
@ -158,315 +40,229 @@ 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
|
||||
</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 > 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 “style” 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 “atom_style hybrid sphere dipole”. 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 & 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>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
<footer>
|
||||
|
||||
|
||||
<hr/>
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|
||||
<P><B>(Grime)</B> Grime and Voth, to appear in J Chem Theory & Computation
|
||||
(2014).
|
||||
</P>
|
||||
</HTML>
|
||||
|
||||
581
doc/balance.html
581
doc/balance.html
@ -1,246 +1,130 @@
|
||||
|
||||
|
||||
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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|
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|
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|
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|
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|
||||
<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>
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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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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to 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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<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="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
|
||||
<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 "x" or "y" or "z", 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
|
||||
<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>
|
||||
</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
|
||||
</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
|
||||
</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 “static” 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 “dynamic” 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 “imbalance factor” 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> < 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 “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 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 “grid” 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, “grid” 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 “grid”
|
||||
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 “grid” 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 “grid” 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 “tiling” 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 “grid” 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
|
||||
“tiling” 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 “grid”
|
||||
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 “comm_style
|
||||
brick” can afterwords be specified for subsequent <a class="reference internal" href="run.html"><em>run</em></a>
|
||||
commands.</p>
|
||||
<p>When a “grid” 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 “tiling” method is specified, the current domain partitioning
|
||||
(“grid” or “tiled”) 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 “grid” 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 “create_box” or “read_data” or “read_restart” 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’s sub-domain 3x
|
||||
larger than the right processor’s sub-domain.</p>
|
||||
<hr class="docutils" />
|
||||
<p>The <em>shift</em> style invokes a “grid” 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 “x” or “y” or “z”. 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’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 “tiled” 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
|
||||
@ -455,89 +333,28 @@ ITEM: SQUARES
|
||||
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
|
||||
</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 “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>
|
||||
</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 “z”
|
||||
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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|
||||
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|
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|
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|
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|
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|
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|
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||||
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|
||||
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|
||||
<P>For 2d simulations, the <I>z</I> style cannot be used. Nor can a "z"
|
||||
appear in <I>dimstr</I> for the <I>shift</I> style.
|
||||
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|
||||
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|
||||
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|
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382
doc/body.html
382
doc/body.html
@ -1,252 +1,138 @@
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<input type="hidden" name="area" value="default" />
|
||||
</form>
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</div>
|
||||
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</div>
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<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
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<ul>
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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_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_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 & scalability</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
|
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<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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</ul>
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<ul class="wy-breadcrumbs">
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<li><a href="Manual.html">Docs</a> »</li>
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<li>Body particles</li>
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<a href="http://lammps.sandia.gov">Website</a>
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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
|
||||
<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
|
||||
</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.
|
||||
</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
|
||||
</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>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
</div>
|
||||
<footer>
|
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|
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|
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|
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|
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|
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|
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current COM and orientiation of the body particle.
|
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</P>
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</HTML>
|
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|
||||
@ -1,256 +1,88 @@
|
||||
|
||||
|
||||
<!DOCTYPE html>
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<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
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<li>bond_style class2 command</li>
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<div class="section" id="bond-style-class2-command">
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<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>
|
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</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
|
||||
<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></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
|
||||
</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>
|
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<P><B>Default:</B> none
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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 & extending LAMMPS</a></li>
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<div class="section" id="bond-coeff-command">
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<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
|
||||
<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.
|
||||
</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 “*” or “<em>n” or “n</em>” or “m*n”. 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
|
||||
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></div>
|
||||
</div>
|
||||
<p>A line in a data file that specifies bond coefficients uses the exact
|
||||
</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 “Bond Coeffs” 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
|
||||
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<P><B>Restrictions:</B>
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<P>This command must come after the simulation box is defined by a
|
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<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.
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</P>
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<P>A bond style must be defined before any bond coefficients are set,
|
||||
either in the input script or in a data file.
|
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</P>
|
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<P><B>Related commands:</B>
|
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<P><A HREF = "bond_style.html">bond_style</A>
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<P><B>Default:</B> none
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<div class="section" id="bond-style-fene-command">
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<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
|
||||
<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></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
|
||||
</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"">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’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
|
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|
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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_python.html">11. Python interface to 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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<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
|
||||
<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></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
|
||||
</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"">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’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
|
||||
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|
||||
|
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<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_packages.html">4. Packages</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_howto.html">6. How-to discussions</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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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to 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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<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="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
|
||||
<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></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
|
||||
</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>
|
||||
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<div class="section" id="bond-style-harmonic-shift-command">
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<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
|
||||
<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></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.
|
||||
</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>
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|
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<div class="section" id="bond-style-harmonic-shift-cut-command">
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<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>
|
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</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
|
||||
<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></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 > 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
|
||||
</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>
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</P>
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<P>This bond style can only be used if LAMMPS was built with the
|
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USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
|
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section for more info on packages.
|
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</P>
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<P><B>Related commands:</B>
|
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</P>
|
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<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>,
|
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<A HREF = "bond_harmonic.html">bond_harmonic</A>,
|
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<A HREF = "bond_harmonicshift.html">bond_harmonicshift</A>
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<P><B>Default:</B> none
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<title>bond_style hybrid command — LAMMPS 15 May 2015 version documentation</title>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<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_packages.html">4. Packages</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_howto.html">6. How-to discussions</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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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<div class="section" id="bond-style-hybrid-command">
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<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
|
||||
<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
|
||||
</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. “harmonic” or “fene” must be added after the bond type, for each
|
||||
line in the “Bond Coeffs” 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>
|
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</P>
|
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<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>
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</P>
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<P><B>Default:</B> none
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<div class="section" id="bond-style-morse-command">
|
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<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
|
||||
<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></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
|
||||
</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.
|
||||
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|
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|
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|
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|
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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>
|
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</P>
|
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<P><B>Default:</B> none
|
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@ -1,218 +1,34 @@
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<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_packages.html">4. Packages</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_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to 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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||||
<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
|
||||
<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>
|
||||
</div>
|
||||
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||||
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<A HREF = "read_data.html">read_data</A> command.
|
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|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B> none
|
||||
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|
||||
<P><B>Default:</B> none
|
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@ -1,254 +1,86 @@
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<div class="section" id="bond-style-nonlinear-command">
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<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
|
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</pre></div>
|
||||
</div>
|
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</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
|
||||
<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></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
|
||||
</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>
|
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|
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<div class="section" id="bond-style-quartic-command">
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<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>
|
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</div>
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</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
|
||||
<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></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.
|
||||
</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 > Rc, LAMMPS “breaks”
|
||||
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
|
||||
<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></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
|
||||
</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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|
||||
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|
||||
|
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|
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|
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dihedral, etc) cannot be used with <I>quartic</I> bonds.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
|
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|
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<div class="section" id="bond-style-command">
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||||
<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
|
||||
<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
|
||||
</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>
|
||||
</div>
|
||||
|
||||
|
||||
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|
||||
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<P><B>Related commands:</B>
|
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</P>
|
||||
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
|
||||
</P>
|
||||
<P><B>Default:</B>
|
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</P>
|
||||
<P>bond_style none
|
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</P>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to 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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<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
|
||||
<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></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
|
||||
</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
|
||||
“#”; blank lines or lines starting with “#” can be used as comments
|
||||
</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 “N” 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 = “N” 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 “FP” 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 “FP” 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 “EQ” 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>
|
||||
<HR>
|
||||
|
||||
|
||||
</div>
|
||||
</div>
|
||||
<footer>
|
||||
|
||||
|
||||
<hr/>
|
||||
|
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<div role="contentinfo">
|
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|
||||
© Copyright .
|
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|
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|
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|
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<script type="text/javascript">
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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>
|
||||
|
||||
@ -1,282 +1,106 @@
|
||||
|
||||
|
||||
<!DOCTYPE html>
|
||||
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
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<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<title>boundary command — LAMMPS 15 May 2015 version documentation</title>
|
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<HTML>
|
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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</CENTER>
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|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<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>
|
||||
|
||||
|
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|
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|
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
|
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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_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_howto.html">6. How-to discussions</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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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to 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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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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||||
<li>boundary command</li>
|
||||
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|
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|
||||
<a href="http://lammps.sandia.gov">Website</a>
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||||
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|
||||
|
||||
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|
||||
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||||
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||||
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||||
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|
||||
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
|
||||
<div itemprop="articleBody">
|
||||
|
||||
<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
|
||||
</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
|
||||
</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>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
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|
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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>
|
||||
|
||||
285
doc/box.html
285
doc/box.html
@ -1,246 +1,69 @@
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<title>box command — LAMMPS 15 May 2015 version documentation</title>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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|
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|
||||
|
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<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>
|
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</PRE>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</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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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to 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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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<div itemprop="articleBody">
|
||||
|
||||
<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
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<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
|
||||
</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’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>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
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|
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|
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|
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|
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|
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|
||||
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|
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|
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|
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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>
|
||||
</HTML>
|
||||
|
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@ -1,188 +1,69 @@
|
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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|
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|
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|
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|
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|
||||
<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
|
||||
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|
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<ul>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
|
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<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_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_howto.html">6. How-to discussions</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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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to 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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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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||||
<div itemprop="articleBody">
|
||||
|
||||
<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
|
||||
<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
|
||||
</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></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
|
||||
</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
|
||||
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></div>
|
||||
</div>
|
||||
<div class="highlight-python"><div class="highlight"><pre>change_box all x final -10 20 boundary f s s
|
||||
</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 “displace_box” version of this
|
||||
</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 “key” 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 “key”. 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"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 “boundary” 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>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
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|
||||
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|
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change_box command is issued, so long as an <A HREF = "undump.html">undump</A> or
|
||||
<A HREF = "unfix.html">unfix</A> command is also used to turn them off.
|
||||
</P>
|
||||
<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.
|
||||
</P>
|
||||
</HTML>
|
||||
|
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245
doc/clear.html
245
doc/clear.html
@ -1,226 +1,43 @@
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<ul>
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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_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_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>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to 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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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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|
||||
<div itemprop="articleBody">
|
||||
|
||||
<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)
|
||||
<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
|
||||
</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>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
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|
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||||
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|
||||
</p>
|
||||
</div>
|
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</div>
|
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|
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|
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|
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|
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|
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<script type="text/javascript">
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|
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|
||||
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|
||||
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 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>
|
||||
</HTML>
|
||||
|
||||
@ -1,329 +1,151 @@
|
||||
|
||||
|
||||
<!DOCTYPE html>
|
||||
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
|
||||
<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
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||||
<head>
|
||||
<meta charset="utf-8">
|
||||
|
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
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|
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<title>comm_modify command — LAMMPS 15 May 2015 version documentation</title>
|
||||
<HTML>
|
||||
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
|
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</CENTER>
|
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|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<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>
|
||||
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<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_packages.html">4. Packages</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_howto.html">6. How-to discussions</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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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to 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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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<li>comm_modify command</li>
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<a href="http://lammps.sandia.gov">Website</a>
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<a href="Section_commands.html#comm">Commands</a>
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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
|
||||
</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
|
||||
</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’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 > 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 “find” 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 “remap v” 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>
|
||||
</div>
|
||||
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|
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|
||||
|
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cutoff = pairwise force cutoff + neighbor skin.
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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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<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
|
||||
<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></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
|
||||
</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 “tiles” 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.
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<P><B>Restrictions:</B> none
|
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</P>
|
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<P><B>Related commands:</B>
|
||||
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|
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<P><A HREF = "comm_modify.html">comm_modify</A>, <A HREF = "processors.html">processors</A>,
|
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<P>The default style is brick.
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588
doc/compute.html
588
doc/compute.html
@ -1,154 +1,34 @@
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|
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<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_tools.html">9. Additional tools</a></li>
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|
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|
||||
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
|
||||
<div itemprop="articleBody">
|
||||
|
||||
<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
|
||||
<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.
|
||||
</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 “atom” in their style, e.g. <em>ke/atom</em>. Computes that produce
|
||||
local quantities have the word “local” in their style,
|
||||
e.g. <em>bond/local</em>. 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
|
||||
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 -> scalar, array -> vector). Using two brackets
|
||||
reduces the dimension twice (array -> 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
|
||||
“intensive” or “extensive” 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
|
||||
“thermo_modify norm” 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 “thermo_temp”,
|
||||
“thermo_press”, and “thermo_pe”, 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
|
||||
</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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|
||||
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|
||||
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|
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|
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<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>
|
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</P>
|
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<P><B>Default:</B> none
|
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<li><a href="Manual.html">Docs</a> »</li>
|
||||
|
||||
<li>compute ackland/atom command</li>
|
||||
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|
||||
|
||||
|
||||
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||||
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|
||||
|
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|
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|
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|
||||
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|
||||
<div itemprop="articleBody">
|
||||
|
||||
<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
|
||||
<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>
|
||||
<HR>
|
||||
|
||||
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|
||||
|
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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||||
<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
|
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<div itemprop="articleBody">
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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
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<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
|
||||
</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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|
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|
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<P><A HREF = "dump.html">dump local</A>, <A HREF = "compute_property_local.html">compute
|
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property/local</A>
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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
|
||||
<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 “<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
|
||||
“all” 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’s
|
||||
angular momentum in “unwrapped” 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 “unwrapped” 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 =
|
||||
</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 “intensive”. 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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|
||||
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|
||||
|
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|
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|
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|
||||
</p>
|
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</div>
|
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</footer>
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|
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</section>
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|
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|
||||
15</A> for an overview of LAMMPS output
|
||||
options.
|
||||
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|
||||
<P>The array values are "intensive". The array values will be in
|
||||
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|
||||
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|
||||
<P><B>Restrictions:</B> none
|
||||
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|
||||
<P><B>Related commands:</B>
|
||||
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|
||||
<P><A HREF = "variable.html">variable angmom() function</A>
|
||||
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|
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|
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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 “c”
|
||||
<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>
|
||||
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|
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<title>compute body/local command — LAMMPS 15 May 2015 version documentation</title>
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<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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||||
<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
|
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</PRE>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<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>compute body/local command</li>
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<div class="section" id="compute-body-local-command">
|
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<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
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<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
|
||||
</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
|
||||
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></div>
|
||||
</div>
|
||||
<p><strong>Output info:</strong></p>
|
||||
<p>This compute calculates a local vector or local array depending on the
|
||||
</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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|
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|
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|
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|
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options.
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<P><A HREF = "dump.html">dump local</A>
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<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
|
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<I>force</I> = bond force
|
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</PRE>
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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
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<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
|
||||
</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
|
||||
</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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|
||||
</div>
|
||||
|
||||
|
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|
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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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|
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</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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||||
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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
|
||||
<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 >= 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
|
||||
</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
|
||||
</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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|
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|
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<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_packages.html">4. Packages</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_howto.html">6. How-to discussions</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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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to 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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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<div itemprop="articleBody">
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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
|
||||
<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 > 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>
|
||||
</div>
|
||||
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|
||||
|
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|
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|
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|
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|
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|
||||
</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>
|
||||
</HTML>
|
||||
|
||||
@ -1,272 +1,104 @@
|
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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
|
||||
<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>
|
||||
|
||||
<A NAME = "Faken"></A>
|
||||
|
||||
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|
||||
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|
||||
<footer>
|
||||
<P><B>(Faken)</B> Faken, Jonsson, Comput Mater Sci, 2, 279 (1994).
|
||||
</P>
|
||||
<A NAME = "Tsuzuki"></A>
|
||||
|
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|
||||
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|
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|
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<P><B>(Tsuzuki)</B> Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (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>
|
||||
<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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|
||||
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|
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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
|
||||
<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 “unwrapped” 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 “unwrapped” 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 “intensive”. 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>
|
||||
</div>
|
||||
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|
||||
|
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|
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from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
|
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section</A> for an overview of LAMMPS output
|
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options.
|
||||
</P>
|
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<P>The vector values are "intensive". The vector values will be in
|
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distance <A HREF = "units.html">units</A>.
|
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</P>
|
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<P><B>Restrictions:</B> none
|
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</P>
|
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<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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</P>
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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
|
||||
<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 “<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
|
||||
“all” 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’s
|
||||
center-of-mass in “unwrapped” 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 “unwrapped” 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 =
|
||||
</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 “intensive”. 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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|
||||
</div>
|
||||
|
||||
|
||||
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|
||||
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|
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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>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
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</HTML>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</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_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to 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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<div itemprop="articleBody">
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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
|
||||
<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 >= 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>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
</div>
|
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<footer>
|
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|
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|
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<hr/>
|
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|
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<div role="contentinfo">
|
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|
||||
© Copyright .
|
||||
</p>
|
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</div>
|
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|
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|
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|
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|
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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
|
||||
</P>
|
||||
</HTML>
|
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|
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@ -1,276 +1,97 @@
|
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<div itemprop="articleBody">
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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
|
||||
<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
|
||||
</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 “*” 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 “*” or “<em>n” or “n</em>” or “m*n”. 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 >= 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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|
||||
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|
||||
|
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|
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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
|
||||
</P>
|
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</HTML>
|
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|
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@ -1,240 +1,68 @@
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<title>compute damage/atom command — LAMMPS 15 May 2015 version documentation</title>
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<HTML>
|
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<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_packages.html">4. Packages</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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|
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<div class="section" id="compute-damage-atom-command">
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<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 “damage” of a Peridymaics particles is based on the bond breakage
|
||||
<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 “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><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) >= 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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|
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|
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|
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<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
|
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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>
|
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<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "compute_dilatation.html">compute dilatation</A>, <A HREF = "compute_plasticity.html">compute
|
||||
plasticity</A>
|
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|
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|
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<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>
|
||||
|
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<PRE> <I>phi</I> = tabulate dihedral angles
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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
|
||||
</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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|
||||
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|
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|
||||
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|
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|
||||
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|
||||
<P><B>Restrictions:</B> none
|
||||
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|
||||
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|
||||
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|
||||
<P><A HREF = "dump.html">dump local</A>, <A HREF = "compute_property_local.html">compute
|
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|
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|
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|
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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 “theta” for each peridynamic particle I is calculated
|
||||
<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) >= 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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|
||||
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|
||||
|
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|
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|
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|
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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
|
||||
</P>
|
||||
</HTML>
|
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|
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@ -1,256 +1,74 @@
|
||||
|
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|
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<!DOCTYPE html>
|
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<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
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|
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<title>compute displace/atom command — LAMMPS 15 May 2015 version documentation</title>
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<div class="section" id="compute-displace-atom-command">
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<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>
|
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<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>
|
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<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
|
||||
<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 “unwrapped” 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 “unwrapped” 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>
|
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a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
|
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|
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options.
|
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</P>
|
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<P>The per-atom array values will be in distance <A HREF = "units.html">units</A>.
|
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|
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|
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|
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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
|
||||
<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 “extensive”. 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>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
</div>
|
||||
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|
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the <A HREF = "atom_style.html">atom_style tri</A> command.
|
||||
</P>
|
||||
<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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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</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_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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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,
|
||||
<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 “extensive”. 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>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
</div>
|
||||
<footer>
|
||||
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||||
|
||||
<hr/>
|
||||
|
||||
<div role="contentinfo">
|
||||
<p>
|
||||
© 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>.
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|
||||
</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>
|
||||
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|
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<P>This compute is part of the RIGID package. It is only enabled if
|
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|
||||
LAMMPS</A> section for more info.
|
||||
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|
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<P><B>Related commands:</B>
|
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|
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<P><A HREF = "compute_erotate_ke_rigid.html">compute ke/rigid</A>
|
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<li>compute erotate/sphere command</li>
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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’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
|
||||
<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 “extensive”. 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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|
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|
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contribute to the rotational energy.
|
||||
</P>
|
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<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "compute_erotate_asphere.html">compute erotate/asphere</A>
|
||||
</P>
|
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|
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<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_perf.html">8. Performance & scalability</a></li>
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||||
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|
||||
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|
||||
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|
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|
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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’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
|
||||
<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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|
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|
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|
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|
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</P>
|
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<P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.
|
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</P>
|
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<P><B>Restrictions:</B> none
|
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|
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|
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|
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<div class="section" id="compute-event-displace-command">
|
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<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 “event” if any particle in the
|
||||
<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,
|
||||
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 “false postives.”</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 “intensive”. 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>
|
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input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
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<P>The scalar value calculated by this compute is "intensive". The
|
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|
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|
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<P>This command can only be used if LAMMPS was built with the REPLICA
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<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
|
||||
|
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<LI>attribute = <I>pair</I> or <I>atom</I>
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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
|
||||
<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
|
||||
</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></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
|
||||
</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’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*<sub>0</sub> 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*<sub>1</sub> 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 &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 λ 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. &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. σ 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 &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*<sub>i</sub> 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
|
||||
&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*<sub>1</sub>-<a href="#id9"><span class="problematic" id="id10">*</span></a>U*<sub>0</sub>. By
|
||||
choosing a very small perturbation &delta; the thermodynamic
|
||||
perturbation method using a very small δ:
|
||||
</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
|
||||
λ 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 δ the thermodynamic
|
||||
integration method can be implemented using a numerical evaluation of
|
||||
the derivative of the potential energy with respect to &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 &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 λ:
|
||||
</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 δ = 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 “lj/cut”. 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 <= 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 “*” or “<em>n” or “n</em>” or “m*n”. 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 <= J are considered; if
|
||||
asterisks imply type pairs where J < 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
|
||||
“van der Waals” 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*<sub>1</sub>-*U*<sub>0</sub>) as c_ID[1], the
|
||||
Boltzmann factor exp(-(*U*<sub>1</sub>-*U*<sub>0</sub>)/*kT</em>), or
|
||||
<em>V*exp(-(*U*<sub>1</sub>-*U*<sub>0</sub>)/*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*<sub>1</sub> 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*<sub>0</sub> 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 “extensive”.</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>
|
||||
|
||||
<P><B>(Mezei)</B> Mezei, J Chem Phys, 86, 7084 (1987)
|
||||
</P>
|
||||
<A NAME = "Bennet"></A>
|
||||
|
||||
<hr/>
|
||||
<P><B>(Bennet)</B> Bennet, J Comput Phys, 22, 245 (1976)
|
||||
</P>
|
||||
<A NAME = "BoreschKarplus"></A>
|
||||
|
||||
<div role="contentinfo">
|
||||
<p>
|
||||
© 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>(BoreschKarplus)</B> Boresch and Karplus, J Phys Chem A, 103, 103 (1999)
|
||||
</P>
|
||||
<A NAME = "AllenTildesley"></A>
|
||||
|
||||
</footer>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
|
||||
</section>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<script type="text/javascript">
|
||||
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|
||||
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|
||||
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<H3>compute group/group command
|
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</H3>
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<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>
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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_perf.html">8. Performance & scalability</a></li>
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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
|
||||
</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
|
||||
</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
|
||||
“extensive”. 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)
|
||||
</P>
|
||||
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|
||||
|
||||
@ -1,257 +1,78 @@
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<div class="section" id="compute-gyration-command">
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<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
|
||||
<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 “squared” 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
|
||||
“unwrapped” 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
|
||||
“unwrapped” 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
|
||||
“intensive”. 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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|
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vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
|
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15</A> for an overview of LAMMPS output
|
||||
options.
|
||||
</P>
|
||||
<P>The scalar and vector values calculated by this compute are
|
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"intensive". The scalar and vector values will be in distance and
|
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distance^2 <A HREF = "units.html">units</A> respectively.
|
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</P>
|
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<P><B>Restrictions:</B> none
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|
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<P><B>Related commands:</B>
|
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</P>
|
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<P><A HREF = "compute_gyration_chunk.html">compute gyration/chunk</A>
|
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</P>
|
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<P><B>Default:</B> none
|
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<title>compute gyration/chunk command — LAMMPS 15 May 2015 version documentation</title>
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<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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|
||||
<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>
|
||||
|
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<PRE> <I>tensor</I> value = none
|
||||
</PRE>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<div class="section" id="compute-gyration-chunk-command">
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<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
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<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
|
||||
</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 “<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
|
||||
“all” 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
|
||||
“unwrapped” 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
|
||||
“unwrapped” 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
|
||||
</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
|
||||
“intensive”. 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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|
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<P>All the vector or array values calculated by this compute are
|
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"intensive". The vector or array values will be in distance
|
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<A HREF = "units.html">units</A>, since they are the square root of values
|
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<P><A HREF = "compute_gyration.html">compute gyration</A>
|
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|
||||
<hr/>
|
||||
|
||||
</div>
|
||||
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
|
||||
<div itemprop="articleBody">
|
||||
|
||||
<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
|
||||
<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 “extensive”, 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 “intensive” value, meaning independent of the number of atoms in
|
||||
the simulation. Note that if the compute is “all”, 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
|
||||
</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
|
||||
</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
|
||||
@ -265,24 +157,19 @@ 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
|
||||
</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
|
||||
</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 &
|
||||
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 "average conductivity: $k[W/mK] @ $T K, ${ndens} /A^3"
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
</div>
|
||||
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|
||||
|
||||
|
||||
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|
||||
|
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|
||||
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|
||||
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|
||||
print "average conductivity: $k[W/mK] @ $T K, ${ndens} /A^3"
|
||||
</PRE>
|
||||
</HTML>
|
||||
|
||||
@ -1,253 +1,79 @@
|
||||
|
||||
|
||||
<!DOCTYPE html>
|
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||||
<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>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<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_packages.html">4. Packages</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_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to 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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||||
<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
|
||||
</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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|
||||
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|
||||
|
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|
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|
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uses local values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
|
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section</A> for an overview of LAMMPS output
|
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options.
|
||||
</P>
|
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<P>The output for <I>chi</I> will be in degrees.
|
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</P>
|
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<P><B>Restrictions:</B> none
|
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|
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|
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<P><A HREF = "dump.html">dump local</A>, <A HREF = "compute_property_local.html">compute
|
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property/local</A>
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<div class="section" id="compute-inertia-chunk-command">
|
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<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
|
||||
<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 “<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
|
||||
“all” 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’s
|
||||
inertia tensor in “unwrapped” 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 “unwrapped” 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 =
|
||||
</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 “intensive”. 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>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
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|
||||
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uses global array values from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
|
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15</A> for an overview of LAMMPS output
|
||||
options.
|
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</P>
|
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<P>The array values are "intensive". The array values will be in
|
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mass*distance^2 <A HREF = "units.html">units</A>.
|
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|
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<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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|
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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>
|
||||
<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 “translational” 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 “extensive”. 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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|
||||
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|
||||
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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
|
||||
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@ -1,234 +1,53 @@
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|
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||||
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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
|
||||
<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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|
||||
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|
||||
|
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|
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|
||||
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|
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|
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|
||||
</P>
|
||||
<P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
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|
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|
||||
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@ -1,261 +1,82 @@
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<div class="section" id="compute-ke-atom-eff-command">
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<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
|
||||
<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 “translational” plus electronic “radial” 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
|
||||
<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></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
|
||||
</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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|
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LAMMPS output options.
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</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
|
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LAMMPS</A> section for more info.
|
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|
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<div class="section" id="compute-ke-eff-command">
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<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
|
||||
<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 “translational” and “radial” (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
|
||||
<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></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
|
||||
</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 “extensive”. 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>
|
||||
</div>
|
||||
</div>
|
||||
|
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|
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|
||||
</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
|
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|
||||
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|
||||
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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,
|
||||
<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 “extensive”. 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>
|
||||
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|
||||
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|
||||
|
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|
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|
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|
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</script>
|
||||
|
||||
|
||||
</body>
|
||||
</html>
|
||||
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>
|
||||
</HTML>
|
||||
|
||||
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Reference in New Issue
Block a user