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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 current"><a class="current reference internal" href="#">9. Additional tools</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="#amber2lmp-tool">9.1. amber2lmp tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#binary2txt-tool">9.2. binary2txt tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#ch2lmp-tool">9.3. ch2lmp tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#chain-tool">9.4. chain tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#colvars-tools">9.5. colvars tools</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#createatoms-tool">9.6. createatoms tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#data2xmovie-tool">9.7. data2xmovie tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#eam-database-tool">9.8. eam database tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#eam-generate-tool">9.9. eam generate tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#eff-tool">9.10. eff tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#emacs-tool">9.11. emacs tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#fep-tool">9.12. fep tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#i-pi-tool">9.13. i-pi tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#ipp-tool">9.14. ipp tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#kate-tool">9.15. kate tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#lmp2arc-tool">9.16. lmp2arc tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#lmp2cfg-tool">9.17. lmp2cfg tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#lmp2vmd-tool">9.18. lmp2vmd tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#matlab-tool">9.19. matlab tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#micelle2d-tool">9.20. micelle2d tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#moltemplate-tool">9.21. moltemplate tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#msi2lmp-tool">9.22. msi2lmp tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#phonon-tool">9.23. phonon tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#polymer-bonding-tool">9.24. polymer bonding tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#pymol-asphere-tool">9.25. pymol_asphere tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#python-tool">9.26. python tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#reax-tool">9.27. reax tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#restart2data-tool">9.28. restart2data tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#vim-tool">9.29. vim tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#xmgrace-tool">9.30. xmgrace tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#xmovie-tool">9.31. xmovie tool</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_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>9. Additional tools</li>
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<div class="section" id="additional-tools">
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<h1>9. Additional tools</h1>
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<p>LAMMPS is designed to be a computational kernel for performing
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molecular dynamics computations. Additional pre- and post-processing
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steps are often necessary to setup and analyze a simulation. A few
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additional tools are provided with the LAMMPS distribution and are
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described in this section.</p>
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<p>Our group has also written and released a separate toolkit called
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<a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</a> which provides tools for doing setup, analysis,
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plotting, and visualization for LAMMPS simulations. Pizza.py is
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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>
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<p>Note that many users write their own setup or analysis tools or use
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other existing codes and convert their output to a LAMMPS input format
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or vice versa. The tools listed here are included in the LAMMPS
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distribution as examples of auxiliary tools. Some of them are not
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actively supported by Sandia, as they were contributed by LAMMPS
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users. If you have problems using them, we can direct you to the
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authors.</p>
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<p>The source code for each of these codes is in the tools sub-directory
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of the LAMMPS distribution. There is a Makefile (which you may need
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to edit for your platform) which will build several of the tools which
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reside in that directory. Some of them are larger packages in their
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own sub-directories with their own Makefiles.</p>
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<ul class="simple">
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<li><a class="reference internal" href="#amber"><span class="std std-ref">amber2lmp</span></a></li>
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<li><a class="reference internal" href="#binary"><span class="std std-ref">binary2txt</span></a></li>
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<li><a class="reference internal" href="#charmm"><span class="std std-ref">ch2lmp</span></a></li>
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<li><a class="reference internal" href="#chain"><span class="std std-ref">chain</span></a></li>
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<li><a class="reference internal" href="#colvars"><span class="std std-ref">colvars</span></a></li>
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<li><a class="reference internal" href="#create"><span class="std std-ref">createatoms</span></a></li>
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<li><a class="reference internal" href="#data"><span class="std std-ref">data2xmovie</span></a></li>
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<li><a class="reference internal" href="#eamdb"><span class="std std-ref">eam database</span></a></li>
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<li><a class="reference internal" href="#eamgn"><span class="std std-ref">eam generate</span></a></li>
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<li><a class="reference internal" href="#eff"><span class="std std-ref">eff</span></a></li>
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<li><a class="reference internal" href="#emacs"><span class="std std-ref">emacs</span></a></li>
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<li><a class="reference internal" href="#fep"><span class="std std-ref">fep</span></a></li>
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<li><a class="reference internal" href="fix_ipi.html#ipi"><span class="std std-ref">i-pi</span></a></li>
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<li><a class="reference internal" href="#ipp"><span class="std std-ref">ipp</span></a></li>
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<li><a class="reference internal" href="#kate"><span class="std std-ref">kate</span></a></li>
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<li><a class="reference internal" href="#arc"><span class="std std-ref">lmp2arc</span></a></li>
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<li><a class="reference internal" href="#cfg"><span class="std std-ref">lmp2cfg</span></a></li>
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<li><a class="reference internal" href="#vmd"><span class="std std-ref">lmp2vmd</span></a></li>
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<li><span class="xref std std-ref">matlab</span></li>
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<li><a class="reference internal" href="#micelle"><span class="std std-ref">micelle2d</span></a></li>
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<li><a class="reference internal" href="#moltemplate"><span class="std std-ref">moltemplate</span></a></li>
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<li><a class="reference internal" href="#msi"><span class="std std-ref">msi2lmp</span></a></li>
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<li><a class="reference internal" href="#phonon"><span class="std std-ref">phonon</span></a></li>
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<li><a class="reference internal" href="#polybond"><span class="std std-ref">polymer bonding</span></a></li>
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<li><span class="xref std std-ref">pymol_asphere</span></li>
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<li><a class="reference internal" href="#pythontools"><span class="std std-ref">python</span></a></li>
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<li><a class="reference internal" href="#reax"><span class="std std-ref">reax</span></a></li>
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<li><a class="reference internal" href="#restart"><span class="std std-ref">restart2data</span></a></li>
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<li><a class="reference internal" href="#vim"><span class="std std-ref">vim</span></a></li>
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<li><a class="reference internal" href="#xmgrace"><span class="std std-ref">xmgrace</span></a></li>
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<li><a class="reference internal" href="#xmovie"><span class="std std-ref">xmovie</span></a></li>
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</ul>
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<hr class="docutils" />
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<div class="section" id="amber2lmp-tool">
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<span id="amber"></span><h2>9.1. amber2lmp tool</h2>
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<p>The amber2lmp sub-directory contains two Python scripts for converting
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files back-and-forth between the AMBER MD code and LAMMPS. See the
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README file in amber2lmp for more information.</p>
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<p>These tools were written by Keir Novik while he was at Queen Mary
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University of London. Keir is no longer there and cannot support
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these tools which are out-of-date with respect to the current LAMMPS
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version (and maybe with respect to AMBER as well). Since we don’t use
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these tools at Sandia, you’ll need to experiment with them and make
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necessary modifications yourself.</p>
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<hr class="docutils" />
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</div>
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<div class="section" id="binary2txt-tool">
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<span id="binary"></span><h2>9.2. binary2txt tool</h2>
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<p>The file binary2txt.cpp converts one or more binary LAMMPS dump file
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into ASCII text files. The syntax for running the tool is</p>
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<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>
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</pre></div>
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</div>
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<p>which creates file1.txt, file2.txt, etc. This tool must be compiled
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on a platform that can read the binary file created by a LAMMPS run,
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since binary files are not compatible across all platforms.</p>
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<hr class="docutils" />
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</div>
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<div class="section" id="ch2lmp-tool">
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<span id="charmm"></span><h2>9.3. ch2lmp tool</h2>
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<p>The ch2lmp sub-directory contains tools for converting files
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back-and-forth between the CHARMM MD code and LAMMPS.</p>
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<p>They are intended to make it easy to use CHARMM as a builder and as a
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post-processor for LAMMPS. Using charmm2lammps.pl, you can convert an
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ensemble built in CHARMM into its LAMMPS equivalent. Using
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lammps2pdb.pl you can convert LAMMPS atom dumps into pdb files.</p>
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<p>See the README file in the ch2lmp sub-directory for more information.</p>
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<p>These tools were created by Pieter in’t Veld (pjintve at sandia.gov)
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and Paul Crozier (pscrozi at sandia.gov) at Sandia.</p>
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<hr class="docutils" />
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</div>
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<div class="section" id="chain-tool">
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<span id="chain"></span><h2>9.4. chain tool</h2>
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<p>The file chain.f creates a LAMMPS data file containing bead-spring
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polymer chains and/or monomer solvent atoms. It uses a text file
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containing chain definition parameters as an input. The created
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chains and solvent atoms can strongly overlap, so LAMMPS needs to run
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the system initially with a “soft” pair potential to un-overlap it.
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The syntax for running the tool is</p>
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<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>
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</pre></div>
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</div>
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<p>See the def.chain or def.chain.ab files in the tools directory for
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examples of definition files. This tool was used to create the
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system for the <a class="reference internal" href="Section_perf.html"><span class="doc">chain benchmark</span></a>.</p>
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<hr class="docutils" />
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</div>
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<div class="section" id="colvars-tools">
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<span id="colvars"></span><h2>9.5. colvars tools</h2>
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<p>The colvars directory contains a collection of tools for postprocessing
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data produced by the colvars collective variable library.
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To compile the tools, edit the makefile for your system and run “make”.</p>
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<p>Please report problems and issues the colvars library and its tools
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at: <a class="reference external" href="https://github.com/colvars/colvars/issues">https://github.com/colvars/colvars/issues</a></p>
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<p>abf_integrate:</p>
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<p>MC-based integration of multidimensional free energy gradient
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Version 20110511</p>
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<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>
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</pre></div>
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</div>
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<p>The LAMMPS interface to the colvars collective variable library, as
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well as these tools, were created by Axel Kohlmeyer (akohlmey at
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gmail.com) at ICTP, Italy.</p>
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<hr class="docutils" />
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</div>
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<div class="section" id="createatoms-tool">
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<span id="create"></span><h2>9.6. createatoms tool</h2>
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<p>The tools/createatoms directory contains a Fortran program called
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createAtoms.f which can generate a variety of interesting crystal
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structures and geometries and output the resulting list of atom
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coordinates in LAMMPS or other formats.</p>
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<p>See the included Manual.pdf for details.</p>
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<p>The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.</p>
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<hr class="docutils" />
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</div>
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<div class="section" id="data2xmovie-tool">
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<span id="data"></span><h2>9.7. data2xmovie tool</h2>
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<p>The file data2xmovie.c converts a LAMMPS data file into a snapshot
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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>
|
|
|
|
|
|
</div>
|
|
</div>
|
|
<footer>
|
|
|
|
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
|
|
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