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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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<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</h1>
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<div class="section" id="may-2016-version">
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<h2>3 May 2016 version</h2>
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</div>
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<div class="section" id="version-info">
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<h2>Version info:</h2>
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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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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
|
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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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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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||||
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
|
||||
Thompson, and Paul Crozier who can be contacted at
|
||||
sjplimp,athomps,pscrozi at sandia.gov. The <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> at
|
||||
<a class="reference external" href="http://lammps.sandia.gov">http://lammps.sandia.gov</a> has more information about the code and its
|
||||
uses.</p>
|
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<hr class="docutils" />
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<p>The LAMMPS documentation is organized into the following sections. If
|
||||
you find errors or omissions in this manual or have suggestions for
|
||||
useful information to add, please send an email to the developers so
|
||||
we can improve the LAMMPS documentation.</p>
|
||||
<p>Once you are familiar with LAMMPS, you may want to bookmark <a class="reference internal" href="Section_commands.html#comm"><span class="std std-ref">this page</span></a> at Section_commands.html#comm since
|
||||
it gives quick access to documentation for all LAMMPS commands.</p>
|
||||
<p><a class="reference external" href="Manual.pdf">PDF file</a> of the entire manual, generated by
|
||||
<a class="reference external" href="http://freecode.com/projects/htmldoc">htmldoc</a></p>
|
||||
<div class="toctree-wrapper compound">
|
||||
<ul>
|
||||
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a><ul>
|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#what-is-lammps">1.1. What is LAMMPS</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-features">1.2. LAMMPS features</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-non-features">1.3. LAMMPS non-features</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#open-source-distribution">1.4. Open source distribution</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#acknowledgments-and-citations">1.5. Acknowledgments and citations</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a><ul>
|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#what-s-in-the-lammps-distribution">2.1. What’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-tool">2.4. Building LAMMPS via the Make.py tool</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>
|
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</ul>
|
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</li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a><ul>
|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#lammps-input-script">3.1. LAMMPS input script</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#parsing-rules">3.2. Parsing rules</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#input-script-structure">3.3. Input script structure</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#commands-listed-by-category">3.4. Commands listed by category</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#individual-commands">3.5. Individual commands</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#fix-styles">3.6. Fix styles</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#compute-styles">3.7. Compute styles</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#pair-style-potentials">3.8. Pair_style potentials</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#bond-style-potentials">3.9. Bond_style potentials</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#angle-style-potentials">3.10. Angle_style potentials</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#dihedral-style-potentials">3.11. Dihedral_style potentials</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#improper-style-potentials">3.12. Improper_style potentials</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#kspace-solvers">3.13. Kspace solvers</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a><ul>
|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#standard-packages">4.1. Standard packages</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-packages">4.2. User packages</a></li>
|
||||
</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>
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||||
<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>
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||||
<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>
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||||
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#drude-induced-dipoles">6.27. Drude induced dipoles</a></li>
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||||
</ul>
|
||||
</li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a><ul>
|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_example.html#lowercase-directories">7.1. Lowercase directories</a></li>
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||||
<li class="toctree-l2"><a class="reference internal" href="Section_example.html#uppercase-directories">7.2. Uppercase directories</a></li>
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||||
</ul>
|
||||
</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><ul>
|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#amber2lmp-tool">9.1. amber2lmp tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#binary2txt-tool">9.2. binary2txt tool</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ch2lmp-tool">9.3. ch2lmp tool</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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|
||||
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|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#emacs-tool">9.11. emacs tool</a></li>
|
||||
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|
||||
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|
||||
<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>
|
||||
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|
||||
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|
||||
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a><ul>
|
||||
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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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|
||||
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#pairwise-potentials">10.10. Pairwise potentials</a></li>
|
||||
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|
||||
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|
||||
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|
||||
<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>
|
||||
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|
||||
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|
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<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>
|
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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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|
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|
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|
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|
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<div class="section" id="accelerating-lammps-performance">
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<h1>5. Accelerating LAMMPS performance</h1>
|
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<p>This section describes various methods for improving LAMMPS
|
||||
performance for different classes of problems running on different
|
||||
kinds of machines.</p>
|
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<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 class="std std-ref">Measuring performance</span></a></li>
|
||||
<li>5.2 <a class="reference internal" href="#acc-2"><span class="std std-ref">Algorithms and code options to boost performace</span></a></li>
|
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<li>5.3 <a class="reference internal" href="#acc-3"><span class="std std-ref">Accelerator packages with optimized styles</span></a></li>
|
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|
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|
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<li>5.3.3 <a class="reference internal" href="accelerate_intel.html"><span class="doc">USER-INTEL package</span></a></li>
|
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<li>5.3.4 <a class="reference internal" href="accelerate_kokkos.html"><span class="doc">KOKKOS package</span></a></li>
|
||||
<li>5.3.5 <a class="reference internal" href="accelerate_omp.html"><span class="doc">USER-OMP package</span></a></li>
|
||||
<li>5.3.6 <a class="reference internal" href="accelerate_opt.html"><span class="doc">OPT package</span></a></li>
|
||||
<li>5.4 <a class="reference internal" href="#acc-4"><span class="std std-ref">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
|
||||
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</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
|
||||
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 class="std std-ref">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
|
||||
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
|
||||
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
|
||||
dominating, you may want to look at GPU or OMP versions of the pair
|
||||
style, as discussed below. Comparing how the percentages change as
|
||||
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
|
||||
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
|
||||
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</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.
|
||||
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>
|
||||
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
|
||||
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
|
||||
staggered PPPM allows one to half the mesh size in each dimension as
|
||||
compared to regular PPPM, which can give around a 4x speedup in the
|
||||
kspace time. However, for low relative accuracy, using staggered PPPM
|
||||
gives little benefit and can be up to 2x slower in the kspace
|
||||
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 note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">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</h2>
|
||||
<p>Accelerated versions of various <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a>,
|
||||
<a class="reference internal" href="fix.html"><span class="doc">fixes</span></a>, <a class="reference internal" href="compute.html"><span class="doc">computes</span></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"><span class="doc">Section packages</span></a>.</p>
|
||||
<p>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"><span class="doc">USER-CUDA</span></a></td>
|
||||
<td>for NVIDIA GPUs</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="accelerate_gpu.html"><span class="doc">GPU</span></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"><span class="doc">USER-INTEL</span></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"><span class="doc">KOKKOS</span></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"><span class="doc">USER-OMP</span></a></td>
|
||||
<td>for OpenMP threading</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="accelerate_opt.html"><span class="doc">OPT</span></a></td>
|
||||
<td>generic CPU optimizations</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>Inverting this list, LAMMPS currently has acceleration support for
|
||||
three kinds of hardware, via the listed packages:</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="10%" />
|
||||
<col width="90%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td>Many-core CPUs</td>
|
||||
<td><a class="reference internal" href="accelerate_intel.html"><span class="doc">USER-INTEL</span></a>, <a class="reference internal" href="accelerate_kokkos.html"><span class="doc">KOKKOS</span></a>, <a class="reference internal" href="accelerate_omp.html"><span class="doc">USER-OMP</span></a>, <a class="reference internal" href="accelerate_opt.html"><span class="doc">OPT</span></a> packages</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>NVIDIA GPUs</td>
|
||||
<td><a class="reference internal" href="accelerate_cuda.html"><span class="doc">USER-CUDA</span></a>, <a class="reference internal" href="accelerate_gpu.html"><span class="doc">GPU</span></a>, <a class="reference internal" href="accelerate_kokkos.html"><span class="doc">KOKKOS</span></a> packages</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>Intel Phi</td>
|
||||
<td><a class="reference internal" href="accelerate_intel.html"><span class="doc">USER-INTEL</span></a>, <a class="reference internal" href="accelerate_kokkos.html"><span class="doc">KOKKOS</span></a> packages</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>Which package is fastest for your hardware may depend on the size
|
||||
problem you are running and what commands (accelerated and
|
||||
non-accelerated) are invoked by your input script. While these doc
|
||||
pages include performance guidelines, there is no substitute for
|
||||
trying out the different packages appropriate to your hardware.</p>
|
||||
<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"><span class="doc">pair_style lj/cut</span></a>:</p>
|
||||
<ul class="simple">
|
||||
<li><a class="reference internal" href="pair_lj.html"><span class="doc">pair_style lj/cut/cuda</span></a></li>
|
||||
<li><a class="reference internal" href="pair_lj.html"><span class="doc">pair_style lj/cut/gpu</span></a></li>
|
||||
<li><a class="reference internal" href="pair_lj.html"><span class="doc">pair_style lj/cut/intel</span></a></li>
|
||||
<li><a class="reference internal" href="pair_lj.html"><span class="doc">pair_style lj/cut/kk</span></a></li>
|
||||
<li><a class="reference internal" href="pair_lj.html"><span class="doc">pair_style lj/cut/omp</span></a></li>
|
||||
<li><a class="reference internal" href="pair_lj.html"><span class="doc">pair_style lj/cut/opt</span></a></li>
|
||||
</ul>
|
||||
<p>To see what accelerate styles are currently available, see
|
||||
<a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">Section_commands 5</span></a> of the manual. The
|
||||
doc pages for individual commands (e.g. <a class="reference internal" href="pair_lj.html"><span class="doc">pair lj/cut</span></a> or
|
||||
<a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></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, OPT 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>
|
||||
</tbody>
|
||||
</table>
|
||||
<div class="line-block">
|
||||
<div class="line">re-build LAMMPS | make machine |</div>
|
||||
</div>
|
||||
<blockquote>
|
||||
<div>mpirun -np 32 lmp_machine -in in.script |</div></blockquote>
|
||||
<blockquote>
|
||||
<div>only for USER-CUDA and KOKKOS packages |</div></blockquote>
|
||||
<blockquote>
|
||||
<div><a class="reference internal" href="package.html"><span class="doc">package</span></a> command, <br>
|
||||
only if defaults need to be changed |</div></blockquote>
|
||||
<blockquote>
|
||||
<div><a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command |</div></blockquote>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
</tbody>
|
||||
</table>
|
||||
<p>Note that the first 4 steps can be done as a single command, using the
|
||||
src/Make.py tool. This tool is discussed in <a class="reference internal" href="Section_start.html#start-4"><span class="std std-ref">Section 2.4</span></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
|
||||
launched, without changing your input script, as illustrated in the
|
||||
individual accelerator sections. Or you can add
|
||||
<a class="reference internal" href="package.html"><span class="doc">package</span></a> and <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> commands to your input
|
||||
script.</p>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">With a few exceptions, you can build a single LAMMPS executable
|
||||
with all its accelerator packages installed. Note however that the
|
||||
USER-INTEL and KOKKOS packages require you to choose one of their
|
||||
hardware options when building for a specific platform. I.e. CPU or
|
||||
Phi option for the USER-INTEL package. Or the OpenMP, Cuda, or Phi
|
||||
option for the KOKKOS package.</p>
|
||||
</div>
|
||||
<p>These are the exceptions. You cannot build a single executable with:</p>
|
||||
<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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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)
|
||||
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
|
||||
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
|
||||
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
|
||||
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</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
|
||||
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,
|
||||
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
|
||||
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)
|
||||
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
|
||||
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 smaller. 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
|
||||
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
|
||||
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
|
||||
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
|
||||
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</h3>
|
||||
<p>The LAMMPS distribution has two directories with sample input scripts
|
||||
for the GPU and USER-CUDA packages.</p>
|
||||
<ul class="simple">
|
||||
<li>lammps/examples/gpu = GPU package files</li>
|
||||
<li>lammps/examples/USER/cuda = USER-CUDA package files</li>
|
||||
</ul>
|
||||
<p>These contain input scripts for identical systems, so they can be used
|
||||
to benchmark the performance of both packages on your system.</p>
|
||||
</div>
|
||||
</div>
|
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<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 current"><a class="current reference internal" href="#">7. Example problems</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="#uppercase-directories">7.2. Uppercase directories</a></li>
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||||
<div class="section" id="example-problems">
|
||||
<h1>7. Example problems</h1>
|
||||
<p>The LAMMPS distribution includes an examples sub-directory with many
|
||||
sample problems. Many are 2d models that run quickly are are
|
||||
straightforward to visualize, requiring at most a couple of minutes to
|
||||
run on a desktop machine. Each problem has an input script (in.*) and
|
||||
produces a log file (log.*) when it runs. Some use a data file
|
||||
(data.*) of initial coordinates as additional input. A few sample log
|
||||
file run 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.date.crack.foo.P means the “crack” example was run on P
|
||||
processors of machine “foo” on that date (i.e. with that version of
|
||||
LAMMPS).</p>
|
||||
<p>Many of the input files have commented-out lines for creating dump
|
||||
files and image files.</p>
|
||||
<p>If you uncomment the <a class="reference internal" href="dump.html"><span class="doc">dump</span></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"><span class="doc">Additional Tools</span></a> section of the LAMMPS documentation.</p>
|
||||
<p>If you uncomment the <a class="reference internal" href="dump.html"><span class="doc">dump image</span></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"><span class="doc">dump image</span></a> doc page.</p>
|
||||
<p>Animations of many of the examples can be viewed on the Movies section
|
||||
of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS web site</a>.</p>
|
||||
<p>There are two kinds of sub-directories in the examples dir. Lowercase
|
||||
dirs contain one or a few simple, quick-to-run problems. Uppercase
|
||||
dirs contain up to several complex scripts that illustrate a
|
||||
particular kind of simulation method or model. Some of these run for
|
||||
longer times, e.g. to measure a particular quantity.</p>
|
||||
<p>Lists of both kinds of directories are given below.</p>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="lowercase-directories">
|
||||
<h2>7.1. Lowercase directories</h2>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="16%" />
|
||||
<col width="84%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td>accelerate</td>
|
||||
<td>run with various acceleration options (OpenMP, GPU, Phi)</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>balance</td>
|
||||
<td>dynamic load balancing, 2d system</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>body</td>
|
||||
<td>body particles, 2d system</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>colloid</td>
|
||||
<td>big colloid particles in a small particle solvent, 2d system</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>comb</td>
|
||||
<td>models using the COMB potential</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>coreshell</td>
|
||||
<td>core/shell model using CORESHELL package</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>deposit</td>
|
||||
<td>deposit atoms and molecules on a surface</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>dipole</td>
|
||||
<td>point dipolar particles, 2d system</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>dreiding</td>
|
||||
<td>methanol via Dreiding FF</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>eim</td>
|
||||
<td>NaCl using the EIM potential</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>ellipse</td>
|
||||
<td>ellipsoidal particles in spherical solvent, 2d system</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>flow</td>
|
||||
<td>Couette and Poiseuille flow in a 2d channel</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>friction</td>
|
||||
<td>frictional contact of spherical asperities between 2d surfaces</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>kim</td>
|
||||
<td>use of potentials in Knowledge Base for Interatomic Models (KIM)</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>python</td>
|
||||
<td>using embedded Python in a LAMMPS input script</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>qeq</td>
|
||||
<td>use of the QEQ package for charge equilibration</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>reax</td>
|
||||
<td>RDX and TATB models using the ReaxFF</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>rigid</td>
|
||||
<td>rigid bodies modeled as independent or coupled</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>shear</td>
|
||||
<td>sideways shear applied to 2d solid, with and without a void</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>snap</td>
|
||||
<td>NVE dynamics for BCC tantalum crystal using SNAP potential</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>srd</td>
|
||||
<td>stochastic rotation dynamics (SRD) particles as solvent</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>streitz</td>
|
||||
<td>use of Streitz/Mintmire potential with charge equilibration</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>vashishta</td>
|
||||
<td>use of the Vashishta potential</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>Here is how you can run and visualize one of the sample problems:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">indent</span>
|
||||
<span class="n">cp</span> <span class="o">../../</span><span class="n">src</span><span class="o">/</span><span class="n">lmp_linux</span> <span class="o">.</span> <span class="c1"># copy LAMMPS executable to this dir</span>
|
||||
<span class="n">lmp_linux</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">indent</span> <span class="c1"># run the problem</span>
|
||||
</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 of snapshots with a
|
||||
variety of 3rd-party tools highlighted on the
|
||||
<a class="reference external" href="http://lammps.sandia.gov/viz.html">Visualization</a> page of the LAMMPS
|
||||
web site.</p>
|
||||
<p>If you uncomment the <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> line(s) in the input
|
||||
script a series of JPG images will be produced by the run (assuming
|
||||
you built LAMMPS with JPG support; see <a class="reference internal" href="Section_start.html"><span class="doc">Section start 2.2</span></a> for details). 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"><span class="doc">dump image</span></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-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">convert</span> <span class="o">-</span><span class="n">loop</span> <span class="mi">1</span> <span class="o">*.</span><span class="n">jpg</span> <span class="n">foo</span><span class="o">.</span><span class="n">gif</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="uppercase-directories">
|
||||
<h2>7.2. Uppercase directories</h2>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="10%" />
|
||||
<col width="90%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td>ASPHERE</td>
|
||||
<td>various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>COUPLE</td>
|
||||
<td>examples of how to use LAMMPS as a library</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>DIFFUSE</td>
|
||||
<td>compute diffusion coefficients via several methods</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>ELASTIC</td>
|
||||
<td>compute elastic constants at zero temperature</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>ELASTIC_T</td>
|
||||
<td>compute elastic constants at finite temperature</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>KAPPA</td>
|
||||
<td>compute thermal conductivity via several methods</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>MC</td>
|
||||
<td>using LAMMPS in a Monte Carlo mode to relax the energy of a system</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>USER</td>
|
||||
<td>examples for USER packages and USER-contributed commands</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>VISCOSITY</td>
|
||||
<td>compute viscosity via several methods</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>Nearly all of these directories have README files which give more
|
||||
details on how to understand and use their contents.</p>
|
||||
<p>The USER directory has a large number of sub-directories which
|
||||
correspond by name to a USER package. They contain scripts that
|
||||
illustrate how to use the command(s) provided in that package. Many
|
||||
of the sub-directories have their own README files which give further
|
||||
instructions. See the <a class="reference internal" href="Section_packages.html"><span class="doc">Section packages</span></a> doc
|
||||
page for more info on specific USER packages.</p>
|
||||
</div>
|
||||
</div>
|
||||
|
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|
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|
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<a href="Section_perf.html" class="btn btn-neutral float-right" title="8. Performance & scalability" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
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|
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|
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<p>
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© Copyright 2013 Sandia Corporation.
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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_modify.html">10. Modifying & extending LAMMPS</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</h1>
|
||||
<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 class="std std-ref">Coming attractions</span></a></div>
|
||||
<div class="line">13.2 <a class="reference internal" href="#hist-2"><span class="std std-ref">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</h2>
|
||||
<p>The <a class="reference external" 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</h2>
|
||||
<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
|
||||
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
|
||||
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
|
||||
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
|
||||
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>
|
||||
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<li class="toctree-l1 current"><a class="current reference internal" href="#">1. Introduction</a><ul>
|
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<li class="toctree-l2"><a class="reference internal" href="#what-is-lammps">1.1. What is LAMMPS</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#lammps-features">1.2. LAMMPS features</a><ul>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#general-features">1.2.1. General features</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#particle-and-model-types">1.2.2. Particle and model types</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#force-fields">1.2.3. Force fields</a></li>
|
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<li class="toctree-l3"><a class="reference internal" href="#atom-creation">1.2.4. Atom creation</a></li>
|
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<li class="toctree-l3"><a class="reference internal" href="#ensembles-constraints-and-boundary-conditions">1.2.5. Ensembles, constraints, and boundary conditions</a></li>
|
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<li class="toctree-l3"><a class="reference internal" href="#integrators">1.2.6. Integrators</a></li>
|
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<li class="toctree-l3"><a class="reference internal" href="#diagnostics">1.2.7. Diagnostics</a></li>
|
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<li class="toctree-l3"><a class="reference internal" href="#output">1.2.8. Output</a></li>
|
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<li class="toctree-l3"><a class="reference internal" href="#multi-replica-models">1.2.9. Multi-replica models</a></li>
|
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<li class="toctree-l3"><a class="reference internal" href="#pre-and-post-processing">1.2.10. Pre- and post-processing</a></li>
|
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<li class="toctree-l3"><a class="reference internal" href="#specialized-features">1.2.11. Specialized features</a></li>
|
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</ul>
|
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</li>
|
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<li class="toctree-l2"><a class="reference internal" href="#lammps-non-features">1.3. LAMMPS non-features</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="#open-source-distribution">1.4. Open source distribution</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="#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></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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||||
<div class="section" id="introduction">
|
||||
<h1>1. Introduction</h1>
|
||||
<p>This section provides an overview of what LAMMPS can and can’t do,
|
||||
describes what it means for LAMMPS to be an open-source code, and
|
||||
acknowledges the funding and people who have contributed to LAMMPS
|
||||
over the years.</p>
|
||||
<div class="line-block">
|
||||
<div class="line">1.1 <a class="reference internal" href="#intro-1"><span class="std std-ref">What is LAMMPS</span></a></div>
|
||||
<div class="line">1.2 <a class="reference internal" href="#intro-2"><span class="std std-ref">LAMMPS features</span></a></div>
|
||||
<div class="line">1.3 <a class="reference internal" href="#intro-3"><span class="std std-ref">LAMMPS non-features</span></a></div>
|
||||
<div class="line">1.4 <a class="reference internal" href="#intro-4"><span class="std std-ref">Open source distribution</span></a></div>
|
||||
<div class="line">1.5 <a class="reference internal" href="#intro-5"><span class="std std-ref">Acknowledgments and citations</span></a></div>
|
||||
<div class="line"><br /></div>
|
||||
</div>
|
||||
<div class="section" id="what-is-lammps">
|
||||
<span id="intro-1"></span><h2>1.1. What is LAMMPS</h2>
|
||||
<p>LAMMPS is a classical molecular dynamics code that models an ensemble
|
||||
of particles in a liquid, solid, or gaseous state. It can model
|
||||
atomic, polymeric, biological, metallic, granular, and coarse-grained
|
||||
systems using a variety of force fields and boundary conditions.</p>
|
||||
<p>For examples of LAMMPS simulations, see the Publications page of the
|
||||
<a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>.</p>
|
||||
<p>LAMMPS runs efficiently on single-processor desktop or laptop
|
||||
machines, but is designed for parallel computers. It will run on any
|
||||
parallel machine that compiles C++ and supports the <a class="reference external" href="http://www-unix.mcs.anl.gov/mpi">MPI</a>
|
||||
message-passing library. This includes distributed- or shared-memory
|
||||
parallel machines and Beowulf-style clusters.</p>
|
||||
<p>LAMMPS can model systems with only a few particles up to millions or
|
||||
billions. See <a class="reference internal" href="Section_perf.html"><span class="doc">Section_perf</span></a> for information on
|
||||
LAMMPS performance and scalability, or the Benchmarks section of the
|
||||
<a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>.</p>
|
||||
<p>LAMMPS is a freely-available open-source code, distributed under the
|
||||
terms of the <a class="reference external" href="http://www.gnu.org/copyleft/gpl.html">GNU Public License</a>, which means you can use or
|
||||
modify the code however you wish. See <a class="reference internal" href="#intro-4"><span class="std std-ref">this section</span></a> for a
|
||||
brief discussion of the open-source philosophy.</p>
|
||||
<p>LAMMPS is designed to be easy to modify or extend with new
|
||||
capabilities, such as new force fields, atom types, boundary
|
||||
conditions, or diagnostics. See <a class="reference internal" href="Section_modify.html"><span class="doc">Section_modify</span></a>
|
||||
for more details.</p>
|
||||
<p>The current version of LAMMPS is written in C++. Earlier versions
|
||||
were written in F77 and F90. See
|
||||
<a class="reference internal" href="Section_history.html"><span class="doc">Section_history</span></a> for more information on
|
||||
different versions. All versions can be downloaded from the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>.</p>
|
||||
<p>LAMMPS was originally developed under a US Department of Energy CRADA
|
||||
(Cooperative Research and Development Agreement) between two DOE labs
|
||||
and 3 companies. It is distributed by <a class="reference external" href="http://www.sandia.gov">Sandia National Labs</a>.
|
||||
See <a class="reference internal" href="#intro-5"><span class="std std-ref">this section</span></a> for more information on LAMMPS funding and
|
||||
individuals who have contributed to LAMMPS.</p>
|
||||
<p>In the most general sense, LAMMPS integrates Newton’s equations of
|
||||
motion for collections of atoms, molecules, or macroscopic particles
|
||||
that interact via short- or long-range forces with a variety of
|
||||
initial and/or boundary conditions. For computational efficiency
|
||||
LAMMPS uses neighbor lists to keep track of nearby particles. The
|
||||
lists are optimized for systems with particles that are repulsive at
|
||||
short distances, so that the local density of particles never becomes
|
||||
too large. On parallel machines, LAMMPS uses spatial-decomposition
|
||||
techniques to partition the simulation domain into small 3d
|
||||
sub-domains, one of which is assigned to each processor. Processors
|
||||
communicate and store “ghost” atom information for atoms that border
|
||||
their sub-domain. LAMMPS is most efficient (in a parallel sense) for
|
||||
systems whose particles fill a 3d rectangular box with roughly uniform
|
||||
density. Papers with technical details of the algorithms used in
|
||||
LAMMPS are listed in <a class="reference internal" href="#intro-5"><span class="std std-ref">this section</span></a>.</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="lammps-features">
|
||||
<span id="intro-2"></span><h2>1.2. LAMMPS features</h2>
|
||||
<p>This section highlights LAMMPS features, with pointers to specific
|
||||
commands which give more details. If LAMMPS doesn’t have your
|
||||
favorite interatomic potential, boundary condition, or atom type, see
|
||||
<a class="reference internal" href="Section_modify.html"><span class="doc">Section_modify</span></a>, which describes how you can add
|
||||
it to LAMMPS.</p>
|
||||
<div class="section" id="general-features">
|
||||
<h3>1.2.1. General features</h3>
|
||||
<ul class="simple">
|
||||
<li>runs on a single processor or in parallel</li>
|
||||
<li>distributed-memory message-passing parallelism (MPI)</li>
|
||||
<li>spatial-decomposition of simulation domain for parallelism</li>
|
||||
<li>open-source distribution</li>
|
||||
<li>highly portable C++</li>
|
||||
<li>optional libraries used: MPI and single-processor FFT</li>
|
||||
<li>GPU (CUDA and OpenCL), Intel(R) Xeon Phi(TM) coprocessors, and OpenMP support for many code features</li>
|
||||
<li>easy to extend with new features and functionality</li>
|
||||
<li>runs from an input script</li>
|
||||
<li>syntax for defining and using variables and formulas</li>
|
||||
<li>syntax for looping over runs and breaking out of loops</li>
|
||||
<li>run one or multiple simulations simultaneously (in parallel) from one script</li>
|
||||
<li>build as library, invoke LAMMPS thru library interface or provided Python wrapper</li>
|
||||
<li>couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="particle-and-model-types">
|
||||
<h3>1.2.2. Particle and model types</h3>
|
||||
<p>(<a class="reference internal" href="atom_style.html"><span class="doc">atom style</span></a> command)</p>
|
||||
<ul class="simple">
|
||||
<li>atoms</li>
|
||||
<li>coarse-grained particles (e.g. bead-spring polymers)</li>
|
||||
<li>united-atom polymers or organic molecules</li>
|
||||
<li>all-atom polymers, organic molecules, proteins, DNA</li>
|
||||
<li>metals</li>
|
||||
<li>granular materials</li>
|
||||
<li>coarse-grained mesoscale models</li>
|
||||
<li>finite-size spherical and ellipsoidal particles</li>
|
||||
<li>finite-size line segment (2d) and triangle (3d) particles</li>
|
||||
<li>point dipole particles</li>
|
||||
<li>rigid collections of particles</li>
|
||||
<li>hybrid combinations of these</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="force-fields">
|
||||
<h3>1.2.3. Force fields</h3>
|
||||
<p>(<a class="reference internal" href="pair_style.html"><span class="doc">pair style</span></a>, <a class="reference internal" href="bond_style.html"><span class="doc">bond style</span></a>,
|
||||
<a class="reference internal" href="angle_style.html"><span class="doc">angle style</span></a>, <a class="reference internal" href="dihedral_style.html"><span class="doc">dihedral style</span></a>,
|
||||
<a class="reference internal" href="improper_style.html"><span class="doc">improper style</span></a>, <a class="reference internal" href="kspace_style.html"><span class="doc">kspace style</span></a>
|
||||
commands)</p>
|
||||
<ul class="simple">
|
||||
<li>pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated</li>
|
||||
<li>charged pairwise potentials: Coulombic, point-dipole</li>
|
||||
<li>manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic</li>
|
||||
<li>long-range interactions for charge, point-dipoles, and LJ dispersion: Ewald, Wolf, PPPM (similar to particle-mesh Ewald)</li>
|
||||
<li>polarization models: <a class="reference internal" href="fix_qeq.html"><span class="doc">QEq</span></a>, <a class="reference internal" href="Section_howto.html#howto-26"><span class="std std-ref">core/shell model</span></a>, <a class="reference internal" href="Section_howto.html#howto-27"><span class="std std-ref">Drude dipole model</span></a></li>
|
||||
<li>charge equilibration (QEq via dynamic, point, shielded, Slater methods)</li>
|
||||
<li>coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO</li>
|
||||
<li>mesoscopic potentials: granular, Peridynamics, SPH</li>
|
||||
<li>electron force field (eFF, AWPMD)</li>
|
||||
<li>bond potentials: harmonic, FENE, Morse, nonlinear, class 2, quartic (breakable)</li>
|
||||
<li>angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, class 2 (COMPASS)</li>
|
||||
<li>dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, class 2 (COMPASS), OPLS</li>
|
||||
<li>improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS)</li>
|
||||
<li>polymer potentials: all-atom, united-atom, bead-spring, breakable</li>
|
||||
<li>water potentials: TIP3P, TIP4P, SPC</li>
|
||||
<li>implicit solvent potentials: hydrodynamic lubrication, Debye</li>
|
||||
<li>force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options</li>
|
||||
<li>access to <a class="reference external" href="http://openkim.org">KIM archive</a> of potentials via <a class="reference internal" href="pair_kim.html"><span class="doc">pair kim</span></a></li>
|
||||
<li>hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation</li>
|
||||
<li>overlaid potentials: superposition of multiple pair potentials</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="atom-creation">
|
||||
<h3>1.2.4. Atom creation</h3>
|
||||
<p>(<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>, <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a>,
|
||||
<a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a>, <a class="reference internal" href="delete_atoms.html"><span class="doc">delete_atoms</span></a>,
|
||||
<a class="reference internal" href="displace_atoms.html"><span class="doc">displace_atoms</span></a>, <a class="reference internal" href="replicate.html"><span class="doc">replicate</span></a> commands)</p>
|
||||
<ul class="simple">
|
||||
<li>read in atom coords from files</li>
|
||||
<li>create atoms on one or more lattices (e.g. grain boundaries)</li>
|
||||
<li>delete geometric or logical groups of atoms (e.g. voids)</li>
|
||||
<li>replicate existing atoms multiple times</li>
|
||||
<li>displace atoms</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="ensembles-constraints-and-boundary-conditions">
|
||||
<h3>1.2.5. Ensembles, constraints, and boundary conditions</h3>
|
||||
<p>(<a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command)</p>
|
||||
<ul class="simple">
|
||||
<li>2d or 3d systems</li>
|
||||
<li>orthogonal or non-orthogonal (triclinic symmetry) simulation domains</li>
|
||||
<li>constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators</li>
|
||||
<li>thermostatting options for groups and geometric regions of atoms</li>
|
||||
<li>pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions</li>
|
||||
<li>simulation box deformation (tensile and shear)</li>
|
||||
<li>harmonic (umbrella) constraint forces</li>
|
||||
<li>rigid body constraints</li>
|
||||
<li>SHAKE bond and angle constraints</li>
|
||||
<li>Monte Carlo bond breaking, formation, swapping</li>
|
||||
<li>atom/molecule insertion and deletion</li>
|
||||
<li>walls of various kinds</li>
|
||||
<li>non-equilibrium molecular dynamics (NEMD)</li>
|
||||
<li>variety of additional boundary conditions and constraints</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="integrators">
|
||||
<h3>1.2.6. Integrators</h3>
|
||||
<p>(<a class="reference internal" href="run.html"><span class="doc">run</span></a>, <a class="reference internal" href="run_style.html"><span class="doc">run_style</span></a>, <a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a> commands)</p>
|
||||
<ul class="simple">
|
||||
<li>velocity-Verlet integrator</li>
|
||||
<li>Brownian dynamics</li>
|
||||
<li>rigid body integration</li>
|
||||
<li>energy minimization via conjugate gradient or steepest descent relaxation</li>
|
||||
<li>rRESPA hierarchical timestepping</li>
|
||||
<li>rerun command for post-processing of dump files</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="diagnostics">
|
||||
<h3>1.2.7. Diagnostics</h3>
|
||||
<ul class="simple">
|
||||
<li>see the various flavors of the <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> and <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> commands</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="output">
|
||||
<h3>1.2.8. Output</h3>
|
||||
<p>(<a class="reference internal" href="dump.html"><span class="doc">dump</span></a>, <a class="reference internal" href="restart.html"><span class="doc">restart</span></a> commands)</p>
|
||||
<ul class="simple">
|
||||
<li>log file of thermodynamic info</li>
|
||||
<li>text dump files of atom coords, velocities, other per-atom quantities</li>
|
||||
<li>binary restart files</li>
|
||||
<li>parallel I/O of dump and restart files</li>
|
||||
<li>per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc)</li>
|
||||
<li>user-defined system-wide (log file) or per-atom (dump file) calculations</li>
|
||||
<li>spatial and time averaging of per-atom quantities</li>
|
||||
<li>time averaging of system-wide quantities</li>
|
||||
<li>atom snapshots in native, XYZ, XTC, DCD, CFG formats</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="multi-replica-models">
|
||||
<h3>1.2.9. Multi-replica models</h3>
|
||||
<p><a class="reference internal" href="neb.html"><span class="doc">nudged elastic band</span></a>
|
||||
<a class="reference internal" href="prd.html"><span class="doc">parallel replica dynamics</span></a>
|
||||
<a class="reference internal" href="tad.html"><span class="doc">temperature accelerated dynamics</span></a>
|
||||
<a class="reference internal" href="temper.html"><span class="doc">parallel tempering</span></a></p>
|
||||
</div>
|
||||
<div class="section" id="pre-and-post-processing">
|
||||
<h3>1.2.10. Pre- and post-processing</h3>
|
||||
<ul class="simple">
|
||||
<li>Various pre- and post-processing serial tools are packaged
|
||||
with LAMMPS; see these <a class="reference internal" href="Section_tools.html"><span class="doc">doc pages</span></a>.</li>
|
||||
<li>Our group has also written and released a separate toolkit called
|
||||
<a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</a> which provides tools for doing setup, analysis,
|
||||
plotting, and visualization for LAMMPS simulations. Pizza.py is
|
||||
written in <a class="reference external" href="http://www.python.org">Python</a> and is available for download from <a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">the Pizza.py WWW site</a>.</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="specialized-features">
|
||||
<h3>1.2.11. Specialized features</h3>
|
||||
<p>These are LAMMPS capabilities which you may not think of as typical
|
||||
molecular dynamics options:</p>
|
||||
<ul class="simple">
|
||||
<li><a class="reference internal" href="balance.html"><span class="doc">static</span></a> and <a class="reference internal" href="fix_balance.html"><span class="doc">dynamic load-balancing</span></a></li>
|
||||
<li><a class="reference internal" href="body.html"><span class="doc">generalized aspherical particles</span></a></li>
|
||||
<li><a class="reference internal" href="fix_srd.html"><span class="doc">stochastic rotation dynamics (SRD)</span></a></li>
|
||||
<li><a class="reference internal" href="fix_imd.html"><span class="doc">real-time visualization and interactive MD</span></a></li>
|
||||
<li>calculate <a class="reference internal" href="compute_xrd.html"><span class="doc">virtual diffraction patterns</span></a></li>
|
||||
<li><a class="reference internal" href="fix_atc.html"><span class="doc">atom-to-continuum coupling</span></a> with finite elements</li>
|
||||
<li>coupled rigid body integration via the <a class="reference internal" href="fix_poems.html"><span class="doc">POEMS</span></a> library</li>
|
||||
<li><a class="reference internal" href="fix_qmmm.html"><span class="doc">QM/MM coupling</span></a></li>
|
||||
<li><a class="reference internal" href="fix_ipi.html"><span class="doc">path-integral molecular dynamics (PIMD)</span></a> and <a class="reference internal" href="fix_pimd.html"><span class="doc">this as well</span></a></li>
|
||||
<li>Monte Carlo via <a class="reference internal" href="fix_gcmc.html"><span class="doc">GCMC</span></a> and <a class="reference internal" href="fix_tfmc.html"><span class="doc">tfMC</span></a> and <span class="xref doc">atom swapping</span></li>
|
||||
<li><a class="reference internal" href="pair_dsmc.html"><span class="doc">Direct Simulation Monte Carlo</span></a> for low-density fluids</li>
|
||||
<li><a class="reference internal" href="pair_peri.html"><span class="doc">Peridynamics mesoscale modeling</span></a></li>
|
||||
<li><a class="reference internal" href="fix_lb_fluid.html"><span class="doc">Lattice Boltzmann fluid</span></a></li>
|
||||
<li><a class="reference internal" href="fix_tmd.html"><span class="doc">targeted</span></a> and <a class="reference internal" href="fix_smd.html"><span class="doc">steered</span></a> molecular dynamics</li>
|
||||
<li><a class="reference internal" href="fix_ttm.html"><span class="doc">two-temperature electron model</span></a></li>
|
||||
</ul>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="lammps-non-features">
|
||||
<span id="intro-3"></span><h2>1.3. LAMMPS non-features</h2>
|
||||
<p>LAMMPS is designed to efficiently compute Newton’s equations of motion
|
||||
for a system of interacting particles. Many of the tools needed to
|
||||
pre- and post-process the data for such simulations are not included
|
||||
in the LAMMPS kernel for several reasons:</p>
|
||||
<ul class="simple">
|
||||
<li>the desire to keep LAMMPS simple</li>
|
||||
<li>they are not parallel operations</li>
|
||||
<li>other codes already do them</li>
|
||||
<li>limited development resources</li>
|
||||
</ul>
|
||||
<p>Specifically, LAMMPS itself does not:</p>
|
||||
<ul class="simple">
|
||||
<li>run thru a GUI</li>
|
||||
<li>build molecular systems</li>
|
||||
<li>assign force-field coefficients automagically</li>
|
||||
<li>perform sophisticated analyses of your MD simulation</li>
|
||||
<li>visualize your MD simulation</li>
|
||||
<li>plot your output data</li>
|
||||
</ul>
|
||||
<p>A few tools for pre- and post-processing tasks are provided as part of
|
||||
the LAMMPS package; they are described in <a class="reference internal" href="Section_tools.html"><span class="doc">this section</span></a>. However, many people use other codes or
|
||||
write their own tools for these tasks.</p>
|
||||
<p>As noted above, our group has also written and released a separate
|
||||
toolkit called <a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</a> which addresses some of the listed
|
||||
bullets. It provides tools for doing setup, analysis, plotting, and
|
||||
visualization for LAMMPS simulations. Pizza.py is written in
|
||||
<a class="reference external" href="http://www.python.org">Python</a> and is available for download from <a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">the Pizza.py WWW site</a>.</p>
|
||||
<p>LAMMPS requires as input a list of initial atom coordinates and types,
|
||||
molecular topology information, and force-field coefficients assigned
|
||||
to all atoms and bonds. LAMMPS will not build molecular systems and
|
||||
assign force-field parameters for you.</p>
|
||||
<p>For atomic systems LAMMPS provides a <a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a>
|
||||
command which places atoms on solid-state lattices (fcc, bcc,
|
||||
user-defined, etc). Assigning small numbers of force field
|
||||
coefficients can be done via the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair coeff</span></a>, <a class="reference internal" href="bond_coeff.html"><span class="doc">bond coeff</span></a>, <a class="reference internal" href="angle_coeff.html"><span class="doc">angle coeff</span></a>, etc commands.
|
||||
For molecular systems or more complicated simulation geometries, users
|
||||
typically use another code as a builder and convert its output to
|
||||
LAMMPS input format, or write their own code to generate atom
|
||||
coordinate and molecular topology for LAMMPS to read in.</p>
|
||||
<p>For complicated molecular systems (e.g. a protein), a multitude of
|
||||
topology information and hundreds of force-field coefficients must
|
||||
typically be specified. We suggest you use a program like
|
||||
<a class="reference external" href="http://www.scripps.edu/brooks">CHARMM</a> or <a class="reference external" href="http://amber.scripps.edu">AMBER</a> or other molecular builders to setup
|
||||
such problems and dump its information to a file. You can then
|
||||
reformat the file as LAMMPS input. Some of the tools in <a class="reference internal" href="Section_tools.html"><span class="doc">this section</span></a> can assist in this process.</p>
|
||||
<p>Similarly, LAMMPS creates output files in a simple format. Most users
|
||||
post-process these files with their own analysis tools or re-format
|
||||
them for input into other programs, including visualization packages.
|
||||
If you are convinced you need to compute something on-the-fly as
|
||||
LAMMPS runs, see <a class="reference internal" href="Section_modify.html"><span class="doc">Section_modify</span></a> for a discussion
|
||||
of how you can use the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> and <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> and
|
||||
<a class="reference internal" href="fix.html"><span class="doc">fix</span></a> commands to print out data of your choosing. Keep in
|
||||
mind that complicated computations can slow down the molecular
|
||||
dynamics timestepping, particularly if the computations are not
|
||||
parallel, so it is often better to leave such analysis to
|
||||
post-processing codes.</p>
|
||||
<p>A very simple (yet fast) visualizer is provided with the LAMMPS
|
||||
package - see the <a class="reference internal" href="Section_tools.html#xmovie"><span class="std std-ref">xmovie</span></a> tool in <a class="reference internal" href="Section_tools.html"><span class="doc">this section</span></a>. It creates xyz projection views of
|
||||
atomic coordinates and animates them. We find it very useful for
|
||||
debugging purposes. For high-quality visualization we recommend the
|
||||
following packages:</p>
|
||||
<ul class="simple">
|
||||
<li><a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD</a></li>
|
||||
<li><a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a></li>
|
||||
<li><a class="reference external" href="http://pymol.sourceforge.net">PyMol</a></li>
|
||||
<li><a class="reference external" href="http://www.bmsc.washington.edu/raster3d/raster3d.html">Raster3d</a></li>
|
||||
<li><a class="reference external" href="http://www.openrasmol.org">RasMol</a></li>
|
||||
</ul>
|
||||
<p>Other features that LAMMPS does not yet (and may never) support are
|
||||
discussed in <a class="reference internal" href="Section_history.html"><span class="doc">Section_history</span></a>.</p>
|
||||
<p>Finally, these are freely-available molecular dynamics codes, most of
|
||||
them parallel, which may be well-suited to the problems you want to
|
||||
model. They can also be used in conjunction with LAMMPS to perform
|
||||
complementary modeling tasks.</p>
|
||||
<ul class="simple">
|
||||
<li><a class="reference external" href="http://www.scripps.edu/brooks">CHARMM</a></li>
|
||||
<li><a class="reference external" href="http://amber.scripps.edu">AMBER</a></li>
|
||||
<li><a class="reference external" href="http://www.ks.uiuc.edu/Research/namd/">NAMD</a></li>
|
||||
<li><a class="reference external" href="http://www.emsl.pnl.gov/docs/nwchem/nwchem.html">NWCHEM</a></li>
|
||||
<li><a class="reference external" href="http://www.cse.clrc.ac.uk/msi/software/DL_POLY">DL_POLY</a></li>
|
||||
<li><a class="reference external" href="http://dasher.wustl.edu/tinker">Tinker</a></li>
|
||||
</ul>
|
||||
<p>CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for
|
||||
modeling biological molecules. CHARMM and AMBER use
|
||||
atom-decomposition (replicated-data) strategies for parallelism; NAMD
|
||||
and NWCHEM use spatial-decomposition approaches, similar to LAMMPS.
|
||||
Tinker is a serial code. DL_POLY includes potentials for a variety of
|
||||
biological and non-biological materials; both a replicated-data and
|
||||
spatial-decomposition version exist.</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="open-source-distribution">
|
||||
<span id="intro-4"></span><h2>1.4. Open source distribution</h2>
|
||||
<p>LAMMPS comes with no warranty of any kind. As each source file states
|
||||
in its header, it is a copyrighted code that is distributed free-of-
|
||||
charge, under the terms of the <a class="reference external" href="http://www.gnu.org/copyleft/gpl.html">GNU Public License</a> (GPL). This
|
||||
is often referred to as open-source distribution - see
|
||||
<a class="reference external" href="http://www.gnu.org">www.gnu.org</a> or <a class="reference external" href="http://www.opensource.org">www.opensource.org</a> for more
|
||||
details. The legal text of the GPL is in the LICENSE file that is
|
||||
included in the LAMMPS distribution.</p>
|
||||
<p>Here is a summary of what the GPL means for LAMMPS users:</p>
|
||||
<p>(1) Anyone is free to use, modify, or extend LAMMPS in any way they
|
||||
choose, including for commercial purposes.</p>
|
||||
<p>(2) If you distribute a modified version of LAMMPS, it must remain
|
||||
open-source, meaning you distribute it under the terms of the GPL.
|
||||
You should clearly annotate such a code as a derivative version of
|
||||
LAMMPS.</p>
|
||||
<p>(3) If you release any code that includes LAMMPS source code, then it
|
||||
must also be open-sourced, meaning you distribute it under the terms
|
||||
of the GPL.</p>
|
||||
<p>(4) If you give LAMMPS files to someone else, the GPL LICENSE file and
|
||||
source file headers (including the copyright and GPL notices) should
|
||||
remain part of the code.</p>
|
||||
<p>In the spirit of an open-source code, these are various ways you can
|
||||
contribute to making LAMMPS better. You can send email to the
|
||||
<a class="reference external" href="http://lammps.sandia.gov/authors.html">developers</a> on any of these
|
||||
items.</p>
|
||||
<ul class="simple">
|
||||
<li>Point prospective users to the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>. Mention it in
|
||||
talks or link to it from your WWW site.</li>
|
||||
<li>If you find an error or omission in this manual or on the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>, or have a suggestion for something to clarify or include,
|
||||
send an email to the
|
||||
<a class="reference external" href="http://lammps.sandia.gov/authors.html">developers</a>.</li>
|
||||
<li>If you find a bug, <a class="reference internal" href="Section_errors.html#err-2"><span class="std std-ref">Section_errors 2</span></a>
|
||||
describes how to report it.</li>
|
||||
<li>If you publish a paper using LAMMPS results, send the citation (and
|
||||
any cool pictures or movies if you like) to add to the Publications,
|
||||
Pictures, and Movies pages of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>, with links
|
||||
and attributions back to you.</li>
|
||||
<li>Create a new Makefile.machine that can be added to the src/MAKE
|
||||
directory.</li>
|
||||
<li>The tools sub-directory of the LAMMPS distribution has various
|
||||
stand-alone codes for pre- and post-processing of LAMMPS data. More
|
||||
details are given in <a class="reference internal" href="Section_tools.html"><span class="doc">Section_tools</span></a>. If you write
|
||||
a new tool that users will find useful, it can be added to the LAMMPS
|
||||
distribution.</li>
|
||||
<li>LAMMPS is designed to be easy to extend with new code for features
|
||||
like potentials, boundary conditions, diagnostic computations, etc.
|
||||
<a class="reference internal" href="Section_modify.html"><span class="doc">This section</span></a> gives details. If you add a
|
||||
feature of general interest, it can be added to the LAMMPS
|
||||
distribution.</li>
|
||||
<li>The Benchmark page of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> lists LAMMPS
|
||||
performance on various platforms. The files needed to run the
|
||||
benchmarks are part of the LAMMPS distribution. If your machine is
|
||||
sufficiently different from those listed, your timing data can be
|
||||
added to the page.</li>
|
||||
<li>You can send feedback for the User Comments page of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>. It might be added to the page. No promises.</li>
|
||||
<li>Cash. Small denominations, unmarked bills preferred. Paper sack OK.
|
||||
Leave on desk. VISA also accepted. Chocolate chip cookies
|
||||
encouraged.</li>
|
||||
</ul>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="acknowledgments-and-citations">
|
||||
<span id="intro-5"></span><h2>1.5. Acknowledgments and citations</h2>
|
||||
<p>LAMMPS development has been funded by the <a class="reference external" href="http://www.doe.gov">US Department of Energy</a> (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life
|
||||
programs and its <a class="reference external" href="http://www.sc.doe.gov/ascr/home.html">OASCR</a> and <a class="reference external" href="http://www.er.doe.gov/production/ober/ober_top.html">OBER</a> offices.</p>
|
||||
<p>Specifically, work on the latest version was funded in part by the US
|
||||
Department of Energy’s Genomics:GTL program
|
||||
(<a class="reference external" href="http://www.doegenomestolife.org">www.doegenomestolife.org</a>) under the <a class="reference external" href="http://www.genomes2life.org">project</a>, “Carbon
|
||||
Sequestration in Synechococcus Sp.: From Molecular Machines to
|
||||
Hierarchical Modeling”.</p>
|
||||
<p>The following paper describe the basic parallel algorithms used in
|
||||
LAMMPS. If you use LAMMPS results in your published work, please cite
|
||||
this paper and include a pointer to the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>
|
||||
(<a class="reference external" href="http://lammps.sandia.gov">http://lammps.sandia.gov</a>):</p>
|
||||
<p>S. J. Plimpton, <strong>Fast Parallel Algorithms for Short-Range Molecular
|
||||
Dynamics</strong>, J Comp Phys, 117, 1-19 (1995).</p>
|
||||
<p>Other papers describing specific algorithms used in LAMMPS are listed
|
||||
under the <a class="reference external" href="http://lammps.sandia.gov/cite.html">Citing LAMMPS link</a> of
|
||||
the LAMMPS WWW page.</p>
|
||||
<p>The <a class="reference external" href="http://lammps.sandia.gov/papers.html">Publications link</a> on the
|
||||
LAMMPS WWW page lists papers that have cited LAMMPS. If your paper is
|
||||
not listed there for some reason, feel free to send us the info. If
|
||||
the simulations in your paper produced cool pictures or animations,
|
||||
we’ll be pleased to add them to the
|
||||
<a class="reference external" href="http://lammps.sandia.gov/pictures.html">Pictures</a> or
|
||||
<a class="reference external" href="http://lammps.sandia.gov/movies.html">Movies</a> pages of the LAMMPS WWW
|
||||
site.</p>
|
||||
<p>The core group of LAMMPS developers is at Sandia National Labs:</p>
|
||||
<ul class="simple">
|
||||
<li>Steve Plimpton, sjplimp at sandia.gov</li>
|
||||
<li>Aidan Thompson, athomps at sandia.gov</li>
|
||||
<li>Paul Crozier, pscrozi at sandia.gov</li>
|
||||
</ul>
|
||||
<p>The following folks are responsible for significant contributions to
|
||||
the code, or other aspects of the LAMMPS development effort. Many of
|
||||
the packages they have written are somewhat unique to LAMMPS and the
|
||||
code would not be as general-purpose as it is without their expertise
|
||||
and efforts.</p>
|
||||
<ul class="simple">
|
||||
<li>Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CG-CMM and USER-OMP packages</li>
|
||||
<li>Roy Pollock (LLNL), Ewald and PPPM solvers</li>
|
||||
<li>Mike Brown (ORNL), brownw at ornl.gov, GPU package</li>
|
||||
<li>Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential</li>
|
||||
<li>Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics</li>
|
||||
<li>Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion</li>
|
||||
<li>Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling</li>
|
||||
<li>Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD</li>
|
||||
<li>Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA package</li>
|
||||
<li>Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field</li>
|
||||
<li>Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling</li>
|
||||
<li>Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF</li>
|
||||
<li>Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SPH package</li>
|
||||
</ul>
|
||||
<p>As discussed in <a class="reference internal" href="Section_history.html"><span class="doc">Section_history</span></a>, LAMMPS
|
||||
originated as a cooperative project between DOE labs and industrial
|
||||
partners. Folks involved in the design and testing of the original
|
||||
version of LAMMPS were the following:</p>
|
||||
<ul class="simple">
|
||||
<li>John Carpenter (Mayo Clinic, formerly at Cray Research)</li>
|
||||
<li>Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)</li>
|
||||
<li>Steve Lustig (Dupont)</li>
|
||||
<li>Jim Belak (LLNL)</li>
|
||||
</ul>
|
||||
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|
||||
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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_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>
|
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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="performance-scalability">
|
||||
<h1>8. Performance & scalability</h1>
|
||||
<p>Current LAMMPS performance is discussed on the Benchmarks page of the
|
||||
<a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> where CPU timings and parallel efficiencies are
|
||||
listed. The page has several sections, which are briefly described
|
||||
below:</p>
|
||||
<ul class="simple">
|
||||
<li>CPU performance on 5 standard problems, strong and weak scaling</li>
|
||||
<li>GPU and Xeon Phi performance on same and related problems</li>
|
||||
<li>Comparison of cost of interatomic potentials</li>
|
||||
<li>Performance of huge, billion-atom problems</li>
|
||||
</ul>
|
||||
<p>The 5 standard problems are as follow:</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
|
||||
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
|
||||
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>Input files for these 5 problems are provided in the bench directory
|
||||
of the LAMMPS distribution. Each has 32,000 atoms and runs for 100
|
||||
timesteps. The size of the problem (number of atoms) can be varied
|
||||
using command-line switches as described in the bench/README file.
|
||||
This is an easy way to test performance and either strong or weak
|
||||
scalability on your machine.</p>
|
||||
<p>The bench directory includes a few log.* files that show performance
|
||||
of these 5 problems on 1 or 4 cores of Linux desktop. The bench/FERMI
|
||||
and bench/KEPLER dirs have input files and scripts and instructions
|
||||
for running the same (or similar) problems using OpenMP or GPU or Xeon
|
||||
Phi acceleration options. See the README files in those dirs and the
|
||||
<a class="reference internal" href="Section_accelerate.html"><span class="doc">Section accelerate</span></a> doc pages for
|
||||
instructions on how to build LAMMPS and run on that kind of hardware.</p>
|
||||
<p>The bench/POTENTIALS directory has input files which correspond to the
|
||||
table of results on the
|
||||
<span class="xref std std-ref">Potentials</span> section of
|
||||
the Benchmarks web page. So you can also run those test problems on
|
||||
your machine.</p>
|
||||
<p>The <span class="xref std std-ref">billion-atom</span> section
|
||||
of the Benchmarks web page has performance data for very large
|
||||
benchmark runs of simple Lennard-Jones (LJ) models, which use the
|
||||
bench/in.lj input script.</p>
|
||||
<hr class="docutils" />
|
||||
<p>For all the benchmarks, a useful metric is the CPU cost per atom per
|
||||
timestep. Since performance scales roughly linearly with problem size
|
||||
and timesteps for all LAMMPS models (i.e. inteatomic or coarse-grained
|
||||
potentials), the run time of any problem using the same model (atom
|
||||
style, force field, cutoff, etc) can then be estimated.</p>
|
||||
<p>Performance on a parallel machine can also be predicted from one-core
|
||||
or one-node 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 parallel
|
||||
efficiencies on these benchmarks above 50% so long as the number of
|
||||
atoms/core is a few 100 or greater, and closer to 100% for large
|
||||
numbers of atoms/core. This is for all-MPI mode with one MPI task per
|
||||
core. For nodes with accelerator options or hardware (OpenMP, GPU,
|
||||
Phi), you should first measure single node performance. Then you can
|
||||
estimate parallel performance for multi-node runs using the same logic
|
||||
as for all-MPI mode, except that now you will typically need many more
|
||||
atoms/node to achieve good scalability.</p>
|
||||
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|
||||
|
||||
|
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<ul class="current">
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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 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 current"><a class="current reference internal" href="#">9. Additional tools</a><ul>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#amber2lmp-tool">9.1. amber2lmp tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#binary2txt-tool">9.2. binary2txt tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#ch2lmp-tool">9.3. ch2lmp tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#chain-tool">9.4. chain tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#colvars-tools">9.5. colvars tools</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#createatoms-tool">9.6. createatoms tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#data2xmovie-tool">9.7. data2xmovie tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#eam-database-tool">9.8. eam database tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#eam-generate-tool">9.9. eam generate tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#eff-tool">9.10. eff tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#emacs-tool">9.11. emacs tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#fep-tool">9.12. fep tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#i-pi-tool">9.13. i-pi tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#ipp-tool">9.14. ipp tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#kate-tool">9.15. kate tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#lmp2arc-tool">9.16. lmp2arc tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#lmp2cfg-tool">9.17. lmp2cfg tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#lmp2vmd-tool">9.18. lmp2vmd tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#matlab-tool">9.19. matlab tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#micelle2d-tool">9.20. micelle2d tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#moltemplate-tool">9.21. moltemplate tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#msi2lmp-tool">9.22. msi2lmp tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#phonon-tool">9.23. phonon tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#polymer-bonding-tool">9.24. polymer bonding tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#pymol-asphere-tool">9.25. pymol_asphere tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#python-tool">9.26. python tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#reax-tool">9.27. reax tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#restart2data-tool">9.28. restart2data tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#vim-tool">9.29. vim tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#xmgrace-tool">9.30. xmgrace tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#xmovie-tool">9.31. xmovie tool</a></li>
|
||||
</ul>
|
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</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="additional-tools">
|
||||
<h1>9. Additional tools</h1>
|
||||
<p>LAMMPS is designed to be a computational kernel for performing
|
||||
molecular dynamics computations. Additional pre- and post-processing
|
||||
steps are often necessary to setup and analyze a simulation. A few
|
||||
additional tools are provided with the LAMMPS distribution and are
|
||||
described in this section.</p>
|
||||
<p>Our group has also written and released a separate toolkit called
|
||||
<a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</a> which provides tools for doing setup, analysis,
|
||||
plotting, and visualization for LAMMPS simulations. Pizza.py is
|
||||
written in <a class="reference external" href="http://www.python.org">Python</a> and is available for download from <a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">the Pizza.py WWW site</a>.</p>
|
||||
<p>Note that many users write their own setup or analysis tools or use
|
||||
other existing codes and convert their output to a LAMMPS input format
|
||||
or vice versa. The tools listed here are included in the LAMMPS
|
||||
distribution as examples of auxiliary tools. Some of them are not
|
||||
actively supported by Sandia, as they were contributed by LAMMPS
|
||||
users. If you have problems using them, we can direct you to the
|
||||
authors.</p>
|
||||
<p>The source code for each of these codes is in the tools sub-directory
|
||||
of the LAMMPS distribution. There is a Makefile (which you may need
|
||||
to edit for your platform) which will build several of the tools which
|
||||
reside in that directory. Some of them are larger packages in their
|
||||
own sub-directories with their own Makefiles.</p>
|
||||
<ul class="simple">
|
||||
<li><a class="reference internal" href="#amber"><span class="std std-ref">amber2lmp</span></a></li>
|
||||
<li><a class="reference internal" href="#binary"><span class="std std-ref">binary2txt</span></a></li>
|
||||
<li><a class="reference internal" href="#charmm"><span class="std std-ref">ch2lmp</span></a></li>
|
||||
<li><a class="reference internal" href="#chain"><span class="std std-ref">chain</span></a></li>
|
||||
<li><a class="reference internal" href="#colvars"><span class="std std-ref">colvars</span></a></li>
|
||||
<li><a class="reference internal" href="#create"><span class="std std-ref">createatoms</span></a></li>
|
||||
<li><a class="reference internal" href="#data"><span class="std std-ref">data2xmovie</span></a></li>
|
||||
<li><a class="reference internal" href="#eamdb"><span class="std std-ref">eam database</span></a></li>
|
||||
<li><a class="reference internal" href="#eamgn"><span class="std std-ref">eam generate</span></a></li>
|
||||
<li><a class="reference internal" href="#eff"><span class="std std-ref">eff</span></a></li>
|
||||
<li><a class="reference internal" href="#emacs"><span class="std std-ref">emacs</span></a></li>
|
||||
<li><a class="reference internal" href="#fep"><span class="std std-ref">fep</span></a></li>
|
||||
<li><a class="reference internal" href="fix_ipi.html#ipi"><span class="std std-ref">i-pi</span></a></li>
|
||||
<li><a class="reference internal" href="#ipp"><span class="std std-ref">ipp</span></a></li>
|
||||
<li><a class="reference internal" href="#kate"><span class="std std-ref">kate</span></a></li>
|
||||
<li><a class="reference internal" href="#arc"><span class="std std-ref">lmp2arc</span></a></li>
|
||||
<li><a class="reference internal" href="#cfg"><span class="std std-ref">lmp2cfg</span></a></li>
|
||||
<li><a class="reference internal" href="#vmd"><span class="std std-ref">lmp2vmd</span></a></li>
|
||||
<li><span class="xref std std-ref">matlab</span></li>
|
||||
<li><a class="reference internal" href="#micelle"><span class="std std-ref">micelle2d</span></a></li>
|
||||
<li><a class="reference internal" href="#moltemplate"><span class="std std-ref">moltemplate</span></a></li>
|
||||
<li><a class="reference internal" href="#msi"><span class="std std-ref">msi2lmp</span></a></li>
|
||||
<li><a class="reference internal" href="#phonon"><span class="std std-ref">phonon</span></a></li>
|
||||
<li><a class="reference internal" href="#polybond"><span class="std std-ref">polymer bonding</span></a></li>
|
||||
<li><span class="xref std std-ref">pymol_asphere</span></li>
|
||||
<li><a class="reference internal" href="#pythontools"><span class="std std-ref">python</span></a></li>
|
||||
<li><a class="reference internal" href="#reax"><span class="std std-ref">reax</span></a></li>
|
||||
<li><a class="reference internal" href="#restart"><span class="std std-ref">restart2data</span></a></li>
|
||||
<li><a class="reference internal" href="#vim"><span class="std std-ref">vim</span></a></li>
|
||||
<li><a class="reference internal" href="#xmgrace"><span class="std std-ref">xmgrace</span></a></li>
|
||||
<li><a class="reference internal" href="#xmovie"><span class="std std-ref">xmovie</span></a></li>
|
||||
</ul>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="amber2lmp-tool">
|
||||
<span id="amber"></span><h2>9.1. amber2lmp tool</h2>
|
||||
<p>The amber2lmp sub-directory contains two Python scripts for converting
|
||||
files back-and-forth between the AMBER MD code and LAMMPS. See the
|
||||
README file in amber2lmp for more information.</p>
|
||||
<p>These tools were written by Keir Novik while he was at Queen Mary
|
||||
University of London. Keir is no longer there and cannot support
|
||||
these tools which are out-of-date with respect to the current LAMMPS
|
||||
version (and maybe with respect to AMBER as well). Since we don’t use
|
||||
these tools at Sandia, you’ll need to experiment with them and make
|
||||
necessary modifications yourself.</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="binary2txt-tool">
|
||||
<span id="binary"></span><h2>9.2. binary2txt tool</h2>
|
||||
<p>The file binary2txt.cpp converts one or more binary LAMMPS dump file
|
||||
into ASCII text files. The syntax for running the tool is</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">binary2txt</span> <span class="n">file1</span> <span class="n">file2</span> <span class="o">...</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>which creates file1.txt, file2.txt, etc. This tool must be compiled
|
||||
on a platform that can read the binary file created by a LAMMPS run,
|
||||
since binary files are not compatible across all platforms.</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="ch2lmp-tool">
|
||||
<span id="charmm"></span><h2>9.3. ch2lmp tool</h2>
|
||||
<p>The ch2lmp sub-directory contains tools for converting files
|
||||
back-and-forth between the CHARMM MD code and LAMMPS.</p>
|
||||
<p>They are intended to make it easy to use CHARMM as a builder and as a
|
||||
post-processor for LAMMPS. Using charmm2lammps.pl, you can convert an
|
||||
ensemble built in CHARMM into its LAMMPS equivalent. Using
|
||||
lammps2pdb.pl you can convert LAMMPS atom dumps into pdb files.</p>
|
||||
<p>See the README file in the ch2lmp sub-directory for more information.</p>
|
||||
<p>These tools were created by Pieter in’t Veld (pjintve at sandia.gov)
|
||||
and Paul Crozier (pscrozi at sandia.gov) at Sandia.</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="chain-tool">
|
||||
<span id="chain"></span><h2>9.4. chain tool</h2>
|
||||
<p>The file chain.f creates a LAMMPS data file containing bead-spring
|
||||
polymer chains and/or monomer solvent atoms. It uses a text file
|
||||
containing chain definition parameters as an input. The created
|
||||
chains and solvent atoms can strongly overlap, so LAMMPS needs to run
|
||||
the system initially with a “soft” pair potential to un-overlap it.
|
||||
The syntax for running the tool is</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">chain</span> <span class="o"><</span> <span class="n">def</span><span class="o">.</span><span class="n">chain</span> <span class="o">></span> <span class="n">data</span><span class="o">.</span><span class="n">file</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>See the def.chain or def.chain.ab files in the tools directory for
|
||||
examples of definition files. This tool was used to create the
|
||||
system for the <a class="reference internal" href="Section_perf.html"><span class="doc">chain benchmark</span></a>.</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="colvars-tools">
|
||||
<span id="colvars"></span><h2>9.5. colvars tools</h2>
|
||||
<p>The colvars directory contains a collection of tools for postprocessing
|
||||
data produced by the colvars collective variable library.
|
||||
To compile the tools, edit the makefile for your system and run “make”.</p>
|
||||
<p>Please report problems and issues the colvars library and its tools
|
||||
at: <a class="reference external" href="https://github.com/colvars/colvars/issues">https://github.com/colvars/colvars/issues</a></p>
|
||||
<p>abf_integrate:</p>
|
||||
<p>MC-based integration of multidimensional free energy gradient
|
||||
Version 20110511</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Syntax</span><span class="p">:</span> <span class="o">./</span><span class="n">abf_integrate</span> <span class="o"><</span> <span class="n">filename</span> <span class="o">></span> <span class="p">[</span><span class="o">-</span><span class="n">n</span> <span class="o"><</span> <span class="n">nsteps</span> <span class="o">></span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">t</span> <span class="o"><</span> <span class="n">temp</span> <span class="o">></span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">m</span> <span class="p">[</span><span class="mi">0</span><span class="o">|</span><span class="mi">1</span><span class="p">]</span> <span class="p">(</span><span class="n">metadynamics</span><span class="p">)]</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span> <span class="o"><</span> <span class="n">hill_height</span> <span class="o">></span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">f</span> <span class="o"><</span> <span class="n">variable_hill_factor</span> <span class="o">></span><span class="p">]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The LAMMPS interface to the colvars collective variable library, as
|
||||
well as these tools, were created by Axel Kohlmeyer (akohlmey at
|
||||
gmail.com) at ICTP, Italy.</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="createatoms-tool">
|
||||
<span id="create"></span><h2>9.6. createatoms tool</h2>
|
||||
<p>The tools/createatoms directory contains a Fortran program called
|
||||
createAtoms.f which can generate a variety of interesting crystal
|
||||
structures and geometries and output the resulting list of atom
|
||||
coordinates in LAMMPS or other formats.</p>
|
||||
<p>See the included Manual.pdf for details.</p>
|
||||
<p>The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="data2xmovie-tool">
|
||||
<span id="data"></span><h2>9.7. data2xmovie tool</h2>
|
||||
<p>The file data2xmovie.c converts a LAMMPS data file into a snapshot
|
||||
suitable for visualizing with the <a class="reference internal" href="#xmovie"><span class="std std-ref">xmovie</span></a> tool, as if it had
|
||||
been output with a dump command from LAMMPS itself. The syntax for
|
||||
running the tool is</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">data2xmovie</span> <span class="p">[</span><span class="n">options</span><span class="p">]</span> <span class="o"><</span> <span class="n">infile</span> <span class="o">></span> <span class="n">outfile</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>See the top of the data2xmovie.c file for a discussion of the options.</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="eam-database-tool">
|
||||
<span id="eamdb"></span><h2>9.8. eam database tool</h2>
|
||||
<p>The tools/eam_database directory contains a Fortran program that will
|
||||
generate EAM alloy setfl potential files for any combination of 16
|
||||
elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti,
|
||||
Zr. The files can then be used with the <a class="reference internal" href="pair_eam.html"><span class="doc">pair_style eam/alloy</span></a> command.</p>
|
||||
<p>The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov,
|
||||
and is based on his paper:</p>
|
||||
<p>X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
|
||||
144113 (2004).</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="eam-generate-tool">
|
||||
<span id="eamgn"></span><h2>9.9. eam generate tool</h2>
|
||||
<p>The tools/eam_generate directory contains several one-file C programs
|
||||
that convert an analytic formula into a tabulated <a class="reference internal" href="pair_eam.html"><span class="doc">embedded atom method (EAM)</span></a> setfl potential file. The potentials they
|
||||
produce are in the potentials directory, and can be used with the
|
||||
<a class="reference internal" href="pair_eam.html"><span class="doc">pair_style eam/alloy</span></a> command.</p>
|
||||
<p>The source files and potentials were provided by Gerolf Ziegenhain
|
||||
(gerolf at ziegenhain.com).</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="eff-tool">
|
||||
<span id="eff"></span><h2>9.10. eff tool</h2>
|
||||
<p>The tools/eff directory contains various scripts for generating
|
||||
structures and post-processing output for simulations using the
|
||||
electron force field (eFF).</p>
|
||||
<p>These tools were provided by Andres Jaramillo-Botero at CalTech
|
||||
(ajaramil at wag.caltech.edu).</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="emacs-tool">
|
||||
<span id="emacs"></span><h2>9.11. emacs tool</h2>
|
||||
<p>The tools/emacs directory contains a Lips add-on file for Emacs that
|
||||
enables a lammps-mode for editing of input scripts when using Emacs,
|
||||
with various highlighting options setup.</p>
|
||||
<p>These tools were provided by Aidan Thompson at Sandia
|
||||
(athomps at sandia.gov).</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="fep-tool">
|
||||
<span id="fep"></span><h2>9.12. fep tool</h2>
|
||||
<p>The tools/fep directory contains Python scripts useful for
|
||||
post-processing results from performing free-energy perturbation
|
||||
simulations using the USER-FEP package.</p>
|
||||
<p>The scripts were contributed by Agilio Padua (Universite Blaise
|
||||
Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr.</p>
|
||||
<p>See README file in the tools/fep directory.</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="i-pi-tool">
|
||||
<span id="ipi"></span><h2>9.13. i-pi tool</h2>
|
||||
<p>The tools/i-pi directory contains a version of the i-PI package, with
|
||||
all the LAMMPS-unrelated files removed. It is provided so that it can
|
||||
be used with the <a class="reference internal" href="fix_ipi.html"><span class="doc">fix ipi</span></a> command to perform
|
||||
path-integral molecular dynamics (PIMD).</p>
|
||||
<p>The i-PI package was created and is maintained by Michele Ceriotti,
|
||||
michele.ceriotti at gmail.com, to interface to a variety of molecular
|
||||
dynamics codes.</p>
|
||||
<p>See the tools/i-pi/manual.pdf file for an overview of i-PI, and the
|
||||
<a class="reference internal" href="fix_ipi.html"><span class="doc">fix ipi</span></a> doc page for further details on running PIMD
|
||||
calculations with LAMMPS.</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="ipp-tool">
|
||||
<span id="ipp"></span><h2>9.14. ipp tool</h2>
|
||||
<p>The tools/ipp directory contains a Perl script ipp which can be used
|
||||
to facilitate the creation of a complicated file (say, a lammps input
|
||||
script or tools/createatoms input file) using a template file.</p>
|
||||
<p>ipp was created and is maintained by Reese Jones (Sandia), rjones at
|
||||
sandia.gov.</p>
|
||||
<p>See two examples in the tools/ipp directory. One of them is for the
|
||||
tools/createatoms tool’s input file.</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="kate-tool">
|
||||
<span id="kate"></span><h2>9.15. kate tool</h2>
|
||||
<p>The file in the tools/kate directory is an add-on to the Kate editor
|
||||
in the KDE suite that allow syntax highlighting of LAMMPS input
|
||||
scripts. See the README.txt file for details.</p>
|
||||
<p>The file was provided by Alessandro Luigi Sellerio
|
||||
(alessandro.sellerio at ieni.cnr.it).</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="lmp2arc-tool">
|
||||
<span id="arc"></span><h2>9.16. lmp2arc tool</h2>
|
||||
<p>The lmp2arc sub-directory contains a tool for converting LAMMPS output
|
||||
files to the format for Accelrys’ Insight MD code (formerly
|
||||
MSI/Biosym and its Discover MD code). See the README file for more
|
||||
information.</p>
|
||||
<p>This tool was written by John Carpenter (Cray), Michael Peachey
|
||||
(Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic
|
||||
(jec at mayo.edu), but still fields questions about the tool.</p>
|
||||
<p>This tool was updated for the current LAMMPS C++ version by Jeff
|
||||
Greathouse at Sandia (jagreat at sandia.gov).</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="lmp2cfg-tool">
|
||||
<span id="cfg"></span><h2>9.17. lmp2cfg tool</h2>
|
||||
<p>The lmp2cfg sub-directory contains a tool for converting LAMMPS output
|
||||
files into a series of <a href="#id1"><span class="problematic" id="id2">*</span></a>.cfg files which can be read into the
|
||||
<a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a> visualizer. See
|
||||
the README file for more information.</p>
|
||||
<p>This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="lmp2vmd-tool">
|
||||
<span id="vmd"></span><h2>9.18. lmp2vmd tool</h2>
|
||||
<p>The lmp2vmd sub-directory contains a README.txt file that describes
|
||||
details of scripts and plugin support within the <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD package</a> for visualizing LAMMPS
|
||||
dump files.</p>
|
||||
<p>The VMD plugins and other supporting scripts were written by Axel
|
||||
Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="matlab-tool">
|
||||
<span id="matlab"></span><h2>9.19. matlab tool</h2>
|
||||
<p>The matlab sub-directory contains several <span class="xref std std-ref">MATLAB</span> scripts for
|
||||
post-processing LAMMPS output. The scripts include readers for log
|
||||
and dump files, a reader for EAM potential files, and a converter that
|
||||
reads LAMMPS dump files and produces CFG files that can be visualized
|
||||
with the <a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a>
|
||||
visualizer.</p>
|
||||
<p>See the README.pdf file for more information.</p>
|
||||
<p>These scripts were written by Arun Subramaniyan at Purdue Univ
|
||||
(asubrama at purdue.edu).</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="micelle2d-tool">
|
||||
<span id="micelle"></span><h2>9.20. micelle2d tool</h2>
|
||||
<p>The file micelle2d.f creates a LAMMPS data file containing short lipid
|
||||
chains in a monomer solution. It uses a text file containing lipid
|
||||
definition parameters as an input. The created molecules and solvent
|
||||
atoms can strongly overlap, so LAMMPS needs to run the system
|
||||
initially with a “soft” pair potential to un-overlap it. The syntax
|
||||
for running the tool is</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">micelle2d</span> <span class="o"><</span> <span class="n">def</span><span class="o">.</span><span class="n">micelle2d</span> <span class="o">></span> <span class="n">data</span><span class="o">.</span><span class="n">file</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>See the def.micelle2d file in the tools directory for an example of a
|
||||
definition file. This tool was used to create the system for the
|
||||
<a class="reference internal" href="Section_example.html"><span class="doc">micelle example</span></a>.</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="moltemplate-tool">
|
||||
<span id="moltemplate"></span><h2>9.21. moltemplate tool</h2>
|
||||
<p>The moltemplate sub-directory contains a Python-based tool for
|
||||
building molecular systems based on a text-file description, and
|
||||
creating LAMMPS data files that encode their molecular topology as
|
||||
lists of bonds, angles, dihedrals, etc. See the README.TXT file for
|
||||
more information.</p>
|
||||
<p>This tool was written by Andrew Jewett (jewett.aij at gmail.com), who
|
||||
supports it. It has its own WWW page at
|
||||
<a class="reference external" href="http://moltemplate.org">http://moltemplate.org</a>.</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="msi2lmp-tool">
|
||||
<span id="msi"></span><h2>9.22. msi2lmp tool</h2>
|
||||
<p>The msi2lmp sub-directory contains a tool for creating LAMMPS input
|
||||
data files from Accelrys’ Insight MD code (formerly MSI/Biosym and
|
||||
its Discover MD code). See the README file for more information.</p>
|
||||
<p>This tool was written by John Carpenter (Cray), Michael Peachey
|
||||
(Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic
|
||||
(jec at mayo.edu), but still fields questions about the tool.</p>
|
||||
<p>This tool may be out-of-date with respect to the current LAMMPS and
|
||||
Insight versions. Since we don’t use it at Sandia, you’ll need to
|
||||
experiment with it yourself.</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="phonon-tool">
|
||||
<span id="phonon"></span><h2>9.23. phonon tool</h2>
|
||||
<p>The phonon sub-directory contains a post-processing tool useful for
|
||||
analyzing the output of the <a class="reference internal" href="fix_phonon.html"><span class="doc">fix phonon</span></a> command in
|
||||
the USER-PHONON package.</p>
|
||||
<p>See the README file for instruction on building the tool and what
|
||||
library it needs. And see the examples/USER/phonon directory
|
||||
for example problems that can be post-processed with this tool.</p>
|
||||
<p>This tool was written by Ling-Ti Kong at Shanghai Jiao Tong
|
||||
University.</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="polymer-bonding-tool">
|
||||
<span id="polybond"></span><h2>9.24. polymer bonding tool</h2>
|
||||
<p>The polybond sub-directory contains a Python-based tool useful for
|
||||
performing “programmable polymer bonding”. The Python file
|
||||
lmpsdata.py provides a “Lmpsdata” class with various methods which can
|
||||
be invoked by a user-written Python script to create data files with
|
||||
complex bonding topologies.</p>
|
||||
<p>See the Manual.pdf for details and example scripts.</p>
|
||||
<p>This tool was written by Zachary Kraus at Georgia Tech.</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="pymol-asphere-tool">
|
||||
<span id="pymol"></span><h2>9.25. pymol_asphere tool</h2>
|
||||
<p>The pymol_asphere sub-directory contains a tool for converting a
|
||||
LAMMPS dump file that contains orientation info for ellipsoidal
|
||||
particles into an input file for the <span class="xref std std-ref">PyMol visualization package</span>.</p>
|
||||
<p>Specifically, the tool triangulates the ellipsoids so they can be
|
||||
viewed as true ellipsoidal particles within PyMol. See the README and
|
||||
examples directory within pymol_asphere for more information.</p>
|
||||
<p>This tool was written by Mike Brown at Sandia.</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="python-tool">
|
||||
<span id="pythontools"></span><h2>9.26. python tool</h2>
|
||||
<p>The python sub-directory contains several Python scripts
|
||||
that perform common LAMMPS post-processing tasks, such as:</p>
|
||||
<ul class="simple">
|
||||
<li>extract thermodynamic info from a log file as columns of numbers</li>
|
||||
<li>plot two columns of thermodynamic info from a log file using GnuPlot</li>
|
||||
<li>sort the snapshots in a dump file by atom ID</li>
|
||||
<li>convert multiple <a class="reference internal" href="neb.html"><span class="doc">NEB</span></a> dump files into one dump file for viz</li>
|
||||
<li>convert dump files into XYZ, CFG, or PDB format for viz by other packages</li>
|
||||
</ul>
|
||||
<p>These are simple scripts built on <a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</a> modules. See the
|
||||
README for more info on Pizza.py and how to use these scripts.</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="reax-tool">
|
||||
<span id="reax"></span><h2>9.27. reax tool</h2>
|
||||
<p>The reax sub-directory contains stand-alond codes that can
|
||||
post-process the output of the <a class="reference internal" href="fix_reax_bonds.html"><span class="doc">fix reax/bonds</span></a>
|
||||
command from a LAMMPS simulation using <a class="reference internal" href="pair_reax.html"><span class="doc">ReaxFF</span></a>. See
|
||||
the README.txt file for more info.</p>
|
||||
<p>These tools were written by Aidan Thompson at Sandia.</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="restart2data-tool">
|
||||
<span id="restart"></span><h2>9.28. restart2data tool</h2>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">This tool is now obsolete and is not included in the current
|
||||
LAMMPS distribution. This is becaues there is now a
|
||||
<a class="reference internal" href="write_data.html"><span class="doc">write_data</span></a> command, which can create a data file
|
||||
from within an input script. Running LAMMPS with the “-r”
|
||||
<a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> as follows:</p>
|
||||
</div>
|
||||
<p>lmp_g++ -r restartfile datafile</p>
|
||||
<p>is the same as running a 2-line input script:</p>
|
||||
<p>read_restart restartfile
|
||||
write_data datafile</p>
|
||||
<p>which will produce the same data file that the restart2data tool used
|
||||
to create. The following information is included in case you have an
|
||||
older version of LAMMPS which still includes the restart2data tool.</p>
|
||||
<p>The file restart2data.cpp converts a binary LAMMPS restart file into
|
||||
an ASCII data file. The syntax for running the tool is</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">restart2data</span> <span class="n">restart</span><span class="o">-</span><span class="n">file</span> <span class="n">data</span><span class="o">-</span><span class="n">file</span> <span class="p">(</span><span class="nb">input</span><span class="o">-</span><span class="n">file</span><span class="p">)</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Input-file is optional and if specified will contain LAMMPS input
|
||||
commands for the masses and force field parameters, instead of putting
|
||||
those in the data-file. Only a few force field styles currently
|
||||
support this option.</p>
|
||||
<p>This tool must be compiled on a platform that can read the binary file
|
||||
created by a LAMMPS run, since binary files are not compatible across
|
||||
all platforms.</p>
|
||||
<p>Note that a text data file has less precision than a binary restart
|
||||
file. Hence, continuing a run from a converted data file will
|
||||
typically not conform as closely to a previous run as will restarting
|
||||
from a binary restart file.</p>
|
||||
<p>If a “%” appears in the specified restart-file, the tool expects a set
|
||||
of multiple files to exist. See the <a class="reference internal" href="restart.html"><span class="doc">restart</span></a> and
|
||||
<a class="reference internal" href="write_restart.html"><span class="doc">write_restart</span></a> commands for info on how such sets
|
||||
of files are written by LAMMPS, and how the files are named.</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="vim-tool">
|
||||
<span id="vim"></span><h2>9.29. vim tool</h2>
|
||||
<p>The files in the tools/vim directory are add-ons to the VIM editor
|
||||
that allow easier editing of LAMMPS input scripts. See the README.txt
|
||||
file for details.</p>
|
||||
<p>These files were provided by Gerolf Ziegenhain (gerolf at
|
||||
ziegenhain.com)</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="xmgrace-tool">
|
||||
<span id="xmgrace"></span><h2>9.30. xmgrace tool</h2>
|
||||
<p>The files in the tools/xmgrace directory can be used to plot the
|
||||
thermodynamic data in LAMMPS log files via the xmgrace plotting
|
||||
package. There are several tools in the directory that can be used in
|
||||
post-processing mode. The lammpsplot.cpp file can be compiled and
|
||||
used to create plots from the current state of a running LAMMPS
|
||||
simulation.</p>
|
||||
<p>See the README file for details.</p>
|
||||
<p>These files were provided by Vikas Varshney (vv0210 at gmail.com)</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="xmovie-tool">
|
||||
<span id="xmovie"></span><h2>9.31. xmovie tool</h2>
|
||||
<p>The xmovie tool is an X-based visualization package that can read
|
||||
LAMMPS dump files and animate them. It is in its own sub-directory
|
||||
with the tools directory. You may need to modify its Makefile so that
|
||||
it can find the appropriate X libraries to link against.</p>
|
||||
<p>The syntax for running xmovie is</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">xmovie</span> <span class="p">[</span><span class="n">options</span><span class="p">]</span> <span class="n">dump</span><span class="o">.</span><span class="n">file1</span> <span class="n">dump</span><span class="o">.</span><span class="n">file2</span> <span class="o">...</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>If you just type “xmovie” you will see a list of options. Note that
|
||||
by default, LAMMPS dump files are in scaled coordinates, so you
|
||||
typically need to use the -scale option with xmovie. When xmovie runs
|
||||
it opens a visualization window and a control window. The control
|
||||
options are straightforward to use.</p>
|
||||
<p>Xmovie was mostly written by Mike Uttormark (U Wisconsin) while he
|
||||
spent a summer at Sandia. It displays 2d projections of a 3d domain.
|
||||
While simple in design, it is an amazingly fast program that can
|
||||
render large numbers of atoms very quickly. It’s a useful tool for
|
||||
debugging LAMMPS input and output and making sure your simulation is
|
||||
doing what you think it should. The animations on the Examples page
|
||||
of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW site</a> were created with xmovie.</p>
|
||||
<p>I’ve lost contact with Mike, so I hope he’s comfortable with us
|
||||
distributing his great tool!</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
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|
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© Copyright 2013 Sandia Corporation.
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@ -35,7 +35,7 @@ Examples
|
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Description
|
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"""""""""""
|
||||
|
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DOG Perform constant NVE integration to update position and velocity for
|
||||
Perform constant NVE integration to update position and velocity for
|
||||
atoms in the group each timestep. V is volume; E is energy. This
|
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creates a system trajectory consistent with the microcanonical
|
||||
ensemble.
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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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<p><a class="reference internal" href="Section_accelerate.html"><span class="doc">Return to Section accelerate overview</span></a></p>
|
||||
<div class="section" id="user-cuda-package">
|
||||
<h1>5.USER-CUDA package</h1>
|
||||
<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
|
||||
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
|
||||
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 class="std std-ref">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"><span class="doc">package cuda</span></a> or <a class="reference internal" href="suffix.html"><span class="doc">suffix cuda</span></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
|
||||
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 class="std std-ref">Section 2.4</span></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-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="n">cuda</span> <span class="o">-</span><span class="n">cuda</span> <span class="n">mode</span><span class="o">=</span><span class="n">single</span> <span class="n">arch</span><span class="o">=</span><span class="mi">20</span> <span class="o">-</span><span class="n">o</span> <span class="n">cuda</span> <span class="o">-</span><span class="n">a</span> <span class="n">lib</span><span class="o">-</span><span class="n">cuda</span> <span class="n">file</span> <span class="n">mpi</span>
|
||||
</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-default"><div class="highlight"><pre><span></span><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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">lammps</span><span class="o">/</span><span class="n">src</span>
|
||||
<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">user</span><span class="o">-</span><span class="n">cuda</span>
|
||||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</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
|
||||
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
|
||||
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 class="std std-ref">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"><span class="doc">package cuda 1</span></a>
|
||||
command which sets various USER-CUDA options to default values, as
|
||||
discussed on the <a class="reference internal" href="package.html"><span class="doc">package</span></a> command doc page.</p>
|
||||
<p>Use the “-sf cuda” <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">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 class="std std-ref">command-line switch</span></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"><span class="doc">package cuda</span></a> options.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_machine</span> <span class="o">-</span><span class="n">c</span> <span class="n">on</span> <span class="o">-</span><span class="n">sf</span> <span class="n">cuda</span> <span class="o">-</span><span class="n">pk</span> <span class="n">cuda</span> <span class="mi">1</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 1 MPI task uses 1 GPU</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">c</span> <span class="n">on</span> <span class="o">-</span><span class="n">sf</span> <span class="n">cuda</span> <span class="o">-</span><span class="n">pk</span> <span class="n">cuda</span> <span class="mi">2</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 2 MPI tasks use 2 GPUs on a single 16-core (or whatever) node</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">24</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">2</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">c</span> <span class="n">on</span> <span class="o">-</span><span class="n">sf</span> <span class="n">cuda</span> <span class="o">-</span><span class="n">pk</span> <span class="n">cuda</span> <span class="mi">2</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># ditto on 12 16-core nodes</span>
|
||||
</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"><span class="doc">package</span></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"><span class="doc">package cuda</span></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"><span class="doc">newton</span></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 class="std std-ref">command-line switch</span></a> to enable the USER-CUDA package.</p>
|
||||
<p>Use the <a class="reference internal" href="suffix.html"><span class="doc">suffix cuda</span></a> command, or you can explicitly add a
|
||||
“cuda” suffix to individual styles in your input script, e.g.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">cuda</span> <span class="mf">2.5</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>You only need to use the <a class="reference internal" href="package.html"><span class="doc">package cuda</span></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 class="std std-ref">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
|
||||
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
|
||||
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
|
||||
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
|
||||
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</h2>
|
||||
<p>None.</p>
|
||||
</div>
|
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</div>
|
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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_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>
|
||||
<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>
|
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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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<a href="http://lammps.sandia.gov">Website</a>
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<p><a class="reference internal" href="Section_accelerate.html"><span class="doc">Return to Section accelerate overview</span></a></p>
|
||||
<div class="section" id="gpu-package">
|
||||
<h1>5.GPU package</h1>
|
||||
<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"><span class="doc">kspace_style pppm</span></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
|
||||
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
|
||||
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
|
||||
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
|
||||
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 class="std std-ref">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"><span class="doc">package gpu</span></a> or <a class="reference internal" href="suffix.html"><span class="doc">suffix gpu</span></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 class="std std-ref">Section 2.4</span></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-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="n">gpu</span> <span class="o">-</span><span class="n">gpu</span> <span class="n">mode</span><span class="o">=</span><span class="n">single</span> <span class="n">arch</span><span class="o">=</span><span class="mi">31</span> <span class="o">-</span><span class="n">o</span> <span class="n">gpu</span> <span class="o">-</span><span class="n">a</span> <span class="n">lib</span><span class="o">-</span><span class="n">gpu</span> <span class="n">file</span> <span class="n">mpi</span>
|
||||
</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
|
||||
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
|
||||
for different GPU choices, e.g. Fermi vs Kepler. It also lists the
|
||||
possible precision settings:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">CUDA_PREC</span> <span class="o">=</span> <span class="o">-</span><span class="n">D_SINGLE_SINGLE</span> <span class="c1"># 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="c1"># 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="c1"># accumulation of forces, etc, in double</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<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-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="o">-</span><span class="n">f</span> <span class="n">Makefile</span><span class="o">.</span><span class="n">machine</span>
|
||||
</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
|
||||
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-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">lammps</span><span class="o">/</span><span class="n">src</span>
|
||||
<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">gpu</span>
|
||||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</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)
|
||||
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
|
||||
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
|
||||
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 class="std std-ref">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 class="std std-ref">command-line switch</span></a> to
|
||||
set Ng = # of GPUs/node to use.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">gpu</span> <span class="o">-</span><span class="n">pk</span> <span class="n">gpu</span> <span class="mi">1</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 1 MPI task uses 1 GPU</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">12</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">gpu</span> <span class="o">-</span><span class="n">pk</span> <span class="n">gpu</span> <span class="mi">2</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">48</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">12</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">gpu</span> <span class="o">-</span><span class="n">pk</span> <span class="n">gpu</span> <span class="mi">2</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># ditto on 4 16-core nodes</span>
|
||||
</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"><span class="doc">package gpu 1</span></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"><span class="doc">package</span></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"><span class="doc">package gpu</span></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"><span class="doc">suffix gpu</span></a> command, or you can explicitly add an
|
||||
“gpu” suffix to individual styles in your input script, e.g.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">gpu</span> <span class="mf">2.5</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>You must also use the <a class="reference internal" href="package.html"><span class="doc">package gpu</span></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 class="std std-ref">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
|
||||
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
|
||||
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
|
||||
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
|
||||
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"><span class="doc">package gpu</span></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"><span class="doc">packakge</span></a> command
|
||||
doc page for details.</li>
|
||||
<li>As described by the <a class="reference internal" href="package.html"><span class="doc">package gpu</span></a> command, GPU
|
||||
accelerated pair styles can perform computations asynchronously with
|
||||
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"><span class="doc">bond</span></a>,
|
||||
<a class="reference internal" href="angle_style.html"><span class="doc">angle</span></a>, <a class="reference internal" href="dihedral_style.html"><span class="doc">dihedral</span></a>,
|
||||
<a class="reference internal" href="improper_style.html"><span class="doc">improper</span></a>, and <a class="reference internal" href="kspace_style.html"><span class="doc">long-range</span></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,
|
||||
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
|
||||
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”.
|
||||
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</h2>
|
||||
<p>None.</p>
|
||||
</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>
|
||||
<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_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"><span class="doc">Return to Section accelerate overview</span></a></p>
|
||||
<div class="section" id="user-intel-package">
|
||||
<h1>5.USER-INTEL package</h1>
|
||||
<p>The USER-INTEL package was developed by Mike Brown at Intel
|
||||
Corporation. It provides two methods for accelerating simulations,
|
||||
depending on the hardware you have. The first is acceleration on
|
||||
Intel(R) CPUs by running in single, mixed, or double precision with
|
||||
vectorization. The second is acceleration on Intel(R) Xeon Phi(TM)
|
||||
coprocessors via offloading neighbor list and non-bonded force
|
||||
calculations to the Phi. The same C++ code is used in both cases.
|
||||
When offloading to a coprocessor from a CPU, the same routine is run
|
||||
twice, once on the CPU and once with an offload flag.</p>
|
||||
<p>Note that the USER-INTEL package supports use of the Phi in “offload”
|
||||
mode, not “native” mode like the <a class="reference internal" href="accelerate_kokkos.html"><span class="doc">KOKKOS package</span></a>.</p>
|
||||
<p>Also note that the USER-INTEL package can be used in tandem with the
|
||||
<a class="reference internal" href="accelerate_omp.html"><span class="doc">USER-OMP package</span></a>. This is useful when
|
||||
offloading pair style computations to the Phi, 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>As illustrated below, if LAMMPS is built with both the USER-INTEL and
|
||||
USER-OMP packages, this dual mode of operation is made easier to use,
|
||||
via the “-suffix hybrid intel omp” <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> or the <a class="reference internal" href="suffix.html"><span class="doc">suffix hybrid intel omp</span></a> command. Both set a second-choice suffix to “omp” so
|
||||
that styles from the USER-INTEL package will be used if available,
|
||||
with styles from the USER-OMP package as a second choice.</p>
|
||||
<p>Here is a quick overview of how to use the USER-INTEL package for CPU
|
||||
acceleration, assuming one or more 16-core nodes. More details
|
||||
follow.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">use</span> <span class="n">an</span> <span class="n">Intel</span> <span class="n">compiler</span>
|
||||
<span class="n">use</span> <span class="n">these</span> <span class="n">CCFLAGS</span> <span class="n">settings</span> <span class="ow">in</span> <span class="n">Makefile</span><span class="o">.</span><span class="n">machine</span><span class="p">:</span> <span class="o">-</span><span class="n">fopenmp</span><span class="p">,</span> <span class="o">-</span><span class="n">DLAMMPS_MEMALIGN</span><span class="o">=</span><span class="mi">64</span><span class="p">,</span> <span class="o">-</span><span class="n">restrict</span><span class="p">,</span> <span class="o">-</span><span class="n">xHost</span><span class="p">,</span> <span class="o">-</span><span class="n">fno</span><span class="o">-</span><span class="n">alias</span><span class="p">,</span> <span class="o">-</span><span class="n">ansi</span><span class="o">-</span><span class="n">alias</span><span class="p">,</span> <span class="o">-</span><span class="n">override</span><span class="o">-</span><span class="n">limits</span>
|
||||
<span class="n">use</span> <span class="n">these</span> <span class="n">LINKFLAGS</span> <span class="n">settings</span> <span class="ow">in</span> <span class="n">Makefile</span><span class="o">.</span><span class="n">machine</span><span class="p">:</span> <span class="o">-</span><span class="n">fopenmp</span><span class="p">,</span> <span class="o">-</span><span class="n">xHost</span>
|
||||
<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">user</span><span class="o">-</span><span class="n">intel</span> <span class="n">yes</span><span class="o">-</span><span class="n">user</span><span class="o">-</span><span class="n">omp</span> <span class="c1"># including user-omp is optional</span>
|
||||
<span class="n">make</span> <span class="n">mpi</span> <span class="c1"># build with the USER-INTEL package, if settings (including compiler) added to Makefile.mpi</span>
|
||||
<span class="n">make</span> <span class="n">intel_cpu</span> <span class="c1"># or Makefile.intel_cpu already has settings, uses Intel MPI wrapper</span>
|
||||
<span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">v</span> <span class="o">-</span><span class="n">p</span> <span class="n">intel</span> <span class="n">omp</span> <span class="o">-</span><span class="n">intel</span> <span class="n">cpu</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">mpich_icc</span> <span class="c1"># or one-line build via Make.py for MPICH</span>
|
||||
<span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">v</span> <span class="o">-</span><span class="n">p</span> <span class="n">intel</span> <span class="n">omp</span> <span class="o">-</span><span class="n">intel</span> <span class="n">cpu</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">ompi_icc</span> <span class="c1"># or for OpenMPI</span>
|
||||
<span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">v</span> <span class="o">-</span><span class="n">p</span> <span class="n">intel</span> <span class="n">omp</span> <span class="o">-</span><span class="n">intel</span> <span class="n">cpu</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">intel_cpu</span> <span class="c1"># or for Intel MPI wrapper</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">intel</span> <span class="o">-</span><span class="n">pk</span> <span class="n">intel</span> <span class="mi">0</span> <span class="n">omp</span> <span class="mi">16</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 1 node, 1 MPI task/node, 16 threads/task, no USER-OMP</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">32</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">intel</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 2 nodess, 16 MPI tasks/node, no threads, no USER-OMP</span>
|
||||
<span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">hybrid</span> <span class="n">intel</span> <span class="n">omp</span> <span class="o">-</span><span class="n">pk</span> <span class="n">intel</span> <span class="mi">0</span> <span class="n">omp</span> <span class="mi">16</span> <span class="o">-</span><span class="n">pk</span> <span class="n">omp</span> <span class="mi">16</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 1 node, 1 MPI task/node, 16 threads/task, with USER-OMP</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">32</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">4</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">hybrid</span> <span class="n">intel</span> <span class="n">omp</span> <span class="o">-</span><span class="n">pk</span> <span class="n">omp</span> <span class="mi">4</span> <span class="o">-</span><span class="n">pk</span> <span class="n">omp</span> <span class="mi">4</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 8 nodes, 4 MPI tasks/node, 4 threads/task, with USER-OMP</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Here is a quick overview of how to use the USER-INTEL package for the
|
||||
same CPUs as above (16 cores/node), with an additional Xeon Phi(TM)
|
||||
coprocessor per node. More details follow.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Same</span> <span class="k">as</span> <span class="n">above</span> <span class="k">for</span> <span class="n">building</span><span class="p">,</span> <span class="k">with</span> <span class="n">these</span> <span class="n">additions</span><span class="o">/</span><span class="n">changes</span><span class="p">:</span>
|
||||
<span class="n">add</span> <span class="n">the</span> <span class="n">flag</span> <span class="o">-</span><span class="n">DLMP_INTEL_OFFLOAD</span> <span class="n">to</span> <span class="n">CCFLAGS</span> <span class="ow">in</span> <span class="n">Makefile</span><span class="o">.</span><span class="n">machine</span>
|
||||
<span class="n">add</span> <span class="n">the</span> <span class="n">flag</span> <span class="o">-</span><span class="n">offload</span> <span class="n">to</span> <span class="n">LINKFLAGS</span> <span class="ow">in</span> <span class="n">Makefile</span><span class="o">.</span><span class="n">machine</span>
|
||||
<span class="k">for</span> <span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="n">change</span> <span class="s2">"-intel cpu"</span> <span class="n">to</span> <span class="s2">"-intel phi"</span><span class="p">,</span> <span class="ow">and</span> <span class="s2">"file intel_cpu"</span> <span class="n">to</span> <span class="s2">"file intel_phi"</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">32</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">intel</span> <span class="o">-</span><span class="n">pk</span> <span class="n">intel</span> <span class="mi">1</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 2 nodes, 16 MPI tasks/node, 240 total threads on coprocessor, no USER-OMP</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">16</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">8</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">intel</span> <span class="o">-</span><span class="n">pk</span> <span class="n">intel</span> <span class="mi">1</span> <span class="n">omp</span> <span class="mi">2</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 2 nodes, 8 MPI tasks/node, 2 threads/task, 240 total threads on coprocessor, no USER-OMP</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">32</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">8</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">hybrid</span> <span class="n">intel</span> <span class="n">omp</span> <span class="o">-</span><span class="n">pk</span> <span class="n">intel</span> <span class="mi">1</span> <span class="n">omp</span> <span class="mi">2</span> <span class="o">-</span><span class="n">pk</span> <span class="n">omp</span> <span class="mi">2</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 4 nodes, 8 MPI tasks/node, 2 threads/task, 240 total threads on coprocessor, with USER-OMP</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p><strong>Required hardware/software:</strong></p>
|
||||
<p>Your compiler must support the OpenMP interface. Use of an Intel(R)
|
||||
C++ compiler is recommended, but not required. However, g++ will not
|
||||
recognize some of the settings listed above, so they cannot be used.
|
||||
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>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>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><strong>Building LAMMPS with the USER-INTEL package:</strong></p>
|
||||
<p>The lines above illustrate how to include/build with the USER-INTEL
|
||||
package, for either CPU or Phi support, in two steps, using the “make”
|
||||
command. Or how to do it with one command via the src/Make.py script,
|
||||
described in <a class="reference internal" href="Section_start.html#start-4"><span class="std std-ref">Section 2.4</span></a> of the manual.
|
||||
Type “Make.py -h” for help. Because the mechanism for specifing what
|
||||
compiler to use (Intel in this case) is different for different MPI
|
||||
wrappers, 3 versions of the Make.py command are shown.</p>
|
||||
<p>Note that if you build with support for a Phi coprocessor, the same
|
||||
binary can be used on nodes with or without coprocessors installed.
|
||||
However, if you do not have coprocessors on your system, building
|
||||
without offload support will produce a smaller binary.</p>
|
||||
<p>If you also build with the USER-OMP package, you can use styles from
|
||||
both packages, as described below.</p>
|
||||
<p>Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must
|
||||
include “-fopenmp”. Likewise, if you use an Intel compiler, the
|
||||
CCFLAGS setting must include “-restrict”. For Phi support, the
|
||||
“-DLMP_INTEL_OFFLOAD” (CCFLAGS) and “-offload” (LINKFLAGS) settings
|
||||
are required. The other settings listed above are optional, but will
|
||||
typically improve performance. The Make.py command will add all of
|
||||
these automatically.</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 enables vectorization
|
||||
with the Intel(R) compiler. Otherwise, you must provide the correct
|
||||
compute node architecture to the -x option (e.g. -xAVX).</p>
|
||||
<p>Example machines 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 has support for
|
||||
offload to Phi coprocessors; the former does not.</p>
|
||||
<p><strong>Run 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
|
||||
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 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. If both packages
|
||||
are used, it must be done for both packages, and the same thread count
|
||||
value should be used for both. 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>When using the USER-INTEL package for the Phi, you also need to
|
||||
specify the number of coprocessor/node and optionally 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>As in the lines above, use the “-sf intel” or “-sf hybrid intel omp”
|
||||
<a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a>, which will
|
||||
automatically append “intel” to styles that support it. In the second
|
||||
case, “omp” will be appended if an “intel” style does not exist.</p>
|
||||
<p>Note that if either switch is used, it also invokes a default command:
|
||||
<a class="reference internal" href="package.html"><span class="doc">package intel 1</span></a>. If the “-sf hybrid intel omp” switch
|
||||
is used, the default USER-OMP command <a class="reference internal" href="package.html"><span class="doc">package omp 0</span></a> is
|
||||
also invoked (if LAMMPS was built with USER-OMP). 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 (ignored if USER-INTEL is built for CPU-only),
|
||||
and the precision mode to “mixed” (default value).</p>
|
||||
<p>You can also use the “-pk intel Nphi” <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> to explicitly set Nphi = # of Xeon
|
||||
Phi(TM) coprocessors/node, as well as additional options. Nphi should
|
||||
be >= 1 if LAMMPS was built with coprocessor support, otherswise Nphi
|
||||
= 0 for a CPU-only build. 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 class="std std-ref">command-line switch</span></a> is
|
||||
used to limit the coprocessor threads per MPI task. See the <a class="reference internal" href="package.html"><span class="doc">package intel</span></a> command for details, including the default values
|
||||
used for all its options if not specified, and how to set the number
|
||||
of OpenMP threads via the OMP_NUM_THREADS environment variable if
|
||||
desired.</p>
|
||||
<p>If LAMMPS was built with the USER-OMP package, you can also use the
|
||||
“-pk omp Nt” <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> to
|
||||
explicitly set Nt = # of OpenMP threads per MPI task to use, as well
|
||||
as additional options. Nt should be the same threads per MPI task as
|
||||
set for the USER-INTEL package, e.g. via the “-pk intel Nphi omp Nt”
|
||||
command. Again, see the <a class="reference internal" href="package.html"><span class="doc">package omp</span></a> command for
|
||||
details, including the default values used for all its options if 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,
|
||||
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"><span class="doc">suffix intel</span></a> or <a class="reference internal" href="suffix.html"><span class="doc">suffix hybrid intel omp</span></a> commands, or you can explicitly add an “intel” or
|
||||
“omp” suffix to individual styles in your input script, e.g.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">intel</span> <span class="mf">2.5</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>You must also use the <a class="reference internal" href="package.html"><span class="doc">package intel</span></a> command, unless the
|
||||
“-sf intel” or “-pk intel” <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switches</span></a> were used. It specifies how many
|
||||
coprocessors/node to use, as well as other OpenMP threading and
|
||||
coprocessor options. The <a class="reference internal" href="package.html"><span class="doc">package</span></a> 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"><span class="doc">package omp</span></a> command to enable that package, unless
|
||||
the “-sf hybrid intel omp” or “-pk omp” <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switches</span></a> were used. It specifies how many
|
||||
OpenMP threads per MPI task to use (should be same as the setting for
|
||||
the USER-INTEL package), 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 (CPU only) 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
|
||||
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
|
||||
LAMMPS web site for performance of the USER-INTEL package on different
|
||||
hardware.</p>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">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 (CPU) 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"><span class="doc">package intel</span></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>
|
||||
</div>
|
||||
<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"><span class="doc">package intel</span></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
|
||||
automatically get affinity to a subset of the hardware threads
|
||||
available on the coprocessor. For example, if your card has 61 cores,
|
||||
with 60 cores available for offload and 4 hardware threads per core
|
||||
(240 total threads), running with 24 MPI tasks per node will cause
|
||||
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"><span class="doc">package intel</span></a> command.</li>
|
||||
<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"><span class="doc">package intel</span></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
|
||||
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
|
||||
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)
|
||||
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"><span class="doc">atom sorting</span></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,
|
||||
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"><span class="doc">package intel</span></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"><span class="doc">newton</span></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</h2>
|
||||
<p>When offloading to a coprocessor, <a class="reference internal" href="pair_hybrid.html"><span class="doc">hybrid</span></a> styles
|
||||
that require skip lists for neighbor builds cannot be offloaded.
|
||||
Using <a class="reference internal" href="pair_hybrid.html"><span class="doc">hybrid/overlay</span></a> is allowed. Only one intel
|
||||
accelerated style may be used with hybrid styles.
|
||||
<a class="reference internal" href="special_bonds.html"><span class="doc">Special_bonds</span></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"><span class="doc">run_style respa</span></a> command; only the “pair” option is
|
||||
supported.</p>
|
||||
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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 class="wy-breadcrumbs-aside">
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<a href="http://lammps.sandia.gov">Website</a>
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<p><a class="reference internal" href="Section_accelerate.html"><span class="doc">Return to Section accelerate overview</span></a></p>
|
||||
<div class="section" id="kokkos-package">
|
||||
<h1>5.KOKKOS package</h1>
|
||||
<p>The KOKKOS package was developed primarily 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
|
||||
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
|
||||
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
|
||||
CPU.</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. 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 currently provides support for 3 modes of execution (per MPI
|
||||
task). These are OpenMP (for many-core CPUs), Cuda (for NVIDIA GPUs),
|
||||
and OpenMP (for Intel Phi). Note that the KOKKOS package supports
|
||||
running on the Phi in native mode, not offload mode like the
|
||||
USER-INTEL package supports. You choose the mode at build time to
|
||||
produce an executable compatible with specific hardware.</p>
|
||||
<p>Here is a quick overview of how to use the KOKKOS package
|
||||
for CPU acceleration, assuming one or more 16-core nodes.
|
||||
More details follow.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">use</span> <span class="n">a</span> <span class="n">C</span><span class="o">++</span><span class="mi">11</span> <span class="n">compatible</span> <span class="n">compiler</span>
|
||||
<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span>
|
||||
<span class="n">make</span> <span class="n">mpi</span> <span class="n">KOKKOS_DEVICES</span><span class="o">=</span><span class="n">OpenMP</span> <span class="c1"># build with the KOKKOS package</span>
|
||||
<span class="n">make</span> <span class="n">kokkos_omp</span> <span class="c1"># or Makefile.kokkos_omp already has variable set</span>
|
||||
<span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">v</span> <span class="o">-</span><span class="n">p</span> <span class="n">kokkos</span> <span class="o">-</span><span class="n">kokkos</span> <span class="n">omp</span> <span class="o">-</span><span class="n">o</span> <span class="n">mpi</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">mpi</span> <span class="c1"># or one-line build via Make.py</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">16</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># 1 node, 16 MPI tasks/node, no threads</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">1</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">16</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># 2 nodes, 1 MPI task/node, 16 threads/task</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">8</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># 1 node, 2 MPI tasks/node, 8 threads/task</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">32</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">4</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">4</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># 8 nodes, 4 MPI tasks/node, 4 threads/task</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<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>Here is a quick overview of how to use the KOKKOS package for GPUs,
|
||||
assuming one or more nodes, each with 16 cores and a GPU. More
|
||||
details follow.</p>
|
||||
<p>discuss use of NVCC, which Makefiles to examine</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">use</span> <span class="n">a</span> <span class="n">C</span><span class="o">++</span><span class="mi">11</span> <span class="n">compatible</span> <span class="n">compiler</span>
|
||||
<span class="n">KOKKOS_DEVICES</span> <span class="o">=</span> <span class="n">Cuda</span><span class="p">,</span> <span class="n">OpenMP</span>
|
||||
<span class="n">KOKKOS_ARCH</span> <span class="o">=</span> <span class="n">Kepler35</span>
|
||||
<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span>
|
||||
<span class="n">make</span> <span class="n">machine</span>
|
||||
<span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="n">kokkos</span> <span class="o">-</span><span class="n">kokkos</span> <span class="n">cuda</span> <span class="n">arch</span><span class="o">=</span><span class="mi">31</span> <span class="o">-</span><span class="n">o</span> <span class="n">kokkos_cuda</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">kokkos_cuda</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">1</span> <span class="n">lmp_cuda</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">6</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># one MPI task, 6 threads on CPU</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">4</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">1</span> <span class="n">lmp_cuda</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">6</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># ditto on 4 nodes</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="n">lmp_cuda</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">8</span> <span class="n">g</span> <span class="mi">2</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># two MPI tasks, 8 threads per CPU</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">32</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">2</span> <span class="n">lmp_cuda</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">8</span> <span class="n">g</span> <span class="mi">2</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># ditto on 16 nodes</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Here is a quick overview of how to use the KOKKOS package
|
||||
for the Intel Phi:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">use</span> <span class="n">a</span> <span class="n">C</span><span class="o">++</span><span class="mi">11</span> <span class="n">compatible</span> <span class="n">compiler</span>
|
||||
<span class="n">KOKKOS_DEVICES</span> <span class="o">=</span> <span class="n">OpenMP</span>
|
||||
<span class="n">KOKKOS_ARCH</span> <span class="o">=</span> <span class="n">KNC</span>
|
||||
<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span>
|
||||
<span class="n">make</span> <span class="n">machine</span>
|
||||
<span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="n">kokkos</span> <span class="o">-</span><span class="n">kokkos</span> <span class="n">phi</span> <span class="o">-</span><span class="n">o</span> <span class="n">kokkos_phi</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">mpi</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">host</span><span class="o">=</span><span class="n">MIC</span><span class="p">,</span> <span class="n">Intel</span> <span class="n">Phi</span> <span class="k">with</span> <span class="mi">61</span> <span class="n">cores</span> <span class="p">(</span><span class="mi">240</span> <span class="n">threads</span><span class="o">/</span><span class="n">phi</span> <span class="n">via</span> <span class="mi">4</span><span class="n">x</span> <span class="n">hardware</span> <span class="n">threading</span><span class="p">):</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">1</span> <span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">240</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># 1 MPI task on 1 Phi, 1*240 = 240</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">30</span> <span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">8</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># 30 MPI tasks on 1 Phi, 30*8 = 240</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">12</span> <span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">20</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># 12 MPI tasks on 1 Phi, 12*20 = 240</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">96</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">12</span> <span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">20</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># ditto on 8 Phis</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p><strong>Required hardware/software:</strong></p>
|
||||
<p>Kokkos support within LAMMPS must be built with a C++11 compatible
|
||||
compiler. If using gcc, version 4.8.1 or later is required.</p>
|
||||
<p>To build with Kokkos support for CPUs, your compiler must support the
|
||||
OpenMP interface. You should have one or more multi-core CPUs so that
|
||||
multiple threads can be launched by each MPI task running on a CPU.</p>
|
||||
<p>To build with Kokkos support for NVIDIA GPUs, NVIDIA Cuda software
|
||||
version 6.5 or later must be installed on your system. See the
|
||||
discussion for the <a class="reference internal" href="accelerate_cuda.html"><span class="doc">USER-CUDA</span></a> and
|
||||
<a class="reference internal" href="accelerate_gpu.html"><span class="doc">GPU</span></a> packages for details of how to check and do
|
||||
this.</p>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">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 with Kokkos support for Intel Xeon Phi coprocessors, your
|
||||
sysmte must be configured to use them in “native” mode, not “offload”
|
||||
mode like the USER-INTEL package supports.</p>
|
||||
<p><strong>Building LAMMPS with the KOKKOS package:</strong></p>
|
||||
<p>You must choose at build time whether to build for CPUs (OpenMP),
|
||||
GPUs, 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 class="std std-ref">Section 2.4</span></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>
|
||||
<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 class="std std-ref">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"><span class="doc">package kokkos</span></a> or <a class="reference internal" href="suffix.html"><span class="doc">suffix kk</span></a> commands respectively to your input script.</p>
|
||||
<p>Or you can follow these steps:</p>
|
||||
<p>CPU-only (run all-MPI or with OpenMP threading):</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">lammps</span><span class="o">/</span><span class="n">src</span>
|
||||
<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span>
|
||||
<span class="n">make</span> <span class="n">g</span><span class="o">++</span> <span class="n">KOKKOS_DEVICES</span><span class="o">=</span><span class="n">OpenMP</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Intel Xeon Phi:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">lammps</span><span class="o">/</span><span class="n">src</span>
|
||||
<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span>
|
||||
<span class="n">make</span> <span class="n">g</span><span class="o">++</span> <span class="n">KOKKOS_DEVICES</span><span class="o">=</span><span class="n">OpenMP</span> <span class="n">KOKKOS_ARCH</span><span class="o">=</span><span class="n">KNC</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>CPUs and GPUs:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">lammps</span><span class="o">/</span><span class="n">src</span>
|
||||
<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span>
|
||||
<span class="n">make</span> <span class="n">cuda</span> <span class="n">KOKKOS_DEVICES</span><span class="o">=</span><span class="n">Cuda</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<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 note">
|
||||
<p class="first admonition-title">Note</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 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
|
||||
makefile, e.g. src/MAKE/Makefile.g++ in the first two examples above,
|
||||
with a line like:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><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
|
||||
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 note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">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 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 note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">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.
|
||||
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
|
||||
(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
|
||||
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
|
||||
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.
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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 class="std std-ref">command-line switch</span></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 class="std std-ref">documented here</span></a>. The two most commonly used
|
||||
options are:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="n">Nt</span> <span class="n">g</span> <span class="n">Ng</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<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
|
||||
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
|
||||
additional arguments) which sets various KOKKOS options to default
|
||||
values, as discussed on the <a class="reference internal" href="package.html"><span class="doc">package</span></a> command doc page.</p>
|
||||
<p>Use the “-sf kk” <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">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 class="std std-ref">command-line switch</span></a> if
|
||||
you wish to change any of the default <a class="reference internal" href="package.html"><span class="doc">package kokkos</span></a>
|
||||
optionns set by the “-k on” <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a>.</p>
|
||||
<p>Note that the default for the <a class="reference internal" href="package.html"><span class="doc">package kokkos</span></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"><span class="doc">newton</span></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 class="std std-ref">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
|
||||
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 class="std std-ref">command-line switch</span></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"><span class="doc">suffix kk</span></a> command, or you can explicitly add a
|
||||
“kk” suffix to individual styles in your input script, e.g.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">kk</span> <span class="mf">2.5</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>You only need to use the <a class="reference internal" href="package.html"><span class="doc">package kokkos</span></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 class="std std-ref">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 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,
|
||||
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,
|
||||
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
|
||||
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"><span class="doc">package kokkos</span></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
|
||||
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 class="std std-ref">command-line switch</span></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
|
||||
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-default"><div class="highlight"><pre><span></span><span class="n">OpenMPI</span> <span class="mf">1.8</span><span class="p">:</span> <span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="o">-</span><span class="n">bind</span><span class="o">-</span><span class="n">to</span> <span class="n">socket</span> <span class="o">-</span><span class="nb">map</span><span class="o">-</span><span class="n">by</span> <span class="n">socket</span> <span class="o">./</span><span class="n">lmp_openmpi</span> <span class="o">...</span>
|
||||
<span class="n">Mvapich2</span> <span class="mf">2.0</span><span class="p">:</span> <span class="n">mpiexec</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="o">-</span><span class="n">bind</span><span class="o">-</span><span class="n">to</span> <span class="n">socket</span> <span class="o">-</span><span class="nb">map</span><span class="o">-</span><span class="n">by</span> <span class="n">socket</span> <span class="o">./</span><span class="n">lmp_mvapich</span> <span class="o">...</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<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 class="std std-ref">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,
|
||||
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 class="std std-ref">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 class="std std-ref">command-line switch</span></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
|
||||
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 note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">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"><span class="doc">thermo</span></a> or <a class="reference internal" href="dump.html"><span class="doc">dump</span></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
|
||||
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)
|
||||
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
|
||||
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
|
||||
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
|
||||
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</h2>
|
||||
<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
|
||||
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>
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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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<p><a class="reference internal" href="Section_accelerate.html"><span class="doc">Return to Section accelerate overview</span></a></p>
|
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<div class="section" id="user-omp-package">
|
||||
<h1>5.USER-OMP package</h1>
|
||||
<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, assuming
|
||||
one or more 16-core nodes. More details follow.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">use</span> <span class="o">-</span><span class="n">fopenmp</span> <span class="k">with</span> <span class="n">CCFLAGS</span> <span class="ow">and</span> <span class="n">LINKFLAGS</span> <span class="ow">in</span> <span class="n">Makefile</span><span class="o">.</span><span class="n">machine</span>
|
||||
<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">user</span><span class="o">-</span><span class="n">omp</span>
|
||||
<span class="n">make</span> <span class="n">mpi</span> <span class="c1"># build with USER-OMP package, if settings added to Makefile.mpi</span>
|
||||
<span class="n">make</span> <span class="n">omp</span> <span class="c1"># or Makefile.omp already has settings</span>
|
||||
<span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">v</span> <span class="o">-</span><span class="n">p</span> <span class="n">omp</span> <span class="o">-</span><span class="n">o</span> <span class="n">mpi</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">mpi</span> <span class="c1"># or one-line build via Make.py</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">sf</span> <span class="n">omp</span> <span class="o">-</span><span class="n">pk</span> <span class="n">omp</span> <span class="mi">16</span> <span class="o"><</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 1 MPI task, 16 threads</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">4</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">sf</span> <span class="n">omp</span> <span class="o">-</span><span class="n">pk</span> <span class="n">omp</span> <span class="mi">4</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 4 MPI tasks, 4 threads/task</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">32</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">4</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">sf</span> <span class="n">omp</span> <span class="o">-</span><span class="n">pk</span> <span class="n">omp</span> <span class="mi">4</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 8 nodes, 4 MPI tasks/node, 4 threads/task</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p><strong>Required hardware/software:</strong></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
|
||||
each MPI task running on a CPU.</p>
|
||||
<p><strong>Building LAMMPS with the USER-OMP package:</strong></p>
|
||||
<p>The lines above illustrate how to include/build with the USER-OMP
|
||||
package in two steps, using the “make” command. Or how to do it with
|
||||
one command via the src/Make.py script, described in <a class="reference internal" href="Section_start.html#start-4"><span class="std std-ref">Section 2.4</span></a> of the manual. Type “Make.py -h” for
|
||||
help.</p>
|
||||
<p>Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must
|
||||
include “-fopenmp”. Likewise, if you use an Intel compiler, the
|
||||
CCFLAGS setting must include “-restrict”. The Make.py command will
|
||||
add these automatically.</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
|
||||
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 OpenMP 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>As in the lines above, use the “-sf omp” <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a>, which will automatically append
|
||||
“omp” to styles that support it. The “-sf omp” switch also issues a
|
||||
default <a class="reference internal" href="package.html"><span class="doc">package omp 0</span></a> command, which will set the
|
||||
number of threads per MPI task via the OMP_NUM_THREADS environment
|
||||
variable.</p>
|
||||
<p>You can also use the “-pk omp Nt” <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a>, to explicitly set Nt = # of OpenMP
|
||||
threads per MPI task to use, as well as additional options. Its
|
||||
syntax is the same as the <a class="reference internal" href="package.html"><span class="doc">package omp</span></a> command whose doc
|
||||
page gives details, including the default values used if it is not
|
||||
specified. It also gives more details on how to set the number of
|
||||
threads via the OMP_NUM_THREADS environment variable.</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"><span class="doc">suffix omp</span></a> command, or you can explicitly add an
|
||||
“omp” suffix to individual styles in your input script, e.g.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">omp</span> <span class="mf">2.5</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>You must also use the <a class="reference internal" href="package.html"><span class="doc">package omp</span></a> command to enable the
|
||||
USER-OMP package. When you do this you also specify how many threads
|
||||
per MPI task to use. The command doc page explains other options and
|
||||
how to set the number of threads via the OMP_NUM_THREADS environment
|
||||
variable.</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
|
||||
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, described in <a class="reference internal" href="accelerate_opt.html"><span class="doc">Section accelerate 5.3.6</span></a>.</p>
|
||||
<p>With multiple threads/task, the optimal choice of number 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
|
||||
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
|
||||
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
|
||||
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
|
||||
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"><span class="doc">domain decomposition scheme</span></a> or
|
||||
<a class="reference internal" href="balance.html"><span class="doc">load-balancing</span></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
|
||||
where MPI parallelism is maxed out. For example, this can happen when
|
||||
using the <a class="reference internal" href="kspace_style.html"><span class="doc">PPPM solver</span></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"><span class="doc">kspace_style</span></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"><span class="doc">run_style verlet/split</span></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
|
||||
when there is at least one MPI task per physical CPU chip, 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>NOTE: By default, several current MPI implementations use a processor
|
||||
affinity setting that restricts each MPI task to a single CPU core.
|
||||
Using multi-threading in this mode will force all threads to share the
|
||||
one 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</h2>
|
||||
<p>None.</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
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</div>
|
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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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<p><a class="reference internal" href="Section_accelerate.html"><span class="doc">Return to Section accelerate overview</span></a></p>
|
||||
<div class="section" id="opt-package">
|
||||
<h1>5.OPT package</h1>
|
||||
<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. More details
|
||||
follow.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">opt</span>
|
||||
<span class="n">make</span> <span class="n">mpi</span> <span class="c1"># build with the OPT package</span>
|
||||
<span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">v</span> <span class="o">-</span><span class="n">p</span> <span class="n">opt</span> <span class="o">-</span><span class="n">o</span> <span class="n">mpi</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">mpi</span> <span class="c1"># or one-line build via Make.py</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">sf</span> <span class="n">opt</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># run in serial</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">4</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">sf</span> <span class="n">opt</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># run in parallel</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p><strong>Required hardware/software:</strong></p>
|
||||
<p>None.</p>
|
||||
<p><strong>Building LAMMPS with the OPT package:</strong></p>
|
||||
<p>The lines above illustrate how to build LAMMPS with the OPT package in
|
||||
two steps, using the “make” command. Or how to do it with one command
|
||||
via the src/Make.py script, described in <a class="reference internal" href="Section_start.html#start-4"><span class="std std-ref">Section 2.4</span></a> of the manual. Type “Make.py -h” for
|
||||
help.</p>
|
||||
<p>Note that if you use an Intel compiler to build with the OPT package,
|
||||
the CCFLAGS setting in your Makefile.machine must include “-restrict”.
|
||||
The Make.py command will add this automatically.</p>
|
||||
<p><strong>Run with the OPT package from the command line:</strong></p>
|
||||
<p>As in the lines above, use the “-sf opt” <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a>, which will automatically append
|
||||
“opt” to styles that support it.</p>
|
||||
<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"><span class="doc">suffix opt</span></a> command, or you can explicitly add an
|
||||
“opt” suffix to individual styles in your input script, e.g.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">opt</span> <span class="mf">2.5</span>
|
||||
</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
|
||||
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>Just try out an OPT pair style to see how it performs.</p>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<p>None.</p>
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<div class="section" id="angle-style-charmm-command">
|
||||
<span id="index-0"></span><h1>angle_style charmm command</h1>
|
||||
</div>
|
||||
<div class="section" id="angle-style-charmm-intel-command">
|
||||
<h1>angle_style charmm/intel command</h1>
|
||||
</div>
|
||||
<div class="section" id="angle-style-charmm-kk-command">
|
||||
<h1>angle_style charmm/kk command</h1>
|
||||
</div>
|
||||
<div class="section" id="angle-style-charmm-omp-command">
|
||||
<h1>angle_style charmm/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">charmm</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">charmm</span>
|
||||
<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="mf">300.0</span> <span class="mf">107.0</span> <span class="mf">50.0</span> <span class="mf">3.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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
|
||||
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 class="std std-ref">(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"><span class="doc">angle_coeff</span></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"><span class="doc">read_data</span></a>
|
||||
or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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</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 class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></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>
|
||||
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<li>angle_style class2 command</li>
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<div class="section" id="angle-style-class2-command">
|
||||
<span id="index-0"></span><h1>angle_style class2 command</h1>
|
||||
</div>
|
||||
<div class="section" id="angle-style-class2-omp-command">
|
||||
<h1>angle_style class2/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">class2</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">class2</span>
|
||||
<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">75.0</span>
|
||||
<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="n">bb</span> <span class="mf">10.5872</span> <span class="mf">1.0119</span> <span class="mf">1.5228</span>
|
||||
<span class="n">angle_coeff</span> <span class="o">*</span> <span class="n">ba</span> <span class="mf">3.6551</span> <span class="mf">24.895</span> <span class="mf">1.0119</span> <span class="mf">1.5228</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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
|
||||
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 class="std std-ref">(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"><span class="doc">angle_coeff</span></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"><span class="doc">read_data</span></a> or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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"><span class="doc">angle_coeff</span></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"><span class="doc">angle_coeff</span></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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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</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 class="std std-ref">Making LAMMPS</span></a> section
|
||||
for more info on packages.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></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>
|
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<div class="section" id="angle-coeff-command">
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<span id="index-0"></span><h1>angle_coeff command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_coeff</span> <span class="n">N</span> <span class="n">args</span>
|
||||
</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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_coeff</span> <span class="mi">1</span> <span class="mf">300.0</span> <span class="mf">107.0</span>
|
||||
<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">5.0</span>
|
||||
<span class="n">angle_coeff</span> <span class="mi">2</span><span class="o">*</span><span class="mi">10</span> <span class="mf">5.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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"><span class="doc">read_data</span></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,
|
||||
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
|
||||
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-default"><div class="highlight"><pre><span></span><span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">200.0</span> <span class="mf">107.0</span> <span class="mf">1.2</span>
|
||||
<span class="n">angle_coeff</span> <span class="mi">2</span> <span class="mf">50.0</span> <span class="mf">107.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<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-default"><div class="highlight"><pre><span></span><span class="mi">1</span> <span class="mf">300.0</span> <span class="mf">107.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The <a class="reference internal" href="angle_class2.html"><span class="doc">angle_style class2</span></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
|
||||
the style to display the formula it computes and coefficients
|
||||
specified by the associated <a class="reference internal" href="#"><span class="doc">angle_coeff</span></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 class="std std-ref">this page</span></a>.</p>
|
||||
<ul class="simple">
|
||||
<li><a class="reference internal" href="angle_none.html"><span class="doc">angle_style none</span></a> - turn off angle interactions</li>
|
||||
<li><a class="reference internal" href="angle_hybrid.html"><span class="doc">angle_style hybrid</span></a> - define multiple styles of angle interactions</li>
|
||||
<li><a class="reference internal" href="angle_charmm.html"><span class="doc">angle_style charmm</span></a> - CHARMM angle</li>
|
||||
<li><a class="reference internal" href="angle_class2.html"><span class="doc">angle_style class2</span></a> - COMPASS (class 2) angle</li>
|
||||
<li><a class="reference internal" href="angle_cosine.html"><span class="doc">angle_style cosine</span></a> - cosine angle potential</li>
|
||||
<li><a class="reference internal" href="angle_cosine_delta.html"><span class="doc">angle_style cosine/delta</span></a> - difference of cosines angle potential</li>
|
||||
<li><a class="reference internal" href="angle_cosine_periodic.html"><span class="doc">angle_style cosine/periodic</span></a> - DREIDING angle</li>
|
||||
<li><a class="reference internal" href="angle_cosine_squared.html"><span class="doc">angle_style cosine/squared</span></a> - cosine squared angle potential</li>
|
||||
<li><a class="reference internal" href="angle_harmonic.html"><span class="doc">angle_style harmonic</span></a> - harmonic angle</li>
|
||||
<li><a class="reference internal" href="angle_table.html"><span class="doc">angle_style table</span></a> - tabulated by angle</li>
|
||||
</ul>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<p>This command must come after the simulation box is defined by a
|
||||
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>, <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>, or
|
||||
<a class="reference internal" href="create_box.html"><span class="doc">create_box</span></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</h2>
|
||||
<p><a class="reference internal" href="angle_style.html"><span class="doc">angle_style</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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|
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|
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</p>
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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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<div class="section" id="angle-style-cosine-command">
|
||||
<span id="index-0"></span><h1>angle_style cosine command</h1>
|
||||
</div>
|
||||
<div class="section" id="angle-style-cosine-omp-command">
|
||||
<h1>angle_style cosine/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span>
|
||||
<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">75.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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"><span class="doc">angle_coeff</span></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"><span class="doc">read_data</span></a>
|
||||
or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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</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 class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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© Copyright 2013 Sandia Corporation.
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</p>
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</div>
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<li>angle_style cosine/delta command</li>
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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</h1>
|
||||
</div>
|
||||
<div class="section" id="angle-style-cosine-delta-omp-command">
|
||||
<h1>angle_style cosine/delta/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">delta</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">delta</span>
|
||||
<span class="n">angle_coeff</span> <span class="mi">2</span><span class="o">*</span><span class="mi">4</span> <span class="mf">75.0</span> <span class="mf">100.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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"><span class="doc">angle_coeff</span></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"><span class="doc">read_data</span></a>
|
||||
or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
|
||||
more instructions on how to use the accelerated styles effectively.</p>
|
||||
</div>
|
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<hr class="docutils" />
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</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 class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a>, <a class="reference internal" href="angle_cosine_squared.html"><span class="doc">angle_style cosine/squared</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
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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</h1>
|
||||
</div>
|
||||
<div class="section" id="angle-style-cosine-periodic-omp-command">
|
||||
<h1>angle_style cosine/periodic/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">periodic</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">periodic</span>
|
||||
<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">75.0</span> <span class="mi">1</span> <span class="mi">6</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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 class="std std-ref">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 class="std std-ref">(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"><span class="doc">angle_coeff</span></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"><span class="doc">read_data</span></a>
|
||||
or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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
|
||||
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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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</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 class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></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>
|
||||
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<div class="section" id="angle-style-cosine-shift-command">
|
||||
<span id="index-0"></span><h1>angle_style cosine/shift command</h1>
|
||||
</div>
|
||||
<div class="section" id="angle-style-cosine-shift-omp-command">
|
||||
<h1>angle_style cosine/shift/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span>
|
||||
<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">10.0</span> <span class="mf">45.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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
|
||||
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"><span class="doc">angle_coeff</span></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"><span class="doc">read_data</span></a>
|
||||
or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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</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 class="std std-ref">Making LAMMPS</span></a>
|
||||
section for more info on packages.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a>,
|
||||
<span class="xref doc">angle_cosineshiftexp</span></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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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</h1>
|
||||
</div>
|
||||
<div class="section" id="angle-style-cosine-shift-exp-omp-command">
|
||||
<h1>angle_style cosine/shift/exp/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">exp</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">exp</span>
|
||||
<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">10.0</span> <span class="mf">45.0</span> <span class="mf">2.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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
|
||||
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
|
||||
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"><span class="doc">angle_coeff</span></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"><span class="doc">read_data</span></a>
|
||||
or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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</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 class="std std-ref">Making LAMMPS</span></a>
|
||||
section for more info on packages.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a>,
|
||||
<span class="xref doc">angle_cosineshift</span>,
|
||||
<span class="xref doc">dihedral_cosineshift</span></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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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</h1>
|
||||
</div>
|
||||
<div class="section" id="angle-style-cosine-squared-omp-command">
|
||||
<h1>angle_style cosine/squared/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">squared</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">squared</span>
|
||||
<span class="n">angle_coeff</span> <span class="mi">2</span><span class="o">*</span><span class="mi">4</span> <span class="mf">75.0</span> <span class="mf">100.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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"><span class="doc">angle_coeff</span></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"><span class="doc">read_data</span></a>
|
||||
or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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</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 class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
</div>
|
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© Copyright 2013 Sandia Corporation.
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</p>
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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</h1>
|
||||
</div>
|
||||
<div class="section" id="angle-style-dipole-omp-command">
|
||||
<h1>angle_style dipole/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">dipole</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">dipole</span>
|
||||
<span class="n">angle_coeff</span> <span class="mi">6</span> <span class="mf">2.1</span> <span class="mf">180.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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 class="std std-ref">(Orsi)</span></a>. Specifically, the <em>dipole</em> 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 class="std std-ref">(Allen)</span></a>:</p>
|
||||
<img alt="_images/angle_dipole_torque.jpg" class="align-center" src="_images/angle_dipole_torque.jpg" />
|
||||
<p>Example: if gamma0 is set to 0 degrees, the torque generated by
|
||||
the potential will tend to align the dipole along the reference
|
||||
direction defined by the (bond) vector r_ij (in other words, mu_j is
|
||||
restrained to point towards atom ‘i’).</p>
|
||||
<p>The dipolar torque T_j must be counterbalanced in order to conserve
|
||||
the local angular momentum. This is achieved via an additional force
|
||||
couple generating a torque equivalent to the opposite of T_j:</p>
|
||||
<img alt="_images/angle_dipole_couple.jpg" class="align-center" src="_images/angle_dipole_couple.jpg" />
|
||||
<p>where F_i and F_j are applied on atoms i and j, respectively.</p>
|
||||
<p>The following coefficients must be defined for each angle type via the
|
||||
<a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></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"><span class="doc">read_data</span></a>
|
||||
or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
|
||||
more instructions on how to use the accelerated styles effectively.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</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 note">
|
||||
<p class="first admonition-title">Note</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 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</h2>
|
||||
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a>, <a class="reference internal" href="angle_hybrid.html"><span class="doc">angle_hybrid</span></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>
|
||||
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<div class="section" id="angle-style-fourier-command">
|
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<span id="index-0"></span><h1>angle_style fourier command</h1>
|
||||
</div>
|
||||
<div class="section" id="angle-style-fourier-omp-command">
|
||||
<h1>angle_style fourier/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">fourier</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<p>angle_style fourier
|
||||
angle_coeff 75.0 1.0 1.0 1.0</p>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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"><span class="doc">angle_coeff</span></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"><span class="doc">read_data</span></a>
|
||||
or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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</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 class="std std-ref">Making LAMMPS</span></a>
|
||||
section for more info on packages.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a></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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<div class="section" id="angle-style-fourier-simple-command">
|
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<span id="index-0"></span><h1>angle_style fourier/simple command</h1>
|
||||
</div>
|
||||
<div class="section" id="angle-style-fourier-simple-omp-command">
|
||||
<h1>angle_style fourier/simple/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">fourier</span><span class="o">/</span><span class="n">simple</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<p>angle_style fourier/simple
|
||||
angle_coeff 100.0 -1.0 1.0</p>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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"><span class="doc">angle_coeff</span></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"><span class="doc">read_data</span></a>
|
||||
or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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</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 class="std std-ref">Making LAMMPS</span></a>
|
||||
section for more info on packages.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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© Copyright 2013 Sandia Corporation.
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<div class="section" id="angle-style-harmonic-command">
|
||||
<span id="index-0"></span><h1>angle_style harmonic command</h1>
|
||||
</div>
|
||||
<div class="section" id="angle-style-harmonic-intel-command">
|
||||
<h1>angle_style harmonic/intel command</h1>
|
||||
</div>
|
||||
<div class="section" id="angle-style-harmonic-kk-command">
|
||||
<h1>angle_style harmonic/kk command</h1>
|
||||
</div>
|
||||
<div class="section" id="angle-style-harmonic-omp-command">
|
||||
<h1>angle_style harmonic/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">harmonic</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">harmonic</span>
|
||||
<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="mf">300.0</span> <span class="mf">107.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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"><span class="doc">angle_coeff</span></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"><span class="doc">read_data</span></a>
|
||||
or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
|
||||
more instructions on how to use the accelerated styles effectively.</p>
|
||||
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|
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<hr class="docutils" />
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</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 class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
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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</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">hybrid</span> <span class="n">style1</span> <span class="n">style2</span> <span class="o">...</span>
|
||||
</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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">hybrid</span> <span class="n">harmonic</span> <span class="n">cosine</span>
|
||||
<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="n">harmonic</span> <span class="mf">80.0</span> <span class="mf">30.0</span>
|
||||
<span class="n">angle_coeff</span> <span class="mi">2</span><span class="o">*</span> <span class="n">cosine</span> <span class="mf">50.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<p>The <em>hybrid</em> 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"><span class="doc">angle_coeff</span></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>
|
||||
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"><span class="doc">read_data</span></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-default"><div class="highlight"><pre><span></span><span class="n">Angle</span> <span class="n">Coeffs</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="mi">1</span> <span class="n">harmonic</span> <span class="mf">80.0</span> <span class="mf">30.0</span>
|
||||
<span class="mi">2</span> <span class="n">cosine</span> <span class="mf">50.0</span>
|
||||
<span class="o">...</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>If <em>class2</em> 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
|
||||
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-default"><div class="highlight"><pre><span></span><span class="n">BondBond</span> <span class="n">Coeffs</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="mi">1</span> <span class="n">skip</span>
|
||||
<span class="mi">2</span> <span class="n">class2</span> <span class="mf">3.6512</span> <span class="mf">1.0119</span> <span class="mf">1.0119</span>
|
||||
<span class="o">...</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Note that it is not necessary to use the angle style <em>skip</em> 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
|
||||
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</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 class="std std-ref">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"><span class="doc">binary restart files</span></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</h2>
|
||||
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
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<div class="section" id="angle-style-none-command">
|
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<span id="index-0"></span><h1>angle_style none command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">none</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">none</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<p>Using an angle style of none means angle forces and energies 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"><span class="doc">read_data</span></a> command.</p>
|
||||
<p>See the <a class="reference internal" href="angle_zero.html"><span class="doc">angle_style zero</span></a> command for a way to
|
||||
calculate angle statistics, but compute no angle interactions.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="angle_zero.html"><span class="doc">angle_style zero</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
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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 itemprop="articleBody">
|
||||
|
||||
<div class="section" id="angle-style-quartic-command">
|
||||
<span id="index-0"></span><h1>angle_style quartic command</h1>
|
||||
</div>
|
||||
<div class="section" id="angle-style-quartic-omp-command">
|
||||
<h1>angle_style quartic/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">quartic</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">quartic</span>
|
||||
<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="mf">129.1948</span> <span class="mf">56.8726</span> <span class="o">-</span><span class="mf">25.9442</span> <span class="o">-</span><span class="mf">14.2221</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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"><span class="doc">angle_coeff</span></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"><span class="doc">read_data</span></a>
|
||||
or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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</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 class="std std-ref">Making LAMMPS</span></a>
|
||||
section for more info on packages.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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</p>
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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_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_errors.html">12. Errors</a></li>
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<div class="section" id="angle-style-sdk-command">
|
||||
<span id="index-0"></span><h1>angle_style sdk command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">sdk</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">sdk</span><span class="o">/</span><span class="n">omp</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">sdk</span>
|
||||
<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="mf">300.0</span> <span class="mf">107.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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
|
||||
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"><span class="doc">pair_style lj/sdk</span></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"><span class="doc">angle_coeff</span></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
|
||||
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</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 class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a>, <a class="reference internal" href="angle_harmonic.html"><span class="doc">angle_style harmonic</span></a>, <a class="reference internal" href="pair_sdk.html"><span class="doc">pair_style lj/sdk</span></a>,
|
||||
<a class="reference internal" href="pair_sdk.html"><span class="doc">pair_style lj/sdk/coul/long</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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|
||||
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|
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</p>
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<div class="section" id="angle-style-command">
|
||||
<span id="index-0"></span><h1>angle_style command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">style</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>style = <em>none</em> or <em>hybrid</em> or <em>charmm</em> or <em>class2</em> or <em>cosine</em> or <em>cosine/squared</em> or <em>harmonic</em></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">harmonic</span>
|
||||
<span class="n">angle_style</span> <span class="n">charmm</span>
|
||||
<span class="n">angle_style</span> <span class="n">hybrid</span> <span class="n">harmonic</span> <span class="n">cosine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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"><span class="doc">read_data</span></a> or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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"><span class="doc">angle_coeff</span></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"><span class="doc">angle_coeff</span></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"><span class="doc">read_restart</span></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 note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">When both an angle and pair style is defined, the
|
||||
<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></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
|
||||
the style to display the formula it computes and coefficients
|
||||
specified by the associated <a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></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 class="std std-ref">this page</span></a>.</p>
|
||||
<ul class="simple">
|
||||
<li><a class="reference internal" href="angle_none.html"><span class="doc">angle_style none</span></a> - turn off angle interactions</li>
|
||||
<li><a class="reference internal" href="angle_zero.html"><span class="doc">angle_style zero</span></a> - topology but no interactions</li>
|
||||
<li><a class="reference internal" href="angle_hybrid.html"><span class="doc">angle_style hybrid</span></a> - define multiple styles of angle interactions</li>
|
||||
<li><a class="reference internal" href="angle_charmm.html"><span class="doc">angle_style charmm</span></a> - CHARMM angle</li>
|
||||
<li><a class="reference internal" href="angle_class2.html"><span class="doc">angle_style class2</span></a> - COMPASS (class 2) angle</li>
|
||||
<li><a class="reference internal" href="angle_cosine.html"><span class="doc">angle_style cosine</span></a> - cosine angle potential</li>
|
||||
<li><a class="reference internal" href="angle_cosine_delta.html"><span class="doc">angle_style cosine/delta</span></a> - difference of cosines angle potential</li>
|
||||
<li><a class="reference internal" href="angle_cosine_periodic.html"><span class="doc">angle_style cosine/periodic</span></a> - DREIDING angle</li>
|
||||
<li><a class="reference internal" href="angle_cosine_squared.html"><span class="doc">angle_style cosine/squared</span></a> - cosine squared angle potential</li>
|
||||
<li><a class="reference internal" href="angle_harmonic.html"><span class="doc">angle_style harmonic</span></a> - harmonic angle</li>
|
||||
<li><a class="reference internal" href="angle_table.html"><span class="doc">angle_style table</span></a> - tabulated by angle</li>
|
||||
</ul>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</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 class="std std-ref">Making LAMMPS</span></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</h2>
|
||||
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a></p>
|
||||
</div>
|
||||
<div class="section" id="default">
|
||||
<h2>Default</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">none</span>
|
||||
</pre></div>
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<div class="section" id="angle-style-table-command">
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<span id="index-0"></span><h1>angle_style table command</h1>
|
||||
</div>
|
||||
<div class="section" id="angle-style-table-omp-command">
|
||||
<h1>angle_style table/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">table</span> <span class="n">style</span> <span class="n">N</span>
|
||||
</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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">table</span> <span class="n">linear</span> <span class="mi">1000</span>
|
||||
<span class="n">angle_coeff</span> <span class="mi">3</span> <span class="n">file</span><span class="o">.</span><span class="n">table</span> <span class="n">ENTRY1</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<p>Style <em>table</em> creates interpolation tables of length <em>N</em> 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"><span class="doc">angle_coeff</span></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
|
||||
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
|
||||
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
|
||||
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"><span class="doc">angle_coeff</span></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
|
||||
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-default"><div class="highlight"><pre><span></span><span class="c1"># Angle potential for harmonic (one or more comment or blank lines)</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">HAM</span> <span class="p">(</span><span class="n">keyword</span> <span class="ow">is</span> <span class="n">the</span> <span class="n">first</span> <span class="n">text</span> <span class="n">on</span> <span class="n">line</span><span class="p">)</span>
|
||||
<span class="n">N</span> <span class="mi">181</span> <span class="n">FP</span> <span class="mi">0</span> <span class="mi">0</span> <span class="n">EQ</span> <span class="mf">90.0</span> <span class="p">(</span><span class="n">N</span><span class="p">,</span> <span class="n">FP</span><span class="p">,</span> <span class="n">EQ</span> <span class="n">parameters</span><span class="p">)</span>
|
||||
<span class="p">(</span><span class="n">blank</span> <span class="n">line</span><span class="p">)</span>
|
||||
<span class="n">N</span> <span class="mi">181</span> <span class="n">FP</span> <span class="mi">0</span> <span class="mi">0</span> <span class="p">(</span><span class="n">N</span><span class="p">,</span> <span class="n">FP</span> <span class="n">parameters</span><span class="p">)</span>
|
||||
<span class="mi">1</span> <span class="mf">0.0</span> <span class="mf">200.5</span> <span class="mf">2.5</span> <span class="p">(</span><span class="n">index</span><span class="p">,</span> <span class="n">angle</span><span class="p">,</span> <span class="n">energy</span><span class="p">,</span> <span class="n">derivative</span><span class="p">)</span>
|
||||
<span class="mi">2</span> <span class="mf">1.0</span> <span class="mf">198.0</span> <span class="mf">2.5</span>
|
||||
<span class="o">...</span>
|
||||
<span class="mi">181</span> <span class="mf">180.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
|
||||
</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
|
||||
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"><span class="doc">angle_coeff</span></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"><span class="doc">angle_style table</span></a> command. Let
|
||||
Ntable = <em>N</em> 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
|
||||
values at Ntable different points. The resulting tables of length
|
||||
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
|
||||
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
|
||||
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"><span class="doc">fix shake</span></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
|
||||
term is the energy of the 3-atom configuration for the specified
|
||||
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
|
||||
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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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</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 class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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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_tools.html">9. Additional tools</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-zero-command">
|
||||
<span id="index-0"></span><h1>angle_style zero command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<pre class="literal-block">
|
||||
angle_style zero <em>nocoeff</em>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">zero</span>
|
||||
<span class="n">angle_style</span> <span class="n">zero</span> <span class="n">nocoeff</span>
|
||||
<span class="n">angle_coeff</span> <span class="o">*</span>
|
||||
<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">120.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<p>Using an angle style of zero means angle forces and energies are not
|
||||
computed, but the geometry of angle triplets is still accessible to
|
||||
other commands.</p>
|
||||
<p>As an example, the <a class="reference internal" href="compute_angle_local.html"><span class="doc">compute angle/local</span></a>
|
||||
command can be used to compute the theta values for the list of
|
||||
triplets of angle atoms listed in the data file read by the
|
||||
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command. If no angle style is defined,
|
||||
this command cannot be used.</p>
|
||||
<p>The optional <em>nocoeff</em> flag allows to read data files with AngleCoeff
|
||||
section for any angle style. Similarly, any angle_coeff commands
|
||||
will only be checked for the angle type number and the rest ignored.</p>
|
||||
<p>Note that the <a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a> command must be used for
|
||||
all angle types. If specified, there can be only one value, which is
|
||||
going to be used to assign an equilibrium angle, e.g. for use with
|
||||
<a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="angle_none.html"><span class="doc">angle_style none</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
</div>
|
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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="atom-modify-command">
|
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<span id="index-0"></span><h1>atom_modify command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_modify</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
|
||||
</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
|
||||
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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_modify</span> <span class="nb">map</span> <span class="nb">hash</span>
|
||||
<span class="n">atom_modify</span> <span class="nb">map</span> <span class="n">array</span> <span class="n">sort</span> <span class="mi">10000</span> <span class="mf">2.0</span>
|
||||
<span class="n">atom_modify</span> <span class="n">first</span> <span class="n">colloid</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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"><span class="doc">atom_style</span></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"><span class="doc">create atoms</span></a> or
|
||||
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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
|
||||
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"><span class="doc">atom styles</span></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
|
||||
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 class="std std-ref">Section 2.2</span></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
|
||||
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
|
||||
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
|
||||
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
|
||||
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"><span class="doc">velocity loop all</span></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"><span class="doc">group</span></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"><span class="doc">neigh_modify include</span></a> and <a class="reference internal" href="comm_modify.html"><span class="doc">comm_modify group</span></a>
|
||||
commands are two examples of commands that require this setting to
|
||||
work efficiently. Several <a class="reference internal" href="fix.html"><span class="doc">fixes</span></a>, most notably time
|
||||
integration fixes like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></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
|
||||
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
|
||||
cache performance and thus speed-up a LAMMPS simulation, as discussed
|
||||
in a paper by <a class="reference internal" href="#meloni"><span class="std std-ref">(Meloni)</span></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
|
||||
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"><span class="doc">neighbor</span></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
|
||||
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 note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">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"><span class="doc">velocity create</span></a>, and <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></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"><span class="doc">dump</span></a> file will also typically change
|
||||
if sorting is enabled.</p>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</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</h2>
|
||||
<p>By default, <em>id</em> is yes. By default, atomic systems (no bond topology
|
||||
info) do not use a map. For molecular systems (with bond topology
|
||||
info), a map is used. The default map style is array if no atom ID is
|
||||
larger than 1 million, otherwise the default is hash. By default, a
|
||||
“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>
|
||||
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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>atom_style command</li>
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<a href="http://lammps.sandia.gov">Website</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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|
||||
<div class="section" id="atom-style-command">
|
||||
<span id="index-0"></span><h1>atom_style command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">style</span> <span class="n">args</span>
|
||||
</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>dpd</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>smd</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 the following
|
||||
<em>body</em> 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"><span class="doc">body</span></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"><span class="doc">molecule</span></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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">atomic</span>
|
||||
<span class="n">atom_style</span> <span class="n">bond</span>
|
||||
<span class="n">atom_style</span> <span class="n">full</span>
|
||||
<span class="n">atom_style</span> <span class="n">full</span><span class="o">/</span><span class="n">cuda</span>
|
||||
<span class="n">atom_style</span> <span class="n">body</span> <span class="n">nparticle</span> <span class="mi">2</span> <span class="mi">10</span>
|
||||
<span class="n">atom_style</span> <span class="n">hybrid</span> <span class="n">charge</span> <span class="n">bond</span>
|
||||
<span class="n">atom_style</span> <span class="n">hybrid</span> <span class="n">charge</span> <span class="n">body</span> <span class="n">nparticle</span> <span class="mi">2</span> <span class="mi">5</span>
|
||||
<span class="n">atom_style</span> <span class="n">template</span> <span class="n">myMols</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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"><span class="doc">read_data</span></a>,
|
||||
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>, or <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a>
|
||||
command.</p>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">Many of the atom styles discussed here are only enabled if
|
||||
LAMMPS was built with a specific package, as listed below in the
|
||||
Restrictions section.</p>
|
||||
</div>
|
||||
<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
|
||||
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,
|
||||
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"><span class="doc">read_data</span></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"><span class="doc">read_data</span></a>, <a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a>, and
|
||||
<a class="reference internal" href="set.html"><span class="doc">set</span></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>dpd</em></td>
|
||||
<td>internal temperature and internal energies</td>
|
||||
<td>DPD particles</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><em>electron</em></td>
|
||||
<td>charge and spin and eradius</td>
|
||||
<td>electronic force field</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><em>ellipsoid</em></td>
|
||||
<td>shape, quaternion, angular momentum</td>
|
||||
<td>aspherical particles</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><em>full</em></td>
|
||||
<td>molecular + charge</td>
|
||||
<td>bio-molecules</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><em>line</em></td>
|
||||
<td>end points, angular velocity</td>
|
||||
<td>rigid bodies</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><em>meso</em></td>
|
||||
<td>rho, e, cv</td>
|
||||
<td>SPH particles</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><em>molecular</em></td>
|
||||
<td>bonds, angles, dihedrals, impropers</td>
|
||||
<td>uncharged molecules</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><em>peri</em></td>
|
||||
<td>mass, volume</td>
|
||||
<td>mesocopic Peridynamic models</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><em>smd</em></td>
|
||||
<td>volume, kernel diameter, contact radius, mass</td>
|
||||
<td>solid and fluid SPH particles</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 note">
|
||||
<p class="first admonition-title">Note</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"><span class="doc">fix property/atom</span></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"><span class="doc">fix property/atom</span></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 class="std std-ref">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"><span class="doc">mass</span></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
|
||||
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
|
||||
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>dipole</em> style, a point dipole is defined for each point
|
||||
particle. Note that if you wish the particles to be finite-size
|
||||
spheres as in a Stockmayer potential for a dipolar fluid, so that the
|
||||
particles can rotate due to dipole-dipole interactions, then you need
|
||||
to use atom_style hybrid sphere dipole, which will assign both a
|
||||
diameter and dipole moment to each particle.</p>
|
||||
<p>For the <em>electron</em> 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>dpd</em> style is for dissipative particle dynamics (DPD) particles
|
||||
which store the particle internal temperature (dpdTheta), internal
|
||||
conductive energy (uCond) and internal mechanical energy (uMech).</p>
|
||||
<p>The <em>meso</em> style is for smoothed particle hydrodynamics (SPH)
|
||||
particles which store a density (rho), energy (e), and heat capacity
|
||||
(cv).</p>
|
||||
<p>The <em>smd</em> style is for a general formulation of Smooth Particle
|
||||
Hydrodynamics. Both fluids and solids can be modeled. Particles
|
||||
store the mass and volume of an integration point, a kernel diameter
|
||||
used for calculating the field variables (e.g. stress and deformation)
|
||||
and a contact radius for calculating repulsive forces which prevent
|
||||
individual physical bodies from penetretating each other.</p>
|
||||
<p>The <em>wavepacket</em> style is similar to <em>electron</em>, 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
|
||||
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
|
||||
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>
|
||||
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
|
||||
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 class="std std-ref">(Grime)</span></a>, for examples of how this
|
||||
can be advantageous for large-scale coarse-grained systems.</p>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">When using the <em>template</em> style with a <a class="reference internal" href="molecule.html"><span class="doc">molecule template</span></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"><span class="doc">read_data</span></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,
|
||||
such as surface meshes of discrete points, collections of
|
||||
sub-particles, deformable objects, etc.</p>
|
||||
<p>The <a class="reference internal" href="body.html"><span class="doc">body</span></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"><span class="doc">body</span></a> doc page.</p>
|
||||
<hr class="docutils" />
|
||||
<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
|
||||
single style which defines all needed properties of all atoms. For
|
||||
example, as mentioned above, if you want dipolar particles which will
|
||||
rotate due to torque, you 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
|
||||
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"><span class="doc">this section</span></a>.</p>
|
||||
<hr class="docutils" />
|
||||
<p>Styles with a <em>cuda</em> or <em>kk</em> 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"><span class="doc">Section_accelerate</span></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,
|
||||
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
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
|
||||
more instructions on how to use the accelerated styles effectively.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<p>This command cannot be used after the simulation box is defined by a
|
||||
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command.</p>
|
||||
<p>Many of the styles listed above are only enabled if LAMMPS was built
|
||||
with a specific package, as listed below. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</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.</p>
|
||||
<p>The <em>line</em> and <em>tri</em> styles are part of the ASPHERE package.</p>
|
||||
<p>The <em>body</em> style is part of the BODY package.</p>
|
||||
<p>The <em>dipole</em> style is part of the DIPOLE package.</p>
|
||||
<p>The <em>peri</em> style is part of the PERI package for Peridynamics.</p>
|
||||
<p>The <em>electron</em> style is part of the USER-EFF package for <a class="reference internal" href="pair_eff.html"><span class="doc">electronic force fields</span></a>.</p>
|
||||
<p>The <em>dpd</em> style is part of the USER-DPD package for dissipative
|
||||
particle dynamics (DPD).</p>
|
||||
<p>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.</p>
|
||||
<p>The <em>wavepacket</em> style is part of the USER-AWPMD package for the
|
||||
<a class="reference internal" href="pair_awpmd.html"><span class="doc">antisymmetrized wave packet MD method</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>, <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a></p>
|
||||
</div>
|
||||
<div class="section" id="default">
|
||||
<h2>Default</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>
|
||||
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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_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</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">balance</span> <span class="n">thresh</span> <span class="n">style</span> <span class="n">args</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
|
||||
</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>,<em>y</em>,<em>z</em>)</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
|
||||
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
|
||||
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
|
||||
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
|
||||
Niter = # of times to iterate within each dimension of dimstr sequence
|
||||
stopthresh = stop balancing when this imbalance threshhold is reached
|
||||
<em>rcb</em> args = none
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>zero or more keyword/value pairs may be appended</li>
|
||||
<li>keyword = <em>out</em></li>
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>out</em> value = filename
|
||||
filename = write each processor's sub-domain to a file
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">balance</span> <span class="mf">0.9</span> <span class="n">x</span> <span class="n">uniform</span> <span class="n">y</span> <span class="mf">0.4</span> <span class="mf">0.5</span> <span class="mf">0.6</span>
|
||||
<span class="n">balance</span> <span class="mf">1.2</span> <span class="n">shift</span> <span class="n">xz</span> <span class="mi">5</span> <span class="mf">1.1</span>
|
||||
<span class="n">balance</span> <span class="mf">1.0</span> <span class="n">shift</span> <span class="n">xz</span> <span class="mi">5</span> <span class="mf">1.1</span>
|
||||
<span class="n">balance</span> <span class="mf">1.1</span> <span class="n">rcb</span>
|
||||
<span class="n">balance</span> <span class="mf">1.0</span> <span class="n">shift</span> <span class="n">x</span> <span class="mi">20</span> <span class="mf">1.0</span> <span class="n">out</span> <span class="n">tmp</span><span class="o">.</span><span class="n">balance</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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
|
||||
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"><span class="doc">fix balance</span></a> command, which can adjust processor
|
||||
sub-domain sizes and shapes on-the-fly during a <a class="reference internal" href="run.html"><span class="doc">run</span></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"><span class="doc">processors</span></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
|
||||
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
|
||||
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 note">
|
||||
<p class="first admonition-title">Note</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"><span class="doc">comm_style brick</span></a> command can then
|
||||
be used to replace a current <a class="reference internal" href="comm_style.html"><span class="doc">comm_style tiled</span></a>
|
||||
setting.</p>
|
||||
</div>
|
||||
<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
|
||||
(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 note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">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 (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"><span class="doc">create_atoms</span></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 note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">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 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"><span class="doc">kspace_style</span></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>,<em>y</em>,<em>z</em>), 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
|
||||
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 class=""
|
||||
data-lightbox="group-default"
|
||||
href="_images/balance_uniform.jpg"
|
||||
title=""
|
||||
data-title=""
|
||||
><img src="_images/balance_uniform.jpg"
|
||||
class="align-center"
|
||||
width="25%"
|
||||
height="auto"
|
||||
alt=""/>
|
||||
</a><a class=""
|
||||
data-lightbox="group-default"
|
||||
href="_images/balance_nonuniform.jpg"
|
||||
title=""
|
||||
data-title=""
|
||||
><img src="_images/balance_nonuniform.jpg"
|
||||
class="align-center"
|
||||
width="25%"
|
||||
height="auto"
|
||||
alt=""/>
|
||||
</a><a class=""
|
||||
data-lightbox="group-default"
|
||||
href="_images/balance_rcb.jpg"
|
||||
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
|
||||
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"><span class="doc">comm_style</span></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"><span class="doc">comm_style tiled</span></a>. Note that it can be useful to use a “grid”
|
||||
method with <a class="reference internal" href="comm_style.html"><span class="doc">comm_style tiled</span></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"><span class="doc">run</span></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
|
||||
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
|
||||
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"><span class="doc">processors</span></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
|
||||
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"><span class="doc">fix balance shift</span></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,
|
||||
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
|
||||
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
|
||||
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
|
||||
that the bounds used for each bisectioning take advantage of
|
||||
information from neighboring cuts if possible. At each iteration, the
|
||||
count of particles on either side of each plane is tallied. If the
|
||||
counts do not match the target value for the plane, the position of
|
||||
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
|
||||
assigned, particles are migrated to their new owning processor, and
|
||||
the balance procedure ends.</p>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">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. 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 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.
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
upper side. (If the processor count is odd, one side gets an extra
|
||||
processor.) The cut is positioned so that the number of atoms in the
|
||||
lower box is exactly the number that the processors assigned to that
|
||||
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
|
||||
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
|
||||
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
|
||||
visualizing mesh files. An example is shown here for a balancing by 4
|
||||
processors for a 2d problem:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">ITEM</span><span class="p">:</span> <span class="n">TIMESTEP</span>
|
||||
<span class="mi">0</span>
|
||||
<span class="n">ITEM</span><span class="p">:</span> <span class="n">NUMBER</span> <span class="n">OF</span> <span class="n">NODES</span>
|
||||
<span class="mi">16</span>
|
||||
<span class="n">ITEM</span><span class="p">:</span> <span class="n">BOX</span> <span class="n">BOUNDS</span>
|
||||
<span class="mi">0</span> <span class="mi">10</span>
|
||||
<span class="mi">0</span> <span class="mi">10</span>
|
||||
<span class="mi">0</span> <span class="mi">10</span>
|
||||
<span class="n">ITEM</span><span class="p">:</span> <span class="n">NODES</span>
|
||||
<span class="mi">1</span> <span class="mi">1</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span>
|
||||
<span class="mi">2</span> <span class="mi">1</span> <span class="mi">5</span> <span class="mi">0</span> <span class="mi">0</span>
|
||||
<span class="mi">3</span> <span class="mi">1</span> <span class="mi">5</span> <span class="mi">5</span> <span class="mi">0</span>
|
||||
<span class="mi">4</span> <span class="mi">1</span> <span class="mi">0</span> <span class="mi">5</span> <span class="mi">0</span>
|
||||
<span class="mi">5</span> <span class="mi">1</span> <span class="mi">5</span> <span class="mi">0</span> <span class="mi">0</span>
|
||||
<span class="mi">6</span> <span class="mi">1</span> <span class="mi">10</span> <span class="mi">0</span> <span class="mi">0</span>
|
||||
<span class="mi">7</span> <span class="mi">1</span> <span class="mi">10</span> <span class="mi">5</span> <span class="mi">0</span>
|
||||
<span class="mi">8</span> <span class="mi">1</span> <span class="mi">5</span> <span class="mi">5</span> <span class="mi">0</span>
|
||||
<span class="mi">9</span> <span class="mi">1</span> <span class="mi">0</span> <span class="mi">5</span> <span class="mi">0</span>
|
||||
<span class="mi">10</span> <span class="mi">1</span> <span class="mi">5</span> <span class="mi">5</span> <span class="mi">0</span>
|
||||
<span class="mi">11</span> <span class="mi">1</span> <span class="mi">5</span> <span class="mi">10</span> <span class="mi">0</span>
|
||||
<span class="mi">12</span> <span class="mi">1</span> <span class="mi">10</span> <span class="mi">5</span> <span class="mi">0</span>
|
||||
<span class="mi">13</span> <span class="mi">1</span> <span class="mi">5</span> <span class="mi">5</span> <span class="mi">0</span>
|
||||
<span class="mi">14</span> <span class="mi">1</span> <span class="mi">10</span> <span class="mi">5</span> <span class="mi">0</span>
|
||||
<span class="mi">15</span> <span class="mi">1</span> <span class="mi">10</span> <span class="mi">10</span> <span class="mi">0</span>
|
||||
<span class="mi">16</span> <span class="mi">1</span> <span class="mi">5</span> <span class="mi">10</span> <span class="mi">0</span>
|
||||
<span class="n">ITEM</span><span class="p">:</span> <span class="n">TIMESTEP</span>
|
||||
<span class="mi">0</span>
|
||||
<span class="n">ITEM</span><span class="p">:</span> <span class="n">NUMBER</span> <span class="n">OF</span> <span class="n">SQUARES</span>
|
||||
<span class="mi">4</span>
|
||||
<span class="n">ITEM</span><span class="p">:</span> <span class="n">SQUARES</span>
|
||||
<span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">4</span>
|
||||
<span class="mi">2</span> <span class="mi">1</span> <span class="mi">5</span> <span class="mi">6</span> <span class="mi">7</span> <span class="mi">8</span>
|
||||
<span class="mi">3</span> <span class="mi">1</span> <span class="mi">9</span> <span class="mi">10</span> <span class="mi">11</span> <span class="mi">12</span>
|
||||
<span class="mi">4</span> <span class="mi">1</span> <span class="mi">13</span> <span class="mi">14</span> <span class="mi">15</span> <span class="mi">16</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<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</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</h2>
|
||||
<p><a class="reference internal" href="processors.html"><span class="doc">processors</span></a>, <a class="reference internal" href="fix_balance.html"><span class="doc">fix balance</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
</div>
|
||||
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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>Body particles</li>
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<a href="http://lammps.sandia.gov">Website</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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||||
<div class="section" id="body-particles">
|
||||
<h1>Body particles</h1>
|
||||
<p><strong>Overview:</strong></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 class="std std-ref">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"><span class="doc">atom_style body</span></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"><span class="doc">atom_style body</span></a> command.</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="35%" />
|
||||
<col width="65%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td><em>nparticle</em></td>
|
||||
<td>rigid body with N sub-particles</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><em>rounded/polygon</em></td>
|
||||
<td>2d convex polygon with N vertices</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<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>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">The rounded/polygon style listed in the table above and
|
||||
described below has not yet been relesed in LAMMPS. It will be soon.</p>
|
||||
</div>
|
||||
<p>We hope to add more styles in the future. See <a class="reference internal" href="Section_modify.html#mod-12"><span class="std std-ref">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
|
||||
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"><span class="doc">fix rigid</span></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"><span class="doc">fix rigid</span></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
|
||||
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"><span class="doc">fix rigid</span></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
|
||||
style, when particle/particle interactions are more complex than what
|
||||
the <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></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
|
||||
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"><span class="doc">fix nve/body</span></a></td>
|
||||
<td>integrate motion of a body particle in NVE ensemble</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="fix_nvt_body.html"><span class="doc">fix nvt/body</span></a></td>
|
||||
<td>ditto for NVT ensemble</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="fix_npt_body.html"><span class="doc">fix npt/body</span></a></td>
|
||||
<td>ditto for NPT ensemble</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="fix_nph_body.html"><span class="doc">fix nph/body</span></a></td>
|
||||
<td>ditto for NPH ensemble</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="compute_body_local.html"><span class="doc">compute body/local</span></a></td>
|
||||
<td>store sub-particle attributes of a body particle</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="compute_temp_body.html"><span class="doc">compute temp/body</span></a></td>
|
||||
<td>compute temperature of body particles</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="dump.html"><span class="doc">dump local</span></a></td>
|
||||
<td>output sub-particle attributes of a body particle</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a></td>
|
||||
<td>output body particle attributes as an image</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
|
||||
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"><span class="doc">fix rigid</span></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-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">body</span> <span class="n">nparticle</span> <span class="n">Nmin</span> <span class="n">Nmax</span>
|
||||
<span class="n">Nmin</span> <span class="o">=</span> <span class="n">minimum</span> <span class="c1"># of sub-particles in any body in the system</span>
|
||||
<span class="n">Nmax</span> <span class="o">=</span> <span class="n">maximum</span> <span class="c1"># of sub-particles in any body in the system</span>
|
||||
</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"><span class="doc">read_data</span></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-default"><div class="highlight"><pre><span></span><span class="n">atom</span><span class="o">-</span><span class="n">ID</span> <span class="mi">1</span> <span class="n">M</span>
|
||||
<span class="n">N</span>
|
||||
<span class="n">ixx</span> <span class="n">iyy</span> <span class="n">izz</span> <span class="n">ixy</span> <span class="n">ixz</span> <span class="n">iyz</span>
|
||||
<span class="n">x1</span> <span class="n">y1</span> <span class="n">z1</span>
|
||||
<span class="o">...</span>
|
||||
<span class="n">xN</span> <span class="n">yN</span> <span class="n">zN</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<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. These values can be listed on
|
||||
as many lines as you wish; see the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command
|
||||
for more details.</p>
|
||||
<p>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 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, as is the total mass
|
||||
of the body particle.</p>
|
||||
<p>The <a class="reference internal" href="pair_body.html"><span class="doc">pair_style body</span></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"><span class="doc">compute body/local</span></a> and <a class="reference internal" href="dump.html"><span class="doc">dump local</span></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-default"><div class="highlight"><pre><span></span><span class="mi">1</span> <span class="o">=</span> <span class="n">x</span> <span class="n">position</span> <span class="n">of</span> <span class="n">sub</span><span class="o">-</span><span class="n">particle</span>
|
||||
<span class="mi">2</span> <span class="o">=</span> <span class="n">y</span> <span class="n">position</span> <span class="n">of</span> <span class="n">sub</span><span class="o">-</span><span class="n">particle</span>
|
||||
<span class="mi">3</span> <span class="o">=</span> <span class="n">z</span> <span class="n">position</span> <span class="n">of</span> <span class="n">sub</span><span class="o">-</span><span class="n">particle</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<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 orientation of the body particle.</p>
|
||||
<p>For images created by the <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> command, if the
|
||||
<em>body</em> keyword is set, then each body particle is drawn as a
|
||||
collection of spheres, one for each sub-particle. The size of each
|
||||
sphere is determined by the <em>bflag1</em> parameter for the <em>body</em> keyword.
|
||||
The <em>bflag2</em> argument is ignored.</p>
|
||||
<hr class="docutils" />
|
||||
<p><strong>Specifics of body style rounded/polygon:</strong></p>
|
||||
<p>The <em>rounded/polygon</em> body style represents body particles as a convex
|
||||
polygon with a variable number N > 2 of vertices, which can only be
|
||||
used for 2d models. One example use of this body style is for 2d
|
||||
discrete element models, as described in <a class="reference internal" href="#fraige"><span class="std std-ref">Fraige</span></a>. Similar to
|
||||
body style <em>nparticle</em>, the atom_style body command for this body
|
||||
style takes two additional arguments:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">body</span> <span class="n">rounded</span><span class="o">/</span><span class="n">polygon</span> <span class="n">Nmin</span> <span class="n">Nmax</span>
|
||||
<span class="n">Nmin</span> <span class="o">=</span> <span class="n">minimum</span> <span class="c1"># of vertices in any body in the system</span>
|
||||
<span class="n">Nmax</span> <span class="o">=</span> <span class="n">maximum</span> <span class="c1"># of vertices in any body in the system</span>
|
||||
</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"><span class="doc">read_data</span></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-default"><div class="highlight"><pre><span></span><span class="n">atom</span><span class="o">-</span><span class="n">ID</span> <span class="mi">1</span> <span class="n">M</span>
|
||||
<span class="n">N</span>
|
||||
<span class="n">ixx</span> <span class="n">iyy</span> <span class="n">izz</span> <span class="n">ixy</span> <span class="n">ixz</span> <span class="n">iyz</span>
|
||||
<span class="n">x1</span> <span class="n">y1</span> <span class="n">z1</span>
|
||||
<span class="o">...</span>
|
||||
<span class="n">xN</span> <span class="n">yN</span> <span class="n">zN</span>
|
||||
<span class="n">i</span> <span class="n">j</span> <span class="n">j</span> <span class="n">k</span> <span class="n">k</span> <span class="o">...</span>
|
||||
<span class="n">radius</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>N is the number of vertices in the body particle. M = 6 + 3*N + 2*N +
|
||||
1. 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
|
||||
vertices (x1 to zN) as 3N values, followed by 2N vertex indices
|
||||
corresponding to the end points of the N edges, followed by a single
|
||||
radius value = the smallest circle encompassing the polygon. That
|
||||
last value is used to facilitate the body/body contact detection.
|
||||
These floating-point values can be listed on as many lines as you
|
||||
wish; see the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command for more details.</p>
|
||||
<p>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 respect to the prinicpal axes of the
|
||||
rigid body itself. LAMMPS performs the latter calculation internally.
|
||||
The coordinates of each vertex 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>For example, the following information would specify a square
|
||||
particles whose edge length is sqrt(2):</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="mi">3</span> <span class="mi">1</span> <span class="mi">27</span>
|
||||
<span class="mi">4</span>
|
||||
<span class="mi">1</span> <span class="mi">1</span> <span class="mi">4</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span>
|
||||
<span class="o">-</span><span class="mf">0.7071</span> <span class="o">-</span><span class="mf">0.7071</span> <span class="mi">0</span>
|
||||
<span class="o">-</span><span class="mf">0.7071</span> <span class="mf">0.7071</span> <span class="mi">0</span>
|
||||
<span class="mf">0.7071</span> <span class="mf">0.7071</span> <span class="mi">0</span>
|
||||
<span class="mf">0.7071</span> <span class="o">-</span><span class="mf">0.7071</span> <span class="mi">0</span>
|
||||
<span class="mi">0</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">3</span> <span class="mi">0</span>
|
||||
<span class="mf">1.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The <span class="xref doc">pair_style body/rounded/polygon</span> command
|
||||
can be used with this body style to compute body/body interactions.</p>
|
||||
<p>For output purposes via the <a class="reference internal" href="compute_body_local.html"><span class="doc">compute body/local</span></a> and <a class="reference internal" href="dump.html"><span class="doc">dump local</span></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-default"><div class="highlight"><pre><span></span><span class="mi">1</span> <span class="o">=</span> <span class="n">x</span> <span class="n">position</span> <span class="n">of</span> <span class="n">vertex</span>
|
||||
<span class="mi">2</span> <span class="o">=</span> <span class="n">y</span> <span class="n">position</span> <span class="n">of</span> <span class="n">vertex</span>
|
||||
<span class="mi">3</span> <span class="o">=</span> <span class="n">z</span> <span class="n">position</span> <span class="n">of</span> <span class="n">vertex</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>These values are the current position of the vertex 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 orientation of the body particle.</p>
|
||||
<p>For images created by the <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> command, if the
|
||||
<em>body</em> keyword is set, then each body particle is drawn as a convex
|
||||
polygon consisting of N line segments. Note that the line segments
|
||||
are drawn between the N vertices, which does not correspond exactly to
|
||||
the physical extent of the body (because the <a class="reference external" href="pair_body_rounded_polygon.cpp">pair_style rounded/polygon</a> defines finite-size
|
||||
spheres at those point and the line segments between the spheres are
|
||||
tangent to the spheres). The drawn diameter of each line segment is
|
||||
determined by the <em>bflag1</em> parameter for the <em>body</em> keyword. The
|
||||
<em>bflag2</em> argument is ignored.</p>
|
||||
<hr class="docutils" />
|
||||
<p id="fraige"><strong>(Fraige)</strong> F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds,
|
||||
Particuology, 6, 455 (2008).</p>
|
||||
</div>
|
||||
|
||||
|
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|
||||
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|
||||
<footer>
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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_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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||||
<div class="section" id="bond-style-class2-command">
|
||||
<span id="index-0"></span><h1>bond_style class2 command</h1>
|
||||
</div>
|
||||
<div class="section" id="bond-style-class2-omp-command">
|
||||
<h1>bond_style class2/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">class2</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">class2</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">100.0</span> <span class="mf">80.0</span> <span class="mf">80.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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 class="std std-ref">(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"><span class="doc">bond_coeff</span></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"><span class="doc">read_data</span></a>
|
||||
or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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</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 class="std std-ref">Making LAMMPS</span></a> section
|
||||
for more info on packages.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a>, <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></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>
|
||||
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|
||||
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|
||||
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<div class="section" id="bond-coeff-command">
|
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<span id="index-0"></span><h1>bond_coeff command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_coeff</span> <span class="n">N</span> <span class="n">args</span>
|
||||
</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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_coeff</span> <span class="mi">5</span> <span class="mf">80.0</span> <span class="mf">1.2</span>
|
||||
<span class="n">bond_coeff</span> <span class="o">*</span> <span class="mf">30.0</span> <span class="mf">1.5</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">1</span><span class="o">*</span><span class="mi">4</span> <span class="mf">30.0</span> <span class="mf">1.5</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="n">harmonic</span> <span class="mf">200.0</span> <span class="mf">1.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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"><span class="doc">read_data</span></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,
|
||||
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
|
||||
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-default"><div class="highlight"><pre><span></span><span class="n">bond_coeff</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">1.2</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">2</span> <span class="mf">200.0</span> <span class="mf">1.2</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<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-default"><div class="highlight"><pre><span></span><span class="mi">5</span> <span class="mf">80.0</span> <span class="mf">1.2</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<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="#"><span class="doc">bond_coeff</span></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 class="std std-ref">this page</span></a>.</p>
|
||||
<ul class="simple">
|
||||
<li><a class="reference internal" href="bond_none.html"><span class="doc">bond_style none</span></a> - turn off bonded interactions</li>
|
||||
<li><a class="reference internal" href="bond_hybrid.html"><span class="doc">bond_style hybrid</span></a> - define multiple styles of bond interactions</li>
|
||||
<li><a class="reference internal" href="bond_class2.html"><span class="doc">bond_style class2</span></a> - COMPASS (class 2) bond</li>
|
||||
<li><a class="reference internal" href="bond_fene.html"><span class="doc">bond_style fene</span></a> - FENE (finite-extensible non-linear elastic) bond</li>
|
||||
<li><a class="reference internal" href="bond_fene_expand.html"><span class="doc">bond_style fene/expand</span></a> - FENE bonds with variable size particles</li>
|
||||
<li><a class="reference internal" href="bond_harmonic.html"><span class="doc">bond_style harmonic</span></a> - harmonic bond</li>
|
||||
<li><a class="reference internal" href="bond_morse.html"><span class="doc">bond_style morse</span></a> - Morse bond</li>
|
||||
<li><a class="reference internal" href="bond_nonlinear.html"><span class="doc">bond_style nonlinear</span></a> - nonlinear bond</li>
|
||||
<li><a class="reference internal" href="bond_quartic.html"><span class="doc">bond_style quartic</span></a> - breakable quartic bond</li>
|
||||
<li><a class="reference internal" href="bond_table.html"><span class="doc">bond_style table</span></a> - tabulated by bond length</li>
|
||||
</ul>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<p>This command must come after the simulation box is defined by a
|
||||
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>, <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>, or
|
||||
<a class="reference internal" href="create_box.html"><span class="doc">create_box</span></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</h2>
|
||||
<p><a class="reference internal" href="bond_style.html"><span class="doc">bond_style</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
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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</h1>
|
||||
</div>
|
||||
<div class="section" id="bond-style-fene-kk-command">
|
||||
<h1>bond_style fene/kk command</h1>
|
||||
</div>
|
||||
<div class="section" id="bond-style-fene-omp-command">
|
||||
<h1>bond_style fene/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">fene</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">fene</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="mf">30.0</span> <span class="mf">1.5</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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 class="std std-ref">(Kremer)</span></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"><span class="doc">bond_coeff</span></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"><span class="doc">read_data</span></a>
|
||||
or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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</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 class="std std-ref">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"><span class="doc">special_bonds lj/coul 0 1 1</span></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">
|
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<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a>, <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></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>
|
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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="bond-style-fene-expand-command">
|
||||
<span id="index-0"></span><h1>bond_style fene/expand command</h1>
|
||||
</div>
|
||||
<div class="section" id="bond-style-fene-expand-omp-command">
|
||||
<h1>bond_style fene/expand/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">fene</span><span class="o">/</span><span class="n">expand</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">fene</span><span class="o">/</span><span class="n">expand</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="mf">30.0</span> <span class="mf">1.5</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">0.5</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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 class="std std-ref">(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
|
||||
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"><span class="doc">bond_coeff</span></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"><span class="doc">read_data</span></a>
|
||||
or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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</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 class="std std-ref">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"><span class="doc">special_bonds lj/coul 0 1 1</span></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</h2>
|
||||
<p><a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a>, <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></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>
|
||||
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|
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|
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<div class="section" id="bond-style-harmonic-command">
|
||||
<span id="index-0"></span><h1>bond_style harmonic command</h1>
|
||||
</div>
|
||||
<div class="section" id="bond-style-harmonic-intel-command">
|
||||
<h1>bond_style harmonic/intel command</h1>
|
||||
</div>
|
||||
<div class="section" id="bond-style-harmonic-kk-command">
|
||||
<h1>bond_style harmonic/kk command</h1>
|
||||
</div>
|
||||
<div class="section" id="bond-style-harmonic-omp-command">
|
||||
<h1>bond_style harmonic/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">5</span> <span class="mf">80.0</span> <span class="mf">1.2</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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"><span class="doc">bond_coeff</span></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"><span class="doc">read_data</span></a>
|
||||
or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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</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 class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a>, <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
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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</h1>
|
||||
</div>
|
||||
<div class="section" id="bond-style-harmonic-shift-omp-command">
|
||||
<h1>bond_style harmonic/shift/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span><span class="o">/</span><span class="n">shift</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span><span class="o">/</span><span class="n">shift</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">5</span> <span class="mf">10.0</span> <span class="mf">0.5</span> <span class="mf">1.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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.
|
||||
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"><span class="doc">bond_coeff</span></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"><span class="doc">read_data</span></a>
|
||||
or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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</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 class="std std-ref">Making LAMMPS</span></a>
|
||||
section for more info on packages.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
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<div class="section" id="bond-style-harmonic-shift-cut-command">
|
||||
<span id="index-0"></span><h1>bond_style harmonic/shift/cut command</h1>
|
||||
</div>
|
||||
<div class="section" id="bond-style-harmonic-shift-cut-omp-command">
|
||||
<h1>bond_style harmonic/shift/cut/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">cut</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">cut</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">5</span> <span class="mf">10.0</span> <span class="mf">0.5</span> <span class="mf">1.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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"><span class="doc">bond_coeff</span></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"><span class="doc">read_data</span></a>
|
||||
or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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</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 class="std std-ref">Making LAMMPS</span></a>
|
||||
section for more info on packages.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a>, <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a>,
|
||||
<a class="reference internal" href="bond_harmonic.html"><span class="doc">bond_harmonic</span></a>,
|
||||
<span class="xref doc">bond_harmonicshift</span></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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<li>bond_style hybrid command</li>
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||||
<div class="section" id="bond-style-hybrid-command">
|
||||
<span id="index-0"></span><h1>bond_style hybrid command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">hybrid</span> <span class="n">style1</span> <span class="n">style2</span> <span class="o">...</span>
|
||||
</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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">hybrid</span> <span class="n">harmonic</span> <span class="n">fene</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="n">harmonic</span> <span class="mf">80.0</span> <span class="mf">1.2</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">2</span><span class="o">*</span> <span class="n">fene</span> <span class="mf">30.0</span> <span class="mf">1.5</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<p>The <em>hybrid</em> 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"><span class="doc">bond_coeff</span></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>
|
||||
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"><span class="doc">read_data</span></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-default"><div class="highlight"><pre><span></span><span class="n">Bond</span> <span class="n">Coeffs</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="mi">1</span> <span class="n">harmonic</span> <span class="mf">80.0</span> <span class="mf">1.2</span>
|
||||
<span class="mi">2</span> <span class="n">fene</span> <span class="mf">30.0</span> <span class="mf">1.5</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
|
||||
<span class="o">...</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>A bond style of <em>none</em> 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</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 class="std std-ref">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"><span class="doc">binary restart files</span></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</h2>
|
||||
<p><a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a>, <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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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="bond-style-morse-command">
|
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<span id="index-0"></span><h1>bond_style morse command</h1>
|
||||
</div>
|
||||
<div class="section" id="bond-style-morse-omp-command">
|
||||
<h1>bond_style morse/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">morse</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">morse</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">5</span> <span class="mf">1.0</span> <span class="mf">2.0</span> <span class="mf">1.2</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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"><span class="doc">bond_coeff</span></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"><span class="doc">read_data</span></a>
|
||||
or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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</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 class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a>, <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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<div class="section" id="bond-style-none-command">
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<span id="index-0"></span><h1>bond_style none command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">none</span>
|
||||
</pre></div>
|
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</div>
|
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|
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<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">none</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<p>Using a bond style of none means bond forces and energies 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"><span class="doc">read_data</span></a> command.</p>
|
||||
<p>See the <a class="reference internal" href="bond_zero.html"><span class="doc">bond_style zero</span></a> command for a way to
|
||||
calculate bond statistics, but compute no bond interactions.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
<p><strong>Related commands:</strong> none</p>
|
||||
<p><a class="reference internal" href="bond_zero.html"><span class="doc">bond_style zero</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
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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</h1>
|
||||
</div>
|
||||
<div class="section" id="bond-style-nonlinear-omp-command">
|
||||
<h1>bond_style nonlinear/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">nonlinear</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">nonlinear</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">2</span> <span class="mf">100.0</span> <span class="mf">1.1</span> <span class="mf">1.4</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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 class="std std-ref">(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"><span class="doc">bond_coeff</span></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"><span class="doc">read_data</span></a>
|
||||
or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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</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 class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a>, <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></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>
|
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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</h1>
|
||||
</div>
|
||||
<div class="section" id="bond-style-quartic-omp-command">
|
||||
<h1>bond_style quartic/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">quartic</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">quartic</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">2</span> <span class="mi">1200</span> <span class="o">-</span><span class="mf">0.55</span> <span class="mf">0.25</span> <span class="mf">1.3</span> <span class="mf">34.6878</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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.
|
||||
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"><span class="doc">bond_coeff</span></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"><span class="doc">read_data</span></a>
|
||||
or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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
|
||||
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"><span class="doc">bond_coeff</span></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”
|
||||
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
|
||||
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"><span class="doc">pair_style</span></a> command, whether the bond is broken or
|
||||
not. This means that <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></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"><span class="doc">dump local</span></a> command, bonds with type 0 are not included. The
|
||||
<a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a> command can also be used to query the
|
||||
status of broken bonds or permanently delete them, e.g.:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">stats</span>
|
||||
<span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">bond</span> <span class="mi">0</span> <span class="n">remove</span>
|
||||
</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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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</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 class="std std-ref">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"><span class="doc">special_bonds</span></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</h2>
|
||||
<p><a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a>, <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a></p>
|
||||
<p><strong>Default:</strong> none</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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<div class="section" id="bond-style-command">
|
||||
<span id="index-0"></span><h1>bond_style command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">style</span> <span class="n">args</span>
|
||||
</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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span>
|
||||
<span class="n">bond_style</span> <span class="n">fene</span>
|
||||
<span class="n">bond_style</span> <span class="n">hybrid</span> <span class="n">harmonic</span> <span class="n">fene</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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"><span class="doc">pair_style</span></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"><span class="doc">read_data</span></a> or
|
||||
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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"><span class="doc">bond_coeff</span></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"><span class="doc">bond_coeff</span></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"><span class="doc">read_restart</span></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 note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">When both a bond and pair style is defined, the
|
||||
<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></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
|
||||
the style to display the formula it computes and coefficients
|
||||
specified by the associated <a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></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 class="std std-ref">this page</span></a>.</p>
|
||||
<ul class="simple">
|
||||
<li><a class="reference internal" href="bond_none.html"><span class="doc">bond_style none</span></a> - turn off bonded interactions</li>
|
||||
<li><a class="reference internal" href="bond_zero.html"><span class="doc">bond_style zero</span></a> - topology but no interactions</li>
|
||||
<li><a class="reference internal" href="bond_hybrid.html"><span class="doc">bond_style hybrid</span></a> - define multiple styles of bond interactions</li>
|
||||
<li><a class="reference internal" href="bond_class2.html"><span class="doc">bond_style class2</span></a> - COMPASS (class 2) bond</li>
|
||||
<li><a class="reference internal" href="bond_fene.html"><span class="doc">bond_style fene</span></a> - FENE (finite-extensible non-linear elastic) bond</li>
|
||||
<li><a class="reference internal" href="bond_fene_expand.html"><span class="doc">bond_style fene/expand</span></a> - FENE bonds with variable size particles</li>
|
||||
<li><a class="reference internal" href="bond_harmonic.html"><span class="doc">bond_style harmonic</span></a> - harmonic bond</li>
|
||||
<li><a class="reference internal" href="bond_morse.html"><span class="doc">bond_style morse</span></a> - Morse bond</li>
|
||||
<li><a class="reference internal" href="bond_nonlinear.html"><span class="doc">bond_style nonlinear</span></a> - nonlinear bond</li>
|
||||
<li><a class="reference internal" href="bond_quartic.html"><span class="doc">bond_style quartic</span></a> - breakable quartic bond</li>
|
||||
<li><a class="reference internal" href="bond_table.html"><span class="doc">bond_style table</span></a> - tabulated by bond length</li>
|
||||
</ul>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</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 class="std std-ref">Making LAMMPS</span></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</h2>
|
||||
<p><a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a>, <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a></p>
|
||||
</div>
|
||||
<div class="section" id="default">
|
||||
<h2>Default</h2>
|
||||
<p>bond_style none</p>
|
||||
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|
||||
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|
||||
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<div class="section" id="bond-style-table-command">
|
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<span id="index-0"></span><h1>bond_style table command</h1>
|
||||
</div>
|
||||
<div class="section" id="bond-style-table-omp-command">
|
||||
<h1>bond_style table/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">table</span> <span class="n">style</span> <span class="n">N</span>
|
||||
</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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">table</span> <span class="n">linear</span> <span class="mi">1000</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="n">file</span><span class="o">.</span><span class="n">table</span> <span class="n">ENTRY1</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<p>Style <em>table</em> creates interpolation tables of length <em>N</em> 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"><span class="doc">bond_coeff</span></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>
|
||||
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
|
||||
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
|
||||
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"><span class="doc">bond_coeff</span></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
|
||||
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-default"><div class="highlight"><pre><span></span><span class="c1"># Bond potential for harmonic (one or more comment or blank lines)</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">HAM</span> <span class="p">(</span><span class="n">keyword</span> <span class="ow">is</span> <span class="n">the</span> <span class="n">first</span> <span class="n">text</span> <span class="n">on</span> <span class="n">line</span><span class="p">)</span>
|
||||
<span class="n">N</span> <span class="mi">101</span> <span class="n">FP</span> <span class="mi">0</span> <span class="mi">0</span> <span class="n">EQ</span> <span class="mf">0.5</span> <span class="p">(</span><span class="n">N</span><span class="p">,</span> <span class="n">FP</span><span class="p">,</span> <span class="n">EQ</span> <span class="n">parameters</span><span class="p">)</span>
|
||||
<span class="p">(</span><span class="n">blank</span> <span class="n">line</span><span class="p">)</span>
|
||||
<span class="mi">1</span> <span class="mf">0.00</span> <span class="mf">338.0000</span> <span class="mf">1352.0000</span> <span class="p">(</span><span class="n">index</span><span class="p">,</span> <span class="n">bond</span><span class="o">-</span><span class="n">length</span><span class="p">,</span> <span class="n">energy</span><span class="p">,</span> <span class="n">force</span><span class="p">)</span>
|
||||
<span class="mi">2</span> <span class="mf">0.01</span> <span class="mf">324.6152</span> <span class="mf">1324.9600</span>
|
||||
<span class="o">...</span>
|
||||
<span class="mi">101</span> <span class="mf">1.00</span> <span class="mf">338.0000</span> <span class="o">-</span><span class="mf">1352.0000</span>
|
||||
</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
|
||||
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"><span class="doc">bond_coeff</span></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"><span class="doc">bond_style table</span></a> command. Let
|
||||
Ntable = <em>N</em> 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
|
||||
values at Ntable different points. The resulting tables of length
|
||||
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
|
||||
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
|
||||
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"><span class="doc">fix shake</span></a> command. If not used, the equilibrium bond
|
||||
length is to the distance in the table with the lowest potential energy.</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
|
||||
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
|
||||
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"><span class="doc">Section_accelerate</span></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,
|
||||
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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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</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 class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a>, <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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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_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>
|
||||
<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-write-command">
|
||||
<span id="index-0"></span><h1>bond_write command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_write</span> <span class="n">btype</span> <span class="n">N</span> <span class="n">inner</span> <span class="n">outer</span> <span class="n">file</span> <span class="n">keyword</span> <span class="n">itype</span> <span class="n">jtype</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>btype = bond types</li>
|
||||
<li>N = # of values</li>
|
||||
<li>inner,outer = inner and outer bond length (distance units)</li>
|
||||
<li>file = name of file to write values to</li>
|
||||
<li>keyword = section name in file for this set of tabulated values</li>
|
||||
<li>itype,jtype = 2 atom types (optional)</li>
|
||||
<li></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_write</span> <span class="mi">1</span> <span class="mi">500</span> <span class="mf">0.5</span> <span class="mf">3.5</span> <span class="n">table</span><span class="o">.</span><span class="n">txt</span> <span class="n">Harmonic_1</span>
|
||||
<span class="n">bond_write</span> <span class="mi">3</span> <span class="mi">1000</span> <span class="mf">0.1</span> <span class="mf">6.0</span> <span class="n">table</span><span class="o">.</span><span class="n">txt</span> <span class="n">Morse</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<p>Write energy and force values to a file as a function of distance for
|
||||
the currently defined bond potential. This is useful for plotting the
|
||||
potential function or otherwise debugging its values. If the file
|
||||
already exists, the table of values is appended to the end of the file
|
||||
to allow multiple tables of energy and force to be included in one
|
||||
file.</p>
|
||||
<p>The energy and force values are computed at distances from inner to
|
||||
outer for 2 interacting atoms forming a bond of type btype, using the
|
||||
appropriate <a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a> coefficients. N evenly spaced
|
||||
distances are used.</p>
|
||||
<p>For example, for N = 7, inner = 1.0, and outer = 4.0,
|
||||
values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0.</p>
|
||||
<p>The file is written in the format used as input for the
|
||||
<a class="reference internal" href="bond_style.html"><span class="doc">bond_style</span></a> <em>table</em> option with <em>keyword</em> as the
|
||||
section name. Each line written to the file lists an index number
|
||||
(1-N), a distance (in distance units), an energy (in energy units),
|
||||
and a force (in force units).</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<p>All force field coefficients for bond and other kinds of interactions
|
||||
must be set before this command can be invoked.</p>
|
||||
<p>Due to how the bond force is computed, an inner value > 0.0 must
|
||||
be specified even if the potential has a finite value at r = 0.0.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="bond_table.html"><span class="doc">bond_style table</span></a>,
|
||||
<a class="reference internal" href="bond_style.html"><span class="doc">bond_style</span></a>, <a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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||||
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||||
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|
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<div class="section" id="bond-style-zero-command">
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<span id="index-0"></span><h1>bond_style zero command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<pre class="literal-block">
|
||||
bond_style zero <em>nocoeff</em>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">zero</span>
|
||||
<span class="n">bond_style</span> <span class="n">zero</span> <span class="n">nocoeff</span>
|
||||
<span class="n">bond_coeff</span> <span class="o">*</span>
|
||||
<span class="n">bond_coeff</span> <span class="o">*</span> <span class="mf">2.14</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<p>Using an bond style of zero means bond forces and energies are not
|
||||
computed, but the geometry of bond pairs is still accessible to other
|
||||
commands.</p>
|
||||
<p>As an example, the <a class="reference internal" href="compute_bond_local.html"><span class="doc">compute bond/local</span></a>
|
||||
command can be used to compute distances for the list of pairs of bond
|
||||
atoms listed in the data file read by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>
|
||||
command. If no bond style is defined, this command cannot be used.</p>
|
||||
<p>The optional <em>nocoeff</em> flag allows to read data files with a BondCoeff
|
||||
section for any bond style. Similarly, any bond_coeff commands
|
||||
will only be checked for the bond type number and the rest ignored.</p>
|
||||
<p>Note that the <a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a> command must be used for
|
||||
all bond types. If specified, there can be only one value, which is
|
||||
going to be used to assign an equilibrium distance, e.g. for use with
|
||||
<a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="bond_none.html"><span class="doc">bond_style none</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
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<div class="section" id="boundary-command">
|
||||
<span id="index-0"></span><h1>boundary command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">boundary</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span>
|
||||
</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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">boundary</span> <span class="n">p</span> <span class="n">p</span> <span class="n">f</span>
|
||||
<span class="n">boundary</span> <span class="n">p</span> <span class="n">fs</span> <span class="n">p</span>
|
||||
<span class="n">boundary</span> <span class="n">s</span> <span class="n">f</span> <span class="n">fm</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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"><span class="doc">read_data</span></a>,
|
||||
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>, or <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a>
|
||||
commands.</p>
|
||||
<p>The style <em>p</em> 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"><span class="doc">fix npt</span></a> and <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></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
|
||||
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
|
||||
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"><span class="doc">thermo_modify lost</span></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
|
||||
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
|
||||
specified in the data or restart file or set by the
|
||||
<a class="reference internal" href="create_box.html"><span class="doc">create_box</span></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 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 class="std std-ref">Section_howto 12</span></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</h2>
|
||||
<p>This command cannot be used after the simulation box is defined by a
|
||||
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command or
|
||||
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command. See the
|
||||
<a class="reference internal" href="change_box.html"><span class="doc">change_box</span></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</h2>
|
||||
<p>See the <a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a> command for a discussion
|
||||
of lost atoms.</p>
|
||||
</div>
|
||||
<div class="section" id="default">
|
||||
<h2>Default</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">boundary</span> <span class="n">p</span> <span class="n">p</span> <span class="n">p</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
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<hr/>
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<div role="contentinfo">
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<p>
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© Copyright 2013 Sandia Corporation.
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</p>
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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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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div itemprop="articleBody">
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||||
<div class="section" id="box-command">
|
||||
<span id="index-0"></span><h1>box command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">box</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
|
||||
</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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">box</span> <span class="n">tilt</span> <span class="n">large</span>
|
||||
<span class="n">box</span> <span class="n">tilt</span> <span class="n">small</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<p>Set attributes of the simulation box.</p>
|
||||
<p>For triclinic (non-orthogonal) simulation boxes, the <em>tilt</em> keyword
|
||||
allows simulation domains to be created with arbitrary tilt factors,
|
||||
e.g. via the <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> or
|
||||
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> commands. Tilt factors determine how
|
||||
skewed the triclinic box is; see <a class="reference internal" href="Section_howto.html#howto-12"><span class="std std-ref">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
|
||||
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
|
||||
less efficiently, due to the large volume of communication needed to
|
||||
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</h2>
|
||||
<p>This command cannot be used after the simulation box is defined by a
|
||||
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command or
|
||||
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command.</p>
|
||||
<p><strong>Related commands:</strong> none</p>
|
||||
</div>
|
||||
<div class="section" id="default">
|
||||
<h2>Default</h2>
|
||||
<p>The default value is tilt = small.</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
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</div>
|
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© Copyright 2013 Sandia Corporation.
|
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</p>
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</div>
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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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|
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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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>change_box 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 role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
|
||||
<div itemprop="articleBody">
|
||||
|
||||
<div class="section" id="change-box-command">
|
||||
<span id="index-0"></span><h1>change_box command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">parameter</span> <span class="n">args</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">args</span> <span class="o">...</span>
|
||||
</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
|
||||
lo hi = box boundaries after displacement (distance units)
|
||||
<em>delta</em> values = dlo dhi
|
||||
dlo dhi = change in box boundaries after displacement (distance units)
|
||||
<em>scale</em> 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
|
||||
tilt = tilt factor after displacement (distance units)
|
||||
<em>delta</em> 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>
|
||||
lattice = distances are defined in lattice units
|
||||
box = distances are defined in simulation box units
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">xy</span> <span class="n">final</span> <span class="o">-</span><span class="mf">2.0</span> <span class="n">z</span> <span class="n">final</span> <span class="mf">0.0</span> <span class="mf">5.0</span> <span class="n">boundary</span> <span class="n">p</span> <span class="n">p</span> <span class="n">f</span> <span class="n">remap</span> <span class="n">units</span> <span class="n">box</span>
|
||||
<span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">y</span> <span class="n">volume</span> <span class="n">z</span> <span class="n">volume</span> <span class="n">remap</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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
|
||||
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"><span class="doc">boundary</span></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"><span class="doc">create_box</span></a> or <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or
|
||||
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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"><span class="doc">fix npt</span></a> or <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></a> commands.
|
||||
The <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a>, <a class="reference internal" href="read_data.html"><span class="doc">read data</span></a>, and
|
||||
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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 class="std std-ref">Section_howto 12</span></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
|
||||
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"><span class="doc">boundary</span></a> command)
|
||||
which may change simulation box boundaries, and atoms are migrated to
|
||||
new owning processors.</p>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">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"><span class="doc">create_atoms</span></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>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">final</span> <span class="o">-</span><span class="mi">10</span> <span class="mi">20</span>
|
||||
<span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">single</span> <span class="o">-</span><span class="mi">5</span> <span class="mi">5</span> <span class="mi">5</span> <span class="c1"># this will fail to insert an atom</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">final</span> <span class="o">-</span><span class="mi">10</span> <span class="mi">20</span> <span class="n">boundary</span> <span class="n">f</span> <span class="n">s</span> <span class="n">s</span>
|
||||
<span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">single</span> <span class="o">-</span><span class="mi">5</span> <span class="mi">5</span> <span class="mi">5</span>
|
||||
<span class="n">change_box</span> <span class="n">boundary</span> <span class="n">s</span> <span class="n">s</span> <span class="n">s</span> <span class="c1"># this will work</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">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 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 note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">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
|
||||
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 note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">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"><span class="doc">processors</span></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 note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">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 class="std std-ref">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
|
||||
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
|
||||
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
|
||||
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
|
||||
the overall box volume remains constant with respect to the operation
|
||||
performed by the preceding keyword. The <em>volume</em> 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>
|
||||
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-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">y</span> <span class="n">volume</span> <span class="n">z</span> <span class="n">volume</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The <em>volume</em> 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-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">z</span> <span class="n">volume</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<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-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span><span class="s2">"x scale 1.1 y volume z volume</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<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-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">z</span> <span class="n">volume</span> <span class="n">y</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">z</span> <span class="n">volume</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">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
|
||||
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
|
||||
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
|
||||
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
|
||||
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,
|
||||
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
|
||||
factor must be between -5 and 5. Similarly, both xz and yz must be
|
||||
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"><span class="doc">boundary</span></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
|
||||
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
|
||||
current box edge in that dimension, so that the box will become no
|
||||
smaller. See the <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></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"><span class="doc">read_data</span></a> or
|
||||
<a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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"><span class="doc">read_restart</span></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 class="std std-ref">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"><span class="doc">create_box</span></a>,
|
||||
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>, or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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 class="std std-ref">non-equilibrium MD (NEMD) simulation</span></a> can be run with deformation
|
||||
via the <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></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
|
||||
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
|
||||
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
|
||||
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
|
||||
boundaries. Also, any shrink-wrapping of non-periodic boundaries (see
|
||||
the <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></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"><span class="doc">units</span></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"><span class="doc">lattice</span></a> command must have
|
||||
been previously used to define the lattice spacing.</p>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</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"><span class="doc">dumps</span></a> can
|
||||
be active, nor can a <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a> or <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></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"><span class="doc">undump</span></a> or
|
||||
<a class="reference internal" href="unfix.html"><span class="doc">unfix</span></a> command is also used to turn them off.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></a>, <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a></p>
|
||||
</div>
|
||||
<div class="section" id="default">
|
||||
<h2>Default</h2>
|
||||
<p>The option default is units = lattice.</p>
|
||||
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|
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|
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|
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|
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<div class="section" id="clear-command">
|
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<span id="index-0"></span><h1>clear command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">clear</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="p">(</span><span class="n">commands</span> <span class="k">for</span> <span class="mi">1</span><span class="n">st</span> <span class="n">simulation</span><span class="p">)</span>
|
||||
<span class="n">clear</span>
|
||||
<span class="p">(</span><span class="n">commands</span> <span class="k">for</span> <span class="mi">2</span><span class="n">nd</span> <span class="n">simulation</span><span class="p">)</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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"><span class="doc">shell</span></a> command), log file status
|
||||
(<a class="reference internal" href="log.html"><span class="doc">log</span></a> command), echo status (<a class="reference internal" href="echo.html"><span class="doc">echo</span></a> command), and
|
||||
input script variables (<a class="reference internal" href="variable.html"><span class="doc">variable</span></a> command).</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
<p><strong>Related commands:</strong> none</p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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|
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</p>
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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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|
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<div class="section" id="comm-modify-command">
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<span id="index-0"></span><h1>comm_modify command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">comm_modify</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
|
||||
</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>cutoff/multi</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>cutoff/multi</em> type value
|
||||
type = atom type or type range (supports asterisk notation)
|
||||
value = Rcut (distance units) = communicate atoms for selected types 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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">comm_modify</span> <span class="n">mode</span> <span class="n">multi</span>
|
||||
<span class="n">comm_modify</span> <span class="n">mode</span> <span class="n">multi</span> <span class="n">group</span> <span class="n">solvent</span>
|
||||
<span class="n">comm_modift</span> <span class="n">mode</span> <span class="n">multi</span> <span class="n">cutoff</span><span class="o">/</span><span class="n">multi</span> <span class="mi">1</span> <span class="mf">10.0</span> <span class="n">cutoff</span><span class="o">/</span><span class="n">multi</span> <span class="mi">2</span><span class="o">*</span><span class="mi">4</span> <span class="mf">15.0</span>
|
||||
<span class="n">comm_modify</span> <span class="n">vel</span> <span class="n">yes</span>
|
||||
<span class="n">comm_modify</span> <span class="n">mode</span> <span class="n">single</span> <span class="n">cutoff</span> <span class="mf">5.0</span> <span class="n">vel</span> <span class="n">yes</span>
|
||||
<span class="n">comm_modify</span> <span class="n">cutoff</span><span class="o">/</span><span class="n">multi</span> <span class="o">*</span> <span class="mf">0.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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 note">
|
||||
<p class="first admonition-title">Note</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"><span class="doc">comm_style</span></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
|
||||
information for ghost atoms that are within a single distance from its
|
||||
sub-domain. The distance is by default the maximum of the neighbor
|
||||
cutoff across 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
|
||||
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"><span class="doc">neighbor multi</span></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 extend the ghost cutoff distance
|
||||
for communication mode <em>single</em>, 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"><span class="doc">neighbor</span></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 the provided cutoff is smaller, the provided value will be ignored
|
||||
and the ghost cutoff is set to the neighbor cutoff. Specifying a
|
||||
cutoff value of 0.0 will reset any previous value to the default.</p>
|
||||
<p>The <em>cutoff/multi</em> option is equivalent to <em>cutoff</em>, but applies to
|
||||
communication mode <em>multi</em> instead. Since in this case the communication
|
||||
cutoffs are determined per atom type, a type specifier is needed and
|
||||
cutoff for one or multiple types can be extended. Also ranges of types
|
||||
using the usual asterisk notation can be given.</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
|
||||
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"><span class="doc">newton bond</span></a>
|
||||
setting. For newton bond <em>off</em>, 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 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
|
||||
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"><span class="doc">fix</span></a> or <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> or
|
||||
<a class="reference internal" href="pair_style.html"><span class="doc">pairwise potential</span></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 note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">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 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"><span class="doc">neigh_modify cluster</span></a> command.</p>
|
||||
</div>
|
||||
<p>The <em>group</em> 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"><span class="doc">atom_modify first</span></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"><span class="doc">atom_style</span></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
|
||||
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"><span class="doc">fix deform</span></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</h2>
|
||||
<p>Communication mode <em>multi</em> is currently only available for
|
||||
<a class="reference internal" href="comm_style.html"><span class="doc">comm_style</span></a> <em>brick</em>.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="comm_style.html"><span class="doc">comm_style</span></a>, <a class="reference internal" href="neighbor.html"><span class="doc">neighbor</span></a></p>
|
||||
</div>
|
||||
<div class="section" id="default">
|
||||
<h2>Default</h2>
|
||||
<p>The option defauls are mode = single, group = all, cutoff = 0.0, vel =
|
||||
no. The cutoff default of 0.0 means that ghost cutoff = neighbor
|
||||
cutoff = pairwise force cutoff + neighbor skin.</p>
|
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<div class="section" id="comm-style-command">
|
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<span id="index-0"></span><h1>comm_style command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">comm_style</span> <span class="n">style</span>
|
||||
</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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">comm_style</span> <span class="n">brick</span>
|
||||
<span class="n">comm_style</span> <span class="n">tiled</span>
|
||||
</pre></div>
|
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|
||||
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|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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
|
||||
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"><span class="doc">balance</span></a> or <a class="reference internal" href="fix_balance.html"><span class="doc">fix balance</span></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
|
||||
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"><span class="doc">create_box</span></a>
|
||||
or <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
|
||||
commands. For both the <em>brick</em> and <em>tiled</em> styles, the initial
|
||||
decomposition will be the same, as described by
|
||||
<a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> and <a class="reference internal" href="processors.html"><span class="doc">processors</span></a>
|
||||
commands. The decomposition can be changed via the
|
||||
<a class="reference internal" href="balance.html"><span class="doc">balance</span></a> or <a class="reference internal" href="fix_balance.html"><span class="doc">fix balance</span></a> commands.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
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|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="comm_modify.html"><span class="doc">comm_modify</span></a>, <a class="reference internal" href="processors.html"><span class="doc">processors</span></a>,
|
||||
<a class="reference internal" href="balance.html"><span class="doc">balance</span></a>, <a class="reference internal" href="fix_balance.html"><span class="doc">fix balance</span></a></p>
|
||||
</div>
|
||||
<div class="section" id="default">
|
||||
<h2>Default</h2>
|
||||
<p>The default style is brick.</p>
|
||||
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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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<div class="section" id="compute-command">
|
||||
<span id="index-0"></span><h1>compute command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">style</span> <span class="n">args</span>
|
||||
</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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">temp</span>
|
||||
<span class="n">compute</span> <span class="n">newtemp</span> <span class="n">flow</span> <span class="n">temp</span><span class="o">/</span><span class="n">partial</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">0</span>
|
||||
<span class="n">compute</span> <span class="mi">3</span> <span class="nb">all</span> <span class="n">ke</span><span class="o">/</span><span class="n">atom</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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
|
||||
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 class="std std-ref">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,
|
||||
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.
|
||||
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 (with only a few
|
||||
exceptions, as documented by individual compute commands).</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
|
||||
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
|
||||
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"><span class="doc">variables</span></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
|
||||
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"><span class="doc">thermo_style custom</span></a> or <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a> command.
|
||||
Or the values can be referenced in a <a class="reference internal" href="variable.html"><span class="doc">variable equal</span></a> or
|
||||
<a class="reference internal" href="variable.html"><span class="doc">variable atom</span></a> command.</li>
|
||||
<li>Per-atom values can be output via the <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> command
|
||||
or the <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a> command. Or they can be
|
||||
time-averaged via the <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a> command or
|
||||
reduced by the <a class="reference internal" href="compute_reduce.html"><span class="doc">compute reduce</span></a> command. Or the
|
||||
per-atom values can be referenced in an <a class="reference internal" href="variable.html"><span class="doc">atom-style variable</span></a>.</li>
|
||||
<li>Local values can be reduced by the <a class="reference internal" href="compute_reduce.html"><span class="doc">compute reduce</span></a> command, or histogrammed by the <a class="reference internal" href="fix_ave_histo.html"><span class="doc">fix ave/histo</span></a> command, or output by the <a class="reference internal" href="dump.html"><span class="doc">dump local</span></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
|
||||
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"><span class="doc">Thermodynamic output</span></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.
|
||||
If a compute value is accessed in another way, e.g. by a
|
||||
<a class="reference internal" href="variable.html"><span class="doc">variable</span></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-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">thermo_temp</span> <span class="nb">all</span> <span class="n">temp</span>
|
||||
<span class="n">compute</span> <span class="n">thermo_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">thermo_temp</span>
|
||||
<span class="n">compute</span> <span class="n">thermo_pe</span> <span class="nb">all</span> <span class="n">pe</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<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"><span class="doc">thermo_style</span></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"><span class="doc">fix</span></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"><span class="doc">thermo_modify</span></a> and <a class="reference internal" href="fix_modify.html"><span class="doc">fix modify</span></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"><span class="doc">compute_modify</span></a> command.</p>
|
||||
<p>Computes can be deleted with the <a class="reference internal" href="uncompute.html"><span class="doc">uncompute</span></a> command.</p>
|
||||
<p>Code for new computes can be added to LAMMPS (see <a class="reference internal" href="Section_modify.html"><span class="doc">this section</span></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
|
||||
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 class="std std-ref">this page</span></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 class="std std-ref">this page</span></a>.</p>
|
||||
<ul class="simple">
|
||||
<li><a class="reference internal" href="compute_bond_local.html"><span class="doc">angle/local</span></a> - theta and energy of each angle</li>
|
||||
<li><a class="reference internal" href="compute_angmom_chunk.html"><span class="doc">angmom/chunk</span></a> - angular momentum for each chunk</li>
|
||||
<li><a class="reference internal" href="compute_body_local.html"><span class="doc">body/local</span></a> - attributes of body sub-particles</li>
|
||||
<li><a class="reference internal" href="compute_bond.html"><span class="doc">bond</span></a> - values computed by a bond style</li>
|
||||
<li><a class="reference internal" href="compute_bond_local.html"><span class="doc">bond/local</span></a> - distance and energy of each bond</li>
|
||||
<li><a class="reference internal" href="compute_centro_atom.html"><span class="doc">centro/atom</span></a> - centro-symmetry parameter for each atom</li>
|
||||
<li><a class="reference internal" href="compute_chunk_atom.html"><span class="doc">chunk/atom</span></a> - assign chunk IDs to each atom</li>
|
||||
<li><a class="reference internal" href="compute_cluster_atom.html"><span class="doc">cluster/atom</span></a> - cluster ID for each atom</li>
|
||||
<li><a class="reference internal" href="compute_cna_atom.html"><span class="doc">cna/atom</span></a> - common neighbor analysis (CNA) for each atom</li>
|
||||
<li><a class="reference internal" href="compute_com.html"><span class="doc">com</span></a> - center-of-mass of group of atoms</li>
|
||||
<li><a class="reference internal" href="compute_com_chunk.html"><span class="doc">com/chunk</span></a> - center-of-mass for each chunk</li>
|
||||
<li><a class="reference internal" href="compute_contact_atom.html"><span class="doc">contact/atom</span></a> - contact count for each spherical particle</li>
|
||||
<li><a class="reference internal" href="compute_coord_atom.html"><span class="doc">coord/atom</span></a> - coordination number for each atom</li>
|
||||
<li><a class="reference internal" href="compute_damage_atom.html"><span class="doc">damage/atom</span></a> - Peridynamic damage for each atom</li>
|
||||
<li><a class="reference internal" href="compute_dihedral_local.html"><span class="doc">dihedral/local</span></a> - angle of each dihedral</li>
|
||||
<li><a class="reference internal" href="compute_dilatation_atom.html"><span class="doc">dilatation/atom</span></a> - Peridynamic dilatation for each atom</li>
|
||||
<li><a class="reference internal" href="compute_displace_atom.html"><span class="doc">displace/atom</span></a> - displacement of each atom</li>
|
||||
<li><a class="reference internal" href="compute_erotate_asphere.html"><span class="doc">erotate/asphere</span></a> - rotational energy of aspherical particles</li>
|
||||
<li><a class="reference internal" href="compute_erotate_rigid.html"><span class="doc">erotate/rigid</span></a> - rotational energy of rigid bodies</li>
|
||||
<li><a class="reference internal" href="compute_erotate_sphere.html"><span class="doc">erotate/sphere</span></a> - rotational energy of spherical particles</li>
|
||||
<li><a class="reference internal" href="compute_erotate_sphere.html"><span class="doc">erotate/sphere/atom</span></a> - rotational energy for each spherical particle</li>
|
||||
<li><a class="reference internal" href="compute_event_displace.html"><span class="doc">event/displace</span></a> - detect event on atom displacement</li>
|
||||
<li><a class="reference internal" href="compute_group_group.html"><span class="doc">group/group</span></a> - energy/force between two groups of atoms</li>
|
||||
<li><a class="reference internal" href="compute_gyration.html"><span class="doc">gyration</span></a> - radius of gyration of group of atoms</li>
|
||||
<li><a class="reference internal" href="compute_gyration_chunk.html"><span class="doc">gyration/chunk</span></a> - radius of gyration for each chunk</li>
|
||||
<li><a class="reference internal" href="compute_heat_flux.html"><span class="doc">heat/flux</span></a> - heat flux through a group of atoms</li>
|
||||
<li><a class="reference internal" href="compute_hexorder_atom.html"><span class="doc">hexorder/atom</span></a> - bond orientational order parameter q6</li>
|
||||
<li><a class="reference internal" href="compute_improper_local.html"><span class="doc">improper/local</span></a> - angle of each improper</li>
|
||||
<li><a class="reference internal" href="compute_inertia_chunk.html"><span class="doc">inertia/chunk</span></a> - inertia tensor for each chunk</li>
|
||||
<li><a class="reference internal" href="compute_ke.html"><span class="doc">ke</span></a> - translational kinetic energy</li>
|
||||
<li><a class="reference internal" href="compute_ke_atom.html"><span class="doc">ke/atom</span></a> - kinetic energy for each atom</li>
|
||||
<li><a class="reference internal" href="compute_ke_rigid.html"><span class="doc">ke/rigid</span></a> - translational kinetic energy of rigid bodies</li>
|
||||
<li><a class="reference internal" href="compute_msd.html"><span class="doc">msd</span></a> - mean-squared displacement of group of atoms</li>
|
||||
<li><a class="reference internal" href="compute_msd_chunk.html"><span class="doc">msd/chunk</span></a> - mean-squared displacement for each chunk</li>
|
||||
<li><a class="reference internal" href="compute_msd_nongauss.html"><span class="doc">msd/nongauss</span></a> - MSD and non-Gaussian parameter of group of atoms</li>
|
||||
<li><a class="reference internal" href="compute_omega_chunk.html"><span class="doc">omega/chunk</span></a> - angular velocity for each chunk</li>
|
||||
<li><a class="reference internal" href="compute_orientorder_atom.html"><span class="doc">orientorder/atom</span></a> - Steinhardt bond orientational order parameters Ql</li>
|
||||
<li><a class="reference internal" href="compute_pair.html"><span class="doc">pair</span></a> - values computed by a pair style</li>
|
||||
<li><a class="reference internal" href="compute_pair_local.html"><span class="doc">pair/local</span></a> - distance/energy/force of each pairwise interaction</li>
|
||||
<li><a class="reference internal" href="compute_pe.html"><span class="doc">pe</span></a> - potential energy</li>
|
||||
<li><a class="reference internal" href="compute_pe_atom.html"><span class="doc">pe/atom</span></a> - potential energy for each atom</li>
|
||||
<li><a class="reference internal" href="compute_plasticity_atom.html"><span class="doc">plasticity/atom</span></a> - Peridynamic plasticity for each atom</li>
|
||||
<li><a class="reference internal" href="compute_pressure.html"><span class="doc">pressure</span></a> - total pressure and pressure tensor</li>
|
||||
<li><a class="reference internal" href="compute_property_atom.html"><span class="doc">property/atom</span></a> - convert atom attributes to per-atom vectors/arrays</li>
|
||||
<li><a class="reference internal" href="compute_property_local.html"><span class="doc">property/local</span></a> - convert local attributes to localvectors/arrays</li>
|
||||
<li><a class="reference internal" href="compute_property_chunk.html"><span class="doc">property/chunk</span></a> - extract various per-chunk attributes</li>
|
||||
<li><a class="reference internal" href="compute_rdf.html"><span class="doc">rdf</span></a> - radial distribution function g(r) histogram of group of atoms</li>
|
||||
<li><a class="reference internal" href="compute_reduce.html"><span class="doc">reduce</span></a> - combine per-atom quantities into a single global value</li>
|
||||
<li><a class="reference internal" href="compute_reduce.html"><span class="doc">reduce/region</span></a> - same as compute reduce, within a region</li>
|
||||
<li><a class="reference internal" href="compute_slice.html"><span class="doc">slice</span></a> - extract values from global vector or array</li>
|
||||
<li><a class="reference internal" href="compute_sna_atom.html"><span class="doc">sna/atom</span></a> - calculate bispectrum coefficients for each atom</li>
|
||||
<li><a class="reference internal" href="compute_sna_atom.html"><span class="doc">snad/atom</span></a> - derivative of bispectrum coefficients for each atom</li>
|
||||
<li><a class="reference internal" href="compute_sna_atom.html"><span class="doc">snav/atom</span></a> - virial contribution from bispectrum coefficients for each atom</li>
|
||||
<li><a class="reference internal" href="compute_stress_atom.html"><span class="doc">stress/atom</span></a> - stress tensor for each atom</li>
|
||||
<li><a class="reference internal" href="compute_temp.html"><span class="doc">temp</span></a> - temperature of group of atoms</li>
|
||||
<li><a class="reference internal" href="compute_temp_asphere.html"><span class="doc">temp/asphere</span></a> - temperature of aspherical particles</li>
|
||||
<li><a class="reference internal" href="compute_temp_body.html"><span class="doc">temp/body</span></a> - temperature of body particles</li>
|
||||
<li><a class="reference internal" href="compute_temp_chunk.html"><span class="doc">temp/chunk</span></a> - temperature of each chunk</li>
|
||||
<li><a class="reference internal" href="compute_temp_com.html"><span class="doc">temp/com</span></a> - temperature after subtracting center-of-mass velocity</li>
|
||||
<li><a class="reference internal" href="compute_temp_deform.html"><span class="doc">temp/deform</span></a> - temperature excluding box deformation velocity</li>
|
||||
<li><a class="reference internal" href="compute_temp_partial.html"><span class="doc">temp/partial</span></a> - temperature excluding one or more dimensions of velocity</li>
|
||||
<li><a class="reference internal" href="compute_temp_profile.html"><span class="doc">temp/profile</span></a> - temperature excluding a binned velocity profile</li>
|
||||
<li><a class="reference internal" href="compute_temp_ramp.html"><span class="doc">temp/ramp</span></a> - temperature excluding ramped velocity component</li>
|
||||
<li><a class="reference internal" href="compute_temp_region.html"><span class="doc">temp/region</span></a> - temperature of a region of atoms</li>
|
||||
<li><a class="reference internal" href="compute_temp_sphere.html"><span class="doc">temp/sphere</span></a> - temperature of spherical particles</li>
|
||||
<li><a class="reference internal" href="compute_ti.html"><span class="doc">ti</span></a> - thermodyanmic integration free energy values</li>
|
||||
<li><a class="reference internal" href="compute_torque_chunk.html"><span class="doc">torque/chunk</span></a> - torque applied on each chunk</li>
|
||||
<li><a class="reference internal" href="compute_vacf.html"><span class="doc">vacf</span></a> - velocity-autocorrelation function of group of atoms</li>
|
||||
<li><a class="reference internal" href="compute_vcm_chunk.html"><span class="doc">vcm/chunk</span></a> - velocity of center-of-mass for each chunk</li>
|
||||
<li><a class="reference internal" href="compute_voronoi_atom.html"><span class="doc">voronoi/atom</span></a> - Voronoi volume and neighbors for each atom</li>
|
||||
</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 class="std std-ref">this page</span></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 class="std std-ref">this page</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="uncompute.html"><span class="doc">uncompute</span></a>, <a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify</span></a>, <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a>, <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a>,
|
||||
<a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>, <a class="reference internal" href="fix_ave_histo.html"><span class="doc">fix ave/histo</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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|
||||
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||||
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|
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<div class="section" id="compute-ackland-atom-command">
|
||||
<span id="index-0"></span><h1>compute ackland/atom command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">ackland</span><span class="o">/</span><span class="n">atom</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
|
||||
<li>ackland/atom = style name of this compute command</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ackland</span><span class="o">/</span><span class="n">atom</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<p>Defines a computation that calculates the local lattice structure
|
||||
according to the formulation given in <a class="reference internal" href="#ackland"><span class="std std-ref">(Ackland)</span></a>.</p>
|
||||
<p>In contrast to the <a class="reference internal" href="compute_centro_atom.html"><span class="doc">centro-symmetry parameter</span></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
|
||||
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
|
||||
any command that uses per-atom values from a compute as input. See
|
||||
<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of
|
||||
LAMMPS output options.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</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 class="std std-ref">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</h2>
|
||||
<p><a class="reference internal" href="compute_centro_atom.html"><span class="doc">compute centro/atom</span></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>
|
||||
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<div class="section" id="compute-angle-command">
|
||||
<span id="index-0"></span><h1>compute angle command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">angle</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
|
||||
<li>angle = style name of this compute command</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">angle</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<p>Define a computation that extracts the angle energy calculated by each
|
||||
of the angle sub-styles used in the “angle_style
|
||||
hybrid” angle_hybrid.html command. These values are made accessible
|
||||
for output or further processing by other commands. The group
|
||||
specified for this command is ignored.</p>
|
||||
<p>This compute is useful when using <a class="reference internal" href="angle_hybrid.html"><span class="doc">angle_style hybrid</span></a> if you want to know the portion of the total
|
||||
energy contributed by one or more of the hybrid sub-styles.</p>
|
||||
<p><strong>Output info:</strong></p>
|
||||
<p>This compute calculates a global vector of length N where N is the
|
||||
number of sub_styles defined by the <a class="reference internal" href="angle_style.html"><span class="doc">angle_style hybrid</span></a> command, which can be accessed by indices
|
||||
1-N. 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 class="std std-ref">this section</span></a> for an overview of LAMMPS output
|
||||
options.</p>
|
||||
<p>The vector values are “extensive” and will be in energy
|
||||
<a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="compute_pe.html"><span class="doc">compute pe</span></a>, <a class="reference internal" href="compute_pair.html"><span class="doc">compute pair</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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|
||||
<div class="section" id="compute-angle-local-command">
|
||||
<span id="index-0"></span><h1>compute angle/local command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">angle</span><span class="o">/</span><span class="n">local</span> <span class="n">input1</span> <span class="n">input2</span> <span class="o">...</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">angle</span><span class="o">/</span><span class="n">local</span> <span class="n">theta</span>
|
||||
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">angle</span><span class="o">/</span><span class="n">local</span> <span class="n">eng</span> <span class="n">theta</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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
|
||||
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"><span class="doc">angle_style</span></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"><span class="doc">fix shake</span></a> or <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></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
|
||||
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"><span class="doc">compute property/local</span></a> command can be combined
|
||||
with data from this command and output by the <a class="reference internal" href="dump.html"><span class="doc">dump local</span></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
|
||||
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 class="std std-ref">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"><span class="doc">units</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="dump.html"><span class="doc">dump local</span></a>, <a class="reference internal" href="compute_property_local.html"><span class="doc">compute property/local</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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<div class="section" id="compute-angmom-chunk-command">
|
||||
<span id="index-0"></span><h1>compute angmom/chunk command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">angmom</span><span class="o">/</span><span class="n">chunk</span> <span class="n">chunkID</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></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"><span class="doc">compute chunk/atom</span></a> command</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="n">fluid</span> <span class="n">angmom</span><span class="o">/</span><span class="n">chunk</span> <span class="n">molchunk</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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"><span class="doc">compute chunk/atom</span></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"><span class="doc">compute chunk/atom</span></a> doc page and “<a class="reference internal" href="Section_howto.html#howto-23"><span class="std std-ref">Section_howto 23</span></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
|
||||
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"><span class="doc">compute chunk/atom</span></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 note">
|
||||
<p class="first admonition-title">Note</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"><span class="doc">dump custom</span></a> command for a discussion
|
||||
of “unwrapped” coordinates. See the Atoms section of the
|
||||
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></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"><span class="doc">set image</span></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"><span class="doc">fix ave/time</span></a>
|
||||
command, for example:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
|
||||
<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">angmom</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
|
||||
</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"><span class="doc">compute chunk/atom</span></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 class="std std-ref">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"><span class="doc">units</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="variable.html"><span class="doc">variable angmom() function</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
</div>
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<div class="section" id="compute-basal-atom-command">
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<span id="index-0"></span><h1>compute basal/atom command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">basal</span><span class="o">/</span><span class="n">atom</span>
|
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</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
|
||||
<li>basal/atom = style name of this compute command</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">basal</span><span class="o">/</span><span class="n">atom</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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
|
||||
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 class="std std-ref">(Barrett)</span></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
|
||||
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 class="std std-ref">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</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 class="std std-ref">Making LAMMPS</span></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</h2>
|
||||
<p><a class="reference internal" href="compute_centro_atom.html"><span class="doc">compute centro/atom</span></a>, <a class="reference internal" href="compute_ackland_atom.html"><span class="doc">compute ackland/atom</span></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>
|
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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</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">body</span><span class="o">/</span><span class="n">local</span> <span class="n">input1</span> <span class="n">input2</span> <span class="o">...</span>
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|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></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>id</em> or <em>type</em> or <em>integer</em></li>
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>id</em> = atom ID of the body particle
|
||||
<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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">body</span><span class="o">/</span><span class="n">local</span> <span class="nb">type</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span>
|
||||
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">body</span><span class="o">/</span><span class="n">local</span> <span class="mi">3</span> <span class="mi">6</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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 class="std std-ref">Section_howto 14</span></a>
|
||||
of the manual and the <a class="reference internal" href="body.html"><span class="doc">body</span></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>id</em> keyword
|
||||
will store the ID of the particle.</p>
|
||||
<p>For both body particles and non-body particles, the <em>type</em> keyword
|
||||
will store the type of the particle.</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.
|
||||
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
|
||||
by the body style for each sub-particle. The body style, as specified
|
||||
by the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style body</span></a>, determines how many fields
|
||||
exist and what they are. See the <a class="reference internal" href="body.html"><span class="doc">body</span></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"><span class="doc">dump local</span></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"><span class="doc">dump atom or custom</span></a>
|
||||
command.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">body</span><span class="o">/</span><span class="n">local</span> <span class="nb">type</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span>
|
||||
<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1000</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="n">index</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p><strong>Output info:</strong></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 class="std std-ref">this section</span></a> for an overview of LAMMPS output
|
||||
options.</p>
|
||||
<p>The <a class="reference internal" href="units.html"><span class="doc">units</span></a> for output values depend on the body style.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="dump.html"><span class="doc">dump local</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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|
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|
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<div class="section" id="compute-bond-command">
|
||||
<span id="index-0"></span><h1>compute bond command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">bond</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
|
||||
<li>bond = style name of this compute command</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">bond</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<p>Define a computation that extracts the bond energy calculated by each
|
||||
of the bond sub-styles used in the <a class="reference internal" href="bond_hybrid.html"><span class="doc">bond_style hybrid</span></a> command. These values are made accessible
|
||||
for output or further processing by other commands. The group
|
||||
specified for this command is ignored.</p>
|
||||
<p>This compute is useful when using <a class="reference internal" href="bond_hybrid.html"><span class="doc">bond_style hybrid</span></a>
|
||||
if you want to know the portion of the total energy contributed by one
|
||||
or more of the hybrid sub-styles.</p>
|
||||
<p><strong>Output info:</strong></p>
|
||||
<p>This compute calculates a global vector of length N where N is the
|
||||
number of sub_styles defined by the <a class="reference internal" href="bond_style.html"><span class="doc">bond_style hybrid</span></a> command, which can be accessed by indices 1-N.
|
||||
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 class="std std-ref">this section</span></a> for an overview of LAMMPS output
|
||||
options.</p>
|
||||
<p>The vector values are “extensive” and will be in energy
|
||||
<a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="compute_pe.html"><span class="doc">compute pe</span></a>, <a class="reference internal" href="compute_pair.html"><span class="doc">compute pair</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
</div>
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</div>
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<div class="section" id="compute-bond-local-command">
|
||||
<span id="index-0"></span><h1>compute bond/local command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">bond</span><span class="o">/</span><span class="n">local</span> <span class="n">input1</span> <span class="n">input2</span> <span class="o">...</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">bond</span><span class="o">/</span><span class="n">local</span> <span class="n">eng</span>
|
||||
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">bond</span><span class="o">/</span><span class="n">local</span> <span class="n">dist</span> <span class="n">eng</span> <span class="n">force</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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
|
||||
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"><span class="doc">bond_style</span></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"><span class="doc">fix shake</span></a> or
|
||||
<a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></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"><span class="doc">compute property/local</span></a> command can be combined
|
||||
with data from this command and output by the <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a>
|
||||
command in a consistent way.</p>
|
||||
<p>Here is an example of how to do this:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">local</span> <span class="n">batom1</span> <span class="n">batom2</span> <span class="n">btype</span>
|
||||
<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">bond</span><span class="o">/</span><span class="n">local</span> <span class="n">dist</span> <span class="n">eng</span>
|
||||
<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1000</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="n">index</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p><strong>Output info:</strong></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 class="std std-ref">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"><span class="doc">units</span></a>. The
|
||||
output for <em>eng</em> will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>. The output for
|
||||
<em>force</em> will be in force <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="dump.html"><span class="doc">dump local</span></a>, <a class="reference internal" href="compute_property_local.html"><span class="doc">compute property/local</span></a></p>
|
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<div class="section" id="compute-centro-atom-command">
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<span id="index-0"></span><h1>compute centro/atom command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">centro</span><span class="o">/</span><span class="n">atom</span> <span class="n">lattice</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">centro</span><span class="o">/</span><span class="n">atom</span> <span class="n">fcc</span>
|
||||
</pre></div>
|
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|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">centro</span><span class="o">/</span><span class="n">atom</span> <span class="mi">8</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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 class="std std-ref">(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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
any command that uses per-atom values from a compute as input. See
|
||||
<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">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
|
||||
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
|
||||
simulation into gold (FCC). These were provided by Jon Zimmerman
|
||||
(Sandia):</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Bulk</span> <span class="n">lattice</span> <span class="o">=</span> <span class="mi">0</span>
|
||||
<span class="n">Dislocation</span> <span class="n">core</span> <span class="o">~</span> <span class="mf">1.0</span> <span class="p">(</span><span class="mf">0.5</span> <span class="n">to</span> <span class="mf">1.25</span><span class="p">)</span>
|
||||
<span class="n">Stacking</span> <span class="n">faults</span> <span class="o">~</span> <span class="mf">5.0</span> <span class="p">(</span><span class="mf">4.0</span> <span class="n">to</span> <span class="mf">6.0</span><span class="p">)</span>
|
||||
<span class="n">Free</span> <span class="n">surface</span> <span class="o">~</span> <span class="mf">23.0</span>
|
||||
</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-default"><div class="highlight"><pre><span></span><span class="n">Bulk</span> <span class="n">lattice</span> <span class="o">=</span> <span class="mi">0</span>
|
||||
<span class="n">Dislocation</span> <span class="n">core</span> <span class="o">~</span> <span class="mf">0.06</span> <span class="p">(</span><span class="mf">0.03</span> <span class="n">to</span> <span class="mf">0.075</span><span class="p">)</span>
|
||||
<span class="n">Stacking</span> <span class="n">faults</span> <span class="o">~</span> <span class="mf">0.3</span> <span class="p">(</span><span class="mf">0.24</span> <span class="n">to</span> <span class="mf">0.36</span><span class="p">)</span>
|
||||
<span class="n">Free</span> <span class="n">surface</span> <span class="o">~</span> <span class="mf">1.38</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<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</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="compute_cna_atom.html"><span class="doc">compute cna/atom</span></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>
|
||||
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|
||||
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|
||||
|
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<div class="section" id="compute-chunk-atom-command">
|
||||
<span id="index-0"></span><h1>compute chunk/atom command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">style</span> <span class="n">args</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
|
||||
<li>chunk/atom = style name of this compute command</li>
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
style = <em>bin/1d</em> or <em>bin/2d</em> or <em>bin/3d</em> or <em>bin/sphere</em> or <em>type</em> or <em>molecule</em> or <em>compute/fix/variable</em>
|
||||
<em>bin/1d</em> args = dim origin delta
|
||||
dim = <em>x</em> or <em>y</em> or <em>z</em>
|
||||
origin = <em>lower</em> or <em>center</em> or <em>upper</em> or coordinate value (distance units)
|
||||
delta = thickness of spatial bins in dim (distance units)
|
||||
<em>bin/2d</em> args = dim origin delta dim origin delta
|
||||
dim = <em>x</em> or <em>y</em> or <em>z</em>
|
||||
origin = <em>lower</em> or <em>center</em> or <em>upper</em> or coordinate value (distance units)
|
||||
delta = thickness of spatial bins in dim (distance units)
|
||||
<em>bin/3d</em> args = dim origin delta dim origin delta dim origin delta
|
||||
dim = <em>x</em> or <em>y</em> or <em>z</em>
|
||||
origin = <em>lower</em> or <em>center</em> or <em>upper</em> or coordinate value (distance units)
|
||||
delta = thickness of spatial bins in dim (distance units)
|
||||
<em>bin/sphere</em> args = xorig yorig zorig rmin rmax nsbin
|
||||
xorig,yorig,zorig = center point of sphere
|
||||
srmin,srmax = bin from sphere radius rmin to rmax
|
||||
nsbin = # of spherical shell bins between rmin and rmax
|
||||
<em>bin/cylinder</em> args = dim origin delta c1 c2 rmin rmax ncbin
|
||||
dim = <em>x</em> or <em>y</em> or <em>z</em> = axis of cylinder axis
|
||||
origin = <em>lower</em> or <em>center</em> or <em>upper</em> or coordinate value (distance units)
|
||||
delta = thickness of spatial bins in dim (distance units)
|
||||
c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
|
||||
crmin,crmax = bin from cylinder radius rmin to rmax (distance units)
|
||||
ncbin = # of concentric circle bins between rmin and rmax
|
||||
<em>type</em> args = none
|
||||
<em>molecule</em> args = none
|
||||
<em>compute/fix/variable</em> = c_ID, c_ID[I], f_ID, f_ID[I], v_name with no args
|
||||
c_ID = per-atom vector calculated by a compute with ID
|
||||
c_ID[I] = Ith column of per-atom array calculated by a compute with ID
|
||||
f_ID = per-atom vector calculated by a fix with ID
|
||||
f_ID[I] = Ith column of per-atom array calculated by a fix with ID
|
||||
v_name = per-atom vector calculated by an atom-style variable with name
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>zero or more keyword/values pairs may be appended</li>
|
||||
<li>keyword = <em>region</em> or <em>nchunk</em> or <em>static</em> or <em>compress</em> or <em>bound</em> or <em>discard</em> or <em>pbc</em> or <em>units</em></li>
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>region</em> value = region-ID
|
||||
region-ID = ID of region atoms must be in to be part of a chunk
|
||||
<em>nchunk</em> value = <em>once</em> or <em>every</em>
|
||||
once = only compute the number of chunks once
|
||||
every = re-compute the number of chunks whenever invoked
|
||||
<em>limit</em> values = 0 or Nc max or Nc exact
|
||||
0 = no limit on the number of chunks
|
||||
Nc max = limit number of chunks to be <= Nc
|
||||
Nc exact = set number of chunks to exactly Nc
|
||||
<em>ids</em> value = <em>once</em> or <em>nfreq</em> or <em>every</em>
|
||||
once = assign chunk IDs to atoms only once, they persist thereafter
|
||||
nfreq = assign chunk IDs to atoms only once every Nfreq steps (if invoked by <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> which sets Nfreq)
|
||||
every = assign chunk IDs to atoms whenever invoked
|
||||
<em>compress</em> value = <em>yes</em> or <em>no</em>
|
||||
yes = compress chunk IDs to eliminate IDs with no atoms
|
||||
no = do not compress chunk IDs even if some IDs have no atoms
|
||||
<em>discard</em> value = <em>yes</em> or <em>no</em> or <em>mixed</em>
|
||||
yes = discard atoms with out-of-range chunk IDs by assigning a chunk ID = 0
|
||||
no = keep atoms with out-of-range chunk IDs by assigning a valid chunk ID
|
||||
mixed = keep or discard such atoms according to spatial binning rule
|
||||
<em>bound</em> values = x/y/z lo hi
|
||||
x/y/z = <em>x</em> or <em>y</em> or <em>z</em> to bound sptial bins in this dimension
|
||||
lo = <em>lower</em> or coordinate value (distance units)
|
||||
hi = <em>upper</em> or coordinate value (distance units)
|
||||
<em>pbc</em> value = <em>no</em> or <em>yes</em>
|
||||
yes = use periodic distance for bin/sphere and bin/cylinder styles
|
||||
<em>units</em> value = <em>box</em> or <em>lattice</em> or <em>reduced</em>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="nb">type</span>
|
||||
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="nb">bin</span><span class="o">/</span><span class="mi">1</span><span class="n">d</span> <span class="n">z</span> <span class="n">lower</span> <span class="mf">0.02</span> <span class="n">units</span> <span class="n">reduced</span>
|
||||
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="nb">bin</span><span class="o">/</span><span class="mi">2</span><span class="n">d</span> <span class="n">z</span> <span class="n">lower</span> <span class="mf">1.0</span> <span class="n">y</span> <span class="mf">0.0</span> <span class="mf">2.5</span>
|
||||
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span> <span class="n">region</span> <span class="n">sphere</span> <span class="n">nchunk</span> <span class="n">once</span> <span class="n">ids</span> <span class="n">once</span> <span class="n">compress</span> <span class="n">yes</span>
|
||||
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="nb">bin</span><span class="o">/</span><span class="n">sphere</span> <span class="mi">5</span> <span class="mi">5</span> <span class="mi">5</span> <span class="mf">2.0</span> <span class="mf">5.0</span> <span class="mi">5</span> <span class="n">discard</span> <span class="n">yes</span>
|
||||
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="nb">bin</span><span class="o">/</span><span class="n">cylinder</span> <span class="n">z</span> <span class="n">lower</span> <span class="mi">2</span> <span class="mi">10</span> <span class="mi">10</span> <span class="mf">2.0</span> <span class="mf">5.0</span> <span class="mi">3</span> <span class="n">discard</span> <span class="n">yes</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<p>Define a computation that calculates an integer chunk ID from 1 to
|
||||
Nchunk for each atom in the group. Values of chunk IDs are determined
|
||||
by the <em>style</em> of chunk, which can be based on atom type or molecule
|
||||
ID or spatial binning or a per-atom property or value calculated by
|
||||
another <a class="reference internal" href="compute.html"><span class="doc">compute</span></a>, <a class="reference internal" href="fix.html"><span class="doc">fix</span></a>, or <a class="reference internal" href="variable.html"><span class="doc">atom-style variable</span></a>. Per-atom chunk IDs can be used by other
|
||||
computes with “chunk” in their style name, such as <a class="reference internal" href="compute_com_chunk.html"><span class="doc">compute com/chunk</span></a> or <a class="reference internal" href="compute_msd_chunk.html"><span class="doc">compute msd/chunk</span></a>. Or they can be used by the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> command to sum and time average a
|
||||
variety of per-atom properties over the atoms in each chunk. Or they
|
||||
can simply be accessed by any command that uses per-atom values from a
|
||||
compute as input, as discussed in <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a>.</p>
|
||||
<p>See <a class="reference internal" href="Section_howto.html#howto-23"><span class="std std-ref">Section_howto 23</span></a> for an overview of
|
||||
how this compute can be used with a variety of other commands to
|
||||
tabulate properties of a simulation. The howto section gives several
|
||||
examples of input script commands that can be used to calculate
|
||||
interesting properties.</p>
|
||||
<p>Conceptually it is important to realize that this compute does two
|
||||
simple things. First, it sets the value of <em>Nchunk</em> = the number of
|
||||
chunks, which can be a constant value or change over time. Second, it
|
||||
assigns each atom to a chunk via a chunk ID. Chunk IDs range from 1
|
||||
to <em>Nchunk</em> inclusive; some chunks may have no atoms assigned to them.
|
||||
Atoms that do not belong to any chunk are assigned a value of 0. Note
|
||||
that the two operations are not always performed together. For
|
||||
example, spatial bins can be setup once (which sets <em>Nchunk</em>), and
|
||||
atoms assigned to those bins many times thereafter (setting their
|
||||
chunk IDs).</p>
|
||||
<p>All other commands in LAMMPS that use chunk IDs assume there are
|
||||
<em>Nchunk</em> number of chunks, and that every atom is assigned to one of
|
||||
those chunks, or not assigned to any chunk.</p>
|
||||
<p>There are many options for specifying for how and when <em>Nchunk</em> is
|
||||
calculated, and how and when chunk IDs are assigned to atoms. The
|
||||
details depend on the chunk <em>style</em> and its <em>args</em>, as well as
|
||||
optional keyword settings. They can also depend on whether a <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> command is using this compute, since
|
||||
that command requires <em>Nchunk</em> to remain static across windows of
|
||||
timesteps it specifies, while it accumulates per-chunk averages.</p>
|
||||
<p>The details are described below.</p>
|
||||
<p>The different chunk styles operate as follows. For each style, how it
|
||||
calculates <em>Nchunk</em> and assigns chunk IDs to atoms is explained. Note
|
||||
that using the optional keywords can change both of those actions, as
|
||||
described further below where the keywords are discussed.</p>
|
||||
<hr class="docutils" />
|
||||
<p>The <em>binning</em> styles perform a spatial binning of atoms, and assign an
|
||||
atom the chunk ID corresponding to the bin number it is in. <em>Nchunk</em>
|
||||
is set to the number of bins, which can change if the simulation box
|
||||
size changes.</p>
|
||||
<p>The <em>bin/1d</em>, <em>bin/2d</em>, and <em>bin/3d</em> styles define bins as 1d layers
|
||||
(slabs), 2d pencils, or 3d boxes. The <em>dim</em>, <em>origin</em>, and <em>delta</em>
|
||||
settings are specified 1, 2, or 3 times. For 2d or 3d bins, there is
|
||||
no restriction on specifying dim = x before dim = y or z, or dim = y
|
||||
before dim = z. Bins in a particular <em>dim</em> have a bin size in that
|
||||
dimension given by <em>delta</em>. In each dimension, bins are defined
|
||||
relative to a specified <em>origin</em>, which may be the lower/upper edge of
|
||||
the simulation box (in that dimension), or its center point, or a
|
||||
specified coordinate value. Starting at the origin, sufficient bins
|
||||
are created in both directions to completely span the simulation box
|
||||
or the bounds specified by the optional <em>bounds</em> keyword.</p>
|
||||
<p>For orthogonal simulation boxes, the bins are layers, pencils, or
|
||||
boxes aligned with the xyz coordinate axes. For triclinic
|
||||
(non-orthogonal) simulation boxes, the bin faces are parallel to the
|
||||
tilted faces of the simulation box. See <a class="reference internal" href="Section_howto.html#howto-12"><span class="std std-ref">this section</span></a> of the manual for a discussion of
|
||||
the geometry of triclinic boxes in LAMMPS. As described there, a
|
||||
tilted simulation box has edge vectors a,b,c. In that nomenclature,
|
||||
bins in the x dimension have faces with normals in the “b” cross “c”
|
||||
direction. Bins in y have faces normal to the “a” cross “c”
|
||||
direction. And bins in z have faces normal to the “a” cross “b”
|
||||
direction. Note that in order to define the size and position of
|
||||
these bins in an unambiguous fashion, the <em>units</em> option must be set
|
||||
to <em>reduced</em> when using a triclinic simulation box, as noted below.</p>
|
||||
<p>The meaning of <em>origin</em> and <em>delta</em> for triclinic boxes is as follows.
|
||||
Consider a triclinic box with bins that are 1d layers or slabs in the
|
||||
x dimension. No matter how the box is tilted, an <em>origin</em> of 0.0
|
||||
means start layers at the lower “b” cross “c” plane of the simulation
|
||||
box and an <em>origin</em> of 1.0 means to start layers at the upper “b”
|
||||
cross “c” face of the box. A <em>delta</em> value of 0.1 in <em>reduced</em> units
|
||||
means there will be 10 layers from 0.0 to 1.0, regardless of the
|
||||
current size or shape of the simulation box.</p>
|
||||
<p>The <em>bin/sphere</em> style defines a set of spherical shell bins around
|
||||
the origin (<em>xorig</em>,<em>yorig</em>,<em>zorig</em>), using <em>nsbin</em> bins with radii
|
||||
equally spaced between <em>srmin</em> and <em>srmax</em>. This is effectively a 1d
|
||||
vector of bins. For example, if <em>srmin</em> = 1.0 and <em>srmax</em> = 10.0 and
|
||||
<em>nsbin</em> = 9, then the first bin spans 1.0 < r < 2.0, and the last bin
|
||||
spans 9.0 < r 10.0. The geometry of the bins is the same whether the
|
||||
simulation box is orthogonal or triclinic; i.e. the spherical shells
|
||||
are not tilted or scaled differently in different dimensions to
|
||||
transform them into ellipsoidal shells.</p>
|
||||
<p>The <em>bin/cylinder</em> style defines bins for a cylinder oriented along
|
||||
the axis <em>dim</em> with the axis coordinates in the other two radial
|
||||
dimensions at (<em>c1</em>,<em>c2</em>). For dim = x, c1/c2 = y/z; for dim = y,
|
||||
c1/c2 = x/z; for dim = z, c1/c2 = x/y. This is effectively a 2d array
|
||||
of bins. The first dimension is along the cylinder axis, the second
|
||||
dimension is radially outward from the cylinder axis. The bin size
|
||||
and positions along the cylinder axis are specified by the <em>origin</em>
|
||||
and <em>delta</em> values, the same as for the <em>bin/1d</em>, <em>bin/2d</em>, and
|
||||
<em>bin/3d</em> styles. There are <em>ncbin</em> concentric circle bins in the
|
||||
radial direction from the cylinder axis with radii equally spaced
|
||||
between <em>crmin</em> and <em>crmax</em>. For example, if <em>crmin</em> = 1.0 and
|
||||
<em>crmax</em> = 10.0 and <em>ncbin</em> = 9, then the first bin spans 1.0 < r <
|
||||
2.0, and the last bin spans 9.0 < r 10.0. The geometry of the bins in
|
||||
the radial dimensions is the same whether the simulation box is
|
||||
orthogonal or triclinic; i.e. the concetric circles are not tilted or
|
||||
scaled differently in the two different dimensions to transform them
|
||||
into ellipses.</p>
|
||||
<p>The created bins (and hence the chunk IDs) are numbered consecutively
|
||||
from 1 to the number of bins = <em>Nchunk</em>. For <em>bin2d</em> and <em>bin3d</em>, the
|
||||
numbering varies most rapidly in the first dimension (which could be
|
||||
x, y, or z), next rapidly in the 2nd dimension, and most slowly in the
|
||||
3rd dimension. For <em>bin/sphere</em>, the bin with smallest radii is chunk
|
||||
1 and the bni with largest radii is chunk Nchunk = <em>ncbin</em>. For
|
||||
<em>bin/cylinder</em>, the numbering varies most rapidly in the dimension
|
||||
along the cylinder axis and most slowly in the radial direction.</p>
|
||||
<p>Each time this compute is invoked, each atom is mapped to a bin based
|
||||
on its current position. Note that between reneighboring timesteps,
|
||||
atoms can move outside the current simulation box. If the box is
|
||||
periodic (in that dimension) the atom is remapping into the periodic
|
||||
box for purposes of binning. If the box in not periodic, the atom may
|
||||
have moved outside the bounds of all bins. If an atom is not inside
|
||||
any bin, the <em>discard</em> keyword is used to determine how a chunk ID is
|
||||
assigned to the atom.</p>
|
||||
<hr class="docutils" />
|
||||
<p>The <em>type</em> style uses the atom type as the chunk ID. <em>Nchunk</em> is set
|
||||
to the number of atom types defined for the simulation, e.g. via the
|
||||
<a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> or <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> commands.</p>
|
||||
<hr class="docutils" />
|
||||
<p>The <em>molecule</em> style uses the molecule ID of each atom as its chunk
|
||||
ID. <em>Nchunk</em> is set to the largest chunk ID. Note that this excludes
|
||||
molecule IDs for atoms which are not in the specified group or
|
||||
optional region.</p>
|
||||
<p>There is no requirement that all atoms in a particular molecule are
|
||||
assigned the same chunk ID (zero or non-zero), though you probably
|
||||
want that to be the case, if you wish to compute a per-molecule
|
||||
property. LAMMPS will issue a warning if that is not the case, but
|
||||
only the first time that <em>Nchunk</em> is calculated.</p>
|
||||
<p>Note that atoms with a molecule ID = 0, which may be non-molecular
|
||||
solvent atoms, have an out-of-range chunk ID. These atoms are
|
||||
discarded (not assigned to any chunk) or assigned to <em>Nchunk</em>,
|
||||
depending on the value of the <em>discard</em> keyword.</p>
|
||||
<hr class="docutils" />
|
||||
<p>The <em>compute/fix/variable</em> styles set the chunk ID of each atom based
|
||||
on a quantity calculated and stored by a compute, fix, or variable.
|
||||
In each case, it must be a per-atom quantity. In each case the
|
||||
referenced floating point values are converted to an integer chunk ID
|
||||
as follows. The floating point value is truncated (rounded down) to
|
||||
an integer value. If the integer value is <= 0, then a chunk ID of 0
|
||||
is assigned to the atom. If the integer value is > 0, it becomes the
|
||||
chunk ID to the atom. <em>Nchunk</em> is set to the largest chunk ID. Note
|
||||
that this excludes atoms which are not in the specified group or
|
||||
optional region.</p>
|
||||
<p>If the style begins with “<a href="#id1"><span class="problematic" id="id2">c_</span></a>”, a compute ID must follow which has been
|
||||
previously defined in the input script. If no bracketed integer is
|
||||
appended, the per-atom vector calculated by the compute is used. If a
|
||||
bracketed integer is appended, the Ith column of the per-atom array
|
||||
calculated by the compute is used. Users can also write code for
|
||||
their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
|
||||
<p>If the style begins with “<a href="#id3"><span class="problematic" id="id4">f_</span></a>”, a fix ID must follow which has been
|
||||
previously defined in the input script. If no bracketed integer is
|
||||
appended, the per-atom vector calculated by the fix is used. If a
|
||||
bracketed integer is appended, the Ith column of the per-atom array
|
||||
calculated by the fix is used. Note that some fixes only produce
|
||||
their values on certain timesteps, which must be compatible with the
|
||||
timestep on which this compute accesses the fix, else an error
|
||||
results. Users can also write code for their own fix styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
|
||||
<p>If a value begins with “<a href="#id5"><span class="problematic" id="id6">v_</span></a>”, a variable name for an <em>atom</em> or
|
||||
<em>atomfile</em> style <a class="reference internal" href="variable.html"><span class="doc">variable</span></a> must follow which has been
|
||||
previously defined in the input script. Variables of style <em>atom</em> can
|
||||
reference thermodynamic keywords and various per-atom attributes, or
|
||||
invoke other computes, fixes, or variables when they are evaluated, so
|
||||
this is a very general means of generating per-atom quantities to
|
||||
treat as a chunk ID.</p>
|
||||
<p>Normally, <em>Nchunk</em> = the number of chunks, is re-calculated every time
|
||||
this fix is invoked, though the value may or may not change. As
|
||||
explained below, the <em>nchunk</em> keyword can be set to <em>once</em> which means
|
||||
<em>Nchunk</em> will never change.</p>
|
||||
<p>If a <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> command uses this compute, it
|
||||
can also turn off the re-calculation of <em>Nchunk</em> for one or more
|
||||
windows of timesteps. The extent of the windows, during which Nchunk
|
||||
is held constant, are determined by the <em>Nevery</em>, <em>Nrepeat</em>, <em>Nfreq</em>
|
||||
values and the <em>ave</em> keyword setting that are used by the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> command.</p>
|
||||
<p>Specifically, if <em>ave</em> = <em>one</em>, then for each span of <em>Nfreq</em>
|
||||
timesteps, <em>Nchunk</em> is held constant between the first timestep when
|
||||
averaging is done (within the Nfreq-length window), and the last
|
||||
timestep when averaging is done (multiple of Nfreq). If <em>ave</em> =
|
||||
<em>running</em> or <em>window</em>, then <em>Nchunk</em> is held constant forever,
|
||||
starting on the first timestep when the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> command invokes this compute.</p>
|
||||
<p>Note that multiple <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> commands can use
|
||||
the same compute chunk/atom compute. However, the time windows they
|
||||
induce for holding <em>Nchunk</em> constant must be identical, else an error
|
||||
will be generated.</p>
|
||||
<p>The various optional keywords operate as follows. Note that some of
|
||||
them function differently or are ignored by different chunk styles.
|
||||
Some of them also have different default values, depending on
|
||||
the chunk style, as listed below.</p>
|
||||
<p>The <em>region</em> keyword applies to all chunk styles. If used, an atom
|
||||
must be in both the specified group and the specified geometric
|
||||
<a class="reference internal" href="region.html"><span class="doc">region</span></a> to be assigned to a chunk.</p>
|
||||
<hr class="docutils" />
|
||||
<p>The <em>nchunk</em> keyword applies to all chunk styles. It specifies how
|
||||
often <em>Nchunk</em> is recalculated, which in turn can affect the chunk IDs
|
||||
assigned to individual atoms.</p>
|
||||
<p>If <em>nchunk</em> is set to <em>once</em>, then <em>Nchunk</em> is only calculated once,
|
||||
the first time this compute is invoked. If <em>nchunk</em> is set to
|
||||
<em>every</em>, then <em>Nchunk</em> is re-calculated every time the compute is
|
||||
invoked. Note that, as described above, the use of this compute
|
||||
by the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> command can override
|
||||
the <em>every</em> setting.</p>
|
||||
<p>The default values for <em>nchunk</em> are listed below and depend on the
|
||||
chunk style and other system and keyword settings. They attempt to
|
||||
represent typical use cases for the various chunk styles. The
|
||||
<em>nchunk</em> value can always be set explicitly if desired.</p>
|
||||
<hr class="docutils" />
|
||||
<p>The <em>limit</em> keyword can be used to limit the calculated value of
|
||||
<em>Nchunk</em> = the number of chunks. The limit is applied each time
|
||||
<em>Nchunk</em> is calculated, which also limits the chunk IDs assigned to
|
||||
any atom. The <em>limit</em> keyword is used by all chunk styles except the
|
||||
<em>binning</em> styles, which ignore it. This is because the number of bins
|
||||
can be tailored using the <em>bound</em> keyword (described below) which
|
||||
effectively limits the size of <em>Nchunk</em>.</p>
|
||||
<p>If <em>limit</em> is set to <em>Nc</em> = 0, then no limit is imposed on <em>Nchunk</em>,
|
||||
though the <em>compress</em> keyword can still be used to reduce <em>Nchunk</em>, as
|
||||
described below.</p>
|
||||
<p>If <em>Nc</em> > 0, then the effect of the <em>limit</em> keyword depends on whether
|
||||
the <em>compress</em> keyword is also used with a setting of <em>yes</em>, and
|
||||
whether the <em>compress</em> keyword is specified before the <em>limit</em> keyword
|
||||
or after.</p>
|
||||
<p>In all cases, <em>Nchunk</em> is first calculated in the usual way for each
|
||||
chunk style, as described above.</p>
|
||||
<p>First, here is what occurs if <em>compress yes</em> is not set. If <em>limit</em>
|
||||
is set to <em>Nc max</em>, then <em>Nchunk</em> is reset to the smaller of <em>Nchunk</em>
|
||||
and <em>Nc</em>. If <em>limit</em> is set to <em>Nc exact</em>, then <em>Nchunk</em> is reset to
|
||||
<em>Nc</em>, whether the original <em>Nchunk</em> was larger or smaller than <em>Nc</em>.
|
||||
If <em>Nchunk</em> shrank due to the <em>limit</em> setting, then atom chunk IDs >
|
||||
<em>Nchunk</em> will be reset to 0 or <em>Nchunk</em>, depending on the setting of
|
||||
the <em>discard</em> keyword. If <em>Nchunk</em> grew, there will simply be some
|
||||
chunks with no atoms assigned to them.</p>
|
||||
<p>If <em>compress yes</em> is set, and the <em>compress</em> keyword comes before the
|
||||
<em>limit</em> keyword, the compression operation is performed first, as
|
||||
described below, which resets <em>Nchunk</em>. The <em>limit</em> keyword is then
|
||||
applied to the new <em>Nchunk</em> value, exactly as described in the
|
||||
preceeding paragraph. Note that in this case, all atoms will end up
|
||||
with chunk IDs <= <em>Nc</em>, but their original values (e.g. molecule ID or
|
||||
compute/fix/variable value) may have been > <em>Nc</em>, because of the
|
||||
compression operation.</p>
|
||||
<p>If <em>compress yes</em> is set, and the <em>compress</em> keyword comes after the
|
||||
<em>limit</em> keyword, then the <em>limit</em> value of <em>Nc</em> is applied first to
|
||||
the uncompressed value of <em>Nchunk</em>, but only if <em>Nc</em> < <em>Nchunk</em>
|
||||
(whether <em>Nc max</em> or <em>Nc exact</em> is used). This effectively means all
|
||||
atoms with chunk IDs > <em>Nc</em> have their chunk IDs reset to 0 or <em>Nc</em>,
|
||||
depending on the setting of the <em>discard</em> keyword. The compression
|
||||
operation is then performed, which may shrink <em>Nchunk</em> further. If
|
||||
the new <em>Nchunk</em> < <em>Nc</em> and <em>limit</em> = <em>Nc exact</em> is specified, then
|
||||
<em>Nchunk</em> is reset to <em>Nc</em>, which results in extra chunks with no atoms
|
||||
assigned to them. Note that in this case, all atoms will end up with
|
||||
chunk IDs <= <em>Nc</em>, and their original values (e.g. molecule ID or
|
||||
compute/fix/variable value) will also have been <= <em>Nc</em>.</p>
|
||||
<hr class="docutils" />
|
||||
<p>The <em>ids</em> keyword applies to all chunk styles. If the setting is
|
||||
<em>once</em> then the chunk IDs assigned to atoms the first time this
|
||||
compute is invoked will be permanent, and never be re-computed.</p>
|
||||
<p>If the setting is <em>nfreq</em> and if a <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>
|
||||
command is using this compute, then in each of the <em>Nchunk</em> = constant
|
||||
time windows (discussed above), the chunk ID’s assigned to atoms on
|
||||
the first step of the time window will persist until the end of the
|
||||
time window.</p>
|
||||
<p>If the setting is <em>every</em>, which is the default, then chunk IDs are
|
||||
re-calculated on any timestep this compute is invoked.</p>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">If you want the persistent chunk-IDs calculated by this compute
|
||||
to be continuous when running from a <a class="reference internal" href="read_restart.html"><span class="doc">restart file</span></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 chunk IDs from the restart file.</p>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<p>The <em>compress</em> keyword applies to all chunk styles and affects how
|
||||
<em>Nchunk</em> is calculated, which in turn affects the chunk IDs assigned
|
||||
to each atom. It is useful for converting a “sparse” set of chunk IDs
|
||||
(with many IDs that have no atoms assigned to them), into a “dense”
|
||||
set of IDs, where every chunk has one or more atoms assigned to it.</p>
|
||||
<p>Two possible use cases are as follows. If a large simulation box is
|
||||
mostly empty space, then the <em>binning</em> style may produce many bins
|
||||
with no atoms. If <em>compress</em> is set to <em>yes</em>, only bins with atoms
|
||||
will be contribute to <em>Nchunk</em>. Likewise, the <em>molecule</em> or
|
||||
<em>compute/fix/variable</em> styles may produce large <em>Nchunk</em> values. For
|
||||
example, the <a class="reference internal" href="compute_cluster_atom.html"><span class="doc">compute cluster/atom</span></a> command
|
||||
assigns every atom an atom ID for one of the atoms it is clustered
|
||||
with. For a million-atom system with 5 clusters, there would only be
|
||||
5 unique chunk IDs, but the largest chunk ID might be 1 million,
|
||||
resulting in <em>Nchunk</em> = 1 million. If <em>compress</em> is set to <em>yes</em>,
|
||||
<em>Nchunk</em> will be reset to 5.</p>
|
||||
<p>If <em>compress</em> is set to <em>no</em>, which is the default, no compression is
|
||||
done. If it is set to <em>yes</em>, all chunk IDs with no atoms are removed
|
||||
from the list of chunk IDs, and the list is sorted. The remaining
|
||||
chunk IDs are renumbered from 1 to <em>Nchunk</em> where <em>Nchunk</em> is the new
|
||||
length of the list. The chunk IDs assigned to each atom reflect
|
||||
the new renumbering from 1 to <em>Nchunk</em>.</p>
|
||||
<p>The original chunk IDs (before renumbering) can be accessed by the
|
||||
<a class="reference internal" href="compute_property_chunk.html"><span class="doc">compute property/chunk</span></a> command and its
|
||||
<em>id</em> keyword, or by the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> command
|
||||
which outputs the original IDs as one of the columns in its global
|
||||
output array. For example, using the “compute cluster/atom” command
|
||||
discussed above, the original 5 unique chunk IDs might be atom IDs
|
||||
(27,4982,58374,857838,1000000). After compresion, these will be
|
||||
renumbered to (1,2,3,4,5). The original values (27,...,1000000) can
|
||||
be output to a file by the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> command,
|
||||
or by using the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a> command in
|
||||
conjunction with the <a class="reference internal" href="compute_property_chunk.html"><span class="doc">compute property/chunk</span></a> command.</p>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">The compression operation requires global communication across
|
||||
all processors to share their chunk ID values. It can require large
|
||||
memory on every processor to store them, even after they are
|
||||
compressed, if there are are a large number of unique chunk IDs with
|
||||
atoms assigned to them. It uses a STL map to find unique chunk IDs
|
||||
and store them in sorted order. Each time an atom is assigned a
|
||||
compressed chunk ID, it must access the STL map. All of this means
|
||||
that compression can be expensive, both in memory and CPU time. The
|
||||
use of the <em>limit</em> keyword in conjunction with the <em>compress</em> keyword
|
||||
can affect these costs, depending on which keyword is used first. So
|
||||
use this option with care.</p>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<p>The <em>discard</em> keyword applies to all chunk styles. It affects what
|
||||
chunk IDs are assigned to atoms that do not match one of the valid
|
||||
chunk IDs from 1 to <em>Nchunk</em>. Note that it does not apply to atoms
|
||||
that are not in the specified group or optionally specified region.
|
||||
Those atoms are always assigned a chunk ID = 0.</p>
|
||||
<p>If the calculated chunk ID for an atom is not within the range 1 to
|
||||
<em>Nchunk</em> then it is a “discard” atom. Note that <em>Nchunk</em> may have
|
||||
been shrunk by the <em>limit</em> keyword. Or the <em>compress</em> keyword may
|
||||
have eliminated chunk IDs that were valid before the compression took
|
||||
place, and are now not in the compressed list. Also note that for the
|
||||
<em>molecule</em> chunk style, if new molecules are added to the system,
|
||||
their chunk IDs may exceed a previously calculated <em>Nchunk</em>.
|
||||
Likewise, evaluation of a compute/fix/variable on a later timestep may
|
||||
return chunk IDs that are invalid for the previously calculated
|
||||
<em>Nchunk</em>.</p>
|
||||
<p>All the chunk styles except the <em>binning</em> styles, must use <em>discard</em>
|
||||
set to either <em>yes</em> or <em>no</em>. If <em>discard</em> is set to <em>yes</em>, which is
|
||||
the default, then every “discard” atom has its chunk ID set to 0. If
|
||||
<em>discard</em> is set to <em>no</em>, every “discard” atom has its chunk ID set to
|
||||
<em>Nchunk</em>. I.e. it becomes part of the last chunk.</p>
|
||||
<p>The <em>binning</em> styles use the <em>discard</em> keyword to decide whether to
|
||||
discard atoms outside the spatial domain covered by bins, or to assign
|
||||
them to the bin they are nearest to.</p>
|
||||
<p>For the <em>bin/1d</em>, <em>bin/2d</em>, <em>bin/3d</em> styles the details are as
|
||||
follows. If <em>discard</em> is set to <em>yes</em>, an out-of-domain atom will
|
||||
have its chunk ID set to 0. If <em>discard</em> is set to <em>no</em>, the atom
|
||||
will have its chunk ID set to the first or last bin in that dimension.
|
||||
If <em>discard</em> is set to <em>mixed</em>, which is the default, it will only
|
||||
have its chunk ID set to the first or last bin if bins extend to the
|
||||
simulation box boundary in that dimension. This is the case if the
|
||||
<em>bound</em> keyword settings are <em>lower</em> and <em>upper</em>, which is the
|
||||
default. If the <em>bound</em> keyword settings are numeric values, then the
|
||||
atom will have its chunk ID set to 0 if it is outside the bounds of
|
||||
any bin. Note that in this case, it is possible that the first or
|
||||
last bin extends beyond the numeric <em>bounds</em> settings, depending on
|
||||
the specified <em>origin</em>. If this is the case, the chunk ID of the atom
|
||||
is only set to 0 if it is outside the first or last bin, not if it is
|
||||
simply outside the numeric <em>bounds</em> setting.</p>
|
||||
<p>For the <em>bin/sphere</em> style the details are as follows. If <em>discard</em>
|
||||
is set to <em>yes</em>, an out-of-domain atom will have its chunk ID set to
|
||||
0. If <em>discard</em> is set to <em>no</em> or <em>mixed</em>, the atom will have its
|
||||
chunk ID set to the first or last bin, i.e. the innermost or outermost
|
||||
spherical shell. If the distance of the atom from the origin is less
|
||||
than <em>rmin</em>, it will be assigned to the first bin. If the distance of
|
||||
the atom from the origin is greater than <em>rmax</em>, it will be assigned
|
||||
to the last bin.</p>
|
||||
<p>For the <em>bin/cylinder</em> style the details are as follows. If <em>discard</em>
|
||||
is set to <em>yes</em>, an out-of-domain atom will have its chunk ID set to
|
||||
0. If <em>discard</em> is set to <em>no</em>, the atom will have its chunk ID set
|
||||
to the first or last bin in both the radial and axis dimensions. If
|
||||
<em>discard</em> is set to <em>mixed</em>, which is the default, the the radial
|
||||
dimension is treated the same as for <em>discard</em> = no. But for the axis
|
||||
dimensinon, it will only have its chunk ID set to the first or last
|
||||
bin if bins extend to the simulation box boundary in the axis
|
||||
dimension. This is the case if the <em>bound</em> keyword settings are
|
||||
<em>lower</em> and <em>upper</em>, which is the default. If the <em>bound</em> keyword
|
||||
settings are numeric values, then the atom will have its chunk ID set
|
||||
to 0 if it is outside the bounds of any bin. Note that in this case,
|
||||
it is possible that the first or last bin extends beyond the numeric
|
||||
<em>bounds</em> settings, depending on the specified <em>origin</em>. If this is
|
||||
the case, the chunk ID of the atom is only set to 0 if it is outside
|
||||
the first or last bin, not if it is simply outside the numeric
|
||||
<em>bounds</em> setting.</p>
|
||||
<p>If <em>discard</em> is set to <em>no</em> or <em>mixed</em>, the atom will have its
|
||||
chunk ID set to the first or last bin, i.e. the innermost or outermost
|
||||
spherical shell. If the distance of the atom from the origin is less
|
||||
than <em>rmin</em>, it will be assigned to the first bin. If the distance of
|
||||
the atom from the origin is greater than <em>rmax</em>, it will be assigned
|
||||
to the last bin.</p>
|
||||
<hr class="docutils" />
|
||||
<p>The <em>bound</em> keyword only applies to the <em>bin/1d</em>, <em>bin/2d</em>, <em>bin/3d</em>
|
||||
styles and to the axis dimension of the <em>bin/cylinder</em> style;
|
||||
otherwise it is ignored. It can be used one or more times to limit
|
||||
the extent of bin coverage in a specified dimension, i.e. to only bin
|
||||
a portion of the box. If the <em>lo</em> setting is <em>lower</em> or the <em>hi</em>
|
||||
setting is <em>upper</em>, the bin extent in that direction extends to the
|
||||
box boundary. If a numeric value is used for <em>lo</em> and/or <em>hi</em>, then
|
||||
the bin extent in the <em>lo</em> or <em>hi</em> direction extends only to that
|
||||
value, which is assumed to be inside (or at least near) the simulation
|
||||
box boundaries, though LAMMPS does not check for this. Note that
|
||||
using the <em>bound</em> keyword typically reduces the total number of bins
|
||||
and thus the number of chunks <em>Nchunk</em>.</p>
|
||||
<p>The <em>pbc</em> keyword only applies to the <em>bin/sphere</em> and <em>bin/cylinder</em>
|
||||
styles. If set to <em>yes</em>, the distance an atom is from the sphere
|
||||
origin or cylinder axis is calculated in a minimum image sense with
|
||||
respect to periodic dimensions, when determining which bin the atom is
|
||||
in. I.e. if x is a periodic dimension and the distance between the
|
||||
atom and the sphere center in the x dimension is greater than 0.5 *
|
||||
simulation box length in x, then a box length is subtracted to give a
|
||||
distance < 0.5 * simulation box length. This allosws the sphere or
|
||||
cylinder center to be near a box edge, and atoms on the other side of
|
||||
the periodic box will still be close to the center point/axis. Note
|
||||
that with a setting of <em>yes</em>, the outer sphere or cylinder radius must
|
||||
also be <= 0.5 * simulation box length in any periodic dimension
|
||||
except for the cylinder axis dimension, or an error is generated.</p>
|
||||
<p>The <em>units</em> keyword only applies to the <em>binning</em> styles; otherwise it
|
||||
is ignored. For the <em>bin/1d</em>, <em>bin/2d</em>, <em>bin/3d</em> styles, it
|
||||
determines the meaning of the distance units used for the bin sizes
|
||||
<em>delta</em> and for <em>origin</em> and <em>bounds</em> values if they are coordinate
|
||||
values. For the <em>bin/sphere</em> style it determines the meaning of the
|
||||
distance units used for <em>xorig</em>,<em>yorig</em>,<em>zorig</em> and the radii <em>srmin</em>
|
||||
and <em>srmax</em>. For the <em>bin/cylinder</em> style it determines the meaning
|
||||
of the distance units used for <em>delta</em>,<em>c1</em>,<em>c2</em> and the radii <em>crmin</em>
|
||||
and <em>crmax</em>.</p>
|
||||
<p>For orthogonal simulation boxes, any of the 3 options may
|
||||
be used. For non-orthogonal (triclinic) simulation boxes, only the
|
||||
<em>reduced</em> option may be used.</p>
|
||||
<p>A <em>box</em> value selects standard distance units as defined by the
|
||||
<a class="reference internal" href="units.html"><span class="doc">units</span></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"><span class="doc">lattice</span></a> command must have been previously used to
|
||||
define the lattice spacing. A <em>reduced</em> value means normalized
|
||||
unitless values between 0 and 1, which represent the lower and upper
|
||||
faces of the simulation box respectively. Thus an <em>origin</em> value of
|
||||
0.5 means the center of the box in any dimension. A <em>delta</em> value of
|
||||
0.1 means 10 bins span the box in that dimension.</p>
|
||||
<p>Note that for the <em>bin/sphere</em> style, the radii <em>srmin</em> and <em>srmax</em> are
|
||||
scaled by the lattice spacing or reduced value of the <em>x</em> dimension.</p>
|
||||
<p>Note that for the <em>bin/cylinder</em> style, the radii <em>crmin</em> and <em>crmax</em>
|
||||
are scaled by the lattice spacing or reduced value of the 1st
|
||||
dimension perpendicular to the cylinder axis. E.g. y for an x-axis
|
||||
cylinder, x for a y-axis cylinder, and x for a z-axis cylinder.</p>
|
||||
<hr class="docutils" />
|
||||
<p><strong>Output info:</strong></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 class="std std-ref">Section_howto 15</span></a> for an overview of
|
||||
LAMMPS output options.</p>
|
||||
<p>The per-atom vector values are unitless chunk IDs, ranging from 1 to
|
||||
<em>Nchunk</em> (inclusive) for atoms assigned to chunks, and 0 for atoms not
|
||||
belonging to a chunk.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<p>Even if the <em>nchunk</em> keyword is set to <em>once</em>, the chunk IDs assigned
|
||||
to each atom are not stored in a restart files. This means you cannot
|
||||
expect those assignments to persist in a restarted simulation.
|
||||
Instead you must re-specify this command and assign atoms to chunks when
|
||||
the restarted simulation begins.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a></p>
|
||||
</div>
|
||||
<div class="section" id="default">
|
||||
<h2>Default</h2>
|
||||
<p>The option defaults are as follows:</p>
|
||||
<ul class="simple">
|
||||
<li>region = none</li>
|
||||
<li>nchunk = every, if compress is yes, overriding other defaults listed here</li>
|
||||
<li>nchunk = once, for type style</li>
|
||||
<li>nchunk = once, for mol style if region is none</li>
|
||||
<li>nchunk = every, for mol style if region is set</li>
|
||||
<li>nchunk = once, for binning style if the simulation box size is static or units = reduced</li>
|
||||
<li>nchunk = every, for binning style if the simulation box size is dynamic and units is lattice or box</li>
|
||||
<li>nchunk = every, for compute/fix/variable style</li>
|
||||
<li>limit = 0</li>
|
||||
<li>ids = every</li>
|
||||
<li>compress = no</li>
|
||||
<li>discard = yes, for all styles except binning</li>
|
||||
<li>discard = mixed, for binning styles</li>
|
||||
<li>bound = lower and upper in all dimensions</li>
|
||||
<li>pbc = no</li>
|
||||
<li>units = lattice</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
</div>
|
||||
<footer>
|
||||
|
||||
|
||||
<hr/>
|
||||
|
||||
<div role="contentinfo">
|
||||
<p>
|
||||
© Copyright 2013 Sandia Corporation.
|
||||
</p>
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<div class="section" id="compute-cluster-atom-command">
|
||||
<span id="index-0"></span><h1>compute cluster/atom command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">cluster</span><span class="o">/</span><span class="n">atom</span> <span class="n">cutoff</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">cluster</span><span class="o">/</span><span class="n">atom</span> <span class="mf">1.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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
|
||||
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
|
||||
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>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">If you have a bonded system, then the settings of
|
||||
<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></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"><span class="doc">special_bonds</span></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 when computing the clusters. This
|
||||
does not apply when using long-range coulomb (<em>coul/long</em>, <em>coul/msm</em>,
|
||||
<em>coul/wolf</em> or similar. One way to get around this would be to set
|
||||
special_bond scaling factors to very tiny numbers that are not exactly
|
||||
zero (e.g. 1.0e-50). Another workaround is to write a dump file, and
|
||||
use the <a class="reference internal" href="rerun.html"><span class="doc">rerun</span></a> command to compute the clusters for
|
||||
snapshots in the dump file. The rerun script can use a
|
||||
<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command that includes all pairs in
|
||||
the neighbor list.</p>
|
||||
</div>
|
||||
<p><strong>Output info:</strong></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 class="std std-ref">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</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="compute_coord_atom.html"><span class="doc">compute coord/atom</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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<div class="section" id="compute-cna-atom-command">
|
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<span id="index-0"></span><h1>compute cna/atom command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">cna</span><span class="o">/</span><span class="n">atom</span> <span class="n">cutoff</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">cna</span><span class="o">/</span><span class="n">atom</span> <span class="mf">3.08</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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 class="std std-ref">(Faken)</span></a>
|
||||
and <a class="reference internal" href="#tsuzuki"><span class="std std-ref">(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
|
||||
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.
|
||||
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
|
||||
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
|
||||
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"><span class="doc">neighbor</span></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
|
||||
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
|
||||
any command that uses per-atom values from a compute as input. See
|
||||
<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">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</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="compute_centro_atom.html"><span class="doc">compute centro/atom</span></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>
|
||||
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|
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<div class="section" id="compute-com-command">
|
||||
<span id="index-0"></span><h1>compute com command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">com</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
|
||||
<li>com = style name of this compute command</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">com</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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 note">
|
||||
<p class="first admonition-title">Note</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"><span class="doc">dump custom</span></a> command for a discussion of
|
||||
“unwrapped” coordinates. See the Atoms section of the
|
||||
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></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"><span class="doc">set image</span></a> command.</p>
|
||||
</div>
|
||||
<p><strong>Output info:</strong></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 class="std std-ref">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"><span class="doc">units</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="compute_com_chunk.html"><span class="doc">compute com/chunk</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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<div class="section" id="compute-com-chunk-command">
|
||||
<span id="index-0"></span><h1>compute com/chunk command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">com</span><span class="o">/</span><span class="n">chunk</span> <span class="n">chunkID</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></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"><span class="doc">compute chunk/atom</span></a> command</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="n">fluid</span> <span class="n">com</span><span class="o">/</span><span class="n">chunk</span> <span class="n">molchunk</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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"><span class="doc">compute chunk/atom</span></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"><span class="doc">compute chunk/atom</span></a> doc page and “<a class="reference internal" href="Section_howto.html#howto-23"><span class="std std-ref">Section_howto 23</span></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
|
||||
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"><span class="doc">compute chunk/atom</span></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 note">
|
||||
<p class="first admonition-title">Note</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"><span class="doc">dump custom</span></a> command
|
||||
for a discussion of “unwrapped” coordinates. See the Atoms section of
|
||||
the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></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"><span class="doc">set image</span></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"><span class="doc">fix ave/time</span></a>
|
||||
command, for example:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
|
||||
<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">com</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
|
||||
</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"><span class="doc">compute chunk/atom</span></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 class="std std-ref">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"><span class="doc">units</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="compute_com.html"><span class="doc">compute com</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
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<div class="section" id="compute-contact-atom-command">
|
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<span id="index-0"></span><h1>compute contact/atom command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">contact</span><span class="o">/</span><span class="n">atom</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
|
||||
<li>contact/atom = style name of this compute command</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">contact</span><span class="o">/</span><span class="n">atom</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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
|
||||
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
|
||||
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 class="std std-ref">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</h2>
|
||||
<p>This compute requires that atoms store a radius as defined by the
|
||||
<a class="reference internal" href="atom_style.html"><span class="doc">atom_style sphere</span></a> command.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="compute_coord_atom.html"><span class="doc">compute coord/atom</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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|
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<div class="section" id="compute-coord-atom-command">
|
||||
<span id="index-0"></span><h1>compute coord/atom command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">coord</span><span class="o">/</span><span class="n">atom</span> <span class="n">cutoff</span> <span class="n">type1</span> <span class="n">type2</span> <span class="o">...</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">coord</span><span class="o">/</span><span class="n">atom</span> <span class="mf">2.0</span>
|
||||
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">coord</span><span class="o">/</span><span class="n">atom</span> <span class="mf">6.0</span> <span class="mi">1</span> <span class="mi">2</span>
|
||||
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">coord</span><span class="o">/</span><span class="n">atom</span> <span class="mf">6.0</span> <span class="mi">2</span><span class="o">*</span><span class="mi">4</span> <span class="mi">5</span><span class="o">*</span><span class="mi">8</span> <span class="o">*</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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 note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">If you have a bonded system, then the settings of
|
||||
<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></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"><span class="doc">special_bonds</span></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"><span class="doc">rerun</span></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"><span class="doc">special_bonds</span></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>
|
||||
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 class="std std-ref">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</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="compute_cluster_atom.html"><span class="doc">compute cluster/atom</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
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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</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">damage</span><span class="o">/</span><span class="n">atom</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
|
||||
<li>damage/atom = style name of this compute command</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">damage</span><span class="o">/</span><span class="n">atom</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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"><span class="doc">Peridynamics models</span></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
|
||||
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
|
||||
any command that uses per-atom values from a compute as input. See
|
||||
<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">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</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 class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><span class="xref doc">compute dilatation</span>, <span class="xref doc">compute plasticity</span></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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<div class="section" id="compute-dihedral-command">
|
||||
<span id="index-0"></span><h1>compute dihedral command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">dihedral</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
|
||||
<li>dihedral = style name of this compute command</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">dihedral</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<p>Define a computation that extracts the dihedral energy calculated by
|
||||
each of the dihedral sub-styles used in the <a class="reference internal" href="dihedral_hybrid.html"><span class="doc">dihedral_style hybrid</span></a> command. These values are made
|
||||
accessible for output or further processing by other commands. The
|
||||
group specified for this command is ignored.</p>
|
||||
<p>This compute is useful when using <a class="reference internal" href="dihedral_hybrid.html"><span class="doc">dihedral_style hybrid</span></a> if you want to know the portion of the
|
||||
total energy contributed by one or more of the hybrid sub-styles.</p>
|
||||
<p><strong>Output info:</strong></p>
|
||||
<p>This compute calculates a global vector of length N where N is the
|
||||
number of sub_styles defined by the <a class="reference internal" href="dihedral_style.html"><span class="doc">dihedral_style hybrid</span></a> command. which can be accessed by indices
|
||||
1-N. 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 class="std std-ref">this section</span></a> for an overview of LAMMPS output
|
||||
options.</p>
|
||||
<p>The vector values are “extensive” and will be in energy
|
||||
<a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="compute_pe.html"><span class="doc">compute pe</span></a>, <a class="reference internal" href="compute_pair.html"><span class="doc">compute pair</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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||||
<div class="section" id="compute-dihedral-local-command">
|
||||
<span id="index-0"></span><h1>compute dihedral/local command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">dihedral</span><span class="o">/</span><span class="n">local</span> <span class="n">input1</span> <span class="n">input2</span> <span class="o">...</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">dihedral</span><span class="o">/</span><span class="n">local</span> <span class="n">phi</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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
|
||||
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
|
||||
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"><span class="doc">compute property/local</span></a> command can be combined
|
||||
with data from this command and output by the <a class="reference internal" href="dump.html"><span class="doc">dump local</span></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
|
||||
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 class="std std-ref">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</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="dump.html"><span class="doc">dump local</span></a>, <a class="reference internal" href="compute_property_local.html"><span class="doc">compute property/local</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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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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<div class="section" id="compute-dilatation-atom-command">
|
||||
<span id="index-0"></span><h1>compute dilatation/atom command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">dilatation</span><span class="o">/</span><span class="n">atom</span>
|
||||
</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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">dilatation</span><span class="o">/</span><span class="n">atom</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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"><span class="doc">Peridynamics models</span></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
|
||||
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"><span class="doc">pair styles</span></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
|
||||
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</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 class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><span class="xref doc">compute damage</span>, <span class="xref doc">compute plasticity</span></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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<div class="section" id="compute-dipole-chunk-command">
|
||||
<span id="index-0"></span><h1>compute dipole/chunk command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">dipole</span><span class="o">/</span><span class="n">chunk</span> <span class="n">chunkID</span> <span class="n">charge</span><span class="o">-</span><span class="n">correction</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
|
||||
<li>dipole/chunk = style name of this compute command</li>
|
||||
<li>chunkID = ID of <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command</li>
|
||||
<li>charge-correction = <em>mass</em> or <em>geometry</em>, use COM or geometric center for charged chunk correction (optional)</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="n">fluid</span> <span class="n">dipole</span><span class="o">/</span><span class="n">chunk</span> <span class="n">molchunk</span>
|
||||
<span class="n">compute</span> <span class="n">dw</span> <span class="n">water</span> <span class="n">dipole</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">1</span> <span class="n">geometry</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<p>Define a computation that calculates the dipole vector and total dipole
|
||||
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"><span class="doc">compute chunk/atom</span></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"><span class="doc">compute chunk/atom</span></a> doc page and “<a class="reference internal" href="Section_howto.html#howto-23"><span class="std std-ref">Section_howto 23</span></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 dipole vector
|
||||
and the total dipole moment for each chunk, which includes all effects
|
||||
due to atoms passing thru periodic boundaries. For chunks with a net
|
||||
charge the resulting dipole is made position independent by subtracting
|
||||
the position vector of the center of mass or geometric center times the
|
||||
net charge from the computed dipole vector.</p>
|
||||
<p>Note that only atoms in the specified group contribute to the
|
||||
calculation. The <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></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 note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">The coordinates of an atom contribute to the chunk’s
|
||||
dipole in “unwrapped” form, by using the image flags
|
||||
associated with each atom. See the <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> command
|
||||
for a discussion of “unwrapped” coordinates. See the Atoms section of
|
||||
the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></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"><span class="doc">set image</span></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"><span class="doc">fix ave/time</span></a>
|
||||
command, for example:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
|
||||
<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">dipole</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
|
||||
</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"><span class="doc">compute chunk/atom</span></a> command. The number of columns =
|
||||
4 for the x,y,z dipole vector components and the total dipole 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 class="std std-ref">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
|
||||
dipole units, i.e. charge units times distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="compute_com_chunk.html"><span class="doc">compute com/chunk</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
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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</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">displace</span><span class="o">/</span><span class="n">atom</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
|
||||
<li>displace/atom = style name of this compute command</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">displace</span><span class="o">/</span><span class="n">atom</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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.
|
||||
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
|
||||
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 note">
|
||||
<p class="first admonition-title">Note</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"><span class="doc">dump custom</span></a> command for a discussion of “unwrapped” coordinates.
|
||||
See the Atoms section of the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></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"><span class="doc">set image</span></a> command.</p>
|
||||
</div>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</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"><span class="doc">restart file</span></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
|
||||
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 class="std std-ref">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"><span class="doc">units</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="compute_msd.html"><span class="doc">compute msd</span></a>, <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a>, <a class="reference internal" href="fix_store_state.html"><span class="doc">fix store/state</span></a></p>
|
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<p><strong>Default:</strong> none</p>
|
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||||
<div class="section" id="compute-dpd-command">
|
||||
<span id="index-0"></span><h1>compute dpd command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">dpd</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
|
||||
<li>dpd = style name of this compute command</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">dpd</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<p>Define a computation that accumulates the total internal conductive
|
||||
energy (U_cond), the total internal mechanical energy (U_mech), the
|
||||
total internal energy (U) and the <em>harmonic</em> average of the internal
|
||||
temperature (dpdTheta) for the entire system of particles. See the
|
||||
<a class="reference internal" href="compute_dpd_atom.html"><span class="doc">compute dpd/atom</span></a> command if you want
|
||||
per-particle internal energies and internal temperatures.</p>
|
||||
<p>The system internal properties are computed according to the following
|
||||
relations:</p>
|
||||
<img alt="_images/compute_dpd.jpg" class="align-center" src="_images/compute_dpd.jpg" />
|
||||
<p>where N is the number of particles in the system</p>
|
||||
<hr class="docutils" />
|
||||
<p><strong>Output info:</strong></p>
|
||||
<p>This compute calculates a global vector of length 5 (U_cond, U_mech,
|
||||
U, dpdTheta, N_particles), which can be accessed by indices 1-5. See
|
||||
<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS
|
||||
output options.</p>
|
||||
<p>The vector values will be in energy and temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<p>The compute <em>dpd</em> is only available if LAMMPS is built with the
|
||||
USER-DPD package and requires the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dpd</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="compute_dpd_atom.html"><span class="doc">compute dpd/atom</span></a>,
|
||||
<a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
<hr class="docutils" />
|
||||
<p id="larentzos"><strong>(Larentzos)</strong> J.P. Larentzos, J.K. Brennan, J.D. Moore, and
|
||||
W.D. Mattson, “LAMMPS Implementation of Constant Energy Dissipative
|
||||
Particle Dynamics (DPD-E)”, ARL-TR-6863, U.S. Army Research
|
||||
Laboratory, Aberdeen Proving Ground, MD (2014).</p>
|
||||
</div>
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||||
</div>
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<div class="section" id="compute-dpd-atom-command">
|
||||
<span id="index-0"></span><h1>compute dpd/atom command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">dpd</span><span class="o">/</span><span class="n">atom</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
|
||||
<li>dpd/atom = style name of this compute command</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<p>compute 1 all dpd/atom</p>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<p>Define a computation that accesses the per-particle internal
|
||||
conductive energy (u_cond), internal mechanical energy (u_mech) and
|
||||
internal temperatures (dpdTheta) for each particle in a group. See
|
||||
the <a class="reference internal" href="compute_dpd.html"><span class="doc">compute dpd</span></a> command if you want the total
|
||||
internal conductive energy, the total internal mechanical energy, and
|
||||
average internal temperature of the entire system or group of dpd
|
||||
particles.</p>
|
||||
<p><strong>Output info:</strong></p>
|
||||
<p>This compute calculates a per-particle array with 3 columns (u_cond,
|
||||
u_mech, dpdTheta), which can be accessed by indices 1-3 by any command
|
||||
that uses per-particle values from a compute as input. See
|
||||
<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto15</span></a> for an overview of
|
||||
LAMMPS output options.</p>
|
||||
<p>The per-particle array values will be in energy (u_cond, u_mech) and
|
||||
temperature (dpdTheta) <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<p>The compute <em>dpd/atom</em> is only available if LAMMPS is built with the
|
||||
USER-DPD package.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a>, <a class="reference internal" href="compute_dpd.html"><span class="doc">compute dpd</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
<hr class="docutils" />
|
||||
<p id="larentzos"><strong>(Larentzos)</strong> J.P. Larentzos, J.K. Brennan, J.D. Moore, and
|
||||
W.D. Mattson, “LAMMPS Implementation of Constant Energy Dissipative
|
||||
Particle Dynamics (DPD-E)”, ARL-TR-6863, U.S. Army Research
|
||||
Laboratory, Aberdeen Proving Ground, MD (2014).</p>
|
||||
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<div class="section" id="compute-erotate-asphere-command">
|
||||
<span id="index-0"></span><h1>compute erotate/asphere command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">erotate</span><span class="o">/</span><span class="n">asphere</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
|
||||
<li>erotate/asphere = style name of this compute command</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">erotate</span><span class="o">/</span><span class="n">asphere</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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"><span class="doc">atom_style</span></a> and <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></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 note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">For <a class="reference internal" href="dimension.html"><span class="doc">2d models</span></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
|
||||
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 class="std std-ref">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"><span class="doc">units</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<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"><span class="doc">atom_style ellipsoid</span></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"><span class="doc">atom_style line</span></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"><span class="doc">atom_style tri</span></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"><span class="doc">compute erotate/sphere</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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|
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|
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<div class="section" id="compute-erotate-rigid-command">
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<span id="index-0"></span><h1>compute erotate/rigid command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">erotate</span><span class="o">/</span><span class="n">rigid</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID</span>
|
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</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">erotate</span><span class="o">/</span><span class="n">rigid</span> <span class="n">myRigid</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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"><span class="doc">fix rigid</span></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"><span class="doc">fix rigid</span></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
|
||||
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 class="std std-ref">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"><span class="doc">units</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</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 class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><span class="xref doc">compute ke/rigid</span></p>
|
||||
<p><strong>Default:</strong> none</p>
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<div class="section" id="compute-erotate-sphere-command">
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<span id="index-0"></span><h1>compute erotate/sphere command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">erotate</span><span class="o">/</span><span class="n">sphere</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
|
||||
<li>erotate/sphere = style name of this compute command</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">erotate</span><span class="o">/</span><span class="n">sphere</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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 note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">For <a class="reference internal" href="dimension.html"><span class="doc">2d models</span></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
|
||||
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 class="std std-ref">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"><span class="doc">units</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</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"><span class="doc">atom_style sphere</span></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</h2>
|
||||
<p><a class="reference internal" href="compute_erotate_asphere.html"><span class="doc">compute erotate/asphere</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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<div class="section" id="compute-erotate-sphere-atom-command">
|
||||
<span id="index-0"></span><h1>compute erotate/sphere/atom command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">erotate</span><span class="o">/</span><span class="n">sphere</span><span class="o">/</span><span class="n">atom</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
|
||||
<li>erotate/sphere/atom = style name of this compute command</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">erotate</span><span class="o">/</span><span class="n">sphere</span><span class="o">/</span><span class="n">atom</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</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 note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">For <a class="reference internal" href="dimension.html"><span class="doc">2d models</span></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
|
||||
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
|
||||
any command that uses per-atom values from a compute as input. See
|
||||
<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">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"><span class="doc">units</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
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<div class="section" id="compute-event-displace-command">
|
||||
<span id="index-0"></span><h1>compute event/displace command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">event</span><span class="o">/</span><span class="n">displace</span> <span class="n">threshold</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">event</span><span class="o">/</span><span class="n">displace</span> <span class="mf">0.5</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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"><span class="doc">prd</span></a> and <a class="reference internal" href="tad.html"><span class="doc">tad</span></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
|
||||
moved far enough, and equal to 1 if one or more particles have moved
|
||||
further than the threshold distance.</p>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">If the system is undergoing significant center-of-mass motion,
|
||||
due to thermal motion, an external force, or an initial net momentum,
|
||||
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
|
||||
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 class="std std-ref">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</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 class="std std-ref">Making LAMMPS</span></a> section
|
||||
for more info on packages.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="prd.html"><span class="doc">prd</span></a>, <a class="reference internal" href="tad.html"><span class="doc">tad</span></a></p>
|
||||
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|
||||
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<div class="section" id="compute-fep-command">
|
||||
<span id="index-0"></span><h1>compute fep command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">fep</span> <span class="n">temp</span> <span class="n">attribute</span> <span class="n">args</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in the <a class="reference internal" href="compute.html"><span class="doc">compute</span></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
|
||||
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
|
||||
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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">fep</span> <span class="mi">298</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="n">epsilon</span> <span class="mi">1</span> <span class="o">*</span> <span class="n">v_delta</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="n">sigma</span> <span class="mi">1</span> <span class="o">*</span> <span class="n">v_delta</span> <span class="n">volume</span> <span class="n">yes</span>
|
||||
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">fep</span> <span class="mi">300</span> <span class="n">atom</span> <span class="n">charge</span> <span class="mi">2</span> <span class="n">v_delta</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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
|
||||
background term corresponding to interaction sites whose parameters
|
||||
remain constant, a reference term <em>U</em><sub>0</sub> corresponding to the
|
||||
initial interactions of the atoms that will undergo perturbation, and
|
||||
a term <em>U</em><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
|
||||
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"><span class="doc">fix adapt</span></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 class="std std-ref">(Mezei)</span></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 <em>w</em><sub>i</sub> are weights of a numerical quadrature. The <a class="reference internal" href="fix_adapt.html"><span class="doc">fix adapt</span></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 <em>U</em><sub>1</sub>-<em>U</em><sub>0</sub>. By
|
||||
choosing a very small perturbation &delta; the thermodynamic
|
||||
integration method can be implemented using a numerical evaluation of
|
||||
the derivative of the potential energy with respect to &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 class="std std-ref">(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
|
||||
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 class="std std-ref">(Pearlman)</span></a>. The latter does not require modification of
|
||||
bond lengths, angles or other internal coordinates.</p>
|
||||
<p>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 class="std std-ref">(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"><span class="doc">pair_style</span></a> and <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></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
|
||||
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"><span class="doc">lj/cut</span></a></td>
|
||||
<td>epsilon,sigma</td>
|
||||
<td>type pairs</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_lj.html"><span class="doc">lj/cut/coul/cut</span></a></td>
|
||||
<td>epsilon,sigma</td>
|
||||
<td>type pairs</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_lj.html"><span class="doc">lj/cut/coul/long</span></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"><span class="doc">lj/cut/soft</span></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"><span class="doc">coul/cut/soft</span></a></td>
|
||||
<td>lambda</td>
|
||||
<td>type pairs</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">coul/long/soft</span></a></td>
|
||||
<td>lambda</td>
|
||||
<td>type pairs</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">lj/cut/coul/cut/soft</span></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"><span class="doc">lj/cut/coul/long/soft</span></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"><span class="doc">lj/cut/tip4p/long/soft</span></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"><span class="doc">tip4p/long/soft</span></a></td>
|
||||
<td>lambda</td>
|
||||
<td>type pairs</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">lj/charmm/coul/long/soft</span></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"><span class="doc">born</span></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"><span class="doc">buck</span></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
|
||||
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"><span class="doc">pair_coeff</span></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
|
||||
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 =
|
||||
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"><span class="doc">pair_style hybrid or hybrid/overlay</span></a> is being
|
||||
used, then the <em>pstyle</em> 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"><span class="doc">pair_coeff</span></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"><span class="doc">equal-style variable</span></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"><span class="doc">equal-style variable</span></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"><span class="doc">pair_modify</span></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
|
||||
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 class="std std-ref">(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</em><sub>1</sub>-<em>U</em><sub>0</sub>) as c_ID[1], the
|
||||
Boltzmann factor exp(-(<em>U</em><sub>1</sub>-<em>U</em><sub>0</sub>)/<em>kT</em>), or
|
||||
<em>V</em>exp(-(<em>U</em><sub>1</sub>-<em>U</em><sub>0</sub>)/<em>kT</em>), as c_ID[2] and the
|
||||
volume of the simulation box <em>V</em> as c_ID[3]. <em>U</em><sub>1</sub> is the
|
||||
pair potential energy obtained with the perturbed parameters and
|
||||
<em>U</em><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 class="std std-ref">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"><span class="doc">fix ave/time</span></a>.</p>
|
||||
<p>The values calculated by this compute are “extensive”.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</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 class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="fix_adapt_fep.html"><span class="doc">fix adapt/fep</span></a>, <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></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</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>
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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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<div class="section" id="compute-group-group-command">
|
||||
<span id="index-0"></span><h1>compute group/group command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">group</span><span class="o">/</span><span class="n">group</span> <span class="n">group2</span><span class="o">-</span><span class="n">ID</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></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</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="n">lower</span> <span class="n">group</span><span class="o">/</span><span class="n">group</span> <span class="n">upper</span>
|
||||
<span class="n">compute</span> <span class="mi">1</span> <span class="n">lower</span> <span class="n">group</span><span class="o">/</span><span class="n">group</span> <span class="n">upper</span> <span class="n">kspace</span> <span class="n">yes</span>
|
||||
<span class="n">compute</span> <span class="n">mine</span> <span class="n">fluid</span> <span class="n">group</span><span class="o">/</span><span class="n">group</span> <span class="n">wall</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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
|
||||
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>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">The energies computed by the <em>pair</em> keyword do not include tail
|
||||
corrections, even if they are enabled via the
|
||||
<a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> command.</p>
|
||||
</div>
|
||||
<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"><span class="doc">kspace_style</span></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
|
||||
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 class="std std-ref">(Bogusz)</span></a>. If the
|
||||
<em>boundary</em> keyword is set to <em>yes</em>, which is the default, and <em>kspace</em>
|
||||
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
|
||||
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
|
||||
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>.
|
||||
The individual contributions can be summed in a
|
||||
<a class="reference internal" href="variable.html"><span class="doc">variable</span></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
|
||||
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 class="std std-ref">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"><span class="doc">units</span></a>.
|
||||
The vector values will be in force <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<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"><span class="doc">Tersoff</span></a> and
|
||||
<a class="reference internal" href="pair_sw.html"><span class="doc">Stillinger-Weber</span></a> cannot be used. <a class="reference internal" href="pair_eam.html"><span class="doc">EAM</span></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</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>
|
||||
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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>
|
||||
<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>
|
||||
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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||||
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||||
<div class="section" id="compute-gyration-command">
|
||||
<span id="index-0"></span><h1>compute gyration command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">gyration</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
|
||||
<li>gyration = style name of this compute command</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="n">molecule</span> <span class="n">gyration</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
<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
|
||||
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 note">
|
||||
<p class="first admonition-title">Note</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"><span class="doc">dump custom</span></a> command for a discussion of “unwrapped” coordinates.
|
||||
See the Atoms section of the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></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"><span class="doc">set image</span></a> command.</p>
|
||||
</div>
|
||||
<p><strong>Output info:</strong></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 class="std std-ref">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"><span class="doc">units</span></a> respectively.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
<p><a class="reference internal" href="compute_gyration_chunk.html"><span class="doc">compute gyration/chunk</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
</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">
|
||||
<p>
|
||||
© Copyright 2013 Sandia Corporation.
|
||||
</p>
|
||||
</div>
|
||||
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|
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|
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